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' => 'HOM05D001460', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '433', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p22980' => 'bna', 'A01p32340' => 'bna', 'A03p42970' => 'bna', 'A05p25880' => 'bna', 'Aa31LG8G9320' => 'aar', 'Aa31LG8G9330' => 'aar', 'Aa31LG8G9340' => 'aar', 'Aa31sc221G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1034' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1528' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.829' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2222' => 'aag', 'Ah.12g058830' => 'amhyb', 'Ah.12g058840' => 'amhyb', 'AL3G37160' => 'aly', 'AL7G41310' => 'aly', 'Aqoxy5G00395' => 'aox', 'Aqoxy5G00396' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0C8NZA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5185HY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JZ1PRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MD3LS0' => 'arhy', 'AT3G22840' => 'ath', 'AT4G14690' => 'ath', 'ATR0665G054' => 'atr', 'Atru.chr4.2344' => 'acertr', 'Atru.chr4.2346' => 'acertr', 'Atru.chr4.2347' => 'acertr', 'Atru.chr4.2348' => 'acertr', 'Atru.chr4.2355' => 'acertr', 'Atru.chr4.2356' => 'acertr', 'Atru.chr4.2358' => 'acertr', 'Atru.chr4.2359' => 'acertr', 'Atru.chr4.2360' => 'acertr', 'Atru.chr4.2361' => 'acertr', 'AUR62030476' => 'cqu', 'AUR62030478' => 'cqu', 'AUR62030819' => 'cqu', 'AUR62030820' => 'cqu', 'BcaB03g14648' => 'bca', 'BcaB04g20492' => 'bca', 'BcaB06g26399' => 'bca', 'BcaC01g03416' => 'bca', 'BcaC01g03419' => 'bca', 'BcaC01g03421' => 'bca', 'BcaC01g03424' => 'bca', 'BcaC05g28012' => 'bca', 'BcaC09g49212' => 'bca', 'BcaC09g50140' => 'bca', 'BcaNung00346' => 'bca', 'BolC1t02785H' => 'bol', 'BolC1t04095H' => 'bol', 'BolC3t17545H' => 'bol', 'BolC5t32769H' => 'bol', 'BraA01t02211Z' => 'bra', 'BraA01t03359Z' => 'bra', 'BraA03t13441Z' => 'bra', 'BraA05t21476Z' => 'bra', 'C01p28420' => 'bna', 'C01p41350' => 'bna', 'C03p52750' => 'bna', 'C03p52780' => 'bna', 'C05p40270' => 'bna', 'CAN.G1437.9' => 'can', 'CANSAT78G0035' => 'cansat', 'CANSAT78G1036' => 'cansat', 'CANSAT78G2272' => 'cansat', 'CANSAT78G2478' => 'cansat', 'CARHR098700' => 'chi', 'CARHR221120' => 'chi', 'CARHR221150' => 'chi', 'Carub.0003s2297' => 'cru', 'Carub.0007s2749' => 'cru', 'Carub.0007s2750' => 'cru', 'Carub.0007s2751' => 'cru', 'Ca_10849_v3' => 'car', 'Cc03_g04300' => 'ccan', 'CDE02G3648' => 'cde', 'CDE05G0060' => 'cde', 'CDE05G0692' => 'cde', 'CDE05G2285' => 'cde', 'CDE05G2884' => 'cde', 'CDE05G3072' => 'cde', 'Cfa008439' => 'cfa', 'Cfa008441' => 'cfa', 'Cfa008443' => 'cfa', 'Cfa008448' => 'cfa', 'Ciclev10005974m.g' => 'ccl', 'Ciclev10006006m.g' => 'ccl', 'Ciclev10006775m.g' => 'ccl', 'CiPaw.02G120400' => 'cil', 'CiPaw.02G120500' => 'cil', 'CiPaw.02G120600' => 'cil', 'ClCG05G004850' => 'cla', 'COL.COLO4_21566' => 'col', 'Cpa.g.sc44.124' => 'cpa', 'Cre07.g320400' => 'cre', 'Cre07.g320450' => 'cre', 'Cre08.g384650' => 'cre', 'Cre09.g393173' => 'cre', 'Cre09.g394325' => 'cre', 'Cre14.g626750' => 'cre', 'Cre16.g679250' => 'cre', 'CsaV3_3G012890' => 'csa', 'CSS0010865' => 'camsi', 'CSS0044338' => 'camsi', 'DCAR_002366' => 'dca', 'DCAR_030687' => 'dca', 'DCAR_030688' => 'dca', 'Dinv14047' => 'din', 'Dinv14048' => 'din', 'Duzib151G0105' => 'dzi', 'Duzib151G0114' => 'dzi', 'Duzib212G1029' => 'dzi', 'ECA232G3536' => 'eca', 'ECA240G0786' => 'eca', 'ECA240G1802' => 'eca', 'ECA240G3760' => 'eca', 'ECA240G3920' => 'eca', 'EL10Ac5g12536' => 'bvu', 'EL10Ac5g12537' => 'bvu', 'EL10Ac5g12538' => 'bvu', 'Eucgr.B01004' => 'egr', 'Eucgr.B01006' => 'egr', 'Eucgr.B01007' => 'egr', 'Eucgr.B01008' => 'egr', 'Eucgr.B01895' => 'egr', 'Eucgr.B01896' => 'egr', 'FAN04G1456' => 'fan', 'FAN08G1769' => 'fan', 'FAN08G2160' => 'fan', 'FAN13G2403' => 'fan', 'FAN13G3303' => 'fan', 'FAN15G2435' => 'fan', 'FAN17G0672' => 'fan', 'FAN17G2441' => 'fan', 'FAN18G1024' => 'fan', 'FAN22G1458' => 'fan', 'FAN24G0037' => 'fan', 'FAN24G0429' => 'fan', 'FAN24G2387' => 'fan', 'FAN27G2746' => 'fan', 'FvH4_2g20400' => 'fve', 'FvH4_2g20420' => 'fve', 'FvH4_2g20430' => 'fve', 'FvH4_4g01270' => 'fve', 'FvH4_4g01290' => 'fve', 'FvH4_4g01300' => 'fve', 'FvH4_4g01310' => 'fve', 'FvH4_4g01330' => 'fve', 'FvH4_5g09070' => 'fve', 'Glyma.10G243800' => 'gma', 'Glyma.20G150600' => 'gma', 'Gohir.A09G219200' => 'ghi', 'Gohir.A09G219300' => 'ghi', 'Gohir.D09G221400' => 'ghi', 'Gohir.D09G221500' => 'ghi', 'Gorai.006G242600' => 'gra', 'Gorai.006G242700' => 'gra', 'GSVIVG01018044001' => 'vvi', 'HanXRQChr03g0083821' => 'han', 'HanXRQChr03g0083841' => 'han', 'HanXRQChr03g0083881' => 'han', 'HanXRQChr03g0083901' => 'han', 'HanXRQChr03g0083921' => 'han', 'HanXRQChr03g0085331' => 'han', 'HanXRQChr03g0085361' => 'han', 'HanXRQChr03g0085411' => 'han', 'HanXRQChr03g0085421' => 'han', 'HanXRQChr03g0085431' => 'han', 'HanXRQChr08g0221991' => 'han', 'HanXRQChr11g0336061' => 'han', 'HanXRQChr11g0336411' => 'han', 'Haze_11234' => 'cav', 'Hma1.2p1_0549F.1_g177010' => 'hma', 'Hma1.2p1_0602F.1_g187630' => 'hma', 'Hund14876' => 'sun', 'Hund14879' => 'sun', 'Lalb_Chr06g0160741' => 'lal', 'Lalb_Chr21g0304781' => 'lal', 'Lj3A726G19' => 'lonja', 'Lj3A726T23' => 'lonja', 'Lj3A726T24' => 'lonja', 'Lj3A726T25' => 'lonja', 'Lj3A727T17' => 'lonja', 'Lj3C726T0' => 'lonja', 'Lj3C726T2' => 'lonja', 'Lj3P725T35' => 'lonja', 'Lj3P727T10' => 'lonja', 'Lj3P727T12' => 'lonja', 'Lj3P727T14' => 'lonja', 'Lj5g0023109' => 'lja', 'Lj6P646T44' => 'lonja', 'Lsat_1_v5_gn_6_75760' => 'lsa', 'Lsat_1_v5_gn_6_75800' => 'lsa', 'Lsat_1_v5_gn_6_75900' => 'lsa', 'Lsat_1_v5_gn_6_76240' => 'lsa', 'Lsat_1_v5_gn_6_76441' => 'lsa', 'Lsat_1_v5_gn_6_76700' => 'lsa', 'Lsat_1_v5_gn_6_76760' => 'lsa', 'Manes.15G033100' => 'mes', 'Mapoly0004s0074' => 'mpo', 'Mapoly0004s0075' => 'mpo', 'Mapoly0004s0163' => 'mpo', 'Mapoly0004s0164' => 'mpo', 'Mapoly0021s0018' => 'mpo', 'Mapoly0041s0136' => 'mpo', 'Mapoly0041s0137' => 'mpo', 'Mapoly0041s0138' => 'mpo', 'Mapoly0041s0139' => 'mpo', 'Mapoly0041s0141' => 'mpo', 'Mapoly0041s0142' => 'mpo', 'Mapoly0041s0143' => 'mpo', 'Mapoly0041s0144' => 'mpo', 'Mapoly0041s0145' => 'mpo', 'Mapoly0047s0106' => 'mpo', 'Mapoly0047s0108' => 'mpo', 'Mapoly0050s0051' => 'mpo', 'Mapoly0050s0052' => 'mpo', 'Mapoly0050s0053' => 'mpo', 'Mapoly0058s0013' => 'mpo', 'Mapoly0091s0078' => 'mpo', 'Mapoly0091s0079' => 'mpo', 'Mapoly0091s0080' => 'mpo', 'Mapoly0091s0081' => 'mpo', 'Mapoly0278s0004' => 'mpo', 'Mapoly0278s0005' => 'mpo', 'Mapoly0278s0006' => 'mpo', 'MBI11_g30648_MAGBIO' => 'mbi', 'MCO03G194' => 'mco', 'MCO03G590' => 'mco', 'MCO07G312' => 'mco', 'MCO10G318' => 'mco', 'MCO12G244' => 'mco', 'MCO13G148' => 'mco', 'MCO13G194' => 'mco', 'MCO16G238' => 'mco', 'MD06G1134100' => 'mdo', 'MD13G1200100' => 'mdo', 'MD13G1200300' => 'mdo', 'MD13G1200600' => 'mdo', 'MD14G1150400' => 'mdo', 'MD16G1200000' => 'mdo', 'Medtr1g102570' => 'mtr', 'Medtr1g102780' => 'mtr', 'Medtr1g102800' => 'mtr', 'Medtr1g102810' => 'mtr', 'Medtr1g102830' => 'mtr', 'MELO3C006499.2' => 'cme', 'Migut.G00385' => 'egut', 'MSTRG.4063' => 'ama', 'Nitab4.5_0000090g0260' => 'nta', 'Nitab4.5_0000977g0030' => 'nta', 'Nitab4.5_0002541g0040' => 'nta', 'Nitab4.5_0007068g0040' => 'nta', 'Nn005s41408' => 'nnu', 'Nn005s41410' => 'nnu', 'Oeu010310.1' => 'oeu', 'Oeu010311.1' => 'oeu', 'Oeu043472.1' => 'oeu', 'Os01g0246400' => 'osa', 'Os04g0267950' => 'osa', 'Os07g0178700' => 'osa', 'Os07g0178800' => 'osa', 'Peaxi162Scf00316g00046' => 'pax', 'Peaxi162Scf00316g00049' => 'pax', 'Peaxi162Scf00316g00059' => 'pax', 'Peaxi162Scf00316g00328' => 'pax', 'Peaxi162Scf00316g00329' => 'pax', 'Peaxi162Scf00316g00411' => 'pax', 'Peaxi162Scf00316g00521' => 'pax', 'Peaxi162Scf00492g00068' => 'pax', 'Peaxi162Scf35631g00002' => 'pax', 'PGR142G3720' => 'pgr', 'PGSC0003DMG400006442' => 'stu', 'Phvul.007G062000' => 'pvu', 'Potri.008G157750' => 'ptr', 'Potri.008G157900' => 'ptr', 'Potri.008G158000' => 'ptr', 'Potri.008G158200' => 'ptr', 'Pp3c11_7280' => 'ppa', 'Pp3c11_7980' => 'ppa', 'Pp3c12_19450' => 'ppa', 'Pp3c14_1480' => 'ppa', 'Pp3c14_1501' => 'ppa', 'Pp3c16_4900' => 'ppa', 'Pp3c16_5010' => 'ppa', 'Pp3c16_5060' => 'ppa', 'Pp3c19_18250' => 'ppa', 'Pp3c23_8530' => 'ppa', 'Pp3c23_8550' => 'ppa', 'Pp3c24_9670' => 'ppa', 'Pp3c2_21390' => 'ppa', 'Pp3c2_31380' => 'ppa', 'Pp3c3_16620' => 'ppa', 'Pp3c3_8090' => 'ppa', 'Pp3c3_8110' => 'ppa', 'Pp3c3_8130' => 'ppa', 'Pp3c3_8150' => 'ppa', 'Pp3c4_14320' => 'ppa', 'Pp3c6_2560' => 'ppa', 'Pp3c9_16700' => 'ppa', 'PRCOL_00000234' => 'pco', 'PRCOL_00000235' => 'pco', 'PRCOL_00000777' => 'pco', 'PRCOL_00002344' => 'pco', 'PRCOL_00002372' => 'pco', 'PRCOL_00006120' => 'pco', 'Prupe.1G021400' => 'ppe', 'Prupe.1G021500' => 'ppe', 'Prupe.1G021600' => 'ppe', 'Prupe.1G021700' => 'ppe', 'Prupe.1G021800' => 'ppe', 'Prupe.5G145100' => 'ppe', 'Psat6g204040' => 'psa', 'Psat6g204800' => 'psa', 'Psat6g204920' => 'psa', 'Psat6g204960' => 'psa', 'Psat6g205080' => 'psa', 'PSO017G0271' => 'pso', 'PSO017G1276' => 'pso', 'PSO017G1429' => 'pso', 'PSO017G1861' => 'pso', 'PSO017G2787' => 'pso', 'PSO017G4466' => 'pso', 'PSO017G5118' => 'pso', 'PSO017G5420' => 'pso', 'PSO063G3678' => 'pso', 'PSO210G0546' => 'pso', 'PSO317G0001' => 'pso', 'PSO357G0512' => 'pso', 'PSO478G2682' => 'pso', 'PSO647G0001' => 'pso', 'PSO675G0001' => 'pso', 'PSO675G2699' => 'pso', 'PSO675G2849' => 'pso', 'PSO675G4991' => 'pso', 'PSO689G0001' => 'pso', 'QL06p000916' => 'qlo', 'QL06p000921' => 'qlo', 'QL06p001398' => 'qlo', 'QL06p001407' => 'qlo', 'QL06p002031' => 'qlo', 'RcHm_v2.0_Chr4g0387791' => 'rch', 'RcHm_v2.0_Chr4g0387801' => 'rch', 'RcHm_v2.0_Chr6g0286501' => 'rch', 'RcHm_v2.0_Chr6g0286511' => 'rch', 'RcHm_v2.0_Chr6g0286521' => 'rch', 'RcHm_v2.0_Chr6g0286531' => 'rch', 'RcHm_v2.0_Chr7g0189141' => 'rch', 'Rhsim02G0028700' => 'rsi', 'Rhsim02G0028800' => 'rsi', 'Rhsim02G0028900' => 'rsi', 'Rhsim02G0029000' => 'rsi', 'Rhsim02G0029100' => 'rsi', 'Rhsim02G0029200' => 'rsi', 'Rhsim02G0029300' => 'rsi', 'Rhsim02G0029400' => 'rsi', 'Rhsim02G0029500' => 'rsi', 'Rhsim02G0029600' => 'rsi', 'RhsimUnG0024000' => 'rsi', 'RhsimUnG0024100' => 'rsi', 'RhsimUnG0024200' => 'rsi', 'RhsimUnG0024300' => 'rsi', 'RhsimUnG0024400' => 'rsi', 'RhsimUnG0024500' => 'rsi', 'RhsimUnG0024700' => 'rsi', 'RhsimUnG0024800' => 'rsi', 'RhsimUnG0024900' => 'rsi', 'RhsimUnG0025100' => 'rsi', 'Sabra08G0120200' => 'sbr', 'Sabra08G0120300' => 'sbr', 'Sabra08G0120500' => 'sbr', 'Sabra08G0120600' => 'sbr', 'Sabra10G0158900' => 'sbr', 'SalBow2G3492' => 'sbo', 'Sc13g0004760' => 'sci', 'Sc13g0004770' => 'sci', 'Sed0003417' => 'sed', 'Sed0019750' => 'sed', 'SEGI_03419' => 'sgi', 'SEGI_05907' => 'sgi', 'SEGI_10682' => 'sgi', 'SEGI_13528' => 'sgi', 'SEGI_16081' => 'sgi', 'SEGI_19370' => 'sgi', 'SEGI_21015' => 'sgi', 'SEGI_21944' => 'sgi', 'SEGI_32906' => 'sgi', 'SEGI_33093' => 'sgi', 'SEGI_36110' => 'sgi', 'SEGI_40397' => 'sgi', 'SGA_v2.0_scaffold191G40426' => 'sas', 'SGA_v2.0_scaffold353G49717' => 'sas', 'SGA_v2.0_scaffold50G18550' => 'sas', 'SMO119G0173' => 'smo', 'SMO172G0002' => 'smo', 'Solyc09g082690.3' => 'sly', 'Solyc09g082700.2' => 'sly', 'Sopen09g031550' => 'spe', 'Sopen09g031560' => 'spe', 'Sp3g20540' => 'spa', 'Sp7g07580' => 'spa', 'TAR134G0002' => 'tar', 'TAR236G0001' => 'tar', 'TAR365G0892' => 'tar', 'TAR636G0166' => 'tar', 'TAR636G0646' => 'tar', 'TAR636G0869' => 'tar', 'TAR636G1317' => 'tar', 'TAR636G1744' => 'tar', 'TAR636G3358' => 'tar', 'TAR636G3436' => 'tar', 'THA.LOC104803047' => 'tha', 'Thecc.04G238900' => 'tca', 'Thhalv10021557m.g' => 'esa', 'Thhalv10026318m.g' => 'esa', 'Thhalv10026335m.g' => 'esa', 'TPR.G17433' => 'tpr', 'TPR.G18915' => 'tpr', 'TPR.G26125' => 'tpr', 'TWI09G0677' => 'twi', 'TWI73G0287' => 'twi', 'unitig_748.g8326' => 'ugi', 'vmacro15370' => 'vma', 'vmacro15371' => 'vma', 'vmacro15372' => 'vma', 'vmacro15373' => 'vma', 'vmacro15374' => 'vma', 'VMungo0720G2826' => 'vmu', 'Zm00001eb116960' => 'zma', 'Zm00001eb301260' => 'zma', 'Zm00001eb301270' => 'zma' ), 'gf_id' => 'HOM05D001460', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001460' ), 'data_identifier' => 'HOM05D001460', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001460', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '433', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p22980' => 'bna', 'A01p32340' => 'bna', 'A03p42970' => 'bna', 'A05p25880' => 'bna', 'Aa31LG8G9320' => 'aar', 'Aa31LG8G9330' => 'aar', 'Aa31LG8G9340' => 'aar', 'Aa31sc221G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1034' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1528' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.829' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2222' => 'aag', 'Ah.12g058830' => 'amhyb', 'Ah.12g058840' => 'amhyb', 'AL3G37160' => 'aly', 'AL7G41310' => 'aly', 'Aqoxy5G00395' => 'aox', 'Aqoxy5G00396' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0C8NZA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5185HY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JZ1PRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MD3LS0' => 'arhy', 'AT3G22840' => 'ath', 'AT4G14690' => 'ath', 'ATR0665G054' => 'atr', 'Atru.chr4.2344' => 'acertr', 'Atru.chr4.2346' => 'acertr', 'Atru.chr4.2347' => 'acertr', 'Atru.chr4.2348' => 'acertr', 'Atru.chr4.2355' => 'acertr', 'Atru.chr4.2356' => 'acertr', 'Atru.chr4.2358' => 'acertr', 'Atru.chr4.2359' => 'acertr', 'Atru.chr4.2360' => 'acertr', 'Atru.chr4.2361' => 'acertr', 'AUR62030476' => 'cqu', 'AUR62030478' => 'cqu', 'AUR62030819' => 'cqu', 'AUR62030820' => 'cqu', 'BcaB03g14648' => 'bca', 'BcaB04g20492' => 'bca', 'BcaB06g26399' => 'bca', 'BcaC01g03416' => 'bca', 'BcaC01g03419' => 'bca', 'BcaC01g03421' => 'bca', 'BcaC01g03424' => 'bca', 'BcaC05g28012' => 'bca', 'BcaC09g49212' => 'bca', 'BcaC09g50140' => 'bca', 'BcaNung00346' => 'bca', 'BolC1t02785H' => 'bol', 'BolC1t04095H' => 'bol', 'BolC3t17545H' => 'bol', 'BolC5t32769H' => 'bol', 'BraA01t02211Z' => 'bra', 'BraA01t03359Z' => 'bra', 'BraA03t13441Z' => 'bra', 'BraA05t21476Z' => 'bra', 'C01p28420' => 'bna', 'C01p41350' => 'bna', 'C03p52750' => 'bna', 'C03p52780' => 'bna', 'C05p40270' => 'bna', 'CAN.G1437.9' => 'can', 'CANSAT78G0035' => 'cansat', 'CANSAT78G1036' => 'cansat', 'CANSAT78G2272' => 'cansat', 'CANSAT78G2478' => 'cansat', 'CARHR098700' => 'chi', 'CARHR221120' => 'chi', 'CARHR221150' => 'chi', 'Carub.0003s2297' => 'cru', 'Carub.0007s2749' => 'cru', 'Carub.0007s2750' => 'cru', 'Carub.0007s2751' => 'cru', 'Ca_10849_v3' => 'car', 'Cc03_g04300' => 'ccan', 'CDE02G3648' => 'cde', 'CDE05G0060' => 'cde', 'CDE05G0692' => 'cde', 'CDE05G2285' => 'cde', 'CDE05G2884' => 'cde', 'CDE05G3072' => 'cde', 'Cfa008439' => 'cfa', 'Cfa008441' => 'cfa', 'Cfa008443' => 'cfa', 'Cfa008448' => 'cfa', 'Ciclev10005974m.g' => 'ccl', 'Ciclev10006006m.g' => 'ccl', 'Ciclev10006775m.g' => 'ccl', 'CiPaw.02G120400' => 'cil', 'CiPaw.02G120500' => 'cil', 'CiPaw.02G120600' => 'cil', 'ClCG05G004850' => 'cla', 'COL.COLO4_21566' => 'col', 'Cpa.g.sc44.124' => 'cpa', 'Cre07.g320400' => 'cre', 'Cre07.g320450' => 'cre', 'Cre08.g384650' => 'cre', 'Cre09.g393173' => 'cre', 'Cre09.g394325' => 'cre', 'Cre14.g626750' => 'cre', 'Cre16.g679250' => 'cre', 'CsaV3_3G012890' => 'csa', 'CSS0010865' => 'camsi', 'CSS0044338' => 'camsi', 'DCAR_002366' => 'dca', 'DCAR_030687' => 'dca', 'DCAR_030688' => 'dca', 'Dinv14047' => 'din', 'Dinv14048' => 'din', 'Duzib151G0105' => 'dzi', 'Duzib151G0114' => 'dzi', 'Duzib212G1029' => 'dzi', 'ECA232G3536' => 'eca', 'ECA240G0786' => 'eca', 'ECA240G1802' => 'eca', 'ECA240G3760' => 'eca', 'ECA240G3920' => 'eca', 'EL10Ac5g12536' => 'bvu', 'EL10Ac5g12537' => 'bvu', 'EL10Ac5g12538' => 'bvu', 'Eucgr.B01004' => 'egr', 'Eucgr.B01006' => 'egr', 'Eucgr.B01007' => 'egr', 'Eucgr.B01008' => 'egr', 'Eucgr.B01895' => 'egr', 'Eucgr.B01896' => 'egr', 'FAN04G1456' => 'fan', 'FAN08G1769' => 'fan', 'FAN08G2160' => 'fan', 'FAN13G2403' => 'fan', 'FAN13G3303' => 'fan', 'FAN15G2435' => 'fan', 'FAN17G0672' => 'fan', 'FAN17G2441' => 'fan', 'FAN18G1024' => 'fan', 'FAN22G1458' => 'fan', 'FAN24G0037' => 'fan', 'FAN24G0429' => 'fan', 'FAN24G2387' => 'fan', 'FAN27G2746' => 'fan', 'FvH4_2g20400' => 'fve', 'FvH4_2g20420' => 'fve', 'FvH4_2g20430' => 'fve', 'FvH4_4g01270' => 'fve', 'FvH4_4g01290' => 'fve', 'FvH4_4g01300' => 'fve', 'FvH4_4g01310' => 'fve', 'FvH4_4g01330' => 'fve', 'FvH4_5g09070' => 'fve', 'Glyma.10G243800' => 'gma', 'Glyma.20G150600' => 'gma', 'Gohir.A09G219200' => 'ghi', 'Gohir.A09G219300' => 'ghi', 'Gohir.D09G221400' => 'ghi', 'Gohir.D09G221500' => 'ghi', 'Gorai.006G242600' => 'gra', 'Gorai.006G242700' => 'gra', 'GSVIVG01018044001' => 'vvi', 'HanXRQChr03g0083821' => 'han', 'HanXRQChr03g0083841' => 'han', 'HanXRQChr03g0083881' => 'han', 'HanXRQChr03g0083901' => 'han', 'HanXRQChr03g0083921' => 'han', 'HanXRQChr03g0085331' => 'han', 'HanXRQChr03g0085361' => 'han', 'HanXRQChr03g0085411' => 'han', 'HanXRQChr03g0085421' => 'han', 'HanXRQChr03g0085431' => 'han', 'HanXRQChr08g0221991' => 'han', 'HanXRQChr11g0336061' => 'han', 'HanXRQChr11g0336411' => 'han', 'Haze_11234' => 'cav', 'Hma1.2p1_0549F.1_g177010' => 'hma', 'Hma1.2p1_0602F.1_g187630' => 'hma', 'Hund14876' => 'sun', 'Hund14879' => 'sun', 'Lalb_Chr06g0160741' => 'lal', 'Lalb_Chr21g0304781' => 'lal', 'Lj3A726G19' => 'lonja', 'Lj3A726T23' => 'lonja', 'Lj3A726T24' => 'lonja', 'Lj3A726T25' => 'lonja', 'Lj3A727T17' => 'lonja', 'Lj3C726T0' => 'lonja', 'Lj3C726T2' => 'lonja', 'Lj3P725T35' => 'lonja', 'Lj3P727T10' => 'lonja', 'Lj3P727T12' => 'lonja', 'Lj3P727T14' => 'lonja', 'Lj5g0023109' => 'lja', 'Lj6P646T44' => 'lonja', 'Lsat_1_v5_gn_6_75760' => 'lsa', 'Lsat_1_v5_gn_6_75800' => 'lsa', 'Lsat_1_v5_gn_6_75900' => 'lsa', 'Lsat_1_v5_gn_6_76240' => 'lsa', 'Lsat_1_v5_gn_6_76441' => 'lsa', 'Lsat_1_v5_gn_6_76700' => 'lsa', 'Lsat_1_v5_gn_6_76760' => 'lsa', 'Manes.15G033100' => 'mes', 'Mapoly0004s0074' => 'mpo', 'Mapoly0004s0075' => 'mpo', 'Mapoly0004s0163' => 'mpo', 'Mapoly0004s0164' => 'mpo', 'Mapoly0021s0018' => 'mpo', 'Mapoly0041s0136' => 'mpo', 'Mapoly0041s0137' => 'mpo', 'Mapoly0041s0138' => 'mpo', 'Mapoly0041s0139' => 'mpo', 'Mapoly0041s0141' => 'mpo', 'Mapoly0041s0142' => 'mpo', 'Mapoly0041s0143' => 'mpo', 'Mapoly0041s0144' => 'mpo', 'Mapoly0041s0145' => 'mpo', 'Mapoly0047s0106' => 'mpo', 'Mapoly0047s0108' => 'mpo', 'Mapoly0050s0051' => 'mpo', 'Mapoly0050s0052' => 'mpo', 'Mapoly0050s0053' => 'mpo', 'Mapoly0058s0013' => 'mpo', 'Mapoly0091s0078' => 'mpo', 'Mapoly0091s0079' => 'mpo', 'Mapoly0091s0080' => 'mpo', 'Mapoly0091s0081' => 'mpo', 'Mapoly0278s0004' => 'mpo', 'Mapoly0278s0005' => 'mpo', 'Mapoly0278s0006' => 'mpo', 'MBI11_g30648_MAGBIO' => 'mbi', 'MCO03G194' => 'mco', 'MCO03G590' => 'mco', 'MCO07G312' => 'mco', 'MCO10G318' => 'mco', 'MCO12G244' => 'mco', 'MCO13G148' => 'mco', 'MCO13G194' => 'mco', 'MCO16G238' => 'mco', 'MD06G1134100' => 'mdo', 'MD13G1200100' => 'mdo', 'MD13G1200300' => 'mdo', 'MD13G1200600' => 'mdo', 'MD14G1150400' => 'mdo', 'MD16G1200000' => 'mdo', 'Medtr1g102570' => 'mtr', 'Medtr1g102780' => 'mtr', 'Medtr1g102800' => 'mtr', 'Medtr1g102810' => 'mtr', 'Medtr1g102830' => 'mtr', 'MELO3C006499.2' => 'cme', 'Migut.G00385' => 'egut', 'MSTRG.4063' => 'ama', 'Nitab4.5_0000090g0260' => 'nta', 'Nitab4.5_0000977g0030' => 'nta', 'Nitab4.5_0002541g0040' => 'nta', 'Nitab4.5_0007068g0040' => 'nta', 'Nn005s41408' => 'nnu', 'Nn005s41410' => 'nnu', 'Oeu010310.1' => 'oeu', 'Oeu010311.1' => 'oeu', 'Oeu043472.1' => 'oeu', 'Os01g0246400' => 'osa', 'Os04g0267950' => 'osa', 'Os07g0178700' => 'osa', 'Os07g0178800' => 'osa', 'Peaxi162Scf00316g00046' => 'pax', 'Peaxi162Scf00316g00049' => 'pax', 'Peaxi162Scf00316g00059' => 'pax', 'Peaxi162Scf00316g00328' => 'pax', 'Peaxi162Scf00316g00329' => 'pax', 'Peaxi162Scf00316g00411' => 'pax', 'Peaxi162Scf00316g00521' => 'pax', 'Peaxi162Scf00492g00068' => 'pax', 'Peaxi162Scf35631g00002' => 'pax', 'PGR142G3720' => 'pgr', 'PGSC0003DMG400006442' => 'stu', 'Phvul.007G062000' => 'pvu', 'Potri.008G157750' => 'ptr', 'Potri.008G157900' => 'ptr', 'Potri.008G158000' => 'ptr', 'Potri.008G158200' => 'ptr', 'Pp3c11_7280' => 'ppa', 'Pp3c11_7980' => 'ppa', 'Pp3c12_19450' => 'ppa', 'Pp3c14_1480' => 'ppa', 'Pp3c14_1501' => 'ppa', 'Pp3c16_4900' => 'ppa', 'Pp3c16_5010' => 'ppa', 'Pp3c16_5060' => 'ppa', 'Pp3c19_18250' => 'ppa', 'Pp3c23_8530' => 'ppa', 'Pp3c23_8550' => 'ppa', 'Pp3c24_9670' => 'ppa', 'Pp3c2_21390' => 'ppa', 'Pp3c2_31380' => 'ppa', 'Pp3c3_16620' => 'ppa', 'Pp3c3_8090' => 'ppa', 'Pp3c3_8110' => 'ppa', 'Pp3c3_8130' => 'ppa', 'Pp3c3_8150' => 'ppa', 'Pp3c4_14320' => 'ppa', 'Pp3c6_2560' => 'ppa', 'Pp3c9_16700' => 'ppa', 'PRCOL_00000234' => 'pco', 'PRCOL_00000235' => 'pco', 'PRCOL_00000777' => 'pco', 'PRCOL_00002344' => 'pco', 'PRCOL_00002372' => 'pco', 'PRCOL_00006120' => 'pco', 'Prupe.1G021400' => 'ppe', 'Prupe.1G021500' => 'ppe', 'Prupe.1G021600' => 'ppe', 'Prupe.1G021700' => 'ppe', 'Prupe.1G021800' => 'ppe', 'Prupe.5G145100' => 'ppe', 'Psat6g204040' => 'psa', 'Psat6g204800' => 'psa', 'Psat6g204920' => 'psa', 'Psat6g204960' => 'psa', 'Psat6g205080' => 'psa', 'PSO017G0271' => 'pso', 'PSO017G1276' => 'pso', 'PSO017G1429' => 'pso', 'PSO017G1861' => 'pso', 'PSO017G2787' => 'pso', 'PSO017G4466' => 'pso', 'PSO017G5118' => 'pso', 'PSO017G5420' => 'pso', 'PSO063G3678' => 'pso', 'PSO210G0546' => 'pso', 'PSO317G0001' => 'pso', 'PSO357G0512' => 'pso', 'PSO478G2682' => 'pso', 'PSO647G0001' => 'pso', 'PSO675G0001' => 'pso', 'PSO675G2699' => 'pso', 'PSO675G2849' => 'pso', 'PSO675G4991' => 'pso', 'PSO689G0001' => 'pso', 'QL06p000916' => 'qlo', 'QL06p000921' => 'qlo', 'QL06p001398' => 'qlo', 'QL06p001407' => 'qlo', 'QL06p002031' => 'qlo', 'RcHm_v2.0_Chr4g0387791' => 'rch', 'RcHm_v2.0_Chr4g0387801' => 'rch', 'RcHm_v2.0_Chr6g0286501' => 'rch', 'RcHm_v2.0_Chr6g0286511' => 'rch', 'RcHm_v2.0_Chr6g0286521' => 'rch', 'RcHm_v2.0_Chr6g0286531' => 'rch', 'RcHm_v2.0_Chr7g0189141' => 'rch', 'Rhsim02G0028700' => 'rsi', 'Rhsim02G0028800' => 'rsi', 'Rhsim02G0028900' => 'rsi', 'Rhsim02G0029000' => 'rsi', 'Rhsim02G0029100' => 'rsi', 'Rhsim02G0029200' => 'rsi', 'Rhsim02G0029300' => 'rsi', 'Rhsim02G0029400' => 'rsi', 'Rhsim02G0029500' => 'rsi', 'Rhsim02G0029600' => 'rsi', 'RhsimUnG0024000' => 'rsi', 'RhsimUnG0024100' => 'rsi', 'RhsimUnG0024200' => 'rsi', 'RhsimUnG0024300' => 'rsi', 'RhsimUnG0024400' => 'rsi', 'RhsimUnG0024500' => 'rsi', 'RhsimUnG0024700' => 'rsi', 'RhsimUnG0024800' => 'rsi', 'RhsimUnG0024900' => 'rsi', 'RhsimUnG0025100' => 'rsi', 'Sabra08G0120200' => 'sbr', 'Sabra08G0120300' => 'sbr', 'Sabra08G0120500' => 'sbr', 'Sabra08G0120600' => 'sbr', 'Sabra10G0158900' => 'sbr', 'SalBow2G3492' => 'sbo', 'Sc13g0004760' => 'sci', 'Sc13g0004770' => 'sci', 'Sed0003417' => 'sed', 'Sed0019750' => 'sed', 'SEGI_03419' => 'sgi', 'SEGI_05907' => 'sgi', 'SEGI_10682' => 'sgi', 'SEGI_13528' => 'sgi', 'SEGI_16081' => 'sgi', 'SEGI_19370' => 'sgi', 'SEGI_21015' => 'sgi', 'SEGI_21944' => 'sgi', 'SEGI_32906' => 'sgi', 'SEGI_33093' => 'sgi', 'SEGI_36110' => 'sgi', 'SEGI_40397' => 'sgi', 'SGA_v2.0_scaffold191G40426' => 'sas', 'SGA_v2.0_scaffold353G49717' => 'sas', 'SGA_v2.0_scaffold50G18550' => 'sas', 'SMO119G0173' => 'smo', 'SMO172G0002' => 'smo', 'Solyc09g082690.3' => 'sly', 'Solyc09g082700.2' => 'sly', 'Sopen09g031550' => 'spe', 'Sopen09g031560' => 'spe', 'Sp3g20540' => 'spa', 'Sp7g07580' => 'spa', 'TAR134G0002' => 'tar', 'TAR236G0001' => 'tar', 'TAR365G0892' => 'tar', 'TAR636G0166' => 'tar', 'TAR636G0646' => 'tar', 'TAR636G0869' => 'tar', 'TAR636G1317' => 'tar', 'TAR636G1744' => 'tar', 'TAR636G3358' => 'tar', 'TAR636G3436' => 'tar', 'THA.LOC104803047' => 'tha', 'Thecc.04G238900' => 'tca', 'Thhalv10021557m.g' => 'esa', 'Thhalv10026318m.g' => 'esa', 'Thhalv10026335m.g' => 'esa', 'TPR.G17433' => 'tpr', 'TPR.G18915' => 'tpr', 'TPR.G26125' => 'tpr', 'TWI09G0677' => 'twi', 'TWI73G0287' => 'twi', 'unitig_748.g8326' => 'ugi', 'vmacro15370' => 'vma', 'vmacro15371' => 'vma', 'vmacro15372' => 'vma', 'vmacro15373' => 'vma', 'vmacro15374' => 'vma', 'VMungo0720G2826' => 'vmu', 'Zm00001eb116960' => 'zma', 'Zm00001eb301260' => 'zma', 'Zm00001eb301270' => 'zma' ) $gf_id = 'HOM05D001460' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001460' ) $data_identifier = 'HOM05D001460' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 4, 'aag' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 2, 'aox' => (int) 2, 'arhy' => (int) 4, 'ath' => (int) 2, 'atr' => (int) 1, 'acertr' => (int) 10, 'cqu' => (int) 4, 'bca' => (int) 11, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 1, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 1, 'ccan' => (int) 1, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 1, 'col' => (int) 1, 'cpa' => (int) 1, 'cre' => (int) 7, 'csa' => (int) 1, 'camsi' => (int) 2, 'dca' => (int) 3, 'din' => (int) 2, 'dzi' => (int) 3, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 14, 'fve' => (int) 9, 'gma' => (int) 2, 'ghi' => (int) 4, 'gra' => (int) 2, 'vvi' => (int) 1, 'han' => (int) 13, 'cav' => (int) 1, 'hma' => (int) 2, 'sun' => (int) 2, 'lal' => (int) 2, 'lonja' => (int) 12, 'lja' => (int) 1, 'lsa' => (int) 7, 'mes' => (int) 1, 'mpo' => (int) 27, 'mbi' => (int) 1, 'mco' => (int) 8, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 1, 'egut' => (int) 1, 'ama' => (int) 1, 'nta' => (int) 4, 'nnu' => (int) 2, 'oeu' => (int) 3, 'osa' => (int) 4, 'pax' => (int) 9, 'pgr' => (int) 1, 'stu' => (int) 1, 'pvu' => (int) 1, 'ptr' => (int) 4, 'ppa' => (int) 22, 'pco' => (int) 6, 'ppe' => (int) 6, 'psa' => (int) 5, 'pso' => (int) 19, 'qlo' => (int) 5, 'rch' => (int) 7, 'rsi' => (int) 20, 'sbr' => (int) 5, 'sbo' => (int) 1, 'sci' => (int) 2, 'sed' => (int) 2, 'sgi' => (int) 12, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 2, 'tar' => (int) 10, 'tha' => (int) 1, 'tca' => (int) 1, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 2, 'ugi' => (int) 1, 'vma' => (int) 5, 'vmu' => (int) 1, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb301270' $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' => 'HOM05D001460', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '433', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p22980' => 'bna', 'A01p32340' => 'bna', 'A03p42970' => 'bna', 'A05p25880' => 'bna', 'Aa31LG8G9320' => 'aar', 'Aa31LG8G9330' => 'aar', 'Aa31LG8G9340' => 'aar', 'Aa31sc221G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1034' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1528' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.829' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2222' => 'aag', 'Ah.12g058830' => 'amhyb', 'Ah.12g058840' => 'amhyb', 'AL3G37160' => 'aly', 'AL7G41310' => 'aly', 'Aqoxy5G00395' => 'aox', 'Aqoxy5G00396' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0C8NZA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5185HY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JZ1PRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MD3LS0' => 'arhy', 'AT3G22840' => 'ath', 'AT4G14690' => 'ath', 'ATR0665G054' => 'atr', 'Atru.chr4.2344' => 'acertr', 'Atru.chr4.2346' => 'acertr', 'Atru.chr4.2347' => 'acertr', 'Atru.chr4.2348' => 'acertr', 'Atru.chr4.2355' => 'acertr', 'Atru.chr4.2356' => 'acertr', 'Atru.chr4.2358' => 'acertr', 'Atru.chr4.2359' => 'acertr', 'Atru.chr4.2360' => 'acertr', 'Atru.chr4.2361' => 'acertr', 'AUR62030476' => 'cqu', 'AUR62030478' => 'cqu', 'AUR62030819' => 'cqu', 'AUR62030820' => 'cqu', 'BcaB03g14648' => 'bca', 'BcaB04g20492' => 'bca', 'BcaB06g26399' => 'bca', 'BcaC01g03416' => 'bca', 'BcaC01g03419' => 'bca', 'BcaC01g03421' => 'bca', 'BcaC01g03424' => 'bca', 'BcaC05g28012' => 'bca', 'BcaC09g49212' => 'bca', 'BcaC09g50140' => 'bca', 'BcaNung00346' => 'bca', 'BolC1t02785H' => 'bol', 'BolC1t04095H' => 'bol', 'BolC3t17545H' => 'bol', 'BolC5t32769H' => 'bol', 'BraA01t02211Z' => 'bra', 'BraA01t03359Z' => 'bra', 'BraA03t13441Z' => 'bra', 'BraA05t21476Z' => 'bra', 'C01p28420' => 'bna', 'C01p41350' => 'bna', 'C03p52750' => 'bna', 'C03p52780' => 'bna', 'C05p40270' => 'bna', 'CAN.G1437.9' => 'can', 'CANSAT78G0035' => 'cansat', 'CANSAT78G1036' => 'cansat', 'CANSAT78G2272' => 'cansat', 'CANSAT78G2478' => 'cansat', 'CARHR098700' => 'chi', 'CARHR221120' => 'chi', 'CARHR221150' => 'chi', 'Carub.0003s2297' => 'cru', 'Carub.0007s2749' => 'cru', 'Carub.0007s2750' => 'cru', 'Carub.0007s2751' => 'cru', 'Ca_10849_v3' => 'car', 'Cc03_g04300' => 'ccan', 'CDE02G3648' => 'cde', 'CDE05G0060' => 'cde', 'CDE05G0692' => 'cde', 'CDE05G2285' => 'cde', 'CDE05G2884' => 'cde', 'CDE05G3072' => 'cde', 'Cfa008439' => 'cfa', 'Cfa008441' => 'cfa', 'Cfa008443' => 'cfa', 'Cfa008448' => 'cfa', 'Ciclev10005974m.g' => 'ccl', 'Ciclev10006006m.g' => 'ccl', 'Ciclev10006775m.g' => 'ccl', 'CiPaw.02G120400' => 'cil', 'CiPaw.02G120500' => 'cil', 'CiPaw.02G120600' => 'cil', 'ClCG05G004850' => 'cla', 'COL.COLO4_21566' => 'col', 'Cpa.g.sc44.124' => 'cpa', 'Cre07.g320400' => 'cre', 'Cre07.g320450' => 'cre', 'Cre08.g384650' => 'cre', 'Cre09.g393173' => 'cre', 'Cre09.g394325' => 'cre', 'Cre14.g626750' => 'cre', 'Cre16.g679250' => 'cre', 'CsaV3_3G012890' => 'csa', 'CSS0010865' => 'camsi', 'CSS0044338' => 'camsi', 'DCAR_002366' => 'dca', 'DCAR_030687' => 'dca', 'DCAR_030688' => 'dca', 'Dinv14047' => 'din', 'Dinv14048' => 'din', 'Duzib151G0105' => 'dzi', 'Duzib151G0114' => 'dzi', 'Duzib212G1029' => 'dzi', 'ECA232G3536' => 'eca', 'ECA240G0786' => 'eca', 'ECA240G1802' => 'eca', 'ECA240G3760' => 'eca', 'ECA240G3920' => 'eca', 'EL10Ac5g12536' => 'bvu', 'EL10Ac5g12537' => 'bvu', 'EL10Ac5g12538' => 'bvu', 'Eucgr.B01004' => 'egr', 'Eucgr.B01006' => 'egr', 'Eucgr.B01007' => 'egr', 'Eucgr.B01008' => 'egr', 'Eucgr.B01895' => 'egr', 'Eucgr.B01896' => 'egr', 'FAN04G1456' => 'fan', 'FAN08G1769' => 'fan', 'FAN08G2160' => 'fan', 'FAN13G2403' => 'fan', 'FAN13G3303' => 'fan', 'FAN15G2435' => 'fan', 'FAN17G0672' => 'fan', 'FAN17G2441' => 'fan', 'FAN18G1024' => 'fan', 'FAN22G1458' => 'fan', 'FAN24G0037' => 'fan', 'FAN24G0429' => 'fan', 'FAN24G2387' => 'fan', 'FAN27G2746' => 'fan', 'FvH4_2g20400' => 'fve', 'FvH4_2g20420' => 'fve', 'FvH4_2g20430' => 'fve', 'FvH4_4g01270' => 'fve', 'FvH4_4g01290' => 'fve', 'FvH4_4g01300' => 'fve', 'FvH4_4g01310' => 'fve', 'FvH4_4g01330' => 'fve', 'FvH4_5g09070' => 'fve', 'Glyma.10G243800' => 'gma', 'Glyma.20G150600' => 'gma', 'Gohir.A09G219200' => 'ghi', 'Gohir.A09G219300' => 'ghi', 'Gohir.D09G221400' => 'ghi', 'Gohir.D09G221500' => 'ghi', 'Gorai.006G242600' => 'gra', 'Gorai.006G242700' => 'gra', 'GSVIVG01018044001' => 'vvi', 'HanXRQChr03g0083821' => 'han', 'HanXRQChr03g0083841' => 'han', 'HanXRQChr03g0083881' => 'han', 'HanXRQChr03g0083901' => 'han', 'HanXRQChr03g0083921' => 'han', 'HanXRQChr03g0085331' => 'han', 'HanXRQChr03g0085361' => 'han', 'HanXRQChr03g0085411' => 'han', 'HanXRQChr03g0085421' => 'han', 'HanXRQChr03g0085431' => 'han', 'HanXRQChr08g0221991' => 'han', 'HanXRQChr11g0336061' => 'han', 'HanXRQChr11g0336411' => 'han', 'Haze_11234' => 'cav', 'Hma1.2p1_0549F.1_g177010' => 'hma', 'Hma1.2p1_0602F.1_g187630' => 'hma', 'Hund14876' => 'sun', 'Hund14879' => 'sun', 'Lalb_Chr06g0160741' => 'lal', 'Lalb_Chr21g0304781' => 'lal', 'Lj3A726G19' => 'lonja', 'Lj3A726T23' => 'lonja', 'Lj3A726T24' => 'lonja', 'Lj3A726T25' => 'lonja', 'Lj3A727T17' => 'lonja', 'Lj3C726T0' => 'lonja', 'Lj3C726T2' => 'lonja', 'Lj3P725T35' => 'lonja', 'Lj3P727T10' => 'lonja', 'Lj3P727T12' => 'lonja', 'Lj3P727T14' => 'lonja', 'Lj5g0023109' => 'lja', 'Lj6P646T44' => 'lonja', 'Lsat_1_v5_gn_6_75760' => 'lsa', 'Lsat_1_v5_gn_6_75800' => 'lsa', 'Lsat_1_v5_gn_6_75900' => 'lsa', 'Lsat_1_v5_gn_6_76240' => 'lsa', 'Lsat_1_v5_gn_6_76441' => 'lsa', 'Lsat_1_v5_gn_6_76700' => 'lsa', 'Lsat_1_v5_gn_6_76760' => 'lsa', 'Manes.15G033100' => 'mes', 'Mapoly0004s0074' => 'mpo', 'Mapoly0004s0075' => 'mpo', 'Mapoly0004s0163' => 'mpo', 'Mapoly0004s0164' => 'mpo', 'Mapoly0021s0018' => 'mpo', 'Mapoly0041s0136' => 'mpo', 'Mapoly0041s0137' => 'mpo', 'Mapoly0041s0138' => 'mpo', 'Mapoly0041s0139' => 'mpo', 'Mapoly0041s0141' => 'mpo', 'Mapoly0041s0142' => 'mpo', 'Mapoly0041s0143' => 'mpo', 'Mapoly0041s0144' => 'mpo', 'Mapoly0041s0145' => 'mpo', 'Mapoly0047s0106' => 'mpo', 'Mapoly0047s0108' => 'mpo', 'Mapoly0050s0051' => 'mpo', 'Mapoly0050s0052' => 'mpo', 'Mapoly0050s0053' => 'mpo', 'Mapoly0058s0013' => 'mpo', 'Mapoly0091s0078' => 'mpo', 'Mapoly0091s0079' => 'mpo', 'Mapoly0091s0080' => 'mpo', 'Mapoly0091s0081' => 'mpo', 'Mapoly0278s0004' => 'mpo', 'Mapoly0278s0005' => 'mpo', 'Mapoly0278s0006' => 'mpo', 'MBI11_g30648_MAGBIO' => 'mbi', 'MCO03G194' => 'mco', 'MCO03G590' => 'mco', 'MCO07G312' => 'mco', 'MCO10G318' => 'mco', 'MCO12G244' => 'mco', 'MCO13G148' => 'mco', 'MCO13G194' => 'mco', 'MCO16G238' => 'mco', 'MD06G1134100' => 'mdo', 'MD13G1200100' => 'mdo', 'MD13G1200300' => 'mdo', 'MD13G1200600' => 'mdo', 'MD14G1150400' => 'mdo', 'MD16G1200000' => 'mdo', 'Medtr1g102570' => 'mtr', 'Medtr1g102780' => 'mtr', 'Medtr1g102800' => 'mtr', 'Medtr1g102810' => 'mtr', 'Medtr1g102830' => 'mtr', 'MELO3C006499.2' => 'cme', 'Migut.G00385' => 'egut', 'MSTRG.4063' => 'ama', 'Nitab4.5_0000090g0260' => 'nta', 'Nitab4.5_0000977g0030' => 'nta', 'Nitab4.5_0002541g0040' => 'nta', 'Nitab4.5_0007068g0040' => 'nta', 'Nn005s41408' => 'nnu', 'Nn005s41410' => 'nnu', 'Oeu010310.1' => 'oeu', 'Oeu010311.1' => 'oeu', 'Oeu043472.1' => 'oeu', 'Os01g0246400' => 'osa', 'Os04g0267950' => 'osa', 'Os07g0178700' => 'osa', 'Os07g0178800' => 'osa', 'Peaxi162Scf00316g00046' => 'pax', 'Peaxi162Scf00316g00049' => 'pax', 'Peaxi162Scf00316g00059' => 'pax', 'Peaxi162Scf00316g00328' => 'pax', 'Peaxi162Scf00316g00329' => 'pax', 'Peaxi162Scf00316g00411' => 'pax', 'Peaxi162Scf00316g00521' => 'pax', 'Peaxi162Scf00492g00068' => 'pax', 'Peaxi162Scf35631g00002' => 'pax', 'PGR142G3720' => 'pgr', 'PGSC0003DMG400006442' => 'stu', 'Phvul.007G062000' => 'pvu', 'Potri.008G157750' => 'ptr', 'Potri.008G157900' => 'ptr', 'Potri.008G158000' => 'ptr', 'Potri.008G158200' => 'ptr', 'Pp3c11_7280' => 'ppa', 'Pp3c11_7980' => 'ppa', 'Pp3c12_19450' => 'ppa', 'Pp3c14_1480' => 'ppa', 'Pp3c14_1501' => 'ppa', 'Pp3c16_4900' => 'ppa', 'Pp3c16_5010' => 'ppa', 'Pp3c16_5060' => 'ppa', 'Pp3c19_18250' => 'ppa', 'Pp3c23_8530' => 'ppa', 'Pp3c23_8550' => 'ppa', 'Pp3c24_9670' => 'ppa', 'Pp3c2_21390' => 'ppa', 'Pp3c2_31380' => 'ppa', 'Pp3c3_16620' => 'ppa', 'Pp3c3_8090' => 'ppa', 'Pp3c3_8110' => 'ppa', 'Pp3c3_8130' => 'ppa', 'Pp3c3_8150' => 'ppa', 'Pp3c4_14320' => 'ppa', 'Pp3c6_2560' => 'ppa', 'Pp3c9_16700' => 'ppa', 'PRCOL_00000234' => 'pco', 'PRCOL_00000235' => 'pco', 'PRCOL_00000777' => 'pco', 'PRCOL_00002344' => 'pco', 'PRCOL_00002372' => 'pco', 'PRCOL_00006120' => 'pco', 'Prupe.1G021400' => 'ppe', 'Prupe.1G021500' => 'ppe', 'Prupe.1G021600' => 'ppe', 'Prupe.1G021700' => 'ppe', 'Prupe.1G021800' => 'ppe', 'Prupe.5G145100' => 'ppe', 'Psat6g204040' => 'psa', 'Psat6g204800' => 'psa', 'Psat6g204920' => 'psa', 'Psat6g204960' => 'psa', 'Psat6g205080' => 'psa', 'PSO017G0271' => 'pso', 'PSO017G1276' => 'pso', 'PSO017G1429' => 'pso', 'PSO017G1861' => 'pso', 'PSO017G2787' => 'pso', 'PSO017G4466' => 'pso', 'PSO017G5118' => 'pso', 'PSO017G5420' => 'pso', 'PSO063G3678' => 'pso', 'PSO210G0546' => 'pso', 'PSO317G0001' => 'pso', 'PSO357G0512' => 'pso', 'PSO478G2682' => 'pso', 'PSO647G0001' => 'pso', 'PSO675G0001' => 'pso', 'PSO675G2699' => 'pso', 'PSO675G2849' => 'pso', 'PSO675G4991' => 'pso', 'PSO689G0001' => 'pso', 'QL06p000916' => 'qlo', 'QL06p000921' => 'qlo', 'QL06p001398' => 'qlo', 'QL06p001407' => 'qlo', 'QL06p002031' => 'qlo', 'RcHm_v2.0_Chr4g0387791' => 'rch', 'RcHm_v2.0_Chr4g0387801' => 'rch', 'RcHm_v2.0_Chr6g0286501' => 'rch', 'RcHm_v2.0_Chr6g0286511' => 'rch', 'RcHm_v2.0_Chr6g0286521' => 'rch', 'RcHm_v2.0_Chr6g0286531' => 'rch', 'RcHm_v2.0_Chr7g0189141' => 'rch', 'Rhsim02G0028700' => 'rsi', 'Rhsim02G0028800' => 'rsi', 'Rhsim02G0028900' => 'rsi', 'Rhsim02G0029000' => 'rsi', 'Rhsim02G0029100' => 'rsi', 'Rhsim02G0029200' => 'rsi', 'Rhsim02G0029300' => 'rsi', 'Rhsim02G0029400' => 'rsi', 'Rhsim02G0029500' => 'rsi', 'Rhsim02G0029600' => 'rsi', 'RhsimUnG0024000' => 'rsi', 'RhsimUnG0024100' => 'rsi', 'RhsimUnG0024200' => 'rsi', 'RhsimUnG0024300' => 'rsi', 'RhsimUnG0024400' => 'rsi', 'RhsimUnG0024500' => 'rsi', 'RhsimUnG0024700' => 'rsi', 'RhsimUnG0024800' => 'rsi', 'RhsimUnG0024900' => 'rsi', 'RhsimUnG0025100' => 'rsi', 'Sabra08G0120200' => 'sbr', 'Sabra08G0120300' => 'sbr', 'Sabra08G0120500' => 'sbr', 'Sabra08G0120600' => 'sbr', 'Sabra10G0158900' => 'sbr', 'SalBow2G3492' => 'sbo', 'Sc13g0004760' => 'sci', 'Sc13g0004770' => 'sci', 'Sed0003417' => 'sed', 'Sed0019750' => 'sed', 'SEGI_03419' => 'sgi', 'SEGI_05907' => 'sgi', 'SEGI_10682' => 'sgi', 'SEGI_13528' => 'sgi', 'SEGI_16081' => 'sgi', 'SEGI_19370' => 'sgi', 'SEGI_21015' => 'sgi', 'SEGI_21944' => 'sgi', 'SEGI_32906' => 'sgi', 'SEGI_33093' => 'sgi', 'SEGI_36110' => 'sgi', 'SEGI_40397' => 'sgi', 'SGA_v2.0_scaffold191G40426' => 'sas', 'SGA_v2.0_scaffold353G49717' => 'sas', 'SGA_v2.0_scaffold50G18550' => 'sas', 'SMO119G0173' => 'smo', 'SMO172G0002' => 'smo', 'Solyc09g082690.3' => 'sly', 'Solyc09g082700.2' => 'sly', 'Sopen09g031550' => 'spe', 'Sopen09g031560' => 'spe', 'Sp3g20540' => 'spa', 'Sp7g07580' => 'spa', 'TAR134G0002' => 'tar', 'TAR236G0001' => 'tar', 'TAR365G0892' => 'tar', 'TAR636G0166' => 'tar', 'TAR636G0646' => 'tar', 'TAR636G0869' => 'tar', 'TAR636G1317' => 'tar', 'TAR636G1744' => 'tar', 'TAR636G3358' => 'tar', 'TAR636G3436' => 'tar', 'THA.LOC104803047' => 'tha', 'Thecc.04G238900' => 'tca', 'Thhalv10021557m.g' => 'esa', 'Thhalv10026318m.g' => 'esa', 'Thhalv10026335m.g' => 'esa', 'TPR.G17433' => 'tpr', 'TPR.G18915' => 'tpr', 'TPR.G26125' => 'tpr', 'TWI09G0677' => 'twi', 'TWI73G0287' => 'twi', 'unitig_748.g8326' => 'ugi', 'vmacro15370' => 'vma', 'vmacro15371' => 'vma', 'vmacro15372' => 'vma', 'vmacro15373' => 'vma', 'vmacro15374' => 'vma', 'VMungo0720G2826' => 'vmu', 'Zm00001eb116960' => 'zma', 'Zm00001eb301260' => 'zma', 'Zm00001eb301270' => 'zma' ), 'gf_id' => 'HOM05D001460', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001460' ), 'data_identifier' => 'HOM05D001460', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001460', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '433', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p22980' => 'bna', 'A01p32340' => 'bna', 'A03p42970' => 'bna', 'A05p25880' => 'bna', 'Aa31LG8G9320' => 'aar', 'Aa31LG8G9330' => 'aar', 'Aa31LG8G9340' => 'aar', 'Aa31sc221G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1034' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1528' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.829' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2222' => 'aag', 'Ah.12g058830' => 'amhyb', 'Ah.12g058840' => 'amhyb', 'AL3G37160' => 'aly', 'AL7G41310' => 'aly', 'Aqoxy5G00395' => 'aox', 'Aqoxy5G00396' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0C8NZA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5185HY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JZ1PRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MD3LS0' => 'arhy', 'AT3G22840' => 'ath', 'AT4G14690' => 'ath', 'ATR0665G054' => 'atr', 'Atru.chr4.2344' => 'acertr', 'Atru.chr4.2346' => 'acertr', 'Atru.chr4.2347' => 'acertr', 'Atru.chr4.2348' => 'acertr', 'Atru.chr4.2355' => 'acertr', 'Atru.chr4.2356' => 'acertr', 'Atru.chr4.2358' => 'acertr', 'Atru.chr4.2359' => 'acertr', 'Atru.chr4.2360' => 'acertr', 'Atru.chr4.2361' => 'acertr', 'AUR62030476' => 'cqu', 'AUR62030478' => 'cqu', 'AUR62030819' => 'cqu', 'AUR62030820' => 'cqu', 'BcaB03g14648' => 'bca', 'BcaB04g20492' => 'bca', 'BcaB06g26399' => 'bca', 'BcaC01g03416' => 'bca', 'BcaC01g03419' => 'bca', 'BcaC01g03421' => 'bca', 'BcaC01g03424' => 'bca', 'BcaC05g28012' => 'bca', 'BcaC09g49212' => 'bca', 'BcaC09g50140' => 'bca', 'BcaNung00346' => 'bca', 'BolC1t02785H' => 'bol', 'BolC1t04095H' => 'bol', 'BolC3t17545H' => 'bol', 'BolC5t32769H' => 'bol', 'BraA01t02211Z' => 'bra', 'BraA01t03359Z' => 'bra', 'BraA03t13441Z' => 'bra', 'BraA05t21476Z' => 'bra', 'C01p28420' => 'bna', 'C01p41350' => 'bna', 'C03p52750' => 'bna', 'C03p52780' => 'bna', 'C05p40270' => 'bna', 'CAN.G1437.9' => 'can', 'CANSAT78G0035' => 'cansat', 'CANSAT78G1036' => 'cansat', 'CANSAT78G2272' => 'cansat', 'CANSAT78G2478' => 'cansat', 'CARHR098700' => 'chi', 'CARHR221120' => 'chi', 'CARHR221150' => 'chi', 'Carub.0003s2297' => 'cru', 'Carub.0007s2749' => 'cru', 'Carub.0007s2750' => 'cru', 'Carub.0007s2751' => 'cru', 'Ca_10849_v3' => 'car', 'Cc03_g04300' => 'ccan', 'CDE02G3648' => 'cde', 'CDE05G0060' => 'cde', 'CDE05G0692' => 'cde', 'CDE05G2285' => 'cde', 'CDE05G2884' => 'cde', 'CDE05G3072' => 'cde', 'Cfa008439' => 'cfa', 'Cfa008441' => 'cfa', 'Cfa008443' => 'cfa', 'Cfa008448' => 'cfa', 'Ciclev10005974m.g' => 'ccl', 'Ciclev10006006m.g' => 'ccl', 'Ciclev10006775m.g' => 'ccl', 'CiPaw.02G120400' => 'cil', 'CiPaw.02G120500' => 'cil', 'CiPaw.02G120600' => 'cil', 'ClCG05G004850' => 'cla', 'COL.COLO4_21566' => 'col', 'Cpa.g.sc44.124' => 'cpa', 'Cre07.g320400' => 'cre', 'Cre07.g320450' => 'cre', 'Cre08.g384650' => 'cre', 'Cre09.g393173' => 'cre', 'Cre09.g394325' => 'cre', 'Cre14.g626750' => 'cre', 'Cre16.g679250' => 'cre', 'CsaV3_3G012890' => 'csa', 'CSS0010865' => 'camsi', 'CSS0044338' => 'camsi', 'DCAR_002366' => 'dca', 'DCAR_030687' => 'dca', 'DCAR_030688' => 'dca', 'Dinv14047' => 'din', 'Dinv14048' => 'din', 'Duzib151G0105' => 'dzi', 'Duzib151G0114' => 'dzi', 'Duzib212G1029' => 'dzi', 'ECA232G3536' => 'eca', 'ECA240G0786' => 'eca', 'ECA240G1802' => 'eca', 'ECA240G3760' => 'eca', 'ECA240G3920' => 'eca', 'EL10Ac5g12536' => 'bvu', 'EL10Ac5g12537' => 'bvu', 'EL10Ac5g12538' => 'bvu', 'Eucgr.B01004' => 'egr', 'Eucgr.B01006' => 'egr', 'Eucgr.B01007' => 'egr', 'Eucgr.B01008' => 'egr', 'Eucgr.B01895' => 'egr', 'Eucgr.B01896' => 'egr', 'FAN04G1456' => 'fan', 'FAN08G1769' => 'fan', 'FAN08G2160' => 'fan', 'FAN13G2403' => 'fan', 'FAN13G3303' => 'fan', 'FAN15G2435' => 'fan', 'FAN17G0672' => 'fan', 'FAN17G2441' => 'fan', 'FAN18G1024' => 'fan', 'FAN22G1458' => 'fan', 'FAN24G0037' => 'fan', 'FAN24G0429' => 'fan', 'FAN24G2387' => 'fan', 'FAN27G2746' => 'fan', 'FvH4_2g20400' => 'fve', 'FvH4_2g20420' => 'fve', 'FvH4_2g20430' => 'fve', 'FvH4_4g01270' => 'fve', 'FvH4_4g01290' => 'fve', 'FvH4_4g01300' => 'fve', 'FvH4_4g01310' => 'fve', 'FvH4_4g01330' => 'fve', 'FvH4_5g09070' => 'fve', 'Glyma.10G243800' => 'gma', 'Glyma.20G150600' => 'gma', 'Gohir.A09G219200' => 'ghi', 'Gohir.A09G219300' => 'ghi', 'Gohir.D09G221400' => 'ghi', 'Gohir.D09G221500' => 'ghi', 'Gorai.006G242600' => 'gra', 'Gorai.006G242700' => 'gra', 'GSVIVG01018044001' => 'vvi', 'HanXRQChr03g0083821' => 'han', 'HanXRQChr03g0083841' => 'han', 'HanXRQChr03g0083881' => 'han', 'HanXRQChr03g0083901' => 'han', 'HanXRQChr03g0083921' => 'han', 'HanXRQChr03g0085331' => 'han', 'HanXRQChr03g0085361' => 'han', 'HanXRQChr03g0085411' => 'han', 'HanXRQChr03g0085421' => 'han', 'HanXRQChr03g0085431' => 'han', 'HanXRQChr08g0221991' => 'han', 'HanXRQChr11g0336061' => 'han', 'HanXRQChr11g0336411' => 'han', 'Haze_11234' => 'cav', 'Hma1.2p1_0549F.1_g177010' => 'hma', 'Hma1.2p1_0602F.1_g187630' => 'hma', 'Hund14876' => 'sun', 'Hund14879' => 'sun', 'Lalb_Chr06g0160741' => 'lal', 'Lalb_Chr21g0304781' => 'lal', 'Lj3A726G19' => 'lonja', 'Lj3A726T23' => 'lonja', 'Lj3A726T24' => 'lonja', 'Lj3A726T25' => 'lonja', 'Lj3A727T17' => 'lonja', 'Lj3C726T0' => 'lonja', 'Lj3C726T2' => 'lonja', 'Lj3P725T35' => 'lonja', 'Lj3P727T10' => 'lonja', 'Lj3P727T12' => 'lonja', 'Lj3P727T14' => 'lonja', 'Lj5g0023109' => 'lja', 'Lj6P646T44' => 'lonja', 'Lsat_1_v5_gn_6_75760' => 'lsa', 'Lsat_1_v5_gn_6_75800' => 'lsa', 'Lsat_1_v5_gn_6_75900' => 'lsa', 'Lsat_1_v5_gn_6_76240' => 'lsa', 'Lsat_1_v5_gn_6_76441' => 'lsa', 'Lsat_1_v5_gn_6_76700' => 'lsa', 'Lsat_1_v5_gn_6_76760' => 'lsa', 'Manes.15G033100' => 'mes', 'Mapoly0004s0074' => 'mpo', 'Mapoly0004s0075' => 'mpo', 'Mapoly0004s0163' => 'mpo', 'Mapoly0004s0164' => 'mpo', 'Mapoly0021s0018' => 'mpo', 'Mapoly0041s0136' => 'mpo', 'Mapoly0041s0137' => 'mpo', 'Mapoly0041s0138' => 'mpo', 'Mapoly0041s0139' => 'mpo', 'Mapoly0041s0141' => 'mpo', 'Mapoly0041s0142' => 'mpo', 'Mapoly0041s0143' => 'mpo', 'Mapoly0041s0144' => 'mpo', 'Mapoly0041s0145' => 'mpo', 'Mapoly0047s0106' => 'mpo', 'Mapoly0047s0108' => 'mpo', 'Mapoly0050s0051' => 'mpo', 'Mapoly0050s0052' => 'mpo', 'Mapoly0050s0053' => 'mpo', 'Mapoly0058s0013' => 'mpo', 'Mapoly0091s0078' => 'mpo', 'Mapoly0091s0079' => 'mpo', 'Mapoly0091s0080' => 'mpo', 'Mapoly0091s0081' => 'mpo', 'Mapoly0278s0004' => 'mpo', 'Mapoly0278s0005' => 'mpo', 'Mapoly0278s0006' => 'mpo', 'MBI11_g30648_MAGBIO' => 'mbi', 'MCO03G194' => 'mco', 'MCO03G590' => 'mco', 'MCO07G312' => 'mco', 'MCO10G318' => 'mco', 'MCO12G244' => 'mco', 'MCO13G148' => 'mco', 'MCO13G194' => 'mco', 'MCO16G238' => 'mco', 'MD06G1134100' => 'mdo', 'MD13G1200100' => 'mdo', 'MD13G1200300' => 'mdo', 'MD13G1200600' => 'mdo', 'MD14G1150400' => 'mdo', 'MD16G1200000' => 'mdo', 'Medtr1g102570' => 'mtr', 'Medtr1g102780' => 'mtr', 'Medtr1g102800' => 'mtr', 'Medtr1g102810' => 'mtr', 'Medtr1g102830' => 'mtr', 'MELO3C006499.2' => 'cme', 'Migut.G00385' => 'egut', 'MSTRG.4063' => 'ama', 'Nitab4.5_0000090g0260' => 'nta', 'Nitab4.5_0000977g0030' => 'nta', 'Nitab4.5_0002541g0040' => 'nta', 'Nitab4.5_0007068g0040' => 'nta', 'Nn005s41408' => 'nnu', 'Nn005s41410' => 'nnu', 'Oeu010310.1' => 'oeu', 'Oeu010311.1' => 'oeu', 'Oeu043472.1' => 'oeu', 'Os01g0246400' => 'osa', 'Os04g0267950' => 'osa', 'Os07g0178700' => 'osa', 'Os07g0178800' => 'osa', 'Peaxi162Scf00316g00046' => 'pax', 'Peaxi162Scf00316g00049' => 'pax', 'Peaxi162Scf00316g00059' => 'pax', 'Peaxi162Scf00316g00328' => 'pax', 'Peaxi162Scf00316g00329' => 'pax', 'Peaxi162Scf00316g00411' => 'pax', 'Peaxi162Scf00316g00521' => 'pax', 'Peaxi162Scf00492g00068' => 'pax', 'Peaxi162Scf35631g00002' => 'pax', 'PGR142G3720' => 'pgr', 'PGSC0003DMG400006442' => 'stu', 'Phvul.007G062000' => 'pvu', 'Potri.008G157750' => 'ptr', 'Potri.008G157900' => 'ptr', 'Potri.008G158000' => 'ptr', 'Potri.008G158200' => 'ptr', 'Pp3c11_7280' => 'ppa', 'Pp3c11_7980' => 'ppa', 'Pp3c12_19450' => 'ppa', 'Pp3c14_1480' => 'ppa', 'Pp3c14_1501' => 'ppa', 'Pp3c16_4900' => 'ppa', 'Pp3c16_5010' => 'ppa', 'Pp3c16_5060' => 'ppa', 'Pp3c19_18250' => 'ppa', 'Pp3c23_8530' => 'ppa', 'Pp3c23_8550' => 'ppa', 'Pp3c24_9670' => 'ppa', 'Pp3c2_21390' => 'ppa', 'Pp3c2_31380' => 'ppa', 'Pp3c3_16620' => 'ppa', 'Pp3c3_8090' => 'ppa', 'Pp3c3_8110' => 'ppa', 'Pp3c3_8130' => 'ppa', 'Pp3c3_8150' => 'ppa', 'Pp3c4_14320' => 'ppa', 'Pp3c6_2560' => 'ppa', 'Pp3c9_16700' => 'ppa', 'PRCOL_00000234' => 'pco', 'PRCOL_00000235' => 'pco', 'PRCOL_00000777' => 'pco', 'PRCOL_00002344' => 'pco', 'PRCOL_00002372' => 'pco', 'PRCOL_00006120' => 'pco', 'Prupe.1G021400' => 'ppe', 'Prupe.1G021500' => 'ppe', 'Prupe.1G021600' => 'ppe', 'Prupe.1G021700' => 'ppe', 'Prupe.1G021800' => 'ppe', 'Prupe.5G145100' => 'ppe', 'Psat6g204040' => 'psa', 'Psat6g204800' => 'psa', 'Psat6g204920' => 'psa', 'Psat6g204960' => 'psa', 'Psat6g205080' => 'psa', 'PSO017G0271' => 'pso', 'PSO017G1276' => 'pso', 'PSO017G1429' => 'pso', 'PSO017G1861' => 'pso', 'PSO017G2787' => 'pso', 'PSO017G4466' => 'pso', 'PSO017G5118' => 'pso', 'PSO017G5420' => 'pso', 'PSO063G3678' => 'pso', 'PSO210G0546' => 'pso', 'PSO317G0001' => 'pso', 'PSO357G0512' => 'pso', 'PSO478G2682' => 'pso', 'PSO647G0001' => 'pso', 'PSO675G0001' => 'pso', 'PSO675G2699' => 'pso', 'PSO675G2849' => 'pso', 'PSO675G4991' => 'pso', 'PSO689G0001' => 'pso', 'QL06p000916' => 'qlo', 'QL06p000921' => 'qlo', 'QL06p001398' => 'qlo', 'QL06p001407' => 'qlo', 'QL06p002031' => 'qlo', 'RcHm_v2.0_Chr4g0387791' => 'rch', 'RcHm_v2.0_Chr4g0387801' => 'rch', 'RcHm_v2.0_Chr6g0286501' => 'rch', 'RcHm_v2.0_Chr6g0286511' => 'rch', 'RcHm_v2.0_Chr6g0286521' => 'rch', 'RcHm_v2.0_Chr6g0286531' => 'rch', 'RcHm_v2.0_Chr7g0189141' => 'rch', 'Rhsim02G0028700' => 'rsi', 'Rhsim02G0028800' => 'rsi', 'Rhsim02G0028900' => 'rsi', 'Rhsim02G0029000' => 'rsi', 'Rhsim02G0029100' => 'rsi', 'Rhsim02G0029200' => 'rsi', 'Rhsim02G0029300' => 'rsi', 'Rhsim02G0029400' => 'rsi', 'Rhsim02G0029500' => 'rsi', 'Rhsim02G0029600' => 'rsi', 'RhsimUnG0024000' => 'rsi', 'RhsimUnG0024100' => 'rsi', 'RhsimUnG0024200' => 'rsi', 'RhsimUnG0024300' => 'rsi', 'RhsimUnG0024400' => 'rsi', 'RhsimUnG0024500' => 'rsi', 'RhsimUnG0024700' => 'rsi', 'RhsimUnG0024800' => 'rsi', 'RhsimUnG0024900' => 'rsi', 'RhsimUnG0025100' => 'rsi', 'Sabra08G0120200' => 'sbr', 'Sabra08G0120300' => 'sbr', 'Sabra08G0120500' => 'sbr', 'Sabra08G0120600' => 'sbr', 'Sabra10G0158900' => 'sbr', 'SalBow2G3492' => 'sbo', 'Sc13g0004760' => 'sci', 'Sc13g0004770' => 'sci', 'Sed0003417' => 'sed', 'Sed0019750' => 'sed', 'SEGI_03419' => 'sgi', 'SEGI_05907' => 'sgi', 'SEGI_10682' => 'sgi', 'SEGI_13528' => 'sgi', 'SEGI_16081' => 'sgi', 'SEGI_19370' => 'sgi', 'SEGI_21015' => 'sgi', 'SEGI_21944' => 'sgi', 'SEGI_32906' => 'sgi', 'SEGI_33093' => 'sgi', 'SEGI_36110' => 'sgi', 'SEGI_40397' => 'sgi', 'SGA_v2.0_scaffold191G40426' => 'sas', 'SGA_v2.0_scaffold353G49717' => 'sas', 'SGA_v2.0_scaffold50G18550' => 'sas', 'SMO119G0173' => 'smo', 'SMO172G0002' => 'smo', 'Solyc09g082690.3' => 'sly', 'Solyc09g082700.2' => 'sly', 'Sopen09g031550' => 'spe', 'Sopen09g031560' => 'spe', 'Sp3g20540' => 'spa', 'Sp7g07580' => 'spa', 'TAR134G0002' => 'tar', 'TAR236G0001' => 'tar', 'TAR365G0892' => 'tar', 'TAR636G0166' => 'tar', 'TAR636G0646' => 'tar', 'TAR636G0869' => 'tar', 'TAR636G1317' => 'tar', 'TAR636G1744' => 'tar', 'TAR636G3358' => 'tar', 'TAR636G3436' => 'tar', 'THA.LOC104803047' => 'tha', 'Thecc.04G238900' => 'tca', 'Thhalv10021557m.g' => 'esa', 'Thhalv10026318m.g' => 'esa', 'Thhalv10026335m.g' => 'esa', 'TPR.G17433' => 'tpr', 'TPR.G18915' => 'tpr', 'TPR.G26125' => 'tpr', 'TWI09G0677' => 'twi', 'TWI73G0287' => 'twi', 'unitig_748.g8326' => 'ugi', 'vmacro15370' => 'vma', 'vmacro15371' => 'vma', 'vmacro15372' => 'vma', 'vmacro15373' => 'vma', 'vmacro15374' => 'vma', 'VMungo0720G2826' => 'vmu', 'Zm00001eb116960' => 'zma', 'Zm00001eb301260' => 'zma', 'Zm00001eb301270' => 'zma' ) $gf_id = 'HOM05D001460' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001460' ) $data_identifier = 'HOM05D001460' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 4, 'aag' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 2, 'aox' => (int) 2, 'arhy' => (int) 4, 'ath' => (int) 2, 'atr' => (int) 1, 'acertr' => (int) 10, 'cqu' => (int) 4, 'bca' => (int) 11, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 1, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 1, 'ccan' => (int) 1, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 1, 'col' => (int) 1, 'cpa' => (int) 1, 'cre' => (int) 7, 'csa' => (int) 1, 'camsi' => (int) 2, 'dca' => (int) 3, 'din' => (int) 2, 'dzi' => (int) 3, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 14, 'fve' => (int) 9, 'gma' => (int) 2, 'ghi' => (int) 4, 'gra' => (int) 2, 'vvi' => (int) 1, 'han' => (int) 13, 'cav' => (int) 1, 'hma' => (int) 2, 'sun' => (int) 2, 'lal' => (int) 2, 'lonja' => (int) 12, 'lja' => (int) 1, 'lsa' => (int) 7, 'mes' => (int) 1, 'mpo' => (int) 27, 'mbi' => (int) 1, 'mco' => (int) 8, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 1, 'egut' => (int) 1, 'ama' => (int) 1, 'nta' => (int) 4, 'nnu' => (int) 2, 'oeu' => (int) 3, 'osa' => (int) 4, 'pax' => (int) 9, 'pgr' => (int) 1, 'stu' => (int) 1, 'pvu' => (int) 1, 'ptr' => (int) 4, 'ppa' => (int) 22, 'pco' => (int) 6, 'ppe' => (int) 6, 'psa' => (int) 5, 'pso' => (int) 19, 'qlo' => (int) 5, 'rch' => (int) 7, 'rsi' => (int) 20, 'sbr' => (int) 5, 'sbo' => (int) 1, 'sci' => (int) 2, 'sed' => (int) 2, 'sgi' => (int) 12, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 2, 'tar' => (int) 10, 'tha' => (int) 1, 'tca' => (int) 1, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 2, 'ugi' => (int) 1, 'vma' => (int) 5, 'vmu' => (int) 1, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb301270' $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' => 'HOM05D001460', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '433', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p22980' => 'bna', 'A01p32340' => 'bna', 'A03p42970' => 'bna', 'A05p25880' => 'bna', 'Aa31LG8G9320' => 'aar', 'Aa31LG8G9330' => 'aar', 'Aa31LG8G9340' => 'aar', 'Aa31sc221G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1034' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1528' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.829' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2222' => 'aag', 'Ah.12g058830' => 'amhyb', 'Ah.12g058840' => 'amhyb', 'AL3G37160' => 'aly', 'AL7G41310' => 'aly', 'Aqoxy5G00395' => 'aox', 'Aqoxy5G00396' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0C8NZA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5185HY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JZ1PRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MD3LS0' => 'arhy', 'AT3G22840' => 'ath', 'AT4G14690' => 'ath', 'ATR0665G054' => 'atr', 'Atru.chr4.2344' => 'acertr', 'Atru.chr4.2346' => 'acertr', 'Atru.chr4.2347' => 'acertr', 'Atru.chr4.2348' => 'acertr', 'Atru.chr4.2355' => 'acertr', 'Atru.chr4.2356' => 'acertr', 'Atru.chr4.2358' => 'acertr', 'Atru.chr4.2359' => 'acertr', 'Atru.chr4.2360' => 'acertr', 'Atru.chr4.2361' => 'acertr', 'AUR62030476' => 'cqu', 'AUR62030478' => 'cqu', 'AUR62030819' => 'cqu', 'AUR62030820' => 'cqu', 'BcaB03g14648' => 'bca', 'BcaB04g20492' => 'bca', 'BcaB06g26399' => 'bca', 'BcaC01g03416' => 'bca', 'BcaC01g03419' => 'bca', 'BcaC01g03421' => 'bca', 'BcaC01g03424' => 'bca', 'BcaC05g28012' => 'bca', 'BcaC09g49212' => 'bca', 'BcaC09g50140' => 'bca', 'BcaNung00346' => 'bca', 'BolC1t02785H' => 'bol', 'BolC1t04095H' => 'bol', 'BolC3t17545H' => 'bol', 'BolC5t32769H' => 'bol', 'BraA01t02211Z' => 'bra', 'BraA01t03359Z' => 'bra', 'BraA03t13441Z' => 'bra', 'BraA05t21476Z' => 'bra', 'C01p28420' => 'bna', 'C01p41350' => 'bna', 'C03p52750' => 'bna', 'C03p52780' => 'bna', 'C05p40270' => 'bna', 'CAN.G1437.9' => 'can', 'CANSAT78G0035' => 'cansat', 'CANSAT78G1036' => 'cansat', 'CANSAT78G2272' => 'cansat', 'CANSAT78G2478' => 'cansat', 'CARHR098700' => 'chi', 'CARHR221120' => 'chi', 'CARHR221150' => 'chi', 'Carub.0003s2297' => 'cru', 'Carub.0007s2749' => 'cru', 'Carub.0007s2750' => 'cru', 'Carub.0007s2751' => 'cru', 'Ca_10849_v3' => 'car', 'Cc03_g04300' => 'ccan', 'CDE02G3648' => 'cde', 'CDE05G0060' => 'cde', 'CDE05G0692' => 'cde', 'CDE05G2285' => 'cde', 'CDE05G2884' => 'cde', 'CDE05G3072' => 'cde', 'Cfa008439' => 'cfa', 'Cfa008441' => 'cfa', 'Cfa008443' => 'cfa', 'Cfa008448' => 'cfa', 'Ciclev10005974m.g' => 'ccl', 'Ciclev10006006m.g' => 'ccl', 'Ciclev10006775m.g' => 'ccl', 'CiPaw.02G120400' => 'cil', 'CiPaw.02G120500' => 'cil', 'CiPaw.02G120600' => 'cil', 'ClCG05G004850' => 'cla', 'COL.COLO4_21566' => 'col', 'Cpa.g.sc44.124' => 'cpa', 'Cre07.g320400' => 'cre', 'Cre07.g320450' => 'cre', 'Cre08.g384650' => 'cre', 'Cre09.g393173' => 'cre', 'Cre09.g394325' => 'cre', 'Cre14.g626750' => 'cre', 'Cre16.g679250' => 'cre', 'CsaV3_3G012890' => 'csa', 'CSS0010865' => 'camsi', 'CSS0044338' => 'camsi', 'DCAR_002366' => 'dca', 'DCAR_030687' => 'dca', 'DCAR_030688' => 'dca', 'Dinv14047' => 'din', 'Dinv14048' => 'din', 'Duzib151G0105' => 'dzi', 'Duzib151G0114' => 'dzi', 'Duzib212G1029' => 'dzi', 'ECA232G3536' => 'eca', 'ECA240G0786' => 'eca', 'ECA240G1802' => 'eca', 'ECA240G3760' => 'eca', 'ECA240G3920' => 'eca', 'EL10Ac5g12536' => 'bvu', 'EL10Ac5g12537' => 'bvu', 'EL10Ac5g12538' => 'bvu', 'Eucgr.B01004' => 'egr', 'Eucgr.B01006' => 'egr', 'Eucgr.B01007' => 'egr', 'Eucgr.B01008' => 'egr', 'Eucgr.B01895' => 'egr', 'Eucgr.B01896' => 'egr', 'FAN04G1456' => 'fan', 'FAN08G1769' => 'fan', 'FAN08G2160' => 'fan', 'FAN13G2403' => 'fan', 'FAN13G3303' => 'fan', 'FAN15G2435' => 'fan', 'FAN17G0672' => 'fan', 'FAN17G2441' => 'fan', 'FAN18G1024' => 'fan', 'FAN22G1458' => 'fan', 'FAN24G0037' => 'fan', 'FAN24G0429' => 'fan', 'FAN24G2387' => 'fan', 'FAN27G2746' => 'fan', 'FvH4_2g20400' => 'fve', 'FvH4_2g20420' => 'fve', 'FvH4_2g20430' => 'fve', 'FvH4_4g01270' => 'fve', 'FvH4_4g01290' => 'fve', 'FvH4_4g01300' => 'fve', 'FvH4_4g01310' => 'fve', 'FvH4_4g01330' => 'fve', 'FvH4_5g09070' => 'fve', 'Glyma.10G243800' => 'gma', 'Glyma.20G150600' => 'gma', 'Gohir.A09G219200' => 'ghi', 'Gohir.A09G219300' => 'ghi', 'Gohir.D09G221400' => 'ghi', 'Gohir.D09G221500' => 'ghi', 'Gorai.006G242600' => 'gra', 'Gorai.006G242700' => 'gra', 'GSVIVG01018044001' => 'vvi', 'HanXRQChr03g0083821' => 'han', 'HanXRQChr03g0083841' => 'han', 'HanXRQChr03g0083881' => 'han', 'HanXRQChr03g0083901' => 'han', 'HanXRQChr03g0083921' => 'han', 'HanXRQChr03g0085331' => 'han', 'HanXRQChr03g0085361' => 'han', 'HanXRQChr03g0085411' => 'han', 'HanXRQChr03g0085421' => 'han', 'HanXRQChr03g0085431' => 'han', 'HanXRQChr08g0221991' => 'han', 'HanXRQChr11g0336061' => 'han', 'HanXRQChr11g0336411' => 'han', 'Haze_11234' => 'cav', 'Hma1.2p1_0549F.1_g177010' => 'hma', 'Hma1.2p1_0602F.1_g187630' => 'hma', 'Hund14876' => 'sun', 'Hund14879' => 'sun', 'Lalb_Chr06g0160741' => 'lal', 'Lalb_Chr21g0304781' => 'lal', 'Lj3A726G19' => 'lonja', 'Lj3A726T23' => 'lonja', 'Lj3A726T24' => 'lonja', 'Lj3A726T25' => 'lonja', 'Lj3A727T17' => 'lonja', 'Lj3C726T0' => 'lonja', 'Lj3C726T2' => 'lonja', 'Lj3P725T35' => 'lonja', 'Lj3P727T10' => 'lonja', 'Lj3P727T12' => 'lonja', 'Lj3P727T14' => 'lonja', 'Lj5g0023109' => 'lja', 'Lj6P646T44' => 'lonja', 'Lsat_1_v5_gn_6_75760' => 'lsa', 'Lsat_1_v5_gn_6_75800' => 'lsa', 'Lsat_1_v5_gn_6_75900' => 'lsa', 'Lsat_1_v5_gn_6_76240' => 'lsa', 'Lsat_1_v5_gn_6_76441' => 'lsa', 'Lsat_1_v5_gn_6_76700' => 'lsa', 'Lsat_1_v5_gn_6_76760' => 'lsa', 'Manes.15G033100' => 'mes', 'Mapoly0004s0074' => 'mpo', 'Mapoly0004s0075' => 'mpo', 'Mapoly0004s0163' => 'mpo', 'Mapoly0004s0164' => 'mpo', 'Mapoly0021s0018' => 'mpo', 'Mapoly0041s0136' => 'mpo', 'Mapoly0041s0137' => 'mpo', 'Mapoly0041s0138' => 'mpo', 'Mapoly0041s0139' => 'mpo', 'Mapoly0041s0141' => 'mpo', 'Mapoly0041s0142' => 'mpo', 'Mapoly0041s0143' => 'mpo', 'Mapoly0041s0144' => 'mpo', 'Mapoly0041s0145' => 'mpo', 'Mapoly0047s0106' => 'mpo', 'Mapoly0047s0108' => 'mpo', 'Mapoly0050s0051' => 'mpo', 'Mapoly0050s0052' => 'mpo', 'Mapoly0050s0053' => 'mpo', 'Mapoly0058s0013' => 'mpo', 'Mapoly0091s0078' => 'mpo', 'Mapoly0091s0079' => 'mpo', 'Mapoly0091s0080' => 'mpo', 'Mapoly0091s0081' => 'mpo', 'Mapoly0278s0004' => 'mpo', 'Mapoly0278s0005' => 'mpo', 'Mapoly0278s0006' => 'mpo', 'MBI11_g30648_MAGBIO' => 'mbi', 'MCO03G194' => 'mco', 'MCO03G590' => 'mco', 'MCO07G312' => 'mco', 'MCO10G318' => 'mco', 'MCO12G244' => 'mco', 'MCO13G148' => 'mco', 'MCO13G194' => 'mco', 'MCO16G238' => 'mco', 'MD06G1134100' => 'mdo', 'MD13G1200100' => 'mdo', 'MD13G1200300' => 'mdo', 'MD13G1200600' => 'mdo', 'MD14G1150400' => 'mdo', 'MD16G1200000' => 'mdo', 'Medtr1g102570' => 'mtr', 'Medtr1g102780' => 'mtr', 'Medtr1g102800' => 'mtr', 'Medtr1g102810' => 'mtr', 'Medtr1g102830' => 'mtr', 'MELO3C006499.2' => 'cme', 'Migut.G00385' => 'egut', 'MSTRG.4063' => 'ama', 'Nitab4.5_0000090g0260' => 'nta', 'Nitab4.5_0000977g0030' => 'nta', 'Nitab4.5_0002541g0040' => 'nta', 'Nitab4.5_0007068g0040' => 'nta', 'Nn005s41408' => 'nnu', 'Nn005s41410' => 'nnu', 'Oeu010310.1' => 'oeu', 'Oeu010311.1' => 'oeu', 'Oeu043472.1' => 'oeu', 'Os01g0246400' => 'osa', 'Os04g0267950' => 'osa', 'Os07g0178700' => 'osa', 'Os07g0178800' => 'osa', 'Peaxi162Scf00316g00046' => 'pax', 'Peaxi162Scf00316g00049' => 'pax', 'Peaxi162Scf00316g00059' => 'pax', 'Peaxi162Scf00316g00328' => 'pax', 'Peaxi162Scf00316g00329' => 'pax', 'Peaxi162Scf00316g00411' => 'pax', 'Peaxi162Scf00316g00521' => 'pax', 'Peaxi162Scf00492g00068' => 'pax', 'Peaxi162Scf35631g00002' => 'pax', 'PGR142G3720' => 'pgr', 'PGSC0003DMG400006442' => 'stu', 'Phvul.007G062000' => 'pvu', 'Potri.008G157750' => 'ptr', 'Potri.008G157900' => 'ptr', 'Potri.008G158000' => 'ptr', 'Potri.008G158200' => 'ptr', 'Pp3c11_7280' => 'ppa', 'Pp3c11_7980' => 'ppa', 'Pp3c12_19450' => 'ppa', 'Pp3c14_1480' => 'ppa', 'Pp3c14_1501' => 'ppa', 'Pp3c16_4900' => 'ppa', 'Pp3c16_5010' => 'ppa', 'Pp3c16_5060' => 'ppa', 'Pp3c19_18250' => 'ppa', 'Pp3c23_8530' => 'ppa', 'Pp3c23_8550' => 'ppa', 'Pp3c24_9670' => 'ppa', 'Pp3c2_21390' => 'ppa', 'Pp3c2_31380' => 'ppa', 'Pp3c3_16620' => 'ppa', 'Pp3c3_8090' => 'ppa', 'Pp3c3_8110' => 'ppa', 'Pp3c3_8130' => 'ppa', 'Pp3c3_8150' => 'ppa', 'Pp3c4_14320' => 'ppa', 'Pp3c6_2560' => 'ppa', 'Pp3c9_16700' => 'ppa', 'PRCOL_00000234' => 'pco', 'PRCOL_00000235' => 'pco', 'PRCOL_00000777' => 'pco', 'PRCOL_00002344' => 'pco', 'PRCOL_00002372' => 'pco', 'PRCOL_00006120' => 'pco', 'Prupe.1G021400' => 'ppe', 'Prupe.1G021500' => 'ppe', 'Prupe.1G021600' => 'ppe', 'Prupe.1G021700' => 'ppe', 'Prupe.1G021800' => 'ppe', 'Prupe.5G145100' => 'ppe', 'Psat6g204040' => 'psa', 'Psat6g204800' => 'psa', 'Psat6g204920' => 'psa', 'Psat6g204960' => 'psa', 'Psat6g205080' => 'psa', 'PSO017G0271' => 'pso', 'PSO017G1276' => 'pso', 'PSO017G1429' => 'pso', 'PSO017G1861' => 'pso', 'PSO017G2787' => 'pso', 'PSO017G4466' => 'pso', 'PSO017G5118' => 'pso', 'PSO017G5420' => 'pso', 'PSO063G3678' => 'pso', 'PSO210G0546' => 'pso', 'PSO317G0001' => 'pso', 'PSO357G0512' => 'pso', 'PSO478G2682' => 'pso', 'PSO647G0001' => 'pso', 'PSO675G0001' => 'pso', 'PSO675G2699' => 'pso', 'PSO675G2849' => 'pso', 'PSO675G4991' => 'pso', 'PSO689G0001' => 'pso', 'QL06p000916' => 'qlo', 'QL06p000921' => 'qlo', 'QL06p001398' => 'qlo', 'QL06p001407' => 'qlo', 'QL06p002031' => 'qlo', 'RcHm_v2.0_Chr4g0387791' => 'rch', 'RcHm_v2.0_Chr4g0387801' => 'rch', 'RcHm_v2.0_Chr6g0286501' => 'rch', 'RcHm_v2.0_Chr6g0286511' => 'rch', 'RcHm_v2.0_Chr6g0286521' => 'rch', 'RcHm_v2.0_Chr6g0286531' => 'rch', 'RcHm_v2.0_Chr7g0189141' => 'rch', 'Rhsim02G0028700' => 'rsi', 'Rhsim02G0028800' => 'rsi', 'Rhsim02G0028900' => 'rsi', 'Rhsim02G0029000' => 'rsi', 'Rhsim02G0029100' => 'rsi', 'Rhsim02G0029200' => 'rsi', 'Rhsim02G0029300' => 'rsi', 'Rhsim02G0029400' => 'rsi', 'Rhsim02G0029500' => 'rsi', 'Rhsim02G0029600' => 'rsi', 'RhsimUnG0024000' => 'rsi', 'RhsimUnG0024100' => 'rsi', 'RhsimUnG0024200' => 'rsi', 'RhsimUnG0024300' => 'rsi', 'RhsimUnG0024400' => 'rsi', 'RhsimUnG0024500' => 'rsi', 'RhsimUnG0024700' => 'rsi', 'RhsimUnG0024800' => 'rsi', 'RhsimUnG0024900' => 'rsi', 'RhsimUnG0025100' => 'rsi', 'Sabra08G0120200' => 'sbr', 'Sabra08G0120300' => 'sbr', 'Sabra08G0120500' => 'sbr', 'Sabra08G0120600' => 'sbr', 'Sabra10G0158900' => 'sbr', 'SalBow2G3492' => 'sbo', 'Sc13g0004760' => 'sci', 'Sc13g0004770' => 'sci', 'Sed0003417' => 'sed', 'Sed0019750' => 'sed', 'SEGI_03419' => 'sgi', 'SEGI_05907' => 'sgi', 'SEGI_10682' => 'sgi', 'SEGI_13528' => 'sgi', 'SEGI_16081' => 'sgi', 'SEGI_19370' => 'sgi', 'SEGI_21015' => 'sgi', 'SEGI_21944' => 'sgi', 'SEGI_32906' => 'sgi', 'SEGI_33093' => 'sgi', 'SEGI_36110' => 'sgi', 'SEGI_40397' => 'sgi', 'SGA_v2.0_scaffold191G40426' => 'sas', 'SGA_v2.0_scaffold353G49717' => 'sas', 'SGA_v2.0_scaffold50G18550' => 'sas', 'SMO119G0173' => 'smo', 'SMO172G0002' => 'smo', 'Solyc09g082690.3' => 'sly', 'Solyc09g082700.2' => 'sly', 'Sopen09g031550' => 'spe', 'Sopen09g031560' => 'spe', 'Sp3g20540' => 'spa', 'Sp7g07580' => 'spa', 'TAR134G0002' => 'tar', 'TAR236G0001' => 'tar', 'TAR365G0892' => 'tar', 'TAR636G0166' => 'tar', 'TAR636G0646' => 'tar', 'TAR636G0869' => 'tar', 'TAR636G1317' => 'tar', 'TAR636G1744' => 'tar', 'TAR636G3358' => 'tar', 'TAR636G3436' => 'tar', 'THA.LOC104803047' => 'tha', 'Thecc.04G238900' => 'tca', 'Thhalv10021557m.g' => 'esa', 'Thhalv10026318m.g' => 'esa', 'Thhalv10026335m.g' => 'esa', 'TPR.G17433' => 'tpr', 'TPR.G18915' => 'tpr', 'TPR.G26125' => 'tpr', 'TWI09G0677' => 'twi', 'TWI73G0287' => 'twi', 'unitig_748.g8326' => 'ugi', 'vmacro15370' => 'vma', 'vmacro15371' => 'vma', 'vmacro15372' => 'vma', 'vmacro15373' => 'vma', 'vmacro15374' => 'vma', 'VMungo0720G2826' => 'vmu', 'Zm00001eb116960' => 'zma', 'Zm00001eb301260' => 'zma', 'Zm00001eb301270' => 'zma' ), 'gf_id' => 'HOM05D001460', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001460' ), 'data_identifier' => 'HOM05D001460', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001460', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '433', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p22980' => 'bna', 'A01p32340' => 'bna', 'A03p42970' => 'bna', 'A05p25880' => 'bna', 'Aa31LG8G9320' => 'aar', 'Aa31LG8G9330' => 'aar', 'Aa31LG8G9340' => 'aar', 'Aa31sc221G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1034' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1528' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.829' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2222' => 'aag', 'Ah.12g058830' => 'amhyb', 'Ah.12g058840' => 'amhyb', 'AL3G37160' => 'aly', 'AL7G41310' => 'aly', 'Aqoxy5G00395' => 'aox', 'Aqoxy5G00396' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0C8NZA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5185HY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JZ1PRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MD3LS0' => 'arhy', 'AT3G22840' => 'ath', 'AT4G14690' => 'ath', 'ATR0665G054' => 'atr', 'Atru.chr4.2344' => 'acertr', 'Atru.chr4.2346' => 'acertr', 'Atru.chr4.2347' => 'acertr', 'Atru.chr4.2348' => 'acertr', 'Atru.chr4.2355' => 'acertr', 'Atru.chr4.2356' => 'acertr', 'Atru.chr4.2358' => 'acertr', 'Atru.chr4.2359' => 'acertr', 'Atru.chr4.2360' => 'acertr', 'Atru.chr4.2361' => 'acertr', 'AUR62030476' => 'cqu', 'AUR62030478' => 'cqu', 'AUR62030819' => 'cqu', 'AUR62030820' => 'cqu', 'BcaB03g14648' => 'bca', 'BcaB04g20492' => 'bca', 'BcaB06g26399' => 'bca', 'BcaC01g03416' => 'bca', 'BcaC01g03419' => 'bca', 'BcaC01g03421' => 'bca', 'BcaC01g03424' => 'bca', 'BcaC05g28012' => 'bca', 'BcaC09g49212' => 'bca', 'BcaC09g50140' => 'bca', 'BcaNung00346' => 'bca', 'BolC1t02785H' => 'bol', 'BolC1t04095H' => 'bol', 'BolC3t17545H' => 'bol', 'BolC5t32769H' => 'bol', 'BraA01t02211Z' => 'bra', 'BraA01t03359Z' => 'bra', 'BraA03t13441Z' => 'bra', 'BraA05t21476Z' => 'bra', 'C01p28420' => 'bna', 'C01p41350' => 'bna', 'C03p52750' => 'bna', 'C03p52780' => 'bna', 'C05p40270' => 'bna', 'CAN.G1437.9' => 'can', 'CANSAT78G0035' => 'cansat', 'CANSAT78G1036' => 'cansat', 'CANSAT78G2272' => 'cansat', 'CANSAT78G2478' => 'cansat', 'CARHR098700' => 'chi', 'CARHR221120' => 'chi', 'CARHR221150' => 'chi', 'Carub.0003s2297' => 'cru', 'Carub.0007s2749' => 'cru', 'Carub.0007s2750' => 'cru', 'Carub.0007s2751' => 'cru', 'Ca_10849_v3' => 'car', 'Cc03_g04300' => 'ccan', 'CDE02G3648' => 'cde', 'CDE05G0060' => 'cde', 'CDE05G0692' => 'cde', 'CDE05G2285' => 'cde', 'CDE05G2884' => 'cde', 'CDE05G3072' => 'cde', 'Cfa008439' => 'cfa', 'Cfa008441' => 'cfa', 'Cfa008443' => 'cfa', 'Cfa008448' => 'cfa', 'Ciclev10005974m.g' => 'ccl', 'Ciclev10006006m.g' => 'ccl', 'Ciclev10006775m.g' => 'ccl', 'CiPaw.02G120400' => 'cil', 'CiPaw.02G120500' => 'cil', 'CiPaw.02G120600' => 'cil', 'ClCG05G004850' => 'cla', 'COL.COLO4_21566' => 'col', 'Cpa.g.sc44.124' => 'cpa', 'Cre07.g320400' => 'cre', 'Cre07.g320450' => 'cre', 'Cre08.g384650' => 'cre', 'Cre09.g393173' => 'cre', 'Cre09.g394325' => 'cre', 'Cre14.g626750' => 'cre', 'Cre16.g679250' => 'cre', 'CsaV3_3G012890' => 'csa', 'CSS0010865' => 'camsi', 'CSS0044338' => 'camsi', 'DCAR_002366' => 'dca', 'DCAR_030687' => 'dca', 'DCAR_030688' => 'dca', 'Dinv14047' => 'din', 'Dinv14048' => 'din', 'Duzib151G0105' => 'dzi', 'Duzib151G0114' => 'dzi', 'Duzib212G1029' => 'dzi', 'ECA232G3536' => 'eca', 'ECA240G0786' => 'eca', 'ECA240G1802' => 'eca', 'ECA240G3760' => 'eca', 'ECA240G3920' => 'eca', 'EL10Ac5g12536' => 'bvu', 'EL10Ac5g12537' => 'bvu', 'EL10Ac5g12538' => 'bvu', 'Eucgr.B01004' => 'egr', 'Eucgr.B01006' => 'egr', 'Eucgr.B01007' => 'egr', 'Eucgr.B01008' => 'egr', 'Eucgr.B01895' => 'egr', 'Eucgr.B01896' => 'egr', 'FAN04G1456' => 'fan', 'FAN08G1769' => 'fan', 'FAN08G2160' => 'fan', 'FAN13G2403' => 'fan', 'FAN13G3303' => 'fan', 'FAN15G2435' => 'fan', 'FAN17G0672' => 'fan', 'FAN17G2441' => 'fan', 'FAN18G1024' => 'fan', 'FAN22G1458' => 'fan', 'FAN24G0037' => 'fan', 'FAN24G0429' => 'fan', 'FAN24G2387' => 'fan', 'FAN27G2746' => 'fan', 'FvH4_2g20400' => 'fve', 'FvH4_2g20420' => 'fve', 'FvH4_2g20430' => 'fve', 'FvH4_4g01270' => 'fve', 'FvH4_4g01290' => 'fve', 'FvH4_4g01300' => 'fve', 'FvH4_4g01310' => 'fve', 'FvH4_4g01330' => 'fve', 'FvH4_5g09070' => 'fve', 'Glyma.10G243800' => 'gma', 'Glyma.20G150600' => 'gma', 'Gohir.A09G219200' => 'ghi', 'Gohir.A09G219300' => 'ghi', 'Gohir.D09G221400' => 'ghi', 'Gohir.D09G221500' => 'ghi', 'Gorai.006G242600' => 'gra', 'Gorai.006G242700' => 'gra', 'GSVIVG01018044001' => 'vvi', 'HanXRQChr03g0083821' => 'han', 'HanXRQChr03g0083841' => 'han', 'HanXRQChr03g0083881' => 'han', 'HanXRQChr03g0083901' => 'han', 'HanXRQChr03g0083921' => 'han', 'HanXRQChr03g0085331' => 'han', 'HanXRQChr03g0085361' => 'han', 'HanXRQChr03g0085411' => 'han', 'HanXRQChr03g0085421' => 'han', 'HanXRQChr03g0085431' => 'han', 'HanXRQChr08g0221991' => 'han', 'HanXRQChr11g0336061' => 'han', 'HanXRQChr11g0336411' => 'han', 'Haze_11234' => 'cav', 'Hma1.2p1_0549F.1_g177010' => 'hma', 'Hma1.2p1_0602F.1_g187630' => 'hma', 'Hund14876' => 'sun', 'Hund14879' => 'sun', 'Lalb_Chr06g0160741' => 'lal', 'Lalb_Chr21g0304781' => 'lal', 'Lj3A726G19' => 'lonja', 'Lj3A726T23' => 'lonja', 'Lj3A726T24' => 'lonja', 'Lj3A726T25' => 'lonja', 'Lj3A727T17' => 'lonja', 'Lj3C726T0' => 'lonja', 'Lj3C726T2' => 'lonja', 'Lj3P725T35' => 'lonja', 'Lj3P727T10' => 'lonja', 'Lj3P727T12' => 'lonja', 'Lj3P727T14' => 'lonja', 'Lj5g0023109' => 'lja', 'Lj6P646T44' => 'lonja', 'Lsat_1_v5_gn_6_75760' => 'lsa', 'Lsat_1_v5_gn_6_75800' => 'lsa', 'Lsat_1_v5_gn_6_75900' => 'lsa', 'Lsat_1_v5_gn_6_76240' => 'lsa', 'Lsat_1_v5_gn_6_76441' => 'lsa', 'Lsat_1_v5_gn_6_76700' => 'lsa', 'Lsat_1_v5_gn_6_76760' => 'lsa', 'Manes.15G033100' => 'mes', 'Mapoly0004s0074' => 'mpo', 'Mapoly0004s0075' => 'mpo', 'Mapoly0004s0163' => 'mpo', 'Mapoly0004s0164' => 'mpo', 'Mapoly0021s0018' => 'mpo', 'Mapoly0041s0136' => 'mpo', 'Mapoly0041s0137' => 'mpo', 'Mapoly0041s0138' => 'mpo', 'Mapoly0041s0139' => 'mpo', 'Mapoly0041s0141' => 'mpo', 'Mapoly0041s0142' => 'mpo', 'Mapoly0041s0143' => 'mpo', 'Mapoly0041s0144' => 'mpo', 'Mapoly0041s0145' => 'mpo', 'Mapoly0047s0106' => 'mpo', 'Mapoly0047s0108' => 'mpo', 'Mapoly0050s0051' => 'mpo', 'Mapoly0050s0052' => 'mpo', 'Mapoly0050s0053' => 'mpo', 'Mapoly0058s0013' => 'mpo', 'Mapoly0091s0078' => 'mpo', 'Mapoly0091s0079' => 'mpo', 'Mapoly0091s0080' => 'mpo', 'Mapoly0091s0081' => 'mpo', 'Mapoly0278s0004' => 'mpo', 'Mapoly0278s0005' => 'mpo', 'Mapoly0278s0006' => 'mpo', 'MBI11_g30648_MAGBIO' => 'mbi', 'MCO03G194' => 'mco', 'MCO03G590' => 'mco', 'MCO07G312' => 'mco', 'MCO10G318' => 'mco', 'MCO12G244' => 'mco', 'MCO13G148' => 'mco', 'MCO13G194' => 'mco', 'MCO16G238' => 'mco', 'MD06G1134100' => 'mdo', 'MD13G1200100' => 'mdo', 'MD13G1200300' => 'mdo', 'MD13G1200600' => 'mdo', 'MD14G1150400' => 'mdo', 'MD16G1200000' => 'mdo', 'Medtr1g102570' => 'mtr', 'Medtr1g102780' => 'mtr', 'Medtr1g102800' => 'mtr', 'Medtr1g102810' => 'mtr', 'Medtr1g102830' => 'mtr', 'MELO3C006499.2' => 'cme', 'Migut.G00385' => 'egut', 'MSTRG.4063' => 'ama', 'Nitab4.5_0000090g0260' => 'nta', 'Nitab4.5_0000977g0030' => 'nta', 'Nitab4.5_0002541g0040' => 'nta', 'Nitab4.5_0007068g0040' => 'nta', 'Nn005s41408' => 'nnu', 'Nn005s41410' => 'nnu', 'Oeu010310.1' => 'oeu', 'Oeu010311.1' => 'oeu', 'Oeu043472.1' => 'oeu', 'Os01g0246400' => 'osa', 'Os04g0267950' => 'osa', 'Os07g0178700' => 'osa', 'Os07g0178800' => 'osa', 'Peaxi162Scf00316g00046' => 'pax', 'Peaxi162Scf00316g00049' => 'pax', 'Peaxi162Scf00316g00059' => 'pax', 'Peaxi162Scf00316g00328' => 'pax', 'Peaxi162Scf00316g00329' => 'pax', 'Peaxi162Scf00316g00411' => 'pax', 'Peaxi162Scf00316g00521' => 'pax', 'Peaxi162Scf00492g00068' => 'pax', 'Peaxi162Scf35631g00002' => 'pax', 'PGR142G3720' => 'pgr', 'PGSC0003DMG400006442' => 'stu', 'Phvul.007G062000' => 'pvu', 'Potri.008G157750' => 'ptr', 'Potri.008G157900' => 'ptr', 'Potri.008G158000' => 'ptr', 'Potri.008G158200' => 'ptr', 'Pp3c11_7280' => 'ppa', 'Pp3c11_7980' => 'ppa', 'Pp3c12_19450' => 'ppa', 'Pp3c14_1480' => 'ppa', 'Pp3c14_1501' => 'ppa', 'Pp3c16_4900' => 'ppa', 'Pp3c16_5010' => 'ppa', 'Pp3c16_5060' => 'ppa', 'Pp3c19_18250' => 'ppa', 'Pp3c23_8530' => 'ppa', 'Pp3c23_8550' => 'ppa', 'Pp3c24_9670' => 'ppa', 'Pp3c2_21390' => 'ppa', 'Pp3c2_31380' => 'ppa', 'Pp3c3_16620' => 'ppa', 'Pp3c3_8090' => 'ppa', 'Pp3c3_8110' => 'ppa', 'Pp3c3_8130' => 'ppa', 'Pp3c3_8150' => 'ppa', 'Pp3c4_14320' => 'ppa', 'Pp3c6_2560' => 'ppa', 'Pp3c9_16700' => 'ppa', 'PRCOL_00000234' => 'pco', 'PRCOL_00000235' => 'pco', 'PRCOL_00000777' => 'pco', 'PRCOL_00002344' => 'pco', 'PRCOL_00002372' => 'pco', 'PRCOL_00006120' => 'pco', 'Prupe.1G021400' => 'ppe', 'Prupe.1G021500' => 'ppe', 'Prupe.1G021600' => 'ppe', 'Prupe.1G021700' => 'ppe', 'Prupe.1G021800' => 'ppe', 'Prupe.5G145100' => 'ppe', 'Psat6g204040' => 'psa', 'Psat6g204800' => 'psa', 'Psat6g204920' => 'psa', 'Psat6g204960' => 'psa', 'Psat6g205080' => 'psa', 'PSO017G0271' => 'pso', 'PSO017G1276' => 'pso', 'PSO017G1429' => 'pso', 'PSO017G1861' => 'pso', 'PSO017G2787' => 'pso', 'PSO017G4466' => 'pso', 'PSO017G5118' => 'pso', 'PSO017G5420' => 'pso', 'PSO063G3678' => 'pso', 'PSO210G0546' => 'pso', 'PSO317G0001' => 'pso', 'PSO357G0512' => 'pso', 'PSO478G2682' => 'pso', 'PSO647G0001' => 'pso', 'PSO675G0001' => 'pso', 'PSO675G2699' => 'pso', 'PSO675G2849' => 'pso', 'PSO675G4991' => 'pso', 'PSO689G0001' => 'pso', 'QL06p000916' => 'qlo', 'QL06p000921' => 'qlo', 'QL06p001398' => 'qlo', 'QL06p001407' => 'qlo', 'QL06p002031' => 'qlo', 'RcHm_v2.0_Chr4g0387791' => 'rch', 'RcHm_v2.0_Chr4g0387801' => 'rch', 'RcHm_v2.0_Chr6g0286501' => 'rch', 'RcHm_v2.0_Chr6g0286511' => 'rch', 'RcHm_v2.0_Chr6g0286521' => 'rch', 'RcHm_v2.0_Chr6g0286531' => 'rch', 'RcHm_v2.0_Chr7g0189141' => 'rch', 'Rhsim02G0028700' => 'rsi', 'Rhsim02G0028800' => 'rsi', 'Rhsim02G0028900' => 'rsi', 'Rhsim02G0029000' => 'rsi', 'Rhsim02G0029100' => 'rsi', 'Rhsim02G0029200' => 'rsi', 'Rhsim02G0029300' => 'rsi', 'Rhsim02G0029400' => 'rsi', 'Rhsim02G0029500' => 'rsi', 'Rhsim02G0029600' => 'rsi', 'RhsimUnG0024000' => 'rsi', 'RhsimUnG0024100' => 'rsi', 'RhsimUnG0024200' => 'rsi', 'RhsimUnG0024300' => 'rsi', 'RhsimUnG0024400' => 'rsi', 'RhsimUnG0024500' => 'rsi', 'RhsimUnG0024700' => 'rsi', 'RhsimUnG0024800' => 'rsi', 'RhsimUnG0024900' => 'rsi', 'RhsimUnG0025100' => 'rsi', 'Sabra08G0120200' => 'sbr', 'Sabra08G0120300' => 'sbr', 'Sabra08G0120500' => 'sbr', 'Sabra08G0120600' => 'sbr', 'Sabra10G0158900' => 'sbr', 'SalBow2G3492' => 'sbo', 'Sc13g0004760' => 'sci', 'Sc13g0004770' => 'sci', 'Sed0003417' => 'sed', 'Sed0019750' => 'sed', 'SEGI_03419' => 'sgi', 'SEGI_05907' => 'sgi', 'SEGI_10682' => 'sgi', 'SEGI_13528' => 'sgi', 'SEGI_16081' => 'sgi', 'SEGI_19370' => 'sgi', 'SEGI_21015' => 'sgi', 'SEGI_21944' => 'sgi', 'SEGI_32906' => 'sgi', 'SEGI_33093' => 'sgi', 'SEGI_36110' => 'sgi', 'SEGI_40397' => 'sgi', 'SGA_v2.0_scaffold191G40426' => 'sas', 'SGA_v2.0_scaffold353G49717' => 'sas', 'SGA_v2.0_scaffold50G18550' => 'sas', 'SMO119G0173' => 'smo', 'SMO172G0002' => 'smo', 'Solyc09g082690.3' => 'sly', 'Solyc09g082700.2' => 'sly', 'Sopen09g031550' => 'spe', 'Sopen09g031560' => 'spe', 'Sp3g20540' => 'spa', 'Sp7g07580' => 'spa', 'TAR134G0002' => 'tar', 'TAR236G0001' => 'tar', 'TAR365G0892' => 'tar', 'TAR636G0166' => 'tar', 'TAR636G0646' => 'tar', 'TAR636G0869' => 'tar', 'TAR636G1317' => 'tar', 'TAR636G1744' => 'tar', 'TAR636G3358' => 'tar', 'TAR636G3436' => 'tar', 'THA.LOC104803047' => 'tha', 'Thecc.04G238900' => 'tca', 'Thhalv10021557m.g' => 'esa', 'Thhalv10026318m.g' => 'esa', 'Thhalv10026335m.g' => 'esa', 'TPR.G17433' => 'tpr', 'TPR.G18915' => 'tpr', 'TPR.G26125' => 'tpr', 'TWI09G0677' => 'twi', 'TWI73G0287' => 'twi', 'unitig_748.g8326' => 'ugi', 'vmacro15370' => 'vma', 'vmacro15371' => 'vma', 'vmacro15372' => 'vma', 'vmacro15373' => 'vma', 'vmacro15374' => 'vma', 'VMungo0720G2826' => 'vmu', 'Zm00001eb116960' => 'zma', 'Zm00001eb301260' => 'zma', 'Zm00001eb301270' => 'zma' ) $gf_id = 'HOM05D001460' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001460' ) $data_identifier = 'HOM05D001460' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 4, 'aag' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 2, 'aox' => (int) 2, 'arhy' => (int) 4, 'ath' => (int) 2, 'atr' => (int) 1, 'acertr' => (int) 10, 'cqu' => (int) 4, 'bca' => (int) 11, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 1, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 1, 'ccan' => (int) 1, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 1, 'col' => (int) 1, 'cpa' => (int) 1, 'cre' => (int) 7, 'csa' => (int) 1, 'camsi' => (int) 2, 'dca' => (int) 3, 'din' => (int) 2, 'dzi' => (int) 3, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 14, 'fve' => (int) 9, 'gma' => (int) 2, 'ghi' => (int) 4, 'gra' => (int) 2, 'vvi' => (int) 1, 'han' => (int) 13, 'cav' => (int) 1, 'hma' => (int) 2, 'sun' => (int) 2, 'lal' => (int) 2, 'lonja' => (int) 12, 'lja' => (int) 1, 'lsa' => (int) 7, 'mes' => (int) 1, 'mpo' => (int) 27, 'mbi' => (int) 1, 'mco' => (int) 8, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 1, 'egut' => (int) 1, 'ama' => (int) 1, 'nta' => (int) 4, 'nnu' => (int) 2, 'oeu' => (int) 3, 'osa' => (int) 4, 'pax' => (int) 9, 'pgr' => (int) 1, 'stu' => (int) 1, 'pvu' => (int) 1, 'ptr' => (int) 4, 'ppa' => (int) 22, 'pco' => (int) 6, 'ppe' => (int) 6, 'psa' => (int) 5, 'pso' => (int) 19, 'qlo' => (int) 5, 'rch' => (int) 7, 'rsi' => (int) 20, 'sbr' => (int) 5, 'sbo' => (int) 1, 'sci' => (int) 2, 'sed' => (int) 2, 'sgi' => (int) 12, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 2, 'tar' => (int) 10, 'tha' => (int) 1, 'tca' => (int) 1, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 2, 'ugi' => (int) 1, 'vma' => (int) 5, 'vmu' => (int) 1, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb301270' $species_info = array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ) $local_species = 'aar' $disabled = '' $selected = '' $num_hits = (int) 0include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001460', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '433', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p22980' => 'bna', 'A01p32340' => 'bna', 'A03p42970' => 'bna', 'A05p25880' => 'bna', 'Aa31LG8G9320' => 'aar', 'Aa31LG8G9330' => 'aar', 'Aa31LG8G9340' => 'aar', 'Aa31sc221G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1034' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1528' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.829' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2222' => 'aag', 'Ah.12g058830' => 'amhyb', 'Ah.12g058840' => 'amhyb', 'AL3G37160' => 'aly', 'AL7G41310' => 'aly', 'Aqoxy5G00395' => 'aox', 'Aqoxy5G00396' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0C8NZA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5185HY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JZ1PRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MD3LS0' => 'arhy', 'AT3G22840' => 'ath', 'AT4G14690' => 'ath', 'ATR0665G054' => 'atr', 'Atru.chr4.2344' => 'acertr', 'Atru.chr4.2346' => 'acertr', 'Atru.chr4.2347' => 'acertr', 'Atru.chr4.2348' => 'acertr', 'Atru.chr4.2355' => 'acertr', 'Atru.chr4.2356' => 'acertr', 'Atru.chr4.2358' => 'acertr', 'Atru.chr4.2359' => 'acertr', 'Atru.chr4.2360' => 'acertr', 'Atru.chr4.2361' => 'acertr', 'AUR62030476' => 'cqu', 'AUR62030478' => 'cqu', 'AUR62030819' => 'cqu', 'AUR62030820' => 'cqu', 'BcaB03g14648' => 'bca', 'BcaB04g20492' => 'bca', 'BcaB06g26399' => 'bca', 'BcaC01g03416' => 'bca', 'BcaC01g03419' => 'bca', 'BcaC01g03421' => 'bca', 'BcaC01g03424' => 'bca', 'BcaC05g28012' => 'bca', 'BcaC09g49212' => 'bca', 'BcaC09g50140' => 'bca', 'BcaNung00346' => 'bca', 'BolC1t02785H' => 'bol', 'BolC1t04095H' => 'bol', 'BolC3t17545H' => 'bol', 'BolC5t32769H' => 'bol', 'BraA01t02211Z' => 'bra', 'BraA01t03359Z' => 'bra', 'BraA03t13441Z' => 'bra', 'BraA05t21476Z' => 'bra', 'C01p28420' => 'bna', 'C01p41350' => 'bna', 'C03p52750' => 'bna', 'C03p52780' => 'bna', 'C05p40270' => 'bna', 'CAN.G1437.9' => 'can', 'CANSAT78G0035' => 'cansat', 'CANSAT78G1036' => 'cansat', 'CANSAT78G2272' => 'cansat', 'CANSAT78G2478' => 'cansat', 'CARHR098700' => 'chi', 'CARHR221120' => 'chi', 'CARHR221150' => 'chi', 'Carub.0003s2297' => 'cru', 'Carub.0007s2749' => 'cru', 'Carub.0007s2750' => 'cru', 'Carub.0007s2751' => 'cru', 'Ca_10849_v3' => 'car', 'Cc03_g04300' => 'ccan', 'CDE02G3648' => 'cde', 'CDE05G0060' => 'cde', 'CDE05G0692' => 'cde', 'CDE05G2285' => 'cde', 'CDE05G2884' => 'cde', 'CDE05G3072' => 'cde', 'Cfa008439' => 'cfa', 'Cfa008441' => 'cfa', 'Cfa008443' => 'cfa', 'Cfa008448' => 'cfa', 'Ciclev10005974m.g' => 'ccl', 'Ciclev10006006m.g' => 'ccl', 'Ciclev10006775m.g' => 'ccl', 'CiPaw.02G120400' => 'cil', 'CiPaw.02G120500' => 'cil', 'CiPaw.02G120600' => 'cil', 'ClCG05G004850' => 'cla', 'COL.COLO4_21566' => 'col', 'Cpa.g.sc44.124' => 'cpa', 'Cre07.g320400' => 'cre', 'Cre07.g320450' => 'cre', 'Cre08.g384650' => 'cre', 'Cre09.g393173' => 'cre', 'Cre09.g394325' => 'cre', 'Cre14.g626750' => 'cre', 'Cre16.g679250' => 'cre', 'CsaV3_3G012890' => 'csa', 'CSS0010865' => 'camsi', 'CSS0044338' => 'camsi', 'DCAR_002366' => 'dca', 'DCAR_030687' => 'dca', 'DCAR_030688' => 'dca', 'Dinv14047' => 'din', 'Dinv14048' => 'din', 'Duzib151G0105' => 'dzi', 'Duzib151G0114' => 'dzi', 'Duzib212G1029' => 'dzi', 'ECA232G3536' => 'eca', 'ECA240G0786' => 'eca', 'ECA240G1802' => 'eca', 'ECA240G3760' => 'eca', 'ECA240G3920' => 'eca', 'EL10Ac5g12536' => 'bvu', 'EL10Ac5g12537' => 'bvu', 'EL10Ac5g12538' => 'bvu', 'Eucgr.B01004' => 'egr', 'Eucgr.B01006' => 'egr', 'Eucgr.B01007' => 'egr', 'Eucgr.B01008' => 'egr', 'Eucgr.B01895' => 'egr', 'Eucgr.B01896' => 'egr', 'FAN04G1456' => 'fan', 'FAN08G1769' => 'fan', 'FAN08G2160' => 'fan', 'FAN13G2403' => 'fan', 'FAN13G3303' => 'fan', 'FAN15G2435' => 'fan', 'FAN17G0672' => 'fan', 'FAN17G2441' => 'fan', 'FAN18G1024' => 'fan', 'FAN22G1458' => 'fan', 'FAN24G0037' => 'fan', 'FAN24G0429' => 'fan', 'FAN24G2387' => 'fan', 'FAN27G2746' => 'fan', 'FvH4_2g20400' => 'fve', 'FvH4_2g20420' => 'fve', 'FvH4_2g20430' => 'fve', 'FvH4_4g01270' => 'fve', 'FvH4_4g01290' => 'fve', 'FvH4_4g01300' => 'fve', 'FvH4_4g01310' => 'fve', 'FvH4_4g01330' => 'fve', 'FvH4_5g09070' => 'fve', 'Glyma.10G243800' => 'gma', 'Glyma.20G150600' => 'gma', 'Gohir.A09G219200' => 'ghi', 'Gohir.A09G219300' => 'ghi', 'Gohir.D09G221400' => 'ghi', 'Gohir.D09G221500' => 'ghi', 'Gorai.006G242600' => 'gra', 'Gorai.006G242700' => 'gra', 'GSVIVG01018044001' => 'vvi', 'HanXRQChr03g0083821' => 'han', 'HanXRQChr03g0083841' => 'han', 'HanXRQChr03g0083881' => 'han', 'HanXRQChr03g0083901' => 'han', 'HanXRQChr03g0083921' => 'han', 'HanXRQChr03g0085331' => 'han', 'HanXRQChr03g0085361' => 'han', 'HanXRQChr03g0085411' => 'han', 'HanXRQChr03g0085421' => 'han', 'HanXRQChr03g0085431' => 'han', 'HanXRQChr08g0221991' => 'han', 'HanXRQChr11g0336061' => 'han', 'HanXRQChr11g0336411' => 'han', 'Haze_11234' => 'cav', 'Hma1.2p1_0549F.1_g177010' => 'hma', 'Hma1.2p1_0602F.1_g187630' => 'hma', 'Hund14876' => 'sun', 'Hund14879' => 'sun', 'Lalb_Chr06g0160741' => 'lal', 'Lalb_Chr21g0304781' => 'lal', 'Lj3A726G19' => 'lonja', 'Lj3A726T23' => 'lonja', 'Lj3A726T24' => 'lonja', 'Lj3A726T25' => 'lonja', 'Lj3A727T17' => 'lonja', 'Lj3C726T0' => 'lonja', 'Lj3C726T2' => 'lonja', 'Lj3P725T35' => 'lonja', 'Lj3P727T10' => 'lonja', 'Lj3P727T12' => 'lonja', 'Lj3P727T14' => 'lonja', 'Lj5g0023109' => 'lja', 'Lj6P646T44' => 'lonja', 'Lsat_1_v5_gn_6_75760' => 'lsa', 'Lsat_1_v5_gn_6_75800' => 'lsa', 'Lsat_1_v5_gn_6_75900' => 'lsa', 'Lsat_1_v5_gn_6_76240' => 'lsa', 'Lsat_1_v5_gn_6_76441' => 'lsa', 'Lsat_1_v5_gn_6_76700' => 'lsa', 'Lsat_1_v5_gn_6_76760' => 'lsa', 'Manes.15G033100' => 'mes', 'Mapoly0004s0074' => 'mpo', 'Mapoly0004s0075' => 'mpo', 'Mapoly0004s0163' => 'mpo', 'Mapoly0004s0164' => 'mpo', 'Mapoly0021s0018' => 'mpo', 'Mapoly0041s0136' => 'mpo', 'Mapoly0041s0137' => 'mpo', 'Mapoly0041s0138' => 'mpo', 'Mapoly0041s0139' => 'mpo', 'Mapoly0041s0141' => 'mpo', 'Mapoly0041s0142' => 'mpo', 'Mapoly0041s0143' => 'mpo', 'Mapoly0041s0144' => 'mpo', 'Mapoly0041s0145' => 'mpo', 'Mapoly0047s0106' => 'mpo', 'Mapoly0047s0108' => 'mpo', 'Mapoly0050s0051' => 'mpo', 'Mapoly0050s0052' => 'mpo', 'Mapoly0050s0053' => 'mpo', 'Mapoly0058s0013' => 'mpo', 'Mapoly0091s0078' => 'mpo', 'Mapoly0091s0079' => 'mpo', 'Mapoly0091s0080' => 'mpo', 'Mapoly0091s0081' => 'mpo', 'Mapoly0278s0004' => 'mpo', 'Mapoly0278s0005' => 'mpo', 'Mapoly0278s0006' => 'mpo', 'MBI11_g30648_MAGBIO' => 'mbi', 'MCO03G194' => 'mco', 'MCO03G590' => 'mco', 'MCO07G312' => 'mco', 'MCO10G318' => 'mco', 'MCO12G244' => 'mco', 'MCO13G148' => 'mco', 'MCO13G194' => 'mco', 'MCO16G238' => 'mco', 'MD06G1134100' => 'mdo', 'MD13G1200100' => 'mdo', 'MD13G1200300' => 'mdo', 'MD13G1200600' => 'mdo', 'MD14G1150400' => 'mdo', 'MD16G1200000' => 'mdo', 'Medtr1g102570' => 'mtr', 'Medtr1g102780' => 'mtr', 'Medtr1g102800' => 'mtr', 'Medtr1g102810' => 'mtr', 'Medtr1g102830' => 'mtr', 'MELO3C006499.2' => 'cme', 'Migut.G00385' => 'egut', 'MSTRG.4063' => 'ama', 'Nitab4.5_0000090g0260' => 'nta', 'Nitab4.5_0000977g0030' => 'nta', 'Nitab4.5_0002541g0040' => 'nta', 'Nitab4.5_0007068g0040' => 'nta', 'Nn005s41408' => 'nnu', 'Nn005s41410' => 'nnu', 'Oeu010310.1' => 'oeu', 'Oeu010311.1' => 'oeu', 'Oeu043472.1' => 'oeu', 'Os01g0246400' => 'osa', 'Os04g0267950' => 'osa', 'Os07g0178700' => 'osa', 'Os07g0178800' => 'osa', 'Peaxi162Scf00316g00046' => 'pax', 'Peaxi162Scf00316g00049' => 'pax', 'Peaxi162Scf00316g00059' => 'pax', 'Peaxi162Scf00316g00328' => 'pax', 'Peaxi162Scf00316g00329' => 'pax', 'Peaxi162Scf00316g00411' => 'pax', 'Peaxi162Scf00316g00521' => 'pax', 'Peaxi162Scf00492g00068' => 'pax', 'Peaxi162Scf35631g00002' => 'pax', 'PGR142G3720' => 'pgr', 'PGSC0003DMG400006442' => 'stu', 'Phvul.007G062000' => 'pvu', 'Potri.008G157750' => 'ptr', 'Potri.008G157900' => 'ptr', 'Potri.008G158000' => 'ptr', 'Potri.008G158200' => 'ptr', 'Pp3c11_7280' => 'ppa', 'Pp3c11_7980' => 'ppa', 'Pp3c12_19450' => 'ppa', 'Pp3c14_1480' => 'ppa', 'Pp3c14_1501' => 'ppa', 'Pp3c16_4900' => 'ppa', 'Pp3c16_5010' => 'ppa', 'Pp3c16_5060' => 'ppa', 'Pp3c19_18250' => 'ppa', 'Pp3c23_8530' => 'ppa', 'Pp3c23_8550' => 'ppa', 'Pp3c24_9670' => 'ppa', 'Pp3c2_21390' => 'ppa', 'Pp3c2_31380' => 'ppa', 'Pp3c3_16620' => 'ppa', 'Pp3c3_8090' => 'ppa', 'Pp3c3_8110' => 'ppa', 'Pp3c3_8130' => 'ppa', 'Pp3c3_8150' => 'ppa', 'Pp3c4_14320' => 'ppa', 'Pp3c6_2560' => 'ppa', 'Pp3c9_16700' => 'ppa', 'PRCOL_00000234' => 'pco', 'PRCOL_00000235' => 'pco', 'PRCOL_00000777' => 'pco', 'PRCOL_00002344' => 'pco', 'PRCOL_00002372' => 'pco', 'PRCOL_00006120' => 'pco', 'Prupe.1G021400' => 'ppe', 'Prupe.1G021500' => 'ppe', 'Prupe.1G021600' => 'ppe', 'Prupe.1G021700' => 'ppe', 'Prupe.1G021800' => 'ppe', 'Prupe.5G145100' => 'ppe', 'Psat6g204040' => 'psa', 'Psat6g204800' => 'psa', 'Psat6g204920' => 'psa', 'Psat6g204960' => 'psa', 'Psat6g205080' => 'psa', 'PSO017G0271' => 'pso', 'PSO017G1276' => 'pso', 'PSO017G1429' => 'pso', 'PSO017G1861' => 'pso', 'PSO017G2787' => 'pso', 'PSO017G4466' => 'pso', 'PSO017G5118' => 'pso', 'PSO017G5420' => 'pso', 'PSO063G3678' => 'pso', 'PSO210G0546' => 'pso', 'PSO317G0001' => 'pso', 'PSO357G0512' => 'pso', 'PSO478G2682' => 'pso', 'PSO647G0001' => 'pso', 'PSO675G0001' => 'pso', 'PSO675G2699' => 'pso', 'PSO675G2849' => 'pso', 'PSO675G4991' => 'pso', 'PSO689G0001' => 'pso', 'QL06p000916' => 'qlo', 'QL06p000921' => 'qlo', 'QL06p001398' => 'qlo', 'QL06p001407' => 'qlo', 'QL06p002031' => 'qlo', 'RcHm_v2.0_Chr4g0387791' => 'rch', 'RcHm_v2.0_Chr4g0387801' => 'rch', 'RcHm_v2.0_Chr6g0286501' => 'rch', 'RcHm_v2.0_Chr6g0286511' => 'rch', 'RcHm_v2.0_Chr6g0286521' => 'rch', 'RcHm_v2.0_Chr6g0286531' => 'rch', 'RcHm_v2.0_Chr7g0189141' => 'rch', 'Rhsim02G0028700' => 'rsi', 'Rhsim02G0028800' => 'rsi', 'Rhsim02G0028900' => 'rsi', 'Rhsim02G0029000' => 'rsi', 'Rhsim02G0029100' => 'rsi', 'Rhsim02G0029200' => 'rsi', 'Rhsim02G0029300' => 'rsi', 'Rhsim02G0029400' => 'rsi', 'Rhsim02G0029500' => 'rsi', 'Rhsim02G0029600' => 'rsi', 'RhsimUnG0024000' => 'rsi', 'RhsimUnG0024100' => 'rsi', 'RhsimUnG0024200' => 'rsi', 'RhsimUnG0024300' => 'rsi', 'RhsimUnG0024400' => 'rsi', 'RhsimUnG0024500' => 'rsi', 'RhsimUnG0024700' => 'rsi', 'RhsimUnG0024800' => 'rsi', 'RhsimUnG0024900' => 'rsi', 'RhsimUnG0025100' => 'rsi', 'Sabra08G0120200' => 'sbr', 'Sabra08G0120300' => 'sbr', 'Sabra08G0120500' => 'sbr', 'Sabra08G0120600' => 'sbr', 'Sabra10G0158900' => 'sbr', 'SalBow2G3492' => 'sbo', 'Sc13g0004760' => 'sci', 'Sc13g0004770' => 'sci', 'Sed0003417' => 'sed', 'Sed0019750' => 'sed', 'SEGI_03419' => 'sgi', 'SEGI_05907' => 'sgi', 'SEGI_10682' => 'sgi', 'SEGI_13528' => 'sgi', 'SEGI_16081' => 'sgi', 'SEGI_19370' => 'sgi', 'SEGI_21015' => 'sgi', 'SEGI_21944' => 'sgi', 'SEGI_32906' => 'sgi', 'SEGI_33093' => 'sgi', 'SEGI_36110' => 'sgi', 'SEGI_40397' => 'sgi', 'SGA_v2.0_scaffold191G40426' => 'sas', 'SGA_v2.0_scaffold353G49717' => 'sas', 'SGA_v2.0_scaffold50G18550' => 'sas', 'SMO119G0173' => 'smo', 'SMO172G0002' => 'smo', 'Solyc09g082690.3' => 'sly', 'Solyc09g082700.2' => 'sly', 'Sopen09g031550' => 'spe', 'Sopen09g031560' => 'spe', 'Sp3g20540' => 'spa', 'Sp7g07580' => 'spa', 'TAR134G0002' => 'tar', 'TAR236G0001' => 'tar', 'TAR365G0892' => 'tar', 'TAR636G0166' => 'tar', 'TAR636G0646' => 'tar', 'TAR636G0869' => 'tar', 'TAR636G1317' => 'tar', 'TAR636G1744' => 'tar', 'TAR636G3358' => 'tar', 'TAR636G3436' => 'tar', 'THA.LOC104803047' => 'tha', 'Thecc.04G238900' => 'tca', 'Thhalv10021557m.g' => 'esa', 'Thhalv10026318m.g' => 'esa', 'Thhalv10026335m.g' => 'esa', 'TPR.G17433' => 'tpr', 'TPR.G18915' => 'tpr', 'TPR.G26125' => 'tpr', 'TWI09G0677' => 'twi', 'TWI73G0287' => 'twi', 'unitig_748.g8326' => 'ugi', 'vmacro15370' => 'vma', 'vmacro15371' => 'vma', 'vmacro15372' => 'vma', 'vmacro15373' => 'vma', 'vmacro15374' => 'vma', 'VMungo0720G2826' => 'vmu', 'Zm00001eb116960' => 'zma', 'Zm00001eb301260' => 'zma', 'Zm00001eb301270' => 'zma' ), 'gf_id' => 'HOM05D001460', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001460' ), 'data_identifier' => 'HOM05D001460', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001460', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '433', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p22980' => 'bna', 'A01p32340' => 'bna', 'A03p42970' => 'bna', 'A05p25880' => 'bna', 'Aa31LG8G9320' => 'aar', 'Aa31LG8G9330' => 'aar', 'Aa31LG8G9340' => 'aar', 'Aa31sc221G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1034' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1528' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.829' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2222' => 'aag', 'Ah.12g058830' => 'amhyb', 'Ah.12g058840' => 'amhyb', 'AL3G37160' => 'aly', 'AL7G41310' => 'aly', 'Aqoxy5G00395' => 'aox', 'Aqoxy5G00396' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0C8NZA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5185HY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JZ1PRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MD3LS0' => 'arhy', 'AT3G22840' => 'ath', 'AT4G14690' => 'ath', 'ATR0665G054' => 'atr', 'Atru.chr4.2344' => 'acertr', 'Atru.chr4.2346' => 'acertr', 'Atru.chr4.2347' => 'acertr', 'Atru.chr4.2348' => 'acertr', 'Atru.chr4.2355' => 'acertr', 'Atru.chr4.2356' => 'acertr', 'Atru.chr4.2358' => 'acertr', 'Atru.chr4.2359' => 'acertr', 'Atru.chr4.2360' => 'acertr', 'Atru.chr4.2361' => 'acertr', 'AUR62030476' => 'cqu', 'AUR62030478' => 'cqu', 'AUR62030819' => 'cqu', 'AUR62030820' => 'cqu', 'BcaB03g14648' => 'bca', 'BcaB04g20492' => 'bca', 'BcaB06g26399' => 'bca', 'BcaC01g03416' => 'bca', 'BcaC01g03419' => 'bca', 'BcaC01g03421' => 'bca', 'BcaC01g03424' => 'bca', 'BcaC05g28012' => 'bca', 'BcaC09g49212' => 'bca', 'BcaC09g50140' => 'bca', 'BcaNung00346' => 'bca', 'BolC1t02785H' => 'bol', 'BolC1t04095H' => 'bol', 'BolC3t17545H' => 'bol', 'BolC5t32769H' => 'bol', 'BraA01t02211Z' => 'bra', 'BraA01t03359Z' => 'bra', 'BraA03t13441Z' => 'bra', 'BraA05t21476Z' => 'bra', 'C01p28420' => 'bna', 'C01p41350' => 'bna', 'C03p52750' => 'bna', 'C03p52780' => 'bna', 'C05p40270' => 'bna', 'CAN.G1437.9' => 'can', 'CANSAT78G0035' => 'cansat', 'CANSAT78G1036' => 'cansat', 'CANSAT78G2272' => 'cansat', 'CANSAT78G2478' => 'cansat', 'CARHR098700' => 'chi', 'CARHR221120' => 'chi', 'CARHR221150' => 'chi', 'Carub.0003s2297' => 'cru', 'Carub.0007s2749' => 'cru', 'Carub.0007s2750' => 'cru', 'Carub.0007s2751' => 'cru', 'Ca_10849_v3' => 'car', 'Cc03_g04300' => 'ccan', 'CDE02G3648' => 'cde', 'CDE05G0060' => 'cde', 'CDE05G0692' => 'cde', 'CDE05G2285' => 'cde', 'CDE05G2884' => 'cde', 'CDE05G3072' => 'cde', 'Cfa008439' => 'cfa', 'Cfa008441' => 'cfa', 'Cfa008443' => 'cfa', 'Cfa008448' => 'cfa', 'Ciclev10005974m.g' => 'ccl', 'Ciclev10006006m.g' => 'ccl', 'Ciclev10006775m.g' => 'ccl', 'CiPaw.02G120400' => 'cil', 'CiPaw.02G120500' => 'cil', 'CiPaw.02G120600' => 'cil', 'ClCG05G004850' => 'cla', 'COL.COLO4_21566' => 'col', 'Cpa.g.sc44.124' => 'cpa', 'Cre07.g320400' => 'cre', 'Cre07.g320450' => 'cre', 'Cre08.g384650' => 'cre', 'Cre09.g393173' => 'cre', 'Cre09.g394325' => 'cre', 'Cre14.g626750' => 'cre', 'Cre16.g679250' => 'cre', 'CsaV3_3G012890' => 'csa', 'CSS0010865' => 'camsi', 'CSS0044338' => 'camsi', 'DCAR_002366' => 'dca', 'DCAR_030687' => 'dca', 'DCAR_030688' => 'dca', 'Dinv14047' => 'din', 'Dinv14048' => 'din', 'Duzib151G0105' => 'dzi', 'Duzib151G0114' => 'dzi', 'Duzib212G1029' => 'dzi', 'ECA232G3536' => 'eca', 'ECA240G0786' => 'eca', 'ECA240G1802' => 'eca', 'ECA240G3760' => 'eca', 'ECA240G3920' => 'eca', 'EL10Ac5g12536' => 'bvu', 'EL10Ac5g12537' => 'bvu', 'EL10Ac5g12538' => 'bvu', 'Eucgr.B01004' => 'egr', 'Eucgr.B01006' => 'egr', 'Eucgr.B01007' => 'egr', 'Eucgr.B01008' => 'egr', 'Eucgr.B01895' => 'egr', 'Eucgr.B01896' => 'egr', 'FAN04G1456' => 'fan', 'FAN08G1769' => 'fan', 'FAN08G2160' => 'fan', 'FAN13G2403' => 'fan', 'FAN13G3303' => 'fan', 'FAN15G2435' => 'fan', 'FAN17G0672' => 'fan', 'FAN17G2441' => 'fan', 'FAN18G1024' => 'fan', 'FAN22G1458' => 'fan', 'FAN24G0037' => 'fan', 'FAN24G0429' => 'fan', 'FAN24G2387' => 'fan', 'FAN27G2746' => 'fan', 'FvH4_2g20400' => 'fve', 'FvH4_2g20420' => 'fve', 'FvH4_2g20430' => 'fve', 'FvH4_4g01270' => 'fve', 'FvH4_4g01290' => 'fve', 'FvH4_4g01300' => 'fve', 'FvH4_4g01310' => 'fve', 'FvH4_4g01330' => 'fve', 'FvH4_5g09070' => 'fve', 'Glyma.10G243800' => 'gma', 'Glyma.20G150600' => 'gma', 'Gohir.A09G219200' => 'ghi', 'Gohir.A09G219300' => 'ghi', 'Gohir.D09G221400' => 'ghi', 'Gohir.D09G221500' => 'ghi', 'Gorai.006G242600' => 'gra', 'Gorai.006G242700' => 'gra', 'GSVIVG01018044001' => 'vvi', 'HanXRQChr03g0083821' => 'han', 'HanXRQChr03g0083841' => 'han', 'HanXRQChr03g0083881' => 'han', 'HanXRQChr03g0083901' => 'han', 'HanXRQChr03g0083921' => 'han', 'HanXRQChr03g0085331' => 'han', 'HanXRQChr03g0085361' => 'han', 'HanXRQChr03g0085411' => 'han', 'HanXRQChr03g0085421' => 'han', 'HanXRQChr03g0085431' => 'han', 'HanXRQChr08g0221991' => 'han', 'HanXRQChr11g0336061' => 'han', 'HanXRQChr11g0336411' => 'han', 'Haze_11234' => 'cav', 'Hma1.2p1_0549F.1_g177010' => 'hma', 'Hma1.2p1_0602F.1_g187630' => 'hma', 'Hund14876' => 'sun', 'Hund14879' => 'sun', 'Lalb_Chr06g0160741' => 'lal', 'Lalb_Chr21g0304781' => 'lal', 'Lj3A726G19' => 'lonja', 'Lj3A726T23' => 'lonja', 'Lj3A726T24' => 'lonja', 'Lj3A726T25' => 'lonja', 'Lj3A727T17' => 'lonja', 'Lj3C726T0' => 'lonja', 'Lj3C726T2' => 'lonja', 'Lj3P725T35' => 'lonja', 'Lj3P727T10' => 'lonja', 'Lj3P727T12' => 'lonja', 'Lj3P727T14' => 'lonja', 'Lj5g0023109' => 'lja', 'Lj6P646T44' => 'lonja', 'Lsat_1_v5_gn_6_75760' => 'lsa', 'Lsat_1_v5_gn_6_75800' => 'lsa', 'Lsat_1_v5_gn_6_75900' => 'lsa', 'Lsat_1_v5_gn_6_76240' => 'lsa', 'Lsat_1_v5_gn_6_76441' => 'lsa', 'Lsat_1_v5_gn_6_76700' => 'lsa', 'Lsat_1_v5_gn_6_76760' => 'lsa', 'Manes.15G033100' => 'mes', 'Mapoly0004s0074' => 'mpo', 'Mapoly0004s0075' => 'mpo', 'Mapoly0004s0163' => 'mpo', 'Mapoly0004s0164' => 'mpo', 'Mapoly0021s0018' => 'mpo', 'Mapoly0041s0136' => 'mpo', 'Mapoly0041s0137' => 'mpo', 'Mapoly0041s0138' => 'mpo', 'Mapoly0041s0139' => 'mpo', 'Mapoly0041s0141' => 'mpo', 'Mapoly0041s0142' => 'mpo', 'Mapoly0041s0143' => 'mpo', 'Mapoly0041s0144' => 'mpo', 'Mapoly0041s0145' => 'mpo', 'Mapoly0047s0106' => 'mpo', 'Mapoly0047s0108' => 'mpo', 'Mapoly0050s0051' => 'mpo', 'Mapoly0050s0052' => 'mpo', 'Mapoly0050s0053' => 'mpo', 'Mapoly0058s0013' => 'mpo', 'Mapoly0091s0078' => 'mpo', 'Mapoly0091s0079' => 'mpo', 'Mapoly0091s0080' => 'mpo', 'Mapoly0091s0081' => 'mpo', 'Mapoly0278s0004' => 'mpo', 'Mapoly0278s0005' => 'mpo', 'Mapoly0278s0006' => 'mpo', 'MBI11_g30648_MAGBIO' => 'mbi', 'MCO03G194' => 'mco', 'MCO03G590' => 'mco', 'MCO07G312' => 'mco', 'MCO10G318' => 'mco', 'MCO12G244' => 'mco', 'MCO13G148' => 'mco', 'MCO13G194' => 'mco', 'MCO16G238' => 'mco', 'MD06G1134100' => 'mdo', 'MD13G1200100' => 'mdo', 'MD13G1200300' => 'mdo', 'MD13G1200600' => 'mdo', 'MD14G1150400' => 'mdo', 'MD16G1200000' => 'mdo', 'Medtr1g102570' => 'mtr', 'Medtr1g102780' => 'mtr', 'Medtr1g102800' => 'mtr', 'Medtr1g102810' => 'mtr', 'Medtr1g102830' => 'mtr', 'MELO3C006499.2' => 'cme', 'Migut.G00385' => 'egut', 'MSTRG.4063' => 'ama', 'Nitab4.5_0000090g0260' => 'nta', 'Nitab4.5_0000977g0030' => 'nta', 'Nitab4.5_0002541g0040' => 'nta', 'Nitab4.5_0007068g0040' => 'nta', 'Nn005s41408' => 'nnu', 'Nn005s41410' => 'nnu', 'Oeu010310.1' => 'oeu', 'Oeu010311.1' => 'oeu', 'Oeu043472.1' => 'oeu', 'Os01g0246400' => 'osa', 'Os04g0267950' => 'osa', 'Os07g0178700' => 'osa', 'Os07g0178800' => 'osa', 'Peaxi162Scf00316g00046' => 'pax', 'Peaxi162Scf00316g00049' => 'pax', 'Peaxi162Scf00316g00059' => 'pax', 'Peaxi162Scf00316g00328' => 'pax', 'Peaxi162Scf00316g00329' => 'pax', 'Peaxi162Scf00316g00411' => 'pax', 'Peaxi162Scf00316g00521' => 'pax', 'Peaxi162Scf00492g00068' => 'pax', 'Peaxi162Scf35631g00002' => 'pax', 'PGR142G3720' => 'pgr', 'PGSC0003DMG400006442' => 'stu', 'Phvul.007G062000' => 'pvu', 'Potri.008G157750' => 'ptr', 'Potri.008G157900' => 'ptr', 'Potri.008G158000' => 'ptr', 'Potri.008G158200' => 'ptr', 'Pp3c11_7280' => 'ppa', 'Pp3c11_7980' => 'ppa', 'Pp3c12_19450' => 'ppa', 'Pp3c14_1480' => 'ppa', 'Pp3c14_1501' => 'ppa', 'Pp3c16_4900' => 'ppa', 'Pp3c16_5010' => 'ppa', 'Pp3c16_5060' => 'ppa', 'Pp3c19_18250' => 'ppa', 'Pp3c23_8530' => 'ppa', 'Pp3c23_8550' => 'ppa', 'Pp3c24_9670' => 'ppa', 'Pp3c2_21390' => 'ppa', 'Pp3c2_31380' => 'ppa', 'Pp3c3_16620' => 'ppa', 'Pp3c3_8090' => 'ppa', 'Pp3c3_8110' => 'ppa', 'Pp3c3_8130' => 'ppa', 'Pp3c3_8150' => 'ppa', 'Pp3c4_14320' => 'ppa', 'Pp3c6_2560' => 'ppa', 'Pp3c9_16700' => 'ppa', 'PRCOL_00000234' => 'pco', 'PRCOL_00000235' => 'pco', 'PRCOL_00000777' => 'pco', 'PRCOL_00002344' => 'pco', 'PRCOL_00002372' => 'pco', 'PRCOL_00006120' => 'pco', 'Prupe.1G021400' => 'ppe', 'Prupe.1G021500' => 'ppe', 'Prupe.1G021600' => 'ppe', 'Prupe.1G021700' => 'ppe', 'Prupe.1G021800' => 'ppe', 'Prupe.5G145100' => 'ppe', 'Psat6g204040' => 'psa', 'Psat6g204800' => 'psa', 'Psat6g204920' => 'psa', 'Psat6g204960' => 'psa', 'Psat6g205080' => 'psa', 'PSO017G0271' => 'pso', 'PSO017G1276' => 'pso', 'PSO017G1429' => 'pso', 'PSO017G1861' => 'pso', 'PSO017G2787' => 'pso', 'PSO017G4466' => 'pso', 'PSO017G5118' => 'pso', 'PSO017G5420' => 'pso', 'PSO063G3678' => 'pso', 'PSO210G0546' => 'pso', 'PSO317G0001' => 'pso', 'PSO357G0512' => 'pso', 'PSO478G2682' => 'pso', 'PSO647G0001' => 'pso', 'PSO675G0001' => 'pso', 'PSO675G2699' => 'pso', 'PSO675G2849' => 'pso', 'PSO675G4991' => 'pso', 'PSO689G0001' => 'pso', 'QL06p000916' => 'qlo', 'QL06p000921' => 'qlo', 'QL06p001398' => 'qlo', 'QL06p001407' => 'qlo', 'QL06p002031' => 'qlo', 'RcHm_v2.0_Chr4g0387791' => 'rch', 'RcHm_v2.0_Chr4g0387801' => 'rch', 'RcHm_v2.0_Chr6g0286501' => 'rch', 'RcHm_v2.0_Chr6g0286511' => 'rch', 'RcHm_v2.0_Chr6g0286521' => 'rch', 'RcHm_v2.0_Chr6g0286531' => 'rch', 'RcHm_v2.0_Chr7g0189141' => 'rch', 'Rhsim02G0028700' => 'rsi', 'Rhsim02G0028800' => 'rsi', 'Rhsim02G0028900' => 'rsi', 'Rhsim02G0029000' => 'rsi', 'Rhsim02G0029100' => 'rsi', 'Rhsim02G0029200' => 'rsi', 'Rhsim02G0029300' => 'rsi', 'Rhsim02G0029400' => 'rsi', 'Rhsim02G0029500' => 'rsi', 'Rhsim02G0029600' => 'rsi', 'RhsimUnG0024000' => 'rsi', 'RhsimUnG0024100' => 'rsi', 'RhsimUnG0024200' => 'rsi', 'RhsimUnG0024300' => 'rsi', 'RhsimUnG0024400' => 'rsi', 'RhsimUnG0024500' => 'rsi', 'RhsimUnG0024700' => 'rsi', 'RhsimUnG0024800' => 'rsi', 'RhsimUnG0024900' => 'rsi', 'RhsimUnG0025100' => 'rsi', 'Sabra08G0120200' => 'sbr', 'Sabra08G0120300' => 'sbr', 'Sabra08G0120500' => 'sbr', 'Sabra08G0120600' => 'sbr', 'Sabra10G0158900' => 'sbr', 'SalBow2G3492' => 'sbo', 'Sc13g0004760' => 'sci', 'Sc13g0004770' => 'sci', 'Sed0003417' => 'sed', 'Sed0019750' => 'sed', 'SEGI_03419' => 'sgi', 'SEGI_05907' => 'sgi', 'SEGI_10682' => 'sgi', 'SEGI_13528' => 'sgi', 'SEGI_16081' => 'sgi', 'SEGI_19370' => 'sgi', 'SEGI_21015' => 'sgi', 'SEGI_21944' => 'sgi', 'SEGI_32906' => 'sgi', 'SEGI_33093' => 'sgi', 'SEGI_36110' => 'sgi', 'SEGI_40397' => 'sgi', 'SGA_v2.0_scaffold191G40426' => 'sas', 'SGA_v2.0_scaffold353G49717' => 'sas', 'SGA_v2.0_scaffold50G18550' => 'sas', 'SMO119G0173' => 'smo', 'SMO172G0002' => 'smo', 'Solyc09g082690.3' => 'sly', 'Solyc09g082700.2' => 'sly', 'Sopen09g031550' => 'spe', 'Sopen09g031560' => 'spe', 'Sp3g20540' => 'spa', 'Sp7g07580' => 'spa', 'TAR134G0002' => 'tar', 'TAR236G0001' => 'tar', 'TAR365G0892' => 'tar', 'TAR636G0166' => 'tar', 'TAR636G0646' => 'tar', 'TAR636G0869' => 'tar', 'TAR636G1317' => 'tar', 'TAR636G1744' => 'tar', 'TAR636G3358' => 'tar', 'TAR636G3436' => 'tar', 'THA.LOC104803047' => 'tha', 'Thecc.04G238900' => 'tca', 'Thhalv10021557m.g' => 'esa', 'Thhalv10026318m.g' => 'esa', 'Thhalv10026335m.g' => 'esa', 'TPR.G17433' => 'tpr', 'TPR.G18915' => 'tpr', 'TPR.G26125' => 'tpr', 'TWI09G0677' => 'twi', 'TWI73G0287' => 'twi', 'unitig_748.g8326' => 'ugi', 'vmacro15370' => 'vma', 'vmacro15371' => 'vma', 'vmacro15372' => 'vma', 'vmacro15373' => 'vma', 'vmacro15374' => 'vma', 'VMungo0720G2826' => 'vmu', 'Zm00001eb116960' => 'zma', 'Zm00001eb301260' => 'zma', 'Zm00001eb301270' => 'zma' ) $gf_id = 'HOM05D001460' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001460' ) $data_identifier = 'HOM05D001460' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 4, 'aag' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 2, 'aox' => (int) 2, 'arhy' => (int) 4, 'ath' => (int) 2, 'atr' => (int) 1, 'acertr' => (int) 10, 'cqu' => (int) 4, 'bca' => (int) 11, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 1, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 1, 'ccan' => (int) 1, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 1, 'col' => (int) 1, 'cpa' => (int) 1, 'cre' => (int) 7, 'csa' => (int) 1, 'camsi' => (int) 2, 'dca' => (int) 3, 'din' => (int) 2, 'dzi' => (int) 3, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 14, 'fve' => (int) 9, 'gma' => (int) 2, 'ghi' => (int) 4, 'gra' => (int) 2, 'vvi' => (int) 1, 'han' => (int) 13, 'cav' => (int) 1, 'hma' => (int) 2, 'sun' => (int) 2, 'lal' => (int) 2, 'lonja' => (int) 12, 'lja' => (int) 1, 'lsa' => (int) 7, 'mes' => (int) 1, 'mpo' => (int) 27, 'mbi' => (int) 1, 'mco' => (int) 8, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 1, 'egut' => (int) 1, 'ama' => (int) 1, 'nta' => (int) 4, 'nnu' => (int) 2, 'oeu' => (int) 3, 'osa' => (int) 4, 'pax' => (int) 9, 'pgr' => (int) 1, 'stu' => (int) 1, 'pvu' => (int) 1, 'ptr' => (int) 4, 'ppa' => (int) 22, 'pco' => (int) 6, 'ppe' => (int) 6, 'psa' => (int) 5, 'pso' => (int) 19, 'qlo' => (int) 5, 'rch' => (int) 7, 'rsi' => (int) 20, 'sbr' => (int) 5, 'sbo' => (int) 1, 'sci' => (int) 2, 'sed' => (int) 2, 'sgi' => (int) 12, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 2, 'tar' => (int) 10, 'tha' => (int) 1, 'tca' => (int) 1, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 2, 'ugi' => (int) 1, 'vma' => (int) 5, 'vmu' => (int) 1, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb301270' $species_info = array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ) $local_species = 'aar' $disabled = '' $selected = '' $num_hits = (int) 0
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001460', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '433', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p22980' => 'bna', 'A01p32340' => 'bna', 'A03p42970' => 'bna', 'A05p25880' => 'bna', 'Aa31LG8G9320' => 'aar', 'Aa31LG8G9330' => 'aar', 'Aa31LG8G9340' => 'aar', 'Aa31sc221G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1034' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1528' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.829' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2222' => 'aag', 'Ah.12g058830' => 'amhyb', 'Ah.12g058840' => 'amhyb', 'AL3G37160' => 'aly', 'AL7G41310' => 'aly', 'Aqoxy5G00395' => 'aox', 'Aqoxy5G00396' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0C8NZA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5185HY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JZ1PRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MD3LS0' => 'arhy', 'AT3G22840' => 'ath', 'AT4G14690' => 'ath', 'ATR0665G054' => 'atr', 'Atru.chr4.2344' => 'acertr', 'Atru.chr4.2346' => 'acertr', 'Atru.chr4.2347' => 'acertr', 'Atru.chr4.2348' => 'acertr', 'Atru.chr4.2355' => 'acertr', 'Atru.chr4.2356' => 'acertr', 'Atru.chr4.2358' => 'acertr', 'Atru.chr4.2359' => 'acertr', 'Atru.chr4.2360' => 'acertr', 'Atru.chr4.2361' => 'acertr', 'AUR62030476' => 'cqu', 'AUR62030478' => 'cqu', 'AUR62030819' => 'cqu', 'AUR62030820' => 'cqu', 'BcaB03g14648' => 'bca', 'BcaB04g20492' => 'bca', 'BcaB06g26399' => 'bca', 'BcaC01g03416' => 'bca', 'BcaC01g03419' => 'bca', 'BcaC01g03421' => 'bca', 'BcaC01g03424' => 'bca', 'BcaC05g28012' => 'bca', 'BcaC09g49212' => 'bca', 'BcaC09g50140' => 'bca', 'BcaNung00346' => 'bca', 'BolC1t02785H' => 'bol', 'BolC1t04095H' => 'bol', 'BolC3t17545H' => 'bol', 'BolC5t32769H' => 'bol', 'BraA01t02211Z' => 'bra', 'BraA01t03359Z' => 'bra', 'BraA03t13441Z' => 'bra', 'BraA05t21476Z' => 'bra', 'C01p28420' => 'bna', 'C01p41350' => 'bna', 'C03p52750' => 'bna', 'C03p52780' => 'bna', 'C05p40270' => 'bna', 'CAN.G1437.9' => 'can', 'CANSAT78G0035' => 'cansat', 'CANSAT78G1036' => 'cansat', 'CANSAT78G2272' => 'cansat', 'CANSAT78G2478' => 'cansat', 'CARHR098700' => 'chi', 'CARHR221120' => 'chi', 'CARHR221150' => 'chi', 'Carub.0003s2297' => 'cru', 'Carub.0007s2749' => 'cru', 'Carub.0007s2750' => 'cru', 'Carub.0007s2751' => 'cru', 'Ca_10849_v3' => 'car', 'Cc03_g04300' => 'ccan', 'CDE02G3648' => 'cde', 'CDE05G0060' => 'cde', 'CDE05G0692' => 'cde', 'CDE05G2285' => 'cde', 'CDE05G2884' => 'cde', 'CDE05G3072' => 'cde', 'Cfa008439' => 'cfa', 'Cfa008441' => 'cfa', 'Cfa008443' => 'cfa', 'Cfa008448' => 'cfa', 'Ciclev10005974m.g' => 'ccl', 'Ciclev10006006m.g' => 'ccl', 'Ciclev10006775m.g' => 'ccl', 'CiPaw.02G120400' => 'cil', 'CiPaw.02G120500' => 'cil', 'CiPaw.02G120600' => 'cil', 'ClCG05G004850' => 'cla', 'COL.COLO4_21566' => 'col', 'Cpa.g.sc44.124' => 'cpa', 'Cre07.g320400' => 'cre', 'Cre07.g320450' => 'cre', 'Cre08.g384650' => 'cre', 'Cre09.g393173' => 'cre', 'Cre09.g394325' => 'cre', 'Cre14.g626750' => 'cre', 'Cre16.g679250' => 'cre', 'CsaV3_3G012890' => 'csa', 'CSS0010865' => 'camsi', 'CSS0044338' => 'camsi', 'DCAR_002366' => 'dca', 'DCAR_030687' => 'dca', 'DCAR_030688' => 'dca', 'Dinv14047' => 'din', 'Dinv14048' => 'din', 'Duzib151G0105' => 'dzi', 'Duzib151G0114' => 'dzi', 'Duzib212G1029' => 'dzi', 'ECA232G3536' => 'eca', 'ECA240G0786' => 'eca', 'ECA240G1802' => 'eca', 'ECA240G3760' => 'eca', 'ECA240G3920' => 'eca', 'EL10Ac5g12536' => 'bvu', 'EL10Ac5g12537' => 'bvu', 'EL10Ac5g12538' => 'bvu', 'Eucgr.B01004' => 'egr', 'Eucgr.B01006' => 'egr', 'Eucgr.B01007' => 'egr', 'Eucgr.B01008' => 'egr', 'Eucgr.B01895' => 'egr', 'Eucgr.B01896' => 'egr', 'FAN04G1456' => 'fan', 'FAN08G1769' => 'fan', 'FAN08G2160' => 'fan', 'FAN13G2403' => 'fan', 'FAN13G3303' => 'fan', 'FAN15G2435' => 'fan', 'FAN17G0672' => 'fan', 'FAN17G2441' => 'fan', 'FAN18G1024' => 'fan', 'FAN22G1458' => 'fan', 'FAN24G0037' => 'fan', 'FAN24G0429' => 'fan', 'FAN24G2387' => 'fan', 'FAN27G2746' => 'fan', 'FvH4_2g20400' => 'fve', 'FvH4_2g20420' => 'fve', 'FvH4_2g20430' => 'fve', 'FvH4_4g01270' => 'fve', 'FvH4_4g01290' => 'fve', 'FvH4_4g01300' => 'fve', 'FvH4_4g01310' => 'fve', 'FvH4_4g01330' => 'fve', 'FvH4_5g09070' => 'fve', 'Glyma.10G243800' => 'gma', 'Glyma.20G150600' => 'gma', 'Gohir.A09G219200' => 'ghi', 'Gohir.A09G219300' => 'ghi', 'Gohir.D09G221400' => 'ghi', 'Gohir.D09G221500' => 'ghi', 'Gorai.006G242600' => 'gra', 'Gorai.006G242700' => 'gra', 'GSVIVG01018044001' => 'vvi', 'HanXRQChr03g0083821' => 'han', 'HanXRQChr03g0083841' => 'han', 'HanXRQChr03g0083881' => 'han', 'HanXRQChr03g0083901' => 'han', 'HanXRQChr03g0083921' => 'han', 'HanXRQChr03g0085331' => 'han', 'HanXRQChr03g0085361' => 'han', 'HanXRQChr03g0085411' => 'han', 'HanXRQChr03g0085421' => 'han', 'HanXRQChr03g0085431' => 'han', 'HanXRQChr08g0221991' => 'han', 'HanXRQChr11g0336061' => 'han', 'HanXRQChr11g0336411' => 'han', 'Haze_11234' => 'cav', 'Hma1.2p1_0549F.1_g177010' => 'hma', 'Hma1.2p1_0602F.1_g187630' => 'hma', 'Hund14876' => 'sun', 'Hund14879' => 'sun', 'Lalb_Chr06g0160741' => 'lal', 'Lalb_Chr21g0304781' => 'lal', 'Lj3A726G19' => 'lonja', 'Lj3A726T23' => 'lonja', 'Lj3A726T24' => 'lonja', 'Lj3A726T25' => 'lonja', 'Lj3A727T17' => 'lonja', 'Lj3C726T0' => 'lonja', 'Lj3C726T2' => 'lonja', 'Lj3P725T35' => 'lonja', 'Lj3P727T10' => 'lonja', 'Lj3P727T12' => 'lonja', 'Lj3P727T14' => 'lonja', 'Lj5g0023109' => 'lja', 'Lj6P646T44' => 'lonja', 'Lsat_1_v5_gn_6_75760' => 'lsa', 'Lsat_1_v5_gn_6_75800' => 'lsa', 'Lsat_1_v5_gn_6_75900' => 'lsa', 'Lsat_1_v5_gn_6_76240' => 'lsa', 'Lsat_1_v5_gn_6_76441' => 'lsa', 'Lsat_1_v5_gn_6_76700' => 'lsa', 'Lsat_1_v5_gn_6_76760' => 'lsa', 'Manes.15G033100' => 'mes', 'Mapoly0004s0074' => 'mpo', 'Mapoly0004s0075' => 'mpo', 'Mapoly0004s0163' => 'mpo', 'Mapoly0004s0164' => 'mpo', 'Mapoly0021s0018' => 'mpo', 'Mapoly0041s0136' => 'mpo', 'Mapoly0041s0137' => 'mpo', 'Mapoly0041s0138' => 'mpo', 'Mapoly0041s0139' => 'mpo', 'Mapoly0041s0141' => 'mpo', 'Mapoly0041s0142' => 'mpo', 'Mapoly0041s0143' => 'mpo', 'Mapoly0041s0144' => 'mpo', 'Mapoly0041s0145' => 'mpo', 'Mapoly0047s0106' => 'mpo', 'Mapoly0047s0108' => 'mpo', 'Mapoly0050s0051' => 'mpo', 'Mapoly0050s0052' => 'mpo', 'Mapoly0050s0053' => 'mpo', 'Mapoly0058s0013' => 'mpo', 'Mapoly0091s0078' => 'mpo', 'Mapoly0091s0079' => 'mpo', 'Mapoly0091s0080' => 'mpo', 'Mapoly0091s0081' => 'mpo', 'Mapoly0278s0004' => 'mpo', 'Mapoly0278s0005' => 'mpo', 'Mapoly0278s0006' => 'mpo', 'MBI11_g30648_MAGBIO' => 'mbi', 'MCO03G194' => 'mco', 'MCO03G590' => 'mco', 'MCO07G312' => 'mco', 'MCO10G318' => 'mco', 'MCO12G244' => 'mco', 'MCO13G148' => 'mco', 'MCO13G194' => 'mco', 'MCO16G238' => 'mco', 'MD06G1134100' => 'mdo', 'MD13G1200100' => 'mdo', 'MD13G1200300' => 'mdo', 'MD13G1200600' => 'mdo', 'MD14G1150400' => 'mdo', 'MD16G1200000' => 'mdo', 'Medtr1g102570' => 'mtr', 'Medtr1g102780' => 'mtr', 'Medtr1g102800' => 'mtr', 'Medtr1g102810' => 'mtr', 'Medtr1g102830' => 'mtr', 'MELO3C006499.2' => 'cme', 'Migut.G00385' => 'egut', 'MSTRG.4063' => 'ama', 'Nitab4.5_0000090g0260' => 'nta', 'Nitab4.5_0000977g0030' => 'nta', 'Nitab4.5_0002541g0040' => 'nta', 'Nitab4.5_0007068g0040' => 'nta', 'Nn005s41408' => 'nnu', 'Nn005s41410' => 'nnu', 'Oeu010310.1' => 'oeu', 'Oeu010311.1' => 'oeu', 'Oeu043472.1' => 'oeu', 'Os01g0246400' => 'osa', 'Os04g0267950' => 'osa', 'Os07g0178700' => 'osa', 'Os07g0178800' => 'osa', 'Peaxi162Scf00316g00046' => 'pax', 'Peaxi162Scf00316g00049' => 'pax', 'Peaxi162Scf00316g00059' => 'pax', 'Peaxi162Scf00316g00328' => 'pax', 'Peaxi162Scf00316g00329' => 'pax', 'Peaxi162Scf00316g00411' => 'pax', 'Peaxi162Scf00316g00521' => 'pax', 'Peaxi162Scf00492g00068' => 'pax', 'Peaxi162Scf35631g00002' => 'pax', 'PGR142G3720' => 'pgr', 'PGSC0003DMG400006442' => 'stu', 'Phvul.007G062000' => 'pvu', 'Potri.008G157750' => 'ptr', 'Potri.008G157900' => 'ptr', 'Potri.008G158000' => 'ptr', 'Potri.008G158200' => 'ptr', 'Pp3c11_7280' => 'ppa', 'Pp3c11_7980' => 'ppa', 'Pp3c12_19450' => 'ppa', 'Pp3c14_1480' => 'ppa', 'Pp3c14_1501' => 'ppa', 'Pp3c16_4900' => 'ppa', 'Pp3c16_5010' => 'ppa', 'Pp3c16_5060' => 'ppa', 'Pp3c19_18250' => 'ppa', 'Pp3c23_8530' => 'ppa', 'Pp3c23_8550' => 'ppa', 'Pp3c24_9670' => 'ppa', 'Pp3c2_21390' => 'ppa', 'Pp3c2_31380' => 'ppa', 'Pp3c3_16620' => 'ppa', 'Pp3c3_8090' => 'ppa', 'Pp3c3_8110' => 'ppa', 'Pp3c3_8130' => 'ppa', 'Pp3c3_8150' => 'ppa', 'Pp3c4_14320' => 'ppa', 'Pp3c6_2560' => 'ppa', 'Pp3c9_16700' => 'ppa', 'PRCOL_00000234' => 'pco', 'PRCOL_00000235' => 'pco', 'PRCOL_00000777' => 'pco', 'PRCOL_00002344' => 'pco', 'PRCOL_00002372' => 'pco', 'PRCOL_00006120' => 'pco', 'Prupe.1G021400' => 'ppe', 'Prupe.1G021500' => 'ppe', 'Prupe.1G021600' => 'ppe', 'Prupe.1G021700' => 'ppe', 'Prupe.1G021800' => 'ppe', 'Prupe.5G145100' => 'ppe', 'Psat6g204040' => 'psa', 'Psat6g204800' => 'psa', 'Psat6g204920' => 'psa', 'Psat6g204960' => 'psa', 'Psat6g205080' => 'psa', 'PSO017G0271' => 'pso', 'PSO017G1276' => 'pso', 'PSO017G1429' => 'pso', 'PSO017G1861' => 'pso', 'PSO017G2787' => 'pso', 'PSO017G4466' => 'pso', 'PSO017G5118' => 'pso', 'PSO017G5420' => 'pso', 'PSO063G3678' => 'pso', 'PSO210G0546' => 'pso', 'PSO317G0001' => 'pso', 'PSO357G0512' => 'pso', 'PSO478G2682' => 'pso', 'PSO647G0001' => 'pso', 'PSO675G0001' => 'pso', 'PSO675G2699' => 'pso', 'PSO675G2849' => 'pso', 'PSO675G4991' => 'pso', 'PSO689G0001' => 'pso', 'QL06p000916' => 'qlo', 'QL06p000921' => 'qlo', 'QL06p001398' => 'qlo', 'QL06p001407' => 'qlo', 'QL06p002031' => 'qlo', 'RcHm_v2.0_Chr4g0387791' => 'rch', 'RcHm_v2.0_Chr4g0387801' => 'rch', 'RcHm_v2.0_Chr6g0286501' => 'rch', 'RcHm_v2.0_Chr6g0286511' => 'rch', 'RcHm_v2.0_Chr6g0286521' => 'rch', 'RcHm_v2.0_Chr6g0286531' => 'rch', 'RcHm_v2.0_Chr7g0189141' => 'rch', 'Rhsim02G0028700' => 'rsi', 'Rhsim02G0028800' => 'rsi', 'Rhsim02G0028900' => 'rsi', 'Rhsim02G0029000' => 'rsi', 'Rhsim02G0029100' => 'rsi', 'Rhsim02G0029200' => 'rsi', 'Rhsim02G0029300' => 'rsi', 'Rhsim02G0029400' => 'rsi', 'Rhsim02G0029500' => 'rsi', 'Rhsim02G0029600' => 'rsi', 'RhsimUnG0024000' => 'rsi', 'RhsimUnG0024100' => 'rsi', 'RhsimUnG0024200' => 'rsi', 'RhsimUnG0024300' => 'rsi', 'RhsimUnG0024400' => 'rsi', 'RhsimUnG0024500' => 'rsi', 'RhsimUnG0024700' => 'rsi', 'RhsimUnG0024800' => 'rsi', 'RhsimUnG0024900' => 'rsi', 'RhsimUnG0025100' => 'rsi', 'Sabra08G0120200' => 'sbr', 'Sabra08G0120300' => 'sbr', 'Sabra08G0120500' => 'sbr', 'Sabra08G0120600' => 'sbr', 'Sabra10G0158900' => 'sbr', 'SalBow2G3492' => 'sbo', 'Sc13g0004760' => 'sci', 'Sc13g0004770' => 'sci', 'Sed0003417' => 'sed', 'Sed0019750' => 'sed', 'SEGI_03419' => 'sgi', 'SEGI_05907' => 'sgi', 'SEGI_10682' => 'sgi', 'SEGI_13528' => 'sgi', 'SEGI_16081' => 'sgi', 'SEGI_19370' => 'sgi', 'SEGI_21015' => 'sgi', 'SEGI_21944' => 'sgi', 'SEGI_32906' => 'sgi', 'SEGI_33093' => 'sgi', 'SEGI_36110' => 'sgi', 'SEGI_40397' => 'sgi', 'SGA_v2.0_scaffold191G40426' => 'sas', 'SGA_v2.0_scaffold353G49717' => 'sas', 'SGA_v2.0_scaffold50G18550' => 'sas', 'SMO119G0173' => 'smo', 'SMO172G0002' => 'smo', 'Solyc09g082690.3' => 'sly', 'Solyc09g082700.2' => 'sly', 'Sopen09g031550' => 'spe', 'Sopen09g031560' => 'spe', 'Sp3g20540' => 'spa', 'Sp7g07580' => 'spa', 'TAR134G0002' => 'tar', 'TAR236G0001' => 'tar', 'TAR365G0892' => 'tar', 'TAR636G0166' => 'tar', 'TAR636G0646' => 'tar', 'TAR636G0869' => 'tar', 'TAR636G1317' => 'tar', 'TAR636G1744' => 'tar', 'TAR636G3358' => 'tar', 'TAR636G3436' => 'tar', 'THA.LOC104803047' => 'tha', 'Thecc.04G238900' => 'tca', 'Thhalv10021557m.g' => 'esa', 'Thhalv10026318m.g' => 'esa', 'Thhalv10026335m.g' => 'esa', 'TPR.G17433' => 'tpr', 'TPR.G18915' => 'tpr', 'TPR.G26125' => 'tpr', 'TWI09G0677' => 'twi', 'TWI73G0287' => 'twi', 'unitig_748.g8326' => 'ugi', 'vmacro15370' => 'vma', 'vmacro15371' => 'vma', 'vmacro15372' => 'vma', 'vmacro15373' => 'vma', 'vmacro15374' => 'vma', 'VMungo0720G2826' => 'vmu', 'Zm00001eb116960' => 'zma', 'Zm00001eb301260' => 'zma', 'Zm00001eb301270' => 'zma' ), 'gf_id' => 'HOM05D001460', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001460' ), 'data_identifier' => 'HOM05D001460', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001460', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '433', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p22980' => 'bna', 'A01p32340' => 'bna', 'A03p42970' => 'bna', 'A05p25880' => 'bna', 'Aa31LG8G9320' => 'aar', 'Aa31LG8G9330' => 'aar', 'Aa31LG8G9340' => 'aar', 'Aa31sc221G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1034' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1528' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.829' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2222' => 'aag', 'Ah.12g058830' => 'amhyb', 'Ah.12g058840' => 'amhyb', 'AL3G37160' => 'aly', 'AL7G41310' => 'aly', 'Aqoxy5G00395' => 'aox', 'Aqoxy5G00396' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0C8NZA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5185HY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JZ1PRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MD3LS0' => 'arhy', 'AT3G22840' => 'ath', 'AT4G14690' => 'ath', 'ATR0665G054' => 'atr', 'Atru.chr4.2344' => 'acertr', 'Atru.chr4.2346' => 'acertr', 'Atru.chr4.2347' => 'acertr', 'Atru.chr4.2348' => 'acertr', 'Atru.chr4.2355' => 'acertr', 'Atru.chr4.2356' => 'acertr', 'Atru.chr4.2358' => 'acertr', 'Atru.chr4.2359' => 'acertr', 'Atru.chr4.2360' => 'acertr', 'Atru.chr4.2361' => 'acertr', 'AUR62030476' => 'cqu', 'AUR62030478' => 'cqu', 'AUR62030819' => 'cqu', 'AUR62030820' => 'cqu', 'BcaB03g14648' => 'bca', 'BcaB04g20492' => 'bca', 'BcaB06g26399' => 'bca', 'BcaC01g03416' => 'bca', 'BcaC01g03419' => 'bca', 'BcaC01g03421' => 'bca', 'BcaC01g03424' => 'bca', 'BcaC05g28012' => 'bca', 'BcaC09g49212' => 'bca', 'BcaC09g50140' => 'bca', 'BcaNung00346' => 'bca', 'BolC1t02785H' => 'bol', 'BolC1t04095H' => 'bol', 'BolC3t17545H' => 'bol', 'BolC5t32769H' => 'bol', 'BraA01t02211Z' => 'bra', 'BraA01t03359Z' => 'bra', 'BraA03t13441Z' => 'bra', 'BraA05t21476Z' => 'bra', 'C01p28420' => 'bna', 'C01p41350' => 'bna', 'C03p52750' => 'bna', 'C03p52780' => 'bna', 'C05p40270' => 'bna', 'CAN.G1437.9' => 'can', 'CANSAT78G0035' => 'cansat', 'CANSAT78G1036' => 'cansat', 'CANSAT78G2272' => 'cansat', 'CANSAT78G2478' => 'cansat', 'CARHR098700' => 'chi', 'CARHR221120' => 'chi', 'CARHR221150' => 'chi', 'Carub.0003s2297' => 'cru', 'Carub.0007s2749' => 'cru', 'Carub.0007s2750' => 'cru', 'Carub.0007s2751' => 'cru', 'Ca_10849_v3' => 'car', 'Cc03_g04300' => 'ccan', 'CDE02G3648' => 'cde', 'CDE05G0060' => 'cde', 'CDE05G0692' => 'cde', 'CDE05G2285' => 'cde', 'CDE05G2884' => 'cde', 'CDE05G3072' => 'cde', 'Cfa008439' => 'cfa', 'Cfa008441' => 'cfa', 'Cfa008443' => 'cfa', 'Cfa008448' => 'cfa', 'Ciclev10005974m.g' => 'ccl', 'Ciclev10006006m.g' => 'ccl', 'Ciclev10006775m.g' => 'ccl', 'CiPaw.02G120400' => 'cil', 'CiPaw.02G120500' => 'cil', 'CiPaw.02G120600' => 'cil', 'ClCG05G004850' => 'cla', 'COL.COLO4_21566' => 'col', 'Cpa.g.sc44.124' => 'cpa', 'Cre07.g320400' => 'cre', 'Cre07.g320450' => 'cre', 'Cre08.g384650' => 'cre', 'Cre09.g393173' => 'cre', 'Cre09.g394325' => 'cre', 'Cre14.g626750' => 'cre', 'Cre16.g679250' => 'cre', 'CsaV3_3G012890' => 'csa', 'CSS0010865' => 'camsi', 'CSS0044338' => 'camsi', 'DCAR_002366' => 'dca', 'DCAR_030687' => 'dca', 'DCAR_030688' => 'dca', 'Dinv14047' => 'din', 'Dinv14048' => 'din', 'Duzib151G0105' => 'dzi', 'Duzib151G0114' => 'dzi', 'Duzib212G1029' => 'dzi', 'ECA232G3536' => 'eca', 'ECA240G0786' => 'eca', 'ECA240G1802' => 'eca', 'ECA240G3760' => 'eca', 'ECA240G3920' => 'eca', 'EL10Ac5g12536' => 'bvu', 'EL10Ac5g12537' => 'bvu', 'EL10Ac5g12538' => 'bvu', 'Eucgr.B01004' => 'egr', 'Eucgr.B01006' => 'egr', 'Eucgr.B01007' => 'egr', 'Eucgr.B01008' => 'egr', 'Eucgr.B01895' => 'egr', 'Eucgr.B01896' => 'egr', 'FAN04G1456' => 'fan', 'FAN08G1769' => 'fan', 'FAN08G2160' => 'fan', 'FAN13G2403' => 'fan', 'FAN13G3303' => 'fan', 'FAN15G2435' => 'fan', 'FAN17G0672' => 'fan', 'FAN17G2441' => 'fan', 'FAN18G1024' => 'fan', 'FAN22G1458' => 'fan', 'FAN24G0037' => 'fan', 'FAN24G0429' => 'fan', 'FAN24G2387' => 'fan', 'FAN27G2746' => 'fan', 'FvH4_2g20400' => 'fve', 'FvH4_2g20420' => 'fve', 'FvH4_2g20430' => 'fve', 'FvH4_4g01270' => 'fve', 'FvH4_4g01290' => 'fve', 'FvH4_4g01300' => 'fve', 'FvH4_4g01310' => 'fve', 'FvH4_4g01330' => 'fve', 'FvH4_5g09070' => 'fve', 'Glyma.10G243800' => 'gma', 'Glyma.20G150600' => 'gma', 'Gohir.A09G219200' => 'ghi', 'Gohir.A09G219300' => 'ghi', 'Gohir.D09G221400' => 'ghi', 'Gohir.D09G221500' => 'ghi', 'Gorai.006G242600' => 'gra', 'Gorai.006G242700' => 'gra', 'GSVIVG01018044001' => 'vvi', 'HanXRQChr03g0083821' => 'han', 'HanXRQChr03g0083841' => 'han', 'HanXRQChr03g0083881' => 'han', 'HanXRQChr03g0083901' => 'han', 'HanXRQChr03g0083921' => 'han', 'HanXRQChr03g0085331' => 'han', 'HanXRQChr03g0085361' => 'han', 'HanXRQChr03g0085411' => 'han', 'HanXRQChr03g0085421' => 'han', 'HanXRQChr03g0085431' => 'han', 'HanXRQChr08g0221991' => 'han', 'HanXRQChr11g0336061' => 'han', 'HanXRQChr11g0336411' => 'han', 'Haze_11234' => 'cav', 'Hma1.2p1_0549F.1_g177010' => 'hma', 'Hma1.2p1_0602F.1_g187630' => 'hma', 'Hund14876' => 'sun', 'Hund14879' => 'sun', 'Lalb_Chr06g0160741' => 'lal', 'Lalb_Chr21g0304781' => 'lal', 'Lj3A726G19' => 'lonja', 'Lj3A726T23' => 'lonja', 'Lj3A726T24' => 'lonja', 'Lj3A726T25' => 'lonja', 'Lj3A727T17' => 'lonja', 'Lj3C726T0' => 'lonja', 'Lj3C726T2' => 'lonja', 'Lj3P725T35' => 'lonja', 'Lj3P727T10' => 'lonja', 'Lj3P727T12' => 'lonja', 'Lj3P727T14' => 'lonja', 'Lj5g0023109' => 'lja', 'Lj6P646T44' => 'lonja', 'Lsat_1_v5_gn_6_75760' => 'lsa', 'Lsat_1_v5_gn_6_75800' => 'lsa', 'Lsat_1_v5_gn_6_75900' => 'lsa', 'Lsat_1_v5_gn_6_76240' => 'lsa', 'Lsat_1_v5_gn_6_76441' => 'lsa', 'Lsat_1_v5_gn_6_76700' => 'lsa', 'Lsat_1_v5_gn_6_76760' => 'lsa', 'Manes.15G033100' => 'mes', 'Mapoly0004s0074' => 'mpo', 'Mapoly0004s0075' => 'mpo', 'Mapoly0004s0163' => 'mpo', 'Mapoly0004s0164' => 'mpo', 'Mapoly0021s0018' => 'mpo', 'Mapoly0041s0136' => 'mpo', 'Mapoly0041s0137' => 'mpo', 'Mapoly0041s0138' => 'mpo', 'Mapoly0041s0139' => 'mpo', 'Mapoly0041s0141' => 'mpo', 'Mapoly0041s0142' => 'mpo', 'Mapoly0041s0143' => 'mpo', 'Mapoly0041s0144' => 'mpo', 'Mapoly0041s0145' => 'mpo', 'Mapoly0047s0106' => 'mpo', 'Mapoly0047s0108' => 'mpo', 'Mapoly0050s0051' => 'mpo', 'Mapoly0050s0052' => 'mpo', 'Mapoly0050s0053' => 'mpo', 'Mapoly0058s0013' => 'mpo', 'Mapoly0091s0078' => 'mpo', 'Mapoly0091s0079' => 'mpo', 'Mapoly0091s0080' => 'mpo', 'Mapoly0091s0081' => 'mpo', 'Mapoly0278s0004' => 'mpo', 'Mapoly0278s0005' => 'mpo', 'Mapoly0278s0006' => 'mpo', 'MBI11_g30648_MAGBIO' => 'mbi', 'MCO03G194' => 'mco', 'MCO03G590' => 'mco', 'MCO07G312' => 'mco', 'MCO10G318' => 'mco', 'MCO12G244' => 'mco', 'MCO13G148' => 'mco', 'MCO13G194' => 'mco', 'MCO16G238' => 'mco', 'MD06G1134100' => 'mdo', 'MD13G1200100' => 'mdo', 'MD13G1200300' => 'mdo', 'MD13G1200600' => 'mdo', 'MD14G1150400' => 'mdo', 'MD16G1200000' => 'mdo', 'Medtr1g102570' => 'mtr', 'Medtr1g102780' => 'mtr', 'Medtr1g102800' => 'mtr', 'Medtr1g102810' => 'mtr', 'Medtr1g102830' => 'mtr', 'MELO3C006499.2' => 'cme', 'Migut.G00385' => 'egut', 'MSTRG.4063' => 'ama', 'Nitab4.5_0000090g0260' => 'nta', 'Nitab4.5_0000977g0030' => 'nta', 'Nitab4.5_0002541g0040' => 'nta', 'Nitab4.5_0007068g0040' => 'nta', 'Nn005s41408' => 'nnu', 'Nn005s41410' => 'nnu', 'Oeu010310.1' => 'oeu', 'Oeu010311.1' => 'oeu', 'Oeu043472.1' => 'oeu', 'Os01g0246400' => 'osa', 'Os04g0267950' => 'osa', 'Os07g0178700' => 'osa', 'Os07g0178800' => 'osa', 'Peaxi162Scf00316g00046' => 'pax', 'Peaxi162Scf00316g00049' => 'pax', 'Peaxi162Scf00316g00059' => 'pax', 'Peaxi162Scf00316g00328' => 'pax', 'Peaxi162Scf00316g00329' => 'pax', 'Peaxi162Scf00316g00411' => 'pax', 'Peaxi162Scf00316g00521' => 'pax', 'Peaxi162Scf00492g00068' => 'pax', 'Peaxi162Scf35631g00002' => 'pax', 'PGR142G3720' => 'pgr', 'PGSC0003DMG400006442' => 'stu', 'Phvul.007G062000' => 'pvu', 'Potri.008G157750' => 'ptr', 'Potri.008G157900' => 'ptr', 'Potri.008G158000' => 'ptr', 'Potri.008G158200' => 'ptr', 'Pp3c11_7280' => 'ppa', 'Pp3c11_7980' => 'ppa', 'Pp3c12_19450' => 'ppa', 'Pp3c14_1480' => 'ppa', 'Pp3c14_1501' => 'ppa', 'Pp3c16_4900' => 'ppa', 'Pp3c16_5010' => 'ppa', 'Pp3c16_5060' => 'ppa', 'Pp3c19_18250' => 'ppa', 'Pp3c23_8530' => 'ppa', 'Pp3c23_8550' => 'ppa', 'Pp3c24_9670' => 'ppa', 'Pp3c2_21390' => 'ppa', 'Pp3c2_31380' => 'ppa', 'Pp3c3_16620' => 'ppa', 'Pp3c3_8090' => 'ppa', 'Pp3c3_8110' => 'ppa', 'Pp3c3_8130' => 'ppa', 'Pp3c3_8150' => 'ppa', 'Pp3c4_14320' => 'ppa', 'Pp3c6_2560' => 'ppa', 'Pp3c9_16700' => 'ppa', 'PRCOL_00000234' => 'pco', 'PRCOL_00000235' => 'pco', 'PRCOL_00000777' => 'pco', 'PRCOL_00002344' => 'pco', 'PRCOL_00002372' => 'pco', 'PRCOL_00006120' => 'pco', 'Prupe.1G021400' => 'ppe', 'Prupe.1G021500' => 'ppe', 'Prupe.1G021600' => 'ppe', 'Prupe.1G021700' => 'ppe', 'Prupe.1G021800' => 'ppe', 'Prupe.5G145100' => 'ppe', 'Psat6g204040' => 'psa', 'Psat6g204800' => 'psa', 'Psat6g204920' => 'psa', 'Psat6g204960' => 'psa', 'Psat6g205080' => 'psa', 'PSO017G0271' => 'pso', 'PSO017G1276' => 'pso', 'PSO017G1429' => 'pso', 'PSO017G1861' => 'pso', 'PSO017G2787' => 'pso', 'PSO017G4466' => 'pso', 'PSO017G5118' => 'pso', 'PSO017G5420' => 'pso', 'PSO063G3678' => 'pso', 'PSO210G0546' => 'pso', 'PSO317G0001' => 'pso', 'PSO357G0512' => 'pso', 'PSO478G2682' => 'pso', 'PSO647G0001' => 'pso', 'PSO675G0001' => 'pso', 'PSO675G2699' => 'pso', 'PSO675G2849' => 'pso', 'PSO675G4991' => 'pso', 'PSO689G0001' => 'pso', 'QL06p000916' => 'qlo', 'QL06p000921' => 'qlo', 'QL06p001398' => 'qlo', 'QL06p001407' => 'qlo', 'QL06p002031' => 'qlo', 'RcHm_v2.0_Chr4g0387791' => 'rch', 'RcHm_v2.0_Chr4g0387801' => 'rch', 'RcHm_v2.0_Chr6g0286501' => 'rch', 'RcHm_v2.0_Chr6g0286511' => 'rch', 'RcHm_v2.0_Chr6g0286521' => 'rch', 'RcHm_v2.0_Chr6g0286531' => 'rch', 'RcHm_v2.0_Chr7g0189141' => 'rch', 'Rhsim02G0028700' => 'rsi', 'Rhsim02G0028800' => 'rsi', 'Rhsim02G0028900' => 'rsi', 'Rhsim02G0029000' => 'rsi', 'Rhsim02G0029100' => 'rsi', 'Rhsim02G0029200' => 'rsi', 'Rhsim02G0029300' => 'rsi', 'Rhsim02G0029400' => 'rsi', 'Rhsim02G0029500' => 'rsi', 'Rhsim02G0029600' => 'rsi', 'RhsimUnG0024000' => 'rsi', 'RhsimUnG0024100' => 'rsi', 'RhsimUnG0024200' => 'rsi', 'RhsimUnG0024300' => 'rsi', 'RhsimUnG0024400' => 'rsi', 'RhsimUnG0024500' => 'rsi', 'RhsimUnG0024700' => 'rsi', 'RhsimUnG0024800' => 'rsi', 'RhsimUnG0024900' => 'rsi', 'RhsimUnG0025100' => 'rsi', 'Sabra08G0120200' => 'sbr', 'Sabra08G0120300' => 'sbr', 'Sabra08G0120500' => 'sbr', 'Sabra08G0120600' => 'sbr', 'Sabra10G0158900' => 'sbr', 'SalBow2G3492' => 'sbo', 'Sc13g0004760' => 'sci', 'Sc13g0004770' => 'sci', 'Sed0003417' => 'sed', 'Sed0019750' => 'sed', 'SEGI_03419' => 'sgi', 'SEGI_05907' => 'sgi', 'SEGI_10682' => 'sgi', 'SEGI_13528' => 'sgi', 'SEGI_16081' => 'sgi', 'SEGI_19370' => 'sgi', 'SEGI_21015' => 'sgi', 'SEGI_21944' => 'sgi', 'SEGI_32906' => 'sgi', 'SEGI_33093' => 'sgi', 'SEGI_36110' => 'sgi', 'SEGI_40397' => 'sgi', 'SGA_v2.0_scaffold191G40426' => 'sas', 'SGA_v2.0_scaffold353G49717' => 'sas', 'SGA_v2.0_scaffold50G18550' => 'sas', 'SMO119G0173' => 'smo', 'SMO172G0002' => 'smo', 'Solyc09g082690.3' => 'sly', 'Solyc09g082700.2' => 'sly', 'Sopen09g031550' => 'spe', 'Sopen09g031560' => 'spe', 'Sp3g20540' => 'spa', 'Sp7g07580' => 'spa', 'TAR134G0002' => 'tar', 'TAR236G0001' => 'tar', 'TAR365G0892' => 'tar', 'TAR636G0166' => 'tar', 'TAR636G0646' => 'tar', 'TAR636G0869' => 'tar', 'TAR636G1317' => 'tar', 'TAR636G1744' => 'tar', 'TAR636G3358' => 'tar', 'TAR636G3436' => 'tar', 'THA.LOC104803047' => 'tha', 'Thecc.04G238900' => 'tca', 'Thhalv10021557m.g' => 'esa', 'Thhalv10026318m.g' => 'esa', 'Thhalv10026335m.g' => 'esa', 'TPR.G17433' => 'tpr', 'TPR.G18915' => 'tpr', 'TPR.G26125' => 'tpr', 'TWI09G0677' => 'twi', 'TWI73G0287' => 'twi', 'unitig_748.g8326' => 'ugi', 'vmacro15370' => 'vma', 'vmacro15371' => 'vma', 'vmacro15372' => 'vma', 'vmacro15373' => 'vma', 'vmacro15374' => 'vma', 'VMungo0720G2826' => 'vmu', 'Zm00001eb116960' => 'zma', 'Zm00001eb301260' => 'zma', 'Zm00001eb301270' => 'zma' ) $gf_id = 'HOM05D001460' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001460' ) $data_identifier = 'HOM05D001460' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 4, 'aag' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 2, 'aox' => (int) 2, 'arhy' => (int) 4, 'ath' => (int) 2, 'atr' => (int) 1, 'acertr' => (int) 10, 'cqu' => (int) 4, 'bca' => (int) 11, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 1, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 1, 'ccan' => (int) 1, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 1, 'col' => (int) 1, 'cpa' => (int) 1, 'cre' => (int) 7, 'csa' => (int) 1, 'camsi' => (int) 2, 'dca' => (int) 3, 'din' => (int) 2, 'dzi' => (int) 3, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 14, 'fve' => (int) 9, 'gma' => (int) 2, 'ghi' => (int) 4, 'gra' => (int) 2, 'vvi' => (int) 1, 'han' => (int) 13, 'cav' => (int) 1, 'hma' => (int) 2, 'sun' => (int) 2, 'lal' => (int) 2, 'lonja' => (int) 12, 'lja' => (int) 1, 'lsa' => (int) 7, 'mes' => (int) 1, 'mpo' => (int) 27, 'mbi' => (int) 1, 'mco' => (int) 8, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 1, 'egut' => (int) 1, 'ama' => (int) 1, 'nta' => (int) 4, 'nnu' => (int) 2, 'oeu' => (int) 3, 'osa' => (int) 4, 'pax' => (int) 9, 'pgr' => (int) 1, 'stu' => (int) 1, 'pvu' => (int) 1, 'ptr' => (int) 4, 'ppa' => (int) 22, 'pco' => (int) 6, 'ppe' => (int) 6, 'psa' => (int) 5, 'pso' => (int) 19, 'qlo' => (int) 5, 'rch' => (int) 7, 'rsi' => (int) 20, 'sbr' => (int) 5, 'sbo' => (int) 1, 'sci' => (int) 2, 'sed' => (int) 2, 'sgi' => (int) 12, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 2, 'tar' => (int) 10, 'tha' => (int) 1, 'tca' => (int) 1, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 2, 'ugi' => (int) 1, 'vma' => (int) 5, 'vmu' => (int) 1, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb301270' $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' => 'HOM05D001460', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '433', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p22980' => 'bna', 'A01p32340' => 'bna', 'A03p42970' => 'bna', 'A05p25880' => 'bna', 'Aa31LG8G9320' => 'aar', 'Aa31LG8G9330' => 'aar', 'Aa31LG8G9340' => 'aar', 'Aa31sc221G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1034' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1528' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.829' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2222' => 'aag', 'Ah.12g058830' => 'amhyb', 'Ah.12g058840' => 'amhyb', 'AL3G37160' => 'aly', 'AL7G41310' => 'aly', 'Aqoxy5G00395' => 'aox', 'Aqoxy5G00396' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0C8NZA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5185HY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JZ1PRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MD3LS0' => 'arhy', 'AT3G22840' => 'ath', 'AT4G14690' => 'ath', 'ATR0665G054' => 'atr', 'Atru.chr4.2344' => 'acertr', 'Atru.chr4.2346' => 'acertr', 'Atru.chr4.2347' => 'acertr', 'Atru.chr4.2348' => 'acertr', 'Atru.chr4.2355' => 'acertr', 'Atru.chr4.2356' => 'acertr', 'Atru.chr4.2358' => 'acertr', 'Atru.chr4.2359' => 'acertr', 'Atru.chr4.2360' => 'acertr', 'Atru.chr4.2361' => 'acertr', 'AUR62030476' => 'cqu', 'AUR62030478' => 'cqu', 'AUR62030819' => 'cqu', 'AUR62030820' => 'cqu', 'BcaB03g14648' => 'bca', 'BcaB04g20492' => 'bca', 'BcaB06g26399' => 'bca', 'BcaC01g03416' => 'bca', 'BcaC01g03419' => 'bca', 'BcaC01g03421' => 'bca', 'BcaC01g03424' => 'bca', 'BcaC05g28012' => 'bca', 'BcaC09g49212' => 'bca', 'BcaC09g50140' => 'bca', 'BcaNung00346' => 'bca', 'BolC1t02785H' => 'bol', 'BolC1t04095H' => 'bol', 'BolC3t17545H' => 'bol', 'BolC5t32769H' => 'bol', 'BraA01t02211Z' => 'bra', 'BraA01t03359Z' => 'bra', 'BraA03t13441Z' => 'bra', 'BraA05t21476Z' => 'bra', 'C01p28420' => 'bna', 'C01p41350' => 'bna', 'C03p52750' => 'bna', 'C03p52780' => 'bna', 'C05p40270' => 'bna', 'CAN.G1437.9' => 'can', 'CANSAT78G0035' => 'cansat', 'CANSAT78G1036' => 'cansat', 'CANSAT78G2272' => 'cansat', 'CANSAT78G2478' => 'cansat', 'CARHR098700' => 'chi', 'CARHR221120' => 'chi', 'CARHR221150' => 'chi', 'Carub.0003s2297' => 'cru', 'Carub.0007s2749' => 'cru', 'Carub.0007s2750' => 'cru', 'Carub.0007s2751' => 'cru', 'Ca_10849_v3' => 'car', 'Cc03_g04300' => 'ccan', 'CDE02G3648' => 'cde', 'CDE05G0060' => 'cde', 'CDE05G0692' => 'cde', 'CDE05G2285' => 'cde', 'CDE05G2884' => 'cde', 'CDE05G3072' => 'cde', 'Cfa008439' => 'cfa', 'Cfa008441' => 'cfa', 'Cfa008443' => 'cfa', 'Cfa008448' => 'cfa', 'Ciclev10005974m.g' => 'ccl', 'Ciclev10006006m.g' => 'ccl', 'Ciclev10006775m.g' => 'ccl', 'CiPaw.02G120400' => 'cil', 'CiPaw.02G120500' => 'cil', 'CiPaw.02G120600' => 'cil', 'ClCG05G004850' => 'cla', 'COL.COLO4_21566' => 'col', 'Cpa.g.sc44.124' => 'cpa', 'Cre07.g320400' => 'cre', 'Cre07.g320450' => 'cre', 'Cre08.g384650' => 'cre', 'Cre09.g393173' => 'cre', 'Cre09.g394325' => 'cre', 'Cre14.g626750' => 'cre', 'Cre16.g679250' => 'cre', 'CsaV3_3G012890' => 'csa', 'CSS0010865' => 'camsi', 'CSS0044338' => 'camsi', 'DCAR_002366' => 'dca', 'DCAR_030687' => 'dca', 'DCAR_030688' => 'dca', 'Dinv14047' => 'din', 'Dinv14048' => 'din', 'Duzib151G0105' => 'dzi', 'Duzib151G0114' => 'dzi', 'Duzib212G1029' => 'dzi', 'ECA232G3536' => 'eca', 'ECA240G0786' => 'eca', 'ECA240G1802' => 'eca', 'ECA240G3760' => 'eca', 'ECA240G3920' => 'eca', 'EL10Ac5g12536' => 'bvu', 'EL10Ac5g12537' => 'bvu', 'EL10Ac5g12538' => 'bvu', 'Eucgr.B01004' => 'egr', 'Eucgr.B01006' => 'egr', 'Eucgr.B01007' => 'egr', 'Eucgr.B01008' => 'egr', 'Eucgr.B01895' => 'egr', 'Eucgr.B01896' => 'egr', 'FAN04G1456' => 'fan', 'FAN08G1769' => 'fan', 'FAN08G2160' => 'fan', 'FAN13G2403' => 'fan', 'FAN13G3303' => 'fan', 'FAN15G2435' => 'fan', 'FAN17G0672' => 'fan', 'FAN17G2441' => 'fan', 'FAN18G1024' => 'fan', 'FAN22G1458' => 'fan', 'FAN24G0037' => 'fan', 'FAN24G0429' => 'fan', 'FAN24G2387' => 'fan', 'FAN27G2746' => 'fan', 'FvH4_2g20400' => 'fve', 'FvH4_2g20420' => 'fve', 'FvH4_2g20430' => 'fve', 'FvH4_4g01270' => 'fve', 'FvH4_4g01290' => 'fve', 'FvH4_4g01300' => 'fve', 'FvH4_4g01310' => 'fve', 'FvH4_4g01330' => 'fve', 'FvH4_5g09070' => 'fve', 'Glyma.10G243800' => 'gma', 'Glyma.20G150600' => 'gma', 'Gohir.A09G219200' => 'ghi', 'Gohir.A09G219300' => 'ghi', 'Gohir.D09G221400' => 'ghi', 'Gohir.D09G221500' => 'ghi', 'Gorai.006G242600' => 'gra', 'Gorai.006G242700' => 'gra', 'GSVIVG01018044001' => 'vvi', 'HanXRQChr03g0083821' => 'han', 'HanXRQChr03g0083841' => 'han', 'HanXRQChr03g0083881' => 'han', 'HanXRQChr03g0083901' => 'han', 'HanXRQChr03g0083921' => 'han', 'HanXRQChr03g0085331' => 'han', 'HanXRQChr03g0085361' => 'han', 'HanXRQChr03g0085411' => 'han', 'HanXRQChr03g0085421' => 'han', 'HanXRQChr03g0085431' => 'han', 'HanXRQChr08g0221991' => 'han', 'HanXRQChr11g0336061' => 'han', 'HanXRQChr11g0336411' => 'han', 'Haze_11234' => 'cav', 'Hma1.2p1_0549F.1_g177010' => 'hma', 'Hma1.2p1_0602F.1_g187630' => 'hma', 'Hund14876' => 'sun', 'Hund14879' => 'sun', 'Lalb_Chr06g0160741' => 'lal', 'Lalb_Chr21g0304781' => 'lal', 'Lj3A726G19' => 'lonja', 'Lj3A726T23' => 'lonja', 'Lj3A726T24' => 'lonja', 'Lj3A726T25' => 'lonja', 'Lj3A727T17' => 'lonja', 'Lj3C726T0' => 'lonja', 'Lj3C726T2' => 'lonja', 'Lj3P725T35' => 'lonja', 'Lj3P727T10' => 'lonja', 'Lj3P727T12' => 'lonja', 'Lj3P727T14' => 'lonja', 'Lj5g0023109' => 'lja', 'Lj6P646T44' => 'lonja', 'Lsat_1_v5_gn_6_75760' => 'lsa', 'Lsat_1_v5_gn_6_75800' => 'lsa', 'Lsat_1_v5_gn_6_75900' => 'lsa', 'Lsat_1_v5_gn_6_76240' => 'lsa', 'Lsat_1_v5_gn_6_76441' => 'lsa', 'Lsat_1_v5_gn_6_76700' => 'lsa', 'Lsat_1_v5_gn_6_76760' => 'lsa', 'Manes.15G033100' => 'mes', 'Mapoly0004s0074' => 'mpo', 'Mapoly0004s0075' => 'mpo', 'Mapoly0004s0163' => 'mpo', 'Mapoly0004s0164' => 'mpo', 'Mapoly0021s0018' => 'mpo', 'Mapoly0041s0136' => 'mpo', 'Mapoly0041s0137' => 'mpo', 'Mapoly0041s0138' => 'mpo', 'Mapoly0041s0139' => 'mpo', 'Mapoly0041s0141' => 'mpo', 'Mapoly0041s0142' => 'mpo', 'Mapoly0041s0143' => 'mpo', 'Mapoly0041s0144' => 'mpo', 'Mapoly0041s0145' => 'mpo', 'Mapoly0047s0106' => 'mpo', 'Mapoly0047s0108' => 'mpo', 'Mapoly0050s0051' => 'mpo', 'Mapoly0050s0052' => 'mpo', 'Mapoly0050s0053' => 'mpo', 'Mapoly0058s0013' => 'mpo', 'Mapoly0091s0078' => 'mpo', 'Mapoly0091s0079' => 'mpo', 'Mapoly0091s0080' => 'mpo', 'Mapoly0091s0081' => 'mpo', 'Mapoly0278s0004' => 'mpo', 'Mapoly0278s0005' => 'mpo', 'Mapoly0278s0006' => 'mpo', 'MBI11_g30648_MAGBIO' => 'mbi', 'MCO03G194' => 'mco', 'MCO03G590' => 'mco', 'MCO07G312' => 'mco', 'MCO10G318' => 'mco', 'MCO12G244' => 'mco', 'MCO13G148' => 'mco', 'MCO13G194' => 'mco', 'MCO16G238' => 'mco', 'MD06G1134100' => 'mdo', 'MD13G1200100' => 'mdo', 'MD13G1200300' => 'mdo', 'MD13G1200600' => 'mdo', 'MD14G1150400' => 'mdo', 'MD16G1200000' => 'mdo', 'Medtr1g102570' => 'mtr', 'Medtr1g102780' => 'mtr', 'Medtr1g102800' => 'mtr', 'Medtr1g102810' => 'mtr', 'Medtr1g102830' => 'mtr', 'MELO3C006499.2' => 'cme', 'Migut.G00385' => 'egut', 'MSTRG.4063' => 'ama', 'Nitab4.5_0000090g0260' => 'nta', 'Nitab4.5_0000977g0030' => 'nta', 'Nitab4.5_0002541g0040' => 'nta', 'Nitab4.5_0007068g0040' => 'nta', 'Nn005s41408' => 'nnu', 'Nn005s41410' => 'nnu', 'Oeu010310.1' => 'oeu', 'Oeu010311.1' => 'oeu', 'Oeu043472.1' => 'oeu', 'Os01g0246400' => 'osa', 'Os04g0267950' => 'osa', 'Os07g0178700' => 'osa', 'Os07g0178800' => 'osa', 'Peaxi162Scf00316g00046' => 'pax', 'Peaxi162Scf00316g00049' => 'pax', 'Peaxi162Scf00316g00059' => 'pax', 'Peaxi162Scf00316g00328' => 'pax', 'Peaxi162Scf00316g00329' => 'pax', 'Peaxi162Scf00316g00411' => 'pax', 'Peaxi162Scf00316g00521' => 'pax', 'Peaxi162Scf00492g00068' => 'pax', 'Peaxi162Scf35631g00002' => 'pax', 'PGR142G3720' => 'pgr', 'PGSC0003DMG400006442' => 'stu', 'Phvul.007G062000' => 'pvu', 'Potri.008G157750' => 'ptr', 'Potri.008G157900' => 'ptr', 'Potri.008G158000' => 'ptr', 'Potri.008G158200' => 'ptr', 'Pp3c11_7280' => 'ppa', 'Pp3c11_7980' => 'ppa', 'Pp3c12_19450' => 'ppa', 'Pp3c14_1480' => 'ppa', 'Pp3c14_1501' => 'ppa', 'Pp3c16_4900' => 'ppa', 'Pp3c16_5010' => 'ppa', 'Pp3c16_5060' => 'ppa', 'Pp3c19_18250' => 'ppa', 'Pp3c23_8530' => 'ppa', 'Pp3c23_8550' => 'ppa', 'Pp3c24_9670' => 'ppa', 'Pp3c2_21390' => 'ppa', 'Pp3c2_31380' => 'ppa', 'Pp3c3_16620' => 'ppa', 'Pp3c3_8090' => 'ppa', 'Pp3c3_8110' => 'ppa', 'Pp3c3_8130' => 'ppa', 'Pp3c3_8150' => 'ppa', 'Pp3c4_14320' => 'ppa', 'Pp3c6_2560' => 'ppa', 'Pp3c9_16700' => 'ppa', 'PRCOL_00000234' => 'pco', 'PRCOL_00000235' => 'pco', 'PRCOL_00000777' => 'pco', 'PRCOL_00002344' => 'pco', 'PRCOL_00002372' => 'pco', 'PRCOL_00006120' => 'pco', 'Prupe.1G021400' => 'ppe', 'Prupe.1G021500' => 'ppe', 'Prupe.1G021600' => 'ppe', 'Prupe.1G021700' => 'ppe', 'Prupe.1G021800' => 'ppe', 'Prupe.5G145100' => 'ppe', 'Psat6g204040' => 'psa', 'Psat6g204800' => 'psa', 'Psat6g204920' => 'psa', 'Psat6g204960' => 'psa', 'Psat6g205080' => 'psa', 'PSO017G0271' => 'pso', 'PSO017G1276' => 'pso', 'PSO017G1429' => 'pso', 'PSO017G1861' => 'pso', 'PSO017G2787' => 'pso', 'PSO017G4466' => 'pso', 'PSO017G5118' => 'pso', 'PSO017G5420' => 'pso', 'PSO063G3678' => 'pso', 'PSO210G0546' => 'pso', 'PSO317G0001' => 'pso', 'PSO357G0512' => 'pso', 'PSO478G2682' => 'pso', 'PSO647G0001' => 'pso', 'PSO675G0001' => 'pso', 'PSO675G2699' => 'pso', 'PSO675G2849' => 'pso', 'PSO675G4991' => 'pso', 'PSO689G0001' => 'pso', 'QL06p000916' => 'qlo', 'QL06p000921' => 'qlo', 'QL06p001398' => 'qlo', 'QL06p001407' => 'qlo', 'QL06p002031' => 'qlo', 'RcHm_v2.0_Chr4g0387791' => 'rch', 'RcHm_v2.0_Chr4g0387801' => 'rch', 'RcHm_v2.0_Chr6g0286501' => 'rch', 'RcHm_v2.0_Chr6g0286511' => 'rch', 'RcHm_v2.0_Chr6g0286521' => 'rch', 'RcHm_v2.0_Chr6g0286531' => 'rch', 'RcHm_v2.0_Chr7g0189141' => 'rch', 'Rhsim02G0028700' => 'rsi', 'Rhsim02G0028800' => 'rsi', 'Rhsim02G0028900' => 'rsi', 'Rhsim02G0029000' => 'rsi', 'Rhsim02G0029100' => 'rsi', 'Rhsim02G0029200' => 'rsi', 'Rhsim02G0029300' => 'rsi', 'Rhsim02G0029400' => 'rsi', 'Rhsim02G0029500' => 'rsi', 'Rhsim02G0029600' => 'rsi', 'RhsimUnG0024000' => 'rsi', 'RhsimUnG0024100' => 'rsi', 'RhsimUnG0024200' => 'rsi', 'RhsimUnG0024300' => 'rsi', 'RhsimUnG0024400' => 'rsi', 'RhsimUnG0024500' => 'rsi', 'RhsimUnG0024700' => 'rsi', 'RhsimUnG0024800' => 'rsi', 'RhsimUnG0024900' => 'rsi', 'RhsimUnG0025100' => 'rsi', 'Sabra08G0120200' => 'sbr', 'Sabra08G0120300' => 'sbr', 'Sabra08G0120500' => 'sbr', 'Sabra08G0120600' => 'sbr', 'Sabra10G0158900' => 'sbr', 'SalBow2G3492' => 'sbo', 'Sc13g0004760' => 'sci', 'Sc13g0004770' => 'sci', 'Sed0003417' => 'sed', 'Sed0019750' => 'sed', 'SEGI_03419' => 'sgi', 'SEGI_05907' => 'sgi', 'SEGI_10682' => 'sgi', 'SEGI_13528' => 'sgi', 'SEGI_16081' => 'sgi', 'SEGI_19370' => 'sgi', 'SEGI_21015' => 'sgi', 'SEGI_21944' => 'sgi', 'SEGI_32906' => 'sgi', 'SEGI_33093' => 'sgi', 'SEGI_36110' => 'sgi', 'SEGI_40397' => 'sgi', 'SGA_v2.0_scaffold191G40426' => 'sas', 'SGA_v2.0_scaffold353G49717' => 'sas', 'SGA_v2.0_scaffold50G18550' => 'sas', 'SMO119G0173' => 'smo', 'SMO172G0002' => 'smo', 'Solyc09g082690.3' => 'sly', 'Solyc09g082700.2' => 'sly', 'Sopen09g031550' => 'spe', 'Sopen09g031560' => 'spe', 'Sp3g20540' => 'spa', 'Sp7g07580' => 'spa', 'TAR134G0002' => 'tar', 'TAR236G0001' => 'tar', 'TAR365G0892' => 'tar', 'TAR636G0166' => 'tar', 'TAR636G0646' => 'tar', 'TAR636G0869' => 'tar', 'TAR636G1317' => 'tar', 'TAR636G1744' => 'tar', 'TAR636G3358' => 'tar', 'TAR636G3436' => 'tar', 'THA.LOC104803047' => 'tha', 'Thecc.04G238900' => 'tca', 'Thhalv10021557m.g' => 'esa', 'Thhalv10026318m.g' => 'esa', 'Thhalv10026335m.g' => 'esa', 'TPR.G17433' => 'tpr', 'TPR.G18915' => 'tpr', 'TPR.G26125' => 'tpr', 'TWI09G0677' => 'twi', 'TWI73G0287' => 'twi', 'unitig_748.g8326' => 'ugi', 'vmacro15370' => 'vma', 'vmacro15371' => 'vma', 'vmacro15372' => 'vma', 'vmacro15373' => 'vma', 'vmacro15374' => 'vma', 'VMungo0720G2826' => 'vmu', 'Zm00001eb116960' => 'zma', 'Zm00001eb301260' => 'zma', 'Zm00001eb301270' => 'zma' ), 'gf_id' => 'HOM05D001460', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001460' ), 'data_identifier' => 'HOM05D001460', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001460', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '433', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p22980' => 'bna', 'A01p32340' => 'bna', 'A03p42970' => 'bna', 'A05p25880' => 'bna', 'Aa31LG8G9320' => 'aar', 'Aa31LG8G9330' => 'aar', 'Aa31LG8G9340' => 'aar', 'Aa31sc221G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1034' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1528' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.829' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2222' => 'aag', 'Ah.12g058830' => 'amhyb', 'Ah.12g058840' => 'amhyb', 'AL3G37160' => 'aly', 'AL7G41310' => 'aly', 'Aqoxy5G00395' => 'aox', 'Aqoxy5G00396' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0C8NZA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5185HY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JZ1PRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MD3LS0' => 'arhy', 'AT3G22840' => 'ath', 'AT4G14690' => 'ath', 'ATR0665G054' => 'atr', 'Atru.chr4.2344' => 'acertr', 'Atru.chr4.2346' => 'acertr', 'Atru.chr4.2347' => 'acertr', 'Atru.chr4.2348' => 'acertr', 'Atru.chr4.2355' => 'acertr', 'Atru.chr4.2356' => 'acertr', 'Atru.chr4.2358' => 'acertr', 'Atru.chr4.2359' => 'acertr', 'Atru.chr4.2360' => 'acertr', 'Atru.chr4.2361' => 'acertr', 'AUR62030476' => 'cqu', 'AUR62030478' => 'cqu', 'AUR62030819' => 'cqu', 'AUR62030820' => 'cqu', 'BcaB03g14648' => 'bca', 'BcaB04g20492' => 'bca', 'BcaB06g26399' => 'bca', 'BcaC01g03416' => 'bca', 'BcaC01g03419' => 'bca', 'BcaC01g03421' => 'bca', 'BcaC01g03424' => 'bca', 'BcaC05g28012' => 'bca', 'BcaC09g49212' => 'bca', 'BcaC09g50140' => 'bca', 'BcaNung00346' => 'bca', 'BolC1t02785H' => 'bol', 'BolC1t04095H' => 'bol', 'BolC3t17545H' => 'bol', 'BolC5t32769H' => 'bol', 'BraA01t02211Z' => 'bra', 'BraA01t03359Z' => 'bra', 'BraA03t13441Z' => 'bra', 'BraA05t21476Z' => 'bra', 'C01p28420' => 'bna', 'C01p41350' => 'bna', 'C03p52750' => 'bna', 'C03p52780' => 'bna', 'C05p40270' => 'bna', 'CAN.G1437.9' => 'can', 'CANSAT78G0035' => 'cansat', 'CANSAT78G1036' => 'cansat', 'CANSAT78G2272' => 'cansat', 'CANSAT78G2478' => 'cansat', 'CARHR098700' => 'chi', 'CARHR221120' => 'chi', 'CARHR221150' => 'chi', 'Carub.0003s2297' => 'cru', 'Carub.0007s2749' => 'cru', 'Carub.0007s2750' => 'cru', 'Carub.0007s2751' => 'cru', 'Ca_10849_v3' => 'car', 'Cc03_g04300' => 'ccan', 'CDE02G3648' => 'cde', 'CDE05G0060' => 'cde', 'CDE05G0692' => 'cde', 'CDE05G2285' => 'cde', 'CDE05G2884' => 'cde', 'CDE05G3072' => 'cde', 'Cfa008439' => 'cfa', 'Cfa008441' => 'cfa', 'Cfa008443' => 'cfa', 'Cfa008448' => 'cfa', 'Ciclev10005974m.g' => 'ccl', 'Ciclev10006006m.g' => 'ccl', 'Ciclev10006775m.g' => 'ccl', 'CiPaw.02G120400' => 'cil', 'CiPaw.02G120500' => 'cil', 'CiPaw.02G120600' => 'cil', 'ClCG05G004850' => 'cla', 'COL.COLO4_21566' => 'col', 'Cpa.g.sc44.124' => 'cpa', 'Cre07.g320400' => 'cre', 'Cre07.g320450' => 'cre', 'Cre08.g384650' => 'cre', 'Cre09.g393173' => 'cre', 'Cre09.g394325' => 'cre', 'Cre14.g626750' => 'cre', 'Cre16.g679250' => 'cre', 'CsaV3_3G012890' => 'csa', 'CSS0010865' => 'camsi', 'CSS0044338' => 'camsi', 'DCAR_002366' => 'dca', 'DCAR_030687' => 'dca', 'DCAR_030688' => 'dca', 'Dinv14047' => 'din', 'Dinv14048' => 'din', 'Duzib151G0105' => 'dzi', 'Duzib151G0114' => 'dzi', 'Duzib212G1029' => 'dzi', 'ECA232G3536' => 'eca', 'ECA240G0786' => 'eca', 'ECA240G1802' => 'eca', 'ECA240G3760' => 'eca', 'ECA240G3920' => 'eca', 'EL10Ac5g12536' => 'bvu', 'EL10Ac5g12537' => 'bvu', 'EL10Ac5g12538' => 'bvu', 'Eucgr.B01004' => 'egr', 'Eucgr.B01006' => 'egr', 'Eucgr.B01007' => 'egr', 'Eucgr.B01008' => 'egr', 'Eucgr.B01895' => 'egr', 'Eucgr.B01896' => 'egr', 'FAN04G1456' => 'fan', 'FAN08G1769' => 'fan', 'FAN08G2160' => 'fan', 'FAN13G2403' => 'fan', 'FAN13G3303' => 'fan', 'FAN15G2435' => 'fan', 'FAN17G0672' => 'fan', 'FAN17G2441' => 'fan', 'FAN18G1024' => 'fan', 'FAN22G1458' => 'fan', 'FAN24G0037' => 'fan', 'FAN24G0429' => 'fan', 'FAN24G2387' => 'fan', 'FAN27G2746' => 'fan', 'FvH4_2g20400' => 'fve', 'FvH4_2g20420' => 'fve', 'FvH4_2g20430' => 'fve', 'FvH4_4g01270' => 'fve', 'FvH4_4g01290' => 'fve', 'FvH4_4g01300' => 'fve', 'FvH4_4g01310' => 'fve', 'FvH4_4g01330' => 'fve', 'FvH4_5g09070' => 'fve', 'Glyma.10G243800' => 'gma', 'Glyma.20G150600' => 'gma', 'Gohir.A09G219200' => 'ghi', 'Gohir.A09G219300' => 'ghi', 'Gohir.D09G221400' => 'ghi', 'Gohir.D09G221500' => 'ghi', 'Gorai.006G242600' => 'gra', 'Gorai.006G242700' => 'gra', 'GSVIVG01018044001' => 'vvi', 'HanXRQChr03g0083821' => 'han', 'HanXRQChr03g0083841' => 'han', 'HanXRQChr03g0083881' => 'han', 'HanXRQChr03g0083901' => 'han', 'HanXRQChr03g0083921' => 'han', 'HanXRQChr03g0085331' => 'han', 'HanXRQChr03g0085361' => 'han', 'HanXRQChr03g0085411' => 'han', 'HanXRQChr03g0085421' => 'han', 'HanXRQChr03g0085431' => 'han', 'HanXRQChr08g0221991' => 'han', 'HanXRQChr11g0336061' => 'han', 'HanXRQChr11g0336411' => 'han', 'Haze_11234' => 'cav', 'Hma1.2p1_0549F.1_g177010' => 'hma', 'Hma1.2p1_0602F.1_g187630' => 'hma', 'Hund14876' => 'sun', 'Hund14879' => 'sun', 'Lalb_Chr06g0160741' => 'lal', 'Lalb_Chr21g0304781' => 'lal', 'Lj3A726G19' => 'lonja', 'Lj3A726T23' => 'lonja', 'Lj3A726T24' => 'lonja', 'Lj3A726T25' => 'lonja', 'Lj3A727T17' => 'lonja', 'Lj3C726T0' => 'lonja', 'Lj3C726T2' => 'lonja', 'Lj3P725T35' => 'lonja', 'Lj3P727T10' => 'lonja', 'Lj3P727T12' => 'lonja', 'Lj3P727T14' => 'lonja', 'Lj5g0023109' => 'lja', 'Lj6P646T44' => 'lonja', 'Lsat_1_v5_gn_6_75760' => 'lsa', 'Lsat_1_v5_gn_6_75800' => 'lsa', 'Lsat_1_v5_gn_6_75900' => 'lsa', 'Lsat_1_v5_gn_6_76240' => 'lsa', 'Lsat_1_v5_gn_6_76441' => 'lsa', 'Lsat_1_v5_gn_6_76700' => 'lsa', 'Lsat_1_v5_gn_6_76760' => 'lsa', 'Manes.15G033100' => 'mes', 'Mapoly0004s0074' => 'mpo', 'Mapoly0004s0075' => 'mpo', 'Mapoly0004s0163' => 'mpo', 'Mapoly0004s0164' => 'mpo', 'Mapoly0021s0018' => 'mpo', 'Mapoly0041s0136' => 'mpo', 'Mapoly0041s0137' => 'mpo', 'Mapoly0041s0138' => 'mpo', 'Mapoly0041s0139' => 'mpo', 'Mapoly0041s0141' => 'mpo', 'Mapoly0041s0142' => 'mpo', 'Mapoly0041s0143' => 'mpo', 'Mapoly0041s0144' => 'mpo', 'Mapoly0041s0145' => 'mpo', 'Mapoly0047s0106' => 'mpo', 'Mapoly0047s0108' => 'mpo', 'Mapoly0050s0051' => 'mpo', 'Mapoly0050s0052' => 'mpo', 'Mapoly0050s0053' => 'mpo', 'Mapoly0058s0013' => 'mpo', 'Mapoly0091s0078' => 'mpo', 'Mapoly0091s0079' => 'mpo', 'Mapoly0091s0080' => 'mpo', 'Mapoly0091s0081' => 'mpo', 'Mapoly0278s0004' => 'mpo', 'Mapoly0278s0005' => 'mpo', 'Mapoly0278s0006' => 'mpo', 'MBI11_g30648_MAGBIO' => 'mbi', 'MCO03G194' => 'mco', 'MCO03G590' => 'mco', 'MCO07G312' => 'mco', 'MCO10G318' => 'mco', 'MCO12G244' => 'mco', 'MCO13G148' => 'mco', 'MCO13G194' => 'mco', 'MCO16G238' => 'mco', 'MD06G1134100' => 'mdo', 'MD13G1200100' => 'mdo', 'MD13G1200300' => 'mdo', 'MD13G1200600' => 'mdo', 'MD14G1150400' => 'mdo', 'MD16G1200000' => 'mdo', 'Medtr1g102570' => 'mtr', 'Medtr1g102780' => 'mtr', 'Medtr1g102800' => 'mtr', 'Medtr1g102810' => 'mtr', 'Medtr1g102830' => 'mtr', 'MELO3C006499.2' => 'cme', 'Migut.G00385' => 'egut', 'MSTRG.4063' => 'ama', 'Nitab4.5_0000090g0260' => 'nta', 'Nitab4.5_0000977g0030' => 'nta', 'Nitab4.5_0002541g0040' => 'nta', 'Nitab4.5_0007068g0040' => 'nta', 'Nn005s41408' => 'nnu', 'Nn005s41410' => 'nnu', 'Oeu010310.1' => 'oeu', 'Oeu010311.1' => 'oeu', 'Oeu043472.1' => 'oeu', 'Os01g0246400' => 'osa', 'Os04g0267950' => 'osa', 'Os07g0178700' => 'osa', 'Os07g0178800' => 'osa', 'Peaxi162Scf00316g00046' => 'pax', 'Peaxi162Scf00316g00049' => 'pax', 'Peaxi162Scf00316g00059' => 'pax', 'Peaxi162Scf00316g00328' => 'pax', 'Peaxi162Scf00316g00329' => 'pax', 'Peaxi162Scf00316g00411' => 'pax', 'Peaxi162Scf00316g00521' => 'pax', 'Peaxi162Scf00492g00068' => 'pax', 'Peaxi162Scf35631g00002' => 'pax', 'PGR142G3720' => 'pgr', 'PGSC0003DMG400006442' => 'stu', 'Phvul.007G062000' => 'pvu', 'Potri.008G157750' => 'ptr', 'Potri.008G157900' => 'ptr', 'Potri.008G158000' => 'ptr', 'Potri.008G158200' => 'ptr', 'Pp3c11_7280' => 'ppa', 'Pp3c11_7980' => 'ppa', 'Pp3c12_19450' => 'ppa', 'Pp3c14_1480' => 'ppa', 'Pp3c14_1501' => 'ppa', 'Pp3c16_4900' => 'ppa', 'Pp3c16_5010' => 'ppa', 'Pp3c16_5060' => 'ppa', 'Pp3c19_18250' => 'ppa', 'Pp3c23_8530' => 'ppa', 'Pp3c23_8550' => 'ppa', 'Pp3c24_9670' => 'ppa', 'Pp3c2_21390' => 'ppa', 'Pp3c2_31380' => 'ppa', 'Pp3c3_16620' => 'ppa', 'Pp3c3_8090' => 'ppa', 'Pp3c3_8110' => 'ppa', 'Pp3c3_8130' => 'ppa', 'Pp3c3_8150' => 'ppa', 'Pp3c4_14320' => 'ppa', 'Pp3c6_2560' => 'ppa', 'Pp3c9_16700' => 'ppa', 'PRCOL_00000234' => 'pco', 'PRCOL_00000235' => 'pco', 'PRCOL_00000777' => 'pco', 'PRCOL_00002344' => 'pco', 'PRCOL_00002372' => 'pco', 'PRCOL_00006120' => 'pco', 'Prupe.1G021400' => 'ppe', 'Prupe.1G021500' => 'ppe', 'Prupe.1G021600' => 'ppe', 'Prupe.1G021700' => 'ppe', 'Prupe.1G021800' => 'ppe', 'Prupe.5G145100' => 'ppe', 'Psat6g204040' => 'psa', 'Psat6g204800' => 'psa', 'Psat6g204920' => 'psa', 'Psat6g204960' => 'psa', 'Psat6g205080' => 'psa', 'PSO017G0271' => 'pso', 'PSO017G1276' => 'pso', 'PSO017G1429' => 'pso', 'PSO017G1861' => 'pso', 'PSO017G2787' => 'pso', 'PSO017G4466' => 'pso', 'PSO017G5118' => 'pso', 'PSO017G5420' => 'pso', 'PSO063G3678' => 'pso', 'PSO210G0546' => 'pso', 'PSO317G0001' => 'pso', 'PSO357G0512' => 'pso', 'PSO478G2682' => 'pso', 'PSO647G0001' => 'pso', 'PSO675G0001' => 'pso', 'PSO675G2699' => 'pso', 'PSO675G2849' => 'pso', 'PSO675G4991' => 'pso', 'PSO689G0001' => 'pso', 'QL06p000916' => 'qlo', 'QL06p000921' => 'qlo', 'QL06p001398' => 'qlo', 'QL06p001407' => 'qlo', 'QL06p002031' => 'qlo', 'RcHm_v2.0_Chr4g0387791' => 'rch', 'RcHm_v2.0_Chr4g0387801' => 'rch', 'RcHm_v2.0_Chr6g0286501' => 'rch', 'RcHm_v2.0_Chr6g0286511' => 'rch', 'RcHm_v2.0_Chr6g0286521' => 'rch', 'RcHm_v2.0_Chr6g0286531' => 'rch', 'RcHm_v2.0_Chr7g0189141' => 'rch', 'Rhsim02G0028700' => 'rsi', 'Rhsim02G0028800' => 'rsi', 'Rhsim02G0028900' => 'rsi', 'Rhsim02G0029000' => 'rsi', 'Rhsim02G0029100' => 'rsi', 'Rhsim02G0029200' => 'rsi', 'Rhsim02G0029300' => 'rsi', 'Rhsim02G0029400' => 'rsi', 'Rhsim02G0029500' => 'rsi', 'Rhsim02G0029600' => 'rsi', 'RhsimUnG0024000' => 'rsi', 'RhsimUnG0024100' => 'rsi', 'RhsimUnG0024200' => 'rsi', 'RhsimUnG0024300' => 'rsi', 'RhsimUnG0024400' => 'rsi', 'RhsimUnG0024500' => 'rsi', 'RhsimUnG0024700' => 'rsi', 'RhsimUnG0024800' => 'rsi', 'RhsimUnG0024900' => 'rsi', 'RhsimUnG0025100' => 'rsi', 'Sabra08G0120200' => 'sbr', 'Sabra08G0120300' => 'sbr', 'Sabra08G0120500' => 'sbr', 'Sabra08G0120600' => 'sbr', 'Sabra10G0158900' => 'sbr', 'SalBow2G3492' => 'sbo', 'Sc13g0004760' => 'sci', 'Sc13g0004770' => 'sci', 'Sed0003417' => 'sed', 'Sed0019750' => 'sed', 'SEGI_03419' => 'sgi', 'SEGI_05907' => 'sgi', 'SEGI_10682' => 'sgi', 'SEGI_13528' => 'sgi', 'SEGI_16081' => 'sgi', 'SEGI_19370' => 'sgi', 'SEGI_21015' => 'sgi', 'SEGI_21944' => 'sgi', 'SEGI_32906' => 'sgi', 'SEGI_33093' => 'sgi', 'SEGI_36110' => 'sgi', 'SEGI_40397' => 'sgi', 'SGA_v2.0_scaffold191G40426' => 'sas', 'SGA_v2.0_scaffold353G49717' => 'sas', 'SGA_v2.0_scaffold50G18550' => 'sas', 'SMO119G0173' => 'smo', 'SMO172G0002' => 'smo', 'Solyc09g082690.3' => 'sly', 'Solyc09g082700.2' => 'sly', 'Sopen09g031550' => 'spe', 'Sopen09g031560' => 'spe', 'Sp3g20540' => 'spa', 'Sp7g07580' => 'spa', 'TAR134G0002' => 'tar', 'TAR236G0001' => 'tar', 'TAR365G0892' => 'tar', 'TAR636G0166' => 'tar', 'TAR636G0646' => 'tar', 'TAR636G0869' => 'tar', 'TAR636G1317' => 'tar', 'TAR636G1744' => 'tar', 'TAR636G3358' => 'tar', 'TAR636G3436' => 'tar', 'THA.LOC104803047' => 'tha', 'Thecc.04G238900' => 'tca', 'Thhalv10021557m.g' => 'esa', 'Thhalv10026318m.g' => 'esa', 'Thhalv10026335m.g' => 'esa', 'TPR.G17433' => 'tpr', 'TPR.G18915' => 'tpr', 'TPR.G26125' => 'tpr', 'TWI09G0677' => 'twi', 'TWI73G0287' => 'twi', 'unitig_748.g8326' => 'ugi', 'vmacro15370' => 'vma', 'vmacro15371' => 'vma', 'vmacro15372' => 'vma', 'vmacro15373' => 'vma', 'vmacro15374' => 'vma', 'VMungo0720G2826' => 'vmu', 'Zm00001eb116960' => 'zma', 'Zm00001eb301260' => 'zma', 'Zm00001eb301270' => 'zma' ) $gf_id = 'HOM05D001460' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001460' ) $data_identifier = 'HOM05D001460' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 4, 'aag' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 2, 'aox' => (int) 2, 'arhy' => (int) 4, 'ath' => (int) 2, 'atr' => (int) 1, 'acertr' => (int) 10, 'cqu' => (int) 4, 'bca' => (int) 11, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 1, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 1, 'ccan' => (int) 1, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 1, 'col' => (int) 1, 'cpa' => (int) 1, 'cre' => (int) 7, 'csa' => (int) 1, 'camsi' => (int) 2, 'dca' => (int) 3, 'din' => (int) 2, 'dzi' => (int) 3, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 14, 'fve' => (int) 9, 'gma' => (int) 2, 'ghi' => (int) 4, 'gra' => (int) 2, 'vvi' => (int) 1, 'han' => (int) 13, 'cav' => (int) 1, 'hma' => (int) 2, 'sun' => (int) 2, 'lal' => (int) 2, 'lonja' => (int) 12, 'lja' => (int) 1, 'lsa' => (int) 7, 'mes' => (int) 1, 'mpo' => (int) 27, 'mbi' => (int) 1, 'mco' => (int) 8, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 1, 'egut' => (int) 1, 'ama' => (int) 1, 'nta' => (int) 4, 'nnu' => (int) 2, 'oeu' => (int) 3, 'osa' => (int) 4, 'pax' => (int) 9, 'pgr' => (int) 1, 'stu' => (int) 1, 'pvu' => (int) 1, 'ptr' => (int) 4, 'ppa' => (int) 22, 'pco' => (int) 6, 'ppe' => (int) 6, 'psa' => (int) 5, 'pso' => (int) 19, 'qlo' => (int) 5, 'rch' => (int) 7, 'rsi' => (int) 20, 'sbr' => (int) 5, 'sbo' => (int) 1, 'sci' => (int) 2, 'sed' => (int) 2, 'sgi' => (int) 12, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 2, 'tar' => (int) 10, 'tha' => (int) 1, 'tca' => (int) 1, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 2, 'ugi' => (int) 1, 'vma' => (int) 5, 'vmu' => (int) 1, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb301270' $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' => 'HOM05D001460', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '433', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p22980' => 'bna', 'A01p32340' => 'bna', 'A03p42970' => 'bna', 'A05p25880' => 'bna', 'Aa31LG8G9320' => 'aar', 'Aa31LG8G9330' => 'aar', 'Aa31LG8G9340' => 'aar', 'Aa31sc221G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1034' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1528' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.829' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2222' => 'aag', 'Ah.12g058830' => 'amhyb', 'Ah.12g058840' => 'amhyb', 'AL3G37160' => 'aly', 'AL7G41310' => 'aly', 'Aqoxy5G00395' => 'aox', 'Aqoxy5G00396' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0C8NZA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5185HY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JZ1PRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MD3LS0' => 'arhy', 'AT3G22840' => 'ath', 'AT4G14690' => 'ath', 'ATR0665G054' => 'atr', 'Atru.chr4.2344' => 'acertr', 'Atru.chr4.2346' => 'acertr', 'Atru.chr4.2347' => 'acertr', 'Atru.chr4.2348' => 'acertr', 'Atru.chr4.2355' => 'acertr', 'Atru.chr4.2356' => 'acertr', 'Atru.chr4.2358' => 'acertr', 'Atru.chr4.2359' => 'acertr', 'Atru.chr4.2360' => 'acertr', 'Atru.chr4.2361' => 'acertr', 'AUR62030476' => 'cqu', 'AUR62030478' => 'cqu', 'AUR62030819' => 'cqu', 'AUR62030820' => 'cqu', 'BcaB03g14648' => 'bca', 'BcaB04g20492' => 'bca', 'BcaB06g26399' => 'bca', 'BcaC01g03416' => 'bca', 'BcaC01g03419' => 'bca', 'BcaC01g03421' => 'bca', 'BcaC01g03424' => 'bca', 'BcaC05g28012' => 'bca', 'BcaC09g49212' => 'bca', 'BcaC09g50140' => 'bca', 'BcaNung00346' => 'bca', 'BolC1t02785H' => 'bol', 'BolC1t04095H' => 'bol', 'BolC3t17545H' => 'bol', 'BolC5t32769H' => 'bol', 'BraA01t02211Z' => 'bra', 'BraA01t03359Z' => 'bra', 'BraA03t13441Z' => 'bra', 'BraA05t21476Z' => 'bra', 'C01p28420' => 'bna', 'C01p41350' => 'bna', 'C03p52750' => 'bna', 'C03p52780' => 'bna', 'C05p40270' => 'bna', 'CAN.G1437.9' => 'can', 'CANSAT78G0035' => 'cansat', 'CANSAT78G1036' => 'cansat', 'CANSAT78G2272' => 'cansat', 'CANSAT78G2478' => 'cansat', 'CARHR098700' => 'chi', 'CARHR221120' => 'chi', 'CARHR221150' => 'chi', 'Carub.0003s2297' => 'cru', 'Carub.0007s2749' => 'cru', 'Carub.0007s2750' => 'cru', 'Carub.0007s2751' => 'cru', 'Ca_10849_v3' => 'car', 'Cc03_g04300' => 'ccan', 'CDE02G3648' => 'cde', 'CDE05G0060' => 'cde', 'CDE05G0692' => 'cde', 'CDE05G2285' => 'cde', 'CDE05G2884' => 'cde', 'CDE05G3072' => 'cde', 'Cfa008439' => 'cfa', 'Cfa008441' => 'cfa', 'Cfa008443' => 'cfa', 'Cfa008448' => 'cfa', 'Ciclev10005974m.g' => 'ccl', 'Ciclev10006006m.g' => 'ccl', 'Ciclev10006775m.g' => 'ccl', 'CiPaw.02G120400' => 'cil', 'CiPaw.02G120500' => 'cil', 'CiPaw.02G120600' => 'cil', 'ClCG05G004850' => 'cla', 'COL.COLO4_21566' => 'col', 'Cpa.g.sc44.124' => 'cpa', 'Cre07.g320400' => 'cre', 'Cre07.g320450' => 'cre', 'Cre08.g384650' => 'cre', 'Cre09.g393173' => 'cre', 'Cre09.g394325' => 'cre', 'Cre14.g626750' => 'cre', 'Cre16.g679250' => 'cre', 'CsaV3_3G012890' => 'csa', 'CSS0010865' => 'camsi', 'CSS0044338' => 'camsi', 'DCAR_002366' => 'dca', 'DCAR_030687' => 'dca', 'DCAR_030688' => 'dca', 'Dinv14047' => 'din', 'Dinv14048' => 'din', 'Duzib151G0105' => 'dzi', 'Duzib151G0114' => 'dzi', 'Duzib212G1029' => 'dzi', 'ECA232G3536' => 'eca', 'ECA240G0786' => 'eca', 'ECA240G1802' => 'eca', 'ECA240G3760' => 'eca', 'ECA240G3920' => 'eca', 'EL10Ac5g12536' => 'bvu', 'EL10Ac5g12537' => 'bvu', 'EL10Ac5g12538' => 'bvu', 'Eucgr.B01004' => 'egr', 'Eucgr.B01006' => 'egr', 'Eucgr.B01007' => 'egr', 'Eucgr.B01008' => 'egr', 'Eucgr.B01895' => 'egr', 'Eucgr.B01896' => 'egr', 'FAN04G1456' => 'fan', 'FAN08G1769' => 'fan', 'FAN08G2160' => 'fan', 'FAN13G2403' => 'fan', 'FAN13G3303' => 'fan', 'FAN15G2435' => 'fan', 'FAN17G0672' => 'fan', 'FAN17G2441' => 'fan', 'FAN18G1024' => 'fan', 'FAN22G1458' => 'fan', 'FAN24G0037' => 'fan', 'FAN24G0429' => 'fan', 'FAN24G2387' => 'fan', 'FAN27G2746' => 'fan', 'FvH4_2g20400' => 'fve', 'FvH4_2g20420' => 'fve', 'FvH4_2g20430' => 'fve', 'FvH4_4g01270' => 'fve', 'FvH4_4g01290' => 'fve', 'FvH4_4g01300' => 'fve', 'FvH4_4g01310' => 'fve', 'FvH4_4g01330' => 'fve', 'FvH4_5g09070' => 'fve', 'Glyma.10G243800' => 'gma', 'Glyma.20G150600' => 'gma', 'Gohir.A09G219200' => 'ghi', 'Gohir.A09G219300' => 'ghi', 'Gohir.D09G221400' => 'ghi', 'Gohir.D09G221500' => 'ghi', 'Gorai.006G242600' => 'gra', 'Gorai.006G242700' => 'gra', 'GSVIVG01018044001' => 'vvi', 'HanXRQChr03g0083821' => 'han', 'HanXRQChr03g0083841' => 'han', 'HanXRQChr03g0083881' => 'han', 'HanXRQChr03g0083901' => 'han', 'HanXRQChr03g0083921' => 'han', 'HanXRQChr03g0085331' => 'han', 'HanXRQChr03g0085361' => 'han', 'HanXRQChr03g0085411' => 'han', 'HanXRQChr03g0085421' => 'han', 'HanXRQChr03g0085431' => 'han', 'HanXRQChr08g0221991' => 'han', 'HanXRQChr11g0336061' => 'han', 'HanXRQChr11g0336411' => 'han', 'Haze_11234' => 'cav', 'Hma1.2p1_0549F.1_g177010' => 'hma', 'Hma1.2p1_0602F.1_g187630' => 'hma', 'Hund14876' => 'sun', 'Hund14879' => 'sun', 'Lalb_Chr06g0160741' => 'lal', 'Lalb_Chr21g0304781' => 'lal', 'Lj3A726G19' => 'lonja', 'Lj3A726T23' => 'lonja', 'Lj3A726T24' => 'lonja', 'Lj3A726T25' => 'lonja', 'Lj3A727T17' => 'lonja', 'Lj3C726T0' => 'lonja', 'Lj3C726T2' => 'lonja', 'Lj3P725T35' => 'lonja', 'Lj3P727T10' => 'lonja', 'Lj3P727T12' => 'lonja', 'Lj3P727T14' => 'lonja', 'Lj5g0023109' => 'lja', 'Lj6P646T44' => 'lonja', 'Lsat_1_v5_gn_6_75760' => 'lsa', 'Lsat_1_v5_gn_6_75800' => 'lsa', 'Lsat_1_v5_gn_6_75900' => 'lsa', 'Lsat_1_v5_gn_6_76240' => 'lsa', 'Lsat_1_v5_gn_6_76441' => 'lsa', 'Lsat_1_v5_gn_6_76700' => 'lsa', 'Lsat_1_v5_gn_6_76760' => 'lsa', 'Manes.15G033100' => 'mes', 'Mapoly0004s0074' => 'mpo', 'Mapoly0004s0075' => 'mpo', 'Mapoly0004s0163' => 'mpo', 'Mapoly0004s0164' => 'mpo', 'Mapoly0021s0018' => 'mpo', 'Mapoly0041s0136' => 'mpo', 'Mapoly0041s0137' => 'mpo', 'Mapoly0041s0138' => 'mpo', 'Mapoly0041s0139' => 'mpo', 'Mapoly0041s0141' => 'mpo', 'Mapoly0041s0142' => 'mpo', 'Mapoly0041s0143' => 'mpo', 'Mapoly0041s0144' => 'mpo', 'Mapoly0041s0145' => 'mpo', 'Mapoly0047s0106' => 'mpo', 'Mapoly0047s0108' => 'mpo', 'Mapoly0050s0051' => 'mpo', 'Mapoly0050s0052' => 'mpo', 'Mapoly0050s0053' => 'mpo', 'Mapoly0058s0013' => 'mpo', 'Mapoly0091s0078' => 'mpo', 'Mapoly0091s0079' => 'mpo', 'Mapoly0091s0080' => 'mpo', 'Mapoly0091s0081' => 'mpo', 'Mapoly0278s0004' => 'mpo', 'Mapoly0278s0005' => 'mpo', 'Mapoly0278s0006' => 'mpo', 'MBI11_g30648_MAGBIO' => 'mbi', 'MCO03G194' => 'mco', 'MCO03G590' => 'mco', 'MCO07G312' => 'mco', 'MCO10G318' => 'mco', 'MCO12G244' => 'mco', 'MCO13G148' => 'mco', 'MCO13G194' => 'mco', 'MCO16G238' => 'mco', 'MD06G1134100' => 'mdo', 'MD13G1200100' => 'mdo', 'MD13G1200300' => 'mdo', 'MD13G1200600' => 'mdo', 'MD14G1150400' => 'mdo', 'MD16G1200000' => 'mdo', 'Medtr1g102570' => 'mtr', 'Medtr1g102780' => 'mtr', 'Medtr1g102800' => 'mtr', 'Medtr1g102810' => 'mtr', 'Medtr1g102830' => 'mtr', 'MELO3C006499.2' => 'cme', 'Migut.G00385' => 'egut', 'MSTRG.4063' => 'ama', 'Nitab4.5_0000090g0260' => 'nta', 'Nitab4.5_0000977g0030' => 'nta', 'Nitab4.5_0002541g0040' => 'nta', 'Nitab4.5_0007068g0040' => 'nta', 'Nn005s41408' => 'nnu', 'Nn005s41410' => 'nnu', 'Oeu010310.1' => 'oeu', 'Oeu010311.1' => 'oeu', 'Oeu043472.1' => 'oeu', 'Os01g0246400' => 'osa', 'Os04g0267950' => 'osa', 'Os07g0178700' => 'osa', 'Os07g0178800' => 'osa', 'Peaxi162Scf00316g00046' => 'pax', 'Peaxi162Scf00316g00049' => 'pax', 'Peaxi162Scf00316g00059' => 'pax', 'Peaxi162Scf00316g00328' => 'pax', 'Peaxi162Scf00316g00329' => 'pax', 'Peaxi162Scf00316g00411' => 'pax', 'Peaxi162Scf00316g00521' => 'pax', 'Peaxi162Scf00492g00068' => 'pax', 'Peaxi162Scf35631g00002' => 'pax', 'PGR142G3720' => 'pgr', 'PGSC0003DMG400006442' => 'stu', 'Phvul.007G062000' => 'pvu', 'Potri.008G157750' => 'ptr', 'Potri.008G157900' => 'ptr', 'Potri.008G158000' => 'ptr', 'Potri.008G158200' => 'ptr', 'Pp3c11_7280' => 'ppa', 'Pp3c11_7980' => 'ppa', 'Pp3c12_19450' => 'ppa', 'Pp3c14_1480' => 'ppa', 'Pp3c14_1501' => 'ppa', 'Pp3c16_4900' => 'ppa', 'Pp3c16_5010' => 'ppa', 'Pp3c16_5060' => 'ppa', 'Pp3c19_18250' => 'ppa', 'Pp3c23_8530' => 'ppa', 'Pp3c23_8550' => 'ppa', 'Pp3c24_9670' => 'ppa', 'Pp3c2_21390' => 'ppa', 'Pp3c2_31380' => 'ppa', 'Pp3c3_16620' => 'ppa', 'Pp3c3_8090' => 'ppa', 'Pp3c3_8110' => 'ppa', 'Pp3c3_8130' => 'ppa', 'Pp3c3_8150' => 'ppa', 'Pp3c4_14320' => 'ppa', 'Pp3c6_2560' => 'ppa', 'Pp3c9_16700' => 'ppa', 'PRCOL_00000234' => 'pco', 'PRCOL_00000235' => 'pco', 'PRCOL_00000777' => 'pco', 'PRCOL_00002344' => 'pco', 'PRCOL_00002372' => 'pco', 'PRCOL_00006120' => 'pco', 'Prupe.1G021400' => 'ppe', 'Prupe.1G021500' => 'ppe', 'Prupe.1G021600' => 'ppe', 'Prupe.1G021700' => 'ppe', 'Prupe.1G021800' => 'ppe', 'Prupe.5G145100' => 'ppe', 'Psat6g204040' => 'psa', 'Psat6g204800' => 'psa', 'Psat6g204920' => 'psa', 'Psat6g204960' => 'psa', 'Psat6g205080' => 'psa', 'PSO017G0271' => 'pso', 'PSO017G1276' => 'pso', 'PSO017G1429' => 'pso', 'PSO017G1861' => 'pso', 'PSO017G2787' => 'pso', 'PSO017G4466' => 'pso', 'PSO017G5118' => 'pso', 'PSO017G5420' => 'pso', 'PSO063G3678' => 'pso', 'PSO210G0546' => 'pso', 'PSO317G0001' => 'pso', 'PSO357G0512' => 'pso', 'PSO478G2682' => 'pso', 'PSO647G0001' => 'pso', 'PSO675G0001' => 'pso', 'PSO675G2699' => 'pso', 'PSO675G2849' => 'pso', 'PSO675G4991' => 'pso', 'PSO689G0001' => 'pso', 'QL06p000916' => 'qlo', 'QL06p000921' => 'qlo', 'QL06p001398' => 'qlo', 'QL06p001407' => 'qlo', 'QL06p002031' => 'qlo', 'RcHm_v2.0_Chr4g0387791' => 'rch', 'RcHm_v2.0_Chr4g0387801' => 'rch', 'RcHm_v2.0_Chr6g0286501' => 'rch', 'RcHm_v2.0_Chr6g0286511' => 'rch', 'RcHm_v2.0_Chr6g0286521' => 'rch', 'RcHm_v2.0_Chr6g0286531' => 'rch', 'RcHm_v2.0_Chr7g0189141' => 'rch', 'Rhsim02G0028700' => 'rsi', 'Rhsim02G0028800' => 'rsi', 'Rhsim02G0028900' => 'rsi', 'Rhsim02G0029000' => 'rsi', 'Rhsim02G0029100' => 'rsi', 'Rhsim02G0029200' => 'rsi', 'Rhsim02G0029300' => 'rsi', 'Rhsim02G0029400' => 'rsi', 'Rhsim02G0029500' => 'rsi', 'Rhsim02G0029600' => 'rsi', 'RhsimUnG0024000' => 'rsi', 'RhsimUnG0024100' => 'rsi', 'RhsimUnG0024200' => 'rsi', 'RhsimUnG0024300' => 'rsi', 'RhsimUnG0024400' => 'rsi', 'RhsimUnG0024500' => 'rsi', 'RhsimUnG0024700' => 'rsi', 'RhsimUnG0024800' => 'rsi', 'RhsimUnG0024900' => 'rsi', 'RhsimUnG0025100' => 'rsi', 'Sabra08G0120200' => 'sbr', 'Sabra08G0120300' => 'sbr', 'Sabra08G0120500' => 'sbr', 'Sabra08G0120600' => 'sbr', 'Sabra10G0158900' => 'sbr', 'SalBow2G3492' => 'sbo', 'Sc13g0004760' => 'sci', 'Sc13g0004770' => 'sci', 'Sed0003417' => 'sed', 'Sed0019750' => 'sed', 'SEGI_03419' => 'sgi', 'SEGI_05907' => 'sgi', 'SEGI_10682' => 'sgi', 'SEGI_13528' => 'sgi', 'SEGI_16081' => 'sgi', 'SEGI_19370' => 'sgi', 'SEGI_21015' => 'sgi', 'SEGI_21944' => 'sgi', 'SEGI_32906' => 'sgi', 'SEGI_33093' => 'sgi', 'SEGI_36110' => 'sgi', 'SEGI_40397' => 'sgi', 'SGA_v2.0_scaffold191G40426' => 'sas', 'SGA_v2.0_scaffold353G49717' => 'sas', 'SGA_v2.0_scaffold50G18550' => 'sas', 'SMO119G0173' => 'smo', 'SMO172G0002' => 'smo', 'Solyc09g082690.3' => 'sly', 'Solyc09g082700.2' => 'sly', 'Sopen09g031550' => 'spe', 'Sopen09g031560' => 'spe', 'Sp3g20540' => 'spa', 'Sp7g07580' => 'spa', 'TAR134G0002' => 'tar', 'TAR236G0001' => 'tar', 'TAR365G0892' => 'tar', 'TAR636G0166' => 'tar', 'TAR636G0646' => 'tar', 'TAR636G0869' => 'tar', 'TAR636G1317' => 'tar', 'TAR636G1744' => 'tar', 'TAR636G3358' => 'tar', 'TAR636G3436' => 'tar', 'THA.LOC104803047' => 'tha', 'Thecc.04G238900' => 'tca', 'Thhalv10021557m.g' => 'esa', 'Thhalv10026318m.g' => 'esa', 'Thhalv10026335m.g' => 'esa', 'TPR.G17433' => 'tpr', 'TPR.G18915' => 'tpr', 'TPR.G26125' => 'tpr', 'TWI09G0677' => 'twi', 'TWI73G0287' => 'twi', 'unitig_748.g8326' => 'ugi', 'vmacro15370' => 'vma', 'vmacro15371' => 'vma', 'vmacro15372' => 'vma', 'vmacro15373' => 'vma', 'vmacro15374' => 'vma', 'VMungo0720G2826' => 'vmu', 'Zm00001eb116960' => 'zma', 'Zm00001eb301260' => 'zma', 'Zm00001eb301270' => 'zma' ), 'gf_id' => 'HOM05D001460', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001460' ), 'data_identifier' => 'HOM05D001460', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001460', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '433', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p22980' => 'bna', 'A01p32340' => 'bna', 'A03p42970' => 'bna', 'A05p25880' => 'bna', 'Aa31LG8G9320' => 'aar', 'Aa31LG8G9330' => 'aar', 'Aa31LG8G9340' => 'aar', 'Aa31sc221G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1034' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1528' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.829' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2222' => 'aag', 'Ah.12g058830' => 'amhyb', 'Ah.12g058840' => 'amhyb', 'AL3G37160' => 'aly', 'AL7G41310' => 'aly', 'Aqoxy5G00395' => 'aox', 'Aqoxy5G00396' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0C8NZA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5185HY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JZ1PRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MD3LS0' => 'arhy', 'AT3G22840' => 'ath', 'AT4G14690' => 'ath', 'ATR0665G054' => 'atr', 'Atru.chr4.2344' => 'acertr', 'Atru.chr4.2346' => 'acertr', 'Atru.chr4.2347' => 'acertr', 'Atru.chr4.2348' => 'acertr', 'Atru.chr4.2355' => 'acertr', 'Atru.chr4.2356' => 'acertr', 'Atru.chr4.2358' => 'acertr', 'Atru.chr4.2359' => 'acertr', 'Atru.chr4.2360' => 'acertr', 'Atru.chr4.2361' => 'acertr', 'AUR62030476' => 'cqu', 'AUR62030478' => 'cqu', 'AUR62030819' => 'cqu', 'AUR62030820' => 'cqu', 'BcaB03g14648' => 'bca', 'BcaB04g20492' => 'bca', 'BcaB06g26399' => 'bca', 'BcaC01g03416' => 'bca', 'BcaC01g03419' => 'bca', 'BcaC01g03421' => 'bca', 'BcaC01g03424' => 'bca', 'BcaC05g28012' => 'bca', 'BcaC09g49212' => 'bca', 'BcaC09g50140' => 'bca', 'BcaNung00346' => 'bca', 'BolC1t02785H' => 'bol', 'BolC1t04095H' => 'bol', 'BolC3t17545H' => 'bol', 'BolC5t32769H' => 'bol', 'BraA01t02211Z' => 'bra', 'BraA01t03359Z' => 'bra', 'BraA03t13441Z' => 'bra', 'BraA05t21476Z' => 'bra', 'C01p28420' => 'bna', 'C01p41350' => 'bna', 'C03p52750' => 'bna', 'C03p52780' => 'bna', 'C05p40270' => 'bna', 'CAN.G1437.9' => 'can', 'CANSAT78G0035' => 'cansat', 'CANSAT78G1036' => 'cansat', 'CANSAT78G2272' => 'cansat', 'CANSAT78G2478' => 'cansat', 'CARHR098700' => 'chi', 'CARHR221120' => 'chi', 'CARHR221150' => 'chi', 'Carub.0003s2297' => 'cru', 'Carub.0007s2749' => 'cru', 'Carub.0007s2750' => 'cru', 'Carub.0007s2751' => 'cru', 'Ca_10849_v3' => 'car', 'Cc03_g04300' => 'ccan', 'CDE02G3648' => 'cde', 'CDE05G0060' => 'cde', 'CDE05G0692' => 'cde', 'CDE05G2285' => 'cde', 'CDE05G2884' => 'cde', 'CDE05G3072' => 'cde', 'Cfa008439' => 'cfa', 'Cfa008441' => 'cfa', 'Cfa008443' => 'cfa', 'Cfa008448' => 'cfa', 'Ciclev10005974m.g' => 'ccl', 'Ciclev10006006m.g' => 'ccl', 'Ciclev10006775m.g' => 'ccl', 'CiPaw.02G120400' => 'cil', 'CiPaw.02G120500' => 'cil', 'CiPaw.02G120600' => 'cil', 'ClCG05G004850' => 'cla', 'COL.COLO4_21566' => 'col', 'Cpa.g.sc44.124' => 'cpa', 'Cre07.g320400' => 'cre', 'Cre07.g320450' => 'cre', 'Cre08.g384650' => 'cre', 'Cre09.g393173' => 'cre', 'Cre09.g394325' => 'cre', 'Cre14.g626750' => 'cre', 'Cre16.g679250' => 'cre', 'CsaV3_3G012890' => 'csa', 'CSS0010865' => 'camsi', 'CSS0044338' => 'camsi', 'DCAR_002366' => 'dca', 'DCAR_030687' => 'dca', 'DCAR_030688' => 'dca', 'Dinv14047' => 'din', 'Dinv14048' => 'din', 'Duzib151G0105' => 'dzi', 'Duzib151G0114' => 'dzi', 'Duzib212G1029' => 'dzi', 'ECA232G3536' => 'eca', 'ECA240G0786' => 'eca', 'ECA240G1802' => 'eca', 'ECA240G3760' => 'eca', 'ECA240G3920' => 'eca', 'EL10Ac5g12536' => 'bvu', 'EL10Ac5g12537' => 'bvu', 'EL10Ac5g12538' => 'bvu', 'Eucgr.B01004' => 'egr', 'Eucgr.B01006' => 'egr', 'Eucgr.B01007' => 'egr', 'Eucgr.B01008' => 'egr', 'Eucgr.B01895' => 'egr', 'Eucgr.B01896' => 'egr', 'FAN04G1456' => 'fan', 'FAN08G1769' => 'fan', 'FAN08G2160' => 'fan', 'FAN13G2403' => 'fan', 'FAN13G3303' => 'fan', 'FAN15G2435' => 'fan', 'FAN17G0672' => 'fan', 'FAN17G2441' => 'fan', 'FAN18G1024' => 'fan', 'FAN22G1458' => 'fan', 'FAN24G0037' => 'fan', 'FAN24G0429' => 'fan', 'FAN24G2387' => 'fan', 'FAN27G2746' => 'fan', 'FvH4_2g20400' => 'fve', 'FvH4_2g20420' => 'fve', 'FvH4_2g20430' => 'fve', 'FvH4_4g01270' => 'fve', 'FvH4_4g01290' => 'fve', 'FvH4_4g01300' => 'fve', 'FvH4_4g01310' => 'fve', 'FvH4_4g01330' => 'fve', 'FvH4_5g09070' => 'fve', 'Glyma.10G243800' => 'gma', 'Glyma.20G150600' => 'gma', 'Gohir.A09G219200' => 'ghi', 'Gohir.A09G219300' => 'ghi', 'Gohir.D09G221400' => 'ghi', 'Gohir.D09G221500' => 'ghi', 'Gorai.006G242600' => 'gra', 'Gorai.006G242700' => 'gra', 'GSVIVG01018044001' => 'vvi', 'HanXRQChr03g0083821' => 'han', 'HanXRQChr03g0083841' => 'han', 'HanXRQChr03g0083881' => 'han', 'HanXRQChr03g0083901' => 'han', 'HanXRQChr03g0083921' => 'han', 'HanXRQChr03g0085331' => 'han', 'HanXRQChr03g0085361' => 'han', 'HanXRQChr03g0085411' => 'han', 'HanXRQChr03g0085421' => 'han', 'HanXRQChr03g0085431' => 'han', 'HanXRQChr08g0221991' => 'han', 'HanXRQChr11g0336061' => 'han', 'HanXRQChr11g0336411' => 'han', 'Haze_11234' => 'cav', 'Hma1.2p1_0549F.1_g177010' => 'hma', 'Hma1.2p1_0602F.1_g187630' => 'hma', 'Hund14876' => 'sun', 'Hund14879' => 'sun', 'Lalb_Chr06g0160741' => 'lal', 'Lalb_Chr21g0304781' => 'lal', 'Lj3A726G19' => 'lonja', 'Lj3A726T23' => 'lonja', 'Lj3A726T24' => 'lonja', 'Lj3A726T25' => 'lonja', 'Lj3A727T17' => 'lonja', 'Lj3C726T0' => 'lonja', 'Lj3C726T2' => 'lonja', 'Lj3P725T35' => 'lonja', 'Lj3P727T10' => 'lonja', 'Lj3P727T12' => 'lonja', 'Lj3P727T14' => 'lonja', 'Lj5g0023109' => 'lja', 'Lj6P646T44' => 'lonja', 'Lsat_1_v5_gn_6_75760' => 'lsa', 'Lsat_1_v5_gn_6_75800' => 'lsa', 'Lsat_1_v5_gn_6_75900' => 'lsa', 'Lsat_1_v5_gn_6_76240' => 'lsa', 'Lsat_1_v5_gn_6_76441' => 'lsa', 'Lsat_1_v5_gn_6_76700' => 'lsa', 'Lsat_1_v5_gn_6_76760' => 'lsa', 'Manes.15G033100' => 'mes', 'Mapoly0004s0074' => 'mpo', 'Mapoly0004s0075' => 'mpo', 'Mapoly0004s0163' => 'mpo', 'Mapoly0004s0164' => 'mpo', 'Mapoly0021s0018' => 'mpo', 'Mapoly0041s0136' => 'mpo', 'Mapoly0041s0137' => 'mpo', 'Mapoly0041s0138' => 'mpo', 'Mapoly0041s0139' => 'mpo', 'Mapoly0041s0141' => 'mpo', 'Mapoly0041s0142' => 'mpo', 'Mapoly0041s0143' => 'mpo', 'Mapoly0041s0144' => 'mpo', 'Mapoly0041s0145' => 'mpo', 'Mapoly0047s0106' => 'mpo', 'Mapoly0047s0108' => 'mpo', 'Mapoly0050s0051' => 'mpo', 'Mapoly0050s0052' => 'mpo', 'Mapoly0050s0053' => 'mpo', 'Mapoly0058s0013' => 'mpo', 'Mapoly0091s0078' => 'mpo', 'Mapoly0091s0079' => 'mpo', 'Mapoly0091s0080' => 'mpo', 'Mapoly0091s0081' => 'mpo', 'Mapoly0278s0004' => 'mpo', 'Mapoly0278s0005' => 'mpo', 'Mapoly0278s0006' => 'mpo', 'MBI11_g30648_MAGBIO' => 'mbi', 'MCO03G194' => 'mco', 'MCO03G590' => 'mco', 'MCO07G312' => 'mco', 'MCO10G318' => 'mco', 'MCO12G244' => 'mco', 'MCO13G148' => 'mco', 'MCO13G194' => 'mco', 'MCO16G238' => 'mco', 'MD06G1134100' => 'mdo', 'MD13G1200100' => 'mdo', 'MD13G1200300' => 'mdo', 'MD13G1200600' => 'mdo', 'MD14G1150400' => 'mdo', 'MD16G1200000' => 'mdo', 'Medtr1g102570' => 'mtr', 'Medtr1g102780' => 'mtr', 'Medtr1g102800' => 'mtr', 'Medtr1g102810' => 'mtr', 'Medtr1g102830' => 'mtr', 'MELO3C006499.2' => 'cme', 'Migut.G00385' => 'egut', 'MSTRG.4063' => 'ama', 'Nitab4.5_0000090g0260' => 'nta', 'Nitab4.5_0000977g0030' => 'nta', 'Nitab4.5_0002541g0040' => 'nta', 'Nitab4.5_0007068g0040' => 'nta', 'Nn005s41408' => 'nnu', 'Nn005s41410' => 'nnu', 'Oeu010310.1' => 'oeu', 'Oeu010311.1' => 'oeu', 'Oeu043472.1' => 'oeu', 'Os01g0246400' => 'osa', 'Os04g0267950' => 'osa', 'Os07g0178700' => 'osa', 'Os07g0178800' => 'osa', 'Peaxi162Scf00316g00046' => 'pax', 'Peaxi162Scf00316g00049' => 'pax', 'Peaxi162Scf00316g00059' => 'pax', 'Peaxi162Scf00316g00328' => 'pax', 'Peaxi162Scf00316g00329' => 'pax', 'Peaxi162Scf00316g00411' => 'pax', 'Peaxi162Scf00316g00521' => 'pax', 'Peaxi162Scf00492g00068' => 'pax', 'Peaxi162Scf35631g00002' => 'pax', 'PGR142G3720' => 'pgr', 'PGSC0003DMG400006442' => 'stu', 'Phvul.007G062000' => 'pvu', 'Potri.008G157750' => 'ptr', 'Potri.008G157900' => 'ptr', 'Potri.008G158000' => 'ptr', 'Potri.008G158200' => 'ptr', 'Pp3c11_7280' => 'ppa', 'Pp3c11_7980' => 'ppa', 'Pp3c12_19450' => 'ppa', 'Pp3c14_1480' => 'ppa', 'Pp3c14_1501' => 'ppa', 'Pp3c16_4900' => 'ppa', 'Pp3c16_5010' => 'ppa', 'Pp3c16_5060' => 'ppa', 'Pp3c19_18250' => 'ppa', 'Pp3c23_8530' => 'ppa', 'Pp3c23_8550' => 'ppa', 'Pp3c24_9670' => 'ppa', 'Pp3c2_21390' => 'ppa', 'Pp3c2_31380' => 'ppa', 'Pp3c3_16620' => 'ppa', 'Pp3c3_8090' => 'ppa', 'Pp3c3_8110' => 'ppa', 'Pp3c3_8130' => 'ppa', 'Pp3c3_8150' => 'ppa', 'Pp3c4_14320' => 'ppa', 'Pp3c6_2560' => 'ppa', 'Pp3c9_16700' => 'ppa', 'PRCOL_00000234' => 'pco', 'PRCOL_00000235' => 'pco', 'PRCOL_00000777' => 'pco', 'PRCOL_00002344' => 'pco', 'PRCOL_00002372' => 'pco', 'PRCOL_00006120' => 'pco', 'Prupe.1G021400' => 'ppe', 'Prupe.1G021500' => 'ppe', 'Prupe.1G021600' => 'ppe', 'Prupe.1G021700' => 'ppe', 'Prupe.1G021800' => 'ppe', 'Prupe.5G145100' => 'ppe', 'Psat6g204040' => 'psa', 'Psat6g204800' => 'psa', 'Psat6g204920' => 'psa', 'Psat6g204960' => 'psa', 'Psat6g205080' => 'psa', 'PSO017G0271' => 'pso', 'PSO017G1276' => 'pso', 'PSO017G1429' => 'pso', 'PSO017G1861' => 'pso', 'PSO017G2787' => 'pso', 'PSO017G4466' => 'pso', 'PSO017G5118' => 'pso', 'PSO017G5420' => 'pso', 'PSO063G3678' => 'pso', 'PSO210G0546' => 'pso', 'PSO317G0001' => 'pso', 'PSO357G0512' => 'pso', 'PSO478G2682' => 'pso', 'PSO647G0001' => 'pso', 'PSO675G0001' => 'pso', 'PSO675G2699' => 'pso', 'PSO675G2849' => 'pso', 'PSO675G4991' => 'pso', 'PSO689G0001' => 'pso', 'QL06p000916' => 'qlo', 'QL06p000921' => 'qlo', 'QL06p001398' => 'qlo', 'QL06p001407' => 'qlo', 'QL06p002031' => 'qlo', 'RcHm_v2.0_Chr4g0387791' => 'rch', 'RcHm_v2.0_Chr4g0387801' => 'rch', 'RcHm_v2.0_Chr6g0286501' => 'rch', 'RcHm_v2.0_Chr6g0286511' => 'rch', 'RcHm_v2.0_Chr6g0286521' => 'rch', 'RcHm_v2.0_Chr6g0286531' => 'rch', 'RcHm_v2.0_Chr7g0189141' => 'rch', 'Rhsim02G0028700' => 'rsi', 'Rhsim02G0028800' => 'rsi', 'Rhsim02G0028900' => 'rsi', 'Rhsim02G0029000' => 'rsi', 'Rhsim02G0029100' => 'rsi', 'Rhsim02G0029200' => 'rsi', 'Rhsim02G0029300' => 'rsi', 'Rhsim02G0029400' => 'rsi', 'Rhsim02G0029500' => 'rsi', 'Rhsim02G0029600' => 'rsi', 'RhsimUnG0024000' => 'rsi', 'RhsimUnG0024100' => 'rsi', 'RhsimUnG0024200' => 'rsi', 'RhsimUnG0024300' => 'rsi', 'RhsimUnG0024400' => 'rsi', 'RhsimUnG0024500' => 'rsi', 'RhsimUnG0024700' => 'rsi', 'RhsimUnG0024800' => 'rsi', 'RhsimUnG0024900' => 'rsi', 'RhsimUnG0025100' => 'rsi', 'Sabra08G0120200' => 'sbr', 'Sabra08G0120300' => 'sbr', 'Sabra08G0120500' => 'sbr', 'Sabra08G0120600' => 'sbr', 'Sabra10G0158900' => 'sbr', 'SalBow2G3492' => 'sbo', 'Sc13g0004760' => 'sci', 'Sc13g0004770' => 'sci', 'Sed0003417' => 'sed', 'Sed0019750' => 'sed', 'SEGI_03419' => 'sgi', 'SEGI_05907' => 'sgi', 'SEGI_10682' => 'sgi', 'SEGI_13528' => 'sgi', 'SEGI_16081' => 'sgi', 'SEGI_19370' => 'sgi', 'SEGI_21015' => 'sgi', 'SEGI_21944' => 'sgi', 'SEGI_32906' => 'sgi', 'SEGI_33093' => 'sgi', 'SEGI_36110' => 'sgi', 'SEGI_40397' => 'sgi', 'SGA_v2.0_scaffold191G40426' => 'sas', 'SGA_v2.0_scaffold353G49717' => 'sas', 'SGA_v2.0_scaffold50G18550' => 'sas', 'SMO119G0173' => 'smo', 'SMO172G0002' => 'smo', 'Solyc09g082690.3' => 'sly', 'Solyc09g082700.2' => 'sly', 'Sopen09g031550' => 'spe', 'Sopen09g031560' => 'spe', 'Sp3g20540' => 'spa', 'Sp7g07580' => 'spa', 'TAR134G0002' => 'tar', 'TAR236G0001' => 'tar', 'TAR365G0892' => 'tar', 'TAR636G0166' => 'tar', 'TAR636G0646' => 'tar', 'TAR636G0869' => 'tar', 'TAR636G1317' => 'tar', 'TAR636G1744' => 'tar', 'TAR636G3358' => 'tar', 'TAR636G3436' => 'tar', 'THA.LOC104803047' => 'tha', 'Thecc.04G238900' => 'tca', 'Thhalv10021557m.g' => 'esa', 'Thhalv10026318m.g' => 'esa', 'Thhalv10026335m.g' => 'esa', 'TPR.G17433' => 'tpr', 'TPR.G18915' => 'tpr', 'TPR.G26125' => 'tpr', 'TWI09G0677' => 'twi', 'TWI73G0287' => 'twi', 'unitig_748.g8326' => 'ugi', 'vmacro15370' => 'vma', 'vmacro15371' => 'vma', 'vmacro15372' => 'vma', 'vmacro15373' => 'vma', 'vmacro15374' => 'vma', 'VMungo0720G2826' => 'vmu', 'Zm00001eb116960' => 'zma', 'Zm00001eb301260' => 'zma', 'Zm00001eb301270' => 'zma' ) $gf_id = 'HOM05D001460' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001460' ) $data_identifier = 'HOM05D001460' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 4, 'aag' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 2, 'aox' => (int) 2, 'arhy' => (int) 4, 'ath' => (int) 2, 'atr' => (int) 1, 'acertr' => (int) 10, 'cqu' => (int) 4, 'bca' => (int) 11, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 1, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 1, 'ccan' => (int) 1, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 1, 'col' => (int) 1, 'cpa' => (int) 1, 'cre' => (int) 7, 'csa' => (int) 1, 'camsi' => (int) 2, 'dca' => (int) 3, 'din' => (int) 2, 'dzi' => (int) 3, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 14, 'fve' => (int) 9, 'gma' => (int) 2, 'ghi' => (int) 4, 'gra' => (int) 2, 'vvi' => (int) 1, 'han' => (int) 13, 'cav' => (int) 1, 'hma' => (int) 2, 'sun' => (int) 2, 'lal' => (int) 2, 'lonja' => (int) 12, 'lja' => (int) 1, 'lsa' => (int) 7, 'mes' => (int) 1, 'mpo' => (int) 27, 'mbi' => (int) 1, 'mco' => (int) 8, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 1, 'egut' => (int) 1, 'ama' => (int) 1, 'nta' => (int) 4, 'nnu' => (int) 2, 'oeu' => (int) 3, 'osa' => (int) 4, 'pax' => (int) 9, 'pgr' => (int) 1, 'stu' => (int) 1, 'pvu' => (int) 1, 'ptr' => (int) 4, 'ppa' => (int) 22, 'pco' => (int) 6, 'ppe' => (int) 6, 'psa' => (int) 5, 'pso' => (int) 19, 'qlo' => (int) 5, 'rch' => (int) 7, 'rsi' => (int) 20, 'sbr' => (int) 5, 'sbo' => (int) 1, 'sci' => (int) 2, 'sed' => (int) 2, 'sgi' => (int) 12, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 2, 'tar' => (int) 10, 'tha' => (int) 1, 'tca' => (int) 1, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 2, 'ugi' => (int) 1, 'vma' => (int) 5, 'vmu' => (int) 1, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb301270' $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' => 'HOM05D001460', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '433', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p22980' => 'bna', 'A01p32340' => 'bna', 'A03p42970' => 'bna', 'A05p25880' => 'bna', 'Aa31LG8G9320' => 'aar', 'Aa31LG8G9330' => 'aar', 'Aa31LG8G9340' => 'aar', 'Aa31sc221G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1034' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1528' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.829' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2222' => 'aag', 'Ah.12g058830' => 'amhyb', 'Ah.12g058840' => 'amhyb', 'AL3G37160' => 'aly', 'AL7G41310' => 'aly', 'Aqoxy5G00395' => 'aox', 'Aqoxy5G00396' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0C8NZA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5185HY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JZ1PRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MD3LS0' => 'arhy', 'AT3G22840' => 'ath', 'AT4G14690' => 'ath', 'ATR0665G054' => 'atr', 'Atru.chr4.2344' => 'acertr', 'Atru.chr4.2346' => 'acertr', 'Atru.chr4.2347' => 'acertr', 'Atru.chr4.2348' => 'acertr', 'Atru.chr4.2355' => 'acertr', 'Atru.chr4.2356' => 'acertr', 'Atru.chr4.2358' => 'acertr', 'Atru.chr4.2359' => 'acertr', 'Atru.chr4.2360' => 'acertr', 'Atru.chr4.2361' => 'acertr', 'AUR62030476' => 'cqu', 'AUR62030478' => 'cqu', 'AUR62030819' => 'cqu', 'AUR62030820' => 'cqu', 'BcaB03g14648' => 'bca', 'BcaB04g20492' => 'bca', 'BcaB06g26399' => 'bca', 'BcaC01g03416' => 'bca', 'BcaC01g03419' => 'bca', 'BcaC01g03421' => 'bca', 'BcaC01g03424' => 'bca', 'BcaC05g28012' => 'bca', 'BcaC09g49212' => 'bca', 'BcaC09g50140' => 'bca', 'BcaNung00346' => 'bca', 'BolC1t02785H' => 'bol', 'BolC1t04095H' => 'bol', 'BolC3t17545H' => 'bol', 'BolC5t32769H' => 'bol', 'BraA01t02211Z' => 'bra', 'BraA01t03359Z' => 'bra', 'BraA03t13441Z' => 'bra', 'BraA05t21476Z' => 'bra', 'C01p28420' => 'bna', 'C01p41350' => 'bna', 'C03p52750' => 'bna', 'C03p52780' => 'bna', 'C05p40270' => 'bna', 'CAN.G1437.9' => 'can', 'CANSAT78G0035' => 'cansat', 'CANSAT78G1036' => 'cansat', 'CANSAT78G2272' => 'cansat', 'CANSAT78G2478' => 'cansat', 'CARHR098700' => 'chi', 'CARHR221120' => 'chi', 'CARHR221150' => 'chi', 'Carub.0003s2297' => 'cru', 'Carub.0007s2749' => 'cru', 'Carub.0007s2750' => 'cru', 'Carub.0007s2751' => 'cru', 'Ca_10849_v3' => 'car', 'Cc03_g04300' => 'ccan', 'CDE02G3648' => 'cde', 'CDE05G0060' => 'cde', 'CDE05G0692' => 'cde', 'CDE05G2285' => 'cde', 'CDE05G2884' => 'cde', 'CDE05G3072' => 'cde', 'Cfa008439' => 'cfa', 'Cfa008441' => 'cfa', 'Cfa008443' => 'cfa', 'Cfa008448' => 'cfa', 'Ciclev10005974m.g' => 'ccl', 'Ciclev10006006m.g' => 'ccl', 'Ciclev10006775m.g' => 'ccl', 'CiPaw.02G120400' => 'cil', 'CiPaw.02G120500' => 'cil', 'CiPaw.02G120600' => 'cil', 'ClCG05G004850' => 'cla', 'COL.COLO4_21566' => 'col', 'Cpa.g.sc44.124' => 'cpa', 'Cre07.g320400' => 'cre', 'Cre07.g320450' => 'cre', 'Cre08.g384650' => 'cre', 'Cre09.g393173' => 'cre', 'Cre09.g394325' => 'cre', 'Cre14.g626750' => 'cre', 'Cre16.g679250' => 'cre', 'CsaV3_3G012890' => 'csa', 'CSS0010865' => 'camsi', 'CSS0044338' => 'camsi', 'DCAR_002366' => 'dca', 'DCAR_030687' => 'dca', 'DCAR_030688' => 'dca', 'Dinv14047' => 'din', 'Dinv14048' => 'din', 'Duzib151G0105' => 'dzi', 'Duzib151G0114' => 'dzi', 'Duzib212G1029' => 'dzi', 'ECA232G3536' => 'eca', 'ECA240G0786' => 'eca', 'ECA240G1802' => 'eca', 'ECA240G3760' => 'eca', 'ECA240G3920' => 'eca', 'EL10Ac5g12536' => 'bvu', 'EL10Ac5g12537' => 'bvu', 'EL10Ac5g12538' => 'bvu', 'Eucgr.B01004' => 'egr', 'Eucgr.B01006' => 'egr', 'Eucgr.B01007' => 'egr', 'Eucgr.B01008' => 'egr', 'Eucgr.B01895' => 'egr', 'Eucgr.B01896' => 'egr', 'FAN04G1456' => 'fan', 'FAN08G1769' => 'fan', 'FAN08G2160' => 'fan', 'FAN13G2403' => 'fan', 'FAN13G3303' => 'fan', 'FAN15G2435' => 'fan', 'FAN17G0672' => 'fan', 'FAN17G2441' => 'fan', 'FAN18G1024' => 'fan', 'FAN22G1458' => 'fan', 'FAN24G0037' => 'fan', 'FAN24G0429' => 'fan', 'FAN24G2387' => 'fan', 'FAN27G2746' => 'fan', 'FvH4_2g20400' => 'fve', 'FvH4_2g20420' => 'fve', 'FvH4_2g20430' => 'fve', 'FvH4_4g01270' => 'fve', 'FvH4_4g01290' => 'fve', 'FvH4_4g01300' => 'fve', 'FvH4_4g01310' => 'fve', 'FvH4_4g01330' => 'fve', 'FvH4_5g09070' => 'fve', 'Glyma.10G243800' => 'gma', 'Glyma.20G150600' => 'gma', 'Gohir.A09G219200' => 'ghi', 'Gohir.A09G219300' => 'ghi', 'Gohir.D09G221400' => 'ghi', 'Gohir.D09G221500' => 'ghi', 'Gorai.006G242600' => 'gra', 'Gorai.006G242700' => 'gra', 'GSVIVG01018044001' => 'vvi', 'HanXRQChr03g0083821' => 'han', 'HanXRQChr03g0083841' => 'han', 'HanXRQChr03g0083881' => 'han', 'HanXRQChr03g0083901' => 'han', 'HanXRQChr03g0083921' => 'han', 'HanXRQChr03g0085331' => 'han', 'HanXRQChr03g0085361' => 'han', 'HanXRQChr03g0085411' => 'han', 'HanXRQChr03g0085421' => 'han', 'HanXRQChr03g0085431' => 'han', 'HanXRQChr08g0221991' => 'han', 'HanXRQChr11g0336061' => 'han', 'HanXRQChr11g0336411' => 'han', 'Haze_11234' => 'cav', 'Hma1.2p1_0549F.1_g177010' => 'hma', 'Hma1.2p1_0602F.1_g187630' => 'hma', 'Hund14876' => 'sun', 'Hund14879' => 'sun', 'Lalb_Chr06g0160741' => 'lal', 'Lalb_Chr21g0304781' => 'lal', 'Lj3A726G19' => 'lonja', 'Lj3A726T23' => 'lonja', 'Lj3A726T24' => 'lonja', 'Lj3A726T25' => 'lonja', 'Lj3A727T17' => 'lonja', 'Lj3C726T0' => 'lonja', 'Lj3C726T2' => 'lonja', 'Lj3P725T35' => 'lonja', 'Lj3P727T10' => 'lonja', 'Lj3P727T12' => 'lonja', 'Lj3P727T14' => 'lonja', 'Lj5g0023109' => 'lja', 'Lj6P646T44' => 'lonja', 'Lsat_1_v5_gn_6_75760' => 'lsa', 'Lsat_1_v5_gn_6_75800' => 'lsa', 'Lsat_1_v5_gn_6_75900' => 'lsa', 'Lsat_1_v5_gn_6_76240' => 'lsa', 'Lsat_1_v5_gn_6_76441' => 'lsa', 'Lsat_1_v5_gn_6_76700' => 'lsa', 'Lsat_1_v5_gn_6_76760' => 'lsa', 'Manes.15G033100' => 'mes', 'Mapoly0004s0074' => 'mpo', 'Mapoly0004s0075' => 'mpo', 'Mapoly0004s0163' => 'mpo', 'Mapoly0004s0164' => 'mpo', 'Mapoly0021s0018' => 'mpo', 'Mapoly0041s0136' => 'mpo', 'Mapoly0041s0137' => 'mpo', 'Mapoly0041s0138' => 'mpo', 'Mapoly0041s0139' => 'mpo', 'Mapoly0041s0141' => 'mpo', 'Mapoly0041s0142' => 'mpo', 'Mapoly0041s0143' => 'mpo', 'Mapoly0041s0144' => 'mpo', 'Mapoly0041s0145' => 'mpo', 'Mapoly0047s0106' => 'mpo', 'Mapoly0047s0108' => 'mpo', 'Mapoly0050s0051' => 'mpo', 'Mapoly0050s0052' => 'mpo', 'Mapoly0050s0053' => 'mpo', 'Mapoly0058s0013' => 'mpo', 'Mapoly0091s0078' => 'mpo', 'Mapoly0091s0079' => 'mpo', 'Mapoly0091s0080' => 'mpo', 'Mapoly0091s0081' => 'mpo', 'Mapoly0278s0004' => 'mpo', 'Mapoly0278s0005' => 'mpo', 'Mapoly0278s0006' => 'mpo', 'MBI11_g30648_MAGBIO' => 'mbi', 'MCO03G194' => 'mco', 'MCO03G590' => 'mco', 'MCO07G312' => 'mco', 'MCO10G318' => 'mco', 'MCO12G244' => 'mco', 'MCO13G148' => 'mco', 'MCO13G194' => 'mco', 'MCO16G238' => 'mco', 'MD06G1134100' => 'mdo', 'MD13G1200100' => 'mdo', 'MD13G1200300' => 'mdo', 'MD13G1200600' => 'mdo', 'MD14G1150400' => 'mdo', 'MD16G1200000' => 'mdo', 'Medtr1g102570' => 'mtr', 'Medtr1g102780' => 'mtr', 'Medtr1g102800' => 'mtr', 'Medtr1g102810' => 'mtr', 'Medtr1g102830' => 'mtr', 'MELO3C006499.2' => 'cme', 'Migut.G00385' => 'egut', 'MSTRG.4063' => 'ama', 'Nitab4.5_0000090g0260' => 'nta', 'Nitab4.5_0000977g0030' => 'nta', 'Nitab4.5_0002541g0040' => 'nta', 'Nitab4.5_0007068g0040' => 'nta', 'Nn005s41408' => 'nnu', 'Nn005s41410' => 'nnu', 'Oeu010310.1' => 'oeu', 'Oeu010311.1' => 'oeu', 'Oeu043472.1' => 'oeu', 'Os01g0246400' => 'osa', 'Os04g0267950' => 'osa', 'Os07g0178700' => 'osa', 'Os07g0178800' => 'osa', 'Peaxi162Scf00316g00046' => 'pax', 'Peaxi162Scf00316g00049' => 'pax', 'Peaxi162Scf00316g00059' => 'pax', 'Peaxi162Scf00316g00328' => 'pax', 'Peaxi162Scf00316g00329' => 'pax', 'Peaxi162Scf00316g00411' => 'pax', 'Peaxi162Scf00316g00521' => 'pax', 'Peaxi162Scf00492g00068' => 'pax', 'Peaxi162Scf35631g00002' => 'pax', 'PGR142G3720' => 'pgr', 'PGSC0003DMG400006442' => 'stu', 'Phvul.007G062000' => 'pvu', 'Potri.008G157750' => 'ptr', 'Potri.008G157900' => 'ptr', 'Potri.008G158000' => 'ptr', 'Potri.008G158200' => 'ptr', 'Pp3c11_7280' => 'ppa', 'Pp3c11_7980' => 'ppa', 'Pp3c12_19450' => 'ppa', 'Pp3c14_1480' => 'ppa', 'Pp3c14_1501' => 'ppa', 'Pp3c16_4900' => 'ppa', 'Pp3c16_5010' => 'ppa', 'Pp3c16_5060' => 'ppa', 'Pp3c19_18250' => 'ppa', 'Pp3c23_8530' => 'ppa', 'Pp3c23_8550' => 'ppa', 'Pp3c24_9670' => 'ppa', 'Pp3c2_21390' => 'ppa', 'Pp3c2_31380' => 'ppa', 'Pp3c3_16620' => 'ppa', 'Pp3c3_8090' => 'ppa', 'Pp3c3_8110' => 'ppa', 'Pp3c3_8130' => 'ppa', 'Pp3c3_8150' => 'ppa', 'Pp3c4_14320' => 'ppa', 'Pp3c6_2560' => 'ppa', 'Pp3c9_16700' => 'ppa', 'PRCOL_00000234' => 'pco', 'PRCOL_00000235' => 'pco', 'PRCOL_00000777' => 'pco', 'PRCOL_00002344' => 'pco', 'PRCOL_00002372' => 'pco', 'PRCOL_00006120' => 'pco', 'Prupe.1G021400' => 'ppe', 'Prupe.1G021500' => 'ppe', 'Prupe.1G021600' => 'ppe', 'Prupe.1G021700' => 'ppe', 'Prupe.1G021800' => 'ppe', 'Prupe.5G145100' => 'ppe', 'Psat6g204040' => 'psa', 'Psat6g204800' => 'psa', 'Psat6g204920' => 'psa', 'Psat6g204960' => 'psa', 'Psat6g205080' => 'psa', 'PSO017G0271' => 'pso', 'PSO017G1276' => 'pso', 'PSO017G1429' => 'pso', 'PSO017G1861' => 'pso', 'PSO017G2787' => 'pso', 'PSO017G4466' => 'pso', 'PSO017G5118' => 'pso', 'PSO017G5420' => 'pso', 'PSO063G3678' => 'pso', 'PSO210G0546' => 'pso', 'PSO317G0001' => 'pso', 'PSO357G0512' => 'pso', 'PSO478G2682' => 'pso', 'PSO647G0001' => 'pso', 'PSO675G0001' => 'pso', 'PSO675G2699' => 'pso', 'PSO675G2849' => 'pso', 'PSO675G4991' => 'pso', 'PSO689G0001' => 'pso', 'QL06p000916' => 'qlo', 'QL06p000921' => 'qlo', 'QL06p001398' => 'qlo', 'QL06p001407' => 'qlo', 'QL06p002031' => 'qlo', 'RcHm_v2.0_Chr4g0387791' => 'rch', 'RcHm_v2.0_Chr4g0387801' => 'rch', 'RcHm_v2.0_Chr6g0286501' => 'rch', 'RcHm_v2.0_Chr6g0286511' => 'rch', 'RcHm_v2.0_Chr6g0286521' => 'rch', 'RcHm_v2.0_Chr6g0286531' => 'rch', 'RcHm_v2.0_Chr7g0189141' => 'rch', 'Rhsim02G0028700' => 'rsi', 'Rhsim02G0028800' => 'rsi', 'Rhsim02G0028900' => 'rsi', 'Rhsim02G0029000' => 'rsi', 'Rhsim02G0029100' => 'rsi', 'Rhsim02G0029200' => 'rsi', 'Rhsim02G0029300' => 'rsi', 'Rhsim02G0029400' => 'rsi', 'Rhsim02G0029500' => 'rsi', 'Rhsim02G0029600' => 'rsi', 'RhsimUnG0024000' => 'rsi', 'RhsimUnG0024100' => 'rsi', 'RhsimUnG0024200' => 'rsi', 'RhsimUnG0024300' => 'rsi', 'RhsimUnG0024400' => 'rsi', 'RhsimUnG0024500' => 'rsi', 'RhsimUnG0024700' => 'rsi', 'RhsimUnG0024800' => 'rsi', 'RhsimUnG0024900' => 'rsi', 'RhsimUnG0025100' => 'rsi', 'Sabra08G0120200' => 'sbr', 'Sabra08G0120300' => 'sbr', 'Sabra08G0120500' => 'sbr', 'Sabra08G0120600' => 'sbr', 'Sabra10G0158900' => 'sbr', 'SalBow2G3492' => 'sbo', 'Sc13g0004760' => 'sci', 'Sc13g0004770' => 'sci', 'Sed0003417' => 'sed', 'Sed0019750' => 'sed', 'SEGI_03419' => 'sgi', 'SEGI_05907' => 'sgi', 'SEGI_10682' => 'sgi', 'SEGI_13528' => 'sgi', 'SEGI_16081' => 'sgi', 'SEGI_19370' => 'sgi', 'SEGI_21015' => 'sgi', 'SEGI_21944' => 'sgi', 'SEGI_32906' => 'sgi', 'SEGI_33093' => 'sgi', 'SEGI_36110' => 'sgi', 'SEGI_40397' => 'sgi', 'SGA_v2.0_scaffold191G40426' => 'sas', 'SGA_v2.0_scaffold353G49717' => 'sas', 'SGA_v2.0_scaffold50G18550' => 'sas', 'SMO119G0173' => 'smo', 'SMO172G0002' => 'smo', 'Solyc09g082690.3' => 'sly', 'Solyc09g082700.2' => 'sly', 'Sopen09g031550' => 'spe', 'Sopen09g031560' => 'spe', 'Sp3g20540' => 'spa', 'Sp7g07580' => 'spa', 'TAR134G0002' => 'tar', 'TAR236G0001' => 'tar', 'TAR365G0892' => 'tar', 'TAR636G0166' => 'tar', 'TAR636G0646' => 'tar', 'TAR636G0869' => 'tar', 'TAR636G1317' => 'tar', 'TAR636G1744' => 'tar', 'TAR636G3358' => 'tar', 'TAR636G3436' => 'tar', 'THA.LOC104803047' => 'tha', 'Thecc.04G238900' => 'tca', 'Thhalv10021557m.g' => 'esa', 'Thhalv10026318m.g' => 'esa', 'Thhalv10026335m.g' => 'esa', 'TPR.G17433' => 'tpr', 'TPR.G18915' => 'tpr', 'TPR.G26125' => 'tpr', 'TWI09G0677' => 'twi', 'TWI73G0287' => 'twi', 'unitig_748.g8326' => 'ugi', 'vmacro15370' => 'vma', 'vmacro15371' => 'vma', 'vmacro15372' => 'vma', 'vmacro15373' => 'vma', 'vmacro15374' => 'vma', 'VMungo0720G2826' => 'vmu', 'Zm00001eb116960' => 'zma', 'Zm00001eb301260' => 'zma', 'Zm00001eb301270' => 'zma' ), 'gf_id' => 'HOM05D001460', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001460' ), 'data_identifier' => 'HOM05D001460', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001460', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '433', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p22980' => 'bna', 'A01p32340' => 'bna', 'A03p42970' => 'bna', 'A05p25880' => 'bna', 'Aa31LG8G9320' => 'aar', 'Aa31LG8G9330' => 'aar', 'Aa31LG8G9340' => 'aar', 'Aa31sc221G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1034' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1528' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.829' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2222' => 'aag', 'Ah.12g058830' => 'amhyb', 'Ah.12g058840' => 'amhyb', 'AL3G37160' => 'aly', 'AL7G41310' => 'aly', 'Aqoxy5G00395' => 'aox', 'Aqoxy5G00396' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0C8NZA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5185HY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JZ1PRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MD3LS0' => 'arhy', 'AT3G22840' => 'ath', 'AT4G14690' => 'ath', 'ATR0665G054' => 'atr', 'Atru.chr4.2344' => 'acertr', 'Atru.chr4.2346' => 'acertr', 'Atru.chr4.2347' => 'acertr', 'Atru.chr4.2348' => 'acertr', 'Atru.chr4.2355' => 'acertr', 'Atru.chr4.2356' => 'acertr', 'Atru.chr4.2358' => 'acertr', 'Atru.chr4.2359' => 'acertr', 'Atru.chr4.2360' => 'acertr', 'Atru.chr4.2361' => 'acertr', 'AUR62030476' => 'cqu', 'AUR62030478' => 'cqu', 'AUR62030819' => 'cqu', 'AUR62030820' => 'cqu', 'BcaB03g14648' => 'bca', 'BcaB04g20492' => 'bca', 'BcaB06g26399' => 'bca', 'BcaC01g03416' => 'bca', 'BcaC01g03419' => 'bca', 'BcaC01g03421' => 'bca', 'BcaC01g03424' => 'bca', 'BcaC05g28012' => 'bca', 'BcaC09g49212' => 'bca', 'BcaC09g50140' => 'bca', 'BcaNung00346' => 'bca', 'BolC1t02785H' => 'bol', 'BolC1t04095H' => 'bol', 'BolC3t17545H' => 'bol', 'BolC5t32769H' => 'bol', 'BraA01t02211Z' => 'bra', 'BraA01t03359Z' => 'bra', 'BraA03t13441Z' => 'bra', 'BraA05t21476Z' => 'bra', 'C01p28420' => 'bna', 'C01p41350' => 'bna', 'C03p52750' => 'bna', 'C03p52780' => 'bna', 'C05p40270' => 'bna', 'CAN.G1437.9' => 'can', 'CANSAT78G0035' => 'cansat', 'CANSAT78G1036' => 'cansat', 'CANSAT78G2272' => 'cansat', 'CANSAT78G2478' => 'cansat', 'CARHR098700' => 'chi', 'CARHR221120' => 'chi', 'CARHR221150' => 'chi', 'Carub.0003s2297' => 'cru', 'Carub.0007s2749' => 'cru', 'Carub.0007s2750' => 'cru', 'Carub.0007s2751' => 'cru', 'Ca_10849_v3' => 'car', 'Cc03_g04300' => 'ccan', 'CDE02G3648' => 'cde', 'CDE05G0060' => 'cde', 'CDE05G0692' => 'cde', 'CDE05G2285' => 'cde', 'CDE05G2884' => 'cde', 'CDE05G3072' => 'cde', 'Cfa008439' => 'cfa', 'Cfa008441' => 'cfa', 'Cfa008443' => 'cfa', 'Cfa008448' => 'cfa', 'Ciclev10005974m.g' => 'ccl', 'Ciclev10006006m.g' => 'ccl', 'Ciclev10006775m.g' => 'ccl', 'CiPaw.02G120400' => 'cil', 'CiPaw.02G120500' => 'cil', 'CiPaw.02G120600' => 'cil', 'ClCG05G004850' => 'cla', 'COL.COLO4_21566' => 'col', 'Cpa.g.sc44.124' => 'cpa', 'Cre07.g320400' => 'cre', 'Cre07.g320450' => 'cre', 'Cre08.g384650' => 'cre', 'Cre09.g393173' => 'cre', 'Cre09.g394325' => 'cre', 'Cre14.g626750' => 'cre', 'Cre16.g679250' => 'cre', 'CsaV3_3G012890' => 'csa', 'CSS0010865' => 'camsi', 'CSS0044338' => 'camsi', 'DCAR_002366' => 'dca', 'DCAR_030687' => 'dca', 'DCAR_030688' => 'dca', 'Dinv14047' => 'din', 'Dinv14048' => 'din', 'Duzib151G0105' => 'dzi', 'Duzib151G0114' => 'dzi', 'Duzib212G1029' => 'dzi', 'ECA232G3536' => 'eca', 'ECA240G0786' => 'eca', 'ECA240G1802' => 'eca', 'ECA240G3760' => 'eca', 'ECA240G3920' => 'eca', 'EL10Ac5g12536' => 'bvu', 'EL10Ac5g12537' => 'bvu', 'EL10Ac5g12538' => 'bvu', 'Eucgr.B01004' => 'egr', 'Eucgr.B01006' => 'egr', 'Eucgr.B01007' => 'egr', 'Eucgr.B01008' => 'egr', 'Eucgr.B01895' => 'egr', 'Eucgr.B01896' => 'egr', 'FAN04G1456' => 'fan', 'FAN08G1769' => 'fan', 'FAN08G2160' => 'fan', 'FAN13G2403' => 'fan', 'FAN13G3303' => 'fan', 'FAN15G2435' => 'fan', 'FAN17G0672' => 'fan', 'FAN17G2441' => 'fan', 'FAN18G1024' => 'fan', 'FAN22G1458' => 'fan', 'FAN24G0037' => 'fan', 'FAN24G0429' => 'fan', 'FAN24G2387' => 'fan', 'FAN27G2746' => 'fan', 'FvH4_2g20400' => 'fve', 'FvH4_2g20420' => 'fve', 'FvH4_2g20430' => 'fve', 'FvH4_4g01270' => 'fve', 'FvH4_4g01290' => 'fve', 'FvH4_4g01300' => 'fve', 'FvH4_4g01310' => 'fve', 'FvH4_4g01330' => 'fve', 'FvH4_5g09070' => 'fve', 'Glyma.10G243800' => 'gma', 'Glyma.20G150600' => 'gma', 'Gohir.A09G219200' => 'ghi', 'Gohir.A09G219300' => 'ghi', 'Gohir.D09G221400' => 'ghi', 'Gohir.D09G221500' => 'ghi', 'Gorai.006G242600' => 'gra', 'Gorai.006G242700' => 'gra', 'GSVIVG01018044001' => 'vvi', 'HanXRQChr03g0083821' => 'han', 'HanXRQChr03g0083841' => 'han', 'HanXRQChr03g0083881' => 'han', 'HanXRQChr03g0083901' => 'han', 'HanXRQChr03g0083921' => 'han', 'HanXRQChr03g0085331' => 'han', 'HanXRQChr03g0085361' => 'han', 'HanXRQChr03g0085411' => 'han', 'HanXRQChr03g0085421' => 'han', 'HanXRQChr03g0085431' => 'han', 'HanXRQChr08g0221991' => 'han', 'HanXRQChr11g0336061' => 'han', 'HanXRQChr11g0336411' => 'han', 'Haze_11234' => 'cav', 'Hma1.2p1_0549F.1_g177010' => 'hma', 'Hma1.2p1_0602F.1_g187630' => 'hma', 'Hund14876' => 'sun', 'Hund14879' => 'sun', 'Lalb_Chr06g0160741' => 'lal', 'Lalb_Chr21g0304781' => 'lal', 'Lj3A726G19' => 'lonja', 'Lj3A726T23' => 'lonja', 'Lj3A726T24' => 'lonja', 'Lj3A726T25' => 'lonja', 'Lj3A727T17' => 'lonja', 'Lj3C726T0' => 'lonja', 'Lj3C726T2' => 'lonja', 'Lj3P725T35' => 'lonja', 'Lj3P727T10' => 'lonja', 'Lj3P727T12' => 'lonja', 'Lj3P727T14' => 'lonja', 'Lj5g0023109' => 'lja', 'Lj6P646T44' => 'lonja', 'Lsat_1_v5_gn_6_75760' => 'lsa', 'Lsat_1_v5_gn_6_75800' => 'lsa', 'Lsat_1_v5_gn_6_75900' => 'lsa', 'Lsat_1_v5_gn_6_76240' => 'lsa', 'Lsat_1_v5_gn_6_76441' => 'lsa', 'Lsat_1_v5_gn_6_76700' => 'lsa', 'Lsat_1_v5_gn_6_76760' => 'lsa', 'Manes.15G033100' => 'mes', 'Mapoly0004s0074' => 'mpo', 'Mapoly0004s0075' => 'mpo', 'Mapoly0004s0163' => 'mpo', 'Mapoly0004s0164' => 'mpo', 'Mapoly0021s0018' => 'mpo', 'Mapoly0041s0136' => 'mpo', 'Mapoly0041s0137' => 'mpo', 'Mapoly0041s0138' => 'mpo', 'Mapoly0041s0139' => 'mpo', 'Mapoly0041s0141' => 'mpo', 'Mapoly0041s0142' => 'mpo', 'Mapoly0041s0143' => 'mpo', 'Mapoly0041s0144' => 'mpo', 'Mapoly0041s0145' => 'mpo', 'Mapoly0047s0106' => 'mpo', 'Mapoly0047s0108' => 'mpo', 'Mapoly0050s0051' => 'mpo', 'Mapoly0050s0052' => 'mpo', 'Mapoly0050s0053' => 'mpo', 'Mapoly0058s0013' => 'mpo', 'Mapoly0091s0078' => 'mpo', 'Mapoly0091s0079' => 'mpo', 'Mapoly0091s0080' => 'mpo', 'Mapoly0091s0081' => 'mpo', 'Mapoly0278s0004' => 'mpo', 'Mapoly0278s0005' => 'mpo', 'Mapoly0278s0006' => 'mpo', 'MBI11_g30648_MAGBIO' => 'mbi', 'MCO03G194' => 'mco', 'MCO03G590' => 'mco', 'MCO07G312' => 'mco', 'MCO10G318' => 'mco', 'MCO12G244' => 'mco', 'MCO13G148' => 'mco', 'MCO13G194' => 'mco', 'MCO16G238' => 'mco', 'MD06G1134100' => 'mdo', 'MD13G1200100' => 'mdo', 'MD13G1200300' => 'mdo', 'MD13G1200600' => 'mdo', 'MD14G1150400' => 'mdo', 'MD16G1200000' => 'mdo', 'Medtr1g102570' => 'mtr', 'Medtr1g102780' => 'mtr', 'Medtr1g102800' => 'mtr', 'Medtr1g102810' => 'mtr', 'Medtr1g102830' => 'mtr', 'MELO3C006499.2' => 'cme', 'Migut.G00385' => 'egut', 'MSTRG.4063' => 'ama', 'Nitab4.5_0000090g0260' => 'nta', 'Nitab4.5_0000977g0030' => 'nta', 'Nitab4.5_0002541g0040' => 'nta', 'Nitab4.5_0007068g0040' => 'nta', 'Nn005s41408' => 'nnu', 'Nn005s41410' => 'nnu', 'Oeu010310.1' => 'oeu', 'Oeu010311.1' => 'oeu', 'Oeu043472.1' => 'oeu', 'Os01g0246400' => 'osa', 'Os04g0267950' => 'osa', 'Os07g0178700' => 'osa', 'Os07g0178800' => 'osa', 'Peaxi162Scf00316g00046' => 'pax', 'Peaxi162Scf00316g00049' => 'pax', 'Peaxi162Scf00316g00059' => 'pax', 'Peaxi162Scf00316g00328' => 'pax', 'Peaxi162Scf00316g00329' => 'pax', 'Peaxi162Scf00316g00411' => 'pax', 'Peaxi162Scf00316g00521' => 'pax', 'Peaxi162Scf00492g00068' => 'pax', 'Peaxi162Scf35631g00002' => 'pax', 'PGR142G3720' => 'pgr', 'PGSC0003DMG400006442' => 'stu', 'Phvul.007G062000' => 'pvu', 'Potri.008G157750' => 'ptr', 'Potri.008G157900' => 'ptr', 'Potri.008G158000' => 'ptr', 'Potri.008G158200' => 'ptr', 'Pp3c11_7280' => 'ppa', 'Pp3c11_7980' => 'ppa', 'Pp3c12_19450' => 'ppa', 'Pp3c14_1480' => 'ppa', 'Pp3c14_1501' => 'ppa', 'Pp3c16_4900' => 'ppa', 'Pp3c16_5010' => 'ppa', 'Pp3c16_5060' => 'ppa', 'Pp3c19_18250' => 'ppa', 'Pp3c23_8530' => 'ppa', 'Pp3c23_8550' => 'ppa', 'Pp3c24_9670' => 'ppa', 'Pp3c2_21390' => 'ppa', 'Pp3c2_31380' => 'ppa', 'Pp3c3_16620' => 'ppa', 'Pp3c3_8090' => 'ppa', 'Pp3c3_8110' => 'ppa', 'Pp3c3_8130' => 'ppa', 'Pp3c3_8150' => 'ppa', 'Pp3c4_14320' => 'ppa', 'Pp3c6_2560' => 'ppa', 'Pp3c9_16700' => 'ppa', 'PRCOL_00000234' => 'pco', 'PRCOL_00000235' => 'pco', 'PRCOL_00000777' => 'pco', 'PRCOL_00002344' => 'pco', 'PRCOL_00002372' => 'pco', 'PRCOL_00006120' => 'pco', 'Prupe.1G021400' => 'ppe', 'Prupe.1G021500' => 'ppe', 'Prupe.1G021600' => 'ppe', 'Prupe.1G021700' => 'ppe', 'Prupe.1G021800' => 'ppe', 'Prupe.5G145100' => 'ppe', 'Psat6g204040' => 'psa', 'Psat6g204800' => 'psa', 'Psat6g204920' => 'psa', 'Psat6g204960' => 'psa', 'Psat6g205080' => 'psa', 'PSO017G0271' => 'pso', 'PSO017G1276' => 'pso', 'PSO017G1429' => 'pso', 'PSO017G1861' => 'pso', 'PSO017G2787' => 'pso', 'PSO017G4466' => 'pso', 'PSO017G5118' => 'pso', 'PSO017G5420' => 'pso', 'PSO063G3678' => 'pso', 'PSO210G0546' => 'pso', 'PSO317G0001' => 'pso', 'PSO357G0512' => 'pso', 'PSO478G2682' => 'pso', 'PSO647G0001' => 'pso', 'PSO675G0001' => 'pso', 'PSO675G2699' => 'pso', 'PSO675G2849' => 'pso', 'PSO675G4991' => 'pso', 'PSO689G0001' => 'pso', 'QL06p000916' => 'qlo', 'QL06p000921' => 'qlo', 'QL06p001398' => 'qlo', 'QL06p001407' => 'qlo', 'QL06p002031' => 'qlo', 'RcHm_v2.0_Chr4g0387791' => 'rch', 'RcHm_v2.0_Chr4g0387801' => 'rch', 'RcHm_v2.0_Chr6g0286501' => 'rch', 'RcHm_v2.0_Chr6g0286511' => 'rch', 'RcHm_v2.0_Chr6g0286521' => 'rch', 'RcHm_v2.0_Chr6g0286531' => 'rch', 'RcHm_v2.0_Chr7g0189141' => 'rch', 'Rhsim02G0028700' => 'rsi', 'Rhsim02G0028800' => 'rsi', 'Rhsim02G0028900' => 'rsi', 'Rhsim02G0029000' => 'rsi', 'Rhsim02G0029100' => 'rsi', 'Rhsim02G0029200' => 'rsi', 'Rhsim02G0029300' => 'rsi', 'Rhsim02G0029400' => 'rsi', 'Rhsim02G0029500' => 'rsi', 'Rhsim02G0029600' => 'rsi', 'RhsimUnG0024000' => 'rsi', 'RhsimUnG0024100' => 'rsi', 'RhsimUnG0024200' => 'rsi', 'RhsimUnG0024300' => 'rsi', 'RhsimUnG0024400' => 'rsi', 'RhsimUnG0024500' => 'rsi', 'RhsimUnG0024700' => 'rsi', 'RhsimUnG0024800' => 'rsi', 'RhsimUnG0024900' => 'rsi', 'RhsimUnG0025100' => 'rsi', 'Sabra08G0120200' => 'sbr', 'Sabra08G0120300' => 'sbr', 'Sabra08G0120500' => 'sbr', 'Sabra08G0120600' => 'sbr', 'Sabra10G0158900' => 'sbr', 'SalBow2G3492' => 'sbo', 'Sc13g0004760' => 'sci', 'Sc13g0004770' => 'sci', 'Sed0003417' => 'sed', 'Sed0019750' => 'sed', 'SEGI_03419' => 'sgi', 'SEGI_05907' => 'sgi', 'SEGI_10682' => 'sgi', 'SEGI_13528' => 'sgi', 'SEGI_16081' => 'sgi', 'SEGI_19370' => 'sgi', 'SEGI_21015' => 'sgi', 'SEGI_21944' => 'sgi', 'SEGI_32906' => 'sgi', 'SEGI_33093' => 'sgi', 'SEGI_36110' => 'sgi', 'SEGI_40397' => 'sgi', 'SGA_v2.0_scaffold191G40426' => 'sas', 'SGA_v2.0_scaffold353G49717' => 'sas', 'SGA_v2.0_scaffold50G18550' => 'sas', 'SMO119G0173' => 'smo', 'SMO172G0002' => 'smo', 'Solyc09g082690.3' => 'sly', 'Solyc09g082700.2' => 'sly', 'Sopen09g031550' => 'spe', 'Sopen09g031560' => 'spe', 'Sp3g20540' => 'spa', 'Sp7g07580' => 'spa', 'TAR134G0002' => 'tar', 'TAR236G0001' => 'tar', 'TAR365G0892' => 'tar', 'TAR636G0166' => 'tar', 'TAR636G0646' => 'tar', 'TAR636G0869' => 'tar', 'TAR636G1317' => 'tar', 'TAR636G1744' => 'tar', 'TAR636G3358' => 'tar', 'TAR636G3436' => 'tar', 'THA.LOC104803047' => 'tha', 'Thecc.04G238900' => 'tca', 'Thhalv10021557m.g' => 'esa', 'Thhalv10026318m.g' => 'esa', 'Thhalv10026335m.g' => 'esa', 'TPR.G17433' => 'tpr', 'TPR.G18915' => 'tpr', 'TPR.G26125' => 'tpr', 'TWI09G0677' => 'twi', 'TWI73G0287' => 'twi', 'unitig_748.g8326' => 'ugi', 'vmacro15370' => 'vma', 'vmacro15371' => 'vma', 'vmacro15372' => 'vma', 'vmacro15373' => 'vma', 'vmacro15374' => 'vma', 'VMungo0720G2826' => 'vmu', 'Zm00001eb116960' => 'zma', 'Zm00001eb301260' => 'zma', 'Zm00001eb301270' => 'zma' ) $gf_id = 'HOM05D001460' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001460' ) $data_identifier = 'HOM05D001460' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 4, 'aag' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 2, 'aox' => (int) 2, 'arhy' => (int) 4, 'ath' => (int) 2, 'atr' => (int) 1, 'acertr' => (int) 10, 'cqu' => (int) 4, 'bca' => (int) 11, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 1, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 1, 'ccan' => (int) 1, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 1, 'col' => (int) 1, 'cpa' => (int) 1, 'cre' => (int) 7, 'csa' => (int) 1, 'camsi' => (int) 2, 'dca' => (int) 3, 'din' => (int) 2, 'dzi' => (int) 3, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 14, 'fve' => (int) 9, 'gma' => (int) 2, 'ghi' => (int) 4, 'gra' => (int) 2, 'vvi' => (int) 1, 'han' => (int) 13, 'cav' => (int) 1, 'hma' => (int) 2, 'sun' => (int) 2, 'lal' => (int) 2, 'lonja' => (int) 12, 'lja' => (int) 1, 'lsa' => (int) 7, 'mes' => (int) 1, 'mpo' => (int) 27, 'mbi' => (int) 1, 'mco' => (int) 8, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 1, 'egut' => (int) 1, 'ama' => (int) 1, 'nta' => (int) 4, 'nnu' => (int) 2, 'oeu' => (int) 3, 'osa' => (int) 4, 'pax' => (int) 9, 'pgr' => (int) 1, 'stu' => (int) 1, 'pvu' => (int) 1, 'ptr' => (int) 4, 'ppa' => (int) 22, 'pco' => (int) 6, 'ppe' => (int) 6, 'psa' => (int) 5, 'pso' => (int) 19, 'qlo' => (int) 5, 'rch' => (int) 7, 'rsi' => (int) 20, 'sbr' => (int) 5, 'sbo' => (int) 1, 'sci' => (int) 2, 'sed' => (int) 2, 'sgi' => (int) 12, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 2, 'tar' => (int) 10, 'tha' => (int) 1, 'tca' => (int) 1, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 2, 'ugi' => (int) 1, 'vma' => (int) 5, 'vmu' => (int) 1, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb301270' $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' => 'HOM05D001460', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '433', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p22980' => 'bna', 'A01p32340' => 'bna', 'A03p42970' => 'bna', 'A05p25880' => 'bna', 'Aa31LG8G9320' => 'aar', 'Aa31LG8G9330' => 'aar', 'Aa31LG8G9340' => 'aar', 'Aa31sc221G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1034' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1528' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.829' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2222' => 'aag', 'Ah.12g058830' => 'amhyb', 'Ah.12g058840' => 'amhyb', 'AL3G37160' => 'aly', 'AL7G41310' => 'aly', 'Aqoxy5G00395' => 'aox', 'Aqoxy5G00396' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0C8NZA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5185HY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JZ1PRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MD3LS0' => 'arhy', 'AT3G22840' => 'ath', 'AT4G14690' => 'ath', 'ATR0665G054' => 'atr', 'Atru.chr4.2344' => 'acertr', 'Atru.chr4.2346' => 'acertr', 'Atru.chr4.2347' => 'acertr', 'Atru.chr4.2348' => 'acertr', 'Atru.chr4.2355' => 'acertr', 'Atru.chr4.2356' => 'acertr', 'Atru.chr4.2358' => 'acertr', 'Atru.chr4.2359' => 'acertr', 'Atru.chr4.2360' => 'acertr', 'Atru.chr4.2361' => 'acertr', 'AUR62030476' => 'cqu', 'AUR62030478' => 'cqu', 'AUR62030819' => 'cqu', 'AUR62030820' => 'cqu', 'BcaB03g14648' => 'bca', 'BcaB04g20492' => 'bca', 'BcaB06g26399' => 'bca', 'BcaC01g03416' => 'bca', 'BcaC01g03419' => 'bca', 'BcaC01g03421' => 'bca', 'BcaC01g03424' => 'bca', 'BcaC05g28012' => 'bca', 'BcaC09g49212' => 'bca', 'BcaC09g50140' => 'bca', 'BcaNung00346' => 'bca', 'BolC1t02785H' => 'bol', 'BolC1t04095H' => 'bol', 'BolC3t17545H' => 'bol', 'BolC5t32769H' => 'bol', 'BraA01t02211Z' => 'bra', 'BraA01t03359Z' => 'bra', 'BraA03t13441Z' => 'bra', 'BraA05t21476Z' => 'bra', 'C01p28420' => 'bna', 'C01p41350' => 'bna', 'C03p52750' => 'bna', 'C03p52780' => 'bna', 'C05p40270' => 'bna', 'CAN.G1437.9' => 'can', 'CANSAT78G0035' => 'cansat', 'CANSAT78G1036' => 'cansat', 'CANSAT78G2272' => 'cansat', 'CANSAT78G2478' => 'cansat', 'CARHR098700' => 'chi', 'CARHR221120' => 'chi', 'CARHR221150' => 'chi', 'Carub.0003s2297' => 'cru', 'Carub.0007s2749' => 'cru', 'Carub.0007s2750' => 'cru', 'Carub.0007s2751' => 'cru', 'Ca_10849_v3' => 'car', 'Cc03_g04300' => 'ccan', 'CDE02G3648' => 'cde', 'CDE05G0060' => 'cde', 'CDE05G0692' => 'cde', 'CDE05G2285' => 'cde', 'CDE05G2884' => 'cde', 'CDE05G3072' => 'cde', 'Cfa008439' => 'cfa', 'Cfa008441' => 'cfa', 'Cfa008443' => 'cfa', 'Cfa008448' => 'cfa', 'Ciclev10005974m.g' => 'ccl', 'Ciclev10006006m.g' => 'ccl', 'Ciclev10006775m.g' => 'ccl', 'CiPaw.02G120400' => 'cil', 'CiPaw.02G120500' => 'cil', 'CiPaw.02G120600' => 'cil', 'ClCG05G004850' => 'cla', 'COL.COLO4_21566' => 'col', 'Cpa.g.sc44.124' => 'cpa', 'Cre07.g320400' => 'cre', 'Cre07.g320450' => 'cre', 'Cre08.g384650' => 'cre', 'Cre09.g393173' => 'cre', 'Cre09.g394325' => 'cre', 'Cre14.g626750' => 'cre', 'Cre16.g679250' => 'cre', 'CsaV3_3G012890' => 'csa', 'CSS0010865' => 'camsi', 'CSS0044338' => 'camsi', 'DCAR_002366' => 'dca', 'DCAR_030687' => 'dca', 'DCAR_030688' => 'dca', 'Dinv14047' => 'din', 'Dinv14048' => 'din', 'Duzib151G0105' => 'dzi', 'Duzib151G0114' => 'dzi', 'Duzib212G1029' => 'dzi', 'ECA232G3536' => 'eca', 'ECA240G0786' => 'eca', 'ECA240G1802' => 'eca', 'ECA240G3760' => 'eca', 'ECA240G3920' => 'eca', 'EL10Ac5g12536' => 'bvu', 'EL10Ac5g12537' => 'bvu', 'EL10Ac5g12538' => 'bvu', 'Eucgr.B01004' => 'egr', 'Eucgr.B01006' => 'egr', 'Eucgr.B01007' => 'egr', 'Eucgr.B01008' => 'egr', 'Eucgr.B01895' => 'egr', 'Eucgr.B01896' => 'egr', 'FAN04G1456' => 'fan', 'FAN08G1769' => 'fan', 'FAN08G2160' => 'fan', 'FAN13G2403' => 'fan', 'FAN13G3303' => 'fan', 'FAN15G2435' => 'fan', 'FAN17G0672' => 'fan', 'FAN17G2441' => 'fan', 'FAN18G1024' => 'fan', 'FAN22G1458' => 'fan', 'FAN24G0037' => 'fan', 'FAN24G0429' => 'fan', 'FAN24G2387' => 'fan', 'FAN27G2746' => 'fan', 'FvH4_2g20400' => 'fve', 'FvH4_2g20420' => 'fve', 'FvH4_2g20430' => 'fve', 'FvH4_4g01270' => 'fve', 'FvH4_4g01290' => 'fve', 'FvH4_4g01300' => 'fve', 'FvH4_4g01310' => 'fve', 'FvH4_4g01330' => 'fve', 'FvH4_5g09070' => 'fve', 'Glyma.10G243800' => 'gma', 'Glyma.20G150600' => 'gma', 'Gohir.A09G219200' => 'ghi', 'Gohir.A09G219300' => 'ghi', 'Gohir.D09G221400' => 'ghi', 'Gohir.D09G221500' => 'ghi', 'Gorai.006G242600' => 'gra', 'Gorai.006G242700' => 'gra', 'GSVIVG01018044001' => 'vvi', 'HanXRQChr03g0083821' => 'han', 'HanXRQChr03g0083841' => 'han', 'HanXRQChr03g0083881' => 'han', 'HanXRQChr03g0083901' => 'han', 'HanXRQChr03g0083921' => 'han', 'HanXRQChr03g0085331' => 'han', 'HanXRQChr03g0085361' => 'han', 'HanXRQChr03g0085411' => 'han', 'HanXRQChr03g0085421' => 'han', 'HanXRQChr03g0085431' => 'han', 'HanXRQChr08g0221991' => 'han', 'HanXRQChr11g0336061' => 'han', 'HanXRQChr11g0336411' => 'han', 'Haze_11234' => 'cav', 'Hma1.2p1_0549F.1_g177010' => 'hma', 'Hma1.2p1_0602F.1_g187630' => 'hma', 'Hund14876' => 'sun', 'Hund14879' => 'sun', 'Lalb_Chr06g0160741' => 'lal', 'Lalb_Chr21g0304781' => 'lal', 'Lj3A726G19' => 'lonja', 'Lj3A726T23' => 'lonja', 'Lj3A726T24' => 'lonja', 'Lj3A726T25' => 'lonja', 'Lj3A727T17' => 'lonja', 'Lj3C726T0' => 'lonja', 'Lj3C726T2' => 'lonja', 'Lj3P725T35' => 'lonja', 'Lj3P727T10' => 'lonja', 'Lj3P727T12' => 'lonja', 'Lj3P727T14' => 'lonja', 'Lj5g0023109' => 'lja', 'Lj6P646T44' => 'lonja', 'Lsat_1_v5_gn_6_75760' => 'lsa', 'Lsat_1_v5_gn_6_75800' => 'lsa', 'Lsat_1_v5_gn_6_75900' => 'lsa', 'Lsat_1_v5_gn_6_76240' => 'lsa', 'Lsat_1_v5_gn_6_76441' => 'lsa', 'Lsat_1_v5_gn_6_76700' => 'lsa', 'Lsat_1_v5_gn_6_76760' => 'lsa', 'Manes.15G033100' => 'mes', 'Mapoly0004s0074' => 'mpo', 'Mapoly0004s0075' => 'mpo', 'Mapoly0004s0163' => 'mpo', 'Mapoly0004s0164' => 'mpo', 'Mapoly0021s0018' => 'mpo', 'Mapoly0041s0136' => 'mpo', 'Mapoly0041s0137' => 'mpo', 'Mapoly0041s0138' => 'mpo', 'Mapoly0041s0139' => 'mpo', 'Mapoly0041s0141' => 'mpo', 'Mapoly0041s0142' => 'mpo', 'Mapoly0041s0143' => 'mpo', 'Mapoly0041s0144' => 'mpo', 'Mapoly0041s0145' => 'mpo', 'Mapoly0047s0106' => 'mpo', 'Mapoly0047s0108' => 'mpo', 'Mapoly0050s0051' => 'mpo', 'Mapoly0050s0052' => 'mpo', 'Mapoly0050s0053' => 'mpo', 'Mapoly0058s0013' => 'mpo', 'Mapoly0091s0078' => 'mpo', 'Mapoly0091s0079' => 'mpo', 'Mapoly0091s0080' => 'mpo', 'Mapoly0091s0081' => 'mpo', 'Mapoly0278s0004' => 'mpo', 'Mapoly0278s0005' => 'mpo', 'Mapoly0278s0006' => 'mpo', 'MBI11_g30648_MAGBIO' => 'mbi', 'MCO03G194' => 'mco', 'MCO03G590' => 'mco', 'MCO07G312' => 'mco', 'MCO10G318' => 'mco', 'MCO12G244' => 'mco', 'MCO13G148' => 'mco', 'MCO13G194' => 'mco', 'MCO16G238' => 'mco', 'MD06G1134100' => 'mdo', 'MD13G1200100' => 'mdo', 'MD13G1200300' => 'mdo', 'MD13G1200600' => 'mdo', 'MD14G1150400' => 'mdo', 'MD16G1200000' => 'mdo', 'Medtr1g102570' => 'mtr', 'Medtr1g102780' => 'mtr', 'Medtr1g102800' => 'mtr', 'Medtr1g102810' => 'mtr', 'Medtr1g102830' => 'mtr', 'MELO3C006499.2' => 'cme', 'Migut.G00385' => 'egut', 'MSTRG.4063' => 'ama', 'Nitab4.5_0000090g0260' => 'nta', 'Nitab4.5_0000977g0030' => 'nta', 'Nitab4.5_0002541g0040' => 'nta', 'Nitab4.5_0007068g0040' => 'nta', 'Nn005s41408' => 'nnu', 'Nn005s41410' => 'nnu', 'Oeu010310.1' => 'oeu', 'Oeu010311.1' => 'oeu', 'Oeu043472.1' => 'oeu', 'Os01g0246400' => 'osa', 'Os04g0267950' => 'osa', 'Os07g0178700' => 'osa', 'Os07g0178800' => 'osa', 'Peaxi162Scf00316g00046' => 'pax', 'Peaxi162Scf00316g00049' => 'pax', 'Peaxi162Scf00316g00059' => 'pax', 'Peaxi162Scf00316g00328' => 'pax', 'Peaxi162Scf00316g00329' => 'pax', 'Peaxi162Scf00316g00411' => 'pax', 'Peaxi162Scf00316g00521' => 'pax', 'Peaxi162Scf00492g00068' => 'pax', 'Peaxi162Scf35631g00002' => 'pax', 'PGR142G3720' => 'pgr', 'PGSC0003DMG400006442' => 'stu', 'Phvul.007G062000' => 'pvu', 'Potri.008G157750' => 'ptr', 'Potri.008G157900' => 'ptr', 'Potri.008G158000' => 'ptr', 'Potri.008G158200' => 'ptr', 'Pp3c11_7280' => 'ppa', 'Pp3c11_7980' => 'ppa', 'Pp3c12_19450' => 'ppa', 'Pp3c14_1480' => 'ppa', 'Pp3c14_1501' => 'ppa', 'Pp3c16_4900' => 'ppa', 'Pp3c16_5010' => 'ppa', 'Pp3c16_5060' => 'ppa', 'Pp3c19_18250' => 'ppa', 'Pp3c23_8530' => 'ppa', 'Pp3c23_8550' => 'ppa', 'Pp3c24_9670' => 'ppa', 'Pp3c2_21390' => 'ppa', 'Pp3c2_31380' => 'ppa', 'Pp3c3_16620' => 'ppa', 'Pp3c3_8090' => 'ppa', 'Pp3c3_8110' => 'ppa', 'Pp3c3_8130' => 'ppa', 'Pp3c3_8150' => 'ppa', 'Pp3c4_14320' => 'ppa', 'Pp3c6_2560' => 'ppa', 'Pp3c9_16700' => 'ppa', 'PRCOL_00000234' => 'pco', 'PRCOL_00000235' => 'pco', 'PRCOL_00000777' => 'pco', 'PRCOL_00002344' => 'pco', 'PRCOL_00002372' => 'pco', 'PRCOL_00006120' => 'pco', 'Prupe.1G021400' => 'ppe', 'Prupe.1G021500' => 'ppe', 'Prupe.1G021600' => 'ppe', 'Prupe.1G021700' => 'ppe', 'Prupe.1G021800' => 'ppe', 'Prupe.5G145100' => 'ppe', 'Psat6g204040' => 'psa', 'Psat6g204800' => 'psa', 'Psat6g204920' => 'psa', 'Psat6g204960' => 'psa', 'Psat6g205080' => 'psa', 'PSO017G0271' => 'pso', 'PSO017G1276' => 'pso', 'PSO017G1429' => 'pso', 'PSO017G1861' => 'pso', 'PSO017G2787' => 'pso', 'PSO017G4466' => 'pso', 'PSO017G5118' => 'pso', 'PSO017G5420' => 'pso', 'PSO063G3678' => 'pso', 'PSO210G0546' => 'pso', 'PSO317G0001' => 'pso', 'PSO357G0512' => 'pso', 'PSO478G2682' => 'pso', 'PSO647G0001' => 'pso', 'PSO675G0001' => 'pso', 'PSO675G2699' => 'pso', 'PSO675G2849' => 'pso', 'PSO675G4991' => 'pso', 'PSO689G0001' => 'pso', 'QL06p000916' => 'qlo', 'QL06p000921' => 'qlo', 'QL06p001398' => 'qlo', 'QL06p001407' => 'qlo', 'QL06p002031' => 'qlo', 'RcHm_v2.0_Chr4g0387791' => 'rch', 'RcHm_v2.0_Chr4g0387801' => 'rch', 'RcHm_v2.0_Chr6g0286501' => 'rch', 'RcHm_v2.0_Chr6g0286511' => 'rch', 'RcHm_v2.0_Chr6g0286521' => 'rch', 'RcHm_v2.0_Chr6g0286531' => 'rch', 'RcHm_v2.0_Chr7g0189141' => 'rch', 'Rhsim02G0028700' => 'rsi', 'Rhsim02G0028800' => 'rsi', 'Rhsim02G0028900' => 'rsi', 'Rhsim02G0029000' => 'rsi', 'Rhsim02G0029100' => 'rsi', 'Rhsim02G0029200' => 'rsi', 'Rhsim02G0029300' => 'rsi', 'Rhsim02G0029400' => 'rsi', 'Rhsim02G0029500' => 'rsi', 'Rhsim02G0029600' => 'rsi', 'RhsimUnG0024000' => 'rsi', 'RhsimUnG0024100' => 'rsi', 'RhsimUnG0024200' => 'rsi', 'RhsimUnG0024300' => 'rsi', 'RhsimUnG0024400' => 'rsi', 'RhsimUnG0024500' => 'rsi', 'RhsimUnG0024700' => 'rsi', 'RhsimUnG0024800' => 'rsi', 'RhsimUnG0024900' => 'rsi', 'RhsimUnG0025100' => 'rsi', 'Sabra08G0120200' => 'sbr', 'Sabra08G0120300' => 'sbr', 'Sabra08G0120500' => 'sbr', 'Sabra08G0120600' => 'sbr', 'Sabra10G0158900' => 'sbr', 'SalBow2G3492' => 'sbo', 'Sc13g0004760' => 'sci', 'Sc13g0004770' => 'sci', 'Sed0003417' => 'sed', 'Sed0019750' => 'sed', 'SEGI_03419' => 'sgi', 'SEGI_05907' => 'sgi', 'SEGI_10682' => 'sgi', 'SEGI_13528' => 'sgi', 'SEGI_16081' => 'sgi', 'SEGI_19370' => 'sgi', 'SEGI_21015' => 'sgi', 'SEGI_21944' => 'sgi', 'SEGI_32906' => 'sgi', 'SEGI_33093' => 'sgi', 'SEGI_36110' => 'sgi', 'SEGI_40397' => 'sgi', 'SGA_v2.0_scaffold191G40426' => 'sas', 'SGA_v2.0_scaffold353G49717' => 'sas', 'SGA_v2.0_scaffold50G18550' => 'sas', 'SMO119G0173' => 'smo', 'SMO172G0002' => 'smo', 'Solyc09g082690.3' => 'sly', 'Solyc09g082700.2' => 'sly', 'Sopen09g031550' => 'spe', 'Sopen09g031560' => 'spe', 'Sp3g20540' => 'spa', 'Sp7g07580' => 'spa', 'TAR134G0002' => 'tar', 'TAR236G0001' => 'tar', 'TAR365G0892' => 'tar', 'TAR636G0166' => 'tar', 'TAR636G0646' => 'tar', 'TAR636G0869' => 'tar', 'TAR636G1317' => 'tar', 'TAR636G1744' => 'tar', 'TAR636G3358' => 'tar', 'TAR636G3436' => 'tar', 'THA.LOC104803047' => 'tha', 'Thecc.04G238900' => 'tca', 'Thhalv10021557m.g' => 'esa', 'Thhalv10026318m.g' => 'esa', 'Thhalv10026335m.g' => 'esa', 'TPR.G17433' => 'tpr', 'TPR.G18915' => 'tpr', 'TPR.G26125' => 'tpr', 'TWI09G0677' => 'twi', 'TWI73G0287' => 'twi', 'unitig_748.g8326' => 'ugi', 'vmacro15370' => 'vma', 'vmacro15371' => 'vma', 'vmacro15372' => 'vma', 'vmacro15373' => 'vma', 'vmacro15374' => 'vma', 'VMungo0720G2826' => 'vmu', 'Zm00001eb116960' => 'zma', 'Zm00001eb301260' => 'zma', 'Zm00001eb301270' => 'zma' ), 'gf_id' => 'HOM05D001460', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001460' ), 'data_identifier' => 'HOM05D001460', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001460', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '433', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p22980' => 'bna', 'A01p32340' => 'bna', 'A03p42970' => 'bna', 'A05p25880' => 'bna', 'Aa31LG8G9320' => 'aar', 'Aa31LG8G9330' => 'aar', 'Aa31LG8G9340' => 'aar', 'Aa31sc221G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1034' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1528' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.829' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2222' => 'aag', 'Ah.12g058830' => 'amhyb', 'Ah.12g058840' => 'amhyb', 'AL3G37160' => 'aly', 'AL7G41310' => 'aly', 'Aqoxy5G00395' => 'aox', 'Aqoxy5G00396' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0C8NZA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5185HY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JZ1PRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MD3LS0' => 'arhy', 'AT3G22840' => 'ath', 'AT4G14690' => 'ath', 'ATR0665G054' => 'atr', 'Atru.chr4.2344' => 'acertr', 'Atru.chr4.2346' => 'acertr', 'Atru.chr4.2347' => 'acertr', 'Atru.chr4.2348' => 'acertr', 'Atru.chr4.2355' => 'acertr', 'Atru.chr4.2356' => 'acertr', 'Atru.chr4.2358' => 'acertr', 'Atru.chr4.2359' => 'acertr', 'Atru.chr4.2360' => 'acertr', 'Atru.chr4.2361' => 'acertr', 'AUR62030476' => 'cqu', 'AUR62030478' => 'cqu', 'AUR62030819' => 'cqu', 'AUR62030820' => 'cqu', 'BcaB03g14648' => 'bca', 'BcaB04g20492' => 'bca', 'BcaB06g26399' => 'bca', 'BcaC01g03416' => 'bca', 'BcaC01g03419' => 'bca', 'BcaC01g03421' => 'bca', 'BcaC01g03424' => 'bca', 'BcaC05g28012' => 'bca', 'BcaC09g49212' => 'bca', 'BcaC09g50140' => 'bca', 'BcaNung00346' => 'bca', 'BolC1t02785H' => 'bol', 'BolC1t04095H' => 'bol', 'BolC3t17545H' => 'bol', 'BolC5t32769H' => 'bol', 'BraA01t02211Z' => 'bra', 'BraA01t03359Z' => 'bra', 'BraA03t13441Z' => 'bra', 'BraA05t21476Z' => 'bra', 'C01p28420' => 'bna', 'C01p41350' => 'bna', 'C03p52750' => 'bna', 'C03p52780' => 'bna', 'C05p40270' => 'bna', 'CAN.G1437.9' => 'can', 'CANSAT78G0035' => 'cansat', 'CANSAT78G1036' => 'cansat', 'CANSAT78G2272' => 'cansat', 'CANSAT78G2478' => 'cansat', 'CARHR098700' => 'chi', 'CARHR221120' => 'chi', 'CARHR221150' => 'chi', 'Carub.0003s2297' => 'cru', 'Carub.0007s2749' => 'cru', 'Carub.0007s2750' => 'cru', 'Carub.0007s2751' => 'cru', 'Ca_10849_v3' => 'car', 'Cc03_g04300' => 'ccan', 'CDE02G3648' => 'cde', 'CDE05G0060' => 'cde', 'CDE05G0692' => 'cde', 'CDE05G2285' => 'cde', 'CDE05G2884' => 'cde', 'CDE05G3072' => 'cde', 'Cfa008439' => 'cfa', 'Cfa008441' => 'cfa', 'Cfa008443' => 'cfa', 'Cfa008448' => 'cfa', 'Ciclev10005974m.g' => 'ccl', 'Ciclev10006006m.g' => 'ccl', 'Ciclev10006775m.g' => 'ccl', 'CiPaw.02G120400' => 'cil', 'CiPaw.02G120500' => 'cil', 'CiPaw.02G120600' => 'cil', 'ClCG05G004850' => 'cla', 'COL.COLO4_21566' => 'col', 'Cpa.g.sc44.124' => 'cpa', 'Cre07.g320400' => 'cre', 'Cre07.g320450' => 'cre', 'Cre08.g384650' => 'cre', 'Cre09.g393173' => 'cre', 'Cre09.g394325' => 'cre', 'Cre14.g626750' => 'cre', 'Cre16.g679250' => 'cre', 'CsaV3_3G012890' => 'csa', 'CSS0010865' => 'camsi', 'CSS0044338' => 'camsi', 'DCAR_002366' => 'dca', 'DCAR_030687' => 'dca', 'DCAR_030688' => 'dca', 'Dinv14047' => 'din', 'Dinv14048' => 'din', 'Duzib151G0105' => 'dzi', 'Duzib151G0114' => 'dzi', 'Duzib212G1029' => 'dzi', 'ECA232G3536' => 'eca', 'ECA240G0786' => 'eca', 'ECA240G1802' => 'eca', 'ECA240G3760' => 'eca', 'ECA240G3920' => 'eca', 'EL10Ac5g12536' => 'bvu', 'EL10Ac5g12537' => 'bvu', 'EL10Ac5g12538' => 'bvu', 'Eucgr.B01004' => 'egr', 'Eucgr.B01006' => 'egr', 'Eucgr.B01007' => 'egr', 'Eucgr.B01008' => 'egr', 'Eucgr.B01895' => 'egr', 'Eucgr.B01896' => 'egr', 'FAN04G1456' => 'fan', 'FAN08G1769' => 'fan', 'FAN08G2160' => 'fan', 'FAN13G2403' => 'fan', 'FAN13G3303' => 'fan', 'FAN15G2435' => 'fan', 'FAN17G0672' => 'fan', 'FAN17G2441' => 'fan', 'FAN18G1024' => 'fan', 'FAN22G1458' => 'fan', 'FAN24G0037' => 'fan', 'FAN24G0429' => 'fan', 'FAN24G2387' => 'fan', 'FAN27G2746' => 'fan', 'FvH4_2g20400' => 'fve', 'FvH4_2g20420' => 'fve', 'FvH4_2g20430' => 'fve', 'FvH4_4g01270' => 'fve', 'FvH4_4g01290' => 'fve', 'FvH4_4g01300' => 'fve', 'FvH4_4g01310' => 'fve', 'FvH4_4g01330' => 'fve', 'FvH4_5g09070' => 'fve', 'Glyma.10G243800' => 'gma', 'Glyma.20G150600' => 'gma', 'Gohir.A09G219200' => 'ghi', 'Gohir.A09G219300' => 'ghi', 'Gohir.D09G221400' => 'ghi', 'Gohir.D09G221500' => 'ghi', 'Gorai.006G242600' => 'gra', 'Gorai.006G242700' => 'gra', 'GSVIVG01018044001' => 'vvi', 'HanXRQChr03g0083821' => 'han', 'HanXRQChr03g0083841' => 'han', 'HanXRQChr03g0083881' => 'han', 'HanXRQChr03g0083901' => 'han', 'HanXRQChr03g0083921' => 'han', 'HanXRQChr03g0085331' => 'han', 'HanXRQChr03g0085361' => 'han', 'HanXRQChr03g0085411' => 'han', 'HanXRQChr03g0085421' => 'han', 'HanXRQChr03g0085431' => 'han', 'HanXRQChr08g0221991' => 'han', 'HanXRQChr11g0336061' => 'han', 'HanXRQChr11g0336411' => 'han', 'Haze_11234' => 'cav', 'Hma1.2p1_0549F.1_g177010' => 'hma', 'Hma1.2p1_0602F.1_g187630' => 'hma', 'Hund14876' => 'sun', 'Hund14879' => 'sun', 'Lalb_Chr06g0160741' => 'lal', 'Lalb_Chr21g0304781' => 'lal', 'Lj3A726G19' => 'lonja', 'Lj3A726T23' => 'lonja', 'Lj3A726T24' => 'lonja', 'Lj3A726T25' => 'lonja', 'Lj3A727T17' => 'lonja', 'Lj3C726T0' => 'lonja', 'Lj3C726T2' => 'lonja', 'Lj3P725T35' => 'lonja', 'Lj3P727T10' => 'lonja', 'Lj3P727T12' => 'lonja', 'Lj3P727T14' => 'lonja', 'Lj5g0023109' => 'lja', 'Lj6P646T44' => 'lonja', 'Lsat_1_v5_gn_6_75760' => 'lsa', 'Lsat_1_v5_gn_6_75800' => 'lsa', 'Lsat_1_v5_gn_6_75900' => 'lsa', 'Lsat_1_v5_gn_6_76240' => 'lsa', 'Lsat_1_v5_gn_6_76441' => 'lsa', 'Lsat_1_v5_gn_6_76700' => 'lsa', 'Lsat_1_v5_gn_6_76760' => 'lsa', 'Manes.15G033100' => 'mes', 'Mapoly0004s0074' => 'mpo', 'Mapoly0004s0075' => 'mpo', 'Mapoly0004s0163' => 'mpo', 'Mapoly0004s0164' => 'mpo', 'Mapoly0021s0018' => 'mpo', 'Mapoly0041s0136' => 'mpo', 'Mapoly0041s0137' => 'mpo', 'Mapoly0041s0138' => 'mpo', 'Mapoly0041s0139' => 'mpo', 'Mapoly0041s0141' => 'mpo', 'Mapoly0041s0142' => 'mpo', 'Mapoly0041s0143' => 'mpo', 'Mapoly0041s0144' => 'mpo', 'Mapoly0041s0145' => 'mpo', 'Mapoly0047s0106' => 'mpo', 'Mapoly0047s0108' => 'mpo', 'Mapoly0050s0051' => 'mpo', 'Mapoly0050s0052' => 'mpo', 'Mapoly0050s0053' => 'mpo', 'Mapoly0058s0013' => 'mpo', 'Mapoly0091s0078' => 'mpo', 'Mapoly0091s0079' => 'mpo', 'Mapoly0091s0080' => 'mpo', 'Mapoly0091s0081' => 'mpo', 'Mapoly0278s0004' => 'mpo', 'Mapoly0278s0005' => 'mpo', 'Mapoly0278s0006' => 'mpo', 'MBI11_g30648_MAGBIO' => 'mbi', 'MCO03G194' => 'mco', 'MCO03G590' => 'mco', 'MCO07G312' => 'mco', 'MCO10G318' => 'mco', 'MCO12G244' => 'mco', 'MCO13G148' => 'mco', 'MCO13G194' => 'mco', 'MCO16G238' => 'mco', 'MD06G1134100' => 'mdo', 'MD13G1200100' => 'mdo', 'MD13G1200300' => 'mdo', 'MD13G1200600' => 'mdo', 'MD14G1150400' => 'mdo', 'MD16G1200000' => 'mdo', 'Medtr1g102570' => 'mtr', 'Medtr1g102780' => 'mtr', 'Medtr1g102800' => 'mtr', 'Medtr1g102810' => 'mtr', 'Medtr1g102830' => 'mtr', 'MELO3C006499.2' => 'cme', 'Migut.G00385' => 'egut', 'MSTRG.4063' => 'ama', 'Nitab4.5_0000090g0260' => 'nta', 'Nitab4.5_0000977g0030' => 'nta', 'Nitab4.5_0002541g0040' => 'nta', 'Nitab4.5_0007068g0040' => 'nta', 'Nn005s41408' => 'nnu', 'Nn005s41410' => 'nnu', 'Oeu010310.1' => 'oeu', 'Oeu010311.1' => 'oeu', 'Oeu043472.1' => 'oeu', 'Os01g0246400' => 'osa', 'Os04g0267950' => 'osa', 'Os07g0178700' => 'osa', 'Os07g0178800' => 'osa', 'Peaxi162Scf00316g00046' => 'pax', 'Peaxi162Scf00316g00049' => 'pax', 'Peaxi162Scf00316g00059' => 'pax', 'Peaxi162Scf00316g00328' => 'pax', 'Peaxi162Scf00316g00329' => 'pax', 'Peaxi162Scf00316g00411' => 'pax', 'Peaxi162Scf00316g00521' => 'pax', 'Peaxi162Scf00492g00068' => 'pax', 'Peaxi162Scf35631g00002' => 'pax', 'PGR142G3720' => 'pgr', 'PGSC0003DMG400006442' => 'stu', 'Phvul.007G062000' => 'pvu', 'Potri.008G157750' => 'ptr', 'Potri.008G157900' => 'ptr', 'Potri.008G158000' => 'ptr', 'Potri.008G158200' => 'ptr', 'Pp3c11_7280' => 'ppa', 'Pp3c11_7980' => 'ppa', 'Pp3c12_19450' => 'ppa', 'Pp3c14_1480' => 'ppa', 'Pp3c14_1501' => 'ppa', 'Pp3c16_4900' => 'ppa', 'Pp3c16_5010' => 'ppa', 'Pp3c16_5060' => 'ppa', 'Pp3c19_18250' => 'ppa', 'Pp3c23_8530' => 'ppa', 'Pp3c23_8550' => 'ppa', 'Pp3c24_9670' => 'ppa', 'Pp3c2_21390' => 'ppa', 'Pp3c2_31380' => 'ppa', 'Pp3c3_16620' => 'ppa', 'Pp3c3_8090' => 'ppa', 'Pp3c3_8110' => 'ppa', 'Pp3c3_8130' => 'ppa', 'Pp3c3_8150' => 'ppa', 'Pp3c4_14320' => 'ppa', 'Pp3c6_2560' => 'ppa', 'Pp3c9_16700' => 'ppa', 'PRCOL_00000234' => 'pco', 'PRCOL_00000235' => 'pco', 'PRCOL_00000777' => 'pco', 'PRCOL_00002344' => 'pco', 'PRCOL_00002372' => 'pco', 'PRCOL_00006120' => 'pco', 'Prupe.1G021400' => 'ppe', 'Prupe.1G021500' => 'ppe', 'Prupe.1G021600' => 'ppe', 'Prupe.1G021700' => 'ppe', 'Prupe.1G021800' => 'ppe', 'Prupe.5G145100' => 'ppe', 'Psat6g204040' => 'psa', 'Psat6g204800' => 'psa', 'Psat6g204920' => 'psa', 'Psat6g204960' => 'psa', 'Psat6g205080' => 'psa', 'PSO017G0271' => 'pso', 'PSO017G1276' => 'pso', 'PSO017G1429' => 'pso', 'PSO017G1861' => 'pso', 'PSO017G2787' => 'pso', 'PSO017G4466' => 'pso', 'PSO017G5118' => 'pso', 'PSO017G5420' => 'pso', 'PSO063G3678' => 'pso', 'PSO210G0546' => 'pso', 'PSO317G0001' => 'pso', 'PSO357G0512' => 'pso', 'PSO478G2682' => 'pso', 'PSO647G0001' => 'pso', 'PSO675G0001' => 'pso', 'PSO675G2699' => 'pso', 'PSO675G2849' => 'pso', 'PSO675G4991' => 'pso', 'PSO689G0001' => 'pso', 'QL06p000916' => 'qlo', 'QL06p000921' => 'qlo', 'QL06p001398' => 'qlo', 'QL06p001407' => 'qlo', 'QL06p002031' => 'qlo', 'RcHm_v2.0_Chr4g0387791' => 'rch', 'RcHm_v2.0_Chr4g0387801' => 'rch', 'RcHm_v2.0_Chr6g0286501' => 'rch', 'RcHm_v2.0_Chr6g0286511' => 'rch', 'RcHm_v2.0_Chr6g0286521' => 'rch', 'RcHm_v2.0_Chr6g0286531' => 'rch', 'RcHm_v2.0_Chr7g0189141' => 'rch', 'Rhsim02G0028700' => 'rsi', 'Rhsim02G0028800' => 'rsi', 'Rhsim02G0028900' => 'rsi', 'Rhsim02G0029000' => 'rsi', 'Rhsim02G0029100' => 'rsi', 'Rhsim02G0029200' => 'rsi', 'Rhsim02G0029300' => 'rsi', 'Rhsim02G0029400' => 'rsi', 'Rhsim02G0029500' => 'rsi', 'Rhsim02G0029600' => 'rsi', 'RhsimUnG0024000' => 'rsi', 'RhsimUnG0024100' => 'rsi', 'RhsimUnG0024200' => 'rsi', 'RhsimUnG0024300' => 'rsi', 'RhsimUnG0024400' => 'rsi', 'RhsimUnG0024500' => 'rsi', 'RhsimUnG0024700' => 'rsi', 'RhsimUnG0024800' => 'rsi', 'RhsimUnG0024900' => 'rsi', 'RhsimUnG0025100' => 'rsi', 'Sabra08G0120200' => 'sbr', 'Sabra08G0120300' => 'sbr', 'Sabra08G0120500' => 'sbr', 'Sabra08G0120600' => 'sbr', 'Sabra10G0158900' => 'sbr', 'SalBow2G3492' => 'sbo', 'Sc13g0004760' => 'sci', 'Sc13g0004770' => 'sci', 'Sed0003417' => 'sed', 'Sed0019750' => 'sed', 'SEGI_03419' => 'sgi', 'SEGI_05907' => 'sgi', 'SEGI_10682' => 'sgi', 'SEGI_13528' => 'sgi', 'SEGI_16081' => 'sgi', 'SEGI_19370' => 'sgi', 'SEGI_21015' => 'sgi', 'SEGI_21944' => 'sgi', 'SEGI_32906' => 'sgi', 'SEGI_33093' => 'sgi', 'SEGI_36110' => 'sgi', 'SEGI_40397' => 'sgi', 'SGA_v2.0_scaffold191G40426' => 'sas', 'SGA_v2.0_scaffold353G49717' => 'sas', 'SGA_v2.0_scaffold50G18550' => 'sas', 'SMO119G0173' => 'smo', 'SMO172G0002' => 'smo', 'Solyc09g082690.3' => 'sly', 'Solyc09g082700.2' => 'sly', 'Sopen09g031550' => 'spe', 'Sopen09g031560' => 'spe', 'Sp3g20540' => 'spa', 'Sp7g07580' => 'spa', 'TAR134G0002' => 'tar', 'TAR236G0001' => 'tar', 'TAR365G0892' => 'tar', 'TAR636G0166' => 'tar', 'TAR636G0646' => 'tar', 'TAR636G0869' => 'tar', 'TAR636G1317' => 'tar', 'TAR636G1744' => 'tar', 'TAR636G3358' => 'tar', 'TAR636G3436' => 'tar', 'THA.LOC104803047' => 'tha', 'Thecc.04G238900' => 'tca', 'Thhalv10021557m.g' => 'esa', 'Thhalv10026318m.g' => 'esa', 'Thhalv10026335m.g' => 'esa', 'TPR.G17433' => 'tpr', 'TPR.G18915' => 'tpr', 'TPR.G26125' => 'tpr', 'TWI09G0677' => 'twi', 'TWI73G0287' => 'twi', 'unitig_748.g8326' => 'ugi', 'vmacro15370' => 'vma', 'vmacro15371' => 'vma', 'vmacro15372' => 'vma', 'vmacro15373' => 'vma', 'vmacro15374' => 'vma', 'VMungo0720G2826' => 'vmu', 'Zm00001eb116960' => 'zma', 'Zm00001eb301260' => 'zma', 'Zm00001eb301270' => 'zma' ) $gf_id = 'HOM05D001460' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001460' ) $data_identifier = 'HOM05D001460' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 4, 'aag' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 2, 'aox' => (int) 2, 'arhy' => (int) 4, 'ath' => (int) 2, 'atr' => (int) 1, 'acertr' => (int) 10, 'cqu' => (int) 4, 'bca' => (int) 11, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 1, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 1, 'ccan' => (int) 1, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 1, 'col' => (int) 1, 'cpa' => (int) 1, 'cre' => (int) 7, 'csa' => (int) 1, 'camsi' => (int) 2, 'dca' => (int) 3, 'din' => (int) 2, 'dzi' => (int) 3, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 14, 'fve' => (int) 9, 'gma' => (int) 2, 'ghi' => (int) 4, 'gra' => (int) 2, 'vvi' => (int) 1, 'han' => (int) 13, 'cav' => (int) 1, 'hma' => (int) 2, 'sun' => (int) 2, 'lal' => (int) 2, 'lonja' => (int) 12, 'lja' => (int) 1, 'lsa' => (int) 7, 'mes' => (int) 1, 'mpo' => (int) 27, 'mbi' => (int) 1, 'mco' => (int) 8, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 1, 'egut' => (int) 1, 'ama' => (int) 1, 'nta' => (int) 4, 'nnu' => (int) 2, 'oeu' => (int) 3, 'osa' => (int) 4, 'pax' => (int) 9, 'pgr' => (int) 1, 'stu' => (int) 1, 'pvu' => (int) 1, 'ptr' => (int) 4, 'ppa' => (int) 22, 'pco' => (int) 6, 'ppe' => (int) 6, 'psa' => (int) 5, 'pso' => (int) 19, 'qlo' => (int) 5, 'rch' => (int) 7, 'rsi' => (int) 20, 'sbr' => (int) 5, 'sbo' => (int) 1, 'sci' => (int) 2, 'sed' => (int) 2, 'sgi' => (int) 12, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 2, 'tar' => (int) 10, 'tha' => (int) 1, 'tca' => (int) 1, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 2, 'ugi' => (int) 1, 'vma' => (int) 5, 'vmu' => (int) 1, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb301270' $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' => 'HOM05D001460', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '433', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p22980' => 'bna', 'A01p32340' => 'bna', 'A03p42970' => 'bna', 'A05p25880' => 'bna', 'Aa31LG8G9320' => 'aar', 'Aa31LG8G9330' => 'aar', 'Aa31LG8G9340' => 'aar', 'Aa31sc221G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1034' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1528' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.829' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2222' => 'aag', 'Ah.12g058830' => 'amhyb', 'Ah.12g058840' => 'amhyb', 'AL3G37160' => 'aly', 'AL7G41310' => 'aly', 'Aqoxy5G00395' => 'aox', 'Aqoxy5G00396' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0C8NZA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5185HY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JZ1PRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MD3LS0' => 'arhy', 'AT3G22840' => 'ath', 'AT4G14690' => 'ath', 'ATR0665G054' => 'atr', 'Atru.chr4.2344' => 'acertr', 'Atru.chr4.2346' => 'acertr', 'Atru.chr4.2347' => 'acertr', 'Atru.chr4.2348' => 'acertr', 'Atru.chr4.2355' => 'acertr', 'Atru.chr4.2356' => 'acertr', 'Atru.chr4.2358' => 'acertr', 'Atru.chr4.2359' => 'acertr', 'Atru.chr4.2360' => 'acertr', 'Atru.chr4.2361' => 'acertr', 'AUR62030476' => 'cqu', 'AUR62030478' => 'cqu', 'AUR62030819' => 'cqu', 'AUR62030820' => 'cqu', 'BcaB03g14648' => 'bca', 'BcaB04g20492' => 'bca', 'BcaB06g26399' => 'bca', 'BcaC01g03416' => 'bca', 'BcaC01g03419' => 'bca', 'BcaC01g03421' => 'bca', 'BcaC01g03424' => 'bca', 'BcaC05g28012' => 'bca', 'BcaC09g49212' => 'bca', 'BcaC09g50140' => 'bca', 'BcaNung00346' => 'bca', 'BolC1t02785H' => 'bol', 'BolC1t04095H' => 'bol', 'BolC3t17545H' => 'bol', 'BolC5t32769H' => 'bol', 'BraA01t02211Z' => 'bra', 'BraA01t03359Z' => 'bra', 'BraA03t13441Z' => 'bra', 'BraA05t21476Z' => 'bra', 'C01p28420' => 'bna', 'C01p41350' => 'bna', 'C03p52750' => 'bna', 'C03p52780' => 'bna', 'C05p40270' => 'bna', 'CAN.G1437.9' => 'can', 'CANSAT78G0035' => 'cansat', 'CANSAT78G1036' => 'cansat', 'CANSAT78G2272' => 'cansat', 'CANSAT78G2478' => 'cansat', 'CARHR098700' => 'chi', 'CARHR221120' => 'chi', 'CARHR221150' => 'chi', 'Carub.0003s2297' => 'cru', 'Carub.0007s2749' => 'cru', 'Carub.0007s2750' => 'cru', 'Carub.0007s2751' => 'cru', 'Ca_10849_v3' => 'car', 'Cc03_g04300' => 'ccan', 'CDE02G3648' => 'cde', 'CDE05G0060' => 'cde', 'CDE05G0692' => 'cde', 'CDE05G2285' => 'cde', 'CDE05G2884' => 'cde', 'CDE05G3072' => 'cde', 'Cfa008439' => 'cfa', 'Cfa008441' => 'cfa', 'Cfa008443' => 'cfa', 'Cfa008448' => 'cfa', 'Ciclev10005974m.g' => 'ccl', 'Ciclev10006006m.g' => 'ccl', 'Ciclev10006775m.g' => 'ccl', 'CiPaw.02G120400' => 'cil', 'CiPaw.02G120500' => 'cil', 'CiPaw.02G120600' => 'cil', 'ClCG05G004850' => 'cla', 'COL.COLO4_21566' => 'col', 'Cpa.g.sc44.124' => 'cpa', 'Cre07.g320400' => 'cre', 'Cre07.g320450' => 'cre', 'Cre08.g384650' => 'cre', 'Cre09.g393173' => 'cre', 'Cre09.g394325' => 'cre', 'Cre14.g626750' => 'cre', 'Cre16.g679250' => 'cre', 'CsaV3_3G012890' => 'csa', 'CSS0010865' => 'camsi', 'CSS0044338' => 'camsi', 'DCAR_002366' => 'dca', 'DCAR_030687' => 'dca', 'DCAR_030688' => 'dca', 'Dinv14047' => 'din', 'Dinv14048' => 'din', 'Duzib151G0105' => 'dzi', 'Duzib151G0114' => 'dzi', 'Duzib212G1029' => 'dzi', 'ECA232G3536' => 'eca', 'ECA240G0786' => 'eca', 'ECA240G1802' => 'eca', 'ECA240G3760' => 'eca', 'ECA240G3920' => 'eca', 'EL10Ac5g12536' => 'bvu', 'EL10Ac5g12537' => 'bvu', 'EL10Ac5g12538' => 'bvu', 'Eucgr.B01004' => 'egr', 'Eucgr.B01006' => 'egr', 'Eucgr.B01007' => 'egr', 'Eucgr.B01008' => 'egr', 'Eucgr.B01895' => 'egr', 'Eucgr.B01896' => 'egr', 'FAN04G1456' => 'fan', 'FAN08G1769' => 'fan', 'FAN08G2160' => 'fan', 'FAN13G2403' => 'fan', 'FAN13G3303' => 'fan', 'FAN15G2435' => 'fan', 'FAN17G0672' => 'fan', 'FAN17G2441' => 'fan', 'FAN18G1024' => 'fan', 'FAN22G1458' => 'fan', 'FAN24G0037' => 'fan', 'FAN24G0429' => 'fan', 'FAN24G2387' => 'fan', 'FAN27G2746' => 'fan', 'FvH4_2g20400' => 'fve', 'FvH4_2g20420' => 'fve', 'FvH4_2g20430' => 'fve', 'FvH4_4g01270' => 'fve', 'FvH4_4g01290' => 'fve', 'FvH4_4g01300' => 'fve', 'FvH4_4g01310' => 'fve', 'FvH4_4g01330' => 'fve', 'FvH4_5g09070' => 'fve', 'Glyma.10G243800' => 'gma', 'Glyma.20G150600' => 'gma', 'Gohir.A09G219200' => 'ghi', 'Gohir.A09G219300' => 'ghi', 'Gohir.D09G221400' => 'ghi', 'Gohir.D09G221500' => 'ghi', 'Gorai.006G242600' => 'gra', 'Gorai.006G242700' => 'gra', 'GSVIVG01018044001' => 'vvi', 'HanXRQChr03g0083821' => 'han', 'HanXRQChr03g0083841' => 'han', 'HanXRQChr03g0083881' => 'han', 'HanXRQChr03g0083901' => 'han', 'HanXRQChr03g0083921' => 'han', 'HanXRQChr03g0085331' => 'han', 'HanXRQChr03g0085361' => 'han', 'HanXRQChr03g0085411' => 'han', 'HanXRQChr03g0085421' => 'han', 'HanXRQChr03g0085431' => 'han', 'HanXRQChr08g0221991' => 'han', 'HanXRQChr11g0336061' => 'han', 'HanXRQChr11g0336411' => 'han', 'Haze_11234' => 'cav', 'Hma1.2p1_0549F.1_g177010' => 'hma', 'Hma1.2p1_0602F.1_g187630' => 'hma', 'Hund14876' => 'sun', 'Hund14879' => 'sun', 'Lalb_Chr06g0160741' => 'lal', 'Lalb_Chr21g0304781' => 'lal', 'Lj3A726G19' => 'lonja', 'Lj3A726T23' => 'lonja', 'Lj3A726T24' => 'lonja', 'Lj3A726T25' => 'lonja', 'Lj3A727T17' => 'lonja', 'Lj3C726T0' => 'lonja', 'Lj3C726T2' => 'lonja', 'Lj3P725T35' => 'lonja', 'Lj3P727T10' => 'lonja', 'Lj3P727T12' => 'lonja', 'Lj3P727T14' => 'lonja', 'Lj5g0023109' => 'lja', 'Lj6P646T44' => 'lonja', 'Lsat_1_v5_gn_6_75760' => 'lsa', 'Lsat_1_v5_gn_6_75800' => 'lsa', 'Lsat_1_v5_gn_6_75900' => 'lsa', 'Lsat_1_v5_gn_6_76240' => 'lsa', 'Lsat_1_v5_gn_6_76441' => 'lsa', 'Lsat_1_v5_gn_6_76700' => 'lsa', 'Lsat_1_v5_gn_6_76760' => 'lsa', 'Manes.15G033100' => 'mes', 'Mapoly0004s0074' => 'mpo', 'Mapoly0004s0075' => 'mpo', 'Mapoly0004s0163' => 'mpo', 'Mapoly0004s0164' => 'mpo', 'Mapoly0021s0018' => 'mpo', 'Mapoly0041s0136' => 'mpo', 'Mapoly0041s0137' => 'mpo', 'Mapoly0041s0138' => 'mpo', 'Mapoly0041s0139' => 'mpo', 'Mapoly0041s0141' => 'mpo', 'Mapoly0041s0142' => 'mpo', 'Mapoly0041s0143' => 'mpo', 'Mapoly0041s0144' => 'mpo', 'Mapoly0041s0145' => 'mpo', 'Mapoly0047s0106' => 'mpo', 'Mapoly0047s0108' => 'mpo', 'Mapoly0050s0051' => 'mpo', 'Mapoly0050s0052' => 'mpo', 'Mapoly0050s0053' => 'mpo', 'Mapoly0058s0013' => 'mpo', 'Mapoly0091s0078' => 'mpo', 'Mapoly0091s0079' => 'mpo', 'Mapoly0091s0080' => 'mpo', 'Mapoly0091s0081' => 'mpo', 'Mapoly0278s0004' => 'mpo', 'Mapoly0278s0005' => 'mpo', 'Mapoly0278s0006' => 'mpo', 'MBI11_g30648_MAGBIO' => 'mbi', 'MCO03G194' => 'mco', 'MCO03G590' => 'mco', 'MCO07G312' => 'mco', 'MCO10G318' => 'mco', 'MCO12G244' => 'mco', 'MCO13G148' => 'mco', 'MCO13G194' => 'mco', 'MCO16G238' => 'mco', 'MD06G1134100' => 'mdo', 'MD13G1200100' => 'mdo', 'MD13G1200300' => 'mdo', 'MD13G1200600' => 'mdo', 'MD14G1150400' => 'mdo', 'MD16G1200000' => 'mdo', 'Medtr1g102570' => 'mtr', 'Medtr1g102780' => 'mtr', 'Medtr1g102800' => 'mtr', 'Medtr1g102810' => 'mtr', 'Medtr1g102830' => 'mtr', 'MELO3C006499.2' => 'cme', 'Migut.G00385' => 'egut', 'MSTRG.4063' => 'ama', 'Nitab4.5_0000090g0260' => 'nta', 'Nitab4.5_0000977g0030' => 'nta', 'Nitab4.5_0002541g0040' => 'nta', 'Nitab4.5_0007068g0040' => 'nta', 'Nn005s41408' => 'nnu', 'Nn005s41410' => 'nnu', 'Oeu010310.1' => 'oeu', 'Oeu010311.1' => 'oeu', 'Oeu043472.1' => 'oeu', 'Os01g0246400' => 'osa', 'Os04g0267950' => 'osa', 'Os07g0178700' => 'osa', 'Os07g0178800' => 'osa', 'Peaxi162Scf00316g00046' => 'pax', 'Peaxi162Scf00316g00049' => 'pax', 'Peaxi162Scf00316g00059' => 'pax', 'Peaxi162Scf00316g00328' => 'pax', 'Peaxi162Scf00316g00329' => 'pax', 'Peaxi162Scf00316g00411' => 'pax', 'Peaxi162Scf00316g00521' => 'pax', 'Peaxi162Scf00492g00068' => 'pax', 'Peaxi162Scf35631g00002' => 'pax', 'PGR142G3720' => 'pgr', 'PGSC0003DMG400006442' => 'stu', 'Phvul.007G062000' => 'pvu', 'Potri.008G157750' => 'ptr', 'Potri.008G157900' => 'ptr', 'Potri.008G158000' => 'ptr', 'Potri.008G158200' => 'ptr', 'Pp3c11_7280' => 'ppa', 'Pp3c11_7980' => 'ppa', 'Pp3c12_19450' => 'ppa', 'Pp3c14_1480' => 'ppa', 'Pp3c14_1501' => 'ppa', 'Pp3c16_4900' => 'ppa', 'Pp3c16_5010' => 'ppa', 'Pp3c16_5060' => 'ppa', 'Pp3c19_18250' => 'ppa', 'Pp3c23_8530' => 'ppa', 'Pp3c23_8550' => 'ppa', 'Pp3c24_9670' => 'ppa', 'Pp3c2_21390' => 'ppa', 'Pp3c2_31380' => 'ppa', 'Pp3c3_16620' => 'ppa', 'Pp3c3_8090' => 'ppa', 'Pp3c3_8110' => 'ppa', 'Pp3c3_8130' => 'ppa', 'Pp3c3_8150' => 'ppa', 'Pp3c4_14320' => 'ppa', 'Pp3c6_2560' => 'ppa', 'Pp3c9_16700' => 'ppa', 'PRCOL_00000234' => 'pco', 'PRCOL_00000235' => 'pco', 'PRCOL_00000777' => 'pco', 'PRCOL_00002344' => 'pco', 'PRCOL_00002372' => 'pco', 'PRCOL_00006120' => 'pco', 'Prupe.1G021400' => 'ppe', 'Prupe.1G021500' => 'ppe', 'Prupe.1G021600' => 'ppe', 'Prupe.1G021700' => 'ppe', 'Prupe.1G021800' => 'ppe', 'Prupe.5G145100' => 'ppe', 'Psat6g204040' => 'psa', 'Psat6g204800' => 'psa', 'Psat6g204920' => 'psa', 'Psat6g204960' => 'psa', 'Psat6g205080' => 'psa', 'PSO017G0271' => 'pso', 'PSO017G1276' => 'pso', 'PSO017G1429' => 'pso', 'PSO017G1861' => 'pso', 'PSO017G2787' => 'pso', 'PSO017G4466' => 'pso', 'PSO017G5118' => 'pso', 'PSO017G5420' => 'pso', 'PSO063G3678' => 'pso', 'PSO210G0546' => 'pso', 'PSO317G0001' => 'pso', 'PSO357G0512' => 'pso', 'PSO478G2682' => 'pso', 'PSO647G0001' => 'pso', 'PSO675G0001' => 'pso', 'PSO675G2699' => 'pso', 'PSO675G2849' => 'pso', 'PSO675G4991' => 'pso', 'PSO689G0001' => 'pso', 'QL06p000916' => 'qlo', 'QL06p000921' => 'qlo', 'QL06p001398' => 'qlo', 'QL06p001407' => 'qlo', 'QL06p002031' => 'qlo', 'RcHm_v2.0_Chr4g0387791' => 'rch', 'RcHm_v2.0_Chr4g0387801' => 'rch', 'RcHm_v2.0_Chr6g0286501' => 'rch', 'RcHm_v2.0_Chr6g0286511' => 'rch', 'RcHm_v2.0_Chr6g0286521' => 'rch', 'RcHm_v2.0_Chr6g0286531' => 'rch', 'RcHm_v2.0_Chr7g0189141' => 'rch', 'Rhsim02G0028700' => 'rsi', 'Rhsim02G0028800' => 'rsi', 'Rhsim02G0028900' => 'rsi', 'Rhsim02G0029000' => 'rsi', 'Rhsim02G0029100' => 'rsi', 'Rhsim02G0029200' => 'rsi', 'Rhsim02G0029300' => 'rsi', 'Rhsim02G0029400' => 'rsi', 'Rhsim02G0029500' => 'rsi', 'Rhsim02G0029600' => 'rsi', 'RhsimUnG0024000' => 'rsi', 'RhsimUnG0024100' => 'rsi', 'RhsimUnG0024200' => 'rsi', 'RhsimUnG0024300' => 'rsi', 'RhsimUnG0024400' => 'rsi', 'RhsimUnG0024500' => 'rsi', 'RhsimUnG0024700' => 'rsi', 'RhsimUnG0024800' => 'rsi', 'RhsimUnG0024900' => 'rsi', 'RhsimUnG0025100' => 'rsi', 'Sabra08G0120200' => 'sbr', 'Sabra08G0120300' => 'sbr', 'Sabra08G0120500' => 'sbr', 'Sabra08G0120600' => 'sbr', 'Sabra10G0158900' => 'sbr', 'SalBow2G3492' => 'sbo', 'Sc13g0004760' => 'sci', 'Sc13g0004770' => 'sci', 'Sed0003417' => 'sed', 'Sed0019750' => 'sed', 'SEGI_03419' => 'sgi', 'SEGI_05907' => 'sgi', 'SEGI_10682' => 'sgi', 'SEGI_13528' => 'sgi', 'SEGI_16081' => 'sgi', 'SEGI_19370' => 'sgi', 'SEGI_21015' => 'sgi', 'SEGI_21944' => 'sgi', 'SEGI_32906' => 'sgi', 'SEGI_33093' => 'sgi', 'SEGI_36110' => 'sgi', 'SEGI_40397' => 'sgi', 'SGA_v2.0_scaffold191G40426' => 'sas', 'SGA_v2.0_scaffold353G49717' => 'sas', 'SGA_v2.0_scaffold50G18550' => 'sas', 'SMO119G0173' => 'smo', 'SMO172G0002' => 'smo', 'Solyc09g082690.3' => 'sly', 'Solyc09g082700.2' => 'sly', 'Sopen09g031550' => 'spe', 'Sopen09g031560' => 'spe', 'Sp3g20540' => 'spa', 'Sp7g07580' => 'spa', 'TAR134G0002' => 'tar', 'TAR236G0001' => 'tar', 'TAR365G0892' => 'tar', 'TAR636G0166' => 'tar', 'TAR636G0646' => 'tar', 'TAR636G0869' => 'tar', 'TAR636G1317' => 'tar', 'TAR636G1744' => 'tar', 'TAR636G3358' => 'tar', 'TAR636G3436' => 'tar', 'THA.LOC104803047' => 'tha', 'Thecc.04G238900' => 'tca', 'Thhalv10021557m.g' => 'esa', 'Thhalv10026318m.g' => 'esa', 'Thhalv10026335m.g' => 'esa', 'TPR.G17433' => 'tpr', 'TPR.G18915' => 'tpr', 'TPR.G26125' => 'tpr', 'TWI09G0677' => 'twi', 'TWI73G0287' => 'twi', 'unitig_748.g8326' => 'ugi', 'vmacro15370' => 'vma', 'vmacro15371' => 'vma', 'vmacro15372' => 'vma', 'vmacro15373' => 'vma', 'vmacro15374' => 'vma', 'VMungo0720G2826' => 'vmu', 'Zm00001eb116960' => 'zma', 'Zm00001eb301260' => 'zma', 'Zm00001eb301270' => 'zma' ), 'gf_id' => 'HOM05D001460', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001460' ), 'data_identifier' => 'HOM05D001460', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001460', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '433', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p22980' => 'bna', 'A01p32340' => 'bna', 'A03p42970' => 'bna', 'A05p25880' => 'bna', 'Aa31LG8G9320' => 'aar', 'Aa31LG8G9330' => 'aar', 'Aa31LG8G9340' => 'aar', 'Aa31sc221G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1034' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1528' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.829' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2222' => 'aag', 'Ah.12g058830' => 'amhyb', 'Ah.12g058840' => 'amhyb', 'AL3G37160' => 'aly', 'AL7G41310' => 'aly', 'Aqoxy5G00395' => 'aox', 'Aqoxy5G00396' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0C8NZA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5185HY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JZ1PRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MD3LS0' => 'arhy', 'AT3G22840' => 'ath', 'AT4G14690' => 'ath', 'ATR0665G054' => 'atr', 'Atru.chr4.2344' => 'acertr', 'Atru.chr4.2346' => 'acertr', 'Atru.chr4.2347' => 'acertr', 'Atru.chr4.2348' => 'acertr', 'Atru.chr4.2355' => 'acertr', 'Atru.chr4.2356' => 'acertr', 'Atru.chr4.2358' => 'acertr', 'Atru.chr4.2359' => 'acertr', 'Atru.chr4.2360' => 'acertr', 'Atru.chr4.2361' => 'acertr', 'AUR62030476' => 'cqu', 'AUR62030478' => 'cqu', 'AUR62030819' => 'cqu', 'AUR62030820' => 'cqu', 'BcaB03g14648' => 'bca', 'BcaB04g20492' => 'bca', 'BcaB06g26399' => 'bca', 'BcaC01g03416' => 'bca', 'BcaC01g03419' => 'bca', 'BcaC01g03421' => 'bca', 'BcaC01g03424' => 'bca', 'BcaC05g28012' => 'bca', 'BcaC09g49212' => 'bca', 'BcaC09g50140' => 'bca', 'BcaNung00346' => 'bca', 'BolC1t02785H' => 'bol', 'BolC1t04095H' => 'bol', 'BolC3t17545H' => 'bol', 'BolC5t32769H' => 'bol', 'BraA01t02211Z' => 'bra', 'BraA01t03359Z' => 'bra', 'BraA03t13441Z' => 'bra', 'BraA05t21476Z' => 'bra', 'C01p28420' => 'bna', 'C01p41350' => 'bna', 'C03p52750' => 'bna', 'C03p52780' => 'bna', 'C05p40270' => 'bna', 'CAN.G1437.9' => 'can', 'CANSAT78G0035' => 'cansat', 'CANSAT78G1036' => 'cansat', 'CANSAT78G2272' => 'cansat', 'CANSAT78G2478' => 'cansat', 'CARHR098700' => 'chi', 'CARHR221120' => 'chi', 'CARHR221150' => 'chi', 'Carub.0003s2297' => 'cru', 'Carub.0007s2749' => 'cru', 'Carub.0007s2750' => 'cru', 'Carub.0007s2751' => 'cru', 'Ca_10849_v3' => 'car', 'Cc03_g04300' => 'ccan', 'CDE02G3648' => 'cde', 'CDE05G0060' => 'cde', 'CDE05G0692' => 'cde', 'CDE05G2285' => 'cde', 'CDE05G2884' => 'cde', 'CDE05G3072' => 'cde', 'Cfa008439' => 'cfa', 'Cfa008441' => 'cfa', 'Cfa008443' => 'cfa', 'Cfa008448' => 'cfa', 'Ciclev10005974m.g' => 'ccl', 'Ciclev10006006m.g' => 'ccl', 'Ciclev10006775m.g' => 'ccl', 'CiPaw.02G120400' => 'cil', 'CiPaw.02G120500' => 'cil', 'CiPaw.02G120600' => 'cil', 'ClCG05G004850' => 'cla', 'COL.COLO4_21566' => 'col', 'Cpa.g.sc44.124' => 'cpa', 'Cre07.g320400' => 'cre', 'Cre07.g320450' => 'cre', 'Cre08.g384650' => 'cre', 'Cre09.g393173' => 'cre', 'Cre09.g394325' => 'cre', 'Cre14.g626750' => 'cre', 'Cre16.g679250' => 'cre', 'CsaV3_3G012890' => 'csa', 'CSS0010865' => 'camsi', 'CSS0044338' => 'camsi', 'DCAR_002366' => 'dca', 'DCAR_030687' => 'dca', 'DCAR_030688' => 'dca', 'Dinv14047' => 'din', 'Dinv14048' => 'din', 'Duzib151G0105' => 'dzi', 'Duzib151G0114' => 'dzi', 'Duzib212G1029' => 'dzi', 'ECA232G3536' => 'eca', 'ECA240G0786' => 'eca', 'ECA240G1802' => 'eca', 'ECA240G3760' => 'eca', 'ECA240G3920' => 'eca', 'EL10Ac5g12536' => 'bvu', 'EL10Ac5g12537' => 'bvu', 'EL10Ac5g12538' => 'bvu', 'Eucgr.B01004' => 'egr', 'Eucgr.B01006' => 'egr', 'Eucgr.B01007' => 'egr', 'Eucgr.B01008' => 'egr', 'Eucgr.B01895' => 'egr', 'Eucgr.B01896' => 'egr', 'FAN04G1456' => 'fan', 'FAN08G1769' => 'fan', 'FAN08G2160' => 'fan', 'FAN13G2403' => 'fan', 'FAN13G3303' => 'fan', 'FAN15G2435' => 'fan', 'FAN17G0672' => 'fan', 'FAN17G2441' => 'fan', 'FAN18G1024' => 'fan', 'FAN22G1458' => 'fan', 'FAN24G0037' => 'fan', 'FAN24G0429' => 'fan', 'FAN24G2387' => 'fan', 'FAN27G2746' => 'fan', 'FvH4_2g20400' => 'fve', 'FvH4_2g20420' => 'fve', 'FvH4_2g20430' => 'fve', 'FvH4_4g01270' => 'fve', 'FvH4_4g01290' => 'fve', 'FvH4_4g01300' => 'fve', 'FvH4_4g01310' => 'fve', 'FvH4_4g01330' => 'fve', 'FvH4_5g09070' => 'fve', 'Glyma.10G243800' => 'gma', 'Glyma.20G150600' => 'gma', 'Gohir.A09G219200' => 'ghi', 'Gohir.A09G219300' => 'ghi', 'Gohir.D09G221400' => 'ghi', 'Gohir.D09G221500' => 'ghi', 'Gorai.006G242600' => 'gra', 'Gorai.006G242700' => 'gra', 'GSVIVG01018044001' => 'vvi', 'HanXRQChr03g0083821' => 'han', 'HanXRQChr03g0083841' => 'han', 'HanXRQChr03g0083881' => 'han', 'HanXRQChr03g0083901' => 'han', 'HanXRQChr03g0083921' => 'han', 'HanXRQChr03g0085331' => 'han', 'HanXRQChr03g0085361' => 'han', 'HanXRQChr03g0085411' => 'han', 'HanXRQChr03g0085421' => 'han', 'HanXRQChr03g0085431' => 'han', 'HanXRQChr08g0221991' => 'han', 'HanXRQChr11g0336061' => 'han', 'HanXRQChr11g0336411' => 'han', 'Haze_11234' => 'cav', 'Hma1.2p1_0549F.1_g177010' => 'hma', 'Hma1.2p1_0602F.1_g187630' => 'hma', 'Hund14876' => 'sun', 'Hund14879' => 'sun', 'Lalb_Chr06g0160741' => 'lal', 'Lalb_Chr21g0304781' => 'lal', 'Lj3A726G19' => 'lonja', 'Lj3A726T23' => 'lonja', 'Lj3A726T24' => 'lonja', 'Lj3A726T25' => 'lonja', 'Lj3A727T17' => 'lonja', 'Lj3C726T0' => 'lonja', 'Lj3C726T2' => 'lonja', 'Lj3P725T35' => 'lonja', 'Lj3P727T10' => 'lonja', 'Lj3P727T12' => 'lonja', 'Lj3P727T14' => 'lonja', 'Lj5g0023109' => 'lja', 'Lj6P646T44' => 'lonja', 'Lsat_1_v5_gn_6_75760' => 'lsa', 'Lsat_1_v5_gn_6_75800' => 'lsa', 'Lsat_1_v5_gn_6_75900' => 'lsa', 'Lsat_1_v5_gn_6_76240' => 'lsa', 'Lsat_1_v5_gn_6_76441' => 'lsa', 'Lsat_1_v5_gn_6_76700' => 'lsa', 'Lsat_1_v5_gn_6_76760' => 'lsa', 'Manes.15G033100' => 'mes', 'Mapoly0004s0074' => 'mpo', 'Mapoly0004s0075' => 'mpo', 'Mapoly0004s0163' => 'mpo', 'Mapoly0004s0164' => 'mpo', 'Mapoly0021s0018' => 'mpo', 'Mapoly0041s0136' => 'mpo', 'Mapoly0041s0137' => 'mpo', 'Mapoly0041s0138' => 'mpo', 'Mapoly0041s0139' => 'mpo', 'Mapoly0041s0141' => 'mpo', 'Mapoly0041s0142' => 'mpo', 'Mapoly0041s0143' => 'mpo', 'Mapoly0041s0144' => 'mpo', 'Mapoly0041s0145' => 'mpo', 'Mapoly0047s0106' => 'mpo', 'Mapoly0047s0108' => 'mpo', 'Mapoly0050s0051' => 'mpo', 'Mapoly0050s0052' => 'mpo', 'Mapoly0050s0053' => 'mpo', 'Mapoly0058s0013' => 'mpo', 'Mapoly0091s0078' => 'mpo', 'Mapoly0091s0079' => 'mpo', 'Mapoly0091s0080' => 'mpo', 'Mapoly0091s0081' => 'mpo', 'Mapoly0278s0004' => 'mpo', 'Mapoly0278s0005' => 'mpo', 'Mapoly0278s0006' => 'mpo', 'MBI11_g30648_MAGBIO' => 'mbi', 'MCO03G194' => 'mco', 'MCO03G590' => 'mco', 'MCO07G312' => 'mco', 'MCO10G318' => 'mco', 'MCO12G244' => 'mco', 'MCO13G148' => 'mco', 'MCO13G194' => 'mco', 'MCO16G238' => 'mco', 'MD06G1134100' => 'mdo', 'MD13G1200100' => 'mdo', 'MD13G1200300' => 'mdo', 'MD13G1200600' => 'mdo', 'MD14G1150400' => 'mdo', 'MD16G1200000' => 'mdo', 'Medtr1g102570' => 'mtr', 'Medtr1g102780' => 'mtr', 'Medtr1g102800' => 'mtr', 'Medtr1g102810' => 'mtr', 'Medtr1g102830' => 'mtr', 'MELO3C006499.2' => 'cme', 'Migut.G00385' => 'egut', 'MSTRG.4063' => 'ama', 'Nitab4.5_0000090g0260' => 'nta', 'Nitab4.5_0000977g0030' => 'nta', 'Nitab4.5_0002541g0040' => 'nta', 'Nitab4.5_0007068g0040' => 'nta', 'Nn005s41408' => 'nnu', 'Nn005s41410' => 'nnu', 'Oeu010310.1' => 'oeu', 'Oeu010311.1' => 'oeu', 'Oeu043472.1' => 'oeu', 'Os01g0246400' => 'osa', 'Os04g0267950' => 'osa', 'Os07g0178700' => 'osa', 'Os07g0178800' => 'osa', 'Peaxi162Scf00316g00046' => 'pax', 'Peaxi162Scf00316g00049' => 'pax', 'Peaxi162Scf00316g00059' => 'pax', 'Peaxi162Scf00316g00328' => 'pax', 'Peaxi162Scf00316g00329' => 'pax', 'Peaxi162Scf00316g00411' => 'pax', 'Peaxi162Scf00316g00521' => 'pax', 'Peaxi162Scf00492g00068' => 'pax', 'Peaxi162Scf35631g00002' => 'pax', 'PGR142G3720' => 'pgr', 'PGSC0003DMG400006442' => 'stu', 'Phvul.007G062000' => 'pvu', 'Potri.008G157750' => 'ptr', 'Potri.008G157900' => 'ptr', 'Potri.008G158000' => 'ptr', 'Potri.008G158200' => 'ptr', 'Pp3c11_7280' => 'ppa', 'Pp3c11_7980' => 'ppa', 'Pp3c12_19450' => 'ppa', 'Pp3c14_1480' => 'ppa', 'Pp3c14_1501' => 'ppa', 'Pp3c16_4900' => 'ppa', 'Pp3c16_5010' => 'ppa', 'Pp3c16_5060' => 'ppa', 'Pp3c19_18250' => 'ppa', 'Pp3c23_8530' => 'ppa', 'Pp3c23_8550' => 'ppa', 'Pp3c24_9670' => 'ppa', 'Pp3c2_21390' => 'ppa', 'Pp3c2_31380' => 'ppa', 'Pp3c3_16620' => 'ppa', 'Pp3c3_8090' => 'ppa', 'Pp3c3_8110' => 'ppa', 'Pp3c3_8130' => 'ppa', 'Pp3c3_8150' => 'ppa', 'Pp3c4_14320' => 'ppa', 'Pp3c6_2560' => 'ppa', 'Pp3c9_16700' => 'ppa', 'PRCOL_00000234' => 'pco', 'PRCOL_00000235' => 'pco', 'PRCOL_00000777' => 'pco', 'PRCOL_00002344' => 'pco', 'PRCOL_00002372' => 'pco', 'PRCOL_00006120' => 'pco', 'Prupe.1G021400' => 'ppe', 'Prupe.1G021500' => 'ppe', 'Prupe.1G021600' => 'ppe', 'Prupe.1G021700' => 'ppe', 'Prupe.1G021800' => 'ppe', 'Prupe.5G145100' => 'ppe', 'Psat6g204040' => 'psa', 'Psat6g204800' => 'psa', 'Psat6g204920' => 'psa', 'Psat6g204960' => 'psa', 'Psat6g205080' => 'psa', 'PSO017G0271' => 'pso', 'PSO017G1276' => 'pso', 'PSO017G1429' => 'pso', 'PSO017G1861' => 'pso', 'PSO017G2787' => 'pso', 'PSO017G4466' => 'pso', 'PSO017G5118' => 'pso', 'PSO017G5420' => 'pso', 'PSO063G3678' => 'pso', 'PSO210G0546' => 'pso', 'PSO317G0001' => 'pso', 'PSO357G0512' => 'pso', 'PSO478G2682' => 'pso', 'PSO647G0001' => 'pso', 'PSO675G0001' => 'pso', 'PSO675G2699' => 'pso', 'PSO675G2849' => 'pso', 'PSO675G4991' => 'pso', 'PSO689G0001' => 'pso', 'QL06p000916' => 'qlo', 'QL06p000921' => 'qlo', 'QL06p001398' => 'qlo', 'QL06p001407' => 'qlo', 'QL06p002031' => 'qlo', 'RcHm_v2.0_Chr4g0387791' => 'rch', 'RcHm_v2.0_Chr4g0387801' => 'rch', 'RcHm_v2.0_Chr6g0286501' => 'rch', 'RcHm_v2.0_Chr6g0286511' => 'rch', 'RcHm_v2.0_Chr6g0286521' => 'rch', 'RcHm_v2.0_Chr6g0286531' => 'rch', 'RcHm_v2.0_Chr7g0189141' => 'rch', 'Rhsim02G0028700' => 'rsi', 'Rhsim02G0028800' => 'rsi', 'Rhsim02G0028900' => 'rsi', 'Rhsim02G0029000' => 'rsi', 'Rhsim02G0029100' => 'rsi', 'Rhsim02G0029200' => 'rsi', 'Rhsim02G0029300' => 'rsi', 'Rhsim02G0029400' => 'rsi', 'Rhsim02G0029500' => 'rsi', 'Rhsim02G0029600' => 'rsi', 'RhsimUnG0024000' => 'rsi', 'RhsimUnG0024100' => 'rsi', 'RhsimUnG0024200' => 'rsi', 'RhsimUnG0024300' => 'rsi', 'RhsimUnG0024400' => 'rsi', 'RhsimUnG0024500' => 'rsi', 'RhsimUnG0024700' => 'rsi', 'RhsimUnG0024800' => 'rsi', 'RhsimUnG0024900' => 'rsi', 'RhsimUnG0025100' => 'rsi', 'Sabra08G0120200' => 'sbr', 'Sabra08G0120300' => 'sbr', 'Sabra08G0120500' => 'sbr', 'Sabra08G0120600' => 'sbr', 'Sabra10G0158900' => 'sbr', 'SalBow2G3492' => 'sbo', 'Sc13g0004760' => 'sci', 'Sc13g0004770' => 'sci', 'Sed0003417' => 'sed', 'Sed0019750' => 'sed', 'SEGI_03419' => 'sgi', 'SEGI_05907' => 'sgi', 'SEGI_10682' => 'sgi', 'SEGI_13528' => 'sgi', 'SEGI_16081' => 'sgi', 'SEGI_19370' => 'sgi', 'SEGI_21015' => 'sgi', 'SEGI_21944' => 'sgi', 'SEGI_32906' => 'sgi', 'SEGI_33093' => 'sgi', 'SEGI_36110' => 'sgi', 'SEGI_40397' => 'sgi', 'SGA_v2.0_scaffold191G40426' => 'sas', 'SGA_v2.0_scaffold353G49717' => 'sas', 'SGA_v2.0_scaffold50G18550' => 'sas', 'SMO119G0173' => 'smo', 'SMO172G0002' => 'smo', 'Solyc09g082690.3' => 'sly', 'Solyc09g082700.2' => 'sly', 'Sopen09g031550' => 'spe', 'Sopen09g031560' => 'spe', 'Sp3g20540' => 'spa', 'Sp7g07580' => 'spa', 'TAR134G0002' => 'tar', 'TAR236G0001' => 'tar', 'TAR365G0892' => 'tar', 'TAR636G0166' => 'tar', 'TAR636G0646' => 'tar', 'TAR636G0869' => 'tar', 'TAR636G1317' => 'tar', 'TAR636G1744' => 'tar', 'TAR636G3358' => 'tar', 'TAR636G3436' => 'tar', 'THA.LOC104803047' => 'tha', 'Thecc.04G238900' => 'tca', 'Thhalv10021557m.g' => 'esa', 'Thhalv10026318m.g' => 'esa', 'Thhalv10026335m.g' => 'esa', 'TPR.G17433' => 'tpr', 'TPR.G18915' => 'tpr', 'TPR.G26125' => 'tpr', 'TWI09G0677' => 'twi', 'TWI73G0287' => 'twi', 'unitig_748.g8326' => 'ugi', 'vmacro15370' => 'vma', 'vmacro15371' => 'vma', 'vmacro15372' => 'vma', 'vmacro15373' => 'vma', 'vmacro15374' => 'vma', 'VMungo0720G2826' => 'vmu', 'Zm00001eb116960' => 'zma', 'Zm00001eb301260' => 'zma', 'Zm00001eb301270' => 'zma' ) $gf_id = 'HOM05D001460' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001460' ) $data_identifier = 'HOM05D001460' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 4, 'aag' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 2, 'aox' => (int) 2, 'arhy' => (int) 4, 'ath' => (int) 2, 'atr' => (int) 1, 'acertr' => (int) 10, 'cqu' => (int) 4, 'bca' => (int) 11, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 1, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 1, 'ccan' => (int) 1, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 1, 'col' => (int) 1, 'cpa' => (int) 1, 'cre' => (int) 7, 'csa' => (int) 1, 'camsi' => (int) 2, 'dca' => (int) 3, 'din' => (int) 2, 'dzi' => (int) 3, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 14, 'fve' => (int) 9, 'gma' => (int) 2, 'ghi' => (int) 4, 'gra' => (int) 2, 'vvi' => (int) 1, 'han' => (int) 13, 'cav' => (int) 1, 'hma' => (int) 2, 'sun' => (int) 2, 'lal' => (int) 2, 'lonja' => (int) 12, 'lja' => (int) 1, 'lsa' => (int) 7, 'mes' => (int) 1, 'mpo' => (int) 27, 'mbi' => (int) 1, 'mco' => (int) 8, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 1, 'egut' => (int) 1, 'ama' => (int) 1, 'nta' => (int) 4, 'nnu' => (int) 2, 'oeu' => (int) 3, 'osa' => (int) 4, 'pax' => (int) 9, 'pgr' => (int) 1, 'stu' => (int) 1, 'pvu' => (int) 1, 'ptr' => (int) 4, 'ppa' => (int) 22, 'pco' => (int) 6, 'ppe' => (int) 6, 'psa' => (int) 5, 'pso' => (int) 19, 'qlo' => (int) 5, 'rch' => (int) 7, 'rsi' => (int) 20, 'sbr' => (int) 5, 'sbo' => (int) 1, 'sci' => (int) 2, 'sed' => (int) 2, 'sgi' => (int) 12, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 2, 'tar' => (int) 10, 'tha' => (int) 1, 'tca' => (int) 1, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 2, 'ugi' => (int) 1, 'vma' => (int) 5, 'vmu' => (int) 1, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb301270' $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' => 'HOM05D001460', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '433', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p22980' => 'bna', 'A01p32340' => 'bna', 'A03p42970' => 'bna', 'A05p25880' => 'bna', 'Aa31LG8G9320' => 'aar', 'Aa31LG8G9330' => 'aar', 'Aa31LG8G9340' => 'aar', 'Aa31sc221G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1034' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1528' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.829' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2222' => 'aag', 'Ah.12g058830' => 'amhyb', 'Ah.12g058840' => 'amhyb', 'AL3G37160' => 'aly', 'AL7G41310' => 'aly', 'Aqoxy5G00395' => 'aox', 'Aqoxy5G00396' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0C8NZA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5185HY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JZ1PRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MD3LS0' => 'arhy', 'AT3G22840' => 'ath', 'AT4G14690' => 'ath', 'ATR0665G054' => 'atr', 'Atru.chr4.2344' => 'acertr', 'Atru.chr4.2346' => 'acertr', 'Atru.chr4.2347' => 'acertr', 'Atru.chr4.2348' => 'acertr', 'Atru.chr4.2355' => 'acertr', 'Atru.chr4.2356' => 'acertr', 'Atru.chr4.2358' => 'acertr', 'Atru.chr4.2359' => 'acertr', 'Atru.chr4.2360' => 'acertr', 'Atru.chr4.2361' => 'acertr', 'AUR62030476' => 'cqu', 'AUR62030478' => 'cqu', 'AUR62030819' => 'cqu', 'AUR62030820' => 'cqu', 'BcaB03g14648' => 'bca', 'BcaB04g20492' => 'bca', 'BcaB06g26399' => 'bca', 'BcaC01g03416' => 'bca', 'BcaC01g03419' => 'bca', 'BcaC01g03421' => 'bca', 'BcaC01g03424' => 'bca', 'BcaC05g28012' => 'bca', 'BcaC09g49212' => 'bca', 'BcaC09g50140' => 'bca', 'BcaNung00346' => 'bca', 'BolC1t02785H' => 'bol', 'BolC1t04095H' => 'bol', 'BolC3t17545H' => 'bol', 'BolC5t32769H' => 'bol', 'BraA01t02211Z' => 'bra', 'BraA01t03359Z' => 'bra', 'BraA03t13441Z' => 'bra', 'BraA05t21476Z' => 'bra', 'C01p28420' => 'bna', 'C01p41350' => 'bna', 'C03p52750' => 'bna', 'C03p52780' => 'bna', 'C05p40270' => 'bna', 'CAN.G1437.9' => 'can', 'CANSAT78G0035' => 'cansat', 'CANSAT78G1036' => 'cansat', 'CANSAT78G2272' => 'cansat', 'CANSAT78G2478' => 'cansat', 'CARHR098700' => 'chi', 'CARHR221120' => 'chi', 'CARHR221150' => 'chi', 'Carub.0003s2297' => 'cru', 'Carub.0007s2749' => 'cru', 'Carub.0007s2750' => 'cru', 'Carub.0007s2751' => 'cru', 'Ca_10849_v3' => 'car', 'Cc03_g04300' => 'ccan', 'CDE02G3648' => 'cde', 'CDE05G0060' => 'cde', 'CDE05G0692' => 'cde', 'CDE05G2285' => 'cde', 'CDE05G2884' => 'cde', 'CDE05G3072' => 'cde', 'Cfa008439' => 'cfa', 'Cfa008441' => 'cfa', 'Cfa008443' => 'cfa', 'Cfa008448' => 'cfa', 'Ciclev10005974m.g' => 'ccl', 'Ciclev10006006m.g' => 'ccl', 'Ciclev10006775m.g' => 'ccl', 'CiPaw.02G120400' => 'cil', 'CiPaw.02G120500' => 'cil', 'CiPaw.02G120600' => 'cil', 'ClCG05G004850' => 'cla', 'COL.COLO4_21566' => 'col', 'Cpa.g.sc44.124' => 'cpa', 'Cre07.g320400' => 'cre', 'Cre07.g320450' => 'cre', 'Cre08.g384650' => 'cre', 'Cre09.g393173' => 'cre', 'Cre09.g394325' => 'cre', 'Cre14.g626750' => 'cre', 'Cre16.g679250' => 'cre', 'CsaV3_3G012890' => 'csa', 'CSS0010865' => 'camsi', 'CSS0044338' => 'camsi', 'DCAR_002366' => 'dca', 'DCAR_030687' => 'dca', 'DCAR_030688' => 'dca', 'Dinv14047' => 'din', 'Dinv14048' => 'din', 'Duzib151G0105' => 'dzi', 'Duzib151G0114' => 'dzi', 'Duzib212G1029' => 'dzi', 'ECA232G3536' => 'eca', 'ECA240G0786' => 'eca', 'ECA240G1802' => 'eca', 'ECA240G3760' => 'eca', 'ECA240G3920' => 'eca', 'EL10Ac5g12536' => 'bvu', 'EL10Ac5g12537' => 'bvu', 'EL10Ac5g12538' => 'bvu', 'Eucgr.B01004' => 'egr', 'Eucgr.B01006' => 'egr', 'Eucgr.B01007' => 'egr', 'Eucgr.B01008' => 'egr', 'Eucgr.B01895' => 'egr', 'Eucgr.B01896' => 'egr', 'FAN04G1456' => 'fan', 'FAN08G1769' => 'fan', 'FAN08G2160' => 'fan', 'FAN13G2403' => 'fan', 'FAN13G3303' => 'fan', 'FAN15G2435' => 'fan', 'FAN17G0672' => 'fan', 'FAN17G2441' => 'fan', 'FAN18G1024' => 'fan', 'FAN22G1458' => 'fan', 'FAN24G0037' => 'fan', 'FAN24G0429' => 'fan', 'FAN24G2387' => 'fan', 'FAN27G2746' => 'fan', 'FvH4_2g20400' => 'fve', 'FvH4_2g20420' => 'fve', 'FvH4_2g20430' => 'fve', 'FvH4_4g01270' => 'fve', 'FvH4_4g01290' => 'fve', 'FvH4_4g01300' => 'fve', 'FvH4_4g01310' => 'fve', 'FvH4_4g01330' => 'fve', 'FvH4_5g09070' => 'fve', 'Glyma.10G243800' => 'gma', 'Glyma.20G150600' => 'gma', 'Gohir.A09G219200' => 'ghi', 'Gohir.A09G219300' => 'ghi', 'Gohir.D09G221400' => 'ghi', 'Gohir.D09G221500' => 'ghi', 'Gorai.006G242600' => 'gra', 'Gorai.006G242700' => 'gra', 'GSVIVG01018044001' => 'vvi', 'HanXRQChr03g0083821' => 'han', 'HanXRQChr03g0083841' => 'han', 'HanXRQChr03g0083881' => 'han', 'HanXRQChr03g0083901' => 'han', 'HanXRQChr03g0083921' => 'han', 'HanXRQChr03g0085331' => 'han', 'HanXRQChr03g0085361' => 'han', 'HanXRQChr03g0085411' => 'han', 'HanXRQChr03g0085421' => 'han', 'HanXRQChr03g0085431' => 'han', 'HanXRQChr08g0221991' => 'han', 'HanXRQChr11g0336061' => 'han', 'HanXRQChr11g0336411' => 'han', 'Haze_11234' => 'cav', 'Hma1.2p1_0549F.1_g177010' => 'hma', 'Hma1.2p1_0602F.1_g187630' => 'hma', 'Hund14876' => 'sun', 'Hund14879' => 'sun', 'Lalb_Chr06g0160741' => 'lal', 'Lalb_Chr21g0304781' => 'lal', 'Lj3A726G19' => 'lonja', 'Lj3A726T23' => 'lonja', 'Lj3A726T24' => 'lonja', 'Lj3A726T25' => 'lonja', 'Lj3A727T17' => 'lonja', 'Lj3C726T0' => 'lonja', 'Lj3C726T2' => 'lonja', 'Lj3P725T35' => 'lonja', 'Lj3P727T10' => 'lonja', 'Lj3P727T12' => 'lonja', 'Lj3P727T14' => 'lonja', 'Lj5g0023109' => 'lja', 'Lj6P646T44' => 'lonja', 'Lsat_1_v5_gn_6_75760' => 'lsa', 'Lsat_1_v5_gn_6_75800' => 'lsa', 'Lsat_1_v5_gn_6_75900' => 'lsa', 'Lsat_1_v5_gn_6_76240' => 'lsa', 'Lsat_1_v5_gn_6_76441' => 'lsa', 'Lsat_1_v5_gn_6_76700' => 'lsa', 'Lsat_1_v5_gn_6_76760' => 'lsa', 'Manes.15G033100' => 'mes', 'Mapoly0004s0074' => 'mpo', 'Mapoly0004s0075' => 'mpo', 'Mapoly0004s0163' => 'mpo', 'Mapoly0004s0164' => 'mpo', 'Mapoly0021s0018' => 'mpo', 'Mapoly0041s0136' => 'mpo', 'Mapoly0041s0137' => 'mpo', 'Mapoly0041s0138' => 'mpo', 'Mapoly0041s0139' => 'mpo', 'Mapoly0041s0141' => 'mpo', 'Mapoly0041s0142' => 'mpo', 'Mapoly0041s0143' => 'mpo', 'Mapoly0041s0144' => 'mpo', 'Mapoly0041s0145' => 'mpo', 'Mapoly0047s0106' => 'mpo', 'Mapoly0047s0108' => 'mpo', 'Mapoly0050s0051' => 'mpo', 'Mapoly0050s0052' => 'mpo', 'Mapoly0050s0053' => 'mpo', 'Mapoly0058s0013' => 'mpo', 'Mapoly0091s0078' => 'mpo', 'Mapoly0091s0079' => 'mpo', 'Mapoly0091s0080' => 'mpo', 'Mapoly0091s0081' => 'mpo', 'Mapoly0278s0004' => 'mpo', 'Mapoly0278s0005' => 'mpo', 'Mapoly0278s0006' => 'mpo', 'MBI11_g30648_MAGBIO' => 'mbi', 'MCO03G194' => 'mco', 'MCO03G590' => 'mco', 'MCO07G312' => 'mco', 'MCO10G318' => 'mco', 'MCO12G244' => 'mco', 'MCO13G148' => 'mco', 'MCO13G194' => 'mco', 'MCO16G238' => 'mco', 'MD06G1134100' => 'mdo', 'MD13G1200100' => 'mdo', 'MD13G1200300' => 'mdo', 'MD13G1200600' => 'mdo', 'MD14G1150400' => 'mdo', 'MD16G1200000' => 'mdo', 'Medtr1g102570' => 'mtr', 'Medtr1g102780' => 'mtr', 'Medtr1g102800' => 'mtr', 'Medtr1g102810' => 'mtr', 'Medtr1g102830' => 'mtr', 'MELO3C006499.2' => 'cme', 'Migut.G00385' => 'egut', 'MSTRG.4063' => 'ama', 'Nitab4.5_0000090g0260' => 'nta', 'Nitab4.5_0000977g0030' => 'nta', 'Nitab4.5_0002541g0040' => 'nta', 'Nitab4.5_0007068g0040' => 'nta', 'Nn005s41408' => 'nnu', 'Nn005s41410' => 'nnu', 'Oeu010310.1' => 'oeu', 'Oeu010311.1' => 'oeu', 'Oeu043472.1' => 'oeu', 'Os01g0246400' => 'osa', 'Os04g0267950' => 'osa', 'Os07g0178700' => 'osa', 'Os07g0178800' => 'osa', 'Peaxi162Scf00316g00046' => 'pax', 'Peaxi162Scf00316g00049' => 'pax', 'Peaxi162Scf00316g00059' => 'pax', 'Peaxi162Scf00316g00328' => 'pax', 'Peaxi162Scf00316g00329' => 'pax', 'Peaxi162Scf00316g00411' => 'pax', 'Peaxi162Scf00316g00521' => 'pax', 'Peaxi162Scf00492g00068' => 'pax', 'Peaxi162Scf35631g00002' => 'pax', 'PGR142G3720' => 'pgr', 'PGSC0003DMG400006442' => 'stu', 'Phvul.007G062000' => 'pvu', 'Potri.008G157750' => 'ptr', 'Potri.008G157900' => 'ptr', 'Potri.008G158000' => 'ptr', 'Potri.008G158200' => 'ptr', 'Pp3c11_7280' => 'ppa', 'Pp3c11_7980' => 'ppa', 'Pp3c12_19450' => 'ppa', 'Pp3c14_1480' => 'ppa', 'Pp3c14_1501' => 'ppa', 'Pp3c16_4900' => 'ppa', 'Pp3c16_5010' => 'ppa', 'Pp3c16_5060' => 'ppa', 'Pp3c19_18250' => 'ppa', 'Pp3c23_8530' => 'ppa', 'Pp3c23_8550' => 'ppa', 'Pp3c24_9670' => 'ppa', 'Pp3c2_21390' => 'ppa', 'Pp3c2_31380' => 'ppa', 'Pp3c3_16620' => 'ppa', 'Pp3c3_8090' => 'ppa', 'Pp3c3_8110' => 'ppa', 'Pp3c3_8130' => 'ppa', 'Pp3c3_8150' => 'ppa', 'Pp3c4_14320' => 'ppa', 'Pp3c6_2560' => 'ppa', 'Pp3c9_16700' => 'ppa', 'PRCOL_00000234' => 'pco', 'PRCOL_00000235' => 'pco', 'PRCOL_00000777' => 'pco', 'PRCOL_00002344' => 'pco', 'PRCOL_00002372' => 'pco', 'PRCOL_00006120' => 'pco', 'Prupe.1G021400' => 'ppe', 'Prupe.1G021500' => 'ppe', 'Prupe.1G021600' => 'ppe', 'Prupe.1G021700' => 'ppe', 'Prupe.1G021800' => 'ppe', 'Prupe.5G145100' => 'ppe', 'Psat6g204040' => 'psa', 'Psat6g204800' => 'psa', 'Psat6g204920' => 'psa', 'Psat6g204960' => 'psa', 'Psat6g205080' => 'psa', 'PSO017G0271' => 'pso', 'PSO017G1276' => 'pso', 'PSO017G1429' => 'pso', 'PSO017G1861' => 'pso', 'PSO017G2787' => 'pso', 'PSO017G4466' => 'pso', 'PSO017G5118' => 'pso', 'PSO017G5420' => 'pso', 'PSO063G3678' => 'pso', 'PSO210G0546' => 'pso', 'PSO317G0001' => 'pso', 'PSO357G0512' => 'pso', 'PSO478G2682' => 'pso', 'PSO647G0001' => 'pso', 'PSO675G0001' => 'pso', 'PSO675G2699' => 'pso', 'PSO675G2849' => 'pso', 'PSO675G4991' => 'pso', 'PSO689G0001' => 'pso', 'QL06p000916' => 'qlo', 'QL06p000921' => 'qlo', 'QL06p001398' => 'qlo', 'QL06p001407' => 'qlo', 'QL06p002031' => 'qlo', 'RcHm_v2.0_Chr4g0387791' => 'rch', 'RcHm_v2.0_Chr4g0387801' => 'rch', 'RcHm_v2.0_Chr6g0286501' => 'rch', 'RcHm_v2.0_Chr6g0286511' => 'rch', 'RcHm_v2.0_Chr6g0286521' => 'rch', 'RcHm_v2.0_Chr6g0286531' => 'rch', 'RcHm_v2.0_Chr7g0189141' => 'rch', 'Rhsim02G0028700' => 'rsi', 'Rhsim02G0028800' => 'rsi', 'Rhsim02G0028900' => 'rsi', 'Rhsim02G0029000' => 'rsi', 'Rhsim02G0029100' => 'rsi', 'Rhsim02G0029200' => 'rsi', 'Rhsim02G0029300' => 'rsi', 'Rhsim02G0029400' => 'rsi', 'Rhsim02G0029500' => 'rsi', 'Rhsim02G0029600' => 'rsi', 'RhsimUnG0024000' => 'rsi', 'RhsimUnG0024100' => 'rsi', 'RhsimUnG0024200' => 'rsi', 'RhsimUnG0024300' => 'rsi', 'RhsimUnG0024400' => 'rsi', 'RhsimUnG0024500' => 'rsi', 'RhsimUnG0024700' => 'rsi', 'RhsimUnG0024800' => 'rsi', 'RhsimUnG0024900' => 'rsi', 'RhsimUnG0025100' => 'rsi', 'Sabra08G0120200' => 'sbr', 'Sabra08G0120300' => 'sbr', 'Sabra08G0120500' => 'sbr', 'Sabra08G0120600' => 'sbr', 'Sabra10G0158900' => 'sbr', 'SalBow2G3492' => 'sbo', 'Sc13g0004760' => 'sci', 'Sc13g0004770' => 'sci', 'Sed0003417' => 'sed', 'Sed0019750' => 'sed', 'SEGI_03419' => 'sgi', 'SEGI_05907' => 'sgi', 'SEGI_10682' => 'sgi', 'SEGI_13528' => 'sgi', 'SEGI_16081' => 'sgi', 'SEGI_19370' => 'sgi', 'SEGI_21015' => 'sgi', 'SEGI_21944' => 'sgi', 'SEGI_32906' => 'sgi', 'SEGI_33093' => 'sgi', 'SEGI_36110' => 'sgi', 'SEGI_40397' => 'sgi', 'SGA_v2.0_scaffold191G40426' => 'sas', 'SGA_v2.0_scaffold353G49717' => 'sas', 'SGA_v2.0_scaffold50G18550' => 'sas', 'SMO119G0173' => 'smo', 'SMO172G0002' => 'smo', 'Solyc09g082690.3' => 'sly', 'Solyc09g082700.2' => 'sly', 'Sopen09g031550' => 'spe', 'Sopen09g031560' => 'spe', 'Sp3g20540' => 'spa', 'Sp7g07580' => 'spa', 'TAR134G0002' => 'tar', 'TAR236G0001' => 'tar', 'TAR365G0892' => 'tar', 'TAR636G0166' => 'tar', 'TAR636G0646' => 'tar', 'TAR636G0869' => 'tar', 'TAR636G1317' => 'tar', 'TAR636G1744' => 'tar', 'TAR636G3358' => 'tar', 'TAR636G3436' => 'tar', 'THA.LOC104803047' => 'tha', 'Thecc.04G238900' => 'tca', 'Thhalv10021557m.g' => 'esa', 'Thhalv10026318m.g' => 'esa', 'Thhalv10026335m.g' => 'esa', 'TPR.G17433' => 'tpr', 'TPR.G18915' => 'tpr', 'TPR.G26125' => 'tpr', 'TWI09G0677' => 'twi', 'TWI73G0287' => 'twi', 'unitig_748.g8326' => 'ugi', 'vmacro15370' => 'vma', 'vmacro15371' => 'vma', 'vmacro15372' => 'vma', 'vmacro15373' => 'vma', 'vmacro15374' => 'vma', 'VMungo0720G2826' => 'vmu', 'Zm00001eb116960' => 'zma', 'Zm00001eb301260' => 'zma', 'Zm00001eb301270' => 'zma' ), 'gf_id' => 'HOM05D001460', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001460' ), 'data_identifier' => 'HOM05D001460', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001460', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '433', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p22980' => 'bna', 'A01p32340' => 'bna', 'A03p42970' => 'bna', 'A05p25880' => 'bna', 'Aa31LG8G9320' => 'aar', 'Aa31LG8G9330' => 'aar', 'Aa31LG8G9340' => 'aar', 'Aa31sc221G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1034' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1528' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.829' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2222' => 'aag', 'Ah.12g058830' => 'amhyb', 'Ah.12g058840' => 'amhyb', 'AL3G37160' => 'aly', 'AL7G41310' => 'aly', 'Aqoxy5G00395' => 'aox', 'Aqoxy5G00396' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0C8NZA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5185HY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JZ1PRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MD3LS0' => 'arhy', 'AT3G22840' => 'ath', 'AT4G14690' => 'ath', 'ATR0665G054' => 'atr', 'Atru.chr4.2344' => 'acertr', 'Atru.chr4.2346' => 'acertr', 'Atru.chr4.2347' => 'acertr', 'Atru.chr4.2348' => 'acertr', 'Atru.chr4.2355' => 'acertr', 'Atru.chr4.2356' => 'acertr', 'Atru.chr4.2358' => 'acertr', 'Atru.chr4.2359' => 'acertr', 'Atru.chr4.2360' => 'acertr', 'Atru.chr4.2361' => 'acertr', 'AUR62030476' => 'cqu', 'AUR62030478' => 'cqu', 'AUR62030819' => 'cqu', 'AUR62030820' => 'cqu', 'BcaB03g14648' => 'bca', 'BcaB04g20492' => 'bca', 'BcaB06g26399' => 'bca', 'BcaC01g03416' => 'bca', 'BcaC01g03419' => 'bca', 'BcaC01g03421' => 'bca', 'BcaC01g03424' => 'bca', 'BcaC05g28012' => 'bca', 'BcaC09g49212' => 'bca', 'BcaC09g50140' => 'bca', 'BcaNung00346' => 'bca', 'BolC1t02785H' => 'bol', 'BolC1t04095H' => 'bol', 'BolC3t17545H' => 'bol', 'BolC5t32769H' => 'bol', 'BraA01t02211Z' => 'bra', 'BraA01t03359Z' => 'bra', 'BraA03t13441Z' => 'bra', 'BraA05t21476Z' => 'bra', 'C01p28420' => 'bna', 'C01p41350' => 'bna', 'C03p52750' => 'bna', 'C03p52780' => 'bna', 'C05p40270' => 'bna', 'CAN.G1437.9' => 'can', 'CANSAT78G0035' => 'cansat', 'CANSAT78G1036' => 'cansat', 'CANSAT78G2272' => 'cansat', 'CANSAT78G2478' => 'cansat', 'CARHR098700' => 'chi', 'CARHR221120' => 'chi', 'CARHR221150' => 'chi', 'Carub.0003s2297' => 'cru', 'Carub.0007s2749' => 'cru', 'Carub.0007s2750' => 'cru', 'Carub.0007s2751' => 'cru', 'Ca_10849_v3' => 'car', 'Cc03_g04300' => 'ccan', 'CDE02G3648' => 'cde', 'CDE05G0060' => 'cde', 'CDE05G0692' => 'cde', 'CDE05G2285' => 'cde', 'CDE05G2884' => 'cde', 'CDE05G3072' => 'cde', 'Cfa008439' => 'cfa', 'Cfa008441' => 'cfa', 'Cfa008443' => 'cfa', 'Cfa008448' => 'cfa', 'Ciclev10005974m.g' => 'ccl', 'Ciclev10006006m.g' => 'ccl', 'Ciclev10006775m.g' => 'ccl', 'CiPaw.02G120400' => 'cil', 'CiPaw.02G120500' => 'cil', 'CiPaw.02G120600' => 'cil', 'ClCG05G004850' => 'cla', 'COL.COLO4_21566' => 'col', 'Cpa.g.sc44.124' => 'cpa', 'Cre07.g320400' => 'cre', 'Cre07.g320450' => 'cre', 'Cre08.g384650' => 'cre', 'Cre09.g393173' => 'cre', 'Cre09.g394325' => 'cre', 'Cre14.g626750' => 'cre', 'Cre16.g679250' => 'cre', 'CsaV3_3G012890' => 'csa', 'CSS0010865' => 'camsi', 'CSS0044338' => 'camsi', 'DCAR_002366' => 'dca', 'DCAR_030687' => 'dca', 'DCAR_030688' => 'dca', 'Dinv14047' => 'din', 'Dinv14048' => 'din', 'Duzib151G0105' => 'dzi', 'Duzib151G0114' => 'dzi', 'Duzib212G1029' => 'dzi', 'ECA232G3536' => 'eca', 'ECA240G0786' => 'eca', 'ECA240G1802' => 'eca', 'ECA240G3760' => 'eca', 'ECA240G3920' => 'eca', 'EL10Ac5g12536' => 'bvu', 'EL10Ac5g12537' => 'bvu', 'EL10Ac5g12538' => 'bvu', 'Eucgr.B01004' => 'egr', 'Eucgr.B01006' => 'egr', 'Eucgr.B01007' => 'egr', 'Eucgr.B01008' => 'egr', 'Eucgr.B01895' => 'egr', 'Eucgr.B01896' => 'egr', 'FAN04G1456' => 'fan', 'FAN08G1769' => 'fan', 'FAN08G2160' => 'fan', 'FAN13G2403' => 'fan', 'FAN13G3303' => 'fan', 'FAN15G2435' => 'fan', 'FAN17G0672' => 'fan', 'FAN17G2441' => 'fan', 'FAN18G1024' => 'fan', 'FAN22G1458' => 'fan', 'FAN24G0037' => 'fan', 'FAN24G0429' => 'fan', 'FAN24G2387' => 'fan', 'FAN27G2746' => 'fan', 'FvH4_2g20400' => 'fve', 'FvH4_2g20420' => 'fve', 'FvH4_2g20430' => 'fve', 'FvH4_4g01270' => 'fve', 'FvH4_4g01290' => 'fve', 'FvH4_4g01300' => 'fve', 'FvH4_4g01310' => 'fve', 'FvH4_4g01330' => 'fve', 'FvH4_5g09070' => 'fve', 'Glyma.10G243800' => 'gma', 'Glyma.20G150600' => 'gma', 'Gohir.A09G219200' => 'ghi', 'Gohir.A09G219300' => 'ghi', 'Gohir.D09G221400' => 'ghi', 'Gohir.D09G221500' => 'ghi', 'Gorai.006G242600' => 'gra', 'Gorai.006G242700' => 'gra', 'GSVIVG01018044001' => 'vvi', 'HanXRQChr03g0083821' => 'han', 'HanXRQChr03g0083841' => 'han', 'HanXRQChr03g0083881' => 'han', 'HanXRQChr03g0083901' => 'han', 'HanXRQChr03g0083921' => 'han', 'HanXRQChr03g0085331' => 'han', 'HanXRQChr03g0085361' => 'han', 'HanXRQChr03g0085411' => 'han', 'HanXRQChr03g0085421' => 'han', 'HanXRQChr03g0085431' => 'han', 'HanXRQChr08g0221991' => 'han', 'HanXRQChr11g0336061' => 'han', 'HanXRQChr11g0336411' => 'han', 'Haze_11234' => 'cav', 'Hma1.2p1_0549F.1_g177010' => 'hma', 'Hma1.2p1_0602F.1_g187630' => 'hma', 'Hund14876' => 'sun', 'Hund14879' => 'sun', 'Lalb_Chr06g0160741' => 'lal', 'Lalb_Chr21g0304781' => 'lal', 'Lj3A726G19' => 'lonja', 'Lj3A726T23' => 'lonja', 'Lj3A726T24' => 'lonja', 'Lj3A726T25' => 'lonja', 'Lj3A727T17' => 'lonja', 'Lj3C726T0' => 'lonja', 'Lj3C726T2' => 'lonja', 'Lj3P725T35' => 'lonja', 'Lj3P727T10' => 'lonja', 'Lj3P727T12' => 'lonja', 'Lj3P727T14' => 'lonja', 'Lj5g0023109' => 'lja', 'Lj6P646T44' => 'lonja', 'Lsat_1_v5_gn_6_75760' => 'lsa', 'Lsat_1_v5_gn_6_75800' => 'lsa', 'Lsat_1_v5_gn_6_75900' => 'lsa', 'Lsat_1_v5_gn_6_76240' => 'lsa', 'Lsat_1_v5_gn_6_76441' => 'lsa', 'Lsat_1_v5_gn_6_76700' => 'lsa', 'Lsat_1_v5_gn_6_76760' => 'lsa', 'Manes.15G033100' => 'mes', 'Mapoly0004s0074' => 'mpo', 'Mapoly0004s0075' => 'mpo', 'Mapoly0004s0163' => 'mpo', 'Mapoly0004s0164' => 'mpo', 'Mapoly0021s0018' => 'mpo', 'Mapoly0041s0136' => 'mpo', 'Mapoly0041s0137' => 'mpo', 'Mapoly0041s0138' => 'mpo', 'Mapoly0041s0139' => 'mpo', 'Mapoly0041s0141' => 'mpo', 'Mapoly0041s0142' => 'mpo', 'Mapoly0041s0143' => 'mpo', 'Mapoly0041s0144' => 'mpo', 'Mapoly0041s0145' => 'mpo', 'Mapoly0047s0106' => 'mpo', 'Mapoly0047s0108' => 'mpo', 'Mapoly0050s0051' => 'mpo', 'Mapoly0050s0052' => 'mpo', 'Mapoly0050s0053' => 'mpo', 'Mapoly0058s0013' => 'mpo', 'Mapoly0091s0078' => 'mpo', 'Mapoly0091s0079' => 'mpo', 'Mapoly0091s0080' => 'mpo', 'Mapoly0091s0081' => 'mpo', 'Mapoly0278s0004' => 'mpo', 'Mapoly0278s0005' => 'mpo', 'Mapoly0278s0006' => 'mpo', 'MBI11_g30648_MAGBIO' => 'mbi', 'MCO03G194' => 'mco', 'MCO03G590' => 'mco', 'MCO07G312' => 'mco', 'MCO10G318' => 'mco', 'MCO12G244' => 'mco', 'MCO13G148' => 'mco', 'MCO13G194' => 'mco', 'MCO16G238' => 'mco', 'MD06G1134100' => 'mdo', 'MD13G1200100' => 'mdo', 'MD13G1200300' => 'mdo', 'MD13G1200600' => 'mdo', 'MD14G1150400' => 'mdo', 'MD16G1200000' => 'mdo', 'Medtr1g102570' => 'mtr', 'Medtr1g102780' => 'mtr', 'Medtr1g102800' => 'mtr', 'Medtr1g102810' => 'mtr', 'Medtr1g102830' => 'mtr', 'MELO3C006499.2' => 'cme', 'Migut.G00385' => 'egut', 'MSTRG.4063' => 'ama', 'Nitab4.5_0000090g0260' => 'nta', 'Nitab4.5_0000977g0030' => 'nta', 'Nitab4.5_0002541g0040' => 'nta', 'Nitab4.5_0007068g0040' => 'nta', 'Nn005s41408' => 'nnu', 'Nn005s41410' => 'nnu', 'Oeu010310.1' => 'oeu', 'Oeu010311.1' => 'oeu', 'Oeu043472.1' => 'oeu', 'Os01g0246400' => 'osa', 'Os04g0267950' => 'osa', 'Os07g0178700' => 'osa', 'Os07g0178800' => 'osa', 'Peaxi162Scf00316g00046' => 'pax', 'Peaxi162Scf00316g00049' => 'pax', 'Peaxi162Scf00316g00059' => 'pax', 'Peaxi162Scf00316g00328' => 'pax', 'Peaxi162Scf00316g00329' => 'pax', 'Peaxi162Scf00316g00411' => 'pax', 'Peaxi162Scf00316g00521' => 'pax', 'Peaxi162Scf00492g00068' => 'pax', 'Peaxi162Scf35631g00002' => 'pax', 'PGR142G3720' => 'pgr', 'PGSC0003DMG400006442' => 'stu', 'Phvul.007G062000' => 'pvu', 'Potri.008G157750' => 'ptr', 'Potri.008G157900' => 'ptr', 'Potri.008G158000' => 'ptr', 'Potri.008G158200' => 'ptr', 'Pp3c11_7280' => 'ppa', 'Pp3c11_7980' => 'ppa', 'Pp3c12_19450' => 'ppa', 'Pp3c14_1480' => 'ppa', 'Pp3c14_1501' => 'ppa', 'Pp3c16_4900' => 'ppa', 'Pp3c16_5010' => 'ppa', 'Pp3c16_5060' => 'ppa', 'Pp3c19_18250' => 'ppa', 'Pp3c23_8530' => 'ppa', 'Pp3c23_8550' => 'ppa', 'Pp3c24_9670' => 'ppa', 'Pp3c2_21390' => 'ppa', 'Pp3c2_31380' => 'ppa', 'Pp3c3_16620' => 'ppa', 'Pp3c3_8090' => 'ppa', 'Pp3c3_8110' => 'ppa', 'Pp3c3_8130' => 'ppa', 'Pp3c3_8150' => 'ppa', 'Pp3c4_14320' => 'ppa', 'Pp3c6_2560' => 'ppa', 'Pp3c9_16700' => 'ppa', 'PRCOL_00000234' => 'pco', 'PRCOL_00000235' => 'pco', 'PRCOL_00000777' => 'pco', 'PRCOL_00002344' => 'pco', 'PRCOL_00002372' => 'pco', 'PRCOL_00006120' => 'pco', 'Prupe.1G021400' => 'ppe', 'Prupe.1G021500' => 'ppe', 'Prupe.1G021600' => 'ppe', 'Prupe.1G021700' => 'ppe', 'Prupe.1G021800' => 'ppe', 'Prupe.5G145100' => 'ppe', 'Psat6g204040' => 'psa', 'Psat6g204800' => 'psa', 'Psat6g204920' => 'psa', 'Psat6g204960' => 'psa', 'Psat6g205080' => 'psa', 'PSO017G0271' => 'pso', 'PSO017G1276' => 'pso', 'PSO017G1429' => 'pso', 'PSO017G1861' => 'pso', 'PSO017G2787' => 'pso', 'PSO017G4466' => 'pso', 'PSO017G5118' => 'pso', 'PSO017G5420' => 'pso', 'PSO063G3678' => 'pso', 'PSO210G0546' => 'pso', 'PSO317G0001' => 'pso', 'PSO357G0512' => 'pso', 'PSO478G2682' => 'pso', 'PSO647G0001' => 'pso', 'PSO675G0001' => 'pso', 'PSO675G2699' => 'pso', 'PSO675G2849' => 'pso', 'PSO675G4991' => 'pso', 'PSO689G0001' => 'pso', 'QL06p000916' => 'qlo', 'QL06p000921' => 'qlo', 'QL06p001398' => 'qlo', 'QL06p001407' => 'qlo', 'QL06p002031' => 'qlo', 'RcHm_v2.0_Chr4g0387791' => 'rch', 'RcHm_v2.0_Chr4g0387801' => 'rch', 'RcHm_v2.0_Chr6g0286501' => 'rch', 'RcHm_v2.0_Chr6g0286511' => 'rch', 'RcHm_v2.0_Chr6g0286521' => 'rch', 'RcHm_v2.0_Chr6g0286531' => 'rch', 'RcHm_v2.0_Chr7g0189141' => 'rch', 'Rhsim02G0028700' => 'rsi', 'Rhsim02G0028800' => 'rsi', 'Rhsim02G0028900' => 'rsi', 'Rhsim02G0029000' => 'rsi', 'Rhsim02G0029100' => 'rsi', 'Rhsim02G0029200' => 'rsi', 'Rhsim02G0029300' => 'rsi', 'Rhsim02G0029400' => 'rsi', 'Rhsim02G0029500' => 'rsi', 'Rhsim02G0029600' => 'rsi', 'RhsimUnG0024000' => 'rsi', 'RhsimUnG0024100' => 'rsi', 'RhsimUnG0024200' => 'rsi', 'RhsimUnG0024300' => 'rsi', 'RhsimUnG0024400' => 'rsi', 'RhsimUnG0024500' => 'rsi', 'RhsimUnG0024700' => 'rsi', 'RhsimUnG0024800' => 'rsi', 'RhsimUnG0024900' => 'rsi', 'RhsimUnG0025100' => 'rsi', 'Sabra08G0120200' => 'sbr', 'Sabra08G0120300' => 'sbr', 'Sabra08G0120500' => 'sbr', 'Sabra08G0120600' => 'sbr', 'Sabra10G0158900' => 'sbr', 'SalBow2G3492' => 'sbo', 'Sc13g0004760' => 'sci', 'Sc13g0004770' => 'sci', 'Sed0003417' => 'sed', 'Sed0019750' => 'sed', 'SEGI_03419' => 'sgi', 'SEGI_05907' => 'sgi', 'SEGI_10682' => 'sgi', 'SEGI_13528' => 'sgi', 'SEGI_16081' => 'sgi', 'SEGI_19370' => 'sgi', 'SEGI_21015' => 'sgi', 'SEGI_21944' => 'sgi', 'SEGI_32906' => 'sgi', 'SEGI_33093' => 'sgi', 'SEGI_36110' => 'sgi', 'SEGI_40397' => 'sgi', 'SGA_v2.0_scaffold191G40426' => 'sas', 'SGA_v2.0_scaffold353G49717' => 'sas', 'SGA_v2.0_scaffold50G18550' => 'sas', 'SMO119G0173' => 'smo', 'SMO172G0002' => 'smo', 'Solyc09g082690.3' => 'sly', 'Solyc09g082700.2' => 'sly', 'Sopen09g031550' => 'spe', 'Sopen09g031560' => 'spe', 'Sp3g20540' => 'spa', 'Sp7g07580' => 'spa', 'TAR134G0002' => 'tar', 'TAR236G0001' => 'tar', 'TAR365G0892' => 'tar', 'TAR636G0166' => 'tar', 'TAR636G0646' => 'tar', 'TAR636G0869' => 'tar', 'TAR636G1317' => 'tar', 'TAR636G1744' => 'tar', 'TAR636G3358' => 'tar', 'TAR636G3436' => 'tar', 'THA.LOC104803047' => 'tha', 'Thecc.04G238900' => 'tca', 'Thhalv10021557m.g' => 'esa', 'Thhalv10026318m.g' => 'esa', 'Thhalv10026335m.g' => 'esa', 'TPR.G17433' => 'tpr', 'TPR.G18915' => 'tpr', 'TPR.G26125' => 'tpr', 'TWI09G0677' => 'twi', 'TWI73G0287' => 'twi', 'unitig_748.g8326' => 'ugi', 'vmacro15370' => 'vma', 'vmacro15371' => 'vma', 'vmacro15372' => 'vma', 'vmacro15373' => 'vma', 'vmacro15374' => 'vma', 'VMungo0720G2826' => 'vmu', 'Zm00001eb116960' => 'zma', 'Zm00001eb301260' => 'zma', 'Zm00001eb301270' => 'zma' ) $gf_id = 'HOM05D001460' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001460' ) $data_identifier = 'HOM05D001460' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 4, 'aag' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 2, 'aox' => (int) 2, 'arhy' => (int) 4, 'ath' => (int) 2, 'atr' => (int) 1, 'acertr' => (int) 10, 'cqu' => (int) 4, 'bca' => (int) 11, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 1, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 1, 'ccan' => (int) 1, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 1, 'col' => (int) 1, 'cpa' => (int) 1, 'cre' => (int) 7, 'csa' => (int) 1, 'camsi' => (int) 2, 'dca' => (int) 3, 'din' => (int) 2, 'dzi' => (int) 3, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 14, 'fve' => (int) 9, 'gma' => (int) 2, 'ghi' => (int) 4, 'gra' => (int) 2, 'vvi' => (int) 1, 'han' => (int) 13, 'cav' => (int) 1, 'hma' => (int) 2, 'sun' => (int) 2, 'lal' => (int) 2, 'lonja' => (int) 12, 'lja' => (int) 1, 'lsa' => (int) 7, 'mes' => (int) 1, 'mpo' => (int) 27, 'mbi' => (int) 1, 'mco' => (int) 8, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 1, 'egut' => (int) 1, 'ama' => (int) 1, 'nta' => (int) 4, 'nnu' => (int) 2, 'oeu' => (int) 3, 'osa' => (int) 4, 'pax' => (int) 9, 'pgr' => (int) 1, 'stu' => (int) 1, 'pvu' => (int) 1, 'ptr' => (int) 4, 'ppa' => (int) 22, 'pco' => (int) 6, 'ppe' => (int) 6, 'psa' => (int) 5, 'pso' => (int) 19, 'qlo' => (int) 5, 'rch' => (int) 7, 'rsi' => (int) 20, 'sbr' => (int) 5, 'sbo' => (int) 1, 'sci' => (int) 2, 'sed' => (int) 2, 'sgi' => (int) 12, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 2, 'tar' => (int) 10, 'tha' => (int) 1, 'tca' => (int) 1, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 2, 'ugi' => (int) 1, 'vma' => (int) 5, 'vmu' => (int) 1, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb301270' $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' => 'HOM05D001460', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '433', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p22980' => 'bna', 'A01p32340' => 'bna', 'A03p42970' => 'bna', 'A05p25880' => 'bna', 'Aa31LG8G9320' => 'aar', 'Aa31LG8G9330' => 'aar', 'Aa31LG8G9340' => 'aar', 'Aa31sc221G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1034' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1528' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.829' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2222' => 'aag', 'Ah.12g058830' => 'amhyb', 'Ah.12g058840' => 'amhyb', 'AL3G37160' => 'aly', 'AL7G41310' => 'aly', 'Aqoxy5G00395' => 'aox', 'Aqoxy5G00396' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0C8NZA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5185HY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JZ1PRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MD3LS0' => 'arhy', 'AT3G22840' => 'ath', 'AT4G14690' => 'ath', 'ATR0665G054' => 'atr', 'Atru.chr4.2344' => 'acertr', 'Atru.chr4.2346' => 'acertr', 'Atru.chr4.2347' => 'acertr', 'Atru.chr4.2348' => 'acertr', 'Atru.chr4.2355' => 'acertr', 'Atru.chr4.2356' => 'acertr', 'Atru.chr4.2358' => 'acertr', 'Atru.chr4.2359' => 'acertr', 'Atru.chr4.2360' => 'acertr', 'Atru.chr4.2361' => 'acertr', 'AUR62030476' => 'cqu', 'AUR62030478' => 'cqu', 'AUR62030819' => 'cqu', 'AUR62030820' => 'cqu', 'BcaB03g14648' => 'bca', 'BcaB04g20492' => 'bca', 'BcaB06g26399' => 'bca', 'BcaC01g03416' => 'bca', 'BcaC01g03419' => 'bca', 'BcaC01g03421' => 'bca', 'BcaC01g03424' => 'bca', 'BcaC05g28012' => 'bca', 'BcaC09g49212' => 'bca', 'BcaC09g50140' => 'bca', 'BcaNung00346' => 'bca', 'BolC1t02785H' => 'bol', 'BolC1t04095H' => 'bol', 'BolC3t17545H' => 'bol', 'BolC5t32769H' => 'bol', 'BraA01t02211Z' => 'bra', 'BraA01t03359Z' => 'bra', 'BraA03t13441Z' => 'bra', 'BraA05t21476Z' => 'bra', 'C01p28420' => 'bna', 'C01p41350' => 'bna', 'C03p52750' => 'bna', 'C03p52780' => 'bna', 'C05p40270' => 'bna', 'CAN.G1437.9' => 'can', 'CANSAT78G0035' => 'cansat', 'CANSAT78G1036' => 'cansat', 'CANSAT78G2272' => 'cansat', 'CANSAT78G2478' => 'cansat', 'CARHR098700' => 'chi', 'CARHR221120' => 'chi', 'CARHR221150' => 'chi', 'Carub.0003s2297' => 'cru', 'Carub.0007s2749' => 'cru', 'Carub.0007s2750' => 'cru', 'Carub.0007s2751' => 'cru', 'Ca_10849_v3' => 'car', 'Cc03_g04300' => 'ccan', 'CDE02G3648' => 'cde', 'CDE05G0060' => 'cde', 'CDE05G0692' => 'cde', 'CDE05G2285' => 'cde', 'CDE05G2884' => 'cde', 'CDE05G3072' => 'cde', 'Cfa008439' => 'cfa', 'Cfa008441' => 'cfa', 'Cfa008443' => 'cfa', 'Cfa008448' => 'cfa', 'Ciclev10005974m.g' => 'ccl', 'Ciclev10006006m.g' => 'ccl', 'Ciclev10006775m.g' => 'ccl', 'CiPaw.02G120400' => 'cil', 'CiPaw.02G120500' => 'cil', 'CiPaw.02G120600' => 'cil', 'ClCG05G004850' => 'cla', 'COL.COLO4_21566' => 'col', 'Cpa.g.sc44.124' => 'cpa', 'Cre07.g320400' => 'cre', 'Cre07.g320450' => 'cre', 'Cre08.g384650' => 'cre', 'Cre09.g393173' => 'cre', 'Cre09.g394325' => 'cre', 'Cre14.g626750' => 'cre', 'Cre16.g679250' => 'cre', 'CsaV3_3G012890' => 'csa', 'CSS0010865' => 'camsi', 'CSS0044338' => 'camsi', 'DCAR_002366' => 'dca', 'DCAR_030687' => 'dca', 'DCAR_030688' => 'dca', 'Dinv14047' => 'din', 'Dinv14048' => 'din', 'Duzib151G0105' => 'dzi', 'Duzib151G0114' => 'dzi', 'Duzib212G1029' => 'dzi', 'ECA232G3536' => 'eca', 'ECA240G0786' => 'eca', 'ECA240G1802' => 'eca', 'ECA240G3760' => 'eca', 'ECA240G3920' => 'eca', 'EL10Ac5g12536' => 'bvu', 'EL10Ac5g12537' => 'bvu', 'EL10Ac5g12538' => 'bvu', 'Eucgr.B01004' => 'egr', 'Eucgr.B01006' => 'egr', 'Eucgr.B01007' => 'egr', 'Eucgr.B01008' => 'egr', 'Eucgr.B01895' => 'egr', 'Eucgr.B01896' => 'egr', 'FAN04G1456' => 'fan', 'FAN08G1769' => 'fan', 'FAN08G2160' => 'fan', 'FAN13G2403' => 'fan', 'FAN13G3303' => 'fan', 'FAN15G2435' => 'fan', 'FAN17G0672' => 'fan', 'FAN17G2441' => 'fan', 'FAN18G1024' => 'fan', 'FAN22G1458' => 'fan', 'FAN24G0037' => 'fan', 'FAN24G0429' => 'fan', 'FAN24G2387' => 'fan', 'FAN27G2746' => 'fan', 'FvH4_2g20400' => 'fve', 'FvH4_2g20420' => 'fve', 'FvH4_2g20430' => 'fve', 'FvH4_4g01270' => 'fve', 'FvH4_4g01290' => 'fve', 'FvH4_4g01300' => 'fve', 'FvH4_4g01310' => 'fve', 'FvH4_4g01330' => 'fve', 'FvH4_5g09070' => 'fve', 'Glyma.10G243800' => 'gma', 'Glyma.20G150600' => 'gma', 'Gohir.A09G219200' => 'ghi', 'Gohir.A09G219300' => 'ghi', 'Gohir.D09G221400' => 'ghi', 'Gohir.D09G221500' => 'ghi', 'Gorai.006G242600' => 'gra', 'Gorai.006G242700' => 'gra', 'GSVIVG01018044001' => 'vvi', 'HanXRQChr03g0083821' => 'han', 'HanXRQChr03g0083841' => 'han', 'HanXRQChr03g0083881' => 'han', 'HanXRQChr03g0083901' => 'han', 'HanXRQChr03g0083921' => 'han', 'HanXRQChr03g0085331' => 'han', 'HanXRQChr03g0085361' => 'han', 'HanXRQChr03g0085411' => 'han', 'HanXRQChr03g0085421' => 'han', 'HanXRQChr03g0085431' => 'han', 'HanXRQChr08g0221991' => 'han', 'HanXRQChr11g0336061' => 'han', 'HanXRQChr11g0336411' => 'han', 'Haze_11234' => 'cav', 'Hma1.2p1_0549F.1_g177010' => 'hma', 'Hma1.2p1_0602F.1_g187630' => 'hma', 'Hund14876' => 'sun', 'Hund14879' => 'sun', 'Lalb_Chr06g0160741' => 'lal', 'Lalb_Chr21g0304781' => 'lal', 'Lj3A726G19' => 'lonja', 'Lj3A726T23' => 'lonja', 'Lj3A726T24' => 'lonja', 'Lj3A726T25' => 'lonja', 'Lj3A727T17' => 'lonja', 'Lj3C726T0' => 'lonja', 'Lj3C726T2' => 'lonja', 'Lj3P725T35' => 'lonja', 'Lj3P727T10' => 'lonja', 'Lj3P727T12' => 'lonja', 'Lj3P727T14' => 'lonja', 'Lj5g0023109' => 'lja', 'Lj6P646T44' => 'lonja', 'Lsat_1_v5_gn_6_75760' => 'lsa', 'Lsat_1_v5_gn_6_75800' => 'lsa', 'Lsat_1_v5_gn_6_75900' => 'lsa', 'Lsat_1_v5_gn_6_76240' => 'lsa', 'Lsat_1_v5_gn_6_76441' => 'lsa', 'Lsat_1_v5_gn_6_76700' => 'lsa', 'Lsat_1_v5_gn_6_76760' => 'lsa', 'Manes.15G033100' => 'mes', 'Mapoly0004s0074' => 'mpo', 'Mapoly0004s0075' => 'mpo', 'Mapoly0004s0163' => 'mpo', 'Mapoly0004s0164' => 'mpo', 'Mapoly0021s0018' => 'mpo', 'Mapoly0041s0136' => 'mpo', 'Mapoly0041s0137' => 'mpo', 'Mapoly0041s0138' => 'mpo', 'Mapoly0041s0139' => 'mpo', 'Mapoly0041s0141' => 'mpo', 'Mapoly0041s0142' => 'mpo', 'Mapoly0041s0143' => 'mpo', 'Mapoly0041s0144' => 'mpo', 'Mapoly0041s0145' => 'mpo', 'Mapoly0047s0106' => 'mpo', 'Mapoly0047s0108' => 'mpo', 'Mapoly0050s0051' => 'mpo', 'Mapoly0050s0052' => 'mpo', 'Mapoly0050s0053' => 'mpo', 'Mapoly0058s0013' => 'mpo', 'Mapoly0091s0078' => 'mpo', 'Mapoly0091s0079' => 'mpo', 'Mapoly0091s0080' => 'mpo', 'Mapoly0091s0081' => 'mpo', 'Mapoly0278s0004' => 'mpo', 'Mapoly0278s0005' => 'mpo', 'Mapoly0278s0006' => 'mpo', 'MBI11_g30648_MAGBIO' => 'mbi', 'MCO03G194' => 'mco', 'MCO03G590' => 'mco', 'MCO07G312' => 'mco', 'MCO10G318' => 'mco', 'MCO12G244' => 'mco', 'MCO13G148' => 'mco', 'MCO13G194' => 'mco', 'MCO16G238' => 'mco', 'MD06G1134100' => 'mdo', 'MD13G1200100' => 'mdo', 'MD13G1200300' => 'mdo', 'MD13G1200600' => 'mdo', 'MD14G1150400' => 'mdo', 'MD16G1200000' => 'mdo', 'Medtr1g102570' => 'mtr', 'Medtr1g102780' => 'mtr', 'Medtr1g102800' => 'mtr', 'Medtr1g102810' => 'mtr', 'Medtr1g102830' => 'mtr', 'MELO3C006499.2' => 'cme', 'Migut.G00385' => 'egut', 'MSTRG.4063' => 'ama', 'Nitab4.5_0000090g0260' => 'nta', 'Nitab4.5_0000977g0030' => 'nta', 'Nitab4.5_0002541g0040' => 'nta', 'Nitab4.5_0007068g0040' => 'nta', 'Nn005s41408' => 'nnu', 'Nn005s41410' => 'nnu', 'Oeu010310.1' => 'oeu', 'Oeu010311.1' => 'oeu', 'Oeu043472.1' => 'oeu', 'Os01g0246400' => 'osa', 'Os04g0267950' => 'osa', 'Os07g0178700' => 'osa', 'Os07g0178800' => 'osa', 'Peaxi162Scf00316g00046' => 'pax', 'Peaxi162Scf00316g00049' => 'pax', 'Peaxi162Scf00316g00059' => 'pax', 'Peaxi162Scf00316g00328' => 'pax', 'Peaxi162Scf00316g00329' => 'pax', 'Peaxi162Scf00316g00411' => 'pax', 'Peaxi162Scf00316g00521' => 'pax', 'Peaxi162Scf00492g00068' => 'pax', 'Peaxi162Scf35631g00002' => 'pax', 'PGR142G3720' => 'pgr', 'PGSC0003DMG400006442' => 'stu', 'Phvul.007G062000' => 'pvu', 'Potri.008G157750' => 'ptr', 'Potri.008G157900' => 'ptr', 'Potri.008G158000' => 'ptr', 'Potri.008G158200' => 'ptr', 'Pp3c11_7280' => 'ppa', 'Pp3c11_7980' => 'ppa', 'Pp3c12_19450' => 'ppa', 'Pp3c14_1480' => 'ppa', 'Pp3c14_1501' => 'ppa', 'Pp3c16_4900' => 'ppa', 'Pp3c16_5010' => 'ppa', 'Pp3c16_5060' => 'ppa', 'Pp3c19_18250' => 'ppa', 'Pp3c23_8530' => 'ppa', 'Pp3c23_8550' => 'ppa', 'Pp3c24_9670' => 'ppa', 'Pp3c2_21390' => 'ppa', 'Pp3c2_31380' => 'ppa', 'Pp3c3_16620' => 'ppa', 'Pp3c3_8090' => 'ppa', 'Pp3c3_8110' => 'ppa', 'Pp3c3_8130' => 'ppa', 'Pp3c3_8150' => 'ppa', 'Pp3c4_14320' => 'ppa', 'Pp3c6_2560' => 'ppa', 'Pp3c9_16700' => 'ppa', 'PRCOL_00000234' => 'pco', 'PRCOL_00000235' => 'pco', 'PRCOL_00000777' => 'pco', 'PRCOL_00002344' => 'pco', 'PRCOL_00002372' => 'pco', 'PRCOL_00006120' => 'pco', 'Prupe.1G021400' => 'ppe', 'Prupe.1G021500' => 'ppe', 'Prupe.1G021600' => 'ppe', 'Prupe.1G021700' => 'ppe', 'Prupe.1G021800' => 'ppe', 'Prupe.5G145100' => 'ppe', 'Psat6g204040' => 'psa', 'Psat6g204800' => 'psa', 'Psat6g204920' => 'psa', 'Psat6g204960' => 'psa', 'Psat6g205080' => 'psa', 'PSO017G0271' => 'pso', 'PSO017G1276' => 'pso', 'PSO017G1429' => 'pso', 'PSO017G1861' => 'pso', 'PSO017G2787' => 'pso', 'PSO017G4466' => 'pso', 'PSO017G5118' => 'pso', 'PSO017G5420' => 'pso', 'PSO063G3678' => 'pso', 'PSO210G0546' => 'pso', 'PSO317G0001' => 'pso', 'PSO357G0512' => 'pso', 'PSO478G2682' => 'pso', 'PSO647G0001' => 'pso', 'PSO675G0001' => 'pso', 'PSO675G2699' => 'pso', 'PSO675G2849' => 'pso', 'PSO675G4991' => 'pso', 'PSO689G0001' => 'pso', 'QL06p000916' => 'qlo', 'QL06p000921' => 'qlo', 'QL06p001398' => 'qlo', 'QL06p001407' => 'qlo', 'QL06p002031' => 'qlo', 'RcHm_v2.0_Chr4g0387791' => 'rch', 'RcHm_v2.0_Chr4g0387801' => 'rch', 'RcHm_v2.0_Chr6g0286501' => 'rch', 'RcHm_v2.0_Chr6g0286511' => 'rch', 'RcHm_v2.0_Chr6g0286521' => 'rch', 'RcHm_v2.0_Chr6g0286531' => 'rch', 'RcHm_v2.0_Chr7g0189141' => 'rch', 'Rhsim02G0028700' => 'rsi', 'Rhsim02G0028800' => 'rsi', 'Rhsim02G0028900' => 'rsi', 'Rhsim02G0029000' => 'rsi', 'Rhsim02G0029100' => 'rsi', 'Rhsim02G0029200' => 'rsi', 'Rhsim02G0029300' => 'rsi', 'Rhsim02G0029400' => 'rsi', 'Rhsim02G0029500' => 'rsi', 'Rhsim02G0029600' => 'rsi', 'RhsimUnG0024000' => 'rsi', 'RhsimUnG0024100' => 'rsi', 'RhsimUnG0024200' => 'rsi', 'RhsimUnG0024300' => 'rsi', 'RhsimUnG0024400' => 'rsi', 'RhsimUnG0024500' => 'rsi', 'RhsimUnG0024700' => 'rsi', 'RhsimUnG0024800' => 'rsi', 'RhsimUnG0024900' => 'rsi', 'RhsimUnG0025100' => 'rsi', 'Sabra08G0120200' => 'sbr', 'Sabra08G0120300' => 'sbr', 'Sabra08G0120500' => 'sbr', 'Sabra08G0120600' => 'sbr', 'Sabra10G0158900' => 'sbr', 'SalBow2G3492' => 'sbo', 'Sc13g0004760' => 'sci', 'Sc13g0004770' => 'sci', 'Sed0003417' => 'sed', 'Sed0019750' => 'sed', 'SEGI_03419' => 'sgi', 'SEGI_05907' => 'sgi', 'SEGI_10682' => 'sgi', 'SEGI_13528' => 'sgi', 'SEGI_16081' => 'sgi', 'SEGI_19370' => 'sgi', 'SEGI_21015' => 'sgi', 'SEGI_21944' => 'sgi', 'SEGI_32906' => 'sgi', 'SEGI_33093' => 'sgi', 'SEGI_36110' => 'sgi', 'SEGI_40397' => 'sgi', 'SGA_v2.0_scaffold191G40426' => 'sas', 'SGA_v2.0_scaffold353G49717' => 'sas', 'SGA_v2.0_scaffold50G18550' => 'sas', 'SMO119G0173' => 'smo', 'SMO172G0002' => 'smo', 'Solyc09g082690.3' => 'sly', 'Solyc09g082700.2' => 'sly', 'Sopen09g031550' => 'spe', 'Sopen09g031560' => 'spe', 'Sp3g20540' => 'spa', 'Sp7g07580' => 'spa', 'TAR134G0002' => 'tar', 'TAR236G0001' => 'tar', 'TAR365G0892' => 'tar', 'TAR636G0166' => 'tar', 'TAR636G0646' => 'tar', 'TAR636G0869' => 'tar', 'TAR636G1317' => 'tar', 'TAR636G1744' => 'tar', 'TAR636G3358' => 'tar', 'TAR636G3436' => 'tar', 'THA.LOC104803047' => 'tha', 'Thecc.04G238900' => 'tca', 'Thhalv10021557m.g' => 'esa', 'Thhalv10026318m.g' => 'esa', 'Thhalv10026335m.g' => 'esa', 'TPR.G17433' => 'tpr', 'TPR.G18915' => 'tpr', 'TPR.G26125' => 'tpr', 'TWI09G0677' => 'twi', 'TWI73G0287' => 'twi', 'unitig_748.g8326' => 'ugi', 'vmacro15370' => 'vma', 'vmacro15371' => 'vma', 'vmacro15372' => 'vma', 'vmacro15373' => 'vma', 'vmacro15374' => 'vma', 'VMungo0720G2826' => 'vmu', 'Zm00001eb116960' => 'zma', 'Zm00001eb301260' => 'zma', 'Zm00001eb301270' => 'zma' ), 'gf_id' => 'HOM05D001460', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001460' ), 'data_identifier' => 'HOM05D001460', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001460', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '433', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p22980' => 'bna', 'A01p32340' => 'bna', 'A03p42970' => 'bna', 'A05p25880' => 'bna', 'Aa31LG8G9320' => 'aar', 'Aa31LG8G9330' => 'aar', 'Aa31LG8G9340' => 'aar', 'Aa31sc221G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1034' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1528' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.829' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2222' => 'aag', 'Ah.12g058830' => 'amhyb', 'Ah.12g058840' => 'amhyb', 'AL3G37160' => 'aly', 'AL7G41310' => 'aly', 'Aqoxy5G00395' => 'aox', 'Aqoxy5G00396' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0C8NZA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5185HY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JZ1PRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MD3LS0' => 'arhy', 'AT3G22840' => 'ath', 'AT4G14690' => 'ath', 'ATR0665G054' => 'atr', 'Atru.chr4.2344' => 'acertr', 'Atru.chr4.2346' => 'acertr', 'Atru.chr4.2347' => 'acertr', 'Atru.chr4.2348' => 'acertr', 'Atru.chr4.2355' => 'acertr', 'Atru.chr4.2356' => 'acertr', 'Atru.chr4.2358' => 'acertr', 'Atru.chr4.2359' => 'acertr', 'Atru.chr4.2360' => 'acertr', 'Atru.chr4.2361' => 'acertr', 'AUR62030476' => 'cqu', 'AUR62030478' => 'cqu', 'AUR62030819' => 'cqu', 'AUR62030820' => 'cqu', 'BcaB03g14648' => 'bca', 'BcaB04g20492' => 'bca', 'BcaB06g26399' => 'bca', 'BcaC01g03416' => 'bca', 'BcaC01g03419' => 'bca', 'BcaC01g03421' => 'bca', 'BcaC01g03424' => 'bca', 'BcaC05g28012' => 'bca', 'BcaC09g49212' => 'bca', 'BcaC09g50140' => 'bca', 'BcaNung00346' => 'bca', 'BolC1t02785H' => 'bol', 'BolC1t04095H' => 'bol', 'BolC3t17545H' => 'bol', 'BolC5t32769H' => 'bol', 'BraA01t02211Z' => 'bra', 'BraA01t03359Z' => 'bra', 'BraA03t13441Z' => 'bra', 'BraA05t21476Z' => 'bra', 'C01p28420' => 'bna', 'C01p41350' => 'bna', 'C03p52750' => 'bna', 'C03p52780' => 'bna', 'C05p40270' => 'bna', 'CAN.G1437.9' => 'can', 'CANSAT78G0035' => 'cansat', 'CANSAT78G1036' => 'cansat', 'CANSAT78G2272' => 'cansat', 'CANSAT78G2478' => 'cansat', 'CARHR098700' => 'chi', 'CARHR221120' => 'chi', 'CARHR221150' => 'chi', 'Carub.0003s2297' => 'cru', 'Carub.0007s2749' => 'cru', 'Carub.0007s2750' => 'cru', 'Carub.0007s2751' => 'cru', 'Ca_10849_v3' => 'car', 'Cc03_g04300' => 'ccan', 'CDE02G3648' => 'cde', 'CDE05G0060' => 'cde', 'CDE05G0692' => 'cde', 'CDE05G2285' => 'cde', 'CDE05G2884' => 'cde', 'CDE05G3072' => 'cde', 'Cfa008439' => 'cfa', 'Cfa008441' => 'cfa', 'Cfa008443' => 'cfa', 'Cfa008448' => 'cfa', 'Ciclev10005974m.g' => 'ccl', 'Ciclev10006006m.g' => 'ccl', 'Ciclev10006775m.g' => 'ccl', 'CiPaw.02G120400' => 'cil', 'CiPaw.02G120500' => 'cil', 'CiPaw.02G120600' => 'cil', 'ClCG05G004850' => 'cla', 'COL.COLO4_21566' => 'col', 'Cpa.g.sc44.124' => 'cpa', 'Cre07.g320400' => 'cre', 'Cre07.g320450' => 'cre', 'Cre08.g384650' => 'cre', 'Cre09.g393173' => 'cre', 'Cre09.g394325' => 'cre', 'Cre14.g626750' => 'cre', 'Cre16.g679250' => 'cre', 'CsaV3_3G012890' => 'csa', 'CSS0010865' => 'camsi', 'CSS0044338' => 'camsi', 'DCAR_002366' => 'dca', 'DCAR_030687' => 'dca', 'DCAR_030688' => 'dca', 'Dinv14047' => 'din', 'Dinv14048' => 'din', 'Duzib151G0105' => 'dzi', 'Duzib151G0114' => 'dzi', 'Duzib212G1029' => 'dzi', 'ECA232G3536' => 'eca', 'ECA240G0786' => 'eca', 'ECA240G1802' => 'eca', 'ECA240G3760' => 'eca', 'ECA240G3920' => 'eca', 'EL10Ac5g12536' => 'bvu', 'EL10Ac5g12537' => 'bvu', 'EL10Ac5g12538' => 'bvu', 'Eucgr.B01004' => 'egr', 'Eucgr.B01006' => 'egr', 'Eucgr.B01007' => 'egr', 'Eucgr.B01008' => 'egr', 'Eucgr.B01895' => 'egr', 'Eucgr.B01896' => 'egr', 'FAN04G1456' => 'fan', 'FAN08G1769' => 'fan', 'FAN08G2160' => 'fan', 'FAN13G2403' => 'fan', 'FAN13G3303' => 'fan', 'FAN15G2435' => 'fan', 'FAN17G0672' => 'fan', 'FAN17G2441' => 'fan', 'FAN18G1024' => 'fan', 'FAN22G1458' => 'fan', 'FAN24G0037' => 'fan', 'FAN24G0429' => 'fan', 'FAN24G2387' => 'fan', 'FAN27G2746' => 'fan', 'FvH4_2g20400' => 'fve', 'FvH4_2g20420' => 'fve', 'FvH4_2g20430' => 'fve', 'FvH4_4g01270' => 'fve', 'FvH4_4g01290' => 'fve', 'FvH4_4g01300' => 'fve', 'FvH4_4g01310' => 'fve', 'FvH4_4g01330' => 'fve', 'FvH4_5g09070' => 'fve', 'Glyma.10G243800' => 'gma', 'Glyma.20G150600' => 'gma', 'Gohir.A09G219200' => 'ghi', 'Gohir.A09G219300' => 'ghi', 'Gohir.D09G221400' => 'ghi', 'Gohir.D09G221500' => 'ghi', 'Gorai.006G242600' => 'gra', 'Gorai.006G242700' => 'gra', 'GSVIVG01018044001' => 'vvi', 'HanXRQChr03g0083821' => 'han', 'HanXRQChr03g0083841' => 'han', 'HanXRQChr03g0083881' => 'han', 'HanXRQChr03g0083901' => 'han', 'HanXRQChr03g0083921' => 'han', 'HanXRQChr03g0085331' => 'han', 'HanXRQChr03g0085361' => 'han', 'HanXRQChr03g0085411' => 'han', 'HanXRQChr03g0085421' => 'han', 'HanXRQChr03g0085431' => 'han', 'HanXRQChr08g0221991' => 'han', 'HanXRQChr11g0336061' => 'han', 'HanXRQChr11g0336411' => 'han', 'Haze_11234' => 'cav', 'Hma1.2p1_0549F.1_g177010' => 'hma', 'Hma1.2p1_0602F.1_g187630' => 'hma', 'Hund14876' => 'sun', 'Hund14879' => 'sun', 'Lalb_Chr06g0160741' => 'lal', 'Lalb_Chr21g0304781' => 'lal', 'Lj3A726G19' => 'lonja', 'Lj3A726T23' => 'lonja', 'Lj3A726T24' => 'lonja', 'Lj3A726T25' => 'lonja', 'Lj3A727T17' => 'lonja', 'Lj3C726T0' => 'lonja', 'Lj3C726T2' => 'lonja', 'Lj3P725T35' => 'lonja', 'Lj3P727T10' => 'lonja', 'Lj3P727T12' => 'lonja', 'Lj3P727T14' => 'lonja', 'Lj5g0023109' => 'lja', 'Lj6P646T44' => 'lonja', 'Lsat_1_v5_gn_6_75760' => 'lsa', 'Lsat_1_v5_gn_6_75800' => 'lsa', 'Lsat_1_v5_gn_6_75900' => 'lsa', 'Lsat_1_v5_gn_6_76240' => 'lsa', 'Lsat_1_v5_gn_6_76441' => 'lsa', 'Lsat_1_v5_gn_6_76700' => 'lsa', 'Lsat_1_v5_gn_6_76760' => 'lsa', 'Manes.15G033100' => 'mes', 'Mapoly0004s0074' => 'mpo', 'Mapoly0004s0075' => 'mpo', 'Mapoly0004s0163' => 'mpo', 'Mapoly0004s0164' => 'mpo', 'Mapoly0021s0018' => 'mpo', 'Mapoly0041s0136' => 'mpo', 'Mapoly0041s0137' => 'mpo', 'Mapoly0041s0138' => 'mpo', 'Mapoly0041s0139' => 'mpo', 'Mapoly0041s0141' => 'mpo', 'Mapoly0041s0142' => 'mpo', 'Mapoly0041s0143' => 'mpo', 'Mapoly0041s0144' => 'mpo', 'Mapoly0041s0145' => 'mpo', 'Mapoly0047s0106' => 'mpo', 'Mapoly0047s0108' => 'mpo', 'Mapoly0050s0051' => 'mpo', 'Mapoly0050s0052' => 'mpo', 'Mapoly0050s0053' => 'mpo', 'Mapoly0058s0013' => 'mpo', 'Mapoly0091s0078' => 'mpo', 'Mapoly0091s0079' => 'mpo', 'Mapoly0091s0080' => 'mpo', 'Mapoly0091s0081' => 'mpo', 'Mapoly0278s0004' => 'mpo', 'Mapoly0278s0005' => 'mpo', 'Mapoly0278s0006' => 'mpo', 'MBI11_g30648_MAGBIO' => 'mbi', 'MCO03G194' => 'mco', 'MCO03G590' => 'mco', 'MCO07G312' => 'mco', 'MCO10G318' => 'mco', 'MCO12G244' => 'mco', 'MCO13G148' => 'mco', 'MCO13G194' => 'mco', 'MCO16G238' => 'mco', 'MD06G1134100' => 'mdo', 'MD13G1200100' => 'mdo', 'MD13G1200300' => 'mdo', 'MD13G1200600' => 'mdo', 'MD14G1150400' => 'mdo', 'MD16G1200000' => 'mdo', 'Medtr1g102570' => 'mtr', 'Medtr1g102780' => 'mtr', 'Medtr1g102800' => 'mtr', 'Medtr1g102810' => 'mtr', 'Medtr1g102830' => 'mtr', 'MELO3C006499.2' => 'cme', 'Migut.G00385' => 'egut', 'MSTRG.4063' => 'ama', 'Nitab4.5_0000090g0260' => 'nta', 'Nitab4.5_0000977g0030' => 'nta', 'Nitab4.5_0002541g0040' => 'nta', 'Nitab4.5_0007068g0040' => 'nta', 'Nn005s41408' => 'nnu', 'Nn005s41410' => 'nnu', 'Oeu010310.1' => 'oeu', 'Oeu010311.1' => 'oeu', 'Oeu043472.1' => 'oeu', 'Os01g0246400' => 'osa', 'Os04g0267950' => 'osa', 'Os07g0178700' => 'osa', 'Os07g0178800' => 'osa', 'Peaxi162Scf00316g00046' => 'pax', 'Peaxi162Scf00316g00049' => 'pax', 'Peaxi162Scf00316g00059' => 'pax', 'Peaxi162Scf00316g00328' => 'pax', 'Peaxi162Scf00316g00329' => 'pax', 'Peaxi162Scf00316g00411' => 'pax', 'Peaxi162Scf00316g00521' => 'pax', 'Peaxi162Scf00492g00068' => 'pax', 'Peaxi162Scf35631g00002' => 'pax', 'PGR142G3720' => 'pgr', 'PGSC0003DMG400006442' => 'stu', 'Phvul.007G062000' => 'pvu', 'Potri.008G157750' => 'ptr', 'Potri.008G157900' => 'ptr', 'Potri.008G158000' => 'ptr', 'Potri.008G158200' => 'ptr', 'Pp3c11_7280' => 'ppa', 'Pp3c11_7980' => 'ppa', 'Pp3c12_19450' => 'ppa', 'Pp3c14_1480' => 'ppa', 'Pp3c14_1501' => 'ppa', 'Pp3c16_4900' => 'ppa', 'Pp3c16_5010' => 'ppa', 'Pp3c16_5060' => 'ppa', 'Pp3c19_18250' => 'ppa', 'Pp3c23_8530' => 'ppa', 'Pp3c23_8550' => 'ppa', 'Pp3c24_9670' => 'ppa', 'Pp3c2_21390' => 'ppa', 'Pp3c2_31380' => 'ppa', 'Pp3c3_16620' => 'ppa', 'Pp3c3_8090' => 'ppa', 'Pp3c3_8110' => 'ppa', 'Pp3c3_8130' => 'ppa', 'Pp3c3_8150' => 'ppa', 'Pp3c4_14320' => 'ppa', 'Pp3c6_2560' => 'ppa', 'Pp3c9_16700' => 'ppa', 'PRCOL_00000234' => 'pco', 'PRCOL_00000235' => 'pco', 'PRCOL_00000777' => 'pco', 'PRCOL_00002344' => 'pco', 'PRCOL_00002372' => 'pco', 'PRCOL_00006120' => 'pco', 'Prupe.1G021400' => 'ppe', 'Prupe.1G021500' => 'ppe', 'Prupe.1G021600' => 'ppe', 'Prupe.1G021700' => 'ppe', 'Prupe.1G021800' => 'ppe', 'Prupe.5G145100' => 'ppe', 'Psat6g204040' => 'psa', 'Psat6g204800' => 'psa', 'Psat6g204920' => 'psa', 'Psat6g204960' => 'psa', 'Psat6g205080' => 'psa', 'PSO017G0271' => 'pso', 'PSO017G1276' => 'pso', 'PSO017G1429' => 'pso', 'PSO017G1861' => 'pso', 'PSO017G2787' => 'pso', 'PSO017G4466' => 'pso', 'PSO017G5118' => 'pso', 'PSO017G5420' => 'pso', 'PSO063G3678' => 'pso', 'PSO210G0546' => 'pso', 'PSO317G0001' => 'pso', 'PSO357G0512' => 'pso', 'PSO478G2682' => 'pso', 'PSO647G0001' => 'pso', 'PSO675G0001' => 'pso', 'PSO675G2699' => 'pso', 'PSO675G2849' => 'pso', 'PSO675G4991' => 'pso', 'PSO689G0001' => 'pso', 'QL06p000916' => 'qlo', 'QL06p000921' => 'qlo', 'QL06p001398' => 'qlo', 'QL06p001407' => 'qlo', 'QL06p002031' => 'qlo', 'RcHm_v2.0_Chr4g0387791' => 'rch', 'RcHm_v2.0_Chr4g0387801' => 'rch', 'RcHm_v2.0_Chr6g0286501' => 'rch', 'RcHm_v2.0_Chr6g0286511' => 'rch', 'RcHm_v2.0_Chr6g0286521' => 'rch', 'RcHm_v2.0_Chr6g0286531' => 'rch', 'RcHm_v2.0_Chr7g0189141' => 'rch', 'Rhsim02G0028700' => 'rsi', 'Rhsim02G0028800' => 'rsi', 'Rhsim02G0028900' => 'rsi', 'Rhsim02G0029000' => 'rsi', 'Rhsim02G0029100' => 'rsi', 'Rhsim02G0029200' => 'rsi', 'Rhsim02G0029300' => 'rsi', 'Rhsim02G0029400' => 'rsi', 'Rhsim02G0029500' => 'rsi', 'Rhsim02G0029600' => 'rsi', 'RhsimUnG0024000' => 'rsi', 'RhsimUnG0024100' => 'rsi', 'RhsimUnG0024200' => 'rsi', 'RhsimUnG0024300' => 'rsi', 'RhsimUnG0024400' => 'rsi', 'RhsimUnG0024500' => 'rsi', 'RhsimUnG0024700' => 'rsi', 'RhsimUnG0024800' => 'rsi', 'RhsimUnG0024900' => 'rsi', 'RhsimUnG0025100' => 'rsi', 'Sabra08G0120200' => 'sbr', 'Sabra08G0120300' => 'sbr', 'Sabra08G0120500' => 'sbr', 'Sabra08G0120600' => 'sbr', 'Sabra10G0158900' => 'sbr', 'SalBow2G3492' => 'sbo', 'Sc13g0004760' => 'sci', 'Sc13g0004770' => 'sci', 'Sed0003417' => 'sed', 'Sed0019750' => 'sed', 'SEGI_03419' => 'sgi', 'SEGI_05907' => 'sgi', 'SEGI_10682' => 'sgi', 'SEGI_13528' => 'sgi', 'SEGI_16081' => 'sgi', 'SEGI_19370' => 'sgi', 'SEGI_21015' => 'sgi', 'SEGI_21944' => 'sgi', 'SEGI_32906' => 'sgi', 'SEGI_33093' => 'sgi', 'SEGI_36110' => 'sgi', 'SEGI_40397' => 'sgi', 'SGA_v2.0_scaffold191G40426' => 'sas', 'SGA_v2.0_scaffold353G49717' => 'sas', 'SGA_v2.0_scaffold50G18550' => 'sas', 'SMO119G0173' => 'smo', 'SMO172G0002' => 'smo', 'Solyc09g082690.3' => 'sly', 'Solyc09g082700.2' => 'sly', 'Sopen09g031550' => 'spe', 'Sopen09g031560' => 'spe', 'Sp3g20540' => 'spa', 'Sp7g07580' => 'spa', 'TAR134G0002' => 'tar', 'TAR236G0001' => 'tar', 'TAR365G0892' => 'tar', 'TAR636G0166' => 'tar', 'TAR636G0646' => 'tar', 'TAR636G0869' => 'tar', 'TAR636G1317' => 'tar', 'TAR636G1744' => 'tar', 'TAR636G3358' => 'tar', 'TAR636G3436' => 'tar', 'THA.LOC104803047' => 'tha', 'Thecc.04G238900' => 'tca', 'Thhalv10021557m.g' => 'esa', 'Thhalv10026318m.g' => 'esa', 'Thhalv10026335m.g' => 'esa', 'TPR.G17433' => 'tpr', 'TPR.G18915' => 'tpr', 'TPR.G26125' => 'tpr', 'TWI09G0677' => 'twi', 'TWI73G0287' => 'twi', 'unitig_748.g8326' => 'ugi', 'vmacro15370' => 'vma', 'vmacro15371' => 'vma', 'vmacro15372' => 'vma', 'vmacro15373' => 'vma', 'vmacro15374' => 'vma', 'VMungo0720G2826' => 'vmu', 'Zm00001eb116960' => 'zma', 'Zm00001eb301260' => 'zma', 'Zm00001eb301270' => 'zma' ) $gf_id = 'HOM05D001460' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001460' ) $data_identifier = 'HOM05D001460' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 4, 'aag' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 2, 'aox' => (int) 2, 'arhy' => (int) 4, 'ath' => (int) 2, 'atr' => (int) 1, 'acertr' => (int) 10, 'cqu' => (int) 4, 'bca' => (int) 11, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 1, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 1, 'ccan' => (int) 1, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 1, 'col' => (int) 1, 'cpa' => (int) 1, 'cre' => (int) 7, 'csa' => (int) 1, 'camsi' => (int) 2, 'dca' => (int) 3, 'din' => (int) 2, 'dzi' => (int) 3, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 14, 'fve' => (int) 9, 'gma' => (int) 2, 'ghi' => (int) 4, 'gra' => (int) 2, 'vvi' => (int) 1, 'han' => (int) 13, 'cav' => (int) 1, 'hma' => (int) 2, 'sun' => (int) 2, 'lal' => (int) 2, 'lonja' => (int) 12, 'lja' => (int) 1, 'lsa' => (int) 7, 'mes' => (int) 1, 'mpo' => (int) 27, 'mbi' => (int) 1, 'mco' => (int) 8, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 1, 'egut' => (int) 1, 'ama' => (int) 1, 'nta' => (int) 4, 'nnu' => (int) 2, 'oeu' => (int) 3, 'osa' => (int) 4, 'pax' => (int) 9, 'pgr' => (int) 1, 'stu' => (int) 1, 'pvu' => (int) 1, 'ptr' => (int) 4, 'ppa' => (int) 22, 'pco' => (int) 6, 'ppe' => (int) 6, 'psa' => (int) 5, 'pso' => (int) 19, 'qlo' => (int) 5, 'rch' => (int) 7, 'rsi' => (int) 20, 'sbr' => (int) 5, 'sbo' => (int) 1, 'sci' => (int) 2, 'sed' => (int) 2, 'sgi' => (int) 12, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 2, 'tar' => (int) 10, 'tha' => (int) 1, 'tca' => (int) 1, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 2, 'ugi' => (int) 1, 'vma' => (int) 5, 'vmu' => (int) 1, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb301270' $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' => 'HOM05D001460', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '433', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p22980' => 'bna', 'A01p32340' => 'bna', 'A03p42970' => 'bna', 'A05p25880' => 'bna', 'Aa31LG8G9320' => 'aar', 'Aa31LG8G9330' => 'aar', 'Aa31LG8G9340' => 'aar', 'Aa31sc221G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1034' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1528' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.829' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2222' => 'aag', 'Ah.12g058830' => 'amhyb', 'Ah.12g058840' => 'amhyb', 'AL3G37160' => 'aly', 'AL7G41310' => 'aly', 'Aqoxy5G00395' => 'aox', 'Aqoxy5G00396' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0C8NZA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5185HY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JZ1PRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MD3LS0' => 'arhy', 'AT3G22840' => 'ath', 'AT4G14690' => 'ath', 'ATR0665G054' => 'atr', 'Atru.chr4.2344' => 'acertr', 'Atru.chr4.2346' => 'acertr', 'Atru.chr4.2347' => 'acertr', 'Atru.chr4.2348' => 'acertr', 'Atru.chr4.2355' => 'acertr', 'Atru.chr4.2356' => 'acertr', 'Atru.chr4.2358' => 'acertr', 'Atru.chr4.2359' => 'acertr', 'Atru.chr4.2360' => 'acertr', 'Atru.chr4.2361' => 'acertr', 'AUR62030476' => 'cqu', 'AUR62030478' => 'cqu', 'AUR62030819' => 'cqu', 'AUR62030820' => 'cqu', 'BcaB03g14648' => 'bca', 'BcaB04g20492' => 'bca', 'BcaB06g26399' => 'bca', 'BcaC01g03416' => 'bca', 'BcaC01g03419' => 'bca', 'BcaC01g03421' => 'bca', 'BcaC01g03424' => 'bca', 'BcaC05g28012' => 'bca', 'BcaC09g49212' => 'bca', 'BcaC09g50140' => 'bca', 'BcaNung00346' => 'bca', 'BolC1t02785H' => 'bol', 'BolC1t04095H' => 'bol', 'BolC3t17545H' => 'bol', 'BolC5t32769H' => 'bol', 'BraA01t02211Z' => 'bra', 'BraA01t03359Z' => 'bra', 'BraA03t13441Z' => 'bra', 'BraA05t21476Z' => 'bra', 'C01p28420' => 'bna', 'C01p41350' => 'bna', 'C03p52750' => 'bna', 'C03p52780' => 'bna', 'C05p40270' => 'bna', 'CAN.G1437.9' => 'can', 'CANSAT78G0035' => 'cansat', 'CANSAT78G1036' => 'cansat', 'CANSAT78G2272' => 'cansat', 'CANSAT78G2478' => 'cansat', 'CARHR098700' => 'chi', 'CARHR221120' => 'chi', 'CARHR221150' => 'chi', 'Carub.0003s2297' => 'cru', 'Carub.0007s2749' => 'cru', 'Carub.0007s2750' => 'cru', 'Carub.0007s2751' => 'cru', 'Ca_10849_v3' => 'car', 'Cc03_g04300' => 'ccan', 'CDE02G3648' => 'cde', 'CDE05G0060' => 'cde', 'CDE05G0692' => 'cde', 'CDE05G2285' => 'cde', 'CDE05G2884' => 'cde', 'CDE05G3072' => 'cde', 'Cfa008439' => 'cfa', 'Cfa008441' => 'cfa', 'Cfa008443' => 'cfa', 'Cfa008448' => 'cfa', 'Ciclev10005974m.g' => 'ccl', 'Ciclev10006006m.g' => 'ccl', 'Ciclev10006775m.g' => 'ccl', 'CiPaw.02G120400' => 'cil', 'CiPaw.02G120500' => 'cil', 'CiPaw.02G120600' => 'cil', 'ClCG05G004850' => 'cla', 'COL.COLO4_21566' => 'col', 'Cpa.g.sc44.124' => 'cpa', 'Cre07.g320400' => 'cre', 'Cre07.g320450' => 'cre', 'Cre08.g384650' => 'cre', 'Cre09.g393173' => 'cre', 'Cre09.g394325' => 'cre', 'Cre14.g626750' => 'cre', 'Cre16.g679250' => 'cre', 'CsaV3_3G012890' => 'csa', 'CSS0010865' => 'camsi', 'CSS0044338' => 'camsi', 'DCAR_002366' => 'dca', 'DCAR_030687' => 'dca', 'DCAR_030688' => 'dca', 'Dinv14047' => 'din', 'Dinv14048' => 'din', 'Duzib151G0105' => 'dzi', 'Duzib151G0114' => 'dzi', 'Duzib212G1029' => 'dzi', 'ECA232G3536' => 'eca', 'ECA240G0786' => 'eca', 'ECA240G1802' => 'eca', 'ECA240G3760' => 'eca', 'ECA240G3920' => 'eca', 'EL10Ac5g12536' => 'bvu', 'EL10Ac5g12537' => 'bvu', 'EL10Ac5g12538' => 'bvu', 'Eucgr.B01004' => 'egr', 'Eucgr.B01006' => 'egr', 'Eucgr.B01007' => 'egr', 'Eucgr.B01008' => 'egr', 'Eucgr.B01895' => 'egr', 'Eucgr.B01896' => 'egr', 'FAN04G1456' => 'fan', 'FAN08G1769' => 'fan', 'FAN08G2160' => 'fan', 'FAN13G2403' => 'fan', 'FAN13G3303' => 'fan', 'FAN15G2435' => 'fan', 'FAN17G0672' => 'fan', 'FAN17G2441' => 'fan', 'FAN18G1024' => 'fan', 'FAN22G1458' => 'fan', 'FAN24G0037' => 'fan', 'FAN24G0429' => 'fan', 'FAN24G2387' => 'fan', 'FAN27G2746' => 'fan', 'FvH4_2g20400' => 'fve', 'FvH4_2g20420' => 'fve', 'FvH4_2g20430' => 'fve', 'FvH4_4g01270' => 'fve', 'FvH4_4g01290' => 'fve', 'FvH4_4g01300' => 'fve', 'FvH4_4g01310' => 'fve', 'FvH4_4g01330' => 'fve', 'FvH4_5g09070' => 'fve', 'Glyma.10G243800' => 'gma', 'Glyma.20G150600' => 'gma', 'Gohir.A09G219200' => 'ghi', 'Gohir.A09G219300' => 'ghi', 'Gohir.D09G221400' => 'ghi', 'Gohir.D09G221500' => 'ghi', 'Gorai.006G242600' => 'gra', 'Gorai.006G242700' => 'gra', 'GSVIVG01018044001' => 'vvi', 'HanXRQChr03g0083821' => 'han', 'HanXRQChr03g0083841' => 'han', 'HanXRQChr03g0083881' => 'han', 'HanXRQChr03g0083901' => 'han', 'HanXRQChr03g0083921' => 'han', 'HanXRQChr03g0085331' => 'han', 'HanXRQChr03g0085361' => 'han', 'HanXRQChr03g0085411' => 'han', 'HanXRQChr03g0085421' => 'han', 'HanXRQChr03g0085431' => 'han', 'HanXRQChr08g0221991' => 'han', 'HanXRQChr11g0336061' => 'han', 'HanXRQChr11g0336411' => 'han', 'Haze_11234' => 'cav', 'Hma1.2p1_0549F.1_g177010' => 'hma', 'Hma1.2p1_0602F.1_g187630' => 'hma', 'Hund14876' => 'sun', 'Hund14879' => 'sun', 'Lalb_Chr06g0160741' => 'lal', 'Lalb_Chr21g0304781' => 'lal', 'Lj3A726G19' => 'lonja', 'Lj3A726T23' => 'lonja', 'Lj3A726T24' => 'lonja', 'Lj3A726T25' => 'lonja', 'Lj3A727T17' => 'lonja', 'Lj3C726T0' => 'lonja', 'Lj3C726T2' => 'lonja', 'Lj3P725T35' => 'lonja', 'Lj3P727T10' => 'lonja', 'Lj3P727T12' => 'lonja', 'Lj3P727T14' => 'lonja', 'Lj5g0023109' => 'lja', 'Lj6P646T44' => 'lonja', 'Lsat_1_v5_gn_6_75760' => 'lsa', 'Lsat_1_v5_gn_6_75800' => 'lsa', 'Lsat_1_v5_gn_6_75900' => 'lsa', 'Lsat_1_v5_gn_6_76240' => 'lsa', 'Lsat_1_v5_gn_6_76441' => 'lsa', 'Lsat_1_v5_gn_6_76700' => 'lsa', 'Lsat_1_v5_gn_6_76760' => 'lsa', 'Manes.15G033100' => 'mes', 'Mapoly0004s0074' => 'mpo', 'Mapoly0004s0075' => 'mpo', 'Mapoly0004s0163' => 'mpo', 'Mapoly0004s0164' => 'mpo', 'Mapoly0021s0018' => 'mpo', 'Mapoly0041s0136' => 'mpo', 'Mapoly0041s0137' => 'mpo', 'Mapoly0041s0138' => 'mpo', 'Mapoly0041s0139' => 'mpo', 'Mapoly0041s0141' => 'mpo', 'Mapoly0041s0142' => 'mpo', 'Mapoly0041s0143' => 'mpo', 'Mapoly0041s0144' => 'mpo', 'Mapoly0041s0145' => 'mpo', 'Mapoly0047s0106' => 'mpo', 'Mapoly0047s0108' => 'mpo', 'Mapoly0050s0051' => 'mpo', 'Mapoly0050s0052' => 'mpo', 'Mapoly0050s0053' => 'mpo', 'Mapoly0058s0013' => 'mpo', 'Mapoly0091s0078' => 'mpo', 'Mapoly0091s0079' => 'mpo', 'Mapoly0091s0080' => 'mpo', 'Mapoly0091s0081' => 'mpo', 'Mapoly0278s0004' => 'mpo', 'Mapoly0278s0005' => 'mpo', 'Mapoly0278s0006' => 'mpo', 'MBI11_g30648_MAGBIO' => 'mbi', 'MCO03G194' => 'mco', 'MCO03G590' => 'mco', 'MCO07G312' => 'mco', 'MCO10G318' => 'mco', 'MCO12G244' => 'mco', 'MCO13G148' => 'mco', 'MCO13G194' => 'mco', 'MCO16G238' => 'mco', 'MD06G1134100' => 'mdo', 'MD13G1200100' => 'mdo', 'MD13G1200300' => 'mdo', 'MD13G1200600' => 'mdo', 'MD14G1150400' => 'mdo', 'MD16G1200000' => 'mdo', 'Medtr1g102570' => 'mtr', 'Medtr1g102780' => 'mtr', 'Medtr1g102800' => 'mtr', 'Medtr1g102810' => 'mtr', 'Medtr1g102830' => 'mtr', 'MELO3C006499.2' => 'cme', 'Migut.G00385' => 'egut', 'MSTRG.4063' => 'ama', 'Nitab4.5_0000090g0260' => 'nta', 'Nitab4.5_0000977g0030' => 'nta', 'Nitab4.5_0002541g0040' => 'nta', 'Nitab4.5_0007068g0040' => 'nta', 'Nn005s41408' => 'nnu', 'Nn005s41410' => 'nnu', 'Oeu010310.1' => 'oeu', 'Oeu010311.1' => 'oeu', 'Oeu043472.1' => 'oeu', 'Os01g0246400' => 'osa', 'Os04g0267950' => 'osa', 'Os07g0178700' => 'osa', 'Os07g0178800' => 'osa', 'Peaxi162Scf00316g00046' => 'pax', 'Peaxi162Scf00316g00049' => 'pax', 'Peaxi162Scf00316g00059' => 'pax', 'Peaxi162Scf00316g00328' => 'pax', 'Peaxi162Scf00316g00329' => 'pax', 'Peaxi162Scf00316g00411' => 'pax', 'Peaxi162Scf00316g00521' => 'pax', 'Peaxi162Scf00492g00068' => 'pax', 'Peaxi162Scf35631g00002' => 'pax', 'PGR142G3720' => 'pgr', 'PGSC0003DMG400006442' => 'stu', 'Phvul.007G062000' => 'pvu', 'Potri.008G157750' => 'ptr', 'Potri.008G157900' => 'ptr', 'Potri.008G158000' => 'ptr', 'Potri.008G158200' => 'ptr', 'Pp3c11_7280' => 'ppa', 'Pp3c11_7980' => 'ppa', 'Pp3c12_19450' => 'ppa', 'Pp3c14_1480' => 'ppa', 'Pp3c14_1501' => 'ppa', 'Pp3c16_4900' => 'ppa', 'Pp3c16_5010' => 'ppa', 'Pp3c16_5060' => 'ppa', 'Pp3c19_18250' => 'ppa', 'Pp3c23_8530' => 'ppa', 'Pp3c23_8550' => 'ppa', 'Pp3c24_9670' => 'ppa', 'Pp3c2_21390' => 'ppa', 'Pp3c2_31380' => 'ppa', 'Pp3c3_16620' => 'ppa', 'Pp3c3_8090' => 'ppa', 'Pp3c3_8110' => 'ppa', 'Pp3c3_8130' => 'ppa', 'Pp3c3_8150' => 'ppa', 'Pp3c4_14320' => 'ppa', 'Pp3c6_2560' => 'ppa', 'Pp3c9_16700' => 'ppa', 'PRCOL_00000234' => 'pco', 'PRCOL_00000235' => 'pco', 'PRCOL_00000777' => 'pco', 'PRCOL_00002344' => 'pco', 'PRCOL_00002372' => 'pco', 'PRCOL_00006120' => 'pco', 'Prupe.1G021400' => 'ppe', 'Prupe.1G021500' => 'ppe', 'Prupe.1G021600' => 'ppe', 'Prupe.1G021700' => 'ppe', 'Prupe.1G021800' => 'ppe', 'Prupe.5G145100' => 'ppe', 'Psat6g204040' => 'psa', 'Psat6g204800' => 'psa', 'Psat6g204920' => 'psa', 'Psat6g204960' => 'psa', 'Psat6g205080' => 'psa', 'PSO017G0271' => 'pso', 'PSO017G1276' => 'pso', 'PSO017G1429' => 'pso', 'PSO017G1861' => 'pso', 'PSO017G2787' => 'pso', 'PSO017G4466' => 'pso', 'PSO017G5118' => 'pso', 'PSO017G5420' => 'pso', 'PSO063G3678' => 'pso', 'PSO210G0546' => 'pso', 'PSO317G0001' => 'pso', 'PSO357G0512' => 'pso', 'PSO478G2682' => 'pso', 'PSO647G0001' => 'pso', 'PSO675G0001' => 'pso', 'PSO675G2699' => 'pso', 'PSO675G2849' => 'pso', 'PSO675G4991' => 'pso', 'PSO689G0001' => 'pso', 'QL06p000916' => 'qlo', 'QL06p000921' => 'qlo', 'QL06p001398' => 'qlo', 'QL06p001407' => 'qlo', 'QL06p002031' => 'qlo', 'RcHm_v2.0_Chr4g0387791' => 'rch', 'RcHm_v2.0_Chr4g0387801' => 'rch', 'RcHm_v2.0_Chr6g0286501' => 'rch', 'RcHm_v2.0_Chr6g0286511' => 'rch', 'RcHm_v2.0_Chr6g0286521' => 'rch', 'RcHm_v2.0_Chr6g0286531' => 'rch', 'RcHm_v2.0_Chr7g0189141' => 'rch', 'Rhsim02G0028700' => 'rsi', 'Rhsim02G0028800' => 'rsi', 'Rhsim02G0028900' => 'rsi', 'Rhsim02G0029000' => 'rsi', 'Rhsim02G0029100' => 'rsi', 'Rhsim02G0029200' => 'rsi', 'Rhsim02G0029300' => 'rsi', 'Rhsim02G0029400' => 'rsi', 'Rhsim02G0029500' => 'rsi', 'Rhsim02G0029600' => 'rsi', 'RhsimUnG0024000' => 'rsi', 'RhsimUnG0024100' => 'rsi', 'RhsimUnG0024200' => 'rsi', 'RhsimUnG0024300' => 'rsi', 'RhsimUnG0024400' => 'rsi', 'RhsimUnG0024500' => 'rsi', 'RhsimUnG0024700' => 'rsi', 'RhsimUnG0024800' => 'rsi', 'RhsimUnG0024900' => 'rsi', 'RhsimUnG0025100' => 'rsi', 'Sabra08G0120200' => 'sbr', 'Sabra08G0120300' => 'sbr', 'Sabra08G0120500' => 'sbr', 'Sabra08G0120600' => 'sbr', 'Sabra10G0158900' => 'sbr', 'SalBow2G3492' => 'sbo', 'Sc13g0004760' => 'sci', 'Sc13g0004770' => 'sci', 'Sed0003417' => 'sed', 'Sed0019750' => 'sed', 'SEGI_03419' => 'sgi', 'SEGI_05907' => 'sgi', 'SEGI_10682' => 'sgi', 'SEGI_13528' => 'sgi', 'SEGI_16081' => 'sgi', 'SEGI_19370' => 'sgi', 'SEGI_21015' => 'sgi', 'SEGI_21944' => 'sgi', 'SEGI_32906' => 'sgi', 'SEGI_33093' => 'sgi', 'SEGI_36110' => 'sgi', 'SEGI_40397' => 'sgi', 'SGA_v2.0_scaffold191G40426' => 'sas', 'SGA_v2.0_scaffold353G49717' => 'sas', 'SGA_v2.0_scaffold50G18550' => 'sas', 'SMO119G0173' => 'smo', 'SMO172G0002' => 'smo', 'Solyc09g082690.3' => 'sly', 'Solyc09g082700.2' => 'sly', 'Sopen09g031550' => 'spe', 'Sopen09g031560' => 'spe', 'Sp3g20540' => 'spa', 'Sp7g07580' => 'spa', 'TAR134G0002' => 'tar', 'TAR236G0001' => 'tar', 'TAR365G0892' => 'tar', 'TAR636G0166' => 'tar', 'TAR636G0646' => 'tar', 'TAR636G0869' => 'tar', 'TAR636G1317' => 'tar', 'TAR636G1744' => 'tar', 'TAR636G3358' => 'tar', 'TAR636G3436' => 'tar', 'THA.LOC104803047' => 'tha', 'Thecc.04G238900' => 'tca', 'Thhalv10021557m.g' => 'esa', 'Thhalv10026318m.g' => 'esa', 'Thhalv10026335m.g' => 'esa', 'TPR.G17433' => 'tpr', 'TPR.G18915' => 'tpr', 'TPR.G26125' => 'tpr', 'TWI09G0677' => 'twi', 'TWI73G0287' => 'twi', 'unitig_748.g8326' => 'ugi', 'vmacro15370' => 'vma', 'vmacro15371' => 'vma', 'vmacro15372' => 'vma', 'vmacro15373' => 'vma', 'vmacro15374' => 'vma', 'VMungo0720G2826' => 'vmu', 'Zm00001eb116960' => 'zma', 'Zm00001eb301260' => 'zma', 'Zm00001eb301270' => 'zma' ), 'gf_id' => 'HOM05D001460', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001460' ), 'data_identifier' => 'HOM05D001460', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001460', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '433', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p22980' => 'bna', 'A01p32340' => 'bna', 'A03p42970' => 'bna', 'A05p25880' => 'bna', 'Aa31LG8G9320' => 'aar', 'Aa31LG8G9330' => 'aar', 'Aa31LG8G9340' => 'aar', 'Aa31sc221G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1034' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1528' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.829' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2222' => 'aag', 'Ah.12g058830' => 'amhyb', 'Ah.12g058840' => 'amhyb', 'AL3G37160' => 'aly', 'AL7G41310' => 'aly', 'Aqoxy5G00395' => 'aox', 'Aqoxy5G00396' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0C8NZA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5185HY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JZ1PRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MD3LS0' => 'arhy', 'AT3G22840' => 'ath', 'AT4G14690' => 'ath', 'ATR0665G054' => 'atr', 'Atru.chr4.2344' => 'acertr', 'Atru.chr4.2346' => 'acertr', 'Atru.chr4.2347' => 'acertr', 'Atru.chr4.2348' => 'acertr', 'Atru.chr4.2355' => 'acertr', 'Atru.chr4.2356' => 'acertr', 'Atru.chr4.2358' => 'acertr', 'Atru.chr4.2359' => 'acertr', 'Atru.chr4.2360' => 'acertr', 'Atru.chr4.2361' => 'acertr', 'AUR62030476' => 'cqu', 'AUR62030478' => 'cqu', 'AUR62030819' => 'cqu', 'AUR62030820' => 'cqu', 'BcaB03g14648' => 'bca', 'BcaB04g20492' => 'bca', 'BcaB06g26399' => 'bca', 'BcaC01g03416' => 'bca', 'BcaC01g03419' => 'bca', 'BcaC01g03421' => 'bca', 'BcaC01g03424' => 'bca', 'BcaC05g28012' => 'bca', 'BcaC09g49212' => 'bca', 'BcaC09g50140' => 'bca', 'BcaNung00346' => 'bca', 'BolC1t02785H' => 'bol', 'BolC1t04095H' => 'bol', 'BolC3t17545H' => 'bol', 'BolC5t32769H' => 'bol', 'BraA01t02211Z' => 'bra', 'BraA01t03359Z' => 'bra', 'BraA03t13441Z' => 'bra', 'BraA05t21476Z' => 'bra', 'C01p28420' => 'bna', 'C01p41350' => 'bna', 'C03p52750' => 'bna', 'C03p52780' => 'bna', 'C05p40270' => 'bna', 'CAN.G1437.9' => 'can', 'CANSAT78G0035' => 'cansat', 'CANSAT78G1036' => 'cansat', 'CANSAT78G2272' => 'cansat', 'CANSAT78G2478' => 'cansat', 'CARHR098700' => 'chi', 'CARHR221120' => 'chi', 'CARHR221150' => 'chi', 'Carub.0003s2297' => 'cru', 'Carub.0007s2749' => 'cru', 'Carub.0007s2750' => 'cru', 'Carub.0007s2751' => 'cru', 'Ca_10849_v3' => 'car', 'Cc03_g04300' => 'ccan', 'CDE02G3648' => 'cde', 'CDE05G0060' => 'cde', 'CDE05G0692' => 'cde', 'CDE05G2285' => 'cde', 'CDE05G2884' => 'cde', 'CDE05G3072' => 'cde', 'Cfa008439' => 'cfa', 'Cfa008441' => 'cfa', 'Cfa008443' => 'cfa', 'Cfa008448' => 'cfa', 'Ciclev10005974m.g' => 'ccl', 'Ciclev10006006m.g' => 'ccl', 'Ciclev10006775m.g' => 'ccl', 'CiPaw.02G120400' => 'cil', 'CiPaw.02G120500' => 'cil', 'CiPaw.02G120600' => 'cil', 'ClCG05G004850' => 'cla', 'COL.COLO4_21566' => 'col', 'Cpa.g.sc44.124' => 'cpa', 'Cre07.g320400' => 'cre', 'Cre07.g320450' => 'cre', 'Cre08.g384650' => 'cre', 'Cre09.g393173' => 'cre', 'Cre09.g394325' => 'cre', 'Cre14.g626750' => 'cre', 'Cre16.g679250' => 'cre', 'CsaV3_3G012890' => 'csa', 'CSS0010865' => 'camsi', 'CSS0044338' => 'camsi', 'DCAR_002366' => 'dca', 'DCAR_030687' => 'dca', 'DCAR_030688' => 'dca', 'Dinv14047' => 'din', 'Dinv14048' => 'din', 'Duzib151G0105' => 'dzi', 'Duzib151G0114' => 'dzi', 'Duzib212G1029' => 'dzi', 'ECA232G3536' => 'eca', 'ECA240G0786' => 'eca', 'ECA240G1802' => 'eca', 'ECA240G3760' => 'eca', 'ECA240G3920' => 'eca', 'EL10Ac5g12536' => 'bvu', 'EL10Ac5g12537' => 'bvu', 'EL10Ac5g12538' => 'bvu', 'Eucgr.B01004' => 'egr', 'Eucgr.B01006' => 'egr', 'Eucgr.B01007' => 'egr', 'Eucgr.B01008' => 'egr', 'Eucgr.B01895' => 'egr', 'Eucgr.B01896' => 'egr', 'FAN04G1456' => 'fan', 'FAN08G1769' => 'fan', 'FAN08G2160' => 'fan', 'FAN13G2403' => 'fan', 'FAN13G3303' => 'fan', 'FAN15G2435' => 'fan', 'FAN17G0672' => 'fan', 'FAN17G2441' => 'fan', 'FAN18G1024' => 'fan', 'FAN22G1458' => 'fan', 'FAN24G0037' => 'fan', 'FAN24G0429' => 'fan', 'FAN24G2387' => 'fan', 'FAN27G2746' => 'fan', 'FvH4_2g20400' => 'fve', 'FvH4_2g20420' => 'fve', 'FvH4_2g20430' => 'fve', 'FvH4_4g01270' => 'fve', 'FvH4_4g01290' => 'fve', 'FvH4_4g01300' => 'fve', 'FvH4_4g01310' => 'fve', 'FvH4_4g01330' => 'fve', 'FvH4_5g09070' => 'fve', 'Glyma.10G243800' => 'gma', 'Glyma.20G150600' => 'gma', 'Gohir.A09G219200' => 'ghi', 'Gohir.A09G219300' => 'ghi', 'Gohir.D09G221400' => 'ghi', 'Gohir.D09G221500' => 'ghi', 'Gorai.006G242600' => 'gra', 'Gorai.006G242700' => 'gra', 'GSVIVG01018044001' => 'vvi', 'HanXRQChr03g0083821' => 'han', 'HanXRQChr03g0083841' => 'han', 'HanXRQChr03g0083881' => 'han', 'HanXRQChr03g0083901' => 'han', 'HanXRQChr03g0083921' => 'han', 'HanXRQChr03g0085331' => 'han', 'HanXRQChr03g0085361' => 'han', 'HanXRQChr03g0085411' => 'han', 'HanXRQChr03g0085421' => 'han', 'HanXRQChr03g0085431' => 'han', 'HanXRQChr08g0221991' => 'han', 'HanXRQChr11g0336061' => 'han', 'HanXRQChr11g0336411' => 'han', 'Haze_11234' => 'cav', 'Hma1.2p1_0549F.1_g177010' => 'hma', 'Hma1.2p1_0602F.1_g187630' => 'hma', 'Hund14876' => 'sun', 'Hund14879' => 'sun', 'Lalb_Chr06g0160741' => 'lal', 'Lalb_Chr21g0304781' => 'lal', 'Lj3A726G19' => 'lonja', 'Lj3A726T23' => 'lonja', 'Lj3A726T24' => 'lonja', 'Lj3A726T25' => 'lonja', 'Lj3A727T17' => 'lonja', 'Lj3C726T0' => 'lonja', 'Lj3C726T2' => 'lonja', 'Lj3P725T35' => 'lonja', 'Lj3P727T10' => 'lonja', 'Lj3P727T12' => 'lonja', 'Lj3P727T14' => 'lonja', 'Lj5g0023109' => 'lja', 'Lj6P646T44' => 'lonja', 'Lsat_1_v5_gn_6_75760' => 'lsa', 'Lsat_1_v5_gn_6_75800' => 'lsa', 'Lsat_1_v5_gn_6_75900' => 'lsa', 'Lsat_1_v5_gn_6_76240' => 'lsa', 'Lsat_1_v5_gn_6_76441' => 'lsa', 'Lsat_1_v5_gn_6_76700' => 'lsa', 'Lsat_1_v5_gn_6_76760' => 'lsa', 'Manes.15G033100' => 'mes', 'Mapoly0004s0074' => 'mpo', 'Mapoly0004s0075' => 'mpo', 'Mapoly0004s0163' => 'mpo', 'Mapoly0004s0164' => 'mpo', 'Mapoly0021s0018' => 'mpo', 'Mapoly0041s0136' => 'mpo', 'Mapoly0041s0137' => 'mpo', 'Mapoly0041s0138' => 'mpo', 'Mapoly0041s0139' => 'mpo', 'Mapoly0041s0141' => 'mpo', 'Mapoly0041s0142' => 'mpo', 'Mapoly0041s0143' => 'mpo', 'Mapoly0041s0144' => 'mpo', 'Mapoly0041s0145' => 'mpo', 'Mapoly0047s0106' => 'mpo', 'Mapoly0047s0108' => 'mpo', 'Mapoly0050s0051' => 'mpo', 'Mapoly0050s0052' => 'mpo', 'Mapoly0050s0053' => 'mpo', 'Mapoly0058s0013' => 'mpo', 'Mapoly0091s0078' => 'mpo', 'Mapoly0091s0079' => 'mpo', 'Mapoly0091s0080' => 'mpo', 'Mapoly0091s0081' => 'mpo', 'Mapoly0278s0004' => 'mpo', 'Mapoly0278s0005' => 'mpo', 'Mapoly0278s0006' => 'mpo', 'MBI11_g30648_MAGBIO' => 'mbi', 'MCO03G194' => 'mco', 'MCO03G590' => 'mco', 'MCO07G312' => 'mco', 'MCO10G318' => 'mco', 'MCO12G244' => 'mco', 'MCO13G148' => 'mco', 'MCO13G194' => 'mco', 'MCO16G238' => 'mco', 'MD06G1134100' => 'mdo', 'MD13G1200100' => 'mdo', 'MD13G1200300' => 'mdo', 'MD13G1200600' => 'mdo', 'MD14G1150400' => 'mdo', 'MD16G1200000' => 'mdo', 'Medtr1g102570' => 'mtr', 'Medtr1g102780' => 'mtr', 'Medtr1g102800' => 'mtr', 'Medtr1g102810' => 'mtr', 'Medtr1g102830' => 'mtr', 'MELO3C006499.2' => 'cme', 'Migut.G00385' => 'egut', 'MSTRG.4063' => 'ama', 'Nitab4.5_0000090g0260' => 'nta', 'Nitab4.5_0000977g0030' => 'nta', 'Nitab4.5_0002541g0040' => 'nta', 'Nitab4.5_0007068g0040' => 'nta', 'Nn005s41408' => 'nnu', 'Nn005s41410' => 'nnu', 'Oeu010310.1' => 'oeu', 'Oeu010311.1' => 'oeu', 'Oeu043472.1' => 'oeu', 'Os01g0246400' => 'osa', 'Os04g0267950' => 'osa', 'Os07g0178700' => 'osa', 'Os07g0178800' => 'osa', 'Peaxi162Scf00316g00046' => 'pax', 'Peaxi162Scf00316g00049' => 'pax', 'Peaxi162Scf00316g00059' => 'pax', 'Peaxi162Scf00316g00328' => 'pax', 'Peaxi162Scf00316g00329' => 'pax', 'Peaxi162Scf00316g00411' => 'pax', 'Peaxi162Scf00316g00521' => 'pax', 'Peaxi162Scf00492g00068' => 'pax', 'Peaxi162Scf35631g00002' => 'pax', 'PGR142G3720' => 'pgr', 'PGSC0003DMG400006442' => 'stu', 'Phvul.007G062000' => 'pvu', 'Potri.008G157750' => 'ptr', 'Potri.008G157900' => 'ptr', 'Potri.008G158000' => 'ptr', 'Potri.008G158200' => 'ptr', 'Pp3c11_7280' => 'ppa', 'Pp3c11_7980' => 'ppa', 'Pp3c12_19450' => 'ppa', 'Pp3c14_1480' => 'ppa', 'Pp3c14_1501' => 'ppa', 'Pp3c16_4900' => 'ppa', 'Pp3c16_5010' => 'ppa', 'Pp3c16_5060' => 'ppa', 'Pp3c19_18250' => 'ppa', 'Pp3c23_8530' => 'ppa', 'Pp3c23_8550' => 'ppa', 'Pp3c24_9670' => 'ppa', 'Pp3c2_21390' => 'ppa', 'Pp3c2_31380' => 'ppa', 'Pp3c3_16620' => 'ppa', 'Pp3c3_8090' => 'ppa', 'Pp3c3_8110' => 'ppa', 'Pp3c3_8130' => 'ppa', 'Pp3c3_8150' => 'ppa', 'Pp3c4_14320' => 'ppa', 'Pp3c6_2560' => 'ppa', 'Pp3c9_16700' => 'ppa', 'PRCOL_00000234' => 'pco', 'PRCOL_00000235' => 'pco', 'PRCOL_00000777' => 'pco', 'PRCOL_00002344' => 'pco', 'PRCOL_00002372' => 'pco', 'PRCOL_00006120' => 'pco', 'Prupe.1G021400' => 'ppe', 'Prupe.1G021500' => 'ppe', 'Prupe.1G021600' => 'ppe', 'Prupe.1G021700' => 'ppe', 'Prupe.1G021800' => 'ppe', 'Prupe.5G145100' => 'ppe', 'Psat6g204040' => 'psa', 'Psat6g204800' => 'psa', 'Psat6g204920' => 'psa', 'Psat6g204960' => 'psa', 'Psat6g205080' => 'psa', 'PSO017G0271' => 'pso', 'PSO017G1276' => 'pso', 'PSO017G1429' => 'pso', 'PSO017G1861' => 'pso', 'PSO017G2787' => 'pso', 'PSO017G4466' => 'pso', 'PSO017G5118' => 'pso', 'PSO017G5420' => 'pso', 'PSO063G3678' => 'pso', 'PSO210G0546' => 'pso', 'PSO317G0001' => 'pso', 'PSO357G0512' => 'pso', 'PSO478G2682' => 'pso', 'PSO647G0001' => 'pso', 'PSO675G0001' => 'pso', 'PSO675G2699' => 'pso', 'PSO675G2849' => 'pso', 'PSO675G4991' => 'pso', 'PSO689G0001' => 'pso', 'QL06p000916' => 'qlo', 'QL06p000921' => 'qlo', 'QL06p001398' => 'qlo', 'QL06p001407' => 'qlo', 'QL06p002031' => 'qlo', 'RcHm_v2.0_Chr4g0387791' => 'rch', 'RcHm_v2.0_Chr4g0387801' => 'rch', 'RcHm_v2.0_Chr6g0286501' => 'rch', 'RcHm_v2.0_Chr6g0286511' => 'rch', 'RcHm_v2.0_Chr6g0286521' => 'rch', 'RcHm_v2.0_Chr6g0286531' => 'rch', 'RcHm_v2.0_Chr7g0189141' => 'rch', 'Rhsim02G0028700' => 'rsi', 'Rhsim02G0028800' => 'rsi', 'Rhsim02G0028900' => 'rsi', 'Rhsim02G0029000' => 'rsi', 'Rhsim02G0029100' => 'rsi', 'Rhsim02G0029200' => 'rsi', 'Rhsim02G0029300' => 'rsi', 'Rhsim02G0029400' => 'rsi', 'Rhsim02G0029500' => 'rsi', 'Rhsim02G0029600' => 'rsi', 'RhsimUnG0024000' => 'rsi', 'RhsimUnG0024100' => 'rsi', 'RhsimUnG0024200' => 'rsi', 'RhsimUnG0024300' => 'rsi', 'RhsimUnG0024400' => 'rsi', 'RhsimUnG0024500' => 'rsi', 'RhsimUnG0024700' => 'rsi', 'RhsimUnG0024800' => 'rsi', 'RhsimUnG0024900' => 'rsi', 'RhsimUnG0025100' => 'rsi', 'Sabra08G0120200' => 'sbr', 'Sabra08G0120300' => 'sbr', 'Sabra08G0120500' => 'sbr', 'Sabra08G0120600' => 'sbr', 'Sabra10G0158900' => 'sbr', 'SalBow2G3492' => 'sbo', 'Sc13g0004760' => 'sci', 'Sc13g0004770' => 'sci', 'Sed0003417' => 'sed', 'Sed0019750' => 'sed', 'SEGI_03419' => 'sgi', 'SEGI_05907' => 'sgi', 'SEGI_10682' => 'sgi', 'SEGI_13528' => 'sgi', 'SEGI_16081' => 'sgi', 'SEGI_19370' => 'sgi', 'SEGI_21015' => 'sgi', 'SEGI_21944' => 'sgi', 'SEGI_32906' => 'sgi', 'SEGI_33093' => 'sgi', 'SEGI_36110' => 'sgi', 'SEGI_40397' => 'sgi', 'SGA_v2.0_scaffold191G40426' => 'sas', 'SGA_v2.0_scaffold353G49717' => 'sas', 'SGA_v2.0_scaffold50G18550' => 'sas', 'SMO119G0173' => 'smo', 'SMO172G0002' => 'smo', 'Solyc09g082690.3' => 'sly', 'Solyc09g082700.2' => 'sly', 'Sopen09g031550' => 'spe', 'Sopen09g031560' => 'spe', 'Sp3g20540' => 'spa', 'Sp7g07580' => 'spa', 'TAR134G0002' => 'tar', 'TAR236G0001' => 'tar', 'TAR365G0892' => 'tar', 'TAR636G0166' => 'tar', 'TAR636G0646' => 'tar', 'TAR636G0869' => 'tar', 'TAR636G1317' => 'tar', 'TAR636G1744' => 'tar', 'TAR636G3358' => 'tar', 'TAR636G3436' => 'tar', 'THA.LOC104803047' => 'tha', 'Thecc.04G238900' => 'tca', 'Thhalv10021557m.g' => 'esa', 'Thhalv10026318m.g' => 'esa', 'Thhalv10026335m.g' => 'esa', 'TPR.G17433' => 'tpr', 'TPR.G18915' => 'tpr', 'TPR.G26125' => 'tpr', 'TWI09G0677' => 'twi', 'TWI73G0287' => 'twi', 'unitig_748.g8326' => 'ugi', 'vmacro15370' => 'vma', 'vmacro15371' => 'vma', 'vmacro15372' => 'vma', 'vmacro15373' => 'vma', 'vmacro15374' => 'vma', 'VMungo0720G2826' => 'vmu', 'Zm00001eb116960' => 'zma', 'Zm00001eb301260' => 'zma', 'Zm00001eb301270' => 'zma' ) $gf_id = 'HOM05D001460' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001460' ) $data_identifier = 'HOM05D001460' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 4, 'aag' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 2, 'aox' => (int) 2, 'arhy' => (int) 4, 'ath' => (int) 2, 'atr' => (int) 1, 'acertr' => (int) 10, 'cqu' => (int) 4, 'bca' => (int) 11, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 1, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 1, 'ccan' => (int) 1, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 1, 'col' => (int) 1, 'cpa' => (int) 1, 'cre' => (int) 7, 'csa' => (int) 1, 'camsi' => (int) 2, 'dca' => (int) 3, 'din' => (int) 2, 'dzi' => (int) 3, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 14, 'fve' => (int) 9, 'gma' => (int) 2, 'ghi' => (int) 4, 'gra' => (int) 2, 'vvi' => (int) 1, 'han' => (int) 13, 'cav' => (int) 1, 'hma' => (int) 2, 'sun' => (int) 2, 'lal' => (int) 2, 'lonja' => (int) 12, 'lja' => (int) 1, 'lsa' => (int) 7, 'mes' => (int) 1, 'mpo' => (int) 27, 'mbi' => (int) 1, 'mco' => (int) 8, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 1, 'egut' => (int) 1, 'ama' => (int) 1, 'nta' => (int) 4, 'nnu' => (int) 2, 'oeu' => (int) 3, 'osa' => (int) 4, 'pax' => (int) 9, 'pgr' => (int) 1, 'stu' => (int) 1, 'pvu' => (int) 1, 'ptr' => (int) 4, 'ppa' => (int) 22, 'pco' => (int) 6, 'ppe' => (int) 6, 'psa' => (int) 5, 'pso' => (int) 19, 'qlo' => (int) 5, 'rch' => (int) 7, 'rsi' => (int) 20, 'sbr' => (int) 5, 'sbo' => (int) 1, 'sci' => (int) 2, 'sed' => (int) 2, 'sgi' => (int) 12, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 2, 'tar' => (int) 10, 'tha' => (int) 1, 'tca' => (int) 1, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 2, 'ugi' => (int) 1, 'vma' => (int) 5, 'vmu' => (int) 1, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb301270' $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' => 'HOM05D001460', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '433', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p22980' => 'bna', 'A01p32340' => 'bna', 'A03p42970' => 'bna', 'A05p25880' => 'bna', 'Aa31LG8G9320' => 'aar', 'Aa31LG8G9330' => 'aar', 'Aa31LG8G9340' => 'aar', 'Aa31sc221G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1034' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1528' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.829' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2222' => 'aag', 'Ah.12g058830' => 'amhyb', 'Ah.12g058840' => 'amhyb', 'AL3G37160' => 'aly', 'AL7G41310' => 'aly', 'Aqoxy5G00395' => 'aox', 'Aqoxy5G00396' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0C8NZA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5185HY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JZ1PRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MD3LS0' => 'arhy', 'AT3G22840' => 'ath', 'AT4G14690' => 'ath', 'ATR0665G054' => 'atr', 'Atru.chr4.2344' => 'acertr', 'Atru.chr4.2346' => 'acertr', 'Atru.chr4.2347' => 'acertr', 'Atru.chr4.2348' => 'acertr', 'Atru.chr4.2355' => 'acertr', 'Atru.chr4.2356' => 'acertr', 'Atru.chr4.2358' => 'acertr', 'Atru.chr4.2359' => 'acertr', 'Atru.chr4.2360' => 'acertr', 'Atru.chr4.2361' => 'acertr', 'AUR62030476' => 'cqu', 'AUR62030478' => 'cqu', 'AUR62030819' => 'cqu', 'AUR62030820' => 'cqu', 'BcaB03g14648' => 'bca', 'BcaB04g20492' => 'bca', 'BcaB06g26399' => 'bca', 'BcaC01g03416' => 'bca', 'BcaC01g03419' => 'bca', 'BcaC01g03421' => 'bca', 'BcaC01g03424' => 'bca', 'BcaC05g28012' => 'bca', 'BcaC09g49212' => 'bca', 'BcaC09g50140' => 'bca', 'BcaNung00346' => 'bca', 'BolC1t02785H' => 'bol', 'BolC1t04095H' => 'bol', 'BolC3t17545H' => 'bol', 'BolC5t32769H' => 'bol', 'BraA01t02211Z' => 'bra', 'BraA01t03359Z' => 'bra', 'BraA03t13441Z' => 'bra', 'BraA05t21476Z' => 'bra', 'C01p28420' => 'bna', 'C01p41350' => 'bna', 'C03p52750' => 'bna', 'C03p52780' => 'bna', 'C05p40270' => 'bna', 'CAN.G1437.9' => 'can', 'CANSAT78G0035' => 'cansat', 'CANSAT78G1036' => 'cansat', 'CANSAT78G2272' => 'cansat', 'CANSAT78G2478' => 'cansat', 'CARHR098700' => 'chi', 'CARHR221120' => 'chi', 'CARHR221150' => 'chi', 'Carub.0003s2297' => 'cru', 'Carub.0007s2749' => 'cru', 'Carub.0007s2750' => 'cru', 'Carub.0007s2751' => 'cru', 'Ca_10849_v3' => 'car', 'Cc03_g04300' => 'ccan', 'CDE02G3648' => 'cde', 'CDE05G0060' => 'cde', 'CDE05G0692' => 'cde', 'CDE05G2285' => 'cde', 'CDE05G2884' => 'cde', 'CDE05G3072' => 'cde', 'Cfa008439' => 'cfa', 'Cfa008441' => 'cfa', 'Cfa008443' => 'cfa', 'Cfa008448' => 'cfa', 'Ciclev10005974m.g' => 'ccl', 'Ciclev10006006m.g' => 'ccl', 'Ciclev10006775m.g' => 'ccl', 'CiPaw.02G120400' => 'cil', 'CiPaw.02G120500' => 'cil', 'CiPaw.02G120600' => 'cil', 'ClCG05G004850' => 'cla', 'COL.COLO4_21566' => 'col', 'Cpa.g.sc44.124' => 'cpa', 'Cre07.g320400' => 'cre', 'Cre07.g320450' => 'cre', 'Cre08.g384650' => 'cre', 'Cre09.g393173' => 'cre', 'Cre09.g394325' => 'cre', 'Cre14.g626750' => 'cre', 'Cre16.g679250' => 'cre', 'CsaV3_3G012890' => 'csa', 'CSS0010865' => 'camsi', 'CSS0044338' => 'camsi', 'DCAR_002366' => 'dca', 'DCAR_030687' => 'dca', 'DCAR_030688' => 'dca', 'Dinv14047' => 'din', 'Dinv14048' => 'din', 'Duzib151G0105' => 'dzi', 'Duzib151G0114' => 'dzi', 'Duzib212G1029' => 'dzi', 'ECA232G3536' => 'eca', 'ECA240G0786' => 'eca', 'ECA240G1802' => 'eca', 'ECA240G3760' => 'eca', 'ECA240G3920' => 'eca', 'EL10Ac5g12536' => 'bvu', 'EL10Ac5g12537' => 'bvu', 'EL10Ac5g12538' => 'bvu', 'Eucgr.B01004' => 'egr', 'Eucgr.B01006' => 'egr', 'Eucgr.B01007' => 'egr', 'Eucgr.B01008' => 'egr', 'Eucgr.B01895' => 'egr', 'Eucgr.B01896' => 'egr', 'FAN04G1456' => 'fan', 'FAN08G1769' => 'fan', 'FAN08G2160' => 'fan', 'FAN13G2403' => 'fan', 'FAN13G3303' => 'fan', 'FAN15G2435' => 'fan', 'FAN17G0672' => 'fan', 'FAN17G2441' => 'fan', 'FAN18G1024' => 'fan', 'FAN22G1458' => 'fan', 'FAN24G0037' => 'fan', 'FAN24G0429' => 'fan', 'FAN24G2387' => 'fan', 'FAN27G2746' => 'fan', 'FvH4_2g20400' => 'fve', 'FvH4_2g20420' => 'fve', 'FvH4_2g20430' => 'fve', 'FvH4_4g01270' => 'fve', 'FvH4_4g01290' => 'fve', 'FvH4_4g01300' => 'fve', 'FvH4_4g01310' => 'fve', 'FvH4_4g01330' => 'fve', 'FvH4_5g09070' => 'fve', 'Glyma.10G243800' => 'gma', 'Glyma.20G150600' => 'gma', 'Gohir.A09G219200' => 'ghi', 'Gohir.A09G219300' => 'ghi', 'Gohir.D09G221400' => 'ghi', 'Gohir.D09G221500' => 'ghi', 'Gorai.006G242600' => 'gra', 'Gorai.006G242700' => 'gra', 'GSVIVG01018044001' => 'vvi', 'HanXRQChr03g0083821' => 'han', 'HanXRQChr03g0083841' => 'han', 'HanXRQChr03g0083881' => 'han', 'HanXRQChr03g0083901' => 'han', 'HanXRQChr03g0083921' => 'han', 'HanXRQChr03g0085331' => 'han', 'HanXRQChr03g0085361' => 'han', 'HanXRQChr03g0085411' => 'han', 'HanXRQChr03g0085421' => 'han', 'HanXRQChr03g0085431' => 'han', 'HanXRQChr08g0221991' => 'han', 'HanXRQChr11g0336061' => 'han', 'HanXRQChr11g0336411' => 'han', 'Haze_11234' => 'cav', 'Hma1.2p1_0549F.1_g177010' => 'hma', 'Hma1.2p1_0602F.1_g187630' => 'hma', 'Hund14876' => 'sun', 'Hund14879' => 'sun', 'Lalb_Chr06g0160741' => 'lal', 'Lalb_Chr21g0304781' => 'lal', 'Lj3A726G19' => 'lonja', 'Lj3A726T23' => 'lonja', 'Lj3A726T24' => 'lonja', 'Lj3A726T25' => 'lonja', 'Lj3A727T17' => 'lonja', 'Lj3C726T0' => 'lonja', 'Lj3C726T2' => 'lonja', 'Lj3P725T35' => 'lonja', 'Lj3P727T10' => 'lonja', 'Lj3P727T12' => 'lonja', 'Lj3P727T14' => 'lonja', 'Lj5g0023109' => 'lja', 'Lj6P646T44' => 'lonja', 'Lsat_1_v5_gn_6_75760' => 'lsa', 'Lsat_1_v5_gn_6_75800' => 'lsa', 'Lsat_1_v5_gn_6_75900' => 'lsa', 'Lsat_1_v5_gn_6_76240' => 'lsa', 'Lsat_1_v5_gn_6_76441' => 'lsa', 'Lsat_1_v5_gn_6_76700' => 'lsa', 'Lsat_1_v5_gn_6_76760' => 'lsa', 'Manes.15G033100' => 'mes', 'Mapoly0004s0074' => 'mpo', 'Mapoly0004s0075' => 'mpo', 'Mapoly0004s0163' => 'mpo', 'Mapoly0004s0164' => 'mpo', 'Mapoly0021s0018' => 'mpo', 'Mapoly0041s0136' => 'mpo', 'Mapoly0041s0137' => 'mpo', 'Mapoly0041s0138' => 'mpo', 'Mapoly0041s0139' => 'mpo', 'Mapoly0041s0141' => 'mpo', 'Mapoly0041s0142' => 'mpo', 'Mapoly0041s0143' => 'mpo', 'Mapoly0041s0144' => 'mpo', 'Mapoly0041s0145' => 'mpo', 'Mapoly0047s0106' => 'mpo', 'Mapoly0047s0108' => 'mpo', 'Mapoly0050s0051' => 'mpo', 'Mapoly0050s0052' => 'mpo', 'Mapoly0050s0053' => 'mpo', 'Mapoly0058s0013' => 'mpo', 'Mapoly0091s0078' => 'mpo', 'Mapoly0091s0079' => 'mpo', 'Mapoly0091s0080' => 'mpo', 'Mapoly0091s0081' => 'mpo', 'Mapoly0278s0004' => 'mpo', 'Mapoly0278s0005' => 'mpo', 'Mapoly0278s0006' => 'mpo', 'MBI11_g30648_MAGBIO' => 'mbi', 'MCO03G194' => 'mco', 'MCO03G590' => 'mco', 'MCO07G312' => 'mco', 'MCO10G318' => 'mco', 'MCO12G244' => 'mco', 'MCO13G148' => 'mco', 'MCO13G194' => 'mco', 'MCO16G238' => 'mco', 'MD06G1134100' => 'mdo', 'MD13G1200100' => 'mdo', 'MD13G1200300' => 'mdo', 'MD13G1200600' => 'mdo', 'MD14G1150400' => 'mdo', 'MD16G1200000' => 'mdo', 'Medtr1g102570' => 'mtr', 'Medtr1g102780' => 'mtr', 'Medtr1g102800' => 'mtr', 'Medtr1g102810' => 'mtr', 'Medtr1g102830' => 'mtr', 'MELO3C006499.2' => 'cme', 'Migut.G00385' => 'egut', 'MSTRG.4063' => 'ama', 'Nitab4.5_0000090g0260' => 'nta', 'Nitab4.5_0000977g0030' => 'nta', 'Nitab4.5_0002541g0040' => 'nta', 'Nitab4.5_0007068g0040' => 'nta', 'Nn005s41408' => 'nnu', 'Nn005s41410' => 'nnu', 'Oeu010310.1' => 'oeu', 'Oeu010311.1' => 'oeu', 'Oeu043472.1' => 'oeu', 'Os01g0246400' => 'osa', 'Os04g0267950' => 'osa', 'Os07g0178700' => 'osa', 'Os07g0178800' => 'osa', 'Peaxi162Scf00316g00046' => 'pax', 'Peaxi162Scf00316g00049' => 'pax', 'Peaxi162Scf00316g00059' => 'pax', 'Peaxi162Scf00316g00328' => 'pax', 'Peaxi162Scf00316g00329' => 'pax', 'Peaxi162Scf00316g00411' => 'pax', 'Peaxi162Scf00316g00521' => 'pax', 'Peaxi162Scf00492g00068' => 'pax', 'Peaxi162Scf35631g00002' => 'pax', 'PGR142G3720' => 'pgr', 'PGSC0003DMG400006442' => 'stu', 'Phvul.007G062000' => 'pvu', 'Potri.008G157750' => 'ptr', 'Potri.008G157900' => 'ptr', 'Potri.008G158000' => 'ptr', 'Potri.008G158200' => 'ptr', 'Pp3c11_7280' => 'ppa', 'Pp3c11_7980' => 'ppa', 'Pp3c12_19450' => 'ppa', 'Pp3c14_1480' => 'ppa', 'Pp3c14_1501' => 'ppa', 'Pp3c16_4900' => 'ppa', 'Pp3c16_5010' => 'ppa', 'Pp3c16_5060' => 'ppa', 'Pp3c19_18250' => 'ppa', 'Pp3c23_8530' => 'ppa', 'Pp3c23_8550' => 'ppa', 'Pp3c24_9670' => 'ppa', 'Pp3c2_21390' => 'ppa', 'Pp3c2_31380' => 'ppa', 'Pp3c3_16620' => 'ppa', 'Pp3c3_8090' => 'ppa', 'Pp3c3_8110' => 'ppa', 'Pp3c3_8130' => 'ppa', 'Pp3c3_8150' => 'ppa', 'Pp3c4_14320' => 'ppa', 'Pp3c6_2560' => 'ppa', 'Pp3c9_16700' => 'ppa', 'PRCOL_00000234' => 'pco', 'PRCOL_00000235' => 'pco', 'PRCOL_00000777' => 'pco', 'PRCOL_00002344' => 'pco', 'PRCOL_00002372' => 'pco', 'PRCOL_00006120' => 'pco', 'Prupe.1G021400' => 'ppe', 'Prupe.1G021500' => 'ppe', 'Prupe.1G021600' => 'ppe', 'Prupe.1G021700' => 'ppe', 'Prupe.1G021800' => 'ppe', 'Prupe.5G145100' => 'ppe', 'Psat6g204040' => 'psa', 'Psat6g204800' => 'psa', 'Psat6g204920' => 'psa', 'Psat6g204960' => 'psa', 'Psat6g205080' => 'psa', 'PSO017G0271' => 'pso', 'PSO017G1276' => 'pso', 'PSO017G1429' => 'pso', 'PSO017G1861' => 'pso', 'PSO017G2787' => 'pso', 'PSO017G4466' => 'pso', 'PSO017G5118' => 'pso', 'PSO017G5420' => 'pso', 'PSO063G3678' => 'pso', 'PSO210G0546' => 'pso', 'PSO317G0001' => 'pso', 'PSO357G0512' => 'pso', 'PSO478G2682' => 'pso', 'PSO647G0001' => 'pso', 'PSO675G0001' => 'pso', 'PSO675G2699' => 'pso', 'PSO675G2849' => 'pso', 'PSO675G4991' => 'pso', 'PSO689G0001' => 'pso', 'QL06p000916' => 'qlo', 'QL06p000921' => 'qlo', 'QL06p001398' => 'qlo', 'QL06p001407' => 'qlo', 'QL06p002031' => 'qlo', 'RcHm_v2.0_Chr4g0387791' => 'rch', 'RcHm_v2.0_Chr4g0387801' => 'rch', 'RcHm_v2.0_Chr6g0286501' => 'rch', 'RcHm_v2.0_Chr6g0286511' => 'rch', 'RcHm_v2.0_Chr6g0286521' => 'rch', 'RcHm_v2.0_Chr6g0286531' => 'rch', 'RcHm_v2.0_Chr7g0189141' => 'rch', 'Rhsim02G0028700' => 'rsi', 'Rhsim02G0028800' => 'rsi', 'Rhsim02G0028900' => 'rsi', 'Rhsim02G0029000' => 'rsi', 'Rhsim02G0029100' => 'rsi', 'Rhsim02G0029200' => 'rsi', 'Rhsim02G0029300' => 'rsi', 'Rhsim02G0029400' => 'rsi', 'Rhsim02G0029500' => 'rsi', 'Rhsim02G0029600' => 'rsi', 'RhsimUnG0024000' => 'rsi', 'RhsimUnG0024100' => 'rsi', 'RhsimUnG0024200' => 'rsi', 'RhsimUnG0024300' => 'rsi', 'RhsimUnG0024400' => 'rsi', 'RhsimUnG0024500' => 'rsi', 'RhsimUnG0024700' => 'rsi', 'RhsimUnG0024800' => 'rsi', 'RhsimUnG0024900' => 'rsi', 'RhsimUnG0025100' => 'rsi', 'Sabra08G0120200' => 'sbr', 'Sabra08G0120300' => 'sbr', 'Sabra08G0120500' => 'sbr', 'Sabra08G0120600' => 'sbr', 'Sabra10G0158900' => 'sbr', 'SalBow2G3492' => 'sbo', 'Sc13g0004760' => 'sci', 'Sc13g0004770' => 'sci', 'Sed0003417' => 'sed', 'Sed0019750' => 'sed', 'SEGI_03419' => 'sgi', 'SEGI_05907' => 'sgi', 'SEGI_10682' => 'sgi', 'SEGI_13528' => 'sgi', 'SEGI_16081' => 'sgi', 'SEGI_19370' => 'sgi', 'SEGI_21015' => 'sgi', 'SEGI_21944' => 'sgi', 'SEGI_32906' => 'sgi', 'SEGI_33093' => 'sgi', 'SEGI_36110' => 'sgi', 'SEGI_40397' => 'sgi', 'SGA_v2.0_scaffold191G40426' => 'sas', 'SGA_v2.0_scaffold353G49717' => 'sas', 'SGA_v2.0_scaffold50G18550' => 'sas', 'SMO119G0173' => 'smo', 'SMO172G0002' => 'smo', 'Solyc09g082690.3' => 'sly', 'Solyc09g082700.2' => 'sly', 'Sopen09g031550' => 'spe', 'Sopen09g031560' => 'spe', 'Sp3g20540' => 'spa', 'Sp7g07580' => 'spa', 'TAR134G0002' => 'tar', 'TAR236G0001' => 'tar', 'TAR365G0892' => 'tar', 'TAR636G0166' => 'tar', 'TAR636G0646' => 'tar', 'TAR636G0869' => 'tar', 'TAR636G1317' => 'tar', 'TAR636G1744' => 'tar', 'TAR636G3358' => 'tar', 'TAR636G3436' => 'tar', 'THA.LOC104803047' => 'tha', 'Thecc.04G238900' => 'tca', 'Thhalv10021557m.g' => 'esa', 'Thhalv10026318m.g' => 'esa', 'Thhalv10026335m.g' => 'esa', 'TPR.G17433' => 'tpr', 'TPR.G18915' => 'tpr', 'TPR.G26125' => 'tpr', 'TWI09G0677' => 'twi', 'TWI73G0287' => 'twi', 'unitig_748.g8326' => 'ugi', 'vmacro15370' => 'vma', 'vmacro15371' => 'vma', 'vmacro15372' => 'vma', 'vmacro15373' => 'vma', 'vmacro15374' => 'vma', 'VMungo0720G2826' => 'vmu', 'Zm00001eb116960' => 'zma', 'Zm00001eb301260' => 'zma', 'Zm00001eb301270' => 'zma' ), 'gf_id' => 'HOM05D001460', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001460' ), 'data_identifier' => 'HOM05D001460', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001460', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '433', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p22980' => 'bna', 'A01p32340' => 'bna', 'A03p42970' => 'bna', 'A05p25880' => 'bna', 'Aa31LG8G9320' => 'aar', 'Aa31LG8G9330' => 'aar', 'Aa31LG8G9340' => 'aar', 'Aa31sc221G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1034' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1528' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.829' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2222' => 'aag', 'Ah.12g058830' => 'amhyb', 'Ah.12g058840' => 'amhyb', 'AL3G37160' => 'aly', 'AL7G41310' => 'aly', 'Aqoxy5G00395' => 'aox', 'Aqoxy5G00396' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0C8NZA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5185HY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JZ1PRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MD3LS0' => 'arhy', 'AT3G22840' => 'ath', 'AT4G14690' => 'ath', 'ATR0665G054' => 'atr', 'Atru.chr4.2344' => 'acertr', 'Atru.chr4.2346' => 'acertr', 'Atru.chr4.2347' => 'acertr', 'Atru.chr4.2348' => 'acertr', 'Atru.chr4.2355' => 'acertr', 'Atru.chr4.2356' => 'acertr', 'Atru.chr4.2358' => 'acertr', 'Atru.chr4.2359' => 'acertr', 'Atru.chr4.2360' => 'acertr', 'Atru.chr4.2361' => 'acertr', 'AUR62030476' => 'cqu', 'AUR62030478' => 'cqu', 'AUR62030819' => 'cqu', 'AUR62030820' => 'cqu', 'BcaB03g14648' => 'bca', 'BcaB04g20492' => 'bca', 'BcaB06g26399' => 'bca', 'BcaC01g03416' => 'bca', 'BcaC01g03419' => 'bca', 'BcaC01g03421' => 'bca', 'BcaC01g03424' => 'bca', 'BcaC05g28012' => 'bca', 'BcaC09g49212' => 'bca', 'BcaC09g50140' => 'bca', 'BcaNung00346' => 'bca', 'BolC1t02785H' => 'bol', 'BolC1t04095H' => 'bol', 'BolC3t17545H' => 'bol', 'BolC5t32769H' => 'bol', 'BraA01t02211Z' => 'bra', 'BraA01t03359Z' => 'bra', 'BraA03t13441Z' => 'bra', 'BraA05t21476Z' => 'bra', 'C01p28420' => 'bna', 'C01p41350' => 'bna', 'C03p52750' => 'bna', 'C03p52780' => 'bna', 'C05p40270' => 'bna', 'CAN.G1437.9' => 'can', 'CANSAT78G0035' => 'cansat', 'CANSAT78G1036' => 'cansat', 'CANSAT78G2272' => 'cansat', 'CANSAT78G2478' => 'cansat', 'CARHR098700' => 'chi', 'CARHR221120' => 'chi', 'CARHR221150' => 'chi', 'Carub.0003s2297' => 'cru', 'Carub.0007s2749' => 'cru', 'Carub.0007s2750' => 'cru', 'Carub.0007s2751' => 'cru', 'Ca_10849_v3' => 'car', 'Cc03_g04300' => 'ccan', 'CDE02G3648' => 'cde', 'CDE05G0060' => 'cde', 'CDE05G0692' => 'cde', 'CDE05G2285' => 'cde', 'CDE05G2884' => 'cde', 'CDE05G3072' => 'cde', 'Cfa008439' => 'cfa', 'Cfa008441' => 'cfa', 'Cfa008443' => 'cfa', 'Cfa008448' => 'cfa', 'Ciclev10005974m.g' => 'ccl', 'Ciclev10006006m.g' => 'ccl', 'Ciclev10006775m.g' => 'ccl', 'CiPaw.02G120400' => 'cil', 'CiPaw.02G120500' => 'cil', 'CiPaw.02G120600' => 'cil', 'ClCG05G004850' => 'cla', 'COL.COLO4_21566' => 'col', 'Cpa.g.sc44.124' => 'cpa', 'Cre07.g320400' => 'cre', 'Cre07.g320450' => 'cre', 'Cre08.g384650' => 'cre', 'Cre09.g393173' => 'cre', 'Cre09.g394325' => 'cre', 'Cre14.g626750' => 'cre', 'Cre16.g679250' => 'cre', 'CsaV3_3G012890' => 'csa', 'CSS0010865' => 'camsi', 'CSS0044338' => 'camsi', 'DCAR_002366' => 'dca', 'DCAR_030687' => 'dca', 'DCAR_030688' => 'dca', 'Dinv14047' => 'din', 'Dinv14048' => 'din', 'Duzib151G0105' => 'dzi', 'Duzib151G0114' => 'dzi', 'Duzib212G1029' => 'dzi', 'ECA232G3536' => 'eca', 'ECA240G0786' => 'eca', 'ECA240G1802' => 'eca', 'ECA240G3760' => 'eca', 'ECA240G3920' => 'eca', 'EL10Ac5g12536' => 'bvu', 'EL10Ac5g12537' => 'bvu', 'EL10Ac5g12538' => 'bvu', 'Eucgr.B01004' => 'egr', 'Eucgr.B01006' => 'egr', 'Eucgr.B01007' => 'egr', 'Eucgr.B01008' => 'egr', 'Eucgr.B01895' => 'egr', 'Eucgr.B01896' => 'egr', 'FAN04G1456' => 'fan', 'FAN08G1769' => 'fan', 'FAN08G2160' => 'fan', 'FAN13G2403' => 'fan', 'FAN13G3303' => 'fan', 'FAN15G2435' => 'fan', 'FAN17G0672' => 'fan', 'FAN17G2441' => 'fan', 'FAN18G1024' => 'fan', 'FAN22G1458' => 'fan', 'FAN24G0037' => 'fan', 'FAN24G0429' => 'fan', 'FAN24G2387' => 'fan', 'FAN27G2746' => 'fan', 'FvH4_2g20400' => 'fve', 'FvH4_2g20420' => 'fve', 'FvH4_2g20430' => 'fve', 'FvH4_4g01270' => 'fve', 'FvH4_4g01290' => 'fve', 'FvH4_4g01300' => 'fve', 'FvH4_4g01310' => 'fve', 'FvH4_4g01330' => 'fve', 'FvH4_5g09070' => 'fve', 'Glyma.10G243800' => 'gma', 'Glyma.20G150600' => 'gma', 'Gohir.A09G219200' => 'ghi', 'Gohir.A09G219300' => 'ghi', 'Gohir.D09G221400' => 'ghi', 'Gohir.D09G221500' => 'ghi', 'Gorai.006G242600' => 'gra', 'Gorai.006G242700' => 'gra', 'GSVIVG01018044001' => 'vvi', 'HanXRQChr03g0083821' => 'han', 'HanXRQChr03g0083841' => 'han', 'HanXRQChr03g0083881' => 'han', 'HanXRQChr03g0083901' => 'han', 'HanXRQChr03g0083921' => 'han', 'HanXRQChr03g0085331' => 'han', 'HanXRQChr03g0085361' => 'han', 'HanXRQChr03g0085411' => 'han', 'HanXRQChr03g0085421' => 'han', 'HanXRQChr03g0085431' => 'han', 'HanXRQChr08g0221991' => 'han', 'HanXRQChr11g0336061' => 'han', 'HanXRQChr11g0336411' => 'han', 'Haze_11234' => 'cav', 'Hma1.2p1_0549F.1_g177010' => 'hma', 'Hma1.2p1_0602F.1_g187630' => 'hma', 'Hund14876' => 'sun', 'Hund14879' => 'sun', 'Lalb_Chr06g0160741' => 'lal', 'Lalb_Chr21g0304781' => 'lal', 'Lj3A726G19' => 'lonja', 'Lj3A726T23' => 'lonja', 'Lj3A726T24' => 'lonja', 'Lj3A726T25' => 'lonja', 'Lj3A727T17' => 'lonja', 'Lj3C726T0' => 'lonja', 'Lj3C726T2' => 'lonja', 'Lj3P725T35' => 'lonja', 'Lj3P727T10' => 'lonja', 'Lj3P727T12' => 'lonja', 'Lj3P727T14' => 'lonja', 'Lj5g0023109' => 'lja', 'Lj6P646T44' => 'lonja', 'Lsat_1_v5_gn_6_75760' => 'lsa', 'Lsat_1_v5_gn_6_75800' => 'lsa', 'Lsat_1_v5_gn_6_75900' => 'lsa', 'Lsat_1_v5_gn_6_76240' => 'lsa', 'Lsat_1_v5_gn_6_76441' => 'lsa', 'Lsat_1_v5_gn_6_76700' => 'lsa', 'Lsat_1_v5_gn_6_76760' => 'lsa', 'Manes.15G033100' => 'mes', 'Mapoly0004s0074' => 'mpo', 'Mapoly0004s0075' => 'mpo', 'Mapoly0004s0163' => 'mpo', 'Mapoly0004s0164' => 'mpo', 'Mapoly0021s0018' => 'mpo', 'Mapoly0041s0136' => 'mpo', 'Mapoly0041s0137' => 'mpo', 'Mapoly0041s0138' => 'mpo', 'Mapoly0041s0139' => 'mpo', 'Mapoly0041s0141' => 'mpo', 'Mapoly0041s0142' => 'mpo', 'Mapoly0041s0143' => 'mpo', 'Mapoly0041s0144' => 'mpo', 'Mapoly0041s0145' => 'mpo', 'Mapoly0047s0106' => 'mpo', 'Mapoly0047s0108' => 'mpo', 'Mapoly0050s0051' => 'mpo', 'Mapoly0050s0052' => 'mpo', 'Mapoly0050s0053' => 'mpo', 'Mapoly0058s0013' => 'mpo', 'Mapoly0091s0078' => 'mpo', 'Mapoly0091s0079' => 'mpo', 'Mapoly0091s0080' => 'mpo', 'Mapoly0091s0081' => 'mpo', 'Mapoly0278s0004' => 'mpo', 'Mapoly0278s0005' => 'mpo', 'Mapoly0278s0006' => 'mpo', 'MBI11_g30648_MAGBIO' => 'mbi', 'MCO03G194' => 'mco', 'MCO03G590' => 'mco', 'MCO07G312' => 'mco', 'MCO10G318' => 'mco', 'MCO12G244' => 'mco', 'MCO13G148' => 'mco', 'MCO13G194' => 'mco', 'MCO16G238' => 'mco', 'MD06G1134100' => 'mdo', 'MD13G1200100' => 'mdo', 'MD13G1200300' => 'mdo', 'MD13G1200600' => 'mdo', 'MD14G1150400' => 'mdo', 'MD16G1200000' => 'mdo', 'Medtr1g102570' => 'mtr', 'Medtr1g102780' => 'mtr', 'Medtr1g102800' => 'mtr', 'Medtr1g102810' => 'mtr', 'Medtr1g102830' => 'mtr', 'MELO3C006499.2' => 'cme', 'Migut.G00385' => 'egut', 'MSTRG.4063' => 'ama', 'Nitab4.5_0000090g0260' => 'nta', 'Nitab4.5_0000977g0030' => 'nta', 'Nitab4.5_0002541g0040' => 'nta', 'Nitab4.5_0007068g0040' => 'nta', 'Nn005s41408' => 'nnu', 'Nn005s41410' => 'nnu', 'Oeu010310.1' => 'oeu', 'Oeu010311.1' => 'oeu', 'Oeu043472.1' => 'oeu', 'Os01g0246400' => 'osa', 'Os04g0267950' => 'osa', 'Os07g0178700' => 'osa', 'Os07g0178800' => 'osa', 'Peaxi162Scf00316g00046' => 'pax', 'Peaxi162Scf00316g00049' => 'pax', 'Peaxi162Scf00316g00059' => 'pax', 'Peaxi162Scf00316g00328' => 'pax', 'Peaxi162Scf00316g00329' => 'pax', 'Peaxi162Scf00316g00411' => 'pax', 'Peaxi162Scf00316g00521' => 'pax', 'Peaxi162Scf00492g00068' => 'pax', 'Peaxi162Scf35631g00002' => 'pax', 'PGR142G3720' => 'pgr', 'PGSC0003DMG400006442' => 'stu', 'Phvul.007G062000' => 'pvu', 'Potri.008G157750' => 'ptr', 'Potri.008G157900' => 'ptr', 'Potri.008G158000' => 'ptr', 'Potri.008G158200' => 'ptr', 'Pp3c11_7280' => 'ppa', 'Pp3c11_7980' => 'ppa', 'Pp3c12_19450' => 'ppa', 'Pp3c14_1480' => 'ppa', 'Pp3c14_1501' => 'ppa', 'Pp3c16_4900' => 'ppa', 'Pp3c16_5010' => 'ppa', 'Pp3c16_5060' => 'ppa', 'Pp3c19_18250' => 'ppa', 'Pp3c23_8530' => 'ppa', 'Pp3c23_8550' => 'ppa', 'Pp3c24_9670' => 'ppa', 'Pp3c2_21390' => 'ppa', 'Pp3c2_31380' => 'ppa', 'Pp3c3_16620' => 'ppa', 'Pp3c3_8090' => 'ppa', 'Pp3c3_8110' => 'ppa', 'Pp3c3_8130' => 'ppa', 'Pp3c3_8150' => 'ppa', 'Pp3c4_14320' => 'ppa', 'Pp3c6_2560' => 'ppa', 'Pp3c9_16700' => 'ppa', 'PRCOL_00000234' => 'pco', 'PRCOL_00000235' => 'pco', 'PRCOL_00000777' => 'pco', 'PRCOL_00002344' => 'pco', 'PRCOL_00002372' => 'pco', 'PRCOL_00006120' => 'pco', 'Prupe.1G021400' => 'ppe', 'Prupe.1G021500' => 'ppe', 'Prupe.1G021600' => 'ppe', 'Prupe.1G021700' => 'ppe', 'Prupe.1G021800' => 'ppe', 'Prupe.5G145100' => 'ppe', 'Psat6g204040' => 'psa', 'Psat6g204800' => 'psa', 'Psat6g204920' => 'psa', 'Psat6g204960' => 'psa', 'Psat6g205080' => 'psa', 'PSO017G0271' => 'pso', 'PSO017G1276' => 'pso', 'PSO017G1429' => 'pso', 'PSO017G1861' => 'pso', 'PSO017G2787' => 'pso', 'PSO017G4466' => 'pso', 'PSO017G5118' => 'pso', 'PSO017G5420' => 'pso', 'PSO063G3678' => 'pso', 'PSO210G0546' => 'pso', 'PSO317G0001' => 'pso', 'PSO357G0512' => 'pso', 'PSO478G2682' => 'pso', 'PSO647G0001' => 'pso', 'PSO675G0001' => 'pso', 'PSO675G2699' => 'pso', 'PSO675G2849' => 'pso', 'PSO675G4991' => 'pso', 'PSO689G0001' => 'pso', 'QL06p000916' => 'qlo', 'QL06p000921' => 'qlo', 'QL06p001398' => 'qlo', 'QL06p001407' => 'qlo', 'QL06p002031' => 'qlo', 'RcHm_v2.0_Chr4g0387791' => 'rch', 'RcHm_v2.0_Chr4g0387801' => 'rch', 'RcHm_v2.0_Chr6g0286501' => 'rch', 'RcHm_v2.0_Chr6g0286511' => 'rch', 'RcHm_v2.0_Chr6g0286521' => 'rch', 'RcHm_v2.0_Chr6g0286531' => 'rch', 'RcHm_v2.0_Chr7g0189141' => 'rch', 'Rhsim02G0028700' => 'rsi', 'Rhsim02G0028800' => 'rsi', 'Rhsim02G0028900' => 'rsi', 'Rhsim02G0029000' => 'rsi', 'Rhsim02G0029100' => 'rsi', 'Rhsim02G0029200' => 'rsi', 'Rhsim02G0029300' => 'rsi', 'Rhsim02G0029400' => 'rsi', 'Rhsim02G0029500' => 'rsi', 'Rhsim02G0029600' => 'rsi', 'RhsimUnG0024000' => 'rsi', 'RhsimUnG0024100' => 'rsi', 'RhsimUnG0024200' => 'rsi', 'RhsimUnG0024300' => 'rsi', 'RhsimUnG0024400' => 'rsi', 'RhsimUnG0024500' => 'rsi', 'RhsimUnG0024700' => 'rsi', 'RhsimUnG0024800' => 'rsi', 'RhsimUnG0024900' => 'rsi', 'RhsimUnG0025100' => 'rsi', 'Sabra08G0120200' => 'sbr', 'Sabra08G0120300' => 'sbr', 'Sabra08G0120500' => 'sbr', 'Sabra08G0120600' => 'sbr', 'Sabra10G0158900' => 'sbr', 'SalBow2G3492' => 'sbo', 'Sc13g0004760' => 'sci', 'Sc13g0004770' => 'sci', 'Sed0003417' => 'sed', 'Sed0019750' => 'sed', 'SEGI_03419' => 'sgi', 'SEGI_05907' => 'sgi', 'SEGI_10682' => 'sgi', 'SEGI_13528' => 'sgi', 'SEGI_16081' => 'sgi', 'SEGI_19370' => 'sgi', 'SEGI_21015' => 'sgi', 'SEGI_21944' => 'sgi', 'SEGI_32906' => 'sgi', 'SEGI_33093' => 'sgi', 'SEGI_36110' => 'sgi', 'SEGI_40397' => 'sgi', 'SGA_v2.0_scaffold191G40426' => 'sas', 'SGA_v2.0_scaffold353G49717' => 'sas', 'SGA_v2.0_scaffold50G18550' => 'sas', 'SMO119G0173' => 'smo', 'SMO172G0002' => 'smo', 'Solyc09g082690.3' => 'sly', 'Solyc09g082700.2' => 'sly', 'Sopen09g031550' => 'spe', 'Sopen09g031560' => 'spe', 'Sp3g20540' => 'spa', 'Sp7g07580' => 'spa', 'TAR134G0002' => 'tar', 'TAR236G0001' => 'tar', 'TAR365G0892' => 'tar', 'TAR636G0166' => 'tar', 'TAR636G0646' => 'tar', 'TAR636G0869' => 'tar', 'TAR636G1317' => 'tar', 'TAR636G1744' => 'tar', 'TAR636G3358' => 'tar', 'TAR636G3436' => 'tar', 'THA.LOC104803047' => 'tha', 'Thecc.04G238900' => 'tca', 'Thhalv10021557m.g' => 'esa', 'Thhalv10026318m.g' => 'esa', 'Thhalv10026335m.g' => 'esa', 'TPR.G17433' => 'tpr', 'TPR.G18915' => 'tpr', 'TPR.G26125' => 'tpr', 'TWI09G0677' => 'twi', 'TWI73G0287' => 'twi', 'unitig_748.g8326' => 'ugi', 'vmacro15370' => 'vma', 'vmacro15371' => 'vma', 'vmacro15372' => 'vma', 'vmacro15373' => 'vma', 'vmacro15374' => 'vma', 'VMungo0720G2826' => 'vmu', 'Zm00001eb116960' => 'zma', 'Zm00001eb301260' => 'zma', 'Zm00001eb301270' => 'zma' ) $gf_id = 'HOM05D001460' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001460' ) $data_identifier = 'HOM05D001460' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 4, 'aag' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 2, 'aox' => (int) 2, 'arhy' => (int) 4, 'ath' => (int) 2, 'atr' => (int) 1, 'acertr' => (int) 10, 'cqu' => (int) 4, 'bca' => (int) 11, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 1, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 1, 'ccan' => (int) 1, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 1, 'col' => (int) 1, 'cpa' => (int) 1, 'cre' => (int) 7, 'csa' => (int) 1, 'camsi' => (int) 2, 'dca' => (int) 3, 'din' => (int) 2, 'dzi' => (int) 3, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 14, 'fve' => (int) 9, 'gma' => (int) 2, 'ghi' => (int) 4, 'gra' => (int) 2, 'vvi' => (int) 1, 'han' => (int) 13, 'cav' => (int) 1, 'hma' => (int) 2, 'sun' => (int) 2, 'lal' => (int) 2, 'lonja' => (int) 12, 'lja' => (int) 1, 'lsa' => (int) 7, 'mes' => (int) 1, 'mpo' => (int) 27, 'mbi' => (int) 1, 'mco' => (int) 8, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 1, 'egut' => (int) 1, 'ama' => (int) 1, 'nta' => (int) 4, 'nnu' => (int) 2, 'oeu' => (int) 3, 'osa' => (int) 4, 'pax' => (int) 9, 'pgr' => (int) 1, 'stu' => (int) 1, 'pvu' => (int) 1, 'ptr' => (int) 4, 'ppa' => (int) 22, 'pco' => (int) 6, 'ppe' => (int) 6, 'psa' => (int) 5, 'pso' => (int) 19, 'qlo' => (int) 5, 'rch' => (int) 7, 'rsi' => (int) 20, 'sbr' => (int) 5, 'sbo' => (int) 1, 'sci' => (int) 2, 'sed' => (int) 2, 'sgi' => (int) 12, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 2, 'tar' => (int) 10, 'tha' => (int) 1, 'tca' => (int) 1, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 2, 'ugi' => (int) 1, 'vma' => (int) 5, 'vmu' => (int) 1, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb301270' $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' => 'HOM05D001460', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '433', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p22980' => 'bna', 'A01p32340' => 'bna', 'A03p42970' => 'bna', 'A05p25880' => 'bna', 'Aa31LG8G9320' => 'aar', 'Aa31LG8G9330' => 'aar', 'Aa31LG8G9340' => 'aar', 'Aa31sc221G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1034' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1528' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.829' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2222' => 'aag', 'Ah.12g058830' => 'amhyb', 'Ah.12g058840' => 'amhyb', 'AL3G37160' => 'aly', 'AL7G41310' => 'aly', 'Aqoxy5G00395' => 'aox', 'Aqoxy5G00396' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0C8NZA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5185HY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JZ1PRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MD3LS0' => 'arhy', 'AT3G22840' => 'ath', 'AT4G14690' => 'ath', 'ATR0665G054' => 'atr', 'Atru.chr4.2344' => 'acertr', 'Atru.chr4.2346' => 'acertr', 'Atru.chr4.2347' => 'acertr', 'Atru.chr4.2348' => 'acertr', 'Atru.chr4.2355' => 'acertr', 'Atru.chr4.2356' => 'acertr', 'Atru.chr4.2358' => 'acertr', 'Atru.chr4.2359' => 'acertr', 'Atru.chr4.2360' => 'acertr', 'Atru.chr4.2361' => 'acertr', 'AUR62030476' => 'cqu', 'AUR62030478' => 'cqu', 'AUR62030819' => 'cqu', 'AUR62030820' => 'cqu', 'BcaB03g14648' => 'bca', 'BcaB04g20492' => 'bca', 'BcaB06g26399' => 'bca', 'BcaC01g03416' => 'bca', 'BcaC01g03419' => 'bca', 'BcaC01g03421' => 'bca', 'BcaC01g03424' => 'bca', 'BcaC05g28012' => 'bca', 'BcaC09g49212' => 'bca', 'BcaC09g50140' => 'bca', 'BcaNung00346' => 'bca', 'BolC1t02785H' => 'bol', 'BolC1t04095H' => 'bol', 'BolC3t17545H' => 'bol', 'BolC5t32769H' => 'bol', 'BraA01t02211Z' => 'bra', 'BraA01t03359Z' => 'bra', 'BraA03t13441Z' => 'bra', 'BraA05t21476Z' => 'bra', 'C01p28420' => 'bna', 'C01p41350' => 'bna', 'C03p52750' => 'bna', 'C03p52780' => 'bna', 'C05p40270' => 'bna', 'CAN.G1437.9' => 'can', 'CANSAT78G0035' => 'cansat', 'CANSAT78G1036' => 'cansat', 'CANSAT78G2272' => 'cansat', 'CANSAT78G2478' => 'cansat', 'CARHR098700' => 'chi', 'CARHR221120' => 'chi', 'CARHR221150' => 'chi', 'Carub.0003s2297' => 'cru', 'Carub.0007s2749' => 'cru', 'Carub.0007s2750' => 'cru', 'Carub.0007s2751' => 'cru', 'Ca_10849_v3' => 'car', 'Cc03_g04300' => 'ccan', 'CDE02G3648' => 'cde', 'CDE05G0060' => 'cde', 'CDE05G0692' => 'cde', 'CDE05G2285' => 'cde', 'CDE05G2884' => 'cde', 'CDE05G3072' => 'cde', 'Cfa008439' => 'cfa', 'Cfa008441' => 'cfa', 'Cfa008443' => 'cfa', 'Cfa008448' => 'cfa', 'Ciclev10005974m.g' => 'ccl', 'Ciclev10006006m.g' => 'ccl', 'Ciclev10006775m.g' => 'ccl', 'CiPaw.02G120400' => 'cil', 'CiPaw.02G120500' => 'cil', 'CiPaw.02G120600' => 'cil', 'ClCG05G004850' => 'cla', 'COL.COLO4_21566' => 'col', 'Cpa.g.sc44.124' => 'cpa', 'Cre07.g320400' => 'cre', 'Cre07.g320450' => 'cre', 'Cre08.g384650' => 'cre', 'Cre09.g393173' => 'cre', 'Cre09.g394325' => 'cre', 'Cre14.g626750' => 'cre', 'Cre16.g679250' => 'cre', 'CsaV3_3G012890' => 'csa', 'CSS0010865' => 'camsi', 'CSS0044338' => 'camsi', 'DCAR_002366' => 'dca', 'DCAR_030687' => 'dca', 'DCAR_030688' => 'dca', 'Dinv14047' => 'din', 'Dinv14048' => 'din', 'Duzib151G0105' => 'dzi', 'Duzib151G0114' => 'dzi', 'Duzib212G1029' => 'dzi', 'ECA232G3536' => 'eca', 'ECA240G0786' => 'eca', 'ECA240G1802' => 'eca', 'ECA240G3760' => 'eca', 'ECA240G3920' => 'eca', 'EL10Ac5g12536' => 'bvu', 'EL10Ac5g12537' => 'bvu', 'EL10Ac5g12538' => 'bvu', 'Eucgr.B01004' => 'egr', 'Eucgr.B01006' => 'egr', 'Eucgr.B01007' => 'egr', 'Eucgr.B01008' => 'egr', 'Eucgr.B01895' => 'egr', 'Eucgr.B01896' => 'egr', 'FAN04G1456' => 'fan', 'FAN08G1769' => 'fan', 'FAN08G2160' => 'fan', 'FAN13G2403' => 'fan', 'FAN13G3303' => 'fan', 'FAN15G2435' => 'fan', 'FAN17G0672' => 'fan', 'FAN17G2441' => 'fan', 'FAN18G1024' => 'fan', 'FAN22G1458' => 'fan', 'FAN24G0037' => 'fan', 'FAN24G0429' => 'fan', 'FAN24G2387' => 'fan', 'FAN27G2746' => 'fan', 'FvH4_2g20400' => 'fve', 'FvH4_2g20420' => 'fve', 'FvH4_2g20430' => 'fve', 'FvH4_4g01270' => 'fve', 'FvH4_4g01290' => 'fve', 'FvH4_4g01300' => 'fve', 'FvH4_4g01310' => 'fve', 'FvH4_4g01330' => 'fve', 'FvH4_5g09070' => 'fve', 'Glyma.10G243800' => 'gma', 'Glyma.20G150600' => 'gma', 'Gohir.A09G219200' => 'ghi', 'Gohir.A09G219300' => 'ghi', 'Gohir.D09G221400' => 'ghi', 'Gohir.D09G221500' => 'ghi', 'Gorai.006G242600' => 'gra', 'Gorai.006G242700' => 'gra', 'GSVIVG01018044001' => 'vvi', 'HanXRQChr03g0083821' => 'han', 'HanXRQChr03g0083841' => 'han', 'HanXRQChr03g0083881' => 'han', 'HanXRQChr03g0083901' => 'han', 'HanXRQChr03g0083921' => 'han', 'HanXRQChr03g0085331' => 'han', 'HanXRQChr03g0085361' => 'han', 'HanXRQChr03g0085411' => 'han', 'HanXRQChr03g0085421' => 'han', 'HanXRQChr03g0085431' => 'han', 'HanXRQChr08g0221991' => 'han', 'HanXRQChr11g0336061' => 'han', 'HanXRQChr11g0336411' => 'han', 'Haze_11234' => 'cav', 'Hma1.2p1_0549F.1_g177010' => 'hma', 'Hma1.2p1_0602F.1_g187630' => 'hma', 'Hund14876' => 'sun', 'Hund14879' => 'sun', 'Lalb_Chr06g0160741' => 'lal', 'Lalb_Chr21g0304781' => 'lal', 'Lj3A726G19' => 'lonja', 'Lj3A726T23' => 'lonja', 'Lj3A726T24' => 'lonja', 'Lj3A726T25' => 'lonja', 'Lj3A727T17' => 'lonja', 'Lj3C726T0' => 'lonja', 'Lj3C726T2' => 'lonja', 'Lj3P725T35' => 'lonja', 'Lj3P727T10' => 'lonja', 'Lj3P727T12' => 'lonja', 'Lj3P727T14' => 'lonja', 'Lj5g0023109' => 'lja', 'Lj6P646T44' => 'lonja', 'Lsat_1_v5_gn_6_75760' => 'lsa', 'Lsat_1_v5_gn_6_75800' => 'lsa', 'Lsat_1_v5_gn_6_75900' => 'lsa', 'Lsat_1_v5_gn_6_76240' => 'lsa', 'Lsat_1_v5_gn_6_76441' => 'lsa', 'Lsat_1_v5_gn_6_76700' => 'lsa', 'Lsat_1_v5_gn_6_76760' => 'lsa', 'Manes.15G033100' => 'mes', 'Mapoly0004s0074' => 'mpo', 'Mapoly0004s0075' => 'mpo', 'Mapoly0004s0163' => 'mpo', 'Mapoly0004s0164' => 'mpo', 'Mapoly0021s0018' => 'mpo', 'Mapoly0041s0136' => 'mpo', 'Mapoly0041s0137' => 'mpo', 'Mapoly0041s0138' => 'mpo', 'Mapoly0041s0139' => 'mpo', 'Mapoly0041s0141' => 'mpo', 'Mapoly0041s0142' => 'mpo', 'Mapoly0041s0143' => 'mpo', 'Mapoly0041s0144' => 'mpo', 'Mapoly0041s0145' => 'mpo', 'Mapoly0047s0106' => 'mpo', 'Mapoly0047s0108' => 'mpo', 'Mapoly0050s0051' => 'mpo', 'Mapoly0050s0052' => 'mpo', 'Mapoly0050s0053' => 'mpo', 'Mapoly0058s0013' => 'mpo', 'Mapoly0091s0078' => 'mpo', 'Mapoly0091s0079' => 'mpo', 'Mapoly0091s0080' => 'mpo', 'Mapoly0091s0081' => 'mpo', 'Mapoly0278s0004' => 'mpo', 'Mapoly0278s0005' => 'mpo', 'Mapoly0278s0006' => 'mpo', 'MBI11_g30648_MAGBIO' => 'mbi', 'MCO03G194' => 'mco', 'MCO03G590' => 'mco', 'MCO07G312' => 'mco', 'MCO10G318' => 'mco', 'MCO12G244' => 'mco', 'MCO13G148' => 'mco', 'MCO13G194' => 'mco', 'MCO16G238' => 'mco', 'MD06G1134100' => 'mdo', 'MD13G1200100' => 'mdo', 'MD13G1200300' => 'mdo', 'MD13G1200600' => 'mdo', 'MD14G1150400' => 'mdo', 'MD16G1200000' => 'mdo', 'Medtr1g102570' => 'mtr', 'Medtr1g102780' => 'mtr', 'Medtr1g102800' => 'mtr', 'Medtr1g102810' => 'mtr', 'Medtr1g102830' => 'mtr', 'MELO3C006499.2' => 'cme', 'Migut.G00385' => 'egut', 'MSTRG.4063' => 'ama', 'Nitab4.5_0000090g0260' => 'nta', 'Nitab4.5_0000977g0030' => 'nta', 'Nitab4.5_0002541g0040' => 'nta', 'Nitab4.5_0007068g0040' => 'nta', 'Nn005s41408' => 'nnu', 'Nn005s41410' => 'nnu', 'Oeu010310.1' => 'oeu', 'Oeu010311.1' => 'oeu', 'Oeu043472.1' => 'oeu', 'Os01g0246400' => 'osa', 'Os04g0267950' => 'osa', 'Os07g0178700' => 'osa', 'Os07g0178800' => 'osa', 'Peaxi162Scf00316g00046' => 'pax', 'Peaxi162Scf00316g00049' => 'pax', 'Peaxi162Scf00316g00059' => 'pax', 'Peaxi162Scf00316g00328' => 'pax', 'Peaxi162Scf00316g00329' => 'pax', 'Peaxi162Scf00316g00411' => 'pax', 'Peaxi162Scf00316g00521' => 'pax', 'Peaxi162Scf00492g00068' => 'pax', 'Peaxi162Scf35631g00002' => 'pax', 'PGR142G3720' => 'pgr', 'PGSC0003DMG400006442' => 'stu', 'Phvul.007G062000' => 'pvu', 'Potri.008G157750' => 'ptr', 'Potri.008G157900' => 'ptr', 'Potri.008G158000' => 'ptr', 'Potri.008G158200' => 'ptr', 'Pp3c11_7280' => 'ppa', 'Pp3c11_7980' => 'ppa', 'Pp3c12_19450' => 'ppa', 'Pp3c14_1480' => 'ppa', 'Pp3c14_1501' => 'ppa', 'Pp3c16_4900' => 'ppa', 'Pp3c16_5010' => 'ppa', 'Pp3c16_5060' => 'ppa', 'Pp3c19_18250' => 'ppa', 'Pp3c23_8530' => 'ppa', 'Pp3c23_8550' => 'ppa', 'Pp3c24_9670' => 'ppa', 'Pp3c2_21390' => 'ppa', 'Pp3c2_31380' => 'ppa', 'Pp3c3_16620' => 'ppa', 'Pp3c3_8090' => 'ppa', 'Pp3c3_8110' => 'ppa', 'Pp3c3_8130' => 'ppa', 'Pp3c3_8150' => 'ppa', 'Pp3c4_14320' => 'ppa', 'Pp3c6_2560' => 'ppa', 'Pp3c9_16700' => 'ppa', 'PRCOL_00000234' => 'pco', 'PRCOL_00000235' => 'pco', 'PRCOL_00000777' => 'pco', 'PRCOL_00002344' => 'pco', 'PRCOL_00002372' => 'pco', 'PRCOL_00006120' => 'pco', 'Prupe.1G021400' => 'ppe', 'Prupe.1G021500' => 'ppe', 'Prupe.1G021600' => 'ppe', 'Prupe.1G021700' => 'ppe', 'Prupe.1G021800' => 'ppe', 'Prupe.5G145100' => 'ppe', 'Psat6g204040' => 'psa', 'Psat6g204800' => 'psa', 'Psat6g204920' => 'psa', 'Psat6g204960' => 'psa', 'Psat6g205080' => 'psa', 'PSO017G0271' => 'pso', 'PSO017G1276' => 'pso', 'PSO017G1429' => 'pso', 'PSO017G1861' => 'pso', 'PSO017G2787' => 'pso', 'PSO017G4466' => 'pso', 'PSO017G5118' => 'pso', 'PSO017G5420' => 'pso', 'PSO063G3678' => 'pso', 'PSO210G0546' => 'pso', 'PSO317G0001' => 'pso', 'PSO357G0512' => 'pso', 'PSO478G2682' => 'pso', 'PSO647G0001' => 'pso', 'PSO675G0001' => 'pso', 'PSO675G2699' => 'pso', 'PSO675G2849' => 'pso', 'PSO675G4991' => 'pso', 'PSO689G0001' => 'pso', 'QL06p000916' => 'qlo', 'QL06p000921' => 'qlo', 'QL06p001398' => 'qlo', 'QL06p001407' => 'qlo', 'QL06p002031' => 'qlo', 'RcHm_v2.0_Chr4g0387791' => 'rch', 'RcHm_v2.0_Chr4g0387801' => 'rch', 'RcHm_v2.0_Chr6g0286501' => 'rch', 'RcHm_v2.0_Chr6g0286511' => 'rch', 'RcHm_v2.0_Chr6g0286521' => 'rch', 'RcHm_v2.0_Chr6g0286531' => 'rch', 'RcHm_v2.0_Chr7g0189141' => 'rch', 'Rhsim02G0028700' => 'rsi', 'Rhsim02G0028800' => 'rsi', 'Rhsim02G0028900' => 'rsi', 'Rhsim02G0029000' => 'rsi', 'Rhsim02G0029100' => 'rsi', 'Rhsim02G0029200' => 'rsi', 'Rhsim02G0029300' => 'rsi', 'Rhsim02G0029400' => 'rsi', 'Rhsim02G0029500' => 'rsi', 'Rhsim02G0029600' => 'rsi', 'RhsimUnG0024000' => 'rsi', 'RhsimUnG0024100' => 'rsi', 'RhsimUnG0024200' => 'rsi', 'RhsimUnG0024300' => 'rsi', 'RhsimUnG0024400' => 'rsi', 'RhsimUnG0024500' => 'rsi', 'RhsimUnG0024700' => 'rsi', 'RhsimUnG0024800' => 'rsi', 'RhsimUnG0024900' => 'rsi', 'RhsimUnG0025100' => 'rsi', 'Sabra08G0120200' => 'sbr', 'Sabra08G0120300' => 'sbr', 'Sabra08G0120500' => 'sbr', 'Sabra08G0120600' => 'sbr', 'Sabra10G0158900' => 'sbr', 'SalBow2G3492' => 'sbo', 'Sc13g0004760' => 'sci', 'Sc13g0004770' => 'sci', 'Sed0003417' => 'sed', 'Sed0019750' => 'sed', 'SEGI_03419' => 'sgi', 'SEGI_05907' => 'sgi', 'SEGI_10682' => 'sgi', 'SEGI_13528' => 'sgi', 'SEGI_16081' => 'sgi', 'SEGI_19370' => 'sgi', 'SEGI_21015' => 'sgi', 'SEGI_21944' => 'sgi', 'SEGI_32906' => 'sgi', 'SEGI_33093' => 'sgi', 'SEGI_36110' => 'sgi', 'SEGI_40397' => 'sgi', 'SGA_v2.0_scaffold191G40426' => 'sas', 'SGA_v2.0_scaffold353G49717' => 'sas', 'SGA_v2.0_scaffold50G18550' => 'sas', 'SMO119G0173' => 'smo', 'SMO172G0002' => 'smo', 'Solyc09g082690.3' => 'sly', 'Solyc09g082700.2' => 'sly', 'Sopen09g031550' => 'spe', 'Sopen09g031560' => 'spe', 'Sp3g20540' => 'spa', 'Sp7g07580' => 'spa', 'TAR134G0002' => 'tar', 'TAR236G0001' => 'tar', 'TAR365G0892' => 'tar', 'TAR636G0166' => 'tar', 'TAR636G0646' => 'tar', 'TAR636G0869' => 'tar', 'TAR636G1317' => 'tar', 'TAR636G1744' => 'tar', 'TAR636G3358' => 'tar', 'TAR636G3436' => 'tar', 'THA.LOC104803047' => 'tha', 'Thecc.04G238900' => 'tca', 'Thhalv10021557m.g' => 'esa', 'Thhalv10026318m.g' => 'esa', 'Thhalv10026335m.g' => 'esa', 'TPR.G17433' => 'tpr', 'TPR.G18915' => 'tpr', 'TPR.G26125' => 'tpr', 'TWI09G0677' => 'twi', 'TWI73G0287' => 'twi', 'unitig_748.g8326' => 'ugi', 'vmacro15370' => 'vma', 'vmacro15371' => 'vma', 'vmacro15372' => 'vma', 'vmacro15373' => 'vma', 'vmacro15374' => 'vma', 'VMungo0720G2826' => 'vmu', 'Zm00001eb116960' => 'zma', 'Zm00001eb301260' => 'zma', 'Zm00001eb301270' => 'zma' ), 'gf_id' => 'HOM05D001460', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001460' ), 'data_identifier' => 'HOM05D001460', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001460', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '433', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p22980' => 'bna', 'A01p32340' => 'bna', 'A03p42970' => 'bna', 'A05p25880' => 'bna', 'Aa31LG8G9320' => 'aar', 'Aa31LG8G9330' => 'aar', 'Aa31LG8G9340' => 'aar', 'Aa31sc221G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1034' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1528' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.829' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2222' => 'aag', 'Ah.12g058830' => 'amhyb', 'Ah.12g058840' => 'amhyb', 'AL3G37160' => 'aly', 'AL7G41310' => 'aly', 'Aqoxy5G00395' => 'aox', 'Aqoxy5G00396' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0C8NZA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5185HY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JZ1PRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MD3LS0' => 'arhy', 'AT3G22840' => 'ath', 'AT4G14690' => 'ath', 'ATR0665G054' => 'atr', 'Atru.chr4.2344' => 'acertr', 'Atru.chr4.2346' => 'acertr', 'Atru.chr4.2347' => 'acertr', 'Atru.chr4.2348' => 'acertr', 'Atru.chr4.2355' => 'acertr', 'Atru.chr4.2356' => 'acertr', 'Atru.chr4.2358' => 'acertr', 'Atru.chr4.2359' => 'acertr', 'Atru.chr4.2360' => 'acertr', 'Atru.chr4.2361' => 'acertr', 'AUR62030476' => 'cqu', 'AUR62030478' => 'cqu', 'AUR62030819' => 'cqu', 'AUR62030820' => 'cqu', 'BcaB03g14648' => 'bca', 'BcaB04g20492' => 'bca', 'BcaB06g26399' => 'bca', 'BcaC01g03416' => 'bca', 'BcaC01g03419' => 'bca', 'BcaC01g03421' => 'bca', 'BcaC01g03424' => 'bca', 'BcaC05g28012' => 'bca', 'BcaC09g49212' => 'bca', 'BcaC09g50140' => 'bca', 'BcaNung00346' => 'bca', 'BolC1t02785H' => 'bol', 'BolC1t04095H' => 'bol', 'BolC3t17545H' => 'bol', 'BolC5t32769H' => 'bol', 'BraA01t02211Z' => 'bra', 'BraA01t03359Z' => 'bra', 'BraA03t13441Z' => 'bra', 'BraA05t21476Z' => 'bra', 'C01p28420' => 'bna', 'C01p41350' => 'bna', 'C03p52750' => 'bna', 'C03p52780' => 'bna', 'C05p40270' => 'bna', 'CAN.G1437.9' => 'can', 'CANSAT78G0035' => 'cansat', 'CANSAT78G1036' => 'cansat', 'CANSAT78G2272' => 'cansat', 'CANSAT78G2478' => 'cansat', 'CARHR098700' => 'chi', 'CARHR221120' => 'chi', 'CARHR221150' => 'chi', 'Carub.0003s2297' => 'cru', 'Carub.0007s2749' => 'cru', 'Carub.0007s2750' => 'cru', 'Carub.0007s2751' => 'cru', 'Ca_10849_v3' => 'car', 'Cc03_g04300' => 'ccan', 'CDE02G3648' => 'cde', 'CDE05G0060' => 'cde', 'CDE05G0692' => 'cde', 'CDE05G2285' => 'cde', 'CDE05G2884' => 'cde', 'CDE05G3072' => 'cde', 'Cfa008439' => 'cfa', 'Cfa008441' => 'cfa', 'Cfa008443' => 'cfa', 'Cfa008448' => 'cfa', 'Ciclev10005974m.g' => 'ccl', 'Ciclev10006006m.g' => 'ccl', 'Ciclev10006775m.g' => 'ccl', 'CiPaw.02G120400' => 'cil', 'CiPaw.02G120500' => 'cil', 'CiPaw.02G120600' => 'cil', 'ClCG05G004850' => 'cla', 'COL.COLO4_21566' => 'col', 'Cpa.g.sc44.124' => 'cpa', 'Cre07.g320400' => 'cre', 'Cre07.g320450' => 'cre', 'Cre08.g384650' => 'cre', 'Cre09.g393173' => 'cre', 'Cre09.g394325' => 'cre', 'Cre14.g626750' => 'cre', 'Cre16.g679250' => 'cre', 'CsaV3_3G012890' => 'csa', 'CSS0010865' => 'camsi', 'CSS0044338' => 'camsi', 'DCAR_002366' => 'dca', 'DCAR_030687' => 'dca', 'DCAR_030688' => 'dca', 'Dinv14047' => 'din', 'Dinv14048' => 'din', 'Duzib151G0105' => 'dzi', 'Duzib151G0114' => 'dzi', 'Duzib212G1029' => 'dzi', 'ECA232G3536' => 'eca', 'ECA240G0786' => 'eca', 'ECA240G1802' => 'eca', 'ECA240G3760' => 'eca', 'ECA240G3920' => 'eca', 'EL10Ac5g12536' => 'bvu', 'EL10Ac5g12537' => 'bvu', 'EL10Ac5g12538' => 'bvu', 'Eucgr.B01004' => 'egr', 'Eucgr.B01006' => 'egr', 'Eucgr.B01007' => 'egr', 'Eucgr.B01008' => 'egr', 'Eucgr.B01895' => 'egr', 'Eucgr.B01896' => 'egr', 'FAN04G1456' => 'fan', 'FAN08G1769' => 'fan', 'FAN08G2160' => 'fan', 'FAN13G2403' => 'fan', 'FAN13G3303' => 'fan', 'FAN15G2435' => 'fan', 'FAN17G0672' => 'fan', 'FAN17G2441' => 'fan', 'FAN18G1024' => 'fan', 'FAN22G1458' => 'fan', 'FAN24G0037' => 'fan', 'FAN24G0429' => 'fan', 'FAN24G2387' => 'fan', 'FAN27G2746' => 'fan', 'FvH4_2g20400' => 'fve', 'FvH4_2g20420' => 'fve', 'FvH4_2g20430' => 'fve', 'FvH4_4g01270' => 'fve', 'FvH4_4g01290' => 'fve', 'FvH4_4g01300' => 'fve', 'FvH4_4g01310' => 'fve', 'FvH4_4g01330' => 'fve', 'FvH4_5g09070' => 'fve', 'Glyma.10G243800' => 'gma', 'Glyma.20G150600' => 'gma', 'Gohir.A09G219200' => 'ghi', 'Gohir.A09G219300' => 'ghi', 'Gohir.D09G221400' => 'ghi', 'Gohir.D09G221500' => 'ghi', 'Gorai.006G242600' => 'gra', 'Gorai.006G242700' => 'gra', 'GSVIVG01018044001' => 'vvi', 'HanXRQChr03g0083821' => 'han', 'HanXRQChr03g0083841' => 'han', 'HanXRQChr03g0083881' => 'han', 'HanXRQChr03g0083901' => 'han', 'HanXRQChr03g0083921' => 'han', 'HanXRQChr03g0085331' => 'han', 'HanXRQChr03g0085361' => 'han', 'HanXRQChr03g0085411' => 'han', 'HanXRQChr03g0085421' => 'han', 'HanXRQChr03g0085431' => 'han', 'HanXRQChr08g0221991' => 'han', 'HanXRQChr11g0336061' => 'han', 'HanXRQChr11g0336411' => 'han', 'Haze_11234' => 'cav', 'Hma1.2p1_0549F.1_g177010' => 'hma', 'Hma1.2p1_0602F.1_g187630' => 'hma', 'Hund14876' => 'sun', 'Hund14879' => 'sun', 'Lalb_Chr06g0160741' => 'lal', 'Lalb_Chr21g0304781' => 'lal', 'Lj3A726G19' => 'lonja', 'Lj3A726T23' => 'lonja', 'Lj3A726T24' => 'lonja', 'Lj3A726T25' => 'lonja', 'Lj3A727T17' => 'lonja', 'Lj3C726T0' => 'lonja', 'Lj3C726T2' => 'lonja', 'Lj3P725T35' => 'lonja', 'Lj3P727T10' => 'lonja', 'Lj3P727T12' => 'lonja', 'Lj3P727T14' => 'lonja', 'Lj5g0023109' => 'lja', 'Lj6P646T44' => 'lonja', 'Lsat_1_v5_gn_6_75760' => 'lsa', 'Lsat_1_v5_gn_6_75800' => 'lsa', 'Lsat_1_v5_gn_6_75900' => 'lsa', 'Lsat_1_v5_gn_6_76240' => 'lsa', 'Lsat_1_v5_gn_6_76441' => 'lsa', 'Lsat_1_v5_gn_6_76700' => 'lsa', 'Lsat_1_v5_gn_6_76760' => 'lsa', 'Manes.15G033100' => 'mes', 'Mapoly0004s0074' => 'mpo', 'Mapoly0004s0075' => 'mpo', 'Mapoly0004s0163' => 'mpo', 'Mapoly0004s0164' => 'mpo', 'Mapoly0021s0018' => 'mpo', 'Mapoly0041s0136' => 'mpo', 'Mapoly0041s0137' => 'mpo', 'Mapoly0041s0138' => 'mpo', 'Mapoly0041s0139' => 'mpo', 'Mapoly0041s0141' => 'mpo', 'Mapoly0041s0142' => 'mpo', 'Mapoly0041s0143' => 'mpo', 'Mapoly0041s0144' => 'mpo', 'Mapoly0041s0145' => 'mpo', 'Mapoly0047s0106' => 'mpo', 'Mapoly0047s0108' => 'mpo', 'Mapoly0050s0051' => 'mpo', 'Mapoly0050s0052' => 'mpo', 'Mapoly0050s0053' => 'mpo', 'Mapoly0058s0013' => 'mpo', 'Mapoly0091s0078' => 'mpo', 'Mapoly0091s0079' => 'mpo', 'Mapoly0091s0080' => 'mpo', 'Mapoly0091s0081' => 'mpo', 'Mapoly0278s0004' => 'mpo', 'Mapoly0278s0005' => 'mpo', 'Mapoly0278s0006' => 'mpo', 'MBI11_g30648_MAGBIO' => 'mbi', 'MCO03G194' => 'mco', 'MCO03G590' => 'mco', 'MCO07G312' => 'mco', 'MCO10G318' => 'mco', 'MCO12G244' => 'mco', 'MCO13G148' => 'mco', 'MCO13G194' => 'mco', 'MCO16G238' => 'mco', 'MD06G1134100' => 'mdo', 'MD13G1200100' => 'mdo', 'MD13G1200300' => 'mdo', 'MD13G1200600' => 'mdo', 'MD14G1150400' => 'mdo', 'MD16G1200000' => 'mdo', 'Medtr1g102570' => 'mtr', 'Medtr1g102780' => 'mtr', 'Medtr1g102800' => 'mtr', 'Medtr1g102810' => 'mtr', 'Medtr1g102830' => 'mtr', 'MELO3C006499.2' => 'cme', 'Migut.G00385' => 'egut', 'MSTRG.4063' => 'ama', 'Nitab4.5_0000090g0260' => 'nta', 'Nitab4.5_0000977g0030' => 'nta', 'Nitab4.5_0002541g0040' => 'nta', 'Nitab4.5_0007068g0040' => 'nta', 'Nn005s41408' => 'nnu', 'Nn005s41410' => 'nnu', 'Oeu010310.1' => 'oeu', 'Oeu010311.1' => 'oeu', 'Oeu043472.1' => 'oeu', 'Os01g0246400' => 'osa', 'Os04g0267950' => 'osa', 'Os07g0178700' => 'osa', 'Os07g0178800' => 'osa', 'Peaxi162Scf00316g00046' => 'pax', 'Peaxi162Scf00316g00049' => 'pax', 'Peaxi162Scf00316g00059' => 'pax', 'Peaxi162Scf00316g00328' => 'pax', 'Peaxi162Scf00316g00329' => 'pax', 'Peaxi162Scf00316g00411' => 'pax', 'Peaxi162Scf00316g00521' => 'pax', 'Peaxi162Scf00492g00068' => 'pax', 'Peaxi162Scf35631g00002' => 'pax', 'PGR142G3720' => 'pgr', 'PGSC0003DMG400006442' => 'stu', 'Phvul.007G062000' => 'pvu', 'Potri.008G157750' => 'ptr', 'Potri.008G157900' => 'ptr', 'Potri.008G158000' => 'ptr', 'Potri.008G158200' => 'ptr', 'Pp3c11_7280' => 'ppa', 'Pp3c11_7980' => 'ppa', 'Pp3c12_19450' => 'ppa', 'Pp3c14_1480' => 'ppa', 'Pp3c14_1501' => 'ppa', 'Pp3c16_4900' => 'ppa', 'Pp3c16_5010' => 'ppa', 'Pp3c16_5060' => 'ppa', 'Pp3c19_18250' => 'ppa', 'Pp3c23_8530' => 'ppa', 'Pp3c23_8550' => 'ppa', 'Pp3c24_9670' => 'ppa', 'Pp3c2_21390' => 'ppa', 'Pp3c2_31380' => 'ppa', 'Pp3c3_16620' => 'ppa', 'Pp3c3_8090' => 'ppa', 'Pp3c3_8110' => 'ppa', 'Pp3c3_8130' => 'ppa', 'Pp3c3_8150' => 'ppa', 'Pp3c4_14320' => 'ppa', 'Pp3c6_2560' => 'ppa', 'Pp3c9_16700' => 'ppa', 'PRCOL_00000234' => 'pco', 'PRCOL_00000235' => 'pco', 'PRCOL_00000777' => 'pco', 'PRCOL_00002344' => 'pco', 'PRCOL_00002372' => 'pco', 'PRCOL_00006120' => 'pco', 'Prupe.1G021400' => 'ppe', 'Prupe.1G021500' => 'ppe', 'Prupe.1G021600' => 'ppe', 'Prupe.1G021700' => 'ppe', 'Prupe.1G021800' => 'ppe', 'Prupe.5G145100' => 'ppe', 'Psat6g204040' => 'psa', 'Psat6g204800' => 'psa', 'Psat6g204920' => 'psa', 'Psat6g204960' => 'psa', 'Psat6g205080' => 'psa', 'PSO017G0271' => 'pso', 'PSO017G1276' => 'pso', 'PSO017G1429' => 'pso', 'PSO017G1861' => 'pso', 'PSO017G2787' => 'pso', 'PSO017G4466' => 'pso', 'PSO017G5118' => 'pso', 'PSO017G5420' => 'pso', 'PSO063G3678' => 'pso', 'PSO210G0546' => 'pso', 'PSO317G0001' => 'pso', 'PSO357G0512' => 'pso', 'PSO478G2682' => 'pso', 'PSO647G0001' => 'pso', 'PSO675G0001' => 'pso', 'PSO675G2699' => 'pso', 'PSO675G2849' => 'pso', 'PSO675G4991' => 'pso', 'PSO689G0001' => 'pso', 'QL06p000916' => 'qlo', 'QL06p000921' => 'qlo', 'QL06p001398' => 'qlo', 'QL06p001407' => 'qlo', 'QL06p002031' => 'qlo', 'RcHm_v2.0_Chr4g0387791' => 'rch', 'RcHm_v2.0_Chr4g0387801' => 'rch', 'RcHm_v2.0_Chr6g0286501' => 'rch', 'RcHm_v2.0_Chr6g0286511' => 'rch', 'RcHm_v2.0_Chr6g0286521' => 'rch', 'RcHm_v2.0_Chr6g0286531' => 'rch', 'RcHm_v2.0_Chr7g0189141' => 'rch', 'Rhsim02G0028700' => 'rsi', 'Rhsim02G0028800' => 'rsi', 'Rhsim02G0028900' => 'rsi', 'Rhsim02G0029000' => 'rsi', 'Rhsim02G0029100' => 'rsi', 'Rhsim02G0029200' => 'rsi', 'Rhsim02G0029300' => 'rsi', 'Rhsim02G0029400' => 'rsi', 'Rhsim02G0029500' => 'rsi', 'Rhsim02G0029600' => 'rsi', 'RhsimUnG0024000' => 'rsi', 'RhsimUnG0024100' => 'rsi', 'RhsimUnG0024200' => 'rsi', 'RhsimUnG0024300' => 'rsi', 'RhsimUnG0024400' => 'rsi', 'RhsimUnG0024500' => 'rsi', 'RhsimUnG0024700' => 'rsi', 'RhsimUnG0024800' => 'rsi', 'RhsimUnG0024900' => 'rsi', 'RhsimUnG0025100' => 'rsi', 'Sabra08G0120200' => 'sbr', 'Sabra08G0120300' => 'sbr', 'Sabra08G0120500' => 'sbr', 'Sabra08G0120600' => 'sbr', 'Sabra10G0158900' => 'sbr', 'SalBow2G3492' => 'sbo', 'Sc13g0004760' => 'sci', 'Sc13g0004770' => 'sci', 'Sed0003417' => 'sed', 'Sed0019750' => 'sed', 'SEGI_03419' => 'sgi', 'SEGI_05907' => 'sgi', 'SEGI_10682' => 'sgi', 'SEGI_13528' => 'sgi', 'SEGI_16081' => 'sgi', 'SEGI_19370' => 'sgi', 'SEGI_21015' => 'sgi', 'SEGI_21944' => 'sgi', 'SEGI_32906' => 'sgi', 'SEGI_33093' => 'sgi', 'SEGI_36110' => 'sgi', 'SEGI_40397' => 'sgi', 'SGA_v2.0_scaffold191G40426' => 'sas', 'SGA_v2.0_scaffold353G49717' => 'sas', 'SGA_v2.0_scaffold50G18550' => 'sas', 'SMO119G0173' => 'smo', 'SMO172G0002' => 'smo', 'Solyc09g082690.3' => 'sly', 'Solyc09g082700.2' => 'sly', 'Sopen09g031550' => 'spe', 'Sopen09g031560' => 'spe', 'Sp3g20540' => 'spa', 'Sp7g07580' => 'spa', 'TAR134G0002' => 'tar', 'TAR236G0001' => 'tar', 'TAR365G0892' => 'tar', 'TAR636G0166' => 'tar', 'TAR636G0646' => 'tar', 'TAR636G0869' => 'tar', 'TAR636G1317' => 'tar', 'TAR636G1744' => 'tar', 'TAR636G3358' => 'tar', 'TAR636G3436' => 'tar', 'THA.LOC104803047' => 'tha', 'Thecc.04G238900' => 'tca', 'Thhalv10021557m.g' => 'esa', 'Thhalv10026318m.g' => 'esa', 'Thhalv10026335m.g' => 'esa', 'TPR.G17433' => 'tpr', 'TPR.G18915' => 'tpr', 'TPR.G26125' => 'tpr', 'TWI09G0677' => 'twi', 'TWI73G0287' => 'twi', 'unitig_748.g8326' => 'ugi', 'vmacro15370' => 'vma', 'vmacro15371' => 'vma', 'vmacro15372' => 'vma', 'vmacro15373' => 'vma', 'vmacro15374' => 'vma', 'VMungo0720G2826' => 'vmu', 'Zm00001eb116960' => 'zma', 'Zm00001eb301260' => 'zma', 'Zm00001eb301270' => 'zma' ) $gf_id = 'HOM05D001460' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001460' ) $data_identifier = 'HOM05D001460' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 4, 'aag' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 2, 'aox' => (int) 2, 'arhy' => (int) 4, 'ath' => (int) 2, 'atr' => (int) 1, 'acertr' => (int) 10, 'cqu' => (int) 4, 'bca' => (int) 11, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 1, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 1, 'ccan' => (int) 1, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 1, 'col' => (int) 1, 'cpa' => (int) 1, 'cre' => (int) 7, 'csa' => (int) 1, 'camsi' => (int) 2, 'dca' => (int) 3, 'din' => (int) 2, 'dzi' => (int) 3, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 14, 'fve' => (int) 9, 'gma' => (int) 2, 'ghi' => (int) 4, 'gra' => (int) 2, 'vvi' => (int) 1, 'han' => (int) 13, 'cav' => (int) 1, 'hma' => (int) 2, 'sun' => (int) 2, 'lal' => (int) 2, 'lonja' => (int) 12, 'lja' => (int) 1, 'lsa' => (int) 7, 'mes' => (int) 1, 'mpo' => (int) 27, 'mbi' => (int) 1, 'mco' => (int) 8, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 1, 'egut' => (int) 1, 'ama' => (int) 1, 'nta' => (int) 4, 'nnu' => (int) 2, 'oeu' => (int) 3, 'osa' => (int) 4, 'pax' => (int) 9, 'pgr' => (int) 1, 'stu' => (int) 1, 'pvu' => (int) 1, 'ptr' => (int) 4, 'ppa' => (int) 22, 'pco' => (int) 6, 'ppe' => (int) 6, 'psa' => (int) 5, 'pso' => (int) 19, 'qlo' => (int) 5, 'rch' => (int) 7, 'rsi' => (int) 20, 'sbr' => (int) 5, 'sbo' => (int) 1, 'sci' => (int) 2, 'sed' => (int) 2, 'sgi' => (int) 12, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 2, 'tar' => (int) 10, 'tha' => (int) 1, 'tca' => (int) 1, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 2, 'ugi' => (int) 1, 'vma' => (int) 5, 'vmu' => (int) 1, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb301270' $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' => 'HOM05D001460', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '433', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p22980' => 'bna', 'A01p32340' => 'bna', 'A03p42970' => 'bna', 'A05p25880' => 'bna', 'Aa31LG8G9320' => 'aar', 'Aa31LG8G9330' => 'aar', 'Aa31LG8G9340' => 'aar', 'Aa31sc221G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1034' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1528' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.829' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2222' => 'aag', 'Ah.12g058830' => 'amhyb', 'Ah.12g058840' => 'amhyb', 'AL3G37160' => 'aly', 'AL7G41310' => 'aly', 'Aqoxy5G00395' => 'aox', 'Aqoxy5G00396' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0C8NZA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5185HY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JZ1PRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MD3LS0' => 'arhy', 'AT3G22840' => 'ath', 'AT4G14690' => 'ath', 'ATR0665G054' => 'atr', 'Atru.chr4.2344' => 'acertr', 'Atru.chr4.2346' => 'acertr', 'Atru.chr4.2347' => 'acertr', 'Atru.chr4.2348' => 'acertr', 'Atru.chr4.2355' => 'acertr', 'Atru.chr4.2356' => 'acertr', 'Atru.chr4.2358' => 'acertr', 'Atru.chr4.2359' => 'acertr', 'Atru.chr4.2360' => 'acertr', 'Atru.chr4.2361' => 'acertr', 'AUR62030476' => 'cqu', 'AUR62030478' => 'cqu', 'AUR62030819' => 'cqu', 'AUR62030820' => 'cqu', 'BcaB03g14648' => 'bca', 'BcaB04g20492' => 'bca', 'BcaB06g26399' => 'bca', 'BcaC01g03416' => 'bca', 'BcaC01g03419' => 'bca', 'BcaC01g03421' => 'bca', 'BcaC01g03424' => 'bca', 'BcaC05g28012' => 'bca', 'BcaC09g49212' => 'bca', 'BcaC09g50140' => 'bca', 'BcaNung00346' => 'bca', 'BolC1t02785H' => 'bol', 'BolC1t04095H' => 'bol', 'BolC3t17545H' => 'bol', 'BolC5t32769H' => 'bol', 'BraA01t02211Z' => 'bra', 'BraA01t03359Z' => 'bra', 'BraA03t13441Z' => 'bra', 'BraA05t21476Z' => 'bra', 'C01p28420' => 'bna', 'C01p41350' => 'bna', 'C03p52750' => 'bna', 'C03p52780' => 'bna', 'C05p40270' => 'bna', 'CAN.G1437.9' => 'can', 'CANSAT78G0035' => 'cansat', 'CANSAT78G1036' => 'cansat', 'CANSAT78G2272' => 'cansat', 'CANSAT78G2478' => 'cansat', 'CARHR098700' => 'chi', 'CARHR221120' => 'chi', 'CARHR221150' => 'chi', 'Carub.0003s2297' => 'cru', 'Carub.0007s2749' => 'cru', 'Carub.0007s2750' => 'cru', 'Carub.0007s2751' => 'cru', 'Ca_10849_v3' => 'car', 'Cc03_g04300' => 'ccan', 'CDE02G3648' => 'cde', 'CDE05G0060' => 'cde', 'CDE05G0692' => 'cde', 'CDE05G2285' => 'cde', 'CDE05G2884' => 'cde', 'CDE05G3072' => 'cde', 'Cfa008439' => 'cfa', 'Cfa008441' => 'cfa', 'Cfa008443' => 'cfa', 'Cfa008448' => 'cfa', 'Ciclev10005974m.g' => 'ccl', 'Ciclev10006006m.g' => 'ccl', 'Ciclev10006775m.g' => 'ccl', 'CiPaw.02G120400' => 'cil', 'CiPaw.02G120500' => 'cil', 'CiPaw.02G120600' => 'cil', 'ClCG05G004850' => 'cla', 'COL.COLO4_21566' => 'col', 'Cpa.g.sc44.124' => 'cpa', 'Cre07.g320400' => 'cre', 'Cre07.g320450' => 'cre', 'Cre08.g384650' => 'cre', 'Cre09.g393173' => 'cre', 'Cre09.g394325' => 'cre', 'Cre14.g626750' => 'cre', 'Cre16.g679250' => 'cre', 'CsaV3_3G012890' => 'csa', 'CSS0010865' => 'camsi', 'CSS0044338' => 'camsi', 'DCAR_002366' => 'dca', 'DCAR_030687' => 'dca', 'DCAR_030688' => 'dca', 'Dinv14047' => 'din', 'Dinv14048' => 'din', 'Duzib151G0105' => 'dzi', 'Duzib151G0114' => 'dzi', 'Duzib212G1029' => 'dzi', 'ECA232G3536' => 'eca', 'ECA240G0786' => 'eca', 'ECA240G1802' => 'eca', 'ECA240G3760' => 'eca', 'ECA240G3920' => 'eca', 'EL10Ac5g12536' => 'bvu', 'EL10Ac5g12537' => 'bvu', 'EL10Ac5g12538' => 'bvu', 'Eucgr.B01004' => 'egr', 'Eucgr.B01006' => 'egr', 'Eucgr.B01007' => 'egr', 'Eucgr.B01008' => 'egr', 'Eucgr.B01895' => 'egr', 'Eucgr.B01896' => 'egr', 'FAN04G1456' => 'fan', 'FAN08G1769' => 'fan', 'FAN08G2160' => 'fan', 'FAN13G2403' => 'fan', 'FAN13G3303' => 'fan', 'FAN15G2435' => 'fan', 'FAN17G0672' => 'fan', 'FAN17G2441' => 'fan', 'FAN18G1024' => 'fan', 'FAN22G1458' => 'fan', 'FAN24G0037' => 'fan', 'FAN24G0429' => 'fan', 'FAN24G2387' => 'fan', 'FAN27G2746' => 'fan', 'FvH4_2g20400' => 'fve', 'FvH4_2g20420' => 'fve', 'FvH4_2g20430' => 'fve', 'FvH4_4g01270' => 'fve', 'FvH4_4g01290' => 'fve', 'FvH4_4g01300' => 'fve', 'FvH4_4g01310' => 'fve', 'FvH4_4g01330' => 'fve', 'FvH4_5g09070' => 'fve', 'Glyma.10G243800' => 'gma', 'Glyma.20G150600' => 'gma', 'Gohir.A09G219200' => 'ghi', 'Gohir.A09G219300' => 'ghi', 'Gohir.D09G221400' => 'ghi', 'Gohir.D09G221500' => 'ghi', 'Gorai.006G242600' => 'gra', 'Gorai.006G242700' => 'gra', 'GSVIVG01018044001' => 'vvi', 'HanXRQChr03g0083821' => 'han', 'HanXRQChr03g0083841' => 'han', 'HanXRQChr03g0083881' => 'han', 'HanXRQChr03g0083901' => 'han', 'HanXRQChr03g0083921' => 'han', 'HanXRQChr03g0085331' => 'han', 'HanXRQChr03g0085361' => 'han', 'HanXRQChr03g0085411' => 'han', 'HanXRQChr03g0085421' => 'han', 'HanXRQChr03g0085431' => 'han', 'HanXRQChr08g0221991' => 'han', 'HanXRQChr11g0336061' => 'han', 'HanXRQChr11g0336411' => 'han', 'Haze_11234' => 'cav', 'Hma1.2p1_0549F.1_g177010' => 'hma', 'Hma1.2p1_0602F.1_g187630' => 'hma', 'Hund14876' => 'sun', 'Hund14879' => 'sun', 'Lalb_Chr06g0160741' => 'lal', 'Lalb_Chr21g0304781' => 'lal', 'Lj3A726G19' => 'lonja', 'Lj3A726T23' => 'lonja', 'Lj3A726T24' => 'lonja', 'Lj3A726T25' => 'lonja', 'Lj3A727T17' => 'lonja', 'Lj3C726T0' => 'lonja', 'Lj3C726T2' => 'lonja', 'Lj3P725T35' => 'lonja', 'Lj3P727T10' => 'lonja', 'Lj3P727T12' => 'lonja', 'Lj3P727T14' => 'lonja', 'Lj5g0023109' => 'lja', 'Lj6P646T44' => 'lonja', 'Lsat_1_v5_gn_6_75760' => 'lsa', 'Lsat_1_v5_gn_6_75800' => 'lsa', 'Lsat_1_v5_gn_6_75900' => 'lsa', 'Lsat_1_v5_gn_6_76240' => 'lsa', 'Lsat_1_v5_gn_6_76441' => 'lsa', 'Lsat_1_v5_gn_6_76700' => 'lsa', 'Lsat_1_v5_gn_6_76760' => 'lsa', 'Manes.15G033100' => 'mes', 'Mapoly0004s0074' => 'mpo', 'Mapoly0004s0075' => 'mpo', 'Mapoly0004s0163' => 'mpo', 'Mapoly0004s0164' => 'mpo', 'Mapoly0021s0018' => 'mpo', 'Mapoly0041s0136' => 'mpo', 'Mapoly0041s0137' => 'mpo', 'Mapoly0041s0138' => 'mpo', 'Mapoly0041s0139' => 'mpo', 'Mapoly0041s0141' => 'mpo', 'Mapoly0041s0142' => 'mpo', 'Mapoly0041s0143' => 'mpo', 'Mapoly0041s0144' => 'mpo', 'Mapoly0041s0145' => 'mpo', 'Mapoly0047s0106' => 'mpo', 'Mapoly0047s0108' => 'mpo', 'Mapoly0050s0051' => 'mpo', 'Mapoly0050s0052' => 'mpo', 'Mapoly0050s0053' => 'mpo', 'Mapoly0058s0013' => 'mpo', 'Mapoly0091s0078' => 'mpo', 'Mapoly0091s0079' => 'mpo', 'Mapoly0091s0080' => 'mpo', 'Mapoly0091s0081' => 'mpo', 'Mapoly0278s0004' => 'mpo', 'Mapoly0278s0005' => 'mpo', 'Mapoly0278s0006' => 'mpo', 'MBI11_g30648_MAGBIO' => 'mbi', 'MCO03G194' => 'mco', 'MCO03G590' => 'mco', 'MCO07G312' => 'mco', 'MCO10G318' => 'mco', 'MCO12G244' => 'mco', 'MCO13G148' => 'mco', 'MCO13G194' => 'mco', 'MCO16G238' => 'mco', 'MD06G1134100' => 'mdo', 'MD13G1200100' => 'mdo', 'MD13G1200300' => 'mdo', 'MD13G1200600' => 'mdo', 'MD14G1150400' => 'mdo', 'MD16G1200000' => 'mdo', 'Medtr1g102570' => 'mtr', 'Medtr1g102780' => 'mtr', 'Medtr1g102800' => 'mtr', 'Medtr1g102810' => 'mtr', 'Medtr1g102830' => 'mtr', 'MELO3C006499.2' => 'cme', 'Migut.G00385' => 'egut', 'MSTRG.4063' => 'ama', 'Nitab4.5_0000090g0260' => 'nta', 'Nitab4.5_0000977g0030' => 'nta', 'Nitab4.5_0002541g0040' => 'nta', 'Nitab4.5_0007068g0040' => 'nta', 'Nn005s41408' => 'nnu', 'Nn005s41410' => 'nnu', 'Oeu010310.1' => 'oeu', 'Oeu010311.1' => 'oeu', 'Oeu043472.1' => 'oeu', 'Os01g0246400' => 'osa', 'Os04g0267950' => 'osa', 'Os07g0178700' => 'osa', 'Os07g0178800' => 'osa', 'Peaxi162Scf00316g00046' => 'pax', 'Peaxi162Scf00316g00049' => 'pax', 'Peaxi162Scf00316g00059' => 'pax', 'Peaxi162Scf00316g00328' => 'pax', 'Peaxi162Scf00316g00329' => 'pax', 'Peaxi162Scf00316g00411' => 'pax', 'Peaxi162Scf00316g00521' => 'pax', 'Peaxi162Scf00492g00068' => 'pax', 'Peaxi162Scf35631g00002' => 'pax', 'PGR142G3720' => 'pgr', 'PGSC0003DMG400006442' => 'stu', 'Phvul.007G062000' => 'pvu', 'Potri.008G157750' => 'ptr', 'Potri.008G157900' => 'ptr', 'Potri.008G158000' => 'ptr', 'Potri.008G158200' => 'ptr', 'Pp3c11_7280' => 'ppa', 'Pp3c11_7980' => 'ppa', 'Pp3c12_19450' => 'ppa', 'Pp3c14_1480' => 'ppa', 'Pp3c14_1501' => 'ppa', 'Pp3c16_4900' => 'ppa', 'Pp3c16_5010' => 'ppa', 'Pp3c16_5060' => 'ppa', 'Pp3c19_18250' => 'ppa', 'Pp3c23_8530' => 'ppa', 'Pp3c23_8550' => 'ppa', 'Pp3c24_9670' => 'ppa', 'Pp3c2_21390' => 'ppa', 'Pp3c2_31380' => 'ppa', 'Pp3c3_16620' => 'ppa', 'Pp3c3_8090' => 'ppa', 'Pp3c3_8110' => 'ppa', 'Pp3c3_8130' => 'ppa', 'Pp3c3_8150' => 'ppa', 'Pp3c4_14320' => 'ppa', 'Pp3c6_2560' => 'ppa', 'Pp3c9_16700' => 'ppa', 'PRCOL_00000234' => 'pco', 'PRCOL_00000235' => 'pco', 'PRCOL_00000777' => 'pco', 'PRCOL_00002344' => 'pco', 'PRCOL_00002372' => 'pco', 'PRCOL_00006120' => 'pco', 'Prupe.1G021400' => 'ppe', 'Prupe.1G021500' => 'ppe', 'Prupe.1G021600' => 'ppe', 'Prupe.1G021700' => 'ppe', 'Prupe.1G021800' => 'ppe', 'Prupe.5G145100' => 'ppe', 'Psat6g204040' => 'psa', 'Psat6g204800' => 'psa', 'Psat6g204920' => 'psa', 'Psat6g204960' => 'psa', 'Psat6g205080' => 'psa', 'PSO017G0271' => 'pso', 'PSO017G1276' => 'pso', 'PSO017G1429' => 'pso', 'PSO017G1861' => 'pso', 'PSO017G2787' => 'pso', 'PSO017G4466' => 'pso', 'PSO017G5118' => 'pso', 'PSO017G5420' => 'pso', 'PSO063G3678' => 'pso', 'PSO210G0546' => 'pso', 'PSO317G0001' => 'pso', 'PSO357G0512' => 'pso', 'PSO478G2682' => 'pso', 'PSO647G0001' => 'pso', 'PSO675G0001' => 'pso', 'PSO675G2699' => 'pso', 'PSO675G2849' => 'pso', 'PSO675G4991' => 'pso', 'PSO689G0001' => 'pso', 'QL06p000916' => 'qlo', 'QL06p000921' => 'qlo', 'QL06p001398' => 'qlo', 'QL06p001407' => 'qlo', 'QL06p002031' => 'qlo', 'RcHm_v2.0_Chr4g0387791' => 'rch', 'RcHm_v2.0_Chr4g0387801' => 'rch', 'RcHm_v2.0_Chr6g0286501' => 'rch', 'RcHm_v2.0_Chr6g0286511' => 'rch', 'RcHm_v2.0_Chr6g0286521' => 'rch', 'RcHm_v2.0_Chr6g0286531' => 'rch', 'RcHm_v2.0_Chr7g0189141' => 'rch', 'Rhsim02G0028700' => 'rsi', 'Rhsim02G0028800' => 'rsi', 'Rhsim02G0028900' => 'rsi', 'Rhsim02G0029000' => 'rsi', 'Rhsim02G0029100' => 'rsi', 'Rhsim02G0029200' => 'rsi', 'Rhsim02G0029300' => 'rsi', 'Rhsim02G0029400' => 'rsi', 'Rhsim02G0029500' => 'rsi', 'Rhsim02G0029600' => 'rsi', 'RhsimUnG0024000' => 'rsi', 'RhsimUnG0024100' => 'rsi', 'RhsimUnG0024200' => 'rsi', 'RhsimUnG0024300' => 'rsi', 'RhsimUnG0024400' => 'rsi', 'RhsimUnG0024500' => 'rsi', 'RhsimUnG0024700' => 'rsi', 'RhsimUnG0024800' => 'rsi', 'RhsimUnG0024900' => 'rsi', 'RhsimUnG0025100' => 'rsi', 'Sabra08G0120200' => 'sbr', 'Sabra08G0120300' => 'sbr', 'Sabra08G0120500' => 'sbr', 'Sabra08G0120600' => 'sbr', 'Sabra10G0158900' => 'sbr', 'SalBow2G3492' => 'sbo', 'Sc13g0004760' => 'sci', 'Sc13g0004770' => 'sci', 'Sed0003417' => 'sed', 'Sed0019750' => 'sed', 'SEGI_03419' => 'sgi', 'SEGI_05907' => 'sgi', 'SEGI_10682' => 'sgi', 'SEGI_13528' => 'sgi', 'SEGI_16081' => 'sgi', 'SEGI_19370' => 'sgi', 'SEGI_21015' => 'sgi', 'SEGI_21944' => 'sgi', 'SEGI_32906' => 'sgi', 'SEGI_33093' => 'sgi', 'SEGI_36110' => 'sgi', 'SEGI_40397' => 'sgi', 'SGA_v2.0_scaffold191G40426' => 'sas', 'SGA_v2.0_scaffold353G49717' => 'sas', 'SGA_v2.0_scaffold50G18550' => 'sas', 'SMO119G0173' => 'smo', 'SMO172G0002' => 'smo', 'Solyc09g082690.3' => 'sly', 'Solyc09g082700.2' => 'sly', 'Sopen09g031550' => 'spe', 'Sopen09g031560' => 'spe', 'Sp3g20540' => 'spa', 'Sp7g07580' => 'spa', 'TAR134G0002' => 'tar', 'TAR236G0001' => 'tar', 'TAR365G0892' => 'tar', 'TAR636G0166' => 'tar', 'TAR636G0646' => 'tar', 'TAR636G0869' => 'tar', 'TAR636G1317' => 'tar', 'TAR636G1744' => 'tar', 'TAR636G3358' => 'tar', 'TAR636G3436' => 'tar', 'THA.LOC104803047' => 'tha', 'Thecc.04G238900' => 'tca', 'Thhalv10021557m.g' => 'esa', 'Thhalv10026318m.g' => 'esa', 'Thhalv10026335m.g' => 'esa', 'TPR.G17433' => 'tpr', 'TPR.G18915' => 'tpr', 'TPR.G26125' => 'tpr', 'TWI09G0677' => 'twi', 'TWI73G0287' => 'twi', 'unitig_748.g8326' => 'ugi', 'vmacro15370' => 'vma', 'vmacro15371' => 'vma', 'vmacro15372' => 'vma', 'vmacro15373' => 'vma', 'vmacro15374' => 'vma', 'VMungo0720G2826' => 'vmu', 'Zm00001eb116960' => 'zma', 'Zm00001eb301260' => 'zma', 'Zm00001eb301270' => 'zma' ), 'gf_id' => 'HOM05D001460', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001460' ), 'data_identifier' => 'HOM05D001460', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001460', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '433', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p22980' => 'bna', 'A01p32340' => 'bna', 'A03p42970' => 'bna', 'A05p25880' => 'bna', 'Aa31LG8G9320' => 'aar', 'Aa31LG8G9330' => 'aar', 'Aa31LG8G9340' => 'aar', 'Aa31sc221G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1034' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1528' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.829' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2222' => 'aag', 'Ah.12g058830' => 'amhyb', 'Ah.12g058840' => 'amhyb', 'AL3G37160' => 'aly', 'AL7G41310' => 'aly', 'Aqoxy5G00395' => 'aox', 'Aqoxy5G00396' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0C8NZA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5185HY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JZ1PRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MD3LS0' => 'arhy', 'AT3G22840' => 'ath', 'AT4G14690' => 'ath', 'ATR0665G054' => 'atr', 'Atru.chr4.2344' => 'acertr', 'Atru.chr4.2346' => 'acertr', 'Atru.chr4.2347' => 'acertr', 'Atru.chr4.2348' => 'acertr', 'Atru.chr4.2355' => 'acertr', 'Atru.chr4.2356' => 'acertr', 'Atru.chr4.2358' => 'acertr', 'Atru.chr4.2359' => 'acertr', 'Atru.chr4.2360' => 'acertr', 'Atru.chr4.2361' => 'acertr', 'AUR62030476' => 'cqu', 'AUR62030478' => 'cqu', 'AUR62030819' => 'cqu', 'AUR62030820' => 'cqu', 'BcaB03g14648' => 'bca', 'BcaB04g20492' => 'bca', 'BcaB06g26399' => 'bca', 'BcaC01g03416' => 'bca', 'BcaC01g03419' => 'bca', 'BcaC01g03421' => 'bca', 'BcaC01g03424' => 'bca', 'BcaC05g28012' => 'bca', 'BcaC09g49212' => 'bca', 'BcaC09g50140' => 'bca', 'BcaNung00346' => 'bca', 'BolC1t02785H' => 'bol', 'BolC1t04095H' => 'bol', 'BolC3t17545H' => 'bol', 'BolC5t32769H' => 'bol', 'BraA01t02211Z' => 'bra', 'BraA01t03359Z' => 'bra', 'BraA03t13441Z' => 'bra', 'BraA05t21476Z' => 'bra', 'C01p28420' => 'bna', 'C01p41350' => 'bna', 'C03p52750' => 'bna', 'C03p52780' => 'bna', 'C05p40270' => 'bna', 'CAN.G1437.9' => 'can', 'CANSAT78G0035' => 'cansat', 'CANSAT78G1036' => 'cansat', 'CANSAT78G2272' => 'cansat', 'CANSAT78G2478' => 'cansat', 'CARHR098700' => 'chi', 'CARHR221120' => 'chi', 'CARHR221150' => 'chi', 'Carub.0003s2297' => 'cru', 'Carub.0007s2749' => 'cru', 'Carub.0007s2750' => 'cru', 'Carub.0007s2751' => 'cru', 'Ca_10849_v3' => 'car', 'Cc03_g04300' => 'ccan', 'CDE02G3648' => 'cde', 'CDE05G0060' => 'cde', 'CDE05G0692' => 'cde', 'CDE05G2285' => 'cde', 'CDE05G2884' => 'cde', 'CDE05G3072' => 'cde', 'Cfa008439' => 'cfa', 'Cfa008441' => 'cfa', 'Cfa008443' => 'cfa', 'Cfa008448' => 'cfa', 'Ciclev10005974m.g' => 'ccl', 'Ciclev10006006m.g' => 'ccl', 'Ciclev10006775m.g' => 'ccl', 'CiPaw.02G120400' => 'cil', 'CiPaw.02G120500' => 'cil', 'CiPaw.02G120600' => 'cil', 'ClCG05G004850' => 'cla', 'COL.COLO4_21566' => 'col', 'Cpa.g.sc44.124' => 'cpa', 'Cre07.g320400' => 'cre', 'Cre07.g320450' => 'cre', 'Cre08.g384650' => 'cre', 'Cre09.g393173' => 'cre', 'Cre09.g394325' => 'cre', 'Cre14.g626750' => 'cre', 'Cre16.g679250' => 'cre', 'CsaV3_3G012890' => 'csa', 'CSS0010865' => 'camsi', 'CSS0044338' => 'camsi', 'DCAR_002366' => 'dca', 'DCAR_030687' => 'dca', 'DCAR_030688' => 'dca', 'Dinv14047' => 'din', 'Dinv14048' => 'din', 'Duzib151G0105' => 'dzi', 'Duzib151G0114' => 'dzi', 'Duzib212G1029' => 'dzi', 'ECA232G3536' => 'eca', 'ECA240G0786' => 'eca', 'ECA240G1802' => 'eca', 'ECA240G3760' => 'eca', 'ECA240G3920' => 'eca', 'EL10Ac5g12536' => 'bvu', 'EL10Ac5g12537' => 'bvu', 'EL10Ac5g12538' => 'bvu', 'Eucgr.B01004' => 'egr', 'Eucgr.B01006' => 'egr', 'Eucgr.B01007' => 'egr', 'Eucgr.B01008' => 'egr', 'Eucgr.B01895' => 'egr', 'Eucgr.B01896' => 'egr', 'FAN04G1456' => 'fan', 'FAN08G1769' => 'fan', 'FAN08G2160' => 'fan', 'FAN13G2403' => 'fan', 'FAN13G3303' => 'fan', 'FAN15G2435' => 'fan', 'FAN17G0672' => 'fan', 'FAN17G2441' => 'fan', 'FAN18G1024' => 'fan', 'FAN22G1458' => 'fan', 'FAN24G0037' => 'fan', 'FAN24G0429' => 'fan', 'FAN24G2387' => 'fan', 'FAN27G2746' => 'fan', 'FvH4_2g20400' => 'fve', 'FvH4_2g20420' => 'fve', 'FvH4_2g20430' => 'fve', 'FvH4_4g01270' => 'fve', 'FvH4_4g01290' => 'fve', 'FvH4_4g01300' => 'fve', 'FvH4_4g01310' => 'fve', 'FvH4_4g01330' => 'fve', 'FvH4_5g09070' => 'fve', 'Glyma.10G243800' => 'gma', 'Glyma.20G150600' => 'gma', 'Gohir.A09G219200' => 'ghi', 'Gohir.A09G219300' => 'ghi', 'Gohir.D09G221400' => 'ghi', 'Gohir.D09G221500' => 'ghi', 'Gorai.006G242600' => 'gra', 'Gorai.006G242700' => 'gra', 'GSVIVG01018044001' => 'vvi', 'HanXRQChr03g0083821' => 'han', 'HanXRQChr03g0083841' => 'han', 'HanXRQChr03g0083881' => 'han', 'HanXRQChr03g0083901' => 'han', 'HanXRQChr03g0083921' => 'han', 'HanXRQChr03g0085331' => 'han', 'HanXRQChr03g0085361' => 'han', 'HanXRQChr03g0085411' => 'han', 'HanXRQChr03g0085421' => 'han', 'HanXRQChr03g0085431' => 'han', 'HanXRQChr08g0221991' => 'han', 'HanXRQChr11g0336061' => 'han', 'HanXRQChr11g0336411' => 'han', 'Haze_11234' => 'cav', 'Hma1.2p1_0549F.1_g177010' => 'hma', 'Hma1.2p1_0602F.1_g187630' => 'hma', 'Hund14876' => 'sun', 'Hund14879' => 'sun', 'Lalb_Chr06g0160741' => 'lal', 'Lalb_Chr21g0304781' => 'lal', 'Lj3A726G19' => 'lonja', 'Lj3A726T23' => 'lonja', 'Lj3A726T24' => 'lonja', 'Lj3A726T25' => 'lonja', 'Lj3A727T17' => 'lonja', 'Lj3C726T0' => 'lonja', 'Lj3C726T2' => 'lonja', 'Lj3P725T35' => 'lonja', 'Lj3P727T10' => 'lonja', 'Lj3P727T12' => 'lonja', 'Lj3P727T14' => 'lonja', 'Lj5g0023109' => 'lja', 'Lj6P646T44' => 'lonja', 'Lsat_1_v5_gn_6_75760' => 'lsa', 'Lsat_1_v5_gn_6_75800' => 'lsa', 'Lsat_1_v5_gn_6_75900' => 'lsa', 'Lsat_1_v5_gn_6_76240' => 'lsa', 'Lsat_1_v5_gn_6_76441' => 'lsa', 'Lsat_1_v5_gn_6_76700' => 'lsa', 'Lsat_1_v5_gn_6_76760' => 'lsa', 'Manes.15G033100' => 'mes', 'Mapoly0004s0074' => 'mpo', 'Mapoly0004s0075' => 'mpo', 'Mapoly0004s0163' => 'mpo', 'Mapoly0004s0164' => 'mpo', 'Mapoly0021s0018' => 'mpo', 'Mapoly0041s0136' => 'mpo', 'Mapoly0041s0137' => 'mpo', 'Mapoly0041s0138' => 'mpo', 'Mapoly0041s0139' => 'mpo', 'Mapoly0041s0141' => 'mpo', 'Mapoly0041s0142' => 'mpo', 'Mapoly0041s0143' => 'mpo', 'Mapoly0041s0144' => 'mpo', 'Mapoly0041s0145' => 'mpo', 'Mapoly0047s0106' => 'mpo', 'Mapoly0047s0108' => 'mpo', 'Mapoly0050s0051' => 'mpo', 'Mapoly0050s0052' => 'mpo', 'Mapoly0050s0053' => 'mpo', 'Mapoly0058s0013' => 'mpo', 'Mapoly0091s0078' => 'mpo', 'Mapoly0091s0079' => 'mpo', 'Mapoly0091s0080' => 'mpo', 'Mapoly0091s0081' => 'mpo', 'Mapoly0278s0004' => 'mpo', 'Mapoly0278s0005' => 'mpo', 'Mapoly0278s0006' => 'mpo', 'MBI11_g30648_MAGBIO' => 'mbi', 'MCO03G194' => 'mco', 'MCO03G590' => 'mco', 'MCO07G312' => 'mco', 'MCO10G318' => 'mco', 'MCO12G244' => 'mco', 'MCO13G148' => 'mco', 'MCO13G194' => 'mco', 'MCO16G238' => 'mco', 'MD06G1134100' => 'mdo', 'MD13G1200100' => 'mdo', 'MD13G1200300' => 'mdo', 'MD13G1200600' => 'mdo', 'MD14G1150400' => 'mdo', 'MD16G1200000' => 'mdo', 'Medtr1g102570' => 'mtr', 'Medtr1g102780' => 'mtr', 'Medtr1g102800' => 'mtr', 'Medtr1g102810' => 'mtr', 'Medtr1g102830' => 'mtr', 'MELO3C006499.2' => 'cme', 'Migut.G00385' => 'egut', 'MSTRG.4063' => 'ama', 'Nitab4.5_0000090g0260' => 'nta', 'Nitab4.5_0000977g0030' => 'nta', 'Nitab4.5_0002541g0040' => 'nta', 'Nitab4.5_0007068g0040' => 'nta', 'Nn005s41408' => 'nnu', 'Nn005s41410' => 'nnu', 'Oeu010310.1' => 'oeu', 'Oeu010311.1' => 'oeu', 'Oeu043472.1' => 'oeu', 'Os01g0246400' => 'osa', 'Os04g0267950' => 'osa', 'Os07g0178700' => 'osa', 'Os07g0178800' => 'osa', 'Peaxi162Scf00316g00046' => 'pax', 'Peaxi162Scf00316g00049' => 'pax', 'Peaxi162Scf00316g00059' => 'pax', 'Peaxi162Scf00316g00328' => 'pax', 'Peaxi162Scf00316g00329' => 'pax', 'Peaxi162Scf00316g00411' => 'pax', 'Peaxi162Scf00316g00521' => 'pax', 'Peaxi162Scf00492g00068' => 'pax', 'Peaxi162Scf35631g00002' => 'pax', 'PGR142G3720' => 'pgr', 'PGSC0003DMG400006442' => 'stu', 'Phvul.007G062000' => 'pvu', 'Potri.008G157750' => 'ptr', 'Potri.008G157900' => 'ptr', 'Potri.008G158000' => 'ptr', 'Potri.008G158200' => 'ptr', 'Pp3c11_7280' => 'ppa', 'Pp3c11_7980' => 'ppa', 'Pp3c12_19450' => 'ppa', 'Pp3c14_1480' => 'ppa', 'Pp3c14_1501' => 'ppa', 'Pp3c16_4900' => 'ppa', 'Pp3c16_5010' => 'ppa', 'Pp3c16_5060' => 'ppa', 'Pp3c19_18250' => 'ppa', 'Pp3c23_8530' => 'ppa', 'Pp3c23_8550' => 'ppa', 'Pp3c24_9670' => 'ppa', 'Pp3c2_21390' => 'ppa', 'Pp3c2_31380' => 'ppa', 'Pp3c3_16620' => 'ppa', 'Pp3c3_8090' => 'ppa', 'Pp3c3_8110' => 'ppa', 'Pp3c3_8130' => 'ppa', 'Pp3c3_8150' => 'ppa', 'Pp3c4_14320' => 'ppa', 'Pp3c6_2560' => 'ppa', 'Pp3c9_16700' => 'ppa', 'PRCOL_00000234' => 'pco', 'PRCOL_00000235' => 'pco', 'PRCOL_00000777' => 'pco', 'PRCOL_00002344' => 'pco', 'PRCOL_00002372' => 'pco', 'PRCOL_00006120' => 'pco', 'Prupe.1G021400' => 'ppe', 'Prupe.1G021500' => 'ppe', 'Prupe.1G021600' => 'ppe', 'Prupe.1G021700' => 'ppe', 'Prupe.1G021800' => 'ppe', 'Prupe.5G145100' => 'ppe', 'Psat6g204040' => 'psa', 'Psat6g204800' => 'psa', 'Psat6g204920' => 'psa', 'Psat6g204960' => 'psa', 'Psat6g205080' => 'psa', 'PSO017G0271' => 'pso', 'PSO017G1276' => 'pso', 'PSO017G1429' => 'pso', 'PSO017G1861' => 'pso', 'PSO017G2787' => 'pso', 'PSO017G4466' => 'pso', 'PSO017G5118' => 'pso', 'PSO017G5420' => 'pso', 'PSO063G3678' => 'pso', 'PSO210G0546' => 'pso', 'PSO317G0001' => 'pso', 'PSO357G0512' => 'pso', 'PSO478G2682' => 'pso', 'PSO647G0001' => 'pso', 'PSO675G0001' => 'pso', 'PSO675G2699' => 'pso', 'PSO675G2849' => 'pso', 'PSO675G4991' => 'pso', 'PSO689G0001' => 'pso', 'QL06p000916' => 'qlo', 'QL06p000921' => 'qlo', 'QL06p001398' => 'qlo', 'QL06p001407' => 'qlo', 'QL06p002031' => 'qlo', 'RcHm_v2.0_Chr4g0387791' => 'rch', 'RcHm_v2.0_Chr4g0387801' => 'rch', 'RcHm_v2.0_Chr6g0286501' => 'rch', 'RcHm_v2.0_Chr6g0286511' => 'rch', 'RcHm_v2.0_Chr6g0286521' => 'rch', 'RcHm_v2.0_Chr6g0286531' => 'rch', 'RcHm_v2.0_Chr7g0189141' => 'rch', 'Rhsim02G0028700' => 'rsi', 'Rhsim02G0028800' => 'rsi', 'Rhsim02G0028900' => 'rsi', 'Rhsim02G0029000' => 'rsi', 'Rhsim02G0029100' => 'rsi', 'Rhsim02G0029200' => 'rsi', 'Rhsim02G0029300' => 'rsi', 'Rhsim02G0029400' => 'rsi', 'Rhsim02G0029500' => 'rsi', 'Rhsim02G0029600' => 'rsi', 'RhsimUnG0024000' => 'rsi', 'RhsimUnG0024100' => 'rsi', 'RhsimUnG0024200' => 'rsi', 'RhsimUnG0024300' => 'rsi', 'RhsimUnG0024400' => 'rsi', 'RhsimUnG0024500' => 'rsi', 'RhsimUnG0024700' => 'rsi', 'RhsimUnG0024800' => 'rsi', 'RhsimUnG0024900' => 'rsi', 'RhsimUnG0025100' => 'rsi', 'Sabra08G0120200' => 'sbr', 'Sabra08G0120300' => 'sbr', 'Sabra08G0120500' => 'sbr', 'Sabra08G0120600' => 'sbr', 'Sabra10G0158900' => 'sbr', 'SalBow2G3492' => 'sbo', 'Sc13g0004760' => 'sci', 'Sc13g0004770' => 'sci', 'Sed0003417' => 'sed', 'Sed0019750' => 'sed', 'SEGI_03419' => 'sgi', 'SEGI_05907' => 'sgi', 'SEGI_10682' => 'sgi', 'SEGI_13528' => 'sgi', 'SEGI_16081' => 'sgi', 'SEGI_19370' => 'sgi', 'SEGI_21015' => 'sgi', 'SEGI_21944' => 'sgi', 'SEGI_32906' => 'sgi', 'SEGI_33093' => 'sgi', 'SEGI_36110' => 'sgi', 'SEGI_40397' => 'sgi', 'SGA_v2.0_scaffold191G40426' => 'sas', 'SGA_v2.0_scaffold353G49717' => 'sas', 'SGA_v2.0_scaffold50G18550' => 'sas', 'SMO119G0173' => 'smo', 'SMO172G0002' => 'smo', 'Solyc09g082690.3' => 'sly', 'Solyc09g082700.2' => 'sly', 'Sopen09g031550' => 'spe', 'Sopen09g031560' => 'spe', 'Sp3g20540' => 'spa', 'Sp7g07580' => 'spa', 'TAR134G0002' => 'tar', 'TAR236G0001' => 'tar', 'TAR365G0892' => 'tar', 'TAR636G0166' => 'tar', 'TAR636G0646' => 'tar', 'TAR636G0869' => 'tar', 'TAR636G1317' => 'tar', 'TAR636G1744' => 'tar', 'TAR636G3358' => 'tar', 'TAR636G3436' => 'tar', 'THA.LOC104803047' => 'tha', 'Thecc.04G238900' => 'tca', 'Thhalv10021557m.g' => 'esa', 'Thhalv10026318m.g' => 'esa', 'Thhalv10026335m.g' => 'esa', 'TPR.G17433' => 'tpr', 'TPR.G18915' => 'tpr', 'TPR.G26125' => 'tpr', 'TWI09G0677' => 'twi', 'TWI73G0287' => 'twi', 'unitig_748.g8326' => 'ugi', 'vmacro15370' => 'vma', 'vmacro15371' => 'vma', 'vmacro15372' => 'vma', 'vmacro15373' => 'vma', 'vmacro15374' => 'vma', 'VMungo0720G2826' => 'vmu', 'Zm00001eb116960' => 'zma', 'Zm00001eb301260' => 'zma', 'Zm00001eb301270' => 'zma' ) $gf_id = 'HOM05D001460' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001460' ) $data_identifier = 'HOM05D001460' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 4, 'aag' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 2, 'aox' => (int) 2, 'arhy' => (int) 4, 'ath' => (int) 2, 'atr' => (int) 1, 'acertr' => (int) 10, 'cqu' => (int) 4, 'bca' => (int) 11, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 1, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 1, 'ccan' => (int) 1, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 1, 'col' => (int) 1, 'cpa' => (int) 1, 'cre' => (int) 7, 'csa' => (int) 1, 'camsi' => (int) 2, 'dca' => (int) 3, 'din' => (int) 2, 'dzi' => (int) 3, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 14, 'fve' => (int) 9, 'gma' => (int) 2, 'ghi' => (int) 4, 'gra' => (int) 2, 'vvi' => (int) 1, 'han' => (int) 13, 'cav' => (int) 1, 'hma' => (int) 2, 'sun' => (int) 2, 'lal' => (int) 2, 'lonja' => (int) 12, 'lja' => (int) 1, 'lsa' => (int) 7, 'mes' => (int) 1, 'mpo' => (int) 27, 'mbi' => (int) 1, 'mco' => (int) 8, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 1, 'egut' => (int) 1, 'ama' => (int) 1, 'nta' => (int) 4, 'nnu' => (int) 2, 'oeu' => (int) 3, 'osa' => (int) 4, 'pax' => (int) 9, 'pgr' => (int) 1, 'stu' => (int) 1, 'pvu' => (int) 1, 'ptr' => (int) 4, 'ppa' => (int) 22, 'pco' => (int) 6, 'ppe' => (int) 6, 'psa' => (int) 5, 'pso' => (int) 19, 'qlo' => (int) 5, 'rch' => (int) 7, 'rsi' => (int) 20, 'sbr' => (int) 5, 'sbo' => (int) 1, 'sci' => (int) 2, 'sed' => (int) 2, 'sgi' => (int) 12, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 2, 'tar' => (int) 10, 'tha' => (int) 1, 'tca' => (int) 1, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 2, 'ugi' => (int) 1, 'vma' => (int) 5, 'vmu' => (int) 1, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb301270' $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' => 'HOM05D001460', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '433', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p22980' => 'bna', 'A01p32340' => 'bna', 'A03p42970' => 'bna', 'A05p25880' => 'bna', 'Aa31LG8G9320' => 'aar', 'Aa31LG8G9330' => 'aar', 'Aa31LG8G9340' => 'aar', 'Aa31sc221G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1034' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1528' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.829' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2222' => 'aag', 'Ah.12g058830' => 'amhyb', 'Ah.12g058840' => 'amhyb', 'AL3G37160' => 'aly', 'AL7G41310' => 'aly', 'Aqoxy5G00395' => 'aox', 'Aqoxy5G00396' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0C8NZA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5185HY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JZ1PRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MD3LS0' => 'arhy', 'AT3G22840' => 'ath', 'AT4G14690' => 'ath', 'ATR0665G054' => 'atr', 'Atru.chr4.2344' => 'acertr', 'Atru.chr4.2346' => 'acertr', 'Atru.chr4.2347' => 'acertr', 'Atru.chr4.2348' => 'acertr', 'Atru.chr4.2355' => 'acertr', 'Atru.chr4.2356' => 'acertr', 'Atru.chr4.2358' => 'acertr', 'Atru.chr4.2359' => 'acertr', 'Atru.chr4.2360' => 'acertr', 'Atru.chr4.2361' => 'acertr', 'AUR62030476' => 'cqu', 'AUR62030478' => 'cqu', 'AUR62030819' => 'cqu', 'AUR62030820' => 'cqu', 'BcaB03g14648' => 'bca', 'BcaB04g20492' => 'bca', 'BcaB06g26399' => 'bca', 'BcaC01g03416' => 'bca', 'BcaC01g03419' => 'bca', 'BcaC01g03421' => 'bca', 'BcaC01g03424' => 'bca', 'BcaC05g28012' => 'bca', 'BcaC09g49212' => 'bca', 'BcaC09g50140' => 'bca', 'BcaNung00346' => 'bca', 'BolC1t02785H' => 'bol', 'BolC1t04095H' => 'bol', 'BolC3t17545H' => 'bol', 'BolC5t32769H' => 'bol', 'BraA01t02211Z' => 'bra', 'BraA01t03359Z' => 'bra', 'BraA03t13441Z' => 'bra', 'BraA05t21476Z' => 'bra', 'C01p28420' => 'bna', 'C01p41350' => 'bna', 'C03p52750' => 'bna', 'C03p52780' => 'bna', 'C05p40270' => 'bna', 'CAN.G1437.9' => 'can', 'CANSAT78G0035' => 'cansat', 'CANSAT78G1036' => 'cansat', 'CANSAT78G2272' => 'cansat', 'CANSAT78G2478' => 'cansat', 'CARHR098700' => 'chi', 'CARHR221120' => 'chi', 'CARHR221150' => 'chi', 'Carub.0003s2297' => 'cru', 'Carub.0007s2749' => 'cru', 'Carub.0007s2750' => 'cru', 'Carub.0007s2751' => 'cru', 'Ca_10849_v3' => 'car', 'Cc03_g04300' => 'ccan', 'CDE02G3648' => 'cde', 'CDE05G0060' => 'cde', 'CDE05G0692' => 'cde', 'CDE05G2285' => 'cde', 'CDE05G2884' => 'cde', 'CDE05G3072' => 'cde', 'Cfa008439' => 'cfa', 'Cfa008441' => 'cfa', 'Cfa008443' => 'cfa', 'Cfa008448' => 'cfa', 'Ciclev10005974m.g' => 'ccl', 'Ciclev10006006m.g' => 'ccl', 'Ciclev10006775m.g' => 'ccl', 'CiPaw.02G120400' => 'cil', 'CiPaw.02G120500' => 'cil', 'CiPaw.02G120600' => 'cil', 'ClCG05G004850' => 'cla', 'COL.COLO4_21566' => 'col', 'Cpa.g.sc44.124' => 'cpa', 'Cre07.g320400' => 'cre', 'Cre07.g320450' => 'cre', 'Cre08.g384650' => 'cre', 'Cre09.g393173' => 'cre', 'Cre09.g394325' => 'cre', 'Cre14.g626750' => 'cre', 'Cre16.g679250' => 'cre', 'CsaV3_3G012890' => 'csa', 'CSS0010865' => 'camsi', 'CSS0044338' => 'camsi', 'DCAR_002366' => 'dca', 'DCAR_030687' => 'dca', 'DCAR_030688' => 'dca', 'Dinv14047' => 'din', 'Dinv14048' => 'din', 'Duzib151G0105' => 'dzi', 'Duzib151G0114' => 'dzi', 'Duzib212G1029' => 'dzi', 'ECA232G3536' => 'eca', 'ECA240G0786' => 'eca', 'ECA240G1802' => 'eca', 'ECA240G3760' => 'eca', 'ECA240G3920' => 'eca', 'EL10Ac5g12536' => 'bvu', 'EL10Ac5g12537' => 'bvu', 'EL10Ac5g12538' => 'bvu', 'Eucgr.B01004' => 'egr', 'Eucgr.B01006' => 'egr', 'Eucgr.B01007' => 'egr', 'Eucgr.B01008' => 'egr', 'Eucgr.B01895' => 'egr', 'Eucgr.B01896' => 'egr', 'FAN04G1456' => 'fan', 'FAN08G1769' => 'fan', 'FAN08G2160' => 'fan', 'FAN13G2403' => 'fan', 'FAN13G3303' => 'fan', 'FAN15G2435' => 'fan', 'FAN17G0672' => 'fan', 'FAN17G2441' => 'fan', 'FAN18G1024' => 'fan', 'FAN22G1458' => 'fan', 'FAN24G0037' => 'fan', 'FAN24G0429' => 'fan', 'FAN24G2387' => 'fan', 'FAN27G2746' => 'fan', 'FvH4_2g20400' => 'fve', 'FvH4_2g20420' => 'fve', 'FvH4_2g20430' => 'fve', 'FvH4_4g01270' => 'fve', 'FvH4_4g01290' => 'fve', 'FvH4_4g01300' => 'fve', 'FvH4_4g01310' => 'fve', 'FvH4_4g01330' => 'fve', 'FvH4_5g09070' => 'fve', 'Glyma.10G243800' => 'gma', 'Glyma.20G150600' => 'gma', 'Gohir.A09G219200' => 'ghi', 'Gohir.A09G219300' => 'ghi', 'Gohir.D09G221400' => 'ghi', 'Gohir.D09G221500' => 'ghi', 'Gorai.006G242600' => 'gra', 'Gorai.006G242700' => 'gra', 'GSVIVG01018044001' => 'vvi', 'HanXRQChr03g0083821' => 'han', 'HanXRQChr03g0083841' => 'han', 'HanXRQChr03g0083881' => 'han', 'HanXRQChr03g0083901' => 'han', 'HanXRQChr03g0083921' => 'han', 'HanXRQChr03g0085331' => 'han', 'HanXRQChr03g0085361' => 'han', 'HanXRQChr03g0085411' => 'han', 'HanXRQChr03g0085421' => 'han', 'HanXRQChr03g0085431' => 'han', 'HanXRQChr08g0221991' => 'han', 'HanXRQChr11g0336061' => 'han', 'HanXRQChr11g0336411' => 'han', 'Haze_11234' => 'cav', 'Hma1.2p1_0549F.1_g177010' => 'hma', 'Hma1.2p1_0602F.1_g187630' => 'hma', 'Hund14876' => 'sun', 'Hund14879' => 'sun', 'Lalb_Chr06g0160741' => 'lal', 'Lalb_Chr21g0304781' => 'lal', 'Lj3A726G19' => 'lonja', 'Lj3A726T23' => 'lonja', 'Lj3A726T24' => 'lonja', 'Lj3A726T25' => 'lonja', 'Lj3A727T17' => 'lonja', 'Lj3C726T0' => 'lonja', 'Lj3C726T2' => 'lonja', 'Lj3P725T35' => 'lonja', 'Lj3P727T10' => 'lonja', 'Lj3P727T12' => 'lonja', 'Lj3P727T14' => 'lonja', 'Lj5g0023109' => 'lja', 'Lj6P646T44' => 'lonja', 'Lsat_1_v5_gn_6_75760' => 'lsa', 'Lsat_1_v5_gn_6_75800' => 'lsa', 'Lsat_1_v5_gn_6_75900' => 'lsa', 'Lsat_1_v5_gn_6_76240' => 'lsa', 'Lsat_1_v5_gn_6_76441' => 'lsa', 'Lsat_1_v5_gn_6_76700' => 'lsa', 'Lsat_1_v5_gn_6_76760' => 'lsa', 'Manes.15G033100' => 'mes', 'Mapoly0004s0074' => 'mpo', 'Mapoly0004s0075' => 'mpo', 'Mapoly0004s0163' => 'mpo', 'Mapoly0004s0164' => 'mpo', 'Mapoly0021s0018' => 'mpo', 'Mapoly0041s0136' => 'mpo', 'Mapoly0041s0137' => 'mpo', 'Mapoly0041s0138' => 'mpo', 'Mapoly0041s0139' => 'mpo', 'Mapoly0041s0141' => 'mpo', 'Mapoly0041s0142' => 'mpo', 'Mapoly0041s0143' => 'mpo', 'Mapoly0041s0144' => 'mpo', 'Mapoly0041s0145' => 'mpo', 'Mapoly0047s0106' => 'mpo', 'Mapoly0047s0108' => 'mpo', 'Mapoly0050s0051' => 'mpo', 'Mapoly0050s0052' => 'mpo', 'Mapoly0050s0053' => 'mpo', 'Mapoly0058s0013' => 'mpo', 'Mapoly0091s0078' => 'mpo', 'Mapoly0091s0079' => 'mpo', 'Mapoly0091s0080' => 'mpo', 'Mapoly0091s0081' => 'mpo', 'Mapoly0278s0004' => 'mpo', 'Mapoly0278s0005' => 'mpo', 'Mapoly0278s0006' => 'mpo', 'MBI11_g30648_MAGBIO' => 'mbi', 'MCO03G194' => 'mco', 'MCO03G590' => 'mco', 'MCO07G312' => 'mco', 'MCO10G318' => 'mco', 'MCO12G244' => 'mco', 'MCO13G148' => 'mco', 'MCO13G194' => 'mco', 'MCO16G238' => 'mco', 'MD06G1134100' => 'mdo', 'MD13G1200100' => 'mdo', 'MD13G1200300' => 'mdo', 'MD13G1200600' => 'mdo', 'MD14G1150400' => 'mdo', 'MD16G1200000' => 'mdo', 'Medtr1g102570' => 'mtr', 'Medtr1g102780' => 'mtr', 'Medtr1g102800' => 'mtr', 'Medtr1g102810' => 'mtr', 'Medtr1g102830' => 'mtr', 'MELO3C006499.2' => 'cme', 'Migut.G00385' => 'egut', 'MSTRG.4063' => 'ama', 'Nitab4.5_0000090g0260' => 'nta', 'Nitab4.5_0000977g0030' => 'nta', 'Nitab4.5_0002541g0040' => 'nta', 'Nitab4.5_0007068g0040' => 'nta', 'Nn005s41408' => 'nnu', 'Nn005s41410' => 'nnu', 'Oeu010310.1' => 'oeu', 'Oeu010311.1' => 'oeu', 'Oeu043472.1' => 'oeu', 'Os01g0246400' => 'osa', 'Os04g0267950' => 'osa', 'Os07g0178700' => 'osa', 'Os07g0178800' => 'osa', 'Peaxi162Scf00316g00046' => 'pax', 'Peaxi162Scf00316g00049' => 'pax', 'Peaxi162Scf00316g00059' => 'pax', 'Peaxi162Scf00316g00328' => 'pax', 'Peaxi162Scf00316g00329' => 'pax', 'Peaxi162Scf00316g00411' => 'pax', 'Peaxi162Scf00316g00521' => 'pax', 'Peaxi162Scf00492g00068' => 'pax', 'Peaxi162Scf35631g00002' => 'pax', 'PGR142G3720' => 'pgr', 'PGSC0003DMG400006442' => 'stu', 'Phvul.007G062000' => 'pvu', 'Potri.008G157750' => 'ptr', 'Potri.008G157900' => 'ptr', 'Potri.008G158000' => 'ptr', 'Potri.008G158200' => 'ptr', 'Pp3c11_7280' => 'ppa', 'Pp3c11_7980' => 'ppa', 'Pp3c12_19450' => 'ppa', 'Pp3c14_1480' => 'ppa', 'Pp3c14_1501' => 'ppa', 'Pp3c16_4900' => 'ppa', 'Pp3c16_5010' => 'ppa', 'Pp3c16_5060' => 'ppa', 'Pp3c19_18250' => 'ppa', 'Pp3c23_8530' => 'ppa', 'Pp3c23_8550' => 'ppa', 'Pp3c24_9670' => 'ppa', 'Pp3c2_21390' => 'ppa', 'Pp3c2_31380' => 'ppa', 'Pp3c3_16620' => 'ppa', 'Pp3c3_8090' => 'ppa', 'Pp3c3_8110' => 'ppa', 'Pp3c3_8130' => 'ppa', 'Pp3c3_8150' => 'ppa', 'Pp3c4_14320' => 'ppa', 'Pp3c6_2560' => 'ppa', 'Pp3c9_16700' => 'ppa', 'PRCOL_00000234' => 'pco', 'PRCOL_00000235' => 'pco', 'PRCOL_00000777' => 'pco', 'PRCOL_00002344' => 'pco', 'PRCOL_00002372' => 'pco', 'PRCOL_00006120' => 'pco', 'Prupe.1G021400' => 'ppe', 'Prupe.1G021500' => 'ppe', 'Prupe.1G021600' => 'ppe', 'Prupe.1G021700' => 'ppe', 'Prupe.1G021800' => 'ppe', 'Prupe.5G145100' => 'ppe', 'Psat6g204040' => 'psa', 'Psat6g204800' => 'psa', 'Psat6g204920' => 'psa', 'Psat6g204960' => 'psa', 'Psat6g205080' => 'psa', 'PSO017G0271' => 'pso', 'PSO017G1276' => 'pso', 'PSO017G1429' => 'pso', 'PSO017G1861' => 'pso', 'PSO017G2787' => 'pso', 'PSO017G4466' => 'pso', 'PSO017G5118' => 'pso', 'PSO017G5420' => 'pso', 'PSO063G3678' => 'pso', 'PSO210G0546' => 'pso', 'PSO317G0001' => 'pso', 'PSO357G0512' => 'pso', 'PSO478G2682' => 'pso', 'PSO647G0001' => 'pso', 'PSO675G0001' => 'pso', 'PSO675G2699' => 'pso', 'PSO675G2849' => 'pso', 'PSO675G4991' => 'pso', 'PSO689G0001' => 'pso', 'QL06p000916' => 'qlo', 'QL06p000921' => 'qlo', 'QL06p001398' => 'qlo', 'QL06p001407' => 'qlo', 'QL06p002031' => 'qlo', 'RcHm_v2.0_Chr4g0387791' => 'rch', 'RcHm_v2.0_Chr4g0387801' => 'rch', 'RcHm_v2.0_Chr6g0286501' => 'rch', 'RcHm_v2.0_Chr6g0286511' => 'rch', 'RcHm_v2.0_Chr6g0286521' => 'rch', 'RcHm_v2.0_Chr6g0286531' => 'rch', 'RcHm_v2.0_Chr7g0189141' => 'rch', 'Rhsim02G0028700' => 'rsi', 'Rhsim02G0028800' => 'rsi', 'Rhsim02G0028900' => 'rsi', 'Rhsim02G0029000' => 'rsi', 'Rhsim02G0029100' => 'rsi', 'Rhsim02G0029200' => 'rsi', 'Rhsim02G0029300' => 'rsi', 'Rhsim02G0029400' => 'rsi', 'Rhsim02G0029500' => 'rsi', 'Rhsim02G0029600' => 'rsi', 'RhsimUnG0024000' => 'rsi', 'RhsimUnG0024100' => 'rsi', 'RhsimUnG0024200' => 'rsi', 'RhsimUnG0024300' => 'rsi', 'RhsimUnG0024400' => 'rsi', 'RhsimUnG0024500' => 'rsi', 'RhsimUnG0024700' => 'rsi', 'RhsimUnG0024800' => 'rsi', 'RhsimUnG0024900' => 'rsi', 'RhsimUnG0025100' => 'rsi', 'Sabra08G0120200' => 'sbr', 'Sabra08G0120300' => 'sbr', 'Sabra08G0120500' => 'sbr', 'Sabra08G0120600' => 'sbr', 'Sabra10G0158900' => 'sbr', 'SalBow2G3492' => 'sbo', 'Sc13g0004760' => 'sci', 'Sc13g0004770' => 'sci', 'Sed0003417' => 'sed', 'Sed0019750' => 'sed', 'SEGI_03419' => 'sgi', 'SEGI_05907' => 'sgi', 'SEGI_10682' => 'sgi', 'SEGI_13528' => 'sgi', 'SEGI_16081' => 'sgi', 'SEGI_19370' => 'sgi', 'SEGI_21015' => 'sgi', 'SEGI_21944' => 'sgi', 'SEGI_32906' => 'sgi', 'SEGI_33093' => 'sgi', 'SEGI_36110' => 'sgi', 'SEGI_40397' => 'sgi', 'SGA_v2.0_scaffold191G40426' => 'sas', 'SGA_v2.0_scaffold353G49717' => 'sas', 'SGA_v2.0_scaffold50G18550' => 'sas', 'SMO119G0173' => 'smo', 'SMO172G0002' => 'smo', 'Solyc09g082690.3' => 'sly', 'Solyc09g082700.2' => 'sly', 'Sopen09g031550' => 'spe', 'Sopen09g031560' => 'spe', 'Sp3g20540' => 'spa', 'Sp7g07580' => 'spa', 'TAR134G0002' => 'tar', 'TAR236G0001' => 'tar', 'TAR365G0892' => 'tar', 'TAR636G0166' => 'tar', 'TAR636G0646' => 'tar', 'TAR636G0869' => 'tar', 'TAR636G1317' => 'tar', 'TAR636G1744' => 'tar', 'TAR636G3358' => 'tar', 'TAR636G3436' => 'tar', 'THA.LOC104803047' => 'tha', 'Thecc.04G238900' => 'tca', 'Thhalv10021557m.g' => 'esa', 'Thhalv10026318m.g' => 'esa', 'Thhalv10026335m.g' => 'esa', 'TPR.G17433' => 'tpr', 'TPR.G18915' => 'tpr', 'TPR.G26125' => 'tpr', 'TWI09G0677' => 'twi', 'TWI73G0287' => 'twi', 'unitig_748.g8326' => 'ugi', 'vmacro15370' => 'vma', 'vmacro15371' => 'vma', 'vmacro15372' => 'vma', 'vmacro15373' => 'vma', 'vmacro15374' => 'vma', 'VMungo0720G2826' => 'vmu', 'Zm00001eb116960' => 'zma', 'Zm00001eb301260' => 'zma', 'Zm00001eb301270' => 'zma' ), 'gf_id' => 'HOM05D001460', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001460' ), 'data_identifier' => 'HOM05D001460', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001460', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '433', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p22980' => 'bna', 'A01p32340' => 'bna', 'A03p42970' => 'bna', 'A05p25880' => 'bna', 'Aa31LG8G9320' => 'aar', 'Aa31LG8G9330' => 'aar', 'Aa31LG8G9340' => 'aar', 'Aa31sc221G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1034' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1528' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.829' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2222' => 'aag', 'Ah.12g058830' => 'amhyb', 'Ah.12g058840' => 'amhyb', 'AL3G37160' => 'aly', 'AL7G41310' => 'aly', 'Aqoxy5G00395' => 'aox', 'Aqoxy5G00396' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0C8NZA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5185HY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JZ1PRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MD3LS0' => 'arhy', 'AT3G22840' => 'ath', 'AT4G14690' => 'ath', 'ATR0665G054' => 'atr', 'Atru.chr4.2344' => 'acertr', 'Atru.chr4.2346' => 'acertr', 'Atru.chr4.2347' => 'acertr', 'Atru.chr4.2348' => 'acertr', 'Atru.chr4.2355' => 'acertr', 'Atru.chr4.2356' => 'acertr', 'Atru.chr4.2358' => 'acertr', 'Atru.chr4.2359' => 'acertr', 'Atru.chr4.2360' => 'acertr', 'Atru.chr4.2361' => 'acertr', 'AUR62030476' => 'cqu', 'AUR62030478' => 'cqu', 'AUR62030819' => 'cqu', 'AUR62030820' => 'cqu', 'BcaB03g14648' => 'bca', 'BcaB04g20492' => 'bca', 'BcaB06g26399' => 'bca', 'BcaC01g03416' => 'bca', 'BcaC01g03419' => 'bca', 'BcaC01g03421' => 'bca', 'BcaC01g03424' => 'bca', 'BcaC05g28012' => 'bca', 'BcaC09g49212' => 'bca', 'BcaC09g50140' => 'bca', 'BcaNung00346' => 'bca', 'BolC1t02785H' => 'bol', 'BolC1t04095H' => 'bol', 'BolC3t17545H' => 'bol', 'BolC5t32769H' => 'bol', 'BraA01t02211Z' => 'bra', 'BraA01t03359Z' => 'bra', 'BraA03t13441Z' => 'bra', 'BraA05t21476Z' => 'bra', 'C01p28420' => 'bna', 'C01p41350' => 'bna', 'C03p52750' => 'bna', 'C03p52780' => 'bna', 'C05p40270' => 'bna', 'CAN.G1437.9' => 'can', 'CANSAT78G0035' => 'cansat', 'CANSAT78G1036' => 'cansat', 'CANSAT78G2272' => 'cansat', 'CANSAT78G2478' => 'cansat', 'CARHR098700' => 'chi', 'CARHR221120' => 'chi', 'CARHR221150' => 'chi', 'Carub.0003s2297' => 'cru', 'Carub.0007s2749' => 'cru', 'Carub.0007s2750' => 'cru', 'Carub.0007s2751' => 'cru', 'Ca_10849_v3' => 'car', 'Cc03_g04300' => 'ccan', 'CDE02G3648' => 'cde', 'CDE05G0060' => 'cde', 'CDE05G0692' => 'cde', 'CDE05G2285' => 'cde', 'CDE05G2884' => 'cde', 'CDE05G3072' => 'cde', 'Cfa008439' => 'cfa', 'Cfa008441' => 'cfa', 'Cfa008443' => 'cfa', 'Cfa008448' => 'cfa', 'Ciclev10005974m.g' => 'ccl', 'Ciclev10006006m.g' => 'ccl', 'Ciclev10006775m.g' => 'ccl', 'CiPaw.02G120400' => 'cil', 'CiPaw.02G120500' => 'cil', 'CiPaw.02G120600' => 'cil', 'ClCG05G004850' => 'cla', 'COL.COLO4_21566' => 'col', 'Cpa.g.sc44.124' => 'cpa', 'Cre07.g320400' => 'cre', 'Cre07.g320450' => 'cre', 'Cre08.g384650' => 'cre', 'Cre09.g393173' => 'cre', 'Cre09.g394325' => 'cre', 'Cre14.g626750' => 'cre', 'Cre16.g679250' => 'cre', 'CsaV3_3G012890' => 'csa', 'CSS0010865' => 'camsi', 'CSS0044338' => 'camsi', 'DCAR_002366' => 'dca', 'DCAR_030687' => 'dca', 'DCAR_030688' => 'dca', 'Dinv14047' => 'din', 'Dinv14048' => 'din', 'Duzib151G0105' => 'dzi', 'Duzib151G0114' => 'dzi', 'Duzib212G1029' => 'dzi', 'ECA232G3536' => 'eca', 'ECA240G0786' => 'eca', 'ECA240G1802' => 'eca', 'ECA240G3760' => 'eca', 'ECA240G3920' => 'eca', 'EL10Ac5g12536' => 'bvu', 'EL10Ac5g12537' => 'bvu', 'EL10Ac5g12538' => 'bvu', 'Eucgr.B01004' => 'egr', 'Eucgr.B01006' => 'egr', 'Eucgr.B01007' => 'egr', 'Eucgr.B01008' => 'egr', 'Eucgr.B01895' => 'egr', 'Eucgr.B01896' => 'egr', 'FAN04G1456' => 'fan', 'FAN08G1769' => 'fan', 'FAN08G2160' => 'fan', 'FAN13G2403' => 'fan', 'FAN13G3303' => 'fan', 'FAN15G2435' => 'fan', 'FAN17G0672' => 'fan', 'FAN17G2441' => 'fan', 'FAN18G1024' => 'fan', 'FAN22G1458' => 'fan', 'FAN24G0037' => 'fan', 'FAN24G0429' => 'fan', 'FAN24G2387' => 'fan', 'FAN27G2746' => 'fan', 'FvH4_2g20400' => 'fve', 'FvH4_2g20420' => 'fve', 'FvH4_2g20430' => 'fve', 'FvH4_4g01270' => 'fve', 'FvH4_4g01290' => 'fve', 'FvH4_4g01300' => 'fve', 'FvH4_4g01310' => 'fve', 'FvH4_4g01330' => 'fve', 'FvH4_5g09070' => 'fve', 'Glyma.10G243800' => 'gma', 'Glyma.20G150600' => 'gma', 'Gohir.A09G219200' => 'ghi', 'Gohir.A09G219300' => 'ghi', 'Gohir.D09G221400' => 'ghi', 'Gohir.D09G221500' => 'ghi', 'Gorai.006G242600' => 'gra', 'Gorai.006G242700' => 'gra', 'GSVIVG01018044001' => 'vvi', 'HanXRQChr03g0083821' => 'han', 'HanXRQChr03g0083841' => 'han', 'HanXRQChr03g0083881' => 'han', 'HanXRQChr03g0083901' => 'han', 'HanXRQChr03g0083921' => 'han', 'HanXRQChr03g0085331' => 'han', 'HanXRQChr03g0085361' => 'han', 'HanXRQChr03g0085411' => 'han', 'HanXRQChr03g0085421' => 'han', 'HanXRQChr03g0085431' => 'han', 'HanXRQChr08g0221991' => 'han', 'HanXRQChr11g0336061' => 'han', 'HanXRQChr11g0336411' => 'han', 'Haze_11234' => 'cav', 'Hma1.2p1_0549F.1_g177010' => 'hma', 'Hma1.2p1_0602F.1_g187630' => 'hma', 'Hund14876' => 'sun', 'Hund14879' => 'sun', 'Lalb_Chr06g0160741' => 'lal', 'Lalb_Chr21g0304781' => 'lal', 'Lj3A726G19' => 'lonja', 'Lj3A726T23' => 'lonja', 'Lj3A726T24' => 'lonja', 'Lj3A726T25' => 'lonja', 'Lj3A727T17' => 'lonja', 'Lj3C726T0' => 'lonja', 'Lj3C726T2' => 'lonja', 'Lj3P725T35' => 'lonja', 'Lj3P727T10' => 'lonja', 'Lj3P727T12' => 'lonja', 'Lj3P727T14' => 'lonja', 'Lj5g0023109' => 'lja', 'Lj6P646T44' => 'lonja', 'Lsat_1_v5_gn_6_75760' => 'lsa', 'Lsat_1_v5_gn_6_75800' => 'lsa', 'Lsat_1_v5_gn_6_75900' => 'lsa', 'Lsat_1_v5_gn_6_76240' => 'lsa', 'Lsat_1_v5_gn_6_76441' => 'lsa', 'Lsat_1_v5_gn_6_76700' => 'lsa', 'Lsat_1_v5_gn_6_76760' => 'lsa', 'Manes.15G033100' => 'mes', 'Mapoly0004s0074' => 'mpo', 'Mapoly0004s0075' => 'mpo', 'Mapoly0004s0163' => 'mpo', 'Mapoly0004s0164' => 'mpo', 'Mapoly0021s0018' => 'mpo', 'Mapoly0041s0136' => 'mpo', 'Mapoly0041s0137' => 'mpo', 'Mapoly0041s0138' => 'mpo', 'Mapoly0041s0139' => 'mpo', 'Mapoly0041s0141' => 'mpo', 'Mapoly0041s0142' => 'mpo', 'Mapoly0041s0143' => 'mpo', 'Mapoly0041s0144' => 'mpo', 'Mapoly0041s0145' => 'mpo', 'Mapoly0047s0106' => 'mpo', 'Mapoly0047s0108' => 'mpo', 'Mapoly0050s0051' => 'mpo', 'Mapoly0050s0052' => 'mpo', 'Mapoly0050s0053' => 'mpo', 'Mapoly0058s0013' => 'mpo', 'Mapoly0091s0078' => 'mpo', 'Mapoly0091s0079' => 'mpo', 'Mapoly0091s0080' => 'mpo', 'Mapoly0091s0081' => 'mpo', 'Mapoly0278s0004' => 'mpo', 'Mapoly0278s0005' => 'mpo', 'Mapoly0278s0006' => 'mpo', 'MBI11_g30648_MAGBIO' => 'mbi', 'MCO03G194' => 'mco', 'MCO03G590' => 'mco', 'MCO07G312' => 'mco', 'MCO10G318' => 'mco', 'MCO12G244' => 'mco', 'MCO13G148' => 'mco', 'MCO13G194' => 'mco', 'MCO16G238' => 'mco', 'MD06G1134100' => 'mdo', 'MD13G1200100' => 'mdo', 'MD13G1200300' => 'mdo', 'MD13G1200600' => 'mdo', 'MD14G1150400' => 'mdo', 'MD16G1200000' => 'mdo', 'Medtr1g102570' => 'mtr', 'Medtr1g102780' => 'mtr', 'Medtr1g102800' => 'mtr', 'Medtr1g102810' => 'mtr', 'Medtr1g102830' => 'mtr', 'MELO3C006499.2' => 'cme', 'Migut.G00385' => 'egut', 'MSTRG.4063' => 'ama', 'Nitab4.5_0000090g0260' => 'nta', 'Nitab4.5_0000977g0030' => 'nta', 'Nitab4.5_0002541g0040' => 'nta', 'Nitab4.5_0007068g0040' => 'nta', 'Nn005s41408' => 'nnu', 'Nn005s41410' => 'nnu', 'Oeu010310.1' => 'oeu', 'Oeu010311.1' => 'oeu', 'Oeu043472.1' => 'oeu', 'Os01g0246400' => 'osa', 'Os04g0267950' => 'osa', 'Os07g0178700' => 'osa', 'Os07g0178800' => 'osa', 'Peaxi162Scf00316g00046' => 'pax', 'Peaxi162Scf00316g00049' => 'pax', 'Peaxi162Scf00316g00059' => 'pax', 'Peaxi162Scf00316g00328' => 'pax', 'Peaxi162Scf00316g00329' => 'pax', 'Peaxi162Scf00316g00411' => 'pax', 'Peaxi162Scf00316g00521' => 'pax', 'Peaxi162Scf00492g00068' => 'pax', 'Peaxi162Scf35631g00002' => 'pax', 'PGR142G3720' => 'pgr', 'PGSC0003DMG400006442' => 'stu', 'Phvul.007G062000' => 'pvu', 'Potri.008G157750' => 'ptr', 'Potri.008G157900' => 'ptr', 'Potri.008G158000' => 'ptr', 'Potri.008G158200' => 'ptr', 'Pp3c11_7280' => 'ppa', 'Pp3c11_7980' => 'ppa', 'Pp3c12_19450' => 'ppa', 'Pp3c14_1480' => 'ppa', 'Pp3c14_1501' => 'ppa', 'Pp3c16_4900' => 'ppa', 'Pp3c16_5010' => 'ppa', 'Pp3c16_5060' => 'ppa', 'Pp3c19_18250' => 'ppa', 'Pp3c23_8530' => 'ppa', 'Pp3c23_8550' => 'ppa', 'Pp3c24_9670' => 'ppa', 'Pp3c2_21390' => 'ppa', 'Pp3c2_31380' => 'ppa', 'Pp3c3_16620' => 'ppa', 'Pp3c3_8090' => 'ppa', 'Pp3c3_8110' => 'ppa', 'Pp3c3_8130' => 'ppa', 'Pp3c3_8150' => 'ppa', 'Pp3c4_14320' => 'ppa', 'Pp3c6_2560' => 'ppa', 'Pp3c9_16700' => 'ppa', 'PRCOL_00000234' => 'pco', 'PRCOL_00000235' => 'pco', 'PRCOL_00000777' => 'pco', 'PRCOL_00002344' => 'pco', 'PRCOL_00002372' => 'pco', 'PRCOL_00006120' => 'pco', 'Prupe.1G021400' => 'ppe', 'Prupe.1G021500' => 'ppe', 'Prupe.1G021600' => 'ppe', 'Prupe.1G021700' => 'ppe', 'Prupe.1G021800' => 'ppe', 'Prupe.5G145100' => 'ppe', 'Psat6g204040' => 'psa', 'Psat6g204800' => 'psa', 'Psat6g204920' => 'psa', 'Psat6g204960' => 'psa', 'Psat6g205080' => 'psa', 'PSO017G0271' => 'pso', 'PSO017G1276' => 'pso', 'PSO017G1429' => 'pso', 'PSO017G1861' => 'pso', 'PSO017G2787' => 'pso', 'PSO017G4466' => 'pso', 'PSO017G5118' => 'pso', 'PSO017G5420' => 'pso', 'PSO063G3678' => 'pso', 'PSO210G0546' => 'pso', 'PSO317G0001' => 'pso', 'PSO357G0512' => 'pso', 'PSO478G2682' => 'pso', 'PSO647G0001' => 'pso', 'PSO675G0001' => 'pso', 'PSO675G2699' => 'pso', 'PSO675G2849' => 'pso', 'PSO675G4991' => 'pso', 'PSO689G0001' => 'pso', 'QL06p000916' => 'qlo', 'QL06p000921' => 'qlo', 'QL06p001398' => 'qlo', 'QL06p001407' => 'qlo', 'QL06p002031' => 'qlo', 'RcHm_v2.0_Chr4g0387791' => 'rch', 'RcHm_v2.0_Chr4g0387801' => 'rch', 'RcHm_v2.0_Chr6g0286501' => 'rch', 'RcHm_v2.0_Chr6g0286511' => 'rch', 'RcHm_v2.0_Chr6g0286521' => 'rch', 'RcHm_v2.0_Chr6g0286531' => 'rch', 'RcHm_v2.0_Chr7g0189141' => 'rch', 'Rhsim02G0028700' => 'rsi', 'Rhsim02G0028800' => 'rsi', 'Rhsim02G0028900' => 'rsi', 'Rhsim02G0029000' => 'rsi', 'Rhsim02G0029100' => 'rsi', 'Rhsim02G0029200' => 'rsi', 'Rhsim02G0029300' => 'rsi', 'Rhsim02G0029400' => 'rsi', 'Rhsim02G0029500' => 'rsi', 'Rhsim02G0029600' => 'rsi', 'RhsimUnG0024000' => 'rsi', 'RhsimUnG0024100' => 'rsi', 'RhsimUnG0024200' => 'rsi', 'RhsimUnG0024300' => 'rsi', 'RhsimUnG0024400' => 'rsi', 'RhsimUnG0024500' => 'rsi', 'RhsimUnG0024700' => 'rsi', 'RhsimUnG0024800' => 'rsi', 'RhsimUnG0024900' => 'rsi', 'RhsimUnG0025100' => 'rsi', 'Sabra08G0120200' => 'sbr', 'Sabra08G0120300' => 'sbr', 'Sabra08G0120500' => 'sbr', 'Sabra08G0120600' => 'sbr', 'Sabra10G0158900' => 'sbr', 'SalBow2G3492' => 'sbo', 'Sc13g0004760' => 'sci', 'Sc13g0004770' => 'sci', 'Sed0003417' => 'sed', 'Sed0019750' => 'sed', 'SEGI_03419' => 'sgi', 'SEGI_05907' => 'sgi', 'SEGI_10682' => 'sgi', 'SEGI_13528' => 'sgi', 'SEGI_16081' => 'sgi', 'SEGI_19370' => 'sgi', 'SEGI_21015' => 'sgi', 'SEGI_21944' => 'sgi', 'SEGI_32906' => 'sgi', 'SEGI_33093' => 'sgi', 'SEGI_36110' => 'sgi', 'SEGI_40397' => 'sgi', 'SGA_v2.0_scaffold191G40426' => 'sas', 'SGA_v2.0_scaffold353G49717' => 'sas', 'SGA_v2.0_scaffold50G18550' => 'sas', 'SMO119G0173' => 'smo', 'SMO172G0002' => 'smo', 'Solyc09g082690.3' => 'sly', 'Solyc09g082700.2' => 'sly', 'Sopen09g031550' => 'spe', 'Sopen09g031560' => 'spe', 'Sp3g20540' => 'spa', 'Sp7g07580' => 'spa', 'TAR134G0002' => 'tar', 'TAR236G0001' => 'tar', 'TAR365G0892' => 'tar', 'TAR636G0166' => 'tar', 'TAR636G0646' => 'tar', 'TAR636G0869' => 'tar', 'TAR636G1317' => 'tar', 'TAR636G1744' => 'tar', 'TAR636G3358' => 'tar', 'TAR636G3436' => 'tar', 'THA.LOC104803047' => 'tha', 'Thecc.04G238900' => 'tca', 'Thhalv10021557m.g' => 'esa', 'Thhalv10026318m.g' => 'esa', 'Thhalv10026335m.g' => 'esa', 'TPR.G17433' => 'tpr', 'TPR.G18915' => 'tpr', 'TPR.G26125' => 'tpr', 'TWI09G0677' => 'twi', 'TWI73G0287' => 'twi', 'unitig_748.g8326' => 'ugi', 'vmacro15370' => 'vma', 'vmacro15371' => 'vma', 'vmacro15372' => 'vma', 'vmacro15373' => 'vma', 'vmacro15374' => 'vma', 'VMungo0720G2826' => 'vmu', 'Zm00001eb116960' => 'zma', 'Zm00001eb301260' => 'zma', 'Zm00001eb301270' => 'zma' ) $gf_id = 'HOM05D001460' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001460' ) $data_identifier = 'HOM05D001460' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 4, 'aag' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 2, 'aox' => (int) 2, 'arhy' => (int) 4, 'ath' => (int) 2, 'atr' => (int) 1, 'acertr' => (int) 10, 'cqu' => (int) 4, 'bca' => (int) 11, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 1, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 1, 'ccan' => (int) 1, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 1, 'col' => (int) 1, 'cpa' => (int) 1, 'cre' => (int) 7, 'csa' => (int) 1, 'camsi' => (int) 2, 'dca' => (int) 3, 'din' => (int) 2, 'dzi' => (int) 3, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 14, 'fve' => (int) 9, 'gma' => (int) 2, 'ghi' => (int) 4, 'gra' => (int) 2, 'vvi' => (int) 1, 'han' => (int) 13, 'cav' => (int) 1, 'hma' => (int) 2, 'sun' => (int) 2, 'lal' => (int) 2, 'lonja' => (int) 12, 'lja' => (int) 1, 'lsa' => (int) 7, 'mes' => (int) 1, 'mpo' => (int) 27, 'mbi' => (int) 1, 'mco' => (int) 8, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 1, 'egut' => (int) 1, 'ama' => (int) 1, 'nta' => (int) 4, 'nnu' => (int) 2, 'oeu' => (int) 3, 'osa' => (int) 4, 'pax' => (int) 9, 'pgr' => (int) 1, 'stu' => (int) 1, 'pvu' => (int) 1, 'ptr' => (int) 4, 'ppa' => (int) 22, 'pco' => (int) 6, 'ppe' => (int) 6, 'psa' => (int) 5, 'pso' => (int) 19, 'qlo' => (int) 5, 'rch' => (int) 7, 'rsi' => (int) 20, 'sbr' => (int) 5, 'sbo' => (int) 1, 'sci' => (int) 2, 'sed' => (int) 2, 'sgi' => (int) 12, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 2, 'tar' => (int) 10, 'tha' => (int) 1, 'tca' => (int) 1, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 2, 'ugi' => (int) 1, 'vma' => (int) 5, 'vmu' => (int) 1, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb301270' $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' => 'HOM05D001460', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '433', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p22980' => 'bna', 'A01p32340' => 'bna', 'A03p42970' => 'bna', 'A05p25880' => 'bna', 'Aa31LG8G9320' => 'aar', 'Aa31LG8G9330' => 'aar', 'Aa31LG8G9340' => 'aar', 'Aa31sc221G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1034' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1528' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.829' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2222' => 'aag', 'Ah.12g058830' => 'amhyb', 'Ah.12g058840' => 'amhyb', 'AL3G37160' => 'aly', 'AL7G41310' => 'aly', 'Aqoxy5G00395' => 'aox', 'Aqoxy5G00396' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0C8NZA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5185HY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JZ1PRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MD3LS0' => 'arhy', 'AT3G22840' => 'ath', 'AT4G14690' => 'ath', 'ATR0665G054' => 'atr', 'Atru.chr4.2344' => 'acertr', 'Atru.chr4.2346' => 'acertr', 'Atru.chr4.2347' => 'acertr', 'Atru.chr4.2348' => 'acertr', 'Atru.chr4.2355' => 'acertr', 'Atru.chr4.2356' => 'acertr', 'Atru.chr4.2358' => 'acertr', 'Atru.chr4.2359' => 'acertr', 'Atru.chr4.2360' => 'acertr', 'Atru.chr4.2361' => 'acertr', 'AUR62030476' => 'cqu', 'AUR62030478' => 'cqu', 'AUR62030819' => 'cqu', 'AUR62030820' => 'cqu', 'BcaB03g14648' => 'bca', 'BcaB04g20492' => 'bca', 'BcaB06g26399' => 'bca', 'BcaC01g03416' => 'bca', 'BcaC01g03419' => 'bca', 'BcaC01g03421' => 'bca', 'BcaC01g03424' => 'bca', 'BcaC05g28012' => 'bca', 'BcaC09g49212' => 'bca', 'BcaC09g50140' => 'bca', 'BcaNung00346' => 'bca', 'BolC1t02785H' => 'bol', 'BolC1t04095H' => 'bol', 'BolC3t17545H' => 'bol', 'BolC5t32769H' => 'bol', 'BraA01t02211Z' => 'bra', 'BraA01t03359Z' => 'bra', 'BraA03t13441Z' => 'bra', 'BraA05t21476Z' => 'bra', 'C01p28420' => 'bna', 'C01p41350' => 'bna', 'C03p52750' => 'bna', 'C03p52780' => 'bna', 'C05p40270' => 'bna', 'CAN.G1437.9' => 'can', 'CANSAT78G0035' => 'cansat', 'CANSAT78G1036' => 'cansat', 'CANSAT78G2272' => 'cansat', 'CANSAT78G2478' => 'cansat', 'CARHR098700' => 'chi', 'CARHR221120' => 'chi', 'CARHR221150' => 'chi', 'Carub.0003s2297' => 'cru', 'Carub.0007s2749' => 'cru', 'Carub.0007s2750' => 'cru', 'Carub.0007s2751' => 'cru', 'Ca_10849_v3' => 'car', 'Cc03_g04300' => 'ccan', 'CDE02G3648' => 'cde', 'CDE05G0060' => 'cde', 'CDE05G0692' => 'cde', 'CDE05G2285' => 'cde', 'CDE05G2884' => 'cde', 'CDE05G3072' => 'cde', 'Cfa008439' => 'cfa', 'Cfa008441' => 'cfa', 'Cfa008443' => 'cfa', 'Cfa008448' => 'cfa', 'Ciclev10005974m.g' => 'ccl', 'Ciclev10006006m.g' => 'ccl', 'Ciclev10006775m.g' => 'ccl', 'CiPaw.02G120400' => 'cil', 'CiPaw.02G120500' => 'cil', 'CiPaw.02G120600' => 'cil', 'ClCG05G004850' => 'cla', 'COL.COLO4_21566' => 'col', 'Cpa.g.sc44.124' => 'cpa', 'Cre07.g320400' => 'cre', 'Cre07.g320450' => 'cre', 'Cre08.g384650' => 'cre', 'Cre09.g393173' => 'cre', 'Cre09.g394325' => 'cre', 'Cre14.g626750' => 'cre', 'Cre16.g679250' => 'cre', 'CsaV3_3G012890' => 'csa', 'CSS0010865' => 'camsi', 'CSS0044338' => 'camsi', 'DCAR_002366' => 'dca', 'DCAR_030687' => 'dca', 'DCAR_030688' => 'dca', 'Dinv14047' => 'din', 'Dinv14048' => 'din', 'Duzib151G0105' => 'dzi', 'Duzib151G0114' => 'dzi', 'Duzib212G1029' => 'dzi', 'ECA232G3536' => 'eca', 'ECA240G0786' => 'eca', 'ECA240G1802' => 'eca', 'ECA240G3760' => 'eca', 'ECA240G3920' => 'eca', 'EL10Ac5g12536' => 'bvu', 'EL10Ac5g12537' => 'bvu', 'EL10Ac5g12538' => 'bvu', 'Eucgr.B01004' => 'egr', 'Eucgr.B01006' => 'egr', 'Eucgr.B01007' => 'egr', 'Eucgr.B01008' => 'egr', 'Eucgr.B01895' => 'egr', 'Eucgr.B01896' => 'egr', 'FAN04G1456' => 'fan', 'FAN08G1769' => 'fan', 'FAN08G2160' => 'fan', 'FAN13G2403' => 'fan', 'FAN13G3303' => 'fan', 'FAN15G2435' => 'fan', 'FAN17G0672' => 'fan', 'FAN17G2441' => 'fan', 'FAN18G1024' => 'fan', 'FAN22G1458' => 'fan', 'FAN24G0037' => 'fan', 'FAN24G0429' => 'fan', 'FAN24G2387' => 'fan', 'FAN27G2746' => 'fan', 'FvH4_2g20400' => 'fve', 'FvH4_2g20420' => 'fve', 'FvH4_2g20430' => 'fve', 'FvH4_4g01270' => 'fve', 'FvH4_4g01290' => 'fve', 'FvH4_4g01300' => 'fve', 'FvH4_4g01310' => 'fve', 'FvH4_4g01330' => 'fve', 'FvH4_5g09070' => 'fve', 'Glyma.10G243800' => 'gma', 'Glyma.20G150600' => 'gma', 'Gohir.A09G219200' => 'ghi', 'Gohir.A09G219300' => 'ghi', 'Gohir.D09G221400' => 'ghi', 'Gohir.D09G221500' => 'ghi', 'Gorai.006G242600' => 'gra', 'Gorai.006G242700' => 'gra', 'GSVIVG01018044001' => 'vvi', 'HanXRQChr03g0083821' => 'han', 'HanXRQChr03g0083841' => 'han', 'HanXRQChr03g0083881' => 'han', 'HanXRQChr03g0083901' => 'han', 'HanXRQChr03g0083921' => 'han', 'HanXRQChr03g0085331' => 'han', 'HanXRQChr03g0085361' => 'han', 'HanXRQChr03g0085411' => 'han', 'HanXRQChr03g0085421' => 'han', 'HanXRQChr03g0085431' => 'han', 'HanXRQChr08g0221991' => 'han', 'HanXRQChr11g0336061' => 'han', 'HanXRQChr11g0336411' => 'han', 'Haze_11234' => 'cav', 'Hma1.2p1_0549F.1_g177010' => 'hma', 'Hma1.2p1_0602F.1_g187630' => 'hma', 'Hund14876' => 'sun', 'Hund14879' => 'sun', 'Lalb_Chr06g0160741' => 'lal', 'Lalb_Chr21g0304781' => 'lal', 'Lj3A726G19' => 'lonja', 'Lj3A726T23' => 'lonja', 'Lj3A726T24' => 'lonja', 'Lj3A726T25' => 'lonja', 'Lj3A727T17' => 'lonja', 'Lj3C726T0' => 'lonja', 'Lj3C726T2' => 'lonja', 'Lj3P725T35' => 'lonja', 'Lj3P727T10' => 'lonja', 'Lj3P727T12' => 'lonja', 'Lj3P727T14' => 'lonja', 'Lj5g0023109' => 'lja', 'Lj6P646T44' => 'lonja', 'Lsat_1_v5_gn_6_75760' => 'lsa', 'Lsat_1_v5_gn_6_75800' => 'lsa', 'Lsat_1_v5_gn_6_75900' => 'lsa', 'Lsat_1_v5_gn_6_76240' => 'lsa', 'Lsat_1_v5_gn_6_76441' => 'lsa', 'Lsat_1_v5_gn_6_76700' => 'lsa', 'Lsat_1_v5_gn_6_76760' => 'lsa', 'Manes.15G033100' => 'mes', 'Mapoly0004s0074' => 'mpo', 'Mapoly0004s0075' => 'mpo', 'Mapoly0004s0163' => 'mpo', 'Mapoly0004s0164' => 'mpo', 'Mapoly0021s0018' => 'mpo', 'Mapoly0041s0136' => 'mpo', 'Mapoly0041s0137' => 'mpo', 'Mapoly0041s0138' => 'mpo', 'Mapoly0041s0139' => 'mpo', 'Mapoly0041s0141' => 'mpo', 'Mapoly0041s0142' => 'mpo', 'Mapoly0041s0143' => 'mpo', 'Mapoly0041s0144' => 'mpo', 'Mapoly0041s0145' => 'mpo', 'Mapoly0047s0106' => 'mpo', 'Mapoly0047s0108' => 'mpo', 'Mapoly0050s0051' => 'mpo', 'Mapoly0050s0052' => 'mpo', 'Mapoly0050s0053' => 'mpo', 'Mapoly0058s0013' => 'mpo', 'Mapoly0091s0078' => 'mpo', 'Mapoly0091s0079' => 'mpo', 'Mapoly0091s0080' => 'mpo', 'Mapoly0091s0081' => 'mpo', 'Mapoly0278s0004' => 'mpo', 'Mapoly0278s0005' => 'mpo', 'Mapoly0278s0006' => 'mpo', 'MBI11_g30648_MAGBIO' => 'mbi', 'MCO03G194' => 'mco', 'MCO03G590' => 'mco', 'MCO07G312' => 'mco', 'MCO10G318' => 'mco', 'MCO12G244' => 'mco', 'MCO13G148' => 'mco', 'MCO13G194' => 'mco', 'MCO16G238' => 'mco', 'MD06G1134100' => 'mdo', 'MD13G1200100' => 'mdo', 'MD13G1200300' => 'mdo', 'MD13G1200600' => 'mdo', 'MD14G1150400' => 'mdo', 'MD16G1200000' => 'mdo', 'Medtr1g102570' => 'mtr', 'Medtr1g102780' => 'mtr', 'Medtr1g102800' => 'mtr', 'Medtr1g102810' => 'mtr', 'Medtr1g102830' => 'mtr', 'MELO3C006499.2' => 'cme', 'Migut.G00385' => 'egut', 'MSTRG.4063' => 'ama', 'Nitab4.5_0000090g0260' => 'nta', 'Nitab4.5_0000977g0030' => 'nta', 'Nitab4.5_0002541g0040' => 'nta', 'Nitab4.5_0007068g0040' => 'nta', 'Nn005s41408' => 'nnu', 'Nn005s41410' => 'nnu', 'Oeu010310.1' => 'oeu', 'Oeu010311.1' => 'oeu', 'Oeu043472.1' => 'oeu', 'Os01g0246400' => 'osa', 'Os04g0267950' => 'osa', 'Os07g0178700' => 'osa', 'Os07g0178800' => 'osa', 'Peaxi162Scf00316g00046' => 'pax', 'Peaxi162Scf00316g00049' => 'pax', 'Peaxi162Scf00316g00059' => 'pax', 'Peaxi162Scf00316g00328' => 'pax', 'Peaxi162Scf00316g00329' => 'pax', 'Peaxi162Scf00316g00411' => 'pax', 'Peaxi162Scf00316g00521' => 'pax', 'Peaxi162Scf00492g00068' => 'pax', 'Peaxi162Scf35631g00002' => 'pax', 'PGR142G3720' => 'pgr', 'PGSC0003DMG400006442' => 'stu', 'Phvul.007G062000' => 'pvu', 'Potri.008G157750' => 'ptr', 'Potri.008G157900' => 'ptr', 'Potri.008G158000' => 'ptr', 'Potri.008G158200' => 'ptr', 'Pp3c11_7280' => 'ppa', 'Pp3c11_7980' => 'ppa', 'Pp3c12_19450' => 'ppa', 'Pp3c14_1480' => 'ppa', 'Pp3c14_1501' => 'ppa', 'Pp3c16_4900' => 'ppa', 'Pp3c16_5010' => 'ppa', 'Pp3c16_5060' => 'ppa', 'Pp3c19_18250' => 'ppa', 'Pp3c23_8530' => 'ppa', 'Pp3c23_8550' => 'ppa', 'Pp3c24_9670' => 'ppa', 'Pp3c2_21390' => 'ppa', 'Pp3c2_31380' => 'ppa', 'Pp3c3_16620' => 'ppa', 'Pp3c3_8090' => 'ppa', 'Pp3c3_8110' => 'ppa', 'Pp3c3_8130' => 'ppa', 'Pp3c3_8150' => 'ppa', 'Pp3c4_14320' => 'ppa', 'Pp3c6_2560' => 'ppa', 'Pp3c9_16700' => 'ppa', 'PRCOL_00000234' => 'pco', 'PRCOL_00000235' => 'pco', 'PRCOL_00000777' => 'pco', 'PRCOL_00002344' => 'pco', 'PRCOL_00002372' => 'pco', 'PRCOL_00006120' => 'pco', 'Prupe.1G021400' => 'ppe', 'Prupe.1G021500' => 'ppe', 'Prupe.1G021600' => 'ppe', 'Prupe.1G021700' => 'ppe', 'Prupe.1G021800' => 'ppe', 'Prupe.5G145100' => 'ppe', 'Psat6g204040' => 'psa', 'Psat6g204800' => 'psa', 'Psat6g204920' => 'psa', 'Psat6g204960' => 'psa', 'Psat6g205080' => 'psa', 'PSO017G0271' => 'pso', 'PSO017G1276' => 'pso', 'PSO017G1429' => 'pso', 'PSO017G1861' => 'pso', 'PSO017G2787' => 'pso', 'PSO017G4466' => 'pso', 'PSO017G5118' => 'pso', 'PSO017G5420' => 'pso', 'PSO063G3678' => 'pso', 'PSO210G0546' => 'pso', 'PSO317G0001' => 'pso', 'PSO357G0512' => 'pso', 'PSO478G2682' => 'pso', 'PSO647G0001' => 'pso', 'PSO675G0001' => 'pso', 'PSO675G2699' => 'pso', 'PSO675G2849' => 'pso', 'PSO675G4991' => 'pso', 'PSO689G0001' => 'pso', 'QL06p000916' => 'qlo', 'QL06p000921' => 'qlo', 'QL06p001398' => 'qlo', 'QL06p001407' => 'qlo', 'QL06p002031' => 'qlo', 'RcHm_v2.0_Chr4g0387791' => 'rch', 'RcHm_v2.0_Chr4g0387801' => 'rch', 'RcHm_v2.0_Chr6g0286501' => 'rch', 'RcHm_v2.0_Chr6g0286511' => 'rch', 'RcHm_v2.0_Chr6g0286521' => 'rch', 'RcHm_v2.0_Chr6g0286531' => 'rch', 'RcHm_v2.0_Chr7g0189141' => 'rch', 'Rhsim02G0028700' => 'rsi', 'Rhsim02G0028800' => 'rsi', 'Rhsim02G0028900' => 'rsi', 'Rhsim02G0029000' => 'rsi', 'Rhsim02G0029100' => 'rsi', 'Rhsim02G0029200' => 'rsi', 'Rhsim02G0029300' => 'rsi', 'Rhsim02G0029400' => 'rsi', 'Rhsim02G0029500' => 'rsi', 'Rhsim02G0029600' => 'rsi', 'RhsimUnG0024000' => 'rsi', 'RhsimUnG0024100' => 'rsi', 'RhsimUnG0024200' => 'rsi', 'RhsimUnG0024300' => 'rsi', 'RhsimUnG0024400' => 'rsi', 'RhsimUnG0024500' => 'rsi', 'RhsimUnG0024700' => 'rsi', 'RhsimUnG0024800' => 'rsi', 'RhsimUnG0024900' => 'rsi', 'RhsimUnG0025100' => 'rsi', 'Sabra08G0120200' => 'sbr', 'Sabra08G0120300' => 'sbr', 'Sabra08G0120500' => 'sbr', 'Sabra08G0120600' => 'sbr', 'Sabra10G0158900' => 'sbr', 'SalBow2G3492' => 'sbo', 'Sc13g0004760' => 'sci', 'Sc13g0004770' => 'sci', 'Sed0003417' => 'sed', 'Sed0019750' => 'sed', 'SEGI_03419' => 'sgi', 'SEGI_05907' => 'sgi', 'SEGI_10682' => 'sgi', 'SEGI_13528' => 'sgi', 'SEGI_16081' => 'sgi', 'SEGI_19370' => 'sgi', 'SEGI_21015' => 'sgi', 'SEGI_21944' => 'sgi', 'SEGI_32906' => 'sgi', 'SEGI_33093' => 'sgi', 'SEGI_36110' => 'sgi', 'SEGI_40397' => 'sgi', 'SGA_v2.0_scaffold191G40426' => 'sas', 'SGA_v2.0_scaffold353G49717' => 'sas', 'SGA_v2.0_scaffold50G18550' => 'sas', 'SMO119G0173' => 'smo', 'SMO172G0002' => 'smo', 'Solyc09g082690.3' => 'sly', 'Solyc09g082700.2' => 'sly', 'Sopen09g031550' => 'spe', 'Sopen09g031560' => 'spe', 'Sp3g20540' => 'spa', 'Sp7g07580' => 'spa', 'TAR134G0002' => 'tar', 'TAR236G0001' => 'tar', 'TAR365G0892' => 'tar', 'TAR636G0166' => 'tar', 'TAR636G0646' => 'tar', 'TAR636G0869' => 'tar', 'TAR636G1317' => 'tar', 'TAR636G1744' => 'tar', 'TAR636G3358' => 'tar', 'TAR636G3436' => 'tar', 'THA.LOC104803047' => 'tha', 'Thecc.04G238900' => 'tca', 'Thhalv10021557m.g' => 'esa', 'Thhalv10026318m.g' => 'esa', 'Thhalv10026335m.g' => 'esa', 'TPR.G17433' => 'tpr', 'TPR.G18915' => 'tpr', 'TPR.G26125' => 'tpr', 'TWI09G0677' => 'twi', 'TWI73G0287' => 'twi', 'unitig_748.g8326' => 'ugi', 'vmacro15370' => 'vma', 'vmacro15371' => 'vma', 'vmacro15372' => 'vma', 'vmacro15373' => 'vma', 'vmacro15374' => 'vma', 'VMungo0720G2826' => 'vmu', 'Zm00001eb116960' => 'zma', 'Zm00001eb301260' => 'zma', 'Zm00001eb301270' => 'zma' ), 'gf_id' => 'HOM05D001460', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001460' ), 'data_identifier' => 'HOM05D001460', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001460', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '433', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p22980' => 'bna', 'A01p32340' => 'bna', 'A03p42970' => 'bna', 'A05p25880' => 'bna', 'Aa31LG8G9320' => 'aar', 'Aa31LG8G9330' => 'aar', 'Aa31LG8G9340' => 'aar', 'Aa31sc221G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1034' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1528' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.829' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2222' => 'aag', 'Ah.12g058830' => 'amhyb', 'Ah.12g058840' => 'amhyb', 'AL3G37160' => 'aly', 'AL7G41310' => 'aly', 'Aqoxy5G00395' => 'aox', 'Aqoxy5G00396' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0C8NZA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5185HY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JZ1PRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MD3LS0' => 'arhy', 'AT3G22840' => 'ath', 'AT4G14690' => 'ath', 'ATR0665G054' => 'atr', 'Atru.chr4.2344' => 'acertr', 'Atru.chr4.2346' => 'acertr', 'Atru.chr4.2347' => 'acertr', 'Atru.chr4.2348' => 'acertr', 'Atru.chr4.2355' => 'acertr', 'Atru.chr4.2356' => 'acertr', 'Atru.chr4.2358' => 'acertr', 'Atru.chr4.2359' => 'acertr', 'Atru.chr4.2360' => 'acertr', 'Atru.chr4.2361' => 'acertr', 'AUR62030476' => 'cqu', 'AUR62030478' => 'cqu', 'AUR62030819' => 'cqu', 'AUR62030820' => 'cqu', 'BcaB03g14648' => 'bca', 'BcaB04g20492' => 'bca', 'BcaB06g26399' => 'bca', 'BcaC01g03416' => 'bca', 'BcaC01g03419' => 'bca', 'BcaC01g03421' => 'bca', 'BcaC01g03424' => 'bca', 'BcaC05g28012' => 'bca', 'BcaC09g49212' => 'bca', 'BcaC09g50140' => 'bca', 'BcaNung00346' => 'bca', 'BolC1t02785H' => 'bol', 'BolC1t04095H' => 'bol', 'BolC3t17545H' => 'bol', 'BolC5t32769H' => 'bol', 'BraA01t02211Z' => 'bra', 'BraA01t03359Z' => 'bra', 'BraA03t13441Z' => 'bra', 'BraA05t21476Z' => 'bra', 'C01p28420' => 'bna', 'C01p41350' => 'bna', 'C03p52750' => 'bna', 'C03p52780' => 'bna', 'C05p40270' => 'bna', 'CAN.G1437.9' => 'can', 'CANSAT78G0035' => 'cansat', 'CANSAT78G1036' => 'cansat', 'CANSAT78G2272' => 'cansat', 'CANSAT78G2478' => 'cansat', 'CARHR098700' => 'chi', 'CARHR221120' => 'chi', 'CARHR221150' => 'chi', 'Carub.0003s2297' => 'cru', 'Carub.0007s2749' => 'cru', 'Carub.0007s2750' => 'cru', 'Carub.0007s2751' => 'cru', 'Ca_10849_v3' => 'car', 'Cc03_g04300' => 'ccan', 'CDE02G3648' => 'cde', 'CDE05G0060' => 'cde', 'CDE05G0692' => 'cde', 'CDE05G2285' => 'cde', 'CDE05G2884' => 'cde', 'CDE05G3072' => 'cde', 'Cfa008439' => 'cfa', 'Cfa008441' => 'cfa', 'Cfa008443' => 'cfa', 'Cfa008448' => 'cfa', 'Ciclev10005974m.g' => 'ccl', 'Ciclev10006006m.g' => 'ccl', 'Ciclev10006775m.g' => 'ccl', 'CiPaw.02G120400' => 'cil', 'CiPaw.02G120500' => 'cil', 'CiPaw.02G120600' => 'cil', 'ClCG05G004850' => 'cla', 'COL.COLO4_21566' => 'col', 'Cpa.g.sc44.124' => 'cpa', 'Cre07.g320400' => 'cre', 'Cre07.g320450' => 'cre', 'Cre08.g384650' => 'cre', 'Cre09.g393173' => 'cre', 'Cre09.g394325' => 'cre', 'Cre14.g626750' => 'cre', 'Cre16.g679250' => 'cre', 'CsaV3_3G012890' => 'csa', 'CSS0010865' => 'camsi', 'CSS0044338' => 'camsi', 'DCAR_002366' => 'dca', 'DCAR_030687' => 'dca', 'DCAR_030688' => 'dca', 'Dinv14047' => 'din', 'Dinv14048' => 'din', 'Duzib151G0105' => 'dzi', 'Duzib151G0114' => 'dzi', 'Duzib212G1029' => 'dzi', 'ECA232G3536' => 'eca', 'ECA240G0786' => 'eca', 'ECA240G1802' => 'eca', 'ECA240G3760' => 'eca', 'ECA240G3920' => 'eca', 'EL10Ac5g12536' => 'bvu', 'EL10Ac5g12537' => 'bvu', 'EL10Ac5g12538' => 'bvu', 'Eucgr.B01004' => 'egr', 'Eucgr.B01006' => 'egr', 'Eucgr.B01007' => 'egr', 'Eucgr.B01008' => 'egr', 'Eucgr.B01895' => 'egr', 'Eucgr.B01896' => 'egr', 'FAN04G1456' => 'fan', 'FAN08G1769' => 'fan', 'FAN08G2160' => 'fan', 'FAN13G2403' => 'fan', 'FAN13G3303' => 'fan', 'FAN15G2435' => 'fan', 'FAN17G0672' => 'fan', 'FAN17G2441' => 'fan', 'FAN18G1024' => 'fan', 'FAN22G1458' => 'fan', 'FAN24G0037' => 'fan', 'FAN24G0429' => 'fan', 'FAN24G2387' => 'fan', 'FAN27G2746' => 'fan', 'FvH4_2g20400' => 'fve', 'FvH4_2g20420' => 'fve', 'FvH4_2g20430' => 'fve', 'FvH4_4g01270' => 'fve', 'FvH4_4g01290' => 'fve', 'FvH4_4g01300' => 'fve', 'FvH4_4g01310' => 'fve', 'FvH4_4g01330' => 'fve', 'FvH4_5g09070' => 'fve', 'Glyma.10G243800' => 'gma', 'Glyma.20G150600' => 'gma', 'Gohir.A09G219200' => 'ghi', 'Gohir.A09G219300' => 'ghi', 'Gohir.D09G221400' => 'ghi', 'Gohir.D09G221500' => 'ghi', 'Gorai.006G242600' => 'gra', 'Gorai.006G242700' => 'gra', 'GSVIVG01018044001' => 'vvi', 'HanXRQChr03g0083821' => 'han', 'HanXRQChr03g0083841' => 'han', 'HanXRQChr03g0083881' => 'han', 'HanXRQChr03g0083901' => 'han', 'HanXRQChr03g0083921' => 'han', 'HanXRQChr03g0085331' => 'han', 'HanXRQChr03g0085361' => 'han', 'HanXRQChr03g0085411' => 'han', 'HanXRQChr03g0085421' => 'han', 'HanXRQChr03g0085431' => 'han', 'HanXRQChr08g0221991' => 'han', 'HanXRQChr11g0336061' => 'han', 'HanXRQChr11g0336411' => 'han', 'Haze_11234' => 'cav', 'Hma1.2p1_0549F.1_g177010' => 'hma', 'Hma1.2p1_0602F.1_g187630' => 'hma', 'Hund14876' => 'sun', 'Hund14879' => 'sun', 'Lalb_Chr06g0160741' => 'lal', 'Lalb_Chr21g0304781' => 'lal', 'Lj3A726G19' => 'lonja', 'Lj3A726T23' => 'lonja', 'Lj3A726T24' => 'lonja', 'Lj3A726T25' => 'lonja', 'Lj3A727T17' => 'lonja', 'Lj3C726T0' => 'lonja', 'Lj3C726T2' => 'lonja', 'Lj3P725T35' => 'lonja', 'Lj3P727T10' => 'lonja', 'Lj3P727T12' => 'lonja', 'Lj3P727T14' => 'lonja', 'Lj5g0023109' => 'lja', 'Lj6P646T44' => 'lonja', 'Lsat_1_v5_gn_6_75760' => 'lsa', 'Lsat_1_v5_gn_6_75800' => 'lsa', 'Lsat_1_v5_gn_6_75900' => 'lsa', 'Lsat_1_v5_gn_6_76240' => 'lsa', 'Lsat_1_v5_gn_6_76441' => 'lsa', 'Lsat_1_v5_gn_6_76700' => 'lsa', 'Lsat_1_v5_gn_6_76760' => 'lsa', 'Manes.15G033100' => 'mes', 'Mapoly0004s0074' => 'mpo', 'Mapoly0004s0075' => 'mpo', 'Mapoly0004s0163' => 'mpo', 'Mapoly0004s0164' => 'mpo', 'Mapoly0021s0018' => 'mpo', 'Mapoly0041s0136' => 'mpo', 'Mapoly0041s0137' => 'mpo', 'Mapoly0041s0138' => 'mpo', 'Mapoly0041s0139' => 'mpo', 'Mapoly0041s0141' => 'mpo', 'Mapoly0041s0142' => 'mpo', 'Mapoly0041s0143' => 'mpo', 'Mapoly0041s0144' => 'mpo', 'Mapoly0041s0145' => 'mpo', 'Mapoly0047s0106' => 'mpo', 'Mapoly0047s0108' => 'mpo', 'Mapoly0050s0051' => 'mpo', 'Mapoly0050s0052' => 'mpo', 'Mapoly0050s0053' => 'mpo', 'Mapoly0058s0013' => 'mpo', 'Mapoly0091s0078' => 'mpo', 'Mapoly0091s0079' => 'mpo', 'Mapoly0091s0080' => 'mpo', 'Mapoly0091s0081' => 'mpo', 'Mapoly0278s0004' => 'mpo', 'Mapoly0278s0005' => 'mpo', 'Mapoly0278s0006' => 'mpo', 'MBI11_g30648_MAGBIO' => 'mbi', 'MCO03G194' => 'mco', 'MCO03G590' => 'mco', 'MCO07G312' => 'mco', 'MCO10G318' => 'mco', 'MCO12G244' => 'mco', 'MCO13G148' => 'mco', 'MCO13G194' => 'mco', 'MCO16G238' => 'mco', 'MD06G1134100' => 'mdo', 'MD13G1200100' => 'mdo', 'MD13G1200300' => 'mdo', 'MD13G1200600' => 'mdo', 'MD14G1150400' => 'mdo', 'MD16G1200000' => 'mdo', 'Medtr1g102570' => 'mtr', 'Medtr1g102780' => 'mtr', 'Medtr1g102800' => 'mtr', 'Medtr1g102810' => 'mtr', 'Medtr1g102830' => 'mtr', 'MELO3C006499.2' => 'cme', 'Migut.G00385' => 'egut', 'MSTRG.4063' => 'ama', 'Nitab4.5_0000090g0260' => 'nta', 'Nitab4.5_0000977g0030' => 'nta', 'Nitab4.5_0002541g0040' => 'nta', 'Nitab4.5_0007068g0040' => 'nta', 'Nn005s41408' => 'nnu', 'Nn005s41410' => 'nnu', 'Oeu010310.1' => 'oeu', 'Oeu010311.1' => 'oeu', 'Oeu043472.1' => 'oeu', 'Os01g0246400' => 'osa', 'Os04g0267950' => 'osa', 'Os07g0178700' => 'osa', 'Os07g0178800' => 'osa', 'Peaxi162Scf00316g00046' => 'pax', 'Peaxi162Scf00316g00049' => 'pax', 'Peaxi162Scf00316g00059' => 'pax', 'Peaxi162Scf00316g00328' => 'pax', 'Peaxi162Scf00316g00329' => 'pax', 'Peaxi162Scf00316g00411' => 'pax', 'Peaxi162Scf00316g00521' => 'pax', 'Peaxi162Scf00492g00068' => 'pax', 'Peaxi162Scf35631g00002' => 'pax', 'PGR142G3720' => 'pgr', 'PGSC0003DMG400006442' => 'stu', 'Phvul.007G062000' => 'pvu', 'Potri.008G157750' => 'ptr', 'Potri.008G157900' => 'ptr', 'Potri.008G158000' => 'ptr', 'Potri.008G158200' => 'ptr', 'Pp3c11_7280' => 'ppa', 'Pp3c11_7980' => 'ppa', 'Pp3c12_19450' => 'ppa', 'Pp3c14_1480' => 'ppa', 'Pp3c14_1501' => 'ppa', 'Pp3c16_4900' => 'ppa', 'Pp3c16_5010' => 'ppa', 'Pp3c16_5060' => 'ppa', 'Pp3c19_18250' => 'ppa', 'Pp3c23_8530' => 'ppa', 'Pp3c23_8550' => 'ppa', 'Pp3c24_9670' => 'ppa', 'Pp3c2_21390' => 'ppa', 'Pp3c2_31380' => 'ppa', 'Pp3c3_16620' => 'ppa', 'Pp3c3_8090' => 'ppa', 'Pp3c3_8110' => 'ppa', 'Pp3c3_8130' => 'ppa', 'Pp3c3_8150' => 'ppa', 'Pp3c4_14320' => 'ppa', 'Pp3c6_2560' => 'ppa', 'Pp3c9_16700' => 'ppa', 'PRCOL_00000234' => 'pco', 'PRCOL_00000235' => 'pco', 'PRCOL_00000777' => 'pco', 'PRCOL_00002344' => 'pco', 'PRCOL_00002372' => 'pco', 'PRCOL_00006120' => 'pco', 'Prupe.1G021400' => 'ppe', 'Prupe.1G021500' => 'ppe', 'Prupe.1G021600' => 'ppe', 'Prupe.1G021700' => 'ppe', 'Prupe.1G021800' => 'ppe', 'Prupe.5G145100' => 'ppe', 'Psat6g204040' => 'psa', 'Psat6g204800' => 'psa', 'Psat6g204920' => 'psa', 'Psat6g204960' => 'psa', 'Psat6g205080' => 'psa', 'PSO017G0271' => 'pso', 'PSO017G1276' => 'pso', 'PSO017G1429' => 'pso', 'PSO017G1861' => 'pso', 'PSO017G2787' => 'pso', 'PSO017G4466' => 'pso', 'PSO017G5118' => 'pso', 'PSO017G5420' => 'pso', 'PSO063G3678' => 'pso', 'PSO210G0546' => 'pso', 'PSO317G0001' => 'pso', 'PSO357G0512' => 'pso', 'PSO478G2682' => 'pso', 'PSO647G0001' => 'pso', 'PSO675G0001' => 'pso', 'PSO675G2699' => 'pso', 'PSO675G2849' => 'pso', 'PSO675G4991' => 'pso', 'PSO689G0001' => 'pso', 'QL06p000916' => 'qlo', 'QL06p000921' => 'qlo', 'QL06p001398' => 'qlo', 'QL06p001407' => 'qlo', 'QL06p002031' => 'qlo', 'RcHm_v2.0_Chr4g0387791' => 'rch', 'RcHm_v2.0_Chr4g0387801' => 'rch', 'RcHm_v2.0_Chr6g0286501' => 'rch', 'RcHm_v2.0_Chr6g0286511' => 'rch', 'RcHm_v2.0_Chr6g0286521' => 'rch', 'RcHm_v2.0_Chr6g0286531' => 'rch', 'RcHm_v2.0_Chr7g0189141' => 'rch', 'Rhsim02G0028700' => 'rsi', 'Rhsim02G0028800' => 'rsi', 'Rhsim02G0028900' => 'rsi', 'Rhsim02G0029000' => 'rsi', 'Rhsim02G0029100' => 'rsi', 'Rhsim02G0029200' => 'rsi', 'Rhsim02G0029300' => 'rsi', 'Rhsim02G0029400' => 'rsi', 'Rhsim02G0029500' => 'rsi', 'Rhsim02G0029600' => 'rsi', 'RhsimUnG0024000' => 'rsi', 'RhsimUnG0024100' => 'rsi', 'RhsimUnG0024200' => 'rsi', 'RhsimUnG0024300' => 'rsi', 'RhsimUnG0024400' => 'rsi', 'RhsimUnG0024500' => 'rsi', 'RhsimUnG0024700' => 'rsi', 'RhsimUnG0024800' => 'rsi', 'RhsimUnG0024900' => 'rsi', 'RhsimUnG0025100' => 'rsi', 'Sabra08G0120200' => 'sbr', 'Sabra08G0120300' => 'sbr', 'Sabra08G0120500' => 'sbr', 'Sabra08G0120600' => 'sbr', 'Sabra10G0158900' => 'sbr', 'SalBow2G3492' => 'sbo', 'Sc13g0004760' => 'sci', 'Sc13g0004770' => 'sci', 'Sed0003417' => 'sed', 'Sed0019750' => 'sed', 'SEGI_03419' => 'sgi', 'SEGI_05907' => 'sgi', 'SEGI_10682' => 'sgi', 'SEGI_13528' => 'sgi', 'SEGI_16081' => 'sgi', 'SEGI_19370' => 'sgi', 'SEGI_21015' => 'sgi', 'SEGI_21944' => 'sgi', 'SEGI_32906' => 'sgi', 'SEGI_33093' => 'sgi', 'SEGI_36110' => 'sgi', 'SEGI_40397' => 'sgi', 'SGA_v2.0_scaffold191G40426' => 'sas', 'SGA_v2.0_scaffold353G49717' => 'sas', 'SGA_v2.0_scaffold50G18550' => 'sas', 'SMO119G0173' => 'smo', 'SMO172G0002' => 'smo', 'Solyc09g082690.3' => 'sly', 'Solyc09g082700.2' => 'sly', 'Sopen09g031550' => 'spe', 'Sopen09g031560' => 'spe', 'Sp3g20540' => 'spa', 'Sp7g07580' => 'spa', 'TAR134G0002' => 'tar', 'TAR236G0001' => 'tar', 'TAR365G0892' => 'tar', 'TAR636G0166' => 'tar', 'TAR636G0646' => 'tar', 'TAR636G0869' => 'tar', 'TAR636G1317' => 'tar', 'TAR636G1744' => 'tar', 'TAR636G3358' => 'tar', 'TAR636G3436' => 'tar', 'THA.LOC104803047' => 'tha', 'Thecc.04G238900' => 'tca', 'Thhalv10021557m.g' => 'esa', 'Thhalv10026318m.g' => 'esa', 'Thhalv10026335m.g' => 'esa', 'TPR.G17433' => 'tpr', 'TPR.G18915' => 'tpr', 'TPR.G26125' => 'tpr', 'TWI09G0677' => 'twi', 'TWI73G0287' => 'twi', 'unitig_748.g8326' => 'ugi', 'vmacro15370' => 'vma', 'vmacro15371' => 'vma', 'vmacro15372' => 'vma', 'vmacro15373' => 'vma', 'vmacro15374' => 'vma', 'VMungo0720G2826' => 'vmu', 'Zm00001eb116960' => 'zma', 'Zm00001eb301260' => 'zma', 'Zm00001eb301270' => 'zma' ) $gf_id = 'HOM05D001460' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001460' ) $data_identifier = 'HOM05D001460' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 4, 'aag' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 2, 'aox' => (int) 2, 'arhy' => (int) 4, 'ath' => (int) 2, 'atr' => (int) 1, 'acertr' => (int) 10, 'cqu' => (int) 4, 'bca' => (int) 11, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 1, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 1, 'ccan' => (int) 1, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 1, 'col' => (int) 1, 'cpa' => (int) 1, 'cre' => (int) 7, 'csa' => (int) 1, 'camsi' => (int) 2, 'dca' => (int) 3, 'din' => (int) 2, 'dzi' => (int) 3, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 14, 'fve' => (int) 9, 'gma' => (int) 2, 'ghi' => (int) 4, 'gra' => (int) 2, 'vvi' => (int) 1, 'han' => (int) 13, 'cav' => (int) 1, 'hma' => (int) 2, 'sun' => (int) 2, 'lal' => (int) 2, 'lonja' => (int) 12, 'lja' => (int) 1, 'lsa' => (int) 7, 'mes' => (int) 1, 'mpo' => (int) 27, 'mbi' => (int) 1, 'mco' => (int) 8, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 1, 'egut' => (int) 1, 'ama' => (int) 1, 'nta' => (int) 4, 'nnu' => (int) 2, 'oeu' => (int) 3, 'osa' => (int) 4, 'pax' => (int) 9, 'pgr' => (int) 1, 'stu' => (int) 1, 'pvu' => (int) 1, 'ptr' => (int) 4, 'ppa' => (int) 22, 'pco' => (int) 6, 'ppe' => (int) 6, 'psa' => (int) 5, 'pso' => (int) 19, 'qlo' => (int) 5, 'rch' => (int) 7, 'rsi' => (int) 20, 'sbr' => (int) 5, 'sbo' => (int) 1, 'sci' => (int) 2, 'sed' => (int) 2, 'sgi' => (int) 12, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 2, 'tar' => (int) 10, 'tha' => (int) 1, 'tca' => (int) 1, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 2, 'ugi' => (int) 1, 'vma' => (int) 5, 'vmu' => (int) 1, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb301270' $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' => 'HOM05D001460', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '433', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p22980' => 'bna', 'A01p32340' => 'bna', 'A03p42970' => 'bna', 'A05p25880' => 'bna', 'Aa31LG8G9320' => 'aar', 'Aa31LG8G9330' => 'aar', 'Aa31LG8G9340' => 'aar', 'Aa31sc221G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1034' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1528' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.829' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2222' => 'aag', 'Ah.12g058830' => 'amhyb', 'Ah.12g058840' => 'amhyb', 'AL3G37160' => 'aly', 'AL7G41310' => 'aly', 'Aqoxy5G00395' => 'aox', 'Aqoxy5G00396' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0C8NZA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5185HY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JZ1PRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MD3LS0' => 'arhy', 'AT3G22840' => 'ath', 'AT4G14690' => 'ath', 'ATR0665G054' => 'atr', 'Atru.chr4.2344' => 'acertr', 'Atru.chr4.2346' => 'acertr', 'Atru.chr4.2347' => 'acertr', 'Atru.chr4.2348' => 'acertr', 'Atru.chr4.2355' => 'acertr', 'Atru.chr4.2356' => 'acertr', 'Atru.chr4.2358' => 'acertr', 'Atru.chr4.2359' => 'acertr', 'Atru.chr4.2360' => 'acertr', 'Atru.chr4.2361' => 'acertr', 'AUR62030476' => 'cqu', 'AUR62030478' => 'cqu', 'AUR62030819' => 'cqu', 'AUR62030820' => 'cqu', 'BcaB03g14648' => 'bca', 'BcaB04g20492' => 'bca', 'BcaB06g26399' => 'bca', 'BcaC01g03416' => 'bca', 'BcaC01g03419' => 'bca', 'BcaC01g03421' => 'bca', 'BcaC01g03424' => 'bca', 'BcaC05g28012' => 'bca', 'BcaC09g49212' => 'bca', 'BcaC09g50140' => 'bca', 'BcaNung00346' => 'bca', 'BolC1t02785H' => 'bol', 'BolC1t04095H' => 'bol', 'BolC3t17545H' => 'bol', 'BolC5t32769H' => 'bol', 'BraA01t02211Z' => 'bra', 'BraA01t03359Z' => 'bra', 'BraA03t13441Z' => 'bra', 'BraA05t21476Z' => 'bra', 'C01p28420' => 'bna', 'C01p41350' => 'bna', 'C03p52750' => 'bna', 'C03p52780' => 'bna', 'C05p40270' => 'bna', 'CAN.G1437.9' => 'can', 'CANSAT78G0035' => 'cansat', 'CANSAT78G1036' => 'cansat', 'CANSAT78G2272' => 'cansat', 'CANSAT78G2478' => 'cansat', 'CARHR098700' => 'chi', 'CARHR221120' => 'chi', 'CARHR221150' => 'chi', 'Carub.0003s2297' => 'cru', 'Carub.0007s2749' => 'cru', 'Carub.0007s2750' => 'cru', 'Carub.0007s2751' => 'cru', 'Ca_10849_v3' => 'car', 'Cc03_g04300' => 'ccan', 'CDE02G3648' => 'cde', 'CDE05G0060' => 'cde', 'CDE05G0692' => 'cde', 'CDE05G2285' => 'cde', 'CDE05G2884' => 'cde', 'CDE05G3072' => 'cde', 'Cfa008439' => 'cfa', 'Cfa008441' => 'cfa', 'Cfa008443' => 'cfa', 'Cfa008448' => 'cfa', 'Ciclev10005974m.g' => 'ccl', 'Ciclev10006006m.g' => 'ccl', 'Ciclev10006775m.g' => 'ccl', 'CiPaw.02G120400' => 'cil', 'CiPaw.02G120500' => 'cil', 'CiPaw.02G120600' => 'cil', 'ClCG05G004850' => 'cla', 'COL.COLO4_21566' => 'col', 'Cpa.g.sc44.124' => 'cpa', 'Cre07.g320400' => 'cre', 'Cre07.g320450' => 'cre', 'Cre08.g384650' => 'cre', 'Cre09.g393173' => 'cre', 'Cre09.g394325' => 'cre', 'Cre14.g626750' => 'cre', 'Cre16.g679250' => 'cre', 'CsaV3_3G012890' => 'csa', 'CSS0010865' => 'camsi', 'CSS0044338' => 'camsi', 'DCAR_002366' => 'dca', 'DCAR_030687' => 'dca', 'DCAR_030688' => 'dca', 'Dinv14047' => 'din', 'Dinv14048' => 'din', 'Duzib151G0105' => 'dzi', 'Duzib151G0114' => 'dzi', 'Duzib212G1029' => 'dzi', 'ECA232G3536' => 'eca', 'ECA240G0786' => 'eca', 'ECA240G1802' => 'eca', 'ECA240G3760' => 'eca', 'ECA240G3920' => 'eca', 'EL10Ac5g12536' => 'bvu', 'EL10Ac5g12537' => 'bvu', 'EL10Ac5g12538' => 'bvu', 'Eucgr.B01004' => 'egr', 'Eucgr.B01006' => 'egr', 'Eucgr.B01007' => 'egr', 'Eucgr.B01008' => 'egr', 'Eucgr.B01895' => 'egr', 'Eucgr.B01896' => 'egr', 'FAN04G1456' => 'fan', 'FAN08G1769' => 'fan', 'FAN08G2160' => 'fan', 'FAN13G2403' => 'fan', 'FAN13G3303' => 'fan', 'FAN15G2435' => 'fan', 'FAN17G0672' => 'fan', 'FAN17G2441' => 'fan', 'FAN18G1024' => 'fan', 'FAN22G1458' => 'fan', 'FAN24G0037' => 'fan', 'FAN24G0429' => 'fan', 'FAN24G2387' => 'fan', 'FAN27G2746' => 'fan', 'FvH4_2g20400' => 'fve', 'FvH4_2g20420' => 'fve', 'FvH4_2g20430' => 'fve', 'FvH4_4g01270' => 'fve', 'FvH4_4g01290' => 'fve', 'FvH4_4g01300' => 'fve', 'FvH4_4g01310' => 'fve', 'FvH4_4g01330' => 'fve', 'FvH4_5g09070' => 'fve', 'Glyma.10G243800' => 'gma', 'Glyma.20G150600' => 'gma', 'Gohir.A09G219200' => 'ghi', 'Gohir.A09G219300' => 'ghi', 'Gohir.D09G221400' => 'ghi', 'Gohir.D09G221500' => 'ghi', 'Gorai.006G242600' => 'gra', 'Gorai.006G242700' => 'gra', 'GSVIVG01018044001' => 'vvi', 'HanXRQChr03g0083821' => 'han', 'HanXRQChr03g0083841' => 'han', 'HanXRQChr03g0083881' => 'han', 'HanXRQChr03g0083901' => 'han', 'HanXRQChr03g0083921' => 'han', 'HanXRQChr03g0085331' => 'han', 'HanXRQChr03g0085361' => 'han', 'HanXRQChr03g0085411' => 'han', 'HanXRQChr03g0085421' => 'han', 'HanXRQChr03g0085431' => 'han', 'HanXRQChr08g0221991' => 'han', 'HanXRQChr11g0336061' => 'han', 'HanXRQChr11g0336411' => 'han', 'Haze_11234' => 'cav', 'Hma1.2p1_0549F.1_g177010' => 'hma', 'Hma1.2p1_0602F.1_g187630' => 'hma', 'Hund14876' => 'sun', 'Hund14879' => 'sun', 'Lalb_Chr06g0160741' => 'lal', 'Lalb_Chr21g0304781' => 'lal', 'Lj3A726G19' => 'lonja', 'Lj3A726T23' => 'lonja', 'Lj3A726T24' => 'lonja', 'Lj3A726T25' => 'lonja', 'Lj3A727T17' => 'lonja', 'Lj3C726T0' => 'lonja', 'Lj3C726T2' => 'lonja', 'Lj3P725T35' => 'lonja', 'Lj3P727T10' => 'lonja', 'Lj3P727T12' => 'lonja', 'Lj3P727T14' => 'lonja', 'Lj5g0023109' => 'lja', 'Lj6P646T44' => 'lonja', 'Lsat_1_v5_gn_6_75760' => 'lsa', 'Lsat_1_v5_gn_6_75800' => 'lsa', 'Lsat_1_v5_gn_6_75900' => 'lsa', 'Lsat_1_v5_gn_6_76240' => 'lsa', 'Lsat_1_v5_gn_6_76441' => 'lsa', 'Lsat_1_v5_gn_6_76700' => 'lsa', 'Lsat_1_v5_gn_6_76760' => 'lsa', 'Manes.15G033100' => 'mes', 'Mapoly0004s0074' => 'mpo', 'Mapoly0004s0075' => 'mpo', 'Mapoly0004s0163' => 'mpo', 'Mapoly0004s0164' => 'mpo', 'Mapoly0021s0018' => 'mpo', 'Mapoly0041s0136' => 'mpo', 'Mapoly0041s0137' => 'mpo', 'Mapoly0041s0138' => 'mpo', 'Mapoly0041s0139' => 'mpo', 'Mapoly0041s0141' => 'mpo', 'Mapoly0041s0142' => 'mpo', 'Mapoly0041s0143' => 'mpo', 'Mapoly0041s0144' => 'mpo', 'Mapoly0041s0145' => 'mpo', 'Mapoly0047s0106' => 'mpo', 'Mapoly0047s0108' => 'mpo', 'Mapoly0050s0051' => 'mpo', 'Mapoly0050s0052' => 'mpo', 'Mapoly0050s0053' => 'mpo', 'Mapoly0058s0013' => 'mpo', 'Mapoly0091s0078' => 'mpo', 'Mapoly0091s0079' => 'mpo', 'Mapoly0091s0080' => 'mpo', 'Mapoly0091s0081' => 'mpo', 'Mapoly0278s0004' => 'mpo', 'Mapoly0278s0005' => 'mpo', 'Mapoly0278s0006' => 'mpo', 'MBI11_g30648_MAGBIO' => 'mbi', 'MCO03G194' => 'mco', 'MCO03G590' => 'mco', 'MCO07G312' => 'mco', 'MCO10G318' => 'mco', 'MCO12G244' => 'mco', 'MCO13G148' => 'mco', 'MCO13G194' => 'mco', 'MCO16G238' => 'mco', 'MD06G1134100' => 'mdo', 'MD13G1200100' => 'mdo', 'MD13G1200300' => 'mdo', 'MD13G1200600' => 'mdo', 'MD14G1150400' => 'mdo', 'MD16G1200000' => 'mdo', 'Medtr1g102570' => 'mtr', 'Medtr1g102780' => 'mtr', 'Medtr1g102800' => 'mtr', 'Medtr1g102810' => 'mtr', 'Medtr1g102830' => 'mtr', 'MELO3C006499.2' => 'cme', 'Migut.G00385' => 'egut', 'MSTRG.4063' => 'ama', 'Nitab4.5_0000090g0260' => 'nta', 'Nitab4.5_0000977g0030' => 'nta', 'Nitab4.5_0002541g0040' => 'nta', 'Nitab4.5_0007068g0040' => 'nta', 'Nn005s41408' => 'nnu', 'Nn005s41410' => 'nnu', 'Oeu010310.1' => 'oeu', 'Oeu010311.1' => 'oeu', 'Oeu043472.1' => 'oeu', 'Os01g0246400' => 'osa', 'Os04g0267950' => 'osa', 'Os07g0178700' => 'osa', 'Os07g0178800' => 'osa', 'Peaxi162Scf00316g00046' => 'pax', 'Peaxi162Scf00316g00049' => 'pax', 'Peaxi162Scf00316g00059' => 'pax', 'Peaxi162Scf00316g00328' => 'pax', 'Peaxi162Scf00316g00329' => 'pax', 'Peaxi162Scf00316g00411' => 'pax', 'Peaxi162Scf00316g00521' => 'pax', 'Peaxi162Scf00492g00068' => 'pax', 'Peaxi162Scf35631g00002' => 'pax', 'PGR142G3720' => 'pgr', 'PGSC0003DMG400006442' => 'stu', 'Phvul.007G062000' => 'pvu', 'Potri.008G157750' => 'ptr', 'Potri.008G157900' => 'ptr', 'Potri.008G158000' => 'ptr', 'Potri.008G158200' => 'ptr', 'Pp3c11_7280' => 'ppa', 'Pp3c11_7980' => 'ppa', 'Pp3c12_19450' => 'ppa', 'Pp3c14_1480' => 'ppa', 'Pp3c14_1501' => 'ppa', 'Pp3c16_4900' => 'ppa', 'Pp3c16_5010' => 'ppa', 'Pp3c16_5060' => 'ppa', 'Pp3c19_18250' => 'ppa', 'Pp3c23_8530' => 'ppa', 'Pp3c23_8550' => 'ppa', 'Pp3c24_9670' => 'ppa', 'Pp3c2_21390' => 'ppa', 'Pp3c2_31380' => 'ppa', 'Pp3c3_16620' => 'ppa', 'Pp3c3_8090' => 'ppa', 'Pp3c3_8110' => 'ppa', 'Pp3c3_8130' => 'ppa', 'Pp3c3_8150' => 'ppa', 'Pp3c4_14320' => 'ppa', 'Pp3c6_2560' => 'ppa', 'Pp3c9_16700' => 'ppa', 'PRCOL_00000234' => 'pco', 'PRCOL_00000235' => 'pco', 'PRCOL_00000777' => 'pco', 'PRCOL_00002344' => 'pco', 'PRCOL_00002372' => 'pco', 'PRCOL_00006120' => 'pco', 'Prupe.1G021400' => 'ppe', 'Prupe.1G021500' => 'ppe', 'Prupe.1G021600' => 'ppe', 'Prupe.1G021700' => 'ppe', 'Prupe.1G021800' => 'ppe', 'Prupe.5G145100' => 'ppe', 'Psat6g204040' => 'psa', 'Psat6g204800' => 'psa', 'Psat6g204920' => 'psa', 'Psat6g204960' => 'psa', 'Psat6g205080' => 'psa', 'PSO017G0271' => 'pso', 'PSO017G1276' => 'pso', 'PSO017G1429' => 'pso', 'PSO017G1861' => 'pso', 'PSO017G2787' => 'pso', 'PSO017G4466' => 'pso', 'PSO017G5118' => 'pso', 'PSO017G5420' => 'pso', 'PSO063G3678' => 'pso', 'PSO210G0546' => 'pso', 'PSO317G0001' => 'pso', 'PSO357G0512' => 'pso', 'PSO478G2682' => 'pso', 'PSO647G0001' => 'pso', 'PSO675G0001' => 'pso', 'PSO675G2699' => 'pso', 'PSO675G2849' => 'pso', 'PSO675G4991' => 'pso', 'PSO689G0001' => 'pso', 'QL06p000916' => 'qlo', 'QL06p000921' => 'qlo', 'QL06p001398' => 'qlo', 'QL06p001407' => 'qlo', 'QL06p002031' => 'qlo', 'RcHm_v2.0_Chr4g0387791' => 'rch', 'RcHm_v2.0_Chr4g0387801' => 'rch', 'RcHm_v2.0_Chr6g0286501' => 'rch', 'RcHm_v2.0_Chr6g0286511' => 'rch', 'RcHm_v2.0_Chr6g0286521' => 'rch', 'RcHm_v2.0_Chr6g0286531' => 'rch', 'RcHm_v2.0_Chr7g0189141' => 'rch', 'Rhsim02G0028700' => 'rsi', 'Rhsim02G0028800' => 'rsi', 'Rhsim02G0028900' => 'rsi', 'Rhsim02G0029000' => 'rsi', 'Rhsim02G0029100' => 'rsi', 'Rhsim02G0029200' => 'rsi', 'Rhsim02G0029300' => 'rsi', 'Rhsim02G0029400' => 'rsi', 'Rhsim02G0029500' => 'rsi', 'Rhsim02G0029600' => 'rsi', 'RhsimUnG0024000' => 'rsi', 'RhsimUnG0024100' => 'rsi', 'RhsimUnG0024200' => 'rsi', 'RhsimUnG0024300' => 'rsi', 'RhsimUnG0024400' => 'rsi', 'RhsimUnG0024500' => 'rsi', 'RhsimUnG0024700' => 'rsi', 'RhsimUnG0024800' => 'rsi', 'RhsimUnG0024900' => 'rsi', 'RhsimUnG0025100' => 'rsi', 'Sabra08G0120200' => 'sbr', 'Sabra08G0120300' => 'sbr', 'Sabra08G0120500' => 'sbr', 'Sabra08G0120600' => 'sbr', 'Sabra10G0158900' => 'sbr', 'SalBow2G3492' => 'sbo', 'Sc13g0004760' => 'sci', 'Sc13g0004770' => 'sci', 'Sed0003417' => 'sed', 'Sed0019750' => 'sed', 'SEGI_03419' => 'sgi', 'SEGI_05907' => 'sgi', 'SEGI_10682' => 'sgi', 'SEGI_13528' => 'sgi', 'SEGI_16081' => 'sgi', 'SEGI_19370' => 'sgi', 'SEGI_21015' => 'sgi', 'SEGI_21944' => 'sgi', 'SEGI_32906' => 'sgi', 'SEGI_33093' => 'sgi', 'SEGI_36110' => 'sgi', 'SEGI_40397' => 'sgi', 'SGA_v2.0_scaffold191G40426' => 'sas', 'SGA_v2.0_scaffold353G49717' => 'sas', 'SGA_v2.0_scaffold50G18550' => 'sas', 'SMO119G0173' => 'smo', 'SMO172G0002' => 'smo', 'Solyc09g082690.3' => 'sly', 'Solyc09g082700.2' => 'sly', 'Sopen09g031550' => 'spe', 'Sopen09g031560' => 'spe', 'Sp3g20540' => 'spa', 'Sp7g07580' => 'spa', 'TAR134G0002' => 'tar', 'TAR236G0001' => 'tar', 'TAR365G0892' => 'tar', 'TAR636G0166' => 'tar', 'TAR636G0646' => 'tar', 'TAR636G0869' => 'tar', 'TAR636G1317' => 'tar', 'TAR636G1744' => 'tar', 'TAR636G3358' => 'tar', 'TAR636G3436' => 'tar', 'THA.LOC104803047' => 'tha', 'Thecc.04G238900' => 'tca', 'Thhalv10021557m.g' => 'esa', 'Thhalv10026318m.g' => 'esa', 'Thhalv10026335m.g' => 'esa', 'TPR.G17433' => 'tpr', 'TPR.G18915' => 'tpr', 'TPR.G26125' => 'tpr', 'TWI09G0677' => 'twi', 'TWI73G0287' => 'twi', 'unitig_748.g8326' => 'ugi', 'vmacro15370' => 'vma', 'vmacro15371' => 'vma', 'vmacro15372' => 'vma', 'vmacro15373' => 'vma', 'vmacro15374' => 'vma', 'VMungo0720G2826' => 'vmu', 'Zm00001eb116960' => 'zma', 'Zm00001eb301260' => 'zma', 'Zm00001eb301270' => 'zma' ), 'gf_id' => 'HOM05D001460', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001460' ), 'data_identifier' => 'HOM05D001460', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001460', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '433', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p22980' => 'bna', 'A01p32340' => 'bna', 'A03p42970' => 'bna', 'A05p25880' => 'bna', 'Aa31LG8G9320' => 'aar', 'Aa31LG8G9330' => 'aar', 'Aa31LG8G9340' => 'aar', 'Aa31sc221G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1034' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1528' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.829' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2222' => 'aag', 'Ah.12g058830' => 'amhyb', 'Ah.12g058840' => 'amhyb', 'AL3G37160' => 'aly', 'AL7G41310' => 'aly', 'Aqoxy5G00395' => 'aox', 'Aqoxy5G00396' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0C8NZA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5185HY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JZ1PRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MD3LS0' => 'arhy', 'AT3G22840' => 'ath', 'AT4G14690' => 'ath', 'ATR0665G054' => 'atr', 'Atru.chr4.2344' => 'acertr', 'Atru.chr4.2346' => 'acertr', 'Atru.chr4.2347' => 'acertr', 'Atru.chr4.2348' => 'acertr', 'Atru.chr4.2355' => 'acertr', 'Atru.chr4.2356' => 'acertr', 'Atru.chr4.2358' => 'acertr', 'Atru.chr4.2359' => 'acertr', 'Atru.chr4.2360' => 'acertr', 'Atru.chr4.2361' => 'acertr', 'AUR62030476' => 'cqu', 'AUR62030478' => 'cqu', 'AUR62030819' => 'cqu', 'AUR62030820' => 'cqu', 'BcaB03g14648' => 'bca', 'BcaB04g20492' => 'bca', 'BcaB06g26399' => 'bca', 'BcaC01g03416' => 'bca', 'BcaC01g03419' => 'bca', 'BcaC01g03421' => 'bca', 'BcaC01g03424' => 'bca', 'BcaC05g28012' => 'bca', 'BcaC09g49212' => 'bca', 'BcaC09g50140' => 'bca', 'BcaNung00346' => 'bca', 'BolC1t02785H' => 'bol', 'BolC1t04095H' => 'bol', 'BolC3t17545H' => 'bol', 'BolC5t32769H' => 'bol', 'BraA01t02211Z' => 'bra', 'BraA01t03359Z' => 'bra', 'BraA03t13441Z' => 'bra', 'BraA05t21476Z' => 'bra', 'C01p28420' => 'bna', 'C01p41350' => 'bna', 'C03p52750' => 'bna', 'C03p52780' => 'bna', 'C05p40270' => 'bna', 'CAN.G1437.9' => 'can', 'CANSAT78G0035' => 'cansat', 'CANSAT78G1036' => 'cansat', 'CANSAT78G2272' => 'cansat', 'CANSAT78G2478' => 'cansat', 'CARHR098700' => 'chi', 'CARHR221120' => 'chi', 'CARHR221150' => 'chi', 'Carub.0003s2297' => 'cru', 'Carub.0007s2749' => 'cru', 'Carub.0007s2750' => 'cru', 'Carub.0007s2751' => 'cru', 'Ca_10849_v3' => 'car', 'Cc03_g04300' => 'ccan', 'CDE02G3648' => 'cde', 'CDE05G0060' => 'cde', 'CDE05G0692' => 'cde', 'CDE05G2285' => 'cde', 'CDE05G2884' => 'cde', 'CDE05G3072' => 'cde', 'Cfa008439' => 'cfa', 'Cfa008441' => 'cfa', 'Cfa008443' => 'cfa', 'Cfa008448' => 'cfa', 'Ciclev10005974m.g' => 'ccl', 'Ciclev10006006m.g' => 'ccl', 'Ciclev10006775m.g' => 'ccl', 'CiPaw.02G120400' => 'cil', 'CiPaw.02G120500' => 'cil', 'CiPaw.02G120600' => 'cil', 'ClCG05G004850' => 'cla', 'COL.COLO4_21566' => 'col', 'Cpa.g.sc44.124' => 'cpa', 'Cre07.g320400' => 'cre', 'Cre07.g320450' => 'cre', 'Cre08.g384650' => 'cre', 'Cre09.g393173' => 'cre', 'Cre09.g394325' => 'cre', 'Cre14.g626750' => 'cre', 'Cre16.g679250' => 'cre', 'CsaV3_3G012890' => 'csa', 'CSS0010865' => 'camsi', 'CSS0044338' => 'camsi', 'DCAR_002366' => 'dca', 'DCAR_030687' => 'dca', 'DCAR_030688' => 'dca', 'Dinv14047' => 'din', 'Dinv14048' => 'din', 'Duzib151G0105' => 'dzi', 'Duzib151G0114' => 'dzi', 'Duzib212G1029' => 'dzi', 'ECA232G3536' => 'eca', 'ECA240G0786' => 'eca', 'ECA240G1802' => 'eca', 'ECA240G3760' => 'eca', 'ECA240G3920' => 'eca', 'EL10Ac5g12536' => 'bvu', 'EL10Ac5g12537' => 'bvu', 'EL10Ac5g12538' => 'bvu', 'Eucgr.B01004' => 'egr', 'Eucgr.B01006' => 'egr', 'Eucgr.B01007' => 'egr', 'Eucgr.B01008' => 'egr', 'Eucgr.B01895' => 'egr', 'Eucgr.B01896' => 'egr', 'FAN04G1456' => 'fan', 'FAN08G1769' => 'fan', 'FAN08G2160' => 'fan', 'FAN13G2403' => 'fan', 'FAN13G3303' => 'fan', 'FAN15G2435' => 'fan', 'FAN17G0672' => 'fan', 'FAN17G2441' => 'fan', 'FAN18G1024' => 'fan', 'FAN22G1458' => 'fan', 'FAN24G0037' => 'fan', 'FAN24G0429' => 'fan', 'FAN24G2387' => 'fan', 'FAN27G2746' => 'fan', 'FvH4_2g20400' => 'fve', 'FvH4_2g20420' => 'fve', 'FvH4_2g20430' => 'fve', 'FvH4_4g01270' => 'fve', 'FvH4_4g01290' => 'fve', 'FvH4_4g01300' => 'fve', 'FvH4_4g01310' => 'fve', 'FvH4_4g01330' => 'fve', 'FvH4_5g09070' => 'fve', 'Glyma.10G243800' => 'gma', 'Glyma.20G150600' => 'gma', 'Gohir.A09G219200' => 'ghi', 'Gohir.A09G219300' => 'ghi', 'Gohir.D09G221400' => 'ghi', 'Gohir.D09G221500' => 'ghi', 'Gorai.006G242600' => 'gra', 'Gorai.006G242700' => 'gra', 'GSVIVG01018044001' => 'vvi', 'HanXRQChr03g0083821' => 'han', 'HanXRQChr03g0083841' => 'han', 'HanXRQChr03g0083881' => 'han', 'HanXRQChr03g0083901' => 'han', 'HanXRQChr03g0083921' => 'han', 'HanXRQChr03g0085331' => 'han', 'HanXRQChr03g0085361' => 'han', 'HanXRQChr03g0085411' => 'han', 'HanXRQChr03g0085421' => 'han', 'HanXRQChr03g0085431' => 'han', 'HanXRQChr08g0221991' => 'han', 'HanXRQChr11g0336061' => 'han', 'HanXRQChr11g0336411' => 'han', 'Haze_11234' => 'cav', 'Hma1.2p1_0549F.1_g177010' => 'hma', 'Hma1.2p1_0602F.1_g187630' => 'hma', 'Hund14876' => 'sun', 'Hund14879' => 'sun', 'Lalb_Chr06g0160741' => 'lal', 'Lalb_Chr21g0304781' => 'lal', 'Lj3A726G19' => 'lonja', 'Lj3A726T23' => 'lonja', 'Lj3A726T24' => 'lonja', 'Lj3A726T25' => 'lonja', 'Lj3A727T17' => 'lonja', 'Lj3C726T0' => 'lonja', 'Lj3C726T2' => 'lonja', 'Lj3P725T35' => 'lonja', 'Lj3P727T10' => 'lonja', 'Lj3P727T12' => 'lonja', 'Lj3P727T14' => 'lonja', 'Lj5g0023109' => 'lja', 'Lj6P646T44' => 'lonja', 'Lsat_1_v5_gn_6_75760' => 'lsa', 'Lsat_1_v5_gn_6_75800' => 'lsa', 'Lsat_1_v5_gn_6_75900' => 'lsa', 'Lsat_1_v5_gn_6_76240' => 'lsa', 'Lsat_1_v5_gn_6_76441' => 'lsa', 'Lsat_1_v5_gn_6_76700' => 'lsa', 'Lsat_1_v5_gn_6_76760' => 'lsa', 'Manes.15G033100' => 'mes', 'Mapoly0004s0074' => 'mpo', 'Mapoly0004s0075' => 'mpo', 'Mapoly0004s0163' => 'mpo', 'Mapoly0004s0164' => 'mpo', 'Mapoly0021s0018' => 'mpo', 'Mapoly0041s0136' => 'mpo', 'Mapoly0041s0137' => 'mpo', 'Mapoly0041s0138' => 'mpo', 'Mapoly0041s0139' => 'mpo', 'Mapoly0041s0141' => 'mpo', 'Mapoly0041s0142' => 'mpo', 'Mapoly0041s0143' => 'mpo', 'Mapoly0041s0144' => 'mpo', 'Mapoly0041s0145' => 'mpo', 'Mapoly0047s0106' => 'mpo', 'Mapoly0047s0108' => 'mpo', 'Mapoly0050s0051' => 'mpo', 'Mapoly0050s0052' => 'mpo', 'Mapoly0050s0053' => 'mpo', 'Mapoly0058s0013' => 'mpo', 'Mapoly0091s0078' => 'mpo', 'Mapoly0091s0079' => 'mpo', 'Mapoly0091s0080' => 'mpo', 'Mapoly0091s0081' => 'mpo', 'Mapoly0278s0004' => 'mpo', 'Mapoly0278s0005' => 'mpo', 'Mapoly0278s0006' => 'mpo', 'MBI11_g30648_MAGBIO' => 'mbi', 'MCO03G194' => 'mco', 'MCO03G590' => 'mco', 'MCO07G312' => 'mco', 'MCO10G318' => 'mco', 'MCO12G244' => 'mco', 'MCO13G148' => 'mco', 'MCO13G194' => 'mco', 'MCO16G238' => 'mco', 'MD06G1134100' => 'mdo', 'MD13G1200100' => 'mdo', 'MD13G1200300' => 'mdo', 'MD13G1200600' => 'mdo', 'MD14G1150400' => 'mdo', 'MD16G1200000' => 'mdo', 'Medtr1g102570' => 'mtr', 'Medtr1g102780' => 'mtr', 'Medtr1g102800' => 'mtr', 'Medtr1g102810' => 'mtr', 'Medtr1g102830' => 'mtr', 'MELO3C006499.2' => 'cme', 'Migut.G00385' => 'egut', 'MSTRG.4063' => 'ama', 'Nitab4.5_0000090g0260' => 'nta', 'Nitab4.5_0000977g0030' => 'nta', 'Nitab4.5_0002541g0040' => 'nta', 'Nitab4.5_0007068g0040' => 'nta', 'Nn005s41408' => 'nnu', 'Nn005s41410' => 'nnu', 'Oeu010310.1' => 'oeu', 'Oeu010311.1' => 'oeu', 'Oeu043472.1' => 'oeu', 'Os01g0246400' => 'osa', 'Os04g0267950' => 'osa', 'Os07g0178700' => 'osa', 'Os07g0178800' => 'osa', 'Peaxi162Scf00316g00046' => 'pax', 'Peaxi162Scf00316g00049' => 'pax', 'Peaxi162Scf00316g00059' => 'pax', 'Peaxi162Scf00316g00328' => 'pax', 'Peaxi162Scf00316g00329' => 'pax', 'Peaxi162Scf00316g00411' => 'pax', 'Peaxi162Scf00316g00521' => 'pax', 'Peaxi162Scf00492g00068' => 'pax', 'Peaxi162Scf35631g00002' => 'pax', 'PGR142G3720' => 'pgr', 'PGSC0003DMG400006442' => 'stu', 'Phvul.007G062000' => 'pvu', 'Potri.008G157750' => 'ptr', 'Potri.008G157900' => 'ptr', 'Potri.008G158000' => 'ptr', 'Potri.008G158200' => 'ptr', 'Pp3c11_7280' => 'ppa', 'Pp3c11_7980' => 'ppa', 'Pp3c12_19450' => 'ppa', 'Pp3c14_1480' => 'ppa', 'Pp3c14_1501' => 'ppa', 'Pp3c16_4900' => 'ppa', 'Pp3c16_5010' => 'ppa', 'Pp3c16_5060' => 'ppa', 'Pp3c19_18250' => 'ppa', 'Pp3c23_8530' => 'ppa', 'Pp3c23_8550' => 'ppa', 'Pp3c24_9670' => 'ppa', 'Pp3c2_21390' => 'ppa', 'Pp3c2_31380' => 'ppa', 'Pp3c3_16620' => 'ppa', 'Pp3c3_8090' => 'ppa', 'Pp3c3_8110' => 'ppa', 'Pp3c3_8130' => 'ppa', 'Pp3c3_8150' => 'ppa', 'Pp3c4_14320' => 'ppa', 'Pp3c6_2560' => 'ppa', 'Pp3c9_16700' => 'ppa', 'PRCOL_00000234' => 'pco', 'PRCOL_00000235' => 'pco', 'PRCOL_00000777' => 'pco', 'PRCOL_00002344' => 'pco', 'PRCOL_00002372' => 'pco', 'PRCOL_00006120' => 'pco', 'Prupe.1G021400' => 'ppe', 'Prupe.1G021500' => 'ppe', 'Prupe.1G021600' => 'ppe', 'Prupe.1G021700' => 'ppe', 'Prupe.1G021800' => 'ppe', 'Prupe.5G145100' => 'ppe', 'Psat6g204040' => 'psa', 'Psat6g204800' => 'psa', 'Psat6g204920' => 'psa', 'Psat6g204960' => 'psa', 'Psat6g205080' => 'psa', 'PSO017G0271' => 'pso', 'PSO017G1276' => 'pso', 'PSO017G1429' => 'pso', 'PSO017G1861' => 'pso', 'PSO017G2787' => 'pso', 'PSO017G4466' => 'pso', 'PSO017G5118' => 'pso', 'PSO017G5420' => 'pso', 'PSO063G3678' => 'pso', 'PSO210G0546' => 'pso', 'PSO317G0001' => 'pso', 'PSO357G0512' => 'pso', 'PSO478G2682' => 'pso', 'PSO647G0001' => 'pso', 'PSO675G0001' => 'pso', 'PSO675G2699' => 'pso', 'PSO675G2849' => 'pso', 'PSO675G4991' => 'pso', 'PSO689G0001' => 'pso', 'QL06p000916' => 'qlo', 'QL06p000921' => 'qlo', 'QL06p001398' => 'qlo', 'QL06p001407' => 'qlo', 'QL06p002031' => 'qlo', 'RcHm_v2.0_Chr4g0387791' => 'rch', 'RcHm_v2.0_Chr4g0387801' => 'rch', 'RcHm_v2.0_Chr6g0286501' => 'rch', 'RcHm_v2.0_Chr6g0286511' => 'rch', 'RcHm_v2.0_Chr6g0286521' => 'rch', 'RcHm_v2.0_Chr6g0286531' => 'rch', 'RcHm_v2.0_Chr7g0189141' => 'rch', 'Rhsim02G0028700' => 'rsi', 'Rhsim02G0028800' => 'rsi', 'Rhsim02G0028900' => 'rsi', 'Rhsim02G0029000' => 'rsi', 'Rhsim02G0029100' => 'rsi', 'Rhsim02G0029200' => 'rsi', 'Rhsim02G0029300' => 'rsi', 'Rhsim02G0029400' => 'rsi', 'Rhsim02G0029500' => 'rsi', 'Rhsim02G0029600' => 'rsi', 'RhsimUnG0024000' => 'rsi', 'RhsimUnG0024100' => 'rsi', 'RhsimUnG0024200' => 'rsi', 'RhsimUnG0024300' => 'rsi', 'RhsimUnG0024400' => 'rsi', 'RhsimUnG0024500' => 'rsi', 'RhsimUnG0024700' => 'rsi', 'RhsimUnG0024800' => 'rsi', 'RhsimUnG0024900' => 'rsi', 'RhsimUnG0025100' => 'rsi', 'Sabra08G0120200' => 'sbr', 'Sabra08G0120300' => 'sbr', 'Sabra08G0120500' => 'sbr', 'Sabra08G0120600' => 'sbr', 'Sabra10G0158900' => 'sbr', 'SalBow2G3492' => 'sbo', 'Sc13g0004760' => 'sci', 'Sc13g0004770' => 'sci', 'Sed0003417' => 'sed', 'Sed0019750' => 'sed', 'SEGI_03419' => 'sgi', 'SEGI_05907' => 'sgi', 'SEGI_10682' => 'sgi', 'SEGI_13528' => 'sgi', 'SEGI_16081' => 'sgi', 'SEGI_19370' => 'sgi', 'SEGI_21015' => 'sgi', 'SEGI_21944' => 'sgi', 'SEGI_32906' => 'sgi', 'SEGI_33093' => 'sgi', 'SEGI_36110' => 'sgi', 'SEGI_40397' => 'sgi', 'SGA_v2.0_scaffold191G40426' => 'sas', 'SGA_v2.0_scaffold353G49717' => 'sas', 'SGA_v2.0_scaffold50G18550' => 'sas', 'SMO119G0173' => 'smo', 'SMO172G0002' => 'smo', 'Solyc09g082690.3' => 'sly', 'Solyc09g082700.2' => 'sly', 'Sopen09g031550' => 'spe', 'Sopen09g031560' => 'spe', 'Sp3g20540' => 'spa', 'Sp7g07580' => 'spa', 'TAR134G0002' => 'tar', 'TAR236G0001' => 'tar', 'TAR365G0892' => 'tar', 'TAR636G0166' => 'tar', 'TAR636G0646' => 'tar', 'TAR636G0869' => 'tar', 'TAR636G1317' => 'tar', 'TAR636G1744' => 'tar', 'TAR636G3358' => 'tar', 'TAR636G3436' => 'tar', 'THA.LOC104803047' => 'tha', 'Thecc.04G238900' => 'tca', 'Thhalv10021557m.g' => 'esa', 'Thhalv10026318m.g' => 'esa', 'Thhalv10026335m.g' => 'esa', 'TPR.G17433' => 'tpr', 'TPR.G18915' => 'tpr', 'TPR.G26125' => 'tpr', 'TWI09G0677' => 'twi', 'TWI73G0287' => 'twi', 'unitig_748.g8326' => 'ugi', 'vmacro15370' => 'vma', 'vmacro15371' => 'vma', 'vmacro15372' => 'vma', 'vmacro15373' => 'vma', 'vmacro15374' => 'vma', 'VMungo0720G2826' => 'vmu', 'Zm00001eb116960' => 'zma', 'Zm00001eb301260' => 'zma', 'Zm00001eb301270' => 'zma' ) $gf_id = 'HOM05D001460' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001460' ) $data_identifier = 'HOM05D001460' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 4, 'aag' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 2, 'aox' => (int) 2, 'arhy' => (int) 4, 'ath' => (int) 2, 'atr' => (int) 1, 'acertr' => (int) 10, 'cqu' => (int) 4, 'bca' => (int) 11, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 1, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 1, 'ccan' => (int) 1, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 1, 'col' => (int) 1, 'cpa' => (int) 1, 'cre' => (int) 7, 'csa' => (int) 1, 'camsi' => (int) 2, 'dca' => (int) 3, 'din' => (int) 2, 'dzi' => (int) 3, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 14, 'fve' => (int) 9, 'gma' => (int) 2, 'ghi' => (int) 4, 'gra' => (int) 2, 'vvi' => (int) 1, 'han' => (int) 13, 'cav' => (int) 1, 'hma' => (int) 2, 'sun' => (int) 2, 'lal' => (int) 2, 'lonja' => (int) 12, 'lja' => (int) 1, 'lsa' => (int) 7, 'mes' => (int) 1, 'mpo' => (int) 27, 'mbi' => (int) 1, 'mco' => (int) 8, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 1, 'egut' => (int) 1, 'ama' => (int) 1, 'nta' => (int) 4, 'nnu' => (int) 2, 'oeu' => (int) 3, 'osa' => (int) 4, 'pax' => (int) 9, 'pgr' => (int) 1, 'stu' => (int) 1, 'pvu' => (int) 1, 'ptr' => (int) 4, 'ppa' => (int) 22, 'pco' => (int) 6, 'ppe' => (int) 6, 'psa' => (int) 5, 'pso' => (int) 19, 'qlo' => (int) 5, 'rch' => (int) 7, 'rsi' => (int) 20, 'sbr' => (int) 5, 'sbo' => (int) 1, 'sci' => (int) 2, 'sed' => (int) 2, 'sgi' => (int) 12, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 2, 'tar' => (int) 10, 'tha' => (int) 1, 'tca' => (int) 1, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 2, 'ugi' => (int) 1, 'vma' => (int) 5, 'vmu' => (int) 1, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb301270' $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' => 'HOM05D001460', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '433', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p22980' => 'bna', 'A01p32340' => 'bna', 'A03p42970' => 'bna', 'A05p25880' => 'bna', 'Aa31LG8G9320' => 'aar', 'Aa31LG8G9330' => 'aar', 'Aa31LG8G9340' => 'aar', 'Aa31sc221G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1034' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1528' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.829' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2222' => 'aag', 'Ah.12g058830' => 'amhyb', 'Ah.12g058840' => 'amhyb', 'AL3G37160' => 'aly', 'AL7G41310' => 'aly', 'Aqoxy5G00395' => 'aox', 'Aqoxy5G00396' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0C8NZA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5185HY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JZ1PRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MD3LS0' => 'arhy', 'AT3G22840' => 'ath', 'AT4G14690' => 'ath', 'ATR0665G054' => 'atr', 'Atru.chr4.2344' => 'acertr', 'Atru.chr4.2346' => 'acertr', 'Atru.chr4.2347' => 'acertr', 'Atru.chr4.2348' => 'acertr', 'Atru.chr4.2355' => 'acertr', 'Atru.chr4.2356' => 'acertr', 'Atru.chr4.2358' => 'acertr', 'Atru.chr4.2359' => 'acertr', 'Atru.chr4.2360' => 'acertr', 'Atru.chr4.2361' => 'acertr', 'AUR62030476' => 'cqu', 'AUR62030478' => 'cqu', 'AUR62030819' => 'cqu', 'AUR62030820' => 'cqu', 'BcaB03g14648' => 'bca', 'BcaB04g20492' => 'bca', 'BcaB06g26399' => 'bca', 'BcaC01g03416' => 'bca', 'BcaC01g03419' => 'bca', 'BcaC01g03421' => 'bca', 'BcaC01g03424' => 'bca', 'BcaC05g28012' => 'bca', 'BcaC09g49212' => 'bca', 'BcaC09g50140' => 'bca', 'BcaNung00346' => 'bca', 'BolC1t02785H' => 'bol', 'BolC1t04095H' => 'bol', 'BolC3t17545H' => 'bol', 'BolC5t32769H' => 'bol', 'BraA01t02211Z' => 'bra', 'BraA01t03359Z' => 'bra', 'BraA03t13441Z' => 'bra', 'BraA05t21476Z' => 'bra', 'C01p28420' => 'bna', 'C01p41350' => 'bna', 'C03p52750' => 'bna', 'C03p52780' => 'bna', 'C05p40270' => 'bna', 'CAN.G1437.9' => 'can', 'CANSAT78G0035' => 'cansat', 'CANSAT78G1036' => 'cansat', 'CANSAT78G2272' => 'cansat', 'CANSAT78G2478' => 'cansat', 'CARHR098700' => 'chi', 'CARHR221120' => 'chi', 'CARHR221150' => 'chi', 'Carub.0003s2297' => 'cru', 'Carub.0007s2749' => 'cru', 'Carub.0007s2750' => 'cru', 'Carub.0007s2751' => 'cru', 'Ca_10849_v3' => 'car', 'Cc03_g04300' => 'ccan', 'CDE02G3648' => 'cde', 'CDE05G0060' => 'cde', 'CDE05G0692' => 'cde', 'CDE05G2285' => 'cde', 'CDE05G2884' => 'cde', 'CDE05G3072' => 'cde', 'Cfa008439' => 'cfa', 'Cfa008441' => 'cfa', 'Cfa008443' => 'cfa', 'Cfa008448' => 'cfa', 'Ciclev10005974m.g' => 'ccl', 'Ciclev10006006m.g' => 'ccl', 'Ciclev10006775m.g' => 'ccl', 'CiPaw.02G120400' => 'cil', 'CiPaw.02G120500' => 'cil', 'CiPaw.02G120600' => 'cil', 'ClCG05G004850' => 'cla', 'COL.COLO4_21566' => 'col', 'Cpa.g.sc44.124' => 'cpa', 'Cre07.g320400' => 'cre', 'Cre07.g320450' => 'cre', 'Cre08.g384650' => 'cre', 'Cre09.g393173' => 'cre', 'Cre09.g394325' => 'cre', 'Cre14.g626750' => 'cre', 'Cre16.g679250' => 'cre', 'CsaV3_3G012890' => 'csa', 'CSS0010865' => 'camsi', 'CSS0044338' => 'camsi', 'DCAR_002366' => 'dca', 'DCAR_030687' => 'dca', 'DCAR_030688' => 'dca', 'Dinv14047' => 'din', 'Dinv14048' => 'din', 'Duzib151G0105' => 'dzi', 'Duzib151G0114' => 'dzi', 'Duzib212G1029' => 'dzi', 'ECA232G3536' => 'eca', 'ECA240G0786' => 'eca', 'ECA240G1802' => 'eca', 'ECA240G3760' => 'eca', 'ECA240G3920' => 'eca', 'EL10Ac5g12536' => 'bvu', 'EL10Ac5g12537' => 'bvu', 'EL10Ac5g12538' => 'bvu', 'Eucgr.B01004' => 'egr', 'Eucgr.B01006' => 'egr', 'Eucgr.B01007' => 'egr', 'Eucgr.B01008' => 'egr', 'Eucgr.B01895' => 'egr', 'Eucgr.B01896' => 'egr', 'FAN04G1456' => 'fan', 'FAN08G1769' => 'fan', 'FAN08G2160' => 'fan', 'FAN13G2403' => 'fan', 'FAN13G3303' => 'fan', 'FAN15G2435' => 'fan', 'FAN17G0672' => 'fan', 'FAN17G2441' => 'fan', 'FAN18G1024' => 'fan', 'FAN22G1458' => 'fan', 'FAN24G0037' => 'fan', 'FAN24G0429' => 'fan', 'FAN24G2387' => 'fan', 'FAN27G2746' => 'fan', 'FvH4_2g20400' => 'fve', 'FvH4_2g20420' => 'fve', 'FvH4_2g20430' => 'fve', 'FvH4_4g01270' => 'fve', 'FvH4_4g01290' => 'fve', 'FvH4_4g01300' => 'fve', 'FvH4_4g01310' => 'fve', 'FvH4_4g01330' => 'fve', 'FvH4_5g09070' => 'fve', 'Glyma.10G243800' => 'gma', 'Glyma.20G150600' => 'gma', 'Gohir.A09G219200' => 'ghi', 'Gohir.A09G219300' => 'ghi', 'Gohir.D09G221400' => 'ghi', 'Gohir.D09G221500' => 'ghi', 'Gorai.006G242600' => 'gra', 'Gorai.006G242700' => 'gra', 'GSVIVG01018044001' => 'vvi', 'HanXRQChr03g0083821' => 'han', 'HanXRQChr03g0083841' => 'han', 'HanXRQChr03g0083881' => 'han', 'HanXRQChr03g0083901' => 'han', 'HanXRQChr03g0083921' => 'han', 'HanXRQChr03g0085331' => 'han', 'HanXRQChr03g0085361' => 'han', 'HanXRQChr03g0085411' => 'han', 'HanXRQChr03g0085421' => 'han', 'HanXRQChr03g0085431' => 'han', 'HanXRQChr08g0221991' => 'han', 'HanXRQChr11g0336061' => 'han', 'HanXRQChr11g0336411' => 'han', 'Haze_11234' => 'cav', 'Hma1.2p1_0549F.1_g177010' => 'hma', 'Hma1.2p1_0602F.1_g187630' => 'hma', 'Hund14876' => 'sun', 'Hund14879' => 'sun', 'Lalb_Chr06g0160741' => 'lal', 'Lalb_Chr21g0304781' => 'lal', 'Lj3A726G19' => 'lonja', 'Lj3A726T23' => 'lonja', 'Lj3A726T24' => 'lonja', 'Lj3A726T25' => 'lonja', 'Lj3A727T17' => 'lonja', 'Lj3C726T0' => 'lonja', 'Lj3C726T2' => 'lonja', 'Lj3P725T35' => 'lonja', 'Lj3P727T10' => 'lonja', 'Lj3P727T12' => 'lonja', 'Lj3P727T14' => 'lonja', 'Lj5g0023109' => 'lja', 'Lj6P646T44' => 'lonja', 'Lsat_1_v5_gn_6_75760' => 'lsa', 'Lsat_1_v5_gn_6_75800' => 'lsa', 'Lsat_1_v5_gn_6_75900' => 'lsa', 'Lsat_1_v5_gn_6_76240' => 'lsa', 'Lsat_1_v5_gn_6_76441' => 'lsa', 'Lsat_1_v5_gn_6_76700' => 'lsa', 'Lsat_1_v5_gn_6_76760' => 'lsa', 'Manes.15G033100' => 'mes', 'Mapoly0004s0074' => 'mpo', 'Mapoly0004s0075' => 'mpo', 'Mapoly0004s0163' => 'mpo', 'Mapoly0004s0164' => 'mpo', 'Mapoly0021s0018' => 'mpo', 'Mapoly0041s0136' => 'mpo', 'Mapoly0041s0137' => 'mpo', 'Mapoly0041s0138' => 'mpo', 'Mapoly0041s0139' => 'mpo', 'Mapoly0041s0141' => 'mpo', 'Mapoly0041s0142' => 'mpo', 'Mapoly0041s0143' => 'mpo', 'Mapoly0041s0144' => 'mpo', 'Mapoly0041s0145' => 'mpo', 'Mapoly0047s0106' => 'mpo', 'Mapoly0047s0108' => 'mpo', 'Mapoly0050s0051' => 'mpo', 'Mapoly0050s0052' => 'mpo', 'Mapoly0050s0053' => 'mpo', 'Mapoly0058s0013' => 'mpo', 'Mapoly0091s0078' => 'mpo', 'Mapoly0091s0079' => 'mpo', 'Mapoly0091s0080' => 'mpo', 'Mapoly0091s0081' => 'mpo', 'Mapoly0278s0004' => 'mpo', 'Mapoly0278s0005' => 'mpo', 'Mapoly0278s0006' => 'mpo', 'MBI11_g30648_MAGBIO' => 'mbi', 'MCO03G194' => 'mco', 'MCO03G590' => 'mco', 'MCO07G312' => 'mco', 'MCO10G318' => 'mco', 'MCO12G244' => 'mco', 'MCO13G148' => 'mco', 'MCO13G194' => 'mco', 'MCO16G238' => 'mco', 'MD06G1134100' => 'mdo', 'MD13G1200100' => 'mdo', 'MD13G1200300' => 'mdo', 'MD13G1200600' => 'mdo', 'MD14G1150400' => 'mdo', 'MD16G1200000' => 'mdo', 'Medtr1g102570' => 'mtr', 'Medtr1g102780' => 'mtr', 'Medtr1g102800' => 'mtr', 'Medtr1g102810' => 'mtr', 'Medtr1g102830' => 'mtr', 'MELO3C006499.2' => 'cme', 'Migut.G00385' => 'egut', 'MSTRG.4063' => 'ama', 'Nitab4.5_0000090g0260' => 'nta', 'Nitab4.5_0000977g0030' => 'nta', 'Nitab4.5_0002541g0040' => 'nta', 'Nitab4.5_0007068g0040' => 'nta', 'Nn005s41408' => 'nnu', 'Nn005s41410' => 'nnu', 'Oeu010310.1' => 'oeu', 'Oeu010311.1' => 'oeu', 'Oeu043472.1' => 'oeu', 'Os01g0246400' => 'osa', 'Os04g0267950' => 'osa', 'Os07g0178700' => 'osa', 'Os07g0178800' => 'osa', 'Peaxi162Scf00316g00046' => 'pax', 'Peaxi162Scf00316g00049' => 'pax', 'Peaxi162Scf00316g00059' => 'pax', 'Peaxi162Scf00316g00328' => 'pax', 'Peaxi162Scf00316g00329' => 'pax', 'Peaxi162Scf00316g00411' => 'pax', 'Peaxi162Scf00316g00521' => 'pax', 'Peaxi162Scf00492g00068' => 'pax', 'Peaxi162Scf35631g00002' => 'pax', 'PGR142G3720' => 'pgr', 'PGSC0003DMG400006442' => 'stu', 'Phvul.007G062000' => 'pvu', 'Potri.008G157750' => 'ptr', 'Potri.008G157900' => 'ptr', 'Potri.008G158000' => 'ptr', 'Potri.008G158200' => 'ptr', 'Pp3c11_7280' => 'ppa', 'Pp3c11_7980' => 'ppa', 'Pp3c12_19450' => 'ppa', 'Pp3c14_1480' => 'ppa', 'Pp3c14_1501' => 'ppa', 'Pp3c16_4900' => 'ppa', 'Pp3c16_5010' => 'ppa', 'Pp3c16_5060' => 'ppa', 'Pp3c19_18250' => 'ppa', 'Pp3c23_8530' => 'ppa', 'Pp3c23_8550' => 'ppa', 'Pp3c24_9670' => 'ppa', 'Pp3c2_21390' => 'ppa', 'Pp3c2_31380' => 'ppa', 'Pp3c3_16620' => 'ppa', 'Pp3c3_8090' => 'ppa', 'Pp3c3_8110' => 'ppa', 'Pp3c3_8130' => 'ppa', 'Pp3c3_8150' => 'ppa', 'Pp3c4_14320' => 'ppa', 'Pp3c6_2560' => 'ppa', 'Pp3c9_16700' => 'ppa', 'PRCOL_00000234' => 'pco', 'PRCOL_00000235' => 'pco', 'PRCOL_00000777' => 'pco', 'PRCOL_00002344' => 'pco', 'PRCOL_00002372' => 'pco', 'PRCOL_00006120' => 'pco', 'Prupe.1G021400' => 'ppe', 'Prupe.1G021500' => 'ppe', 'Prupe.1G021600' => 'ppe', 'Prupe.1G021700' => 'ppe', 'Prupe.1G021800' => 'ppe', 'Prupe.5G145100' => 'ppe', 'Psat6g204040' => 'psa', 'Psat6g204800' => 'psa', 'Psat6g204920' => 'psa', 'Psat6g204960' => 'psa', 'Psat6g205080' => 'psa', 'PSO017G0271' => 'pso', 'PSO017G1276' => 'pso', 'PSO017G1429' => 'pso', 'PSO017G1861' => 'pso', 'PSO017G2787' => 'pso', 'PSO017G4466' => 'pso', 'PSO017G5118' => 'pso', 'PSO017G5420' => 'pso', 'PSO063G3678' => 'pso', 'PSO210G0546' => 'pso', 'PSO317G0001' => 'pso', 'PSO357G0512' => 'pso', 'PSO478G2682' => 'pso', 'PSO647G0001' => 'pso', 'PSO675G0001' => 'pso', 'PSO675G2699' => 'pso', 'PSO675G2849' => 'pso', 'PSO675G4991' => 'pso', 'PSO689G0001' => 'pso', 'QL06p000916' => 'qlo', 'QL06p000921' => 'qlo', 'QL06p001398' => 'qlo', 'QL06p001407' => 'qlo', 'QL06p002031' => 'qlo', 'RcHm_v2.0_Chr4g0387791' => 'rch', 'RcHm_v2.0_Chr4g0387801' => 'rch', 'RcHm_v2.0_Chr6g0286501' => 'rch', 'RcHm_v2.0_Chr6g0286511' => 'rch', 'RcHm_v2.0_Chr6g0286521' => 'rch', 'RcHm_v2.0_Chr6g0286531' => 'rch', 'RcHm_v2.0_Chr7g0189141' => 'rch', 'Rhsim02G0028700' => 'rsi', 'Rhsim02G0028800' => 'rsi', 'Rhsim02G0028900' => 'rsi', 'Rhsim02G0029000' => 'rsi', 'Rhsim02G0029100' => 'rsi', 'Rhsim02G0029200' => 'rsi', 'Rhsim02G0029300' => 'rsi', 'Rhsim02G0029400' => 'rsi', 'Rhsim02G0029500' => 'rsi', 'Rhsim02G0029600' => 'rsi', 'RhsimUnG0024000' => 'rsi', 'RhsimUnG0024100' => 'rsi', 'RhsimUnG0024200' => 'rsi', 'RhsimUnG0024300' => 'rsi', 'RhsimUnG0024400' => 'rsi', 'RhsimUnG0024500' => 'rsi', 'RhsimUnG0024700' => 'rsi', 'RhsimUnG0024800' => 'rsi', 'RhsimUnG0024900' => 'rsi', 'RhsimUnG0025100' => 'rsi', 'Sabra08G0120200' => 'sbr', 'Sabra08G0120300' => 'sbr', 'Sabra08G0120500' => 'sbr', 'Sabra08G0120600' => 'sbr', 'Sabra10G0158900' => 'sbr', 'SalBow2G3492' => 'sbo', 'Sc13g0004760' => 'sci', 'Sc13g0004770' => 'sci', 'Sed0003417' => 'sed', 'Sed0019750' => 'sed', 'SEGI_03419' => 'sgi', 'SEGI_05907' => 'sgi', 'SEGI_10682' => 'sgi', 'SEGI_13528' => 'sgi', 'SEGI_16081' => 'sgi', 'SEGI_19370' => 'sgi', 'SEGI_21015' => 'sgi', 'SEGI_21944' => 'sgi', 'SEGI_32906' => 'sgi', 'SEGI_33093' => 'sgi', 'SEGI_36110' => 'sgi', 'SEGI_40397' => 'sgi', 'SGA_v2.0_scaffold191G40426' => 'sas', 'SGA_v2.0_scaffold353G49717' => 'sas', 'SGA_v2.0_scaffold50G18550' => 'sas', 'SMO119G0173' => 'smo', 'SMO172G0002' => 'smo', 'Solyc09g082690.3' => 'sly', 'Solyc09g082700.2' => 'sly', 'Sopen09g031550' => 'spe', 'Sopen09g031560' => 'spe', 'Sp3g20540' => 'spa', 'Sp7g07580' => 'spa', 'TAR134G0002' => 'tar', 'TAR236G0001' => 'tar', 'TAR365G0892' => 'tar', 'TAR636G0166' => 'tar', 'TAR636G0646' => 'tar', 'TAR636G0869' => 'tar', 'TAR636G1317' => 'tar', 'TAR636G1744' => 'tar', 'TAR636G3358' => 'tar', 'TAR636G3436' => 'tar', 'THA.LOC104803047' => 'tha', 'Thecc.04G238900' => 'tca', 'Thhalv10021557m.g' => 'esa', 'Thhalv10026318m.g' => 'esa', 'Thhalv10026335m.g' => 'esa', 'TPR.G17433' => 'tpr', 'TPR.G18915' => 'tpr', 'TPR.G26125' => 'tpr', 'TWI09G0677' => 'twi', 'TWI73G0287' => 'twi', 'unitig_748.g8326' => 'ugi', 'vmacro15370' => 'vma', 'vmacro15371' => 'vma', 'vmacro15372' => 'vma', 'vmacro15373' => 'vma', 'vmacro15374' => 'vma', 'VMungo0720G2826' => 'vmu', 'Zm00001eb116960' => 'zma', 'Zm00001eb301260' => 'zma', 'Zm00001eb301270' => 'zma' ), 'gf_id' => 'HOM05D001460', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001460' ), 'data_identifier' => 'HOM05D001460', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001460', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '433', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p22980' => 'bna', 'A01p32340' => 'bna', 'A03p42970' => 'bna', 'A05p25880' => 'bna', 'Aa31LG8G9320' => 'aar', 'Aa31LG8G9330' => 'aar', 'Aa31LG8G9340' => 'aar', 'Aa31sc221G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1034' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1528' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.829' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2222' => 'aag', 'Ah.12g058830' => 'amhyb', 'Ah.12g058840' => 'amhyb', 'AL3G37160' => 'aly', 'AL7G41310' => 'aly', 'Aqoxy5G00395' => 'aox', 'Aqoxy5G00396' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0C8NZA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5185HY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JZ1PRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MD3LS0' => 'arhy', 'AT3G22840' => 'ath', 'AT4G14690' => 'ath', 'ATR0665G054' => 'atr', 'Atru.chr4.2344' => 'acertr', 'Atru.chr4.2346' => 'acertr', 'Atru.chr4.2347' => 'acertr', 'Atru.chr4.2348' => 'acertr', 'Atru.chr4.2355' => 'acertr', 'Atru.chr4.2356' => 'acertr', 'Atru.chr4.2358' => 'acertr', 'Atru.chr4.2359' => 'acertr', 'Atru.chr4.2360' => 'acertr', 'Atru.chr4.2361' => 'acertr', 'AUR62030476' => 'cqu', 'AUR62030478' => 'cqu', 'AUR62030819' => 'cqu', 'AUR62030820' => 'cqu', 'BcaB03g14648' => 'bca', 'BcaB04g20492' => 'bca', 'BcaB06g26399' => 'bca', 'BcaC01g03416' => 'bca', 'BcaC01g03419' => 'bca', 'BcaC01g03421' => 'bca', 'BcaC01g03424' => 'bca', 'BcaC05g28012' => 'bca', 'BcaC09g49212' => 'bca', 'BcaC09g50140' => 'bca', 'BcaNung00346' => 'bca', 'BolC1t02785H' => 'bol', 'BolC1t04095H' => 'bol', 'BolC3t17545H' => 'bol', 'BolC5t32769H' => 'bol', 'BraA01t02211Z' => 'bra', 'BraA01t03359Z' => 'bra', 'BraA03t13441Z' => 'bra', 'BraA05t21476Z' => 'bra', 'C01p28420' => 'bna', 'C01p41350' => 'bna', 'C03p52750' => 'bna', 'C03p52780' => 'bna', 'C05p40270' => 'bna', 'CAN.G1437.9' => 'can', 'CANSAT78G0035' => 'cansat', 'CANSAT78G1036' => 'cansat', 'CANSAT78G2272' => 'cansat', 'CANSAT78G2478' => 'cansat', 'CARHR098700' => 'chi', 'CARHR221120' => 'chi', 'CARHR221150' => 'chi', 'Carub.0003s2297' => 'cru', 'Carub.0007s2749' => 'cru', 'Carub.0007s2750' => 'cru', 'Carub.0007s2751' => 'cru', 'Ca_10849_v3' => 'car', 'Cc03_g04300' => 'ccan', 'CDE02G3648' => 'cde', 'CDE05G0060' => 'cde', 'CDE05G0692' => 'cde', 'CDE05G2285' => 'cde', 'CDE05G2884' => 'cde', 'CDE05G3072' => 'cde', 'Cfa008439' => 'cfa', 'Cfa008441' => 'cfa', 'Cfa008443' => 'cfa', 'Cfa008448' => 'cfa', 'Ciclev10005974m.g' => 'ccl', 'Ciclev10006006m.g' => 'ccl', 'Ciclev10006775m.g' => 'ccl', 'CiPaw.02G120400' => 'cil', 'CiPaw.02G120500' => 'cil', 'CiPaw.02G120600' => 'cil', 'ClCG05G004850' => 'cla', 'COL.COLO4_21566' => 'col', 'Cpa.g.sc44.124' => 'cpa', 'Cre07.g320400' => 'cre', 'Cre07.g320450' => 'cre', 'Cre08.g384650' => 'cre', 'Cre09.g393173' => 'cre', 'Cre09.g394325' => 'cre', 'Cre14.g626750' => 'cre', 'Cre16.g679250' => 'cre', 'CsaV3_3G012890' => 'csa', 'CSS0010865' => 'camsi', 'CSS0044338' => 'camsi', 'DCAR_002366' => 'dca', 'DCAR_030687' => 'dca', 'DCAR_030688' => 'dca', 'Dinv14047' => 'din', 'Dinv14048' => 'din', 'Duzib151G0105' => 'dzi', 'Duzib151G0114' => 'dzi', 'Duzib212G1029' => 'dzi', 'ECA232G3536' => 'eca', 'ECA240G0786' => 'eca', 'ECA240G1802' => 'eca', 'ECA240G3760' => 'eca', 'ECA240G3920' => 'eca', 'EL10Ac5g12536' => 'bvu', 'EL10Ac5g12537' => 'bvu', 'EL10Ac5g12538' => 'bvu', 'Eucgr.B01004' => 'egr', 'Eucgr.B01006' => 'egr', 'Eucgr.B01007' => 'egr', 'Eucgr.B01008' => 'egr', 'Eucgr.B01895' => 'egr', 'Eucgr.B01896' => 'egr', 'FAN04G1456' => 'fan', 'FAN08G1769' => 'fan', 'FAN08G2160' => 'fan', 'FAN13G2403' => 'fan', 'FAN13G3303' => 'fan', 'FAN15G2435' => 'fan', 'FAN17G0672' => 'fan', 'FAN17G2441' => 'fan', 'FAN18G1024' => 'fan', 'FAN22G1458' => 'fan', 'FAN24G0037' => 'fan', 'FAN24G0429' => 'fan', 'FAN24G2387' => 'fan', 'FAN27G2746' => 'fan', 'FvH4_2g20400' => 'fve', 'FvH4_2g20420' => 'fve', 'FvH4_2g20430' => 'fve', 'FvH4_4g01270' => 'fve', 'FvH4_4g01290' => 'fve', 'FvH4_4g01300' => 'fve', 'FvH4_4g01310' => 'fve', 'FvH4_4g01330' => 'fve', 'FvH4_5g09070' => 'fve', 'Glyma.10G243800' => 'gma', 'Glyma.20G150600' => 'gma', 'Gohir.A09G219200' => 'ghi', 'Gohir.A09G219300' => 'ghi', 'Gohir.D09G221400' => 'ghi', 'Gohir.D09G221500' => 'ghi', 'Gorai.006G242600' => 'gra', 'Gorai.006G242700' => 'gra', 'GSVIVG01018044001' => 'vvi', 'HanXRQChr03g0083821' => 'han', 'HanXRQChr03g0083841' => 'han', 'HanXRQChr03g0083881' => 'han', 'HanXRQChr03g0083901' => 'han', 'HanXRQChr03g0083921' => 'han', 'HanXRQChr03g0085331' => 'han', 'HanXRQChr03g0085361' => 'han', 'HanXRQChr03g0085411' => 'han', 'HanXRQChr03g0085421' => 'han', 'HanXRQChr03g0085431' => 'han', 'HanXRQChr08g0221991' => 'han', 'HanXRQChr11g0336061' => 'han', 'HanXRQChr11g0336411' => 'han', 'Haze_11234' => 'cav', 'Hma1.2p1_0549F.1_g177010' => 'hma', 'Hma1.2p1_0602F.1_g187630' => 'hma', 'Hund14876' => 'sun', 'Hund14879' => 'sun', 'Lalb_Chr06g0160741' => 'lal', 'Lalb_Chr21g0304781' => 'lal', 'Lj3A726G19' => 'lonja', 'Lj3A726T23' => 'lonja', 'Lj3A726T24' => 'lonja', 'Lj3A726T25' => 'lonja', 'Lj3A727T17' => 'lonja', 'Lj3C726T0' => 'lonja', 'Lj3C726T2' => 'lonja', 'Lj3P725T35' => 'lonja', 'Lj3P727T10' => 'lonja', 'Lj3P727T12' => 'lonja', 'Lj3P727T14' => 'lonja', 'Lj5g0023109' => 'lja', 'Lj6P646T44' => 'lonja', 'Lsat_1_v5_gn_6_75760' => 'lsa', 'Lsat_1_v5_gn_6_75800' => 'lsa', 'Lsat_1_v5_gn_6_75900' => 'lsa', 'Lsat_1_v5_gn_6_76240' => 'lsa', 'Lsat_1_v5_gn_6_76441' => 'lsa', 'Lsat_1_v5_gn_6_76700' => 'lsa', 'Lsat_1_v5_gn_6_76760' => 'lsa', 'Manes.15G033100' => 'mes', 'Mapoly0004s0074' => 'mpo', 'Mapoly0004s0075' => 'mpo', 'Mapoly0004s0163' => 'mpo', 'Mapoly0004s0164' => 'mpo', 'Mapoly0021s0018' => 'mpo', 'Mapoly0041s0136' => 'mpo', 'Mapoly0041s0137' => 'mpo', 'Mapoly0041s0138' => 'mpo', 'Mapoly0041s0139' => 'mpo', 'Mapoly0041s0141' => 'mpo', 'Mapoly0041s0142' => 'mpo', 'Mapoly0041s0143' => 'mpo', 'Mapoly0041s0144' => 'mpo', 'Mapoly0041s0145' => 'mpo', 'Mapoly0047s0106' => 'mpo', 'Mapoly0047s0108' => 'mpo', 'Mapoly0050s0051' => 'mpo', 'Mapoly0050s0052' => 'mpo', 'Mapoly0050s0053' => 'mpo', 'Mapoly0058s0013' => 'mpo', 'Mapoly0091s0078' => 'mpo', 'Mapoly0091s0079' => 'mpo', 'Mapoly0091s0080' => 'mpo', 'Mapoly0091s0081' => 'mpo', 'Mapoly0278s0004' => 'mpo', 'Mapoly0278s0005' => 'mpo', 'Mapoly0278s0006' => 'mpo', 'MBI11_g30648_MAGBIO' => 'mbi', 'MCO03G194' => 'mco', 'MCO03G590' => 'mco', 'MCO07G312' => 'mco', 'MCO10G318' => 'mco', 'MCO12G244' => 'mco', 'MCO13G148' => 'mco', 'MCO13G194' => 'mco', 'MCO16G238' => 'mco', 'MD06G1134100' => 'mdo', 'MD13G1200100' => 'mdo', 'MD13G1200300' => 'mdo', 'MD13G1200600' => 'mdo', 'MD14G1150400' => 'mdo', 'MD16G1200000' => 'mdo', 'Medtr1g102570' => 'mtr', 'Medtr1g102780' => 'mtr', 'Medtr1g102800' => 'mtr', 'Medtr1g102810' => 'mtr', 'Medtr1g102830' => 'mtr', 'MELO3C006499.2' => 'cme', 'Migut.G00385' => 'egut', 'MSTRG.4063' => 'ama', 'Nitab4.5_0000090g0260' => 'nta', 'Nitab4.5_0000977g0030' => 'nta', 'Nitab4.5_0002541g0040' => 'nta', 'Nitab4.5_0007068g0040' => 'nta', 'Nn005s41408' => 'nnu', 'Nn005s41410' => 'nnu', 'Oeu010310.1' => 'oeu', 'Oeu010311.1' => 'oeu', 'Oeu043472.1' => 'oeu', 'Os01g0246400' => 'osa', 'Os04g0267950' => 'osa', 'Os07g0178700' => 'osa', 'Os07g0178800' => 'osa', 'Peaxi162Scf00316g00046' => 'pax', 'Peaxi162Scf00316g00049' => 'pax', 'Peaxi162Scf00316g00059' => 'pax', 'Peaxi162Scf00316g00328' => 'pax', 'Peaxi162Scf00316g00329' => 'pax', 'Peaxi162Scf00316g00411' => 'pax', 'Peaxi162Scf00316g00521' => 'pax', 'Peaxi162Scf00492g00068' => 'pax', 'Peaxi162Scf35631g00002' => 'pax', 'PGR142G3720' => 'pgr', 'PGSC0003DMG400006442' => 'stu', 'Phvul.007G062000' => 'pvu', 'Potri.008G157750' => 'ptr', 'Potri.008G157900' => 'ptr', 'Potri.008G158000' => 'ptr', 'Potri.008G158200' => 'ptr', 'Pp3c11_7280' => 'ppa', 'Pp3c11_7980' => 'ppa', 'Pp3c12_19450' => 'ppa', 'Pp3c14_1480' => 'ppa', 'Pp3c14_1501' => 'ppa', 'Pp3c16_4900' => 'ppa', 'Pp3c16_5010' => 'ppa', 'Pp3c16_5060' => 'ppa', 'Pp3c19_18250' => 'ppa', 'Pp3c23_8530' => 'ppa', 'Pp3c23_8550' => 'ppa', 'Pp3c24_9670' => 'ppa', 'Pp3c2_21390' => 'ppa', 'Pp3c2_31380' => 'ppa', 'Pp3c3_16620' => 'ppa', 'Pp3c3_8090' => 'ppa', 'Pp3c3_8110' => 'ppa', 'Pp3c3_8130' => 'ppa', 'Pp3c3_8150' => 'ppa', 'Pp3c4_14320' => 'ppa', 'Pp3c6_2560' => 'ppa', 'Pp3c9_16700' => 'ppa', 'PRCOL_00000234' => 'pco', 'PRCOL_00000235' => 'pco', 'PRCOL_00000777' => 'pco', 'PRCOL_00002344' => 'pco', 'PRCOL_00002372' => 'pco', 'PRCOL_00006120' => 'pco', 'Prupe.1G021400' => 'ppe', 'Prupe.1G021500' => 'ppe', 'Prupe.1G021600' => 'ppe', 'Prupe.1G021700' => 'ppe', 'Prupe.1G021800' => 'ppe', 'Prupe.5G145100' => 'ppe', 'Psat6g204040' => 'psa', 'Psat6g204800' => 'psa', 'Psat6g204920' => 'psa', 'Psat6g204960' => 'psa', 'Psat6g205080' => 'psa', 'PSO017G0271' => 'pso', 'PSO017G1276' => 'pso', 'PSO017G1429' => 'pso', 'PSO017G1861' => 'pso', 'PSO017G2787' => 'pso', 'PSO017G4466' => 'pso', 'PSO017G5118' => 'pso', 'PSO017G5420' => 'pso', 'PSO063G3678' => 'pso', 'PSO210G0546' => 'pso', 'PSO317G0001' => 'pso', 'PSO357G0512' => 'pso', 'PSO478G2682' => 'pso', 'PSO647G0001' => 'pso', 'PSO675G0001' => 'pso', 'PSO675G2699' => 'pso', 'PSO675G2849' => 'pso', 'PSO675G4991' => 'pso', 'PSO689G0001' => 'pso', 'QL06p000916' => 'qlo', 'QL06p000921' => 'qlo', 'QL06p001398' => 'qlo', 'QL06p001407' => 'qlo', 'QL06p002031' => 'qlo', 'RcHm_v2.0_Chr4g0387791' => 'rch', 'RcHm_v2.0_Chr4g0387801' => 'rch', 'RcHm_v2.0_Chr6g0286501' => 'rch', 'RcHm_v2.0_Chr6g0286511' => 'rch', 'RcHm_v2.0_Chr6g0286521' => 'rch', 'RcHm_v2.0_Chr6g0286531' => 'rch', 'RcHm_v2.0_Chr7g0189141' => 'rch', 'Rhsim02G0028700' => 'rsi', 'Rhsim02G0028800' => 'rsi', 'Rhsim02G0028900' => 'rsi', 'Rhsim02G0029000' => 'rsi', 'Rhsim02G0029100' => 'rsi', 'Rhsim02G0029200' => 'rsi', 'Rhsim02G0029300' => 'rsi', 'Rhsim02G0029400' => 'rsi', 'Rhsim02G0029500' => 'rsi', 'Rhsim02G0029600' => 'rsi', 'RhsimUnG0024000' => 'rsi', 'RhsimUnG0024100' => 'rsi', 'RhsimUnG0024200' => 'rsi', 'RhsimUnG0024300' => 'rsi', 'RhsimUnG0024400' => 'rsi', 'RhsimUnG0024500' => 'rsi', 'RhsimUnG0024700' => 'rsi', 'RhsimUnG0024800' => 'rsi', 'RhsimUnG0024900' => 'rsi', 'RhsimUnG0025100' => 'rsi', 'Sabra08G0120200' => 'sbr', 'Sabra08G0120300' => 'sbr', 'Sabra08G0120500' => 'sbr', 'Sabra08G0120600' => 'sbr', 'Sabra10G0158900' => 'sbr', 'SalBow2G3492' => 'sbo', 'Sc13g0004760' => 'sci', 'Sc13g0004770' => 'sci', 'Sed0003417' => 'sed', 'Sed0019750' => 'sed', 'SEGI_03419' => 'sgi', 'SEGI_05907' => 'sgi', 'SEGI_10682' => 'sgi', 'SEGI_13528' => 'sgi', 'SEGI_16081' => 'sgi', 'SEGI_19370' => 'sgi', 'SEGI_21015' => 'sgi', 'SEGI_21944' => 'sgi', 'SEGI_32906' => 'sgi', 'SEGI_33093' => 'sgi', 'SEGI_36110' => 'sgi', 'SEGI_40397' => 'sgi', 'SGA_v2.0_scaffold191G40426' => 'sas', 'SGA_v2.0_scaffold353G49717' => 'sas', 'SGA_v2.0_scaffold50G18550' => 'sas', 'SMO119G0173' => 'smo', 'SMO172G0002' => 'smo', 'Solyc09g082690.3' => 'sly', 'Solyc09g082700.2' => 'sly', 'Sopen09g031550' => 'spe', 'Sopen09g031560' => 'spe', 'Sp3g20540' => 'spa', 'Sp7g07580' => 'spa', 'TAR134G0002' => 'tar', 'TAR236G0001' => 'tar', 'TAR365G0892' => 'tar', 'TAR636G0166' => 'tar', 'TAR636G0646' => 'tar', 'TAR636G0869' => 'tar', 'TAR636G1317' => 'tar', 'TAR636G1744' => 'tar', 'TAR636G3358' => 'tar', 'TAR636G3436' => 'tar', 'THA.LOC104803047' => 'tha', 'Thecc.04G238900' => 'tca', 'Thhalv10021557m.g' => 'esa', 'Thhalv10026318m.g' => 'esa', 'Thhalv10026335m.g' => 'esa', 'TPR.G17433' => 'tpr', 'TPR.G18915' => 'tpr', 'TPR.G26125' => 'tpr', 'TWI09G0677' => 'twi', 'TWI73G0287' => 'twi', 'unitig_748.g8326' => 'ugi', 'vmacro15370' => 'vma', 'vmacro15371' => 'vma', 'vmacro15372' => 'vma', 'vmacro15373' => 'vma', 'vmacro15374' => 'vma', 'VMungo0720G2826' => 'vmu', 'Zm00001eb116960' => 'zma', 'Zm00001eb301260' => 'zma', 'Zm00001eb301270' => 'zma' ) $gf_id = 'HOM05D001460' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001460' ) $data_identifier = 'HOM05D001460' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 4, 'aag' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 2, 'aox' => (int) 2, 'arhy' => (int) 4, 'ath' => (int) 2, 'atr' => (int) 1, 'acertr' => (int) 10, 'cqu' => (int) 4, 'bca' => (int) 11, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 1, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 1, 'ccan' => (int) 1, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 1, 'col' => (int) 1, 'cpa' => (int) 1, 'cre' => (int) 7, 'csa' => (int) 1, 'camsi' => (int) 2, 'dca' => (int) 3, 'din' => (int) 2, 'dzi' => (int) 3, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 14, 'fve' => (int) 9, 'gma' => (int) 2, 'ghi' => (int) 4, 'gra' => (int) 2, 'vvi' => (int) 1, 'han' => (int) 13, 'cav' => (int) 1, 'hma' => (int) 2, 'sun' => (int) 2, 'lal' => (int) 2, 'lonja' => (int) 12, 'lja' => (int) 1, 'lsa' => (int) 7, 'mes' => (int) 1, 'mpo' => (int) 27, 'mbi' => (int) 1, 'mco' => (int) 8, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 1, 'egut' => (int) 1, 'ama' => (int) 1, 'nta' => (int) 4, 'nnu' => (int) 2, 'oeu' => (int) 3, 'osa' => (int) 4, 'pax' => (int) 9, 'pgr' => (int) 1, 'stu' => (int) 1, 'pvu' => (int) 1, 'ptr' => (int) 4, 'ppa' => (int) 22, 'pco' => (int) 6, 'ppe' => (int) 6, 'psa' => (int) 5, 'pso' => (int) 19, 'qlo' => (int) 5, 'rch' => (int) 7, 'rsi' => (int) 20, 'sbr' => (int) 5, 'sbo' => (int) 1, 'sci' => (int) 2, 'sed' => (int) 2, 'sgi' => (int) 12, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 2, 'tar' => (int) 10, 'tha' => (int) 1, 'tca' => (int) 1, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 2, 'ugi' => (int) 1, 'vma' => (int) 5, 'vmu' => (int) 1, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb301270' $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' => 'HOM05D001460', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '433', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p22980' => 'bna', 'A01p32340' => 'bna', 'A03p42970' => 'bna', 'A05p25880' => 'bna', 'Aa31LG8G9320' => 'aar', 'Aa31LG8G9330' => 'aar', 'Aa31LG8G9340' => 'aar', 'Aa31sc221G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1034' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1528' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.829' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2222' => 'aag', 'Ah.12g058830' => 'amhyb', 'Ah.12g058840' => 'amhyb', 'AL3G37160' => 'aly', 'AL7G41310' => 'aly', 'Aqoxy5G00395' => 'aox', 'Aqoxy5G00396' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0C8NZA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5185HY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JZ1PRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MD3LS0' => 'arhy', 'AT3G22840' => 'ath', 'AT4G14690' => 'ath', 'ATR0665G054' => 'atr', 'Atru.chr4.2344' => 'acertr', 'Atru.chr4.2346' => 'acertr', 'Atru.chr4.2347' => 'acertr', 'Atru.chr4.2348' => 'acertr', 'Atru.chr4.2355' => 'acertr', 'Atru.chr4.2356' => 'acertr', 'Atru.chr4.2358' => 'acertr', 'Atru.chr4.2359' => 'acertr', 'Atru.chr4.2360' => 'acertr', 'Atru.chr4.2361' => 'acertr', 'AUR62030476' => 'cqu', 'AUR62030478' => 'cqu', 'AUR62030819' => 'cqu', 'AUR62030820' => 'cqu', 'BcaB03g14648' => 'bca', 'BcaB04g20492' => 'bca', 'BcaB06g26399' => 'bca', 'BcaC01g03416' => 'bca', 'BcaC01g03419' => 'bca', 'BcaC01g03421' => 'bca', 'BcaC01g03424' => 'bca', 'BcaC05g28012' => 'bca', 'BcaC09g49212' => 'bca', 'BcaC09g50140' => 'bca', 'BcaNung00346' => 'bca', 'BolC1t02785H' => 'bol', 'BolC1t04095H' => 'bol', 'BolC3t17545H' => 'bol', 'BolC5t32769H' => 'bol', 'BraA01t02211Z' => 'bra', 'BraA01t03359Z' => 'bra', 'BraA03t13441Z' => 'bra', 'BraA05t21476Z' => 'bra', 'C01p28420' => 'bna', 'C01p41350' => 'bna', 'C03p52750' => 'bna', 'C03p52780' => 'bna', 'C05p40270' => 'bna', 'CAN.G1437.9' => 'can', 'CANSAT78G0035' => 'cansat', 'CANSAT78G1036' => 'cansat', 'CANSAT78G2272' => 'cansat', 'CANSAT78G2478' => 'cansat', 'CARHR098700' => 'chi', 'CARHR221120' => 'chi', 'CARHR221150' => 'chi', 'Carub.0003s2297' => 'cru', 'Carub.0007s2749' => 'cru', 'Carub.0007s2750' => 'cru', 'Carub.0007s2751' => 'cru', 'Ca_10849_v3' => 'car', 'Cc03_g04300' => 'ccan', 'CDE02G3648' => 'cde', 'CDE05G0060' => 'cde', 'CDE05G0692' => 'cde', 'CDE05G2285' => 'cde', 'CDE05G2884' => 'cde', 'CDE05G3072' => 'cde', 'Cfa008439' => 'cfa', 'Cfa008441' => 'cfa', 'Cfa008443' => 'cfa', 'Cfa008448' => 'cfa', 'Ciclev10005974m.g' => 'ccl', 'Ciclev10006006m.g' => 'ccl', 'Ciclev10006775m.g' => 'ccl', 'CiPaw.02G120400' => 'cil', 'CiPaw.02G120500' => 'cil', 'CiPaw.02G120600' => 'cil', 'ClCG05G004850' => 'cla', 'COL.COLO4_21566' => 'col', 'Cpa.g.sc44.124' => 'cpa', 'Cre07.g320400' => 'cre', 'Cre07.g320450' => 'cre', 'Cre08.g384650' => 'cre', 'Cre09.g393173' => 'cre', 'Cre09.g394325' => 'cre', 'Cre14.g626750' => 'cre', 'Cre16.g679250' => 'cre', 'CsaV3_3G012890' => 'csa', 'CSS0010865' => 'camsi', 'CSS0044338' => 'camsi', 'DCAR_002366' => 'dca', 'DCAR_030687' => 'dca', 'DCAR_030688' => 'dca', 'Dinv14047' => 'din', 'Dinv14048' => 'din', 'Duzib151G0105' => 'dzi', 'Duzib151G0114' => 'dzi', 'Duzib212G1029' => 'dzi', 'ECA232G3536' => 'eca', 'ECA240G0786' => 'eca', 'ECA240G1802' => 'eca', 'ECA240G3760' => 'eca', 'ECA240G3920' => 'eca', 'EL10Ac5g12536' => 'bvu', 'EL10Ac5g12537' => 'bvu', 'EL10Ac5g12538' => 'bvu', 'Eucgr.B01004' => 'egr', 'Eucgr.B01006' => 'egr', 'Eucgr.B01007' => 'egr', 'Eucgr.B01008' => 'egr', 'Eucgr.B01895' => 'egr', 'Eucgr.B01896' => 'egr', 'FAN04G1456' => 'fan', 'FAN08G1769' => 'fan', 'FAN08G2160' => 'fan', 'FAN13G2403' => 'fan', 'FAN13G3303' => 'fan', 'FAN15G2435' => 'fan', 'FAN17G0672' => 'fan', 'FAN17G2441' => 'fan', 'FAN18G1024' => 'fan', 'FAN22G1458' => 'fan', 'FAN24G0037' => 'fan', 'FAN24G0429' => 'fan', 'FAN24G2387' => 'fan', 'FAN27G2746' => 'fan', 'FvH4_2g20400' => 'fve', 'FvH4_2g20420' => 'fve', 'FvH4_2g20430' => 'fve', 'FvH4_4g01270' => 'fve', 'FvH4_4g01290' => 'fve', 'FvH4_4g01300' => 'fve', 'FvH4_4g01310' => 'fve', 'FvH4_4g01330' => 'fve', 'FvH4_5g09070' => 'fve', 'Glyma.10G243800' => 'gma', 'Glyma.20G150600' => 'gma', 'Gohir.A09G219200' => 'ghi', 'Gohir.A09G219300' => 'ghi', 'Gohir.D09G221400' => 'ghi', 'Gohir.D09G221500' => 'ghi', 'Gorai.006G242600' => 'gra', 'Gorai.006G242700' => 'gra', 'GSVIVG01018044001' => 'vvi', 'HanXRQChr03g0083821' => 'han', 'HanXRQChr03g0083841' => 'han', 'HanXRQChr03g0083881' => 'han', 'HanXRQChr03g0083901' => 'han', 'HanXRQChr03g0083921' => 'han', 'HanXRQChr03g0085331' => 'han', 'HanXRQChr03g0085361' => 'han', 'HanXRQChr03g0085411' => 'han', 'HanXRQChr03g0085421' => 'han', 'HanXRQChr03g0085431' => 'han', 'HanXRQChr08g0221991' => 'han', 'HanXRQChr11g0336061' => 'han', 'HanXRQChr11g0336411' => 'han', 'Haze_11234' => 'cav', 'Hma1.2p1_0549F.1_g177010' => 'hma', 'Hma1.2p1_0602F.1_g187630' => 'hma', 'Hund14876' => 'sun', 'Hund14879' => 'sun', 'Lalb_Chr06g0160741' => 'lal', 'Lalb_Chr21g0304781' => 'lal', 'Lj3A726G19' => 'lonja', 'Lj3A726T23' => 'lonja', 'Lj3A726T24' => 'lonja', 'Lj3A726T25' => 'lonja', 'Lj3A727T17' => 'lonja', 'Lj3C726T0' => 'lonja', 'Lj3C726T2' => 'lonja', 'Lj3P725T35' => 'lonja', 'Lj3P727T10' => 'lonja', 'Lj3P727T12' => 'lonja', 'Lj3P727T14' => 'lonja', 'Lj5g0023109' => 'lja', 'Lj6P646T44' => 'lonja', 'Lsat_1_v5_gn_6_75760' => 'lsa', 'Lsat_1_v5_gn_6_75800' => 'lsa', 'Lsat_1_v5_gn_6_75900' => 'lsa', 'Lsat_1_v5_gn_6_76240' => 'lsa', 'Lsat_1_v5_gn_6_76441' => 'lsa', 'Lsat_1_v5_gn_6_76700' => 'lsa', 'Lsat_1_v5_gn_6_76760' => 'lsa', 'Manes.15G033100' => 'mes', 'Mapoly0004s0074' => 'mpo', 'Mapoly0004s0075' => 'mpo', 'Mapoly0004s0163' => 'mpo', 'Mapoly0004s0164' => 'mpo', 'Mapoly0021s0018' => 'mpo', 'Mapoly0041s0136' => 'mpo', 'Mapoly0041s0137' => 'mpo', 'Mapoly0041s0138' => 'mpo', 'Mapoly0041s0139' => 'mpo', 'Mapoly0041s0141' => 'mpo', 'Mapoly0041s0142' => 'mpo', 'Mapoly0041s0143' => 'mpo', 'Mapoly0041s0144' => 'mpo', 'Mapoly0041s0145' => 'mpo', 'Mapoly0047s0106' => 'mpo', 'Mapoly0047s0108' => 'mpo', 'Mapoly0050s0051' => 'mpo', 'Mapoly0050s0052' => 'mpo', 'Mapoly0050s0053' => 'mpo', 'Mapoly0058s0013' => 'mpo', 'Mapoly0091s0078' => 'mpo', 'Mapoly0091s0079' => 'mpo', 'Mapoly0091s0080' => 'mpo', 'Mapoly0091s0081' => 'mpo', 'Mapoly0278s0004' => 'mpo', 'Mapoly0278s0005' => 'mpo', 'Mapoly0278s0006' => 'mpo', 'MBI11_g30648_MAGBIO' => 'mbi', 'MCO03G194' => 'mco', 'MCO03G590' => 'mco', 'MCO07G312' => 'mco', 'MCO10G318' => 'mco', 'MCO12G244' => 'mco', 'MCO13G148' => 'mco', 'MCO13G194' => 'mco', 'MCO16G238' => 'mco', 'MD06G1134100' => 'mdo', 'MD13G1200100' => 'mdo', 'MD13G1200300' => 'mdo', 'MD13G1200600' => 'mdo', 'MD14G1150400' => 'mdo', 'MD16G1200000' => 'mdo', 'Medtr1g102570' => 'mtr', 'Medtr1g102780' => 'mtr', 'Medtr1g102800' => 'mtr', 'Medtr1g102810' => 'mtr', 'Medtr1g102830' => 'mtr', 'MELO3C006499.2' => 'cme', 'Migut.G00385' => 'egut', 'MSTRG.4063' => 'ama', 'Nitab4.5_0000090g0260' => 'nta', 'Nitab4.5_0000977g0030' => 'nta', 'Nitab4.5_0002541g0040' => 'nta', 'Nitab4.5_0007068g0040' => 'nta', 'Nn005s41408' => 'nnu', 'Nn005s41410' => 'nnu', 'Oeu010310.1' => 'oeu', 'Oeu010311.1' => 'oeu', 'Oeu043472.1' => 'oeu', 'Os01g0246400' => 'osa', 'Os04g0267950' => 'osa', 'Os07g0178700' => 'osa', 'Os07g0178800' => 'osa', 'Peaxi162Scf00316g00046' => 'pax', 'Peaxi162Scf00316g00049' => 'pax', 'Peaxi162Scf00316g00059' => 'pax', 'Peaxi162Scf00316g00328' => 'pax', 'Peaxi162Scf00316g00329' => 'pax', 'Peaxi162Scf00316g00411' => 'pax', 'Peaxi162Scf00316g00521' => 'pax', 'Peaxi162Scf00492g00068' => 'pax', 'Peaxi162Scf35631g00002' => 'pax', 'PGR142G3720' => 'pgr', 'PGSC0003DMG400006442' => 'stu', 'Phvul.007G062000' => 'pvu', 'Potri.008G157750' => 'ptr', 'Potri.008G157900' => 'ptr', 'Potri.008G158000' => 'ptr', 'Potri.008G158200' => 'ptr', 'Pp3c11_7280' => 'ppa', 'Pp3c11_7980' => 'ppa', 'Pp3c12_19450' => 'ppa', 'Pp3c14_1480' => 'ppa', 'Pp3c14_1501' => 'ppa', 'Pp3c16_4900' => 'ppa', 'Pp3c16_5010' => 'ppa', 'Pp3c16_5060' => 'ppa', 'Pp3c19_18250' => 'ppa', 'Pp3c23_8530' => 'ppa', 'Pp3c23_8550' => 'ppa', 'Pp3c24_9670' => 'ppa', 'Pp3c2_21390' => 'ppa', 'Pp3c2_31380' => 'ppa', 'Pp3c3_16620' => 'ppa', 'Pp3c3_8090' => 'ppa', 'Pp3c3_8110' => 'ppa', 'Pp3c3_8130' => 'ppa', 'Pp3c3_8150' => 'ppa', 'Pp3c4_14320' => 'ppa', 'Pp3c6_2560' => 'ppa', 'Pp3c9_16700' => 'ppa', 'PRCOL_00000234' => 'pco', 'PRCOL_00000235' => 'pco', 'PRCOL_00000777' => 'pco', 'PRCOL_00002344' => 'pco', 'PRCOL_00002372' => 'pco', 'PRCOL_00006120' => 'pco', 'Prupe.1G021400' => 'ppe', 'Prupe.1G021500' => 'ppe', 'Prupe.1G021600' => 'ppe', 'Prupe.1G021700' => 'ppe', 'Prupe.1G021800' => 'ppe', 'Prupe.5G145100' => 'ppe', 'Psat6g204040' => 'psa', 'Psat6g204800' => 'psa', 'Psat6g204920' => 'psa', 'Psat6g204960' => 'psa', 'Psat6g205080' => 'psa', 'PSO017G0271' => 'pso', 'PSO017G1276' => 'pso', 'PSO017G1429' => 'pso', 'PSO017G1861' => 'pso', 'PSO017G2787' => 'pso', 'PSO017G4466' => 'pso', 'PSO017G5118' => 'pso', 'PSO017G5420' => 'pso', 'PSO063G3678' => 'pso', 'PSO210G0546' => 'pso', 'PSO317G0001' => 'pso', 'PSO357G0512' => 'pso', 'PSO478G2682' => 'pso', 'PSO647G0001' => 'pso', 'PSO675G0001' => 'pso', 'PSO675G2699' => 'pso', 'PSO675G2849' => 'pso', 'PSO675G4991' => 'pso', 'PSO689G0001' => 'pso', 'QL06p000916' => 'qlo', 'QL06p000921' => 'qlo', 'QL06p001398' => 'qlo', 'QL06p001407' => 'qlo', 'QL06p002031' => 'qlo', 'RcHm_v2.0_Chr4g0387791' => 'rch', 'RcHm_v2.0_Chr4g0387801' => 'rch', 'RcHm_v2.0_Chr6g0286501' => 'rch', 'RcHm_v2.0_Chr6g0286511' => 'rch', 'RcHm_v2.0_Chr6g0286521' => 'rch', 'RcHm_v2.0_Chr6g0286531' => 'rch', 'RcHm_v2.0_Chr7g0189141' => 'rch', 'Rhsim02G0028700' => 'rsi', 'Rhsim02G0028800' => 'rsi', 'Rhsim02G0028900' => 'rsi', 'Rhsim02G0029000' => 'rsi', 'Rhsim02G0029100' => 'rsi', 'Rhsim02G0029200' => 'rsi', 'Rhsim02G0029300' => 'rsi', 'Rhsim02G0029400' => 'rsi', 'Rhsim02G0029500' => 'rsi', 'Rhsim02G0029600' => 'rsi', 'RhsimUnG0024000' => 'rsi', 'RhsimUnG0024100' => 'rsi', 'RhsimUnG0024200' => 'rsi', 'RhsimUnG0024300' => 'rsi', 'RhsimUnG0024400' => 'rsi', 'RhsimUnG0024500' => 'rsi', 'RhsimUnG0024700' => 'rsi', 'RhsimUnG0024800' => 'rsi', 'RhsimUnG0024900' => 'rsi', 'RhsimUnG0025100' => 'rsi', 'Sabra08G0120200' => 'sbr', 'Sabra08G0120300' => 'sbr', 'Sabra08G0120500' => 'sbr', 'Sabra08G0120600' => 'sbr', 'Sabra10G0158900' => 'sbr', 'SalBow2G3492' => 'sbo', 'Sc13g0004760' => 'sci', 'Sc13g0004770' => 'sci', 'Sed0003417' => 'sed', 'Sed0019750' => 'sed', 'SEGI_03419' => 'sgi', 'SEGI_05907' => 'sgi', 'SEGI_10682' => 'sgi', 'SEGI_13528' => 'sgi', 'SEGI_16081' => 'sgi', 'SEGI_19370' => 'sgi', 'SEGI_21015' => 'sgi', 'SEGI_21944' => 'sgi', 'SEGI_32906' => 'sgi', 'SEGI_33093' => 'sgi', 'SEGI_36110' => 'sgi', 'SEGI_40397' => 'sgi', 'SGA_v2.0_scaffold191G40426' => 'sas', 'SGA_v2.0_scaffold353G49717' => 'sas', 'SGA_v2.0_scaffold50G18550' => 'sas', 'SMO119G0173' => 'smo', 'SMO172G0002' => 'smo', 'Solyc09g082690.3' => 'sly', 'Solyc09g082700.2' => 'sly', 'Sopen09g031550' => 'spe', 'Sopen09g031560' => 'spe', 'Sp3g20540' => 'spa', 'Sp7g07580' => 'spa', 'TAR134G0002' => 'tar', 'TAR236G0001' => 'tar', 'TAR365G0892' => 'tar', 'TAR636G0166' => 'tar', 'TAR636G0646' => 'tar', 'TAR636G0869' => 'tar', 'TAR636G1317' => 'tar', 'TAR636G1744' => 'tar', 'TAR636G3358' => 'tar', 'TAR636G3436' => 'tar', 'THA.LOC104803047' => 'tha', 'Thecc.04G238900' => 'tca', 'Thhalv10021557m.g' => 'esa', 'Thhalv10026318m.g' => 'esa', 'Thhalv10026335m.g' => 'esa', 'TPR.G17433' => 'tpr', 'TPR.G18915' => 'tpr', 'TPR.G26125' => 'tpr', 'TWI09G0677' => 'twi', 'TWI73G0287' => 'twi', 'unitig_748.g8326' => 'ugi', 'vmacro15370' => 'vma', 'vmacro15371' => 'vma', 'vmacro15372' => 'vma', 'vmacro15373' => 'vma', 'vmacro15374' => 'vma', 'VMungo0720G2826' => 'vmu', 'Zm00001eb116960' => 'zma', 'Zm00001eb301260' => 'zma', 'Zm00001eb301270' => 'zma' ), 'gf_id' => 'HOM05D001460', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001460' ), 'data_identifier' => 'HOM05D001460', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001460', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '433', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p22980' => 'bna', 'A01p32340' => 'bna', 'A03p42970' => 'bna', 'A05p25880' => 'bna', 'Aa31LG8G9320' => 'aar', 'Aa31LG8G9330' => 'aar', 'Aa31LG8G9340' => 'aar', 'Aa31sc221G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1034' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1528' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.829' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2222' => 'aag', 'Ah.12g058830' => 'amhyb', 'Ah.12g058840' => 'amhyb', 'AL3G37160' => 'aly', 'AL7G41310' => 'aly', 'Aqoxy5G00395' => 'aox', 'Aqoxy5G00396' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0C8NZA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5185HY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JZ1PRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MD3LS0' => 'arhy', 'AT3G22840' => 'ath', 'AT4G14690' => 'ath', 'ATR0665G054' => 'atr', 'Atru.chr4.2344' => 'acertr', 'Atru.chr4.2346' => 'acertr', 'Atru.chr4.2347' => 'acertr', 'Atru.chr4.2348' => 'acertr', 'Atru.chr4.2355' => 'acertr', 'Atru.chr4.2356' => 'acertr', 'Atru.chr4.2358' => 'acertr', 'Atru.chr4.2359' => 'acertr', 'Atru.chr4.2360' => 'acertr', 'Atru.chr4.2361' => 'acertr', 'AUR62030476' => 'cqu', 'AUR62030478' => 'cqu', 'AUR62030819' => 'cqu', 'AUR62030820' => 'cqu', 'BcaB03g14648' => 'bca', 'BcaB04g20492' => 'bca', 'BcaB06g26399' => 'bca', 'BcaC01g03416' => 'bca', 'BcaC01g03419' => 'bca', 'BcaC01g03421' => 'bca', 'BcaC01g03424' => 'bca', 'BcaC05g28012' => 'bca', 'BcaC09g49212' => 'bca', 'BcaC09g50140' => 'bca', 'BcaNung00346' => 'bca', 'BolC1t02785H' => 'bol', 'BolC1t04095H' => 'bol', 'BolC3t17545H' => 'bol', 'BolC5t32769H' => 'bol', 'BraA01t02211Z' => 'bra', 'BraA01t03359Z' => 'bra', 'BraA03t13441Z' => 'bra', 'BraA05t21476Z' => 'bra', 'C01p28420' => 'bna', 'C01p41350' => 'bna', 'C03p52750' => 'bna', 'C03p52780' => 'bna', 'C05p40270' => 'bna', 'CAN.G1437.9' => 'can', 'CANSAT78G0035' => 'cansat', 'CANSAT78G1036' => 'cansat', 'CANSAT78G2272' => 'cansat', 'CANSAT78G2478' => 'cansat', 'CARHR098700' => 'chi', 'CARHR221120' => 'chi', 'CARHR221150' => 'chi', 'Carub.0003s2297' => 'cru', 'Carub.0007s2749' => 'cru', 'Carub.0007s2750' => 'cru', 'Carub.0007s2751' => 'cru', 'Ca_10849_v3' => 'car', 'Cc03_g04300' => 'ccan', 'CDE02G3648' => 'cde', 'CDE05G0060' => 'cde', 'CDE05G0692' => 'cde', 'CDE05G2285' => 'cde', 'CDE05G2884' => 'cde', 'CDE05G3072' => 'cde', 'Cfa008439' => 'cfa', 'Cfa008441' => 'cfa', 'Cfa008443' => 'cfa', 'Cfa008448' => 'cfa', 'Ciclev10005974m.g' => 'ccl', 'Ciclev10006006m.g' => 'ccl', 'Ciclev10006775m.g' => 'ccl', 'CiPaw.02G120400' => 'cil', 'CiPaw.02G120500' => 'cil', 'CiPaw.02G120600' => 'cil', 'ClCG05G004850' => 'cla', 'COL.COLO4_21566' => 'col', 'Cpa.g.sc44.124' => 'cpa', 'Cre07.g320400' => 'cre', 'Cre07.g320450' => 'cre', 'Cre08.g384650' => 'cre', 'Cre09.g393173' => 'cre', 'Cre09.g394325' => 'cre', 'Cre14.g626750' => 'cre', 'Cre16.g679250' => 'cre', 'CsaV3_3G012890' => 'csa', 'CSS0010865' => 'camsi', 'CSS0044338' => 'camsi', 'DCAR_002366' => 'dca', 'DCAR_030687' => 'dca', 'DCAR_030688' => 'dca', 'Dinv14047' => 'din', 'Dinv14048' => 'din', 'Duzib151G0105' => 'dzi', 'Duzib151G0114' => 'dzi', 'Duzib212G1029' => 'dzi', 'ECA232G3536' => 'eca', 'ECA240G0786' => 'eca', 'ECA240G1802' => 'eca', 'ECA240G3760' => 'eca', 'ECA240G3920' => 'eca', 'EL10Ac5g12536' => 'bvu', 'EL10Ac5g12537' => 'bvu', 'EL10Ac5g12538' => 'bvu', 'Eucgr.B01004' => 'egr', 'Eucgr.B01006' => 'egr', 'Eucgr.B01007' => 'egr', 'Eucgr.B01008' => 'egr', 'Eucgr.B01895' => 'egr', 'Eucgr.B01896' => 'egr', 'FAN04G1456' => 'fan', 'FAN08G1769' => 'fan', 'FAN08G2160' => 'fan', 'FAN13G2403' => 'fan', 'FAN13G3303' => 'fan', 'FAN15G2435' => 'fan', 'FAN17G0672' => 'fan', 'FAN17G2441' => 'fan', 'FAN18G1024' => 'fan', 'FAN22G1458' => 'fan', 'FAN24G0037' => 'fan', 'FAN24G0429' => 'fan', 'FAN24G2387' => 'fan', 'FAN27G2746' => 'fan', 'FvH4_2g20400' => 'fve', 'FvH4_2g20420' => 'fve', 'FvH4_2g20430' => 'fve', 'FvH4_4g01270' => 'fve', 'FvH4_4g01290' => 'fve', 'FvH4_4g01300' => 'fve', 'FvH4_4g01310' => 'fve', 'FvH4_4g01330' => 'fve', 'FvH4_5g09070' => 'fve', 'Glyma.10G243800' => 'gma', 'Glyma.20G150600' => 'gma', 'Gohir.A09G219200' => 'ghi', 'Gohir.A09G219300' => 'ghi', 'Gohir.D09G221400' => 'ghi', 'Gohir.D09G221500' => 'ghi', 'Gorai.006G242600' => 'gra', 'Gorai.006G242700' => 'gra', 'GSVIVG01018044001' => 'vvi', 'HanXRQChr03g0083821' => 'han', 'HanXRQChr03g0083841' => 'han', 'HanXRQChr03g0083881' => 'han', 'HanXRQChr03g0083901' => 'han', 'HanXRQChr03g0083921' => 'han', 'HanXRQChr03g0085331' => 'han', 'HanXRQChr03g0085361' => 'han', 'HanXRQChr03g0085411' => 'han', 'HanXRQChr03g0085421' => 'han', 'HanXRQChr03g0085431' => 'han', 'HanXRQChr08g0221991' => 'han', 'HanXRQChr11g0336061' => 'han', 'HanXRQChr11g0336411' => 'han', 'Haze_11234' => 'cav', 'Hma1.2p1_0549F.1_g177010' => 'hma', 'Hma1.2p1_0602F.1_g187630' => 'hma', 'Hund14876' => 'sun', 'Hund14879' => 'sun', 'Lalb_Chr06g0160741' => 'lal', 'Lalb_Chr21g0304781' => 'lal', 'Lj3A726G19' => 'lonja', 'Lj3A726T23' => 'lonja', 'Lj3A726T24' => 'lonja', 'Lj3A726T25' => 'lonja', 'Lj3A727T17' => 'lonja', 'Lj3C726T0' => 'lonja', 'Lj3C726T2' => 'lonja', 'Lj3P725T35' => 'lonja', 'Lj3P727T10' => 'lonja', 'Lj3P727T12' => 'lonja', 'Lj3P727T14' => 'lonja', 'Lj5g0023109' => 'lja', 'Lj6P646T44' => 'lonja', 'Lsat_1_v5_gn_6_75760' => 'lsa', 'Lsat_1_v5_gn_6_75800' => 'lsa', 'Lsat_1_v5_gn_6_75900' => 'lsa', 'Lsat_1_v5_gn_6_76240' => 'lsa', 'Lsat_1_v5_gn_6_76441' => 'lsa', 'Lsat_1_v5_gn_6_76700' => 'lsa', 'Lsat_1_v5_gn_6_76760' => 'lsa', 'Manes.15G033100' => 'mes', 'Mapoly0004s0074' => 'mpo', 'Mapoly0004s0075' => 'mpo', 'Mapoly0004s0163' => 'mpo', 'Mapoly0004s0164' => 'mpo', 'Mapoly0021s0018' => 'mpo', 'Mapoly0041s0136' => 'mpo', 'Mapoly0041s0137' => 'mpo', 'Mapoly0041s0138' => 'mpo', 'Mapoly0041s0139' => 'mpo', 'Mapoly0041s0141' => 'mpo', 'Mapoly0041s0142' => 'mpo', 'Mapoly0041s0143' => 'mpo', 'Mapoly0041s0144' => 'mpo', 'Mapoly0041s0145' => 'mpo', 'Mapoly0047s0106' => 'mpo', 'Mapoly0047s0108' => 'mpo', 'Mapoly0050s0051' => 'mpo', 'Mapoly0050s0052' => 'mpo', 'Mapoly0050s0053' => 'mpo', 'Mapoly0058s0013' => 'mpo', 'Mapoly0091s0078' => 'mpo', 'Mapoly0091s0079' => 'mpo', 'Mapoly0091s0080' => 'mpo', 'Mapoly0091s0081' => 'mpo', 'Mapoly0278s0004' => 'mpo', 'Mapoly0278s0005' => 'mpo', 'Mapoly0278s0006' => 'mpo', 'MBI11_g30648_MAGBIO' => 'mbi', 'MCO03G194' => 'mco', 'MCO03G590' => 'mco', 'MCO07G312' => 'mco', 'MCO10G318' => 'mco', 'MCO12G244' => 'mco', 'MCO13G148' => 'mco', 'MCO13G194' => 'mco', 'MCO16G238' => 'mco', 'MD06G1134100' => 'mdo', 'MD13G1200100' => 'mdo', 'MD13G1200300' => 'mdo', 'MD13G1200600' => 'mdo', 'MD14G1150400' => 'mdo', 'MD16G1200000' => 'mdo', 'Medtr1g102570' => 'mtr', 'Medtr1g102780' => 'mtr', 'Medtr1g102800' => 'mtr', 'Medtr1g102810' => 'mtr', 'Medtr1g102830' => 'mtr', 'MELO3C006499.2' => 'cme', 'Migut.G00385' => 'egut', 'MSTRG.4063' => 'ama', 'Nitab4.5_0000090g0260' => 'nta', 'Nitab4.5_0000977g0030' => 'nta', 'Nitab4.5_0002541g0040' => 'nta', 'Nitab4.5_0007068g0040' => 'nta', 'Nn005s41408' => 'nnu', 'Nn005s41410' => 'nnu', 'Oeu010310.1' => 'oeu', 'Oeu010311.1' => 'oeu', 'Oeu043472.1' => 'oeu', 'Os01g0246400' => 'osa', 'Os04g0267950' => 'osa', 'Os07g0178700' => 'osa', 'Os07g0178800' => 'osa', 'Peaxi162Scf00316g00046' => 'pax', 'Peaxi162Scf00316g00049' => 'pax', 'Peaxi162Scf00316g00059' => 'pax', 'Peaxi162Scf00316g00328' => 'pax', 'Peaxi162Scf00316g00329' => 'pax', 'Peaxi162Scf00316g00411' => 'pax', 'Peaxi162Scf00316g00521' => 'pax', 'Peaxi162Scf00492g00068' => 'pax', 'Peaxi162Scf35631g00002' => 'pax', 'PGR142G3720' => 'pgr', 'PGSC0003DMG400006442' => 'stu', 'Phvul.007G062000' => 'pvu', 'Potri.008G157750' => 'ptr', 'Potri.008G157900' => 'ptr', 'Potri.008G158000' => 'ptr', 'Potri.008G158200' => 'ptr', 'Pp3c11_7280' => 'ppa', 'Pp3c11_7980' => 'ppa', 'Pp3c12_19450' => 'ppa', 'Pp3c14_1480' => 'ppa', 'Pp3c14_1501' => 'ppa', 'Pp3c16_4900' => 'ppa', 'Pp3c16_5010' => 'ppa', 'Pp3c16_5060' => 'ppa', 'Pp3c19_18250' => 'ppa', 'Pp3c23_8530' => 'ppa', 'Pp3c23_8550' => 'ppa', 'Pp3c24_9670' => 'ppa', 'Pp3c2_21390' => 'ppa', 'Pp3c2_31380' => 'ppa', 'Pp3c3_16620' => 'ppa', 'Pp3c3_8090' => 'ppa', 'Pp3c3_8110' => 'ppa', 'Pp3c3_8130' => 'ppa', 'Pp3c3_8150' => 'ppa', 'Pp3c4_14320' => 'ppa', 'Pp3c6_2560' => 'ppa', 'Pp3c9_16700' => 'ppa', 'PRCOL_00000234' => 'pco', 'PRCOL_00000235' => 'pco', 'PRCOL_00000777' => 'pco', 'PRCOL_00002344' => 'pco', 'PRCOL_00002372' => 'pco', 'PRCOL_00006120' => 'pco', 'Prupe.1G021400' => 'ppe', 'Prupe.1G021500' => 'ppe', 'Prupe.1G021600' => 'ppe', 'Prupe.1G021700' => 'ppe', 'Prupe.1G021800' => 'ppe', 'Prupe.5G145100' => 'ppe', 'Psat6g204040' => 'psa', 'Psat6g204800' => 'psa', 'Psat6g204920' => 'psa', 'Psat6g204960' => 'psa', 'Psat6g205080' => 'psa', 'PSO017G0271' => 'pso', 'PSO017G1276' => 'pso', 'PSO017G1429' => 'pso', 'PSO017G1861' => 'pso', 'PSO017G2787' => 'pso', 'PSO017G4466' => 'pso', 'PSO017G5118' => 'pso', 'PSO017G5420' => 'pso', 'PSO063G3678' => 'pso', 'PSO210G0546' => 'pso', 'PSO317G0001' => 'pso', 'PSO357G0512' => 'pso', 'PSO478G2682' => 'pso', 'PSO647G0001' => 'pso', 'PSO675G0001' => 'pso', 'PSO675G2699' => 'pso', 'PSO675G2849' => 'pso', 'PSO675G4991' => 'pso', 'PSO689G0001' => 'pso', 'QL06p000916' => 'qlo', 'QL06p000921' => 'qlo', 'QL06p001398' => 'qlo', 'QL06p001407' => 'qlo', 'QL06p002031' => 'qlo', 'RcHm_v2.0_Chr4g0387791' => 'rch', 'RcHm_v2.0_Chr4g0387801' => 'rch', 'RcHm_v2.0_Chr6g0286501' => 'rch', 'RcHm_v2.0_Chr6g0286511' => 'rch', 'RcHm_v2.0_Chr6g0286521' => 'rch', 'RcHm_v2.0_Chr6g0286531' => 'rch', 'RcHm_v2.0_Chr7g0189141' => 'rch', 'Rhsim02G0028700' => 'rsi', 'Rhsim02G0028800' => 'rsi', 'Rhsim02G0028900' => 'rsi', 'Rhsim02G0029000' => 'rsi', 'Rhsim02G0029100' => 'rsi', 'Rhsim02G0029200' => 'rsi', 'Rhsim02G0029300' => 'rsi', 'Rhsim02G0029400' => 'rsi', 'Rhsim02G0029500' => 'rsi', 'Rhsim02G0029600' => 'rsi', 'RhsimUnG0024000' => 'rsi', 'RhsimUnG0024100' => 'rsi', 'RhsimUnG0024200' => 'rsi', 'RhsimUnG0024300' => 'rsi', 'RhsimUnG0024400' => 'rsi', 'RhsimUnG0024500' => 'rsi', 'RhsimUnG0024700' => 'rsi', 'RhsimUnG0024800' => 'rsi', 'RhsimUnG0024900' => 'rsi', 'RhsimUnG0025100' => 'rsi', 'Sabra08G0120200' => 'sbr', 'Sabra08G0120300' => 'sbr', 'Sabra08G0120500' => 'sbr', 'Sabra08G0120600' => 'sbr', 'Sabra10G0158900' => 'sbr', 'SalBow2G3492' => 'sbo', 'Sc13g0004760' => 'sci', 'Sc13g0004770' => 'sci', 'Sed0003417' => 'sed', 'Sed0019750' => 'sed', 'SEGI_03419' => 'sgi', 'SEGI_05907' => 'sgi', 'SEGI_10682' => 'sgi', 'SEGI_13528' => 'sgi', 'SEGI_16081' => 'sgi', 'SEGI_19370' => 'sgi', 'SEGI_21015' => 'sgi', 'SEGI_21944' => 'sgi', 'SEGI_32906' => 'sgi', 'SEGI_33093' => 'sgi', 'SEGI_36110' => 'sgi', 'SEGI_40397' => 'sgi', 'SGA_v2.0_scaffold191G40426' => 'sas', 'SGA_v2.0_scaffold353G49717' => 'sas', 'SGA_v2.0_scaffold50G18550' => 'sas', 'SMO119G0173' => 'smo', 'SMO172G0002' => 'smo', 'Solyc09g082690.3' => 'sly', 'Solyc09g082700.2' => 'sly', 'Sopen09g031550' => 'spe', 'Sopen09g031560' => 'spe', 'Sp3g20540' => 'spa', 'Sp7g07580' => 'spa', 'TAR134G0002' => 'tar', 'TAR236G0001' => 'tar', 'TAR365G0892' => 'tar', 'TAR636G0166' => 'tar', 'TAR636G0646' => 'tar', 'TAR636G0869' => 'tar', 'TAR636G1317' => 'tar', 'TAR636G1744' => 'tar', 'TAR636G3358' => 'tar', 'TAR636G3436' => 'tar', 'THA.LOC104803047' => 'tha', 'Thecc.04G238900' => 'tca', 'Thhalv10021557m.g' => 'esa', 'Thhalv10026318m.g' => 'esa', 'Thhalv10026335m.g' => 'esa', 'TPR.G17433' => 'tpr', 'TPR.G18915' => 'tpr', 'TPR.G26125' => 'tpr', 'TWI09G0677' => 'twi', 'TWI73G0287' => 'twi', 'unitig_748.g8326' => 'ugi', 'vmacro15370' => 'vma', 'vmacro15371' => 'vma', 'vmacro15372' => 'vma', 'vmacro15373' => 'vma', 'vmacro15374' => 'vma', 'VMungo0720G2826' => 'vmu', 'Zm00001eb116960' => 'zma', 'Zm00001eb301260' => 'zma', 'Zm00001eb301270' => 'zma' ) $gf_id = 'HOM05D001460' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001460' ) $data_identifier = 'HOM05D001460' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 4, 'aag' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 2, 'aox' => (int) 2, 'arhy' => (int) 4, 'ath' => (int) 2, 'atr' => (int) 1, 'acertr' => (int) 10, 'cqu' => (int) 4, 'bca' => (int) 11, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 1, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 1, 'ccan' => (int) 1, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 1, 'col' => (int) 1, 'cpa' => (int) 1, 'cre' => (int) 7, 'csa' => (int) 1, 'camsi' => (int) 2, 'dca' => (int) 3, 'din' => (int) 2, 'dzi' => (int) 3, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 14, 'fve' => (int) 9, 'gma' => (int) 2, 'ghi' => (int) 4, 'gra' => (int) 2, 'vvi' => (int) 1, 'han' => (int) 13, 'cav' => (int) 1, 'hma' => (int) 2, 'sun' => (int) 2, 'lal' => (int) 2, 'lonja' => (int) 12, 'lja' => (int) 1, 'lsa' => (int) 7, 'mes' => (int) 1, 'mpo' => (int) 27, 'mbi' => (int) 1, 'mco' => (int) 8, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 1, 'egut' => (int) 1, 'ama' => (int) 1, 'nta' => (int) 4, 'nnu' => (int) 2, 'oeu' => (int) 3, 'osa' => (int) 4, 'pax' => (int) 9, 'pgr' => (int) 1, 'stu' => (int) 1, 'pvu' => (int) 1, 'ptr' => (int) 4, 'ppa' => (int) 22, 'pco' => (int) 6, 'ppe' => (int) 6, 'psa' => (int) 5, 'pso' => (int) 19, 'qlo' => (int) 5, 'rch' => (int) 7, 'rsi' => (int) 20, 'sbr' => (int) 5, 'sbo' => (int) 1, 'sci' => (int) 2, 'sed' => (int) 2, 'sgi' => (int) 12, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 2, 'tar' => (int) 10, 'tha' => (int) 1, 'tca' => (int) 1, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 2, 'ugi' => (int) 1, 'vma' => (int) 5, 'vmu' => (int) 1, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb301270' $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' => 'HOM05D001460', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '433', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p22980' => 'bna', 'A01p32340' => 'bna', 'A03p42970' => 'bna', 'A05p25880' => 'bna', 'Aa31LG8G9320' => 'aar', 'Aa31LG8G9330' => 'aar', 'Aa31LG8G9340' => 'aar', 'Aa31sc221G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1034' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1528' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.829' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2222' => 'aag', 'Ah.12g058830' => 'amhyb', 'Ah.12g058840' => 'amhyb', 'AL3G37160' => 'aly', 'AL7G41310' => 'aly', 'Aqoxy5G00395' => 'aox', 'Aqoxy5G00396' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0C8NZA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5185HY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JZ1PRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MD3LS0' => 'arhy', 'AT3G22840' => 'ath', 'AT4G14690' => 'ath', 'ATR0665G054' => 'atr', 'Atru.chr4.2344' => 'acertr', 'Atru.chr4.2346' => 'acertr', 'Atru.chr4.2347' => 'acertr', 'Atru.chr4.2348' => 'acertr', 'Atru.chr4.2355' => 'acertr', 'Atru.chr4.2356' => 'acertr', 'Atru.chr4.2358' => 'acertr', 'Atru.chr4.2359' => 'acertr', 'Atru.chr4.2360' => 'acertr', 'Atru.chr4.2361' => 'acertr', 'AUR62030476' => 'cqu', 'AUR62030478' => 'cqu', 'AUR62030819' => 'cqu', 'AUR62030820' => 'cqu', 'BcaB03g14648' => 'bca', 'BcaB04g20492' => 'bca', 'BcaB06g26399' => 'bca', 'BcaC01g03416' => 'bca', 'BcaC01g03419' => 'bca', 'BcaC01g03421' => 'bca', 'BcaC01g03424' => 'bca', 'BcaC05g28012' => 'bca', 'BcaC09g49212' => 'bca', 'BcaC09g50140' => 'bca', 'BcaNung00346' => 'bca', 'BolC1t02785H' => 'bol', 'BolC1t04095H' => 'bol', 'BolC3t17545H' => 'bol', 'BolC5t32769H' => 'bol', 'BraA01t02211Z' => 'bra', 'BraA01t03359Z' => 'bra', 'BraA03t13441Z' => 'bra', 'BraA05t21476Z' => 'bra', 'C01p28420' => 'bna', 'C01p41350' => 'bna', 'C03p52750' => 'bna', 'C03p52780' => 'bna', 'C05p40270' => 'bna', 'CAN.G1437.9' => 'can', 'CANSAT78G0035' => 'cansat', 'CANSAT78G1036' => 'cansat', 'CANSAT78G2272' => 'cansat', 'CANSAT78G2478' => 'cansat', 'CARHR098700' => 'chi', 'CARHR221120' => 'chi', 'CARHR221150' => 'chi', 'Carub.0003s2297' => 'cru', 'Carub.0007s2749' => 'cru', 'Carub.0007s2750' => 'cru', 'Carub.0007s2751' => 'cru', 'Ca_10849_v3' => 'car', 'Cc03_g04300' => 'ccan', 'CDE02G3648' => 'cde', 'CDE05G0060' => 'cde', 'CDE05G0692' => 'cde', 'CDE05G2285' => 'cde', 'CDE05G2884' => 'cde', 'CDE05G3072' => 'cde', 'Cfa008439' => 'cfa', 'Cfa008441' => 'cfa', 'Cfa008443' => 'cfa', 'Cfa008448' => 'cfa', 'Ciclev10005974m.g' => 'ccl', 'Ciclev10006006m.g' => 'ccl', 'Ciclev10006775m.g' => 'ccl', 'CiPaw.02G120400' => 'cil', 'CiPaw.02G120500' => 'cil', 'CiPaw.02G120600' => 'cil', 'ClCG05G004850' => 'cla', 'COL.COLO4_21566' => 'col', 'Cpa.g.sc44.124' => 'cpa', 'Cre07.g320400' => 'cre', 'Cre07.g320450' => 'cre', 'Cre08.g384650' => 'cre', 'Cre09.g393173' => 'cre', 'Cre09.g394325' => 'cre', 'Cre14.g626750' => 'cre', 'Cre16.g679250' => 'cre', 'CsaV3_3G012890' => 'csa', 'CSS0010865' => 'camsi', 'CSS0044338' => 'camsi', 'DCAR_002366' => 'dca', 'DCAR_030687' => 'dca', 'DCAR_030688' => 'dca', 'Dinv14047' => 'din', 'Dinv14048' => 'din', 'Duzib151G0105' => 'dzi', 'Duzib151G0114' => 'dzi', 'Duzib212G1029' => 'dzi', 'ECA232G3536' => 'eca', 'ECA240G0786' => 'eca', 'ECA240G1802' => 'eca', 'ECA240G3760' => 'eca', 'ECA240G3920' => 'eca', 'EL10Ac5g12536' => 'bvu', 'EL10Ac5g12537' => 'bvu', 'EL10Ac5g12538' => 'bvu', 'Eucgr.B01004' => 'egr', 'Eucgr.B01006' => 'egr', 'Eucgr.B01007' => 'egr', 'Eucgr.B01008' => 'egr', 'Eucgr.B01895' => 'egr', 'Eucgr.B01896' => 'egr', 'FAN04G1456' => 'fan', 'FAN08G1769' => 'fan', 'FAN08G2160' => 'fan', 'FAN13G2403' => 'fan', 'FAN13G3303' => 'fan', 'FAN15G2435' => 'fan', 'FAN17G0672' => 'fan', 'FAN17G2441' => 'fan', 'FAN18G1024' => 'fan', 'FAN22G1458' => 'fan', 'FAN24G0037' => 'fan', 'FAN24G0429' => 'fan', 'FAN24G2387' => 'fan', 'FAN27G2746' => 'fan', 'FvH4_2g20400' => 'fve', 'FvH4_2g20420' => 'fve', 'FvH4_2g20430' => 'fve', 'FvH4_4g01270' => 'fve', 'FvH4_4g01290' => 'fve', 'FvH4_4g01300' => 'fve', 'FvH4_4g01310' => 'fve', 'FvH4_4g01330' => 'fve', 'FvH4_5g09070' => 'fve', 'Glyma.10G243800' => 'gma', 'Glyma.20G150600' => 'gma', 'Gohir.A09G219200' => 'ghi', 'Gohir.A09G219300' => 'ghi', 'Gohir.D09G221400' => 'ghi', 'Gohir.D09G221500' => 'ghi', 'Gorai.006G242600' => 'gra', 'Gorai.006G242700' => 'gra', 'GSVIVG01018044001' => 'vvi', 'HanXRQChr03g0083821' => 'han', 'HanXRQChr03g0083841' => 'han', 'HanXRQChr03g0083881' => 'han', 'HanXRQChr03g0083901' => 'han', 'HanXRQChr03g0083921' => 'han', 'HanXRQChr03g0085331' => 'han', 'HanXRQChr03g0085361' => 'han', 'HanXRQChr03g0085411' => 'han', 'HanXRQChr03g0085421' => 'han', 'HanXRQChr03g0085431' => 'han', 'HanXRQChr08g0221991' => 'han', 'HanXRQChr11g0336061' => 'han', 'HanXRQChr11g0336411' => 'han', 'Haze_11234' => 'cav', 'Hma1.2p1_0549F.1_g177010' => 'hma', 'Hma1.2p1_0602F.1_g187630' => 'hma', 'Hund14876' => 'sun', 'Hund14879' => 'sun', 'Lalb_Chr06g0160741' => 'lal', 'Lalb_Chr21g0304781' => 'lal', 'Lj3A726G19' => 'lonja', 'Lj3A726T23' => 'lonja', 'Lj3A726T24' => 'lonja', 'Lj3A726T25' => 'lonja', 'Lj3A727T17' => 'lonja', 'Lj3C726T0' => 'lonja', 'Lj3C726T2' => 'lonja', 'Lj3P725T35' => 'lonja', 'Lj3P727T10' => 'lonja', 'Lj3P727T12' => 'lonja', 'Lj3P727T14' => 'lonja', 'Lj5g0023109' => 'lja', 'Lj6P646T44' => 'lonja', 'Lsat_1_v5_gn_6_75760' => 'lsa', 'Lsat_1_v5_gn_6_75800' => 'lsa', 'Lsat_1_v5_gn_6_75900' => 'lsa', 'Lsat_1_v5_gn_6_76240' => 'lsa', 'Lsat_1_v5_gn_6_76441' => 'lsa', 'Lsat_1_v5_gn_6_76700' => 'lsa', 'Lsat_1_v5_gn_6_76760' => 'lsa', 'Manes.15G033100' => 'mes', 'Mapoly0004s0074' => 'mpo', 'Mapoly0004s0075' => 'mpo', 'Mapoly0004s0163' => 'mpo', 'Mapoly0004s0164' => 'mpo', 'Mapoly0021s0018' => 'mpo', 'Mapoly0041s0136' => 'mpo', 'Mapoly0041s0137' => 'mpo', 'Mapoly0041s0138' => 'mpo', 'Mapoly0041s0139' => 'mpo', 'Mapoly0041s0141' => 'mpo', 'Mapoly0041s0142' => 'mpo', 'Mapoly0041s0143' => 'mpo', 'Mapoly0041s0144' => 'mpo', 'Mapoly0041s0145' => 'mpo', 'Mapoly0047s0106' => 'mpo', 'Mapoly0047s0108' => 'mpo', 'Mapoly0050s0051' => 'mpo', 'Mapoly0050s0052' => 'mpo', 'Mapoly0050s0053' => 'mpo', 'Mapoly0058s0013' => 'mpo', 'Mapoly0091s0078' => 'mpo', 'Mapoly0091s0079' => 'mpo', 'Mapoly0091s0080' => 'mpo', 'Mapoly0091s0081' => 'mpo', 'Mapoly0278s0004' => 'mpo', 'Mapoly0278s0005' => 'mpo', 'Mapoly0278s0006' => 'mpo', 'MBI11_g30648_MAGBIO' => 'mbi', 'MCO03G194' => 'mco', 'MCO03G590' => 'mco', 'MCO07G312' => 'mco', 'MCO10G318' => 'mco', 'MCO12G244' => 'mco', 'MCO13G148' => 'mco', 'MCO13G194' => 'mco', 'MCO16G238' => 'mco', 'MD06G1134100' => 'mdo', 'MD13G1200100' => 'mdo', 'MD13G1200300' => 'mdo', 'MD13G1200600' => 'mdo', 'MD14G1150400' => 'mdo', 'MD16G1200000' => 'mdo', 'Medtr1g102570' => 'mtr', 'Medtr1g102780' => 'mtr', 'Medtr1g102800' => 'mtr', 'Medtr1g102810' => 'mtr', 'Medtr1g102830' => 'mtr', 'MELO3C006499.2' => 'cme', 'Migut.G00385' => 'egut', 'MSTRG.4063' => 'ama', 'Nitab4.5_0000090g0260' => 'nta', 'Nitab4.5_0000977g0030' => 'nta', 'Nitab4.5_0002541g0040' => 'nta', 'Nitab4.5_0007068g0040' => 'nta', 'Nn005s41408' => 'nnu', 'Nn005s41410' => 'nnu', 'Oeu010310.1' => 'oeu', 'Oeu010311.1' => 'oeu', 'Oeu043472.1' => 'oeu', 'Os01g0246400' => 'osa', 'Os04g0267950' => 'osa', 'Os07g0178700' => 'osa', 'Os07g0178800' => 'osa', 'Peaxi162Scf00316g00046' => 'pax', 'Peaxi162Scf00316g00049' => 'pax', 'Peaxi162Scf00316g00059' => 'pax', 'Peaxi162Scf00316g00328' => 'pax', 'Peaxi162Scf00316g00329' => 'pax', 'Peaxi162Scf00316g00411' => 'pax', 'Peaxi162Scf00316g00521' => 'pax', 'Peaxi162Scf00492g00068' => 'pax', 'Peaxi162Scf35631g00002' => 'pax', 'PGR142G3720' => 'pgr', 'PGSC0003DMG400006442' => 'stu', 'Phvul.007G062000' => 'pvu', 'Potri.008G157750' => 'ptr', 'Potri.008G157900' => 'ptr', 'Potri.008G158000' => 'ptr', 'Potri.008G158200' => 'ptr', 'Pp3c11_7280' => 'ppa', 'Pp3c11_7980' => 'ppa', 'Pp3c12_19450' => 'ppa', 'Pp3c14_1480' => 'ppa', 'Pp3c14_1501' => 'ppa', 'Pp3c16_4900' => 'ppa', 'Pp3c16_5010' => 'ppa', 'Pp3c16_5060' => 'ppa', 'Pp3c19_18250' => 'ppa', 'Pp3c23_8530' => 'ppa', 'Pp3c23_8550' => 'ppa', 'Pp3c24_9670' => 'ppa', 'Pp3c2_21390' => 'ppa', 'Pp3c2_31380' => 'ppa', 'Pp3c3_16620' => 'ppa', 'Pp3c3_8090' => 'ppa', 'Pp3c3_8110' => 'ppa', 'Pp3c3_8130' => 'ppa', 'Pp3c3_8150' => 'ppa', 'Pp3c4_14320' => 'ppa', 'Pp3c6_2560' => 'ppa', 'Pp3c9_16700' => 'ppa', 'PRCOL_00000234' => 'pco', 'PRCOL_00000235' => 'pco', 'PRCOL_00000777' => 'pco', 'PRCOL_00002344' => 'pco', 'PRCOL_00002372' => 'pco', 'PRCOL_00006120' => 'pco', 'Prupe.1G021400' => 'ppe', 'Prupe.1G021500' => 'ppe', 'Prupe.1G021600' => 'ppe', 'Prupe.1G021700' => 'ppe', 'Prupe.1G021800' => 'ppe', 'Prupe.5G145100' => 'ppe', 'Psat6g204040' => 'psa', 'Psat6g204800' => 'psa', 'Psat6g204920' => 'psa', 'Psat6g204960' => 'psa', 'Psat6g205080' => 'psa', 'PSO017G0271' => 'pso', 'PSO017G1276' => 'pso', 'PSO017G1429' => 'pso', 'PSO017G1861' => 'pso', 'PSO017G2787' => 'pso', 'PSO017G4466' => 'pso', 'PSO017G5118' => 'pso', 'PSO017G5420' => 'pso', 'PSO063G3678' => 'pso', 'PSO210G0546' => 'pso', 'PSO317G0001' => 'pso', 'PSO357G0512' => 'pso', 'PSO478G2682' => 'pso', 'PSO647G0001' => 'pso', 'PSO675G0001' => 'pso', 'PSO675G2699' => 'pso', 'PSO675G2849' => 'pso', 'PSO675G4991' => 'pso', 'PSO689G0001' => 'pso', 'QL06p000916' => 'qlo', 'QL06p000921' => 'qlo', 'QL06p001398' => 'qlo', 'QL06p001407' => 'qlo', 'QL06p002031' => 'qlo', 'RcHm_v2.0_Chr4g0387791' => 'rch', 'RcHm_v2.0_Chr4g0387801' => 'rch', 'RcHm_v2.0_Chr6g0286501' => 'rch', 'RcHm_v2.0_Chr6g0286511' => 'rch', 'RcHm_v2.0_Chr6g0286521' => 'rch', 'RcHm_v2.0_Chr6g0286531' => 'rch', 'RcHm_v2.0_Chr7g0189141' => 'rch', 'Rhsim02G0028700' => 'rsi', 'Rhsim02G0028800' => 'rsi', 'Rhsim02G0028900' => 'rsi', 'Rhsim02G0029000' => 'rsi', 'Rhsim02G0029100' => 'rsi', 'Rhsim02G0029200' => 'rsi', 'Rhsim02G0029300' => 'rsi', 'Rhsim02G0029400' => 'rsi', 'Rhsim02G0029500' => 'rsi', 'Rhsim02G0029600' => 'rsi', 'RhsimUnG0024000' => 'rsi', 'RhsimUnG0024100' => 'rsi', 'RhsimUnG0024200' => 'rsi', 'RhsimUnG0024300' => 'rsi', 'RhsimUnG0024400' => 'rsi', 'RhsimUnG0024500' => 'rsi', 'RhsimUnG0024700' => 'rsi', 'RhsimUnG0024800' => 'rsi', 'RhsimUnG0024900' => 'rsi', 'RhsimUnG0025100' => 'rsi', 'Sabra08G0120200' => 'sbr', 'Sabra08G0120300' => 'sbr', 'Sabra08G0120500' => 'sbr', 'Sabra08G0120600' => 'sbr', 'Sabra10G0158900' => 'sbr', 'SalBow2G3492' => 'sbo', 'Sc13g0004760' => 'sci', 'Sc13g0004770' => 'sci', 'Sed0003417' => 'sed', 'Sed0019750' => 'sed', 'SEGI_03419' => 'sgi', 'SEGI_05907' => 'sgi', 'SEGI_10682' => 'sgi', 'SEGI_13528' => 'sgi', 'SEGI_16081' => 'sgi', 'SEGI_19370' => 'sgi', 'SEGI_21015' => 'sgi', 'SEGI_21944' => 'sgi', 'SEGI_32906' => 'sgi', 'SEGI_33093' => 'sgi', 'SEGI_36110' => 'sgi', 'SEGI_40397' => 'sgi', 'SGA_v2.0_scaffold191G40426' => 'sas', 'SGA_v2.0_scaffold353G49717' => 'sas', 'SGA_v2.0_scaffold50G18550' => 'sas', 'SMO119G0173' => 'smo', 'SMO172G0002' => 'smo', 'Solyc09g082690.3' => 'sly', 'Solyc09g082700.2' => 'sly', 'Sopen09g031550' => 'spe', 'Sopen09g031560' => 'spe', 'Sp3g20540' => 'spa', 'Sp7g07580' => 'spa', 'TAR134G0002' => 'tar', 'TAR236G0001' => 'tar', 'TAR365G0892' => 'tar', 'TAR636G0166' => 'tar', 'TAR636G0646' => 'tar', 'TAR636G0869' => 'tar', 'TAR636G1317' => 'tar', 'TAR636G1744' => 'tar', 'TAR636G3358' => 'tar', 'TAR636G3436' => 'tar', 'THA.LOC104803047' => 'tha', 'Thecc.04G238900' => 'tca', 'Thhalv10021557m.g' => 'esa', 'Thhalv10026318m.g' => 'esa', 'Thhalv10026335m.g' => 'esa', 'TPR.G17433' => 'tpr', 'TPR.G18915' => 'tpr', 'TPR.G26125' => 'tpr', 'TWI09G0677' => 'twi', 'TWI73G0287' => 'twi', 'unitig_748.g8326' => 'ugi', 'vmacro15370' => 'vma', 'vmacro15371' => 'vma', 'vmacro15372' => 'vma', 'vmacro15373' => 'vma', 'vmacro15374' => 'vma', 'VMungo0720G2826' => 'vmu', 'Zm00001eb116960' => 'zma', 'Zm00001eb301260' => 'zma', 'Zm00001eb301270' => 'zma' ), 'gf_id' => 'HOM05D001460', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001460' ), 'data_identifier' => 'HOM05D001460', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001460', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '433', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p22980' => 'bna', 'A01p32340' => 'bna', 'A03p42970' => 'bna', 'A05p25880' => 'bna', 'Aa31LG8G9320' => 'aar', 'Aa31LG8G9330' => 'aar', 'Aa31LG8G9340' => 'aar', 'Aa31sc221G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1034' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1528' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.829' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2222' => 'aag', 'Ah.12g058830' => 'amhyb', 'Ah.12g058840' => 'amhyb', 'AL3G37160' => 'aly', 'AL7G41310' => 'aly', 'Aqoxy5G00395' => 'aox', 'Aqoxy5G00396' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0C8NZA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5185HY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JZ1PRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MD3LS0' => 'arhy', 'AT3G22840' => 'ath', 'AT4G14690' => 'ath', 'ATR0665G054' => 'atr', 'Atru.chr4.2344' => 'acertr', 'Atru.chr4.2346' => 'acertr', 'Atru.chr4.2347' => 'acertr', 'Atru.chr4.2348' => 'acertr', 'Atru.chr4.2355' => 'acertr', 'Atru.chr4.2356' => 'acertr', 'Atru.chr4.2358' => 'acertr', 'Atru.chr4.2359' => 'acertr', 'Atru.chr4.2360' => 'acertr', 'Atru.chr4.2361' => 'acertr', 'AUR62030476' => 'cqu', 'AUR62030478' => 'cqu', 'AUR62030819' => 'cqu', 'AUR62030820' => 'cqu', 'BcaB03g14648' => 'bca', 'BcaB04g20492' => 'bca', 'BcaB06g26399' => 'bca', 'BcaC01g03416' => 'bca', 'BcaC01g03419' => 'bca', 'BcaC01g03421' => 'bca', 'BcaC01g03424' => 'bca', 'BcaC05g28012' => 'bca', 'BcaC09g49212' => 'bca', 'BcaC09g50140' => 'bca', 'BcaNung00346' => 'bca', 'BolC1t02785H' => 'bol', 'BolC1t04095H' => 'bol', 'BolC3t17545H' => 'bol', 'BolC5t32769H' => 'bol', 'BraA01t02211Z' => 'bra', 'BraA01t03359Z' => 'bra', 'BraA03t13441Z' => 'bra', 'BraA05t21476Z' => 'bra', 'C01p28420' => 'bna', 'C01p41350' => 'bna', 'C03p52750' => 'bna', 'C03p52780' => 'bna', 'C05p40270' => 'bna', 'CAN.G1437.9' => 'can', 'CANSAT78G0035' => 'cansat', 'CANSAT78G1036' => 'cansat', 'CANSAT78G2272' => 'cansat', 'CANSAT78G2478' => 'cansat', 'CARHR098700' => 'chi', 'CARHR221120' => 'chi', 'CARHR221150' => 'chi', 'Carub.0003s2297' => 'cru', 'Carub.0007s2749' => 'cru', 'Carub.0007s2750' => 'cru', 'Carub.0007s2751' => 'cru', 'Ca_10849_v3' => 'car', 'Cc03_g04300' => 'ccan', 'CDE02G3648' => 'cde', 'CDE05G0060' => 'cde', 'CDE05G0692' => 'cde', 'CDE05G2285' => 'cde', 'CDE05G2884' => 'cde', 'CDE05G3072' => 'cde', 'Cfa008439' => 'cfa', 'Cfa008441' => 'cfa', 'Cfa008443' => 'cfa', 'Cfa008448' => 'cfa', 'Ciclev10005974m.g' => 'ccl', 'Ciclev10006006m.g' => 'ccl', 'Ciclev10006775m.g' => 'ccl', 'CiPaw.02G120400' => 'cil', 'CiPaw.02G120500' => 'cil', 'CiPaw.02G120600' => 'cil', 'ClCG05G004850' => 'cla', 'COL.COLO4_21566' => 'col', 'Cpa.g.sc44.124' => 'cpa', 'Cre07.g320400' => 'cre', 'Cre07.g320450' => 'cre', 'Cre08.g384650' => 'cre', 'Cre09.g393173' => 'cre', 'Cre09.g394325' => 'cre', 'Cre14.g626750' => 'cre', 'Cre16.g679250' => 'cre', 'CsaV3_3G012890' => 'csa', 'CSS0010865' => 'camsi', 'CSS0044338' => 'camsi', 'DCAR_002366' => 'dca', 'DCAR_030687' => 'dca', 'DCAR_030688' => 'dca', 'Dinv14047' => 'din', 'Dinv14048' => 'din', 'Duzib151G0105' => 'dzi', 'Duzib151G0114' => 'dzi', 'Duzib212G1029' => 'dzi', 'ECA232G3536' => 'eca', 'ECA240G0786' => 'eca', 'ECA240G1802' => 'eca', 'ECA240G3760' => 'eca', 'ECA240G3920' => 'eca', 'EL10Ac5g12536' => 'bvu', 'EL10Ac5g12537' => 'bvu', 'EL10Ac5g12538' => 'bvu', 'Eucgr.B01004' => 'egr', 'Eucgr.B01006' => 'egr', 'Eucgr.B01007' => 'egr', 'Eucgr.B01008' => 'egr', 'Eucgr.B01895' => 'egr', 'Eucgr.B01896' => 'egr', 'FAN04G1456' => 'fan', 'FAN08G1769' => 'fan', 'FAN08G2160' => 'fan', 'FAN13G2403' => 'fan', 'FAN13G3303' => 'fan', 'FAN15G2435' => 'fan', 'FAN17G0672' => 'fan', 'FAN17G2441' => 'fan', 'FAN18G1024' => 'fan', 'FAN22G1458' => 'fan', 'FAN24G0037' => 'fan', 'FAN24G0429' => 'fan', 'FAN24G2387' => 'fan', 'FAN27G2746' => 'fan', 'FvH4_2g20400' => 'fve', 'FvH4_2g20420' => 'fve', 'FvH4_2g20430' => 'fve', 'FvH4_4g01270' => 'fve', 'FvH4_4g01290' => 'fve', 'FvH4_4g01300' => 'fve', 'FvH4_4g01310' => 'fve', 'FvH4_4g01330' => 'fve', 'FvH4_5g09070' => 'fve', 'Glyma.10G243800' => 'gma', 'Glyma.20G150600' => 'gma', 'Gohir.A09G219200' => 'ghi', 'Gohir.A09G219300' => 'ghi', 'Gohir.D09G221400' => 'ghi', 'Gohir.D09G221500' => 'ghi', 'Gorai.006G242600' => 'gra', 'Gorai.006G242700' => 'gra', 'GSVIVG01018044001' => 'vvi', 'HanXRQChr03g0083821' => 'han', 'HanXRQChr03g0083841' => 'han', 'HanXRQChr03g0083881' => 'han', 'HanXRQChr03g0083901' => 'han', 'HanXRQChr03g0083921' => 'han', 'HanXRQChr03g0085331' => 'han', 'HanXRQChr03g0085361' => 'han', 'HanXRQChr03g0085411' => 'han', 'HanXRQChr03g0085421' => 'han', 'HanXRQChr03g0085431' => 'han', 'HanXRQChr08g0221991' => 'han', 'HanXRQChr11g0336061' => 'han', 'HanXRQChr11g0336411' => 'han', 'Haze_11234' => 'cav', 'Hma1.2p1_0549F.1_g177010' => 'hma', 'Hma1.2p1_0602F.1_g187630' => 'hma', 'Hund14876' => 'sun', 'Hund14879' => 'sun', 'Lalb_Chr06g0160741' => 'lal', 'Lalb_Chr21g0304781' => 'lal', 'Lj3A726G19' => 'lonja', 'Lj3A726T23' => 'lonja', 'Lj3A726T24' => 'lonja', 'Lj3A726T25' => 'lonja', 'Lj3A727T17' => 'lonja', 'Lj3C726T0' => 'lonja', 'Lj3C726T2' => 'lonja', 'Lj3P725T35' => 'lonja', 'Lj3P727T10' => 'lonja', 'Lj3P727T12' => 'lonja', 'Lj3P727T14' => 'lonja', 'Lj5g0023109' => 'lja', 'Lj6P646T44' => 'lonja', 'Lsat_1_v5_gn_6_75760' => 'lsa', 'Lsat_1_v5_gn_6_75800' => 'lsa', 'Lsat_1_v5_gn_6_75900' => 'lsa', 'Lsat_1_v5_gn_6_76240' => 'lsa', 'Lsat_1_v5_gn_6_76441' => 'lsa', 'Lsat_1_v5_gn_6_76700' => 'lsa', 'Lsat_1_v5_gn_6_76760' => 'lsa', 'Manes.15G033100' => 'mes', 'Mapoly0004s0074' => 'mpo', 'Mapoly0004s0075' => 'mpo', 'Mapoly0004s0163' => 'mpo', 'Mapoly0004s0164' => 'mpo', 'Mapoly0021s0018' => 'mpo', 'Mapoly0041s0136' => 'mpo', 'Mapoly0041s0137' => 'mpo', 'Mapoly0041s0138' => 'mpo', 'Mapoly0041s0139' => 'mpo', 'Mapoly0041s0141' => 'mpo', 'Mapoly0041s0142' => 'mpo', 'Mapoly0041s0143' => 'mpo', 'Mapoly0041s0144' => 'mpo', 'Mapoly0041s0145' => 'mpo', 'Mapoly0047s0106' => 'mpo', 'Mapoly0047s0108' => 'mpo', 'Mapoly0050s0051' => 'mpo', 'Mapoly0050s0052' => 'mpo', 'Mapoly0050s0053' => 'mpo', 'Mapoly0058s0013' => 'mpo', 'Mapoly0091s0078' => 'mpo', 'Mapoly0091s0079' => 'mpo', 'Mapoly0091s0080' => 'mpo', 'Mapoly0091s0081' => 'mpo', 'Mapoly0278s0004' => 'mpo', 'Mapoly0278s0005' => 'mpo', 'Mapoly0278s0006' => 'mpo', 'MBI11_g30648_MAGBIO' => 'mbi', 'MCO03G194' => 'mco', 'MCO03G590' => 'mco', 'MCO07G312' => 'mco', 'MCO10G318' => 'mco', 'MCO12G244' => 'mco', 'MCO13G148' => 'mco', 'MCO13G194' => 'mco', 'MCO16G238' => 'mco', 'MD06G1134100' => 'mdo', 'MD13G1200100' => 'mdo', 'MD13G1200300' => 'mdo', 'MD13G1200600' => 'mdo', 'MD14G1150400' => 'mdo', 'MD16G1200000' => 'mdo', 'Medtr1g102570' => 'mtr', 'Medtr1g102780' => 'mtr', 'Medtr1g102800' => 'mtr', 'Medtr1g102810' => 'mtr', 'Medtr1g102830' => 'mtr', 'MELO3C006499.2' => 'cme', 'Migut.G00385' => 'egut', 'MSTRG.4063' => 'ama', 'Nitab4.5_0000090g0260' => 'nta', 'Nitab4.5_0000977g0030' => 'nta', 'Nitab4.5_0002541g0040' => 'nta', 'Nitab4.5_0007068g0040' => 'nta', 'Nn005s41408' => 'nnu', 'Nn005s41410' => 'nnu', 'Oeu010310.1' => 'oeu', 'Oeu010311.1' => 'oeu', 'Oeu043472.1' => 'oeu', 'Os01g0246400' => 'osa', 'Os04g0267950' => 'osa', 'Os07g0178700' => 'osa', 'Os07g0178800' => 'osa', 'Peaxi162Scf00316g00046' => 'pax', 'Peaxi162Scf00316g00049' => 'pax', 'Peaxi162Scf00316g00059' => 'pax', 'Peaxi162Scf00316g00328' => 'pax', 'Peaxi162Scf00316g00329' => 'pax', 'Peaxi162Scf00316g00411' => 'pax', 'Peaxi162Scf00316g00521' => 'pax', 'Peaxi162Scf00492g00068' => 'pax', 'Peaxi162Scf35631g00002' => 'pax', 'PGR142G3720' => 'pgr', 'PGSC0003DMG400006442' => 'stu', 'Phvul.007G062000' => 'pvu', 'Potri.008G157750' => 'ptr', 'Potri.008G157900' => 'ptr', 'Potri.008G158000' => 'ptr', 'Potri.008G158200' => 'ptr', 'Pp3c11_7280' => 'ppa', 'Pp3c11_7980' => 'ppa', 'Pp3c12_19450' => 'ppa', 'Pp3c14_1480' => 'ppa', 'Pp3c14_1501' => 'ppa', 'Pp3c16_4900' => 'ppa', 'Pp3c16_5010' => 'ppa', 'Pp3c16_5060' => 'ppa', 'Pp3c19_18250' => 'ppa', 'Pp3c23_8530' => 'ppa', 'Pp3c23_8550' => 'ppa', 'Pp3c24_9670' => 'ppa', 'Pp3c2_21390' => 'ppa', 'Pp3c2_31380' => 'ppa', 'Pp3c3_16620' => 'ppa', 'Pp3c3_8090' => 'ppa', 'Pp3c3_8110' => 'ppa', 'Pp3c3_8130' => 'ppa', 'Pp3c3_8150' => 'ppa', 'Pp3c4_14320' => 'ppa', 'Pp3c6_2560' => 'ppa', 'Pp3c9_16700' => 'ppa', 'PRCOL_00000234' => 'pco', 'PRCOL_00000235' => 'pco', 'PRCOL_00000777' => 'pco', 'PRCOL_00002344' => 'pco', 'PRCOL_00002372' => 'pco', 'PRCOL_00006120' => 'pco', 'Prupe.1G021400' => 'ppe', 'Prupe.1G021500' => 'ppe', 'Prupe.1G021600' => 'ppe', 'Prupe.1G021700' => 'ppe', 'Prupe.1G021800' => 'ppe', 'Prupe.5G145100' => 'ppe', 'Psat6g204040' => 'psa', 'Psat6g204800' => 'psa', 'Psat6g204920' => 'psa', 'Psat6g204960' => 'psa', 'Psat6g205080' => 'psa', 'PSO017G0271' => 'pso', 'PSO017G1276' => 'pso', 'PSO017G1429' => 'pso', 'PSO017G1861' => 'pso', 'PSO017G2787' => 'pso', 'PSO017G4466' => 'pso', 'PSO017G5118' => 'pso', 'PSO017G5420' => 'pso', 'PSO063G3678' => 'pso', 'PSO210G0546' => 'pso', 'PSO317G0001' => 'pso', 'PSO357G0512' => 'pso', 'PSO478G2682' => 'pso', 'PSO647G0001' => 'pso', 'PSO675G0001' => 'pso', 'PSO675G2699' => 'pso', 'PSO675G2849' => 'pso', 'PSO675G4991' => 'pso', 'PSO689G0001' => 'pso', 'QL06p000916' => 'qlo', 'QL06p000921' => 'qlo', 'QL06p001398' => 'qlo', 'QL06p001407' => 'qlo', 'QL06p002031' => 'qlo', 'RcHm_v2.0_Chr4g0387791' => 'rch', 'RcHm_v2.0_Chr4g0387801' => 'rch', 'RcHm_v2.0_Chr6g0286501' => 'rch', 'RcHm_v2.0_Chr6g0286511' => 'rch', 'RcHm_v2.0_Chr6g0286521' => 'rch', 'RcHm_v2.0_Chr6g0286531' => 'rch', 'RcHm_v2.0_Chr7g0189141' => 'rch', 'Rhsim02G0028700' => 'rsi', 'Rhsim02G0028800' => 'rsi', 'Rhsim02G0028900' => 'rsi', 'Rhsim02G0029000' => 'rsi', 'Rhsim02G0029100' => 'rsi', 'Rhsim02G0029200' => 'rsi', 'Rhsim02G0029300' => 'rsi', 'Rhsim02G0029400' => 'rsi', 'Rhsim02G0029500' => 'rsi', 'Rhsim02G0029600' => 'rsi', 'RhsimUnG0024000' => 'rsi', 'RhsimUnG0024100' => 'rsi', 'RhsimUnG0024200' => 'rsi', 'RhsimUnG0024300' => 'rsi', 'RhsimUnG0024400' => 'rsi', 'RhsimUnG0024500' => 'rsi', 'RhsimUnG0024700' => 'rsi', 'RhsimUnG0024800' => 'rsi', 'RhsimUnG0024900' => 'rsi', 'RhsimUnG0025100' => 'rsi', 'Sabra08G0120200' => 'sbr', 'Sabra08G0120300' => 'sbr', 'Sabra08G0120500' => 'sbr', 'Sabra08G0120600' => 'sbr', 'Sabra10G0158900' => 'sbr', 'SalBow2G3492' => 'sbo', 'Sc13g0004760' => 'sci', 'Sc13g0004770' => 'sci', 'Sed0003417' => 'sed', 'Sed0019750' => 'sed', 'SEGI_03419' => 'sgi', 'SEGI_05907' => 'sgi', 'SEGI_10682' => 'sgi', 'SEGI_13528' => 'sgi', 'SEGI_16081' => 'sgi', 'SEGI_19370' => 'sgi', 'SEGI_21015' => 'sgi', 'SEGI_21944' => 'sgi', 'SEGI_32906' => 'sgi', 'SEGI_33093' => 'sgi', 'SEGI_36110' => 'sgi', 'SEGI_40397' => 'sgi', 'SGA_v2.0_scaffold191G40426' => 'sas', 'SGA_v2.0_scaffold353G49717' => 'sas', 'SGA_v2.0_scaffold50G18550' => 'sas', 'SMO119G0173' => 'smo', 'SMO172G0002' => 'smo', 'Solyc09g082690.3' => 'sly', 'Solyc09g082700.2' => 'sly', 'Sopen09g031550' => 'spe', 'Sopen09g031560' => 'spe', 'Sp3g20540' => 'spa', 'Sp7g07580' => 'spa', 'TAR134G0002' => 'tar', 'TAR236G0001' => 'tar', 'TAR365G0892' => 'tar', 'TAR636G0166' => 'tar', 'TAR636G0646' => 'tar', 'TAR636G0869' => 'tar', 'TAR636G1317' => 'tar', 'TAR636G1744' => 'tar', 'TAR636G3358' => 'tar', 'TAR636G3436' => 'tar', 'THA.LOC104803047' => 'tha', 'Thecc.04G238900' => 'tca', 'Thhalv10021557m.g' => 'esa', 'Thhalv10026318m.g' => 'esa', 'Thhalv10026335m.g' => 'esa', 'TPR.G17433' => 'tpr', 'TPR.G18915' => 'tpr', 'TPR.G26125' => 'tpr', 'TWI09G0677' => 'twi', 'TWI73G0287' => 'twi', 'unitig_748.g8326' => 'ugi', 'vmacro15370' => 'vma', 'vmacro15371' => 'vma', 'vmacro15372' => 'vma', 'vmacro15373' => 'vma', 'vmacro15374' => 'vma', 'VMungo0720G2826' => 'vmu', 'Zm00001eb116960' => 'zma', 'Zm00001eb301260' => 'zma', 'Zm00001eb301270' => 'zma' ) $gf_id = 'HOM05D001460' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001460' ) $data_identifier = 'HOM05D001460' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 4, 'aag' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 2, 'aox' => (int) 2, 'arhy' => (int) 4, 'ath' => (int) 2, 'atr' => (int) 1, 'acertr' => (int) 10, 'cqu' => (int) 4, 'bca' => (int) 11, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 1, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 1, 'ccan' => (int) 1, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 1, 'col' => (int) 1, 'cpa' => (int) 1, 'cre' => (int) 7, 'csa' => (int) 1, 'camsi' => (int) 2, 'dca' => (int) 3, 'din' => (int) 2, 'dzi' => (int) 3, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 14, 'fve' => (int) 9, 'gma' => (int) 2, 'ghi' => (int) 4, 'gra' => (int) 2, 'vvi' => (int) 1, 'han' => (int) 13, 'cav' => (int) 1, 'hma' => (int) 2, 'sun' => (int) 2, 'lal' => (int) 2, 'lonja' => (int) 12, 'lja' => (int) 1, 'lsa' => (int) 7, 'mes' => (int) 1, 'mpo' => (int) 27, 'mbi' => (int) 1, 'mco' => (int) 8, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 1, 'egut' => (int) 1, 'ama' => (int) 1, 'nta' => (int) 4, 'nnu' => (int) 2, 'oeu' => (int) 3, 'osa' => (int) 4, 'pax' => (int) 9, 'pgr' => (int) 1, 'stu' => (int) 1, 'pvu' => (int) 1, 'ptr' => (int) 4, 'ppa' => (int) 22, 'pco' => (int) 6, 'ppe' => (int) 6, 'psa' => (int) 5, 'pso' => (int) 19, 'qlo' => (int) 5, 'rch' => (int) 7, 'rsi' => (int) 20, 'sbr' => (int) 5, 'sbo' => (int) 1, 'sci' => (int) 2, 'sed' => (int) 2, 'sgi' => (int) 12, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 2, 'tar' => (int) 10, 'tha' => (int) 1, 'tca' => (int) 1, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 2, 'ugi' => (int) 1, 'vma' => (int) 5, 'vmu' => (int) 1, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb301270' $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' => 'HOM05D001460', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '433', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p22980' => 'bna', 'A01p32340' => 'bna', 'A03p42970' => 'bna', 'A05p25880' => 'bna', 'Aa31LG8G9320' => 'aar', 'Aa31LG8G9330' => 'aar', 'Aa31LG8G9340' => 'aar', 'Aa31sc221G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1034' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1528' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.829' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2222' => 'aag', 'Ah.12g058830' => 'amhyb', 'Ah.12g058840' => 'amhyb', 'AL3G37160' => 'aly', 'AL7G41310' => 'aly', 'Aqoxy5G00395' => 'aox', 'Aqoxy5G00396' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0C8NZA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5185HY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JZ1PRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MD3LS0' => 'arhy', 'AT3G22840' => 'ath', 'AT4G14690' => 'ath', 'ATR0665G054' => 'atr', 'Atru.chr4.2344' => 'acertr', 'Atru.chr4.2346' => 'acertr', 'Atru.chr4.2347' => 'acertr', 'Atru.chr4.2348' => 'acertr', 'Atru.chr4.2355' => 'acertr', 'Atru.chr4.2356' => 'acertr', 'Atru.chr4.2358' => 'acertr', 'Atru.chr4.2359' => 'acertr', 'Atru.chr4.2360' => 'acertr', 'Atru.chr4.2361' => 'acertr', 'AUR62030476' => 'cqu', 'AUR62030478' => 'cqu', 'AUR62030819' => 'cqu', 'AUR62030820' => 'cqu', 'BcaB03g14648' => 'bca', 'BcaB04g20492' => 'bca', 'BcaB06g26399' => 'bca', 'BcaC01g03416' => 'bca', 'BcaC01g03419' => 'bca', 'BcaC01g03421' => 'bca', 'BcaC01g03424' => 'bca', 'BcaC05g28012' => 'bca', 'BcaC09g49212' => 'bca', 'BcaC09g50140' => 'bca', 'BcaNung00346' => 'bca', 'BolC1t02785H' => 'bol', 'BolC1t04095H' => 'bol', 'BolC3t17545H' => 'bol', 'BolC5t32769H' => 'bol', 'BraA01t02211Z' => 'bra', 'BraA01t03359Z' => 'bra', 'BraA03t13441Z' => 'bra', 'BraA05t21476Z' => 'bra', 'C01p28420' => 'bna', 'C01p41350' => 'bna', 'C03p52750' => 'bna', 'C03p52780' => 'bna', 'C05p40270' => 'bna', 'CAN.G1437.9' => 'can', 'CANSAT78G0035' => 'cansat', 'CANSAT78G1036' => 'cansat', 'CANSAT78G2272' => 'cansat', 'CANSAT78G2478' => 'cansat', 'CARHR098700' => 'chi', 'CARHR221120' => 'chi', 'CARHR221150' => 'chi', 'Carub.0003s2297' => 'cru', 'Carub.0007s2749' => 'cru', 'Carub.0007s2750' => 'cru', 'Carub.0007s2751' => 'cru', 'Ca_10849_v3' => 'car', 'Cc03_g04300' => 'ccan', 'CDE02G3648' => 'cde', 'CDE05G0060' => 'cde', 'CDE05G0692' => 'cde', 'CDE05G2285' => 'cde', 'CDE05G2884' => 'cde', 'CDE05G3072' => 'cde', 'Cfa008439' => 'cfa', 'Cfa008441' => 'cfa', 'Cfa008443' => 'cfa', 'Cfa008448' => 'cfa', 'Ciclev10005974m.g' => 'ccl', 'Ciclev10006006m.g' => 'ccl', 'Ciclev10006775m.g' => 'ccl', 'CiPaw.02G120400' => 'cil', 'CiPaw.02G120500' => 'cil', 'CiPaw.02G120600' => 'cil', 'ClCG05G004850' => 'cla', 'COL.COLO4_21566' => 'col', 'Cpa.g.sc44.124' => 'cpa', 'Cre07.g320400' => 'cre', 'Cre07.g320450' => 'cre', 'Cre08.g384650' => 'cre', 'Cre09.g393173' => 'cre', 'Cre09.g394325' => 'cre', 'Cre14.g626750' => 'cre', 'Cre16.g679250' => 'cre', 'CsaV3_3G012890' => 'csa', 'CSS0010865' => 'camsi', 'CSS0044338' => 'camsi', 'DCAR_002366' => 'dca', 'DCAR_030687' => 'dca', 'DCAR_030688' => 'dca', 'Dinv14047' => 'din', 'Dinv14048' => 'din', 'Duzib151G0105' => 'dzi', 'Duzib151G0114' => 'dzi', 'Duzib212G1029' => 'dzi', 'ECA232G3536' => 'eca', 'ECA240G0786' => 'eca', 'ECA240G1802' => 'eca', 'ECA240G3760' => 'eca', 'ECA240G3920' => 'eca', 'EL10Ac5g12536' => 'bvu', 'EL10Ac5g12537' => 'bvu', 'EL10Ac5g12538' => 'bvu', 'Eucgr.B01004' => 'egr', 'Eucgr.B01006' => 'egr', 'Eucgr.B01007' => 'egr', 'Eucgr.B01008' => 'egr', 'Eucgr.B01895' => 'egr', 'Eucgr.B01896' => 'egr', 'FAN04G1456' => 'fan', 'FAN08G1769' => 'fan', 'FAN08G2160' => 'fan', 'FAN13G2403' => 'fan', 'FAN13G3303' => 'fan', 'FAN15G2435' => 'fan', 'FAN17G0672' => 'fan', 'FAN17G2441' => 'fan', 'FAN18G1024' => 'fan', 'FAN22G1458' => 'fan', 'FAN24G0037' => 'fan', 'FAN24G0429' => 'fan', 'FAN24G2387' => 'fan', 'FAN27G2746' => 'fan', 'FvH4_2g20400' => 'fve', 'FvH4_2g20420' => 'fve', 'FvH4_2g20430' => 'fve', 'FvH4_4g01270' => 'fve', 'FvH4_4g01290' => 'fve', 'FvH4_4g01300' => 'fve', 'FvH4_4g01310' => 'fve', 'FvH4_4g01330' => 'fve', 'FvH4_5g09070' => 'fve', 'Glyma.10G243800' => 'gma', 'Glyma.20G150600' => 'gma', 'Gohir.A09G219200' => 'ghi', 'Gohir.A09G219300' => 'ghi', 'Gohir.D09G221400' => 'ghi', 'Gohir.D09G221500' => 'ghi', 'Gorai.006G242600' => 'gra', 'Gorai.006G242700' => 'gra', 'GSVIVG01018044001' => 'vvi', 'HanXRQChr03g0083821' => 'han', 'HanXRQChr03g0083841' => 'han', 'HanXRQChr03g0083881' => 'han', 'HanXRQChr03g0083901' => 'han', 'HanXRQChr03g0083921' => 'han', 'HanXRQChr03g0085331' => 'han', 'HanXRQChr03g0085361' => 'han', 'HanXRQChr03g0085411' => 'han', 'HanXRQChr03g0085421' => 'han', 'HanXRQChr03g0085431' => 'han', 'HanXRQChr08g0221991' => 'han', 'HanXRQChr11g0336061' => 'han', 'HanXRQChr11g0336411' => 'han', 'Haze_11234' => 'cav', 'Hma1.2p1_0549F.1_g177010' => 'hma', 'Hma1.2p1_0602F.1_g187630' => 'hma', 'Hund14876' => 'sun', 'Hund14879' => 'sun', 'Lalb_Chr06g0160741' => 'lal', 'Lalb_Chr21g0304781' => 'lal', 'Lj3A726G19' => 'lonja', 'Lj3A726T23' => 'lonja', 'Lj3A726T24' => 'lonja', 'Lj3A726T25' => 'lonja', 'Lj3A727T17' => 'lonja', 'Lj3C726T0' => 'lonja', 'Lj3C726T2' => 'lonja', 'Lj3P725T35' => 'lonja', 'Lj3P727T10' => 'lonja', 'Lj3P727T12' => 'lonja', 'Lj3P727T14' => 'lonja', 'Lj5g0023109' => 'lja', 'Lj6P646T44' => 'lonja', 'Lsat_1_v5_gn_6_75760' => 'lsa', 'Lsat_1_v5_gn_6_75800' => 'lsa', 'Lsat_1_v5_gn_6_75900' => 'lsa', 'Lsat_1_v5_gn_6_76240' => 'lsa', 'Lsat_1_v5_gn_6_76441' => 'lsa', 'Lsat_1_v5_gn_6_76700' => 'lsa', 'Lsat_1_v5_gn_6_76760' => 'lsa', 'Manes.15G033100' => 'mes', 'Mapoly0004s0074' => 'mpo', 'Mapoly0004s0075' => 'mpo', 'Mapoly0004s0163' => 'mpo', 'Mapoly0004s0164' => 'mpo', 'Mapoly0021s0018' => 'mpo', 'Mapoly0041s0136' => 'mpo', 'Mapoly0041s0137' => 'mpo', 'Mapoly0041s0138' => 'mpo', 'Mapoly0041s0139' => 'mpo', 'Mapoly0041s0141' => 'mpo', 'Mapoly0041s0142' => 'mpo', 'Mapoly0041s0143' => 'mpo', 'Mapoly0041s0144' => 'mpo', 'Mapoly0041s0145' => 'mpo', 'Mapoly0047s0106' => 'mpo', 'Mapoly0047s0108' => 'mpo', 'Mapoly0050s0051' => 'mpo', 'Mapoly0050s0052' => 'mpo', 'Mapoly0050s0053' => 'mpo', 'Mapoly0058s0013' => 'mpo', 'Mapoly0091s0078' => 'mpo', 'Mapoly0091s0079' => 'mpo', 'Mapoly0091s0080' => 'mpo', 'Mapoly0091s0081' => 'mpo', 'Mapoly0278s0004' => 'mpo', 'Mapoly0278s0005' => 'mpo', 'Mapoly0278s0006' => 'mpo', 'MBI11_g30648_MAGBIO' => 'mbi', 'MCO03G194' => 'mco', 'MCO03G590' => 'mco', 'MCO07G312' => 'mco', 'MCO10G318' => 'mco', 'MCO12G244' => 'mco', 'MCO13G148' => 'mco', 'MCO13G194' => 'mco', 'MCO16G238' => 'mco', 'MD06G1134100' => 'mdo', 'MD13G1200100' => 'mdo', 'MD13G1200300' => 'mdo', 'MD13G1200600' => 'mdo', 'MD14G1150400' => 'mdo', 'MD16G1200000' => 'mdo', 'Medtr1g102570' => 'mtr', 'Medtr1g102780' => 'mtr', 'Medtr1g102800' => 'mtr', 'Medtr1g102810' => 'mtr', 'Medtr1g102830' => 'mtr', 'MELO3C006499.2' => 'cme', 'Migut.G00385' => 'egut', 'MSTRG.4063' => 'ama', 'Nitab4.5_0000090g0260' => 'nta', 'Nitab4.5_0000977g0030' => 'nta', 'Nitab4.5_0002541g0040' => 'nta', 'Nitab4.5_0007068g0040' => 'nta', 'Nn005s41408' => 'nnu', 'Nn005s41410' => 'nnu', 'Oeu010310.1' => 'oeu', 'Oeu010311.1' => 'oeu', 'Oeu043472.1' => 'oeu', 'Os01g0246400' => 'osa', 'Os04g0267950' => 'osa', 'Os07g0178700' => 'osa', 'Os07g0178800' => 'osa', 'Peaxi162Scf00316g00046' => 'pax', 'Peaxi162Scf00316g00049' => 'pax', 'Peaxi162Scf00316g00059' => 'pax', 'Peaxi162Scf00316g00328' => 'pax', 'Peaxi162Scf00316g00329' => 'pax', 'Peaxi162Scf00316g00411' => 'pax', 'Peaxi162Scf00316g00521' => 'pax', 'Peaxi162Scf00492g00068' => 'pax', 'Peaxi162Scf35631g00002' => 'pax', 'PGR142G3720' => 'pgr', 'PGSC0003DMG400006442' => 'stu', 'Phvul.007G062000' => 'pvu', 'Potri.008G157750' => 'ptr', 'Potri.008G157900' => 'ptr', 'Potri.008G158000' => 'ptr', 'Potri.008G158200' => 'ptr', 'Pp3c11_7280' => 'ppa', 'Pp3c11_7980' => 'ppa', 'Pp3c12_19450' => 'ppa', 'Pp3c14_1480' => 'ppa', 'Pp3c14_1501' => 'ppa', 'Pp3c16_4900' => 'ppa', 'Pp3c16_5010' => 'ppa', 'Pp3c16_5060' => 'ppa', 'Pp3c19_18250' => 'ppa', 'Pp3c23_8530' => 'ppa', 'Pp3c23_8550' => 'ppa', 'Pp3c24_9670' => 'ppa', 'Pp3c2_21390' => 'ppa', 'Pp3c2_31380' => 'ppa', 'Pp3c3_16620' => 'ppa', 'Pp3c3_8090' => 'ppa', 'Pp3c3_8110' => 'ppa', 'Pp3c3_8130' => 'ppa', 'Pp3c3_8150' => 'ppa', 'Pp3c4_14320' => 'ppa', 'Pp3c6_2560' => 'ppa', 'Pp3c9_16700' => 'ppa', 'PRCOL_00000234' => 'pco', 'PRCOL_00000235' => 'pco', 'PRCOL_00000777' => 'pco', 'PRCOL_00002344' => 'pco', 'PRCOL_00002372' => 'pco', 'PRCOL_00006120' => 'pco', 'Prupe.1G021400' => 'ppe', 'Prupe.1G021500' => 'ppe', 'Prupe.1G021600' => 'ppe', 'Prupe.1G021700' => 'ppe', 'Prupe.1G021800' => 'ppe', 'Prupe.5G145100' => 'ppe', 'Psat6g204040' => 'psa', 'Psat6g204800' => 'psa', 'Psat6g204920' => 'psa', 'Psat6g204960' => 'psa', 'Psat6g205080' => 'psa', 'PSO017G0271' => 'pso', 'PSO017G1276' => 'pso', 'PSO017G1429' => 'pso', 'PSO017G1861' => 'pso', 'PSO017G2787' => 'pso', 'PSO017G4466' => 'pso', 'PSO017G5118' => 'pso', 'PSO017G5420' => 'pso', 'PSO063G3678' => 'pso', 'PSO210G0546' => 'pso', 'PSO317G0001' => 'pso', 'PSO357G0512' => 'pso', 'PSO478G2682' => 'pso', 'PSO647G0001' => 'pso', 'PSO675G0001' => 'pso', 'PSO675G2699' => 'pso', 'PSO675G2849' => 'pso', 'PSO675G4991' => 'pso', 'PSO689G0001' => 'pso', 'QL06p000916' => 'qlo', 'QL06p000921' => 'qlo', 'QL06p001398' => 'qlo', 'QL06p001407' => 'qlo', 'QL06p002031' => 'qlo', 'RcHm_v2.0_Chr4g0387791' => 'rch', 'RcHm_v2.0_Chr4g0387801' => 'rch', 'RcHm_v2.0_Chr6g0286501' => 'rch', 'RcHm_v2.0_Chr6g0286511' => 'rch', 'RcHm_v2.0_Chr6g0286521' => 'rch', 'RcHm_v2.0_Chr6g0286531' => 'rch', 'RcHm_v2.0_Chr7g0189141' => 'rch', 'Rhsim02G0028700' => 'rsi', 'Rhsim02G0028800' => 'rsi', 'Rhsim02G0028900' => 'rsi', 'Rhsim02G0029000' => 'rsi', 'Rhsim02G0029100' => 'rsi', 'Rhsim02G0029200' => 'rsi', 'Rhsim02G0029300' => 'rsi', 'Rhsim02G0029400' => 'rsi', 'Rhsim02G0029500' => 'rsi', 'Rhsim02G0029600' => 'rsi', 'RhsimUnG0024000' => 'rsi', 'RhsimUnG0024100' => 'rsi', 'RhsimUnG0024200' => 'rsi', 'RhsimUnG0024300' => 'rsi', 'RhsimUnG0024400' => 'rsi', 'RhsimUnG0024500' => 'rsi', 'RhsimUnG0024700' => 'rsi', 'RhsimUnG0024800' => 'rsi', 'RhsimUnG0024900' => 'rsi', 'RhsimUnG0025100' => 'rsi', 'Sabra08G0120200' => 'sbr', 'Sabra08G0120300' => 'sbr', 'Sabra08G0120500' => 'sbr', 'Sabra08G0120600' => 'sbr', 'Sabra10G0158900' => 'sbr', 'SalBow2G3492' => 'sbo', 'Sc13g0004760' => 'sci', 'Sc13g0004770' => 'sci', 'Sed0003417' => 'sed', 'Sed0019750' => 'sed', 'SEGI_03419' => 'sgi', 'SEGI_05907' => 'sgi', 'SEGI_10682' => 'sgi', 'SEGI_13528' => 'sgi', 'SEGI_16081' => 'sgi', 'SEGI_19370' => 'sgi', 'SEGI_21015' => 'sgi', 'SEGI_21944' => 'sgi', 'SEGI_32906' => 'sgi', 'SEGI_33093' => 'sgi', 'SEGI_36110' => 'sgi', 'SEGI_40397' => 'sgi', 'SGA_v2.0_scaffold191G40426' => 'sas', 'SGA_v2.0_scaffold353G49717' => 'sas', 'SGA_v2.0_scaffold50G18550' => 'sas', 'SMO119G0173' => 'smo', 'SMO172G0002' => 'smo', 'Solyc09g082690.3' => 'sly', 'Solyc09g082700.2' => 'sly', 'Sopen09g031550' => 'spe', 'Sopen09g031560' => 'spe', 'Sp3g20540' => 'spa', 'Sp7g07580' => 'spa', 'TAR134G0002' => 'tar', 'TAR236G0001' => 'tar', 'TAR365G0892' => 'tar', 'TAR636G0166' => 'tar', 'TAR636G0646' => 'tar', 'TAR636G0869' => 'tar', 'TAR636G1317' => 'tar', 'TAR636G1744' => 'tar', 'TAR636G3358' => 'tar', 'TAR636G3436' => 'tar', 'THA.LOC104803047' => 'tha', 'Thecc.04G238900' => 'tca', 'Thhalv10021557m.g' => 'esa', 'Thhalv10026318m.g' => 'esa', 'Thhalv10026335m.g' => 'esa', 'TPR.G17433' => 'tpr', 'TPR.G18915' => 'tpr', 'TPR.G26125' => 'tpr', 'TWI09G0677' => 'twi', 'TWI73G0287' => 'twi', 'unitig_748.g8326' => 'ugi', 'vmacro15370' => 'vma', 'vmacro15371' => 'vma', 'vmacro15372' => 'vma', 'vmacro15373' => 'vma', 'vmacro15374' => 'vma', 'VMungo0720G2826' => 'vmu', 'Zm00001eb116960' => 'zma', 'Zm00001eb301260' => 'zma', 'Zm00001eb301270' => 'zma' ), 'gf_id' => 'HOM05D001460', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001460' ), 'data_identifier' => 'HOM05D001460', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001460', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '433', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p22980' => 'bna', 'A01p32340' => 'bna', 'A03p42970' => 'bna', 'A05p25880' => 'bna', 'Aa31LG8G9320' => 'aar', 'Aa31LG8G9330' => 'aar', 'Aa31LG8G9340' => 'aar', 'Aa31sc221G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1034' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1528' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.829' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2222' => 'aag', 'Ah.12g058830' => 'amhyb', 'Ah.12g058840' => 'amhyb', 'AL3G37160' => 'aly', 'AL7G41310' => 'aly', 'Aqoxy5G00395' => 'aox', 'Aqoxy5G00396' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0C8NZA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5185HY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JZ1PRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MD3LS0' => 'arhy', 'AT3G22840' => 'ath', 'AT4G14690' => 'ath', 'ATR0665G054' => 'atr', 'Atru.chr4.2344' => 'acertr', 'Atru.chr4.2346' => 'acertr', 'Atru.chr4.2347' => 'acertr', 'Atru.chr4.2348' => 'acertr', 'Atru.chr4.2355' => 'acertr', 'Atru.chr4.2356' => 'acertr', 'Atru.chr4.2358' => 'acertr', 'Atru.chr4.2359' => 'acertr', 'Atru.chr4.2360' => 'acertr', 'Atru.chr4.2361' => 'acertr', 'AUR62030476' => 'cqu', 'AUR62030478' => 'cqu', 'AUR62030819' => 'cqu', 'AUR62030820' => 'cqu', 'BcaB03g14648' => 'bca', 'BcaB04g20492' => 'bca', 'BcaB06g26399' => 'bca', 'BcaC01g03416' => 'bca', 'BcaC01g03419' => 'bca', 'BcaC01g03421' => 'bca', 'BcaC01g03424' => 'bca', 'BcaC05g28012' => 'bca', 'BcaC09g49212' => 'bca', 'BcaC09g50140' => 'bca', 'BcaNung00346' => 'bca', 'BolC1t02785H' => 'bol', 'BolC1t04095H' => 'bol', 'BolC3t17545H' => 'bol', 'BolC5t32769H' => 'bol', 'BraA01t02211Z' => 'bra', 'BraA01t03359Z' => 'bra', 'BraA03t13441Z' => 'bra', 'BraA05t21476Z' => 'bra', 'C01p28420' => 'bna', 'C01p41350' => 'bna', 'C03p52750' => 'bna', 'C03p52780' => 'bna', 'C05p40270' => 'bna', 'CAN.G1437.9' => 'can', 'CANSAT78G0035' => 'cansat', 'CANSAT78G1036' => 'cansat', 'CANSAT78G2272' => 'cansat', 'CANSAT78G2478' => 'cansat', 'CARHR098700' => 'chi', 'CARHR221120' => 'chi', 'CARHR221150' => 'chi', 'Carub.0003s2297' => 'cru', 'Carub.0007s2749' => 'cru', 'Carub.0007s2750' => 'cru', 'Carub.0007s2751' => 'cru', 'Ca_10849_v3' => 'car', 'Cc03_g04300' => 'ccan', 'CDE02G3648' => 'cde', 'CDE05G0060' => 'cde', 'CDE05G0692' => 'cde', 'CDE05G2285' => 'cde', 'CDE05G2884' => 'cde', 'CDE05G3072' => 'cde', 'Cfa008439' => 'cfa', 'Cfa008441' => 'cfa', 'Cfa008443' => 'cfa', 'Cfa008448' => 'cfa', 'Ciclev10005974m.g' => 'ccl', 'Ciclev10006006m.g' => 'ccl', 'Ciclev10006775m.g' => 'ccl', 'CiPaw.02G120400' => 'cil', 'CiPaw.02G120500' => 'cil', 'CiPaw.02G120600' => 'cil', 'ClCG05G004850' => 'cla', 'COL.COLO4_21566' => 'col', 'Cpa.g.sc44.124' => 'cpa', 'Cre07.g320400' => 'cre', 'Cre07.g320450' => 'cre', 'Cre08.g384650' => 'cre', 'Cre09.g393173' => 'cre', 'Cre09.g394325' => 'cre', 'Cre14.g626750' => 'cre', 'Cre16.g679250' => 'cre', 'CsaV3_3G012890' => 'csa', 'CSS0010865' => 'camsi', 'CSS0044338' => 'camsi', 'DCAR_002366' => 'dca', 'DCAR_030687' => 'dca', 'DCAR_030688' => 'dca', 'Dinv14047' => 'din', 'Dinv14048' => 'din', 'Duzib151G0105' => 'dzi', 'Duzib151G0114' => 'dzi', 'Duzib212G1029' => 'dzi', 'ECA232G3536' => 'eca', 'ECA240G0786' => 'eca', 'ECA240G1802' => 'eca', 'ECA240G3760' => 'eca', 'ECA240G3920' => 'eca', 'EL10Ac5g12536' => 'bvu', 'EL10Ac5g12537' => 'bvu', 'EL10Ac5g12538' => 'bvu', 'Eucgr.B01004' => 'egr', 'Eucgr.B01006' => 'egr', 'Eucgr.B01007' => 'egr', 'Eucgr.B01008' => 'egr', 'Eucgr.B01895' => 'egr', 'Eucgr.B01896' => 'egr', 'FAN04G1456' => 'fan', 'FAN08G1769' => 'fan', 'FAN08G2160' => 'fan', 'FAN13G2403' => 'fan', 'FAN13G3303' => 'fan', 'FAN15G2435' => 'fan', 'FAN17G0672' => 'fan', 'FAN17G2441' => 'fan', 'FAN18G1024' => 'fan', 'FAN22G1458' => 'fan', 'FAN24G0037' => 'fan', 'FAN24G0429' => 'fan', 'FAN24G2387' => 'fan', 'FAN27G2746' => 'fan', 'FvH4_2g20400' => 'fve', 'FvH4_2g20420' => 'fve', 'FvH4_2g20430' => 'fve', 'FvH4_4g01270' => 'fve', 'FvH4_4g01290' => 'fve', 'FvH4_4g01300' => 'fve', 'FvH4_4g01310' => 'fve', 'FvH4_4g01330' => 'fve', 'FvH4_5g09070' => 'fve', 'Glyma.10G243800' => 'gma', 'Glyma.20G150600' => 'gma', 'Gohir.A09G219200' => 'ghi', 'Gohir.A09G219300' => 'ghi', 'Gohir.D09G221400' => 'ghi', 'Gohir.D09G221500' => 'ghi', 'Gorai.006G242600' => 'gra', 'Gorai.006G242700' => 'gra', 'GSVIVG01018044001' => 'vvi', 'HanXRQChr03g0083821' => 'han', 'HanXRQChr03g0083841' => 'han', 'HanXRQChr03g0083881' => 'han', 'HanXRQChr03g0083901' => 'han', 'HanXRQChr03g0083921' => 'han', 'HanXRQChr03g0085331' => 'han', 'HanXRQChr03g0085361' => 'han', 'HanXRQChr03g0085411' => 'han', 'HanXRQChr03g0085421' => 'han', 'HanXRQChr03g0085431' => 'han', 'HanXRQChr08g0221991' => 'han', 'HanXRQChr11g0336061' => 'han', 'HanXRQChr11g0336411' => 'han', 'Haze_11234' => 'cav', 'Hma1.2p1_0549F.1_g177010' => 'hma', 'Hma1.2p1_0602F.1_g187630' => 'hma', 'Hund14876' => 'sun', 'Hund14879' => 'sun', 'Lalb_Chr06g0160741' => 'lal', 'Lalb_Chr21g0304781' => 'lal', 'Lj3A726G19' => 'lonja', 'Lj3A726T23' => 'lonja', 'Lj3A726T24' => 'lonja', 'Lj3A726T25' => 'lonja', 'Lj3A727T17' => 'lonja', 'Lj3C726T0' => 'lonja', 'Lj3C726T2' => 'lonja', 'Lj3P725T35' => 'lonja', 'Lj3P727T10' => 'lonja', 'Lj3P727T12' => 'lonja', 'Lj3P727T14' => 'lonja', 'Lj5g0023109' => 'lja', 'Lj6P646T44' => 'lonja', 'Lsat_1_v5_gn_6_75760' => 'lsa', 'Lsat_1_v5_gn_6_75800' => 'lsa', 'Lsat_1_v5_gn_6_75900' => 'lsa', 'Lsat_1_v5_gn_6_76240' => 'lsa', 'Lsat_1_v5_gn_6_76441' => 'lsa', 'Lsat_1_v5_gn_6_76700' => 'lsa', 'Lsat_1_v5_gn_6_76760' => 'lsa', 'Manes.15G033100' => 'mes', 'Mapoly0004s0074' => 'mpo', 'Mapoly0004s0075' => 'mpo', 'Mapoly0004s0163' => 'mpo', 'Mapoly0004s0164' => 'mpo', 'Mapoly0021s0018' => 'mpo', 'Mapoly0041s0136' => 'mpo', 'Mapoly0041s0137' => 'mpo', 'Mapoly0041s0138' => 'mpo', 'Mapoly0041s0139' => 'mpo', 'Mapoly0041s0141' => 'mpo', 'Mapoly0041s0142' => 'mpo', 'Mapoly0041s0143' => 'mpo', 'Mapoly0041s0144' => 'mpo', 'Mapoly0041s0145' => 'mpo', 'Mapoly0047s0106' => 'mpo', 'Mapoly0047s0108' => 'mpo', 'Mapoly0050s0051' => 'mpo', 'Mapoly0050s0052' => 'mpo', 'Mapoly0050s0053' => 'mpo', 'Mapoly0058s0013' => 'mpo', 'Mapoly0091s0078' => 'mpo', 'Mapoly0091s0079' => 'mpo', 'Mapoly0091s0080' => 'mpo', 'Mapoly0091s0081' => 'mpo', 'Mapoly0278s0004' => 'mpo', 'Mapoly0278s0005' => 'mpo', 'Mapoly0278s0006' => 'mpo', 'MBI11_g30648_MAGBIO' => 'mbi', 'MCO03G194' => 'mco', 'MCO03G590' => 'mco', 'MCO07G312' => 'mco', 'MCO10G318' => 'mco', 'MCO12G244' => 'mco', 'MCO13G148' => 'mco', 'MCO13G194' => 'mco', 'MCO16G238' => 'mco', 'MD06G1134100' => 'mdo', 'MD13G1200100' => 'mdo', 'MD13G1200300' => 'mdo', 'MD13G1200600' => 'mdo', 'MD14G1150400' => 'mdo', 'MD16G1200000' => 'mdo', 'Medtr1g102570' => 'mtr', 'Medtr1g102780' => 'mtr', 'Medtr1g102800' => 'mtr', 'Medtr1g102810' => 'mtr', 'Medtr1g102830' => 'mtr', 'MELO3C006499.2' => 'cme', 'Migut.G00385' => 'egut', 'MSTRG.4063' => 'ama', 'Nitab4.5_0000090g0260' => 'nta', 'Nitab4.5_0000977g0030' => 'nta', 'Nitab4.5_0002541g0040' => 'nta', 'Nitab4.5_0007068g0040' => 'nta', 'Nn005s41408' => 'nnu', 'Nn005s41410' => 'nnu', 'Oeu010310.1' => 'oeu', 'Oeu010311.1' => 'oeu', 'Oeu043472.1' => 'oeu', 'Os01g0246400' => 'osa', 'Os04g0267950' => 'osa', 'Os07g0178700' => 'osa', 'Os07g0178800' => 'osa', 'Peaxi162Scf00316g00046' => 'pax', 'Peaxi162Scf00316g00049' => 'pax', 'Peaxi162Scf00316g00059' => 'pax', 'Peaxi162Scf00316g00328' => 'pax', 'Peaxi162Scf00316g00329' => 'pax', 'Peaxi162Scf00316g00411' => 'pax', 'Peaxi162Scf00316g00521' => 'pax', 'Peaxi162Scf00492g00068' => 'pax', 'Peaxi162Scf35631g00002' => 'pax', 'PGR142G3720' => 'pgr', 'PGSC0003DMG400006442' => 'stu', 'Phvul.007G062000' => 'pvu', 'Potri.008G157750' => 'ptr', 'Potri.008G157900' => 'ptr', 'Potri.008G158000' => 'ptr', 'Potri.008G158200' => 'ptr', 'Pp3c11_7280' => 'ppa', 'Pp3c11_7980' => 'ppa', 'Pp3c12_19450' => 'ppa', 'Pp3c14_1480' => 'ppa', 'Pp3c14_1501' => 'ppa', 'Pp3c16_4900' => 'ppa', 'Pp3c16_5010' => 'ppa', 'Pp3c16_5060' => 'ppa', 'Pp3c19_18250' => 'ppa', 'Pp3c23_8530' => 'ppa', 'Pp3c23_8550' => 'ppa', 'Pp3c24_9670' => 'ppa', 'Pp3c2_21390' => 'ppa', 'Pp3c2_31380' => 'ppa', 'Pp3c3_16620' => 'ppa', 'Pp3c3_8090' => 'ppa', 'Pp3c3_8110' => 'ppa', 'Pp3c3_8130' => 'ppa', 'Pp3c3_8150' => 'ppa', 'Pp3c4_14320' => 'ppa', 'Pp3c6_2560' => 'ppa', 'Pp3c9_16700' => 'ppa', 'PRCOL_00000234' => 'pco', 'PRCOL_00000235' => 'pco', 'PRCOL_00000777' => 'pco', 'PRCOL_00002344' => 'pco', 'PRCOL_00002372' => 'pco', 'PRCOL_00006120' => 'pco', 'Prupe.1G021400' => 'ppe', 'Prupe.1G021500' => 'ppe', 'Prupe.1G021600' => 'ppe', 'Prupe.1G021700' => 'ppe', 'Prupe.1G021800' => 'ppe', 'Prupe.5G145100' => 'ppe', 'Psat6g204040' => 'psa', 'Psat6g204800' => 'psa', 'Psat6g204920' => 'psa', 'Psat6g204960' => 'psa', 'Psat6g205080' => 'psa', 'PSO017G0271' => 'pso', 'PSO017G1276' => 'pso', 'PSO017G1429' => 'pso', 'PSO017G1861' => 'pso', 'PSO017G2787' => 'pso', 'PSO017G4466' => 'pso', 'PSO017G5118' => 'pso', 'PSO017G5420' => 'pso', 'PSO063G3678' => 'pso', 'PSO210G0546' => 'pso', 'PSO317G0001' => 'pso', 'PSO357G0512' => 'pso', 'PSO478G2682' => 'pso', 'PSO647G0001' => 'pso', 'PSO675G0001' => 'pso', 'PSO675G2699' => 'pso', 'PSO675G2849' => 'pso', 'PSO675G4991' => 'pso', 'PSO689G0001' => 'pso', 'QL06p000916' => 'qlo', 'QL06p000921' => 'qlo', 'QL06p001398' => 'qlo', 'QL06p001407' => 'qlo', 'QL06p002031' => 'qlo', 'RcHm_v2.0_Chr4g0387791' => 'rch', 'RcHm_v2.0_Chr4g0387801' => 'rch', 'RcHm_v2.0_Chr6g0286501' => 'rch', 'RcHm_v2.0_Chr6g0286511' => 'rch', 'RcHm_v2.0_Chr6g0286521' => 'rch', 'RcHm_v2.0_Chr6g0286531' => 'rch', 'RcHm_v2.0_Chr7g0189141' => 'rch', 'Rhsim02G0028700' => 'rsi', 'Rhsim02G0028800' => 'rsi', 'Rhsim02G0028900' => 'rsi', 'Rhsim02G0029000' => 'rsi', 'Rhsim02G0029100' => 'rsi', 'Rhsim02G0029200' => 'rsi', 'Rhsim02G0029300' => 'rsi', 'Rhsim02G0029400' => 'rsi', 'Rhsim02G0029500' => 'rsi', 'Rhsim02G0029600' => 'rsi', 'RhsimUnG0024000' => 'rsi', 'RhsimUnG0024100' => 'rsi', 'RhsimUnG0024200' => 'rsi', 'RhsimUnG0024300' => 'rsi', 'RhsimUnG0024400' => 'rsi', 'RhsimUnG0024500' => 'rsi', 'RhsimUnG0024700' => 'rsi', 'RhsimUnG0024800' => 'rsi', 'RhsimUnG0024900' => 'rsi', 'RhsimUnG0025100' => 'rsi', 'Sabra08G0120200' => 'sbr', 'Sabra08G0120300' => 'sbr', 'Sabra08G0120500' => 'sbr', 'Sabra08G0120600' => 'sbr', 'Sabra10G0158900' => 'sbr', 'SalBow2G3492' => 'sbo', 'Sc13g0004760' => 'sci', 'Sc13g0004770' => 'sci', 'Sed0003417' => 'sed', 'Sed0019750' => 'sed', 'SEGI_03419' => 'sgi', 'SEGI_05907' => 'sgi', 'SEGI_10682' => 'sgi', 'SEGI_13528' => 'sgi', 'SEGI_16081' => 'sgi', 'SEGI_19370' => 'sgi', 'SEGI_21015' => 'sgi', 'SEGI_21944' => 'sgi', 'SEGI_32906' => 'sgi', 'SEGI_33093' => 'sgi', 'SEGI_36110' => 'sgi', 'SEGI_40397' => 'sgi', 'SGA_v2.0_scaffold191G40426' => 'sas', 'SGA_v2.0_scaffold353G49717' => 'sas', 'SGA_v2.0_scaffold50G18550' => 'sas', 'SMO119G0173' => 'smo', 'SMO172G0002' => 'smo', 'Solyc09g082690.3' => 'sly', 'Solyc09g082700.2' => 'sly', 'Sopen09g031550' => 'spe', 'Sopen09g031560' => 'spe', 'Sp3g20540' => 'spa', 'Sp7g07580' => 'spa', 'TAR134G0002' => 'tar', 'TAR236G0001' => 'tar', 'TAR365G0892' => 'tar', 'TAR636G0166' => 'tar', 'TAR636G0646' => 'tar', 'TAR636G0869' => 'tar', 'TAR636G1317' => 'tar', 'TAR636G1744' => 'tar', 'TAR636G3358' => 'tar', 'TAR636G3436' => 'tar', 'THA.LOC104803047' => 'tha', 'Thecc.04G238900' => 'tca', 'Thhalv10021557m.g' => 'esa', 'Thhalv10026318m.g' => 'esa', 'Thhalv10026335m.g' => 'esa', 'TPR.G17433' => 'tpr', 'TPR.G18915' => 'tpr', 'TPR.G26125' => 'tpr', 'TWI09G0677' => 'twi', 'TWI73G0287' => 'twi', 'unitig_748.g8326' => 'ugi', 'vmacro15370' => 'vma', 'vmacro15371' => 'vma', 'vmacro15372' => 'vma', 'vmacro15373' => 'vma', 'vmacro15374' => 'vma', 'VMungo0720G2826' => 'vmu', 'Zm00001eb116960' => 'zma', 'Zm00001eb301260' => 'zma', 'Zm00001eb301270' => 'zma' ) $gf_id = 'HOM05D001460' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001460' ) $data_identifier = 'HOM05D001460' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 4, 'aag' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 2, 'aox' => (int) 2, 'arhy' => (int) 4, 'ath' => (int) 2, 'atr' => (int) 1, 'acertr' => (int) 10, 'cqu' => (int) 4, 'bca' => (int) 11, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 1, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 1, 'ccan' => (int) 1, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 1, 'col' => (int) 1, 'cpa' => (int) 1, 'cre' => (int) 7, 'csa' => (int) 1, 'camsi' => (int) 2, 'dca' => (int) 3, 'din' => (int) 2, 'dzi' => (int) 3, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 14, 'fve' => (int) 9, 'gma' => (int) 2, 'ghi' => (int) 4, 'gra' => (int) 2, 'vvi' => (int) 1, 'han' => (int) 13, 'cav' => (int) 1, 'hma' => (int) 2, 'sun' => (int) 2, 'lal' => (int) 2, 'lonja' => (int) 12, 'lja' => (int) 1, 'lsa' => (int) 7, 'mes' => (int) 1, 'mpo' => (int) 27, 'mbi' => (int) 1, 'mco' => (int) 8, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 1, 'egut' => (int) 1, 'ama' => (int) 1, 'nta' => (int) 4, 'nnu' => (int) 2, 'oeu' => (int) 3, 'osa' => (int) 4, 'pax' => (int) 9, 'pgr' => (int) 1, 'stu' => (int) 1, 'pvu' => (int) 1, 'ptr' => (int) 4, 'ppa' => (int) 22, 'pco' => (int) 6, 'ppe' => (int) 6, 'psa' => (int) 5, 'pso' => (int) 19, 'qlo' => (int) 5, 'rch' => (int) 7, 'rsi' => (int) 20, 'sbr' => (int) 5, 'sbo' => (int) 1, 'sci' => (int) 2, 'sed' => (int) 2, 'sgi' => (int) 12, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 2, 'tar' => (int) 10, 'tha' => (int) 1, 'tca' => (int) 1, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 2, 'ugi' => (int) 1, 'vma' => (int) 5, 'vmu' => (int) 1, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb301270' $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' => 'HOM05D001460', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '433', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p22980' => 'bna', 'A01p32340' => 'bna', 'A03p42970' => 'bna', 'A05p25880' => 'bna', 'Aa31LG8G9320' => 'aar', 'Aa31LG8G9330' => 'aar', 'Aa31LG8G9340' => 'aar', 'Aa31sc221G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1034' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1528' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.829' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2222' => 'aag', 'Ah.12g058830' => 'amhyb', 'Ah.12g058840' => 'amhyb', 'AL3G37160' => 'aly', 'AL7G41310' => 'aly', 'Aqoxy5G00395' => 'aox', 'Aqoxy5G00396' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0C8NZA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5185HY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JZ1PRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MD3LS0' => 'arhy', 'AT3G22840' => 'ath', 'AT4G14690' => 'ath', 'ATR0665G054' => 'atr', 'Atru.chr4.2344' => 'acertr', 'Atru.chr4.2346' => 'acertr', 'Atru.chr4.2347' => 'acertr', 'Atru.chr4.2348' => 'acertr', 'Atru.chr4.2355' => 'acertr', 'Atru.chr4.2356' => 'acertr', 'Atru.chr4.2358' => 'acertr', 'Atru.chr4.2359' => 'acertr', 'Atru.chr4.2360' => 'acertr', 'Atru.chr4.2361' => 'acertr', 'AUR62030476' => 'cqu', 'AUR62030478' => 'cqu', 'AUR62030819' => 'cqu', 'AUR62030820' => 'cqu', 'BcaB03g14648' => 'bca', 'BcaB04g20492' => 'bca', 'BcaB06g26399' => 'bca', 'BcaC01g03416' => 'bca', 'BcaC01g03419' => 'bca', 'BcaC01g03421' => 'bca', 'BcaC01g03424' => 'bca', 'BcaC05g28012' => 'bca', 'BcaC09g49212' => 'bca', 'BcaC09g50140' => 'bca', 'BcaNung00346' => 'bca', 'BolC1t02785H' => 'bol', 'BolC1t04095H' => 'bol', 'BolC3t17545H' => 'bol', 'BolC5t32769H' => 'bol', 'BraA01t02211Z' => 'bra', 'BraA01t03359Z' => 'bra', 'BraA03t13441Z' => 'bra', 'BraA05t21476Z' => 'bra', 'C01p28420' => 'bna', 'C01p41350' => 'bna', 'C03p52750' => 'bna', 'C03p52780' => 'bna', 'C05p40270' => 'bna', 'CAN.G1437.9' => 'can', 'CANSAT78G0035' => 'cansat', 'CANSAT78G1036' => 'cansat', 'CANSAT78G2272' => 'cansat', 'CANSAT78G2478' => 'cansat', 'CARHR098700' => 'chi', 'CARHR221120' => 'chi', 'CARHR221150' => 'chi', 'Carub.0003s2297' => 'cru', 'Carub.0007s2749' => 'cru', 'Carub.0007s2750' => 'cru', 'Carub.0007s2751' => 'cru', 'Ca_10849_v3' => 'car', 'Cc03_g04300' => 'ccan', 'CDE02G3648' => 'cde', 'CDE05G0060' => 'cde', 'CDE05G0692' => 'cde', 'CDE05G2285' => 'cde', 'CDE05G2884' => 'cde', 'CDE05G3072' => 'cde', 'Cfa008439' => 'cfa', 'Cfa008441' => 'cfa', 'Cfa008443' => 'cfa', 'Cfa008448' => 'cfa', 'Ciclev10005974m.g' => 'ccl', 'Ciclev10006006m.g' => 'ccl', 'Ciclev10006775m.g' => 'ccl', 'CiPaw.02G120400' => 'cil', 'CiPaw.02G120500' => 'cil', 'CiPaw.02G120600' => 'cil', 'ClCG05G004850' => 'cla', 'COL.COLO4_21566' => 'col', 'Cpa.g.sc44.124' => 'cpa', 'Cre07.g320400' => 'cre', 'Cre07.g320450' => 'cre', 'Cre08.g384650' => 'cre', 'Cre09.g393173' => 'cre', 'Cre09.g394325' => 'cre', 'Cre14.g626750' => 'cre', 'Cre16.g679250' => 'cre', 'CsaV3_3G012890' => 'csa', 'CSS0010865' => 'camsi', 'CSS0044338' => 'camsi', 'DCAR_002366' => 'dca', 'DCAR_030687' => 'dca', 'DCAR_030688' => 'dca', 'Dinv14047' => 'din', 'Dinv14048' => 'din', 'Duzib151G0105' => 'dzi', 'Duzib151G0114' => 'dzi', 'Duzib212G1029' => 'dzi', 'ECA232G3536' => 'eca', 'ECA240G0786' => 'eca', 'ECA240G1802' => 'eca', 'ECA240G3760' => 'eca', 'ECA240G3920' => 'eca', 'EL10Ac5g12536' => 'bvu', 'EL10Ac5g12537' => 'bvu', 'EL10Ac5g12538' => 'bvu', 'Eucgr.B01004' => 'egr', 'Eucgr.B01006' => 'egr', 'Eucgr.B01007' => 'egr', 'Eucgr.B01008' => 'egr', 'Eucgr.B01895' => 'egr', 'Eucgr.B01896' => 'egr', 'FAN04G1456' => 'fan', 'FAN08G1769' => 'fan', 'FAN08G2160' => 'fan', 'FAN13G2403' => 'fan', 'FAN13G3303' => 'fan', 'FAN15G2435' => 'fan', 'FAN17G0672' => 'fan', 'FAN17G2441' => 'fan', 'FAN18G1024' => 'fan', 'FAN22G1458' => 'fan', 'FAN24G0037' => 'fan', 'FAN24G0429' => 'fan', 'FAN24G2387' => 'fan', 'FAN27G2746' => 'fan', 'FvH4_2g20400' => 'fve', 'FvH4_2g20420' => 'fve', 'FvH4_2g20430' => 'fve', 'FvH4_4g01270' => 'fve', 'FvH4_4g01290' => 'fve', 'FvH4_4g01300' => 'fve', 'FvH4_4g01310' => 'fve', 'FvH4_4g01330' => 'fve', 'FvH4_5g09070' => 'fve', 'Glyma.10G243800' => 'gma', 'Glyma.20G150600' => 'gma', 'Gohir.A09G219200' => 'ghi', 'Gohir.A09G219300' => 'ghi', 'Gohir.D09G221400' => 'ghi', 'Gohir.D09G221500' => 'ghi', 'Gorai.006G242600' => 'gra', 'Gorai.006G242700' => 'gra', 'GSVIVG01018044001' => 'vvi', 'HanXRQChr03g0083821' => 'han', 'HanXRQChr03g0083841' => 'han', 'HanXRQChr03g0083881' => 'han', 'HanXRQChr03g0083901' => 'han', 'HanXRQChr03g0083921' => 'han', 'HanXRQChr03g0085331' => 'han', 'HanXRQChr03g0085361' => 'han', 'HanXRQChr03g0085411' => 'han', 'HanXRQChr03g0085421' => 'han', 'HanXRQChr03g0085431' => 'han', 'HanXRQChr08g0221991' => 'han', 'HanXRQChr11g0336061' => 'han', 'HanXRQChr11g0336411' => 'han', 'Haze_11234' => 'cav', 'Hma1.2p1_0549F.1_g177010' => 'hma', 'Hma1.2p1_0602F.1_g187630' => 'hma', 'Hund14876' => 'sun', 'Hund14879' => 'sun', 'Lalb_Chr06g0160741' => 'lal', 'Lalb_Chr21g0304781' => 'lal', 'Lj3A726G19' => 'lonja', 'Lj3A726T23' => 'lonja', 'Lj3A726T24' => 'lonja', 'Lj3A726T25' => 'lonja', 'Lj3A727T17' => 'lonja', 'Lj3C726T0' => 'lonja', 'Lj3C726T2' => 'lonja', 'Lj3P725T35' => 'lonja', 'Lj3P727T10' => 'lonja', 'Lj3P727T12' => 'lonja', 'Lj3P727T14' => 'lonja', 'Lj5g0023109' => 'lja', 'Lj6P646T44' => 'lonja', 'Lsat_1_v5_gn_6_75760' => 'lsa', 'Lsat_1_v5_gn_6_75800' => 'lsa', 'Lsat_1_v5_gn_6_75900' => 'lsa', 'Lsat_1_v5_gn_6_76240' => 'lsa', 'Lsat_1_v5_gn_6_76441' => 'lsa', 'Lsat_1_v5_gn_6_76700' => 'lsa', 'Lsat_1_v5_gn_6_76760' => 'lsa', 'Manes.15G033100' => 'mes', 'Mapoly0004s0074' => 'mpo', 'Mapoly0004s0075' => 'mpo', 'Mapoly0004s0163' => 'mpo', 'Mapoly0004s0164' => 'mpo', 'Mapoly0021s0018' => 'mpo', 'Mapoly0041s0136' => 'mpo', 'Mapoly0041s0137' => 'mpo', 'Mapoly0041s0138' => 'mpo', 'Mapoly0041s0139' => 'mpo', 'Mapoly0041s0141' => 'mpo', 'Mapoly0041s0142' => 'mpo', 'Mapoly0041s0143' => 'mpo', 'Mapoly0041s0144' => 'mpo', 'Mapoly0041s0145' => 'mpo', 'Mapoly0047s0106' => 'mpo', 'Mapoly0047s0108' => 'mpo', 'Mapoly0050s0051' => 'mpo', 'Mapoly0050s0052' => 'mpo', 'Mapoly0050s0053' => 'mpo', 'Mapoly0058s0013' => 'mpo', 'Mapoly0091s0078' => 'mpo', 'Mapoly0091s0079' => 'mpo', 'Mapoly0091s0080' => 'mpo', 'Mapoly0091s0081' => 'mpo', 'Mapoly0278s0004' => 'mpo', 'Mapoly0278s0005' => 'mpo', 'Mapoly0278s0006' => 'mpo', 'MBI11_g30648_MAGBIO' => 'mbi', 'MCO03G194' => 'mco', 'MCO03G590' => 'mco', 'MCO07G312' => 'mco', 'MCO10G318' => 'mco', 'MCO12G244' => 'mco', 'MCO13G148' => 'mco', 'MCO13G194' => 'mco', 'MCO16G238' => 'mco', 'MD06G1134100' => 'mdo', 'MD13G1200100' => 'mdo', 'MD13G1200300' => 'mdo', 'MD13G1200600' => 'mdo', 'MD14G1150400' => 'mdo', 'MD16G1200000' => 'mdo', 'Medtr1g102570' => 'mtr', 'Medtr1g102780' => 'mtr', 'Medtr1g102800' => 'mtr', 'Medtr1g102810' => 'mtr', 'Medtr1g102830' => 'mtr', 'MELO3C006499.2' => 'cme', 'Migut.G00385' => 'egut', 'MSTRG.4063' => 'ama', 'Nitab4.5_0000090g0260' => 'nta', 'Nitab4.5_0000977g0030' => 'nta', 'Nitab4.5_0002541g0040' => 'nta', 'Nitab4.5_0007068g0040' => 'nta', 'Nn005s41408' => 'nnu', 'Nn005s41410' => 'nnu', 'Oeu010310.1' => 'oeu', 'Oeu010311.1' => 'oeu', 'Oeu043472.1' => 'oeu', 'Os01g0246400' => 'osa', 'Os04g0267950' => 'osa', 'Os07g0178700' => 'osa', 'Os07g0178800' => 'osa', 'Peaxi162Scf00316g00046' => 'pax', 'Peaxi162Scf00316g00049' => 'pax', 'Peaxi162Scf00316g00059' => 'pax', 'Peaxi162Scf00316g00328' => 'pax', 'Peaxi162Scf00316g00329' => 'pax', 'Peaxi162Scf00316g00411' => 'pax', 'Peaxi162Scf00316g00521' => 'pax', 'Peaxi162Scf00492g00068' => 'pax', 'Peaxi162Scf35631g00002' => 'pax', 'PGR142G3720' => 'pgr', 'PGSC0003DMG400006442' => 'stu', 'Phvul.007G062000' => 'pvu', 'Potri.008G157750' => 'ptr', 'Potri.008G157900' => 'ptr', 'Potri.008G158000' => 'ptr', 'Potri.008G158200' => 'ptr', 'Pp3c11_7280' => 'ppa', 'Pp3c11_7980' => 'ppa', 'Pp3c12_19450' => 'ppa', 'Pp3c14_1480' => 'ppa', 'Pp3c14_1501' => 'ppa', 'Pp3c16_4900' => 'ppa', 'Pp3c16_5010' => 'ppa', 'Pp3c16_5060' => 'ppa', 'Pp3c19_18250' => 'ppa', 'Pp3c23_8530' => 'ppa', 'Pp3c23_8550' => 'ppa', 'Pp3c24_9670' => 'ppa', 'Pp3c2_21390' => 'ppa', 'Pp3c2_31380' => 'ppa', 'Pp3c3_16620' => 'ppa', 'Pp3c3_8090' => 'ppa', 'Pp3c3_8110' => 'ppa', 'Pp3c3_8130' => 'ppa', 'Pp3c3_8150' => 'ppa', 'Pp3c4_14320' => 'ppa', 'Pp3c6_2560' => 'ppa', 'Pp3c9_16700' => 'ppa', 'PRCOL_00000234' => 'pco', 'PRCOL_00000235' => 'pco', 'PRCOL_00000777' => 'pco', 'PRCOL_00002344' => 'pco', 'PRCOL_00002372' => 'pco', 'PRCOL_00006120' => 'pco', 'Prupe.1G021400' => 'ppe', 'Prupe.1G021500' => 'ppe', 'Prupe.1G021600' => 'ppe', 'Prupe.1G021700' => 'ppe', 'Prupe.1G021800' => 'ppe', 'Prupe.5G145100' => 'ppe', 'Psat6g204040' => 'psa', 'Psat6g204800' => 'psa', 'Psat6g204920' => 'psa', 'Psat6g204960' => 'psa', 'Psat6g205080' => 'psa', 'PSO017G0271' => 'pso', 'PSO017G1276' => 'pso', 'PSO017G1429' => 'pso', 'PSO017G1861' => 'pso', 'PSO017G2787' => 'pso', 'PSO017G4466' => 'pso', 'PSO017G5118' => 'pso', 'PSO017G5420' => 'pso', 'PSO063G3678' => 'pso', 'PSO210G0546' => 'pso', 'PSO317G0001' => 'pso', 'PSO357G0512' => 'pso', 'PSO478G2682' => 'pso', 'PSO647G0001' => 'pso', 'PSO675G0001' => 'pso', 'PSO675G2699' => 'pso', 'PSO675G2849' => 'pso', 'PSO675G4991' => 'pso', 'PSO689G0001' => 'pso', 'QL06p000916' => 'qlo', 'QL06p000921' => 'qlo', 'QL06p001398' => 'qlo', 'QL06p001407' => 'qlo', 'QL06p002031' => 'qlo', 'RcHm_v2.0_Chr4g0387791' => 'rch', 'RcHm_v2.0_Chr4g0387801' => 'rch', 'RcHm_v2.0_Chr6g0286501' => 'rch', 'RcHm_v2.0_Chr6g0286511' => 'rch', 'RcHm_v2.0_Chr6g0286521' => 'rch', 'RcHm_v2.0_Chr6g0286531' => 'rch', 'RcHm_v2.0_Chr7g0189141' => 'rch', 'Rhsim02G0028700' => 'rsi', 'Rhsim02G0028800' => 'rsi', 'Rhsim02G0028900' => 'rsi', 'Rhsim02G0029000' => 'rsi', 'Rhsim02G0029100' => 'rsi', 'Rhsim02G0029200' => 'rsi', 'Rhsim02G0029300' => 'rsi', 'Rhsim02G0029400' => 'rsi', 'Rhsim02G0029500' => 'rsi', 'Rhsim02G0029600' => 'rsi', 'RhsimUnG0024000' => 'rsi', 'RhsimUnG0024100' => 'rsi', 'RhsimUnG0024200' => 'rsi', 'RhsimUnG0024300' => 'rsi', 'RhsimUnG0024400' => 'rsi', 'RhsimUnG0024500' => 'rsi', 'RhsimUnG0024700' => 'rsi', 'RhsimUnG0024800' => 'rsi', 'RhsimUnG0024900' => 'rsi', 'RhsimUnG0025100' => 'rsi', 'Sabra08G0120200' => 'sbr', 'Sabra08G0120300' => 'sbr', 'Sabra08G0120500' => 'sbr', 'Sabra08G0120600' => 'sbr', 'Sabra10G0158900' => 'sbr', 'SalBow2G3492' => 'sbo', 'Sc13g0004760' => 'sci', 'Sc13g0004770' => 'sci', 'Sed0003417' => 'sed', 'Sed0019750' => 'sed', 'SEGI_03419' => 'sgi', 'SEGI_05907' => 'sgi', 'SEGI_10682' => 'sgi', 'SEGI_13528' => 'sgi', 'SEGI_16081' => 'sgi', 'SEGI_19370' => 'sgi', 'SEGI_21015' => 'sgi', 'SEGI_21944' => 'sgi', 'SEGI_32906' => 'sgi', 'SEGI_33093' => 'sgi', 'SEGI_36110' => 'sgi', 'SEGI_40397' => 'sgi', 'SGA_v2.0_scaffold191G40426' => 'sas', 'SGA_v2.0_scaffold353G49717' => 'sas', 'SGA_v2.0_scaffold50G18550' => 'sas', 'SMO119G0173' => 'smo', 'SMO172G0002' => 'smo', 'Solyc09g082690.3' => 'sly', 'Solyc09g082700.2' => 'sly', 'Sopen09g031550' => 'spe', 'Sopen09g031560' => 'spe', 'Sp3g20540' => 'spa', 'Sp7g07580' => 'spa', 'TAR134G0002' => 'tar', 'TAR236G0001' => 'tar', 'TAR365G0892' => 'tar', 'TAR636G0166' => 'tar', 'TAR636G0646' => 'tar', 'TAR636G0869' => 'tar', 'TAR636G1317' => 'tar', 'TAR636G1744' => 'tar', 'TAR636G3358' => 'tar', 'TAR636G3436' => 'tar', 'THA.LOC104803047' => 'tha', 'Thecc.04G238900' => 'tca', 'Thhalv10021557m.g' => 'esa', 'Thhalv10026318m.g' => 'esa', 'Thhalv10026335m.g' => 'esa', 'TPR.G17433' => 'tpr', 'TPR.G18915' => 'tpr', 'TPR.G26125' => 'tpr', 'TWI09G0677' => 'twi', 'TWI73G0287' => 'twi', 'unitig_748.g8326' => 'ugi', 'vmacro15370' => 'vma', 'vmacro15371' => 'vma', 'vmacro15372' => 'vma', 'vmacro15373' => 'vma', 'vmacro15374' => 'vma', 'VMungo0720G2826' => 'vmu', 'Zm00001eb116960' => 'zma', 'Zm00001eb301260' => 'zma', 'Zm00001eb301270' => 'zma' ), 'gf_id' => 'HOM05D001460', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001460' ), 'data_identifier' => 'HOM05D001460', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001460', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '433', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p22980' => 'bna', 'A01p32340' => 'bna', 'A03p42970' => 'bna', 'A05p25880' => 'bna', 'Aa31LG8G9320' => 'aar', 'Aa31LG8G9330' => 'aar', 'Aa31LG8G9340' => 'aar', 'Aa31sc221G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1034' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1528' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.829' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2222' => 'aag', 'Ah.12g058830' => 'amhyb', 'Ah.12g058840' => 'amhyb', 'AL3G37160' => 'aly', 'AL7G41310' => 'aly', 'Aqoxy5G00395' => 'aox', 'Aqoxy5G00396' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0C8NZA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5185HY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JZ1PRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MD3LS0' => 'arhy', 'AT3G22840' => 'ath', 'AT4G14690' => 'ath', 'ATR0665G054' => 'atr', 'Atru.chr4.2344' => 'acertr', 'Atru.chr4.2346' => 'acertr', 'Atru.chr4.2347' => 'acertr', 'Atru.chr4.2348' => 'acertr', 'Atru.chr4.2355' => 'acertr', 'Atru.chr4.2356' => 'acertr', 'Atru.chr4.2358' => 'acertr', 'Atru.chr4.2359' => 'acertr', 'Atru.chr4.2360' => 'acertr', 'Atru.chr4.2361' => 'acertr', 'AUR62030476' => 'cqu', 'AUR62030478' => 'cqu', 'AUR62030819' => 'cqu', 'AUR62030820' => 'cqu', 'BcaB03g14648' => 'bca', 'BcaB04g20492' => 'bca', 'BcaB06g26399' => 'bca', 'BcaC01g03416' => 'bca', 'BcaC01g03419' => 'bca', 'BcaC01g03421' => 'bca', 'BcaC01g03424' => 'bca', 'BcaC05g28012' => 'bca', 'BcaC09g49212' => 'bca', 'BcaC09g50140' => 'bca', 'BcaNung00346' => 'bca', 'BolC1t02785H' => 'bol', 'BolC1t04095H' => 'bol', 'BolC3t17545H' => 'bol', 'BolC5t32769H' => 'bol', 'BraA01t02211Z' => 'bra', 'BraA01t03359Z' => 'bra', 'BraA03t13441Z' => 'bra', 'BraA05t21476Z' => 'bra', 'C01p28420' => 'bna', 'C01p41350' => 'bna', 'C03p52750' => 'bna', 'C03p52780' => 'bna', 'C05p40270' => 'bna', 'CAN.G1437.9' => 'can', 'CANSAT78G0035' => 'cansat', 'CANSAT78G1036' => 'cansat', 'CANSAT78G2272' => 'cansat', 'CANSAT78G2478' => 'cansat', 'CARHR098700' => 'chi', 'CARHR221120' => 'chi', 'CARHR221150' => 'chi', 'Carub.0003s2297' => 'cru', 'Carub.0007s2749' => 'cru', 'Carub.0007s2750' => 'cru', 'Carub.0007s2751' => 'cru', 'Ca_10849_v3' => 'car', 'Cc03_g04300' => 'ccan', 'CDE02G3648' => 'cde', 'CDE05G0060' => 'cde', 'CDE05G0692' => 'cde', 'CDE05G2285' => 'cde', 'CDE05G2884' => 'cde', 'CDE05G3072' => 'cde', 'Cfa008439' => 'cfa', 'Cfa008441' => 'cfa', 'Cfa008443' => 'cfa', 'Cfa008448' => 'cfa', 'Ciclev10005974m.g' => 'ccl', 'Ciclev10006006m.g' => 'ccl', 'Ciclev10006775m.g' => 'ccl', 'CiPaw.02G120400' => 'cil', 'CiPaw.02G120500' => 'cil', 'CiPaw.02G120600' => 'cil', 'ClCG05G004850' => 'cla', 'COL.COLO4_21566' => 'col', 'Cpa.g.sc44.124' => 'cpa', 'Cre07.g320400' => 'cre', 'Cre07.g320450' => 'cre', 'Cre08.g384650' => 'cre', 'Cre09.g393173' => 'cre', 'Cre09.g394325' => 'cre', 'Cre14.g626750' => 'cre', 'Cre16.g679250' => 'cre', 'CsaV3_3G012890' => 'csa', 'CSS0010865' => 'camsi', 'CSS0044338' => 'camsi', 'DCAR_002366' => 'dca', 'DCAR_030687' => 'dca', 'DCAR_030688' => 'dca', 'Dinv14047' => 'din', 'Dinv14048' => 'din', 'Duzib151G0105' => 'dzi', 'Duzib151G0114' => 'dzi', 'Duzib212G1029' => 'dzi', 'ECA232G3536' => 'eca', 'ECA240G0786' => 'eca', 'ECA240G1802' => 'eca', 'ECA240G3760' => 'eca', 'ECA240G3920' => 'eca', 'EL10Ac5g12536' => 'bvu', 'EL10Ac5g12537' => 'bvu', 'EL10Ac5g12538' => 'bvu', 'Eucgr.B01004' => 'egr', 'Eucgr.B01006' => 'egr', 'Eucgr.B01007' => 'egr', 'Eucgr.B01008' => 'egr', 'Eucgr.B01895' => 'egr', 'Eucgr.B01896' => 'egr', 'FAN04G1456' => 'fan', 'FAN08G1769' => 'fan', 'FAN08G2160' => 'fan', 'FAN13G2403' => 'fan', 'FAN13G3303' => 'fan', 'FAN15G2435' => 'fan', 'FAN17G0672' => 'fan', 'FAN17G2441' => 'fan', 'FAN18G1024' => 'fan', 'FAN22G1458' => 'fan', 'FAN24G0037' => 'fan', 'FAN24G0429' => 'fan', 'FAN24G2387' => 'fan', 'FAN27G2746' => 'fan', 'FvH4_2g20400' => 'fve', 'FvH4_2g20420' => 'fve', 'FvH4_2g20430' => 'fve', 'FvH4_4g01270' => 'fve', 'FvH4_4g01290' => 'fve', 'FvH4_4g01300' => 'fve', 'FvH4_4g01310' => 'fve', 'FvH4_4g01330' => 'fve', 'FvH4_5g09070' => 'fve', 'Glyma.10G243800' => 'gma', 'Glyma.20G150600' => 'gma', 'Gohir.A09G219200' => 'ghi', 'Gohir.A09G219300' => 'ghi', 'Gohir.D09G221400' => 'ghi', 'Gohir.D09G221500' => 'ghi', 'Gorai.006G242600' => 'gra', 'Gorai.006G242700' => 'gra', 'GSVIVG01018044001' => 'vvi', 'HanXRQChr03g0083821' => 'han', 'HanXRQChr03g0083841' => 'han', 'HanXRQChr03g0083881' => 'han', 'HanXRQChr03g0083901' => 'han', 'HanXRQChr03g0083921' => 'han', 'HanXRQChr03g0085331' => 'han', 'HanXRQChr03g0085361' => 'han', 'HanXRQChr03g0085411' => 'han', 'HanXRQChr03g0085421' => 'han', 'HanXRQChr03g0085431' => 'han', 'HanXRQChr08g0221991' => 'han', 'HanXRQChr11g0336061' => 'han', 'HanXRQChr11g0336411' => 'han', 'Haze_11234' => 'cav', 'Hma1.2p1_0549F.1_g177010' => 'hma', 'Hma1.2p1_0602F.1_g187630' => 'hma', 'Hund14876' => 'sun', 'Hund14879' => 'sun', 'Lalb_Chr06g0160741' => 'lal', 'Lalb_Chr21g0304781' => 'lal', 'Lj3A726G19' => 'lonja', 'Lj3A726T23' => 'lonja', 'Lj3A726T24' => 'lonja', 'Lj3A726T25' => 'lonja', 'Lj3A727T17' => 'lonja', 'Lj3C726T0' => 'lonja', 'Lj3C726T2' => 'lonja', 'Lj3P725T35' => 'lonja', 'Lj3P727T10' => 'lonja', 'Lj3P727T12' => 'lonja', 'Lj3P727T14' => 'lonja', 'Lj5g0023109' => 'lja', 'Lj6P646T44' => 'lonja', 'Lsat_1_v5_gn_6_75760' => 'lsa', 'Lsat_1_v5_gn_6_75800' => 'lsa', 'Lsat_1_v5_gn_6_75900' => 'lsa', 'Lsat_1_v5_gn_6_76240' => 'lsa', 'Lsat_1_v5_gn_6_76441' => 'lsa', 'Lsat_1_v5_gn_6_76700' => 'lsa', 'Lsat_1_v5_gn_6_76760' => 'lsa', 'Manes.15G033100' => 'mes', 'Mapoly0004s0074' => 'mpo', 'Mapoly0004s0075' => 'mpo', 'Mapoly0004s0163' => 'mpo', 'Mapoly0004s0164' => 'mpo', 'Mapoly0021s0018' => 'mpo', 'Mapoly0041s0136' => 'mpo', 'Mapoly0041s0137' => 'mpo', 'Mapoly0041s0138' => 'mpo', 'Mapoly0041s0139' => 'mpo', 'Mapoly0041s0141' => 'mpo', 'Mapoly0041s0142' => 'mpo', 'Mapoly0041s0143' => 'mpo', 'Mapoly0041s0144' => 'mpo', 'Mapoly0041s0145' => 'mpo', 'Mapoly0047s0106' => 'mpo', 'Mapoly0047s0108' => 'mpo', 'Mapoly0050s0051' => 'mpo', 'Mapoly0050s0052' => 'mpo', 'Mapoly0050s0053' => 'mpo', 'Mapoly0058s0013' => 'mpo', 'Mapoly0091s0078' => 'mpo', 'Mapoly0091s0079' => 'mpo', 'Mapoly0091s0080' => 'mpo', 'Mapoly0091s0081' => 'mpo', 'Mapoly0278s0004' => 'mpo', 'Mapoly0278s0005' => 'mpo', 'Mapoly0278s0006' => 'mpo', 'MBI11_g30648_MAGBIO' => 'mbi', 'MCO03G194' => 'mco', 'MCO03G590' => 'mco', 'MCO07G312' => 'mco', 'MCO10G318' => 'mco', 'MCO12G244' => 'mco', 'MCO13G148' => 'mco', 'MCO13G194' => 'mco', 'MCO16G238' => 'mco', 'MD06G1134100' => 'mdo', 'MD13G1200100' => 'mdo', 'MD13G1200300' => 'mdo', 'MD13G1200600' => 'mdo', 'MD14G1150400' => 'mdo', 'MD16G1200000' => 'mdo', 'Medtr1g102570' => 'mtr', 'Medtr1g102780' => 'mtr', 'Medtr1g102800' => 'mtr', 'Medtr1g102810' => 'mtr', 'Medtr1g102830' => 'mtr', 'MELO3C006499.2' => 'cme', 'Migut.G00385' => 'egut', 'MSTRG.4063' => 'ama', 'Nitab4.5_0000090g0260' => 'nta', 'Nitab4.5_0000977g0030' => 'nta', 'Nitab4.5_0002541g0040' => 'nta', 'Nitab4.5_0007068g0040' => 'nta', 'Nn005s41408' => 'nnu', 'Nn005s41410' => 'nnu', 'Oeu010310.1' => 'oeu', 'Oeu010311.1' => 'oeu', 'Oeu043472.1' => 'oeu', 'Os01g0246400' => 'osa', 'Os04g0267950' => 'osa', 'Os07g0178700' => 'osa', 'Os07g0178800' => 'osa', 'Peaxi162Scf00316g00046' => 'pax', 'Peaxi162Scf00316g00049' => 'pax', 'Peaxi162Scf00316g00059' => 'pax', 'Peaxi162Scf00316g00328' => 'pax', 'Peaxi162Scf00316g00329' => 'pax', 'Peaxi162Scf00316g00411' => 'pax', 'Peaxi162Scf00316g00521' => 'pax', 'Peaxi162Scf00492g00068' => 'pax', 'Peaxi162Scf35631g00002' => 'pax', 'PGR142G3720' => 'pgr', 'PGSC0003DMG400006442' => 'stu', 'Phvul.007G062000' => 'pvu', 'Potri.008G157750' => 'ptr', 'Potri.008G157900' => 'ptr', 'Potri.008G158000' => 'ptr', 'Potri.008G158200' => 'ptr', 'Pp3c11_7280' => 'ppa', 'Pp3c11_7980' => 'ppa', 'Pp3c12_19450' => 'ppa', 'Pp3c14_1480' => 'ppa', 'Pp3c14_1501' => 'ppa', 'Pp3c16_4900' => 'ppa', 'Pp3c16_5010' => 'ppa', 'Pp3c16_5060' => 'ppa', 'Pp3c19_18250' => 'ppa', 'Pp3c23_8530' => 'ppa', 'Pp3c23_8550' => 'ppa', 'Pp3c24_9670' => 'ppa', 'Pp3c2_21390' => 'ppa', 'Pp3c2_31380' => 'ppa', 'Pp3c3_16620' => 'ppa', 'Pp3c3_8090' => 'ppa', 'Pp3c3_8110' => 'ppa', 'Pp3c3_8130' => 'ppa', 'Pp3c3_8150' => 'ppa', 'Pp3c4_14320' => 'ppa', 'Pp3c6_2560' => 'ppa', 'Pp3c9_16700' => 'ppa', 'PRCOL_00000234' => 'pco', 'PRCOL_00000235' => 'pco', 'PRCOL_00000777' => 'pco', 'PRCOL_00002344' => 'pco', 'PRCOL_00002372' => 'pco', 'PRCOL_00006120' => 'pco', 'Prupe.1G021400' => 'ppe', 'Prupe.1G021500' => 'ppe', 'Prupe.1G021600' => 'ppe', 'Prupe.1G021700' => 'ppe', 'Prupe.1G021800' => 'ppe', 'Prupe.5G145100' => 'ppe', 'Psat6g204040' => 'psa', 'Psat6g204800' => 'psa', 'Psat6g204920' => 'psa', 'Psat6g204960' => 'psa', 'Psat6g205080' => 'psa', 'PSO017G0271' => 'pso', 'PSO017G1276' => 'pso', 'PSO017G1429' => 'pso', 'PSO017G1861' => 'pso', 'PSO017G2787' => 'pso', 'PSO017G4466' => 'pso', 'PSO017G5118' => 'pso', 'PSO017G5420' => 'pso', 'PSO063G3678' => 'pso', 'PSO210G0546' => 'pso', 'PSO317G0001' => 'pso', 'PSO357G0512' => 'pso', 'PSO478G2682' => 'pso', 'PSO647G0001' => 'pso', 'PSO675G0001' => 'pso', 'PSO675G2699' => 'pso', 'PSO675G2849' => 'pso', 'PSO675G4991' => 'pso', 'PSO689G0001' => 'pso', 'QL06p000916' => 'qlo', 'QL06p000921' => 'qlo', 'QL06p001398' => 'qlo', 'QL06p001407' => 'qlo', 'QL06p002031' => 'qlo', 'RcHm_v2.0_Chr4g0387791' => 'rch', 'RcHm_v2.0_Chr4g0387801' => 'rch', 'RcHm_v2.0_Chr6g0286501' => 'rch', 'RcHm_v2.0_Chr6g0286511' => 'rch', 'RcHm_v2.0_Chr6g0286521' => 'rch', 'RcHm_v2.0_Chr6g0286531' => 'rch', 'RcHm_v2.0_Chr7g0189141' => 'rch', 'Rhsim02G0028700' => 'rsi', 'Rhsim02G0028800' => 'rsi', 'Rhsim02G0028900' => 'rsi', 'Rhsim02G0029000' => 'rsi', 'Rhsim02G0029100' => 'rsi', 'Rhsim02G0029200' => 'rsi', 'Rhsim02G0029300' => 'rsi', 'Rhsim02G0029400' => 'rsi', 'Rhsim02G0029500' => 'rsi', 'Rhsim02G0029600' => 'rsi', 'RhsimUnG0024000' => 'rsi', 'RhsimUnG0024100' => 'rsi', 'RhsimUnG0024200' => 'rsi', 'RhsimUnG0024300' => 'rsi', 'RhsimUnG0024400' => 'rsi', 'RhsimUnG0024500' => 'rsi', 'RhsimUnG0024700' => 'rsi', 'RhsimUnG0024800' => 'rsi', 'RhsimUnG0024900' => 'rsi', 'RhsimUnG0025100' => 'rsi', 'Sabra08G0120200' => 'sbr', 'Sabra08G0120300' => 'sbr', 'Sabra08G0120500' => 'sbr', 'Sabra08G0120600' => 'sbr', 'Sabra10G0158900' => 'sbr', 'SalBow2G3492' => 'sbo', 'Sc13g0004760' => 'sci', 'Sc13g0004770' => 'sci', 'Sed0003417' => 'sed', 'Sed0019750' => 'sed', 'SEGI_03419' => 'sgi', 'SEGI_05907' => 'sgi', 'SEGI_10682' => 'sgi', 'SEGI_13528' => 'sgi', 'SEGI_16081' => 'sgi', 'SEGI_19370' => 'sgi', 'SEGI_21015' => 'sgi', 'SEGI_21944' => 'sgi', 'SEGI_32906' => 'sgi', 'SEGI_33093' => 'sgi', 'SEGI_36110' => 'sgi', 'SEGI_40397' => 'sgi', 'SGA_v2.0_scaffold191G40426' => 'sas', 'SGA_v2.0_scaffold353G49717' => 'sas', 'SGA_v2.0_scaffold50G18550' => 'sas', 'SMO119G0173' => 'smo', 'SMO172G0002' => 'smo', 'Solyc09g082690.3' => 'sly', 'Solyc09g082700.2' => 'sly', 'Sopen09g031550' => 'spe', 'Sopen09g031560' => 'spe', 'Sp3g20540' => 'spa', 'Sp7g07580' => 'spa', 'TAR134G0002' => 'tar', 'TAR236G0001' => 'tar', 'TAR365G0892' => 'tar', 'TAR636G0166' => 'tar', 'TAR636G0646' => 'tar', 'TAR636G0869' => 'tar', 'TAR636G1317' => 'tar', 'TAR636G1744' => 'tar', 'TAR636G3358' => 'tar', 'TAR636G3436' => 'tar', 'THA.LOC104803047' => 'tha', 'Thecc.04G238900' => 'tca', 'Thhalv10021557m.g' => 'esa', 'Thhalv10026318m.g' => 'esa', 'Thhalv10026335m.g' => 'esa', 'TPR.G17433' => 'tpr', 'TPR.G18915' => 'tpr', 'TPR.G26125' => 'tpr', 'TWI09G0677' => 'twi', 'TWI73G0287' => 'twi', 'unitig_748.g8326' => 'ugi', 'vmacro15370' => 'vma', 'vmacro15371' => 'vma', 'vmacro15372' => 'vma', 'vmacro15373' => 'vma', 'vmacro15374' => 'vma', 'VMungo0720G2826' => 'vmu', 'Zm00001eb116960' => 'zma', 'Zm00001eb301260' => 'zma', 'Zm00001eb301270' => 'zma' ) $gf_id = 'HOM05D001460' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001460' ) $data_identifier = 'HOM05D001460' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 4, 'aag' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 2, 'aox' => (int) 2, 'arhy' => (int) 4, 'ath' => (int) 2, 'atr' => (int) 1, 'acertr' => (int) 10, 'cqu' => (int) 4, 'bca' => (int) 11, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 1, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 1, 'ccan' => (int) 1, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 1, 'col' => (int) 1, 'cpa' => (int) 1, 'cre' => (int) 7, 'csa' => (int) 1, 'camsi' => (int) 2, 'dca' => (int) 3, 'din' => (int) 2, 'dzi' => (int) 3, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 14, 'fve' => (int) 9, 'gma' => (int) 2, 'ghi' => (int) 4, 'gra' => (int) 2, 'vvi' => (int) 1, 'han' => (int) 13, 'cav' => (int) 1, 'hma' => (int) 2, 'sun' => (int) 2, 'lal' => (int) 2, 'lonja' => (int) 12, 'lja' => (int) 1, 'lsa' => (int) 7, 'mes' => (int) 1, 'mpo' => (int) 27, 'mbi' => (int) 1, 'mco' => (int) 8, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 1, 'egut' => (int) 1, 'ama' => (int) 1, 'nta' => (int) 4, 'nnu' => (int) 2, 'oeu' => (int) 3, 'osa' => (int) 4, 'pax' => (int) 9, 'pgr' => (int) 1, 'stu' => (int) 1, 'pvu' => (int) 1, 'ptr' => (int) 4, 'ppa' => (int) 22, 'pco' => (int) 6, 'ppe' => (int) 6, 'psa' => (int) 5, 'pso' => (int) 19, 'qlo' => (int) 5, 'rch' => (int) 7, 'rsi' => (int) 20, 'sbr' => (int) 5, 'sbo' => (int) 1, 'sci' => (int) 2, 'sed' => (int) 2, 'sgi' => (int) 12, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 2, 'tar' => (int) 10, 'tha' => (int) 1, 'tca' => (int) 1, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 2, 'ugi' => (int) 1, 'vma' => (int) 5, 'vmu' => (int) 1, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb301270' $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' => 'HOM05D001460', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '433', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p22980' => 'bna', 'A01p32340' => 'bna', 'A03p42970' => 'bna', 'A05p25880' => 'bna', 'Aa31LG8G9320' => 'aar', 'Aa31LG8G9330' => 'aar', 'Aa31LG8G9340' => 'aar', 'Aa31sc221G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1034' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1528' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.829' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2222' => 'aag', 'Ah.12g058830' => 'amhyb', 'Ah.12g058840' => 'amhyb', 'AL3G37160' => 'aly', 'AL7G41310' => 'aly', 'Aqoxy5G00395' => 'aox', 'Aqoxy5G00396' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0C8NZA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5185HY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JZ1PRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MD3LS0' => 'arhy', 'AT3G22840' => 'ath', 'AT4G14690' => 'ath', 'ATR0665G054' => 'atr', 'Atru.chr4.2344' => 'acertr', 'Atru.chr4.2346' => 'acertr', 'Atru.chr4.2347' => 'acertr', 'Atru.chr4.2348' => 'acertr', 'Atru.chr4.2355' => 'acertr', 'Atru.chr4.2356' => 'acertr', 'Atru.chr4.2358' => 'acertr', 'Atru.chr4.2359' => 'acertr', 'Atru.chr4.2360' => 'acertr', 'Atru.chr4.2361' => 'acertr', 'AUR62030476' => 'cqu', 'AUR62030478' => 'cqu', 'AUR62030819' => 'cqu', 'AUR62030820' => 'cqu', 'BcaB03g14648' => 'bca', 'BcaB04g20492' => 'bca', 'BcaB06g26399' => 'bca', 'BcaC01g03416' => 'bca', 'BcaC01g03419' => 'bca', 'BcaC01g03421' => 'bca', 'BcaC01g03424' => 'bca', 'BcaC05g28012' => 'bca', 'BcaC09g49212' => 'bca', 'BcaC09g50140' => 'bca', 'BcaNung00346' => 'bca', 'BolC1t02785H' => 'bol', 'BolC1t04095H' => 'bol', 'BolC3t17545H' => 'bol', 'BolC5t32769H' => 'bol', 'BraA01t02211Z' => 'bra', 'BraA01t03359Z' => 'bra', 'BraA03t13441Z' => 'bra', 'BraA05t21476Z' => 'bra', 'C01p28420' => 'bna', 'C01p41350' => 'bna', 'C03p52750' => 'bna', 'C03p52780' => 'bna', 'C05p40270' => 'bna', 'CAN.G1437.9' => 'can', 'CANSAT78G0035' => 'cansat', 'CANSAT78G1036' => 'cansat', 'CANSAT78G2272' => 'cansat', 'CANSAT78G2478' => 'cansat', 'CARHR098700' => 'chi', 'CARHR221120' => 'chi', 'CARHR221150' => 'chi', 'Carub.0003s2297' => 'cru', 'Carub.0007s2749' => 'cru', 'Carub.0007s2750' => 'cru', 'Carub.0007s2751' => 'cru', 'Ca_10849_v3' => 'car', 'Cc03_g04300' => 'ccan', 'CDE02G3648' => 'cde', 'CDE05G0060' => 'cde', 'CDE05G0692' => 'cde', 'CDE05G2285' => 'cde', 'CDE05G2884' => 'cde', 'CDE05G3072' => 'cde', 'Cfa008439' => 'cfa', 'Cfa008441' => 'cfa', 'Cfa008443' => 'cfa', 'Cfa008448' => 'cfa', 'Ciclev10005974m.g' => 'ccl', 'Ciclev10006006m.g' => 'ccl', 'Ciclev10006775m.g' => 'ccl', 'CiPaw.02G120400' => 'cil', 'CiPaw.02G120500' => 'cil', 'CiPaw.02G120600' => 'cil', 'ClCG05G004850' => 'cla', 'COL.COLO4_21566' => 'col', 'Cpa.g.sc44.124' => 'cpa', 'Cre07.g320400' => 'cre', 'Cre07.g320450' => 'cre', 'Cre08.g384650' => 'cre', 'Cre09.g393173' => 'cre', 'Cre09.g394325' => 'cre', 'Cre14.g626750' => 'cre', 'Cre16.g679250' => 'cre', 'CsaV3_3G012890' => 'csa', 'CSS0010865' => 'camsi', 'CSS0044338' => 'camsi', 'DCAR_002366' => 'dca', 'DCAR_030687' => 'dca', 'DCAR_030688' => 'dca', 'Dinv14047' => 'din', 'Dinv14048' => 'din', 'Duzib151G0105' => 'dzi', 'Duzib151G0114' => 'dzi', 'Duzib212G1029' => 'dzi', 'ECA232G3536' => 'eca', 'ECA240G0786' => 'eca', 'ECA240G1802' => 'eca', 'ECA240G3760' => 'eca', 'ECA240G3920' => 'eca', 'EL10Ac5g12536' => 'bvu', 'EL10Ac5g12537' => 'bvu', 'EL10Ac5g12538' => 'bvu', 'Eucgr.B01004' => 'egr', 'Eucgr.B01006' => 'egr', 'Eucgr.B01007' => 'egr', 'Eucgr.B01008' => 'egr', 'Eucgr.B01895' => 'egr', 'Eucgr.B01896' => 'egr', 'FAN04G1456' => 'fan', 'FAN08G1769' => 'fan', 'FAN08G2160' => 'fan', 'FAN13G2403' => 'fan', 'FAN13G3303' => 'fan', 'FAN15G2435' => 'fan', 'FAN17G0672' => 'fan', 'FAN17G2441' => 'fan', 'FAN18G1024' => 'fan', 'FAN22G1458' => 'fan', 'FAN24G0037' => 'fan', 'FAN24G0429' => 'fan', 'FAN24G2387' => 'fan', 'FAN27G2746' => 'fan', 'FvH4_2g20400' => 'fve', 'FvH4_2g20420' => 'fve', 'FvH4_2g20430' => 'fve', 'FvH4_4g01270' => 'fve', 'FvH4_4g01290' => 'fve', 'FvH4_4g01300' => 'fve', 'FvH4_4g01310' => 'fve', 'FvH4_4g01330' => 'fve', 'FvH4_5g09070' => 'fve', 'Glyma.10G243800' => 'gma', 'Glyma.20G150600' => 'gma', 'Gohir.A09G219200' => 'ghi', 'Gohir.A09G219300' => 'ghi', 'Gohir.D09G221400' => 'ghi', 'Gohir.D09G221500' => 'ghi', 'Gorai.006G242600' => 'gra', 'Gorai.006G242700' => 'gra', 'GSVIVG01018044001' => 'vvi', 'HanXRQChr03g0083821' => 'han', 'HanXRQChr03g0083841' => 'han', 'HanXRQChr03g0083881' => 'han', 'HanXRQChr03g0083901' => 'han', 'HanXRQChr03g0083921' => 'han', 'HanXRQChr03g0085331' => 'han', 'HanXRQChr03g0085361' => 'han', 'HanXRQChr03g0085411' => 'han', 'HanXRQChr03g0085421' => 'han', 'HanXRQChr03g0085431' => 'han', 'HanXRQChr08g0221991' => 'han', 'HanXRQChr11g0336061' => 'han', 'HanXRQChr11g0336411' => 'han', 'Haze_11234' => 'cav', 'Hma1.2p1_0549F.1_g177010' => 'hma', 'Hma1.2p1_0602F.1_g187630' => 'hma', 'Hund14876' => 'sun', 'Hund14879' => 'sun', 'Lalb_Chr06g0160741' => 'lal', 'Lalb_Chr21g0304781' => 'lal', 'Lj3A726G19' => 'lonja', 'Lj3A726T23' => 'lonja', 'Lj3A726T24' => 'lonja', 'Lj3A726T25' => 'lonja', 'Lj3A727T17' => 'lonja', 'Lj3C726T0' => 'lonja', 'Lj3C726T2' => 'lonja', 'Lj3P725T35' => 'lonja', 'Lj3P727T10' => 'lonja', 'Lj3P727T12' => 'lonja', 'Lj3P727T14' => 'lonja', 'Lj5g0023109' => 'lja', 'Lj6P646T44' => 'lonja', 'Lsat_1_v5_gn_6_75760' => 'lsa', 'Lsat_1_v5_gn_6_75800' => 'lsa', 'Lsat_1_v5_gn_6_75900' => 'lsa', 'Lsat_1_v5_gn_6_76240' => 'lsa', 'Lsat_1_v5_gn_6_76441' => 'lsa', 'Lsat_1_v5_gn_6_76700' => 'lsa', 'Lsat_1_v5_gn_6_76760' => 'lsa', 'Manes.15G033100' => 'mes', 'Mapoly0004s0074' => 'mpo', 'Mapoly0004s0075' => 'mpo', 'Mapoly0004s0163' => 'mpo', 'Mapoly0004s0164' => 'mpo', 'Mapoly0021s0018' => 'mpo', 'Mapoly0041s0136' => 'mpo', 'Mapoly0041s0137' => 'mpo', 'Mapoly0041s0138' => 'mpo', 'Mapoly0041s0139' => 'mpo', 'Mapoly0041s0141' => 'mpo', 'Mapoly0041s0142' => 'mpo', 'Mapoly0041s0143' => 'mpo', 'Mapoly0041s0144' => 'mpo', 'Mapoly0041s0145' => 'mpo', 'Mapoly0047s0106' => 'mpo', 'Mapoly0047s0108' => 'mpo', 'Mapoly0050s0051' => 'mpo', 'Mapoly0050s0052' => 'mpo', 'Mapoly0050s0053' => 'mpo', 'Mapoly0058s0013' => 'mpo', 'Mapoly0091s0078' => 'mpo', 'Mapoly0091s0079' => 'mpo', 'Mapoly0091s0080' => 'mpo', 'Mapoly0091s0081' => 'mpo', 'Mapoly0278s0004' => 'mpo', 'Mapoly0278s0005' => 'mpo', 'Mapoly0278s0006' => 'mpo', 'MBI11_g30648_MAGBIO' => 'mbi', 'MCO03G194' => 'mco', 'MCO03G590' => 'mco', 'MCO07G312' => 'mco', 'MCO10G318' => 'mco', 'MCO12G244' => 'mco', 'MCO13G148' => 'mco', 'MCO13G194' => 'mco', 'MCO16G238' => 'mco', 'MD06G1134100' => 'mdo', 'MD13G1200100' => 'mdo', 'MD13G1200300' => 'mdo', 'MD13G1200600' => 'mdo', 'MD14G1150400' => 'mdo', 'MD16G1200000' => 'mdo', 'Medtr1g102570' => 'mtr', 'Medtr1g102780' => 'mtr', 'Medtr1g102800' => 'mtr', 'Medtr1g102810' => 'mtr', 'Medtr1g102830' => 'mtr', 'MELO3C006499.2' => 'cme', 'Migut.G00385' => 'egut', 'MSTRG.4063' => 'ama', 'Nitab4.5_0000090g0260' => 'nta', 'Nitab4.5_0000977g0030' => 'nta', 'Nitab4.5_0002541g0040' => 'nta', 'Nitab4.5_0007068g0040' => 'nta', 'Nn005s41408' => 'nnu', 'Nn005s41410' => 'nnu', 'Oeu010310.1' => 'oeu', 'Oeu010311.1' => 'oeu', 'Oeu043472.1' => 'oeu', 'Os01g0246400' => 'osa', 'Os04g0267950' => 'osa', 'Os07g0178700' => 'osa', 'Os07g0178800' => 'osa', 'Peaxi162Scf00316g00046' => 'pax', 'Peaxi162Scf00316g00049' => 'pax', 'Peaxi162Scf00316g00059' => 'pax', 'Peaxi162Scf00316g00328' => 'pax', 'Peaxi162Scf00316g00329' => 'pax', 'Peaxi162Scf00316g00411' => 'pax', 'Peaxi162Scf00316g00521' => 'pax', 'Peaxi162Scf00492g00068' => 'pax', 'Peaxi162Scf35631g00002' => 'pax', 'PGR142G3720' => 'pgr', 'PGSC0003DMG400006442' => 'stu', 'Phvul.007G062000' => 'pvu', 'Potri.008G157750' => 'ptr', 'Potri.008G157900' => 'ptr', 'Potri.008G158000' => 'ptr', 'Potri.008G158200' => 'ptr', 'Pp3c11_7280' => 'ppa', 'Pp3c11_7980' => 'ppa', 'Pp3c12_19450' => 'ppa', 'Pp3c14_1480' => 'ppa', 'Pp3c14_1501' => 'ppa', 'Pp3c16_4900' => 'ppa', 'Pp3c16_5010' => 'ppa', 'Pp3c16_5060' => 'ppa', 'Pp3c19_18250' => 'ppa', 'Pp3c23_8530' => 'ppa', 'Pp3c23_8550' => 'ppa', 'Pp3c24_9670' => 'ppa', 'Pp3c2_21390' => 'ppa', 'Pp3c2_31380' => 'ppa', 'Pp3c3_16620' => 'ppa', 'Pp3c3_8090' => 'ppa', 'Pp3c3_8110' => 'ppa', 'Pp3c3_8130' => 'ppa', 'Pp3c3_8150' => 'ppa', 'Pp3c4_14320' => 'ppa', 'Pp3c6_2560' => 'ppa', 'Pp3c9_16700' => 'ppa', 'PRCOL_00000234' => 'pco', 'PRCOL_00000235' => 'pco', 'PRCOL_00000777' => 'pco', 'PRCOL_00002344' => 'pco', 'PRCOL_00002372' => 'pco', 'PRCOL_00006120' => 'pco', 'Prupe.1G021400' => 'ppe', 'Prupe.1G021500' => 'ppe', 'Prupe.1G021600' => 'ppe', 'Prupe.1G021700' => 'ppe', 'Prupe.1G021800' => 'ppe', 'Prupe.5G145100' => 'ppe', 'Psat6g204040' => 'psa', 'Psat6g204800' => 'psa', 'Psat6g204920' => 'psa', 'Psat6g204960' => 'psa', 'Psat6g205080' => 'psa', 'PSO017G0271' => 'pso', 'PSO017G1276' => 'pso', 'PSO017G1429' => 'pso', 'PSO017G1861' => 'pso', 'PSO017G2787' => 'pso', 'PSO017G4466' => 'pso', 'PSO017G5118' => 'pso', 'PSO017G5420' => 'pso', 'PSO063G3678' => 'pso', 'PSO210G0546' => 'pso', 'PSO317G0001' => 'pso', 'PSO357G0512' => 'pso', 'PSO478G2682' => 'pso', 'PSO647G0001' => 'pso', 'PSO675G0001' => 'pso', 'PSO675G2699' => 'pso', 'PSO675G2849' => 'pso', 'PSO675G4991' => 'pso', 'PSO689G0001' => 'pso', 'QL06p000916' => 'qlo', 'QL06p000921' => 'qlo', 'QL06p001398' => 'qlo', 'QL06p001407' => 'qlo', 'QL06p002031' => 'qlo', 'RcHm_v2.0_Chr4g0387791' => 'rch', 'RcHm_v2.0_Chr4g0387801' => 'rch', 'RcHm_v2.0_Chr6g0286501' => 'rch', 'RcHm_v2.0_Chr6g0286511' => 'rch', 'RcHm_v2.0_Chr6g0286521' => 'rch', 'RcHm_v2.0_Chr6g0286531' => 'rch', 'RcHm_v2.0_Chr7g0189141' => 'rch', 'Rhsim02G0028700' => 'rsi', 'Rhsim02G0028800' => 'rsi', 'Rhsim02G0028900' => 'rsi', 'Rhsim02G0029000' => 'rsi', 'Rhsim02G0029100' => 'rsi', 'Rhsim02G0029200' => 'rsi', 'Rhsim02G0029300' => 'rsi', 'Rhsim02G0029400' => 'rsi', 'Rhsim02G0029500' => 'rsi', 'Rhsim02G0029600' => 'rsi', 'RhsimUnG0024000' => 'rsi', 'RhsimUnG0024100' => 'rsi', 'RhsimUnG0024200' => 'rsi', 'RhsimUnG0024300' => 'rsi', 'RhsimUnG0024400' => 'rsi', 'RhsimUnG0024500' => 'rsi', 'RhsimUnG0024700' => 'rsi', 'RhsimUnG0024800' => 'rsi', 'RhsimUnG0024900' => 'rsi', 'RhsimUnG0025100' => 'rsi', 'Sabra08G0120200' => 'sbr', 'Sabra08G0120300' => 'sbr', 'Sabra08G0120500' => 'sbr', 'Sabra08G0120600' => 'sbr', 'Sabra10G0158900' => 'sbr', 'SalBow2G3492' => 'sbo', 'Sc13g0004760' => 'sci', 'Sc13g0004770' => 'sci', 'Sed0003417' => 'sed', 'Sed0019750' => 'sed', 'SEGI_03419' => 'sgi', 'SEGI_05907' => 'sgi', 'SEGI_10682' => 'sgi', 'SEGI_13528' => 'sgi', 'SEGI_16081' => 'sgi', 'SEGI_19370' => 'sgi', 'SEGI_21015' => 'sgi', 'SEGI_21944' => 'sgi', 'SEGI_32906' => 'sgi', 'SEGI_33093' => 'sgi', 'SEGI_36110' => 'sgi', 'SEGI_40397' => 'sgi', 'SGA_v2.0_scaffold191G40426' => 'sas', 'SGA_v2.0_scaffold353G49717' => 'sas', 'SGA_v2.0_scaffold50G18550' => 'sas', 'SMO119G0173' => 'smo', 'SMO172G0002' => 'smo', 'Solyc09g082690.3' => 'sly', 'Solyc09g082700.2' => 'sly', 'Sopen09g031550' => 'spe', 'Sopen09g031560' => 'spe', 'Sp3g20540' => 'spa', 'Sp7g07580' => 'spa', 'TAR134G0002' => 'tar', 'TAR236G0001' => 'tar', 'TAR365G0892' => 'tar', 'TAR636G0166' => 'tar', 'TAR636G0646' => 'tar', 'TAR636G0869' => 'tar', 'TAR636G1317' => 'tar', 'TAR636G1744' => 'tar', 'TAR636G3358' => 'tar', 'TAR636G3436' => 'tar', 'THA.LOC104803047' => 'tha', 'Thecc.04G238900' => 'tca', 'Thhalv10021557m.g' => 'esa', 'Thhalv10026318m.g' => 'esa', 'Thhalv10026335m.g' => 'esa', 'TPR.G17433' => 'tpr', 'TPR.G18915' => 'tpr', 'TPR.G26125' => 'tpr', 'TWI09G0677' => 'twi', 'TWI73G0287' => 'twi', 'unitig_748.g8326' => 'ugi', 'vmacro15370' => 'vma', 'vmacro15371' => 'vma', 'vmacro15372' => 'vma', 'vmacro15373' => 'vma', 'vmacro15374' => 'vma', 'VMungo0720G2826' => 'vmu', 'Zm00001eb116960' => 'zma', 'Zm00001eb301260' => 'zma', 'Zm00001eb301270' => 'zma' ), 'gf_id' => 'HOM05D001460', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001460' ), 'data_identifier' => 'HOM05D001460', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001460', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '433', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p22980' => 'bna', 'A01p32340' => 'bna', 'A03p42970' => 'bna', 'A05p25880' => 'bna', 'Aa31LG8G9320' => 'aar', 'Aa31LG8G9330' => 'aar', 'Aa31LG8G9340' => 'aar', 'Aa31sc221G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1034' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1528' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.829' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2222' => 'aag', 'Ah.12g058830' => 'amhyb', 'Ah.12g058840' => 'amhyb', 'AL3G37160' => 'aly', 'AL7G41310' => 'aly', 'Aqoxy5G00395' => 'aox', 'Aqoxy5G00396' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0C8NZA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5185HY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JZ1PRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MD3LS0' => 'arhy', 'AT3G22840' => 'ath', 'AT4G14690' => 'ath', 'ATR0665G054' => 'atr', 'Atru.chr4.2344' => 'acertr', 'Atru.chr4.2346' => 'acertr', 'Atru.chr4.2347' => 'acertr', 'Atru.chr4.2348' => 'acertr', 'Atru.chr4.2355' => 'acertr', 'Atru.chr4.2356' => 'acertr', 'Atru.chr4.2358' => 'acertr', 'Atru.chr4.2359' => 'acertr', 'Atru.chr4.2360' => 'acertr', 'Atru.chr4.2361' => 'acertr', 'AUR62030476' => 'cqu', 'AUR62030478' => 'cqu', 'AUR62030819' => 'cqu', 'AUR62030820' => 'cqu', 'BcaB03g14648' => 'bca', 'BcaB04g20492' => 'bca', 'BcaB06g26399' => 'bca', 'BcaC01g03416' => 'bca', 'BcaC01g03419' => 'bca', 'BcaC01g03421' => 'bca', 'BcaC01g03424' => 'bca', 'BcaC05g28012' => 'bca', 'BcaC09g49212' => 'bca', 'BcaC09g50140' => 'bca', 'BcaNung00346' => 'bca', 'BolC1t02785H' => 'bol', 'BolC1t04095H' => 'bol', 'BolC3t17545H' => 'bol', 'BolC5t32769H' => 'bol', 'BraA01t02211Z' => 'bra', 'BraA01t03359Z' => 'bra', 'BraA03t13441Z' => 'bra', 'BraA05t21476Z' => 'bra', 'C01p28420' => 'bna', 'C01p41350' => 'bna', 'C03p52750' => 'bna', 'C03p52780' => 'bna', 'C05p40270' => 'bna', 'CAN.G1437.9' => 'can', 'CANSAT78G0035' => 'cansat', 'CANSAT78G1036' => 'cansat', 'CANSAT78G2272' => 'cansat', 'CANSAT78G2478' => 'cansat', 'CARHR098700' => 'chi', 'CARHR221120' => 'chi', 'CARHR221150' => 'chi', 'Carub.0003s2297' => 'cru', 'Carub.0007s2749' => 'cru', 'Carub.0007s2750' => 'cru', 'Carub.0007s2751' => 'cru', 'Ca_10849_v3' => 'car', 'Cc03_g04300' => 'ccan', 'CDE02G3648' => 'cde', 'CDE05G0060' => 'cde', 'CDE05G0692' => 'cde', 'CDE05G2285' => 'cde', 'CDE05G2884' => 'cde', 'CDE05G3072' => 'cde', 'Cfa008439' => 'cfa', 'Cfa008441' => 'cfa', 'Cfa008443' => 'cfa', 'Cfa008448' => 'cfa', 'Ciclev10005974m.g' => 'ccl', 'Ciclev10006006m.g' => 'ccl', 'Ciclev10006775m.g' => 'ccl', 'CiPaw.02G120400' => 'cil', 'CiPaw.02G120500' => 'cil', 'CiPaw.02G120600' => 'cil', 'ClCG05G004850' => 'cla', 'COL.COLO4_21566' => 'col', 'Cpa.g.sc44.124' => 'cpa', 'Cre07.g320400' => 'cre', 'Cre07.g320450' => 'cre', 'Cre08.g384650' => 'cre', 'Cre09.g393173' => 'cre', 'Cre09.g394325' => 'cre', 'Cre14.g626750' => 'cre', 'Cre16.g679250' => 'cre', 'CsaV3_3G012890' => 'csa', 'CSS0010865' => 'camsi', 'CSS0044338' => 'camsi', 'DCAR_002366' => 'dca', 'DCAR_030687' => 'dca', 'DCAR_030688' => 'dca', 'Dinv14047' => 'din', 'Dinv14048' => 'din', 'Duzib151G0105' => 'dzi', 'Duzib151G0114' => 'dzi', 'Duzib212G1029' => 'dzi', 'ECA232G3536' => 'eca', 'ECA240G0786' => 'eca', 'ECA240G1802' => 'eca', 'ECA240G3760' => 'eca', 'ECA240G3920' => 'eca', 'EL10Ac5g12536' => 'bvu', 'EL10Ac5g12537' => 'bvu', 'EL10Ac5g12538' => 'bvu', 'Eucgr.B01004' => 'egr', 'Eucgr.B01006' => 'egr', 'Eucgr.B01007' => 'egr', 'Eucgr.B01008' => 'egr', 'Eucgr.B01895' => 'egr', 'Eucgr.B01896' => 'egr', 'FAN04G1456' => 'fan', 'FAN08G1769' => 'fan', 'FAN08G2160' => 'fan', 'FAN13G2403' => 'fan', 'FAN13G3303' => 'fan', 'FAN15G2435' => 'fan', 'FAN17G0672' => 'fan', 'FAN17G2441' => 'fan', 'FAN18G1024' => 'fan', 'FAN22G1458' => 'fan', 'FAN24G0037' => 'fan', 'FAN24G0429' => 'fan', 'FAN24G2387' => 'fan', 'FAN27G2746' => 'fan', 'FvH4_2g20400' => 'fve', 'FvH4_2g20420' => 'fve', 'FvH4_2g20430' => 'fve', 'FvH4_4g01270' => 'fve', 'FvH4_4g01290' => 'fve', 'FvH4_4g01300' => 'fve', 'FvH4_4g01310' => 'fve', 'FvH4_4g01330' => 'fve', 'FvH4_5g09070' => 'fve', 'Glyma.10G243800' => 'gma', 'Glyma.20G150600' => 'gma', 'Gohir.A09G219200' => 'ghi', 'Gohir.A09G219300' => 'ghi', 'Gohir.D09G221400' => 'ghi', 'Gohir.D09G221500' => 'ghi', 'Gorai.006G242600' => 'gra', 'Gorai.006G242700' => 'gra', 'GSVIVG01018044001' => 'vvi', 'HanXRQChr03g0083821' => 'han', 'HanXRQChr03g0083841' => 'han', 'HanXRQChr03g0083881' => 'han', 'HanXRQChr03g0083901' => 'han', 'HanXRQChr03g0083921' => 'han', 'HanXRQChr03g0085331' => 'han', 'HanXRQChr03g0085361' => 'han', 'HanXRQChr03g0085411' => 'han', 'HanXRQChr03g0085421' => 'han', 'HanXRQChr03g0085431' => 'han', 'HanXRQChr08g0221991' => 'han', 'HanXRQChr11g0336061' => 'han', 'HanXRQChr11g0336411' => 'han', 'Haze_11234' => 'cav', 'Hma1.2p1_0549F.1_g177010' => 'hma', 'Hma1.2p1_0602F.1_g187630' => 'hma', 'Hund14876' => 'sun', 'Hund14879' => 'sun', 'Lalb_Chr06g0160741' => 'lal', 'Lalb_Chr21g0304781' => 'lal', 'Lj3A726G19' => 'lonja', 'Lj3A726T23' => 'lonja', 'Lj3A726T24' => 'lonja', 'Lj3A726T25' => 'lonja', 'Lj3A727T17' => 'lonja', 'Lj3C726T0' => 'lonja', 'Lj3C726T2' => 'lonja', 'Lj3P725T35' => 'lonja', 'Lj3P727T10' => 'lonja', 'Lj3P727T12' => 'lonja', 'Lj3P727T14' => 'lonja', 'Lj5g0023109' => 'lja', 'Lj6P646T44' => 'lonja', 'Lsat_1_v5_gn_6_75760' => 'lsa', 'Lsat_1_v5_gn_6_75800' => 'lsa', 'Lsat_1_v5_gn_6_75900' => 'lsa', 'Lsat_1_v5_gn_6_76240' => 'lsa', 'Lsat_1_v5_gn_6_76441' => 'lsa', 'Lsat_1_v5_gn_6_76700' => 'lsa', 'Lsat_1_v5_gn_6_76760' => 'lsa', 'Manes.15G033100' => 'mes', 'Mapoly0004s0074' => 'mpo', 'Mapoly0004s0075' => 'mpo', 'Mapoly0004s0163' => 'mpo', 'Mapoly0004s0164' => 'mpo', 'Mapoly0021s0018' => 'mpo', 'Mapoly0041s0136' => 'mpo', 'Mapoly0041s0137' => 'mpo', 'Mapoly0041s0138' => 'mpo', 'Mapoly0041s0139' => 'mpo', 'Mapoly0041s0141' => 'mpo', 'Mapoly0041s0142' => 'mpo', 'Mapoly0041s0143' => 'mpo', 'Mapoly0041s0144' => 'mpo', 'Mapoly0041s0145' => 'mpo', 'Mapoly0047s0106' => 'mpo', 'Mapoly0047s0108' => 'mpo', 'Mapoly0050s0051' => 'mpo', 'Mapoly0050s0052' => 'mpo', 'Mapoly0050s0053' => 'mpo', 'Mapoly0058s0013' => 'mpo', 'Mapoly0091s0078' => 'mpo', 'Mapoly0091s0079' => 'mpo', 'Mapoly0091s0080' => 'mpo', 'Mapoly0091s0081' => 'mpo', 'Mapoly0278s0004' => 'mpo', 'Mapoly0278s0005' => 'mpo', 'Mapoly0278s0006' => 'mpo', 'MBI11_g30648_MAGBIO' => 'mbi', 'MCO03G194' => 'mco', 'MCO03G590' => 'mco', 'MCO07G312' => 'mco', 'MCO10G318' => 'mco', 'MCO12G244' => 'mco', 'MCO13G148' => 'mco', 'MCO13G194' => 'mco', 'MCO16G238' => 'mco', 'MD06G1134100' => 'mdo', 'MD13G1200100' => 'mdo', 'MD13G1200300' => 'mdo', 'MD13G1200600' => 'mdo', 'MD14G1150400' => 'mdo', 'MD16G1200000' => 'mdo', 'Medtr1g102570' => 'mtr', 'Medtr1g102780' => 'mtr', 'Medtr1g102800' => 'mtr', 'Medtr1g102810' => 'mtr', 'Medtr1g102830' => 'mtr', 'MELO3C006499.2' => 'cme', 'Migut.G00385' => 'egut', 'MSTRG.4063' => 'ama', 'Nitab4.5_0000090g0260' => 'nta', 'Nitab4.5_0000977g0030' => 'nta', 'Nitab4.5_0002541g0040' => 'nta', 'Nitab4.5_0007068g0040' => 'nta', 'Nn005s41408' => 'nnu', 'Nn005s41410' => 'nnu', 'Oeu010310.1' => 'oeu', 'Oeu010311.1' => 'oeu', 'Oeu043472.1' => 'oeu', 'Os01g0246400' => 'osa', 'Os04g0267950' => 'osa', 'Os07g0178700' => 'osa', 'Os07g0178800' => 'osa', 'Peaxi162Scf00316g00046' => 'pax', 'Peaxi162Scf00316g00049' => 'pax', 'Peaxi162Scf00316g00059' => 'pax', 'Peaxi162Scf00316g00328' => 'pax', 'Peaxi162Scf00316g00329' => 'pax', 'Peaxi162Scf00316g00411' => 'pax', 'Peaxi162Scf00316g00521' => 'pax', 'Peaxi162Scf00492g00068' => 'pax', 'Peaxi162Scf35631g00002' => 'pax', 'PGR142G3720' => 'pgr', 'PGSC0003DMG400006442' => 'stu', 'Phvul.007G062000' => 'pvu', 'Potri.008G157750' => 'ptr', 'Potri.008G157900' => 'ptr', 'Potri.008G158000' => 'ptr', 'Potri.008G158200' => 'ptr', 'Pp3c11_7280' => 'ppa', 'Pp3c11_7980' => 'ppa', 'Pp3c12_19450' => 'ppa', 'Pp3c14_1480' => 'ppa', 'Pp3c14_1501' => 'ppa', 'Pp3c16_4900' => 'ppa', 'Pp3c16_5010' => 'ppa', 'Pp3c16_5060' => 'ppa', 'Pp3c19_18250' => 'ppa', 'Pp3c23_8530' => 'ppa', 'Pp3c23_8550' => 'ppa', 'Pp3c24_9670' => 'ppa', 'Pp3c2_21390' => 'ppa', 'Pp3c2_31380' => 'ppa', 'Pp3c3_16620' => 'ppa', 'Pp3c3_8090' => 'ppa', 'Pp3c3_8110' => 'ppa', 'Pp3c3_8130' => 'ppa', 'Pp3c3_8150' => 'ppa', 'Pp3c4_14320' => 'ppa', 'Pp3c6_2560' => 'ppa', 'Pp3c9_16700' => 'ppa', 'PRCOL_00000234' => 'pco', 'PRCOL_00000235' => 'pco', 'PRCOL_00000777' => 'pco', 'PRCOL_00002344' => 'pco', 'PRCOL_00002372' => 'pco', 'PRCOL_00006120' => 'pco', 'Prupe.1G021400' => 'ppe', 'Prupe.1G021500' => 'ppe', 'Prupe.1G021600' => 'ppe', 'Prupe.1G021700' => 'ppe', 'Prupe.1G021800' => 'ppe', 'Prupe.5G145100' => 'ppe', 'Psat6g204040' => 'psa', 'Psat6g204800' => 'psa', 'Psat6g204920' => 'psa', 'Psat6g204960' => 'psa', 'Psat6g205080' => 'psa', 'PSO017G0271' => 'pso', 'PSO017G1276' => 'pso', 'PSO017G1429' => 'pso', 'PSO017G1861' => 'pso', 'PSO017G2787' => 'pso', 'PSO017G4466' => 'pso', 'PSO017G5118' => 'pso', 'PSO017G5420' => 'pso', 'PSO063G3678' => 'pso', 'PSO210G0546' => 'pso', 'PSO317G0001' => 'pso', 'PSO357G0512' => 'pso', 'PSO478G2682' => 'pso', 'PSO647G0001' => 'pso', 'PSO675G0001' => 'pso', 'PSO675G2699' => 'pso', 'PSO675G2849' => 'pso', 'PSO675G4991' => 'pso', 'PSO689G0001' => 'pso', 'QL06p000916' => 'qlo', 'QL06p000921' => 'qlo', 'QL06p001398' => 'qlo', 'QL06p001407' => 'qlo', 'QL06p002031' => 'qlo', 'RcHm_v2.0_Chr4g0387791' => 'rch', 'RcHm_v2.0_Chr4g0387801' => 'rch', 'RcHm_v2.0_Chr6g0286501' => 'rch', 'RcHm_v2.0_Chr6g0286511' => 'rch', 'RcHm_v2.0_Chr6g0286521' => 'rch', 'RcHm_v2.0_Chr6g0286531' => 'rch', 'RcHm_v2.0_Chr7g0189141' => 'rch', 'Rhsim02G0028700' => 'rsi', 'Rhsim02G0028800' => 'rsi', 'Rhsim02G0028900' => 'rsi', 'Rhsim02G0029000' => 'rsi', 'Rhsim02G0029100' => 'rsi', 'Rhsim02G0029200' => 'rsi', 'Rhsim02G0029300' => 'rsi', 'Rhsim02G0029400' => 'rsi', 'Rhsim02G0029500' => 'rsi', 'Rhsim02G0029600' => 'rsi', 'RhsimUnG0024000' => 'rsi', 'RhsimUnG0024100' => 'rsi', 'RhsimUnG0024200' => 'rsi', 'RhsimUnG0024300' => 'rsi', 'RhsimUnG0024400' => 'rsi', 'RhsimUnG0024500' => 'rsi', 'RhsimUnG0024700' => 'rsi', 'RhsimUnG0024800' => 'rsi', 'RhsimUnG0024900' => 'rsi', 'RhsimUnG0025100' => 'rsi', 'Sabra08G0120200' => 'sbr', 'Sabra08G0120300' => 'sbr', 'Sabra08G0120500' => 'sbr', 'Sabra08G0120600' => 'sbr', 'Sabra10G0158900' => 'sbr', 'SalBow2G3492' => 'sbo', 'Sc13g0004760' => 'sci', 'Sc13g0004770' => 'sci', 'Sed0003417' => 'sed', 'Sed0019750' => 'sed', 'SEGI_03419' => 'sgi', 'SEGI_05907' => 'sgi', 'SEGI_10682' => 'sgi', 'SEGI_13528' => 'sgi', 'SEGI_16081' => 'sgi', 'SEGI_19370' => 'sgi', 'SEGI_21015' => 'sgi', 'SEGI_21944' => 'sgi', 'SEGI_32906' => 'sgi', 'SEGI_33093' => 'sgi', 'SEGI_36110' => 'sgi', 'SEGI_40397' => 'sgi', 'SGA_v2.0_scaffold191G40426' => 'sas', 'SGA_v2.0_scaffold353G49717' => 'sas', 'SGA_v2.0_scaffold50G18550' => 'sas', 'SMO119G0173' => 'smo', 'SMO172G0002' => 'smo', 'Solyc09g082690.3' => 'sly', 'Solyc09g082700.2' => 'sly', 'Sopen09g031550' => 'spe', 'Sopen09g031560' => 'spe', 'Sp3g20540' => 'spa', 'Sp7g07580' => 'spa', 'TAR134G0002' => 'tar', 'TAR236G0001' => 'tar', 'TAR365G0892' => 'tar', 'TAR636G0166' => 'tar', 'TAR636G0646' => 'tar', 'TAR636G0869' => 'tar', 'TAR636G1317' => 'tar', 'TAR636G1744' => 'tar', 'TAR636G3358' => 'tar', 'TAR636G3436' => 'tar', 'THA.LOC104803047' => 'tha', 'Thecc.04G238900' => 'tca', 'Thhalv10021557m.g' => 'esa', 'Thhalv10026318m.g' => 'esa', 'Thhalv10026335m.g' => 'esa', 'TPR.G17433' => 'tpr', 'TPR.G18915' => 'tpr', 'TPR.G26125' => 'tpr', 'TWI09G0677' => 'twi', 'TWI73G0287' => 'twi', 'unitig_748.g8326' => 'ugi', 'vmacro15370' => 'vma', 'vmacro15371' => 'vma', 'vmacro15372' => 'vma', 'vmacro15373' => 'vma', 'vmacro15374' => 'vma', 'VMungo0720G2826' => 'vmu', 'Zm00001eb116960' => 'zma', 'Zm00001eb301260' => 'zma', 'Zm00001eb301270' => 'zma' ) $gf_id = 'HOM05D001460' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001460' ) $data_identifier = 'HOM05D001460' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 4, 'aag' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 2, 'aox' => (int) 2, 'arhy' => (int) 4, 'ath' => (int) 2, 'atr' => (int) 1, 'acertr' => (int) 10, 'cqu' => (int) 4, 'bca' => (int) 11, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 1, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 1, 'ccan' => (int) 1, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 1, 'col' => (int) 1, 'cpa' => (int) 1, 'cre' => (int) 7, 'csa' => (int) 1, 'camsi' => (int) 2, 'dca' => (int) 3, 'din' => (int) 2, 'dzi' => (int) 3, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 14, 'fve' => (int) 9, 'gma' => (int) 2, 'ghi' => (int) 4, 'gra' => (int) 2, 'vvi' => (int) 1, 'han' => (int) 13, 'cav' => (int) 1, 'hma' => (int) 2, 'sun' => (int) 2, 'lal' => (int) 2, 'lonja' => (int) 12, 'lja' => (int) 1, 'lsa' => (int) 7, 'mes' => (int) 1, 'mpo' => (int) 27, 'mbi' => (int) 1, 'mco' => (int) 8, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 1, 'egut' => (int) 1, 'ama' => (int) 1, 'nta' => (int) 4, 'nnu' => (int) 2, 'oeu' => (int) 3, 'osa' => (int) 4, 'pax' => (int) 9, 'pgr' => (int) 1, 'stu' => (int) 1, 'pvu' => (int) 1, 'ptr' => (int) 4, 'ppa' => (int) 22, 'pco' => (int) 6, 'ppe' => (int) 6, 'psa' => (int) 5, 'pso' => (int) 19, 'qlo' => (int) 5, 'rch' => (int) 7, 'rsi' => (int) 20, 'sbr' => (int) 5, 'sbo' => (int) 1, 'sci' => (int) 2, 'sed' => (int) 2, 'sgi' => (int) 12, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 2, 'tar' => (int) 10, 'tha' => (int) 1, 'tca' => (int) 1, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 2, 'ugi' => (int) 1, 'vma' => (int) 5, 'vmu' => (int) 1, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb301270' $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' => 'HOM05D001460', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '433', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p22980' => 'bna', 'A01p32340' => 'bna', 'A03p42970' => 'bna', 'A05p25880' => 'bna', 'Aa31LG8G9320' => 'aar', 'Aa31LG8G9330' => 'aar', 'Aa31LG8G9340' => 'aar', 'Aa31sc221G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1034' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1528' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.829' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2222' => 'aag', 'Ah.12g058830' => 'amhyb', 'Ah.12g058840' => 'amhyb', 'AL3G37160' => 'aly', 'AL7G41310' => 'aly', 'Aqoxy5G00395' => 'aox', 'Aqoxy5G00396' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0C8NZA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5185HY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JZ1PRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MD3LS0' => 'arhy', 'AT3G22840' => 'ath', 'AT4G14690' => 'ath', 'ATR0665G054' => 'atr', 'Atru.chr4.2344' => 'acertr', 'Atru.chr4.2346' => 'acertr', 'Atru.chr4.2347' => 'acertr', 'Atru.chr4.2348' => 'acertr', 'Atru.chr4.2355' => 'acertr', 'Atru.chr4.2356' => 'acertr', 'Atru.chr4.2358' => 'acertr', 'Atru.chr4.2359' => 'acertr', 'Atru.chr4.2360' => 'acertr', 'Atru.chr4.2361' => 'acertr', 'AUR62030476' => 'cqu', 'AUR62030478' => 'cqu', 'AUR62030819' => 'cqu', 'AUR62030820' => 'cqu', 'BcaB03g14648' => 'bca', 'BcaB04g20492' => 'bca', 'BcaB06g26399' => 'bca', 'BcaC01g03416' => 'bca', 'BcaC01g03419' => 'bca', 'BcaC01g03421' => 'bca', 'BcaC01g03424' => 'bca', 'BcaC05g28012' => 'bca', 'BcaC09g49212' => 'bca', 'BcaC09g50140' => 'bca', 'BcaNung00346' => 'bca', 'BolC1t02785H' => 'bol', 'BolC1t04095H' => 'bol', 'BolC3t17545H' => 'bol', 'BolC5t32769H' => 'bol', 'BraA01t02211Z' => 'bra', 'BraA01t03359Z' => 'bra', 'BraA03t13441Z' => 'bra', 'BraA05t21476Z' => 'bra', 'C01p28420' => 'bna', 'C01p41350' => 'bna', 'C03p52750' => 'bna', 'C03p52780' => 'bna', 'C05p40270' => 'bna', 'CAN.G1437.9' => 'can', 'CANSAT78G0035' => 'cansat', 'CANSAT78G1036' => 'cansat', 'CANSAT78G2272' => 'cansat', 'CANSAT78G2478' => 'cansat', 'CARHR098700' => 'chi', 'CARHR221120' => 'chi', 'CARHR221150' => 'chi', 'Carub.0003s2297' => 'cru', 'Carub.0007s2749' => 'cru', 'Carub.0007s2750' => 'cru', 'Carub.0007s2751' => 'cru', 'Ca_10849_v3' => 'car', 'Cc03_g04300' => 'ccan', 'CDE02G3648' => 'cde', 'CDE05G0060' => 'cde', 'CDE05G0692' => 'cde', 'CDE05G2285' => 'cde', 'CDE05G2884' => 'cde', 'CDE05G3072' => 'cde', 'Cfa008439' => 'cfa', 'Cfa008441' => 'cfa', 'Cfa008443' => 'cfa', 'Cfa008448' => 'cfa', 'Ciclev10005974m.g' => 'ccl', 'Ciclev10006006m.g' => 'ccl', 'Ciclev10006775m.g' => 'ccl', 'CiPaw.02G120400' => 'cil', 'CiPaw.02G120500' => 'cil', 'CiPaw.02G120600' => 'cil', 'ClCG05G004850' => 'cla', 'COL.COLO4_21566' => 'col', 'Cpa.g.sc44.124' => 'cpa', 'Cre07.g320400' => 'cre', 'Cre07.g320450' => 'cre', 'Cre08.g384650' => 'cre', 'Cre09.g393173' => 'cre', 'Cre09.g394325' => 'cre', 'Cre14.g626750' => 'cre', 'Cre16.g679250' => 'cre', 'CsaV3_3G012890' => 'csa', 'CSS0010865' => 'camsi', 'CSS0044338' => 'camsi', 'DCAR_002366' => 'dca', 'DCAR_030687' => 'dca', 'DCAR_030688' => 'dca', 'Dinv14047' => 'din', 'Dinv14048' => 'din', 'Duzib151G0105' => 'dzi', 'Duzib151G0114' => 'dzi', 'Duzib212G1029' => 'dzi', 'ECA232G3536' => 'eca', 'ECA240G0786' => 'eca', 'ECA240G1802' => 'eca', 'ECA240G3760' => 'eca', 'ECA240G3920' => 'eca', 'EL10Ac5g12536' => 'bvu', 'EL10Ac5g12537' => 'bvu', 'EL10Ac5g12538' => 'bvu', 'Eucgr.B01004' => 'egr', 'Eucgr.B01006' => 'egr', 'Eucgr.B01007' => 'egr', 'Eucgr.B01008' => 'egr', 'Eucgr.B01895' => 'egr', 'Eucgr.B01896' => 'egr', 'FAN04G1456' => 'fan', 'FAN08G1769' => 'fan', 'FAN08G2160' => 'fan', 'FAN13G2403' => 'fan', 'FAN13G3303' => 'fan', 'FAN15G2435' => 'fan', 'FAN17G0672' => 'fan', 'FAN17G2441' => 'fan', 'FAN18G1024' => 'fan', 'FAN22G1458' => 'fan', 'FAN24G0037' => 'fan', 'FAN24G0429' => 'fan', 'FAN24G2387' => 'fan', 'FAN27G2746' => 'fan', 'FvH4_2g20400' => 'fve', 'FvH4_2g20420' => 'fve', 'FvH4_2g20430' => 'fve', 'FvH4_4g01270' => 'fve', 'FvH4_4g01290' => 'fve', 'FvH4_4g01300' => 'fve', 'FvH4_4g01310' => 'fve', 'FvH4_4g01330' => 'fve', 'FvH4_5g09070' => 'fve', 'Glyma.10G243800' => 'gma', 'Glyma.20G150600' => 'gma', 'Gohir.A09G219200' => 'ghi', 'Gohir.A09G219300' => 'ghi', 'Gohir.D09G221400' => 'ghi', 'Gohir.D09G221500' => 'ghi', 'Gorai.006G242600' => 'gra', 'Gorai.006G242700' => 'gra', 'GSVIVG01018044001' => 'vvi', 'HanXRQChr03g0083821' => 'han', 'HanXRQChr03g0083841' => 'han', 'HanXRQChr03g0083881' => 'han', 'HanXRQChr03g0083901' => 'han', 'HanXRQChr03g0083921' => 'han', 'HanXRQChr03g0085331' => 'han', 'HanXRQChr03g0085361' => 'han', 'HanXRQChr03g0085411' => 'han', 'HanXRQChr03g0085421' => 'han', 'HanXRQChr03g0085431' => 'han', 'HanXRQChr08g0221991' => 'han', 'HanXRQChr11g0336061' => 'han', 'HanXRQChr11g0336411' => 'han', 'Haze_11234' => 'cav', 'Hma1.2p1_0549F.1_g177010' => 'hma', 'Hma1.2p1_0602F.1_g187630' => 'hma', 'Hund14876' => 'sun', 'Hund14879' => 'sun', 'Lalb_Chr06g0160741' => 'lal', 'Lalb_Chr21g0304781' => 'lal', 'Lj3A726G19' => 'lonja', 'Lj3A726T23' => 'lonja', 'Lj3A726T24' => 'lonja', 'Lj3A726T25' => 'lonja', 'Lj3A727T17' => 'lonja', 'Lj3C726T0' => 'lonja', 'Lj3C726T2' => 'lonja', 'Lj3P725T35' => 'lonja', 'Lj3P727T10' => 'lonja', 'Lj3P727T12' => 'lonja', 'Lj3P727T14' => 'lonja', 'Lj5g0023109' => 'lja', 'Lj6P646T44' => 'lonja', 'Lsat_1_v5_gn_6_75760' => 'lsa', 'Lsat_1_v5_gn_6_75800' => 'lsa', 'Lsat_1_v5_gn_6_75900' => 'lsa', 'Lsat_1_v5_gn_6_76240' => 'lsa', 'Lsat_1_v5_gn_6_76441' => 'lsa', 'Lsat_1_v5_gn_6_76700' => 'lsa', 'Lsat_1_v5_gn_6_76760' => 'lsa', 'Manes.15G033100' => 'mes', 'Mapoly0004s0074' => 'mpo', 'Mapoly0004s0075' => 'mpo', 'Mapoly0004s0163' => 'mpo', 'Mapoly0004s0164' => 'mpo', 'Mapoly0021s0018' => 'mpo', 'Mapoly0041s0136' => 'mpo', 'Mapoly0041s0137' => 'mpo', 'Mapoly0041s0138' => 'mpo', 'Mapoly0041s0139' => 'mpo', 'Mapoly0041s0141' => 'mpo', 'Mapoly0041s0142' => 'mpo', 'Mapoly0041s0143' => 'mpo', 'Mapoly0041s0144' => 'mpo', 'Mapoly0041s0145' => 'mpo', 'Mapoly0047s0106' => 'mpo', 'Mapoly0047s0108' => 'mpo', 'Mapoly0050s0051' => 'mpo', 'Mapoly0050s0052' => 'mpo', 'Mapoly0050s0053' => 'mpo', 'Mapoly0058s0013' => 'mpo', 'Mapoly0091s0078' => 'mpo', 'Mapoly0091s0079' => 'mpo', 'Mapoly0091s0080' => 'mpo', 'Mapoly0091s0081' => 'mpo', 'Mapoly0278s0004' => 'mpo', 'Mapoly0278s0005' => 'mpo', 'Mapoly0278s0006' => 'mpo', 'MBI11_g30648_MAGBIO' => 'mbi', 'MCO03G194' => 'mco', 'MCO03G590' => 'mco', 'MCO07G312' => 'mco', 'MCO10G318' => 'mco', 'MCO12G244' => 'mco', 'MCO13G148' => 'mco', 'MCO13G194' => 'mco', 'MCO16G238' => 'mco', 'MD06G1134100' => 'mdo', 'MD13G1200100' => 'mdo', 'MD13G1200300' => 'mdo', 'MD13G1200600' => 'mdo', 'MD14G1150400' => 'mdo', 'MD16G1200000' => 'mdo', 'Medtr1g102570' => 'mtr', 'Medtr1g102780' => 'mtr', 'Medtr1g102800' => 'mtr', 'Medtr1g102810' => 'mtr', 'Medtr1g102830' => 'mtr', 'MELO3C006499.2' => 'cme', 'Migut.G00385' => 'egut', 'MSTRG.4063' => 'ama', 'Nitab4.5_0000090g0260' => 'nta', 'Nitab4.5_0000977g0030' => 'nta', 'Nitab4.5_0002541g0040' => 'nta', 'Nitab4.5_0007068g0040' => 'nta', 'Nn005s41408' => 'nnu', 'Nn005s41410' => 'nnu', 'Oeu010310.1' => 'oeu', 'Oeu010311.1' => 'oeu', 'Oeu043472.1' => 'oeu', 'Os01g0246400' => 'osa', 'Os04g0267950' => 'osa', 'Os07g0178700' => 'osa', 'Os07g0178800' => 'osa', 'Peaxi162Scf00316g00046' => 'pax', 'Peaxi162Scf00316g00049' => 'pax', 'Peaxi162Scf00316g00059' => 'pax', 'Peaxi162Scf00316g00328' => 'pax', 'Peaxi162Scf00316g00329' => 'pax', 'Peaxi162Scf00316g00411' => 'pax', 'Peaxi162Scf00316g00521' => 'pax', 'Peaxi162Scf00492g00068' => 'pax', 'Peaxi162Scf35631g00002' => 'pax', 'PGR142G3720' => 'pgr', 'PGSC0003DMG400006442' => 'stu', 'Phvul.007G062000' => 'pvu', 'Potri.008G157750' => 'ptr', 'Potri.008G157900' => 'ptr', 'Potri.008G158000' => 'ptr', 'Potri.008G158200' => 'ptr', 'Pp3c11_7280' => 'ppa', 'Pp3c11_7980' => 'ppa', 'Pp3c12_19450' => 'ppa', 'Pp3c14_1480' => 'ppa', 'Pp3c14_1501' => 'ppa', 'Pp3c16_4900' => 'ppa', 'Pp3c16_5010' => 'ppa', 'Pp3c16_5060' => 'ppa', 'Pp3c19_18250' => 'ppa', 'Pp3c23_8530' => 'ppa', 'Pp3c23_8550' => 'ppa', 'Pp3c24_9670' => 'ppa', 'Pp3c2_21390' => 'ppa', 'Pp3c2_31380' => 'ppa', 'Pp3c3_16620' => 'ppa', 'Pp3c3_8090' => 'ppa', 'Pp3c3_8110' => 'ppa', 'Pp3c3_8130' => 'ppa', 'Pp3c3_8150' => 'ppa', 'Pp3c4_14320' => 'ppa', 'Pp3c6_2560' => 'ppa', 'Pp3c9_16700' => 'ppa', 'PRCOL_00000234' => 'pco', 'PRCOL_00000235' => 'pco', 'PRCOL_00000777' => 'pco', 'PRCOL_00002344' => 'pco', 'PRCOL_00002372' => 'pco', 'PRCOL_00006120' => 'pco', 'Prupe.1G021400' => 'ppe', 'Prupe.1G021500' => 'ppe', 'Prupe.1G021600' => 'ppe', 'Prupe.1G021700' => 'ppe', 'Prupe.1G021800' => 'ppe', 'Prupe.5G145100' => 'ppe', 'Psat6g204040' => 'psa', 'Psat6g204800' => 'psa', 'Psat6g204920' => 'psa', 'Psat6g204960' => 'psa', 'Psat6g205080' => 'psa', 'PSO017G0271' => 'pso', 'PSO017G1276' => 'pso', 'PSO017G1429' => 'pso', 'PSO017G1861' => 'pso', 'PSO017G2787' => 'pso', 'PSO017G4466' => 'pso', 'PSO017G5118' => 'pso', 'PSO017G5420' => 'pso', 'PSO063G3678' => 'pso', 'PSO210G0546' => 'pso', 'PSO317G0001' => 'pso', 'PSO357G0512' => 'pso', 'PSO478G2682' => 'pso', 'PSO647G0001' => 'pso', 'PSO675G0001' => 'pso', 'PSO675G2699' => 'pso', 'PSO675G2849' => 'pso', 'PSO675G4991' => 'pso', 'PSO689G0001' => 'pso', 'QL06p000916' => 'qlo', 'QL06p000921' => 'qlo', 'QL06p001398' => 'qlo', 'QL06p001407' => 'qlo', 'QL06p002031' => 'qlo', 'RcHm_v2.0_Chr4g0387791' => 'rch', 'RcHm_v2.0_Chr4g0387801' => 'rch', 'RcHm_v2.0_Chr6g0286501' => 'rch', 'RcHm_v2.0_Chr6g0286511' => 'rch', 'RcHm_v2.0_Chr6g0286521' => 'rch', 'RcHm_v2.0_Chr6g0286531' => 'rch', 'RcHm_v2.0_Chr7g0189141' => 'rch', 'Rhsim02G0028700' => 'rsi', 'Rhsim02G0028800' => 'rsi', 'Rhsim02G0028900' => 'rsi', 'Rhsim02G0029000' => 'rsi', 'Rhsim02G0029100' => 'rsi', 'Rhsim02G0029200' => 'rsi', 'Rhsim02G0029300' => 'rsi', 'Rhsim02G0029400' => 'rsi', 'Rhsim02G0029500' => 'rsi', 'Rhsim02G0029600' => 'rsi', 'RhsimUnG0024000' => 'rsi', 'RhsimUnG0024100' => 'rsi', 'RhsimUnG0024200' => 'rsi', 'RhsimUnG0024300' => 'rsi', 'RhsimUnG0024400' => 'rsi', 'RhsimUnG0024500' => 'rsi', 'RhsimUnG0024700' => 'rsi', 'RhsimUnG0024800' => 'rsi', 'RhsimUnG0024900' => 'rsi', 'RhsimUnG0025100' => 'rsi', 'Sabra08G0120200' => 'sbr', 'Sabra08G0120300' => 'sbr', 'Sabra08G0120500' => 'sbr', 'Sabra08G0120600' => 'sbr', 'Sabra10G0158900' => 'sbr', 'SalBow2G3492' => 'sbo', 'Sc13g0004760' => 'sci', 'Sc13g0004770' => 'sci', 'Sed0003417' => 'sed', 'Sed0019750' => 'sed', 'SEGI_03419' => 'sgi', 'SEGI_05907' => 'sgi', 'SEGI_10682' => 'sgi', 'SEGI_13528' => 'sgi', 'SEGI_16081' => 'sgi', 'SEGI_19370' => 'sgi', 'SEGI_21015' => 'sgi', 'SEGI_21944' => 'sgi', 'SEGI_32906' => 'sgi', 'SEGI_33093' => 'sgi', 'SEGI_36110' => 'sgi', 'SEGI_40397' => 'sgi', 'SGA_v2.0_scaffold191G40426' => 'sas', 'SGA_v2.0_scaffold353G49717' => 'sas', 'SGA_v2.0_scaffold50G18550' => 'sas', 'SMO119G0173' => 'smo', 'SMO172G0002' => 'smo', 'Solyc09g082690.3' => 'sly', 'Solyc09g082700.2' => 'sly', 'Sopen09g031550' => 'spe', 'Sopen09g031560' => 'spe', 'Sp3g20540' => 'spa', 'Sp7g07580' => 'spa', 'TAR134G0002' => 'tar', 'TAR236G0001' => 'tar', 'TAR365G0892' => 'tar', 'TAR636G0166' => 'tar', 'TAR636G0646' => 'tar', 'TAR636G0869' => 'tar', 'TAR636G1317' => 'tar', 'TAR636G1744' => 'tar', 'TAR636G3358' => 'tar', 'TAR636G3436' => 'tar', 'THA.LOC104803047' => 'tha', 'Thecc.04G238900' => 'tca', 'Thhalv10021557m.g' => 'esa', 'Thhalv10026318m.g' => 'esa', 'Thhalv10026335m.g' => 'esa', 'TPR.G17433' => 'tpr', 'TPR.G18915' => 'tpr', 'TPR.G26125' => 'tpr', 'TWI09G0677' => 'twi', 'TWI73G0287' => 'twi', 'unitig_748.g8326' => 'ugi', 'vmacro15370' => 'vma', 'vmacro15371' => 'vma', 'vmacro15372' => 'vma', 'vmacro15373' => 'vma', 'vmacro15374' => 'vma', 'VMungo0720G2826' => 'vmu', 'Zm00001eb116960' => 'zma', 'Zm00001eb301260' => 'zma', 'Zm00001eb301270' => 'zma' ), 'gf_id' => 'HOM05D001460', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001460' ), 'data_identifier' => 'HOM05D001460', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001460', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '433', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p22980' => 'bna', 'A01p32340' => 'bna', 'A03p42970' => 'bna', 'A05p25880' => 'bna', 'Aa31LG8G9320' => 'aar', 'Aa31LG8G9330' => 'aar', 'Aa31LG8G9340' => 'aar', 'Aa31sc221G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1034' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1528' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.829' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2222' => 'aag', 'Ah.12g058830' => 'amhyb', 'Ah.12g058840' => 'amhyb', 'AL3G37160' => 'aly', 'AL7G41310' => 'aly', 'Aqoxy5G00395' => 'aox', 'Aqoxy5G00396' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0C8NZA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5185HY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JZ1PRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MD3LS0' => 'arhy', 'AT3G22840' => 'ath', 'AT4G14690' => 'ath', 'ATR0665G054' => 'atr', 'Atru.chr4.2344' => 'acertr', 'Atru.chr4.2346' => 'acertr', 'Atru.chr4.2347' => 'acertr', 'Atru.chr4.2348' => 'acertr', 'Atru.chr4.2355' => 'acertr', 'Atru.chr4.2356' => 'acertr', 'Atru.chr4.2358' => 'acertr', 'Atru.chr4.2359' => 'acertr', 'Atru.chr4.2360' => 'acertr', 'Atru.chr4.2361' => 'acertr', 'AUR62030476' => 'cqu', 'AUR62030478' => 'cqu', 'AUR62030819' => 'cqu', 'AUR62030820' => 'cqu', 'BcaB03g14648' => 'bca', 'BcaB04g20492' => 'bca', 'BcaB06g26399' => 'bca', 'BcaC01g03416' => 'bca', 'BcaC01g03419' => 'bca', 'BcaC01g03421' => 'bca', 'BcaC01g03424' => 'bca', 'BcaC05g28012' => 'bca', 'BcaC09g49212' => 'bca', 'BcaC09g50140' => 'bca', 'BcaNung00346' => 'bca', 'BolC1t02785H' => 'bol', 'BolC1t04095H' => 'bol', 'BolC3t17545H' => 'bol', 'BolC5t32769H' => 'bol', 'BraA01t02211Z' => 'bra', 'BraA01t03359Z' => 'bra', 'BraA03t13441Z' => 'bra', 'BraA05t21476Z' => 'bra', 'C01p28420' => 'bna', 'C01p41350' => 'bna', 'C03p52750' => 'bna', 'C03p52780' => 'bna', 'C05p40270' => 'bna', 'CAN.G1437.9' => 'can', 'CANSAT78G0035' => 'cansat', 'CANSAT78G1036' => 'cansat', 'CANSAT78G2272' => 'cansat', 'CANSAT78G2478' => 'cansat', 'CARHR098700' => 'chi', 'CARHR221120' => 'chi', 'CARHR221150' => 'chi', 'Carub.0003s2297' => 'cru', 'Carub.0007s2749' => 'cru', 'Carub.0007s2750' => 'cru', 'Carub.0007s2751' => 'cru', 'Ca_10849_v3' => 'car', 'Cc03_g04300' => 'ccan', 'CDE02G3648' => 'cde', 'CDE05G0060' => 'cde', 'CDE05G0692' => 'cde', 'CDE05G2285' => 'cde', 'CDE05G2884' => 'cde', 'CDE05G3072' => 'cde', 'Cfa008439' => 'cfa', 'Cfa008441' => 'cfa', 'Cfa008443' => 'cfa', 'Cfa008448' => 'cfa', 'Ciclev10005974m.g' => 'ccl', 'Ciclev10006006m.g' => 'ccl', 'Ciclev10006775m.g' => 'ccl', 'CiPaw.02G120400' => 'cil', 'CiPaw.02G120500' => 'cil', 'CiPaw.02G120600' => 'cil', 'ClCG05G004850' => 'cla', 'COL.COLO4_21566' => 'col', 'Cpa.g.sc44.124' => 'cpa', 'Cre07.g320400' => 'cre', 'Cre07.g320450' => 'cre', 'Cre08.g384650' => 'cre', 'Cre09.g393173' => 'cre', 'Cre09.g394325' => 'cre', 'Cre14.g626750' => 'cre', 'Cre16.g679250' => 'cre', 'CsaV3_3G012890' => 'csa', 'CSS0010865' => 'camsi', 'CSS0044338' => 'camsi', 'DCAR_002366' => 'dca', 'DCAR_030687' => 'dca', 'DCAR_030688' => 'dca', 'Dinv14047' => 'din', 'Dinv14048' => 'din', 'Duzib151G0105' => 'dzi', 'Duzib151G0114' => 'dzi', 'Duzib212G1029' => 'dzi', 'ECA232G3536' => 'eca', 'ECA240G0786' => 'eca', 'ECA240G1802' => 'eca', 'ECA240G3760' => 'eca', 'ECA240G3920' => 'eca', 'EL10Ac5g12536' => 'bvu', 'EL10Ac5g12537' => 'bvu', 'EL10Ac5g12538' => 'bvu', 'Eucgr.B01004' => 'egr', 'Eucgr.B01006' => 'egr', 'Eucgr.B01007' => 'egr', 'Eucgr.B01008' => 'egr', 'Eucgr.B01895' => 'egr', 'Eucgr.B01896' => 'egr', 'FAN04G1456' => 'fan', 'FAN08G1769' => 'fan', 'FAN08G2160' => 'fan', 'FAN13G2403' => 'fan', 'FAN13G3303' => 'fan', 'FAN15G2435' => 'fan', 'FAN17G0672' => 'fan', 'FAN17G2441' => 'fan', 'FAN18G1024' => 'fan', 'FAN22G1458' => 'fan', 'FAN24G0037' => 'fan', 'FAN24G0429' => 'fan', 'FAN24G2387' => 'fan', 'FAN27G2746' => 'fan', 'FvH4_2g20400' => 'fve', 'FvH4_2g20420' => 'fve', 'FvH4_2g20430' => 'fve', 'FvH4_4g01270' => 'fve', 'FvH4_4g01290' => 'fve', 'FvH4_4g01300' => 'fve', 'FvH4_4g01310' => 'fve', 'FvH4_4g01330' => 'fve', 'FvH4_5g09070' => 'fve', 'Glyma.10G243800' => 'gma', 'Glyma.20G150600' => 'gma', 'Gohir.A09G219200' => 'ghi', 'Gohir.A09G219300' => 'ghi', 'Gohir.D09G221400' => 'ghi', 'Gohir.D09G221500' => 'ghi', 'Gorai.006G242600' => 'gra', 'Gorai.006G242700' => 'gra', 'GSVIVG01018044001' => 'vvi', 'HanXRQChr03g0083821' => 'han', 'HanXRQChr03g0083841' => 'han', 'HanXRQChr03g0083881' => 'han', 'HanXRQChr03g0083901' => 'han', 'HanXRQChr03g0083921' => 'han', 'HanXRQChr03g0085331' => 'han', 'HanXRQChr03g0085361' => 'han', 'HanXRQChr03g0085411' => 'han', 'HanXRQChr03g0085421' => 'han', 'HanXRQChr03g0085431' => 'han', 'HanXRQChr08g0221991' => 'han', 'HanXRQChr11g0336061' => 'han', 'HanXRQChr11g0336411' => 'han', 'Haze_11234' => 'cav', 'Hma1.2p1_0549F.1_g177010' => 'hma', 'Hma1.2p1_0602F.1_g187630' => 'hma', 'Hund14876' => 'sun', 'Hund14879' => 'sun', 'Lalb_Chr06g0160741' => 'lal', 'Lalb_Chr21g0304781' => 'lal', 'Lj3A726G19' => 'lonja', 'Lj3A726T23' => 'lonja', 'Lj3A726T24' => 'lonja', 'Lj3A726T25' => 'lonja', 'Lj3A727T17' => 'lonja', 'Lj3C726T0' => 'lonja', 'Lj3C726T2' => 'lonja', 'Lj3P725T35' => 'lonja', 'Lj3P727T10' => 'lonja', 'Lj3P727T12' => 'lonja', 'Lj3P727T14' => 'lonja', 'Lj5g0023109' => 'lja', 'Lj6P646T44' => 'lonja', 'Lsat_1_v5_gn_6_75760' => 'lsa', 'Lsat_1_v5_gn_6_75800' => 'lsa', 'Lsat_1_v5_gn_6_75900' => 'lsa', 'Lsat_1_v5_gn_6_76240' => 'lsa', 'Lsat_1_v5_gn_6_76441' => 'lsa', 'Lsat_1_v5_gn_6_76700' => 'lsa', 'Lsat_1_v5_gn_6_76760' => 'lsa', 'Manes.15G033100' => 'mes', 'Mapoly0004s0074' => 'mpo', 'Mapoly0004s0075' => 'mpo', 'Mapoly0004s0163' => 'mpo', 'Mapoly0004s0164' => 'mpo', 'Mapoly0021s0018' => 'mpo', 'Mapoly0041s0136' => 'mpo', 'Mapoly0041s0137' => 'mpo', 'Mapoly0041s0138' => 'mpo', 'Mapoly0041s0139' => 'mpo', 'Mapoly0041s0141' => 'mpo', 'Mapoly0041s0142' => 'mpo', 'Mapoly0041s0143' => 'mpo', 'Mapoly0041s0144' => 'mpo', 'Mapoly0041s0145' => 'mpo', 'Mapoly0047s0106' => 'mpo', 'Mapoly0047s0108' => 'mpo', 'Mapoly0050s0051' => 'mpo', 'Mapoly0050s0052' => 'mpo', 'Mapoly0050s0053' => 'mpo', 'Mapoly0058s0013' => 'mpo', 'Mapoly0091s0078' => 'mpo', 'Mapoly0091s0079' => 'mpo', 'Mapoly0091s0080' => 'mpo', 'Mapoly0091s0081' => 'mpo', 'Mapoly0278s0004' => 'mpo', 'Mapoly0278s0005' => 'mpo', 'Mapoly0278s0006' => 'mpo', 'MBI11_g30648_MAGBIO' => 'mbi', 'MCO03G194' => 'mco', 'MCO03G590' => 'mco', 'MCO07G312' => 'mco', 'MCO10G318' => 'mco', 'MCO12G244' => 'mco', 'MCO13G148' => 'mco', 'MCO13G194' => 'mco', 'MCO16G238' => 'mco', 'MD06G1134100' => 'mdo', 'MD13G1200100' => 'mdo', 'MD13G1200300' => 'mdo', 'MD13G1200600' => 'mdo', 'MD14G1150400' => 'mdo', 'MD16G1200000' => 'mdo', 'Medtr1g102570' => 'mtr', 'Medtr1g102780' => 'mtr', 'Medtr1g102800' => 'mtr', 'Medtr1g102810' => 'mtr', 'Medtr1g102830' => 'mtr', 'MELO3C006499.2' => 'cme', 'Migut.G00385' => 'egut', 'MSTRG.4063' => 'ama', 'Nitab4.5_0000090g0260' => 'nta', 'Nitab4.5_0000977g0030' => 'nta', 'Nitab4.5_0002541g0040' => 'nta', 'Nitab4.5_0007068g0040' => 'nta', 'Nn005s41408' => 'nnu', 'Nn005s41410' => 'nnu', 'Oeu010310.1' => 'oeu', 'Oeu010311.1' => 'oeu', 'Oeu043472.1' => 'oeu', 'Os01g0246400' => 'osa', 'Os04g0267950' => 'osa', 'Os07g0178700' => 'osa', 'Os07g0178800' => 'osa', 'Peaxi162Scf00316g00046' => 'pax', 'Peaxi162Scf00316g00049' => 'pax', 'Peaxi162Scf00316g00059' => 'pax', 'Peaxi162Scf00316g00328' => 'pax', 'Peaxi162Scf00316g00329' => 'pax', 'Peaxi162Scf00316g00411' => 'pax', 'Peaxi162Scf00316g00521' => 'pax', 'Peaxi162Scf00492g00068' => 'pax', 'Peaxi162Scf35631g00002' => 'pax', 'PGR142G3720' => 'pgr', 'PGSC0003DMG400006442' => 'stu', 'Phvul.007G062000' => 'pvu', 'Potri.008G157750' => 'ptr', 'Potri.008G157900' => 'ptr', 'Potri.008G158000' => 'ptr', 'Potri.008G158200' => 'ptr', 'Pp3c11_7280' => 'ppa', 'Pp3c11_7980' => 'ppa', 'Pp3c12_19450' => 'ppa', 'Pp3c14_1480' => 'ppa', 'Pp3c14_1501' => 'ppa', 'Pp3c16_4900' => 'ppa', 'Pp3c16_5010' => 'ppa', 'Pp3c16_5060' => 'ppa', 'Pp3c19_18250' => 'ppa', 'Pp3c23_8530' => 'ppa', 'Pp3c23_8550' => 'ppa', 'Pp3c24_9670' => 'ppa', 'Pp3c2_21390' => 'ppa', 'Pp3c2_31380' => 'ppa', 'Pp3c3_16620' => 'ppa', 'Pp3c3_8090' => 'ppa', 'Pp3c3_8110' => 'ppa', 'Pp3c3_8130' => 'ppa', 'Pp3c3_8150' => 'ppa', 'Pp3c4_14320' => 'ppa', 'Pp3c6_2560' => 'ppa', 'Pp3c9_16700' => 'ppa', 'PRCOL_00000234' => 'pco', 'PRCOL_00000235' => 'pco', 'PRCOL_00000777' => 'pco', 'PRCOL_00002344' => 'pco', 'PRCOL_00002372' => 'pco', 'PRCOL_00006120' => 'pco', 'Prupe.1G021400' => 'ppe', 'Prupe.1G021500' => 'ppe', 'Prupe.1G021600' => 'ppe', 'Prupe.1G021700' => 'ppe', 'Prupe.1G021800' => 'ppe', 'Prupe.5G145100' => 'ppe', 'Psat6g204040' => 'psa', 'Psat6g204800' => 'psa', 'Psat6g204920' => 'psa', 'Psat6g204960' => 'psa', 'Psat6g205080' => 'psa', 'PSO017G0271' => 'pso', 'PSO017G1276' => 'pso', 'PSO017G1429' => 'pso', 'PSO017G1861' => 'pso', 'PSO017G2787' => 'pso', 'PSO017G4466' => 'pso', 'PSO017G5118' => 'pso', 'PSO017G5420' => 'pso', 'PSO063G3678' => 'pso', 'PSO210G0546' => 'pso', 'PSO317G0001' => 'pso', 'PSO357G0512' => 'pso', 'PSO478G2682' => 'pso', 'PSO647G0001' => 'pso', 'PSO675G0001' => 'pso', 'PSO675G2699' => 'pso', 'PSO675G2849' => 'pso', 'PSO675G4991' => 'pso', 'PSO689G0001' => 'pso', 'QL06p000916' => 'qlo', 'QL06p000921' => 'qlo', 'QL06p001398' => 'qlo', 'QL06p001407' => 'qlo', 'QL06p002031' => 'qlo', 'RcHm_v2.0_Chr4g0387791' => 'rch', 'RcHm_v2.0_Chr4g0387801' => 'rch', 'RcHm_v2.0_Chr6g0286501' => 'rch', 'RcHm_v2.0_Chr6g0286511' => 'rch', 'RcHm_v2.0_Chr6g0286521' => 'rch', 'RcHm_v2.0_Chr6g0286531' => 'rch', 'RcHm_v2.0_Chr7g0189141' => 'rch', 'Rhsim02G0028700' => 'rsi', 'Rhsim02G0028800' => 'rsi', 'Rhsim02G0028900' => 'rsi', 'Rhsim02G0029000' => 'rsi', 'Rhsim02G0029100' => 'rsi', 'Rhsim02G0029200' => 'rsi', 'Rhsim02G0029300' => 'rsi', 'Rhsim02G0029400' => 'rsi', 'Rhsim02G0029500' => 'rsi', 'Rhsim02G0029600' => 'rsi', 'RhsimUnG0024000' => 'rsi', 'RhsimUnG0024100' => 'rsi', 'RhsimUnG0024200' => 'rsi', 'RhsimUnG0024300' => 'rsi', 'RhsimUnG0024400' => 'rsi', 'RhsimUnG0024500' => 'rsi', 'RhsimUnG0024700' => 'rsi', 'RhsimUnG0024800' => 'rsi', 'RhsimUnG0024900' => 'rsi', 'RhsimUnG0025100' => 'rsi', 'Sabra08G0120200' => 'sbr', 'Sabra08G0120300' => 'sbr', 'Sabra08G0120500' => 'sbr', 'Sabra08G0120600' => 'sbr', 'Sabra10G0158900' => 'sbr', 'SalBow2G3492' => 'sbo', 'Sc13g0004760' => 'sci', 'Sc13g0004770' => 'sci', 'Sed0003417' => 'sed', 'Sed0019750' => 'sed', 'SEGI_03419' => 'sgi', 'SEGI_05907' => 'sgi', 'SEGI_10682' => 'sgi', 'SEGI_13528' => 'sgi', 'SEGI_16081' => 'sgi', 'SEGI_19370' => 'sgi', 'SEGI_21015' => 'sgi', 'SEGI_21944' => 'sgi', 'SEGI_32906' => 'sgi', 'SEGI_33093' => 'sgi', 'SEGI_36110' => 'sgi', 'SEGI_40397' => 'sgi', 'SGA_v2.0_scaffold191G40426' => 'sas', 'SGA_v2.0_scaffold353G49717' => 'sas', 'SGA_v2.0_scaffold50G18550' => 'sas', 'SMO119G0173' => 'smo', 'SMO172G0002' => 'smo', 'Solyc09g082690.3' => 'sly', 'Solyc09g082700.2' => 'sly', 'Sopen09g031550' => 'spe', 'Sopen09g031560' => 'spe', 'Sp3g20540' => 'spa', 'Sp7g07580' => 'spa', 'TAR134G0002' => 'tar', 'TAR236G0001' => 'tar', 'TAR365G0892' => 'tar', 'TAR636G0166' => 'tar', 'TAR636G0646' => 'tar', 'TAR636G0869' => 'tar', 'TAR636G1317' => 'tar', 'TAR636G1744' => 'tar', 'TAR636G3358' => 'tar', 'TAR636G3436' => 'tar', 'THA.LOC104803047' => 'tha', 'Thecc.04G238900' => 'tca', 'Thhalv10021557m.g' => 'esa', 'Thhalv10026318m.g' => 'esa', 'Thhalv10026335m.g' => 'esa', 'TPR.G17433' => 'tpr', 'TPR.G18915' => 'tpr', 'TPR.G26125' => 'tpr', 'TWI09G0677' => 'twi', 'TWI73G0287' => 'twi', 'unitig_748.g8326' => 'ugi', 'vmacro15370' => 'vma', 'vmacro15371' => 'vma', 'vmacro15372' => 'vma', 'vmacro15373' => 'vma', 'vmacro15374' => 'vma', 'VMungo0720G2826' => 'vmu', 'Zm00001eb116960' => 'zma', 'Zm00001eb301260' => 'zma', 'Zm00001eb301270' => 'zma' ) $gf_id = 'HOM05D001460' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001460' ) $data_identifier = 'HOM05D001460' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 4, 'aag' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 2, 'aox' => (int) 2, 'arhy' => (int) 4, 'ath' => (int) 2, 'atr' => (int) 1, 'acertr' => (int) 10, 'cqu' => (int) 4, 'bca' => (int) 11, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 1, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 1, 'ccan' => (int) 1, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 1, 'col' => (int) 1, 'cpa' => (int) 1, 'cre' => (int) 7, 'csa' => (int) 1, 'camsi' => (int) 2, 'dca' => (int) 3, 'din' => (int) 2, 'dzi' => (int) 3, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 14, 'fve' => (int) 9, 'gma' => (int) 2, 'ghi' => (int) 4, 'gra' => (int) 2, 'vvi' => (int) 1, 'han' => (int) 13, 'cav' => (int) 1, 'hma' => (int) 2, 'sun' => (int) 2, 'lal' => (int) 2, 'lonja' => (int) 12, 'lja' => (int) 1, 'lsa' => (int) 7, 'mes' => (int) 1, 'mpo' => (int) 27, 'mbi' => (int) 1, 'mco' => (int) 8, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 1, 'egut' => (int) 1, 'ama' => (int) 1, 'nta' => (int) 4, 'nnu' => (int) 2, 'oeu' => (int) 3, 'osa' => (int) 4, 'pax' => (int) 9, 'pgr' => (int) 1, 'stu' => (int) 1, 'pvu' => (int) 1, 'ptr' => (int) 4, 'ppa' => (int) 22, 'pco' => (int) 6, 'ppe' => (int) 6, 'psa' => (int) 5, 'pso' => (int) 19, 'qlo' => (int) 5, 'rch' => (int) 7, 'rsi' => (int) 20, 'sbr' => (int) 5, 'sbo' => (int) 1, 'sci' => (int) 2, 'sed' => (int) 2, 'sgi' => (int) 12, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 2, 'tar' => (int) 10, 'tha' => (int) 1, 'tca' => (int) 1, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 2, 'ugi' => (int) 1, 'vma' => (int) 5, 'vmu' => (int) 1, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb301270' $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' => 'HOM05D001460', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '433', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p22980' => 'bna', 'A01p32340' => 'bna', 'A03p42970' => 'bna', 'A05p25880' => 'bna', 'Aa31LG8G9320' => 'aar', 'Aa31LG8G9330' => 'aar', 'Aa31LG8G9340' => 'aar', 'Aa31sc221G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1034' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1528' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.829' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2222' => 'aag', 'Ah.12g058830' => 'amhyb', 'Ah.12g058840' => 'amhyb', 'AL3G37160' => 'aly', 'AL7G41310' => 'aly', 'Aqoxy5G00395' => 'aox', 'Aqoxy5G00396' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0C8NZA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5185HY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JZ1PRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MD3LS0' => 'arhy', 'AT3G22840' => 'ath', 'AT4G14690' => 'ath', 'ATR0665G054' => 'atr', 'Atru.chr4.2344' => 'acertr', 'Atru.chr4.2346' => 'acertr', 'Atru.chr4.2347' => 'acertr', 'Atru.chr4.2348' => 'acertr', 'Atru.chr4.2355' => 'acertr', 'Atru.chr4.2356' => 'acertr', 'Atru.chr4.2358' => 'acertr', 'Atru.chr4.2359' => 'acertr', 'Atru.chr4.2360' => 'acertr', 'Atru.chr4.2361' => 'acertr', 'AUR62030476' => 'cqu', 'AUR62030478' => 'cqu', 'AUR62030819' => 'cqu', 'AUR62030820' => 'cqu', 'BcaB03g14648' => 'bca', 'BcaB04g20492' => 'bca', 'BcaB06g26399' => 'bca', 'BcaC01g03416' => 'bca', 'BcaC01g03419' => 'bca', 'BcaC01g03421' => 'bca', 'BcaC01g03424' => 'bca', 'BcaC05g28012' => 'bca', 'BcaC09g49212' => 'bca', 'BcaC09g50140' => 'bca', 'BcaNung00346' => 'bca', 'BolC1t02785H' => 'bol', 'BolC1t04095H' => 'bol', 'BolC3t17545H' => 'bol', 'BolC5t32769H' => 'bol', 'BraA01t02211Z' => 'bra', 'BraA01t03359Z' => 'bra', 'BraA03t13441Z' => 'bra', 'BraA05t21476Z' => 'bra', 'C01p28420' => 'bna', 'C01p41350' => 'bna', 'C03p52750' => 'bna', 'C03p52780' => 'bna', 'C05p40270' => 'bna', 'CAN.G1437.9' => 'can', 'CANSAT78G0035' => 'cansat', 'CANSAT78G1036' => 'cansat', 'CANSAT78G2272' => 'cansat', 'CANSAT78G2478' => 'cansat', 'CARHR098700' => 'chi', 'CARHR221120' => 'chi', 'CARHR221150' => 'chi', 'Carub.0003s2297' => 'cru', 'Carub.0007s2749' => 'cru', 'Carub.0007s2750' => 'cru', 'Carub.0007s2751' => 'cru', 'Ca_10849_v3' => 'car', 'Cc03_g04300' => 'ccan', 'CDE02G3648' => 'cde', 'CDE05G0060' => 'cde', 'CDE05G0692' => 'cde', 'CDE05G2285' => 'cde', 'CDE05G2884' => 'cde', 'CDE05G3072' => 'cde', 'Cfa008439' => 'cfa', 'Cfa008441' => 'cfa', 'Cfa008443' => 'cfa', 'Cfa008448' => 'cfa', 'Ciclev10005974m.g' => 'ccl', 'Ciclev10006006m.g' => 'ccl', 'Ciclev10006775m.g' => 'ccl', 'CiPaw.02G120400' => 'cil', 'CiPaw.02G120500' => 'cil', 'CiPaw.02G120600' => 'cil', 'ClCG05G004850' => 'cla', 'COL.COLO4_21566' => 'col', 'Cpa.g.sc44.124' => 'cpa', 'Cre07.g320400' => 'cre', 'Cre07.g320450' => 'cre', 'Cre08.g384650' => 'cre', 'Cre09.g393173' => 'cre', 'Cre09.g394325' => 'cre', 'Cre14.g626750' => 'cre', 'Cre16.g679250' => 'cre', 'CsaV3_3G012890' => 'csa', 'CSS0010865' => 'camsi', 'CSS0044338' => 'camsi', 'DCAR_002366' => 'dca', 'DCAR_030687' => 'dca', 'DCAR_030688' => 'dca', 'Dinv14047' => 'din', 'Dinv14048' => 'din', 'Duzib151G0105' => 'dzi', 'Duzib151G0114' => 'dzi', 'Duzib212G1029' => 'dzi', 'ECA232G3536' => 'eca', 'ECA240G0786' => 'eca', 'ECA240G1802' => 'eca', 'ECA240G3760' => 'eca', 'ECA240G3920' => 'eca', 'EL10Ac5g12536' => 'bvu', 'EL10Ac5g12537' => 'bvu', 'EL10Ac5g12538' => 'bvu', 'Eucgr.B01004' => 'egr', 'Eucgr.B01006' => 'egr', 'Eucgr.B01007' => 'egr', 'Eucgr.B01008' => 'egr', 'Eucgr.B01895' => 'egr', 'Eucgr.B01896' => 'egr', 'FAN04G1456' => 'fan', 'FAN08G1769' => 'fan', 'FAN08G2160' => 'fan', 'FAN13G2403' => 'fan', 'FAN13G3303' => 'fan', 'FAN15G2435' => 'fan', 'FAN17G0672' => 'fan', 'FAN17G2441' => 'fan', 'FAN18G1024' => 'fan', 'FAN22G1458' => 'fan', 'FAN24G0037' => 'fan', 'FAN24G0429' => 'fan', 'FAN24G2387' => 'fan', 'FAN27G2746' => 'fan', 'FvH4_2g20400' => 'fve', 'FvH4_2g20420' => 'fve', 'FvH4_2g20430' => 'fve', 'FvH4_4g01270' => 'fve', 'FvH4_4g01290' => 'fve', 'FvH4_4g01300' => 'fve', 'FvH4_4g01310' => 'fve', 'FvH4_4g01330' => 'fve', 'FvH4_5g09070' => 'fve', 'Glyma.10G243800' => 'gma', 'Glyma.20G150600' => 'gma', 'Gohir.A09G219200' => 'ghi', 'Gohir.A09G219300' => 'ghi', 'Gohir.D09G221400' => 'ghi', 'Gohir.D09G221500' => 'ghi', 'Gorai.006G242600' => 'gra', 'Gorai.006G242700' => 'gra', 'GSVIVG01018044001' => 'vvi', 'HanXRQChr03g0083821' => 'han', 'HanXRQChr03g0083841' => 'han', 'HanXRQChr03g0083881' => 'han', 'HanXRQChr03g0083901' => 'han', 'HanXRQChr03g0083921' => 'han', 'HanXRQChr03g0085331' => 'han', 'HanXRQChr03g0085361' => 'han', 'HanXRQChr03g0085411' => 'han', 'HanXRQChr03g0085421' => 'han', 'HanXRQChr03g0085431' => 'han', 'HanXRQChr08g0221991' => 'han', 'HanXRQChr11g0336061' => 'han', 'HanXRQChr11g0336411' => 'han', 'Haze_11234' => 'cav', 'Hma1.2p1_0549F.1_g177010' => 'hma', 'Hma1.2p1_0602F.1_g187630' => 'hma', 'Hund14876' => 'sun', 'Hund14879' => 'sun', 'Lalb_Chr06g0160741' => 'lal', 'Lalb_Chr21g0304781' => 'lal', 'Lj3A726G19' => 'lonja', 'Lj3A726T23' => 'lonja', 'Lj3A726T24' => 'lonja', 'Lj3A726T25' => 'lonja', 'Lj3A727T17' => 'lonja', 'Lj3C726T0' => 'lonja', 'Lj3C726T2' => 'lonja', 'Lj3P725T35' => 'lonja', 'Lj3P727T10' => 'lonja', 'Lj3P727T12' => 'lonja', 'Lj3P727T14' => 'lonja', 'Lj5g0023109' => 'lja', 'Lj6P646T44' => 'lonja', 'Lsat_1_v5_gn_6_75760' => 'lsa', 'Lsat_1_v5_gn_6_75800' => 'lsa', 'Lsat_1_v5_gn_6_75900' => 'lsa', 'Lsat_1_v5_gn_6_76240' => 'lsa', 'Lsat_1_v5_gn_6_76441' => 'lsa', 'Lsat_1_v5_gn_6_76700' => 'lsa', 'Lsat_1_v5_gn_6_76760' => 'lsa', 'Manes.15G033100' => 'mes', 'Mapoly0004s0074' => 'mpo', 'Mapoly0004s0075' => 'mpo', 'Mapoly0004s0163' => 'mpo', 'Mapoly0004s0164' => 'mpo', 'Mapoly0021s0018' => 'mpo', 'Mapoly0041s0136' => 'mpo', 'Mapoly0041s0137' => 'mpo', 'Mapoly0041s0138' => 'mpo', 'Mapoly0041s0139' => 'mpo', 'Mapoly0041s0141' => 'mpo', 'Mapoly0041s0142' => 'mpo', 'Mapoly0041s0143' => 'mpo', 'Mapoly0041s0144' => 'mpo', 'Mapoly0041s0145' => 'mpo', 'Mapoly0047s0106' => 'mpo', 'Mapoly0047s0108' => 'mpo', 'Mapoly0050s0051' => 'mpo', 'Mapoly0050s0052' => 'mpo', 'Mapoly0050s0053' => 'mpo', 'Mapoly0058s0013' => 'mpo', 'Mapoly0091s0078' => 'mpo', 'Mapoly0091s0079' => 'mpo', 'Mapoly0091s0080' => 'mpo', 'Mapoly0091s0081' => 'mpo', 'Mapoly0278s0004' => 'mpo', 'Mapoly0278s0005' => 'mpo', 'Mapoly0278s0006' => 'mpo', 'MBI11_g30648_MAGBIO' => 'mbi', 'MCO03G194' => 'mco', 'MCO03G590' => 'mco', 'MCO07G312' => 'mco', 'MCO10G318' => 'mco', 'MCO12G244' => 'mco', 'MCO13G148' => 'mco', 'MCO13G194' => 'mco', 'MCO16G238' => 'mco', 'MD06G1134100' => 'mdo', 'MD13G1200100' => 'mdo', 'MD13G1200300' => 'mdo', 'MD13G1200600' => 'mdo', 'MD14G1150400' => 'mdo', 'MD16G1200000' => 'mdo', 'Medtr1g102570' => 'mtr', 'Medtr1g102780' => 'mtr', 'Medtr1g102800' => 'mtr', 'Medtr1g102810' => 'mtr', 'Medtr1g102830' => 'mtr', 'MELO3C006499.2' => 'cme', 'Migut.G00385' => 'egut', 'MSTRG.4063' => 'ama', 'Nitab4.5_0000090g0260' => 'nta', 'Nitab4.5_0000977g0030' => 'nta', 'Nitab4.5_0002541g0040' => 'nta', 'Nitab4.5_0007068g0040' => 'nta', 'Nn005s41408' => 'nnu', 'Nn005s41410' => 'nnu', 'Oeu010310.1' => 'oeu', 'Oeu010311.1' => 'oeu', 'Oeu043472.1' => 'oeu', 'Os01g0246400' => 'osa', 'Os04g0267950' => 'osa', 'Os07g0178700' => 'osa', 'Os07g0178800' => 'osa', 'Peaxi162Scf00316g00046' => 'pax', 'Peaxi162Scf00316g00049' => 'pax', 'Peaxi162Scf00316g00059' => 'pax', 'Peaxi162Scf00316g00328' => 'pax', 'Peaxi162Scf00316g00329' => 'pax', 'Peaxi162Scf00316g00411' => 'pax', 'Peaxi162Scf00316g00521' => 'pax', 'Peaxi162Scf00492g00068' => 'pax', 'Peaxi162Scf35631g00002' => 'pax', 'PGR142G3720' => 'pgr', 'PGSC0003DMG400006442' => 'stu', 'Phvul.007G062000' => 'pvu', 'Potri.008G157750' => 'ptr', 'Potri.008G157900' => 'ptr', 'Potri.008G158000' => 'ptr', 'Potri.008G158200' => 'ptr', 'Pp3c11_7280' => 'ppa', 'Pp3c11_7980' => 'ppa', 'Pp3c12_19450' => 'ppa', 'Pp3c14_1480' => 'ppa', 'Pp3c14_1501' => 'ppa', 'Pp3c16_4900' => 'ppa', 'Pp3c16_5010' => 'ppa', 'Pp3c16_5060' => 'ppa', 'Pp3c19_18250' => 'ppa', 'Pp3c23_8530' => 'ppa', 'Pp3c23_8550' => 'ppa', 'Pp3c24_9670' => 'ppa', 'Pp3c2_21390' => 'ppa', 'Pp3c2_31380' => 'ppa', 'Pp3c3_16620' => 'ppa', 'Pp3c3_8090' => 'ppa', 'Pp3c3_8110' => 'ppa', 'Pp3c3_8130' => 'ppa', 'Pp3c3_8150' => 'ppa', 'Pp3c4_14320' => 'ppa', 'Pp3c6_2560' => 'ppa', 'Pp3c9_16700' => 'ppa', 'PRCOL_00000234' => 'pco', 'PRCOL_00000235' => 'pco', 'PRCOL_00000777' => 'pco', 'PRCOL_00002344' => 'pco', 'PRCOL_00002372' => 'pco', 'PRCOL_00006120' => 'pco', 'Prupe.1G021400' => 'ppe', 'Prupe.1G021500' => 'ppe', 'Prupe.1G021600' => 'ppe', 'Prupe.1G021700' => 'ppe', 'Prupe.1G021800' => 'ppe', 'Prupe.5G145100' => 'ppe', 'Psat6g204040' => 'psa', 'Psat6g204800' => 'psa', 'Psat6g204920' => 'psa', 'Psat6g204960' => 'psa', 'Psat6g205080' => 'psa', 'PSO017G0271' => 'pso', 'PSO017G1276' => 'pso', 'PSO017G1429' => 'pso', 'PSO017G1861' => 'pso', 'PSO017G2787' => 'pso', 'PSO017G4466' => 'pso', 'PSO017G5118' => 'pso', 'PSO017G5420' => 'pso', 'PSO063G3678' => 'pso', 'PSO210G0546' => 'pso', 'PSO317G0001' => 'pso', 'PSO357G0512' => 'pso', 'PSO478G2682' => 'pso', 'PSO647G0001' => 'pso', 'PSO675G0001' => 'pso', 'PSO675G2699' => 'pso', 'PSO675G2849' => 'pso', 'PSO675G4991' => 'pso', 'PSO689G0001' => 'pso', 'QL06p000916' => 'qlo', 'QL06p000921' => 'qlo', 'QL06p001398' => 'qlo', 'QL06p001407' => 'qlo', 'QL06p002031' => 'qlo', 'RcHm_v2.0_Chr4g0387791' => 'rch', 'RcHm_v2.0_Chr4g0387801' => 'rch', 'RcHm_v2.0_Chr6g0286501' => 'rch', 'RcHm_v2.0_Chr6g0286511' => 'rch', 'RcHm_v2.0_Chr6g0286521' => 'rch', 'RcHm_v2.0_Chr6g0286531' => 'rch', 'RcHm_v2.0_Chr7g0189141' => 'rch', 'Rhsim02G0028700' => 'rsi', 'Rhsim02G0028800' => 'rsi', 'Rhsim02G0028900' => 'rsi', 'Rhsim02G0029000' => 'rsi', 'Rhsim02G0029100' => 'rsi', 'Rhsim02G0029200' => 'rsi', 'Rhsim02G0029300' => 'rsi', 'Rhsim02G0029400' => 'rsi', 'Rhsim02G0029500' => 'rsi', 'Rhsim02G0029600' => 'rsi', 'RhsimUnG0024000' => 'rsi', 'RhsimUnG0024100' => 'rsi', 'RhsimUnG0024200' => 'rsi', 'RhsimUnG0024300' => 'rsi', 'RhsimUnG0024400' => 'rsi', 'RhsimUnG0024500' => 'rsi', 'RhsimUnG0024700' => 'rsi', 'RhsimUnG0024800' => 'rsi', 'RhsimUnG0024900' => 'rsi', 'RhsimUnG0025100' => 'rsi', 'Sabra08G0120200' => 'sbr', 'Sabra08G0120300' => 'sbr', 'Sabra08G0120500' => 'sbr', 'Sabra08G0120600' => 'sbr', 'Sabra10G0158900' => 'sbr', 'SalBow2G3492' => 'sbo', 'Sc13g0004760' => 'sci', 'Sc13g0004770' => 'sci', 'Sed0003417' => 'sed', 'Sed0019750' => 'sed', 'SEGI_03419' => 'sgi', 'SEGI_05907' => 'sgi', 'SEGI_10682' => 'sgi', 'SEGI_13528' => 'sgi', 'SEGI_16081' => 'sgi', 'SEGI_19370' => 'sgi', 'SEGI_21015' => 'sgi', 'SEGI_21944' => 'sgi', 'SEGI_32906' => 'sgi', 'SEGI_33093' => 'sgi', 'SEGI_36110' => 'sgi', 'SEGI_40397' => 'sgi', 'SGA_v2.0_scaffold191G40426' => 'sas', 'SGA_v2.0_scaffold353G49717' => 'sas', 'SGA_v2.0_scaffold50G18550' => 'sas', 'SMO119G0173' => 'smo', 'SMO172G0002' => 'smo', 'Solyc09g082690.3' => 'sly', 'Solyc09g082700.2' => 'sly', 'Sopen09g031550' => 'spe', 'Sopen09g031560' => 'spe', 'Sp3g20540' => 'spa', 'Sp7g07580' => 'spa', 'TAR134G0002' => 'tar', 'TAR236G0001' => 'tar', 'TAR365G0892' => 'tar', 'TAR636G0166' => 'tar', 'TAR636G0646' => 'tar', 'TAR636G0869' => 'tar', 'TAR636G1317' => 'tar', 'TAR636G1744' => 'tar', 'TAR636G3358' => 'tar', 'TAR636G3436' => 'tar', 'THA.LOC104803047' => 'tha', 'Thecc.04G238900' => 'tca', 'Thhalv10021557m.g' => 'esa', 'Thhalv10026318m.g' => 'esa', 'Thhalv10026335m.g' => 'esa', 'TPR.G17433' => 'tpr', 'TPR.G18915' => 'tpr', 'TPR.G26125' => 'tpr', 'TWI09G0677' => 'twi', 'TWI73G0287' => 'twi', 'unitig_748.g8326' => 'ugi', 'vmacro15370' => 'vma', 'vmacro15371' => 'vma', 'vmacro15372' => 'vma', 'vmacro15373' => 'vma', 'vmacro15374' => 'vma', 'VMungo0720G2826' => 'vmu', 'Zm00001eb116960' => 'zma', 'Zm00001eb301260' => 'zma', 'Zm00001eb301270' => 'zma' ), 'gf_id' => 'HOM05D001460', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001460' ), 'data_identifier' => 'HOM05D001460', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001460', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '433', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p22980' => 'bna', 'A01p32340' => 'bna', 'A03p42970' => 'bna', 'A05p25880' => 'bna', 'Aa31LG8G9320' => 'aar', 'Aa31LG8G9330' => 'aar', 'Aa31LG8G9340' => 'aar', 'Aa31sc221G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1034' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1528' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.829' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2222' => 'aag', 'Ah.12g058830' => 'amhyb', 'Ah.12g058840' => 'amhyb', 'AL3G37160' => 'aly', 'AL7G41310' => 'aly', 'Aqoxy5G00395' => 'aox', 'Aqoxy5G00396' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0C8NZA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5185HY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JZ1PRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MD3LS0' => 'arhy', 'AT3G22840' => 'ath', 'AT4G14690' => 'ath', 'ATR0665G054' => 'atr', 'Atru.chr4.2344' => 'acertr', 'Atru.chr4.2346' => 'acertr', 'Atru.chr4.2347' => 'acertr', 'Atru.chr4.2348' => 'acertr', 'Atru.chr4.2355' => 'acertr', 'Atru.chr4.2356' => 'acertr', 'Atru.chr4.2358' => 'acertr', 'Atru.chr4.2359' => 'acertr', 'Atru.chr4.2360' => 'acertr', 'Atru.chr4.2361' => 'acertr', 'AUR62030476' => 'cqu', 'AUR62030478' => 'cqu', 'AUR62030819' => 'cqu', 'AUR62030820' => 'cqu', 'BcaB03g14648' => 'bca', 'BcaB04g20492' => 'bca', 'BcaB06g26399' => 'bca', 'BcaC01g03416' => 'bca', 'BcaC01g03419' => 'bca', 'BcaC01g03421' => 'bca', 'BcaC01g03424' => 'bca', 'BcaC05g28012' => 'bca', 'BcaC09g49212' => 'bca', 'BcaC09g50140' => 'bca', 'BcaNung00346' => 'bca', 'BolC1t02785H' => 'bol', 'BolC1t04095H' => 'bol', 'BolC3t17545H' => 'bol', 'BolC5t32769H' => 'bol', 'BraA01t02211Z' => 'bra', 'BraA01t03359Z' => 'bra', 'BraA03t13441Z' => 'bra', 'BraA05t21476Z' => 'bra', 'C01p28420' => 'bna', 'C01p41350' => 'bna', 'C03p52750' => 'bna', 'C03p52780' => 'bna', 'C05p40270' => 'bna', 'CAN.G1437.9' => 'can', 'CANSAT78G0035' => 'cansat', 'CANSAT78G1036' => 'cansat', 'CANSAT78G2272' => 'cansat', 'CANSAT78G2478' => 'cansat', 'CARHR098700' => 'chi', 'CARHR221120' => 'chi', 'CARHR221150' => 'chi', 'Carub.0003s2297' => 'cru', 'Carub.0007s2749' => 'cru', 'Carub.0007s2750' => 'cru', 'Carub.0007s2751' => 'cru', 'Ca_10849_v3' => 'car', 'Cc03_g04300' => 'ccan', 'CDE02G3648' => 'cde', 'CDE05G0060' => 'cde', 'CDE05G0692' => 'cde', 'CDE05G2285' => 'cde', 'CDE05G2884' => 'cde', 'CDE05G3072' => 'cde', 'Cfa008439' => 'cfa', 'Cfa008441' => 'cfa', 'Cfa008443' => 'cfa', 'Cfa008448' => 'cfa', 'Ciclev10005974m.g' => 'ccl', 'Ciclev10006006m.g' => 'ccl', 'Ciclev10006775m.g' => 'ccl', 'CiPaw.02G120400' => 'cil', 'CiPaw.02G120500' => 'cil', 'CiPaw.02G120600' => 'cil', 'ClCG05G004850' => 'cla', 'COL.COLO4_21566' => 'col', 'Cpa.g.sc44.124' => 'cpa', 'Cre07.g320400' => 'cre', 'Cre07.g320450' => 'cre', 'Cre08.g384650' => 'cre', 'Cre09.g393173' => 'cre', 'Cre09.g394325' => 'cre', 'Cre14.g626750' => 'cre', 'Cre16.g679250' => 'cre', 'CsaV3_3G012890' => 'csa', 'CSS0010865' => 'camsi', 'CSS0044338' => 'camsi', 'DCAR_002366' => 'dca', 'DCAR_030687' => 'dca', 'DCAR_030688' => 'dca', 'Dinv14047' => 'din', 'Dinv14048' => 'din', 'Duzib151G0105' => 'dzi', 'Duzib151G0114' => 'dzi', 'Duzib212G1029' => 'dzi', 'ECA232G3536' => 'eca', 'ECA240G0786' => 'eca', 'ECA240G1802' => 'eca', 'ECA240G3760' => 'eca', 'ECA240G3920' => 'eca', 'EL10Ac5g12536' => 'bvu', 'EL10Ac5g12537' => 'bvu', 'EL10Ac5g12538' => 'bvu', 'Eucgr.B01004' => 'egr', 'Eucgr.B01006' => 'egr', 'Eucgr.B01007' => 'egr', 'Eucgr.B01008' => 'egr', 'Eucgr.B01895' => 'egr', 'Eucgr.B01896' => 'egr', 'FAN04G1456' => 'fan', 'FAN08G1769' => 'fan', 'FAN08G2160' => 'fan', 'FAN13G2403' => 'fan', 'FAN13G3303' => 'fan', 'FAN15G2435' => 'fan', 'FAN17G0672' => 'fan', 'FAN17G2441' => 'fan', 'FAN18G1024' => 'fan', 'FAN22G1458' => 'fan', 'FAN24G0037' => 'fan', 'FAN24G0429' => 'fan', 'FAN24G2387' => 'fan', 'FAN27G2746' => 'fan', 'FvH4_2g20400' => 'fve', 'FvH4_2g20420' => 'fve', 'FvH4_2g20430' => 'fve', 'FvH4_4g01270' => 'fve', 'FvH4_4g01290' => 'fve', 'FvH4_4g01300' => 'fve', 'FvH4_4g01310' => 'fve', 'FvH4_4g01330' => 'fve', 'FvH4_5g09070' => 'fve', 'Glyma.10G243800' => 'gma', 'Glyma.20G150600' => 'gma', 'Gohir.A09G219200' => 'ghi', 'Gohir.A09G219300' => 'ghi', 'Gohir.D09G221400' => 'ghi', 'Gohir.D09G221500' => 'ghi', 'Gorai.006G242600' => 'gra', 'Gorai.006G242700' => 'gra', 'GSVIVG01018044001' => 'vvi', 'HanXRQChr03g0083821' => 'han', 'HanXRQChr03g0083841' => 'han', 'HanXRQChr03g0083881' => 'han', 'HanXRQChr03g0083901' => 'han', 'HanXRQChr03g0083921' => 'han', 'HanXRQChr03g0085331' => 'han', 'HanXRQChr03g0085361' => 'han', 'HanXRQChr03g0085411' => 'han', 'HanXRQChr03g0085421' => 'han', 'HanXRQChr03g0085431' => 'han', 'HanXRQChr08g0221991' => 'han', 'HanXRQChr11g0336061' => 'han', 'HanXRQChr11g0336411' => 'han', 'Haze_11234' => 'cav', 'Hma1.2p1_0549F.1_g177010' => 'hma', 'Hma1.2p1_0602F.1_g187630' => 'hma', 'Hund14876' => 'sun', 'Hund14879' => 'sun', 'Lalb_Chr06g0160741' => 'lal', 'Lalb_Chr21g0304781' => 'lal', 'Lj3A726G19' => 'lonja', 'Lj3A726T23' => 'lonja', 'Lj3A726T24' => 'lonja', 'Lj3A726T25' => 'lonja', 'Lj3A727T17' => 'lonja', 'Lj3C726T0' => 'lonja', 'Lj3C726T2' => 'lonja', 'Lj3P725T35' => 'lonja', 'Lj3P727T10' => 'lonja', 'Lj3P727T12' => 'lonja', 'Lj3P727T14' => 'lonja', 'Lj5g0023109' => 'lja', 'Lj6P646T44' => 'lonja', 'Lsat_1_v5_gn_6_75760' => 'lsa', 'Lsat_1_v5_gn_6_75800' => 'lsa', 'Lsat_1_v5_gn_6_75900' => 'lsa', 'Lsat_1_v5_gn_6_76240' => 'lsa', 'Lsat_1_v5_gn_6_76441' => 'lsa', 'Lsat_1_v5_gn_6_76700' => 'lsa', 'Lsat_1_v5_gn_6_76760' => 'lsa', 'Manes.15G033100' => 'mes', 'Mapoly0004s0074' => 'mpo', 'Mapoly0004s0075' => 'mpo', 'Mapoly0004s0163' => 'mpo', 'Mapoly0004s0164' => 'mpo', 'Mapoly0021s0018' => 'mpo', 'Mapoly0041s0136' => 'mpo', 'Mapoly0041s0137' => 'mpo', 'Mapoly0041s0138' => 'mpo', 'Mapoly0041s0139' => 'mpo', 'Mapoly0041s0141' => 'mpo', 'Mapoly0041s0142' => 'mpo', 'Mapoly0041s0143' => 'mpo', 'Mapoly0041s0144' => 'mpo', 'Mapoly0041s0145' => 'mpo', 'Mapoly0047s0106' => 'mpo', 'Mapoly0047s0108' => 'mpo', 'Mapoly0050s0051' => 'mpo', 'Mapoly0050s0052' => 'mpo', 'Mapoly0050s0053' => 'mpo', 'Mapoly0058s0013' => 'mpo', 'Mapoly0091s0078' => 'mpo', 'Mapoly0091s0079' => 'mpo', 'Mapoly0091s0080' => 'mpo', 'Mapoly0091s0081' => 'mpo', 'Mapoly0278s0004' => 'mpo', 'Mapoly0278s0005' => 'mpo', 'Mapoly0278s0006' => 'mpo', 'MBI11_g30648_MAGBIO' => 'mbi', 'MCO03G194' => 'mco', 'MCO03G590' => 'mco', 'MCO07G312' => 'mco', 'MCO10G318' => 'mco', 'MCO12G244' => 'mco', 'MCO13G148' => 'mco', 'MCO13G194' => 'mco', 'MCO16G238' => 'mco', 'MD06G1134100' => 'mdo', 'MD13G1200100' => 'mdo', 'MD13G1200300' => 'mdo', 'MD13G1200600' => 'mdo', 'MD14G1150400' => 'mdo', 'MD16G1200000' => 'mdo', 'Medtr1g102570' => 'mtr', 'Medtr1g102780' => 'mtr', 'Medtr1g102800' => 'mtr', 'Medtr1g102810' => 'mtr', 'Medtr1g102830' => 'mtr', 'MELO3C006499.2' => 'cme', 'Migut.G00385' => 'egut', 'MSTRG.4063' => 'ama', 'Nitab4.5_0000090g0260' => 'nta', 'Nitab4.5_0000977g0030' => 'nta', 'Nitab4.5_0002541g0040' => 'nta', 'Nitab4.5_0007068g0040' => 'nta', 'Nn005s41408' => 'nnu', 'Nn005s41410' => 'nnu', 'Oeu010310.1' => 'oeu', 'Oeu010311.1' => 'oeu', 'Oeu043472.1' => 'oeu', 'Os01g0246400' => 'osa', 'Os04g0267950' => 'osa', 'Os07g0178700' => 'osa', 'Os07g0178800' => 'osa', 'Peaxi162Scf00316g00046' => 'pax', 'Peaxi162Scf00316g00049' => 'pax', 'Peaxi162Scf00316g00059' => 'pax', 'Peaxi162Scf00316g00328' => 'pax', 'Peaxi162Scf00316g00329' => 'pax', 'Peaxi162Scf00316g00411' => 'pax', 'Peaxi162Scf00316g00521' => 'pax', 'Peaxi162Scf00492g00068' => 'pax', 'Peaxi162Scf35631g00002' => 'pax', 'PGR142G3720' => 'pgr', 'PGSC0003DMG400006442' => 'stu', 'Phvul.007G062000' => 'pvu', 'Potri.008G157750' => 'ptr', 'Potri.008G157900' => 'ptr', 'Potri.008G158000' => 'ptr', 'Potri.008G158200' => 'ptr', 'Pp3c11_7280' => 'ppa', 'Pp3c11_7980' => 'ppa', 'Pp3c12_19450' => 'ppa', 'Pp3c14_1480' => 'ppa', 'Pp3c14_1501' => 'ppa', 'Pp3c16_4900' => 'ppa', 'Pp3c16_5010' => 'ppa', 'Pp3c16_5060' => 'ppa', 'Pp3c19_18250' => 'ppa', 'Pp3c23_8530' => 'ppa', 'Pp3c23_8550' => 'ppa', 'Pp3c24_9670' => 'ppa', 'Pp3c2_21390' => 'ppa', 'Pp3c2_31380' => 'ppa', 'Pp3c3_16620' => 'ppa', 'Pp3c3_8090' => 'ppa', 'Pp3c3_8110' => 'ppa', 'Pp3c3_8130' => 'ppa', 'Pp3c3_8150' => 'ppa', 'Pp3c4_14320' => 'ppa', 'Pp3c6_2560' => 'ppa', 'Pp3c9_16700' => 'ppa', 'PRCOL_00000234' => 'pco', 'PRCOL_00000235' => 'pco', 'PRCOL_00000777' => 'pco', 'PRCOL_00002344' => 'pco', 'PRCOL_00002372' => 'pco', 'PRCOL_00006120' => 'pco', 'Prupe.1G021400' => 'ppe', 'Prupe.1G021500' => 'ppe', 'Prupe.1G021600' => 'ppe', 'Prupe.1G021700' => 'ppe', 'Prupe.1G021800' => 'ppe', 'Prupe.5G145100' => 'ppe', 'Psat6g204040' => 'psa', 'Psat6g204800' => 'psa', 'Psat6g204920' => 'psa', 'Psat6g204960' => 'psa', 'Psat6g205080' => 'psa', 'PSO017G0271' => 'pso', 'PSO017G1276' => 'pso', 'PSO017G1429' => 'pso', 'PSO017G1861' => 'pso', 'PSO017G2787' => 'pso', 'PSO017G4466' => 'pso', 'PSO017G5118' => 'pso', 'PSO017G5420' => 'pso', 'PSO063G3678' => 'pso', 'PSO210G0546' => 'pso', 'PSO317G0001' => 'pso', 'PSO357G0512' => 'pso', 'PSO478G2682' => 'pso', 'PSO647G0001' => 'pso', 'PSO675G0001' => 'pso', 'PSO675G2699' => 'pso', 'PSO675G2849' => 'pso', 'PSO675G4991' => 'pso', 'PSO689G0001' => 'pso', 'QL06p000916' => 'qlo', 'QL06p000921' => 'qlo', 'QL06p001398' => 'qlo', 'QL06p001407' => 'qlo', 'QL06p002031' => 'qlo', 'RcHm_v2.0_Chr4g0387791' => 'rch', 'RcHm_v2.0_Chr4g0387801' => 'rch', 'RcHm_v2.0_Chr6g0286501' => 'rch', 'RcHm_v2.0_Chr6g0286511' => 'rch', 'RcHm_v2.0_Chr6g0286521' => 'rch', 'RcHm_v2.0_Chr6g0286531' => 'rch', 'RcHm_v2.0_Chr7g0189141' => 'rch', 'Rhsim02G0028700' => 'rsi', 'Rhsim02G0028800' => 'rsi', 'Rhsim02G0028900' => 'rsi', 'Rhsim02G0029000' => 'rsi', 'Rhsim02G0029100' => 'rsi', 'Rhsim02G0029200' => 'rsi', 'Rhsim02G0029300' => 'rsi', 'Rhsim02G0029400' => 'rsi', 'Rhsim02G0029500' => 'rsi', 'Rhsim02G0029600' => 'rsi', 'RhsimUnG0024000' => 'rsi', 'RhsimUnG0024100' => 'rsi', 'RhsimUnG0024200' => 'rsi', 'RhsimUnG0024300' => 'rsi', 'RhsimUnG0024400' => 'rsi', 'RhsimUnG0024500' => 'rsi', 'RhsimUnG0024700' => 'rsi', 'RhsimUnG0024800' => 'rsi', 'RhsimUnG0024900' => 'rsi', 'RhsimUnG0025100' => 'rsi', 'Sabra08G0120200' => 'sbr', 'Sabra08G0120300' => 'sbr', 'Sabra08G0120500' => 'sbr', 'Sabra08G0120600' => 'sbr', 'Sabra10G0158900' => 'sbr', 'SalBow2G3492' => 'sbo', 'Sc13g0004760' => 'sci', 'Sc13g0004770' => 'sci', 'Sed0003417' => 'sed', 'Sed0019750' => 'sed', 'SEGI_03419' => 'sgi', 'SEGI_05907' => 'sgi', 'SEGI_10682' => 'sgi', 'SEGI_13528' => 'sgi', 'SEGI_16081' => 'sgi', 'SEGI_19370' => 'sgi', 'SEGI_21015' => 'sgi', 'SEGI_21944' => 'sgi', 'SEGI_32906' => 'sgi', 'SEGI_33093' => 'sgi', 'SEGI_36110' => 'sgi', 'SEGI_40397' => 'sgi', 'SGA_v2.0_scaffold191G40426' => 'sas', 'SGA_v2.0_scaffold353G49717' => 'sas', 'SGA_v2.0_scaffold50G18550' => 'sas', 'SMO119G0173' => 'smo', 'SMO172G0002' => 'smo', 'Solyc09g082690.3' => 'sly', 'Solyc09g082700.2' => 'sly', 'Sopen09g031550' => 'spe', 'Sopen09g031560' => 'spe', 'Sp3g20540' => 'spa', 'Sp7g07580' => 'spa', 'TAR134G0002' => 'tar', 'TAR236G0001' => 'tar', 'TAR365G0892' => 'tar', 'TAR636G0166' => 'tar', 'TAR636G0646' => 'tar', 'TAR636G0869' => 'tar', 'TAR636G1317' => 'tar', 'TAR636G1744' => 'tar', 'TAR636G3358' => 'tar', 'TAR636G3436' => 'tar', 'THA.LOC104803047' => 'tha', 'Thecc.04G238900' => 'tca', 'Thhalv10021557m.g' => 'esa', 'Thhalv10026318m.g' => 'esa', 'Thhalv10026335m.g' => 'esa', 'TPR.G17433' => 'tpr', 'TPR.G18915' => 'tpr', 'TPR.G26125' => 'tpr', 'TWI09G0677' => 'twi', 'TWI73G0287' => 'twi', 'unitig_748.g8326' => 'ugi', 'vmacro15370' => 'vma', 'vmacro15371' => 'vma', 'vmacro15372' => 'vma', 'vmacro15373' => 'vma', 'vmacro15374' => 'vma', 'VMungo0720G2826' => 'vmu', 'Zm00001eb116960' => 'zma', 'Zm00001eb301260' => 'zma', 'Zm00001eb301270' => 'zma' ) $gf_id = 'HOM05D001460' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001460' ) $data_identifier = 'HOM05D001460' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 4, 'aag' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 2, 'aox' => (int) 2, 'arhy' => (int) 4, 'ath' => (int) 2, 'atr' => (int) 1, 'acertr' => (int) 10, 'cqu' => (int) 4, 'bca' => (int) 11, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 1, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 1, 'ccan' => (int) 1, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 1, 'col' => (int) 1, 'cpa' => (int) 1, 'cre' => (int) 7, 'csa' => (int) 1, 'camsi' => (int) 2, 'dca' => (int) 3, 'din' => (int) 2, 'dzi' => (int) 3, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 14, 'fve' => (int) 9, 'gma' => (int) 2, 'ghi' => (int) 4, 'gra' => (int) 2, 'vvi' => (int) 1, 'han' => (int) 13, 'cav' => (int) 1, 'hma' => (int) 2, 'sun' => (int) 2, 'lal' => (int) 2, 'lonja' => (int) 12, 'lja' => (int) 1, 'lsa' => (int) 7, 'mes' => (int) 1, 'mpo' => (int) 27, 'mbi' => (int) 1, 'mco' => (int) 8, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 1, 'egut' => (int) 1, 'ama' => (int) 1, 'nta' => (int) 4, 'nnu' => (int) 2, 'oeu' => (int) 3, 'osa' => (int) 4, 'pax' => (int) 9, 'pgr' => (int) 1, 'stu' => (int) 1, 'pvu' => (int) 1, 'ptr' => (int) 4, 'ppa' => (int) 22, 'pco' => (int) 6, 'ppe' => (int) 6, 'psa' => (int) 5, 'pso' => (int) 19, 'qlo' => (int) 5, 'rch' => (int) 7, 'rsi' => (int) 20, 'sbr' => (int) 5, 'sbo' => (int) 1, 'sci' => (int) 2, 'sed' => (int) 2, 'sgi' => (int) 12, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 2, 'tar' => (int) 10, 'tha' => (int) 1, 'tca' => (int) 1, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 2, 'ugi' => (int) 1, 'vma' => (int) 5, 'vmu' => (int) 1, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb301270' $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' => 'HOM05D001460', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '433', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p22980' => 'bna', 'A01p32340' => 'bna', 'A03p42970' => 'bna', 'A05p25880' => 'bna', 'Aa31LG8G9320' => 'aar', 'Aa31LG8G9330' => 'aar', 'Aa31LG8G9340' => 'aar', 'Aa31sc221G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1034' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1528' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.829' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2222' => 'aag', 'Ah.12g058830' => 'amhyb', 'Ah.12g058840' => 'amhyb', 'AL3G37160' => 'aly', 'AL7G41310' => 'aly', 'Aqoxy5G00395' => 'aox', 'Aqoxy5G00396' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0C8NZA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5185HY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JZ1PRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MD3LS0' => 'arhy', 'AT3G22840' => 'ath', 'AT4G14690' => 'ath', 'ATR0665G054' => 'atr', 'Atru.chr4.2344' => 'acertr', 'Atru.chr4.2346' => 'acertr', 'Atru.chr4.2347' => 'acertr', 'Atru.chr4.2348' => 'acertr', 'Atru.chr4.2355' => 'acertr', 'Atru.chr4.2356' => 'acertr', 'Atru.chr4.2358' => 'acertr', 'Atru.chr4.2359' => 'acertr', 'Atru.chr4.2360' => 'acertr', 'Atru.chr4.2361' => 'acertr', 'AUR62030476' => 'cqu', 'AUR62030478' => 'cqu', 'AUR62030819' => 'cqu', 'AUR62030820' => 'cqu', 'BcaB03g14648' => 'bca', 'BcaB04g20492' => 'bca', 'BcaB06g26399' => 'bca', 'BcaC01g03416' => 'bca', 'BcaC01g03419' => 'bca', 'BcaC01g03421' => 'bca', 'BcaC01g03424' => 'bca', 'BcaC05g28012' => 'bca', 'BcaC09g49212' => 'bca', 'BcaC09g50140' => 'bca', 'BcaNung00346' => 'bca', 'BolC1t02785H' => 'bol', 'BolC1t04095H' => 'bol', 'BolC3t17545H' => 'bol', 'BolC5t32769H' => 'bol', 'BraA01t02211Z' => 'bra', 'BraA01t03359Z' => 'bra', 'BraA03t13441Z' => 'bra', 'BraA05t21476Z' => 'bra', 'C01p28420' => 'bna', 'C01p41350' => 'bna', 'C03p52750' => 'bna', 'C03p52780' => 'bna', 'C05p40270' => 'bna', 'CAN.G1437.9' => 'can', 'CANSAT78G0035' => 'cansat', 'CANSAT78G1036' => 'cansat', 'CANSAT78G2272' => 'cansat', 'CANSAT78G2478' => 'cansat', 'CARHR098700' => 'chi', 'CARHR221120' => 'chi', 'CARHR221150' => 'chi', 'Carub.0003s2297' => 'cru', 'Carub.0007s2749' => 'cru', 'Carub.0007s2750' => 'cru', 'Carub.0007s2751' => 'cru', 'Ca_10849_v3' => 'car', 'Cc03_g04300' => 'ccan', 'CDE02G3648' => 'cde', 'CDE05G0060' => 'cde', 'CDE05G0692' => 'cde', 'CDE05G2285' => 'cde', 'CDE05G2884' => 'cde', 'CDE05G3072' => 'cde', 'Cfa008439' => 'cfa', 'Cfa008441' => 'cfa', 'Cfa008443' => 'cfa', 'Cfa008448' => 'cfa', 'Ciclev10005974m.g' => 'ccl', 'Ciclev10006006m.g' => 'ccl', 'Ciclev10006775m.g' => 'ccl', 'CiPaw.02G120400' => 'cil', 'CiPaw.02G120500' => 'cil', 'CiPaw.02G120600' => 'cil', 'ClCG05G004850' => 'cla', 'COL.COLO4_21566' => 'col', 'Cpa.g.sc44.124' => 'cpa', 'Cre07.g320400' => 'cre', 'Cre07.g320450' => 'cre', 'Cre08.g384650' => 'cre', 'Cre09.g393173' => 'cre', 'Cre09.g394325' => 'cre', 'Cre14.g626750' => 'cre', 'Cre16.g679250' => 'cre', 'CsaV3_3G012890' => 'csa', 'CSS0010865' => 'camsi', 'CSS0044338' => 'camsi', 'DCAR_002366' => 'dca', 'DCAR_030687' => 'dca', 'DCAR_030688' => 'dca', 'Dinv14047' => 'din', 'Dinv14048' => 'din', 'Duzib151G0105' => 'dzi', 'Duzib151G0114' => 'dzi', 'Duzib212G1029' => 'dzi', 'ECA232G3536' => 'eca', 'ECA240G0786' => 'eca', 'ECA240G1802' => 'eca', 'ECA240G3760' => 'eca', 'ECA240G3920' => 'eca', 'EL10Ac5g12536' => 'bvu', 'EL10Ac5g12537' => 'bvu', 'EL10Ac5g12538' => 'bvu', 'Eucgr.B01004' => 'egr', 'Eucgr.B01006' => 'egr', 'Eucgr.B01007' => 'egr', 'Eucgr.B01008' => 'egr', 'Eucgr.B01895' => 'egr', 'Eucgr.B01896' => 'egr', 'FAN04G1456' => 'fan', 'FAN08G1769' => 'fan', 'FAN08G2160' => 'fan', 'FAN13G2403' => 'fan', 'FAN13G3303' => 'fan', 'FAN15G2435' => 'fan', 'FAN17G0672' => 'fan', 'FAN17G2441' => 'fan', 'FAN18G1024' => 'fan', 'FAN22G1458' => 'fan', 'FAN24G0037' => 'fan', 'FAN24G0429' => 'fan', 'FAN24G2387' => 'fan', 'FAN27G2746' => 'fan', 'FvH4_2g20400' => 'fve', 'FvH4_2g20420' => 'fve', 'FvH4_2g20430' => 'fve', 'FvH4_4g01270' => 'fve', 'FvH4_4g01290' => 'fve', 'FvH4_4g01300' => 'fve', 'FvH4_4g01310' => 'fve', 'FvH4_4g01330' => 'fve', 'FvH4_5g09070' => 'fve', 'Glyma.10G243800' => 'gma', 'Glyma.20G150600' => 'gma', 'Gohir.A09G219200' => 'ghi', 'Gohir.A09G219300' => 'ghi', 'Gohir.D09G221400' => 'ghi', 'Gohir.D09G221500' => 'ghi', 'Gorai.006G242600' => 'gra', 'Gorai.006G242700' => 'gra', 'GSVIVG01018044001' => 'vvi', 'HanXRQChr03g0083821' => 'han', 'HanXRQChr03g0083841' => 'han', 'HanXRQChr03g0083881' => 'han', 'HanXRQChr03g0083901' => 'han', 'HanXRQChr03g0083921' => 'han', 'HanXRQChr03g0085331' => 'han', 'HanXRQChr03g0085361' => 'han', 'HanXRQChr03g0085411' => 'han', 'HanXRQChr03g0085421' => 'han', 'HanXRQChr03g0085431' => 'han', 'HanXRQChr08g0221991' => 'han', 'HanXRQChr11g0336061' => 'han', 'HanXRQChr11g0336411' => 'han', 'Haze_11234' => 'cav', 'Hma1.2p1_0549F.1_g177010' => 'hma', 'Hma1.2p1_0602F.1_g187630' => 'hma', 'Hund14876' => 'sun', 'Hund14879' => 'sun', 'Lalb_Chr06g0160741' => 'lal', 'Lalb_Chr21g0304781' => 'lal', 'Lj3A726G19' => 'lonja', 'Lj3A726T23' => 'lonja', 'Lj3A726T24' => 'lonja', 'Lj3A726T25' => 'lonja', 'Lj3A727T17' => 'lonja', 'Lj3C726T0' => 'lonja', 'Lj3C726T2' => 'lonja', 'Lj3P725T35' => 'lonja', 'Lj3P727T10' => 'lonja', 'Lj3P727T12' => 'lonja', 'Lj3P727T14' => 'lonja', 'Lj5g0023109' => 'lja', 'Lj6P646T44' => 'lonja', 'Lsat_1_v5_gn_6_75760' => 'lsa', 'Lsat_1_v5_gn_6_75800' => 'lsa', 'Lsat_1_v5_gn_6_75900' => 'lsa', 'Lsat_1_v5_gn_6_76240' => 'lsa', 'Lsat_1_v5_gn_6_76441' => 'lsa', 'Lsat_1_v5_gn_6_76700' => 'lsa', 'Lsat_1_v5_gn_6_76760' => 'lsa', 'Manes.15G033100' => 'mes', 'Mapoly0004s0074' => 'mpo', 'Mapoly0004s0075' => 'mpo', 'Mapoly0004s0163' => 'mpo', 'Mapoly0004s0164' => 'mpo', 'Mapoly0021s0018' => 'mpo', 'Mapoly0041s0136' => 'mpo', 'Mapoly0041s0137' => 'mpo', 'Mapoly0041s0138' => 'mpo', 'Mapoly0041s0139' => 'mpo', 'Mapoly0041s0141' => 'mpo', 'Mapoly0041s0142' => 'mpo', 'Mapoly0041s0143' => 'mpo', 'Mapoly0041s0144' => 'mpo', 'Mapoly0041s0145' => 'mpo', 'Mapoly0047s0106' => 'mpo', 'Mapoly0047s0108' => 'mpo', 'Mapoly0050s0051' => 'mpo', 'Mapoly0050s0052' => 'mpo', 'Mapoly0050s0053' => 'mpo', 'Mapoly0058s0013' => 'mpo', 'Mapoly0091s0078' => 'mpo', 'Mapoly0091s0079' => 'mpo', 'Mapoly0091s0080' => 'mpo', 'Mapoly0091s0081' => 'mpo', 'Mapoly0278s0004' => 'mpo', 'Mapoly0278s0005' => 'mpo', 'Mapoly0278s0006' => 'mpo', 'MBI11_g30648_MAGBIO' => 'mbi', 'MCO03G194' => 'mco', 'MCO03G590' => 'mco', 'MCO07G312' => 'mco', 'MCO10G318' => 'mco', 'MCO12G244' => 'mco', 'MCO13G148' => 'mco', 'MCO13G194' => 'mco', 'MCO16G238' => 'mco', 'MD06G1134100' => 'mdo', 'MD13G1200100' => 'mdo', 'MD13G1200300' => 'mdo', 'MD13G1200600' => 'mdo', 'MD14G1150400' => 'mdo', 'MD16G1200000' => 'mdo', 'Medtr1g102570' => 'mtr', 'Medtr1g102780' => 'mtr', 'Medtr1g102800' => 'mtr', 'Medtr1g102810' => 'mtr', 'Medtr1g102830' => 'mtr', 'MELO3C006499.2' => 'cme', 'Migut.G00385' => 'egut', 'MSTRG.4063' => 'ama', 'Nitab4.5_0000090g0260' => 'nta', 'Nitab4.5_0000977g0030' => 'nta', 'Nitab4.5_0002541g0040' => 'nta', 'Nitab4.5_0007068g0040' => 'nta', 'Nn005s41408' => 'nnu', 'Nn005s41410' => 'nnu', 'Oeu010310.1' => 'oeu', 'Oeu010311.1' => 'oeu', 'Oeu043472.1' => 'oeu', 'Os01g0246400' => 'osa', 'Os04g0267950' => 'osa', 'Os07g0178700' => 'osa', 'Os07g0178800' => 'osa', 'Peaxi162Scf00316g00046' => 'pax', 'Peaxi162Scf00316g00049' => 'pax', 'Peaxi162Scf00316g00059' => 'pax', 'Peaxi162Scf00316g00328' => 'pax', 'Peaxi162Scf00316g00329' => 'pax', 'Peaxi162Scf00316g00411' => 'pax', 'Peaxi162Scf00316g00521' => 'pax', 'Peaxi162Scf00492g00068' => 'pax', 'Peaxi162Scf35631g00002' => 'pax', 'PGR142G3720' => 'pgr', 'PGSC0003DMG400006442' => 'stu', 'Phvul.007G062000' => 'pvu', 'Potri.008G157750' => 'ptr', 'Potri.008G157900' => 'ptr', 'Potri.008G158000' => 'ptr', 'Potri.008G158200' => 'ptr', 'Pp3c11_7280' => 'ppa', 'Pp3c11_7980' => 'ppa', 'Pp3c12_19450' => 'ppa', 'Pp3c14_1480' => 'ppa', 'Pp3c14_1501' => 'ppa', 'Pp3c16_4900' => 'ppa', 'Pp3c16_5010' => 'ppa', 'Pp3c16_5060' => 'ppa', 'Pp3c19_18250' => 'ppa', 'Pp3c23_8530' => 'ppa', 'Pp3c23_8550' => 'ppa', 'Pp3c24_9670' => 'ppa', 'Pp3c2_21390' => 'ppa', 'Pp3c2_31380' => 'ppa', 'Pp3c3_16620' => 'ppa', 'Pp3c3_8090' => 'ppa', 'Pp3c3_8110' => 'ppa', 'Pp3c3_8130' => 'ppa', 'Pp3c3_8150' => 'ppa', 'Pp3c4_14320' => 'ppa', 'Pp3c6_2560' => 'ppa', 'Pp3c9_16700' => 'ppa', 'PRCOL_00000234' => 'pco', 'PRCOL_00000235' => 'pco', 'PRCOL_00000777' => 'pco', 'PRCOL_00002344' => 'pco', 'PRCOL_00002372' => 'pco', 'PRCOL_00006120' => 'pco', 'Prupe.1G021400' => 'ppe', 'Prupe.1G021500' => 'ppe', 'Prupe.1G021600' => 'ppe', 'Prupe.1G021700' => 'ppe', 'Prupe.1G021800' => 'ppe', 'Prupe.5G145100' => 'ppe', 'Psat6g204040' => 'psa', 'Psat6g204800' => 'psa', 'Psat6g204920' => 'psa', 'Psat6g204960' => 'psa', 'Psat6g205080' => 'psa', 'PSO017G0271' => 'pso', 'PSO017G1276' => 'pso', 'PSO017G1429' => 'pso', 'PSO017G1861' => 'pso', 'PSO017G2787' => 'pso', 'PSO017G4466' => 'pso', 'PSO017G5118' => 'pso', 'PSO017G5420' => 'pso', 'PSO063G3678' => 'pso', 'PSO210G0546' => 'pso', 'PSO317G0001' => 'pso', 'PSO357G0512' => 'pso', 'PSO478G2682' => 'pso', 'PSO647G0001' => 'pso', 'PSO675G0001' => 'pso', 'PSO675G2699' => 'pso', 'PSO675G2849' => 'pso', 'PSO675G4991' => 'pso', 'PSO689G0001' => 'pso', 'QL06p000916' => 'qlo', 'QL06p000921' => 'qlo', 'QL06p001398' => 'qlo', 'QL06p001407' => 'qlo', 'QL06p002031' => 'qlo', 'RcHm_v2.0_Chr4g0387791' => 'rch', 'RcHm_v2.0_Chr4g0387801' => 'rch', 'RcHm_v2.0_Chr6g0286501' => 'rch', 'RcHm_v2.0_Chr6g0286511' => 'rch', 'RcHm_v2.0_Chr6g0286521' => 'rch', 'RcHm_v2.0_Chr6g0286531' => 'rch', 'RcHm_v2.0_Chr7g0189141' => 'rch', 'Rhsim02G0028700' => 'rsi', 'Rhsim02G0028800' => 'rsi', 'Rhsim02G0028900' => 'rsi', 'Rhsim02G0029000' => 'rsi', 'Rhsim02G0029100' => 'rsi', 'Rhsim02G0029200' => 'rsi', 'Rhsim02G0029300' => 'rsi', 'Rhsim02G0029400' => 'rsi', 'Rhsim02G0029500' => 'rsi', 'Rhsim02G0029600' => 'rsi', 'RhsimUnG0024000' => 'rsi', 'RhsimUnG0024100' => 'rsi', 'RhsimUnG0024200' => 'rsi', 'RhsimUnG0024300' => 'rsi', 'RhsimUnG0024400' => 'rsi', 'RhsimUnG0024500' => 'rsi', 'RhsimUnG0024700' => 'rsi', 'RhsimUnG0024800' => 'rsi', 'RhsimUnG0024900' => 'rsi', 'RhsimUnG0025100' => 'rsi', 'Sabra08G0120200' => 'sbr', 'Sabra08G0120300' => 'sbr', 'Sabra08G0120500' => 'sbr', 'Sabra08G0120600' => 'sbr', 'Sabra10G0158900' => 'sbr', 'SalBow2G3492' => 'sbo', 'Sc13g0004760' => 'sci', 'Sc13g0004770' => 'sci', 'Sed0003417' => 'sed', 'Sed0019750' => 'sed', 'SEGI_03419' => 'sgi', 'SEGI_05907' => 'sgi', 'SEGI_10682' => 'sgi', 'SEGI_13528' => 'sgi', 'SEGI_16081' => 'sgi', 'SEGI_19370' => 'sgi', 'SEGI_21015' => 'sgi', 'SEGI_21944' => 'sgi', 'SEGI_32906' => 'sgi', 'SEGI_33093' => 'sgi', 'SEGI_36110' => 'sgi', 'SEGI_40397' => 'sgi', 'SGA_v2.0_scaffold191G40426' => 'sas', 'SGA_v2.0_scaffold353G49717' => 'sas', 'SGA_v2.0_scaffold50G18550' => 'sas', 'SMO119G0173' => 'smo', 'SMO172G0002' => 'smo', 'Solyc09g082690.3' => 'sly', 'Solyc09g082700.2' => 'sly', 'Sopen09g031550' => 'spe', 'Sopen09g031560' => 'spe', 'Sp3g20540' => 'spa', 'Sp7g07580' => 'spa', 'TAR134G0002' => 'tar', 'TAR236G0001' => 'tar', 'TAR365G0892' => 'tar', 'TAR636G0166' => 'tar', 'TAR636G0646' => 'tar', 'TAR636G0869' => 'tar', 'TAR636G1317' => 'tar', 'TAR636G1744' => 'tar', 'TAR636G3358' => 'tar', 'TAR636G3436' => 'tar', 'THA.LOC104803047' => 'tha', 'Thecc.04G238900' => 'tca', 'Thhalv10021557m.g' => 'esa', 'Thhalv10026318m.g' => 'esa', 'Thhalv10026335m.g' => 'esa', 'TPR.G17433' => 'tpr', 'TPR.G18915' => 'tpr', 'TPR.G26125' => 'tpr', 'TWI09G0677' => 'twi', 'TWI73G0287' => 'twi', 'unitig_748.g8326' => 'ugi', 'vmacro15370' => 'vma', 'vmacro15371' => 'vma', 'vmacro15372' => 'vma', 'vmacro15373' => 'vma', 'vmacro15374' => 'vma', 'VMungo0720G2826' => 'vmu', 'Zm00001eb116960' => 'zma', 'Zm00001eb301260' => 'zma', 'Zm00001eb301270' => 'zma' ), 'gf_id' => 'HOM05D001460', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001460' ), 'data_identifier' => 'HOM05D001460', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001460', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '433', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p22980' => 'bna', 'A01p32340' => 'bna', 'A03p42970' => 'bna', 'A05p25880' => 'bna', 'Aa31LG8G9320' => 'aar', 'Aa31LG8G9330' => 'aar', 'Aa31LG8G9340' => 'aar', 'Aa31sc221G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1034' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1528' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.829' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2222' => 'aag', 'Ah.12g058830' => 'amhyb', 'Ah.12g058840' => 'amhyb', 'AL3G37160' => 'aly', 'AL7G41310' => 'aly', 'Aqoxy5G00395' => 'aox', 'Aqoxy5G00396' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0C8NZA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5185HY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JZ1PRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MD3LS0' => 'arhy', 'AT3G22840' => 'ath', 'AT4G14690' => 'ath', 'ATR0665G054' => 'atr', 'Atru.chr4.2344' => 'acertr', 'Atru.chr4.2346' => 'acertr', 'Atru.chr4.2347' => 'acertr', 'Atru.chr4.2348' => 'acertr', 'Atru.chr4.2355' => 'acertr', 'Atru.chr4.2356' => 'acertr', 'Atru.chr4.2358' => 'acertr', 'Atru.chr4.2359' => 'acertr', 'Atru.chr4.2360' => 'acertr', 'Atru.chr4.2361' => 'acertr', 'AUR62030476' => 'cqu', 'AUR62030478' => 'cqu', 'AUR62030819' => 'cqu', 'AUR62030820' => 'cqu', 'BcaB03g14648' => 'bca', 'BcaB04g20492' => 'bca', 'BcaB06g26399' => 'bca', 'BcaC01g03416' => 'bca', 'BcaC01g03419' => 'bca', 'BcaC01g03421' => 'bca', 'BcaC01g03424' => 'bca', 'BcaC05g28012' => 'bca', 'BcaC09g49212' => 'bca', 'BcaC09g50140' => 'bca', 'BcaNung00346' => 'bca', 'BolC1t02785H' => 'bol', 'BolC1t04095H' => 'bol', 'BolC3t17545H' => 'bol', 'BolC5t32769H' => 'bol', 'BraA01t02211Z' => 'bra', 'BraA01t03359Z' => 'bra', 'BraA03t13441Z' => 'bra', 'BraA05t21476Z' => 'bra', 'C01p28420' => 'bna', 'C01p41350' => 'bna', 'C03p52750' => 'bna', 'C03p52780' => 'bna', 'C05p40270' => 'bna', 'CAN.G1437.9' => 'can', 'CANSAT78G0035' => 'cansat', 'CANSAT78G1036' => 'cansat', 'CANSAT78G2272' => 'cansat', 'CANSAT78G2478' => 'cansat', 'CARHR098700' => 'chi', 'CARHR221120' => 'chi', 'CARHR221150' => 'chi', 'Carub.0003s2297' => 'cru', 'Carub.0007s2749' => 'cru', 'Carub.0007s2750' => 'cru', 'Carub.0007s2751' => 'cru', 'Ca_10849_v3' => 'car', 'Cc03_g04300' => 'ccan', 'CDE02G3648' => 'cde', 'CDE05G0060' => 'cde', 'CDE05G0692' => 'cde', 'CDE05G2285' => 'cde', 'CDE05G2884' => 'cde', 'CDE05G3072' => 'cde', 'Cfa008439' => 'cfa', 'Cfa008441' => 'cfa', 'Cfa008443' => 'cfa', 'Cfa008448' => 'cfa', 'Ciclev10005974m.g' => 'ccl', 'Ciclev10006006m.g' => 'ccl', 'Ciclev10006775m.g' => 'ccl', 'CiPaw.02G120400' => 'cil', 'CiPaw.02G120500' => 'cil', 'CiPaw.02G120600' => 'cil', 'ClCG05G004850' => 'cla', 'COL.COLO4_21566' => 'col', 'Cpa.g.sc44.124' => 'cpa', 'Cre07.g320400' => 'cre', 'Cre07.g320450' => 'cre', 'Cre08.g384650' => 'cre', 'Cre09.g393173' => 'cre', 'Cre09.g394325' => 'cre', 'Cre14.g626750' => 'cre', 'Cre16.g679250' => 'cre', 'CsaV3_3G012890' => 'csa', 'CSS0010865' => 'camsi', 'CSS0044338' => 'camsi', 'DCAR_002366' => 'dca', 'DCAR_030687' => 'dca', 'DCAR_030688' => 'dca', 'Dinv14047' => 'din', 'Dinv14048' => 'din', 'Duzib151G0105' => 'dzi', 'Duzib151G0114' => 'dzi', 'Duzib212G1029' => 'dzi', 'ECA232G3536' => 'eca', 'ECA240G0786' => 'eca', 'ECA240G1802' => 'eca', 'ECA240G3760' => 'eca', 'ECA240G3920' => 'eca', 'EL10Ac5g12536' => 'bvu', 'EL10Ac5g12537' => 'bvu', 'EL10Ac5g12538' => 'bvu', 'Eucgr.B01004' => 'egr', 'Eucgr.B01006' => 'egr', 'Eucgr.B01007' => 'egr', 'Eucgr.B01008' => 'egr', 'Eucgr.B01895' => 'egr', 'Eucgr.B01896' => 'egr', 'FAN04G1456' => 'fan', 'FAN08G1769' => 'fan', 'FAN08G2160' => 'fan', 'FAN13G2403' => 'fan', 'FAN13G3303' => 'fan', 'FAN15G2435' => 'fan', 'FAN17G0672' => 'fan', 'FAN17G2441' => 'fan', 'FAN18G1024' => 'fan', 'FAN22G1458' => 'fan', 'FAN24G0037' => 'fan', 'FAN24G0429' => 'fan', 'FAN24G2387' => 'fan', 'FAN27G2746' => 'fan', 'FvH4_2g20400' => 'fve', 'FvH4_2g20420' => 'fve', 'FvH4_2g20430' => 'fve', 'FvH4_4g01270' => 'fve', 'FvH4_4g01290' => 'fve', 'FvH4_4g01300' => 'fve', 'FvH4_4g01310' => 'fve', 'FvH4_4g01330' => 'fve', 'FvH4_5g09070' => 'fve', 'Glyma.10G243800' => 'gma', 'Glyma.20G150600' => 'gma', 'Gohir.A09G219200' => 'ghi', 'Gohir.A09G219300' => 'ghi', 'Gohir.D09G221400' => 'ghi', 'Gohir.D09G221500' => 'ghi', 'Gorai.006G242600' => 'gra', 'Gorai.006G242700' => 'gra', 'GSVIVG01018044001' => 'vvi', 'HanXRQChr03g0083821' => 'han', 'HanXRQChr03g0083841' => 'han', 'HanXRQChr03g0083881' => 'han', 'HanXRQChr03g0083901' => 'han', 'HanXRQChr03g0083921' => 'han', 'HanXRQChr03g0085331' => 'han', 'HanXRQChr03g0085361' => 'han', 'HanXRQChr03g0085411' => 'han', 'HanXRQChr03g0085421' => 'han', 'HanXRQChr03g0085431' => 'han', 'HanXRQChr08g0221991' => 'han', 'HanXRQChr11g0336061' => 'han', 'HanXRQChr11g0336411' => 'han', 'Haze_11234' => 'cav', 'Hma1.2p1_0549F.1_g177010' => 'hma', 'Hma1.2p1_0602F.1_g187630' => 'hma', 'Hund14876' => 'sun', 'Hund14879' => 'sun', 'Lalb_Chr06g0160741' => 'lal', 'Lalb_Chr21g0304781' => 'lal', 'Lj3A726G19' => 'lonja', 'Lj3A726T23' => 'lonja', 'Lj3A726T24' => 'lonja', 'Lj3A726T25' => 'lonja', 'Lj3A727T17' => 'lonja', 'Lj3C726T0' => 'lonja', 'Lj3C726T2' => 'lonja', 'Lj3P725T35' => 'lonja', 'Lj3P727T10' => 'lonja', 'Lj3P727T12' => 'lonja', 'Lj3P727T14' => 'lonja', 'Lj5g0023109' => 'lja', 'Lj6P646T44' => 'lonja', 'Lsat_1_v5_gn_6_75760' => 'lsa', 'Lsat_1_v5_gn_6_75800' => 'lsa', 'Lsat_1_v5_gn_6_75900' => 'lsa', 'Lsat_1_v5_gn_6_76240' => 'lsa', 'Lsat_1_v5_gn_6_76441' => 'lsa', 'Lsat_1_v5_gn_6_76700' => 'lsa', 'Lsat_1_v5_gn_6_76760' => 'lsa', 'Manes.15G033100' => 'mes', 'Mapoly0004s0074' => 'mpo', 'Mapoly0004s0075' => 'mpo', 'Mapoly0004s0163' => 'mpo', 'Mapoly0004s0164' => 'mpo', 'Mapoly0021s0018' => 'mpo', 'Mapoly0041s0136' => 'mpo', 'Mapoly0041s0137' => 'mpo', 'Mapoly0041s0138' => 'mpo', 'Mapoly0041s0139' => 'mpo', 'Mapoly0041s0141' => 'mpo', 'Mapoly0041s0142' => 'mpo', 'Mapoly0041s0143' => 'mpo', 'Mapoly0041s0144' => 'mpo', 'Mapoly0041s0145' => 'mpo', 'Mapoly0047s0106' => 'mpo', 'Mapoly0047s0108' => 'mpo', 'Mapoly0050s0051' => 'mpo', 'Mapoly0050s0052' => 'mpo', 'Mapoly0050s0053' => 'mpo', 'Mapoly0058s0013' => 'mpo', 'Mapoly0091s0078' => 'mpo', 'Mapoly0091s0079' => 'mpo', 'Mapoly0091s0080' => 'mpo', 'Mapoly0091s0081' => 'mpo', 'Mapoly0278s0004' => 'mpo', 'Mapoly0278s0005' => 'mpo', 'Mapoly0278s0006' => 'mpo', 'MBI11_g30648_MAGBIO' => 'mbi', 'MCO03G194' => 'mco', 'MCO03G590' => 'mco', 'MCO07G312' => 'mco', 'MCO10G318' => 'mco', 'MCO12G244' => 'mco', 'MCO13G148' => 'mco', 'MCO13G194' => 'mco', 'MCO16G238' => 'mco', 'MD06G1134100' => 'mdo', 'MD13G1200100' => 'mdo', 'MD13G1200300' => 'mdo', 'MD13G1200600' => 'mdo', 'MD14G1150400' => 'mdo', 'MD16G1200000' => 'mdo', 'Medtr1g102570' => 'mtr', 'Medtr1g102780' => 'mtr', 'Medtr1g102800' => 'mtr', 'Medtr1g102810' => 'mtr', 'Medtr1g102830' => 'mtr', 'MELO3C006499.2' => 'cme', 'Migut.G00385' => 'egut', 'MSTRG.4063' => 'ama', 'Nitab4.5_0000090g0260' => 'nta', 'Nitab4.5_0000977g0030' => 'nta', 'Nitab4.5_0002541g0040' => 'nta', 'Nitab4.5_0007068g0040' => 'nta', 'Nn005s41408' => 'nnu', 'Nn005s41410' => 'nnu', 'Oeu010310.1' => 'oeu', 'Oeu010311.1' => 'oeu', 'Oeu043472.1' => 'oeu', 'Os01g0246400' => 'osa', 'Os04g0267950' => 'osa', 'Os07g0178700' => 'osa', 'Os07g0178800' => 'osa', 'Peaxi162Scf00316g00046' => 'pax', 'Peaxi162Scf00316g00049' => 'pax', 'Peaxi162Scf00316g00059' => 'pax', 'Peaxi162Scf00316g00328' => 'pax', 'Peaxi162Scf00316g00329' => 'pax', 'Peaxi162Scf00316g00411' => 'pax', 'Peaxi162Scf00316g00521' => 'pax', 'Peaxi162Scf00492g00068' => 'pax', 'Peaxi162Scf35631g00002' => 'pax', 'PGR142G3720' => 'pgr', 'PGSC0003DMG400006442' => 'stu', 'Phvul.007G062000' => 'pvu', 'Potri.008G157750' => 'ptr', 'Potri.008G157900' => 'ptr', 'Potri.008G158000' => 'ptr', 'Potri.008G158200' => 'ptr', 'Pp3c11_7280' => 'ppa', 'Pp3c11_7980' => 'ppa', 'Pp3c12_19450' => 'ppa', 'Pp3c14_1480' => 'ppa', 'Pp3c14_1501' => 'ppa', 'Pp3c16_4900' => 'ppa', 'Pp3c16_5010' => 'ppa', 'Pp3c16_5060' => 'ppa', 'Pp3c19_18250' => 'ppa', 'Pp3c23_8530' => 'ppa', 'Pp3c23_8550' => 'ppa', 'Pp3c24_9670' => 'ppa', 'Pp3c2_21390' => 'ppa', 'Pp3c2_31380' => 'ppa', 'Pp3c3_16620' => 'ppa', 'Pp3c3_8090' => 'ppa', 'Pp3c3_8110' => 'ppa', 'Pp3c3_8130' => 'ppa', 'Pp3c3_8150' => 'ppa', 'Pp3c4_14320' => 'ppa', 'Pp3c6_2560' => 'ppa', 'Pp3c9_16700' => 'ppa', 'PRCOL_00000234' => 'pco', 'PRCOL_00000235' => 'pco', 'PRCOL_00000777' => 'pco', 'PRCOL_00002344' => 'pco', 'PRCOL_00002372' => 'pco', 'PRCOL_00006120' => 'pco', 'Prupe.1G021400' => 'ppe', 'Prupe.1G021500' => 'ppe', 'Prupe.1G021600' => 'ppe', 'Prupe.1G021700' => 'ppe', 'Prupe.1G021800' => 'ppe', 'Prupe.5G145100' => 'ppe', 'Psat6g204040' => 'psa', 'Psat6g204800' => 'psa', 'Psat6g204920' => 'psa', 'Psat6g204960' => 'psa', 'Psat6g205080' => 'psa', 'PSO017G0271' => 'pso', 'PSO017G1276' => 'pso', 'PSO017G1429' => 'pso', 'PSO017G1861' => 'pso', 'PSO017G2787' => 'pso', 'PSO017G4466' => 'pso', 'PSO017G5118' => 'pso', 'PSO017G5420' => 'pso', 'PSO063G3678' => 'pso', 'PSO210G0546' => 'pso', 'PSO317G0001' => 'pso', 'PSO357G0512' => 'pso', 'PSO478G2682' => 'pso', 'PSO647G0001' => 'pso', 'PSO675G0001' => 'pso', 'PSO675G2699' => 'pso', 'PSO675G2849' => 'pso', 'PSO675G4991' => 'pso', 'PSO689G0001' => 'pso', 'QL06p000916' => 'qlo', 'QL06p000921' => 'qlo', 'QL06p001398' => 'qlo', 'QL06p001407' => 'qlo', 'QL06p002031' => 'qlo', 'RcHm_v2.0_Chr4g0387791' => 'rch', 'RcHm_v2.0_Chr4g0387801' => 'rch', 'RcHm_v2.0_Chr6g0286501' => 'rch', 'RcHm_v2.0_Chr6g0286511' => 'rch', 'RcHm_v2.0_Chr6g0286521' => 'rch', 'RcHm_v2.0_Chr6g0286531' => 'rch', 'RcHm_v2.0_Chr7g0189141' => 'rch', 'Rhsim02G0028700' => 'rsi', 'Rhsim02G0028800' => 'rsi', 'Rhsim02G0028900' => 'rsi', 'Rhsim02G0029000' => 'rsi', 'Rhsim02G0029100' => 'rsi', 'Rhsim02G0029200' => 'rsi', 'Rhsim02G0029300' => 'rsi', 'Rhsim02G0029400' => 'rsi', 'Rhsim02G0029500' => 'rsi', 'Rhsim02G0029600' => 'rsi', 'RhsimUnG0024000' => 'rsi', 'RhsimUnG0024100' => 'rsi', 'RhsimUnG0024200' => 'rsi', 'RhsimUnG0024300' => 'rsi', 'RhsimUnG0024400' => 'rsi', 'RhsimUnG0024500' => 'rsi', 'RhsimUnG0024700' => 'rsi', 'RhsimUnG0024800' => 'rsi', 'RhsimUnG0024900' => 'rsi', 'RhsimUnG0025100' => 'rsi', 'Sabra08G0120200' => 'sbr', 'Sabra08G0120300' => 'sbr', 'Sabra08G0120500' => 'sbr', 'Sabra08G0120600' => 'sbr', 'Sabra10G0158900' => 'sbr', 'SalBow2G3492' => 'sbo', 'Sc13g0004760' => 'sci', 'Sc13g0004770' => 'sci', 'Sed0003417' => 'sed', 'Sed0019750' => 'sed', 'SEGI_03419' => 'sgi', 'SEGI_05907' => 'sgi', 'SEGI_10682' => 'sgi', 'SEGI_13528' => 'sgi', 'SEGI_16081' => 'sgi', 'SEGI_19370' => 'sgi', 'SEGI_21015' => 'sgi', 'SEGI_21944' => 'sgi', 'SEGI_32906' => 'sgi', 'SEGI_33093' => 'sgi', 'SEGI_36110' => 'sgi', 'SEGI_40397' => 'sgi', 'SGA_v2.0_scaffold191G40426' => 'sas', 'SGA_v2.0_scaffold353G49717' => 'sas', 'SGA_v2.0_scaffold50G18550' => 'sas', 'SMO119G0173' => 'smo', 'SMO172G0002' => 'smo', 'Solyc09g082690.3' => 'sly', 'Solyc09g082700.2' => 'sly', 'Sopen09g031550' => 'spe', 'Sopen09g031560' => 'spe', 'Sp3g20540' => 'spa', 'Sp7g07580' => 'spa', 'TAR134G0002' => 'tar', 'TAR236G0001' => 'tar', 'TAR365G0892' => 'tar', 'TAR636G0166' => 'tar', 'TAR636G0646' => 'tar', 'TAR636G0869' => 'tar', 'TAR636G1317' => 'tar', 'TAR636G1744' => 'tar', 'TAR636G3358' => 'tar', 'TAR636G3436' => 'tar', 'THA.LOC104803047' => 'tha', 'Thecc.04G238900' => 'tca', 'Thhalv10021557m.g' => 'esa', 'Thhalv10026318m.g' => 'esa', 'Thhalv10026335m.g' => 'esa', 'TPR.G17433' => 'tpr', 'TPR.G18915' => 'tpr', 'TPR.G26125' => 'tpr', 'TWI09G0677' => 'twi', 'TWI73G0287' => 'twi', 'unitig_748.g8326' => 'ugi', 'vmacro15370' => 'vma', 'vmacro15371' => 'vma', 'vmacro15372' => 'vma', 'vmacro15373' => 'vma', 'vmacro15374' => 'vma', 'VMungo0720G2826' => 'vmu', 'Zm00001eb116960' => 'zma', 'Zm00001eb301260' => 'zma', 'Zm00001eb301270' => 'zma' ) $gf_id = 'HOM05D001460' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001460' ) $data_identifier = 'HOM05D001460' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 4, 'aag' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 2, 'aox' => (int) 2, 'arhy' => (int) 4, 'ath' => (int) 2, 'atr' => (int) 1, 'acertr' => (int) 10, 'cqu' => (int) 4, 'bca' => (int) 11, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 1, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 1, 'ccan' => (int) 1, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 1, 'col' => (int) 1, 'cpa' => (int) 1, 'cre' => (int) 7, 'csa' => (int) 1, 'camsi' => (int) 2, 'dca' => (int) 3, 'din' => (int) 2, 'dzi' => (int) 3, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 14, 'fve' => (int) 9, 'gma' => (int) 2, 'ghi' => (int) 4, 'gra' => (int) 2, 'vvi' => (int) 1, 'han' => (int) 13, 'cav' => (int) 1, 'hma' => (int) 2, 'sun' => (int) 2, 'lal' => (int) 2, 'lonja' => (int) 12, 'lja' => (int) 1, 'lsa' => (int) 7, 'mes' => (int) 1, 'mpo' => (int) 27, 'mbi' => (int) 1, 'mco' => (int) 8, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 1, 'egut' => (int) 1, 'ama' => (int) 1, 'nta' => (int) 4, 'nnu' => (int) 2, 'oeu' => (int) 3, 'osa' => (int) 4, 'pax' => (int) 9, 'pgr' => (int) 1, 'stu' => (int) 1, 'pvu' => (int) 1, 'ptr' => (int) 4, 'ppa' => (int) 22, 'pco' => (int) 6, 'ppe' => (int) 6, 'psa' => (int) 5, 'pso' => (int) 19, 'qlo' => (int) 5, 'rch' => (int) 7, 'rsi' => (int) 20, 'sbr' => (int) 5, 'sbo' => (int) 1, 'sci' => (int) 2, 'sed' => (int) 2, 'sgi' => (int) 12, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 2, 'tar' => (int) 10, 'tha' => (int) 1, 'tca' => (int) 1, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 2, 'ugi' => (int) 1, 'vma' => (int) 5, 'vmu' => (int) 1, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb301270' $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' => 'HOM05D001460', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '433', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p22980' => 'bna', 'A01p32340' => 'bna', 'A03p42970' => 'bna', 'A05p25880' => 'bna', 'Aa31LG8G9320' => 'aar', 'Aa31LG8G9330' => 'aar', 'Aa31LG8G9340' => 'aar', 'Aa31sc221G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1034' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1528' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.829' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2222' => 'aag', 'Ah.12g058830' => 'amhyb', 'Ah.12g058840' => 'amhyb', 'AL3G37160' => 'aly', 'AL7G41310' => 'aly', 'Aqoxy5G00395' => 'aox', 'Aqoxy5G00396' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0C8NZA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5185HY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JZ1PRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MD3LS0' => 'arhy', 'AT3G22840' => 'ath', 'AT4G14690' => 'ath', 'ATR0665G054' => 'atr', 'Atru.chr4.2344' => 'acertr', 'Atru.chr4.2346' => 'acertr', 'Atru.chr4.2347' => 'acertr', 'Atru.chr4.2348' => 'acertr', 'Atru.chr4.2355' => 'acertr', 'Atru.chr4.2356' => 'acertr', 'Atru.chr4.2358' => 'acertr', 'Atru.chr4.2359' => 'acertr', 'Atru.chr4.2360' => 'acertr', 'Atru.chr4.2361' => 'acertr', 'AUR62030476' => 'cqu', 'AUR62030478' => 'cqu', 'AUR62030819' => 'cqu', 'AUR62030820' => 'cqu', 'BcaB03g14648' => 'bca', 'BcaB04g20492' => 'bca', 'BcaB06g26399' => 'bca', 'BcaC01g03416' => 'bca', 'BcaC01g03419' => 'bca', 'BcaC01g03421' => 'bca', 'BcaC01g03424' => 'bca', 'BcaC05g28012' => 'bca', 'BcaC09g49212' => 'bca', 'BcaC09g50140' => 'bca', 'BcaNung00346' => 'bca', 'BolC1t02785H' => 'bol', 'BolC1t04095H' => 'bol', 'BolC3t17545H' => 'bol', 'BolC5t32769H' => 'bol', 'BraA01t02211Z' => 'bra', 'BraA01t03359Z' => 'bra', 'BraA03t13441Z' => 'bra', 'BraA05t21476Z' => 'bra', 'C01p28420' => 'bna', 'C01p41350' => 'bna', 'C03p52750' => 'bna', 'C03p52780' => 'bna', 'C05p40270' => 'bna', 'CAN.G1437.9' => 'can', 'CANSAT78G0035' => 'cansat', 'CANSAT78G1036' => 'cansat', 'CANSAT78G2272' => 'cansat', 'CANSAT78G2478' => 'cansat', 'CARHR098700' => 'chi', 'CARHR221120' => 'chi', 'CARHR221150' => 'chi', 'Carub.0003s2297' => 'cru', 'Carub.0007s2749' => 'cru', 'Carub.0007s2750' => 'cru', 'Carub.0007s2751' => 'cru', 'Ca_10849_v3' => 'car', 'Cc03_g04300' => 'ccan', 'CDE02G3648' => 'cde', 'CDE05G0060' => 'cde', 'CDE05G0692' => 'cde', 'CDE05G2285' => 'cde', 'CDE05G2884' => 'cde', 'CDE05G3072' => 'cde', 'Cfa008439' => 'cfa', 'Cfa008441' => 'cfa', 'Cfa008443' => 'cfa', 'Cfa008448' => 'cfa', 'Ciclev10005974m.g' => 'ccl', 'Ciclev10006006m.g' => 'ccl', 'Ciclev10006775m.g' => 'ccl', 'CiPaw.02G120400' => 'cil', 'CiPaw.02G120500' => 'cil', 'CiPaw.02G120600' => 'cil', 'ClCG05G004850' => 'cla', 'COL.COLO4_21566' => 'col', 'Cpa.g.sc44.124' => 'cpa', 'Cre07.g320400' => 'cre', 'Cre07.g320450' => 'cre', 'Cre08.g384650' => 'cre', 'Cre09.g393173' => 'cre', 'Cre09.g394325' => 'cre', 'Cre14.g626750' => 'cre', 'Cre16.g679250' => 'cre', 'CsaV3_3G012890' => 'csa', 'CSS0010865' => 'camsi', 'CSS0044338' => 'camsi', 'DCAR_002366' => 'dca', 'DCAR_030687' => 'dca', 'DCAR_030688' => 'dca', 'Dinv14047' => 'din', 'Dinv14048' => 'din', 'Duzib151G0105' => 'dzi', 'Duzib151G0114' => 'dzi', 'Duzib212G1029' => 'dzi', 'ECA232G3536' => 'eca', 'ECA240G0786' => 'eca', 'ECA240G1802' => 'eca', 'ECA240G3760' => 'eca', 'ECA240G3920' => 'eca', 'EL10Ac5g12536' => 'bvu', 'EL10Ac5g12537' => 'bvu', 'EL10Ac5g12538' => 'bvu', 'Eucgr.B01004' => 'egr', 'Eucgr.B01006' => 'egr', 'Eucgr.B01007' => 'egr', 'Eucgr.B01008' => 'egr', 'Eucgr.B01895' => 'egr', 'Eucgr.B01896' => 'egr', 'FAN04G1456' => 'fan', 'FAN08G1769' => 'fan', 'FAN08G2160' => 'fan', 'FAN13G2403' => 'fan', 'FAN13G3303' => 'fan', 'FAN15G2435' => 'fan', 'FAN17G0672' => 'fan', 'FAN17G2441' => 'fan', 'FAN18G1024' => 'fan', 'FAN22G1458' => 'fan', 'FAN24G0037' => 'fan', 'FAN24G0429' => 'fan', 'FAN24G2387' => 'fan', 'FAN27G2746' => 'fan', 'FvH4_2g20400' => 'fve', 'FvH4_2g20420' => 'fve', 'FvH4_2g20430' => 'fve', 'FvH4_4g01270' => 'fve', 'FvH4_4g01290' => 'fve', 'FvH4_4g01300' => 'fve', 'FvH4_4g01310' => 'fve', 'FvH4_4g01330' => 'fve', 'FvH4_5g09070' => 'fve', 'Glyma.10G243800' => 'gma', 'Glyma.20G150600' => 'gma', 'Gohir.A09G219200' => 'ghi', 'Gohir.A09G219300' => 'ghi', 'Gohir.D09G221400' => 'ghi', 'Gohir.D09G221500' => 'ghi', 'Gorai.006G242600' => 'gra', 'Gorai.006G242700' => 'gra', 'GSVIVG01018044001' => 'vvi', 'HanXRQChr03g0083821' => 'han', 'HanXRQChr03g0083841' => 'han', 'HanXRQChr03g0083881' => 'han', 'HanXRQChr03g0083901' => 'han', 'HanXRQChr03g0083921' => 'han', 'HanXRQChr03g0085331' => 'han', 'HanXRQChr03g0085361' => 'han', 'HanXRQChr03g0085411' => 'han', 'HanXRQChr03g0085421' => 'han', 'HanXRQChr03g0085431' => 'han', 'HanXRQChr08g0221991' => 'han', 'HanXRQChr11g0336061' => 'han', 'HanXRQChr11g0336411' => 'han', 'Haze_11234' => 'cav', 'Hma1.2p1_0549F.1_g177010' => 'hma', 'Hma1.2p1_0602F.1_g187630' => 'hma', 'Hund14876' => 'sun', 'Hund14879' => 'sun', 'Lalb_Chr06g0160741' => 'lal', 'Lalb_Chr21g0304781' => 'lal', 'Lj3A726G19' => 'lonja', 'Lj3A726T23' => 'lonja', 'Lj3A726T24' => 'lonja', 'Lj3A726T25' => 'lonja', 'Lj3A727T17' => 'lonja', 'Lj3C726T0' => 'lonja', 'Lj3C726T2' => 'lonja', 'Lj3P725T35' => 'lonja', 'Lj3P727T10' => 'lonja', 'Lj3P727T12' => 'lonja', 'Lj3P727T14' => 'lonja', 'Lj5g0023109' => 'lja', 'Lj6P646T44' => 'lonja', 'Lsat_1_v5_gn_6_75760' => 'lsa', 'Lsat_1_v5_gn_6_75800' => 'lsa', 'Lsat_1_v5_gn_6_75900' => 'lsa', 'Lsat_1_v5_gn_6_76240' => 'lsa', 'Lsat_1_v5_gn_6_76441' => 'lsa', 'Lsat_1_v5_gn_6_76700' => 'lsa', 'Lsat_1_v5_gn_6_76760' => 'lsa', 'Manes.15G033100' => 'mes', 'Mapoly0004s0074' => 'mpo', 'Mapoly0004s0075' => 'mpo', 'Mapoly0004s0163' => 'mpo', 'Mapoly0004s0164' => 'mpo', 'Mapoly0021s0018' => 'mpo', 'Mapoly0041s0136' => 'mpo', 'Mapoly0041s0137' => 'mpo', 'Mapoly0041s0138' => 'mpo', 'Mapoly0041s0139' => 'mpo', 'Mapoly0041s0141' => 'mpo', 'Mapoly0041s0142' => 'mpo', 'Mapoly0041s0143' => 'mpo', 'Mapoly0041s0144' => 'mpo', 'Mapoly0041s0145' => 'mpo', 'Mapoly0047s0106' => 'mpo', 'Mapoly0047s0108' => 'mpo', 'Mapoly0050s0051' => 'mpo', 'Mapoly0050s0052' => 'mpo', 'Mapoly0050s0053' => 'mpo', 'Mapoly0058s0013' => 'mpo', 'Mapoly0091s0078' => 'mpo', 'Mapoly0091s0079' => 'mpo', 'Mapoly0091s0080' => 'mpo', 'Mapoly0091s0081' => 'mpo', 'Mapoly0278s0004' => 'mpo', 'Mapoly0278s0005' => 'mpo', 'Mapoly0278s0006' => 'mpo', 'MBI11_g30648_MAGBIO' => 'mbi', 'MCO03G194' => 'mco', 'MCO03G590' => 'mco', 'MCO07G312' => 'mco', 'MCO10G318' => 'mco', 'MCO12G244' => 'mco', 'MCO13G148' => 'mco', 'MCO13G194' => 'mco', 'MCO16G238' => 'mco', 'MD06G1134100' => 'mdo', 'MD13G1200100' => 'mdo', 'MD13G1200300' => 'mdo', 'MD13G1200600' => 'mdo', 'MD14G1150400' => 'mdo', 'MD16G1200000' => 'mdo', 'Medtr1g102570' => 'mtr', 'Medtr1g102780' => 'mtr', 'Medtr1g102800' => 'mtr', 'Medtr1g102810' => 'mtr', 'Medtr1g102830' => 'mtr', 'MELO3C006499.2' => 'cme', 'Migut.G00385' => 'egut', 'MSTRG.4063' => 'ama', 'Nitab4.5_0000090g0260' => 'nta', 'Nitab4.5_0000977g0030' => 'nta', 'Nitab4.5_0002541g0040' => 'nta', 'Nitab4.5_0007068g0040' => 'nta', 'Nn005s41408' => 'nnu', 'Nn005s41410' => 'nnu', 'Oeu010310.1' => 'oeu', 'Oeu010311.1' => 'oeu', 'Oeu043472.1' => 'oeu', 'Os01g0246400' => 'osa', 'Os04g0267950' => 'osa', 'Os07g0178700' => 'osa', 'Os07g0178800' => 'osa', 'Peaxi162Scf00316g00046' => 'pax', 'Peaxi162Scf00316g00049' => 'pax', 'Peaxi162Scf00316g00059' => 'pax', 'Peaxi162Scf00316g00328' => 'pax', 'Peaxi162Scf00316g00329' => 'pax', 'Peaxi162Scf00316g00411' => 'pax', 'Peaxi162Scf00316g00521' => 'pax', 'Peaxi162Scf00492g00068' => 'pax', 'Peaxi162Scf35631g00002' => 'pax', 'PGR142G3720' => 'pgr', 'PGSC0003DMG400006442' => 'stu', 'Phvul.007G062000' => 'pvu', 'Potri.008G157750' => 'ptr', 'Potri.008G157900' => 'ptr', 'Potri.008G158000' => 'ptr', 'Potri.008G158200' => 'ptr', 'Pp3c11_7280' => 'ppa', 'Pp3c11_7980' => 'ppa', 'Pp3c12_19450' => 'ppa', 'Pp3c14_1480' => 'ppa', 'Pp3c14_1501' => 'ppa', 'Pp3c16_4900' => 'ppa', 'Pp3c16_5010' => 'ppa', 'Pp3c16_5060' => 'ppa', 'Pp3c19_18250' => 'ppa', 'Pp3c23_8530' => 'ppa', 'Pp3c23_8550' => 'ppa', 'Pp3c24_9670' => 'ppa', 'Pp3c2_21390' => 'ppa', 'Pp3c2_31380' => 'ppa', 'Pp3c3_16620' => 'ppa', 'Pp3c3_8090' => 'ppa', 'Pp3c3_8110' => 'ppa', 'Pp3c3_8130' => 'ppa', 'Pp3c3_8150' => 'ppa', 'Pp3c4_14320' => 'ppa', 'Pp3c6_2560' => 'ppa', 'Pp3c9_16700' => 'ppa', 'PRCOL_00000234' => 'pco', 'PRCOL_00000235' => 'pco', 'PRCOL_00000777' => 'pco', 'PRCOL_00002344' => 'pco', 'PRCOL_00002372' => 'pco', 'PRCOL_00006120' => 'pco', 'Prupe.1G021400' => 'ppe', 'Prupe.1G021500' => 'ppe', 'Prupe.1G021600' => 'ppe', 'Prupe.1G021700' => 'ppe', 'Prupe.1G021800' => 'ppe', 'Prupe.5G145100' => 'ppe', 'Psat6g204040' => 'psa', 'Psat6g204800' => 'psa', 'Psat6g204920' => 'psa', 'Psat6g204960' => 'psa', 'Psat6g205080' => 'psa', 'PSO017G0271' => 'pso', 'PSO017G1276' => 'pso', 'PSO017G1429' => 'pso', 'PSO017G1861' => 'pso', 'PSO017G2787' => 'pso', 'PSO017G4466' => 'pso', 'PSO017G5118' => 'pso', 'PSO017G5420' => 'pso', 'PSO063G3678' => 'pso', 'PSO210G0546' => 'pso', 'PSO317G0001' => 'pso', 'PSO357G0512' => 'pso', 'PSO478G2682' => 'pso', 'PSO647G0001' => 'pso', 'PSO675G0001' => 'pso', 'PSO675G2699' => 'pso', 'PSO675G2849' => 'pso', 'PSO675G4991' => 'pso', 'PSO689G0001' => 'pso', 'QL06p000916' => 'qlo', 'QL06p000921' => 'qlo', 'QL06p001398' => 'qlo', 'QL06p001407' => 'qlo', 'QL06p002031' => 'qlo', 'RcHm_v2.0_Chr4g0387791' => 'rch', 'RcHm_v2.0_Chr4g0387801' => 'rch', 'RcHm_v2.0_Chr6g0286501' => 'rch', 'RcHm_v2.0_Chr6g0286511' => 'rch', 'RcHm_v2.0_Chr6g0286521' => 'rch', 'RcHm_v2.0_Chr6g0286531' => 'rch', 'RcHm_v2.0_Chr7g0189141' => 'rch', 'Rhsim02G0028700' => 'rsi', 'Rhsim02G0028800' => 'rsi', 'Rhsim02G0028900' => 'rsi', 'Rhsim02G0029000' => 'rsi', 'Rhsim02G0029100' => 'rsi', 'Rhsim02G0029200' => 'rsi', 'Rhsim02G0029300' => 'rsi', 'Rhsim02G0029400' => 'rsi', 'Rhsim02G0029500' => 'rsi', 'Rhsim02G0029600' => 'rsi', 'RhsimUnG0024000' => 'rsi', 'RhsimUnG0024100' => 'rsi', 'RhsimUnG0024200' => 'rsi', 'RhsimUnG0024300' => 'rsi', 'RhsimUnG0024400' => 'rsi', 'RhsimUnG0024500' => 'rsi', 'RhsimUnG0024700' => 'rsi', 'RhsimUnG0024800' => 'rsi', 'RhsimUnG0024900' => 'rsi', 'RhsimUnG0025100' => 'rsi', 'Sabra08G0120200' => 'sbr', 'Sabra08G0120300' => 'sbr', 'Sabra08G0120500' => 'sbr', 'Sabra08G0120600' => 'sbr', 'Sabra10G0158900' => 'sbr', 'SalBow2G3492' => 'sbo', 'Sc13g0004760' => 'sci', 'Sc13g0004770' => 'sci', 'Sed0003417' => 'sed', 'Sed0019750' => 'sed', 'SEGI_03419' => 'sgi', 'SEGI_05907' => 'sgi', 'SEGI_10682' => 'sgi', 'SEGI_13528' => 'sgi', 'SEGI_16081' => 'sgi', 'SEGI_19370' => 'sgi', 'SEGI_21015' => 'sgi', 'SEGI_21944' => 'sgi', 'SEGI_32906' => 'sgi', 'SEGI_33093' => 'sgi', 'SEGI_36110' => 'sgi', 'SEGI_40397' => 'sgi', 'SGA_v2.0_scaffold191G40426' => 'sas', 'SGA_v2.0_scaffold353G49717' => 'sas', 'SGA_v2.0_scaffold50G18550' => 'sas', 'SMO119G0173' => 'smo', 'SMO172G0002' => 'smo', 'Solyc09g082690.3' => 'sly', 'Solyc09g082700.2' => 'sly', 'Sopen09g031550' => 'spe', 'Sopen09g031560' => 'spe', 'Sp3g20540' => 'spa', 'Sp7g07580' => 'spa', 'TAR134G0002' => 'tar', 'TAR236G0001' => 'tar', 'TAR365G0892' => 'tar', 'TAR636G0166' => 'tar', 'TAR636G0646' => 'tar', 'TAR636G0869' => 'tar', 'TAR636G1317' => 'tar', 'TAR636G1744' => 'tar', 'TAR636G3358' => 'tar', 'TAR636G3436' => 'tar', 'THA.LOC104803047' => 'tha', 'Thecc.04G238900' => 'tca', 'Thhalv10021557m.g' => 'esa', 'Thhalv10026318m.g' => 'esa', 'Thhalv10026335m.g' => 'esa', 'TPR.G17433' => 'tpr', 'TPR.G18915' => 'tpr', 'TPR.G26125' => 'tpr', 'TWI09G0677' => 'twi', 'TWI73G0287' => 'twi', 'unitig_748.g8326' => 'ugi', 'vmacro15370' => 'vma', 'vmacro15371' => 'vma', 'vmacro15372' => 'vma', 'vmacro15373' => 'vma', 'vmacro15374' => 'vma', 'VMungo0720G2826' => 'vmu', 'Zm00001eb116960' => 'zma', 'Zm00001eb301260' => 'zma', 'Zm00001eb301270' => 'zma' ), 'gf_id' => 'HOM05D001460', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001460' ), 'data_identifier' => 'HOM05D001460', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001460', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '433', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p22980' => 'bna', 'A01p32340' => 'bna', 'A03p42970' => 'bna', 'A05p25880' => 'bna', 'Aa31LG8G9320' => 'aar', 'Aa31LG8G9330' => 'aar', 'Aa31LG8G9340' => 'aar', 'Aa31sc221G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1034' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1528' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.829' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2222' => 'aag', 'Ah.12g058830' => 'amhyb', 'Ah.12g058840' => 'amhyb', 'AL3G37160' => 'aly', 'AL7G41310' => 'aly', 'Aqoxy5G00395' => 'aox', 'Aqoxy5G00396' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0C8NZA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5185HY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JZ1PRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MD3LS0' => 'arhy', 'AT3G22840' => 'ath', 'AT4G14690' => 'ath', 'ATR0665G054' => 'atr', 'Atru.chr4.2344' => 'acertr', 'Atru.chr4.2346' => 'acertr', 'Atru.chr4.2347' => 'acertr', 'Atru.chr4.2348' => 'acertr', 'Atru.chr4.2355' => 'acertr', 'Atru.chr4.2356' => 'acertr', 'Atru.chr4.2358' => 'acertr', 'Atru.chr4.2359' => 'acertr', 'Atru.chr4.2360' => 'acertr', 'Atru.chr4.2361' => 'acertr', 'AUR62030476' => 'cqu', 'AUR62030478' => 'cqu', 'AUR62030819' => 'cqu', 'AUR62030820' => 'cqu', 'BcaB03g14648' => 'bca', 'BcaB04g20492' => 'bca', 'BcaB06g26399' => 'bca', 'BcaC01g03416' => 'bca', 'BcaC01g03419' => 'bca', 'BcaC01g03421' => 'bca', 'BcaC01g03424' => 'bca', 'BcaC05g28012' => 'bca', 'BcaC09g49212' => 'bca', 'BcaC09g50140' => 'bca', 'BcaNung00346' => 'bca', 'BolC1t02785H' => 'bol', 'BolC1t04095H' => 'bol', 'BolC3t17545H' => 'bol', 'BolC5t32769H' => 'bol', 'BraA01t02211Z' => 'bra', 'BraA01t03359Z' => 'bra', 'BraA03t13441Z' => 'bra', 'BraA05t21476Z' => 'bra', 'C01p28420' => 'bna', 'C01p41350' => 'bna', 'C03p52750' => 'bna', 'C03p52780' => 'bna', 'C05p40270' => 'bna', 'CAN.G1437.9' => 'can', 'CANSAT78G0035' => 'cansat', 'CANSAT78G1036' => 'cansat', 'CANSAT78G2272' => 'cansat', 'CANSAT78G2478' => 'cansat', 'CARHR098700' => 'chi', 'CARHR221120' => 'chi', 'CARHR221150' => 'chi', 'Carub.0003s2297' => 'cru', 'Carub.0007s2749' => 'cru', 'Carub.0007s2750' => 'cru', 'Carub.0007s2751' => 'cru', 'Ca_10849_v3' => 'car', 'Cc03_g04300' => 'ccan', 'CDE02G3648' => 'cde', 'CDE05G0060' => 'cde', 'CDE05G0692' => 'cde', 'CDE05G2285' => 'cde', 'CDE05G2884' => 'cde', 'CDE05G3072' => 'cde', 'Cfa008439' => 'cfa', 'Cfa008441' => 'cfa', 'Cfa008443' => 'cfa', 'Cfa008448' => 'cfa', 'Ciclev10005974m.g' => 'ccl', 'Ciclev10006006m.g' => 'ccl', 'Ciclev10006775m.g' => 'ccl', 'CiPaw.02G120400' => 'cil', 'CiPaw.02G120500' => 'cil', 'CiPaw.02G120600' => 'cil', 'ClCG05G004850' => 'cla', 'COL.COLO4_21566' => 'col', 'Cpa.g.sc44.124' => 'cpa', 'Cre07.g320400' => 'cre', 'Cre07.g320450' => 'cre', 'Cre08.g384650' => 'cre', 'Cre09.g393173' => 'cre', 'Cre09.g394325' => 'cre', 'Cre14.g626750' => 'cre', 'Cre16.g679250' => 'cre', 'CsaV3_3G012890' => 'csa', 'CSS0010865' => 'camsi', 'CSS0044338' => 'camsi', 'DCAR_002366' => 'dca', 'DCAR_030687' => 'dca', 'DCAR_030688' => 'dca', 'Dinv14047' => 'din', 'Dinv14048' => 'din', 'Duzib151G0105' => 'dzi', 'Duzib151G0114' => 'dzi', 'Duzib212G1029' => 'dzi', 'ECA232G3536' => 'eca', 'ECA240G0786' => 'eca', 'ECA240G1802' => 'eca', 'ECA240G3760' => 'eca', 'ECA240G3920' => 'eca', 'EL10Ac5g12536' => 'bvu', 'EL10Ac5g12537' => 'bvu', 'EL10Ac5g12538' => 'bvu', 'Eucgr.B01004' => 'egr', 'Eucgr.B01006' => 'egr', 'Eucgr.B01007' => 'egr', 'Eucgr.B01008' => 'egr', 'Eucgr.B01895' => 'egr', 'Eucgr.B01896' => 'egr', 'FAN04G1456' => 'fan', 'FAN08G1769' => 'fan', 'FAN08G2160' => 'fan', 'FAN13G2403' => 'fan', 'FAN13G3303' => 'fan', 'FAN15G2435' => 'fan', 'FAN17G0672' => 'fan', 'FAN17G2441' => 'fan', 'FAN18G1024' => 'fan', 'FAN22G1458' => 'fan', 'FAN24G0037' => 'fan', 'FAN24G0429' => 'fan', 'FAN24G2387' => 'fan', 'FAN27G2746' => 'fan', 'FvH4_2g20400' => 'fve', 'FvH4_2g20420' => 'fve', 'FvH4_2g20430' => 'fve', 'FvH4_4g01270' => 'fve', 'FvH4_4g01290' => 'fve', 'FvH4_4g01300' => 'fve', 'FvH4_4g01310' => 'fve', 'FvH4_4g01330' => 'fve', 'FvH4_5g09070' => 'fve', 'Glyma.10G243800' => 'gma', 'Glyma.20G150600' => 'gma', 'Gohir.A09G219200' => 'ghi', 'Gohir.A09G219300' => 'ghi', 'Gohir.D09G221400' => 'ghi', 'Gohir.D09G221500' => 'ghi', 'Gorai.006G242600' => 'gra', 'Gorai.006G242700' => 'gra', 'GSVIVG01018044001' => 'vvi', 'HanXRQChr03g0083821' => 'han', 'HanXRQChr03g0083841' => 'han', 'HanXRQChr03g0083881' => 'han', 'HanXRQChr03g0083901' => 'han', 'HanXRQChr03g0083921' => 'han', 'HanXRQChr03g0085331' => 'han', 'HanXRQChr03g0085361' => 'han', 'HanXRQChr03g0085411' => 'han', 'HanXRQChr03g0085421' => 'han', 'HanXRQChr03g0085431' => 'han', 'HanXRQChr08g0221991' => 'han', 'HanXRQChr11g0336061' => 'han', 'HanXRQChr11g0336411' => 'han', 'Haze_11234' => 'cav', 'Hma1.2p1_0549F.1_g177010' => 'hma', 'Hma1.2p1_0602F.1_g187630' => 'hma', 'Hund14876' => 'sun', 'Hund14879' => 'sun', 'Lalb_Chr06g0160741' => 'lal', 'Lalb_Chr21g0304781' => 'lal', 'Lj3A726G19' => 'lonja', 'Lj3A726T23' => 'lonja', 'Lj3A726T24' => 'lonja', 'Lj3A726T25' => 'lonja', 'Lj3A727T17' => 'lonja', 'Lj3C726T0' => 'lonja', 'Lj3C726T2' => 'lonja', 'Lj3P725T35' => 'lonja', 'Lj3P727T10' => 'lonja', 'Lj3P727T12' => 'lonja', 'Lj3P727T14' => 'lonja', 'Lj5g0023109' => 'lja', 'Lj6P646T44' => 'lonja', 'Lsat_1_v5_gn_6_75760' => 'lsa', 'Lsat_1_v5_gn_6_75800' => 'lsa', 'Lsat_1_v5_gn_6_75900' => 'lsa', 'Lsat_1_v5_gn_6_76240' => 'lsa', 'Lsat_1_v5_gn_6_76441' => 'lsa', 'Lsat_1_v5_gn_6_76700' => 'lsa', 'Lsat_1_v5_gn_6_76760' => 'lsa', 'Manes.15G033100' => 'mes', 'Mapoly0004s0074' => 'mpo', 'Mapoly0004s0075' => 'mpo', 'Mapoly0004s0163' => 'mpo', 'Mapoly0004s0164' => 'mpo', 'Mapoly0021s0018' => 'mpo', 'Mapoly0041s0136' => 'mpo', 'Mapoly0041s0137' => 'mpo', 'Mapoly0041s0138' => 'mpo', 'Mapoly0041s0139' => 'mpo', 'Mapoly0041s0141' => 'mpo', 'Mapoly0041s0142' => 'mpo', 'Mapoly0041s0143' => 'mpo', 'Mapoly0041s0144' => 'mpo', 'Mapoly0041s0145' => 'mpo', 'Mapoly0047s0106' => 'mpo', 'Mapoly0047s0108' => 'mpo', 'Mapoly0050s0051' => 'mpo', 'Mapoly0050s0052' => 'mpo', 'Mapoly0050s0053' => 'mpo', 'Mapoly0058s0013' => 'mpo', 'Mapoly0091s0078' => 'mpo', 'Mapoly0091s0079' => 'mpo', 'Mapoly0091s0080' => 'mpo', 'Mapoly0091s0081' => 'mpo', 'Mapoly0278s0004' => 'mpo', 'Mapoly0278s0005' => 'mpo', 'Mapoly0278s0006' => 'mpo', 'MBI11_g30648_MAGBIO' => 'mbi', 'MCO03G194' => 'mco', 'MCO03G590' => 'mco', 'MCO07G312' => 'mco', 'MCO10G318' => 'mco', 'MCO12G244' => 'mco', 'MCO13G148' => 'mco', 'MCO13G194' => 'mco', 'MCO16G238' => 'mco', 'MD06G1134100' => 'mdo', 'MD13G1200100' => 'mdo', 'MD13G1200300' => 'mdo', 'MD13G1200600' => 'mdo', 'MD14G1150400' => 'mdo', 'MD16G1200000' => 'mdo', 'Medtr1g102570' => 'mtr', 'Medtr1g102780' => 'mtr', 'Medtr1g102800' => 'mtr', 'Medtr1g102810' => 'mtr', 'Medtr1g102830' => 'mtr', 'MELO3C006499.2' => 'cme', 'Migut.G00385' => 'egut', 'MSTRG.4063' => 'ama', 'Nitab4.5_0000090g0260' => 'nta', 'Nitab4.5_0000977g0030' => 'nta', 'Nitab4.5_0002541g0040' => 'nta', 'Nitab4.5_0007068g0040' => 'nta', 'Nn005s41408' => 'nnu', 'Nn005s41410' => 'nnu', 'Oeu010310.1' => 'oeu', 'Oeu010311.1' => 'oeu', 'Oeu043472.1' => 'oeu', 'Os01g0246400' => 'osa', 'Os04g0267950' => 'osa', 'Os07g0178700' => 'osa', 'Os07g0178800' => 'osa', 'Peaxi162Scf00316g00046' => 'pax', 'Peaxi162Scf00316g00049' => 'pax', 'Peaxi162Scf00316g00059' => 'pax', 'Peaxi162Scf00316g00328' => 'pax', 'Peaxi162Scf00316g00329' => 'pax', 'Peaxi162Scf00316g00411' => 'pax', 'Peaxi162Scf00316g00521' => 'pax', 'Peaxi162Scf00492g00068' => 'pax', 'Peaxi162Scf35631g00002' => 'pax', 'PGR142G3720' => 'pgr', 'PGSC0003DMG400006442' => 'stu', 'Phvul.007G062000' => 'pvu', 'Potri.008G157750' => 'ptr', 'Potri.008G157900' => 'ptr', 'Potri.008G158000' => 'ptr', 'Potri.008G158200' => 'ptr', 'Pp3c11_7280' => 'ppa', 'Pp3c11_7980' => 'ppa', 'Pp3c12_19450' => 'ppa', 'Pp3c14_1480' => 'ppa', 'Pp3c14_1501' => 'ppa', 'Pp3c16_4900' => 'ppa', 'Pp3c16_5010' => 'ppa', 'Pp3c16_5060' => 'ppa', 'Pp3c19_18250' => 'ppa', 'Pp3c23_8530' => 'ppa', 'Pp3c23_8550' => 'ppa', 'Pp3c24_9670' => 'ppa', 'Pp3c2_21390' => 'ppa', 'Pp3c2_31380' => 'ppa', 'Pp3c3_16620' => 'ppa', 'Pp3c3_8090' => 'ppa', 'Pp3c3_8110' => 'ppa', 'Pp3c3_8130' => 'ppa', 'Pp3c3_8150' => 'ppa', 'Pp3c4_14320' => 'ppa', 'Pp3c6_2560' => 'ppa', 'Pp3c9_16700' => 'ppa', 'PRCOL_00000234' => 'pco', 'PRCOL_00000235' => 'pco', 'PRCOL_00000777' => 'pco', 'PRCOL_00002344' => 'pco', 'PRCOL_00002372' => 'pco', 'PRCOL_00006120' => 'pco', 'Prupe.1G021400' => 'ppe', 'Prupe.1G021500' => 'ppe', 'Prupe.1G021600' => 'ppe', 'Prupe.1G021700' => 'ppe', 'Prupe.1G021800' => 'ppe', 'Prupe.5G145100' => 'ppe', 'Psat6g204040' => 'psa', 'Psat6g204800' => 'psa', 'Psat6g204920' => 'psa', 'Psat6g204960' => 'psa', 'Psat6g205080' => 'psa', 'PSO017G0271' => 'pso', 'PSO017G1276' => 'pso', 'PSO017G1429' => 'pso', 'PSO017G1861' => 'pso', 'PSO017G2787' => 'pso', 'PSO017G4466' => 'pso', 'PSO017G5118' => 'pso', 'PSO017G5420' => 'pso', 'PSO063G3678' => 'pso', 'PSO210G0546' => 'pso', 'PSO317G0001' => 'pso', 'PSO357G0512' => 'pso', 'PSO478G2682' => 'pso', 'PSO647G0001' => 'pso', 'PSO675G0001' => 'pso', 'PSO675G2699' => 'pso', 'PSO675G2849' => 'pso', 'PSO675G4991' => 'pso', 'PSO689G0001' => 'pso', 'QL06p000916' => 'qlo', 'QL06p000921' => 'qlo', 'QL06p001398' => 'qlo', 'QL06p001407' => 'qlo', 'QL06p002031' => 'qlo', 'RcHm_v2.0_Chr4g0387791' => 'rch', 'RcHm_v2.0_Chr4g0387801' => 'rch', 'RcHm_v2.0_Chr6g0286501' => 'rch', 'RcHm_v2.0_Chr6g0286511' => 'rch', 'RcHm_v2.0_Chr6g0286521' => 'rch', 'RcHm_v2.0_Chr6g0286531' => 'rch', 'RcHm_v2.0_Chr7g0189141' => 'rch', 'Rhsim02G0028700' => 'rsi', 'Rhsim02G0028800' => 'rsi', 'Rhsim02G0028900' => 'rsi', 'Rhsim02G0029000' => 'rsi', 'Rhsim02G0029100' => 'rsi', 'Rhsim02G0029200' => 'rsi', 'Rhsim02G0029300' => 'rsi', 'Rhsim02G0029400' => 'rsi', 'Rhsim02G0029500' => 'rsi', 'Rhsim02G0029600' => 'rsi', 'RhsimUnG0024000' => 'rsi', 'RhsimUnG0024100' => 'rsi', 'RhsimUnG0024200' => 'rsi', 'RhsimUnG0024300' => 'rsi', 'RhsimUnG0024400' => 'rsi', 'RhsimUnG0024500' => 'rsi', 'RhsimUnG0024700' => 'rsi', 'RhsimUnG0024800' => 'rsi', 'RhsimUnG0024900' => 'rsi', 'RhsimUnG0025100' => 'rsi', 'Sabra08G0120200' => 'sbr', 'Sabra08G0120300' => 'sbr', 'Sabra08G0120500' => 'sbr', 'Sabra08G0120600' => 'sbr', 'Sabra10G0158900' => 'sbr', 'SalBow2G3492' => 'sbo', 'Sc13g0004760' => 'sci', 'Sc13g0004770' => 'sci', 'Sed0003417' => 'sed', 'Sed0019750' => 'sed', 'SEGI_03419' => 'sgi', 'SEGI_05907' => 'sgi', 'SEGI_10682' => 'sgi', 'SEGI_13528' => 'sgi', 'SEGI_16081' => 'sgi', 'SEGI_19370' => 'sgi', 'SEGI_21015' => 'sgi', 'SEGI_21944' => 'sgi', 'SEGI_32906' => 'sgi', 'SEGI_33093' => 'sgi', 'SEGI_36110' => 'sgi', 'SEGI_40397' => 'sgi', 'SGA_v2.0_scaffold191G40426' => 'sas', 'SGA_v2.0_scaffold353G49717' => 'sas', 'SGA_v2.0_scaffold50G18550' => 'sas', 'SMO119G0173' => 'smo', 'SMO172G0002' => 'smo', 'Solyc09g082690.3' => 'sly', 'Solyc09g082700.2' => 'sly', 'Sopen09g031550' => 'spe', 'Sopen09g031560' => 'spe', 'Sp3g20540' => 'spa', 'Sp7g07580' => 'spa', 'TAR134G0002' => 'tar', 'TAR236G0001' => 'tar', 'TAR365G0892' => 'tar', 'TAR636G0166' => 'tar', 'TAR636G0646' => 'tar', 'TAR636G0869' => 'tar', 'TAR636G1317' => 'tar', 'TAR636G1744' => 'tar', 'TAR636G3358' => 'tar', 'TAR636G3436' => 'tar', 'THA.LOC104803047' => 'tha', 'Thecc.04G238900' => 'tca', 'Thhalv10021557m.g' => 'esa', 'Thhalv10026318m.g' => 'esa', 'Thhalv10026335m.g' => 'esa', 'TPR.G17433' => 'tpr', 'TPR.G18915' => 'tpr', 'TPR.G26125' => 'tpr', 'TWI09G0677' => 'twi', 'TWI73G0287' => 'twi', 'unitig_748.g8326' => 'ugi', 'vmacro15370' => 'vma', 'vmacro15371' => 'vma', 'vmacro15372' => 'vma', 'vmacro15373' => 'vma', 'vmacro15374' => 'vma', 'VMungo0720G2826' => 'vmu', 'Zm00001eb116960' => 'zma', 'Zm00001eb301260' => 'zma', 'Zm00001eb301270' => 'zma' ) $gf_id = 'HOM05D001460' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001460' ) $data_identifier = 'HOM05D001460' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 4, 'aag' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 2, 'aox' => (int) 2, 'arhy' => (int) 4, 'ath' => (int) 2, 'atr' => (int) 1, 'acertr' => (int) 10, 'cqu' => (int) 4, 'bca' => (int) 11, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 1, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 1, 'ccan' => (int) 1, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 1, 'col' => (int) 1, 'cpa' => (int) 1, 'cre' => (int) 7, 'csa' => (int) 1, 'camsi' => (int) 2, 'dca' => (int) 3, 'din' => (int) 2, 'dzi' => (int) 3, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 14, 'fve' => (int) 9, 'gma' => (int) 2, 'ghi' => (int) 4, 'gra' => (int) 2, 'vvi' => (int) 1, 'han' => (int) 13, 'cav' => (int) 1, 'hma' => (int) 2, 'sun' => (int) 2, 'lal' => (int) 2, 'lonja' => (int) 12, 'lja' => (int) 1, 'lsa' => (int) 7, 'mes' => (int) 1, 'mpo' => (int) 27, 'mbi' => (int) 1, 'mco' => (int) 8, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 1, 'egut' => (int) 1, 'ama' => (int) 1, 'nta' => (int) 4, 'nnu' => (int) 2, 'oeu' => (int) 3, 'osa' => (int) 4, 'pax' => (int) 9, 'pgr' => (int) 1, 'stu' => (int) 1, 'pvu' => (int) 1, 'ptr' => (int) 4, 'ppa' => (int) 22, 'pco' => (int) 6, 'ppe' => (int) 6, 'psa' => (int) 5, 'pso' => (int) 19, 'qlo' => (int) 5, 'rch' => (int) 7, 'rsi' => (int) 20, 'sbr' => (int) 5, 'sbo' => (int) 1, 'sci' => (int) 2, 'sed' => (int) 2, 'sgi' => (int) 12, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 2, 'tar' => (int) 10, 'tha' => (int) 1, 'tca' => (int) 1, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 2, 'ugi' => (int) 1, 'vma' => (int) 5, 'vmu' => (int) 1, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb301270' $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' => 'HOM05D001460', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '433', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p22980' => 'bna', 'A01p32340' => 'bna', 'A03p42970' => 'bna', 'A05p25880' => 'bna', 'Aa31LG8G9320' => 'aar', 'Aa31LG8G9330' => 'aar', 'Aa31LG8G9340' => 'aar', 'Aa31sc221G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1034' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1528' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.829' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2222' => 'aag', 'Ah.12g058830' => 'amhyb', 'Ah.12g058840' => 'amhyb', 'AL3G37160' => 'aly', 'AL7G41310' => 'aly', 'Aqoxy5G00395' => 'aox', 'Aqoxy5G00396' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0C8NZA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5185HY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JZ1PRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MD3LS0' => 'arhy', 'AT3G22840' => 'ath', 'AT4G14690' => 'ath', 'ATR0665G054' => 'atr', 'Atru.chr4.2344' => 'acertr', 'Atru.chr4.2346' => 'acertr', 'Atru.chr4.2347' => 'acertr', 'Atru.chr4.2348' => 'acertr', 'Atru.chr4.2355' => 'acertr', 'Atru.chr4.2356' => 'acertr', 'Atru.chr4.2358' => 'acertr', 'Atru.chr4.2359' => 'acertr', 'Atru.chr4.2360' => 'acertr', 'Atru.chr4.2361' => 'acertr', 'AUR62030476' => 'cqu', 'AUR62030478' => 'cqu', 'AUR62030819' => 'cqu', 'AUR62030820' => 'cqu', 'BcaB03g14648' => 'bca', 'BcaB04g20492' => 'bca', 'BcaB06g26399' => 'bca', 'BcaC01g03416' => 'bca', 'BcaC01g03419' => 'bca', 'BcaC01g03421' => 'bca', 'BcaC01g03424' => 'bca', 'BcaC05g28012' => 'bca', 'BcaC09g49212' => 'bca', 'BcaC09g50140' => 'bca', 'BcaNung00346' => 'bca', 'BolC1t02785H' => 'bol', 'BolC1t04095H' => 'bol', 'BolC3t17545H' => 'bol', 'BolC5t32769H' => 'bol', 'BraA01t02211Z' => 'bra', 'BraA01t03359Z' => 'bra', 'BraA03t13441Z' => 'bra', 'BraA05t21476Z' => 'bra', 'C01p28420' => 'bna', 'C01p41350' => 'bna', 'C03p52750' => 'bna', 'C03p52780' => 'bna', 'C05p40270' => 'bna', 'CAN.G1437.9' => 'can', 'CANSAT78G0035' => 'cansat', 'CANSAT78G1036' => 'cansat', 'CANSAT78G2272' => 'cansat', 'CANSAT78G2478' => 'cansat', 'CARHR098700' => 'chi', 'CARHR221120' => 'chi', 'CARHR221150' => 'chi', 'Carub.0003s2297' => 'cru', 'Carub.0007s2749' => 'cru', 'Carub.0007s2750' => 'cru', 'Carub.0007s2751' => 'cru', 'Ca_10849_v3' => 'car', 'Cc03_g04300' => 'ccan', 'CDE02G3648' => 'cde', 'CDE05G0060' => 'cde', 'CDE05G0692' => 'cde', 'CDE05G2285' => 'cde', 'CDE05G2884' => 'cde', 'CDE05G3072' => 'cde', 'Cfa008439' => 'cfa', 'Cfa008441' => 'cfa', 'Cfa008443' => 'cfa', 'Cfa008448' => 'cfa', 'Ciclev10005974m.g' => 'ccl', 'Ciclev10006006m.g' => 'ccl', 'Ciclev10006775m.g' => 'ccl', 'CiPaw.02G120400' => 'cil', 'CiPaw.02G120500' => 'cil', 'CiPaw.02G120600' => 'cil', 'ClCG05G004850' => 'cla', 'COL.COLO4_21566' => 'col', 'Cpa.g.sc44.124' => 'cpa', 'Cre07.g320400' => 'cre', 'Cre07.g320450' => 'cre', 'Cre08.g384650' => 'cre', 'Cre09.g393173' => 'cre', 'Cre09.g394325' => 'cre', 'Cre14.g626750' => 'cre', 'Cre16.g679250' => 'cre', 'CsaV3_3G012890' => 'csa', 'CSS0010865' => 'camsi', 'CSS0044338' => 'camsi', 'DCAR_002366' => 'dca', 'DCAR_030687' => 'dca', 'DCAR_030688' => 'dca', 'Dinv14047' => 'din', 'Dinv14048' => 'din', 'Duzib151G0105' => 'dzi', 'Duzib151G0114' => 'dzi', 'Duzib212G1029' => 'dzi', 'ECA232G3536' => 'eca', 'ECA240G0786' => 'eca', 'ECA240G1802' => 'eca', 'ECA240G3760' => 'eca', 'ECA240G3920' => 'eca', 'EL10Ac5g12536' => 'bvu', 'EL10Ac5g12537' => 'bvu', 'EL10Ac5g12538' => 'bvu', 'Eucgr.B01004' => 'egr', 'Eucgr.B01006' => 'egr', 'Eucgr.B01007' => 'egr', 'Eucgr.B01008' => 'egr', 'Eucgr.B01895' => 'egr', 'Eucgr.B01896' => 'egr', 'FAN04G1456' => 'fan', 'FAN08G1769' => 'fan', 'FAN08G2160' => 'fan', 'FAN13G2403' => 'fan', 'FAN13G3303' => 'fan', 'FAN15G2435' => 'fan', 'FAN17G0672' => 'fan', 'FAN17G2441' => 'fan', 'FAN18G1024' => 'fan', 'FAN22G1458' => 'fan', 'FAN24G0037' => 'fan', 'FAN24G0429' => 'fan', 'FAN24G2387' => 'fan', 'FAN27G2746' => 'fan', 'FvH4_2g20400' => 'fve', 'FvH4_2g20420' => 'fve', 'FvH4_2g20430' => 'fve', 'FvH4_4g01270' => 'fve', 'FvH4_4g01290' => 'fve', 'FvH4_4g01300' => 'fve', 'FvH4_4g01310' => 'fve', 'FvH4_4g01330' => 'fve', 'FvH4_5g09070' => 'fve', 'Glyma.10G243800' => 'gma', 'Glyma.20G150600' => 'gma', 'Gohir.A09G219200' => 'ghi', 'Gohir.A09G219300' => 'ghi', 'Gohir.D09G221400' => 'ghi', 'Gohir.D09G221500' => 'ghi', 'Gorai.006G242600' => 'gra', 'Gorai.006G242700' => 'gra', 'GSVIVG01018044001' => 'vvi', 'HanXRQChr03g0083821' => 'han', 'HanXRQChr03g0083841' => 'han', 'HanXRQChr03g0083881' => 'han', 'HanXRQChr03g0083901' => 'han', 'HanXRQChr03g0083921' => 'han', 'HanXRQChr03g0085331' => 'han', 'HanXRQChr03g0085361' => 'han', 'HanXRQChr03g0085411' => 'han', 'HanXRQChr03g0085421' => 'han', 'HanXRQChr03g0085431' => 'han', 'HanXRQChr08g0221991' => 'han', 'HanXRQChr11g0336061' => 'han', 'HanXRQChr11g0336411' => 'han', 'Haze_11234' => 'cav', 'Hma1.2p1_0549F.1_g177010' => 'hma', 'Hma1.2p1_0602F.1_g187630' => 'hma', 'Hund14876' => 'sun', 'Hund14879' => 'sun', 'Lalb_Chr06g0160741' => 'lal', 'Lalb_Chr21g0304781' => 'lal', 'Lj3A726G19' => 'lonja', 'Lj3A726T23' => 'lonja', 'Lj3A726T24' => 'lonja', 'Lj3A726T25' => 'lonja', 'Lj3A727T17' => 'lonja', 'Lj3C726T0' => 'lonja', 'Lj3C726T2' => 'lonja', 'Lj3P725T35' => 'lonja', 'Lj3P727T10' => 'lonja', 'Lj3P727T12' => 'lonja', 'Lj3P727T14' => 'lonja', 'Lj5g0023109' => 'lja', 'Lj6P646T44' => 'lonja', 'Lsat_1_v5_gn_6_75760' => 'lsa', 'Lsat_1_v5_gn_6_75800' => 'lsa', 'Lsat_1_v5_gn_6_75900' => 'lsa', 'Lsat_1_v5_gn_6_76240' => 'lsa', 'Lsat_1_v5_gn_6_76441' => 'lsa', 'Lsat_1_v5_gn_6_76700' => 'lsa', 'Lsat_1_v5_gn_6_76760' => 'lsa', 'Manes.15G033100' => 'mes', 'Mapoly0004s0074' => 'mpo', 'Mapoly0004s0075' => 'mpo', 'Mapoly0004s0163' => 'mpo', 'Mapoly0004s0164' => 'mpo', 'Mapoly0021s0018' => 'mpo', 'Mapoly0041s0136' => 'mpo', 'Mapoly0041s0137' => 'mpo', 'Mapoly0041s0138' => 'mpo', 'Mapoly0041s0139' => 'mpo', 'Mapoly0041s0141' => 'mpo', 'Mapoly0041s0142' => 'mpo', 'Mapoly0041s0143' => 'mpo', 'Mapoly0041s0144' => 'mpo', 'Mapoly0041s0145' => 'mpo', 'Mapoly0047s0106' => 'mpo', 'Mapoly0047s0108' => 'mpo', 'Mapoly0050s0051' => 'mpo', 'Mapoly0050s0052' => 'mpo', 'Mapoly0050s0053' => 'mpo', 'Mapoly0058s0013' => 'mpo', 'Mapoly0091s0078' => 'mpo', 'Mapoly0091s0079' => 'mpo', 'Mapoly0091s0080' => 'mpo', 'Mapoly0091s0081' => 'mpo', 'Mapoly0278s0004' => 'mpo', 'Mapoly0278s0005' => 'mpo', 'Mapoly0278s0006' => 'mpo', 'MBI11_g30648_MAGBIO' => 'mbi', 'MCO03G194' => 'mco', 'MCO03G590' => 'mco', 'MCO07G312' => 'mco', 'MCO10G318' => 'mco', 'MCO12G244' => 'mco', 'MCO13G148' => 'mco', 'MCO13G194' => 'mco', 'MCO16G238' => 'mco', 'MD06G1134100' => 'mdo', 'MD13G1200100' => 'mdo', 'MD13G1200300' => 'mdo', 'MD13G1200600' => 'mdo', 'MD14G1150400' => 'mdo', 'MD16G1200000' => 'mdo', 'Medtr1g102570' => 'mtr', 'Medtr1g102780' => 'mtr', 'Medtr1g102800' => 'mtr', 'Medtr1g102810' => 'mtr', 'Medtr1g102830' => 'mtr', 'MELO3C006499.2' => 'cme', 'Migut.G00385' => 'egut', 'MSTRG.4063' => 'ama', 'Nitab4.5_0000090g0260' => 'nta', 'Nitab4.5_0000977g0030' => 'nta', 'Nitab4.5_0002541g0040' => 'nta', 'Nitab4.5_0007068g0040' => 'nta', 'Nn005s41408' => 'nnu', 'Nn005s41410' => 'nnu', 'Oeu010310.1' => 'oeu', 'Oeu010311.1' => 'oeu', 'Oeu043472.1' => 'oeu', 'Os01g0246400' => 'osa', 'Os04g0267950' => 'osa', 'Os07g0178700' => 'osa', 'Os07g0178800' => 'osa', 'Peaxi162Scf00316g00046' => 'pax', 'Peaxi162Scf00316g00049' => 'pax', 'Peaxi162Scf00316g00059' => 'pax', 'Peaxi162Scf00316g00328' => 'pax', 'Peaxi162Scf00316g00329' => 'pax', 'Peaxi162Scf00316g00411' => 'pax', 'Peaxi162Scf00316g00521' => 'pax', 'Peaxi162Scf00492g00068' => 'pax', 'Peaxi162Scf35631g00002' => 'pax', 'PGR142G3720' => 'pgr', 'PGSC0003DMG400006442' => 'stu', 'Phvul.007G062000' => 'pvu', 'Potri.008G157750' => 'ptr', 'Potri.008G157900' => 'ptr', 'Potri.008G158000' => 'ptr', 'Potri.008G158200' => 'ptr', 'Pp3c11_7280' => 'ppa', 'Pp3c11_7980' => 'ppa', 'Pp3c12_19450' => 'ppa', 'Pp3c14_1480' => 'ppa', 'Pp3c14_1501' => 'ppa', 'Pp3c16_4900' => 'ppa', 'Pp3c16_5010' => 'ppa', 'Pp3c16_5060' => 'ppa', 'Pp3c19_18250' => 'ppa', 'Pp3c23_8530' => 'ppa', 'Pp3c23_8550' => 'ppa', 'Pp3c24_9670' => 'ppa', 'Pp3c2_21390' => 'ppa', 'Pp3c2_31380' => 'ppa', 'Pp3c3_16620' => 'ppa', 'Pp3c3_8090' => 'ppa', 'Pp3c3_8110' => 'ppa', 'Pp3c3_8130' => 'ppa', 'Pp3c3_8150' => 'ppa', 'Pp3c4_14320' => 'ppa', 'Pp3c6_2560' => 'ppa', 'Pp3c9_16700' => 'ppa', 'PRCOL_00000234' => 'pco', 'PRCOL_00000235' => 'pco', 'PRCOL_00000777' => 'pco', 'PRCOL_00002344' => 'pco', 'PRCOL_00002372' => 'pco', 'PRCOL_00006120' => 'pco', 'Prupe.1G021400' => 'ppe', 'Prupe.1G021500' => 'ppe', 'Prupe.1G021600' => 'ppe', 'Prupe.1G021700' => 'ppe', 'Prupe.1G021800' => 'ppe', 'Prupe.5G145100' => 'ppe', 'Psat6g204040' => 'psa', 'Psat6g204800' => 'psa', 'Psat6g204920' => 'psa', 'Psat6g204960' => 'psa', 'Psat6g205080' => 'psa', 'PSO017G0271' => 'pso', 'PSO017G1276' => 'pso', 'PSO017G1429' => 'pso', 'PSO017G1861' => 'pso', 'PSO017G2787' => 'pso', 'PSO017G4466' => 'pso', 'PSO017G5118' => 'pso', 'PSO017G5420' => 'pso', 'PSO063G3678' => 'pso', 'PSO210G0546' => 'pso', 'PSO317G0001' => 'pso', 'PSO357G0512' => 'pso', 'PSO478G2682' => 'pso', 'PSO647G0001' => 'pso', 'PSO675G0001' => 'pso', 'PSO675G2699' => 'pso', 'PSO675G2849' => 'pso', 'PSO675G4991' => 'pso', 'PSO689G0001' => 'pso', 'QL06p000916' => 'qlo', 'QL06p000921' => 'qlo', 'QL06p001398' => 'qlo', 'QL06p001407' => 'qlo', 'QL06p002031' => 'qlo', 'RcHm_v2.0_Chr4g0387791' => 'rch', 'RcHm_v2.0_Chr4g0387801' => 'rch', 'RcHm_v2.0_Chr6g0286501' => 'rch', 'RcHm_v2.0_Chr6g0286511' => 'rch', 'RcHm_v2.0_Chr6g0286521' => 'rch', 'RcHm_v2.0_Chr6g0286531' => 'rch', 'RcHm_v2.0_Chr7g0189141' => 'rch', 'Rhsim02G0028700' => 'rsi', 'Rhsim02G0028800' => 'rsi', 'Rhsim02G0028900' => 'rsi', 'Rhsim02G0029000' => 'rsi', 'Rhsim02G0029100' => 'rsi', 'Rhsim02G0029200' => 'rsi', 'Rhsim02G0029300' => 'rsi', 'Rhsim02G0029400' => 'rsi', 'Rhsim02G0029500' => 'rsi', 'Rhsim02G0029600' => 'rsi', 'RhsimUnG0024000' => 'rsi', 'RhsimUnG0024100' => 'rsi', 'RhsimUnG0024200' => 'rsi', 'RhsimUnG0024300' => 'rsi', 'RhsimUnG0024400' => 'rsi', 'RhsimUnG0024500' => 'rsi', 'RhsimUnG0024700' => 'rsi', 'RhsimUnG0024800' => 'rsi', 'RhsimUnG0024900' => 'rsi', 'RhsimUnG0025100' => 'rsi', 'Sabra08G0120200' => 'sbr', 'Sabra08G0120300' => 'sbr', 'Sabra08G0120500' => 'sbr', 'Sabra08G0120600' => 'sbr', 'Sabra10G0158900' => 'sbr', 'SalBow2G3492' => 'sbo', 'Sc13g0004760' => 'sci', 'Sc13g0004770' => 'sci', 'Sed0003417' => 'sed', 'Sed0019750' => 'sed', 'SEGI_03419' => 'sgi', 'SEGI_05907' => 'sgi', 'SEGI_10682' => 'sgi', 'SEGI_13528' => 'sgi', 'SEGI_16081' => 'sgi', 'SEGI_19370' => 'sgi', 'SEGI_21015' => 'sgi', 'SEGI_21944' => 'sgi', 'SEGI_32906' => 'sgi', 'SEGI_33093' => 'sgi', 'SEGI_36110' => 'sgi', 'SEGI_40397' => 'sgi', 'SGA_v2.0_scaffold191G40426' => 'sas', 'SGA_v2.0_scaffold353G49717' => 'sas', 'SGA_v2.0_scaffold50G18550' => 'sas', 'SMO119G0173' => 'smo', 'SMO172G0002' => 'smo', 'Solyc09g082690.3' => 'sly', 'Solyc09g082700.2' => 'sly', 'Sopen09g031550' => 'spe', 'Sopen09g031560' => 'spe', 'Sp3g20540' => 'spa', 'Sp7g07580' => 'spa', 'TAR134G0002' => 'tar', 'TAR236G0001' => 'tar', 'TAR365G0892' => 'tar', 'TAR636G0166' => 'tar', 'TAR636G0646' => 'tar', 'TAR636G0869' => 'tar', 'TAR636G1317' => 'tar', 'TAR636G1744' => 'tar', 'TAR636G3358' => 'tar', 'TAR636G3436' => 'tar', 'THA.LOC104803047' => 'tha', 'Thecc.04G238900' => 'tca', 'Thhalv10021557m.g' => 'esa', 'Thhalv10026318m.g' => 'esa', 'Thhalv10026335m.g' => 'esa', 'TPR.G17433' => 'tpr', 'TPR.G18915' => 'tpr', 'TPR.G26125' => 'tpr', 'TWI09G0677' => 'twi', 'TWI73G0287' => 'twi', 'unitig_748.g8326' => 'ugi', 'vmacro15370' => 'vma', 'vmacro15371' => 'vma', 'vmacro15372' => 'vma', 'vmacro15373' => 'vma', 'vmacro15374' => 'vma', 'VMungo0720G2826' => 'vmu', 'Zm00001eb116960' => 'zma', 'Zm00001eb301260' => 'zma', 'Zm00001eb301270' => 'zma' ), 'gf_id' => 'HOM05D001460', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001460' ), 'data_identifier' => 'HOM05D001460', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001460', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '433', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p22980' => 'bna', 'A01p32340' => 'bna', 'A03p42970' => 'bna', 'A05p25880' => 'bna', 'Aa31LG8G9320' => 'aar', 'Aa31LG8G9330' => 'aar', 'Aa31LG8G9340' => 'aar', 'Aa31sc221G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1034' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1528' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.829' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2222' => 'aag', 'Ah.12g058830' => 'amhyb', 'Ah.12g058840' => 'amhyb', 'AL3G37160' => 'aly', 'AL7G41310' => 'aly', 'Aqoxy5G00395' => 'aox', 'Aqoxy5G00396' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0C8NZA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5185HY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JZ1PRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MD3LS0' => 'arhy', 'AT3G22840' => 'ath', 'AT4G14690' => 'ath', 'ATR0665G054' => 'atr', 'Atru.chr4.2344' => 'acertr', 'Atru.chr4.2346' => 'acertr', 'Atru.chr4.2347' => 'acertr', 'Atru.chr4.2348' => 'acertr', 'Atru.chr4.2355' => 'acertr', 'Atru.chr4.2356' => 'acertr', 'Atru.chr4.2358' => 'acertr', 'Atru.chr4.2359' => 'acertr', 'Atru.chr4.2360' => 'acertr', 'Atru.chr4.2361' => 'acertr', 'AUR62030476' => 'cqu', 'AUR62030478' => 'cqu', 'AUR62030819' => 'cqu', 'AUR62030820' => 'cqu', 'BcaB03g14648' => 'bca', 'BcaB04g20492' => 'bca', 'BcaB06g26399' => 'bca', 'BcaC01g03416' => 'bca', 'BcaC01g03419' => 'bca', 'BcaC01g03421' => 'bca', 'BcaC01g03424' => 'bca', 'BcaC05g28012' => 'bca', 'BcaC09g49212' => 'bca', 'BcaC09g50140' => 'bca', 'BcaNung00346' => 'bca', 'BolC1t02785H' => 'bol', 'BolC1t04095H' => 'bol', 'BolC3t17545H' => 'bol', 'BolC5t32769H' => 'bol', 'BraA01t02211Z' => 'bra', 'BraA01t03359Z' => 'bra', 'BraA03t13441Z' => 'bra', 'BraA05t21476Z' => 'bra', 'C01p28420' => 'bna', 'C01p41350' => 'bna', 'C03p52750' => 'bna', 'C03p52780' => 'bna', 'C05p40270' => 'bna', 'CAN.G1437.9' => 'can', 'CANSAT78G0035' => 'cansat', 'CANSAT78G1036' => 'cansat', 'CANSAT78G2272' => 'cansat', 'CANSAT78G2478' => 'cansat', 'CARHR098700' => 'chi', 'CARHR221120' => 'chi', 'CARHR221150' => 'chi', 'Carub.0003s2297' => 'cru', 'Carub.0007s2749' => 'cru', 'Carub.0007s2750' => 'cru', 'Carub.0007s2751' => 'cru', 'Ca_10849_v3' => 'car', 'Cc03_g04300' => 'ccan', 'CDE02G3648' => 'cde', 'CDE05G0060' => 'cde', 'CDE05G0692' => 'cde', 'CDE05G2285' => 'cde', 'CDE05G2884' => 'cde', 'CDE05G3072' => 'cde', 'Cfa008439' => 'cfa', 'Cfa008441' => 'cfa', 'Cfa008443' => 'cfa', 'Cfa008448' => 'cfa', 'Ciclev10005974m.g' => 'ccl', 'Ciclev10006006m.g' => 'ccl', 'Ciclev10006775m.g' => 'ccl', 'CiPaw.02G120400' => 'cil', 'CiPaw.02G120500' => 'cil', 'CiPaw.02G120600' => 'cil', 'ClCG05G004850' => 'cla', 'COL.COLO4_21566' => 'col', 'Cpa.g.sc44.124' => 'cpa', 'Cre07.g320400' => 'cre', 'Cre07.g320450' => 'cre', 'Cre08.g384650' => 'cre', 'Cre09.g393173' => 'cre', 'Cre09.g394325' => 'cre', 'Cre14.g626750' => 'cre', 'Cre16.g679250' => 'cre', 'CsaV3_3G012890' => 'csa', 'CSS0010865' => 'camsi', 'CSS0044338' => 'camsi', 'DCAR_002366' => 'dca', 'DCAR_030687' => 'dca', 'DCAR_030688' => 'dca', 'Dinv14047' => 'din', 'Dinv14048' => 'din', 'Duzib151G0105' => 'dzi', 'Duzib151G0114' => 'dzi', 'Duzib212G1029' => 'dzi', 'ECA232G3536' => 'eca', 'ECA240G0786' => 'eca', 'ECA240G1802' => 'eca', 'ECA240G3760' => 'eca', 'ECA240G3920' => 'eca', 'EL10Ac5g12536' => 'bvu', 'EL10Ac5g12537' => 'bvu', 'EL10Ac5g12538' => 'bvu', 'Eucgr.B01004' => 'egr', 'Eucgr.B01006' => 'egr', 'Eucgr.B01007' => 'egr', 'Eucgr.B01008' => 'egr', 'Eucgr.B01895' => 'egr', 'Eucgr.B01896' => 'egr', 'FAN04G1456' => 'fan', 'FAN08G1769' => 'fan', 'FAN08G2160' => 'fan', 'FAN13G2403' => 'fan', 'FAN13G3303' => 'fan', 'FAN15G2435' => 'fan', 'FAN17G0672' => 'fan', 'FAN17G2441' => 'fan', 'FAN18G1024' => 'fan', 'FAN22G1458' => 'fan', 'FAN24G0037' => 'fan', 'FAN24G0429' => 'fan', 'FAN24G2387' => 'fan', 'FAN27G2746' => 'fan', 'FvH4_2g20400' => 'fve', 'FvH4_2g20420' => 'fve', 'FvH4_2g20430' => 'fve', 'FvH4_4g01270' => 'fve', 'FvH4_4g01290' => 'fve', 'FvH4_4g01300' => 'fve', 'FvH4_4g01310' => 'fve', 'FvH4_4g01330' => 'fve', 'FvH4_5g09070' => 'fve', 'Glyma.10G243800' => 'gma', 'Glyma.20G150600' => 'gma', 'Gohir.A09G219200' => 'ghi', 'Gohir.A09G219300' => 'ghi', 'Gohir.D09G221400' => 'ghi', 'Gohir.D09G221500' => 'ghi', 'Gorai.006G242600' => 'gra', 'Gorai.006G242700' => 'gra', 'GSVIVG01018044001' => 'vvi', 'HanXRQChr03g0083821' => 'han', 'HanXRQChr03g0083841' => 'han', 'HanXRQChr03g0083881' => 'han', 'HanXRQChr03g0083901' => 'han', 'HanXRQChr03g0083921' => 'han', 'HanXRQChr03g0085331' => 'han', 'HanXRQChr03g0085361' => 'han', 'HanXRQChr03g0085411' => 'han', 'HanXRQChr03g0085421' => 'han', 'HanXRQChr03g0085431' => 'han', 'HanXRQChr08g0221991' => 'han', 'HanXRQChr11g0336061' => 'han', 'HanXRQChr11g0336411' => 'han', 'Haze_11234' => 'cav', 'Hma1.2p1_0549F.1_g177010' => 'hma', 'Hma1.2p1_0602F.1_g187630' => 'hma', 'Hund14876' => 'sun', 'Hund14879' => 'sun', 'Lalb_Chr06g0160741' => 'lal', 'Lalb_Chr21g0304781' => 'lal', 'Lj3A726G19' => 'lonja', 'Lj3A726T23' => 'lonja', 'Lj3A726T24' => 'lonja', 'Lj3A726T25' => 'lonja', 'Lj3A727T17' => 'lonja', 'Lj3C726T0' => 'lonja', 'Lj3C726T2' => 'lonja', 'Lj3P725T35' => 'lonja', 'Lj3P727T10' => 'lonja', 'Lj3P727T12' => 'lonja', 'Lj3P727T14' => 'lonja', 'Lj5g0023109' => 'lja', 'Lj6P646T44' => 'lonja', 'Lsat_1_v5_gn_6_75760' => 'lsa', 'Lsat_1_v5_gn_6_75800' => 'lsa', 'Lsat_1_v5_gn_6_75900' => 'lsa', 'Lsat_1_v5_gn_6_76240' => 'lsa', 'Lsat_1_v5_gn_6_76441' => 'lsa', 'Lsat_1_v5_gn_6_76700' => 'lsa', 'Lsat_1_v5_gn_6_76760' => 'lsa', 'Manes.15G033100' => 'mes', 'Mapoly0004s0074' => 'mpo', 'Mapoly0004s0075' => 'mpo', 'Mapoly0004s0163' => 'mpo', 'Mapoly0004s0164' => 'mpo', 'Mapoly0021s0018' => 'mpo', 'Mapoly0041s0136' => 'mpo', 'Mapoly0041s0137' => 'mpo', 'Mapoly0041s0138' => 'mpo', 'Mapoly0041s0139' => 'mpo', 'Mapoly0041s0141' => 'mpo', 'Mapoly0041s0142' => 'mpo', 'Mapoly0041s0143' => 'mpo', 'Mapoly0041s0144' => 'mpo', 'Mapoly0041s0145' => 'mpo', 'Mapoly0047s0106' => 'mpo', 'Mapoly0047s0108' => 'mpo', 'Mapoly0050s0051' => 'mpo', 'Mapoly0050s0052' => 'mpo', 'Mapoly0050s0053' => 'mpo', 'Mapoly0058s0013' => 'mpo', 'Mapoly0091s0078' => 'mpo', 'Mapoly0091s0079' => 'mpo', 'Mapoly0091s0080' => 'mpo', 'Mapoly0091s0081' => 'mpo', 'Mapoly0278s0004' => 'mpo', 'Mapoly0278s0005' => 'mpo', 'Mapoly0278s0006' => 'mpo', 'MBI11_g30648_MAGBIO' => 'mbi', 'MCO03G194' => 'mco', 'MCO03G590' => 'mco', 'MCO07G312' => 'mco', 'MCO10G318' => 'mco', 'MCO12G244' => 'mco', 'MCO13G148' => 'mco', 'MCO13G194' => 'mco', 'MCO16G238' => 'mco', 'MD06G1134100' => 'mdo', 'MD13G1200100' => 'mdo', 'MD13G1200300' => 'mdo', 'MD13G1200600' => 'mdo', 'MD14G1150400' => 'mdo', 'MD16G1200000' => 'mdo', 'Medtr1g102570' => 'mtr', 'Medtr1g102780' => 'mtr', 'Medtr1g102800' => 'mtr', 'Medtr1g102810' => 'mtr', 'Medtr1g102830' => 'mtr', 'MELO3C006499.2' => 'cme', 'Migut.G00385' => 'egut', 'MSTRG.4063' => 'ama', 'Nitab4.5_0000090g0260' => 'nta', 'Nitab4.5_0000977g0030' => 'nta', 'Nitab4.5_0002541g0040' => 'nta', 'Nitab4.5_0007068g0040' => 'nta', 'Nn005s41408' => 'nnu', 'Nn005s41410' => 'nnu', 'Oeu010310.1' => 'oeu', 'Oeu010311.1' => 'oeu', 'Oeu043472.1' => 'oeu', 'Os01g0246400' => 'osa', 'Os04g0267950' => 'osa', 'Os07g0178700' => 'osa', 'Os07g0178800' => 'osa', 'Peaxi162Scf00316g00046' => 'pax', 'Peaxi162Scf00316g00049' => 'pax', 'Peaxi162Scf00316g00059' => 'pax', 'Peaxi162Scf00316g00328' => 'pax', 'Peaxi162Scf00316g00329' => 'pax', 'Peaxi162Scf00316g00411' => 'pax', 'Peaxi162Scf00316g00521' => 'pax', 'Peaxi162Scf00492g00068' => 'pax', 'Peaxi162Scf35631g00002' => 'pax', 'PGR142G3720' => 'pgr', 'PGSC0003DMG400006442' => 'stu', 'Phvul.007G062000' => 'pvu', 'Potri.008G157750' => 'ptr', 'Potri.008G157900' => 'ptr', 'Potri.008G158000' => 'ptr', 'Potri.008G158200' => 'ptr', 'Pp3c11_7280' => 'ppa', 'Pp3c11_7980' => 'ppa', 'Pp3c12_19450' => 'ppa', 'Pp3c14_1480' => 'ppa', 'Pp3c14_1501' => 'ppa', 'Pp3c16_4900' => 'ppa', 'Pp3c16_5010' => 'ppa', 'Pp3c16_5060' => 'ppa', 'Pp3c19_18250' => 'ppa', 'Pp3c23_8530' => 'ppa', 'Pp3c23_8550' => 'ppa', 'Pp3c24_9670' => 'ppa', 'Pp3c2_21390' => 'ppa', 'Pp3c2_31380' => 'ppa', 'Pp3c3_16620' => 'ppa', 'Pp3c3_8090' => 'ppa', 'Pp3c3_8110' => 'ppa', 'Pp3c3_8130' => 'ppa', 'Pp3c3_8150' => 'ppa', 'Pp3c4_14320' => 'ppa', 'Pp3c6_2560' => 'ppa', 'Pp3c9_16700' => 'ppa', 'PRCOL_00000234' => 'pco', 'PRCOL_00000235' => 'pco', 'PRCOL_00000777' => 'pco', 'PRCOL_00002344' => 'pco', 'PRCOL_00002372' => 'pco', 'PRCOL_00006120' => 'pco', 'Prupe.1G021400' => 'ppe', 'Prupe.1G021500' => 'ppe', 'Prupe.1G021600' => 'ppe', 'Prupe.1G021700' => 'ppe', 'Prupe.1G021800' => 'ppe', 'Prupe.5G145100' => 'ppe', 'Psat6g204040' => 'psa', 'Psat6g204800' => 'psa', 'Psat6g204920' => 'psa', 'Psat6g204960' => 'psa', 'Psat6g205080' => 'psa', 'PSO017G0271' => 'pso', 'PSO017G1276' => 'pso', 'PSO017G1429' => 'pso', 'PSO017G1861' => 'pso', 'PSO017G2787' => 'pso', 'PSO017G4466' => 'pso', 'PSO017G5118' => 'pso', 'PSO017G5420' => 'pso', 'PSO063G3678' => 'pso', 'PSO210G0546' => 'pso', 'PSO317G0001' => 'pso', 'PSO357G0512' => 'pso', 'PSO478G2682' => 'pso', 'PSO647G0001' => 'pso', 'PSO675G0001' => 'pso', 'PSO675G2699' => 'pso', 'PSO675G2849' => 'pso', 'PSO675G4991' => 'pso', 'PSO689G0001' => 'pso', 'QL06p000916' => 'qlo', 'QL06p000921' => 'qlo', 'QL06p001398' => 'qlo', 'QL06p001407' => 'qlo', 'QL06p002031' => 'qlo', 'RcHm_v2.0_Chr4g0387791' => 'rch', 'RcHm_v2.0_Chr4g0387801' => 'rch', 'RcHm_v2.0_Chr6g0286501' => 'rch', 'RcHm_v2.0_Chr6g0286511' => 'rch', 'RcHm_v2.0_Chr6g0286521' => 'rch', 'RcHm_v2.0_Chr6g0286531' => 'rch', 'RcHm_v2.0_Chr7g0189141' => 'rch', 'Rhsim02G0028700' => 'rsi', 'Rhsim02G0028800' => 'rsi', 'Rhsim02G0028900' => 'rsi', 'Rhsim02G0029000' => 'rsi', 'Rhsim02G0029100' => 'rsi', 'Rhsim02G0029200' => 'rsi', 'Rhsim02G0029300' => 'rsi', 'Rhsim02G0029400' => 'rsi', 'Rhsim02G0029500' => 'rsi', 'Rhsim02G0029600' => 'rsi', 'RhsimUnG0024000' => 'rsi', 'RhsimUnG0024100' => 'rsi', 'RhsimUnG0024200' => 'rsi', 'RhsimUnG0024300' => 'rsi', 'RhsimUnG0024400' => 'rsi', 'RhsimUnG0024500' => 'rsi', 'RhsimUnG0024700' => 'rsi', 'RhsimUnG0024800' => 'rsi', 'RhsimUnG0024900' => 'rsi', 'RhsimUnG0025100' => 'rsi', 'Sabra08G0120200' => 'sbr', 'Sabra08G0120300' => 'sbr', 'Sabra08G0120500' => 'sbr', 'Sabra08G0120600' => 'sbr', 'Sabra10G0158900' => 'sbr', 'SalBow2G3492' => 'sbo', 'Sc13g0004760' => 'sci', 'Sc13g0004770' => 'sci', 'Sed0003417' => 'sed', 'Sed0019750' => 'sed', 'SEGI_03419' => 'sgi', 'SEGI_05907' => 'sgi', 'SEGI_10682' => 'sgi', 'SEGI_13528' => 'sgi', 'SEGI_16081' => 'sgi', 'SEGI_19370' => 'sgi', 'SEGI_21015' => 'sgi', 'SEGI_21944' => 'sgi', 'SEGI_32906' => 'sgi', 'SEGI_33093' => 'sgi', 'SEGI_36110' => 'sgi', 'SEGI_40397' => 'sgi', 'SGA_v2.0_scaffold191G40426' => 'sas', 'SGA_v2.0_scaffold353G49717' => 'sas', 'SGA_v2.0_scaffold50G18550' => 'sas', 'SMO119G0173' => 'smo', 'SMO172G0002' => 'smo', 'Solyc09g082690.3' => 'sly', 'Solyc09g082700.2' => 'sly', 'Sopen09g031550' => 'spe', 'Sopen09g031560' => 'spe', 'Sp3g20540' => 'spa', 'Sp7g07580' => 'spa', 'TAR134G0002' => 'tar', 'TAR236G0001' => 'tar', 'TAR365G0892' => 'tar', 'TAR636G0166' => 'tar', 'TAR636G0646' => 'tar', 'TAR636G0869' => 'tar', 'TAR636G1317' => 'tar', 'TAR636G1744' => 'tar', 'TAR636G3358' => 'tar', 'TAR636G3436' => 'tar', 'THA.LOC104803047' => 'tha', 'Thecc.04G238900' => 'tca', 'Thhalv10021557m.g' => 'esa', 'Thhalv10026318m.g' => 'esa', 'Thhalv10026335m.g' => 'esa', 'TPR.G17433' => 'tpr', 'TPR.G18915' => 'tpr', 'TPR.G26125' => 'tpr', 'TWI09G0677' => 'twi', 'TWI73G0287' => 'twi', 'unitig_748.g8326' => 'ugi', 'vmacro15370' => 'vma', 'vmacro15371' => 'vma', 'vmacro15372' => 'vma', 'vmacro15373' => 'vma', 'vmacro15374' => 'vma', 'VMungo0720G2826' => 'vmu', 'Zm00001eb116960' => 'zma', 'Zm00001eb301260' => 'zma', 'Zm00001eb301270' => 'zma' ) $gf_id = 'HOM05D001460' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001460' ) $data_identifier = 'HOM05D001460' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 4, 'aag' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 2, 'aox' => (int) 2, 'arhy' => (int) 4, 'ath' => (int) 2, 'atr' => (int) 1, 'acertr' => (int) 10, 'cqu' => (int) 4, 'bca' => (int) 11, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 1, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 1, 'ccan' => (int) 1, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 1, 'col' => (int) 1, 'cpa' => (int) 1, 'cre' => (int) 7, 'csa' => (int) 1, 'camsi' => (int) 2, 'dca' => (int) 3, 'din' => (int) 2, 'dzi' => (int) 3, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 14, 'fve' => (int) 9, 'gma' => (int) 2, 'ghi' => (int) 4, 'gra' => (int) 2, 'vvi' => (int) 1, 'han' => (int) 13, 'cav' => (int) 1, 'hma' => (int) 2, 'sun' => (int) 2, 'lal' => (int) 2, 'lonja' => (int) 12, 'lja' => (int) 1, 'lsa' => (int) 7, 'mes' => (int) 1, 'mpo' => (int) 27, 'mbi' => (int) 1, 'mco' => (int) 8, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 1, 'egut' => (int) 1, 'ama' => (int) 1, 'nta' => (int) 4, 'nnu' => (int) 2, 'oeu' => (int) 3, 'osa' => (int) 4, 'pax' => (int) 9, 'pgr' => (int) 1, 'stu' => (int) 1, 'pvu' => (int) 1, 'ptr' => (int) 4, 'ppa' => (int) 22, 'pco' => (int) 6, 'ppe' => (int) 6, 'psa' => (int) 5, 'pso' => (int) 19, 'qlo' => (int) 5, 'rch' => (int) 7, 'rsi' => (int) 20, 'sbr' => (int) 5, 'sbo' => (int) 1, 'sci' => (int) 2, 'sed' => (int) 2, 'sgi' => (int) 12, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 2, 'tar' => (int) 10, 'tha' => (int) 1, 'tca' => (int) 1, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 2, 'ugi' => (int) 1, 'vma' => (int) 5, 'vmu' => (int) 1, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb301270' $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' => 'HOM05D001460', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '433', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p22980' => 'bna', 'A01p32340' => 'bna', 'A03p42970' => 'bna', 'A05p25880' => 'bna', 'Aa31LG8G9320' => 'aar', 'Aa31LG8G9330' => 'aar', 'Aa31LG8G9340' => 'aar', 'Aa31sc221G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1034' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1528' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.829' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2222' => 'aag', 'Ah.12g058830' => 'amhyb', 'Ah.12g058840' => 'amhyb', 'AL3G37160' => 'aly', 'AL7G41310' => 'aly', 'Aqoxy5G00395' => 'aox', 'Aqoxy5G00396' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0C8NZA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5185HY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JZ1PRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MD3LS0' => 'arhy', 'AT3G22840' => 'ath', 'AT4G14690' => 'ath', 'ATR0665G054' => 'atr', 'Atru.chr4.2344' => 'acertr', 'Atru.chr4.2346' => 'acertr', 'Atru.chr4.2347' => 'acertr', 'Atru.chr4.2348' => 'acertr', 'Atru.chr4.2355' => 'acertr', 'Atru.chr4.2356' => 'acertr', 'Atru.chr4.2358' => 'acertr', 'Atru.chr4.2359' => 'acertr', 'Atru.chr4.2360' => 'acertr', 'Atru.chr4.2361' => 'acertr', 'AUR62030476' => 'cqu', 'AUR62030478' => 'cqu', 'AUR62030819' => 'cqu', 'AUR62030820' => 'cqu', 'BcaB03g14648' => 'bca', 'BcaB04g20492' => 'bca', 'BcaB06g26399' => 'bca', 'BcaC01g03416' => 'bca', 'BcaC01g03419' => 'bca', 'BcaC01g03421' => 'bca', 'BcaC01g03424' => 'bca', 'BcaC05g28012' => 'bca', 'BcaC09g49212' => 'bca', 'BcaC09g50140' => 'bca', 'BcaNung00346' => 'bca', 'BolC1t02785H' => 'bol', 'BolC1t04095H' => 'bol', 'BolC3t17545H' => 'bol', 'BolC5t32769H' => 'bol', 'BraA01t02211Z' => 'bra', 'BraA01t03359Z' => 'bra', 'BraA03t13441Z' => 'bra', 'BraA05t21476Z' => 'bra', 'C01p28420' => 'bna', 'C01p41350' => 'bna', 'C03p52750' => 'bna', 'C03p52780' => 'bna', 'C05p40270' => 'bna', 'CAN.G1437.9' => 'can', 'CANSAT78G0035' => 'cansat', 'CANSAT78G1036' => 'cansat', 'CANSAT78G2272' => 'cansat', 'CANSAT78G2478' => 'cansat', 'CARHR098700' => 'chi', 'CARHR221120' => 'chi', 'CARHR221150' => 'chi', 'Carub.0003s2297' => 'cru', 'Carub.0007s2749' => 'cru', 'Carub.0007s2750' => 'cru', 'Carub.0007s2751' => 'cru', 'Ca_10849_v3' => 'car', 'Cc03_g04300' => 'ccan', 'CDE02G3648' => 'cde', 'CDE05G0060' => 'cde', 'CDE05G0692' => 'cde', 'CDE05G2285' => 'cde', 'CDE05G2884' => 'cde', 'CDE05G3072' => 'cde', 'Cfa008439' => 'cfa', 'Cfa008441' => 'cfa', 'Cfa008443' => 'cfa', 'Cfa008448' => 'cfa', 'Ciclev10005974m.g' => 'ccl', 'Ciclev10006006m.g' => 'ccl', 'Ciclev10006775m.g' => 'ccl', 'CiPaw.02G120400' => 'cil', 'CiPaw.02G120500' => 'cil', 'CiPaw.02G120600' => 'cil', 'ClCG05G004850' => 'cla', 'COL.COLO4_21566' => 'col', 'Cpa.g.sc44.124' => 'cpa', 'Cre07.g320400' => 'cre', 'Cre07.g320450' => 'cre', 'Cre08.g384650' => 'cre', 'Cre09.g393173' => 'cre', 'Cre09.g394325' => 'cre', 'Cre14.g626750' => 'cre', 'Cre16.g679250' => 'cre', 'CsaV3_3G012890' => 'csa', 'CSS0010865' => 'camsi', 'CSS0044338' => 'camsi', 'DCAR_002366' => 'dca', 'DCAR_030687' => 'dca', 'DCAR_030688' => 'dca', 'Dinv14047' => 'din', 'Dinv14048' => 'din', 'Duzib151G0105' => 'dzi', 'Duzib151G0114' => 'dzi', 'Duzib212G1029' => 'dzi', 'ECA232G3536' => 'eca', 'ECA240G0786' => 'eca', 'ECA240G1802' => 'eca', 'ECA240G3760' => 'eca', 'ECA240G3920' => 'eca', 'EL10Ac5g12536' => 'bvu', 'EL10Ac5g12537' => 'bvu', 'EL10Ac5g12538' => 'bvu', 'Eucgr.B01004' => 'egr', 'Eucgr.B01006' => 'egr', 'Eucgr.B01007' => 'egr', 'Eucgr.B01008' => 'egr', 'Eucgr.B01895' => 'egr', 'Eucgr.B01896' => 'egr', 'FAN04G1456' => 'fan', 'FAN08G1769' => 'fan', 'FAN08G2160' => 'fan', 'FAN13G2403' => 'fan', 'FAN13G3303' => 'fan', 'FAN15G2435' => 'fan', 'FAN17G0672' => 'fan', 'FAN17G2441' => 'fan', 'FAN18G1024' => 'fan', 'FAN22G1458' => 'fan', 'FAN24G0037' => 'fan', 'FAN24G0429' => 'fan', 'FAN24G2387' => 'fan', 'FAN27G2746' => 'fan', 'FvH4_2g20400' => 'fve', 'FvH4_2g20420' => 'fve', 'FvH4_2g20430' => 'fve', 'FvH4_4g01270' => 'fve', 'FvH4_4g01290' => 'fve', 'FvH4_4g01300' => 'fve', 'FvH4_4g01310' => 'fve', 'FvH4_4g01330' => 'fve', 'FvH4_5g09070' => 'fve', 'Glyma.10G243800' => 'gma', 'Glyma.20G150600' => 'gma', 'Gohir.A09G219200' => 'ghi', 'Gohir.A09G219300' => 'ghi', 'Gohir.D09G221400' => 'ghi', 'Gohir.D09G221500' => 'ghi', 'Gorai.006G242600' => 'gra', 'Gorai.006G242700' => 'gra', 'GSVIVG01018044001' => 'vvi', 'HanXRQChr03g0083821' => 'han', 'HanXRQChr03g0083841' => 'han', 'HanXRQChr03g0083881' => 'han', 'HanXRQChr03g0083901' => 'han', 'HanXRQChr03g0083921' => 'han', 'HanXRQChr03g0085331' => 'han', 'HanXRQChr03g0085361' => 'han', 'HanXRQChr03g0085411' => 'han', 'HanXRQChr03g0085421' => 'han', 'HanXRQChr03g0085431' => 'han', 'HanXRQChr08g0221991' => 'han', 'HanXRQChr11g0336061' => 'han', 'HanXRQChr11g0336411' => 'han', 'Haze_11234' => 'cav', 'Hma1.2p1_0549F.1_g177010' => 'hma', 'Hma1.2p1_0602F.1_g187630' => 'hma', 'Hund14876' => 'sun', 'Hund14879' => 'sun', 'Lalb_Chr06g0160741' => 'lal', 'Lalb_Chr21g0304781' => 'lal', 'Lj3A726G19' => 'lonja', 'Lj3A726T23' => 'lonja', 'Lj3A726T24' => 'lonja', 'Lj3A726T25' => 'lonja', 'Lj3A727T17' => 'lonja', 'Lj3C726T0' => 'lonja', 'Lj3C726T2' => 'lonja', 'Lj3P725T35' => 'lonja', 'Lj3P727T10' => 'lonja', 'Lj3P727T12' => 'lonja', 'Lj3P727T14' => 'lonja', 'Lj5g0023109' => 'lja', 'Lj6P646T44' => 'lonja', 'Lsat_1_v5_gn_6_75760' => 'lsa', 'Lsat_1_v5_gn_6_75800' => 'lsa', 'Lsat_1_v5_gn_6_75900' => 'lsa', 'Lsat_1_v5_gn_6_76240' => 'lsa', 'Lsat_1_v5_gn_6_76441' => 'lsa', 'Lsat_1_v5_gn_6_76700' => 'lsa', 'Lsat_1_v5_gn_6_76760' => 'lsa', 'Manes.15G033100' => 'mes', 'Mapoly0004s0074' => 'mpo', 'Mapoly0004s0075' => 'mpo', 'Mapoly0004s0163' => 'mpo', 'Mapoly0004s0164' => 'mpo', 'Mapoly0021s0018' => 'mpo', 'Mapoly0041s0136' => 'mpo', 'Mapoly0041s0137' => 'mpo', 'Mapoly0041s0138' => 'mpo', 'Mapoly0041s0139' => 'mpo', 'Mapoly0041s0141' => 'mpo', 'Mapoly0041s0142' => 'mpo', 'Mapoly0041s0143' => 'mpo', 'Mapoly0041s0144' => 'mpo', 'Mapoly0041s0145' => 'mpo', 'Mapoly0047s0106' => 'mpo', 'Mapoly0047s0108' => 'mpo', 'Mapoly0050s0051' => 'mpo', 'Mapoly0050s0052' => 'mpo', 'Mapoly0050s0053' => 'mpo', 'Mapoly0058s0013' => 'mpo', 'Mapoly0091s0078' => 'mpo', 'Mapoly0091s0079' => 'mpo', 'Mapoly0091s0080' => 'mpo', 'Mapoly0091s0081' => 'mpo', 'Mapoly0278s0004' => 'mpo', 'Mapoly0278s0005' => 'mpo', 'Mapoly0278s0006' => 'mpo', 'MBI11_g30648_MAGBIO' => 'mbi', 'MCO03G194' => 'mco', 'MCO03G590' => 'mco', 'MCO07G312' => 'mco', 'MCO10G318' => 'mco', 'MCO12G244' => 'mco', 'MCO13G148' => 'mco', 'MCO13G194' => 'mco', 'MCO16G238' => 'mco', 'MD06G1134100' => 'mdo', 'MD13G1200100' => 'mdo', 'MD13G1200300' => 'mdo', 'MD13G1200600' => 'mdo', 'MD14G1150400' => 'mdo', 'MD16G1200000' => 'mdo', 'Medtr1g102570' => 'mtr', 'Medtr1g102780' => 'mtr', 'Medtr1g102800' => 'mtr', 'Medtr1g102810' => 'mtr', 'Medtr1g102830' => 'mtr', 'MELO3C006499.2' => 'cme', 'Migut.G00385' => 'egut', 'MSTRG.4063' => 'ama', 'Nitab4.5_0000090g0260' => 'nta', 'Nitab4.5_0000977g0030' => 'nta', 'Nitab4.5_0002541g0040' => 'nta', 'Nitab4.5_0007068g0040' => 'nta', 'Nn005s41408' => 'nnu', 'Nn005s41410' => 'nnu', 'Oeu010310.1' => 'oeu', 'Oeu010311.1' => 'oeu', 'Oeu043472.1' => 'oeu', 'Os01g0246400' => 'osa', 'Os04g0267950' => 'osa', 'Os07g0178700' => 'osa', 'Os07g0178800' => 'osa', 'Peaxi162Scf00316g00046' => 'pax', 'Peaxi162Scf00316g00049' => 'pax', 'Peaxi162Scf00316g00059' => 'pax', 'Peaxi162Scf00316g00328' => 'pax', 'Peaxi162Scf00316g00329' => 'pax', 'Peaxi162Scf00316g00411' => 'pax', 'Peaxi162Scf00316g00521' => 'pax', 'Peaxi162Scf00492g00068' => 'pax', 'Peaxi162Scf35631g00002' => 'pax', 'PGR142G3720' => 'pgr', 'PGSC0003DMG400006442' => 'stu', 'Phvul.007G062000' => 'pvu', 'Potri.008G157750' => 'ptr', 'Potri.008G157900' => 'ptr', 'Potri.008G158000' => 'ptr', 'Potri.008G158200' => 'ptr', 'Pp3c11_7280' => 'ppa', 'Pp3c11_7980' => 'ppa', 'Pp3c12_19450' => 'ppa', 'Pp3c14_1480' => 'ppa', 'Pp3c14_1501' => 'ppa', 'Pp3c16_4900' => 'ppa', 'Pp3c16_5010' => 'ppa', 'Pp3c16_5060' => 'ppa', 'Pp3c19_18250' => 'ppa', 'Pp3c23_8530' => 'ppa', 'Pp3c23_8550' => 'ppa', 'Pp3c24_9670' => 'ppa', 'Pp3c2_21390' => 'ppa', 'Pp3c2_31380' => 'ppa', 'Pp3c3_16620' => 'ppa', 'Pp3c3_8090' => 'ppa', 'Pp3c3_8110' => 'ppa', 'Pp3c3_8130' => 'ppa', 'Pp3c3_8150' => 'ppa', 'Pp3c4_14320' => 'ppa', 'Pp3c6_2560' => 'ppa', 'Pp3c9_16700' => 'ppa', 'PRCOL_00000234' => 'pco', 'PRCOL_00000235' => 'pco', 'PRCOL_00000777' => 'pco', 'PRCOL_00002344' => 'pco', 'PRCOL_00002372' => 'pco', 'PRCOL_00006120' => 'pco', 'Prupe.1G021400' => 'ppe', 'Prupe.1G021500' => 'ppe', 'Prupe.1G021600' => 'ppe', 'Prupe.1G021700' => 'ppe', 'Prupe.1G021800' => 'ppe', 'Prupe.5G145100' => 'ppe', 'Psat6g204040' => 'psa', 'Psat6g204800' => 'psa', 'Psat6g204920' => 'psa', 'Psat6g204960' => 'psa', 'Psat6g205080' => 'psa', 'PSO017G0271' => 'pso', 'PSO017G1276' => 'pso', 'PSO017G1429' => 'pso', 'PSO017G1861' => 'pso', 'PSO017G2787' => 'pso', 'PSO017G4466' => 'pso', 'PSO017G5118' => 'pso', 'PSO017G5420' => 'pso', 'PSO063G3678' => 'pso', 'PSO210G0546' => 'pso', 'PSO317G0001' => 'pso', 'PSO357G0512' => 'pso', 'PSO478G2682' => 'pso', 'PSO647G0001' => 'pso', 'PSO675G0001' => 'pso', 'PSO675G2699' => 'pso', 'PSO675G2849' => 'pso', 'PSO675G4991' => 'pso', 'PSO689G0001' => 'pso', 'QL06p000916' => 'qlo', 'QL06p000921' => 'qlo', 'QL06p001398' => 'qlo', 'QL06p001407' => 'qlo', 'QL06p002031' => 'qlo', 'RcHm_v2.0_Chr4g0387791' => 'rch', 'RcHm_v2.0_Chr4g0387801' => 'rch', 'RcHm_v2.0_Chr6g0286501' => 'rch', 'RcHm_v2.0_Chr6g0286511' => 'rch', 'RcHm_v2.0_Chr6g0286521' => 'rch', 'RcHm_v2.0_Chr6g0286531' => 'rch', 'RcHm_v2.0_Chr7g0189141' => 'rch', 'Rhsim02G0028700' => 'rsi', 'Rhsim02G0028800' => 'rsi', 'Rhsim02G0028900' => 'rsi', 'Rhsim02G0029000' => 'rsi', 'Rhsim02G0029100' => 'rsi', 'Rhsim02G0029200' => 'rsi', 'Rhsim02G0029300' => 'rsi', 'Rhsim02G0029400' => 'rsi', 'Rhsim02G0029500' => 'rsi', 'Rhsim02G0029600' => 'rsi', 'RhsimUnG0024000' => 'rsi', 'RhsimUnG0024100' => 'rsi', 'RhsimUnG0024200' => 'rsi', 'RhsimUnG0024300' => 'rsi', 'RhsimUnG0024400' => 'rsi', 'RhsimUnG0024500' => 'rsi', 'RhsimUnG0024700' => 'rsi', 'RhsimUnG0024800' => 'rsi', 'RhsimUnG0024900' => 'rsi', 'RhsimUnG0025100' => 'rsi', 'Sabra08G0120200' => 'sbr', 'Sabra08G0120300' => 'sbr', 'Sabra08G0120500' => 'sbr', 'Sabra08G0120600' => 'sbr', 'Sabra10G0158900' => 'sbr', 'SalBow2G3492' => 'sbo', 'Sc13g0004760' => 'sci', 'Sc13g0004770' => 'sci', 'Sed0003417' => 'sed', 'Sed0019750' => 'sed', 'SEGI_03419' => 'sgi', 'SEGI_05907' => 'sgi', 'SEGI_10682' => 'sgi', 'SEGI_13528' => 'sgi', 'SEGI_16081' => 'sgi', 'SEGI_19370' => 'sgi', 'SEGI_21015' => 'sgi', 'SEGI_21944' => 'sgi', 'SEGI_32906' => 'sgi', 'SEGI_33093' => 'sgi', 'SEGI_36110' => 'sgi', 'SEGI_40397' => 'sgi', 'SGA_v2.0_scaffold191G40426' => 'sas', 'SGA_v2.0_scaffold353G49717' => 'sas', 'SGA_v2.0_scaffold50G18550' => 'sas', 'SMO119G0173' => 'smo', 'SMO172G0002' => 'smo', 'Solyc09g082690.3' => 'sly', 'Solyc09g082700.2' => 'sly', 'Sopen09g031550' => 'spe', 'Sopen09g031560' => 'spe', 'Sp3g20540' => 'spa', 'Sp7g07580' => 'spa', 'TAR134G0002' => 'tar', 'TAR236G0001' => 'tar', 'TAR365G0892' => 'tar', 'TAR636G0166' => 'tar', 'TAR636G0646' => 'tar', 'TAR636G0869' => 'tar', 'TAR636G1317' => 'tar', 'TAR636G1744' => 'tar', 'TAR636G3358' => 'tar', 'TAR636G3436' => 'tar', 'THA.LOC104803047' => 'tha', 'Thecc.04G238900' => 'tca', 'Thhalv10021557m.g' => 'esa', 'Thhalv10026318m.g' => 'esa', 'Thhalv10026335m.g' => 'esa', 'TPR.G17433' => 'tpr', 'TPR.G18915' => 'tpr', 'TPR.G26125' => 'tpr', 'TWI09G0677' => 'twi', 'TWI73G0287' => 'twi', 'unitig_748.g8326' => 'ugi', 'vmacro15370' => 'vma', 'vmacro15371' => 'vma', 'vmacro15372' => 'vma', 'vmacro15373' => 'vma', 'vmacro15374' => 'vma', 'VMungo0720G2826' => 'vmu', 'Zm00001eb116960' => 'zma', 'Zm00001eb301260' => 'zma', 'Zm00001eb301270' => 'zma' ), 'gf_id' => 'HOM05D001460', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001460' ), 'data_identifier' => 'HOM05D001460', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001460', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '433', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p22980' => 'bna', 'A01p32340' => 'bna', 'A03p42970' => 'bna', 'A05p25880' => 'bna', 'Aa31LG8G9320' => 'aar', 'Aa31LG8G9330' => 'aar', 'Aa31LG8G9340' => 'aar', 'Aa31sc221G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1034' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1528' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.829' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2222' => 'aag', 'Ah.12g058830' => 'amhyb', 'Ah.12g058840' => 'amhyb', 'AL3G37160' => 'aly', 'AL7G41310' => 'aly', 'Aqoxy5G00395' => 'aox', 'Aqoxy5G00396' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0C8NZA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5185HY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JZ1PRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MD3LS0' => 'arhy', 'AT3G22840' => 'ath', 'AT4G14690' => 'ath', 'ATR0665G054' => 'atr', 'Atru.chr4.2344' => 'acertr', 'Atru.chr4.2346' => 'acertr', 'Atru.chr4.2347' => 'acertr', 'Atru.chr4.2348' => 'acertr', 'Atru.chr4.2355' => 'acertr', 'Atru.chr4.2356' => 'acertr', 'Atru.chr4.2358' => 'acertr', 'Atru.chr4.2359' => 'acertr', 'Atru.chr4.2360' => 'acertr', 'Atru.chr4.2361' => 'acertr', 'AUR62030476' => 'cqu', 'AUR62030478' => 'cqu', 'AUR62030819' => 'cqu', 'AUR62030820' => 'cqu', 'BcaB03g14648' => 'bca', 'BcaB04g20492' => 'bca', 'BcaB06g26399' => 'bca', 'BcaC01g03416' => 'bca', 'BcaC01g03419' => 'bca', 'BcaC01g03421' => 'bca', 'BcaC01g03424' => 'bca', 'BcaC05g28012' => 'bca', 'BcaC09g49212' => 'bca', 'BcaC09g50140' => 'bca', 'BcaNung00346' => 'bca', 'BolC1t02785H' => 'bol', 'BolC1t04095H' => 'bol', 'BolC3t17545H' => 'bol', 'BolC5t32769H' => 'bol', 'BraA01t02211Z' => 'bra', 'BraA01t03359Z' => 'bra', 'BraA03t13441Z' => 'bra', 'BraA05t21476Z' => 'bra', 'C01p28420' => 'bna', 'C01p41350' => 'bna', 'C03p52750' => 'bna', 'C03p52780' => 'bna', 'C05p40270' => 'bna', 'CAN.G1437.9' => 'can', 'CANSAT78G0035' => 'cansat', 'CANSAT78G1036' => 'cansat', 'CANSAT78G2272' => 'cansat', 'CANSAT78G2478' => 'cansat', 'CARHR098700' => 'chi', 'CARHR221120' => 'chi', 'CARHR221150' => 'chi', 'Carub.0003s2297' => 'cru', 'Carub.0007s2749' => 'cru', 'Carub.0007s2750' => 'cru', 'Carub.0007s2751' => 'cru', 'Ca_10849_v3' => 'car', 'Cc03_g04300' => 'ccan', 'CDE02G3648' => 'cde', 'CDE05G0060' => 'cde', 'CDE05G0692' => 'cde', 'CDE05G2285' => 'cde', 'CDE05G2884' => 'cde', 'CDE05G3072' => 'cde', 'Cfa008439' => 'cfa', 'Cfa008441' => 'cfa', 'Cfa008443' => 'cfa', 'Cfa008448' => 'cfa', 'Ciclev10005974m.g' => 'ccl', 'Ciclev10006006m.g' => 'ccl', 'Ciclev10006775m.g' => 'ccl', 'CiPaw.02G120400' => 'cil', 'CiPaw.02G120500' => 'cil', 'CiPaw.02G120600' => 'cil', 'ClCG05G004850' => 'cla', 'COL.COLO4_21566' => 'col', 'Cpa.g.sc44.124' => 'cpa', 'Cre07.g320400' => 'cre', 'Cre07.g320450' => 'cre', 'Cre08.g384650' => 'cre', 'Cre09.g393173' => 'cre', 'Cre09.g394325' => 'cre', 'Cre14.g626750' => 'cre', 'Cre16.g679250' => 'cre', 'CsaV3_3G012890' => 'csa', 'CSS0010865' => 'camsi', 'CSS0044338' => 'camsi', 'DCAR_002366' => 'dca', 'DCAR_030687' => 'dca', 'DCAR_030688' => 'dca', 'Dinv14047' => 'din', 'Dinv14048' => 'din', 'Duzib151G0105' => 'dzi', 'Duzib151G0114' => 'dzi', 'Duzib212G1029' => 'dzi', 'ECA232G3536' => 'eca', 'ECA240G0786' => 'eca', 'ECA240G1802' => 'eca', 'ECA240G3760' => 'eca', 'ECA240G3920' => 'eca', 'EL10Ac5g12536' => 'bvu', 'EL10Ac5g12537' => 'bvu', 'EL10Ac5g12538' => 'bvu', 'Eucgr.B01004' => 'egr', 'Eucgr.B01006' => 'egr', 'Eucgr.B01007' => 'egr', 'Eucgr.B01008' => 'egr', 'Eucgr.B01895' => 'egr', 'Eucgr.B01896' => 'egr', 'FAN04G1456' => 'fan', 'FAN08G1769' => 'fan', 'FAN08G2160' => 'fan', 'FAN13G2403' => 'fan', 'FAN13G3303' => 'fan', 'FAN15G2435' => 'fan', 'FAN17G0672' => 'fan', 'FAN17G2441' => 'fan', 'FAN18G1024' => 'fan', 'FAN22G1458' => 'fan', 'FAN24G0037' => 'fan', 'FAN24G0429' => 'fan', 'FAN24G2387' => 'fan', 'FAN27G2746' => 'fan', 'FvH4_2g20400' => 'fve', 'FvH4_2g20420' => 'fve', 'FvH4_2g20430' => 'fve', 'FvH4_4g01270' => 'fve', 'FvH4_4g01290' => 'fve', 'FvH4_4g01300' => 'fve', 'FvH4_4g01310' => 'fve', 'FvH4_4g01330' => 'fve', 'FvH4_5g09070' => 'fve', 'Glyma.10G243800' => 'gma', 'Glyma.20G150600' => 'gma', 'Gohir.A09G219200' => 'ghi', 'Gohir.A09G219300' => 'ghi', 'Gohir.D09G221400' => 'ghi', 'Gohir.D09G221500' => 'ghi', 'Gorai.006G242600' => 'gra', 'Gorai.006G242700' => 'gra', 'GSVIVG01018044001' => 'vvi', 'HanXRQChr03g0083821' => 'han', 'HanXRQChr03g0083841' => 'han', 'HanXRQChr03g0083881' => 'han', 'HanXRQChr03g0083901' => 'han', 'HanXRQChr03g0083921' => 'han', 'HanXRQChr03g0085331' => 'han', 'HanXRQChr03g0085361' => 'han', 'HanXRQChr03g0085411' => 'han', 'HanXRQChr03g0085421' => 'han', 'HanXRQChr03g0085431' => 'han', 'HanXRQChr08g0221991' => 'han', 'HanXRQChr11g0336061' => 'han', 'HanXRQChr11g0336411' => 'han', 'Haze_11234' => 'cav', 'Hma1.2p1_0549F.1_g177010' => 'hma', 'Hma1.2p1_0602F.1_g187630' => 'hma', 'Hund14876' => 'sun', 'Hund14879' => 'sun', 'Lalb_Chr06g0160741' => 'lal', 'Lalb_Chr21g0304781' => 'lal', 'Lj3A726G19' => 'lonja', 'Lj3A726T23' => 'lonja', 'Lj3A726T24' => 'lonja', 'Lj3A726T25' => 'lonja', 'Lj3A727T17' => 'lonja', 'Lj3C726T0' => 'lonja', 'Lj3C726T2' => 'lonja', 'Lj3P725T35' => 'lonja', 'Lj3P727T10' => 'lonja', 'Lj3P727T12' => 'lonja', 'Lj3P727T14' => 'lonja', 'Lj5g0023109' => 'lja', 'Lj6P646T44' => 'lonja', 'Lsat_1_v5_gn_6_75760' => 'lsa', 'Lsat_1_v5_gn_6_75800' => 'lsa', 'Lsat_1_v5_gn_6_75900' => 'lsa', 'Lsat_1_v5_gn_6_76240' => 'lsa', 'Lsat_1_v5_gn_6_76441' => 'lsa', 'Lsat_1_v5_gn_6_76700' => 'lsa', 'Lsat_1_v5_gn_6_76760' => 'lsa', 'Manes.15G033100' => 'mes', 'Mapoly0004s0074' => 'mpo', 'Mapoly0004s0075' => 'mpo', 'Mapoly0004s0163' => 'mpo', 'Mapoly0004s0164' => 'mpo', 'Mapoly0021s0018' => 'mpo', 'Mapoly0041s0136' => 'mpo', 'Mapoly0041s0137' => 'mpo', 'Mapoly0041s0138' => 'mpo', 'Mapoly0041s0139' => 'mpo', 'Mapoly0041s0141' => 'mpo', 'Mapoly0041s0142' => 'mpo', 'Mapoly0041s0143' => 'mpo', 'Mapoly0041s0144' => 'mpo', 'Mapoly0041s0145' => 'mpo', 'Mapoly0047s0106' => 'mpo', 'Mapoly0047s0108' => 'mpo', 'Mapoly0050s0051' => 'mpo', 'Mapoly0050s0052' => 'mpo', 'Mapoly0050s0053' => 'mpo', 'Mapoly0058s0013' => 'mpo', 'Mapoly0091s0078' => 'mpo', 'Mapoly0091s0079' => 'mpo', 'Mapoly0091s0080' => 'mpo', 'Mapoly0091s0081' => 'mpo', 'Mapoly0278s0004' => 'mpo', 'Mapoly0278s0005' => 'mpo', 'Mapoly0278s0006' => 'mpo', 'MBI11_g30648_MAGBIO' => 'mbi', 'MCO03G194' => 'mco', 'MCO03G590' => 'mco', 'MCO07G312' => 'mco', 'MCO10G318' => 'mco', 'MCO12G244' => 'mco', 'MCO13G148' => 'mco', 'MCO13G194' => 'mco', 'MCO16G238' => 'mco', 'MD06G1134100' => 'mdo', 'MD13G1200100' => 'mdo', 'MD13G1200300' => 'mdo', 'MD13G1200600' => 'mdo', 'MD14G1150400' => 'mdo', 'MD16G1200000' => 'mdo', 'Medtr1g102570' => 'mtr', 'Medtr1g102780' => 'mtr', 'Medtr1g102800' => 'mtr', 'Medtr1g102810' => 'mtr', 'Medtr1g102830' => 'mtr', 'MELO3C006499.2' => 'cme', 'Migut.G00385' => 'egut', 'MSTRG.4063' => 'ama', 'Nitab4.5_0000090g0260' => 'nta', 'Nitab4.5_0000977g0030' => 'nta', 'Nitab4.5_0002541g0040' => 'nta', 'Nitab4.5_0007068g0040' => 'nta', 'Nn005s41408' => 'nnu', 'Nn005s41410' => 'nnu', 'Oeu010310.1' => 'oeu', 'Oeu010311.1' => 'oeu', 'Oeu043472.1' => 'oeu', 'Os01g0246400' => 'osa', 'Os04g0267950' => 'osa', 'Os07g0178700' => 'osa', 'Os07g0178800' => 'osa', 'Peaxi162Scf00316g00046' => 'pax', 'Peaxi162Scf00316g00049' => 'pax', 'Peaxi162Scf00316g00059' => 'pax', 'Peaxi162Scf00316g00328' => 'pax', 'Peaxi162Scf00316g00329' => 'pax', 'Peaxi162Scf00316g00411' => 'pax', 'Peaxi162Scf00316g00521' => 'pax', 'Peaxi162Scf00492g00068' => 'pax', 'Peaxi162Scf35631g00002' => 'pax', 'PGR142G3720' => 'pgr', 'PGSC0003DMG400006442' => 'stu', 'Phvul.007G062000' => 'pvu', 'Potri.008G157750' => 'ptr', 'Potri.008G157900' => 'ptr', 'Potri.008G158000' => 'ptr', 'Potri.008G158200' => 'ptr', 'Pp3c11_7280' => 'ppa', 'Pp3c11_7980' => 'ppa', 'Pp3c12_19450' => 'ppa', 'Pp3c14_1480' => 'ppa', 'Pp3c14_1501' => 'ppa', 'Pp3c16_4900' => 'ppa', 'Pp3c16_5010' => 'ppa', 'Pp3c16_5060' => 'ppa', 'Pp3c19_18250' => 'ppa', 'Pp3c23_8530' => 'ppa', 'Pp3c23_8550' => 'ppa', 'Pp3c24_9670' => 'ppa', 'Pp3c2_21390' => 'ppa', 'Pp3c2_31380' => 'ppa', 'Pp3c3_16620' => 'ppa', 'Pp3c3_8090' => 'ppa', 'Pp3c3_8110' => 'ppa', 'Pp3c3_8130' => 'ppa', 'Pp3c3_8150' => 'ppa', 'Pp3c4_14320' => 'ppa', 'Pp3c6_2560' => 'ppa', 'Pp3c9_16700' => 'ppa', 'PRCOL_00000234' => 'pco', 'PRCOL_00000235' => 'pco', 'PRCOL_00000777' => 'pco', 'PRCOL_00002344' => 'pco', 'PRCOL_00002372' => 'pco', 'PRCOL_00006120' => 'pco', 'Prupe.1G021400' => 'ppe', 'Prupe.1G021500' => 'ppe', 'Prupe.1G021600' => 'ppe', 'Prupe.1G021700' => 'ppe', 'Prupe.1G021800' => 'ppe', 'Prupe.5G145100' => 'ppe', 'Psat6g204040' => 'psa', 'Psat6g204800' => 'psa', 'Psat6g204920' => 'psa', 'Psat6g204960' => 'psa', 'Psat6g205080' => 'psa', 'PSO017G0271' => 'pso', 'PSO017G1276' => 'pso', 'PSO017G1429' => 'pso', 'PSO017G1861' => 'pso', 'PSO017G2787' => 'pso', 'PSO017G4466' => 'pso', 'PSO017G5118' => 'pso', 'PSO017G5420' => 'pso', 'PSO063G3678' => 'pso', 'PSO210G0546' => 'pso', 'PSO317G0001' => 'pso', 'PSO357G0512' => 'pso', 'PSO478G2682' => 'pso', 'PSO647G0001' => 'pso', 'PSO675G0001' => 'pso', 'PSO675G2699' => 'pso', 'PSO675G2849' => 'pso', 'PSO675G4991' => 'pso', 'PSO689G0001' => 'pso', 'QL06p000916' => 'qlo', 'QL06p000921' => 'qlo', 'QL06p001398' => 'qlo', 'QL06p001407' => 'qlo', 'QL06p002031' => 'qlo', 'RcHm_v2.0_Chr4g0387791' => 'rch', 'RcHm_v2.0_Chr4g0387801' => 'rch', 'RcHm_v2.0_Chr6g0286501' => 'rch', 'RcHm_v2.0_Chr6g0286511' => 'rch', 'RcHm_v2.0_Chr6g0286521' => 'rch', 'RcHm_v2.0_Chr6g0286531' => 'rch', 'RcHm_v2.0_Chr7g0189141' => 'rch', 'Rhsim02G0028700' => 'rsi', 'Rhsim02G0028800' => 'rsi', 'Rhsim02G0028900' => 'rsi', 'Rhsim02G0029000' => 'rsi', 'Rhsim02G0029100' => 'rsi', 'Rhsim02G0029200' => 'rsi', 'Rhsim02G0029300' => 'rsi', 'Rhsim02G0029400' => 'rsi', 'Rhsim02G0029500' => 'rsi', 'Rhsim02G0029600' => 'rsi', 'RhsimUnG0024000' => 'rsi', 'RhsimUnG0024100' => 'rsi', 'RhsimUnG0024200' => 'rsi', 'RhsimUnG0024300' => 'rsi', 'RhsimUnG0024400' => 'rsi', 'RhsimUnG0024500' => 'rsi', 'RhsimUnG0024700' => 'rsi', 'RhsimUnG0024800' => 'rsi', 'RhsimUnG0024900' => 'rsi', 'RhsimUnG0025100' => 'rsi', 'Sabra08G0120200' => 'sbr', 'Sabra08G0120300' => 'sbr', 'Sabra08G0120500' => 'sbr', 'Sabra08G0120600' => 'sbr', 'Sabra10G0158900' => 'sbr', 'SalBow2G3492' => 'sbo', 'Sc13g0004760' => 'sci', 'Sc13g0004770' => 'sci', 'Sed0003417' => 'sed', 'Sed0019750' => 'sed', 'SEGI_03419' => 'sgi', 'SEGI_05907' => 'sgi', 'SEGI_10682' => 'sgi', 'SEGI_13528' => 'sgi', 'SEGI_16081' => 'sgi', 'SEGI_19370' => 'sgi', 'SEGI_21015' => 'sgi', 'SEGI_21944' => 'sgi', 'SEGI_32906' => 'sgi', 'SEGI_33093' => 'sgi', 'SEGI_36110' => 'sgi', 'SEGI_40397' => 'sgi', 'SGA_v2.0_scaffold191G40426' => 'sas', 'SGA_v2.0_scaffold353G49717' => 'sas', 'SGA_v2.0_scaffold50G18550' => 'sas', 'SMO119G0173' => 'smo', 'SMO172G0002' => 'smo', 'Solyc09g082690.3' => 'sly', 'Solyc09g082700.2' => 'sly', 'Sopen09g031550' => 'spe', 'Sopen09g031560' => 'spe', 'Sp3g20540' => 'spa', 'Sp7g07580' => 'spa', 'TAR134G0002' => 'tar', 'TAR236G0001' => 'tar', 'TAR365G0892' => 'tar', 'TAR636G0166' => 'tar', 'TAR636G0646' => 'tar', 'TAR636G0869' => 'tar', 'TAR636G1317' => 'tar', 'TAR636G1744' => 'tar', 'TAR636G3358' => 'tar', 'TAR636G3436' => 'tar', 'THA.LOC104803047' => 'tha', 'Thecc.04G238900' => 'tca', 'Thhalv10021557m.g' => 'esa', 'Thhalv10026318m.g' => 'esa', 'Thhalv10026335m.g' => 'esa', 'TPR.G17433' => 'tpr', 'TPR.G18915' => 'tpr', 'TPR.G26125' => 'tpr', 'TWI09G0677' => 'twi', 'TWI73G0287' => 'twi', 'unitig_748.g8326' => 'ugi', 'vmacro15370' => 'vma', 'vmacro15371' => 'vma', 'vmacro15372' => 'vma', 'vmacro15373' => 'vma', 'vmacro15374' => 'vma', 'VMungo0720G2826' => 'vmu', 'Zm00001eb116960' => 'zma', 'Zm00001eb301260' => 'zma', 'Zm00001eb301270' => 'zma' ) $gf_id = 'HOM05D001460' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001460' ) $data_identifier = 'HOM05D001460' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 4, 'aag' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 2, 'aox' => (int) 2, 'arhy' => (int) 4, 'ath' => (int) 2, 'atr' => (int) 1, 'acertr' => (int) 10, 'cqu' => (int) 4, 'bca' => (int) 11, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 1, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 1, 'ccan' => (int) 1, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 1, 'col' => (int) 1, 'cpa' => (int) 1, 'cre' => (int) 7, 'csa' => (int) 1, 'camsi' => (int) 2, 'dca' => (int) 3, 'din' => (int) 2, 'dzi' => (int) 3, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 14, 'fve' => (int) 9, 'gma' => (int) 2, 'ghi' => (int) 4, 'gra' => (int) 2, 'vvi' => (int) 1, 'han' => (int) 13, 'cav' => (int) 1, 'hma' => (int) 2, 'sun' => (int) 2, 'lal' => (int) 2, 'lonja' => (int) 12, 'lja' => (int) 1, 'lsa' => (int) 7, 'mes' => (int) 1, 'mpo' => (int) 27, 'mbi' => (int) 1, 'mco' => (int) 8, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 1, 'egut' => (int) 1, 'ama' => (int) 1, 'nta' => (int) 4, 'nnu' => (int) 2, 'oeu' => (int) 3, 'osa' => (int) 4, 'pax' => (int) 9, 'pgr' => (int) 1, 'stu' => (int) 1, 'pvu' => (int) 1, 'ptr' => (int) 4, 'ppa' => (int) 22, 'pco' => (int) 6, 'ppe' => (int) 6, 'psa' => (int) 5, 'pso' => (int) 19, 'qlo' => (int) 5, 'rch' => (int) 7, 'rsi' => (int) 20, 'sbr' => (int) 5, 'sbo' => (int) 1, 'sci' => (int) 2, 'sed' => (int) 2, 'sgi' => (int) 12, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 2, 'tar' => (int) 10, 'tha' => (int) 1, 'tca' => (int) 1, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 2, 'ugi' => (int) 1, 'vma' => (int) 5, 'vmu' => (int) 1, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb301270' $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' => 'HOM05D001460', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '433', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p22980' => 'bna', 'A01p32340' => 'bna', 'A03p42970' => 'bna', 'A05p25880' => 'bna', 'Aa31LG8G9320' => 'aar', 'Aa31LG8G9330' => 'aar', 'Aa31LG8G9340' => 'aar', 'Aa31sc221G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1034' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1528' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.829' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2222' => 'aag', 'Ah.12g058830' => 'amhyb', 'Ah.12g058840' => 'amhyb', 'AL3G37160' => 'aly', 'AL7G41310' => 'aly', 'Aqoxy5G00395' => 'aox', 'Aqoxy5G00396' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0C8NZA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5185HY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JZ1PRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MD3LS0' => 'arhy', 'AT3G22840' => 'ath', 'AT4G14690' => 'ath', 'ATR0665G054' => 'atr', 'Atru.chr4.2344' => 'acertr', 'Atru.chr4.2346' => 'acertr', 'Atru.chr4.2347' => 'acertr', 'Atru.chr4.2348' => 'acertr', 'Atru.chr4.2355' => 'acertr', 'Atru.chr4.2356' => 'acertr', 'Atru.chr4.2358' => 'acertr', 'Atru.chr4.2359' => 'acertr', 'Atru.chr4.2360' => 'acertr', 'Atru.chr4.2361' => 'acertr', 'AUR62030476' => 'cqu', 'AUR62030478' => 'cqu', 'AUR62030819' => 'cqu', 'AUR62030820' => 'cqu', 'BcaB03g14648' => 'bca', 'BcaB04g20492' => 'bca', 'BcaB06g26399' => 'bca', 'BcaC01g03416' => 'bca', 'BcaC01g03419' => 'bca', 'BcaC01g03421' => 'bca', 'BcaC01g03424' => 'bca', 'BcaC05g28012' => 'bca', 'BcaC09g49212' => 'bca', 'BcaC09g50140' => 'bca', 'BcaNung00346' => 'bca', 'BolC1t02785H' => 'bol', 'BolC1t04095H' => 'bol', 'BolC3t17545H' => 'bol', 'BolC5t32769H' => 'bol', 'BraA01t02211Z' => 'bra', 'BraA01t03359Z' => 'bra', 'BraA03t13441Z' => 'bra', 'BraA05t21476Z' => 'bra', 'C01p28420' => 'bna', 'C01p41350' => 'bna', 'C03p52750' => 'bna', 'C03p52780' => 'bna', 'C05p40270' => 'bna', 'CAN.G1437.9' => 'can', 'CANSAT78G0035' => 'cansat', 'CANSAT78G1036' => 'cansat', 'CANSAT78G2272' => 'cansat', 'CANSAT78G2478' => 'cansat', 'CARHR098700' => 'chi', 'CARHR221120' => 'chi', 'CARHR221150' => 'chi', 'Carub.0003s2297' => 'cru', 'Carub.0007s2749' => 'cru', 'Carub.0007s2750' => 'cru', 'Carub.0007s2751' => 'cru', 'Ca_10849_v3' => 'car', 'Cc03_g04300' => 'ccan', 'CDE02G3648' => 'cde', 'CDE05G0060' => 'cde', 'CDE05G0692' => 'cde', 'CDE05G2285' => 'cde', 'CDE05G2884' => 'cde', 'CDE05G3072' => 'cde', 'Cfa008439' => 'cfa', 'Cfa008441' => 'cfa', 'Cfa008443' => 'cfa', 'Cfa008448' => 'cfa', 'Ciclev10005974m.g' => 'ccl', 'Ciclev10006006m.g' => 'ccl', 'Ciclev10006775m.g' => 'ccl', 'CiPaw.02G120400' => 'cil', 'CiPaw.02G120500' => 'cil', 'CiPaw.02G120600' => 'cil', 'ClCG05G004850' => 'cla', 'COL.COLO4_21566' => 'col', 'Cpa.g.sc44.124' => 'cpa', 'Cre07.g320400' => 'cre', 'Cre07.g320450' => 'cre', 'Cre08.g384650' => 'cre', 'Cre09.g393173' => 'cre', 'Cre09.g394325' => 'cre', 'Cre14.g626750' => 'cre', 'Cre16.g679250' => 'cre', 'CsaV3_3G012890' => 'csa', 'CSS0010865' => 'camsi', 'CSS0044338' => 'camsi', 'DCAR_002366' => 'dca', 'DCAR_030687' => 'dca', 'DCAR_030688' => 'dca', 'Dinv14047' => 'din', 'Dinv14048' => 'din', 'Duzib151G0105' => 'dzi', 'Duzib151G0114' => 'dzi', 'Duzib212G1029' => 'dzi', 'ECA232G3536' => 'eca', 'ECA240G0786' => 'eca', 'ECA240G1802' => 'eca', 'ECA240G3760' => 'eca', 'ECA240G3920' => 'eca', 'EL10Ac5g12536' => 'bvu', 'EL10Ac5g12537' => 'bvu', 'EL10Ac5g12538' => 'bvu', 'Eucgr.B01004' => 'egr', 'Eucgr.B01006' => 'egr', 'Eucgr.B01007' => 'egr', 'Eucgr.B01008' => 'egr', 'Eucgr.B01895' => 'egr', 'Eucgr.B01896' => 'egr', 'FAN04G1456' => 'fan', 'FAN08G1769' => 'fan', 'FAN08G2160' => 'fan', 'FAN13G2403' => 'fan', 'FAN13G3303' => 'fan', 'FAN15G2435' => 'fan', 'FAN17G0672' => 'fan', 'FAN17G2441' => 'fan', 'FAN18G1024' => 'fan', 'FAN22G1458' => 'fan', 'FAN24G0037' => 'fan', 'FAN24G0429' => 'fan', 'FAN24G2387' => 'fan', 'FAN27G2746' => 'fan', 'FvH4_2g20400' => 'fve', 'FvH4_2g20420' => 'fve', 'FvH4_2g20430' => 'fve', 'FvH4_4g01270' => 'fve', 'FvH4_4g01290' => 'fve', 'FvH4_4g01300' => 'fve', 'FvH4_4g01310' => 'fve', 'FvH4_4g01330' => 'fve', 'FvH4_5g09070' => 'fve', 'Glyma.10G243800' => 'gma', 'Glyma.20G150600' => 'gma', 'Gohir.A09G219200' => 'ghi', 'Gohir.A09G219300' => 'ghi', 'Gohir.D09G221400' => 'ghi', 'Gohir.D09G221500' => 'ghi', 'Gorai.006G242600' => 'gra', 'Gorai.006G242700' => 'gra', 'GSVIVG01018044001' => 'vvi', 'HanXRQChr03g0083821' => 'han', 'HanXRQChr03g0083841' => 'han', 'HanXRQChr03g0083881' => 'han', 'HanXRQChr03g0083901' => 'han', 'HanXRQChr03g0083921' => 'han', 'HanXRQChr03g0085331' => 'han', 'HanXRQChr03g0085361' => 'han', 'HanXRQChr03g0085411' => 'han', 'HanXRQChr03g0085421' => 'han', 'HanXRQChr03g0085431' => 'han', 'HanXRQChr08g0221991' => 'han', 'HanXRQChr11g0336061' => 'han', 'HanXRQChr11g0336411' => 'han', 'Haze_11234' => 'cav', 'Hma1.2p1_0549F.1_g177010' => 'hma', 'Hma1.2p1_0602F.1_g187630' => 'hma', 'Hund14876' => 'sun', 'Hund14879' => 'sun', 'Lalb_Chr06g0160741' => 'lal', 'Lalb_Chr21g0304781' => 'lal', 'Lj3A726G19' => 'lonja', 'Lj3A726T23' => 'lonja', 'Lj3A726T24' => 'lonja', 'Lj3A726T25' => 'lonja', 'Lj3A727T17' => 'lonja', 'Lj3C726T0' => 'lonja', 'Lj3C726T2' => 'lonja', 'Lj3P725T35' => 'lonja', 'Lj3P727T10' => 'lonja', 'Lj3P727T12' => 'lonja', 'Lj3P727T14' => 'lonja', 'Lj5g0023109' => 'lja', 'Lj6P646T44' => 'lonja', 'Lsat_1_v5_gn_6_75760' => 'lsa', 'Lsat_1_v5_gn_6_75800' => 'lsa', 'Lsat_1_v5_gn_6_75900' => 'lsa', 'Lsat_1_v5_gn_6_76240' => 'lsa', 'Lsat_1_v5_gn_6_76441' => 'lsa', 'Lsat_1_v5_gn_6_76700' => 'lsa', 'Lsat_1_v5_gn_6_76760' => 'lsa', 'Manes.15G033100' => 'mes', 'Mapoly0004s0074' => 'mpo', 'Mapoly0004s0075' => 'mpo', 'Mapoly0004s0163' => 'mpo', 'Mapoly0004s0164' => 'mpo', 'Mapoly0021s0018' => 'mpo', 'Mapoly0041s0136' => 'mpo', 'Mapoly0041s0137' => 'mpo', 'Mapoly0041s0138' => 'mpo', 'Mapoly0041s0139' => 'mpo', 'Mapoly0041s0141' => 'mpo', 'Mapoly0041s0142' => 'mpo', 'Mapoly0041s0143' => 'mpo', 'Mapoly0041s0144' => 'mpo', 'Mapoly0041s0145' => 'mpo', 'Mapoly0047s0106' => 'mpo', 'Mapoly0047s0108' => 'mpo', 'Mapoly0050s0051' => 'mpo', 'Mapoly0050s0052' => 'mpo', 'Mapoly0050s0053' => 'mpo', 'Mapoly0058s0013' => 'mpo', 'Mapoly0091s0078' => 'mpo', 'Mapoly0091s0079' => 'mpo', 'Mapoly0091s0080' => 'mpo', 'Mapoly0091s0081' => 'mpo', 'Mapoly0278s0004' => 'mpo', 'Mapoly0278s0005' => 'mpo', 'Mapoly0278s0006' => 'mpo', 'MBI11_g30648_MAGBIO' => 'mbi', 'MCO03G194' => 'mco', 'MCO03G590' => 'mco', 'MCO07G312' => 'mco', 'MCO10G318' => 'mco', 'MCO12G244' => 'mco', 'MCO13G148' => 'mco', 'MCO13G194' => 'mco', 'MCO16G238' => 'mco', 'MD06G1134100' => 'mdo', 'MD13G1200100' => 'mdo', 'MD13G1200300' => 'mdo', 'MD13G1200600' => 'mdo', 'MD14G1150400' => 'mdo', 'MD16G1200000' => 'mdo', 'Medtr1g102570' => 'mtr', 'Medtr1g102780' => 'mtr', 'Medtr1g102800' => 'mtr', 'Medtr1g102810' => 'mtr', 'Medtr1g102830' => 'mtr', 'MELO3C006499.2' => 'cme', 'Migut.G00385' => 'egut', 'MSTRG.4063' => 'ama', 'Nitab4.5_0000090g0260' => 'nta', 'Nitab4.5_0000977g0030' => 'nta', 'Nitab4.5_0002541g0040' => 'nta', 'Nitab4.5_0007068g0040' => 'nta', 'Nn005s41408' => 'nnu', 'Nn005s41410' => 'nnu', 'Oeu010310.1' => 'oeu', 'Oeu010311.1' => 'oeu', 'Oeu043472.1' => 'oeu', 'Os01g0246400' => 'osa', 'Os04g0267950' => 'osa', 'Os07g0178700' => 'osa', 'Os07g0178800' => 'osa', 'Peaxi162Scf00316g00046' => 'pax', 'Peaxi162Scf00316g00049' => 'pax', 'Peaxi162Scf00316g00059' => 'pax', 'Peaxi162Scf00316g00328' => 'pax', 'Peaxi162Scf00316g00329' => 'pax', 'Peaxi162Scf00316g00411' => 'pax', 'Peaxi162Scf00316g00521' => 'pax', 'Peaxi162Scf00492g00068' => 'pax', 'Peaxi162Scf35631g00002' => 'pax', 'PGR142G3720' => 'pgr', 'PGSC0003DMG400006442' => 'stu', 'Phvul.007G062000' => 'pvu', 'Potri.008G157750' => 'ptr', 'Potri.008G157900' => 'ptr', 'Potri.008G158000' => 'ptr', 'Potri.008G158200' => 'ptr', 'Pp3c11_7280' => 'ppa', 'Pp3c11_7980' => 'ppa', 'Pp3c12_19450' => 'ppa', 'Pp3c14_1480' => 'ppa', 'Pp3c14_1501' => 'ppa', 'Pp3c16_4900' => 'ppa', 'Pp3c16_5010' => 'ppa', 'Pp3c16_5060' => 'ppa', 'Pp3c19_18250' => 'ppa', 'Pp3c23_8530' => 'ppa', 'Pp3c23_8550' => 'ppa', 'Pp3c24_9670' => 'ppa', 'Pp3c2_21390' => 'ppa', 'Pp3c2_31380' => 'ppa', 'Pp3c3_16620' => 'ppa', 'Pp3c3_8090' => 'ppa', 'Pp3c3_8110' => 'ppa', 'Pp3c3_8130' => 'ppa', 'Pp3c3_8150' => 'ppa', 'Pp3c4_14320' => 'ppa', 'Pp3c6_2560' => 'ppa', 'Pp3c9_16700' => 'ppa', 'PRCOL_00000234' => 'pco', 'PRCOL_00000235' => 'pco', 'PRCOL_00000777' => 'pco', 'PRCOL_00002344' => 'pco', 'PRCOL_00002372' => 'pco', 'PRCOL_00006120' => 'pco', 'Prupe.1G021400' => 'ppe', 'Prupe.1G021500' => 'ppe', 'Prupe.1G021600' => 'ppe', 'Prupe.1G021700' => 'ppe', 'Prupe.1G021800' => 'ppe', 'Prupe.5G145100' => 'ppe', 'Psat6g204040' => 'psa', 'Psat6g204800' => 'psa', 'Psat6g204920' => 'psa', 'Psat6g204960' => 'psa', 'Psat6g205080' => 'psa', 'PSO017G0271' => 'pso', 'PSO017G1276' => 'pso', 'PSO017G1429' => 'pso', 'PSO017G1861' => 'pso', 'PSO017G2787' => 'pso', 'PSO017G4466' => 'pso', 'PSO017G5118' => 'pso', 'PSO017G5420' => 'pso', 'PSO063G3678' => 'pso', 'PSO210G0546' => 'pso', 'PSO317G0001' => 'pso', 'PSO357G0512' => 'pso', 'PSO478G2682' => 'pso', 'PSO647G0001' => 'pso', 'PSO675G0001' => 'pso', 'PSO675G2699' => 'pso', 'PSO675G2849' => 'pso', 'PSO675G4991' => 'pso', 'PSO689G0001' => 'pso', 'QL06p000916' => 'qlo', 'QL06p000921' => 'qlo', 'QL06p001398' => 'qlo', 'QL06p001407' => 'qlo', 'QL06p002031' => 'qlo', 'RcHm_v2.0_Chr4g0387791' => 'rch', 'RcHm_v2.0_Chr4g0387801' => 'rch', 'RcHm_v2.0_Chr6g0286501' => 'rch', 'RcHm_v2.0_Chr6g0286511' => 'rch', 'RcHm_v2.0_Chr6g0286521' => 'rch', 'RcHm_v2.0_Chr6g0286531' => 'rch', 'RcHm_v2.0_Chr7g0189141' => 'rch', 'Rhsim02G0028700' => 'rsi', 'Rhsim02G0028800' => 'rsi', 'Rhsim02G0028900' => 'rsi', 'Rhsim02G0029000' => 'rsi', 'Rhsim02G0029100' => 'rsi', 'Rhsim02G0029200' => 'rsi', 'Rhsim02G0029300' => 'rsi', 'Rhsim02G0029400' => 'rsi', 'Rhsim02G0029500' => 'rsi', 'Rhsim02G0029600' => 'rsi', 'RhsimUnG0024000' => 'rsi', 'RhsimUnG0024100' => 'rsi', 'RhsimUnG0024200' => 'rsi', 'RhsimUnG0024300' => 'rsi', 'RhsimUnG0024400' => 'rsi', 'RhsimUnG0024500' => 'rsi', 'RhsimUnG0024700' => 'rsi', 'RhsimUnG0024800' => 'rsi', 'RhsimUnG0024900' => 'rsi', 'RhsimUnG0025100' => 'rsi', 'Sabra08G0120200' => 'sbr', 'Sabra08G0120300' => 'sbr', 'Sabra08G0120500' => 'sbr', 'Sabra08G0120600' => 'sbr', 'Sabra10G0158900' => 'sbr', 'SalBow2G3492' => 'sbo', 'Sc13g0004760' => 'sci', 'Sc13g0004770' => 'sci', 'Sed0003417' => 'sed', 'Sed0019750' => 'sed', 'SEGI_03419' => 'sgi', 'SEGI_05907' => 'sgi', 'SEGI_10682' => 'sgi', 'SEGI_13528' => 'sgi', 'SEGI_16081' => 'sgi', 'SEGI_19370' => 'sgi', 'SEGI_21015' => 'sgi', 'SEGI_21944' => 'sgi', 'SEGI_32906' => 'sgi', 'SEGI_33093' => 'sgi', 'SEGI_36110' => 'sgi', 'SEGI_40397' => 'sgi', 'SGA_v2.0_scaffold191G40426' => 'sas', 'SGA_v2.0_scaffold353G49717' => 'sas', 'SGA_v2.0_scaffold50G18550' => 'sas', 'SMO119G0173' => 'smo', 'SMO172G0002' => 'smo', 'Solyc09g082690.3' => 'sly', 'Solyc09g082700.2' => 'sly', 'Sopen09g031550' => 'spe', 'Sopen09g031560' => 'spe', 'Sp3g20540' => 'spa', 'Sp7g07580' => 'spa', 'TAR134G0002' => 'tar', 'TAR236G0001' => 'tar', 'TAR365G0892' => 'tar', 'TAR636G0166' => 'tar', 'TAR636G0646' => 'tar', 'TAR636G0869' => 'tar', 'TAR636G1317' => 'tar', 'TAR636G1744' => 'tar', 'TAR636G3358' => 'tar', 'TAR636G3436' => 'tar', 'THA.LOC104803047' => 'tha', 'Thecc.04G238900' => 'tca', 'Thhalv10021557m.g' => 'esa', 'Thhalv10026318m.g' => 'esa', 'Thhalv10026335m.g' => 'esa', 'TPR.G17433' => 'tpr', 'TPR.G18915' => 'tpr', 'TPR.G26125' => 'tpr', 'TWI09G0677' => 'twi', 'TWI73G0287' => 'twi', 'unitig_748.g8326' => 'ugi', 'vmacro15370' => 'vma', 'vmacro15371' => 'vma', 'vmacro15372' => 'vma', 'vmacro15373' => 'vma', 'vmacro15374' => 'vma', 'VMungo0720G2826' => 'vmu', 'Zm00001eb116960' => 'zma', 'Zm00001eb301260' => 'zma', 'Zm00001eb301270' => 'zma' ), 'gf_id' => 'HOM05D001460', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001460' ), 'data_identifier' => 'HOM05D001460', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001460', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '433', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p22980' => 'bna', 'A01p32340' => 'bna', 'A03p42970' => 'bna', 'A05p25880' => 'bna', 'Aa31LG8G9320' => 'aar', 'Aa31LG8G9330' => 'aar', 'Aa31LG8G9340' => 'aar', 'Aa31sc221G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1034' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1528' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.829' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2222' => 'aag', 'Ah.12g058830' => 'amhyb', 'Ah.12g058840' => 'amhyb', 'AL3G37160' => 'aly', 'AL7G41310' => 'aly', 'Aqoxy5G00395' => 'aox', 'Aqoxy5G00396' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0C8NZA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5185HY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JZ1PRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MD3LS0' => 'arhy', 'AT3G22840' => 'ath', 'AT4G14690' => 'ath', 'ATR0665G054' => 'atr', 'Atru.chr4.2344' => 'acertr', 'Atru.chr4.2346' => 'acertr', 'Atru.chr4.2347' => 'acertr', 'Atru.chr4.2348' => 'acertr', 'Atru.chr4.2355' => 'acertr', 'Atru.chr4.2356' => 'acertr', 'Atru.chr4.2358' => 'acertr', 'Atru.chr4.2359' => 'acertr', 'Atru.chr4.2360' => 'acertr', 'Atru.chr4.2361' => 'acertr', 'AUR62030476' => 'cqu', 'AUR62030478' => 'cqu', 'AUR62030819' => 'cqu', 'AUR62030820' => 'cqu', 'BcaB03g14648' => 'bca', 'BcaB04g20492' => 'bca', 'BcaB06g26399' => 'bca', 'BcaC01g03416' => 'bca', 'BcaC01g03419' => 'bca', 'BcaC01g03421' => 'bca', 'BcaC01g03424' => 'bca', 'BcaC05g28012' => 'bca', 'BcaC09g49212' => 'bca', 'BcaC09g50140' => 'bca', 'BcaNung00346' => 'bca', 'BolC1t02785H' => 'bol', 'BolC1t04095H' => 'bol', 'BolC3t17545H' => 'bol', 'BolC5t32769H' => 'bol', 'BraA01t02211Z' => 'bra', 'BraA01t03359Z' => 'bra', 'BraA03t13441Z' => 'bra', 'BraA05t21476Z' => 'bra', 'C01p28420' => 'bna', 'C01p41350' => 'bna', 'C03p52750' => 'bna', 'C03p52780' => 'bna', 'C05p40270' => 'bna', 'CAN.G1437.9' => 'can', 'CANSAT78G0035' => 'cansat', 'CANSAT78G1036' => 'cansat', 'CANSAT78G2272' => 'cansat', 'CANSAT78G2478' => 'cansat', 'CARHR098700' => 'chi', 'CARHR221120' => 'chi', 'CARHR221150' => 'chi', 'Carub.0003s2297' => 'cru', 'Carub.0007s2749' => 'cru', 'Carub.0007s2750' => 'cru', 'Carub.0007s2751' => 'cru', 'Ca_10849_v3' => 'car', 'Cc03_g04300' => 'ccan', 'CDE02G3648' => 'cde', 'CDE05G0060' => 'cde', 'CDE05G0692' => 'cde', 'CDE05G2285' => 'cde', 'CDE05G2884' => 'cde', 'CDE05G3072' => 'cde', 'Cfa008439' => 'cfa', 'Cfa008441' => 'cfa', 'Cfa008443' => 'cfa', 'Cfa008448' => 'cfa', 'Ciclev10005974m.g' => 'ccl', 'Ciclev10006006m.g' => 'ccl', 'Ciclev10006775m.g' => 'ccl', 'CiPaw.02G120400' => 'cil', 'CiPaw.02G120500' => 'cil', 'CiPaw.02G120600' => 'cil', 'ClCG05G004850' => 'cla', 'COL.COLO4_21566' => 'col', 'Cpa.g.sc44.124' => 'cpa', 'Cre07.g320400' => 'cre', 'Cre07.g320450' => 'cre', 'Cre08.g384650' => 'cre', 'Cre09.g393173' => 'cre', 'Cre09.g394325' => 'cre', 'Cre14.g626750' => 'cre', 'Cre16.g679250' => 'cre', 'CsaV3_3G012890' => 'csa', 'CSS0010865' => 'camsi', 'CSS0044338' => 'camsi', 'DCAR_002366' => 'dca', 'DCAR_030687' => 'dca', 'DCAR_030688' => 'dca', 'Dinv14047' => 'din', 'Dinv14048' => 'din', 'Duzib151G0105' => 'dzi', 'Duzib151G0114' => 'dzi', 'Duzib212G1029' => 'dzi', 'ECA232G3536' => 'eca', 'ECA240G0786' => 'eca', 'ECA240G1802' => 'eca', 'ECA240G3760' => 'eca', 'ECA240G3920' => 'eca', 'EL10Ac5g12536' => 'bvu', 'EL10Ac5g12537' => 'bvu', 'EL10Ac5g12538' => 'bvu', 'Eucgr.B01004' => 'egr', 'Eucgr.B01006' => 'egr', 'Eucgr.B01007' => 'egr', 'Eucgr.B01008' => 'egr', 'Eucgr.B01895' => 'egr', 'Eucgr.B01896' => 'egr', 'FAN04G1456' => 'fan', 'FAN08G1769' => 'fan', 'FAN08G2160' => 'fan', 'FAN13G2403' => 'fan', 'FAN13G3303' => 'fan', 'FAN15G2435' => 'fan', 'FAN17G0672' => 'fan', 'FAN17G2441' => 'fan', 'FAN18G1024' => 'fan', 'FAN22G1458' => 'fan', 'FAN24G0037' => 'fan', 'FAN24G0429' => 'fan', 'FAN24G2387' => 'fan', 'FAN27G2746' => 'fan', 'FvH4_2g20400' => 'fve', 'FvH4_2g20420' => 'fve', 'FvH4_2g20430' => 'fve', 'FvH4_4g01270' => 'fve', 'FvH4_4g01290' => 'fve', 'FvH4_4g01300' => 'fve', 'FvH4_4g01310' => 'fve', 'FvH4_4g01330' => 'fve', 'FvH4_5g09070' => 'fve', 'Glyma.10G243800' => 'gma', 'Glyma.20G150600' => 'gma', 'Gohir.A09G219200' => 'ghi', 'Gohir.A09G219300' => 'ghi', 'Gohir.D09G221400' => 'ghi', 'Gohir.D09G221500' => 'ghi', 'Gorai.006G242600' => 'gra', 'Gorai.006G242700' => 'gra', 'GSVIVG01018044001' => 'vvi', 'HanXRQChr03g0083821' => 'han', 'HanXRQChr03g0083841' => 'han', 'HanXRQChr03g0083881' => 'han', 'HanXRQChr03g0083901' => 'han', 'HanXRQChr03g0083921' => 'han', 'HanXRQChr03g0085331' => 'han', 'HanXRQChr03g0085361' => 'han', 'HanXRQChr03g0085411' => 'han', 'HanXRQChr03g0085421' => 'han', 'HanXRQChr03g0085431' => 'han', 'HanXRQChr08g0221991' => 'han', 'HanXRQChr11g0336061' => 'han', 'HanXRQChr11g0336411' => 'han', 'Haze_11234' => 'cav', 'Hma1.2p1_0549F.1_g177010' => 'hma', 'Hma1.2p1_0602F.1_g187630' => 'hma', 'Hund14876' => 'sun', 'Hund14879' => 'sun', 'Lalb_Chr06g0160741' => 'lal', 'Lalb_Chr21g0304781' => 'lal', 'Lj3A726G19' => 'lonja', 'Lj3A726T23' => 'lonja', 'Lj3A726T24' => 'lonja', 'Lj3A726T25' => 'lonja', 'Lj3A727T17' => 'lonja', 'Lj3C726T0' => 'lonja', 'Lj3C726T2' => 'lonja', 'Lj3P725T35' => 'lonja', 'Lj3P727T10' => 'lonja', 'Lj3P727T12' => 'lonja', 'Lj3P727T14' => 'lonja', 'Lj5g0023109' => 'lja', 'Lj6P646T44' => 'lonja', 'Lsat_1_v5_gn_6_75760' => 'lsa', 'Lsat_1_v5_gn_6_75800' => 'lsa', 'Lsat_1_v5_gn_6_75900' => 'lsa', 'Lsat_1_v5_gn_6_76240' => 'lsa', 'Lsat_1_v5_gn_6_76441' => 'lsa', 'Lsat_1_v5_gn_6_76700' => 'lsa', 'Lsat_1_v5_gn_6_76760' => 'lsa', 'Manes.15G033100' => 'mes', 'Mapoly0004s0074' => 'mpo', 'Mapoly0004s0075' => 'mpo', 'Mapoly0004s0163' => 'mpo', 'Mapoly0004s0164' => 'mpo', 'Mapoly0021s0018' => 'mpo', 'Mapoly0041s0136' => 'mpo', 'Mapoly0041s0137' => 'mpo', 'Mapoly0041s0138' => 'mpo', 'Mapoly0041s0139' => 'mpo', 'Mapoly0041s0141' => 'mpo', 'Mapoly0041s0142' => 'mpo', 'Mapoly0041s0143' => 'mpo', 'Mapoly0041s0144' => 'mpo', 'Mapoly0041s0145' => 'mpo', 'Mapoly0047s0106' => 'mpo', 'Mapoly0047s0108' => 'mpo', 'Mapoly0050s0051' => 'mpo', 'Mapoly0050s0052' => 'mpo', 'Mapoly0050s0053' => 'mpo', 'Mapoly0058s0013' => 'mpo', 'Mapoly0091s0078' => 'mpo', 'Mapoly0091s0079' => 'mpo', 'Mapoly0091s0080' => 'mpo', 'Mapoly0091s0081' => 'mpo', 'Mapoly0278s0004' => 'mpo', 'Mapoly0278s0005' => 'mpo', 'Mapoly0278s0006' => 'mpo', 'MBI11_g30648_MAGBIO' => 'mbi', 'MCO03G194' => 'mco', 'MCO03G590' => 'mco', 'MCO07G312' => 'mco', 'MCO10G318' => 'mco', 'MCO12G244' => 'mco', 'MCO13G148' => 'mco', 'MCO13G194' => 'mco', 'MCO16G238' => 'mco', 'MD06G1134100' => 'mdo', 'MD13G1200100' => 'mdo', 'MD13G1200300' => 'mdo', 'MD13G1200600' => 'mdo', 'MD14G1150400' => 'mdo', 'MD16G1200000' => 'mdo', 'Medtr1g102570' => 'mtr', 'Medtr1g102780' => 'mtr', 'Medtr1g102800' => 'mtr', 'Medtr1g102810' => 'mtr', 'Medtr1g102830' => 'mtr', 'MELO3C006499.2' => 'cme', 'Migut.G00385' => 'egut', 'MSTRG.4063' => 'ama', 'Nitab4.5_0000090g0260' => 'nta', 'Nitab4.5_0000977g0030' => 'nta', 'Nitab4.5_0002541g0040' => 'nta', 'Nitab4.5_0007068g0040' => 'nta', 'Nn005s41408' => 'nnu', 'Nn005s41410' => 'nnu', 'Oeu010310.1' => 'oeu', 'Oeu010311.1' => 'oeu', 'Oeu043472.1' => 'oeu', 'Os01g0246400' => 'osa', 'Os04g0267950' => 'osa', 'Os07g0178700' => 'osa', 'Os07g0178800' => 'osa', 'Peaxi162Scf00316g00046' => 'pax', 'Peaxi162Scf00316g00049' => 'pax', 'Peaxi162Scf00316g00059' => 'pax', 'Peaxi162Scf00316g00328' => 'pax', 'Peaxi162Scf00316g00329' => 'pax', 'Peaxi162Scf00316g00411' => 'pax', 'Peaxi162Scf00316g00521' => 'pax', 'Peaxi162Scf00492g00068' => 'pax', 'Peaxi162Scf35631g00002' => 'pax', 'PGR142G3720' => 'pgr', 'PGSC0003DMG400006442' => 'stu', 'Phvul.007G062000' => 'pvu', 'Potri.008G157750' => 'ptr', 'Potri.008G157900' => 'ptr', 'Potri.008G158000' => 'ptr', 'Potri.008G158200' => 'ptr', 'Pp3c11_7280' => 'ppa', 'Pp3c11_7980' => 'ppa', 'Pp3c12_19450' => 'ppa', 'Pp3c14_1480' => 'ppa', 'Pp3c14_1501' => 'ppa', 'Pp3c16_4900' => 'ppa', 'Pp3c16_5010' => 'ppa', 'Pp3c16_5060' => 'ppa', 'Pp3c19_18250' => 'ppa', 'Pp3c23_8530' => 'ppa', 'Pp3c23_8550' => 'ppa', 'Pp3c24_9670' => 'ppa', 'Pp3c2_21390' => 'ppa', 'Pp3c2_31380' => 'ppa', 'Pp3c3_16620' => 'ppa', 'Pp3c3_8090' => 'ppa', 'Pp3c3_8110' => 'ppa', 'Pp3c3_8130' => 'ppa', 'Pp3c3_8150' => 'ppa', 'Pp3c4_14320' => 'ppa', 'Pp3c6_2560' => 'ppa', 'Pp3c9_16700' => 'ppa', 'PRCOL_00000234' => 'pco', 'PRCOL_00000235' => 'pco', 'PRCOL_00000777' => 'pco', 'PRCOL_00002344' => 'pco', 'PRCOL_00002372' => 'pco', 'PRCOL_00006120' => 'pco', 'Prupe.1G021400' => 'ppe', 'Prupe.1G021500' => 'ppe', 'Prupe.1G021600' => 'ppe', 'Prupe.1G021700' => 'ppe', 'Prupe.1G021800' => 'ppe', 'Prupe.5G145100' => 'ppe', 'Psat6g204040' => 'psa', 'Psat6g204800' => 'psa', 'Psat6g204920' => 'psa', 'Psat6g204960' => 'psa', 'Psat6g205080' => 'psa', 'PSO017G0271' => 'pso', 'PSO017G1276' => 'pso', 'PSO017G1429' => 'pso', 'PSO017G1861' => 'pso', 'PSO017G2787' => 'pso', 'PSO017G4466' => 'pso', 'PSO017G5118' => 'pso', 'PSO017G5420' => 'pso', 'PSO063G3678' => 'pso', 'PSO210G0546' => 'pso', 'PSO317G0001' => 'pso', 'PSO357G0512' => 'pso', 'PSO478G2682' => 'pso', 'PSO647G0001' => 'pso', 'PSO675G0001' => 'pso', 'PSO675G2699' => 'pso', 'PSO675G2849' => 'pso', 'PSO675G4991' => 'pso', 'PSO689G0001' => 'pso', 'QL06p000916' => 'qlo', 'QL06p000921' => 'qlo', 'QL06p001398' => 'qlo', 'QL06p001407' => 'qlo', 'QL06p002031' => 'qlo', 'RcHm_v2.0_Chr4g0387791' => 'rch', 'RcHm_v2.0_Chr4g0387801' => 'rch', 'RcHm_v2.0_Chr6g0286501' => 'rch', 'RcHm_v2.0_Chr6g0286511' => 'rch', 'RcHm_v2.0_Chr6g0286521' => 'rch', 'RcHm_v2.0_Chr6g0286531' => 'rch', 'RcHm_v2.0_Chr7g0189141' => 'rch', 'Rhsim02G0028700' => 'rsi', 'Rhsim02G0028800' => 'rsi', 'Rhsim02G0028900' => 'rsi', 'Rhsim02G0029000' => 'rsi', 'Rhsim02G0029100' => 'rsi', 'Rhsim02G0029200' => 'rsi', 'Rhsim02G0029300' => 'rsi', 'Rhsim02G0029400' => 'rsi', 'Rhsim02G0029500' => 'rsi', 'Rhsim02G0029600' => 'rsi', 'RhsimUnG0024000' => 'rsi', 'RhsimUnG0024100' => 'rsi', 'RhsimUnG0024200' => 'rsi', 'RhsimUnG0024300' => 'rsi', 'RhsimUnG0024400' => 'rsi', 'RhsimUnG0024500' => 'rsi', 'RhsimUnG0024700' => 'rsi', 'RhsimUnG0024800' => 'rsi', 'RhsimUnG0024900' => 'rsi', 'RhsimUnG0025100' => 'rsi', 'Sabra08G0120200' => 'sbr', 'Sabra08G0120300' => 'sbr', 'Sabra08G0120500' => 'sbr', 'Sabra08G0120600' => 'sbr', 'Sabra10G0158900' => 'sbr', 'SalBow2G3492' => 'sbo', 'Sc13g0004760' => 'sci', 'Sc13g0004770' => 'sci', 'Sed0003417' => 'sed', 'Sed0019750' => 'sed', 'SEGI_03419' => 'sgi', 'SEGI_05907' => 'sgi', 'SEGI_10682' => 'sgi', 'SEGI_13528' => 'sgi', 'SEGI_16081' => 'sgi', 'SEGI_19370' => 'sgi', 'SEGI_21015' => 'sgi', 'SEGI_21944' => 'sgi', 'SEGI_32906' => 'sgi', 'SEGI_33093' => 'sgi', 'SEGI_36110' => 'sgi', 'SEGI_40397' => 'sgi', 'SGA_v2.0_scaffold191G40426' => 'sas', 'SGA_v2.0_scaffold353G49717' => 'sas', 'SGA_v2.0_scaffold50G18550' => 'sas', 'SMO119G0173' => 'smo', 'SMO172G0002' => 'smo', 'Solyc09g082690.3' => 'sly', 'Solyc09g082700.2' => 'sly', 'Sopen09g031550' => 'spe', 'Sopen09g031560' => 'spe', 'Sp3g20540' => 'spa', 'Sp7g07580' => 'spa', 'TAR134G0002' => 'tar', 'TAR236G0001' => 'tar', 'TAR365G0892' => 'tar', 'TAR636G0166' => 'tar', 'TAR636G0646' => 'tar', 'TAR636G0869' => 'tar', 'TAR636G1317' => 'tar', 'TAR636G1744' => 'tar', 'TAR636G3358' => 'tar', 'TAR636G3436' => 'tar', 'THA.LOC104803047' => 'tha', 'Thecc.04G238900' => 'tca', 'Thhalv10021557m.g' => 'esa', 'Thhalv10026318m.g' => 'esa', 'Thhalv10026335m.g' => 'esa', 'TPR.G17433' => 'tpr', 'TPR.G18915' => 'tpr', 'TPR.G26125' => 'tpr', 'TWI09G0677' => 'twi', 'TWI73G0287' => 'twi', 'unitig_748.g8326' => 'ugi', 'vmacro15370' => 'vma', 'vmacro15371' => 'vma', 'vmacro15372' => 'vma', 'vmacro15373' => 'vma', 'vmacro15374' => 'vma', 'VMungo0720G2826' => 'vmu', 'Zm00001eb116960' => 'zma', 'Zm00001eb301260' => 'zma', 'Zm00001eb301270' => 'zma' ) $gf_id = 'HOM05D001460' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001460' ) $data_identifier = 'HOM05D001460' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 4, 'aag' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 2, 'aox' => (int) 2, 'arhy' => (int) 4, 'ath' => (int) 2, 'atr' => (int) 1, 'acertr' => (int) 10, 'cqu' => (int) 4, 'bca' => (int) 11, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 1, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 1, 'ccan' => (int) 1, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 1, 'col' => (int) 1, 'cpa' => (int) 1, 'cre' => (int) 7, 'csa' => (int) 1, 'camsi' => (int) 2, 'dca' => (int) 3, 'din' => (int) 2, 'dzi' => (int) 3, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 14, 'fve' => (int) 9, 'gma' => (int) 2, 'ghi' => (int) 4, 'gra' => (int) 2, 'vvi' => (int) 1, 'han' => (int) 13, 'cav' => (int) 1, 'hma' => (int) 2, 'sun' => (int) 2, 'lal' => (int) 2, 'lonja' => (int) 12, 'lja' => (int) 1, 'lsa' => (int) 7, 'mes' => (int) 1, 'mpo' => (int) 27, 'mbi' => (int) 1, 'mco' => (int) 8, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 1, 'egut' => (int) 1, 'ama' => (int) 1, 'nta' => (int) 4, 'nnu' => (int) 2, 'oeu' => (int) 3, 'osa' => (int) 4, 'pax' => (int) 9, 'pgr' => (int) 1, 'stu' => (int) 1, 'pvu' => (int) 1, 'ptr' => (int) 4, 'ppa' => (int) 22, 'pco' => (int) 6, 'ppe' => (int) 6, 'psa' => (int) 5, 'pso' => (int) 19, 'qlo' => (int) 5, 'rch' => (int) 7, 'rsi' => (int) 20, 'sbr' => (int) 5, 'sbo' => (int) 1, 'sci' => (int) 2, 'sed' => (int) 2, 'sgi' => (int) 12, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 2, 'tar' => (int) 10, 'tha' => (int) 1, 'tca' => (int) 1, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 2, 'ugi' => (int) 1, 'vma' => (int) 5, 'vmu' => (int) 1, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb301270' $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' => 'HOM05D001460', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '433', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p22980' => 'bna', 'A01p32340' => 'bna', 'A03p42970' => 'bna', 'A05p25880' => 'bna', 'Aa31LG8G9320' => 'aar', 'Aa31LG8G9330' => 'aar', 'Aa31LG8G9340' => 'aar', 'Aa31sc221G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1034' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1528' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.829' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2222' => 'aag', 'Ah.12g058830' => 'amhyb', 'Ah.12g058840' => 'amhyb', 'AL3G37160' => 'aly', 'AL7G41310' => 'aly', 'Aqoxy5G00395' => 'aox', 'Aqoxy5G00396' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0C8NZA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5185HY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JZ1PRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MD3LS0' => 'arhy', 'AT3G22840' => 'ath', 'AT4G14690' => 'ath', 'ATR0665G054' => 'atr', 'Atru.chr4.2344' => 'acertr', 'Atru.chr4.2346' => 'acertr', 'Atru.chr4.2347' => 'acertr', 'Atru.chr4.2348' => 'acertr', 'Atru.chr4.2355' => 'acertr', 'Atru.chr4.2356' => 'acertr', 'Atru.chr4.2358' => 'acertr', 'Atru.chr4.2359' => 'acertr', 'Atru.chr4.2360' => 'acertr', 'Atru.chr4.2361' => 'acertr', 'AUR62030476' => 'cqu', 'AUR62030478' => 'cqu', 'AUR62030819' => 'cqu', 'AUR62030820' => 'cqu', 'BcaB03g14648' => 'bca', 'BcaB04g20492' => 'bca', 'BcaB06g26399' => 'bca', 'BcaC01g03416' => 'bca', 'BcaC01g03419' => 'bca', 'BcaC01g03421' => 'bca', 'BcaC01g03424' => 'bca', 'BcaC05g28012' => 'bca', 'BcaC09g49212' => 'bca', 'BcaC09g50140' => 'bca', 'BcaNung00346' => 'bca', 'BolC1t02785H' => 'bol', 'BolC1t04095H' => 'bol', 'BolC3t17545H' => 'bol', 'BolC5t32769H' => 'bol', 'BraA01t02211Z' => 'bra', 'BraA01t03359Z' => 'bra', 'BraA03t13441Z' => 'bra', 'BraA05t21476Z' => 'bra', 'C01p28420' => 'bna', 'C01p41350' => 'bna', 'C03p52750' => 'bna', 'C03p52780' => 'bna', 'C05p40270' => 'bna', 'CAN.G1437.9' => 'can', 'CANSAT78G0035' => 'cansat', 'CANSAT78G1036' => 'cansat', 'CANSAT78G2272' => 'cansat', 'CANSAT78G2478' => 'cansat', 'CARHR098700' => 'chi', 'CARHR221120' => 'chi', 'CARHR221150' => 'chi', 'Carub.0003s2297' => 'cru', 'Carub.0007s2749' => 'cru', 'Carub.0007s2750' => 'cru', 'Carub.0007s2751' => 'cru', 'Ca_10849_v3' => 'car', 'Cc03_g04300' => 'ccan', 'CDE02G3648' => 'cde', 'CDE05G0060' => 'cde', 'CDE05G0692' => 'cde', 'CDE05G2285' => 'cde', 'CDE05G2884' => 'cde', 'CDE05G3072' => 'cde', 'Cfa008439' => 'cfa', 'Cfa008441' => 'cfa', 'Cfa008443' => 'cfa', 'Cfa008448' => 'cfa', 'Ciclev10005974m.g' => 'ccl', 'Ciclev10006006m.g' => 'ccl', 'Ciclev10006775m.g' => 'ccl', 'CiPaw.02G120400' => 'cil', 'CiPaw.02G120500' => 'cil', 'CiPaw.02G120600' => 'cil', 'ClCG05G004850' => 'cla', 'COL.COLO4_21566' => 'col', 'Cpa.g.sc44.124' => 'cpa', 'Cre07.g320400' => 'cre', 'Cre07.g320450' => 'cre', 'Cre08.g384650' => 'cre', 'Cre09.g393173' => 'cre', 'Cre09.g394325' => 'cre', 'Cre14.g626750' => 'cre', 'Cre16.g679250' => 'cre', 'CsaV3_3G012890' => 'csa', 'CSS0010865' => 'camsi', 'CSS0044338' => 'camsi', 'DCAR_002366' => 'dca', 'DCAR_030687' => 'dca', 'DCAR_030688' => 'dca', 'Dinv14047' => 'din', 'Dinv14048' => 'din', 'Duzib151G0105' => 'dzi', 'Duzib151G0114' => 'dzi', 'Duzib212G1029' => 'dzi', 'ECA232G3536' => 'eca', 'ECA240G0786' => 'eca', 'ECA240G1802' => 'eca', 'ECA240G3760' => 'eca', 'ECA240G3920' => 'eca', 'EL10Ac5g12536' => 'bvu', 'EL10Ac5g12537' => 'bvu', 'EL10Ac5g12538' => 'bvu', 'Eucgr.B01004' => 'egr', 'Eucgr.B01006' => 'egr', 'Eucgr.B01007' => 'egr', 'Eucgr.B01008' => 'egr', 'Eucgr.B01895' => 'egr', 'Eucgr.B01896' => 'egr', 'FAN04G1456' => 'fan', 'FAN08G1769' => 'fan', 'FAN08G2160' => 'fan', 'FAN13G2403' => 'fan', 'FAN13G3303' => 'fan', 'FAN15G2435' => 'fan', 'FAN17G0672' => 'fan', 'FAN17G2441' => 'fan', 'FAN18G1024' => 'fan', 'FAN22G1458' => 'fan', 'FAN24G0037' => 'fan', 'FAN24G0429' => 'fan', 'FAN24G2387' => 'fan', 'FAN27G2746' => 'fan', 'FvH4_2g20400' => 'fve', 'FvH4_2g20420' => 'fve', 'FvH4_2g20430' => 'fve', 'FvH4_4g01270' => 'fve', 'FvH4_4g01290' => 'fve', 'FvH4_4g01300' => 'fve', 'FvH4_4g01310' => 'fve', 'FvH4_4g01330' => 'fve', 'FvH4_5g09070' => 'fve', 'Glyma.10G243800' => 'gma', 'Glyma.20G150600' => 'gma', 'Gohir.A09G219200' => 'ghi', 'Gohir.A09G219300' => 'ghi', 'Gohir.D09G221400' => 'ghi', 'Gohir.D09G221500' => 'ghi', 'Gorai.006G242600' => 'gra', 'Gorai.006G242700' => 'gra', 'GSVIVG01018044001' => 'vvi', 'HanXRQChr03g0083821' => 'han', 'HanXRQChr03g0083841' => 'han', 'HanXRQChr03g0083881' => 'han', 'HanXRQChr03g0083901' => 'han', 'HanXRQChr03g0083921' => 'han', 'HanXRQChr03g0085331' => 'han', 'HanXRQChr03g0085361' => 'han', 'HanXRQChr03g0085411' => 'han', 'HanXRQChr03g0085421' => 'han', 'HanXRQChr03g0085431' => 'han', 'HanXRQChr08g0221991' => 'han', 'HanXRQChr11g0336061' => 'han', 'HanXRQChr11g0336411' => 'han', 'Haze_11234' => 'cav', 'Hma1.2p1_0549F.1_g177010' => 'hma', 'Hma1.2p1_0602F.1_g187630' => 'hma', 'Hund14876' => 'sun', 'Hund14879' => 'sun', 'Lalb_Chr06g0160741' => 'lal', 'Lalb_Chr21g0304781' => 'lal', 'Lj3A726G19' => 'lonja', 'Lj3A726T23' => 'lonja', 'Lj3A726T24' => 'lonja', 'Lj3A726T25' => 'lonja', 'Lj3A727T17' => 'lonja', 'Lj3C726T0' => 'lonja', 'Lj3C726T2' => 'lonja', 'Lj3P725T35' => 'lonja', 'Lj3P727T10' => 'lonja', 'Lj3P727T12' => 'lonja', 'Lj3P727T14' => 'lonja', 'Lj5g0023109' => 'lja', 'Lj6P646T44' => 'lonja', 'Lsat_1_v5_gn_6_75760' => 'lsa', 'Lsat_1_v5_gn_6_75800' => 'lsa', 'Lsat_1_v5_gn_6_75900' => 'lsa', 'Lsat_1_v5_gn_6_76240' => 'lsa', 'Lsat_1_v5_gn_6_76441' => 'lsa', 'Lsat_1_v5_gn_6_76700' => 'lsa', 'Lsat_1_v5_gn_6_76760' => 'lsa', 'Manes.15G033100' => 'mes', 'Mapoly0004s0074' => 'mpo', 'Mapoly0004s0075' => 'mpo', 'Mapoly0004s0163' => 'mpo', 'Mapoly0004s0164' => 'mpo', 'Mapoly0021s0018' => 'mpo', 'Mapoly0041s0136' => 'mpo', 'Mapoly0041s0137' => 'mpo', 'Mapoly0041s0138' => 'mpo', 'Mapoly0041s0139' => 'mpo', 'Mapoly0041s0141' => 'mpo', 'Mapoly0041s0142' => 'mpo', 'Mapoly0041s0143' => 'mpo', 'Mapoly0041s0144' => 'mpo', 'Mapoly0041s0145' => 'mpo', 'Mapoly0047s0106' => 'mpo', 'Mapoly0047s0108' => 'mpo', 'Mapoly0050s0051' => 'mpo', 'Mapoly0050s0052' => 'mpo', 'Mapoly0050s0053' => 'mpo', 'Mapoly0058s0013' => 'mpo', 'Mapoly0091s0078' => 'mpo', 'Mapoly0091s0079' => 'mpo', 'Mapoly0091s0080' => 'mpo', 'Mapoly0091s0081' => 'mpo', 'Mapoly0278s0004' => 'mpo', 'Mapoly0278s0005' => 'mpo', 'Mapoly0278s0006' => 'mpo', 'MBI11_g30648_MAGBIO' => 'mbi', 'MCO03G194' => 'mco', 'MCO03G590' => 'mco', 'MCO07G312' => 'mco', 'MCO10G318' => 'mco', 'MCO12G244' => 'mco', 'MCO13G148' => 'mco', 'MCO13G194' => 'mco', 'MCO16G238' => 'mco', 'MD06G1134100' => 'mdo', 'MD13G1200100' => 'mdo', 'MD13G1200300' => 'mdo', 'MD13G1200600' => 'mdo', 'MD14G1150400' => 'mdo', 'MD16G1200000' => 'mdo', 'Medtr1g102570' => 'mtr', 'Medtr1g102780' => 'mtr', 'Medtr1g102800' => 'mtr', 'Medtr1g102810' => 'mtr', 'Medtr1g102830' => 'mtr', 'MELO3C006499.2' => 'cme', 'Migut.G00385' => 'egut', 'MSTRG.4063' => 'ama', 'Nitab4.5_0000090g0260' => 'nta', 'Nitab4.5_0000977g0030' => 'nta', 'Nitab4.5_0002541g0040' => 'nta', 'Nitab4.5_0007068g0040' => 'nta', 'Nn005s41408' => 'nnu', 'Nn005s41410' => 'nnu', 'Oeu010310.1' => 'oeu', 'Oeu010311.1' => 'oeu', 'Oeu043472.1' => 'oeu', 'Os01g0246400' => 'osa', 'Os04g0267950' => 'osa', 'Os07g0178700' => 'osa', 'Os07g0178800' => 'osa', 'Peaxi162Scf00316g00046' => 'pax', 'Peaxi162Scf00316g00049' => 'pax', 'Peaxi162Scf00316g00059' => 'pax', 'Peaxi162Scf00316g00328' => 'pax', 'Peaxi162Scf00316g00329' => 'pax', 'Peaxi162Scf00316g00411' => 'pax', 'Peaxi162Scf00316g00521' => 'pax', 'Peaxi162Scf00492g00068' => 'pax', 'Peaxi162Scf35631g00002' => 'pax', 'PGR142G3720' => 'pgr', 'PGSC0003DMG400006442' => 'stu', 'Phvul.007G062000' => 'pvu', 'Potri.008G157750' => 'ptr', 'Potri.008G157900' => 'ptr', 'Potri.008G158000' => 'ptr', 'Potri.008G158200' => 'ptr', 'Pp3c11_7280' => 'ppa', 'Pp3c11_7980' => 'ppa', 'Pp3c12_19450' => 'ppa', 'Pp3c14_1480' => 'ppa', 'Pp3c14_1501' => 'ppa', 'Pp3c16_4900' => 'ppa', 'Pp3c16_5010' => 'ppa', 'Pp3c16_5060' => 'ppa', 'Pp3c19_18250' => 'ppa', 'Pp3c23_8530' => 'ppa', 'Pp3c23_8550' => 'ppa', 'Pp3c24_9670' => 'ppa', 'Pp3c2_21390' => 'ppa', 'Pp3c2_31380' => 'ppa', 'Pp3c3_16620' => 'ppa', 'Pp3c3_8090' => 'ppa', 'Pp3c3_8110' => 'ppa', 'Pp3c3_8130' => 'ppa', 'Pp3c3_8150' => 'ppa', 'Pp3c4_14320' => 'ppa', 'Pp3c6_2560' => 'ppa', 'Pp3c9_16700' => 'ppa', 'PRCOL_00000234' => 'pco', 'PRCOL_00000235' => 'pco', 'PRCOL_00000777' => 'pco', 'PRCOL_00002344' => 'pco', 'PRCOL_00002372' => 'pco', 'PRCOL_00006120' => 'pco', 'Prupe.1G021400' => 'ppe', 'Prupe.1G021500' => 'ppe', 'Prupe.1G021600' => 'ppe', 'Prupe.1G021700' => 'ppe', 'Prupe.1G021800' => 'ppe', 'Prupe.5G145100' => 'ppe', 'Psat6g204040' => 'psa', 'Psat6g204800' => 'psa', 'Psat6g204920' => 'psa', 'Psat6g204960' => 'psa', 'Psat6g205080' => 'psa', 'PSO017G0271' => 'pso', 'PSO017G1276' => 'pso', 'PSO017G1429' => 'pso', 'PSO017G1861' => 'pso', 'PSO017G2787' => 'pso', 'PSO017G4466' => 'pso', 'PSO017G5118' => 'pso', 'PSO017G5420' => 'pso', 'PSO063G3678' => 'pso', 'PSO210G0546' => 'pso', 'PSO317G0001' => 'pso', 'PSO357G0512' => 'pso', 'PSO478G2682' => 'pso', 'PSO647G0001' => 'pso', 'PSO675G0001' => 'pso', 'PSO675G2699' => 'pso', 'PSO675G2849' => 'pso', 'PSO675G4991' => 'pso', 'PSO689G0001' => 'pso', 'QL06p000916' => 'qlo', 'QL06p000921' => 'qlo', 'QL06p001398' => 'qlo', 'QL06p001407' => 'qlo', 'QL06p002031' => 'qlo', 'RcHm_v2.0_Chr4g0387791' => 'rch', 'RcHm_v2.0_Chr4g0387801' => 'rch', 'RcHm_v2.0_Chr6g0286501' => 'rch', 'RcHm_v2.0_Chr6g0286511' => 'rch', 'RcHm_v2.0_Chr6g0286521' => 'rch', 'RcHm_v2.0_Chr6g0286531' => 'rch', 'RcHm_v2.0_Chr7g0189141' => 'rch', 'Rhsim02G0028700' => 'rsi', 'Rhsim02G0028800' => 'rsi', 'Rhsim02G0028900' => 'rsi', 'Rhsim02G0029000' => 'rsi', 'Rhsim02G0029100' => 'rsi', 'Rhsim02G0029200' => 'rsi', 'Rhsim02G0029300' => 'rsi', 'Rhsim02G0029400' => 'rsi', 'Rhsim02G0029500' => 'rsi', 'Rhsim02G0029600' => 'rsi', 'RhsimUnG0024000' => 'rsi', 'RhsimUnG0024100' => 'rsi', 'RhsimUnG0024200' => 'rsi', 'RhsimUnG0024300' => 'rsi', 'RhsimUnG0024400' => 'rsi', 'RhsimUnG0024500' => 'rsi', 'RhsimUnG0024700' => 'rsi', 'RhsimUnG0024800' => 'rsi', 'RhsimUnG0024900' => 'rsi', 'RhsimUnG0025100' => 'rsi', 'Sabra08G0120200' => 'sbr', 'Sabra08G0120300' => 'sbr', 'Sabra08G0120500' => 'sbr', 'Sabra08G0120600' => 'sbr', 'Sabra10G0158900' => 'sbr', 'SalBow2G3492' => 'sbo', 'Sc13g0004760' => 'sci', 'Sc13g0004770' => 'sci', 'Sed0003417' => 'sed', 'Sed0019750' => 'sed', 'SEGI_03419' => 'sgi', 'SEGI_05907' => 'sgi', 'SEGI_10682' => 'sgi', 'SEGI_13528' => 'sgi', 'SEGI_16081' => 'sgi', 'SEGI_19370' => 'sgi', 'SEGI_21015' => 'sgi', 'SEGI_21944' => 'sgi', 'SEGI_32906' => 'sgi', 'SEGI_33093' => 'sgi', 'SEGI_36110' => 'sgi', 'SEGI_40397' => 'sgi', 'SGA_v2.0_scaffold191G40426' => 'sas', 'SGA_v2.0_scaffold353G49717' => 'sas', 'SGA_v2.0_scaffold50G18550' => 'sas', 'SMO119G0173' => 'smo', 'SMO172G0002' => 'smo', 'Solyc09g082690.3' => 'sly', 'Solyc09g082700.2' => 'sly', 'Sopen09g031550' => 'spe', 'Sopen09g031560' => 'spe', 'Sp3g20540' => 'spa', 'Sp7g07580' => 'spa', 'TAR134G0002' => 'tar', 'TAR236G0001' => 'tar', 'TAR365G0892' => 'tar', 'TAR636G0166' => 'tar', 'TAR636G0646' => 'tar', 'TAR636G0869' => 'tar', 'TAR636G1317' => 'tar', 'TAR636G1744' => 'tar', 'TAR636G3358' => 'tar', 'TAR636G3436' => 'tar', 'THA.LOC104803047' => 'tha', 'Thecc.04G238900' => 'tca', 'Thhalv10021557m.g' => 'esa', 'Thhalv10026318m.g' => 'esa', 'Thhalv10026335m.g' => 'esa', 'TPR.G17433' => 'tpr', 'TPR.G18915' => 'tpr', 'TPR.G26125' => 'tpr', 'TWI09G0677' => 'twi', 'TWI73G0287' => 'twi', 'unitig_748.g8326' => 'ugi', 'vmacro15370' => 'vma', 'vmacro15371' => 'vma', 'vmacro15372' => 'vma', 'vmacro15373' => 'vma', 'vmacro15374' => 'vma', 'VMungo0720G2826' => 'vmu', 'Zm00001eb116960' => 'zma', 'Zm00001eb301260' => 'zma', 'Zm00001eb301270' => 'zma' ), 'gf_id' => 'HOM05D001460', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001460' ), 'data_identifier' => 'HOM05D001460', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001460', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '433', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p22980' => 'bna', 'A01p32340' => 'bna', 'A03p42970' => 'bna', 'A05p25880' => 'bna', 'Aa31LG8G9320' => 'aar', 'Aa31LG8G9330' => 'aar', 'Aa31LG8G9340' => 'aar', 'Aa31sc221G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1034' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1528' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.829' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2222' => 'aag', 'Ah.12g058830' => 'amhyb', 'Ah.12g058840' => 'amhyb', 'AL3G37160' => 'aly', 'AL7G41310' => 'aly', 'Aqoxy5G00395' => 'aox', 'Aqoxy5G00396' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0C8NZA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5185HY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JZ1PRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MD3LS0' => 'arhy', 'AT3G22840' => 'ath', 'AT4G14690' => 'ath', 'ATR0665G054' => 'atr', 'Atru.chr4.2344' => 'acertr', 'Atru.chr4.2346' => 'acertr', 'Atru.chr4.2347' => 'acertr', 'Atru.chr4.2348' => 'acertr', 'Atru.chr4.2355' => 'acertr', 'Atru.chr4.2356' => 'acertr', 'Atru.chr4.2358' => 'acertr', 'Atru.chr4.2359' => 'acertr', 'Atru.chr4.2360' => 'acertr', 'Atru.chr4.2361' => 'acertr', 'AUR62030476' => 'cqu', 'AUR62030478' => 'cqu', 'AUR62030819' => 'cqu', 'AUR62030820' => 'cqu', 'BcaB03g14648' => 'bca', 'BcaB04g20492' => 'bca', 'BcaB06g26399' => 'bca', 'BcaC01g03416' => 'bca', 'BcaC01g03419' => 'bca', 'BcaC01g03421' => 'bca', 'BcaC01g03424' => 'bca', 'BcaC05g28012' => 'bca', 'BcaC09g49212' => 'bca', 'BcaC09g50140' => 'bca', 'BcaNung00346' => 'bca', 'BolC1t02785H' => 'bol', 'BolC1t04095H' => 'bol', 'BolC3t17545H' => 'bol', 'BolC5t32769H' => 'bol', 'BraA01t02211Z' => 'bra', 'BraA01t03359Z' => 'bra', 'BraA03t13441Z' => 'bra', 'BraA05t21476Z' => 'bra', 'C01p28420' => 'bna', 'C01p41350' => 'bna', 'C03p52750' => 'bna', 'C03p52780' => 'bna', 'C05p40270' => 'bna', 'CAN.G1437.9' => 'can', 'CANSAT78G0035' => 'cansat', 'CANSAT78G1036' => 'cansat', 'CANSAT78G2272' => 'cansat', 'CANSAT78G2478' => 'cansat', 'CARHR098700' => 'chi', 'CARHR221120' => 'chi', 'CARHR221150' => 'chi', 'Carub.0003s2297' => 'cru', 'Carub.0007s2749' => 'cru', 'Carub.0007s2750' => 'cru', 'Carub.0007s2751' => 'cru', 'Ca_10849_v3' => 'car', 'Cc03_g04300' => 'ccan', 'CDE02G3648' => 'cde', 'CDE05G0060' => 'cde', 'CDE05G0692' => 'cde', 'CDE05G2285' => 'cde', 'CDE05G2884' => 'cde', 'CDE05G3072' => 'cde', 'Cfa008439' => 'cfa', 'Cfa008441' => 'cfa', 'Cfa008443' => 'cfa', 'Cfa008448' => 'cfa', 'Ciclev10005974m.g' => 'ccl', 'Ciclev10006006m.g' => 'ccl', 'Ciclev10006775m.g' => 'ccl', 'CiPaw.02G120400' => 'cil', 'CiPaw.02G120500' => 'cil', 'CiPaw.02G120600' => 'cil', 'ClCG05G004850' => 'cla', 'COL.COLO4_21566' => 'col', 'Cpa.g.sc44.124' => 'cpa', 'Cre07.g320400' => 'cre', 'Cre07.g320450' => 'cre', 'Cre08.g384650' => 'cre', 'Cre09.g393173' => 'cre', 'Cre09.g394325' => 'cre', 'Cre14.g626750' => 'cre', 'Cre16.g679250' => 'cre', 'CsaV3_3G012890' => 'csa', 'CSS0010865' => 'camsi', 'CSS0044338' => 'camsi', 'DCAR_002366' => 'dca', 'DCAR_030687' => 'dca', 'DCAR_030688' => 'dca', 'Dinv14047' => 'din', 'Dinv14048' => 'din', 'Duzib151G0105' => 'dzi', 'Duzib151G0114' => 'dzi', 'Duzib212G1029' => 'dzi', 'ECA232G3536' => 'eca', 'ECA240G0786' => 'eca', 'ECA240G1802' => 'eca', 'ECA240G3760' => 'eca', 'ECA240G3920' => 'eca', 'EL10Ac5g12536' => 'bvu', 'EL10Ac5g12537' => 'bvu', 'EL10Ac5g12538' => 'bvu', 'Eucgr.B01004' => 'egr', 'Eucgr.B01006' => 'egr', 'Eucgr.B01007' => 'egr', 'Eucgr.B01008' => 'egr', 'Eucgr.B01895' => 'egr', 'Eucgr.B01896' => 'egr', 'FAN04G1456' => 'fan', 'FAN08G1769' => 'fan', 'FAN08G2160' => 'fan', 'FAN13G2403' => 'fan', 'FAN13G3303' => 'fan', 'FAN15G2435' => 'fan', 'FAN17G0672' => 'fan', 'FAN17G2441' => 'fan', 'FAN18G1024' => 'fan', 'FAN22G1458' => 'fan', 'FAN24G0037' => 'fan', 'FAN24G0429' => 'fan', 'FAN24G2387' => 'fan', 'FAN27G2746' => 'fan', 'FvH4_2g20400' => 'fve', 'FvH4_2g20420' => 'fve', 'FvH4_2g20430' => 'fve', 'FvH4_4g01270' => 'fve', 'FvH4_4g01290' => 'fve', 'FvH4_4g01300' => 'fve', 'FvH4_4g01310' => 'fve', 'FvH4_4g01330' => 'fve', 'FvH4_5g09070' => 'fve', 'Glyma.10G243800' => 'gma', 'Glyma.20G150600' => 'gma', 'Gohir.A09G219200' => 'ghi', 'Gohir.A09G219300' => 'ghi', 'Gohir.D09G221400' => 'ghi', 'Gohir.D09G221500' => 'ghi', 'Gorai.006G242600' => 'gra', 'Gorai.006G242700' => 'gra', 'GSVIVG01018044001' => 'vvi', 'HanXRQChr03g0083821' => 'han', 'HanXRQChr03g0083841' => 'han', 'HanXRQChr03g0083881' => 'han', 'HanXRQChr03g0083901' => 'han', 'HanXRQChr03g0083921' => 'han', 'HanXRQChr03g0085331' => 'han', 'HanXRQChr03g0085361' => 'han', 'HanXRQChr03g0085411' => 'han', 'HanXRQChr03g0085421' => 'han', 'HanXRQChr03g0085431' => 'han', 'HanXRQChr08g0221991' => 'han', 'HanXRQChr11g0336061' => 'han', 'HanXRQChr11g0336411' => 'han', 'Haze_11234' => 'cav', 'Hma1.2p1_0549F.1_g177010' => 'hma', 'Hma1.2p1_0602F.1_g187630' => 'hma', 'Hund14876' => 'sun', 'Hund14879' => 'sun', 'Lalb_Chr06g0160741' => 'lal', 'Lalb_Chr21g0304781' => 'lal', 'Lj3A726G19' => 'lonja', 'Lj3A726T23' => 'lonja', 'Lj3A726T24' => 'lonja', 'Lj3A726T25' => 'lonja', 'Lj3A727T17' => 'lonja', 'Lj3C726T0' => 'lonja', 'Lj3C726T2' => 'lonja', 'Lj3P725T35' => 'lonja', 'Lj3P727T10' => 'lonja', 'Lj3P727T12' => 'lonja', 'Lj3P727T14' => 'lonja', 'Lj5g0023109' => 'lja', 'Lj6P646T44' => 'lonja', 'Lsat_1_v5_gn_6_75760' => 'lsa', 'Lsat_1_v5_gn_6_75800' => 'lsa', 'Lsat_1_v5_gn_6_75900' => 'lsa', 'Lsat_1_v5_gn_6_76240' => 'lsa', 'Lsat_1_v5_gn_6_76441' => 'lsa', 'Lsat_1_v5_gn_6_76700' => 'lsa', 'Lsat_1_v5_gn_6_76760' => 'lsa', 'Manes.15G033100' => 'mes', 'Mapoly0004s0074' => 'mpo', 'Mapoly0004s0075' => 'mpo', 'Mapoly0004s0163' => 'mpo', 'Mapoly0004s0164' => 'mpo', 'Mapoly0021s0018' => 'mpo', 'Mapoly0041s0136' => 'mpo', 'Mapoly0041s0137' => 'mpo', 'Mapoly0041s0138' => 'mpo', 'Mapoly0041s0139' => 'mpo', 'Mapoly0041s0141' => 'mpo', 'Mapoly0041s0142' => 'mpo', 'Mapoly0041s0143' => 'mpo', 'Mapoly0041s0144' => 'mpo', 'Mapoly0041s0145' => 'mpo', 'Mapoly0047s0106' => 'mpo', 'Mapoly0047s0108' => 'mpo', 'Mapoly0050s0051' => 'mpo', 'Mapoly0050s0052' => 'mpo', 'Mapoly0050s0053' => 'mpo', 'Mapoly0058s0013' => 'mpo', 'Mapoly0091s0078' => 'mpo', 'Mapoly0091s0079' => 'mpo', 'Mapoly0091s0080' => 'mpo', 'Mapoly0091s0081' => 'mpo', 'Mapoly0278s0004' => 'mpo', 'Mapoly0278s0005' => 'mpo', 'Mapoly0278s0006' => 'mpo', 'MBI11_g30648_MAGBIO' => 'mbi', 'MCO03G194' => 'mco', 'MCO03G590' => 'mco', 'MCO07G312' => 'mco', 'MCO10G318' => 'mco', 'MCO12G244' => 'mco', 'MCO13G148' => 'mco', 'MCO13G194' => 'mco', 'MCO16G238' => 'mco', 'MD06G1134100' => 'mdo', 'MD13G1200100' => 'mdo', 'MD13G1200300' => 'mdo', 'MD13G1200600' => 'mdo', 'MD14G1150400' => 'mdo', 'MD16G1200000' => 'mdo', 'Medtr1g102570' => 'mtr', 'Medtr1g102780' => 'mtr', 'Medtr1g102800' => 'mtr', 'Medtr1g102810' => 'mtr', 'Medtr1g102830' => 'mtr', 'MELO3C006499.2' => 'cme', 'Migut.G00385' => 'egut', 'MSTRG.4063' => 'ama', 'Nitab4.5_0000090g0260' => 'nta', 'Nitab4.5_0000977g0030' => 'nta', 'Nitab4.5_0002541g0040' => 'nta', 'Nitab4.5_0007068g0040' => 'nta', 'Nn005s41408' => 'nnu', 'Nn005s41410' => 'nnu', 'Oeu010310.1' => 'oeu', 'Oeu010311.1' => 'oeu', 'Oeu043472.1' => 'oeu', 'Os01g0246400' => 'osa', 'Os04g0267950' => 'osa', 'Os07g0178700' => 'osa', 'Os07g0178800' => 'osa', 'Peaxi162Scf00316g00046' => 'pax', 'Peaxi162Scf00316g00049' => 'pax', 'Peaxi162Scf00316g00059' => 'pax', 'Peaxi162Scf00316g00328' => 'pax', 'Peaxi162Scf00316g00329' => 'pax', 'Peaxi162Scf00316g00411' => 'pax', 'Peaxi162Scf00316g00521' => 'pax', 'Peaxi162Scf00492g00068' => 'pax', 'Peaxi162Scf35631g00002' => 'pax', 'PGR142G3720' => 'pgr', 'PGSC0003DMG400006442' => 'stu', 'Phvul.007G062000' => 'pvu', 'Potri.008G157750' => 'ptr', 'Potri.008G157900' => 'ptr', 'Potri.008G158000' => 'ptr', 'Potri.008G158200' => 'ptr', 'Pp3c11_7280' => 'ppa', 'Pp3c11_7980' => 'ppa', 'Pp3c12_19450' => 'ppa', 'Pp3c14_1480' => 'ppa', 'Pp3c14_1501' => 'ppa', 'Pp3c16_4900' => 'ppa', 'Pp3c16_5010' => 'ppa', 'Pp3c16_5060' => 'ppa', 'Pp3c19_18250' => 'ppa', 'Pp3c23_8530' => 'ppa', 'Pp3c23_8550' => 'ppa', 'Pp3c24_9670' => 'ppa', 'Pp3c2_21390' => 'ppa', 'Pp3c2_31380' => 'ppa', 'Pp3c3_16620' => 'ppa', 'Pp3c3_8090' => 'ppa', 'Pp3c3_8110' => 'ppa', 'Pp3c3_8130' => 'ppa', 'Pp3c3_8150' => 'ppa', 'Pp3c4_14320' => 'ppa', 'Pp3c6_2560' => 'ppa', 'Pp3c9_16700' => 'ppa', 'PRCOL_00000234' => 'pco', 'PRCOL_00000235' => 'pco', 'PRCOL_00000777' => 'pco', 'PRCOL_00002344' => 'pco', 'PRCOL_00002372' => 'pco', 'PRCOL_00006120' => 'pco', 'Prupe.1G021400' => 'ppe', 'Prupe.1G021500' => 'ppe', 'Prupe.1G021600' => 'ppe', 'Prupe.1G021700' => 'ppe', 'Prupe.1G021800' => 'ppe', 'Prupe.5G145100' => 'ppe', 'Psat6g204040' => 'psa', 'Psat6g204800' => 'psa', 'Psat6g204920' => 'psa', 'Psat6g204960' => 'psa', 'Psat6g205080' => 'psa', 'PSO017G0271' => 'pso', 'PSO017G1276' => 'pso', 'PSO017G1429' => 'pso', 'PSO017G1861' => 'pso', 'PSO017G2787' => 'pso', 'PSO017G4466' => 'pso', 'PSO017G5118' => 'pso', 'PSO017G5420' => 'pso', 'PSO063G3678' => 'pso', 'PSO210G0546' => 'pso', 'PSO317G0001' => 'pso', 'PSO357G0512' => 'pso', 'PSO478G2682' => 'pso', 'PSO647G0001' => 'pso', 'PSO675G0001' => 'pso', 'PSO675G2699' => 'pso', 'PSO675G2849' => 'pso', 'PSO675G4991' => 'pso', 'PSO689G0001' => 'pso', 'QL06p000916' => 'qlo', 'QL06p000921' => 'qlo', 'QL06p001398' => 'qlo', 'QL06p001407' => 'qlo', 'QL06p002031' => 'qlo', 'RcHm_v2.0_Chr4g0387791' => 'rch', 'RcHm_v2.0_Chr4g0387801' => 'rch', 'RcHm_v2.0_Chr6g0286501' => 'rch', 'RcHm_v2.0_Chr6g0286511' => 'rch', 'RcHm_v2.0_Chr6g0286521' => 'rch', 'RcHm_v2.0_Chr6g0286531' => 'rch', 'RcHm_v2.0_Chr7g0189141' => 'rch', 'Rhsim02G0028700' => 'rsi', 'Rhsim02G0028800' => 'rsi', 'Rhsim02G0028900' => 'rsi', 'Rhsim02G0029000' => 'rsi', 'Rhsim02G0029100' => 'rsi', 'Rhsim02G0029200' => 'rsi', 'Rhsim02G0029300' => 'rsi', 'Rhsim02G0029400' => 'rsi', 'Rhsim02G0029500' => 'rsi', 'Rhsim02G0029600' => 'rsi', 'RhsimUnG0024000' => 'rsi', 'RhsimUnG0024100' => 'rsi', 'RhsimUnG0024200' => 'rsi', 'RhsimUnG0024300' => 'rsi', 'RhsimUnG0024400' => 'rsi', 'RhsimUnG0024500' => 'rsi', 'RhsimUnG0024700' => 'rsi', 'RhsimUnG0024800' => 'rsi', 'RhsimUnG0024900' => 'rsi', 'RhsimUnG0025100' => 'rsi', 'Sabra08G0120200' => 'sbr', 'Sabra08G0120300' => 'sbr', 'Sabra08G0120500' => 'sbr', 'Sabra08G0120600' => 'sbr', 'Sabra10G0158900' => 'sbr', 'SalBow2G3492' => 'sbo', 'Sc13g0004760' => 'sci', 'Sc13g0004770' => 'sci', 'Sed0003417' => 'sed', 'Sed0019750' => 'sed', 'SEGI_03419' => 'sgi', 'SEGI_05907' => 'sgi', 'SEGI_10682' => 'sgi', 'SEGI_13528' => 'sgi', 'SEGI_16081' => 'sgi', 'SEGI_19370' => 'sgi', 'SEGI_21015' => 'sgi', 'SEGI_21944' => 'sgi', 'SEGI_32906' => 'sgi', 'SEGI_33093' => 'sgi', 'SEGI_36110' => 'sgi', 'SEGI_40397' => 'sgi', 'SGA_v2.0_scaffold191G40426' => 'sas', 'SGA_v2.0_scaffold353G49717' => 'sas', 'SGA_v2.0_scaffold50G18550' => 'sas', 'SMO119G0173' => 'smo', 'SMO172G0002' => 'smo', 'Solyc09g082690.3' => 'sly', 'Solyc09g082700.2' => 'sly', 'Sopen09g031550' => 'spe', 'Sopen09g031560' => 'spe', 'Sp3g20540' => 'spa', 'Sp7g07580' => 'spa', 'TAR134G0002' => 'tar', 'TAR236G0001' => 'tar', 'TAR365G0892' => 'tar', 'TAR636G0166' => 'tar', 'TAR636G0646' => 'tar', 'TAR636G0869' => 'tar', 'TAR636G1317' => 'tar', 'TAR636G1744' => 'tar', 'TAR636G3358' => 'tar', 'TAR636G3436' => 'tar', 'THA.LOC104803047' => 'tha', 'Thecc.04G238900' => 'tca', 'Thhalv10021557m.g' => 'esa', 'Thhalv10026318m.g' => 'esa', 'Thhalv10026335m.g' => 'esa', 'TPR.G17433' => 'tpr', 'TPR.G18915' => 'tpr', 'TPR.G26125' => 'tpr', 'TWI09G0677' => 'twi', 'TWI73G0287' => 'twi', 'unitig_748.g8326' => 'ugi', 'vmacro15370' => 'vma', 'vmacro15371' => 'vma', 'vmacro15372' => 'vma', 'vmacro15373' => 'vma', 'vmacro15374' => 'vma', 'VMungo0720G2826' => 'vmu', 'Zm00001eb116960' => 'zma', 'Zm00001eb301260' => 'zma', 'Zm00001eb301270' => 'zma' ) $gf_id = 'HOM05D001460' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001460' ) $data_identifier = 'HOM05D001460' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 4, 'aag' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 2, 'aox' => (int) 2, 'arhy' => (int) 4, 'ath' => (int) 2, 'atr' => (int) 1, 'acertr' => (int) 10, 'cqu' => (int) 4, 'bca' => (int) 11, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 1, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 1, 'ccan' => (int) 1, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 1, 'col' => (int) 1, 'cpa' => (int) 1, 'cre' => (int) 7, 'csa' => (int) 1, 'camsi' => (int) 2, 'dca' => (int) 3, 'din' => (int) 2, 'dzi' => (int) 3, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 14, 'fve' => (int) 9, 'gma' => (int) 2, 'ghi' => (int) 4, 'gra' => (int) 2, 'vvi' => (int) 1, 'han' => (int) 13, 'cav' => (int) 1, 'hma' => (int) 2, 'sun' => (int) 2, 'lal' => (int) 2, 'lonja' => (int) 12, 'lja' => (int) 1, 'lsa' => (int) 7, 'mes' => (int) 1, 'mpo' => (int) 27, 'mbi' => (int) 1, 'mco' => (int) 8, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 1, 'egut' => (int) 1, 'ama' => (int) 1, 'nta' => (int) 4, 'nnu' => (int) 2, 'oeu' => (int) 3, 'osa' => (int) 4, 'pax' => (int) 9, 'pgr' => (int) 1, 'stu' => (int) 1, 'pvu' => (int) 1, 'ptr' => (int) 4, 'ppa' => (int) 22, 'pco' => (int) 6, 'ppe' => (int) 6, 'psa' => (int) 5, 'pso' => (int) 19, 'qlo' => (int) 5, 'rch' => (int) 7, 'rsi' => (int) 20, 'sbr' => (int) 5, 'sbo' => (int) 1, 'sci' => (int) 2, 'sed' => (int) 2, 'sgi' => (int) 12, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 2, 'tar' => (int) 10, 'tha' => (int) 1, 'tca' => (int) 1, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 2, 'ugi' => (int) 1, 'vma' => (int) 5, 'vmu' => (int) 1, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb301270' $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' => 'HOM05D001460', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '433', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p22980' => 'bna', 'A01p32340' => 'bna', 'A03p42970' => 'bna', 'A05p25880' => 'bna', 'Aa31LG8G9320' => 'aar', 'Aa31LG8G9330' => 'aar', 'Aa31LG8G9340' => 'aar', 'Aa31sc221G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1034' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1528' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.829' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2222' => 'aag', 'Ah.12g058830' => 'amhyb', 'Ah.12g058840' => 'amhyb', 'AL3G37160' => 'aly', 'AL7G41310' => 'aly', 'Aqoxy5G00395' => 'aox', 'Aqoxy5G00396' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0C8NZA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5185HY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JZ1PRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MD3LS0' => 'arhy', 'AT3G22840' => 'ath', 'AT4G14690' => 'ath', 'ATR0665G054' => 'atr', 'Atru.chr4.2344' => 'acertr', 'Atru.chr4.2346' => 'acertr', 'Atru.chr4.2347' => 'acertr', 'Atru.chr4.2348' => 'acertr', 'Atru.chr4.2355' => 'acertr', 'Atru.chr4.2356' => 'acertr', 'Atru.chr4.2358' => 'acertr', 'Atru.chr4.2359' => 'acertr', 'Atru.chr4.2360' => 'acertr', 'Atru.chr4.2361' => 'acertr', 'AUR62030476' => 'cqu', 'AUR62030478' => 'cqu', 'AUR62030819' => 'cqu', 'AUR62030820' => 'cqu', 'BcaB03g14648' => 'bca', 'BcaB04g20492' => 'bca', 'BcaB06g26399' => 'bca', 'BcaC01g03416' => 'bca', 'BcaC01g03419' => 'bca', 'BcaC01g03421' => 'bca', 'BcaC01g03424' => 'bca', 'BcaC05g28012' => 'bca', 'BcaC09g49212' => 'bca', 'BcaC09g50140' => 'bca', 'BcaNung00346' => 'bca', 'BolC1t02785H' => 'bol', 'BolC1t04095H' => 'bol', 'BolC3t17545H' => 'bol', 'BolC5t32769H' => 'bol', 'BraA01t02211Z' => 'bra', 'BraA01t03359Z' => 'bra', 'BraA03t13441Z' => 'bra', 'BraA05t21476Z' => 'bra', 'C01p28420' => 'bna', 'C01p41350' => 'bna', 'C03p52750' => 'bna', 'C03p52780' => 'bna', 'C05p40270' => 'bna', 'CAN.G1437.9' => 'can', 'CANSAT78G0035' => 'cansat', 'CANSAT78G1036' => 'cansat', 'CANSAT78G2272' => 'cansat', 'CANSAT78G2478' => 'cansat', 'CARHR098700' => 'chi', 'CARHR221120' => 'chi', 'CARHR221150' => 'chi', 'Carub.0003s2297' => 'cru', 'Carub.0007s2749' => 'cru', 'Carub.0007s2750' => 'cru', 'Carub.0007s2751' => 'cru', 'Ca_10849_v3' => 'car', 'Cc03_g04300' => 'ccan', 'CDE02G3648' => 'cde', 'CDE05G0060' => 'cde', 'CDE05G0692' => 'cde', 'CDE05G2285' => 'cde', 'CDE05G2884' => 'cde', 'CDE05G3072' => 'cde', 'Cfa008439' => 'cfa', 'Cfa008441' => 'cfa', 'Cfa008443' => 'cfa', 'Cfa008448' => 'cfa', 'Ciclev10005974m.g' => 'ccl', 'Ciclev10006006m.g' => 'ccl', 'Ciclev10006775m.g' => 'ccl', 'CiPaw.02G120400' => 'cil', 'CiPaw.02G120500' => 'cil', 'CiPaw.02G120600' => 'cil', 'ClCG05G004850' => 'cla', 'COL.COLO4_21566' => 'col', 'Cpa.g.sc44.124' => 'cpa', 'Cre07.g320400' => 'cre', 'Cre07.g320450' => 'cre', 'Cre08.g384650' => 'cre', 'Cre09.g393173' => 'cre', 'Cre09.g394325' => 'cre', 'Cre14.g626750' => 'cre', 'Cre16.g679250' => 'cre', 'CsaV3_3G012890' => 'csa', 'CSS0010865' => 'camsi', 'CSS0044338' => 'camsi', 'DCAR_002366' => 'dca', 'DCAR_030687' => 'dca', 'DCAR_030688' => 'dca', 'Dinv14047' => 'din', 'Dinv14048' => 'din', 'Duzib151G0105' => 'dzi', 'Duzib151G0114' => 'dzi', 'Duzib212G1029' => 'dzi', 'ECA232G3536' => 'eca', 'ECA240G0786' => 'eca', 'ECA240G1802' => 'eca', 'ECA240G3760' => 'eca', 'ECA240G3920' => 'eca', 'EL10Ac5g12536' => 'bvu', 'EL10Ac5g12537' => 'bvu', 'EL10Ac5g12538' => 'bvu', 'Eucgr.B01004' => 'egr', 'Eucgr.B01006' => 'egr', 'Eucgr.B01007' => 'egr', 'Eucgr.B01008' => 'egr', 'Eucgr.B01895' => 'egr', 'Eucgr.B01896' => 'egr', 'FAN04G1456' => 'fan', 'FAN08G1769' => 'fan', 'FAN08G2160' => 'fan', 'FAN13G2403' => 'fan', 'FAN13G3303' => 'fan', 'FAN15G2435' => 'fan', 'FAN17G0672' => 'fan', 'FAN17G2441' => 'fan', 'FAN18G1024' => 'fan', 'FAN22G1458' => 'fan', 'FAN24G0037' => 'fan', 'FAN24G0429' => 'fan', 'FAN24G2387' => 'fan', 'FAN27G2746' => 'fan', 'FvH4_2g20400' => 'fve', 'FvH4_2g20420' => 'fve', 'FvH4_2g20430' => 'fve', 'FvH4_4g01270' => 'fve', 'FvH4_4g01290' => 'fve', 'FvH4_4g01300' => 'fve', 'FvH4_4g01310' => 'fve', 'FvH4_4g01330' => 'fve', 'FvH4_5g09070' => 'fve', 'Glyma.10G243800' => 'gma', 'Glyma.20G150600' => 'gma', 'Gohir.A09G219200' => 'ghi', 'Gohir.A09G219300' => 'ghi', 'Gohir.D09G221400' => 'ghi', 'Gohir.D09G221500' => 'ghi', 'Gorai.006G242600' => 'gra', 'Gorai.006G242700' => 'gra', 'GSVIVG01018044001' => 'vvi', 'HanXRQChr03g0083821' => 'han', 'HanXRQChr03g0083841' => 'han', 'HanXRQChr03g0083881' => 'han', 'HanXRQChr03g0083901' => 'han', 'HanXRQChr03g0083921' => 'han', 'HanXRQChr03g0085331' => 'han', 'HanXRQChr03g0085361' => 'han', 'HanXRQChr03g0085411' => 'han', 'HanXRQChr03g0085421' => 'han', 'HanXRQChr03g0085431' => 'han', 'HanXRQChr08g0221991' => 'han', 'HanXRQChr11g0336061' => 'han', 'HanXRQChr11g0336411' => 'han', 'Haze_11234' => 'cav', 'Hma1.2p1_0549F.1_g177010' => 'hma', 'Hma1.2p1_0602F.1_g187630' => 'hma', 'Hund14876' => 'sun', 'Hund14879' => 'sun', 'Lalb_Chr06g0160741' => 'lal', 'Lalb_Chr21g0304781' => 'lal', 'Lj3A726G19' => 'lonja', 'Lj3A726T23' => 'lonja', 'Lj3A726T24' => 'lonja', 'Lj3A726T25' => 'lonja', 'Lj3A727T17' => 'lonja', 'Lj3C726T0' => 'lonja', 'Lj3C726T2' => 'lonja', 'Lj3P725T35' => 'lonja', 'Lj3P727T10' => 'lonja', 'Lj3P727T12' => 'lonja', 'Lj3P727T14' => 'lonja', 'Lj5g0023109' => 'lja', 'Lj6P646T44' => 'lonja', 'Lsat_1_v5_gn_6_75760' => 'lsa', 'Lsat_1_v5_gn_6_75800' => 'lsa', 'Lsat_1_v5_gn_6_75900' => 'lsa', 'Lsat_1_v5_gn_6_76240' => 'lsa', 'Lsat_1_v5_gn_6_76441' => 'lsa', 'Lsat_1_v5_gn_6_76700' => 'lsa', 'Lsat_1_v5_gn_6_76760' => 'lsa', 'Manes.15G033100' => 'mes', 'Mapoly0004s0074' => 'mpo', 'Mapoly0004s0075' => 'mpo', 'Mapoly0004s0163' => 'mpo', 'Mapoly0004s0164' => 'mpo', 'Mapoly0021s0018' => 'mpo', 'Mapoly0041s0136' => 'mpo', 'Mapoly0041s0137' => 'mpo', 'Mapoly0041s0138' => 'mpo', 'Mapoly0041s0139' => 'mpo', 'Mapoly0041s0141' => 'mpo', 'Mapoly0041s0142' => 'mpo', 'Mapoly0041s0143' => 'mpo', 'Mapoly0041s0144' => 'mpo', 'Mapoly0041s0145' => 'mpo', 'Mapoly0047s0106' => 'mpo', 'Mapoly0047s0108' => 'mpo', 'Mapoly0050s0051' => 'mpo', 'Mapoly0050s0052' => 'mpo', 'Mapoly0050s0053' => 'mpo', 'Mapoly0058s0013' => 'mpo', 'Mapoly0091s0078' => 'mpo', 'Mapoly0091s0079' => 'mpo', 'Mapoly0091s0080' => 'mpo', 'Mapoly0091s0081' => 'mpo', 'Mapoly0278s0004' => 'mpo', 'Mapoly0278s0005' => 'mpo', 'Mapoly0278s0006' => 'mpo', 'MBI11_g30648_MAGBIO' => 'mbi', 'MCO03G194' => 'mco', 'MCO03G590' => 'mco', 'MCO07G312' => 'mco', 'MCO10G318' => 'mco', 'MCO12G244' => 'mco', 'MCO13G148' => 'mco', 'MCO13G194' => 'mco', 'MCO16G238' => 'mco', 'MD06G1134100' => 'mdo', 'MD13G1200100' => 'mdo', 'MD13G1200300' => 'mdo', 'MD13G1200600' => 'mdo', 'MD14G1150400' => 'mdo', 'MD16G1200000' => 'mdo', 'Medtr1g102570' => 'mtr', 'Medtr1g102780' => 'mtr', 'Medtr1g102800' => 'mtr', 'Medtr1g102810' => 'mtr', 'Medtr1g102830' => 'mtr', 'MELO3C006499.2' => 'cme', 'Migut.G00385' => 'egut', 'MSTRG.4063' => 'ama', 'Nitab4.5_0000090g0260' => 'nta', 'Nitab4.5_0000977g0030' => 'nta', 'Nitab4.5_0002541g0040' => 'nta', 'Nitab4.5_0007068g0040' => 'nta', 'Nn005s41408' => 'nnu', 'Nn005s41410' => 'nnu', 'Oeu010310.1' => 'oeu', 'Oeu010311.1' => 'oeu', 'Oeu043472.1' => 'oeu', 'Os01g0246400' => 'osa', 'Os04g0267950' => 'osa', 'Os07g0178700' => 'osa', 'Os07g0178800' => 'osa', 'Peaxi162Scf00316g00046' => 'pax', 'Peaxi162Scf00316g00049' => 'pax', 'Peaxi162Scf00316g00059' => 'pax', 'Peaxi162Scf00316g00328' => 'pax', 'Peaxi162Scf00316g00329' => 'pax', 'Peaxi162Scf00316g00411' => 'pax', 'Peaxi162Scf00316g00521' => 'pax', 'Peaxi162Scf00492g00068' => 'pax', 'Peaxi162Scf35631g00002' => 'pax', 'PGR142G3720' => 'pgr', 'PGSC0003DMG400006442' => 'stu', 'Phvul.007G062000' => 'pvu', 'Potri.008G157750' => 'ptr', 'Potri.008G157900' => 'ptr', 'Potri.008G158000' => 'ptr', 'Potri.008G158200' => 'ptr', 'Pp3c11_7280' => 'ppa', 'Pp3c11_7980' => 'ppa', 'Pp3c12_19450' => 'ppa', 'Pp3c14_1480' => 'ppa', 'Pp3c14_1501' => 'ppa', 'Pp3c16_4900' => 'ppa', 'Pp3c16_5010' => 'ppa', 'Pp3c16_5060' => 'ppa', 'Pp3c19_18250' => 'ppa', 'Pp3c23_8530' => 'ppa', 'Pp3c23_8550' => 'ppa', 'Pp3c24_9670' => 'ppa', 'Pp3c2_21390' => 'ppa', 'Pp3c2_31380' => 'ppa', 'Pp3c3_16620' => 'ppa', 'Pp3c3_8090' => 'ppa', 'Pp3c3_8110' => 'ppa', 'Pp3c3_8130' => 'ppa', 'Pp3c3_8150' => 'ppa', 'Pp3c4_14320' => 'ppa', 'Pp3c6_2560' => 'ppa', 'Pp3c9_16700' => 'ppa', 'PRCOL_00000234' => 'pco', 'PRCOL_00000235' => 'pco', 'PRCOL_00000777' => 'pco', 'PRCOL_00002344' => 'pco', 'PRCOL_00002372' => 'pco', 'PRCOL_00006120' => 'pco', 'Prupe.1G021400' => 'ppe', 'Prupe.1G021500' => 'ppe', 'Prupe.1G021600' => 'ppe', 'Prupe.1G021700' => 'ppe', 'Prupe.1G021800' => 'ppe', 'Prupe.5G145100' => 'ppe', 'Psat6g204040' => 'psa', 'Psat6g204800' => 'psa', 'Psat6g204920' => 'psa', 'Psat6g204960' => 'psa', 'Psat6g205080' => 'psa', 'PSO017G0271' => 'pso', 'PSO017G1276' => 'pso', 'PSO017G1429' => 'pso', 'PSO017G1861' => 'pso', 'PSO017G2787' => 'pso', 'PSO017G4466' => 'pso', 'PSO017G5118' => 'pso', 'PSO017G5420' => 'pso', 'PSO063G3678' => 'pso', 'PSO210G0546' => 'pso', 'PSO317G0001' => 'pso', 'PSO357G0512' => 'pso', 'PSO478G2682' => 'pso', 'PSO647G0001' => 'pso', 'PSO675G0001' => 'pso', 'PSO675G2699' => 'pso', 'PSO675G2849' => 'pso', 'PSO675G4991' => 'pso', 'PSO689G0001' => 'pso', 'QL06p000916' => 'qlo', 'QL06p000921' => 'qlo', 'QL06p001398' => 'qlo', 'QL06p001407' => 'qlo', 'QL06p002031' => 'qlo', 'RcHm_v2.0_Chr4g0387791' => 'rch', 'RcHm_v2.0_Chr4g0387801' => 'rch', 'RcHm_v2.0_Chr6g0286501' => 'rch', 'RcHm_v2.0_Chr6g0286511' => 'rch', 'RcHm_v2.0_Chr6g0286521' => 'rch', 'RcHm_v2.0_Chr6g0286531' => 'rch', 'RcHm_v2.0_Chr7g0189141' => 'rch', 'Rhsim02G0028700' => 'rsi', 'Rhsim02G0028800' => 'rsi', 'Rhsim02G0028900' => 'rsi', 'Rhsim02G0029000' => 'rsi', 'Rhsim02G0029100' => 'rsi', 'Rhsim02G0029200' => 'rsi', 'Rhsim02G0029300' => 'rsi', 'Rhsim02G0029400' => 'rsi', 'Rhsim02G0029500' => 'rsi', 'Rhsim02G0029600' => 'rsi', 'RhsimUnG0024000' => 'rsi', 'RhsimUnG0024100' => 'rsi', 'RhsimUnG0024200' => 'rsi', 'RhsimUnG0024300' => 'rsi', 'RhsimUnG0024400' => 'rsi', 'RhsimUnG0024500' => 'rsi', 'RhsimUnG0024700' => 'rsi', 'RhsimUnG0024800' => 'rsi', 'RhsimUnG0024900' => 'rsi', 'RhsimUnG0025100' => 'rsi', 'Sabra08G0120200' => 'sbr', 'Sabra08G0120300' => 'sbr', 'Sabra08G0120500' => 'sbr', 'Sabra08G0120600' => 'sbr', 'Sabra10G0158900' => 'sbr', 'SalBow2G3492' => 'sbo', 'Sc13g0004760' => 'sci', 'Sc13g0004770' => 'sci', 'Sed0003417' => 'sed', 'Sed0019750' => 'sed', 'SEGI_03419' => 'sgi', 'SEGI_05907' => 'sgi', 'SEGI_10682' => 'sgi', 'SEGI_13528' => 'sgi', 'SEGI_16081' => 'sgi', 'SEGI_19370' => 'sgi', 'SEGI_21015' => 'sgi', 'SEGI_21944' => 'sgi', 'SEGI_32906' => 'sgi', 'SEGI_33093' => 'sgi', 'SEGI_36110' => 'sgi', 'SEGI_40397' => 'sgi', 'SGA_v2.0_scaffold191G40426' => 'sas', 'SGA_v2.0_scaffold353G49717' => 'sas', 'SGA_v2.0_scaffold50G18550' => 'sas', 'SMO119G0173' => 'smo', 'SMO172G0002' => 'smo', 'Solyc09g082690.3' => 'sly', 'Solyc09g082700.2' => 'sly', 'Sopen09g031550' => 'spe', 'Sopen09g031560' => 'spe', 'Sp3g20540' => 'spa', 'Sp7g07580' => 'spa', 'TAR134G0002' => 'tar', 'TAR236G0001' => 'tar', 'TAR365G0892' => 'tar', 'TAR636G0166' => 'tar', 'TAR636G0646' => 'tar', 'TAR636G0869' => 'tar', 'TAR636G1317' => 'tar', 'TAR636G1744' => 'tar', 'TAR636G3358' => 'tar', 'TAR636G3436' => 'tar', 'THA.LOC104803047' => 'tha', 'Thecc.04G238900' => 'tca', 'Thhalv10021557m.g' => 'esa', 'Thhalv10026318m.g' => 'esa', 'Thhalv10026335m.g' => 'esa', 'TPR.G17433' => 'tpr', 'TPR.G18915' => 'tpr', 'TPR.G26125' => 'tpr', 'TWI09G0677' => 'twi', 'TWI73G0287' => 'twi', 'unitig_748.g8326' => 'ugi', 'vmacro15370' => 'vma', 'vmacro15371' => 'vma', 'vmacro15372' => 'vma', 'vmacro15373' => 'vma', 'vmacro15374' => 'vma', 'VMungo0720G2826' => 'vmu', 'Zm00001eb116960' => 'zma', 'Zm00001eb301260' => 'zma', 'Zm00001eb301270' => 'zma' ), 'gf_id' => 'HOM05D001460', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001460' ), 'data_identifier' => 'HOM05D001460', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001460', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '433', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p22980' => 'bna', 'A01p32340' => 'bna', 'A03p42970' => 'bna', 'A05p25880' => 'bna', 'Aa31LG8G9320' => 'aar', 'Aa31LG8G9330' => 'aar', 'Aa31LG8G9340' => 'aar', 'Aa31sc221G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1034' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1528' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.829' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2222' => 'aag', 'Ah.12g058830' => 'amhyb', 'Ah.12g058840' => 'amhyb', 'AL3G37160' => 'aly', 'AL7G41310' => 'aly', 'Aqoxy5G00395' => 'aox', 'Aqoxy5G00396' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0C8NZA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5185HY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JZ1PRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MD3LS0' => 'arhy', 'AT3G22840' => 'ath', 'AT4G14690' => 'ath', 'ATR0665G054' => 'atr', 'Atru.chr4.2344' => 'acertr', 'Atru.chr4.2346' => 'acertr', 'Atru.chr4.2347' => 'acertr', 'Atru.chr4.2348' => 'acertr', 'Atru.chr4.2355' => 'acertr', 'Atru.chr4.2356' => 'acertr', 'Atru.chr4.2358' => 'acertr', 'Atru.chr4.2359' => 'acertr', 'Atru.chr4.2360' => 'acertr', 'Atru.chr4.2361' => 'acertr', 'AUR62030476' => 'cqu', 'AUR62030478' => 'cqu', 'AUR62030819' => 'cqu', 'AUR62030820' => 'cqu', 'BcaB03g14648' => 'bca', 'BcaB04g20492' => 'bca', 'BcaB06g26399' => 'bca', 'BcaC01g03416' => 'bca', 'BcaC01g03419' => 'bca', 'BcaC01g03421' => 'bca', 'BcaC01g03424' => 'bca', 'BcaC05g28012' => 'bca', 'BcaC09g49212' => 'bca', 'BcaC09g50140' => 'bca', 'BcaNung00346' => 'bca', 'BolC1t02785H' => 'bol', 'BolC1t04095H' => 'bol', 'BolC3t17545H' => 'bol', 'BolC5t32769H' => 'bol', 'BraA01t02211Z' => 'bra', 'BraA01t03359Z' => 'bra', 'BraA03t13441Z' => 'bra', 'BraA05t21476Z' => 'bra', 'C01p28420' => 'bna', 'C01p41350' => 'bna', 'C03p52750' => 'bna', 'C03p52780' => 'bna', 'C05p40270' => 'bna', 'CAN.G1437.9' => 'can', 'CANSAT78G0035' => 'cansat', 'CANSAT78G1036' => 'cansat', 'CANSAT78G2272' => 'cansat', 'CANSAT78G2478' => 'cansat', 'CARHR098700' => 'chi', 'CARHR221120' => 'chi', 'CARHR221150' => 'chi', 'Carub.0003s2297' => 'cru', 'Carub.0007s2749' => 'cru', 'Carub.0007s2750' => 'cru', 'Carub.0007s2751' => 'cru', 'Ca_10849_v3' => 'car', 'Cc03_g04300' => 'ccan', 'CDE02G3648' => 'cde', 'CDE05G0060' => 'cde', 'CDE05G0692' => 'cde', 'CDE05G2285' => 'cde', 'CDE05G2884' => 'cde', 'CDE05G3072' => 'cde', 'Cfa008439' => 'cfa', 'Cfa008441' => 'cfa', 'Cfa008443' => 'cfa', 'Cfa008448' => 'cfa', 'Ciclev10005974m.g' => 'ccl', 'Ciclev10006006m.g' => 'ccl', 'Ciclev10006775m.g' => 'ccl', 'CiPaw.02G120400' => 'cil', 'CiPaw.02G120500' => 'cil', 'CiPaw.02G120600' => 'cil', 'ClCG05G004850' => 'cla', 'COL.COLO4_21566' => 'col', 'Cpa.g.sc44.124' => 'cpa', 'Cre07.g320400' => 'cre', 'Cre07.g320450' => 'cre', 'Cre08.g384650' => 'cre', 'Cre09.g393173' => 'cre', 'Cre09.g394325' => 'cre', 'Cre14.g626750' => 'cre', 'Cre16.g679250' => 'cre', 'CsaV3_3G012890' => 'csa', 'CSS0010865' => 'camsi', 'CSS0044338' => 'camsi', 'DCAR_002366' => 'dca', 'DCAR_030687' => 'dca', 'DCAR_030688' => 'dca', 'Dinv14047' => 'din', 'Dinv14048' => 'din', 'Duzib151G0105' => 'dzi', 'Duzib151G0114' => 'dzi', 'Duzib212G1029' => 'dzi', 'ECA232G3536' => 'eca', 'ECA240G0786' => 'eca', 'ECA240G1802' => 'eca', 'ECA240G3760' => 'eca', 'ECA240G3920' => 'eca', 'EL10Ac5g12536' => 'bvu', 'EL10Ac5g12537' => 'bvu', 'EL10Ac5g12538' => 'bvu', 'Eucgr.B01004' => 'egr', 'Eucgr.B01006' => 'egr', 'Eucgr.B01007' => 'egr', 'Eucgr.B01008' => 'egr', 'Eucgr.B01895' => 'egr', 'Eucgr.B01896' => 'egr', 'FAN04G1456' => 'fan', 'FAN08G1769' => 'fan', 'FAN08G2160' => 'fan', 'FAN13G2403' => 'fan', 'FAN13G3303' => 'fan', 'FAN15G2435' => 'fan', 'FAN17G0672' => 'fan', 'FAN17G2441' => 'fan', 'FAN18G1024' => 'fan', 'FAN22G1458' => 'fan', 'FAN24G0037' => 'fan', 'FAN24G0429' => 'fan', 'FAN24G2387' => 'fan', 'FAN27G2746' => 'fan', 'FvH4_2g20400' => 'fve', 'FvH4_2g20420' => 'fve', 'FvH4_2g20430' => 'fve', 'FvH4_4g01270' => 'fve', 'FvH4_4g01290' => 'fve', 'FvH4_4g01300' => 'fve', 'FvH4_4g01310' => 'fve', 'FvH4_4g01330' => 'fve', 'FvH4_5g09070' => 'fve', 'Glyma.10G243800' => 'gma', 'Glyma.20G150600' => 'gma', 'Gohir.A09G219200' => 'ghi', 'Gohir.A09G219300' => 'ghi', 'Gohir.D09G221400' => 'ghi', 'Gohir.D09G221500' => 'ghi', 'Gorai.006G242600' => 'gra', 'Gorai.006G242700' => 'gra', 'GSVIVG01018044001' => 'vvi', 'HanXRQChr03g0083821' => 'han', 'HanXRQChr03g0083841' => 'han', 'HanXRQChr03g0083881' => 'han', 'HanXRQChr03g0083901' => 'han', 'HanXRQChr03g0083921' => 'han', 'HanXRQChr03g0085331' => 'han', 'HanXRQChr03g0085361' => 'han', 'HanXRQChr03g0085411' => 'han', 'HanXRQChr03g0085421' => 'han', 'HanXRQChr03g0085431' => 'han', 'HanXRQChr08g0221991' => 'han', 'HanXRQChr11g0336061' => 'han', 'HanXRQChr11g0336411' => 'han', 'Haze_11234' => 'cav', 'Hma1.2p1_0549F.1_g177010' => 'hma', 'Hma1.2p1_0602F.1_g187630' => 'hma', 'Hund14876' => 'sun', 'Hund14879' => 'sun', 'Lalb_Chr06g0160741' => 'lal', 'Lalb_Chr21g0304781' => 'lal', 'Lj3A726G19' => 'lonja', 'Lj3A726T23' => 'lonja', 'Lj3A726T24' => 'lonja', 'Lj3A726T25' => 'lonja', 'Lj3A727T17' => 'lonja', 'Lj3C726T0' => 'lonja', 'Lj3C726T2' => 'lonja', 'Lj3P725T35' => 'lonja', 'Lj3P727T10' => 'lonja', 'Lj3P727T12' => 'lonja', 'Lj3P727T14' => 'lonja', 'Lj5g0023109' => 'lja', 'Lj6P646T44' => 'lonja', 'Lsat_1_v5_gn_6_75760' => 'lsa', 'Lsat_1_v5_gn_6_75800' => 'lsa', 'Lsat_1_v5_gn_6_75900' => 'lsa', 'Lsat_1_v5_gn_6_76240' => 'lsa', 'Lsat_1_v5_gn_6_76441' => 'lsa', 'Lsat_1_v5_gn_6_76700' => 'lsa', 'Lsat_1_v5_gn_6_76760' => 'lsa', 'Manes.15G033100' => 'mes', 'Mapoly0004s0074' => 'mpo', 'Mapoly0004s0075' => 'mpo', 'Mapoly0004s0163' => 'mpo', 'Mapoly0004s0164' => 'mpo', 'Mapoly0021s0018' => 'mpo', 'Mapoly0041s0136' => 'mpo', 'Mapoly0041s0137' => 'mpo', 'Mapoly0041s0138' => 'mpo', 'Mapoly0041s0139' => 'mpo', 'Mapoly0041s0141' => 'mpo', 'Mapoly0041s0142' => 'mpo', 'Mapoly0041s0143' => 'mpo', 'Mapoly0041s0144' => 'mpo', 'Mapoly0041s0145' => 'mpo', 'Mapoly0047s0106' => 'mpo', 'Mapoly0047s0108' => 'mpo', 'Mapoly0050s0051' => 'mpo', 'Mapoly0050s0052' => 'mpo', 'Mapoly0050s0053' => 'mpo', 'Mapoly0058s0013' => 'mpo', 'Mapoly0091s0078' => 'mpo', 'Mapoly0091s0079' => 'mpo', 'Mapoly0091s0080' => 'mpo', 'Mapoly0091s0081' => 'mpo', 'Mapoly0278s0004' => 'mpo', 'Mapoly0278s0005' => 'mpo', 'Mapoly0278s0006' => 'mpo', 'MBI11_g30648_MAGBIO' => 'mbi', 'MCO03G194' => 'mco', 'MCO03G590' => 'mco', 'MCO07G312' => 'mco', 'MCO10G318' => 'mco', 'MCO12G244' => 'mco', 'MCO13G148' => 'mco', 'MCO13G194' => 'mco', 'MCO16G238' => 'mco', 'MD06G1134100' => 'mdo', 'MD13G1200100' => 'mdo', 'MD13G1200300' => 'mdo', 'MD13G1200600' => 'mdo', 'MD14G1150400' => 'mdo', 'MD16G1200000' => 'mdo', 'Medtr1g102570' => 'mtr', 'Medtr1g102780' => 'mtr', 'Medtr1g102800' => 'mtr', 'Medtr1g102810' => 'mtr', 'Medtr1g102830' => 'mtr', 'MELO3C006499.2' => 'cme', 'Migut.G00385' => 'egut', 'MSTRG.4063' => 'ama', 'Nitab4.5_0000090g0260' => 'nta', 'Nitab4.5_0000977g0030' => 'nta', 'Nitab4.5_0002541g0040' => 'nta', 'Nitab4.5_0007068g0040' => 'nta', 'Nn005s41408' => 'nnu', 'Nn005s41410' => 'nnu', 'Oeu010310.1' => 'oeu', 'Oeu010311.1' => 'oeu', 'Oeu043472.1' => 'oeu', 'Os01g0246400' => 'osa', 'Os04g0267950' => 'osa', 'Os07g0178700' => 'osa', 'Os07g0178800' => 'osa', 'Peaxi162Scf00316g00046' => 'pax', 'Peaxi162Scf00316g00049' => 'pax', 'Peaxi162Scf00316g00059' => 'pax', 'Peaxi162Scf00316g00328' => 'pax', 'Peaxi162Scf00316g00329' => 'pax', 'Peaxi162Scf00316g00411' => 'pax', 'Peaxi162Scf00316g00521' => 'pax', 'Peaxi162Scf00492g00068' => 'pax', 'Peaxi162Scf35631g00002' => 'pax', 'PGR142G3720' => 'pgr', 'PGSC0003DMG400006442' => 'stu', 'Phvul.007G062000' => 'pvu', 'Potri.008G157750' => 'ptr', 'Potri.008G157900' => 'ptr', 'Potri.008G158000' => 'ptr', 'Potri.008G158200' => 'ptr', 'Pp3c11_7280' => 'ppa', 'Pp3c11_7980' => 'ppa', 'Pp3c12_19450' => 'ppa', 'Pp3c14_1480' => 'ppa', 'Pp3c14_1501' => 'ppa', 'Pp3c16_4900' => 'ppa', 'Pp3c16_5010' => 'ppa', 'Pp3c16_5060' => 'ppa', 'Pp3c19_18250' => 'ppa', 'Pp3c23_8530' => 'ppa', 'Pp3c23_8550' => 'ppa', 'Pp3c24_9670' => 'ppa', 'Pp3c2_21390' => 'ppa', 'Pp3c2_31380' => 'ppa', 'Pp3c3_16620' => 'ppa', 'Pp3c3_8090' => 'ppa', 'Pp3c3_8110' => 'ppa', 'Pp3c3_8130' => 'ppa', 'Pp3c3_8150' => 'ppa', 'Pp3c4_14320' => 'ppa', 'Pp3c6_2560' => 'ppa', 'Pp3c9_16700' => 'ppa', 'PRCOL_00000234' => 'pco', 'PRCOL_00000235' => 'pco', 'PRCOL_00000777' => 'pco', 'PRCOL_00002344' => 'pco', 'PRCOL_00002372' => 'pco', 'PRCOL_00006120' => 'pco', 'Prupe.1G021400' => 'ppe', 'Prupe.1G021500' => 'ppe', 'Prupe.1G021600' => 'ppe', 'Prupe.1G021700' => 'ppe', 'Prupe.1G021800' => 'ppe', 'Prupe.5G145100' => 'ppe', 'Psat6g204040' => 'psa', 'Psat6g204800' => 'psa', 'Psat6g204920' => 'psa', 'Psat6g204960' => 'psa', 'Psat6g205080' => 'psa', 'PSO017G0271' => 'pso', 'PSO017G1276' => 'pso', 'PSO017G1429' => 'pso', 'PSO017G1861' => 'pso', 'PSO017G2787' => 'pso', 'PSO017G4466' => 'pso', 'PSO017G5118' => 'pso', 'PSO017G5420' => 'pso', 'PSO063G3678' => 'pso', 'PSO210G0546' => 'pso', 'PSO317G0001' => 'pso', 'PSO357G0512' => 'pso', 'PSO478G2682' => 'pso', 'PSO647G0001' => 'pso', 'PSO675G0001' => 'pso', 'PSO675G2699' => 'pso', 'PSO675G2849' => 'pso', 'PSO675G4991' => 'pso', 'PSO689G0001' => 'pso', 'QL06p000916' => 'qlo', 'QL06p000921' => 'qlo', 'QL06p001398' => 'qlo', 'QL06p001407' => 'qlo', 'QL06p002031' => 'qlo', 'RcHm_v2.0_Chr4g0387791' => 'rch', 'RcHm_v2.0_Chr4g0387801' => 'rch', 'RcHm_v2.0_Chr6g0286501' => 'rch', 'RcHm_v2.0_Chr6g0286511' => 'rch', 'RcHm_v2.0_Chr6g0286521' => 'rch', 'RcHm_v2.0_Chr6g0286531' => 'rch', 'RcHm_v2.0_Chr7g0189141' => 'rch', 'Rhsim02G0028700' => 'rsi', 'Rhsim02G0028800' => 'rsi', 'Rhsim02G0028900' => 'rsi', 'Rhsim02G0029000' => 'rsi', 'Rhsim02G0029100' => 'rsi', 'Rhsim02G0029200' => 'rsi', 'Rhsim02G0029300' => 'rsi', 'Rhsim02G0029400' => 'rsi', 'Rhsim02G0029500' => 'rsi', 'Rhsim02G0029600' => 'rsi', 'RhsimUnG0024000' => 'rsi', 'RhsimUnG0024100' => 'rsi', 'RhsimUnG0024200' => 'rsi', 'RhsimUnG0024300' => 'rsi', 'RhsimUnG0024400' => 'rsi', 'RhsimUnG0024500' => 'rsi', 'RhsimUnG0024700' => 'rsi', 'RhsimUnG0024800' => 'rsi', 'RhsimUnG0024900' => 'rsi', 'RhsimUnG0025100' => 'rsi', 'Sabra08G0120200' => 'sbr', 'Sabra08G0120300' => 'sbr', 'Sabra08G0120500' => 'sbr', 'Sabra08G0120600' => 'sbr', 'Sabra10G0158900' => 'sbr', 'SalBow2G3492' => 'sbo', 'Sc13g0004760' => 'sci', 'Sc13g0004770' => 'sci', 'Sed0003417' => 'sed', 'Sed0019750' => 'sed', 'SEGI_03419' => 'sgi', 'SEGI_05907' => 'sgi', 'SEGI_10682' => 'sgi', 'SEGI_13528' => 'sgi', 'SEGI_16081' => 'sgi', 'SEGI_19370' => 'sgi', 'SEGI_21015' => 'sgi', 'SEGI_21944' => 'sgi', 'SEGI_32906' => 'sgi', 'SEGI_33093' => 'sgi', 'SEGI_36110' => 'sgi', 'SEGI_40397' => 'sgi', 'SGA_v2.0_scaffold191G40426' => 'sas', 'SGA_v2.0_scaffold353G49717' => 'sas', 'SGA_v2.0_scaffold50G18550' => 'sas', 'SMO119G0173' => 'smo', 'SMO172G0002' => 'smo', 'Solyc09g082690.3' => 'sly', 'Solyc09g082700.2' => 'sly', 'Sopen09g031550' => 'spe', 'Sopen09g031560' => 'spe', 'Sp3g20540' => 'spa', 'Sp7g07580' => 'spa', 'TAR134G0002' => 'tar', 'TAR236G0001' => 'tar', 'TAR365G0892' => 'tar', 'TAR636G0166' => 'tar', 'TAR636G0646' => 'tar', 'TAR636G0869' => 'tar', 'TAR636G1317' => 'tar', 'TAR636G1744' => 'tar', 'TAR636G3358' => 'tar', 'TAR636G3436' => 'tar', 'THA.LOC104803047' => 'tha', 'Thecc.04G238900' => 'tca', 'Thhalv10021557m.g' => 'esa', 'Thhalv10026318m.g' => 'esa', 'Thhalv10026335m.g' => 'esa', 'TPR.G17433' => 'tpr', 'TPR.G18915' => 'tpr', 'TPR.G26125' => 'tpr', 'TWI09G0677' => 'twi', 'TWI73G0287' => 'twi', 'unitig_748.g8326' => 'ugi', 'vmacro15370' => 'vma', 'vmacro15371' => 'vma', 'vmacro15372' => 'vma', 'vmacro15373' => 'vma', 'vmacro15374' => 'vma', 'VMungo0720G2826' => 'vmu', 'Zm00001eb116960' => 'zma', 'Zm00001eb301260' => 'zma', 'Zm00001eb301270' => 'zma' ) $gf_id = 'HOM05D001460' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001460' ) $data_identifier = 'HOM05D001460' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 4, 'aag' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 2, 'aox' => (int) 2, 'arhy' => (int) 4, 'ath' => (int) 2, 'atr' => (int) 1, 'acertr' => (int) 10, 'cqu' => (int) 4, 'bca' => (int) 11, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 1, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 1, 'ccan' => (int) 1, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 1, 'col' => (int) 1, 'cpa' => (int) 1, 'cre' => (int) 7, 'csa' => (int) 1, 'camsi' => (int) 2, 'dca' => (int) 3, 'din' => (int) 2, 'dzi' => (int) 3, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 14, 'fve' => (int) 9, 'gma' => (int) 2, 'ghi' => (int) 4, 'gra' => (int) 2, 'vvi' => (int) 1, 'han' => (int) 13, 'cav' => (int) 1, 'hma' => (int) 2, 'sun' => (int) 2, 'lal' => (int) 2, 'lonja' => (int) 12, 'lja' => (int) 1, 'lsa' => (int) 7, 'mes' => (int) 1, 'mpo' => (int) 27, 'mbi' => (int) 1, 'mco' => (int) 8, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 1, 'egut' => (int) 1, 'ama' => (int) 1, 'nta' => (int) 4, 'nnu' => (int) 2, 'oeu' => (int) 3, 'osa' => (int) 4, 'pax' => (int) 9, 'pgr' => (int) 1, 'stu' => (int) 1, 'pvu' => (int) 1, 'ptr' => (int) 4, 'ppa' => (int) 22, 'pco' => (int) 6, 'ppe' => (int) 6, 'psa' => (int) 5, 'pso' => (int) 19, 'qlo' => (int) 5, 'rch' => (int) 7, 'rsi' => (int) 20, 'sbr' => (int) 5, 'sbo' => (int) 1, 'sci' => (int) 2, 'sed' => (int) 2, 'sgi' => (int) 12, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 2, 'tar' => (int) 10, 'tha' => (int) 1, 'tca' => (int) 1, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 2, 'ugi' => (int) 1, 'vma' => (int) 5, 'vmu' => (int) 1, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb301270' $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' => 'HOM05D001460', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '433', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p22980' => 'bna', 'A01p32340' => 'bna', 'A03p42970' => 'bna', 'A05p25880' => 'bna', 'Aa31LG8G9320' => 'aar', 'Aa31LG8G9330' => 'aar', 'Aa31LG8G9340' => 'aar', 'Aa31sc221G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1034' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1528' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.829' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2222' => 'aag', 'Ah.12g058830' => 'amhyb', 'Ah.12g058840' => 'amhyb', 'AL3G37160' => 'aly', 'AL7G41310' => 'aly', 'Aqoxy5G00395' => 'aox', 'Aqoxy5G00396' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0C8NZA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5185HY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JZ1PRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MD3LS0' => 'arhy', 'AT3G22840' => 'ath', 'AT4G14690' => 'ath', 'ATR0665G054' => 'atr', 'Atru.chr4.2344' => 'acertr', 'Atru.chr4.2346' => 'acertr', 'Atru.chr4.2347' => 'acertr', 'Atru.chr4.2348' => 'acertr', 'Atru.chr4.2355' => 'acertr', 'Atru.chr4.2356' => 'acertr', 'Atru.chr4.2358' => 'acertr', 'Atru.chr4.2359' => 'acertr', 'Atru.chr4.2360' => 'acertr', 'Atru.chr4.2361' => 'acertr', 'AUR62030476' => 'cqu', 'AUR62030478' => 'cqu', 'AUR62030819' => 'cqu', 'AUR62030820' => 'cqu', 'BcaB03g14648' => 'bca', 'BcaB04g20492' => 'bca', 'BcaB06g26399' => 'bca', 'BcaC01g03416' => 'bca', 'BcaC01g03419' => 'bca', 'BcaC01g03421' => 'bca', 'BcaC01g03424' => 'bca', 'BcaC05g28012' => 'bca', 'BcaC09g49212' => 'bca', 'BcaC09g50140' => 'bca', 'BcaNung00346' => 'bca', 'BolC1t02785H' => 'bol', 'BolC1t04095H' => 'bol', 'BolC3t17545H' => 'bol', 'BolC5t32769H' => 'bol', 'BraA01t02211Z' => 'bra', 'BraA01t03359Z' => 'bra', 'BraA03t13441Z' => 'bra', 'BraA05t21476Z' => 'bra', 'C01p28420' => 'bna', 'C01p41350' => 'bna', 'C03p52750' => 'bna', 'C03p52780' => 'bna', 'C05p40270' => 'bna', 'CAN.G1437.9' => 'can', 'CANSAT78G0035' => 'cansat', 'CANSAT78G1036' => 'cansat', 'CANSAT78G2272' => 'cansat', 'CANSAT78G2478' => 'cansat', 'CARHR098700' => 'chi', 'CARHR221120' => 'chi', 'CARHR221150' => 'chi', 'Carub.0003s2297' => 'cru', 'Carub.0007s2749' => 'cru', 'Carub.0007s2750' => 'cru', 'Carub.0007s2751' => 'cru', 'Ca_10849_v3' => 'car', 'Cc03_g04300' => 'ccan', 'CDE02G3648' => 'cde', 'CDE05G0060' => 'cde', 'CDE05G0692' => 'cde', 'CDE05G2285' => 'cde', 'CDE05G2884' => 'cde', 'CDE05G3072' => 'cde', 'Cfa008439' => 'cfa', 'Cfa008441' => 'cfa', 'Cfa008443' => 'cfa', 'Cfa008448' => 'cfa', 'Ciclev10005974m.g' => 'ccl', 'Ciclev10006006m.g' => 'ccl', 'Ciclev10006775m.g' => 'ccl', 'CiPaw.02G120400' => 'cil', 'CiPaw.02G120500' => 'cil', 'CiPaw.02G120600' => 'cil', 'ClCG05G004850' => 'cla', 'COL.COLO4_21566' => 'col', 'Cpa.g.sc44.124' => 'cpa', 'Cre07.g320400' => 'cre', 'Cre07.g320450' => 'cre', 'Cre08.g384650' => 'cre', 'Cre09.g393173' => 'cre', 'Cre09.g394325' => 'cre', 'Cre14.g626750' => 'cre', 'Cre16.g679250' => 'cre', 'CsaV3_3G012890' => 'csa', 'CSS0010865' => 'camsi', 'CSS0044338' => 'camsi', 'DCAR_002366' => 'dca', 'DCAR_030687' => 'dca', 'DCAR_030688' => 'dca', 'Dinv14047' => 'din', 'Dinv14048' => 'din', 'Duzib151G0105' => 'dzi', 'Duzib151G0114' => 'dzi', 'Duzib212G1029' => 'dzi', 'ECA232G3536' => 'eca', 'ECA240G0786' => 'eca', 'ECA240G1802' => 'eca', 'ECA240G3760' => 'eca', 'ECA240G3920' => 'eca', 'EL10Ac5g12536' => 'bvu', 'EL10Ac5g12537' => 'bvu', 'EL10Ac5g12538' => 'bvu', 'Eucgr.B01004' => 'egr', 'Eucgr.B01006' => 'egr', 'Eucgr.B01007' => 'egr', 'Eucgr.B01008' => 'egr', 'Eucgr.B01895' => 'egr', 'Eucgr.B01896' => 'egr', 'FAN04G1456' => 'fan', 'FAN08G1769' => 'fan', 'FAN08G2160' => 'fan', 'FAN13G2403' => 'fan', 'FAN13G3303' => 'fan', 'FAN15G2435' => 'fan', 'FAN17G0672' => 'fan', 'FAN17G2441' => 'fan', 'FAN18G1024' => 'fan', 'FAN22G1458' => 'fan', 'FAN24G0037' => 'fan', 'FAN24G0429' => 'fan', 'FAN24G2387' => 'fan', 'FAN27G2746' => 'fan', 'FvH4_2g20400' => 'fve', 'FvH4_2g20420' => 'fve', 'FvH4_2g20430' => 'fve', 'FvH4_4g01270' => 'fve', 'FvH4_4g01290' => 'fve', 'FvH4_4g01300' => 'fve', 'FvH4_4g01310' => 'fve', 'FvH4_4g01330' => 'fve', 'FvH4_5g09070' => 'fve', 'Glyma.10G243800' => 'gma', 'Glyma.20G150600' => 'gma', 'Gohir.A09G219200' => 'ghi', 'Gohir.A09G219300' => 'ghi', 'Gohir.D09G221400' => 'ghi', 'Gohir.D09G221500' => 'ghi', 'Gorai.006G242600' => 'gra', 'Gorai.006G242700' => 'gra', 'GSVIVG01018044001' => 'vvi', 'HanXRQChr03g0083821' => 'han', 'HanXRQChr03g0083841' => 'han', 'HanXRQChr03g0083881' => 'han', 'HanXRQChr03g0083901' => 'han', 'HanXRQChr03g0083921' => 'han', 'HanXRQChr03g0085331' => 'han', 'HanXRQChr03g0085361' => 'han', 'HanXRQChr03g0085411' => 'han', 'HanXRQChr03g0085421' => 'han', 'HanXRQChr03g0085431' => 'han', 'HanXRQChr08g0221991' => 'han', 'HanXRQChr11g0336061' => 'han', 'HanXRQChr11g0336411' => 'han', 'Haze_11234' => 'cav', 'Hma1.2p1_0549F.1_g177010' => 'hma', 'Hma1.2p1_0602F.1_g187630' => 'hma', 'Hund14876' => 'sun', 'Hund14879' => 'sun', 'Lalb_Chr06g0160741' => 'lal', 'Lalb_Chr21g0304781' => 'lal', 'Lj3A726G19' => 'lonja', 'Lj3A726T23' => 'lonja', 'Lj3A726T24' => 'lonja', 'Lj3A726T25' => 'lonja', 'Lj3A727T17' => 'lonja', 'Lj3C726T0' => 'lonja', 'Lj3C726T2' => 'lonja', 'Lj3P725T35' => 'lonja', 'Lj3P727T10' => 'lonja', 'Lj3P727T12' => 'lonja', 'Lj3P727T14' => 'lonja', 'Lj5g0023109' => 'lja', 'Lj6P646T44' => 'lonja', 'Lsat_1_v5_gn_6_75760' => 'lsa', 'Lsat_1_v5_gn_6_75800' => 'lsa', 'Lsat_1_v5_gn_6_75900' => 'lsa', 'Lsat_1_v5_gn_6_76240' => 'lsa', 'Lsat_1_v5_gn_6_76441' => 'lsa', 'Lsat_1_v5_gn_6_76700' => 'lsa', 'Lsat_1_v5_gn_6_76760' => 'lsa', 'Manes.15G033100' => 'mes', 'Mapoly0004s0074' => 'mpo', 'Mapoly0004s0075' => 'mpo', 'Mapoly0004s0163' => 'mpo', 'Mapoly0004s0164' => 'mpo', 'Mapoly0021s0018' => 'mpo', 'Mapoly0041s0136' => 'mpo', 'Mapoly0041s0137' => 'mpo', 'Mapoly0041s0138' => 'mpo', 'Mapoly0041s0139' => 'mpo', 'Mapoly0041s0141' => 'mpo', 'Mapoly0041s0142' => 'mpo', 'Mapoly0041s0143' => 'mpo', 'Mapoly0041s0144' => 'mpo', 'Mapoly0041s0145' => 'mpo', 'Mapoly0047s0106' => 'mpo', 'Mapoly0047s0108' => 'mpo', 'Mapoly0050s0051' => 'mpo', 'Mapoly0050s0052' => 'mpo', 'Mapoly0050s0053' => 'mpo', 'Mapoly0058s0013' => 'mpo', 'Mapoly0091s0078' => 'mpo', 'Mapoly0091s0079' => 'mpo', 'Mapoly0091s0080' => 'mpo', 'Mapoly0091s0081' => 'mpo', 'Mapoly0278s0004' => 'mpo', 'Mapoly0278s0005' => 'mpo', 'Mapoly0278s0006' => 'mpo', 'MBI11_g30648_MAGBIO' => 'mbi', 'MCO03G194' => 'mco', 'MCO03G590' => 'mco', 'MCO07G312' => 'mco', 'MCO10G318' => 'mco', 'MCO12G244' => 'mco', 'MCO13G148' => 'mco', 'MCO13G194' => 'mco', 'MCO16G238' => 'mco', 'MD06G1134100' => 'mdo', 'MD13G1200100' => 'mdo', 'MD13G1200300' => 'mdo', 'MD13G1200600' => 'mdo', 'MD14G1150400' => 'mdo', 'MD16G1200000' => 'mdo', 'Medtr1g102570' => 'mtr', 'Medtr1g102780' => 'mtr', 'Medtr1g102800' => 'mtr', 'Medtr1g102810' => 'mtr', 'Medtr1g102830' => 'mtr', 'MELO3C006499.2' => 'cme', 'Migut.G00385' => 'egut', 'MSTRG.4063' => 'ama', 'Nitab4.5_0000090g0260' => 'nta', 'Nitab4.5_0000977g0030' => 'nta', 'Nitab4.5_0002541g0040' => 'nta', 'Nitab4.5_0007068g0040' => 'nta', 'Nn005s41408' => 'nnu', 'Nn005s41410' => 'nnu', 'Oeu010310.1' => 'oeu', 'Oeu010311.1' => 'oeu', 'Oeu043472.1' => 'oeu', 'Os01g0246400' => 'osa', 'Os04g0267950' => 'osa', 'Os07g0178700' => 'osa', 'Os07g0178800' => 'osa', 'Peaxi162Scf00316g00046' => 'pax', 'Peaxi162Scf00316g00049' => 'pax', 'Peaxi162Scf00316g00059' => 'pax', 'Peaxi162Scf00316g00328' => 'pax', 'Peaxi162Scf00316g00329' => 'pax', 'Peaxi162Scf00316g00411' => 'pax', 'Peaxi162Scf00316g00521' => 'pax', 'Peaxi162Scf00492g00068' => 'pax', 'Peaxi162Scf35631g00002' => 'pax', 'PGR142G3720' => 'pgr', 'PGSC0003DMG400006442' => 'stu', 'Phvul.007G062000' => 'pvu', 'Potri.008G157750' => 'ptr', 'Potri.008G157900' => 'ptr', 'Potri.008G158000' => 'ptr', 'Potri.008G158200' => 'ptr', 'Pp3c11_7280' => 'ppa', 'Pp3c11_7980' => 'ppa', 'Pp3c12_19450' => 'ppa', 'Pp3c14_1480' => 'ppa', 'Pp3c14_1501' => 'ppa', 'Pp3c16_4900' => 'ppa', 'Pp3c16_5010' => 'ppa', 'Pp3c16_5060' => 'ppa', 'Pp3c19_18250' => 'ppa', 'Pp3c23_8530' => 'ppa', 'Pp3c23_8550' => 'ppa', 'Pp3c24_9670' => 'ppa', 'Pp3c2_21390' => 'ppa', 'Pp3c2_31380' => 'ppa', 'Pp3c3_16620' => 'ppa', 'Pp3c3_8090' => 'ppa', 'Pp3c3_8110' => 'ppa', 'Pp3c3_8130' => 'ppa', 'Pp3c3_8150' => 'ppa', 'Pp3c4_14320' => 'ppa', 'Pp3c6_2560' => 'ppa', 'Pp3c9_16700' => 'ppa', 'PRCOL_00000234' => 'pco', 'PRCOL_00000235' => 'pco', 'PRCOL_00000777' => 'pco', 'PRCOL_00002344' => 'pco', 'PRCOL_00002372' => 'pco', 'PRCOL_00006120' => 'pco', 'Prupe.1G021400' => 'ppe', 'Prupe.1G021500' => 'ppe', 'Prupe.1G021600' => 'ppe', 'Prupe.1G021700' => 'ppe', 'Prupe.1G021800' => 'ppe', 'Prupe.5G145100' => 'ppe', 'Psat6g204040' => 'psa', 'Psat6g204800' => 'psa', 'Psat6g204920' => 'psa', 'Psat6g204960' => 'psa', 'Psat6g205080' => 'psa', 'PSO017G0271' => 'pso', 'PSO017G1276' => 'pso', 'PSO017G1429' => 'pso', 'PSO017G1861' => 'pso', 'PSO017G2787' => 'pso', 'PSO017G4466' => 'pso', 'PSO017G5118' => 'pso', 'PSO017G5420' => 'pso', 'PSO063G3678' => 'pso', 'PSO210G0546' => 'pso', 'PSO317G0001' => 'pso', 'PSO357G0512' => 'pso', 'PSO478G2682' => 'pso', 'PSO647G0001' => 'pso', 'PSO675G0001' => 'pso', 'PSO675G2699' => 'pso', 'PSO675G2849' => 'pso', 'PSO675G4991' => 'pso', 'PSO689G0001' => 'pso', 'QL06p000916' => 'qlo', 'QL06p000921' => 'qlo', 'QL06p001398' => 'qlo', 'QL06p001407' => 'qlo', 'QL06p002031' => 'qlo', 'RcHm_v2.0_Chr4g0387791' => 'rch', 'RcHm_v2.0_Chr4g0387801' => 'rch', 'RcHm_v2.0_Chr6g0286501' => 'rch', 'RcHm_v2.0_Chr6g0286511' => 'rch', 'RcHm_v2.0_Chr6g0286521' => 'rch', 'RcHm_v2.0_Chr6g0286531' => 'rch', 'RcHm_v2.0_Chr7g0189141' => 'rch', 'Rhsim02G0028700' => 'rsi', 'Rhsim02G0028800' => 'rsi', 'Rhsim02G0028900' => 'rsi', 'Rhsim02G0029000' => 'rsi', 'Rhsim02G0029100' => 'rsi', 'Rhsim02G0029200' => 'rsi', 'Rhsim02G0029300' => 'rsi', 'Rhsim02G0029400' => 'rsi', 'Rhsim02G0029500' => 'rsi', 'Rhsim02G0029600' => 'rsi', 'RhsimUnG0024000' => 'rsi', 'RhsimUnG0024100' => 'rsi', 'RhsimUnG0024200' => 'rsi', 'RhsimUnG0024300' => 'rsi', 'RhsimUnG0024400' => 'rsi', 'RhsimUnG0024500' => 'rsi', 'RhsimUnG0024700' => 'rsi', 'RhsimUnG0024800' => 'rsi', 'RhsimUnG0024900' => 'rsi', 'RhsimUnG0025100' => 'rsi', 'Sabra08G0120200' => 'sbr', 'Sabra08G0120300' => 'sbr', 'Sabra08G0120500' => 'sbr', 'Sabra08G0120600' => 'sbr', 'Sabra10G0158900' => 'sbr', 'SalBow2G3492' => 'sbo', 'Sc13g0004760' => 'sci', 'Sc13g0004770' => 'sci', 'Sed0003417' => 'sed', 'Sed0019750' => 'sed', 'SEGI_03419' => 'sgi', 'SEGI_05907' => 'sgi', 'SEGI_10682' => 'sgi', 'SEGI_13528' => 'sgi', 'SEGI_16081' => 'sgi', 'SEGI_19370' => 'sgi', 'SEGI_21015' => 'sgi', 'SEGI_21944' => 'sgi', 'SEGI_32906' => 'sgi', 'SEGI_33093' => 'sgi', 'SEGI_36110' => 'sgi', 'SEGI_40397' => 'sgi', 'SGA_v2.0_scaffold191G40426' => 'sas', 'SGA_v2.0_scaffold353G49717' => 'sas', 'SGA_v2.0_scaffold50G18550' => 'sas', 'SMO119G0173' => 'smo', 'SMO172G0002' => 'smo', 'Solyc09g082690.3' => 'sly', 'Solyc09g082700.2' => 'sly', 'Sopen09g031550' => 'spe', 'Sopen09g031560' => 'spe', 'Sp3g20540' => 'spa', 'Sp7g07580' => 'spa', 'TAR134G0002' => 'tar', 'TAR236G0001' => 'tar', 'TAR365G0892' => 'tar', 'TAR636G0166' => 'tar', 'TAR636G0646' => 'tar', 'TAR636G0869' => 'tar', 'TAR636G1317' => 'tar', 'TAR636G1744' => 'tar', 'TAR636G3358' => 'tar', 'TAR636G3436' => 'tar', 'THA.LOC104803047' => 'tha', 'Thecc.04G238900' => 'tca', 'Thhalv10021557m.g' => 'esa', 'Thhalv10026318m.g' => 'esa', 'Thhalv10026335m.g' => 'esa', 'TPR.G17433' => 'tpr', 'TPR.G18915' => 'tpr', 'TPR.G26125' => 'tpr', 'TWI09G0677' => 'twi', 'TWI73G0287' => 'twi', 'unitig_748.g8326' => 'ugi', 'vmacro15370' => 'vma', 'vmacro15371' => 'vma', 'vmacro15372' => 'vma', 'vmacro15373' => 'vma', 'vmacro15374' => 'vma', 'VMungo0720G2826' => 'vmu', 'Zm00001eb116960' => 'zma', 'Zm00001eb301260' => 'zma', 'Zm00001eb301270' => 'zma' ), 'gf_id' => 'HOM05D001460', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001460' ), 'data_identifier' => 'HOM05D001460', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001460', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '433', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p22980' => 'bna', 'A01p32340' => 'bna', 'A03p42970' => 'bna', 'A05p25880' => 'bna', 'Aa31LG8G9320' => 'aar', 'Aa31LG8G9330' => 'aar', 'Aa31LG8G9340' => 'aar', 'Aa31sc221G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1034' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1528' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.829' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2222' => 'aag', 'Ah.12g058830' => 'amhyb', 'Ah.12g058840' => 'amhyb', 'AL3G37160' => 'aly', 'AL7G41310' => 'aly', 'Aqoxy5G00395' => 'aox', 'Aqoxy5G00396' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0C8NZA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5185HY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JZ1PRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MD3LS0' => 'arhy', 'AT3G22840' => 'ath', 'AT4G14690' => 'ath', 'ATR0665G054' => 'atr', 'Atru.chr4.2344' => 'acertr', 'Atru.chr4.2346' => 'acertr', 'Atru.chr4.2347' => 'acertr', 'Atru.chr4.2348' => 'acertr', 'Atru.chr4.2355' => 'acertr', 'Atru.chr4.2356' => 'acertr', 'Atru.chr4.2358' => 'acertr', 'Atru.chr4.2359' => 'acertr', 'Atru.chr4.2360' => 'acertr', 'Atru.chr4.2361' => 'acertr', 'AUR62030476' => 'cqu', 'AUR62030478' => 'cqu', 'AUR62030819' => 'cqu', 'AUR62030820' => 'cqu', 'BcaB03g14648' => 'bca', 'BcaB04g20492' => 'bca', 'BcaB06g26399' => 'bca', 'BcaC01g03416' => 'bca', 'BcaC01g03419' => 'bca', 'BcaC01g03421' => 'bca', 'BcaC01g03424' => 'bca', 'BcaC05g28012' => 'bca', 'BcaC09g49212' => 'bca', 'BcaC09g50140' => 'bca', 'BcaNung00346' => 'bca', 'BolC1t02785H' => 'bol', 'BolC1t04095H' => 'bol', 'BolC3t17545H' => 'bol', 'BolC5t32769H' => 'bol', 'BraA01t02211Z' => 'bra', 'BraA01t03359Z' => 'bra', 'BraA03t13441Z' => 'bra', 'BraA05t21476Z' => 'bra', 'C01p28420' => 'bna', 'C01p41350' => 'bna', 'C03p52750' => 'bna', 'C03p52780' => 'bna', 'C05p40270' => 'bna', 'CAN.G1437.9' => 'can', 'CANSAT78G0035' => 'cansat', 'CANSAT78G1036' => 'cansat', 'CANSAT78G2272' => 'cansat', 'CANSAT78G2478' => 'cansat', 'CARHR098700' => 'chi', 'CARHR221120' => 'chi', 'CARHR221150' => 'chi', 'Carub.0003s2297' => 'cru', 'Carub.0007s2749' => 'cru', 'Carub.0007s2750' => 'cru', 'Carub.0007s2751' => 'cru', 'Ca_10849_v3' => 'car', 'Cc03_g04300' => 'ccan', 'CDE02G3648' => 'cde', 'CDE05G0060' => 'cde', 'CDE05G0692' => 'cde', 'CDE05G2285' => 'cde', 'CDE05G2884' => 'cde', 'CDE05G3072' => 'cde', 'Cfa008439' => 'cfa', 'Cfa008441' => 'cfa', 'Cfa008443' => 'cfa', 'Cfa008448' => 'cfa', 'Ciclev10005974m.g' => 'ccl', 'Ciclev10006006m.g' => 'ccl', 'Ciclev10006775m.g' => 'ccl', 'CiPaw.02G120400' => 'cil', 'CiPaw.02G120500' => 'cil', 'CiPaw.02G120600' => 'cil', 'ClCG05G004850' => 'cla', 'COL.COLO4_21566' => 'col', 'Cpa.g.sc44.124' => 'cpa', 'Cre07.g320400' => 'cre', 'Cre07.g320450' => 'cre', 'Cre08.g384650' => 'cre', 'Cre09.g393173' => 'cre', 'Cre09.g394325' => 'cre', 'Cre14.g626750' => 'cre', 'Cre16.g679250' => 'cre', 'CsaV3_3G012890' => 'csa', 'CSS0010865' => 'camsi', 'CSS0044338' => 'camsi', 'DCAR_002366' => 'dca', 'DCAR_030687' => 'dca', 'DCAR_030688' => 'dca', 'Dinv14047' => 'din', 'Dinv14048' => 'din', 'Duzib151G0105' => 'dzi', 'Duzib151G0114' => 'dzi', 'Duzib212G1029' => 'dzi', 'ECA232G3536' => 'eca', 'ECA240G0786' => 'eca', 'ECA240G1802' => 'eca', 'ECA240G3760' => 'eca', 'ECA240G3920' => 'eca', 'EL10Ac5g12536' => 'bvu', 'EL10Ac5g12537' => 'bvu', 'EL10Ac5g12538' => 'bvu', 'Eucgr.B01004' => 'egr', 'Eucgr.B01006' => 'egr', 'Eucgr.B01007' => 'egr', 'Eucgr.B01008' => 'egr', 'Eucgr.B01895' => 'egr', 'Eucgr.B01896' => 'egr', 'FAN04G1456' => 'fan', 'FAN08G1769' => 'fan', 'FAN08G2160' => 'fan', 'FAN13G2403' => 'fan', 'FAN13G3303' => 'fan', 'FAN15G2435' => 'fan', 'FAN17G0672' => 'fan', 'FAN17G2441' => 'fan', 'FAN18G1024' => 'fan', 'FAN22G1458' => 'fan', 'FAN24G0037' => 'fan', 'FAN24G0429' => 'fan', 'FAN24G2387' => 'fan', 'FAN27G2746' => 'fan', 'FvH4_2g20400' => 'fve', 'FvH4_2g20420' => 'fve', 'FvH4_2g20430' => 'fve', 'FvH4_4g01270' => 'fve', 'FvH4_4g01290' => 'fve', 'FvH4_4g01300' => 'fve', 'FvH4_4g01310' => 'fve', 'FvH4_4g01330' => 'fve', 'FvH4_5g09070' => 'fve', 'Glyma.10G243800' => 'gma', 'Glyma.20G150600' => 'gma', 'Gohir.A09G219200' => 'ghi', 'Gohir.A09G219300' => 'ghi', 'Gohir.D09G221400' => 'ghi', 'Gohir.D09G221500' => 'ghi', 'Gorai.006G242600' => 'gra', 'Gorai.006G242700' => 'gra', 'GSVIVG01018044001' => 'vvi', 'HanXRQChr03g0083821' => 'han', 'HanXRQChr03g0083841' => 'han', 'HanXRQChr03g0083881' => 'han', 'HanXRQChr03g0083901' => 'han', 'HanXRQChr03g0083921' => 'han', 'HanXRQChr03g0085331' => 'han', 'HanXRQChr03g0085361' => 'han', 'HanXRQChr03g0085411' => 'han', 'HanXRQChr03g0085421' => 'han', 'HanXRQChr03g0085431' => 'han', 'HanXRQChr08g0221991' => 'han', 'HanXRQChr11g0336061' => 'han', 'HanXRQChr11g0336411' => 'han', 'Haze_11234' => 'cav', 'Hma1.2p1_0549F.1_g177010' => 'hma', 'Hma1.2p1_0602F.1_g187630' => 'hma', 'Hund14876' => 'sun', 'Hund14879' => 'sun', 'Lalb_Chr06g0160741' => 'lal', 'Lalb_Chr21g0304781' => 'lal', 'Lj3A726G19' => 'lonja', 'Lj3A726T23' => 'lonja', 'Lj3A726T24' => 'lonja', 'Lj3A726T25' => 'lonja', 'Lj3A727T17' => 'lonja', 'Lj3C726T0' => 'lonja', 'Lj3C726T2' => 'lonja', 'Lj3P725T35' => 'lonja', 'Lj3P727T10' => 'lonja', 'Lj3P727T12' => 'lonja', 'Lj3P727T14' => 'lonja', 'Lj5g0023109' => 'lja', 'Lj6P646T44' => 'lonja', 'Lsat_1_v5_gn_6_75760' => 'lsa', 'Lsat_1_v5_gn_6_75800' => 'lsa', 'Lsat_1_v5_gn_6_75900' => 'lsa', 'Lsat_1_v5_gn_6_76240' => 'lsa', 'Lsat_1_v5_gn_6_76441' => 'lsa', 'Lsat_1_v5_gn_6_76700' => 'lsa', 'Lsat_1_v5_gn_6_76760' => 'lsa', 'Manes.15G033100' => 'mes', 'Mapoly0004s0074' => 'mpo', 'Mapoly0004s0075' => 'mpo', 'Mapoly0004s0163' => 'mpo', 'Mapoly0004s0164' => 'mpo', 'Mapoly0021s0018' => 'mpo', 'Mapoly0041s0136' => 'mpo', 'Mapoly0041s0137' => 'mpo', 'Mapoly0041s0138' => 'mpo', 'Mapoly0041s0139' => 'mpo', 'Mapoly0041s0141' => 'mpo', 'Mapoly0041s0142' => 'mpo', 'Mapoly0041s0143' => 'mpo', 'Mapoly0041s0144' => 'mpo', 'Mapoly0041s0145' => 'mpo', 'Mapoly0047s0106' => 'mpo', 'Mapoly0047s0108' => 'mpo', 'Mapoly0050s0051' => 'mpo', 'Mapoly0050s0052' => 'mpo', 'Mapoly0050s0053' => 'mpo', 'Mapoly0058s0013' => 'mpo', 'Mapoly0091s0078' => 'mpo', 'Mapoly0091s0079' => 'mpo', 'Mapoly0091s0080' => 'mpo', 'Mapoly0091s0081' => 'mpo', 'Mapoly0278s0004' => 'mpo', 'Mapoly0278s0005' => 'mpo', 'Mapoly0278s0006' => 'mpo', 'MBI11_g30648_MAGBIO' => 'mbi', 'MCO03G194' => 'mco', 'MCO03G590' => 'mco', 'MCO07G312' => 'mco', 'MCO10G318' => 'mco', 'MCO12G244' => 'mco', 'MCO13G148' => 'mco', 'MCO13G194' => 'mco', 'MCO16G238' => 'mco', 'MD06G1134100' => 'mdo', 'MD13G1200100' => 'mdo', 'MD13G1200300' => 'mdo', 'MD13G1200600' => 'mdo', 'MD14G1150400' => 'mdo', 'MD16G1200000' => 'mdo', 'Medtr1g102570' => 'mtr', 'Medtr1g102780' => 'mtr', 'Medtr1g102800' => 'mtr', 'Medtr1g102810' => 'mtr', 'Medtr1g102830' => 'mtr', 'MELO3C006499.2' => 'cme', 'Migut.G00385' => 'egut', 'MSTRG.4063' => 'ama', 'Nitab4.5_0000090g0260' => 'nta', 'Nitab4.5_0000977g0030' => 'nta', 'Nitab4.5_0002541g0040' => 'nta', 'Nitab4.5_0007068g0040' => 'nta', 'Nn005s41408' => 'nnu', 'Nn005s41410' => 'nnu', 'Oeu010310.1' => 'oeu', 'Oeu010311.1' => 'oeu', 'Oeu043472.1' => 'oeu', 'Os01g0246400' => 'osa', 'Os04g0267950' => 'osa', 'Os07g0178700' => 'osa', 'Os07g0178800' => 'osa', 'Peaxi162Scf00316g00046' => 'pax', 'Peaxi162Scf00316g00049' => 'pax', 'Peaxi162Scf00316g00059' => 'pax', 'Peaxi162Scf00316g00328' => 'pax', 'Peaxi162Scf00316g00329' => 'pax', 'Peaxi162Scf00316g00411' => 'pax', 'Peaxi162Scf00316g00521' => 'pax', 'Peaxi162Scf00492g00068' => 'pax', 'Peaxi162Scf35631g00002' => 'pax', 'PGR142G3720' => 'pgr', 'PGSC0003DMG400006442' => 'stu', 'Phvul.007G062000' => 'pvu', 'Potri.008G157750' => 'ptr', 'Potri.008G157900' => 'ptr', 'Potri.008G158000' => 'ptr', 'Potri.008G158200' => 'ptr', 'Pp3c11_7280' => 'ppa', 'Pp3c11_7980' => 'ppa', 'Pp3c12_19450' => 'ppa', 'Pp3c14_1480' => 'ppa', 'Pp3c14_1501' => 'ppa', 'Pp3c16_4900' => 'ppa', 'Pp3c16_5010' => 'ppa', 'Pp3c16_5060' => 'ppa', 'Pp3c19_18250' => 'ppa', 'Pp3c23_8530' => 'ppa', 'Pp3c23_8550' => 'ppa', 'Pp3c24_9670' => 'ppa', 'Pp3c2_21390' => 'ppa', 'Pp3c2_31380' => 'ppa', 'Pp3c3_16620' => 'ppa', 'Pp3c3_8090' => 'ppa', 'Pp3c3_8110' => 'ppa', 'Pp3c3_8130' => 'ppa', 'Pp3c3_8150' => 'ppa', 'Pp3c4_14320' => 'ppa', 'Pp3c6_2560' => 'ppa', 'Pp3c9_16700' => 'ppa', 'PRCOL_00000234' => 'pco', 'PRCOL_00000235' => 'pco', 'PRCOL_00000777' => 'pco', 'PRCOL_00002344' => 'pco', 'PRCOL_00002372' => 'pco', 'PRCOL_00006120' => 'pco', 'Prupe.1G021400' => 'ppe', 'Prupe.1G021500' => 'ppe', 'Prupe.1G021600' => 'ppe', 'Prupe.1G021700' => 'ppe', 'Prupe.1G021800' => 'ppe', 'Prupe.5G145100' => 'ppe', 'Psat6g204040' => 'psa', 'Psat6g204800' => 'psa', 'Psat6g204920' => 'psa', 'Psat6g204960' => 'psa', 'Psat6g205080' => 'psa', 'PSO017G0271' => 'pso', 'PSO017G1276' => 'pso', 'PSO017G1429' => 'pso', 'PSO017G1861' => 'pso', 'PSO017G2787' => 'pso', 'PSO017G4466' => 'pso', 'PSO017G5118' => 'pso', 'PSO017G5420' => 'pso', 'PSO063G3678' => 'pso', 'PSO210G0546' => 'pso', 'PSO317G0001' => 'pso', 'PSO357G0512' => 'pso', 'PSO478G2682' => 'pso', 'PSO647G0001' => 'pso', 'PSO675G0001' => 'pso', 'PSO675G2699' => 'pso', 'PSO675G2849' => 'pso', 'PSO675G4991' => 'pso', 'PSO689G0001' => 'pso', 'QL06p000916' => 'qlo', 'QL06p000921' => 'qlo', 'QL06p001398' => 'qlo', 'QL06p001407' => 'qlo', 'QL06p002031' => 'qlo', 'RcHm_v2.0_Chr4g0387791' => 'rch', 'RcHm_v2.0_Chr4g0387801' => 'rch', 'RcHm_v2.0_Chr6g0286501' => 'rch', 'RcHm_v2.0_Chr6g0286511' => 'rch', 'RcHm_v2.0_Chr6g0286521' => 'rch', 'RcHm_v2.0_Chr6g0286531' => 'rch', 'RcHm_v2.0_Chr7g0189141' => 'rch', 'Rhsim02G0028700' => 'rsi', 'Rhsim02G0028800' => 'rsi', 'Rhsim02G0028900' => 'rsi', 'Rhsim02G0029000' => 'rsi', 'Rhsim02G0029100' => 'rsi', 'Rhsim02G0029200' => 'rsi', 'Rhsim02G0029300' => 'rsi', 'Rhsim02G0029400' => 'rsi', 'Rhsim02G0029500' => 'rsi', 'Rhsim02G0029600' => 'rsi', 'RhsimUnG0024000' => 'rsi', 'RhsimUnG0024100' => 'rsi', 'RhsimUnG0024200' => 'rsi', 'RhsimUnG0024300' => 'rsi', 'RhsimUnG0024400' => 'rsi', 'RhsimUnG0024500' => 'rsi', 'RhsimUnG0024700' => 'rsi', 'RhsimUnG0024800' => 'rsi', 'RhsimUnG0024900' => 'rsi', 'RhsimUnG0025100' => 'rsi', 'Sabra08G0120200' => 'sbr', 'Sabra08G0120300' => 'sbr', 'Sabra08G0120500' => 'sbr', 'Sabra08G0120600' => 'sbr', 'Sabra10G0158900' => 'sbr', 'SalBow2G3492' => 'sbo', 'Sc13g0004760' => 'sci', 'Sc13g0004770' => 'sci', 'Sed0003417' => 'sed', 'Sed0019750' => 'sed', 'SEGI_03419' => 'sgi', 'SEGI_05907' => 'sgi', 'SEGI_10682' => 'sgi', 'SEGI_13528' => 'sgi', 'SEGI_16081' => 'sgi', 'SEGI_19370' => 'sgi', 'SEGI_21015' => 'sgi', 'SEGI_21944' => 'sgi', 'SEGI_32906' => 'sgi', 'SEGI_33093' => 'sgi', 'SEGI_36110' => 'sgi', 'SEGI_40397' => 'sgi', 'SGA_v2.0_scaffold191G40426' => 'sas', 'SGA_v2.0_scaffold353G49717' => 'sas', 'SGA_v2.0_scaffold50G18550' => 'sas', 'SMO119G0173' => 'smo', 'SMO172G0002' => 'smo', 'Solyc09g082690.3' => 'sly', 'Solyc09g082700.2' => 'sly', 'Sopen09g031550' => 'spe', 'Sopen09g031560' => 'spe', 'Sp3g20540' => 'spa', 'Sp7g07580' => 'spa', 'TAR134G0002' => 'tar', 'TAR236G0001' => 'tar', 'TAR365G0892' => 'tar', 'TAR636G0166' => 'tar', 'TAR636G0646' => 'tar', 'TAR636G0869' => 'tar', 'TAR636G1317' => 'tar', 'TAR636G1744' => 'tar', 'TAR636G3358' => 'tar', 'TAR636G3436' => 'tar', 'THA.LOC104803047' => 'tha', 'Thecc.04G238900' => 'tca', 'Thhalv10021557m.g' => 'esa', 'Thhalv10026318m.g' => 'esa', 'Thhalv10026335m.g' => 'esa', 'TPR.G17433' => 'tpr', 'TPR.G18915' => 'tpr', 'TPR.G26125' => 'tpr', 'TWI09G0677' => 'twi', 'TWI73G0287' => 'twi', 'unitig_748.g8326' => 'ugi', 'vmacro15370' => 'vma', 'vmacro15371' => 'vma', 'vmacro15372' => 'vma', 'vmacro15373' => 'vma', 'vmacro15374' => 'vma', 'VMungo0720G2826' => 'vmu', 'Zm00001eb116960' => 'zma', 'Zm00001eb301260' => 'zma', 'Zm00001eb301270' => 'zma' ) $gf_id = 'HOM05D001460' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001460' ) $data_identifier = 'HOM05D001460' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 4, 'aag' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 2, 'aox' => (int) 2, 'arhy' => (int) 4, 'ath' => (int) 2, 'atr' => (int) 1, 'acertr' => (int) 10, 'cqu' => (int) 4, 'bca' => (int) 11, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 1, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 1, 'ccan' => (int) 1, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 1, 'col' => (int) 1, 'cpa' => (int) 1, 'cre' => (int) 7, 'csa' => (int) 1, 'camsi' => (int) 2, 'dca' => (int) 3, 'din' => (int) 2, 'dzi' => (int) 3, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 14, 'fve' => (int) 9, 'gma' => (int) 2, 'ghi' => (int) 4, 'gra' => (int) 2, 'vvi' => (int) 1, 'han' => (int) 13, 'cav' => (int) 1, 'hma' => (int) 2, 'sun' => (int) 2, 'lal' => (int) 2, 'lonja' => (int) 12, 'lja' => (int) 1, 'lsa' => (int) 7, 'mes' => (int) 1, 'mpo' => (int) 27, 'mbi' => (int) 1, 'mco' => (int) 8, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 1, 'egut' => (int) 1, 'ama' => (int) 1, 'nta' => (int) 4, 'nnu' => (int) 2, 'oeu' => (int) 3, 'osa' => (int) 4, 'pax' => (int) 9, 'pgr' => (int) 1, 'stu' => (int) 1, 'pvu' => (int) 1, 'ptr' => (int) 4, 'ppa' => (int) 22, 'pco' => (int) 6, 'ppe' => (int) 6, 'psa' => (int) 5, 'pso' => (int) 19, 'qlo' => (int) 5, 'rch' => (int) 7, 'rsi' => (int) 20, 'sbr' => (int) 5, 'sbo' => (int) 1, 'sci' => (int) 2, 'sed' => (int) 2, 'sgi' => (int) 12, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 2, 'tar' => (int) 10, 'tha' => (int) 1, 'tca' => (int) 1, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 2, 'ugi' => (int) 1, 'vma' => (int) 5, 'vmu' => (int) 1, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb301270' $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' => 'HOM05D001460', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '433', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p22980' => 'bna', 'A01p32340' => 'bna', 'A03p42970' => 'bna', 'A05p25880' => 'bna', 'Aa31LG8G9320' => 'aar', 'Aa31LG8G9330' => 'aar', 'Aa31LG8G9340' => 'aar', 'Aa31sc221G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1034' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1528' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.829' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2222' => 'aag', 'Ah.12g058830' => 'amhyb', 'Ah.12g058840' => 'amhyb', 'AL3G37160' => 'aly', 'AL7G41310' => 'aly', 'Aqoxy5G00395' => 'aox', 'Aqoxy5G00396' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0C8NZA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5185HY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JZ1PRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MD3LS0' => 'arhy', 'AT3G22840' => 'ath', 'AT4G14690' => 'ath', 'ATR0665G054' => 'atr', 'Atru.chr4.2344' => 'acertr', 'Atru.chr4.2346' => 'acertr', 'Atru.chr4.2347' => 'acertr', 'Atru.chr4.2348' => 'acertr', 'Atru.chr4.2355' => 'acertr', 'Atru.chr4.2356' => 'acertr', 'Atru.chr4.2358' => 'acertr', 'Atru.chr4.2359' => 'acertr', 'Atru.chr4.2360' => 'acertr', 'Atru.chr4.2361' => 'acertr', 'AUR62030476' => 'cqu', 'AUR62030478' => 'cqu', 'AUR62030819' => 'cqu', 'AUR62030820' => 'cqu', 'BcaB03g14648' => 'bca', 'BcaB04g20492' => 'bca', 'BcaB06g26399' => 'bca', 'BcaC01g03416' => 'bca', 'BcaC01g03419' => 'bca', 'BcaC01g03421' => 'bca', 'BcaC01g03424' => 'bca', 'BcaC05g28012' => 'bca', 'BcaC09g49212' => 'bca', 'BcaC09g50140' => 'bca', 'BcaNung00346' => 'bca', 'BolC1t02785H' => 'bol', 'BolC1t04095H' => 'bol', 'BolC3t17545H' => 'bol', 'BolC5t32769H' => 'bol', 'BraA01t02211Z' => 'bra', 'BraA01t03359Z' => 'bra', 'BraA03t13441Z' => 'bra', 'BraA05t21476Z' => 'bra', 'C01p28420' => 'bna', 'C01p41350' => 'bna', 'C03p52750' => 'bna', 'C03p52780' => 'bna', 'C05p40270' => 'bna', 'CAN.G1437.9' => 'can', 'CANSAT78G0035' => 'cansat', 'CANSAT78G1036' => 'cansat', 'CANSAT78G2272' => 'cansat', 'CANSAT78G2478' => 'cansat', 'CARHR098700' => 'chi', 'CARHR221120' => 'chi', 'CARHR221150' => 'chi', 'Carub.0003s2297' => 'cru', 'Carub.0007s2749' => 'cru', 'Carub.0007s2750' => 'cru', 'Carub.0007s2751' => 'cru', 'Ca_10849_v3' => 'car', 'Cc03_g04300' => 'ccan', 'CDE02G3648' => 'cde', 'CDE05G0060' => 'cde', 'CDE05G0692' => 'cde', 'CDE05G2285' => 'cde', 'CDE05G2884' => 'cde', 'CDE05G3072' => 'cde', 'Cfa008439' => 'cfa', 'Cfa008441' => 'cfa', 'Cfa008443' => 'cfa', 'Cfa008448' => 'cfa', 'Ciclev10005974m.g' => 'ccl', 'Ciclev10006006m.g' => 'ccl', 'Ciclev10006775m.g' => 'ccl', 'CiPaw.02G120400' => 'cil', 'CiPaw.02G120500' => 'cil', 'CiPaw.02G120600' => 'cil', 'ClCG05G004850' => 'cla', 'COL.COLO4_21566' => 'col', 'Cpa.g.sc44.124' => 'cpa', 'Cre07.g320400' => 'cre', 'Cre07.g320450' => 'cre', 'Cre08.g384650' => 'cre', 'Cre09.g393173' => 'cre', 'Cre09.g394325' => 'cre', 'Cre14.g626750' => 'cre', 'Cre16.g679250' => 'cre', 'CsaV3_3G012890' => 'csa', 'CSS0010865' => 'camsi', 'CSS0044338' => 'camsi', 'DCAR_002366' => 'dca', 'DCAR_030687' => 'dca', 'DCAR_030688' => 'dca', 'Dinv14047' => 'din', 'Dinv14048' => 'din', 'Duzib151G0105' => 'dzi', 'Duzib151G0114' => 'dzi', 'Duzib212G1029' => 'dzi', 'ECA232G3536' => 'eca', 'ECA240G0786' => 'eca', 'ECA240G1802' => 'eca', 'ECA240G3760' => 'eca', 'ECA240G3920' => 'eca', 'EL10Ac5g12536' => 'bvu', 'EL10Ac5g12537' => 'bvu', 'EL10Ac5g12538' => 'bvu', 'Eucgr.B01004' => 'egr', 'Eucgr.B01006' => 'egr', 'Eucgr.B01007' => 'egr', 'Eucgr.B01008' => 'egr', 'Eucgr.B01895' => 'egr', 'Eucgr.B01896' => 'egr', 'FAN04G1456' => 'fan', 'FAN08G1769' => 'fan', 'FAN08G2160' => 'fan', 'FAN13G2403' => 'fan', 'FAN13G3303' => 'fan', 'FAN15G2435' => 'fan', 'FAN17G0672' => 'fan', 'FAN17G2441' => 'fan', 'FAN18G1024' => 'fan', 'FAN22G1458' => 'fan', 'FAN24G0037' => 'fan', 'FAN24G0429' => 'fan', 'FAN24G2387' => 'fan', 'FAN27G2746' => 'fan', 'FvH4_2g20400' => 'fve', 'FvH4_2g20420' => 'fve', 'FvH4_2g20430' => 'fve', 'FvH4_4g01270' => 'fve', 'FvH4_4g01290' => 'fve', 'FvH4_4g01300' => 'fve', 'FvH4_4g01310' => 'fve', 'FvH4_4g01330' => 'fve', 'FvH4_5g09070' => 'fve', 'Glyma.10G243800' => 'gma', 'Glyma.20G150600' => 'gma', 'Gohir.A09G219200' => 'ghi', 'Gohir.A09G219300' => 'ghi', 'Gohir.D09G221400' => 'ghi', 'Gohir.D09G221500' => 'ghi', 'Gorai.006G242600' => 'gra', 'Gorai.006G242700' => 'gra', 'GSVIVG01018044001' => 'vvi', 'HanXRQChr03g0083821' => 'han', 'HanXRQChr03g0083841' => 'han', 'HanXRQChr03g0083881' => 'han', 'HanXRQChr03g0083901' => 'han', 'HanXRQChr03g0083921' => 'han', 'HanXRQChr03g0085331' => 'han', 'HanXRQChr03g0085361' => 'han', 'HanXRQChr03g0085411' => 'han', 'HanXRQChr03g0085421' => 'han', 'HanXRQChr03g0085431' => 'han', 'HanXRQChr08g0221991' => 'han', 'HanXRQChr11g0336061' => 'han', 'HanXRQChr11g0336411' => 'han', 'Haze_11234' => 'cav', 'Hma1.2p1_0549F.1_g177010' => 'hma', 'Hma1.2p1_0602F.1_g187630' => 'hma', 'Hund14876' => 'sun', 'Hund14879' => 'sun', 'Lalb_Chr06g0160741' => 'lal', 'Lalb_Chr21g0304781' => 'lal', 'Lj3A726G19' => 'lonja', 'Lj3A726T23' => 'lonja', 'Lj3A726T24' => 'lonja', 'Lj3A726T25' => 'lonja', 'Lj3A727T17' => 'lonja', 'Lj3C726T0' => 'lonja', 'Lj3C726T2' => 'lonja', 'Lj3P725T35' => 'lonja', 'Lj3P727T10' => 'lonja', 'Lj3P727T12' => 'lonja', 'Lj3P727T14' => 'lonja', 'Lj5g0023109' => 'lja', 'Lj6P646T44' => 'lonja', 'Lsat_1_v5_gn_6_75760' => 'lsa', 'Lsat_1_v5_gn_6_75800' => 'lsa', 'Lsat_1_v5_gn_6_75900' => 'lsa', 'Lsat_1_v5_gn_6_76240' => 'lsa', 'Lsat_1_v5_gn_6_76441' => 'lsa', 'Lsat_1_v5_gn_6_76700' => 'lsa', 'Lsat_1_v5_gn_6_76760' => 'lsa', 'Manes.15G033100' => 'mes', 'Mapoly0004s0074' => 'mpo', 'Mapoly0004s0075' => 'mpo', 'Mapoly0004s0163' => 'mpo', 'Mapoly0004s0164' => 'mpo', 'Mapoly0021s0018' => 'mpo', 'Mapoly0041s0136' => 'mpo', 'Mapoly0041s0137' => 'mpo', 'Mapoly0041s0138' => 'mpo', 'Mapoly0041s0139' => 'mpo', 'Mapoly0041s0141' => 'mpo', 'Mapoly0041s0142' => 'mpo', 'Mapoly0041s0143' => 'mpo', 'Mapoly0041s0144' => 'mpo', 'Mapoly0041s0145' => 'mpo', 'Mapoly0047s0106' => 'mpo', 'Mapoly0047s0108' => 'mpo', 'Mapoly0050s0051' => 'mpo', 'Mapoly0050s0052' => 'mpo', 'Mapoly0050s0053' => 'mpo', 'Mapoly0058s0013' => 'mpo', 'Mapoly0091s0078' => 'mpo', 'Mapoly0091s0079' => 'mpo', 'Mapoly0091s0080' => 'mpo', 'Mapoly0091s0081' => 'mpo', 'Mapoly0278s0004' => 'mpo', 'Mapoly0278s0005' => 'mpo', 'Mapoly0278s0006' => 'mpo', 'MBI11_g30648_MAGBIO' => 'mbi', 'MCO03G194' => 'mco', 'MCO03G590' => 'mco', 'MCO07G312' => 'mco', 'MCO10G318' => 'mco', 'MCO12G244' => 'mco', 'MCO13G148' => 'mco', 'MCO13G194' => 'mco', 'MCO16G238' => 'mco', 'MD06G1134100' => 'mdo', 'MD13G1200100' => 'mdo', 'MD13G1200300' => 'mdo', 'MD13G1200600' => 'mdo', 'MD14G1150400' => 'mdo', 'MD16G1200000' => 'mdo', 'Medtr1g102570' => 'mtr', 'Medtr1g102780' => 'mtr', 'Medtr1g102800' => 'mtr', 'Medtr1g102810' => 'mtr', 'Medtr1g102830' => 'mtr', 'MELO3C006499.2' => 'cme', 'Migut.G00385' => 'egut', 'MSTRG.4063' => 'ama', 'Nitab4.5_0000090g0260' => 'nta', 'Nitab4.5_0000977g0030' => 'nta', 'Nitab4.5_0002541g0040' => 'nta', 'Nitab4.5_0007068g0040' => 'nta', 'Nn005s41408' => 'nnu', 'Nn005s41410' => 'nnu', 'Oeu010310.1' => 'oeu', 'Oeu010311.1' => 'oeu', 'Oeu043472.1' => 'oeu', 'Os01g0246400' => 'osa', 'Os04g0267950' => 'osa', 'Os07g0178700' => 'osa', 'Os07g0178800' => 'osa', 'Peaxi162Scf00316g00046' => 'pax', 'Peaxi162Scf00316g00049' => 'pax', 'Peaxi162Scf00316g00059' => 'pax', 'Peaxi162Scf00316g00328' => 'pax', 'Peaxi162Scf00316g00329' => 'pax', 'Peaxi162Scf00316g00411' => 'pax', 'Peaxi162Scf00316g00521' => 'pax', 'Peaxi162Scf00492g00068' => 'pax', 'Peaxi162Scf35631g00002' => 'pax', 'PGR142G3720' => 'pgr', 'PGSC0003DMG400006442' => 'stu', 'Phvul.007G062000' => 'pvu', 'Potri.008G157750' => 'ptr', 'Potri.008G157900' => 'ptr', 'Potri.008G158000' => 'ptr', 'Potri.008G158200' => 'ptr', 'Pp3c11_7280' => 'ppa', 'Pp3c11_7980' => 'ppa', 'Pp3c12_19450' => 'ppa', 'Pp3c14_1480' => 'ppa', 'Pp3c14_1501' => 'ppa', 'Pp3c16_4900' => 'ppa', 'Pp3c16_5010' => 'ppa', 'Pp3c16_5060' => 'ppa', 'Pp3c19_18250' => 'ppa', 'Pp3c23_8530' => 'ppa', 'Pp3c23_8550' => 'ppa', 'Pp3c24_9670' => 'ppa', 'Pp3c2_21390' => 'ppa', 'Pp3c2_31380' => 'ppa', 'Pp3c3_16620' => 'ppa', 'Pp3c3_8090' => 'ppa', 'Pp3c3_8110' => 'ppa', 'Pp3c3_8130' => 'ppa', 'Pp3c3_8150' => 'ppa', 'Pp3c4_14320' => 'ppa', 'Pp3c6_2560' => 'ppa', 'Pp3c9_16700' => 'ppa', 'PRCOL_00000234' => 'pco', 'PRCOL_00000235' => 'pco', 'PRCOL_00000777' => 'pco', 'PRCOL_00002344' => 'pco', 'PRCOL_00002372' => 'pco', 'PRCOL_00006120' => 'pco', 'Prupe.1G021400' => 'ppe', 'Prupe.1G021500' => 'ppe', 'Prupe.1G021600' => 'ppe', 'Prupe.1G021700' => 'ppe', 'Prupe.1G021800' => 'ppe', 'Prupe.5G145100' => 'ppe', 'Psat6g204040' => 'psa', 'Psat6g204800' => 'psa', 'Psat6g204920' => 'psa', 'Psat6g204960' => 'psa', 'Psat6g205080' => 'psa', 'PSO017G0271' => 'pso', 'PSO017G1276' => 'pso', 'PSO017G1429' => 'pso', 'PSO017G1861' => 'pso', 'PSO017G2787' => 'pso', 'PSO017G4466' => 'pso', 'PSO017G5118' => 'pso', 'PSO017G5420' => 'pso', 'PSO063G3678' => 'pso', 'PSO210G0546' => 'pso', 'PSO317G0001' => 'pso', 'PSO357G0512' => 'pso', 'PSO478G2682' => 'pso', 'PSO647G0001' => 'pso', 'PSO675G0001' => 'pso', 'PSO675G2699' => 'pso', 'PSO675G2849' => 'pso', 'PSO675G4991' => 'pso', 'PSO689G0001' => 'pso', 'QL06p000916' => 'qlo', 'QL06p000921' => 'qlo', 'QL06p001398' => 'qlo', 'QL06p001407' => 'qlo', 'QL06p002031' => 'qlo', 'RcHm_v2.0_Chr4g0387791' => 'rch', 'RcHm_v2.0_Chr4g0387801' => 'rch', 'RcHm_v2.0_Chr6g0286501' => 'rch', 'RcHm_v2.0_Chr6g0286511' => 'rch', 'RcHm_v2.0_Chr6g0286521' => 'rch', 'RcHm_v2.0_Chr6g0286531' => 'rch', 'RcHm_v2.0_Chr7g0189141' => 'rch', 'Rhsim02G0028700' => 'rsi', 'Rhsim02G0028800' => 'rsi', 'Rhsim02G0028900' => 'rsi', 'Rhsim02G0029000' => 'rsi', 'Rhsim02G0029100' => 'rsi', 'Rhsim02G0029200' => 'rsi', 'Rhsim02G0029300' => 'rsi', 'Rhsim02G0029400' => 'rsi', 'Rhsim02G0029500' => 'rsi', 'Rhsim02G0029600' => 'rsi', 'RhsimUnG0024000' => 'rsi', 'RhsimUnG0024100' => 'rsi', 'RhsimUnG0024200' => 'rsi', 'RhsimUnG0024300' => 'rsi', 'RhsimUnG0024400' => 'rsi', 'RhsimUnG0024500' => 'rsi', 'RhsimUnG0024700' => 'rsi', 'RhsimUnG0024800' => 'rsi', 'RhsimUnG0024900' => 'rsi', 'RhsimUnG0025100' => 'rsi', 'Sabra08G0120200' => 'sbr', 'Sabra08G0120300' => 'sbr', 'Sabra08G0120500' => 'sbr', 'Sabra08G0120600' => 'sbr', 'Sabra10G0158900' => 'sbr', 'SalBow2G3492' => 'sbo', 'Sc13g0004760' => 'sci', 'Sc13g0004770' => 'sci', 'Sed0003417' => 'sed', 'Sed0019750' => 'sed', 'SEGI_03419' => 'sgi', 'SEGI_05907' => 'sgi', 'SEGI_10682' => 'sgi', 'SEGI_13528' => 'sgi', 'SEGI_16081' => 'sgi', 'SEGI_19370' => 'sgi', 'SEGI_21015' => 'sgi', 'SEGI_21944' => 'sgi', 'SEGI_32906' => 'sgi', 'SEGI_33093' => 'sgi', 'SEGI_36110' => 'sgi', 'SEGI_40397' => 'sgi', 'SGA_v2.0_scaffold191G40426' => 'sas', 'SGA_v2.0_scaffold353G49717' => 'sas', 'SGA_v2.0_scaffold50G18550' => 'sas', 'SMO119G0173' => 'smo', 'SMO172G0002' => 'smo', 'Solyc09g082690.3' => 'sly', 'Solyc09g082700.2' => 'sly', 'Sopen09g031550' => 'spe', 'Sopen09g031560' => 'spe', 'Sp3g20540' => 'spa', 'Sp7g07580' => 'spa', 'TAR134G0002' => 'tar', 'TAR236G0001' => 'tar', 'TAR365G0892' => 'tar', 'TAR636G0166' => 'tar', 'TAR636G0646' => 'tar', 'TAR636G0869' => 'tar', 'TAR636G1317' => 'tar', 'TAR636G1744' => 'tar', 'TAR636G3358' => 'tar', 'TAR636G3436' => 'tar', 'THA.LOC104803047' => 'tha', 'Thecc.04G238900' => 'tca', 'Thhalv10021557m.g' => 'esa', 'Thhalv10026318m.g' => 'esa', 'Thhalv10026335m.g' => 'esa', 'TPR.G17433' => 'tpr', 'TPR.G18915' => 'tpr', 'TPR.G26125' => 'tpr', 'TWI09G0677' => 'twi', 'TWI73G0287' => 'twi', 'unitig_748.g8326' => 'ugi', 'vmacro15370' => 'vma', 'vmacro15371' => 'vma', 'vmacro15372' => 'vma', 'vmacro15373' => 'vma', 'vmacro15374' => 'vma', 'VMungo0720G2826' => 'vmu', 'Zm00001eb116960' => 'zma', 'Zm00001eb301260' => 'zma', 'Zm00001eb301270' => 'zma' ), 'gf_id' => 'HOM05D001460', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001460' ), 'data_identifier' => 'HOM05D001460', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001460', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '433', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p22980' => 'bna', 'A01p32340' => 'bna', 'A03p42970' => 'bna', 'A05p25880' => 'bna', 'Aa31LG8G9320' => 'aar', 'Aa31LG8G9330' => 'aar', 'Aa31LG8G9340' => 'aar', 'Aa31sc221G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1034' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1528' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.829' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2222' => 'aag', 'Ah.12g058830' => 'amhyb', 'Ah.12g058840' => 'amhyb', 'AL3G37160' => 'aly', 'AL7G41310' => 'aly', 'Aqoxy5G00395' => 'aox', 'Aqoxy5G00396' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0C8NZA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5185HY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JZ1PRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MD3LS0' => 'arhy', 'AT3G22840' => 'ath', 'AT4G14690' => 'ath', 'ATR0665G054' => 'atr', 'Atru.chr4.2344' => 'acertr', 'Atru.chr4.2346' => 'acertr', 'Atru.chr4.2347' => 'acertr', 'Atru.chr4.2348' => 'acertr', 'Atru.chr4.2355' => 'acertr', 'Atru.chr4.2356' => 'acertr', 'Atru.chr4.2358' => 'acertr', 'Atru.chr4.2359' => 'acertr', 'Atru.chr4.2360' => 'acertr', 'Atru.chr4.2361' => 'acertr', 'AUR62030476' => 'cqu', 'AUR62030478' => 'cqu', 'AUR62030819' => 'cqu', 'AUR62030820' => 'cqu', 'BcaB03g14648' => 'bca', 'BcaB04g20492' => 'bca', 'BcaB06g26399' => 'bca', 'BcaC01g03416' => 'bca', 'BcaC01g03419' => 'bca', 'BcaC01g03421' => 'bca', 'BcaC01g03424' => 'bca', 'BcaC05g28012' => 'bca', 'BcaC09g49212' => 'bca', 'BcaC09g50140' => 'bca', 'BcaNung00346' => 'bca', 'BolC1t02785H' => 'bol', 'BolC1t04095H' => 'bol', 'BolC3t17545H' => 'bol', 'BolC5t32769H' => 'bol', 'BraA01t02211Z' => 'bra', 'BraA01t03359Z' => 'bra', 'BraA03t13441Z' => 'bra', 'BraA05t21476Z' => 'bra', 'C01p28420' => 'bna', 'C01p41350' => 'bna', 'C03p52750' => 'bna', 'C03p52780' => 'bna', 'C05p40270' => 'bna', 'CAN.G1437.9' => 'can', 'CANSAT78G0035' => 'cansat', 'CANSAT78G1036' => 'cansat', 'CANSAT78G2272' => 'cansat', 'CANSAT78G2478' => 'cansat', 'CARHR098700' => 'chi', 'CARHR221120' => 'chi', 'CARHR221150' => 'chi', 'Carub.0003s2297' => 'cru', 'Carub.0007s2749' => 'cru', 'Carub.0007s2750' => 'cru', 'Carub.0007s2751' => 'cru', 'Ca_10849_v3' => 'car', 'Cc03_g04300' => 'ccan', 'CDE02G3648' => 'cde', 'CDE05G0060' => 'cde', 'CDE05G0692' => 'cde', 'CDE05G2285' => 'cde', 'CDE05G2884' => 'cde', 'CDE05G3072' => 'cde', 'Cfa008439' => 'cfa', 'Cfa008441' => 'cfa', 'Cfa008443' => 'cfa', 'Cfa008448' => 'cfa', 'Ciclev10005974m.g' => 'ccl', 'Ciclev10006006m.g' => 'ccl', 'Ciclev10006775m.g' => 'ccl', 'CiPaw.02G120400' => 'cil', 'CiPaw.02G120500' => 'cil', 'CiPaw.02G120600' => 'cil', 'ClCG05G004850' => 'cla', 'COL.COLO4_21566' => 'col', 'Cpa.g.sc44.124' => 'cpa', 'Cre07.g320400' => 'cre', 'Cre07.g320450' => 'cre', 'Cre08.g384650' => 'cre', 'Cre09.g393173' => 'cre', 'Cre09.g394325' => 'cre', 'Cre14.g626750' => 'cre', 'Cre16.g679250' => 'cre', 'CsaV3_3G012890' => 'csa', 'CSS0010865' => 'camsi', 'CSS0044338' => 'camsi', 'DCAR_002366' => 'dca', 'DCAR_030687' => 'dca', 'DCAR_030688' => 'dca', 'Dinv14047' => 'din', 'Dinv14048' => 'din', 'Duzib151G0105' => 'dzi', 'Duzib151G0114' => 'dzi', 'Duzib212G1029' => 'dzi', 'ECA232G3536' => 'eca', 'ECA240G0786' => 'eca', 'ECA240G1802' => 'eca', 'ECA240G3760' => 'eca', 'ECA240G3920' => 'eca', 'EL10Ac5g12536' => 'bvu', 'EL10Ac5g12537' => 'bvu', 'EL10Ac5g12538' => 'bvu', 'Eucgr.B01004' => 'egr', 'Eucgr.B01006' => 'egr', 'Eucgr.B01007' => 'egr', 'Eucgr.B01008' => 'egr', 'Eucgr.B01895' => 'egr', 'Eucgr.B01896' => 'egr', 'FAN04G1456' => 'fan', 'FAN08G1769' => 'fan', 'FAN08G2160' => 'fan', 'FAN13G2403' => 'fan', 'FAN13G3303' => 'fan', 'FAN15G2435' => 'fan', 'FAN17G0672' => 'fan', 'FAN17G2441' => 'fan', 'FAN18G1024' => 'fan', 'FAN22G1458' => 'fan', 'FAN24G0037' => 'fan', 'FAN24G0429' => 'fan', 'FAN24G2387' => 'fan', 'FAN27G2746' => 'fan', 'FvH4_2g20400' => 'fve', 'FvH4_2g20420' => 'fve', 'FvH4_2g20430' => 'fve', 'FvH4_4g01270' => 'fve', 'FvH4_4g01290' => 'fve', 'FvH4_4g01300' => 'fve', 'FvH4_4g01310' => 'fve', 'FvH4_4g01330' => 'fve', 'FvH4_5g09070' => 'fve', 'Glyma.10G243800' => 'gma', 'Glyma.20G150600' => 'gma', 'Gohir.A09G219200' => 'ghi', 'Gohir.A09G219300' => 'ghi', 'Gohir.D09G221400' => 'ghi', 'Gohir.D09G221500' => 'ghi', 'Gorai.006G242600' => 'gra', 'Gorai.006G242700' => 'gra', 'GSVIVG01018044001' => 'vvi', 'HanXRQChr03g0083821' => 'han', 'HanXRQChr03g0083841' => 'han', 'HanXRQChr03g0083881' => 'han', 'HanXRQChr03g0083901' => 'han', 'HanXRQChr03g0083921' => 'han', 'HanXRQChr03g0085331' => 'han', 'HanXRQChr03g0085361' => 'han', 'HanXRQChr03g0085411' => 'han', 'HanXRQChr03g0085421' => 'han', 'HanXRQChr03g0085431' => 'han', 'HanXRQChr08g0221991' => 'han', 'HanXRQChr11g0336061' => 'han', 'HanXRQChr11g0336411' => 'han', 'Haze_11234' => 'cav', 'Hma1.2p1_0549F.1_g177010' => 'hma', 'Hma1.2p1_0602F.1_g187630' => 'hma', 'Hund14876' => 'sun', 'Hund14879' => 'sun', 'Lalb_Chr06g0160741' => 'lal', 'Lalb_Chr21g0304781' => 'lal', 'Lj3A726G19' => 'lonja', 'Lj3A726T23' => 'lonja', 'Lj3A726T24' => 'lonja', 'Lj3A726T25' => 'lonja', 'Lj3A727T17' => 'lonja', 'Lj3C726T0' => 'lonja', 'Lj3C726T2' => 'lonja', 'Lj3P725T35' => 'lonja', 'Lj3P727T10' => 'lonja', 'Lj3P727T12' => 'lonja', 'Lj3P727T14' => 'lonja', 'Lj5g0023109' => 'lja', 'Lj6P646T44' => 'lonja', 'Lsat_1_v5_gn_6_75760' => 'lsa', 'Lsat_1_v5_gn_6_75800' => 'lsa', 'Lsat_1_v5_gn_6_75900' => 'lsa', 'Lsat_1_v5_gn_6_76240' => 'lsa', 'Lsat_1_v5_gn_6_76441' => 'lsa', 'Lsat_1_v5_gn_6_76700' => 'lsa', 'Lsat_1_v5_gn_6_76760' => 'lsa', 'Manes.15G033100' => 'mes', 'Mapoly0004s0074' => 'mpo', 'Mapoly0004s0075' => 'mpo', 'Mapoly0004s0163' => 'mpo', 'Mapoly0004s0164' => 'mpo', 'Mapoly0021s0018' => 'mpo', 'Mapoly0041s0136' => 'mpo', 'Mapoly0041s0137' => 'mpo', 'Mapoly0041s0138' => 'mpo', 'Mapoly0041s0139' => 'mpo', 'Mapoly0041s0141' => 'mpo', 'Mapoly0041s0142' => 'mpo', 'Mapoly0041s0143' => 'mpo', 'Mapoly0041s0144' => 'mpo', 'Mapoly0041s0145' => 'mpo', 'Mapoly0047s0106' => 'mpo', 'Mapoly0047s0108' => 'mpo', 'Mapoly0050s0051' => 'mpo', 'Mapoly0050s0052' => 'mpo', 'Mapoly0050s0053' => 'mpo', 'Mapoly0058s0013' => 'mpo', 'Mapoly0091s0078' => 'mpo', 'Mapoly0091s0079' => 'mpo', 'Mapoly0091s0080' => 'mpo', 'Mapoly0091s0081' => 'mpo', 'Mapoly0278s0004' => 'mpo', 'Mapoly0278s0005' => 'mpo', 'Mapoly0278s0006' => 'mpo', 'MBI11_g30648_MAGBIO' => 'mbi', 'MCO03G194' => 'mco', 'MCO03G590' => 'mco', 'MCO07G312' => 'mco', 'MCO10G318' => 'mco', 'MCO12G244' => 'mco', 'MCO13G148' => 'mco', 'MCO13G194' => 'mco', 'MCO16G238' => 'mco', 'MD06G1134100' => 'mdo', 'MD13G1200100' => 'mdo', 'MD13G1200300' => 'mdo', 'MD13G1200600' => 'mdo', 'MD14G1150400' => 'mdo', 'MD16G1200000' => 'mdo', 'Medtr1g102570' => 'mtr', 'Medtr1g102780' => 'mtr', 'Medtr1g102800' => 'mtr', 'Medtr1g102810' => 'mtr', 'Medtr1g102830' => 'mtr', 'MELO3C006499.2' => 'cme', 'Migut.G00385' => 'egut', 'MSTRG.4063' => 'ama', 'Nitab4.5_0000090g0260' => 'nta', 'Nitab4.5_0000977g0030' => 'nta', 'Nitab4.5_0002541g0040' => 'nta', 'Nitab4.5_0007068g0040' => 'nta', 'Nn005s41408' => 'nnu', 'Nn005s41410' => 'nnu', 'Oeu010310.1' => 'oeu', 'Oeu010311.1' => 'oeu', 'Oeu043472.1' => 'oeu', 'Os01g0246400' => 'osa', 'Os04g0267950' => 'osa', 'Os07g0178700' => 'osa', 'Os07g0178800' => 'osa', 'Peaxi162Scf00316g00046' => 'pax', 'Peaxi162Scf00316g00049' => 'pax', 'Peaxi162Scf00316g00059' => 'pax', 'Peaxi162Scf00316g00328' => 'pax', 'Peaxi162Scf00316g00329' => 'pax', 'Peaxi162Scf00316g00411' => 'pax', 'Peaxi162Scf00316g00521' => 'pax', 'Peaxi162Scf00492g00068' => 'pax', 'Peaxi162Scf35631g00002' => 'pax', 'PGR142G3720' => 'pgr', 'PGSC0003DMG400006442' => 'stu', 'Phvul.007G062000' => 'pvu', 'Potri.008G157750' => 'ptr', 'Potri.008G157900' => 'ptr', 'Potri.008G158000' => 'ptr', 'Potri.008G158200' => 'ptr', 'Pp3c11_7280' => 'ppa', 'Pp3c11_7980' => 'ppa', 'Pp3c12_19450' => 'ppa', 'Pp3c14_1480' => 'ppa', 'Pp3c14_1501' => 'ppa', 'Pp3c16_4900' => 'ppa', 'Pp3c16_5010' => 'ppa', 'Pp3c16_5060' => 'ppa', 'Pp3c19_18250' => 'ppa', 'Pp3c23_8530' => 'ppa', 'Pp3c23_8550' => 'ppa', 'Pp3c24_9670' => 'ppa', 'Pp3c2_21390' => 'ppa', 'Pp3c2_31380' => 'ppa', 'Pp3c3_16620' => 'ppa', 'Pp3c3_8090' => 'ppa', 'Pp3c3_8110' => 'ppa', 'Pp3c3_8130' => 'ppa', 'Pp3c3_8150' => 'ppa', 'Pp3c4_14320' => 'ppa', 'Pp3c6_2560' => 'ppa', 'Pp3c9_16700' => 'ppa', 'PRCOL_00000234' => 'pco', 'PRCOL_00000235' => 'pco', 'PRCOL_00000777' => 'pco', 'PRCOL_00002344' => 'pco', 'PRCOL_00002372' => 'pco', 'PRCOL_00006120' => 'pco', 'Prupe.1G021400' => 'ppe', 'Prupe.1G021500' => 'ppe', 'Prupe.1G021600' => 'ppe', 'Prupe.1G021700' => 'ppe', 'Prupe.1G021800' => 'ppe', 'Prupe.5G145100' => 'ppe', 'Psat6g204040' => 'psa', 'Psat6g204800' => 'psa', 'Psat6g204920' => 'psa', 'Psat6g204960' => 'psa', 'Psat6g205080' => 'psa', 'PSO017G0271' => 'pso', 'PSO017G1276' => 'pso', 'PSO017G1429' => 'pso', 'PSO017G1861' => 'pso', 'PSO017G2787' => 'pso', 'PSO017G4466' => 'pso', 'PSO017G5118' => 'pso', 'PSO017G5420' => 'pso', 'PSO063G3678' => 'pso', 'PSO210G0546' => 'pso', 'PSO317G0001' => 'pso', 'PSO357G0512' => 'pso', 'PSO478G2682' => 'pso', 'PSO647G0001' => 'pso', 'PSO675G0001' => 'pso', 'PSO675G2699' => 'pso', 'PSO675G2849' => 'pso', 'PSO675G4991' => 'pso', 'PSO689G0001' => 'pso', 'QL06p000916' => 'qlo', 'QL06p000921' => 'qlo', 'QL06p001398' => 'qlo', 'QL06p001407' => 'qlo', 'QL06p002031' => 'qlo', 'RcHm_v2.0_Chr4g0387791' => 'rch', 'RcHm_v2.0_Chr4g0387801' => 'rch', 'RcHm_v2.0_Chr6g0286501' => 'rch', 'RcHm_v2.0_Chr6g0286511' => 'rch', 'RcHm_v2.0_Chr6g0286521' => 'rch', 'RcHm_v2.0_Chr6g0286531' => 'rch', 'RcHm_v2.0_Chr7g0189141' => 'rch', 'Rhsim02G0028700' => 'rsi', 'Rhsim02G0028800' => 'rsi', 'Rhsim02G0028900' => 'rsi', 'Rhsim02G0029000' => 'rsi', 'Rhsim02G0029100' => 'rsi', 'Rhsim02G0029200' => 'rsi', 'Rhsim02G0029300' => 'rsi', 'Rhsim02G0029400' => 'rsi', 'Rhsim02G0029500' => 'rsi', 'Rhsim02G0029600' => 'rsi', 'RhsimUnG0024000' => 'rsi', 'RhsimUnG0024100' => 'rsi', 'RhsimUnG0024200' => 'rsi', 'RhsimUnG0024300' => 'rsi', 'RhsimUnG0024400' => 'rsi', 'RhsimUnG0024500' => 'rsi', 'RhsimUnG0024700' => 'rsi', 'RhsimUnG0024800' => 'rsi', 'RhsimUnG0024900' => 'rsi', 'RhsimUnG0025100' => 'rsi', 'Sabra08G0120200' => 'sbr', 'Sabra08G0120300' => 'sbr', 'Sabra08G0120500' => 'sbr', 'Sabra08G0120600' => 'sbr', 'Sabra10G0158900' => 'sbr', 'SalBow2G3492' => 'sbo', 'Sc13g0004760' => 'sci', 'Sc13g0004770' => 'sci', 'Sed0003417' => 'sed', 'Sed0019750' => 'sed', 'SEGI_03419' => 'sgi', 'SEGI_05907' => 'sgi', 'SEGI_10682' => 'sgi', 'SEGI_13528' => 'sgi', 'SEGI_16081' => 'sgi', 'SEGI_19370' => 'sgi', 'SEGI_21015' => 'sgi', 'SEGI_21944' => 'sgi', 'SEGI_32906' => 'sgi', 'SEGI_33093' => 'sgi', 'SEGI_36110' => 'sgi', 'SEGI_40397' => 'sgi', 'SGA_v2.0_scaffold191G40426' => 'sas', 'SGA_v2.0_scaffold353G49717' => 'sas', 'SGA_v2.0_scaffold50G18550' => 'sas', 'SMO119G0173' => 'smo', 'SMO172G0002' => 'smo', 'Solyc09g082690.3' => 'sly', 'Solyc09g082700.2' => 'sly', 'Sopen09g031550' => 'spe', 'Sopen09g031560' => 'spe', 'Sp3g20540' => 'spa', 'Sp7g07580' => 'spa', 'TAR134G0002' => 'tar', 'TAR236G0001' => 'tar', 'TAR365G0892' => 'tar', 'TAR636G0166' => 'tar', 'TAR636G0646' => 'tar', 'TAR636G0869' => 'tar', 'TAR636G1317' => 'tar', 'TAR636G1744' => 'tar', 'TAR636G3358' => 'tar', 'TAR636G3436' => 'tar', 'THA.LOC104803047' => 'tha', 'Thecc.04G238900' => 'tca', 'Thhalv10021557m.g' => 'esa', 'Thhalv10026318m.g' => 'esa', 'Thhalv10026335m.g' => 'esa', 'TPR.G17433' => 'tpr', 'TPR.G18915' => 'tpr', 'TPR.G26125' => 'tpr', 'TWI09G0677' => 'twi', 'TWI73G0287' => 'twi', 'unitig_748.g8326' => 'ugi', 'vmacro15370' => 'vma', 'vmacro15371' => 'vma', 'vmacro15372' => 'vma', 'vmacro15373' => 'vma', 'vmacro15374' => 'vma', 'VMungo0720G2826' => 'vmu', 'Zm00001eb116960' => 'zma', 'Zm00001eb301260' => 'zma', 'Zm00001eb301270' => 'zma' ) $gf_id = 'HOM05D001460' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001460' ) $data_identifier = 'HOM05D001460' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 4, 'aag' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 2, 'aox' => (int) 2, 'arhy' => (int) 4, 'ath' => (int) 2, 'atr' => (int) 1, 'acertr' => (int) 10, 'cqu' => (int) 4, 'bca' => (int) 11, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 1, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 1, 'ccan' => (int) 1, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 1, 'col' => (int) 1, 'cpa' => (int) 1, 'cre' => (int) 7, 'csa' => (int) 1, 'camsi' => (int) 2, 'dca' => (int) 3, 'din' => (int) 2, 'dzi' => (int) 3, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 14, 'fve' => (int) 9, 'gma' => (int) 2, 'ghi' => (int) 4, 'gra' => (int) 2, 'vvi' => (int) 1, 'han' => (int) 13, 'cav' => (int) 1, 'hma' => (int) 2, 'sun' => (int) 2, 'lal' => (int) 2, 'lonja' => (int) 12, 'lja' => (int) 1, 'lsa' => (int) 7, 'mes' => (int) 1, 'mpo' => (int) 27, 'mbi' => (int) 1, 'mco' => (int) 8, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 1, 'egut' => (int) 1, 'ama' => (int) 1, 'nta' => (int) 4, 'nnu' => (int) 2, 'oeu' => (int) 3, 'osa' => (int) 4, 'pax' => (int) 9, 'pgr' => (int) 1, 'stu' => (int) 1, 'pvu' => (int) 1, 'ptr' => (int) 4, 'ppa' => (int) 22, 'pco' => (int) 6, 'ppe' => (int) 6, 'psa' => (int) 5, 'pso' => (int) 19, 'qlo' => (int) 5, 'rch' => (int) 7, 'rsi' => (int) 20, 'sbr' => (int) 5, 'sbo' => (int) 1, 'sci' => (int) 2, 'sed' => (int) 2, 'sgi' => (int) 12, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 2, 'tar' => (int) 10, 'tha' => (int) 1, 'tca' => (int) 1, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 2, 'ugi' => (int) 1, 'vma' => (int) 5, 'vmu' => (int) 1, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb301270' $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' => 'HOM05D001460', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '433', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p22980' => 'bna', 'A01p32340' => 'bna', 'A03p42970' => 'bna', 'A05p25880' => 'bna', 'Aa31LG8G9320' => 'aar', 'Aa31LG8G9330' => 'aar', 'Aa31LG8G9340' => 'aar', 'Aa31sc221G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1034' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1528' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.829' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2222' => 'aag', 'Ah.12g058830' => 'amhyb', 'Ah.12g058840' => 'amhyb', 'AL3G37160' => 'aly', 'AL7G41310' => 'aly', 'Aqoxy5G00395' => 'aox', 'Aqoxy5G00396' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0C8NZA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5185HY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JZ1PRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MD3LS0' => 'arhy', 'AT3G22840' => 'ath', 'AT4G14690' => 'ath', 'ATR0665G054' => 'atr', 'Atru.chr4.2344' => 'acertr', 'Atru.chr4.2346' => 'acertr', 'Atru.chr4.2347' => 'acertr', 'Atru.chr4.2348' => 'acertr', 'Atru.chr4.2355' => 'acertr', 'Atru.chr4.2356' => 'acertr', 'Atru.chr4.2358' => 'acertr', 'Atru.chr4.2359' => 'acertr', 'Atru.chr4.2360' => 'acertr', 'Atru.chr4.2361' => 'acertr', 'AUR62030476' => 'cqu', 'AUR62030478' => 'cqu', 'AUR62030819' => 'cqu', 'AUR62030820' => 'cqu', 'BcaB03g14648' => 'bca', 'BcaB04g20492' => 'bca', 'BcaB06g26399' => 'bca', 'BcaC01g03416' => 'bca', 'BcaC01g03419' => 'bca', 'BcaC01g03421' => 'bca', 'BcaC01g03424' => 'bca', 'BcaC05g28012' => 'bca', 'BcaC09g49212' => 'bca', 'BcaC09g50140' => 'bca', 'BcaNung00346' => 'bca', 'BolC1t02785H' => 'bol', 'BolC1t04095H' => 'bol', 'BolC3t17545H' => 'bol', 'BolC5t32769H' => 'bol', 'BraA01t02211Z' => 'bra', 'BraA01t03359Z' => 'bra', 'BraA03t13441Z' => 'bra', 'BraA05t21476Z' => 'bra', 'C01p28420' => 'bna', 'C01p41350' => 'bna', 'C03p52750' => 'bna', 'C03p52780' => 'bna', 'C05p40270' => 'bna', 'CAN.G1437.9' => 'can', 'CANSAT78G0035' => 'cansat', 'CANSAT78G1036' => 'cansat', 'CANSAT78G2272' => 'cansat', 'CANSAT78G2478' => 'cansat', 'CARHR098700' => 'chi', 'CARHR221120' => 'chi', 'CARHR221150' => 'chi', 'Carub.0003s2297' => 'cru', 'Carub.0007s2749' => 'cru', 'Carub.0007s2750' => 'cru', 'Carub.0007s2751' => 'cru', 'Ca_10849_v3' => 'car', 'Cc03_g04300' => 'ccan', 'CDE02G3648' => 'cde', 'CDE05G0060' => 'cde', 'CDE05G0692' => 'cde', 'CDE05G2285' => 'cde', 'CDE05G2884' => 'cde', 'CDE05G3072' => 'cde', 'Cfa008439' => 'cfa', 'Cfa008441' => 'cfa', 'Cfa008443' => 'cfa', 'Cfa008448' => 'cfa', 'Ciclev10005974m.g' => 'ccl', 'Ciclev10006006m.g' => 'ccl', 'Ciclev10006775m.g' => 'ccl', 'CiPaw.02G120400' => 'cil', 'CiPaw.02G120500' => 'cil', 'CiPaw.02G120600' => 'cil', 'ClCG05G004850' => 'cla', 'COL.COLO4_21566' => 'col', 'Cpa.g.sc44.124' => 'cpa', 'Cre07.g320400' => 'cre', 'Cre07.g320450' => 'cre', 'Cre08.g384650' => 'cre', 'Cre09.g393173' => 'cre', 'Cre09.g394325' => 'cre', 'Cre14.g626750' => 'cre', 'Cre16.g679250' => 'cre', 'CsaV3_3G012890' => 'csa', 'CSS0010865' => 'camsi', 'CSS0044338' => 'camsi', 'DCAR_002366' => 'dca', 'DCAR_030687' => 'dca', 'DCAR_030688' => 'dca', 'Dinv14047' => 'din', 'Dinv14048' => 'din', 'Duzib151G0105' => 'dzi', 'Duzib151G0114' => 'dzi', 'Duzib212G1029' => 'dzi', 'ECA232G3536' => 'eca', 'ECA240G0786' => 'eca', 'ECA240G1802' => 'eca', 'ECA240G3760' => 'eca', 'ECA240G3920' => 'eca', 'EL10Ac5g12536' => 'bvu', 'EL10Ac5g12537' => 'bvu', 'EL10Ac5g12538' => 'bvu', 'Eucgr.B01004' => 'egr', 'Eucgr.B01006' => 'egr', 'Eucgr.B01007' => 'egr', 'Eucgr.B01008' => 'egr', 'Eucgr.B01895' => 'egr', 'Eucgr.B01896' => 'egr', 'FAN04G1456' => 'fan', 'FAN08G1769' => 'fan', 'FAN08G2160' => 'fan', 'FAN13G2403' => 'fan', 'FAN13G3303' => 'fan', 'FAN15G2435' => 'fan', 'FAN17G0672' => 'fan', 'FAN17G2441' => 'fan', 'FAN18G1024' => 'fan', 'FAN22G1458' => 'fan', 'FAN24G0037' => 'fan', 'FAN24G0429' => 'fan', 'FAN24G2387' => 'fan', 'FAN27G2746' => 'fan', 'FvH4_2g20400' => 'fve', 'FvH4_2g20420' => 'fve', 'FvH4_2g20430' => 'fve', 'FvH4_4g01270' => 'fve', 'FvH4_4g01290' => 'fve', 'FvH4_4g01300' => 'fve', 'FvH4_4g01310' => 'fve', 'FvH4_4g01330' => 'fve', 'FvH4_5g09070' => 'fve', 'Glyma.10G243800' => 'gma', 'Glyma.20G150600' => 'gma', 'Gohir.A09G219200' => 'ghi', 'Gohir.A09G219300' => 'ghi', 'Gohir.D09G221400' => 'ghi', 'Gohir.D09G221500' => 'ghi', 'Gorai.006G242600' => 'gra', 'Gorai.006G242700' => 'gra', 'GSVIVG01018044001' => 'vvi', 'HanXRQChr03g0083821' => 'han', 'HanXRQChr03g0083841' => 'han', 'HanXRQChr03g0083881' => 'han', 'HanXRQChr03g0083901' => 'han', 'HanXRQChr03g0083921' => 'han', 'HanXRQChr03g0085331' => 'han', 'HanXRQChr03g0085361' => 'han', 'HanXRQChr03g0085411' => 'han', 'HanXRQChr03g0085421' => 'han', 'HanXRQChr03g0085431' => 'han', 'HanXRQChr08g0221991' => 'han', 'HanXRQChr11g0336061' => 'han', 'HanXRQChr11g0336411' => 'han', 'Haze_11234' => 'cav', 'Hma1.2p1_0549F.1_g177010' => 'hma', 'Hma1.2p1_0602F.1_g187630' => 'hma', 'Hund14876' => 'sun', 'Hund14879' => 'sun', 'Lalb_Chr06g0160741' => 'lal', 'Lalb_Chr21g0304781' => 'lal', 'Lj3A726G19' => 'lonja', 'Lj3A726T23' => 'lonja', 'Lj3A726T24' => 'lonja', 'Lj3A726T25' => 'lonja', 'Lj3A727T17' => 'lonja', 'Lj3C726T0' => 'lonja', 'Lj3C726T2' => 'lonja', 'Lj3P725T35' => 'lonja', 'Lj3P727T10' => 'lonja', 'Lj3P727T12' => 'lonja', 'Lj3P727T14' => 'lonja', 'Lj5g0023109' => 'lja', 'Lj6P646T44' => 'lonja', 'Lsat_1_v5_gn_6_75760' => 'lsa', 'Lsat_1_v5_gn_6_75800' => 'lsa', 'Lsat_1_v5_gn_6_75900' => 'lsa', 'Lsat_1_v5_gn_6_76240' => 'lsa', 'Lsat_1_v5_gn_6_76441' => 'lsa', 'Lsat_1_v5_gn_6_76700' => 'lsa', 'Lsat_1_v5_gn_6_76760' => 'lsa', 'Manes.15G033100' => 'mes', 'Mapoly0004s0074' => 'mpo', 'Mapoly0004s0075' => 'mpo', 'Mapoly0004s0163' => 'mpo', 'Mapoly0004s0164' => 'mpo', 'Mapoly0021s0018' => 'mpo', 'Mapoly0041s0136' => 'mpo', 'Mapoly0041s0137' => 'mpo', 'Mapoly0041s0138' => 'mpo', 'Mapoly0041s0139' => 'mpo', 'Mapoly0041s0141' => 'mpo', 'Mapoly0041s0142' => 'mpo', 'Mapoly0041s0143' => 'mpo', 'Mapoly0041s0144' => 'mpo', 'Mapoly0041s0145' => 'mpo', 'Mapoly0047s0106' => 'mpo', 'Mapoly0047s0108' => 'mpo', 'Mapoly0050s0051' => 'mpo', 'Mapoly0050s0052' => 'mpo', 'Mapoly0050s0053' => 'mpo', 'Mapoly0058s0013' => 'mpo', 'Mapoly0091s0078' => 'mpo', 'Mapoly0091s0079' => 'mpo', 'Mapoly0091s0080' => 'mpo', 'Mapoly0091s0081' => 'mpo', 'Mapoly0278s0004' => 'mpo', 'Mapoly0278s0005' => 'mpo', 'Mapoly0278s0006' => 'mpo', 'MBI11_g30648_MAGBIO' => 'mbi', 'MCO03G194' => 'mco', 'MCO03G590' => 'mco', 'MCO07G312' => 'mco', 'MCO10G318' => 'mco', 'MCO12G244' => 'mco', 'MCO13G148' => 'mco', 'MCO13G194' => 'mco', 'MCO16G238' => 'mco', 'MD06G1134100' => 'mdo', 'MD13G1200100' => 'mdo', 'MD13G1200300' => 'mdo', 'MD13G1200600' => 'mdo', 'MD14G1150400' => 'mdo', 'MD16G1200000' => 'mdo', 'Medtr1g102570' => 'mtr', 'Medtr1g102780' => 'mtr', 'Medtr1g102800' => 'mtr', 'Medtr1g102810' => 'mtr', 'Medtr1g102830' => 'mtr', 'MELO3C006499.2' => 'cme', 'Migut.G00385' => 'egut', 'MSTRG.4063' => 'ama', 'Nitab4.5_0000090g0260' => 'nta', 'Nitab4.5_0000977g0030' => 'nta', 'Nitab4.5_0002541g0040' => 'nta', 'Nitab4.5_0007068g0040' => 'nta', 'Nn005s41408' => 'nnu', 'Nn005s41410' => 'nnu', 'Oeu010310.1' => 'oeu', 'Oeu010311.1' => 'oeu', 'Oeu043472.1' => 'oeu', 'Os01g0246400' => 'osa', 'Os04g0267950' => 'osa', 'Os07g0178700' => 'osa', 'Os07g0178800' => 'osa', 'Peaxi162Scf00316g00046' => 'pax', 'Peaxi162Scf00316g00049' => 'pax', 'Peaxi162Scf00316g00059' => 'pax', 'Peaxi162Scf00316g00328' => 'pax', 'Peaxi162Scf00316g00329' => 'pax', 'Peaxi162Scf00316g00411' => 'pax', 'Peaxi162Scf00316g00521' => 'pax', 'Peaxi162Scf00492g00068' => 'pax', 'Peaxi162Scf35631g00002' => 'pax', 'PGR142G3720' => 'pgr', 'PGSC0003DMG400006442' => 'stu', 'Phvul.007G062000' => 'pvu', 'Potri.008G157750' => 'ptr', 'Potri.008G157900' => 'ptr', 'Potri.008G158000' => 'ptr', 'Potri.008G158200' => 'ptr', 'Pp3c11_7280' => 'ppa', 'Pp3c11_7980' => 'ppa', 'Pp3c12_19450' => 'ppa', 'Pp3c14_1480' => 'ppa', 'Pp3c14_1501' => 'ppa', 'Pp3c16_4900' => 'ppa', 'Pp3c16_5010' => 'ppa', 'Pp3c16_5060' => 'ppa', 'Pp3c19_18250' => 'ppa', 'Pp3c23_8530' => 'ppa', 'Pp3c23_8550' => 'ppa', 'Pp3c24_9670' => 'ppa', 'Pp3c2_21390' => 'ppa', 'Pp3c2_31380' => 'ppa', 'Pp3c3_16620' => 'ppa', 'Pp3c3_8090' => 'ppa', 'Pp3c3_8110' => 'ppa', 'Pp3c3_8130' => 'ppa', 'Pp3c3_8150' => 'ppa', 'Pp3c4_14320' => 'ppa', 'Pp3c6_2560' => 'ppa', 'Pp3c9_16700' => 'ppa', 'PRCOL_00000234' => 'pco', 'PRCOL_00000235' => 'pco', 'PRCOL_00000777' => 'pco', 'PRCOL_00002344' => 'pco', 'PRCOL_00002372' => 'pco', 'PRCOL_00006120' => 'pco', 'Prupe.1G021400' => 'ppe', 'Prupe.1G021500' => 'ppe', 'Prupe.1G021600' => 'ppe', 'Prupe.1G021700' => 'ppe', 'Prupe.1G021800' => 'ppe', 'Prupe.5G145100' => 'ppe', 'Psat6g204040' => 'psa', 'Psat6g204800' => 'psa', 'Psat6g204920' => 'psa', 'Psat6g204960' => 'psa', 'Psat6g205080' => 'psa', 'PSO017G0271' => 'pso', 'PSO017G1276' => 'pso', 'PSO017G1429' => 'pso', 'PSO017G1861' => 'pso', 'PSO017G2787' => 'pso', 'PSO017G4466' => 'pso', 'PSO017G5118' => 'pso', 'PSO017G5420' => 'pso', 'PSO063G3678' => 'pso', 'PSO210G0546' => 'pso', 'PSO317G0001' => 'pso', 'PSO357G0512' => 'pso', 'PSO478G2682' => 'pso', 'PSO647G0001' => 'pso', 'PSO675G0001' => 'pso', 'PSO675G2699' => 'pso', 'PSO675G2849' => 'pso', 'PSO675G4991' => 'pso', 'PSO689G0001' => 'pso', 'QL06p000916' => 'qlo', 'QL06p000921' => 'qlo', 'QL06p001398' => 'qlo', 'QL06p001407' => 'qlo', 'QL06p002031' => 'qlo', 'RcHm_v2.0_Chr4g0387791' => 'rch', 'RcHm_v2.0_Chr4g0387801' => 'rch', 'RcHm_v2.0_Chr6g0286501' => 'rch', 'RcHm_v2.0_Chr6g0286511' => 'rch', 'RcHm_v2.0_Chr6g0286521' => 'rch', 'RcHm_v2.0_Chr6g0286531' => 'rch', 'RcHm_v2.0_Chr7g0189141' => 'rch', 'Rhsim02G0028700' => 'rsi', 'Rhsim02G0028800' => 'rsi', 'Rhsim02G0028900' => 'rsi', 'Rhsim02G0029000' => 'rsi', 'Rhsim02G0029100' => 'rsi', 'Rhsim02G0029200' => 'rsi', 'Rhsim02G0029300' => 'rsi', 'Rhsim02G0029400' => 'rsi', 'Rhsim02G0029500' => 'rsi', 'Rhsim02G0029600' => 'rsi', 'RhsimUnG0024000' => 'rsi', 'RhsimUnG0024100' => 'rsi', 'RhsimUnG0024200' => 'rsi', 'RhsimUnG0024300' => 'rsi', 'RhsimUnG0024400' => 'rsi', 'RhsimUnG0024500' => 'rsi', 'RhsimUnG0024700' => 'rsi', 'RhsimUnG0024800' => 'rsi', 'RhsimUnG0024900' => 'rsi', 'RhsimUnG0025100' => 'rsi', 'Sabra08G0120200' => 'sbr', 'Sabra08G0120300' => 'sbr', 'Sabra08G0120500' => 'sbr', 'Sabra08G0120600' => 'sbr', 'Sabra10G0158900' => 'sbr', 'SalBow2G3492' => 'sbo', 'Sc13g0004760' => 'sci', 'Sc13g0004770' => 'sci', 'Sed0003417' => 'sed', 'Sed0019750' => 'sed', 'SEGI_03419' => 'sgi', 'SEGI_05907' => 'sgi', 'SEGI_10682' => 'sgi', 'SEGI_13528' => 'sgi', 'SEGI_16081' => 'sgi', 'SEGI_19370' => 'sgi', 'SEGI_21015' => 'sgi', 'SEGI_21944' => 'sgi', 'SEGI_32906' => 'sgi', 'SEGI_33093' => 'sgi', 'SEGI_36110' => 'sgi', 'SEGI_40397' => 'sgi', 'SGA_v2.0_scaffold191G40426' => 'sas', 'SGA_v2.0_scaffold353G49717' => 'sas', 'SGA_v2.0_scaffold50G18550' => 'sas', 'SMO119G0173' => 'smo', 'SMO172G0002' => 'smo', 'Solyc09g082690.3' => 'sly', 'Solyc09g082700.2' => 'sly', 'Sopen09g031550' => 'spe', 'Sopen09g031560' => 'spe', 'Sp3g20540' => 'spa', 'Sp7g07580' => 'spa', 'TAR134G0002' => 'tar', 'TAR236G0001' => 'tar', 'TAR365G0892' => 'tar', 'TAR636G0166' => 'tar', 'TAR636G0646' => 'tar', 'TAR636G0869' => 'tar', 'TAR636G1317' => 'tar', 'TAR636G1744' => 'tar', 'TAR636G3358' => 'tar', 'TAR636G3436' => 'tar', 'THA.LOC104803047' => 'tha', 'Thecc.04G238900' => 'tca', 'Thhalv10021557m.g' => 'esa', 'Thhalv10026318m.g' => 'esa', 'Thhalv10026335m.g' => 'esa', 'TPR.G17433' => 'tpr', 'TPR.G18915' => 'tpr', 'TPR.G26125' => 'tpr', 'TWI09G0677' => 'twi', 'TWI73G0287' => 'twi', 'unitig_748.g8326' => 'ugi', 'vmacro15370' => 'vma', 'vmacro15371' => 'vma', 'vmacro15372' => 'vma', 'vmacro15373' => 'vma', 'vmacro15374' => 'vma', 'VMungo0720G2826' => 'vmu', 'Zm00001eb116960' => 'zma', 'Zm00001eb301260' => 'zma', 'Zm00001eb301270' => 'zma' ), 'gf_id' => 'HOM05D001460', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001460' ), 'data_identifier' => 'HOM05D001460', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001460', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '433', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p22980' => 'bna', 'A01p32340' => 'bna', 'A03p42970' => 'bna', 'A05p25880' => 'bna', 'Aa31LG8G9320' => 'aar', 'Aa31LG8G9330' => 'aar', 'Aa31LG8G9340' => 'aar', 'Aa31sc221G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1034' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1528' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.829' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2222' => 'aag', 'Ah.12g058830' => 'amhyb', 'Ah.12g058840' => 'amhyb', 'AL3G37160' => 'aly', 'AL7G41310' => 'aly', 'Aqoxy5G00395' => 'aox', 'Aqoxy5G00396' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0C8NZA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5185HY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JZ1PRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MD3LS0' => 'arhy', 'AT3G22840' => 'ath', 'AT4G14690' => 'ath', 'ATR0665G054' => 'atr', 'Atru.chr4.2344' => 'acertr', 'Atru.chr4.2346' => 'acertr', 'Atru.chr4.2347' => 'acertr', 'Atru.chr4.2348' => 'acertr', 'Atru.chr4.2355' => 'acertr', 'Atru.chr4.2356' => 'acertr', 'Atru.chr4.2358' => 'acertr', 'Atru.chr4.2359' => 'acertr', 'Atru.chr4.2360' => 'acertr', 'Atru.chr4.2361' => 'acertr', 'AUR62030476' => 'cqu', 'AUR62030478' => 'cqu', 'AUR62030819' => 'cqu', 'AUR62030820' => 'cqu', 'BcaB03g14648' => 'bca', 'BcaB04g20492' => 'bca', 'BcaB06g26399' => 'bca', 'BcaC01g03416' => 'bca', 'BcaC01g03419' => 'bca', 'BcaC01g03421' => 'bca', 'BcaC01g03424' => 'bca', 'BcaC05g28012' => 'bca', 'BcaC09g49212' => 'bca', 'BcaC09g50140' => 'bca', 'BcaNung00346' => 'bca', 'BolC1t02785H' => 'bol', 'BolC1t04095H' => 'bol', 'BolC3t17545H' => 'bol', 'BolC5t32769H' => 'bol', 'BraA01t02211Z' => 'bra', 'BraA01t03359Z' => 'bra', 'BraA03t13441Z' => 'bra', 'BraA05t21476Z' => 'bra', 'C01p28420' => 'bna', 'C01p41350' => 'bna', 'C03p52750' => 'bna', 'C03p52780' => 'bna', 'C05p40270' => 'bna', 'CAN.G1437.9' => 'can', 'CANSAT78G0035' => 'cansat', 'CANSAT78G1036' => 'cansat', 'CANSAT78G2272' => 'cansat', 'CANSAT78G2478' => 'cansat', 'CARHR098700' => 'chi', 'CARHR221120' => 'chi', 'CARHR221150' => 'chi', 'Carub.0003s2297' => 'cru', 'Carub.0007s2749' => 'cru', 'Carub.0007s2750' => 'cru', 'Carub.0007s2751' => 'cru', 'Ca_10849_v3' => 'car', 'Cc03_g04300' => 'ccan', 'CDE02G3648' => 'cde', 'CDE05G0060' => 'cde', 'CDE05G0692' => 'cde', 'CDE05G2285' => 'cde', 'CDE05G2884' => 'cde', 'CDE05G3072' => 'cde', 'Cfa008439' => 'cfa', 'Cfa008441' => 'cfa', 'Cfa008443' => 'cfa', 'Cfa008448' => 'cfa', 'Ciclev10005974m.g' => 'ccl', 'Ciclev10006006m.g' => 'ccl', 'Ciclev10006775m.g' => 'ccl', 'CiPaw.02G120400' => 'cil', 'CiPaw.02G120500' => 'cil', 'CiPaw.02G120600' => 'cil', 'ClCG05G004850' => 'cla', 'COL.COLO4_21566' => 'col', 'Cpa.g.sc44.124' => 'cpa', 'Cre07.g320400' => 'cre', 'Cre07.g320450' => 'cre', 'Cre08.g384650' => 'cre', 'Cre09.g393173' => 'cre', 'Cre09.g394325' => 'cre', 'Cre14.g626750' => 'cre', 'Cre16.g679250' => 'cre', 'CsaV3_3G012890' => 'csa', 'CSS0010865' => 'camsi', 'CSS0044338' => 'camsi', 'DCAR_002366' => 'dca', 'DCAR_030687' => 'dca', 'DCAR_030688' => 'dca', 'Dinv14047' => 'din', 'Dinv14048' => 'din', 'Duzib151G0105' => 'dzi', 'Duzib151G0114' => 'dzi', 'Duzib212G1029' => 'dzi', 'ECA232G3536' => 'eca', 'ECA240G0786' => 'eca', 'ECA240G1802' => 'eca', 'ECA240G3760' => 'eca', 'ECA240G3920' => 'eca', 'EL10Ac5g12536' => 'bvu', 'EL10Ac5g12537' => 'bvu', 'EL10Ac5g12538' => 'bvu', 'Eucgr.B01004' => 'egr', 'Eucgr.B01006' => 'egr', 'Eucgr.B01007' => 'egr', 'Eucgr.B01008' => 'egr', 'Eucgr.B01895' => 'egr', 'Eucgr.B01896' => 'egr', 'FAN04G1456' => 'fan', 'FAN08G1769' => 'fan', 'FAN08G2160' => 'fan', 'FAN13G2403' => 'fan', 'FAN13G3303' => 'fan', 'FAN15G2435' => 'fan', 'FAN17G0672' => 'fan', 'FAN17G2441' => 'fan', 'FAN18G1024' => 'fan', 'FAN22G1458' => 'fan', 'FAN24G0037' => 'fan', 'FAN24G0429' => 'fan', 'FAN24G2387' => 'fan', 'FAN27G2746' => 'fan', 'FvH4_2g20400' => 'fve', 'FvH4_2g20420' => 'fve', 'FvH4_2g20430' => 'fve', 'FvH4_4g01270' => 'fve', 'FvH4_4g01290' => 'fve', 'FvH4_4g01300' => 'fve', 'FvH4_4g01310' => 'fve', 'FvH4_4g01330' => 'fve', 'FvH4_5g09070' => 'fve', 'Glyma.10G243800' => 'gma', 'Glyma.20G150600' => 'gma', 'Gohir.A09G219200' => 'ghi', 'Gohir.A09G219300' => 'ghi', 'Gohir.D09G221400' => 'ghi', 'Gohir.D09G221500' => 'ghi', 'Gorai.006G242600' => 'gra', 'Gorai.006G242700' => 'gra', 'GSVIVG01018044001' => 'vvi', 'HanXRQChr03g0083821' => 'han', 'HanXRQChr03g0083841' => 'han', 'HanXRQChr03g0083881' => 'han', 'HanXRQChr03g0083901' => 'han', 'HanXRQChr03g0083921' => 'han', 'HanXRQChr03g0085331' => 'han', 'HanXRQChr03g0085361' => 'han', 'HanXRQChr03g0085411' => 'han', 'HanXRQChr03g0085421' => 'han', 'HanXRQChr03g0085431' => 'han', 'HanXRQChr08g0221991' => 'han', 'HanXRQChr11g0336061' => 'han', 'HanXRQChr11g0336411' => 'han', 'Haze_11234' => 'cav', 'Hma1.2p1_0549F.1_g177010' => 'hma', 'Hma1.2p1_0602F.1_g187630' => 'hma', 'Hund14876' => 'sun', 'Hund14879' => 'sun', 'Lalb_Chr06g0160741' => 'lal', 'Lalb_Chr21g0304781' => 'lal', 'Lj3A726G19' => 'lonja', 'Lj3A726T23' => 'lonja', 'Lj3A726T24' => 'lonja', 'Lj3A726T25' => 'lonja', 'Lj3A727T17' => 'lonja', 'Lj3C726T0' => 'lonja', 'Lj3C726T2' => 'lonja', 'Lj3P725T35' => 'lonja', 'Lj3P727T10' => 'lonja', 'Lj3P727T12' => 'lonja', 'Lj3P727T14' => 'lonja', 'Lj5g0023109' => 'lja', 'Lj6P646T44' => 'lonja', 'Lsat_1_v5_gn_6_75760' => 'lsa', 'Lsat_1_v5_gn_6_75800' => 'lsa', 'Lsat_1_v5_gn_6_75900' => 'lsa', 'Lsat_1_v5_gn_6_76240' => 'lsa', 'Lsat_1_v5_gn_6_76441' => 'lsa', 'Lsat_1_v5_gn_6_76700' => 'lsa', 'Lsat_1_v5_gn_6_76760' => 'lsa', 'Manes.15G033100' => 'mes', 'Mapoly0004s0074' => 'mpo', 'Mapoly0004s0075' => 'mpo', 'Mapoly0004s0163' => 'mpo', 'Mapoly0004s0164' => 'mpo', 'Mapoly0021s0018' => 'mpo', 'Mapoly0041s0136' => 'mpo', 'Mapoly0041s0137' => 'mpo', 'Mapoly0041s0138' => 'mpo', 'Mapoly0041s0139' => 'mpo', 'Mapoly0041s0141' => 'mpo', 'Mapoly0041s0142' => 'mpo', 'Mapoly0041s0143' => 'mpo', 'Mapoly0041s0144' => 'mpo', 'Mapoly0041s0145' => 'mpo', 'Mapoly0047s0106' => 'mpo', 'Mapoly0047s0108' => 'mpo', 'Mapoly0050s0051' => 'mpo', 'Mapoly0050s0052' => 'mpo', 'Mapoly0050s0053' => 'mpo', 'Mapoly0058s0013' => 'mpo', 'Mapoly0091s0078' => 'mpo', 'Mapoly0091s0079' => 'mpo', 'Mapoly0091s0080' => 'mpo', 'Mapoly0091s0081' => 'mpo', 'Mapoly0278s0004' => 'mpo', 'Mapoly0278s0005' => 'mpo', 'Mapoly0278s0006' => 'mpo', 'MBI11_g30648_MAGBIO' => 'mbi', 'MCO03G194' => 'mco', 'MCO03G590' => 'mco', 'MCO07G312' => 'mco', 'MCO10G318' => 'mco', 'MCO12G244' => 'mco', 'MCO13G148' => 'mco', 'MCO13G194' => 'mco', 'MCO16G238' => 'mco', 'MD06G1134100' => 'mdo', 'MD13G1200100' => 'mdo', 'MD13G1200300' => 'mdo', 'MD13G1200600' => 'mdo', 'MD14G1150400' => 'mdo', 'MD16G1200000' => 'mdo', 'Medtr1g102570' => 'mtr', 'Medtr1g102780' => 'mtr', 'Medtr1g102800' => 'mtr', 'Medtr1g102810' => 'mtr', 'Medtr1g102830' => 'mtr', 'MELO3C006499.2' => 'cme', 'Migut.G00385' => 'egut', 'MSTRG.4063' => 'ama', 'Nitab4.5_0000090g0260' => 'nta', 'Nitab4.5_0000977g0030' => 'nta', 'Nitab4.5_0002541g0040' => 'nta', 'Nitab4.5_0007068g0040' => 'nta', 'Nn005s41408' => 'nnu', 'Nn005s41410' => 'nnu', 'Oeu010310.1' => 'oeu', 'Oeu010311.1' => 'oeu', 'Oeu043472.1' => 'oeu', 'Os01g0246400' => 'osa', 'Os04g0267950' => 'osa', 'Os07g0178700' => 'osa', 'Os07g0178800' => 'osa', 'Peaxi162Scf00316g00046' => 'pax', 'Peaxi162Scf00316g00049' => 'pax', 'Peaxi162Scf00316g00059' => 'pax', 'Peaxi162Scf00316g00328' => 'pax', 'Peaxi162Scf00316g00329' => 'pax', 'Peaxi162Scf00316g00411' => 'pax', 'Peaxi162Scf00316g00521' => 'pax', 'Peaxi162Scf00492g00068' => 'pax', 'Peaxi162Scf35631g00002' => 'pax', 'PGR142G3720' => 'pgr', 'PGSC0003DMG400006442' => 'stu', 'Phvul.007G062000' => 'pvu', 'Potri.008G157750' => 'ptr', 'Potri.008G157900' => 'ptr', 'Potri.008G158000' => 'ptr', 'Potri.008G158200' => 'ptr', 'Pp3c11_7280' => 'ppa', 'Pp3c11_7980' => 'ppa', 'Pp3c12_19450' => 'ppa', 'Pp3c14_1480' => 'ppa', 'Pp3c14_1501' => 'ppa', 'Pp3c16_4900' => 'ppa', 'Pp3c16_5010' => 'ppa', 'Pp3c16_5060' => 'ppa', 'Pp3c19_18250' => 'ppa', 'Pp3c23_8530' => 'ppa', 'Pp3c23_8550' => 'ppa', 'Pp3c24_9670' => 'ppa', 'Pp3c2_21390' => 'ppa', 'Pp3c2_31380' => 'ppa', 'Pp3c3_16620' => 'ppa', 'Pp3c3_8090' => 'ppa', 'Pp3c3_8110' => 'ppa', 'Pp3c3_8130' => 'ppa', 'Pp3c3_8150' => 'ppa', 'Pp3c4_14320' => 'ppa', 'Pp3c6_2560' => 'ppa', 'Pp3c9_16700' => 'ppa', 'PRCOL_00000234' => 'pco', 'PRCOL_00000235' => 'pco', 'PRCOL_00000777' => 'pco', 'PRCOL_00002344' => 'pco', 'PRCOL_00002372' => 'pco', 'PRCOL_00006120' => 'pco', 'Prupe.1G021400' => 'ppe', 'Prupe.1G021500' => 'ppe', 'Prupe.1G021600' => 'ppe', 'Prupe.1G021700' => 'ppe', 'Prupe.1G021800' => 'ppe', 'Prupe.5G145100' => 'ppe', 'Psat6g204040' => 'psa', 'Psat6g204800' => 'psa', 'Psat6g204920' => 'psa', 'Psat6g204960' => 'psa', 'Psat6g205080' => 'psa', 'PSO017G0271' => 'pso', 'PSO017G1276' => 'pso', 'PSO017G1429' => 'pso', 'PSO017G1861' => 'pso', 'PSO017G2787' => 'pso', 'PSO017G4466' => 'pso', 'PSO017G5118' => 'pso', 'PSO017G5420' => 'pso', 'PSO063G3678' => 'pso', 'PSO210G0546' => 'pso', 'PSO317G0001' => 'pso', 'PSO357G0512' => 'pso', 'PSO478G2682' => 'pso', 'PSO647G0001' => 'pso', 'PSO675G0001' => 'pso', 'PSO675G2699' => 'pso', 'PSO675G2849' => 'pso', 'PSO675G4991' => 'pso', 'PSO689G0001' => 'pso', 'QL06p000916' => 'qlo', 'QL06p000921' => 'qlo', 'QL06p001398' => 'qlo', 'QL06p001407' => 'qlo', 'QL06p002031' => 'qlo', 'RcHm_v2.0_Chr4g0387791' => 'rch', 'RcHm_v2.0_Chr4g0387801' => 'rch', 'RcHm_v2.0_Chr6g0286501' => 'rch', 'RcHm_v2.0_Chr6g0286511' => 'rch', 'RcHm_v2.0_Chr6g0286521' => 'rch', 'RcHm_v2.0_Chr6g0286531' => 'rch', 'RcHm_v2.0_Chr7g0189141' => 'rch', 'Rhsim02G0028700' => 'rsi', 'Rhsim02G0028800' => 'rsi', 'Rhsim02G0028900' => 'rsi', 'Rhsim02G0029000' => 'rsi', 'Rhsim02G0029100' => 'rsi', 'Rhsim02G0029200' => 'rsi', 'Rhsim02G0029300' => 'rsi', 'Rhsim02G0029400' => 'rsi', 'Rhsim02G0029500' => 'rsi', 'Rhsim02G0029600' => 'rsi', 'RhsimUnG0024000' => 'rsi', 'RhsimUnG0024100' => 'rsi', 'RhsimUnG0024200' => 'rsi', 'RhsimUnG0024300' => 'rsi', 'RhsimUnG0024400' => 'rsi', 'RhsimUnG0024500' => 'rsi', 'RhsimUnG0024700' => 'rsi', 'RhsimUnG0024800' => 'rsi', 'RhsimUnG0024900' => 'rsi', 'RhsimUnG0025100' => 'rsi', 'Sabra08G0120200' => 'sbr', 'Sabra08G0120300' => 'sbr', 'Sabra08G0120500' => 'sbr', 'Sabra08G0120600' => 'sbr', 'Sabra10G0158900' => 'sbr', 'SalBow2G3492' => 'sbo', 'Sc13g0004760' => 'sci', 'Sc13g0004770' => 'sci', 'Sed0003417' => 'sed', 'Sed0019750' => 'sed', 'SEGI_03419' => 'sgi', 'SEGI_05907' => 'sgi', 'SEGI_10682' => 'sgi', 'SEGI_13528' => 'sgi', 'SEGI_16081' => 'sgi', 'SEGI_19370' => 'sgi', 'SEGI_21015' => 'sgi', 'SEGI_21944' => 'sgi', 'SEGI_32906' => 'sgi', 'SEGI_33093' => 'sgi', 'SEGI_36110' => 'sgi', 'SEGI_40397' => 'sgi', 'SGA_v2.0_scaffold191G40426' => 'sas', 'SGA_v2.0_scaffold353G49717' => 'sas', 'SGA_v2.0_scaffold50G18550' => 'sas', 'SMO119G0173' => 'smo', 'SMO172G0002' => 'smo', 'Solyc09g082690.3' => 'sly', 'Solyc09g082700.2' => 'sly', 'Sopen09g031550' => 'spe', 'Sopen09g031560' => 'spe', 'Sp3g20540' => 'spa', 'Sp7g07580' => 'spa', 'TAR134G0002' => 'tar', 'TAR236G0001' => 'tar', 'TAR365G0892' => 'tar', 'TAR636G0166' => 'tar', 'TAR636G0646' => 'tar', 'TAR636G0869' => 'tar', 'TAR636G1317' => 'tar', 'TAR636G1744' => 'tar', 'TAR636G3358' => 'tar', 'TAR636G3436' => 'tar', 'THA.LOC104803047' => 'tha', 'Thecc.04G238900' => 'tca', 'Thhalv10021557m.g' => 'esa', 'Thhalv10026318m.g' => 'esa', 'Thhalv10026335m.g' => 'esa', 'TPR.G17433' => 'tpr', 'TPR.G18915' => 'tpr', 'TPR.G26125' => 'tpr', 'TWI09G0677' => 'twi', 'TWI73G0287' => 'twi', 'unitig_748.g8326' => 'ugi', 'vmacro15370' => 'vma', 'vmacro15371' => 'vma', 'vmacro15372' => 'vma', 'vmacro15373' => 'vma', 'vmacro15374' => 'vma', 'VMungo0720G2826' => 'vmu', 'Zm00001eb116960' => 'zma', 'Zm00001eb301260' => 'zma', 'Zm00001eb301270' => 'zma' ) $gf_id = 'HOM05D001460' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001460' ) $data_identifier = 'HOM05D001460' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 4, 'aag' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 2, 'aox' => (int) 2, 'arhy' => (int) 4, 'ath' => (int) 2, 'atr' => (int) 1, 'acertr' => (int) 10, 'cqu' => (int) 4, 'bca' => (int) 11, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 1, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 1, 'ccan' => (int) 1, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 1, 'col' => (int) 1, 'cpa' => (int) 1, 'cre' => (int) 7, 'csa' => (int) 1, 'camsi' => (int) 2, 'dca' => (int) 3, 'din' => (int) 2, 'dzi' => (int) 3, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 14, 'fve' => (int) 9, 'gma' => (int) 2, 'ghi' => (int) 4, 'gra' => (int) 2, 'vvi' => (int) 1, 'han' => (int) 13, 'cav' => (int) 1, 'hma' => (int) 2, 'sun' => (int) 2, 'lal' => (int) 2, 'lonja' => (int) 12, 'lja' => (int) 1, 'lsa' => (int) 7, 'mes' => (int) 1, 'mpo' => (int) 27, 'mbi' => (int) 1, 'mco' => (int) 8, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 1, 'egut' => (int) 1, 'ama' => (int) 1, 'nta' => (int) 4, 'nnu' => (int) 2, 'oeu' => (int) 3, 'osa' => (int) 4, 'pax' => (int) 9, 'pgr' => (int) 1, 'stu' => (int) 1, 'pvu' => (int) 1, 'ptr' => (int) 4, 'ppa' => (int) 22, 'pco' => (int) 6, 'ppe' => (int) 6, 'psa' => (int) 5, 'pso' => (int) 19, 'qlo' => (int) 5, 'rch' => (int) 7, 'rsi' => (int) 20, 'sbr' => (int) 5, 'sbo' => (int) 1, 'sci' => (int) 2, 'sed' => (int) 2, 'sgi' => (int) 12, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 2, 'tar' => (int) 10, 'tha' => (int) 1, 'tca' => (int) 1, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 2, 'ugi' => (int) 1, 'vma' => (int) 5, 'vmu' => (int) 1, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb301270' $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' => 'HOM05D001460', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '433', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p22980' => 'bna', 'A01p32340' => 'bna', 'A03p42970' => 'bna', 'A05p25880' => 'bna', 'Aa31LG8G9320' => 'aar', 'Aa31LG8G9330' => 'aar', 'Aa31LG8G9340' => 'aar', 'Aa31sc221G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1034' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1528' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.829' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2222' => 'aag', 'Ah.12g058830' => 'amhyb', 'Ah.12g058840' => 'amhyb', 'AL3G37160' => 'aly', 'AL7G41310' => 'aly', 'Aqoxy5G00395' => 'aox', 'Aqoxy5G00396' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0C8NZA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5185HY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JZ1PRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MD3LS0' => 'arhy', 'AT3G22840' => 'ath', 'AT4G14690' => 'ath', 'ATR0665G054' => 'atr', 'Atru.chr4.2344' => 'acertr', 'Atru.chr4.2346' => 'acertr', 'Atru.chr4.2347' => 'acertr', 'Atru.chr4.2348' => 'acertr', 'Atru.chr4.2355' => 'acertr', 'Atru.chr4.2356' => 'acertr', 'Atru.chr4.2358' => 'acertr', 'Atru.chr4.2359' => 'acertr', 'Atru.chr4.2360' => 'acertr', 'Atru.chr4.2361' => 'acertr', 'AUR62030476' => 'cqu', 'AUR62030478' => 'cqu', 'AUR62030819' => 'cqu', 'AUR62030820' => 'cqu', 'BcaB03g14648' => 'bca', 'BcaB04g20492' => 'bca', 'BcaB06g26399' => 'bca', 'BcaC01g03416' => 'bca', 'BcaC01g03419' => 'bca', 'BcaC01g03421' => 'bca', 'BcaC01g03424' => 'bca', 'BcaC05g28012' => 'bca', 'BcaC09g49212' => 'bca', 'BcaC09g50140' => 'bca', 'BcaNung00346' => 'bca', 'BolC1t02785H' => 'bol', 'BolC1t04095H' => 'bol', 'BolC3t17545H' => 'bol', 'BolC5t32769H' => 'bol', 'BraA01t02211Z' => 'bra', 'BraA01t03359Z' => 'bra', 'BraA03t13441Z' => 'bra', 'BraA05t21476Z' => 'bra', 'C01p28420' => 'bna', 'C01p41350' => 'bna', 'C03p52750' => 'bna', 'C03p52780' => 'bna', 'C05p40270' => 'bna', 'CAN.G1437.9' => 'can', 'CANSAT78G0035' => 'cansat', 'CANSAT78G1036' => 'cansat', 'CANSAT78G2272' => 'cansat', 'CANSAT78G2478' => 'cansat', 'CARHR098700' => 'chi', 'CARHR221120' => 'chi', 'CARHR221150' => 'chi', 'Carub.0003s2297' => 'cru', 'Carub.0007s2749' => 'cru', 'Carub.0007s2750' => 'cru', 'Carub.0007s2751' => 'cru', 'Ca_10849_v3' => 'car', 'Cc03_g04300' => 'ccan', 'CDE02G3648' => 'cde', 'CDE05G0060' => 'cde', 'CDE05G0692' => 'cde', 'CDE05G2285' => 'cde', 'CDE05G2884' => 'cde', 'CDE05G3072' => 'cde', 'Cfa008439' => 'cfa', 'Cfa008441' => 'cfa', 'Cfa008443' => 'cfa', 'Cfa008448' => 'cfa', 'Ciclev10005974m.g' => 'ccl', 'Ciclev10006006m.g' => 'ccl', 'Ciclev10006775m.g' => 'ccl', 'CiPaw.02G120400' => 'cil', 'CiPaw.02G120500' => 'cil', 'CiPaw.02G120600' => 'cil', 'ClCG05G004850' => 'cla', 'COL.COLO4_21566' => 'col', 'Cpa.g.sc44.124' => 'cpa', 'Cre07.g320400' => 'cre', 'Cre07.g320450' => 'cre', 'Cre08.g384650' => 'cre', 'Cre09.g393173' => 'cre', 'Cre09.g394325' => 'cre', 'Cre14.g626750' => 'cre', 'Cre16.g679250' => 'cre', 'CsaV3_3G012890' => 'csa', 'CSS0010865' => 'camsi', 'CSS0044338' => 'camsi', 'DCAR_002366' => 'dca', 'DCAR_030687' => 'dca', 'DCAR_030688' => 'dca', 'Dinv14047' => 'din', 'Dinv14048' => 'din', 'Duzib151G0105' => 'dzi', 'Duzib151G0114' => 'dzi', 'Duzib212G1029' => 'dzi', 'ECA232G3536' => 'eca', 'ECA240G0786' => 'eca', 'ECA240G1802' => 'eca', 'ECA240G3760' => 'eca', 'ECA240G3920' => 'eca', 'EL10Ac5g12536' => 'bvu', 'EL10Ac5g12537' => 'bvu', 'EL10Ac5g12538' => 'bvu', 'Eucgr.B01004' => 'egr', 'Eucgr.B01006' => 'egr', 'Eucgr.B01007' => 'egr', 'Eucgr.B01008' => 'egr', 'Eucgr.B01895' => 'egr', 'Eucgr.B01896' => 'egr', 'FAN04G1456' => 'fan', 'FAN08G1769' => 'fan', 'FAN08G2160' => 'fan', 'FAN13G2403' => 'fan', 'FAN13G3303' => 'fan', 'FAN15G2435' => 'fan', 'FAN17G0672' => 'fan', 'FAN17G2441' => 'fan', 'FAN18G1024' => 'fan', 'FAN22G1458' => 'fan', 'FAN24G0037' => 'fan', 'FAN24G0429' => 'fan', 'FAN24G2387' => 'fan', 'FAN27G2746' => 'fan', 'FvH4_2g20400' => 'fve', 'FvH4_2g20420' => 'fve', 'FvH4_2g20430' => 'fve', 'FvH4_4g01270' => 'fve', 'FvH4_4g01290' => 'fve', 'FvH4_4g01300' => 'fve', 'FvH4_4g01310' => 'fve', 'FvH4_4g01330' => 'fve', 'FvH4_5g09070' => 'fve', 'Glyma.10G243800' => 'gma', 'Glyma.20G150600' => 'gma', 'Gohir.A09G219200' => 'ghi', 'Gohir.A09G219300' => 'ghi', 'Gohir.D09G221400' => 'ghi', 'Gohir.D09G221500' => 'ghi', 'Gorai.006G242600' => 'gra', 'Gorai.006G242700' => 'gra', 'GSVIVG01018044001' => 'vvi', 'HanXRQChr03g0083821' => 'han', 'HanXRQChr03g0083841' => 'han', 'HanXRQChr03g0083881' => 'han', 'HanXRQChr03g0083901' => 'han', 'HanXRQChr03g0083921' => 'han', 'HanXRQChr03g0085331' => 'han', 'HanXRQChr03g0085361' => 'han', 'HanXRQChr03g0085411' => 'han', 'HanXRQChr03g0085421' => 'han', 'HanXRQChr03g0085431' => 'han', 'HanXRQChr08g0221991' => 'han', 'HanXRQChr11g0336061' => 'han', 'HanXRQChr11g0336411' => 'han', 'Haze_11234' => 'cav', 'Hma1.2p1_0549F.1_g177010' => 'hma', 'Hma1.2p1_0602F.1_g187630' => 'hma', 'Hund14876' => 'sun', 'Hund14879' => 'sun', 'Lalb_Chr06g0160741' => 'lal', 'Lalb_Chr21g0304781' => 'lal', 'Lj3A726G19' => 'lonja', 'Lj3A726T23' => 'lonja', 'Lj3A726T24' => 'lonja', 'Lj3A726T25' => 'lonja', 'Lj3A727T17' => 'lonja', 'Lj3C726T0' => 'lonja', 'Lj3C726T2' => 'lonja', 'Lj3P725T35' => 'lonja', 'Lj3P727T10' => 'lonja', 'Lj3P727T12' => 'lonja', 'Lj3P727T14' => 'lonja', 'Lj5g0023109' => 'lja', 'Lj6P646T44' => 'lonja', 'Lsat_1_v5_gn_6_75760' => 'lsa', 'Lsat_1_v5_gn_6_75800' => 'lsa', 'Lsat_1_v5_gn_6_75900' => 'lsa', 'Lsat_1_v5_gn_6_76240' => 'lsa', 'Lsat_1_v5_gn_6_76441' => 'lsa', 'Lsat_1_v5_gn_6_76700' => 'lsa', 'Lsat_1_v5_gn_6_76760' => 'lsa', 'Manes.15G033100' => 'mes', 'Mapoly0004s0074' => 'mpo', 'Mapoly0004s0075' => 'mpo', 'Mapoly0004s0163' => 'mpo', 'Mapoly0004s0164' => 'mpo', 'Mapoly0021s0018' => 'mpo', 'Mapoly0041s0136' => 'mpo', 'Mapoly0041s0137' => 'mpo', 'Mapoly0041s0138' => 'mpo', 'Mapoly0041s0139' => 'mpo', 'Mapoly0041s0141' => 'mpo', 'Mapoly0041s0142' => 'mpo', 'Mapoly0041s0143' => 'mpo', 'Mapoly0041s0144' => 'mpo', 'Mapoly0041s0145' => 'mpo', 'Mapoly0047s0106' => 'mpo', 'Mapoly0047s0108' => 'mpo', 'Mapoly0050s0051' => 'mpo', 'Mapoly0050s0052' => 'mpo', 'Mapoly0050s0053' => 'mpo', 'Mapoly0058s0013' => 'mpo', 'Mapoly0091s0078' => 'mpo', 'Mapoly0091s0079' => 'mpo', 'Mapoly0091s0080' => 'mpo', 'Mapoly0091s0081' => 'mpo', 'Mapoly0278s0004' => 'mpo', 'Mapoly0278s0005' => 'mpo', 'Mapoly0278s0006' => 'mpo', 'MBI11_g30648_MAGBIO' => 'mbi', 'MCO03G194' => 'mco', 'MCO03G590' => 'mco', 'MCO07G312' => 'mco', 'MCO10G318' => 'mco', 'MCO12G244' => 'mco', 'MCO13G148' => 'mco', 'MCO13G194' => 'mco', 'MCO16G238' => 'mco', 'MD06G1134100' => 'mdo', 'MD13G1200100' => 'mdo', 'MD13G1200300' => 'mdo', 'MD13G1200600' => 'mdo', 'MD14G1150400' => 'mdo', 'MD16G1200000' => 'mdo', 'Medtr1g102570' => 'mtr', 'Medtr1g102780' => 'mtr', 'Medtr1g102800' => 'mtr', 'Medtr1g102810' => 'mtr', 'Medtr1g102830' => 'mtr', 'MELO3C006499.2' => 'cme', 'Migut.G00385' => 'egut', 'MSTRG.4063' => 'ama', 'Nitab4.5_0000090g0260' => 'nta', 'Nitab4.5_0000977g0030' => 'nta', 'Nitab4.5_0002541g0040' => 'nta', 'Nitab4.5_0007068g0040' => 'nta', 'Nn005s41408' => 'nnu', 'Nn005s41410' => 'nnu', 'Oeu010310.1' => 'oeu', 'Oeu010311.1' => 'oeu', 'Oeu043472.1' => 'oeu', 'Os01g0246400' => 'osa', 'Os04g0267950' => 'osa', 'Os07g0178700' => 'osa', 'Os07g0178800' => 'osa', 'Peaxi162Scf00316g00046' => 'pax', 'Peaxi162Scf00316g00049' => 'pax', 'Peaxi162Scf00316g00059' => 'pax', 'Peaxi162Scf00316g00328' => 'pax', 'Peaxi162Scf00316g00329' => 'pax', 'Peaxi162Scf00316g00411' => 'pax', 'Peaxi162Scf00316g00521' => 'pax', 'Peaxi162Scf00492g00068' => 'pax', 'Peaxi162Scf35631g00002' => 'pax', 'PGR142G3720' => 'pgr', 'PGSC0003DMG400006442' => 'stu', 'Phvul.007G062000' => 'pvu', 'Potri.008G157750' => 'ptr', 'Potri.008G157900' => 'ptr', 'Potri.008G158000' => 'ptr', 'Potri.008G158200' => 'ptr', 'Pp3c11_7280' => 'ppa', 'Pp3c11_7980' => 'ppa', 'Pp3c12_19450' => 'ppa', 'Pp3c14_1480' => 'ppa', 'Pp3c14_1501' => 'ppa', 'Pp3c16_4900' => 'ppa', 'Pp3c16_5010' => 'ppa', 'Pp3c16_5060' => 'ppa', 'Pp3c19_18250' => 'ppa', 'Pp3c23_8530' => 'ppa', 'Pp3c23_8550' => 'ppa', 'Pp3c24_9670' => 'ppa', 'Pp3c2_21390' => 'ppa', 'Pp3c2_31380' => 'ppa', 'Pp3c3_16620' => 'ppa', 'Pp3c3_8090' => 'ppa', 'Pp3c3_8110' => 'ppa', 'Pp3c3_8130' => 'ppa', 'Pp3c3_8150' => 'ppa', 'Pp3c4_14320' => 'ppa', 'Pp3c6_2560' => 'ppa', 'Pp3c9_16700' => 'ppa', 'PRCOL_00000234' => 'pco', 'PRCOL_00000235' => 'pco', 'PRCOL_00000777' => 'pco', 'PRCOL_00002344' => 'pco', 'PRCOL_00002372' => 'pco', 'PRCOL_00006120' => 'pco', 'Prupe.1G021400' => 'ppe', 'Prupe.1G021500' => 'ppe', 'Prupe.1G021600' => 'ppe', 'Prupe.1G021700' => 'ppe', 'Prupe.1G021800' => 'ppe', 'Prupe.5G145100' => 'ppe', 'Psat6g204040' => 'psa', 'Psat6g204800' => 'psa', 'Psat6g204920' => 'psa', 'Psat6g204960' => 'psa', 'Psat6g205080' => 'psa', 'PSO017G0271' => 'pso', 'PSO017G1276' => 'pso', 'PSO017G1429' => 'pso', 'PSO017G1861' => 'pso', 'PSO017G2787' => 'pso', 'PSO017G4466' => 'pso', 'PSO017G5118' => 'pso', 'PSO017G5420' => 'pso', 'PSO063G3678' => 'pso', 'PSO210G0546' => 'pso', 'PSO317G0001' => 'pso', 'PSO357G0512' => 'pso', 'PSO478G2682' => 'pso', 'PSO647G0001' => 'pso', 'PSO675G0001' => 'pso', 'PSO675G2699' => 'pso', 'PSO675G2849' => 'pso', 'PSO675G4991' => 'pso', 'PSO689G0001' => 'pso', 'QL06p000916' => 'qlo', 'QL06p000921' => 'qlo', 'QL06p001398' => 'qlo', 'QL06p001407' => 'qlo', 'QL06p002031' => 'qlo', 'RcHm_v2.0_Chr4g0387791' => 'rch', 'RcHm_v2.0_Chr4g0387801' => 'rch', 'RcHm_v2.0_Chr6g0286501' => 'rch', 'RcHm_v2.0_Chr6g0286511' => 'rch', 'RcHm_v2.0_Chr6g0286521' => 'rch', 'RcHm_v2.0_Chr6g0286531' => 'rch', 'RcHm_v2.0_Chr7g0189141' => 'rch', 'Rhsim02G0028700' => 'rsi', 'Rhsim02G0028800' => 'rsi', 'Rhsim02G0028900' => 'rsi', 'Rhsim02G0029000' => 'rsi', 'Rhsim02G0029100' => 'rsi', 'Rhsim02G0029200' => 'rsi', 'Rhsim02G0029300' => 'rsi', 'Rhsim02G0029400' => 'rsi', 'Rhsim02G0029500' => 'rsi', 'Rhsim02G0029600' => 'rsi', 'RhsimUnG0024000' => 'rsi', 'RhsimUnG0024100' => 'rsi', 'RhsimUnG0024200' => 'rsi', 'RhsimUnG0024300' => 'rsi', 'RhsimUnG0024400' => 'rsi', 'RhsimUnG0024500' => 'rsi', 'RhsimUnG0024700' => 'rsi', 'RhsimUnG0024800' => 'rsi', 'RhsimUnG0024900' => 'rsi', 'RhsimUnG0025100' => 'rsi', 'Sabra08G0120200' => 'sbr', 'Sabra08G0120300' => 'sbr', 'Sabra08G0120500' => 'sbr', 'Sabra08G0120600' => 'sbr', 'Sabra10G0158900' => 'sbr', 'SalBow2G3492' => 'sbo', 'Sc13g0004760' => 'sci', 'Sc13g0004770' => 'sci', 'Sed0003417' => 'sed', 'Sed0019750' => 'sed', 'SEGI_03419' => 'sgi', 'SEGI_05907' => 'sgi', 'SEGI_10682' => 'sgi', 'SEGI_13528' => 'sgi', 'SEGI_16081' => 'sgi', 'SEGI_19370' => 'sgi', 'SEGI_21015' => 'sgi', 'SEGI_21944' => 'sgi', 'SEGI_32906' => 'sgi', 'SEGI_33093' => 'sgi', 'SEGI_36110' => 'sgi', 'SEGI_40397' => 'sgi', 'SGA_v2.0_scaffold191G40426' => 'sas', 'SGA_v2.0_scaffold353G49717' => 'sas', 'SGA_v2.0_scaffold50G18550' => 'sas', 'SMO119G0173' => 'smo', 'SMO172G0002' => 'smo', 'Solyc09g082690.3' => 'sly', 'Solyc09g082700.2' => 'sly', 'Sopen09g031550' => 'spe', 'Sopen09g031560' => 'spe', 'Sp3g20540' => 'spa', 'Sp7g07580' => 'spa', 'TAR134G0002' => 'tar', 'TAR236G0001' => 'tar', 'TAR365G0892' => 'tar', 'TAR636G0166' => 'tar', 'TAR636G0646' => 'tar', 'TAR636G0869' => 'tar', 'TAR636G1317' => 'tar', 'TAR636G1744' => 'tar', 'TAR636G3358' => 'tar', 'TAR636G3436' => 'tar', 'THA.LOC104803047' => 'tha', 'Thecc.04G238900' => 'tca', 'Thhalv10021557m.g' => 'esa', 'Thhalv10026318m.g' => 'esa', 'Thhalv10026335m.g' => 'esa', 'TPR.G17433' => 'tpr', 'TPR.G18915' => 'tpr', 'TPR.G26125' => 'tpr', 'TWI09G0677' => 'twi', 'TWI73G0287' => 'twi', 'unitig_748.g8326' => 'ugi', 'vmacro15370' => 'vma', 'vmacro15371' => 'vma', 'vmacro15372' => 'vma', 'vmacro15373' => 'vma', 'vmacro15374' => 'vma', 'VMungo0720G2826' => 'vmu', 'Zm00001eb116960' => 'zma', 'Zm00001eb301260' => 'zma', 'Zm00001eb301270' => 'zma' ), 'gf_id' => 'HOM05D001460', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001460' ), 'data_identifier' => 'HOM05D001460', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001460', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '433', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p22980' => 'bna', 'A01p32340' => 'bna', 'A03p42970' => 'bna', 'A05p25880' => 'bna', 'Aa31LG8G9320' => 'aar', 'Aa31LG8G9330' => 'aar', 'Aa31LG8G9340' => 'aar', 'Aa31sc221G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1034' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1528' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.829' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2222' => 'aag', 'Ah.12g058830' => 'amhyb', 'Ah.12g058840' => 'amhyb', 'AL3G37160' => 'aly', 'AL7G41310' => 'aly', 'Aqoxy5G00395' => 'aox', 'Aqoxy5G00396' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0C8NZA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5185HY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JZ1PRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MD3LS0' => 'arhy', 'AT3G22840' => 'ath', 'AT4G14690' => 'ath', 'ATR0665G054' => 'atr', 'Atru.chr4.2344' => 'acertr', 'Atru.chr4.2346' => 'acertr', 'Atru.chr4.2347' => 'acertr', 'Atru.chr4.2348' => 'acertr', 'Atru.chr4.2355' => 'acertr', 'Atru.chr4.2356' => 'acertr', 'Atru.chr4.2358' => 'acertr', 'Atru.chr4.2359' => 'acertr', 'Atru.chr4.2360' => 'acertr', 'Atru.chr4.2361' => 'acertr', 'AUR62030476' => 'cqu', 'AUR62030478' => 'cqu', 'AUR62030819' => 'cqu', 'AUR62030820' => 'cqu', 'BcaB03g14648' => 'bca', 'BcaB04g20492' => 'bca', 'BcaB06g26399' => 'bca', 'BcaC01g03416' => 'bca', 'BcaC01g03419' => 'bca', 'BcaC01g03421' => 'bca', 'BcaC01g03424' => 'bca', 'BcaC05g28012' => 'bca', 'BcaC09g49212' => 'bca', 'BcaC09g50140' => 'bca', 'BcaNung00346' => 'bca', 'BolC1t02785H' => 'bol', 'BolC1t04095H' => 'bol', 'BolC3t17545H' => 'bol', 'BolC5t32769H' => 'bol', 'BraA01t02211Z' => 'bra', 'BraA01t03359Z' => 'bra', 'BraA03t13441Z' => 'bra', 'BraA05t21476Z' => 'bra', 'C01p28420' => 'bna', 'C01p41350' => 'bna', 'C03p52750' => 'bna', 'C03p52780' => 'bna', 'C05p40270' => 'bna', 'CAN.G1437.9' => 'can', 'CANSAT78G0035' => 'cansat', 'CANSAT78G1036' => 'cansat', 'CANSAT78G2272' => 'cansat', 'CANSAT78G2478' => 'cansat', 'CARHR098700' => 'chi', 'CARHR221120' => 'chi', 'CARHR221150' => 'chi', 'Carub.0003s2297' => 'cru', 'Carub.0007s2749' => 'cru', 'Carub.0007s2750' => 'cru', 'Carub.0007s2751' => 'cru', 'Ca_10849_v3' => 'car', 'Cc03_g04300' => 'ccan', 'CDE02G3648' => 'cde', 'CDE05G0060' => 'cde', 'CDE05G0692' => 'cde', 'CDE05G2285' => 'cde', 'CDE05G2884' => 'cde', 'CDE05G3072' => 'cde', 'Cfa008439' => 'cfa', 'Cfa008441' => 'cfa', 'Cfa008443' => 'cfa', 'Cfa008448' => 'cfa', 'Ciclev10005974m.g' => 'ccl', 'Ciclev10006006m.g' => 'ccl', 'Ciclev10006775m.g' => 'ccl', 'CiPaw.02G120400' => 'cil', 'CiPaw.02G120500' => 'cil', 'CiPaw.02G120600' => 'cil', 'ClCG05G004850' => 'cla', 'COL.COLO4_21566' => 'col', 'Cpa.g.sc44.124' => 'cpa', 'Cre07.g320400' => 'cre', 'Cre07.g320450' => 'cre', 'Cre08.g384650' => 'cre', 'Cre09.g393173' => 'cre', 'Cre09.g394325' => 'cre', 'Cre14.g626750' => 'cre', 'Cre16.g679250' => 'cre', 'CsaV3_3G012890' => 'csa', 'CSS0010865' => 'camsi', 'CSS0044338' => 'camsi', 'DCAR_002366' => 'dca', 'DCAR_030687' => 'dca', 'DCAR_030688' => 'dca', 'Dinv14047' => 'din', 'Dinv14048' => 'din', 'Duzib151G0105' => 'dzi', 'Duzib151G0114' => 'dzi', 'Duzib212G1029' => 'dzi', 'ECA232G3536' => 'eca', 'ECA240G0786' => 'eca', 'ECA240G1802' => 'eca', 'ECA240G3760' => 'eca', 'ECA240G3920' => 'eca', 'EL10Ac5g12536' => 'bvu', 'EL10Ac5g12537' => 'bvu', 'EL10Ac5g12538' => 'bvu', 'Eucgr.B01004' => 'egr', 'Eucgr.B01006' => 'egr', 'Eucgr.B01007' => 'egr', 'Eucgr.B01008' => 'egr', 'Eucgr.B01895' => 'egr', 'Eucgr.B01896' => 'egr', 'FAN04G1456' => 'fan', 'FAN08G1769' => 'fan', 'FAN08G2160' => 'fan', 'FAN13G2403' => 'fan', 'FAN13G3303' => 'fan', 'FAN15G2435' => 'fan', 'FAN17G0672' => 'fan', 'FAN17G2441' => 'fan', 'FAN18G1024' => 'fan', 'FAN22G1458' => 'fan', 'FAN24G0037' => 'fan', 'FAN24G0429' => 'fan', 'FAN24G2387' => 'fan', 'FAN27G2746' => 'fan', 'FvH4_2g20400' => 'fve', 'FvH4_2g20420' => 'fve', 'FvH4_2g20430' => 'fve', 'FvH4_4g01270' => 'fve', 'FvH4_4g01290' => 'fve', 'FvH4_4g01300' => 'fve', 'FvH4_4g01310' => 'fve', 'FvH4_4g01330' => 'fve', 'FvH4_5g09070' => 'fve', 'Glyma.10G243800' => 'gma', 'Glyma.20G150600' => 'gma', 'Gohir.A09G219200' => 'ghi', 'Gohir.A09G219300' => 'ghi', 'Gohir.D09G221400' => 'ghi', 'Gohir.D09G221500' => 'ghi', 'Gorai.006G242600' => 'gra', 'Gorai.006G242700' => 'gra', 'GSVIVG01018044001' => 'vvi', 'HanXRQChr03g0083821' => 'han', 'HanXRQChr03g0083841' => 'han', 'HanXRQChr03g0083881' => 'han', 'HanXRQChr03g0083901' => 'han', 'HanXRQChr03g0083921' => 'han', 'HanXRQChr03g0085331' => 'han', 'HanXRQChr03g0085361' => 'han', 'HanXRQChr03g0085411' => 'han', 'HanXRQChr03g0085421' => 'han', 'HanXRQChr03g0085431' => 'han', 'HanXRQChr08g0221991' => 'han', 'HanXRQChr11g0336061' => 'han', 'HanXRQChr11g0336411' => 'han', 'Haze_11234' => 'cav', 'Hma1.2p1_0549F.1_g177010' => 'hma', 'Hma1.2p1_0602F.1_g187630' => 'hma', 'Hund14876' => 'sun', 'Hund14879' => 'sun', 'Lalb_Chr06g0160741' => 'lal', 'Lalb_Chr21g0304781' => 'lal', 'Lj3A726G19' => 'lonja', 'Lj3A726T23' => 'lonja', 'Lj3A726T24' => 'lonja', 'Lj3A726T25' => 'lonja', 'Lj3A727T17' => 'lonja', 'Lj3C726T0' => 'lonja', 'Lj3C726T2' => 'lonja', 'Lj3P725T35' => 'lonja', 'Lj3P727T10' => 'lonja', 'Lj3P727T12' => 'lonja', 'Lj3P727T14' => 'lonja', 'Lj5g0023109' => 'lja', 'Lj6P646T44' => 'lonja', 'Lsat_1_v5_gn_6_75760' => 'lsa', 'Lsat_1_v5_gn_6_75800' => 'lsa', 'Lsat_1_v5_gn_6_75900' => 'lsa', 'Lsat_1_v5_gn_6_76240' => 'lsa', 'Lsat_1_v5_gn_6_76441' => 'lsa', 'Lsat_1_v5_gn_6_76700' => 'lsa', 'Lsat_1_v5_gn_6_76760' => 'lsa', 'Manes.15G033100' => 'mes', 'Mapoly0004s0074' => 'mpo', 'Mapoly0004s0075' => 'mpo', 'Mapoly0004s0163' => 'mpo', 'Mapoly0004s0164' => 'mpo', 'Mapoly0021s0018' => 'mpo', 'Mapoly0041s0136' => 'mpo', 'Mapoly0041s0137' => 'mpo', 'Mapoly0041s0138' => 'mpo', 'Mapoly0041s0139' => 'mpo', 'Mapoly0041s0141' => 'mpo', 'Mapoly0041s0142' => 'mpo', 'Mapoly0041s0143' => 'mpo', 'Mapoly0041s0144' => 'mpo', 'Mapoly0041s0145' => 'mpo', 'Mapoly0047s0106' => 'mpo', 'Mapoly0047s0108' => 'mpo', 'Mapoly0050s0051' => 'mpo', 'Mapoly0050s0052' => 'mpo', 'Mapoly0050s0053' => 'mpo', 'Mapoly0058s0013' => 'mpo', 'Mapoly0091s0078' => 'mpo', 'Mapoly0091s0079' => 'mpo', 'Mapoly0091s0080' => 'mpo', 'Mapoly0091s0081' => 'mpo', 'Mapoly0278s0004' => 'mpo', 'Mapoly0278s0005' => 'mpo', 'Mapoly0278s0006' => 'mpo', 'MBI11_g30648_MAGBIO' => 'mbi', 'MCO03G194' => 'mco', 'MCO03G590' => 'mco', 'MCO07G312' => 'mco', 'MCO10G318' => 'mco', 'MCO12G244' => 'mco', 'MCO13G148' => 'mco', 'MCO13G194' => 'mco', 'MCO16G238' => 'mco', 'MD06G1134100' => 'mdo', 'MD13G1200100' => 'mdo', 'MD13G1200300' => 'mdo', 'MD13G1200600' => 'mdo', 'MD14G1150400' => 'mdo', 'MD16G1200000' => 'mdo', 'Medtr1g102570' => 'mtr', 'Medtr1g102780' => 'mtr', 'Medtr1g102800' => 'mtr', 'Medtr1g102810' => 'mtr', 'Medtr1g102830' => 'mtr', 'MELO3C006499.2' => 'cme', 'Migut.G00385' => 'egut', 'MSTRG.4063' => 'ama', 'Nitab4.5_0000090g0260' => 'nta', 'Nitab4.5_0000977g0030' => 'nta', 'Nitab4.5_0002541g0040' => 'nta', 'Nitab4.5_0007068g0040' => 'nta', 'Nn005s41408' => 'nnu', 'Nn005s41410' => 'nnu', 'Oeu010310.1' => 'oeu', 'Oeu010311.1' => 'oeu', 'Oeu043472.1' => 'oeu', 'Os01g0246400' => 'osa', 'Os04g0267950' => 'osa', 'Os07g0178700' => 'osa', 'Os07g0178800' => 'osa', 'Peaxi162Scf00316g00046' => 'pax', 'Peaxi162Scf00316g00049' => 'pax', 'Peaxi162Scf00316g00059' => 'pax', 'Peaxi162Scf00316g00328' => 'pax', 'Peaxi162Scf00316g00329' => 'pax', 'Peaxi162Scf00316g00411' => 'pax', 'Peaxi162Scf00316g00521' => 'pax', 'Peaxi162Scf00492g00068' => 'pax', 'Peaxi162Scf35631g00002' => 'pax', 'PGR142G3720' => 'pgr', 'PGSC0003DMG400006442' => 'stu', 'Phvul.007G062000' => 'pvu', 'Potri.008G157750' => 'ptr', 'Potri.008G157900' => 'ptr', 'Potri.008G158000' => 'ptr', 'Potri.008G158200' => 'ptr', 'Pp3c11_7280' => 'ppa', 'Pp3c11_7980' => 'ppa', 'Pp3c12_19450' => 'ppa', 'Pp3c14_1480' => 'ppa', 'Pp3c14_1501' => 'ppa', 'Pp3c16_4900' => 'ppa', 'Pp3c16_5010' => 'ppa', 'Pp3c16_5060' => 'ppa', 'Pp3c19_18250' => 'ppa', 'Pp3c23_8530' => 'ppa', 'Pp3c23_8550' => 'ppa', 'Pp3c24_9670' => 'ppa', 'Pp3c2_21390' => 'ppa', 'Pp3c2_31380' => 'ppa', 'Pp3c3_16620' => 'ppa', 'Pp3c3_8090' => 'ppa', 'Pp3c3_8110' => 'ppa', 'Pp3c3_8130' => 'ppa', 'Pp3c3_8150' => 'ppa', 'Pp3c4_14320' => 'ppa', 'Pp3c6_2560' => 'ppa', 'Pp3c9_16700' => 'ppa', 'PRCOL_00000234' => 'pco', 'PRCOL_00000235' => 'pco', 'PRCOL_00000777' => 'pco', 'PRCOL_00002344' => 'pco', 'PRCOL_00002372' => 'pco', 'PRCOL_00006120' => 'pco', 'Prupe.1G021400' => 'ppe', 'Prupe.1G021500' => 'ppe', 'Prupe.1G021600' => 'ppe', 'Prupe.1G021700' => 'ppe', 'Prupe.1G021800' => 'ppe', 'Prupe.5G145100' => 'ppe', 'Psat6g204040' => 'psa', 'Psat6g204800' => 'psa', 'Psat6g204920' => 'psa', 'Psat6g204960' => 'psa', 'Psat6g205080' => 'psa', 'PSO017G0271' => 'pso', 'PSO017G1276' => 'pso', 'PSO017G1429' => 'pso', 'PSO017G1861' => 'pso', 'PSO017G2787' => 'pso', 'PSO017G4466' => 'pso', 'PSO017G5118' => 'pso', 'PSO017G5420' => 'pso', 'PSO063G3678' => 'pso', 'PSO210G0546' => 'pso', 'PSO317G0001' => 'pso', 'PSO357G0512' => 'pso', 'PSO478G2682' => 'pso', 'PSO647G0001' => 'pso', 'PSO675G0001' => 'pso', 'PSO675G2699' => 'pso', 'PSO675G2849' => 'pso', 'PSO675G4991' => 'pso', 'PSO689G0001' => 'pso', 'QL06p000916' => 'qlo', 'QL06p000921' => 'qlo', 'QL06p001398' => 'qlo', 'QL06p001407' => 'qlo', 'QL06p002031' => 'qlo', 'RcHm_v2.0_Chr4g0387791' => 'rch', 'RcHm_v2.0_Chr4g0387801' => 'rch', 'RcHm_v2.0_Chr6g0286501' => 'rch', 'RcHm_v2.0_Chr6g0286511' => 'rch', 'RcHm_v2.0_Chr6g0286521' => 'rch', 'RcHm_v2.0_Chr6g0286531' => 'rch', 'RcHm_v2.0_Chr7g0189141' => 'rch', 'Rhsim02G0028700' => 'rsi', 'Rhsim02G0028800' => 'rsi', 'Rhsim02G0028900' => 'rsi', 'Rhsim02G0029000' => 'rsi', 'Rhsim02G0029100' => 'rsi', 'Rhsim02G0029200' => 'rsi', 'Rhsim02G0029300' => 'rsi', 'Rhsim02G0029400' => 'rsi', 'Rhsim02G0029500' => 'rsi', 'Rhsim02G0029600' => 'rsi', 'RhsimUnG0024000' => 'rsi', 'RhsimUnG0024100' => 'rsi', 'RhsimUnG0024200' => 'rsi', 'RhsimUnG0024300' => 'rsi', 'RhsimUnG0024400' => 'rsi', 'RhsimUnG0024500' => 'rsi', 'RhsimUnG0024700' => 'rsi', 'RhsimUnG0024800' => 'rsi', 'RhsimUnG0024900' => 'rsi', 'RhsimUnG0025100' => 'rsi', 'Sabra08G0120200' => 'sbr', 'Sabra08G0120300' => 'sbr', 'Sabra08G0120500' => 'sbr', 'Sabra08G0120600' => 'sbr', 'Sabra10G0158900' => 'sbr', 'SalBow2G3492' => 'sbo', 'Sc13g0004760' => 'sci', 'Sc13g0004770' => 'sci', 'Sed0003417' => 'sed', 'Sed0019750' => 'sed', 'SEGI_03419' => 'sgi', 'SEGI_05907' => 'sgi', 'SEGI_10682' => 'sgi', 'SEGI_13528' => 'sgi', 'SEGI_16081' => 'sgi', 'SEGI_19370' => 'sgi', 'SEGI_21015' => 'sgi', 'SEGI_21944' => 'sgi', 'SEGI_32906' => 'sgi', 'SEGI_33093' => 'sgi', 'SEGI_36110' => 'sgi', 'SEGI_40397' => 'sgi', 'SGA_v2.0_scaffold191G40426' => 'sas', 'SGA_v2.0_scaffold353G49717' => 'sas', 'SGA_v2.0_scaffold50G18550' => 'sas', 'SMO119G0173' => 'smo', 'SMO172G0002' => 'smo', 'Solyc09g082690.3' => 'sly', 'Solyc09g082700.2' => 'sly', 'Sopen09g031550' => 'spe', 'Sopen09g031560' => 'spe', 'Sp3g20540' => 'spa', 'Sp7g07580' => 'spa', 'TAR134G0002' => 'tar', 'TAR236G0001' => 'tar', 'TAR365G0892' => 'tar', 'TAR636G0166' => 'tar', 'TAR636G0646' => 'tar', 'TAR636G0869' => 'tar', 'TAR636G1317' => 'tar', 'TAR636G1744' => 'tar', 'TAR636G3358' => 'tar', 'TAR636G3436' => 'tar', 'THA.LOC104803047' => 'tha', 'Thecc.04G238900' => 'tca', 'Thhalv10021557m.g' => 'esa', 'Thhalv10026318m.g' => 'esa', 'Thhalv10026335m.g' => 'esa', 'TPR.G17433' => 'tpr', 'TPR.G18915' => 'tpr', 'TPR.G26125' => 'tpr', 'TWI09G0677' => 'twi', 'TWI73G0287' => 'twi', 'unitig_748.g8326' => 'ugi', 'vmacro15370' => 'vma', 'vmacro15371' => 'vma', 'vmacro15372' => 'vma', 'vmacro15373' => 'vma', 'vmacro15374' => 'vma', 'VMungo0720G2826' => 'vmu', 'Zm00001eb116960' => 'zma', 'Zm00001eb301260' => 'zma', 'Zm00001eb301270' => 'zma' ) $gf_id = 'HOM05D001460' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001460' ) $data_identifier = 'HOM05D001460' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 4, 'aag' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 2, 'aox' => (int) 2, 'arhy' => (int) 4, 'ath' => (int) 2, 'atr' => (int) 1, 'acertr' => (int) 10, 'cqu' => (int) 4, 'bca' => (int) 11, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 1, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 1, 'ccan' => (int) 1, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 1, 'col' => (int) 1, 'cpa' => (int) 1, 'cre' => (int) 7, 'csa' => (int) 1, 'camsi' => (int) 2, 'dca' => (int) 3, 'din' => (int) 2, 'dzi' => (int) 3, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 14, 'fve' => (int) 9, 'gma' => (int) 2, 'ghi' => (int) 4, 'gra' => (int) 2, 'vvi' => (int) 1, 'han' => (int) 13, 'cav' => (int) 1, 'hma' => (int) 2, 'sun' => (int) 2, 'lal' => (int) 2, 'lonja' => (int) 12, 'lja' => (int) 1, 'lsa' => (int) 7, 'mes' => (int) 1, 'mpo' => (int) 27, 'mbi' => (int) 1, 'mco' => (int) 8, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 1, 'egut' => (int) 1, 'ama' => (int) 1, 'nta' => (int) 4, 'nnu' => (int) 2, 'oeu' => (int) 3, 'osa' => (int) 4, 'pax' => (int) 9, 'pgr' => (int) 1, 'stu' => (int) 1, 'pvu' => (int) 1, 'ptr' => (int) 4, 'ppa' => (int) 22, 'pco' => (int) 6, 'ppe' => (int) 6, 'psa' => (int) 5, 'pso' => (int) 19, 'qlo' => (int) 5, 'rch' => (int) 7, 'rsi' => (int) 20, 'sbr' => (int) 5, 'sbo' => (int) 1, 'sci' => (int) 2, 'sed' => (int) 2, 'sgi' => (int) 12, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 2, 'tar' => (int) 10, 'tha' => (int) 1, 'tca' => (int) 1, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 2, 'ugi' => (int) 1, 'vma' => (int) 5, 'vmu' => (int) 1, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb301270' $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' => 'HOM05D001460', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '433', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p22980' => 'bna', 'A01p32340' => 'bna', 'A03p42970' => 'bna', 'A05p25880' => 'bna', 'Aa31LG8G9320' => 'aar', 'Aa31LG8G9330' => 'aar', 'Aa31LG8G9340' => 'aar', 'Aa31sc221G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1034' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1528' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.829' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2222' => 'aag', 'Ah.12g058830' => 'amhyb', 'Ah.12g058840' => 'amhyb', 'AL3G37160' => 'aly', 'AL7G41310' => 'aly', 'Aqoxy5G00395' => 'aox', 'Aqoxy5G00396' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0C8NZA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5185HY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JZ1PRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MD3LS0' => 'arhy', 'AT3G22840' => 'ath', 'AT4G14690' => 'ath', 'ATR0665G054' => 'atr', 'Atru.chr4.2344' => 'acertr', 'Atru.chr4.2346' => 'acertr', 'Atru.chr4.2347' => 'acertr', 'Atru.chr4.2348' => 'acertr', 'Atru.chr4.2355' => 'acertr', 'Atru.chr4.2356' => 'acertr', 'Atru.chr4.2358' => 'acertr', 'Atru.chr4.2359' => 'acertr', 'Atru.chr4.2360' => 'acertr', 'Atru.chr4.2361' => 'acertr', 'AUR62030476' => 'cqu', 'AUR62030478' => 'cqu', 'AUR62030819' => 'cqu', 'AUR62030820' => 'cqu', 'BcaB03g14648' => 'bca', 'BcaB04g20492' => 'bca', 'BcaB06g26399' => 'bca', 'BcaC01g03416' => 'bca', 'BcaC01g03419' => 'bca', 'BcaC01g03421' => 'bca', 'BcaC01g03424' => 'bca', 'BcaC05g28012' => 'bca', 'BcaC09g49212' => 'bca', 'BcaC09g50140' => 'bca', 'BcaNung00346' => 'bca', 'BolC1t02785H' => 'bol', 'BolC1t04095H' => 'bol', 'BolC3t17545H' => 'bol', 'BolC5t32769H' => 'bol', 'BraA01t02211Z' => 'bra', 'BraA01t03359Z' => 'bra', 'BraA03t13441Z' => 'bra', 'BraA05t21476Z' => 'bra', 'C01p28420' => 'bna', 'C01p41350' => 'bna', 'C03p52750' => 'bna', 'C03p52780' => 'bna', 'C05p40270' => 'bna', 'CAN.G1437.9' => 'can', 'CANSAT78G0035' => 'cansat', 'CANSAT78G1036' => 'cansat', 'CANSAT78G2272' => 'cansat', 'CANSAT78G2478' => 'cansat', 'CARHR098700' => 'chi', 'CARHR221120' => 'chi', 'CARHR221150' => 'chi', 'Carub.0003s2297' => 'cru', 'Carub.0007s2749' => 'cru', 'Carub.0007s2750' => 'cru', 'Carub.0007s2751' => 'cru', 'Ca_10849_v3' => 'car', 'Cc03_g04300' => 'ccan', 'CDE02G3648' => 'cde', 'CDE05G0060' => 'cde', 'CDE05G0692' => 'cde', 'CDE05G2285' => 'cde', 'CDE05G2884' => 'cde', 'CDE05G3072' => 'cde', 'Cfa008439' => 'cfa', 'Cfa008441' => 'cfa', 'Cfa008443' => 'cfa', 'Cfa008448' => 'cfa', 'Ciclev10005974m.g' => 'ccl', 'Ciclev10006006m.g' => 'ccl', 'Ciclev10006775m.g' => 'ccl', 'CiPaw.02G120400' => 'cil', 'CiPaw.02G120500' => 'cil', 'CiPaw.02G120600' => 'cil', 'ClCG05G004850' => 'cla', 'COL.COLO4_21566' => 'col', 'Cpa.g.sc44.124' => 'cpa', 'Cre07.g320400' => 'cre', 'Cre07.g320450' => 'cre', 'Cre08.g384650' => 'cre', 'Cre09.g393173' => 'cre', 'Cre09.g394325' => 'cre', 'Cre14.g626750' => 'cre', 'Cre16.g679250' => 'cre', 'CsaV3_3G012890' => 'csa', 'CSS0010865' => 'camsi', 'CSS0044338' => 'camsi', 'DCAR_002366' => 'dca', 'DCAR_030687' => 'dca', 'DCAR_030688' => 'dca', 'Dinv14047' => 'din', 'Dinv14048' => 'din', 'Duzib151G0105' => 'dzi', 'Duzib151G0114' => 'dzi', 'Duzib212G1029' => 'dzi', 'ECA232G3536' => 'eca', 'ECA240G0786' => 'eca', 'ECA240G1802' => 'eca', 'ECA240G3760' => 'eca', 'ECA240G3920' => 'eca', 'EL10Ac5g12536' => 'bvu', 'EL10Ac5g12537' => 'bvu', 'EL10Ac5g12538' => 'bvu', 'Eucgr.B01004' => 'egr', 'Eucgr.B01006' => 'egr', 'Eucgr.B01007' => 'egr', 'Eucgr.B01008' => 'egr', 'Eucgr.B01895' => 'egr', 'Eucgr.B01896' => 'egr', 'FAN04G1456' => 'fan', 'FAN08G1769' => 'fan', 'FAN08G2160' => 'fan', 'FAN13G2403' => 'fan', 'FAN13G3303' => 'fan', 'FAN15G2435' => 'fan', 'FAN17G0672' => 'fan', 'FAN17G2441' => 'fan', 'FAN18G1024' => 'fan', 'FAN22G1458' => 'fan', 'FAN24G0037' => 'fan', 'FAN24G0429' => 'fan', 'FAN24G2387' => 'fan', 'FAN27G2746' => 'fan', 'FvH4_2g20400' => 'fve', 'FvH4_2g20420' => 'fve', 'FvH4_2g20430' => 'fve', 'FvH4_4g01270' => 'fve', 'FvH4_4g01290' => 'fve', 'FvH4_4g01300' => 'fve', 'FvH4_4g01310' => 'fve', 'FvH4_4g01330' => 'fve', 'FvH4_5g09070' => 'fve', 'Glyma.10G243800' => 'gma', 'Glyma.20G150600' => 'gma', 'Gohir.A09G219200' => 'ghi', 'Gohir.A09G219300' => 'ghi', 'Gohir.D09G221400' => 'ghi', 'Gohir.D09G221500' => 'ghi', 'Gorai.006G242600' => 'gra', 'Gorai.006G242700' => 'gra', 'GSVIVG01018044001' => 'vvi', 'HanXRQChr03g0083821' => 'han', 'HanXRQChr03g0083841' => 'han', 'HanXRQChr03g0083881' => 'han', 'HanXRQChr03g0083901' => 'han', 'HanXRQChr03g0083921' => 'han', 'HanXRQChr03g0085331' => 'han', 'HanXRQChr03g0085361' => 'han', 'HanXRQChr03g0085411' => 'han', 'HanXRQChr03g0085421' => 'han', 'HanXRQChr03g0085431' => 'han', 'HanXRQChr08g0221991' => 'han', 'HanXRQChr11g0336061' => 'han', 'HanXRQChr11g0336411' => 'han', 'Haze_11234' => 'cav', 'Hma1.2p1_0549F.1_g177010' => 'hma', 'Hma1.2p1_0602F.1_g187630' => 'hma', 'Hund14876' => 'sun', 'Hund14879' => 'sun', 'Lalb_Chr06g0160741' => 'lal', 'Lalb_Chr21g0304781' => 'lal', 'Lj3A726G19' => 'lonja', 'Lj3A726T23' => 'lonja', 'Lj3A726T24' => 'lonja', 'Lj3A726T25' => 'lonja', 'Lj3A727T17' => 'lonja', 'Lj3C726T0' => 'lonja', 'Lj3C726T2' => 'lonja', 'Lj3P725T35' => 'lonja', 'Lj3P727T10' => 'lonja', 'Lj3P727T12' => 'lonja', 'Lj3P727T14' => 'lonja', 'Lj5g0023109' => 'lja', 'Lj6P646T44' => 'lonja', 'Lsat_1_v5_gn_6_75760' => 'lsa', 'Lsat_1_v5_gn_6_75800' => 'lsa', 'Lsat_1_v5_gn_6_75900' => 'lsa', 'Lsat_1_v5_gn_6_76240' => 'lsa', 'Lsat_1_v5_gn_6_76441' => 'lsa', 'Lsat_1_v5_gn_6_76700' => 'lsa', 'Lsat_1_v5_gn_6_76760' => 'lsa', 'Manes.15G033100' => 'mes', 'Mapoly0004s0074' => 'mpo', 'Mapoly0004s0075' => 'mpo', 'Mapoly0004s0163' => 'mpo', 'Mapoly0004s0164' => 'mpo', 'Mapoly0021s0018' => 'mpo', 'Mapoly0041s0136' => 'mpo', 'Mapoly0041s0137' => 'mpo', 'Mapoly0041s0138' => 'mpo', 'Mapoly0041s0139' => 'mpo', 'Mapoly0041s0141' => 'mpo', 'Mapoly0041s0142' => 'mpo', 'Mapoly0041s0143' => 'mpo', 'Mapoly0041s0144' => 'mpo', 'Mapoly0041s0145' => 'mpo', 'Mapoly0047s0106' => 'mpo', 'Mapoly0047s0108' => 'mpo', 'Mapoly0050s0051' => 'mpo', 'Mapoly0050s0052' => 'mpo', 'Mapoly0050s0053' => 'mpo', 'Mapoly0058s0013' => 'mpo', 'Mapoly0091s0078' => 'mpo', 'Mapoly0091s0079' => 'mpo', 'Mapoly0091s0080' => 'mpo', 'Mapoly0091s0081' => 'mpo', 'Mapoly0278s0004' => 'mpo', 'Mapoly0278s0005' => 'mpo', 'Mapoly0278s0006' => 'mpo', 'MBI11_g30648_MAGBIO' => 'mbi', 'MCO03G194' => 'mco', 'MCO03G590' => 'mco', 'MCO07G312' => 'mco', 'MCO10G318' => 'mco', 'MCO12G244' => 'mco', 'MCO13G148' => 'mco', 'MCO13G194' => 'mco', 'MCO16G238' => 'mco', 'MD06G1134100' => 'mdo', 'MD13G1200100' => 'mdo', 'MD13G1200300' => 'mdo', 'MD13G1200600' => 'mdo', 'MD14G1150400' => 'mdo', 'MD16G1200000' => 'mdo', 'Medtr1g102570' => 'mtr', 'Medtr1g102780' => 'mtr', 'Medtr1g102800' => 'mtr', 'Medtr1g102810' => 'mtr', 'Medtr1g102830' => 'mtr', 'MELO3C006499.2' => 'cme', 'Migut.G00385' => 'egut', 'MSTRG.4063' => 'ama', 'Nitab4.5_0000090g0260' => 'nta', 'Nitab4.5_0000977g0030' => 'nta', 'Nitab4.5_0002541g0040' => 'nta', 'Nitab4.5_0007068g0040' => 'nta', 'Nn005s41408' => 'nnu', 'Nn005s41410' => 'nnu', 'Oeu010310.1' => 'oeu', 'Oeu010311.1' => 'oeu', 'Oeu043472.1' => 'oeu', 'Os01g0246400' => 'osa', 'Os04g0267950' => 'osa', 'Os07g0178700' => 'osa', 'Os07g0178800' => 'osa', 'Peaxi162Scf00316g00046' => 'pax', 'Peaxi162Scf00316g00049' => 'pax', 'Peaxi162Scf00316g00059' => 'pax', 'Peaxi162Scf00316g00328' => 'pax', 'Peaxi162Scf00316g00329' => 'pax', 'Peaxi162Scf00316g00411' => 'pax', 'Peaxi162Scf00316g00521' => 'pax', 'Peaxi162Scf00492g00068' => 'pax', 'Peaxi162Scf35631g00002' => 'pax', 'PGR142G3720' => 'pgr', 'PGSC0003DMG400006442' => 'stu', 'Phvul.007G062000' => 'pvu', 'Potri.008G157750' => 'ptr', 'Potri.008G157900' => 'ptr', 'Potri.008G158000' => 'ptr', 'Potri.008G158200' => 'ptr', 'Pp3c11_7280' => 'ppa', 'Pp3c11_7980' => 'ppa', 'Pp3c12_19450' => 'ppa', 'Pp3c14_1480' => 'ppa', 'Pp3c14_1501' => 'ppa', 'Pp3c16_4900' => 'ppa', 'Pp3c16_5010' => 'ppa', 'Pp3c16_5060' => 'ppa', 'Pp3c19_18250' => 'ppa', 'Pp3c23_8530' => 'ppa', 'Pp3c23_8550' => 'ppa', 'Pp3c24_9670' => 'ppa', 'Pp3c2_21390' => 'ppa', 'Pp3c2_31380' => 'ppa', 'Pp3c3_16620' => 'ppa', 'Pp3c3_8090' => 'ppa', 'Pp3c3_8110' => 'ppa', 'Pp3c3_8130' => 'ppa', 'Pp3c3_8150' => 'ppa', 'Pp3c4_14320' => 'ppa', 'Pp3c6_2560' => 'ppa', 'Pp3c9_16700' => 'ppa', 'PRCOL_00000234' => 'pco', 'PRCOL_00000235' => 'pco', 'PRCOL_00000777' => 'pco', 'PRCOL_00002344' => 'pco', 'PRCOL_00002372' => 'pco', 'PRCOL_00006120' => 'pco', 'Prupe.1G021400' => 'ppe', 'Prupe.1G021500' => 'ppe', 'Prupe.1G021600' => 'ppe', 'Prupe.1G021700' => 'ppe', 'Prupe.1G021800' => 'ppe', 'Prupe.5G145100' => 'ppe', 'Psat6g204040' => 'psa', 'Psat6g204800' => 'psa', 'Psat6g204920' => 'psa', 'Psat6g204960' => 'psa', 'Psat6g205080' => 'psa', 'PSO017G0271' => 'pso', 'PSO017G1276' => 'pso', 'PSO017G1429' => 'pso', 'PSO017G1861' => 'pso', 'PSO017G2787' => 'pso', 'PSO017G4466' => 'pso', 'PSO017G5118' => 'pso', 'PSO017G5420' => 'pso', 'PSO063G3678' => 'pso', 'PSO210G0546' => 'pso', 'PSO317G0001' => 'pso', 'PSO357G0512' => 'pso', 'PSO478G2682' => 'pso', 'PSO647G0001' => 'pso', 'PSO675G0001' => 'pso', 'PSO675G2699' => 'pso', 'PSO675G2849' => 'pso', 'PSO675G4991' => 'pso', 'PSO689G0001' => 'pso', 'QL06p000916' => 'qlo', 'QL06p000921' => 'qlo', 'QL06p001398' => 'qlo', 'QL06p001407' => 'qlo', 'QL06p002031' => 'qlo', 'RcHm_v2.0_Chr4g0387791' => 'rch', 'RcHm_v2.0_Chr4g0387801' => 'rch', 'RcHm_v2.0_Chr6g0286501' => 'rch', 'RcHm_v2.0_Chr6g0286511' => 'rch', 'RcHm_v2.0_Chr6g0286521' => 'rch', 'RcHm_v2.0_Chr6g0286531' => 'rch', 'RcHm_v2.0_Chr7g0189141' => 'rch', 'Rhsim02G0028700' => 'rsi', 'Rhsim02G0028800' => 'rsi', 'Rhsim02G0028900' => 'rsi', 'Rhsim02G0029000' => 'rsi', 'Rhsim02G0029100' => 'rsi', 'Rhsim02G0029200' => 'rsi', 'Rhsim02G0029300' => 'rsi', 'Rhsim02G0029400' => 'rsi', 'Rhsim02G0029500' => 'rsi', 'Rhsim02G0029600' => 'rsi', 'RhsimUnG0024000' => 'rsi', 'RhsimUnG0024100' => 'rsi', 'RhsimUnG0024200' => 'rsi', 'RhsimUnG0024300' => 'rsi', 'RhsimUnG0024400' => 'rsi', 'RhsimUnG0024500' => 'rsi', 'RhsimUnG0024700' => 'rsi', 'RhsimUnG0024800' => 'rsi', 'RhsimUnG0024900' => 'rsi', 'RhsimUnG0025100' => 'rsi', 'Sabra08G0120200' => 'sbr', 'Sabra08G0120300' => 'sbr', 'Sabra08G0120500' => 'sbr', 'Sabra08G0120600' => 'sbr', 'Sabra10G0158900' => 'sbr', 'SalBow2G3492' => 'sbo', 'Sc13g0004760' => 'sci', 'Sc13g0004770' => 'sci', 'Sed0003417' => 'sed', 'Sed0019750' => 'sed', 'SEGI_03419' => 'sgi', 'SEGI_05907' => 'sgi', 'SEGI_10682' => 'sgi', 'SEGI_13528' => 'sgi', 'SEGI_16081' => 'sgi', 'SEGI_19370' => 'sgi', 'SEGI_21015' => 'sgi', 'SEGI_21944' => 'sgi', 'SEGI_32906' => 'sgi', 'SEGI_33093' => 'sgi', 'SEGI_36110' => 'sgi', 'SEGI_40397' => 'sgi', 'SGA_v2.0_scaffold191G40426' => 'sas', 'SGA_v2.0_scaffold353G49717' => 'sas', 'SGA_v2.0_scaffold50G18550' => 'sas', 'SMO119G0173' => 'smo', 'SMO172G0002' => 'smo', 'Solyc09g082690.3' => 'sly', 'Solyc09g082700.2' => 'sly', 'Sopen09g031550' => 'spe', 'Sopen09g031560' => 'spe', 'Sp3g20540' => 'spa', 'Sp7g07580' => 'spa', 'TAR134G0002' => 'tar', 'TAR236G0001' => 'tar', 'TAR365G0892' => 'tar', 'TAR636G0166' => 'tar', 'TAR636G0646' => 'tar', 'TAR636G0869' => 'tar', 'TAR636G1317' => 'tar', 'TAR636G1744' => 'tar', 'TAR636G3358' => 'tar', 'TAR636G3436' => 'tar', 'THA.LOC104803047' => 'tha', 'Thecc.04G238900' => 'tca', 'Thhalv10021557m.g' => 'esa', 'Thhalv10026318m.g' => 'esa', 'Thhalv10026335m.g' => 'esa', 'TPR.G17433' => 'tpr', 'TPR.G18915' => 'tpr', 'TPR.G26125' => 'tpr', 'TWI09G0677' => 'twi', 'TWI73G0287' => 'twi', 'unitig_748.g8326' => 'ugi', 'vmacro15370' => 'vma', 'vmacro15371' => 'vma', 'vmacro15372' => 'vma', 'vmacro15373' => 'vma', 'vmacro15374' => 'vma', 'VMungo0720G2826' => 'vmu', 'Zm00001eb116960' => 'zma', 'Zm00001eb301260' => 'zma', 'Zm00001eb301270' => 'zma' ), 'gf_id' => 'HOM05D001460', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001460' ), 'data_identifier' => 'HOM05D001460', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001460', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '433', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p22980' => 'bna', 'A01p32340' => 'bna', 'A03p42970' => 'bna', 'A05p25880' => 'bna', 'Aa31LG8G9320' => 'aar', 'Aa31LG8G9330' => 'aar', 'Aa31LG8G9340' => 'aar', 'Aa31sc221G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1034' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1528' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.829' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2222' => 'aag', 'Ah.12g058830' => 'amhyb', 'Ah.12g058840' => 'amhyb', 'AL3G37160' => 'aly', 'AL7G41310' => 'aly', 'Aqoxy5G00395' => 'aox', 'Aqoxy5G00396' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0C8NZA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5185HY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JZ1PRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MD3LS0' => 'arhy', 'AT3G22840' => 'ath', 'AT4G14690' => 'ath', 'ATR0665G054' => 'atr', 'Atru.chr4.2344' => 'acertr', 'Atru.chr4.2346' => 'acertr', 'Atru.chr4.2347' => 'acertr', 'Atru.chr4.2348' => 'acertr', 'Atru.chr4.2355' => 'acertr', 'Atru.chr4.2356' => 'acertr', 'Atru.chr4.2358' => 'acertr', 'Atru.chr4.2359' => 'acertr', 'Atru.chr4.2360' => 'acertr', 'Atru.chr4.2361' => 'acertr', 'AUR62030476' => 'cqu', 'AUR62030478' => 'cqu', 'AUR62030819' => 'cqu', 'AUR62030820' => 'cqu', 'BcaB03g14648' => 'bca', 'BcaB04g20492' => 'bca', 'BcaB06g26399' => 'bca', 'BcaC01g03416' => 'bca', 'BcaC01g03419' => 'bca', 'BcaC01g03421' => 'bca', 'BcaC01g03424' => 'bca', 'BcaC05g28012' => 'bca', 'BcaC09g49212' => 'bca', 'BcaC09g50140' => 'bca', 'BcaNung00346' => 'bca', 'BolC1t02785H' => 'bol', 'BolC1t04095H' => 'bol', 'BolC3t17545H' => 'bol', 'BolC5t32769H' => 'bol', 'BraA01t02211Z' => 'bra', 'BraA01t03359Z' => 'bra', 'BraA03t13441Z' => 'bra', 'BraA05t21476Z' => 'bra', 'C01p28420' => 'bna', 'C01p41350' => 'bna', 'C03p52750' => 'bna', 'C03p52780' => 'bna', 'C05p40270' => 'bna', 'CAN.G1437.9' => 'can', 'CANSAT78G0035' => 'cansat', 'CANSAT78G1036' => 'cansat', 'CANSAT78G2272' => 'cansat', 'CANSAT78G2478' => 'cansat', 'CARHR098700' => 'chi', 'CARHR221120' => 'chi', 'CARHR221150' => 'chi', 'Carub.0003s2297' => 'cru', 'Carub.0007s2749' => 'cru', 'Carub.0007s2750' => 'cru', 'Carub.0007s2751' => 'cru', 'Ca_10849_v3' => 'car', 'Cc03_g04300' => 'ccan', 'CDE02G3648' => 'cde', 'CDE05G0060' => 'cde', 'CDE05G0692' => 'cde', 'CDE05G2285' => 'cde', 'CDE05G2884' => 'cde', 'CDE05G3072' => 'cde', 'Cfa008439' => 'cfa', 'Cfa008441' => 'cfa', 'Cfa008443' => 'cfa', 'Cfa008448' => 'cfa', 'Ciclev10005974m.g' => 'ccl', 'Ciclev10006006m.g' => 'ccl', 'Ciclev10006775m.g' => 'ccl', 'CiPaw.02G120400' => 'cil', 'CiPaw.02G120500' => 'cil', 'CiPaw.02G120600' => 'cil', 'ClCG05G004850' => 'cla', 'COL.COLO4_21566' => 'col', 'Cpa.g.sc44.124' => 'cpa', 'Cre07.g320400' => 'cre', 'Cre07.g320450' => 'cre', 'Cre08.g384650' => 'cre', 'Cre09.g393173' => 'cre', 'Cre09.g394325' => 'cre', 'Cre14.g626750' => 'cre', 'Cre16.g679250' => 'cre', 'CsaV3_3G012890' => 'csa', 'CSS0010865' => 'camsi', 'CSS0044338' => 'camsi', 'DCAR_002366' => 'dca', 'DCAR_030687' => 'dca', 'DCAR_030688' => 'dca', 'Dinv14047' => 'din', 'Dinv14048' => 'din', 'Duzib151G0105' => 'dzi', 'Duzib151G0114' => 'dzi', 'Duzib212G1029' => 'dzi', 'ECA232G3536' => 'eca', 'ECA240G0786' => 'eca', 'ECA240G1802' => 'eca', 'ECA240G3760' => 'eca', 'ECA240G3920' => 'eca', 'EL10Ac5g12536' => 'bvu', 'EL10Ac5g12537' => 'bvu', 'EL10Ac5g12538' => 'bvu', 'Eucgr.B01004' => 'egr', 'Eucgr.B01006' => 'egr', 'Eucgr.B01007' => 'egr', 'Eucgr.B01008' => 'egr', 'Eucgr.B01895' => 'egr', 'Eucgr.B01896' => 'egr', 'FAN04G1456' => 'fan', 'FAN08G1769' => 'fan', 'FAN08G2160' => 'fan', 'FAN13G2403' => 'fan', 'FAN13G3303' => 'fan', 'FAN15G2435' => 'fan', 'FAN17G0672' => 'fan', 'FAN17G2441' => 'fan', 'FAN18G1024' => 'fan', 'FAN22G1458' => 'fan', 'FAN24G0037' => 'fan', 'FAN24G0429' => 'fan', 'FAN24G2387' => 'fan', 'FAN27G2746' => 'fan', 'FvH4_2g20400' => 'fve', 'FvH4_2g20420' => 'fve', 'FvH4_2g20430' => 'fve', 'FvH4_4g01270' => 'fve', 'FvH4_4g01290' => 'fve', 'FvH4_4g01300' => 'fve', 'FvH4_4g01310' => 'fve', 'FvH4_4g01330' => 'fve', 'FvH4_5g09070' => 'fve', 'Glyma.10G243800' => 'gma', 'Glyma.20G150600' => 'gma', 'Gohir.A09G219200' => 'ghi', 'Gohir.A09G219300' => 'ghi', 'Gohir.D09G221400' => 'ghi', 'Gohir.D09G221500' => 'ghi', 'Gorai.006G242600' => 'gra', 'Gorai.006G242700' => 'gra', 'GSVIVG01018044001' => 'vvi', 'HanXRQChr03g0083821' => 'han', 'HanXRQChr03g0083841' => 'han', 'HanXRQChr03g0083881' => 'han', 'HanXRQChr03g0083901' => 'han', 'HanXRQChr03g0083921' => 'han', 'HanXRQChr03g0085331' => 'han', 'HanXRQChr03g0085361' => 'han', 'HanXRQChr03g0085411' => 'han', 'HanXRQChr03g0085421' => 'han', 'HanXRQChr03g0085431' => 'han', 'HanXRQChr08g0221991' => 'han', 'HanXRQChr11g0336061' => 'han', 'HanXRQChr11g0336411' => 'han', 'Haze_11234' => 'cav', 'Hma1.2p1_0549F.1_g177010' => 'hma', 'Hma1.2p1_0602F.1_g187630' => 'hma', 'Hund14876' => 'sun', 'Hund14879' => 'sun', 'Lalb_Chr06g0160741' => 'lal', 'Lalb_Chr21g0304781' => 'lal', 'Lj3A726G19' => 'lonja', 'Lj3A726T23' => 'lonja', 'Lj3A726T24' => 'lonja', 'Lj3A726T25' => 'lonja', 'Lj3A727T17' => 'lonja', 'Lj3C726T0' => 'lonja', 'Lj3C726T2' => 'lonja', 'Lj3P725T35' => 'lonja', 'Lj3P727T10' => 'lonja', 'Lj3P727T12' => 'lonja', 'Lj3P727T14' => 'lonja', 'Lj5g0023109' => 'lja', 'Lj6P646T44' => 'lonja', 'Lsat_1_v5_gn_6_75760' => 'lsa', 'Lsat_1_v5_gn_6_75800' => 'lsa', 'Lsat_1_v5_gn_6_75900' => 'lsa', 'Lsat_1_v5_gn_6_76240' => 'lsa', 'Lsat_1_v5_gn_6_76441' => 'lsa', 'Lsat_1_v5_gn_6_76700' => 'lsa', 'Lsat_1_v5_gn_6_76760' => 'lsa', 'Manes.15G033100' => 'mes', 'Mapoly0004s0074' => 'mpo', 'Mapoly0004s0075' => 'mpo', 'Mapoly0004s0163' => 'mpo', 'Mapoly0004s0164' => 'mpo', 'Mapoly0021s0018' => 'mpo', 'Mapoly0041s0136' => 'mpo', 'Mapoly0041s0137' => 'mpo', 'Mapoly0041s0138' => 'mpo', 'Mapoly0041s0139' => 'mpo', 'Mapoly0041s0141' => 'mpo', 'Mapoly0041s0142' => 'mpo', 'Mapoly0041s0143' => 'mpo', 'Mapoly0041s0144' => 'mpo', 'Mapoly0041s0145' => 'mpo', 'Mapoly0047s0106' => 'mpo', 'Mapoly0047s0108' => 'mpo', 'Mapoly0050s0051' => 'mpo', 'Mapoly0050s0052' => 'mpo', 'Mapoly0050s0053' => 'mpo', 'Mapoly0058s0013' => 'mpo', 'Mapoly0091s0078' => 'mpo', 'Mapoly0091s0079' => 'mpo', 'Mapoly0091s0080' => 'mpo', 'Mapoly0091s0081' => 'mpo', 'Mapoly0278s0004' => 'mpo', 'Mapoly0278s0005' => 'mpo', 'Mapoly0278s0006' => 'mpo', 'MBI11_g30648_MAGBIO' => 'mbi', 'MCO03G194' => 'mco', 'MCO03G590' => 'mco', 'MCO07G312' => 'mco', 'MCO10G318' => 'mco', 'MCO12G244' => 'mco', 'MCO13G148' => 'mco', 'MCO13G194' => 'mco', 'MCO16G238' => 'mco', 'MD06G1134100' => 'mdo', 'MD13G1200100' => 'mdo', 'MD13G1200300' => 'mdo', 'MD13G1200600' => 'mdo', 'MD14G1150400' => 'mdo', 'MD16G1200000' => 'mdo', 'Medtr1g102570' => 'mtr', 'Medtr1g102780' => 'mtr', 'Medtr1g102800' => 'mtr', 'Medtr1g102810' => 'mtr', 'Medtr1g102830' => 'mtr', 'MELO3C006499.2' => 'cme', 'Migut.G00385' => 'egut', 'MSTRG.4063' => 'ama', 'Nitab4.5_0000090g0260' => 'nta', 'Nitab4.5_0000977g0030' => 'nta', 'Nitab4.5_0002541g0040' => 'nta', 'Nitab4.5_0007068g0040' => 'nta', 'Nn005s41408' => 'nnu', 'Nn005s41410' => 'nnu', 'Oeu010310.1' => 'oeu', 'Oeu010311.1' => 'oeu', 'Oeu043472.1' => 'oeu', 'Os01g0246400' => 'osa', 'Os04g0267950' => 'osa', 'Os07g0178700' => 'osa', 'Os07g0178800' => 'osa', 'Peaxi162Scf00316g00046' => 'pax', 'Peaxi162Scf00316g00049' => 'pax', 'Peaxi162Scf00316g00059' => 'pax', 'Peaxi162Scf00316g00328' => 'pax', 'Peaxi162Scf00316g00329' => 'pax', 'Peaxi162Scf00316g00411' => 'pax', 'Peaxi162Scf00316g00521' => 'pax', 'Peaxi162Scf00492g00068' => 'pax', 'Peaxi162Scf35631g00002' => 'pax', 'PGR142G3720' => 'pgr', 'PGSC0003DMG400006442' => 'stu', 'Phvul.007G062000' => 'pvu', 'Potri.008G157750' => 'ptr', 'Potri.008G157900' => 'ptr', 'Potri.008G158000' => 'ptr', 'Potri.008G158200' => 'ptr', 'Pp3c11_7280' => 'ppa', 'Pp3c11_7980' => 'ppa', 'Pp3c12_19450' => 'ppa', 'Pp3c14_1480' => 'ppa', 'Pp3c14_1501' => 'ppa', 'Pp3c16_4900' => 'ppa', 'Pp3c16_5010' => 'ppa', 'Pp3c16_5060' => 'ppa', 'Pp3c19_18250' => 'ppa', 'Pp3c23_8530' => 'ppa', 'Pp3c23_8550' => 'ppa', 'Pp3c24_9670' => 'ppa', 'Pp3c2_21390' => 'ppa', 'Pp3c2_31380' => 'ppa', 'Pp3c3_16620' => 'ppa', 'Pp3c3_8090' => 'ppa', 'Pp3c3_8110' => 'ppa', 'Pp3c3_8130' => 'ppa', 'Pp3c3_8150' => 'ppa', 'Pp3c4_14320' => 'ppa', 'Pp3c6_2560' => 'ppa', 'Pp3c9_16700' => 'ppa', 'PRCOL_00000234' => 'pco', 'PRCOL_00000235' => 'pco', 'PRCOL_00000777' => 'pco', 'PRCOL_00002344' => 'pco', 'PRCOL_00002372' => 'pco', 'PRCOL_00006120' => 'pco', 'Prupe.1G021400' => 'ppe', 'Prupe.1G021500' => 'ppe', 'Prupe.1G021600' => 'ppe', 'Prupe.1G021700' => 'ppe', 'Prupe.1G021800' => 'ppe', 'Prupe.5G145100' => 'ppe', 'Psat6g204040' => 'psa', 'Psat6g204800' => 'psa', 'Psat6g204920' => 'psa', 'Psat6g204960' => 'psa', 'Psat6g205080' => 'psa', 'PSO017G0271' => 'pso', 'PSO017G1276' => 'pso', 'PSO017G1429' => 'pso', 'PSO017G1861' => 'pso', 'PSO017G2787' => 'pso', 'PSO017G4466' => 'pso', 'PSO017G5118' => 'pso', 'PSO017G5420' => 'pso', 'PSO063G3678' => 'pso', 'PSO210G0546' => 'pso', 'PSO317G0001' => 'pso', 'PSO357G0512' => 'pso', 'PSO478G2682' => 'pso', 'PSO647G0001' => 'pso', 'PSO675G0001' => 'pso', 'PSO675G2699' => 'pso', 'PSO675G2849' => 'pso', 'PSO675G4991' => 'pso', 'PSO689G0001' => 'pso', 'QL06p000916' => 'qlo', 'QL06p000921' => 'qlo', 'QL06p001398' => 'qlo', 'QL06p001407' => 'qlo', 'QL06p002031' => 'qlo', 'RcHm_v2.0_Chr4g0387791' => 'rch', 'RcHm_v2.0_Chr4g0387801' => 'rch', 'RcHm_v2.0_Chr6g0286501' => 'rch', 'RcHm_v2.0_Chr6g0286511' => 'rch', 'RcHm_v2.0_Chr6g0286521' => 'rch', 'RcHm_v2.0_Chr6g0286531' => 'rch', 'RcHm_v2.0_Chr7g0189141' => 'rch', 'Rhsim02G0028700' => 'rsi', 'Rhsim02G0028800' => 'rsi', 'Rhsim02G0028900' => 'rsi', 'Rhsim02G0029000' => 'rsi', 'Rhsim02G0029100' => 'rsi', 'Rhsim02G0029200' => 'rsi', 'Rhsim02G0029300' => 'rsi', 'Rhsim02G0029400' => 'rsi', 'Rhsim02G0029500' => 'rsi', 'Rhsim02G0029600' => 'rsi', 'RhsimUnG0024000' => 'rsi', 'RhsimUnG0024100' => 'rsi', 'RhsimUnG0024200' => 'rsi', 'RhsimUnG0024300' => 'rsi', 'RhsimUnG0024400' => 'rsi', 'RhsimUnG0024500' => 'rsi', 'RhsimUnG0024700' => 'rsi', 'RhsimUnG0024800' => 'rsi', 'RhsimUnG0024900' => 'rsi', 'RhsimUnG0025100' => 'rsi', 'Sabra08G0120200' => 'sbr', 'Sabra08G0120300' => 'sbr', 'Sabra08G0120500' => 'sbr', 'Sabra08G0120600' => 'sbr', 'Sabra10G0158900' => 'sbr', 'SalBow2G3492' => 'sbo', 'Sc13g0004760' => 'sci', 'Sc13g0004770' => 'sci', 'Sed0003417' => 'sed', 'Sed0019750' => 'sed', 'SEGI_03419' => 'sgi', 'SEGI_05907' => 'sgi', 'SEGI_10682' => 'sgi', 'SEGI_13528' => 'sgi', 'SEGI_16081' => 'sgi', 'SEGI_19370' => 'sgi', 'SEGI_21015' => 'sgi', 'SEGI_21944' => 'sgi', 'SEGI_32906' => 'sgi', 'SEGI_33093' => 'sgi', 'SEGI_36110' => 'sgi', 'SEGI_40397' => 'sgi', 'SGA_v2.0_scaffold191G40426' => 'sas', 'SGA_v2.0_scaffold353G49717' => 'sas', 'SGA_v2.0_scaffold50G18550' => 'sas', 'SMO119G0173' => 'smo', 'SMO172G0002' => 'smo', 'Solyc09g082690.3' => 'sly', 'Solyc09g082700.2' => 'sly', 'Sopen09g031550' => 'spe', 'Sopen09g031560' => 'spe', 'Sp3g20540' => 'spa', 'Sp7g07580' => 'spa', 'TAR134G0002' => 'tar', 'TAR236G0001' => 'tar', 'TAR365G0892' => 'tar', 'TAR636G0166' => 'tar', 'TAR636G0646' => 'tar', 'TAR636G0869' => 'tar', 'TAR636G1317' => 'tar', 'TAR636G1744' => 'tar', 'TAR636G3358' => 'tar', 'TAR636G3436' => 'tar', 'THA.LOC104803047' => 'tha', 'Thecc.04G238900' => 'tca', 'Thhalv10021557m.g' => 'esa', 'Thhalv10026318m.g' => 'esa', 'Thhalv10026335m.g' => 'esa', 'TPR.G17433' => 'tpr', 'TPR.G18915' => 'tpr', 'TPR.G26125' => 'tpr', 'TWI09G0677' => 'twi', 'TWI73G0287' => 'twi', 'unitig_748.g8326' => 'ugi', 'vmacro15370' => 'vma', 'vmacro15371' => 'vma', 'vmacro15372' => 'vma', 'vmacro15373' => 'vma', 'vmacro15374' => 'vma', 'VMungo0720G2826' => 'vmu', 'Zm00001eb116960' => 'zma', 'Zm00001eb301260' => 'zma', 'Zm00001eb301270' => 'zma' ) $gf_id = 'HOM05D001460' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001460' ) $data_identifier = 'HOM05D001460' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 4, 'aag' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 2, 'aox' => (int) 2, 'arhy' => (int) 4, 'ath' => (int) 2, 'atr' => (int) 1, 'acertr' => (int) 10, 'cqu' => (int) 4, 'bca' => (int) 11, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 1, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 1, 'ccan' => (int) 1, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 1, 'col' => (int) 1, 'cpa' => (int) 1, 'cre' => (int) 7, 'csa' => (int) 1, 'camsi' => (int) 2, 'dca' => (int) 3, 'din' => (int) 2, 'dzi' => (int) 3, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 14, 'fve' => (int) 9, 'gma' => (int) 2, 'ghi' => (int) 4, 'gra' => (int) 2, 'vvi' => (int) 1, 'han' => (int) 13, 'cav' => (int) 1, 'hma' => (int) 2, 'sun' => (int) 2, 'lal' => (int) 2, 'lonja' => (int) 12, 'lja' => (int) 1, 'lsa' => (int) 7, 'mes' => (int) 1, 'mpo' => (int) 27, 'mbi' => (int) 1, 'mco' => (int) 8, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 1, 'egut' => (int) 1, 'ama' => (int) 1, 'nta' => (int) 4, 'nnu' => (int) 2, 'oeu' => (int) 3, 'osa' => (int) 4, 'pax' => (int) 9, 'pgr' => (int) 1, 'stu' => (int) 1, 'pvu' => (int) 1, 'ptr' => (int) 4, 'ppa' => (int) 22, 'pco' => (int) 6, 'ppe' => (int) 6, 'psa' => (int) 5, 'pso' => (int) 19, 'qlo' => (int) 5, 'rch' => (int) 7, 'rsi' => (int) 20, 'sbr' => (int) 5, 'sbo' => (int) 1, 'sci' => (int) 2, 'sed' => (int) 2, 'sgi' => (int) 12, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 2, 'tar' => (int) 10, 'tha' => (int) 1, 'tca' => (int) 1, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 2, 'ugi' => (int) 1, 'vma' => (int) 5, 'vmu' => (int) 1, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb301270' $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' => 'HOM05D001460', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '433', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p22980' => 'bna', 'A01p32340' => 'bna', 'A03p42970' => 'bna', 'A05p25880' => 'bna', 'Aa31LG8G9320' => 'aar', 'Aa31LG8G9330' => 'aar', 'Aa31LG8G9340' => 'aar', 'Aa31sc221G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1034' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1528' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.829' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2222' => 'aag', 'Ah.12g058830' => 'amhyb', 'Ah.12g058840' => 'amhyb', 'AL3G37160' => 'aly', 'AL7G41310' => 'aly', 'Aqoxy5G00395' => 'aox', 'Aqoxy5G00396' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0C8NZA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5185HY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JZ1PRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MD3LS0' => 'arhy', 'AT3G22840' => 'ath', 'AT4G14690' => 'ath', 'ATR0665G054' => 'atr', 'Atru.chr4.2344' => 'acertr', 'Atru.chr4.2346' => 'acertr', 'Atru.chr4.2347' => 'acertr', 'Atru.chr4.2348' => 'acertr', 'Atru.chr4.2355' => 'acertr', 'Atru.chr4.2356' => 'acertr', 'Atru.chr4.2358' => 'acertr', 'Atru.chr4.2359' => 'acertr', 'Atru.chr4.2360' => 'acertr', 'Atru.chr4.2361' => 'acertr', 'AUR62030476' => 'cqu', 'AUR62030478' => 'cqu', 'AUR62030819' => 'cqu', 'AUR62030820' => 'cqu', 'BcaB03g14648' => 'bca', 'BcaB04g20492' => 'bca', 'BcaB06g26399' => 'bca', 'BcaC01g03416' => 'bca', 'BcaC01g03419' => 'bca', 'BcaC01g03421' => 'bca', 'BcaC01g03424' => 'bca', 'BcaC05g28012' => 'bca', 'BcaC09g49212' => 'bca', 'BcaC09g50140' => 'bca', 'BcaNung00346' => 'bca', 'BolC1t02785H' => 'bol', 'BolC1t04095H' => 'bol', 'BolC3t17545H' => 'bol', 'BolC5t32769H' => 'bol', 'BraA01t02211Z' => 'bra', 'BraA01t03359Z' => 'bra', 'BraA03t13441Z' => 'bra', 'BraA05t21476Z' => 'bra', 'C01p28420' => 'bna', 'C01p41350' => 'bna', 'C03p52750' => 'bna', 'C03p52780' => 'bna', 'C05p40270' => 'bna', 'CAN.G1437.9' => 'can', 'CANSAT78G0035' => 'cansat', 'CANSAT78G1036' => 'cansat', 'CANSAT78G2272' => 'cansat', 'CANSAT78G2478' => 'cansat', 'CARHR098700' => 'chi', 'CARHR221120' => 'chi', 'CARHR221150' => 'chi', 'Carub.0003s2297' => 'cru', 'Carub.0007s2749' => 'cru', 'Carub.0007s2750' => 'cru', 'Carub.0007s2751' => 'cru', 'Ca_10849_v3' => 'car', 'Cc03_g04300' => 'ccan', 'CDE02G3648' => 'cde', 'CDE05G0060' => 'cde', 'CDE05G0692' => 'cde', 'CDE05G2285' => 'cde', 'CDE05G2884' => 'cde', 'CDE05G3072' => 'cde', 'Cfa008439' => 'cfa', 'Cfa008441' => 'cfa', 'Cfa008443' => 'cfa', 'Cfa008448' => 'cfa', 'Ciclev10005974m.g' => 'ccl', 'Ciclev10006006m.g' => 'ccl', 'Ciclev10006775m.g' => 'ccl', 'CiPaw.02G120400' => 'cil', 'CiPaw.02G120500' => 'cil', 'CiPaw.02G120600' => 'cil', 'ClCG05G004850' => 'cla', 'COL.COLO4_21566' => 'col', 'Cpa.g.sc44.124' => 'cpa', 'Cre07.g320400' => 'cre', 'Cre07.g320450' => 'cre', 'Cre08.g384650' => 'cre', 'Cre09.g393173' => 'cre', 'Cre09.g394325' => 'cre', 'Cre14.g626750' => 'cre', 'Cre16.g679250' => 'cre', 'CsaV3_3G012890' => 'csa', 'CSS0010865' => 'camsi', 'CSS0044338' => 'camsi', 'DCAR_002366' => 'dca', 'DCAR_030687' => 'dca', 'DCAR_030688' => 'dca', 'Dinv14047' => 'din', 'Dinv14048' => 'din', 'Duzib151G0105' => 'dzi', 'Duzib151G0114' => 'dzi', 'Duzib212G1029' => 'dzi', 'ECA232G3536' => 'eca', 'ECA240G0786' => 'eca', 'ECA240G1802' => 'eca', 'ECA240G3760' => 'eca', 'ECA240G3920' => 'eca', 'EL10Ac5g12536' => 'bvu', 'EL10Ac5g12537' => 'bvu', 'EL10Ac5g12538' => 'bvu', 'Eucgr.B01004' => 'egr', 'Eucgr.B01006' => 'egr', 'Eucgr.B01007' => 'egr', 'Eucgr.B01008' => 'egr', 'Eucgr.B01895' => 'egr', 'Eucgr.B01896' => 'egr', 'FAN04G1456' => 'fan', 'FAN08G1769' => 'fan', 'FAN08G2160' => 'fan', 'FAN13G2403' => 'fan', 'FAN13G3303' => 'fan', 'FAN15G2435' => 'fan', 'FAN17G0672' => 'fan', 'FAN17G2441' => 'fan', 'FAN18G1024' => 'fan', 'FAN22G1458' => 'fan', 'FAN24G0037' => 'fan', 'FAN24G0429' => 'fan', 'FAN24G2387' => 'fan', 'FAN27G2746' => 'fan', 'FvH4_2g20400' => 'fve', 'FvH4_2g20420' => 'fve', 'FvH4_2g20430' => 'fve', 'FvH4_4g01270' => 'fve', 'FvH4_4g01290' => 'fve', 'FvH4_4g01300' => 'fve', 'FvH4_4g01310' => 'fve', 'FvH4_4g01330' => 'fve', 'FvH4_5g09070' => 'fve', 'Glyma.10G243800' => 'gma', 'Glyma.20G150600' => 'gma', 'Gohir.A09G219200' => 'ghi', 'Gohir.A09G219300' => 'ghi', 'Gohir.D09G221400' => 'ghi', 'Gohir.D09G221500' => 'ghi', 'Gorai.006G242600' => 'gra', 'Gorai.006G242700' => 'gra', 'GSVIVG01018044001' => 'vvi', 'HanXRQChr03g0083821' => 'han', 'HanXRQChr03g0083841' => 'han', 'HanXRQChr03g0083881' => 'han', 'HanXRQChr03g0083901' => 'han', 'HanXRQChr03g0083921' => 'han', 'HanXRQChr03g0085331' => 'han', 'HanXRQChr03g0085361' => 'han', 'HanXRQChr03g0085411' => 'han', 'HanXRQChr03g0085421' => 'han', 'HanXRQChr03g0085431' => 'han', 'HanXRQChr08g0221991' => 'han', 'HanXRQChr11g0336061' => 'han', 'HanXRQChr11g0336411' => 'han', 'Haze_11234' => 'cav', 'Hma1.2p1_0549F.1_g177010' => 'hma', 'Hma1.2p1_0602F.1_g187630' => 'hma', 'Hund14876' => 'sun', 'Hund14879' => 'sun', 'Lalb_Chr06g0160741' => 'lal', 'Lalb_Chr21g0304781' => 'lal', 'Lj3A726G19' => 'lonja', 'Lj3A726T23' => 'lonja', 'Lj3A726T24' => 'lonja', 'Lj3A726T25' => 'lonja', 'Lj3A727T17' => 'lonja', 'Lj3C726T0' => 'lonja', 'Lj3C726T2' => 'lonja', 'Lj3P725T35' => 'lonja', 'Lj3P727T10' => 'lonja', 'Lj3P727T12' => 'lonja', 'Lj3P727T14' => 'lonja', 'Lj5g0023109' => 'lja', 'Lj6P646T44' => 'lonja', 'Lsat_1_v5_gn_6_75760' => 'lsa', 'Lsat_1_v5_gn_6_75800' => 'lsa', 'Lsat_1_v5_gn_6_75900' => 'lsa', 'Lsat_1_v5_gn_6_76240' => 'lsa', 'Lsat_1_v5_gn_6_76441' => 'lsa', 'Lsat_1_v5_gn_6_76700' => 'lsa', 'Lsat_1_v5_gn_6_76760' => 'lsa', 'Manes.15G033100' => 'mes', 'Mapoly0004s0074' => 'mpo', 'Mapoly0004s0075' => 'mpo', 'Mapoly0004s0163' => 'mpo', 'Mapoly0004s0164' => 'mpo', 'Mapoly0021s0018' => 'mpo', 'Mapoly0041s0136' => 'mpo', 'Mapoly0041s0137' => 'mpo', 'Mapoly0041s0138' => 'mpo', 'Mapoly0041s0139' => 'mpo', 'Mapoly0041s0141' => 'mpo', 'Mapoly0041s0142' => 'mpo', 'Mapoly0041s0143' => 'mpo', 'Mapoly0041s0144' => 'mpo', 'Mapoly0041s0145' => 'mpo', 'Mapoly0047s0106' => 'mpo', 'Mapoly0047s0108' => 'mpo', 'Mapoly0050s0051' => 'mpo', 'Mapoly0050s0052' => 'mpo', 'Mapoly0050s0053' => 'mpo', 'Mapoly0058s0013' => 'mpo', 'Mapoly0091s0078' => 'mpo', 'Mapoly0091s0079' => 'mpo', 'Mapoly0091s0080' => 'mpo', 'Mapoly0091s0081' => 'mpo', 'Mapoly0278s0004' => 'mpo', 'Mapoly0278s0005' => 'mpo', 'Mapoly0278s0006' => 'mpo', 'MBI11_g30648_MAGBIO' => 'mbi', 'MCO03G194' => 'mco', 'MCO03G590' => 'mco', 'MCO07G312' => 'mco', 'MCO10G318' => 'mco', 'MCO12G244' => 'mco', 'MCO13G148' => 'mco', 'MCO13G194' => 'mco', 'MCO16G238' => 'mco', 'MD06G1134100' => 'mdo', 'MD13G1200100' => 'mdo', 'MD13G1200300' => 'mdo', 'MD13G1200600' => 'mdo', 'MD14G1150400' => 'mdo', 'MD16G1200000' => 'mdo', 'Medtr1g102570' => 'mtr', 'Medtr1g102780' => 'mtr', 'Medtr1g102800' => 'mtr', 'Medtr1g102810' => 'mtr', 'Medtr1g102830' => 'mtr', 'MELO3C006499.2' => 'cme', 'Migut.G00385' => 'egut', 'MSTRG.4063' => 'ama', 'Nitab4.5_0000090g0260' => 'nta', 'Nitab4.5_0000977g0030' => 'nta', 'Nitab4.5_0002541g0040' => 'nta', 'Nitab4.5_0007068g0040' => 'nta', 'Nn005s41408' => 'nnu', 'Nn005s41410' => 'nnu', 'Oeu010310.1' => 'oeu', 'Oeu010311.1' => 'oeu', 'Oeu043472.1' => 'oeu', 'Os01g0246400' => 'osa', 'Os04g0267950' => 'osa', 'Os07g0178700' => 'osa', 'Os07g0178800' => 'osa', 'Peaxi162Scf00316g00046' => 'pax', 'Peaxi162Scf00316g00049' => 'pax', 'Peaxi162Scf00316g00059' => 'pax', 'Peaxi162Scf00316g00328' => 'pax', 'Peaxi162Scf00316g00329' => 'pax', 'Peaxi162Scf00316g00411' => 'pax', 'Peaxi162Scf00316g00521' => 'pax', 'Peaxi162Scf00492g00068' => 'pax', 'Peaxi162Scf35631g00002' => 'pax', 'PGR142G3720' => 'pgr', 'PGSC0003DMG400006442' => 'stu', 'Phvul.007G062000' => 'pvu', 'Potri.008G157750' => 'ptr', 'Potri.008G157900' => 'ptr', 'Potri.008G158000' => 'ptr', 'Potri.008G158200' => 'ptr', 'Pp3c11_7280' => 'ppa', 'Pp3c11_7980' => 'ppa', 'Pp3c12_19450' => 'ppa', 'Pp3c14_1480' => 'ppa', 'Pp3c14_1501' => 'ppa', 'Pp3c16_4900' => 'ppa', 'Pp3c16_5010' => 'ppa', 'Pp3c16_5060' => 'ppa', 'Pp3c19_18250' => 'ppa', 'Pp3c23_8530' => 'ppa', 'Pp3c23_8550' => 'ppa', 'Pp3c24_9670' => 'ppa', 'Pp3c2_21390' => 'ppa', 'Pp3c2_31380' => 'ppa', 'Pp3c3_16620' => 'ppa', 'Pp3c3_8090' => 'ppa', 'Pp3c3_8110' => 'ppa', 'Pp3c3_8130' => 'ppa', 'Pp3c3_8150' => 'ppa', 'Pp3c4_14320' => 'ppa', 'Pp3c6_2560' => 'ppa', 'Pp3c9_16700' => 'ppa', 'PRCOL_00000234' => 'pco', 'PRCOL_00000235' => 'pco', 'PRCOL_00000777' => 'pco', 'PRCOL_00002344' => 'pco', 'PRCOL_00002372' => 'pco', 'PRCOL_00006120' => 'pco', 'Prupe.1G021400' => 'ppe', 'Prupe.1G021500' => 'ppe', 'Prupe.1G021600' => 'ppe', 'Prupe.1G021700' => 'ppe', 'Prupe.1G021800' => 'ppe', 'Prupe.5G145100' => 'ppe', 'Psat6g204040' => 'psa', 'Psat6g204800' => 'psa', 'Psat6g204920' => 'psa', 'Psat6g204960' => 'psa', 'Psat6g205080' => 'psa', 'PSO017G0271' => 'pso', 'PSO017G1276' => 'pso', 'PSO017G1429' => 'pso', 'PSO017G1861' => 'pso', 'PSO017G2787' => 'pso', 'PSO017G4466' => 'pso', 'PSO017G5118' => 'pso', 'PSO017G5420' => 'pso', 'PSO063G3678' => 'pso', 'PSO210G0546' => 'pso', 'PSO317G0001' => 'pso', 'PSO357G0512' => 'pso', 'PSO478G2682' => 'pso', 'PSO647G0001' => 'pso', 'PSO675G0001' => 'pso', 'PSO675G2699' => 'pso', 'PSO675G2849' => 'pso', 'PSO675G4991' => 'pso', 'PSO689G0001' => 'pso', 'QL06p000916' => 'qlo', 'QL06p000921' => 'qlo', 'QL06p001398' => 'qlo', 'QL06p001407' => 'qlo', 'QL06p002031' => 'qlo', 'RcHm_v2.0_Chr4g0387791' => 'rch', 'RcHm_v2.0_Chr4g0387801' => 'rch', 'RcHm_v2.0_Chr6g0286501' => 'rch', 'RcHm_v2.0_Chr6g0286511' => 'rch', 'RcHm_v2.0_Chr6g0286521' => 'rch', 'RcHm_v2.0_Chr6g0286531' => 'rch', 'RcHm_v2.0_Chr7g0189141' => 'rch', 'Rhsim02G0028700' => 'rsi', 'Rhsim02G0028800' => 'rsi', 'Rhsim02G0028900' => 'rsi', 'Rhsim02G0029000' => 'rsi', 'Rhsim02G0029100' => 'rsi', 'Rhsim02G0029200' => 'rsi', 'Rhsim02G0029300' => 'rsi', 'Rhsim02G0029400' => 'rsi', 'Rhsim02G0029500' => 'rsi', 'Rhsim02G0029600' => 'rsi', 'RhsimUnG0024000' => 'rsi', 'RhsimUnG0024100' => 'rsi', 'RhsimUnG0024200' => 'rsi', 'RhsimUnG0024300' => 'rsi', 'RhsimUnG0024400' => 'rsi', 'RhsimUnG0024500' => 'rsi', 'RhsimUnG0024700' => 'rsi', 'RhsimUnG0024800' => 'rsi', 'RhsimUnG0024900' => 'rsi', 'RhsimUnG0025100' => 'rsi', 'Sabra08G0120200' => 'sbr', 'Sabra08G0120300' => 'sbr', 'Sabra08G0120500' => 'sbr', 'Sabra08G0120600' => 'sbr', 'Sabra10G0158900' => 'sbr', 'SalBow2G3492' => 'sbo', 'Sc13g0004760' => 'sci', 'Sc13g0004770' => 'sci', 'Sed0003417' => 'sed', 'Sed0019750' => 'sed', 'SEGI_03419' => 'sgi', 'SEGI_05907' => 'sgi', 'SEGI_10682' => 'sgi', 'SEGI_13528' => 'sgi', 'SEGI_16081' => 'sgi', 'SEGI_19370' => 'sgi', 'SEGI_21015' => 'sgi', 'SEGI_21944' => 'sgi', 'SEGI_32906' => 'sgi', 'SEGI_33093' => 'sgi', 'SEGI_36110' => 'sgi', 'SEGI_40397' => 'sgi', 'SGA_v2.0_scaffold191G40426' => 'sas', 'SGA_v2.0_scaffold353G49717' => 'sas', 'SGA_v2.0_scaffold50G18550' => 'sas', 'SMO119G0173' => 'smo', 'SMO172G0002' => 'smo', 'Solyc09g082690.3' => 'sly', 'Solyc09g082700.2' => 'sly', 'Sopen09g031550' => 'spe', 'Sopen09g031560' => 'spe', 'Sp3g20540' => 'spa', 'Sp7g07580' => 'spa', 'TAR134G0002' => 'tar', 'TAR236G0001' => 'tar', 'TAR365G0892' => 'tar', 'TAR636G0166' => 'tar', 'TAR636G0646' => 'tar', 'TAR636G0869' => 'tar', 'TAR636G1317' => 'tar', 'TAR636G1744' => 'tar', 'TAR636G3358' => 'tar', 'TAR636G3436' => 'tar', 'THA.LOC104803047' => 'tha', 'Thecc.04G238900' => 'tca', 'Thhalv10021557m.g' => 'esa', 'Thhalv10026318m.g' => 'esa', 'Thhalv10026335m.g' => 'esa', 'TPR.G17433' => 'tpr', 'TPR.G18915' => 'tpr', 'TPR.G26125' => 'tpr', 'TWI09G0677' => 'twi', 'TWI73G0287' => 'twi', 'unitig_748.g8326' => 'ugi', 'vmacro15370' => 'vma', 'vmacro15371' => 'vma', 'vmacro15372' => 'vma', 'vmacro15373' => 'vma', 'vmacro15374' => 'vma', 'VMungo0720G2826' => 'vmu', 'Zm00001eb116960' => 'zma', 'Zm00001eb301260' => 'zma', 'Zm00001eb301270' => 'zma' ), 'gf_id' => 'HOM05D001460', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001460' ), 'data_identifier' => 'HOM05D001460', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001460', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '433', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p22980' => 'bna', 'A01p32340' => 'bna', 'A03p42970' => 'bna', 'A05p25880' => 'bna', 'Aa31LG8G9320' => 'aar', 'Aa31LG8G9330' => 'aar', 'Aa31LG8G9340' => 'aar', 'Aa31sc221G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1034' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1528' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.829' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2222' => 'aag', 'Ah.12g058830' => 'amhyb', 'Ah.12g058840' => 'amhyb', 'AL3G37160' => 'aly', 'AL7G41310' => 'aly', 'Aqoxy5G00395' => 'aox', 'Aqoxy5G00396' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0C8NZA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5185HY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JZ1PRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MD3LS0' => 'arhy', 'AT3G22840' => 'ath', 'AT4G14690' => 'ath', 'ATR0665G054' => 'atr', 'Atru.chr4.2344' => 'acertr', 'Atru.chr4.2346' => 'acertr', 'Atru.chr4.2347' => 'acertr', 'Atru.chr4.2348' => 'acertr', 'Atru.chr4.2355' => 'acertr', 'Atru.chr4.2356' => 'acertr', 'Atru.chr4.2358' => 'acertr', 'Atru.chr4.2359' => 'acertr', 'Atru.chr4.2360' => 'acertr', 'Atru.chr4.2361' => 'acertr', 'AUR62030476' => 'cqu', 'AUR62030478' => 'cqu', 'AUR62030819' => 'cqu', 'AUR62030820' => 'cqu', 'BcaB03g14648' => 'bca', 'BcaB04g20492' => 'bca', 'BcaB06g26399' => 'bca', 'BcaC01g03416' => 'bca', 'BcaC01g03419' => 'bca', 'BcaC01g03421' => 'bca', 'BcaC01g03424' => 'bca', 'BcaC05g28012' => 'bca', 'BcaC09g49212' => 'bca', 'BcaC09g50140' => 'bca', 'BcaNung00346' => 'bca', 'BolC1t02785H' => 'bol', 'BolC1t04095H' => 'bol', 'BolC3t17545H' => 'bol', 'BolC5t32769H' => 'bol', 'BraA01t02211Z' => 'bra', 'BraA01t03359Z' => 'bra', 'BraA03t13441Z' => 'bra', 'BraA05t21476Z' => 'bra', 'C01p28420' => 'bna', 'C01p41350' => 'bna', 'C03p52750' => 'bna', 'C03p52780' => 'bna', 'C05p40270' => 'bna', 'CAN.G1437.9' => 'can', 'CANSAT78G0035' => 'cansat', 'CANSAT78G1036' => 'cansat', 'CANSAT78G2272' => 'cansat', 'CANSAT78G2478' => 'cansat', 'CARHR098700' => 'chi', 'CARHR221120' => 'chi', 'CARHR221150' => 'chi', 'Carub.0003s2297' => 'cru', 'Carub.0007s2749' => 'cru', 'Carub.0007s2750' => 'cru', 'Carub.0007s2751' => 'cru', 'Ca_10849_v3' => 'car', 'Cc03_g04300' => 'ccan', 'CDE02G3648' => 'cde', 'CDE05G0060' => 'cde', 'CDE05G0692' => 'cde', 'CDE05G2285' => 'cde', 'CDE05G2884' => 'cde', 'CDE05G3072' => 'cde', 'Cfa008439' => 'cfa', 'Cfa008441' => 'cfa', 'Cfa008443' => 'cfa', 'Cfa008448' => 'cfa', 'Ciclev10005974m.g' => 'ccl', 'Ciclev10006006m.g' => 'ccl', 'Ciclev10006775m.g' => 'ccl', 'CiPaw.02G120400' => 'cil', 'CiPaw.02G120500' => 'cil', 'CiPaw.02G120600' => 'cil', 'ClCG05G004850' => 'cla', 'COL.COLO4_21566' => 'col', 'Cpa.g.sc44.124' => 'cpa', 'Cre07.g320400' => 'cre', 'Cre07.g320450' => 'cre', 'Cre08.g384650' => 'cre', 'Cre09.g393173' => 'cre', 'Cre09.g394325' => 'cre', 'Cre14.g626750' => 'cre', 'Cre16.g679250' => 'cre', 'CsaV3_3G012890' => 'csa', 'CSS0010865' => 'camsi', 'CSS0044338' => 'camsi', 'DCAR_002366' => 'dca', 'DCAR_030687' => 'dca', 'DCAR_030688' => 'dca', 'Dinv14047' => 'din', 'Dinv14048' => 'din', 'Duzib151G0105' => 'dzi', 'Duzib151G0114' => 'dzi', 'Duzib212G1029' => 'dzi', 'ECA232G3536' => 'eca', 'ECA240G0786' => 'eca', 'ECA240G1802' => 'eca', 'ECA240G3760' => 'eca', 'ECA240G3920' => 'eca', 'EL10Ac5g12536' => 'bvu', 'EL10Ac5g12537' => 'bvu', 'EL10Ac5g12538' => 'bvu', 'Eucgr.B01004' => 'egr', 'Eucgr.B01006' => 'egr', 'Eucgr.B01007' => 'egr', 'Eucgr.B01008' => 'egr', 'Eucgr.B01895' => 'egr', 'Eucgr.B01896' => 'egr', 'FAN04G1456' => 'fan', 'FAN08G1769' => 'fan', 'FAN08G2160' => 'fan', 'FAN13G2403' => 'fan', 'FAN13G3303' => 'fan', 'FAN15G2435' => 'fan', 'FAN17G0672' => 'fan', 'FAN17G2441' => 'fan', 'FAN18G1024' => 'fan', 'FAN22G1458' => 'fan', 'FAN24G0037' => 'fan', 'FAN24G0429' => 'fan', 'FAN24G2387' => 'fan', 'FAN27G2746' => 'fan', 'FvH4_2g20400' => 'fve', 'FvH4_2g20420' => 'fve', 'FvH4_2g20430' => 'fve', 'FvH4_4g01270' => 'fve', 'FvH4_4g01290' => 'fve', 'FvH4_4g01300' => 'fve', 'FvH4_4g01310' => 'fve', 'FvH4_4g01330' => 'fve', 'FvH4_5g09070' => 'fve', 'Glyma.10G243800' => 'gma', 'Glyma.20G150600' => 'gma', 'Gohir.A09G219200' => 'ghi', 'Gohir.A09G219300' => 'ghi', 'Gohir.D09G221400' => 'ghi', 'Gohir.D09G221500' => 'ghi', 'Gorai.006G242600' => 'gra', 'Gorai.006G242700' => 'gra', 'GSVIVG01018044001' => 'vvi', 'HanXRQChr03g0083821' => 'han', 'HanXRQChr03g0083841' => 'han', 'HanXRQChr03g0083881' => 'han', 'HanXRQChr03g0083901' => 'han', 'HanXRQChr03g0083921' => 'han', 'HanXRQChr03g0085331' => 'han', 'HanXRQChr03g0085361' => 'han', 'HanXRQChr03g0085411' => 'han', 'HanXRQChr03g0085421' => 'han', 'HanXRQChr03g0085431' => 'han', 'HanXRQChr08g0221991' => 'han', 'HanXRQChr11g0336061' => 'han', 'HanXRQChr11g0336411' => 'han', 'Haze_11234' => 'cav', 'Hma1.2p1_0549F.1_g177010' => 'hma', 'Hma1.2p1_0602F.1_g187630' => 'hma', 'Hund14876' => 'sun', 'Hund14879' => 'sun', 'Lalb_Chr06g0160741' => 'lal', 'Lalb_Chr21g0304781' => 'lal', 'Lj3A726G19' => 'lonja', 'Lj3A726T23' => 'lonja', 'Lj3A726T24' => 'lonja', 'Lj3A726T25' => 'lonja', 'Lj3A727T17' => 'lonja', 'Lj3C726T0' => 'lonja', 'Lj3C726T2' => 'lonja', 'Lj3P725T35' => 'lonja', 'Lj3P727T10' => 'lonja', 'Lj3P727T12' => 'lonja', 'Lj3P727T14' => 'lonja', 'Lj5g0023109' => 'lja', 'Lj6P646T44' => 'lonja', 'Lsat_1_v5_gn_6_75760' => 'lsa', 'Lsat_1_v5_gn_6_75800' => 'lsa', 'Lsat_1_v5_gn_6_75900' => 'lsa', 'Lsat_1_v5_gn_6_76240' => 'lsa', 'Lsat_1_v5_gn_6_76441' => 'lsa', 'Lsat_1_v5_gn_6_76700' => 'lsa', 'Lsat_1_v5_gn_6_76760' => 'lsa', 'Manes.15G033100' => 'mes', 'Mapoly0004s0074' => 'mpo', 'Mapoly0004s0075' => 'mpo', 'Mapoly0004s0163' => 'mpo', 'Mapoly0004s0164' => 'mpo', 'Mapoly0021s0018' => 'mpo', 'Mapoly0041s0136' => 'mpo', 'Mapoly0041s0137' => 'mpo', 'Mapoly0041s0138' => 'mpo', 'Mapoly0041s0139' => 'mpo', 'Mapoly0041s0141' => 'mpo', 'Mapoly0041s0142' => 'mpo', 'Mapoly0041s0143' => 'mpo', 'Mapoly0041s0144' => 'mpo', 'Mapoly0041s0145' => 'mpo', 'Mapoly0047s0106' => 'mpo', 'Mapoly0047s0108' => 'mpo', 'Mapoly0050s0051' => 'mpo', 'Mapoly0050s0052' => 'mpo', 'Mapoly0050s0053' => 'mpo', 'Mapoly0058s0013' => 'mpo', 'Mapoly0091s0078' => 'mpo', 'Mapoly0091s0079' => 'mpo', 'Mapoly0091s0080' => 'mpo', 'Mapoly0091s0081' => 'mpo', 'Mapoly0278s0004' => 'mpo', 'Mapoly0278s0005' => 'mpo', 'Mapoly0278s0006' => 'mpo', 'MBI11_g30648_MAGBIO' => 'mbi', 'MCO03G194' => 'mco', 'MCO03G590' => 'mco', 'MCO07G312' => 'mco', 'MCO10G318' => 'mco', 'MCO12G244' => 'mco', 'MCO13G148' => 'mco', 'MCO13G194' => 'mco', 'MCO16G238' => 'mco', 'MD06G1134100' => 'mdo', 'MD13G1200100' => 'mdo', 'MD13G1200300' => 'mdo', 'MD13G1200600' => 'mdo', 'MD14G1150400' => 'mdo', 'MD16G1200000' => 'mdo', 'Medtr1g102570' => 'mtr', 'Medtr1g102780' => 'mtr', 'Medtr1g102800' => 'mtr', 'Medtr1g102810' => 'mtr', 'Medtr1g102830' => 'mtr', 'MELO3C006499.2' => 'cme', 'Migut.G00385' => 'egut', 'MSTRG.4063' => 'ama', 'Nitab4.5_0000090g0260' => 'nta', 'Nitab4.5_0000977g0030' => 'nta', 'Nitab4.5_0002541g0040' => 'nta', 'Nitab4.5_0007068g0040' => 'nta', 'Nn005s41408' => 'nnu', 'Nn005s41410' => 'nnu', 'Oeu010310.1' => 'oeu', 'Oeu010311.1' => 'oeu', 'Oeu043472.1' => 'oeu', 'Os01g0246400' => 'osa', 'Os04g0267950' => 'osa', 'Os07g0178700' => 'osa', 'Os07g0178800' => 'osa', 'Peaxi162Scf00316g00046' => 'pax', 'Peaxi162Scf00316g00049' => 'pax', 'Peaxi162Scf00316g00059' => 'pax', 'Peaxi162Scf00316g00328' => 'pax', 'Peaxi162Scf00316g00329' => 'pax', 'Peaxi162Scf00316g00411' => 'pax', 'Peaxi162Scf00316g00521' => 'pax', 'Peaxi162Scf00492g00068' => 'pax', 'Peaxi162Scf35631g00002' => 'pax', 'PGR142G3720' => 'pgr', 'PGSC0003DMG400006442' => 'stu', 'Phvul.007G062000' => 'pvu', 'Potri.008G157750' => 'ptr', 'Potri.008G157900' => 'ptr', 'Potri.008G158000' => 'ptr', 'Potri.008G158200' => 'ptr', 'Pp3c11_7280' => 'ppa', 'Pp3c11_7980' => 'ppa', 'Pp3c12_19450' => 'ppa', 'Pp3c14_1480' => 'ppa', 'Pp3c14_1501' => 'ppa', 'Pp3c16_4900' => 'ppa', 'Pp3c16_5010' => 'ppa', 'Pp3c16_5060' => 'ppa', 'Pp3c19_18250' => 'ppa', 'Pp3c23_8530' => 'ppa', 'Pp3c23_8550' => 'ppa', 'Pp3c24_9670' => 'ppa', 'Pp3c2_21390' => 'ppa', 'Pp3c2_31380' => 'ppa', 'Pp3c3_16620' => 'ppa', 'Pp3c3_8090' => 'ppa', 'Pp3c3_8110' => 'ppa', 'Pp3c3_8130' => 'ppa', 'Pp3c3_8150' => 'ppa', 'Pp3c4_14320' => 'ppa', 'Pp3c6_2560' => 'ppa', 'Pp3c9_16700' => 'ppa', 'PRCOL_00000234' => 'pco', 'PRCOL_00000235' => 'pco', 'PRCOL_00000777' => 'pco', 'PRCOL_00002344' => 'pco', 'PRCOL_00002372' => 'pco', 'PRCOL_00006120' => 'pco', 'Prupe.1G021400' => 'ppe', 'Prupe.1G021500' => 'ppe', 'Prupe.1G021600' => 'ppe', 'Prupe.1G021700' => 'ppe', 'Prupe.1G021800' => 'ppe', 'Prupe.5G145100' => 'ppe', 'Psat6g204040' => 'psa', 'Psat6g204800' => 'psa', 'Psat6g204920' => 'psa', 'Psat6g204960' => 'psa', 'Psat6g205080' => 'psa', 'PSO017G0271' => 'pso', 'PSO017G1276' => 'pso', 'PSO017G1429' => 'pso', 'PSO017G1861' => 'pso', 'PSO017G2787' => 'pso', 'PSO017G4466' => 'pso', 'PSO017G5118' => 'pso', 'PSO017G5420' => 'pso', 'PSO063G3678' => 'pso', 'PSO210G0546' => 'pso', 'PSO317G0001' => 'pso', 'PSO357G0512' => 'pso', 'PSO478G2682' => 'pso', 'PSO647G0001' => 'pso', 'PSO675G0001' => 'pso', 'PSO675G2699' => 'pso', 'PSO675G2849' => 'pso', 'PSO675G4991' => 'pso', 'PSO689G0001' => 'pso', 'QL06p000916' => 'qlo', 'QL06p000921' => 'qlo', 'QL06p001398' => 'qlo', 'QL06p001407' => 'qlo', 'QL06p002031' => 'qlo', 'RcHm_v2.0_Chr4g0387791' => 'rch', 'RcHm_v2.0_Chr4g0387801' => 'rch', 'RcHm_v2.0_Chr6g0286501' => 'rch', 'RcHm_v2.0_Chr6g0286511' => 'rch', 'RcHm_v2.0_Chr6g0286521' => 'rch', 'RcHm_v2.0_Chr6g0286531' => 'rch', 'RcHm_v2.0_Chr7g0189141' => 'rch', 'Rhsim02G0028700' => 'rsi', 'Rhsim02G0028800' => 'rsi', 'Rhsim02G0028900' => 'rsi', 'Rhsim02G0029000' => 'rsi', 'Rhsim02G0029100' => 'rsi', 'Rhsim02G0029200' => 'rsi', 'Rhsim02G0029300' => 'rsi', 'Rhsim02G0029400' => 'rsi', 'Rhsim02G0029500' => 'rsi', 'Rhsim02G0029600' => 'rsi', 'RhsimUnG0024000' => 'rsi', 'RhsimUnG0024100' => 'rsi', 'RhsimUnG0024200' => 'rsi', 'RhsimUnG0024300' => 'rsi', 'RhsimUnG0024400' => 'rsi', 'RhsimUnG0024500' => 'rsi', 'RhsimUnG0024700' => 'rsi', 'RhsimUnG0024800' => 'rsi', 'RhsimUnG0024900' => 'rsi', 'RhsimUnG0025100' => 'rsi', 'Sabra08G0120200' => 'sbr', 'Sabra08G0120300' => 'sbr', 'Sabra08G0120500' => 'sbr', 'Sabra08G0120600' => 'sbr', 'Sabra10G0158900' => 'sbr', 'SalBow2G3492' => 'sbo', 'Sc13g0004760' => 'sci', 'Sc13g0004770' => 'sci', 'Sed0003417' => 'sed', 'Sed0019750' => 'sed', 'SEGI_03419' => 'sgi', 'SEGI_05907' => 'sgi', 'SEGI_10682' => 'sgi', 'SEGI_13528' => 'sgi', 'SEGI_16081' => 'sgi', 'SEGI_19370' => 'sgi', 'SEGI_21015' => 'sgi', 'SEGI_21944' => 'sgi', 'SEGI_32906' => 'sgi', 'SEGI_33093' => 'sgi', 'SEGI_36110' => 'sgi', 'SEGI_40397' => 'sgi', 'SGA_v2.0_scaffold191G40426' => 'sas', 'SGA_v2.0_scaffold353G49717' => 'sas', 'SGA_v2.0_scaffold50G18550' => 'sas', 'SMO119G0173' => 'smo', 'SMO172G0002' => 'smo', 'Solyc09g082690.3' => 'sly', 'Solyc09g082700.2' => 'sly', 'Sopen09g031550' => 'spe', 'Sopen09g031560' => 'spe', 'Sp3g20540' => 'spa', 'Sp7g07580' => 'spa', 'TAR134G0002' => 'tar', 'TAR236G0001' => 'tar', 'TAR365G0892' => 'tar', 'TAR636G0166' => 'tar', 'TAR636G0646' => 'tar', 'TAR636G0869' => 'tar', 'TAR636G1317' => 'tar', 'TAR636G1744' => 'tar', 'TAR636G3358' => 'tar', 'TAR636G3436' => 'tar', 'THA.LOC104803047' => 'tha', 'Thecc.04G238900' => 'tca', 'Thhalv10021557m.g' => 'esa', 'Thhalv10026318m.g' => 'esa', 'Thhalv10026335m.g' => 'esa', 'TPR.G17433' => 'tpr', 'TPR.G18915' => 'tpr', 'TPR.G26125' => 'tpr', 'TWI09G0677' => 'twi', 'TWI73G0287' => 'twi', 'unitig_748.g8326' => 'ugi', 'vmacro15370' => 'vma', 'vmacro15371' => 'vma', 'vmacro15372' => 'vma', 'vmacro15373' => 'vma', 'vmacro15374' => 'vma', 'VMungo0720G2826' => 'vmu', 'Zm00001eb116960' => 'zma', 'Zm00001eb301260' => 'zma', 'Zm00001eb301270' => 'zma' ) $gf_id = 'HOM05D001460' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001460' ) $data_identifier = 'HOM05D001460' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 4, 'aag' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 2, 'aox' => (int) 2, 'arhy' => (int) 4, 'ath' => (int) 2, 'atr' => (int) 1, 'acertr' => (int) 10, 'cqu' => (int) 4, 'bca' => (int) 11, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 1, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 1, 'ccan' => (int) 1, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 1, 'col' => (int) 1, 'cpa' => (int) 1, 'cre' => (int) 7, 'csa' => (int) 1, 'camsi' => (int) 2, 'dca' => (int) 3, 'din' => (int) 2, 'dzi' => (int) 3, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 14, 'fve' => (int) 9, 'gma' => (int) 2, 'ghi' => (int) 4, 'gra' => (int) 2, 'vvi' => (int) 1, 'han' => (int) 13, 'cav' => (int) 1, 'hma' => (int) 2, 'sun' => (int) 2, 'lal' => (int) 2, 'lonja' => (int) 12, 'lja' => (int) 1, 'lsa' => (int) 7, 'mes' => (int) 1, 'mpo' => (int) 27, 'mbi' => (int) 1, 'mco' => (int) 8, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 1, 'egut' => (int) 1, 'ama' => (int) 1, 'nta' => (int) 4, 'nnu' => (int) 2, 'oeu' => (int) 3, 'osa' => (int) 4, 'pax' => (int) 9, 'pgr' => (int) 1, 'stu' => (int) 1, 'pvu' => (int) 1, 'ptr' => (int) 4, 'ppa' => (int) 22, 'pco' => (int) 6, 'ppe' => (int) 6, 'psa' => (int) 5, 'pso' => (int) 19, 'qlo' => (int) 5, 'rch' => (int) 7, 'rsi' => (int) 20, 'sbr' => (int) 5, 'sbo' => (int) 1, 'sci' => (int) 2, 'sed' => (int) 2, 'sgi' => (int) 12, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 2, 'tar' => (int) 10, 'tha' => (int) 1, 'tca' => (int) 1, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 2, 'ugi' => (int) 1, 'vma' => (int) 5, 'vmu' => (int) 1, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb301270' $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' => 'HOM05D001460', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '433', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p22980' => 'bna', 'A01p32340' => 'bna', 'A03p42970' => 'bna', 'A05p25880' => 'bna', 'Aa31LG8G9320' => 'aar', 'Aa31LG8G9330' => 'aar', 'Aa31LG8G9340' => 'aar', 'Aa31sc221G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1034' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1528' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.829' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2222' => 'aag', 'Ah.12g058830' => 'amhyb', 'Ah.12g058840' => 'amhyb', 'AL3G37160' => 'aly', 'AL7G41310' => 'aly', 'Aqoxy5G00395' => 'aox', 'Aqoxy5G00396' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0C8NZA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5185HY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JZ1PRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MD3LS0' => 'arhy', 'AT3G22840' => 'ath', 'AT4G14690' => 'ath', 'ATR0665G054' => 'atr', 'Atru.chr4.2344' => 'acertr', 'Atru.chr4.2346' => 'acertr', 'Atru.chr4.2347' => 'acertr', 'Atru.chr4.2348' => 'acertr', 'Atru.chr4.2355' => 'acertr', 'Atru.chr4.2356' => 'acertr', 'Atru.chr4.2358' => 'acertr', 'Atru.chr4.2359' => 'acertr', 'Atru.chr4.2360' => 'acertr', 'Atru.chr4.2361' => 'acertr', 'AUR62030476' => 'cqu', 'AUR62030478' => 'cqu', 'AUR62030819' => 'cqu', 'AUR62030820' => 'cqu', 'BcaB03g14648' => 'bca', 'BcaB04g20492' => 'bca', 'BcaB06g26399' => 'bca', 'BcaC01g03416' => 'bca', 'BcaC01g03419' => 'bca', 'BcaC01g03421' => 'bca', 'BcaC01g03424' => 'bca', 'BcaC05g28012' => 'bca', 'BcaC09g49212' => 'bca', 'BcaC09g50140' => 'bca', 'BcaNung00346' => 'bca', 'BolC1t02785H' => 'bol', 'BolC1t04095H' => 'bol', 'BolC3t17545H' => 'bol', 'BolC5t32769H' => 'bol', 'BraA01t02211Z' => 'bra', 'BraA01t03359Z' => 'bra', 'BraA03t13441Z' => 'bra', 'BraA05t21476Z' => 'bra', 'C01p28420' => 'bna', 'C01p41350' => 'bna', 'C03p52750' => 'bna', 'C03p52780' => 'bna', 'C05p40270' => 'bna', 'CAN.G1437.9' => 'can', 'CANSAT78G0035' => 'cansat', 'CANSAT78G1036' => 'cansat', 'CANSAT78G2272' => 'cansat', 'CANSAT78G2478' => 'cansat', 'CARHR098700' => 'chi', 'CARHR221120' => 'chi', 'CARHR221150' => 'chi', 'Carub.0003s2297' => 'cru', 'Carub.0007s2749' => 'cru', 'Carub.0007s2750' => 'cru', 'Carub.0007s2751' => 'cru', 'Ca_10849_v3' => 'car', 'Cc03_g04300' => 'ccan', 'CDE02G3648' => 'cde', 'CDE05G0060' => 'cde', 'CDE05G0692' => 'cde', 'CDE05G2285' => 'cde', 'CDE05G2884' => 'cde', 'CDE05G3072' => 'cde', 'Cfa008439' => 'cfa', 'Cfa008441' => 'cfa', 'Cfa008443' => 'cfa', 'Cfa008448' => 'cfa', 'Ciclev10005974m.g' => 'ccl', 'Ciclev10006006m.g' => 'ccl', 'Ciclev10006775m.g' => 'ccl', 'CiPaw.02G120400' => 'cil', 'CiPaw.02G120500' => 'cil', 'CiPaw.02G120600' => 'cil', 'ClCG05G004850' => 'cla', 'COL.COLO4_21566' => 'col', 'Cpa.g.sc44.124' => 'cpa', 'Cre07.g320400' => 'cre', 'Cre07.g320450' => 'cre', 'Cre08.g384650' => 'cre', 'Cre09.g393173' => 'cre', 'Cre09.g394325' => 'cre', 'Cre14.g626750' => 'cre', 'Cre16.g679250' => 'cre', 'CsaV3_3G012890' => 'csa', 'CSS0010865' => 'camsi', 'CSS0044338' => 'camsi', 'DCAR_002366' => 'dca', 'DCAR_030687' => 'dca', 'DCAR_030688' => 'dca', 'Dinv14047' => 'din', 'Dinv14048' => 'din', 'Duzib151G0105' => 'dzi', 'Duzib151G0114' => 'dzi', 'Duzib212G1029' => 'dzi', 'ECA232G3536' => 'eca', 'ECA240G0786' => 'eca', 'ECA240G1802' => 'eca', 'ECA240G3760' => 'eca', 'ECA240G3920' => 'eca', 'EL10Ac5g12536' => 'bvu', 'EL10Ac5g12537' => 'bvu', 'EL10Ac5g12538' => 'bvu', 'Eucgr.B01004' => 'egr', 'Eucgr.B01006' => 'egr', 'Eucgr.B01007' => 'egr', 'Eucgr.B01008' => 'egr', 'Eucgr.B01895' => 'egr', 'Eucgr.B01896' => 'egr', 'FAN04G1456' => 'fan', 'FAN08G1769' => 'fan', 'FAN08G2160' => 'fan', 'FAN13G2403' => 'fan', 'FAN13G3303' => 'fan', 'FAN15G2435' => 'fan', 'FAN17G0672' => 'fan', 'FAN17G2441' => 'fan', 'FAN18G1024' => 'fan', 'FAN22G1458' => 'fan', 'FAN24G0037' => 'fan', 'FAN24G0429' => 'fan', 'FAN24G2387' => 'fan', 'FAN27G2746' => 'fan', 'FvH4_2g20400' => 'fve', 'FvH4_2g20420' => 'fve', 'FvH4_2g20430' => 'fve', 'FvH4_4g01270' => 'fve', 'FvH4_4g01290' => 'fve', 'FvH4_4g01300' => 'fve', 'FvH4_4g01310' => 'fve', 'FvH4_4g01330' => 'fve', 'FvH4_5g09070' => 'fve', 'Glyma.10G243800' => 'gma', 'Glyma.20G150600' => 'gma', 'Gohir.A09G219200' => 'ghi', 'Gohir.A09G219300' => 'ghi', 'Gohir.D09G221400' => 'ghi', 'Gohir.D09G221500' => 'ghi', 'Gorai.006G242600' => 'gra', 'Gorai.006G242700' => 'gra', 'GSVIVG01018044001' => 'vvi', 'HanXRQChr03g0083821' => 'han', 'HanXRQChr03g0083841' => 'han', 'HanXRQChr03g0083881' => 'han', 'HanXRQChr03g0083901' => 'han', 'HanXRQChr03g0083921' => 'han', 'HanXRQChr03g0085331' => 'han', 'HanXRQChr03g0085361' => 'han', 'HanXRQChr03g0085411' => 'han', 'HanXRQChr03g0085421' => 'han', 'HanXRQChr03g0085431' => 'han', 'HanXRQChr08g0221991' => 'han', 'HanXRQChr11g0336061' => 'han', 'HanXRQChr11g0336411' => 'han', 'Haze_11234' => 'cav', 'Hma1.2p1_0549F.1_g177010' => 'hma', 'Hma1.2p1_0602F.1_g187630' => 'hma', 'Hund14876' => 'sun', 'Hund14879' => 'sun', 'Lalb_Chr06g0160741' => 'lal', 'Lalb_Chr21g0304781' => 'lal', 'Lj3A726G19' => 'lonja', 'Lj3A726T23' => 'lonja', 'Lj3A726T24' => 'lonja', 'Lj3A726T25' => 'lonja', 'Lj3A727T17' => 'lonja', 'Lj3C726T0' => 'lonja', 'Lj3C726T2' => 'lonja', 'Lj3P725T35' => 'lonja', 'Lj3P727T10' => 'lonja', 'Lj3P727T12' => 'lonja', 'Lj3P727T14' => 'lonja', 'Lj5g0023109' => 'lja', 'Lj6P646T44' => 'lonja', 'Lsat_1_v5_gn_6_75760' => 'lsa', 'Lsat_1_v5_gn_6_75800' => 'lsa', 'Lsat_1_v5_gn_6_75900' => 'lsa', 'Lsat_1_v5_gn_6_76240' => 'lsa', 'Lsat_1_v5_gn_6_76441' => 'lsa', 'Lsat_1_v5_gn_6_76700' => 'lsa', 'Lsat_1_v5_gn_6_76760' => 'lsa', 'Manes.15G033100' => 'mes', 'Mapoly0004s0074' => 'mpo', 'Mapoly0004s0075' => 'mpo', 'Mapoly0004s0163' => 'mpo', 'Mapoly0004s0164' => 'mpo', 'Mapoly0021s0018' => 'mpo', 'Mapoly0041s0136' => 'mpo', 'Mapoly0041s0137' => 'mpo', 'Mapoly0041s0138' => 'mpo', 'Mapoly0041s0139' => 'mpo', 'Mapoly0041s0141' => 'mpo', 'Mapoly0041s0142' => 'mpo', 'Mapoly0041s0143' => 'mpo', 'Mapoly0041s0144' => 'mpo', 'Mapoly0041s0145' => 'mpo', 'Mapoly0047s0106' => 'mpo', 'Mapoly0047s0108' => 'mpo', 'Mapoly0050s0051' => 'mpo', 'Mapoly0050s0052' => 'mpo', 'Mapoly0050s0053' => 'mpo', 'Mapoly0058s0013' => 'mpo', 'Mapoly0091s0078' => 'mpo', 'Mapoly0091s0079' => 'mpo', 'Mapoly0091s0080' => 'mpo', 'Mapoly0091s0081' => 'mpo', 'Mapoly0278s0004' => 'mpo', 'Mapoly0278s0005' => 'mpo', 'Mapoly0278s0006' => 'mpo', 'MBI11_g30648_MAGBIO' => 'mbi', 'MCO03G194' => 'mco', 'MCO03G590' => 'mco', 'MCO07G312' => 'mco', 'MCO10G318' => 'mco', 'MCO12G244' => 'mco', 'MCO13G148' => 'mco', 'MCO13G194' => 'mco', 'MCO16G238' => 'mco', 'MD06G1134100' => 'mdo', 'MD13G1200100' => 'mdo', 'MD13G1200300' => 'mdo', 'MD13G1200600' => 'mdo', 'MD14G1150400' => 'mdo', 'MD16G1200000' => 'mdo', 'Medtr1g102570' => 'mtr', 'Medtr1g102780' => 'mtr', 'Medtr1g102800' => 'mtr', 'Medtr1g102810' => 'mtr', 'Medtr1g102830' => 'mtr', 'MELO3C006499.2' => 'cme', 'Migut.G00385' => 'egut', 'MSTRG.4063' => 'ama', 'Nitab4.5_0000090g0260' => 'nta', 'Nitab4.5_0000977g0030' => 'nta', 'Nitab4.5_0002541g0040' => 'nta', 'Nitab4.5_0007068g0040' => 'nta', 'Nn005s41408' => 'nnu', 'Nn005s41410' => 'nnu', 'Oeu010310.1' => 'oeu', 'Oeu010311.1' => 'oeu', 'Oeu043472.1' => 'oeu', 'Os01g0246400' => 'osa', 'Os04g0267950' => 'osa', 'Os07g0178700' => 'osa', 'Os07g0178800' => 'osa', 'Peaxi162Scf00316g00046' => 'pax', 'Peaxi162Scf00316g00049' => 'pax', 'Peaxi162Scf00316g00059' => 'pax', 'Peaxi162Scf00316g00328' => 'pax', 'Peaxi162Scf00316g00329' => 'pax', 'Peaxi162Scf00316g00411' => 'pax', 'Peaxi162Scf00316g00521' => 'pax', 'Peaxi162Scf00492g00068' => 'pax', 'Peaxi162Scf35631g00002' => 'pax', 'PGR142G3720' => 'pgr', 'PGSC0003DMG400006442' => 'stu', 'Phvul.007G062000' => 'pvu', 'Potri.008G157750' => 'ptr', 'Potri.008G157900' => 'ptr', 'Potri.008G158000' => 'ptr', 'Potri.008G158200' => 'ptr', 'Pp3c11_7280' => 'ppa', 'Pp3c11_7980' => 'ppa', 'Pp3c12_19450' => 'ppa', 'Pp3c14_1480' => 'ppa', 'Pp3c14_1501' => 'ppa', 'Pp3c16_4900' => 'ppa', 'Pp3c16_5010' => 'ppa', 'Pp3c16_5060' => 'ppa', 'Pp3c19_18250' => 'ppa', 'Pp3c23_8530' => 'ppa', 'Pp3c23_8550' => 'ppa', 'Pp3c24_9670' => 'ppa', 'Pp3c2_21390' => 'ppa', 'Pp3c2_31380' => 'ppa', 'Pp3c3_16620' => 'ppa', 'Pp3c3_8090' => 'ppa', 'Pp3c3_8110' => 'ppa', 'Pp3c3_8130' => 'ppa', 'Pp3c3_8150' => 'ppa', 'Pp3c4_14320' => 'ppa', 'Pp3c6_2560' => 'ppa', 'Pp3c9_16700' => 'ppa', 'PRCOL_00000234' => 'pco', 'PRCOL_00000235' => 'pco', 'PRCOL_00000777' => 'pco', 'PRCOL_00002344' => 'pco', 'PRCOL_00002372' => 'pco', 'PRCOL_00006120' => 'pco', 'Prupe.1G021400' => 'ppe', 'Prupe.1G021500' => 'ppe', 'Prupe.1G021600' => 'ppe', 'Prupe.1G021700' => 'ppe', 'Prupe.1G021800' => 'ppe', 'Prupe.5G145100' => 'ppe', 'Psat6g204040' => 'psa', 'Psat6g204800' => 'psa', 'Psat6g204920' => 'psa', 'Psat6g204960' => 'psa', 'Psat6g205080' => 'psa', 'PSO017G0271' => 'pso', 'PSO017G1276' => 'pso', 'PSO017G1429' => 'pso', 'PSO017G1861' => 'pso', 'PSO017G2787' => 'pso', 'PSO017G4466' => 'pso', 'PSO017G5118' => 'pso', 'PSO017G5420' => 'pso', 'PSO063G3678' => 'pso', 'PSO210G0546' => 'pso', 'PSO317G0001' => 'pso', 'PSO357G0512' => 'pso', 'PSO478G2682' => 'pso', 'PSO647G0001' => 'pso', 'PSO675G0001' => 'pso', 'PSO675G2699' => 'pso', 'PSO675G2849' => 'pso', 'PSO675G4991' => 'pso', 'PSO689G0001' => 'pso', 'QL06p000916' => 'qlo', 'QL06p000921' => 'qlo', 'QL06p001398' => 'qlo', 'QL06p001407' => 'qlo', 'QL06p002031' => 'qlo', 'RcHm_v2.0_Chr4g0387791' => 'rch', 'RcHm_v2.0_Chr4g0387801' => 'rch', 'RcHm_v2.0_Chr6g0286501' => 'rch', 'RcHm_v2.0_Chr6g0286511' => 'rch', 'RcHm_v2.0_Chr6g0286521' => 'rch', 'RcHm_v2.0_Chr6g0286531' => 'rch', 'RcHm_v2.0_Chr7g0189141' => 'rch', 'Rhsim02G0028700' => 'rsi', 'Rhsim02G0028800' => 'rsi', 'Rhsim02G0028900' => 'rsi', 'Rhsim02G0029000' => 'rsi', 'Rhsim02G0029100' => 'rsi', 'Rhsim02G0029200' => 'rsi', 'Rhsim02G0029300' => 'rsi', 'Rhsim02G0029400' => 'rsi', 'Rhsim02G0029500' => 'rsi', 'Rhsim02G0029600' => 'rsi', 'RhsimUnG0024000' => 'rsi', 'RhsimUnG0024100' => 'rsi', 'RhsimUnG0024200' => 'rsi', 'RhsimUnG0024300' => 'rsi', 'RhsimUnG0024400' => 'rsi', 'RhsimUnG0024500' => 'rsi', 'RhsimUnG0024700' => 'rsi', 'RhsimUnG0024800' => 'rsi', 'RhsimUnG0024900' => 'rsi', 'RhsimUnG0025100' => 'rsi', 'Sabra08G0120200' => 'sbr', 'Sabra08G0120300' => 'sbr', 'Sabra08G0120500' => 'sbr', 'Sabra08G0120600' => 'sbr', 'Sabra10G0158900' => 'sbr', 'SalBow2G3492' => 'sbo', 'Sc13g0004760' => 'sci', 'Sc13g0004770' => 'sci', 'Sed0003417' => 'sed', 'Sed0019750' => 'sed', 'SEGI_03419' => 'sgi', 'SEGI_05907' => 'sgi', 'SEGI_10682' => 'sgi', 'SEGI_13528' => 'sgi', 'SEGI_16081' => 'sgi', 'SEGI_19370' => 'sgi', 'SEGI_21015' => 'sgi', 'SEGI_21944' => 'sgi', 'SEGI_32906' => 'sgi', 'SEGI_33093' => 'sgi', 'SEGI_36110' => 'sgi', 'SEGI_40397' => 'sgi', 'SGA_v2.0_scaffold191G40426' => 'sas', 'SGA_v2.0_scaffold353G49717' => 'sas', 'SGA_v2.0_scaffold50G18550' => 'sas', 'SMO119G0173' => 'smo', 'SMO172G0002' => 'smo', 'Solyc09g082690.3' => 'sly', 'Solyc09g082700.2' => 'sly', 'Sopen09g031550' => 'spe', 'Sopen09g031560' => 'spe', 'Sp3g20540' => 'spa', 'Sp7g07580' => 'spa', 'TAR134G0002' => 'tar', 'TAR236G0001' => 'tar', 'TAR365G0892' => 'tar', 'TAR636G0166' => 'tar', 'TAR636G0646' => 'tar', 'TAR636G0869' => 'tar', 'TAR636G1317' => 'tar', 'TAR636G1744' => 'tar', 'TAR636G3358' => 'tar', 'TAR636G3436' => 'tar', 'THA.LOC104803047' => 'tha', 'Thecc.04G238900' => 'tca', 'Thhalv10021557m.g' => 'esa', 'Thhalv10026318m.g' => 'esa', 'Thhalv10026335m.g' => 'esa', 'TPR.G17433' => 'tpr', 'TPR.G18915' => 'tpr', 'TPR.G26125' => 'tpr', 'TWI09G0677' => 'twi', 'TWI73G0287' => 'twi', 'unitig_748.g8326' => 'ugi', 'vmacro15370' => 'vma', 'vmacro15371' => 'vma', 'vmacro15372' => 'vma', 'vmacro15373' => 'vma', 'vmacro15374' => 'vma', 'VMungo0720G2826' => 'vmu', 'Zm00001eb116960' => 'zma', 'Zm00001eb301260' => 'zma', 'Zm00001eb301270' => 'zma' ), 'gf_id' => 'HOM05D001460', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001460' ), 'data_identifier' => 'HOM05D001460', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001460', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '433', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p22980' => 'bna', 'A01p32340' => 'bna', 'A03p42970' => 'bna', 'A05p25880' => 'bna', 'Aa31LG8G9320' => 'aar', 'Aa31LG8G9330' => 'aar', 'Aa31LG8G9340' => 'aar', 'Aa31sc221G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1034' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1528' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.829' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2222' => 'aag', 'Ah.12g058830' => 'amhyb', 'Ah.12g058840' => 'amhyb', 'AL3G37160' => 'aly', 'AL7G41310' => 'aly', 'Aqoxy5G00395' => 'aox', 'Aqoxy5G00396' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0C8NZA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5185HY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JZ1PRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MD3LS0' => 'arhy', 'AT3G22840' => 'ath', 'AT4G14690' => 'ath', 'ATR0665G054' => 'atr', 'Atru.chr4.2344' => 'acertr', 'Atru.chr4.2346' => 'acertr', 'Atru.chr4.2347' => 'acertr', 'Atru.chr4.2348' => 'acertr', 'Atru.chr4.2355' => 'acertr', 'Atru.chr4.2356' => 'acertr', 'Atru.chr4.2358' => 'acertr', 'Atru.chr4.2359' => 'acertr', 'Atru.chr4.2360' => 'acertr', 'Atru.chr4.2361' => 'acertr', 'AUR62030476' => 'cqu', 'AUR62030478' => 'cqu', 'AUR62030819' => 'cqu', 'AUR62030820' => 'cqu', 'BcaB03g14648' => 'bca', 'BcaB04g20492' => 'bca', 'BcaB06g26399' => 'bca', 'BcaC01g03416' => 'bca', 'BcaC01g03419' => 'bca', 'BcaC01g03421' => 'bca', 'BcaC01g03424' => 'bca', 'BcaC05g28012' => 'bca', 'BcaC09g49212' => 'bca', 'BcaC09g50140' => 'bca', 'BcaNung00346' => 'bca', 'BolC1t02785H' => 'bol', 'BolC1t04095H' => 'bol', 'BolC3t17545H' => 'bol', 'BolC5t32769H' => 'bol', 'BraA01t02211Z' => 'bra', 'BraA01t03359Z' => 'bra', 'BraA03t13441Z' => 'bra', 'BraA05t21476Z' => 'bra', 'C01p28420' => 'bna', 'C01p41350' => 'bna', 'C03p52750' => 'bna', 'C03p52780' => 'bna', 'C05p40270' => 'bna', 'CAN.G1437.9' => 'can', 'CANSAT78G0035' => 'cansat', 'CANSAT78G1036' => 'cansat', 'CANSAT78G2272' => 'cansat', 'CANSAT78G2478' => 'cansat', 'CARHR098700' => 'chi', 'CARHR221120' => 'chi', 'CARHR221150' => 'chi', 'Carub.0003s2297' => 'cru', 'Carub.0007s2749' => 'cru', 'Carub.0007s2750' => 'cru', 'Carub.0007s2751' => 'cru', 'Ca_10849_v3' => 'car', 'Cc03_g04300' => 'ccan', 'CDE02G3648' => 'cde', 'CDE05G0060' => 'cde', 'CDE05G0692' => 'cde', 'CDE05G2285' => 'cde', 'CDE05G2884' => 'cde', 'CDE05G3072' => 'cde', 'Cfa008439' => 'cfa', 'Cfa008441' => 'cfa', 'Cfa008443' => 'cfa', 'Cfa008448' => 'cfa', 'Ciclev10005974m.g' => 'ccl', 'Ciclev10006006m.g' => 'ccl', 'Ciclev10006775m.g' => 'ccl', 'CiPaw.02G120400' => 'cil', 'CiPaw.02G120500' => 'cil', 'CiPaw.02G120600' => 'cil', 'ClCG05G004850' => 'cla', 'COL.COLO4_21566' => 'col', 'Cpa.g.sc44.124' => 'cpa', 'Cre07.g320400' => 'cre', 'Cre07.g320450' => 'cre', 'Cre08.g384650' => 'cre', 'Cre09.g393173' => 'cre', 'Cre09.g394325' => 'cre', 'Cre14.g626750' => 'cre', 'Cre16.g679250' => 'cre', 'CsaV3_3G012890' => 'csa', 'CSS0010865' => 'camsi', 'CSS0044338' => 'camsi', 'DCAR_002366' => 'dca', 'DCAR_030687' => 'dca', 'DCAR_030688' => 'dca', 'Dinv14047' => 'din', 'Dinv14048' => 'din', 'Duzib151G0105' => 'dzi', 'Duzib151G0114' => 'dzi', 'Duzib212G1029' => 'dzi', 'ECA232G3536' => 'eca', 'ECA240G0786' => 'eca', 'ECA240G1802' => 'eca', 'ECA240G3760' => 'eca', 'ECA240G3920' => 'eca', 'EL10Ac5g12536' => 'bvu', 'EL10Ac5g12537' => 'bvu', 'EL10Ac5g12538' => 'bvu', 'Eucgr.B01004' => 'egr', 'Eucgr.B01006' => 'egr', 'Eucgr.B01007' => 'egr', 'Eucgr.B01008' => 'egr', 'Eucgr.B01895' => 'egr', 'Eucgr.B01896' => 'egr', 'FAN04G1456' => 'fan', 'FAN08G1769' => 'fan', 'FAN08G2160' => 'fan', 'FAN13G2403' => 'fan', 'FAN13G3303' => 'fan', 'FAN15G2435' => 'fan', 'FAN17G0672' => 'fan', 'FAN17G2441' => 'fan', 'FAN18G1024' => 'fan', 'FAN22G1458' => 'fan', 'FAN24G0037' => 'fan', 'FAN24G0429' => 'fan', 'FAN24G2387' => 'fan', 'FAN27G2746' => 'fan', 'FvH4_2g20400' => 'fve', 'FvH4_2g20420' => 'fve', 'FvH4_2g20430' => 'fve', 'FvH4_4g01270' => 'fve', 'FvH4_4g01290' => 'fve', 'FvH4_4g01300' => 'fve', 'FvH4_4g01310' => 'fve', 'FvH4_4g01330' => 'fve', 'FvH4_5g09070' => 'fve', 'Glyma.10G243800' => 'gma', 'Glyma.20G150600' => 'gma', 'Gohir.A09G219200' => 'ghi', 'Gohir.A09G219300' => 'ghi', 'Gohir.D09G221400' => 'ghi', 'Gohir.D09G221500' => 'ghi', 'Gorai.006G242600' => 'gra', 'Gorai.006G242700' => 'gra', 'GSVIVG01018044001' => 'vvi', 'HanXRQChr03g0083821' => 'han', 'HanXRQChr03g0083841' => 'han', 'HanXRQChr03g0083881' => 'han', 'HanXRQChr03g0083901' => 'han', 'HanXRQChr03g0083921' => 'han', 'HanXRQChr03g0085331' => 'han', 'HanXRQChr03g0085361' => 'han', 'HanXRQChr03g0085411' => 'han', 'HanXRQChr03g0085421' => 'han', 'HanXRQChr03g0085431' => 'han', 'HanXRQChr08g0221991' => 'han', 'HanXRQChr11g0336061' => 'han', 'HanXRQChr11g0336411' => 'han', 'Haze_11234' => 'cav', 'Hma1.2p1_0549F.1_g177010' => 'hma', 'Hma1.2p1_0602F.1_g187630' => 'hma', 'Hund14876' => 'sun', 'Hund14879' => 'sun', 'Lalb_Chr06g0160741' => 'lal', 'Lalb_Chr21g0304781' => 'lal', 'Lj3A726G19' => 'lonja', 'Lj3A726T23' => 'lonja', 'Lj3A726T24' => 'lonja', 'Lj3A726T25' => 'lonja', 'Lj3A727T17' => 'lonja', 'Lj3C726T0' => 'lonja', 'Lj3C726T2' => 'lonja', 'Lj3P725T35' => 'lonja', 'Lj3P727T10' => 'lonja', 'Lj3P727T12' => 'lonja', 'Lj3P727T14' => 'lonja', 'Lj5g0023109' => 'lja', 'Lj6P646T44' => 'lonja', 'Lsat_1_v5_gn_6_75760' => 'lsa', 'Lsat_1_v5_gn_6_75800' => 'lsa', 'Lsat_1_v5_gn_6_75900' => 'lsa', 'Lsat_1_v5_gn_6_76240' => 'lsa', 'Lsat_1_v5_gn_6_76441' => 'lsa', 'Lsat_1_v5_gn_6_76700' => 'lsa', 'Lsat_1_v5_gn_6_76760' => 'lsa', 'Manes.15G033100' => 'mes', 'Mapoly0004s0074' => 'mpo', 'Mapoly0004s0075' => 'mpo', 'Mapoly0004s0163' => 'mpo', 'Mapoly0004s0164' => 'mpo', 'Mapoly0021s0018' => 'mpo', 'Mapoly0041s0136' => 'mpo', 'Mapoly0041s0137' => 'mpo', 'Mapoly0041s0138' => 'mpo', 'Mapoly0041s0139' => 'mpo', 'Mapoly0041s0141' => 'mpo', 'Mapoly0041s0142' => 'mpo', 'Mapoly0041s0143' => 'mpo', 'Mapoly0041s0144' => 'mpo', 'Mapoly0041s0145' => 'mpo', 'Mapoly0047s0106' => 'mpo', 'Mapoly0047s0108' => 'mpo', 'Mapoly0050s0051' => 'mpo', 'Mapoly0050s0052' => 'mpo', 'Mapoly0050s0053' => 'mpo', 'Mapoly0058s0013' => 'mpo', 'Mapoly0091s0078' => 'mpo', 'Mapoly0091s0079' => 'mpo', 'Mapoly0091s0080' => 'mpo', 'Mapoly0091s0081' => 'mpo', 'Mapoly0278s0004' => 'mpo', 'Mapoly0278s0005' => 'mpo', 'Mapoly0278s0006' => 'mpo', 'MBI11_g30648_MAGBIO' => 'mbi', 'MCO03G194' => 'mco', 'MCO03G590' => 'mco', 'MCO07G312' => 'mco', 'MCO10G318' => 'mco', 'MCO12G244' => 'mco', 'MCO13G148' => 'mco', 'MCO13G194' => 'mco', 'MCO16G238' => 'mco', 'MD06G1134100' => 'mdo', 'MD13G1200100' => 'mdo', 'MD13G1200300' => 'mdo', 'MD13G1200600' => 'mdo', 'MD14G1150400' => 'mdo', 'MD16G1200000' => 'mdo', 'Medtr1g102570' => 'mtr', 'Medtr1g102780' => 'mtr', 'Medtr1g102800' => 'mtr', 'Medtr1g102810' => 'mtr', 'Medtr1g102830' => 'mtr', 'MELO3C006499.2' => 'cme', 'Migut.G00385' => 'egut', 'MSTRG.4063' => 'ama', 'Nitab4.5_0000090g0260' => 'nta', 'Nitab4.5_0000977g0030' => 'nta', 'Nitab4.5_0002541g0040' => 'nta', 'Nitab4.5_0007068g0040' => 'nta', 'Nn005s41408' => 'nnu', 'Nn005s41410' => 'nnu', 'Oeu010310.1' => 'oeu', 'Oeu010311.1' => 'oeu', 'Oeu043472.1' => 'oeu', 'Os01g0246400' => 'osa', 'Os04g0267950' => 'osa', 'Os07g0178700' => 'osa', 'Os07g0178800' => 'osa', 'Peaxi162Scf00316g00046' => 'pax', 'Peaxi162Scf00316g00049' => 'pax', 'Peaxi162Scf00316g00059' => 'pax', 'Peaxi162Scf00316g00328' => 'pax', 'Peaxi162Scf00316g00329' => 'pax', 'Peaxi162Scf00316g00411' => 'pax', 'Peaxi162Scf00316g00521' => 'pax', 'Peaxi162Scf00492g00068' => 'pax', 'Peaxi162Scf35631g00002' => 'pax', 'PGR142G3720' => 'pgr', 'PGSC0003DMG400006442' => 'stu', 'Phvul.007G062000' => 'pvu', 'Potri.008G157750' => 'ptr', 'Potri.008G157900' => 'ptr', 'Potri.008G158000' => 'ptr', 'Potri.008G158200' => 'ptr', 'Pp3c11_7280' => 'ppa', 'Pp3c11_7980' => 'ppa', 'Pp3c12_19450' => 'ppa', 'Pp3c14_1480' => 'ppa', 'Pp3c14_1501' => 'ppa', 'Pp3c16_4900' => 'ppa', 'Pp3c16_5010' => 'ppa', 'Pp3c16_5060' => 'ppa', 'Pp3c19_18250' => 'ppa', 'Pp3c23_8530' => 'ppa', 'Pp3c23_8550' => 'ppa', 'Pp3c24_9670' => 'ppa', 'Pp3c2_21390' => 'ppa', 'Pp3c2_31380' => 'ppa', 'Pp3c3_16620' => 'ppa', 'Pp3c3_8090' => 'ppa', 'Pp3c3_8110' => 'ppa', 'Pp3c3_8130' => 'ppa', 'Pp3c3_8150' => 'ppa', 'Pp3c4_14320' => 'ppa', 'Pp3c6_2560' => 'ppa', 'Pp3c9_16700' => 'ppa', 'PRCOL_00000234' => 'pco', 'PRCOL_00000235' => 'pco', 'PRCOL_00000777' => 'pco', 'PRCOL_00002344' => 'pco', 'PRCOL_00002372' => 'pco', 'PRCOL_00006120' => 'pco', 'Prupe.1G021400' => 'ppe', 'Prupe.1G021500' => 'ppe', 'Prupe.1G021600' => 'ppe', 'Prupe.1G021700' => 'ppe', 'Prupe.1G021800' => 'ppe', 'Prupe.5G145100' => 'ppe', 'Psat6g204040' => 'psa', 'Psat6g204800' => 'psa', 'Psat6g204920' => 'psa', 'Psat6g204960' => 'psa', 'Psat6g205080' => 'psa', 'PSO017G0271' => 'pso', 'PSO017G1276' => 'pso', 'PSO017G1429' => 'pso', 'PSO017G1861' => 'pso', 'PSO017G2787' => 'pso', 'PSO017G4466' => 'pso', 'PSO017G5118' => 'pso', 'PSO017G5420' => 'pso', 'PSO063G3678' => 'pso', 'PSO210G0546' => 'pso', 'PSO317G0001' => 'pso', 'PSO357G0512' => 'pso', 'PSO478G2682' => 'pso', 'PSO647G0001' => 'pso', 'PSO675G0001' => 'pso', 'PSO675G2699' => 'pso', 'PSO675G2849' => 'pso', 'PSO675G4991' => 'pso', 'PSO689G0001' => 'pso', 'QL06p000916' => 'qlo', 'QL06p000921' => 'qlo', 'QL06p001398' => 'qlo', 'QL06p001407' => 'qlo', 'QL06p002031' => 'qlo', 'RcHm_v2.0_Chr4g0387791' => 'rch', 'RcHm_v2.0_Chr4g0387801' => 'rch', 'RcHm_v2.0_Chr6g0286501' => 'rch', 'RcHm_v2.0_Chr6g0286511' => 'rch', 'RcHm_v2.0_Chr6g0286521' => 'rch', 'RcHm_v2.0_Chr6g0286531' => 'rch', 'RcHm_v2.0_Chr7g0189141' => 'rch', 'Rhsim02G0028700' => 'rsi', 'Rhsim02G0028800' => 'rsi', 'Rhsim02G0028900' => 'rsi', 'Rhsim02G0029000' => 'rsi', 'Rhsim02G0029100' => 'rsi', 'Rhsim02G0029200' => 'rsi', 'Rhsim02G0029300' => 'rsi', 'Rhsim02G0029400' => 'rsi', 'Rhsim02G0029500' => 'rsi', 'Rhsim02G0029600' => 'rsi', 'RhsimUnG0024000' => 'rsi', 'RhsimUnG0024100' => 'rsi', 'RhsimUnG0024200' => 'rsi', 'RhsimUnG0024300' => 'rsi', 'RhsimUnG0024400' => 'rsi', 'RhsimUnG0024500' => 'rsi', 'RhsimUnG0024700' => 'rsi', 'RhsimUnG0024800' => 'rsi', 'RhsimUnG0024900' => 'rsi', 'RhsimUnG0025100' => 'rsi', 'Sabra08G0120200' => 'sbr', 'Sabra08G0120300' => 'sbr', 'Sabra08G0120500' => 'sbr', 'Sabra08G0120600' => 'sbr', 'Sabra10G0158900' => 'sbr', 'SalBow2G3492' => 'sbo', 'Sc13g0004760' => 'sci', 'Sc13g0004770' => 'sci', 'Sed0003417' => 'sed', 'Sed0019750' => 'sed', 'SEGI_03419' => 'sgi', 'SEGI_05907' => 'sgi', 'SEGI_10682' => 'sgi', 'SEGI_13528' => 'sgi', 'SEGI_16081' => 'sgi', 'SEGI_19370' => 'sgi', 'SEGI_21015' => 'sgi', 'SEGI_21944' => 'sgi', 'SEGI_32906' => 'sgi', 'SEGI_33093' => 'sgi', 'SEGI_36110' => 'sgi', 'SEGI_40397' => 'sgi', 'SGA_v2.0_scaffold191G40426' => 'sas', 'SGA_v2.0_scaffold353G49717' => 'sas', 'SGA_v2.0_scaffold50G18550' => 'sas', 'SMO119G0173' => 'smo', 'SMO172G0002' => 'smo', 'Solyc09g082690.3' => 'sly', 'Solyc09g082700.2' => 'sly', 'Sopen09g031550' => 'spe', 'Sopen09g031560' => 'spe', 'Sp3g20540' => 'spa', 'Sp7g07580' => 'spa', 'TAR134G0002' => 'tar', 'TAR236G0001' => 'tar', 'TAR365G0892' => 'tar', 'TAR636G0166' => 'tar', 'TAR636G0646' => 'tar', 'TAR636G0869' => 'tar', 'TAR636G1317' => 'tar', 'TAR636G1744' => 'tar', 'TAR636G3358' => 'tar', 'TAR636G3436' => 'tar', 'THA.LOC104803047' => 'tha', 'Thecc.04G238900' => 'tca', 'Thhalv10021557m.g' => 'esa', 'Thhalv10026318m.g' => 'esa', 'Thhalv10026335m.g' => 'esa', 'TPR.G17433' => 'tpr', 'TPR.G18915' => 'tpr', 'TPR.G26125' => 'tpr', 'TWI09G0677' => 'twi', 'TWI73G0287' => 'twi', 'unitig_748.g8326' => 'ugi', 'vmacro15370' => 'vma', 'vmacro15371' => 'vma', 'vmacro15372' => 'vma', 'vmacro15373' => 'vma', 'vmacro15374' => 'vma', 'VMungo0720G2826' => 'vmu', 'Zm00001eb116960' => 'zma', 'Zm00001eb301260' => 'zma', 'Zm00001eb301270' => 'zma' ) $gf_id = 'HOM05D001460' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001460' ) $data_identifier = 'HOM05D001460' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 4, 'aag' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 2, 'aox' => (int) 2, 'arhy' => (int) 4, 'ath' => (int) 2, 'atr' => (int) 1, 'acertr' => (int) 10, 'cqu' => (int) 4, 'bca' => (int) 11, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 1, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 1, 'ccan' => (int) 1, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 1, 'col' => (int) 1, 'cpa' => (int) 1, 'cre' => (int) 7, 'csa' => (int) 1, 'camsi' => (int) 2, 'dca' => (int) 3, 'din' => (int) 2, 'dzi' => (int) 3, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 14, 'fve' => (int) 9, 'gma' => (int) 2, 'ghi' => (int) 4, 'gra' => (int) 2, 'vvi' => (int) 1, 'han' => (int) 13, 'cav' => (int) 1, 'hma' => (int) 2, 'sun' => (int) 2, 'lal' => (int) 2, 'lonja' => (int) 12, 'lja' => (int) 1, 'lsa' => (int) 7, 'mes' => (int) 1, 'mpo' => (int) 27, 'mbi' => (int) 1, 'mco' => (int) 8, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 1, 'egut' => (int) 1, 'ama' => (int) 1, 'nta' => (int) 4, 'nnu' => (int) 2, 'oeu' => (int) 3, 'osa' => (int) 4, 'pax' => (int) 9, 'pgr' => (int) 1, 'stu' => (int) 1, 'pvu' => (int) 1, 'ptr' => (int) 4, 'ppa' => (int) 22, 'pco' => (int) 6, 'ppe' => (int) 6, 'psa' => (int) 5, 'pso' => (int) 19, 'qlo' => (int) 5, 'rch' => (int) 7, 'rsi' => (int) 20, 'sbr' => (int) 5, 'sbo' => (int) 1, 'sci' => (int) 2, 'sed' => (int) 2, 'sgi' => (int) 12, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 2, 'tar' => (int) 10, 'tha' => (int) 1, 'tca' => (int) 1, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 2, 'ugi' => (int) 1, 'vma' => (int) 5, 'vmu' => (int) 1, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb301270' $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' => 'HOM05D001460', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '433', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p22980' => 'bna', 'A01p32340' => 'bna', 'A03p42970' => 'bna', 'A05p25880' => 'bna', 'Aa31LG8G9320' => 'aar', 'Aa31LG8G9330' => 'aar', 'Aa31LG8G9340' => 'aar', 'Aa31sc221G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1034' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1528' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.829' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2222' => 'aag', 'Ah.12g058830' => 'amhyb', 'Ah.12g058840' => 'amhyb', 'AL3G37160' => 'aly', 'AL7G41310' => 'aly', 'Aqoxy5G00395' => 'aox', 'Aqoxy5G00396' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0C8NZA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5185HY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JZ1PRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MD3LS0' => 'arhy', 'AT3G22840' => 'ath', 'AT4G14690' => 'ath', 'ATR0665G054' => 'atr', 'Atru.chr4.2344' => 'acertr', 'Atru.chr4.2346' => 'acertr', 'Atru.chr4.2347' => 'acertr', 'Atru.chr4.2348' => 'acertr', 'Atru.chr4.2355' => 'acertr', 'Atru.chr4.2356' => 'acertr', 'Atru.chr4.2358' => 'acertr', 'Atru.chr4.2359' => 'acertr', 'Atru.chr4.2360' => 'acertr', 'Atru.chr4.2361' => 'acertr', 'AUR62030476' => 'cqu', 'AUR62030478' => 'cqu', 'AUR62030819' => 'cqu', 'AUR62030820' => 'cqu', 'BcaB03g14648' => 'bca', 'BcaB04g20492' => 'bca', 'BcaB06g26399' => 'bca', 'BcaC01g03416' => 'bca', 'BcaC01g03419' => 'bca', 'BcaC01g03421' => 'bca', 'BcaC01g03424' => 'bca', 'BcaC05g28012' => 'bca', 'BcaC09g49212' => 'bca', 'BcaC09g50140' => 'bca', 'BcaNung00346' => 'bca', 'BolC1t02785H' => 'bol', 'BolC1t04095H' => 'bol', 'BolC3t17545H' => 'bol', 'BolC5t32769H' => 'bol', 'BraA01t02211Z' => 'bra', 'BraA01t03359Z' => 'bra', 'BraA03t13441Z' => 'bra', 'BraA05t21476Z' => 'bra', 'C01p28420' => 'bna', 'C01p41350' => 'bna', 'C03p52750' => 'bna', 'C03p52780' => 'bna', 'C05p40270' => 'bna', 'CAN.G1437.9' => 'can', 'CANSAT78G0035' => 'cansat', 'CANSAT78G1036' => 'cansat', 'CANSAT78G2272' => 'cansat', 'CANSAT78G2478' => 'cansat', 'CARHR098700' => 'chi', 'CARHR221120' => 'chi', 'CARHR221150' => 'chi', 'Carub.0003s2297' => 'cru', 'Carub.0007s2749' => 'cru', 'Carub.0007s2750' => 'cru', 'Carub.0007s2751' => 'cru', 'Ca_10849_v3' => 'car', 'Cc03_g04300' => 'ccan', 'CDE02G3648' => 'cde', 'CDE05G0060' => 'cde', 'CDE05G0692' => 'cde', 'CDE05G2285' => 'cde', 'CDE05G2884' => 'cde', 'CDE05G3072' => 'cde', 'Cfa008439' => 'cfa', 'Cfa008441' => 'cfa', 'Cfa008443' => 'cfa', 'Cfa008448' => 'cfa', 'Ciclev10005974m.g' => 'ccl', 'Ciclev10006006m.g' => 'ccl', 'Ciclev10006775m.g' => 'ccl', 'CiPaw.02G120400' => 'cil', 'CiPaw.02G120500' => 'cil', 'CiPaw.02G120600' => 'cil', 'ClCG05G004850' => 'cla', 'COL.COLO4_21566' => 'col', 'Cpa.g.sc44.124' => 'cpa', 'Cre07.g320400' => 'cre', 'Cre07.g320450' => 'cre', 'Cre08.g384650' => 'cre', 'Cre09.g393173' => 'cre', 'Cre09.g394325' => 'cre', 'Cre14.g626750' => 'cre', 'Cre16.g679250' => 'cre', 'CsaV3_3G012890' => 'csa', 'CSS0010865' => 'camsi', 'CSS0044338' => 'camsi', 'DCAR_002366' => 'dca', 'DCAR_030687' => 'dca', 'DCAR_030688' => 'dca', 'Dinv14047' => 'din', 'Dinv14048' => 'din', 'Duzib151G0105' => 'dzi', 'Duzib151G0114' => 'dzi', 'Duzib212G1029' => 'dzi', 'ECA232G3536' => 'eca', 'ECA240G0786' => 'eca', 'ECA240G1802' => 'eca', 'ECA240G3760' => 'eca', 'ECA240G3920' => 'eca', 'EL10Ac5g12536' => 'bvu', 'EL10Ac5g12537' => 'bvu', 'EL10Ac5g12538' => 'bvu', 'Eucgr.B01004' => 'egr', 'Eucgr.B01006' => 'egr', 'Eucgr.B01007' => 'egr', 'Eucgr.B01008' => 'egr', 'Eucgr.B01895' => 'egr', 'Eucgr.B01896' => 'egr', 'FAN04G1456' => 'fan', 'FAN08G1769' => 'fan', 'FAN08G2160' => 'fan', 'FAN13G2403' => 'fan', 'FAN13G3303' => 'fan', 'FAN15G2435' => 'fan', 'FAN17G0672' => 'fan', 'FAN17G2441' => 'fan', 'FAN18G1024' => 'fan', 'FAN22G1458' => 'fan', 'FAN24G0037' => 'fan', 'FAN24G0429' => 'fan', 'FAN24G2387' => 'fan', 'FAN27G2746' => 'fan', 'FvH4_2g20400' => 'fve', 'FvH4_2g20420' => 'fve', 'FvH4_2g20430' => 'fve', 'FvH4_4g01270' => 'fve', 'FvH4_4g01290' => 'fve', 'FvH4_4g01300' => 'fve', 'FvH4_4g01310' => 'fve', 'FvH4_4g01330' => 'fve', 'FvH4_5g09070' => 'fve', 'Glyma.10G243800' => 'gma', 'Glyma.20G150600' => 'gma', 'Gohir.A09G219200' => 'ghi', 'Gohir.A09G219300' => 'ghi', 'Gohir.D09G221400' => 'ghi', 'Gohir.D09G221500' => 'ghi', 'Gorai.006G242600' => 'gra', 'Gorai.006G242700' => 'gra', 'GSVIVG01018044001' => 'vvi', 'HanXRQChr03g0083821' => 'han', 'HanXRQChr03g0083841' => 'han', 'HanXRQChr03g0083881' => 'han', 'HanXRQChr03g0083901' => 'han', 'HanXRQChr03g0083921' => 'han', 'HanXRQChr03g0085331' => 'han', 'HanXRQChr03g0085361' => 'han', 'HanXRQChr03g0085411' => 'han', 'HanXRQChr03g0085421' => 'han', 'HanXRQChr03g0085431' => 'han', 'HanXRQChr08g0221991' => 'han', 'HanXRQChr11g0336061' => 'han', 'HanXRQChr11g0336411' => 'han', 'Haze_11234' => 'cav', 'Hma1.2p1_0549F.1_g177010' => 'hma', 'Hma1.2p1_0602F.1_g187630' => 'hma', 'Hund14876' => 'sun', 'Hund14879' => 'sun', 'Lalb_Chr06g0160741' => 'lal', 'Lalb_Chr21g0304781' => 'lal', 'Lj3A726G19' => 'lonja', 'Lj3A726T23' => 'lonja', 'Lj3A726T24' => 'lonja', 'Lj3A726T25' => 'lonja', 'Lj3A727T17' => 'lonja', 'Lj3C726T0' => 'lonja', 'Lj3C726T2' => 'lonja', 'Lj3P725T35' => 'lonja', 'Lj3P727T10' => 'lonja', 'Lj3P727T12' => 'lonja', 'Lj3P727T14' => 'lonja', 'Lj5g0023109' => 'lja', 'Lj6P646T44' => 'lonja', 'Lsat_1_v5_gn_6_75760' => 'lsa', 'Lsat_1_v5_gn_6_75800' => 'lsa', 'Lsat_1_v5_gn_6_75900' => 'lsa', 'Lsat_1_v5_gn_6_76240' => 'lsa', 'Lsat_1_v5_gn_6_76441' => 'lsa', 'Lsat_1_v5_gn_6_76700' => 'lsa', 'Lsat_1_v5_gn_6_76760' => 'lsa', 'Manes.15G033100' => 'mes', 'Mapoly0004s0074' => 'mpo', 'Mapoly0004s0075' => 'mpo', 'Mapoly0004s0163' => 'mpo', 'Mapoly0004s0164' => 'mpo', 'Mapoly0021s0018' => 'mpo', 'Mapoly0041s0136' => 'mpo', 'Mapoly0041s0137' => 'mpo', 'Mapoly0041s0138' => 'mpo', 'Mapoly0041s0139' => 'mpo', 'Mapoly0041s0141' => 'mpo', 'Mapoly0041s0142' => 'mpo', 'Mapoly0041s0143' => 'mpo', 'Mapoly0041s0144' => 'mpo', 'Mapoly0041s0145' => 'mpo', 'Mapoly0047s0106' => 'mpo', 'Mapoly0047s0108' => 'mpo', 'Mapoly0050s0051' => 'mpo', 'Mapoly0050s0052' => 'mpo', 'Mapoly0050s0053' => 'mpo', 'Mapoly0058s0013' => 'mpo', 'Mapoly0091s0078' => 'mpo', 'Mapoly0091s0079' => 'mpo', 'Mapoly0091s0080' => 'mpo', 'Mapoly0091s0081' => 'mpo', 'Mapoly0278s0004' => 'mpo', 'Mapoly0278s0005' => 'mpo', 'Mapoly0278s0006' => 'mpo', 'MBI11_g30648_MAGBIO' => 'mbi', 'MCO03G194' => 'mco', 'MCO03G590' => 'mco', 'MCO07G312' => 'mco', 'MCO10G318' => 'mco', 'MCO12G244' => 'mco', 'MCO13G148' => 'mco', 'MCO13G194' => 'mco', 'MCO16G238' => 'mco', 'MD06G1134100' => 'mdo', 'MD13G1200100' => 'mdo', 'MD13G1200300' => 'mdo', 'MD13G1200600' => 'mdo', 'MD14G1150400' => 'mdo', 'MD16G1200000' => 'mdo', 'Medtr1g102570' => 'mtr', 'Medtr1g102780' => 'mtr', 'Medtr1g102800' => 'mtr', 'Medtr1g102810' => 'mtr', 'Medtr1g102830' => 'mtr', 'MELO3C006499.2' => 'cme', 'Migut.G00385' => 'egut', 'MSTRG.4063' => 'ama', 'Nitab4.5_0000090g0260' => 'nta', 'Nitab4.5_0000977g0030' => 'nta', 'Nitab4.5_0002541g0040' => 'nta', 'Nitab4.5_0007068g0040' => 'nta', 'Nn005s41408' => 'nnu', 'Nn005s41410' => 'nnu', 'Oeu010310.1' => 'oeu', 'Oeu010311.1' => 'oeu', 'Oeu043472.1' => 'oeu', 'Os01g0246400' => 'osa', 'Os04g0267950' => 'osa', 'Os07g0178700' => 'osa', 'Os07g0178800' => 'osa', 'Peaxi162Scf00316g00046' => 'pax', 'Peaxi162Scf00316g00049' => 'pax', 'Peaxi162Scf00316g00059' => 'pax', 'Peaxi162Scf00316g00328' => 'pax', 'Peaxi162Scf00316g00329' => 'pax', 'Peaxi162Scf00316g00411' => 'pax', 'Peaxi162Scf00316g00521' => 'pax', 'Peaxi162Scf00492g00068' => 'pax', 'Peaxi162Scf35631g00002' => 'pax', 'PGR142G3720' => 'pgr', 'PGSC0003DMG400006442' => 'stu', 'Phvul.007G062000' => 'pvu', 'Potri.008G157750' => 'ptr', 'Potri.008G157900' => 'ptr', 'Potri.008G158000' => 'ptr', 'Potri.008G158200' => 'ptr', 'Pp3c11_7280' => 'ppa', 'Pp3c11_7980' => 'ppa', 'Pp3c12_19450' => 'ppa', 'Pp3c14_1480' => 'ppa', 'Pp3c14_1501' => 'ppa', 'Pp3c16_4900' => 'ppa', 'Pp3c16_5010' => 'ppa', 'Pp3c16_5060' => 'ppa', 'Pp3c19_18250' => 'ppa', 'Pp3c23_8530' => 'ppa', 'Pp3c23_8550' => 'ppa', 'Pp3c24_9670' => 'ppa', 'Pp3c2_21390' => 'ppa', 'Pp3c2_31380' => 'ppa', 'Pp3c3_16620' => 'ppa', 'Pp3c3_8090' => 'ppa', 'Pp3c3_8110' => 'ppa', 'Pp3c3_8130' => 'ppa', 'Pp3c3_8150' => 'ppa', 'Pp3c4_14320' => 'ppa', 'Pp3c6_2560' => 'ppa', 'Pp3c9_16700' => 'ppa', 'PRCOL_00000234' => 'pco', 'PRCOL_00000235' => 'pco', 'PRCOL_00000777' => 'pco', 'PRCOL_00002344' => 'pco', 'PRCOL_00002372' => 'pco', 'PRCOL_00006120' => 'pco', 'Prupe.1G021400' => 'ppe', 'Prupe.1G021500' => 'ppe', 'Prupe.1G021600' => 'ppe', 'Prupe.1G021700' => 'ppe', 'Prupe.1G021800' => 'ppe', 'Prupe.5G145100' => 'ppe', 'Psat6g204040' => 'psa', 'Psat6g204800' => 'psa', 'Psat6g204920' => 'psa', 'Psat6g204960' => 'psa', 'Psat6g205080' => 'psa', 'PSO017G0271' => 'pso', 'PSO017G1276' => 'pso', 'PSO017G1429' => 'pso', 'PSO017G1861' => 'pso', 'PSO017G2787' => 'pso', 'PSO017G4466' => 'pso', 'PSO017G5118' => 'pso', 'PSO017G5420' => 'pso', 'PSO063G3678' => 'pso', 'PSO210G0546' => 'pso', 'PSO317G0001' => 'pso', 'PSO357G0512' => 'pso', 'PSO478G2682' => 'pso', 'PSO647G0001' => 'pso', 'PSO675G0001' => 'pso', 'PSO675G2699' => 'pso', 'PSO675G2849' => 'pso', 'PSO675G4991' => 'pso', 'PSO689G0001' => 'pso', 'QL06p000916' => 'qlo', 'QL06p000921' => 'qlo', 'QL06p001398' => 'qlo', 'QL06p001407' => 'qlo', 'QL06p002031' => 'qlo', 'RcHm_v2.0_Chr4g0387791' => 'rch', 'RcHm_v2.0_Chr4g0387801' => 'rch', 'RcHm_v2.0_Chr6g0286501' => 'rch', 'RcHm_v2.0_Chr6g0286511' => 'rch', 'RcHm_v2.0_Chr6g0286521' => 'rch', 'RcHm_v2.0_Chr6g0286531' => 'rch', 'RcHm_v2.0_Chr7g0189141' => 'rch', 'Rhsim02G0028700' => 'rsi', 'Rhsim02G0028800' => 'rsi', 'Rhsim02G0028900' => 'rsi', 'Rhsim02G0029000' => 'rsi', 'Rhsim02G0029100' => 'rsi', 'Rhsim02G0029200' => 'rsi', 'Rhsim02G0029300' => 'rsi', 'Rhsim02G0029400' => 'rsi', 'Rhsim02G0029500' => 'rsi', 'Rhsim02G0029600' => 'rsi', 'RhsimUnG0024000' => 'rsi', 'RhsimUnG0024100' => 'rsi', 'RhsimUnG0024200' => 'rsi', 'RhsimUnG0024300' => 'rsi', 'RhsimUnG0024400' => 'rsi', 'RhsimUnG0024500' => 'rsi', 'RhsimUnG0024700' => 'rsi', 'RhsimUnG0024800' => 'rsi', 'RhsimUnG0024900' => 'rsi', 'RhsimUnG0025100' => 'rsi', 'Sabra08G0120200' => 'sbr', 'Sabra08G0120300' => 'sbr', 'Sabra08G0120500' => 'sbr', 'Sabra08G0120600' => 'sbr', 'Sabra10G0158900' => 'sbr', 'SalBow2G3492' => 'sbo', 'Sc13g0004760' => 'sci', 'Sc13g0004770' => 'sci', 'Sed0003417' => 'sed', 'Sed0019750' => 'sed', 'SEGI_03419' => 'sgi', 'SEGI_05907' => 'sgi', 'SEGI_10682' => 'sgi', 'SEGI_13528' => 'sgi', 'SEGI_16081' => 'sgi', 'SEGI_19370' => 'sgi', 'SEGI_21015' => 'sgi', 'SEGI_21944' => 'sgi', 'SEGI_32906' => 'sgi', 'SEGI_33093' => 'sgi', 'SEGI_36110' => 'sgi', 'SEGI_40397' => 'sgi', 'SGA_v2.0_scaffold191G40426' => 'sas', 'SGA_v2.0_scaffold353G49717' => 'sas', 'SGA_v2.0_scaffold50G18550' => 'sas', 'SMO119G0173' => 'smo', 'SMO172G0002' => 'smo', 'Solyc09g082690.3' => 'sly', 'Solyc09g082700.2' => 'sly', 'Sopen09g031550' => 'spe', 'Sopen09g031560' => 'spe', 'Sp3g20540' => 'spa', 'Sp7g07580' => 'spa', 'TAR134G0002' => 'tar', 'TAR236G0001' => 'tar', 'TAR365G0892' => 'tar', 'TAR636G0166' => 'tar', 'TAR636G0646' => 'tar', 'TAR636G0869' => 'tar', 'TAR636G1317' => 'tar', 'TAR636G1744' => 'tar', 'TAR636G3358' => 'tar', 'TAR636G3436' => 'tar', 'THA.LOC104803047' => 'tha', 'Thecc.04G238900' => 'tca', 'Thhalv10021557m.g' => 'esa', 'Thhalv10026318m.g' => 'esa', 'Thhalv10026335m.g' => 'esa', 'TPR.G17433' => 'tpr', 'TPR.G18915' => 'tpr', 'TPR.G26125' => 'tpr', 'TWI09G0677' => 'twi', 'TWI73G0287' => 'twi', 'unitig_748.g8326' => 'ugi', 'vmacro15370' => 'vma', 'vmacro15371' => 'vma', 'vmacro15372' => 'vma', 'vmacro15373' => 'vma', 'vmacro15374' => 'vma', 'VMungo0720G2826' => 'vmu', 'Zm00001eb116960' => 'zma', 'Zm00001eb301260' => 'zma', 'Zm00001eb301270' => 'zma' ), 'gf_id' => 'HOM05D001460', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001460' ), 'data_identifier' => 'HOM05D001460', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001460', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '433', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p22980' => 'bna', 'A01p32340' => 'bna', 'A03p42970' => 'bna', 'A05p25880' => 'bna', 'Aa31LG8G9320' => 'aar', 'Aa31LG8G9330' => 'aar', 'Aa31LG8G9340' => 'aar', 'Aa31sc221G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1034' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1528' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.829' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2222' => 'aag', 'Ah.12g058830' => 'amhyb', 'Ah.12g058840' => 'amhyb', 'AL3G37160' => 'aly', 'AL7G41310' => 'aly', 'Aqoxy5G00395' => 'aox', 'Aqoxy5G00396' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0C8NZA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5185HY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JZ1PRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MD3LS0' => 'arhy', 'AT3G22840' => 'ath', 'AT4G14690' => 'ath', 'ATR0665G054' => 'atr', 'Atru.chr4.2344' => 'acertr', 'Atru.chr4.2346' => 'acertr', 'Atru.chr4.2347' => 'acertr', 'Atru.chr4.2348' => 'acertr', 'Atru.chr4.2355' => 'acertr', 'Atru.chr4.2356' => 'acertr', 'Atru.chr4.2358' => 'acertr', 'Atru.chr4.2359' => 'acertr', 'Atru.chr4.2360' => 'acertr', 'Atru.chr4.2361' => 'acertr', 'AUR62030476' => 'cqu', 'AUR62030478' => 'cqu', 'AUR62030819' => 'cqu', 'AUR62030820' => 'cqu', 'BcaB03g14648' => 'bca', 'BcaB04g20492' => 'bca', 'BcaB06g26399' => 'bca', 'BcaC01g03416' => 'bca', 'BcaC01g03419' => 'bca', 'BcaC01g03421' => 'bca', 'BcaC01g03424' => 'bca', 'BcaC05g28012' => 'bca', 'BcaC09g49212' => 'bca', 'BcaC09g50140' => 'bca', 'BcaNung00346' => 'bca', 'BolC1t02785H' => 'bol', 'BolC1t04095H' => 'bol', 'BolC3t17545H' => 'bol', 'BolC5t32769H' => 'bol', 'BraA01t02211Z' => 'bra', 'BraA01t03359Z' => 'bra', 'BraA03t13441Z' => 'bra', 'BraA05t21476Z' => 'bra', 'C01p28420' => 'bna', 'C01p41350' => 'bna', 'C03p52750' => 'bna', 'C03p52780' => 'bna', 'C05p40270' => 'bna', 'CAN.G1437.9' => 'can', 'CANSAT78G0035' => 'cansat', 'CANSAT78G1036' => 'cansat', 'CANSAT78G2272' => 'cansat', 'CANSAT78G2478' => 'cansat', 'CARHR098700' => 'chi', 'CARHR221120' => 'chi', 'CARHR221150' => 'chi', 'Carub.0003s2297' => 'cru', 'Carub.0007s2749' => 'cru', 'Carub.0007s2750' => 'cru', 'Carub.0007s2751' => 'cru', 'Ca_10849_v3' => 'car', 'Cc03_g04300' => 'ccan', 'CDE02G3648' => 'cde', 'CDE05G0060' => 'cde', 'CDE05G0692' => 'cde', 'CDE05G2285' => 'cde', 'CDE05G2884' => 'cde', 'CDE05G3072' => 'cde', 'Cfa008439' => 'cfa', 'Cfa008441' => 'cfa', 'Cfa008443' => 'cfa', 'Cfa008448' => 'cfa', 'Ciclev10005974m.g' => 'ccl', 'Ciclev10006006m.g' => 'ccl', 'Ciclev10006775m.g' => 'ccl', 'CiPaw.02G120400' => 'cil', 'CiPaw.02G120500' => 'cil', 'CiPaw.02G120600' => 'cil', 'ClCG05G004850' => 'cla', 'COL.COLO4_21566' => 'col', 'Cpa.g.sc44.124' => 'cpa', 'Cre07.g320400' => 'cre', 'Cre07.g320450' => 'cre', 'Cre08.g384650' => 'cre', 'Cre09.g393173' => 'cre', 'Cre09.g394325' => 'cre', 'Cre14.g626750' => 'cre', 'Cre16.g679250' => 'cre', 'CsaV3_3G012890' => 'csa', 'CSS0010865' => 'camsi', 'CSS0044338' => 'camsi', 'DCAR_002366' => 'dca', 'DCAR_030687' => 'dca', 'DCAR_030688' => 'dca', 'Dinv14047' => 'din', 'Dinv14048' => 'din', 'Duzib151G0105' => 'dzi', 'Duzib151G0114' => 'dzi', 'Duzib212G1029' => 'dzi', 'ECA232G3536' => 'eca', 'ECA240G0786' => 'eca', 'ECA240G1802' => 'eca', 'ECA240G3760' => 'eca', 'ECA240G3920' => 'eca', 'EL10Ac5g12536' => 'bvu', 'EL10Ac5g12537' => 'bvu', 'EL10Ac5g12538' => 'bvu', 'Eucgr.B01004' => 'egr', 'Eucgr.B01006' => 'egr', 'Eucgr.B01007' => 'egr', 'Eucgr.B01008' => 'egr', 'Eucgr.B01895' => 'egr', 'Eucgr.B01896' => 'egr', 'FAN04G1456' => 'fan', 'FAN08G1769' => 'fan', 'FAN08G2160' => 'fan', 'FAN13G2403' => 'fan', 'FAN13G3303' => 'fan', 'FAN15G2435' => 'fan', 'FAN17G0672' => 'fan', 'FAN17G2441' => 'fan', 'FAN18G1024' => 'fan', 'FAN22G1458' => 'fan', 'FAN24G0037' => 'fan', 'FAN24G0429' => 'fan', 'FAN24G2387' => 'fan', 'FAN27G2746' => 'fan', 'FvH4_2g20400' => 'fve', 'FvH4_2g20420' => 'fve', 'FvH4_2g20430' => 'fve', 'FvH4_4g01270' => 'fve', 'FvH4_4g01290' => 'fve', 'FvH4_4g01300' => 'fve', 'FvH4_4g01310' => 'fve', 'FvH4_4g01330' => 'fve', 'FvH4_5g09070' => 'fve', 'Glyma.10G243800' => 'gma', 'Glyma.20G150600' => 'gma', 'Gohir.A09G219200' => 'ghi', 'Gohir.A09G219300' => 'ghi', 'Gohir.D09G221400' => 'ghi', 'Gohir.D09G221500' => 'ghi', 'Gorai.006G242600' => 'gra', 'Gorai.006G242700' => 'gra', 'GSVIVG01018044001' => 'vvi', 'HanXRQChr03g0083821' => 'han', 'HanXRQChr03g0083841' => 'han', 'HanXRQChr03g0083881' => 'han', 'HanXRQChr03g0083901' => 'han', 'HanXRQChr03g0083921' => 'han', 'HanXRQChr03g0085331' => 'han', 'HanXRQChr03g0085361' => 'han', 'HanXRQChr03g0085411' => 'han', 'HanXRQChr03g0085421' => 'han', 'HanXRQChr03g0085431' => 'han', 'HanXRQChr08g0221991' => 'han', 'HanXRQChr11g0336061' => 'han', 'HanXRQChr11g0336411' => 'han', 'Haze_11234' => 'cav', 'Hma1.2p1_0549F.1_g177010' => 'hma', 'Hma1.2p1_0602F.1_g187630' => 'hma', 'Hund14876' => 'sun', 'Hund14879' => 'sun', 'Lalb_Chr06g0160741' => 'lal', 'Lalb_Chr21g0304781' => 'lal', 'Lj3A726G19' => 'lonja', 'Lj3A726T23' => 'lonja', 'Lj3A726T24' => 'lonja', 'Lj3A726T25' => 'lonja', 'Lj3A727T17' => 'lonja', 'Lj3C726T0' => 'lonja', 'Lj3C726T2' => 'lonja', 'Lj3P725T35' => 'lonja', 'Lj3P727T10' => 'lonja', 'Lj3P727T12' => 'lonja', 'Lj3P727T14' => 'lonja', 'Lj5g0023109' => 'lja', 'Lj6P646T44' => 'lonja', 'Lsat_1_v5_gn_6_75760' => 'lsa', 'Lsat_1_v5_gn_6_75800' => 'lsa', 'Lsat_1_v5_gn_6_75900' => 'lsa', 'Lsat_1_v5_gn_6_76240' => 'lsa', 'Lsat_1_v5_gn_6_76441' => 'lsa', 'Lsat_1_v5_gn_6_76700' => 'lsa', 'Lsat_1_v5_gn_6_76760' => 'lsa', 'Manes.15G033100' => 'mes', 'Mapoly0004s0074' => 'mpo', 'Mapoly0004s0075' => 'mpo', 'Mapoly0004s0163' => 'mpo', 'Mapoly0004s0164' => 'mpo', 'Mapoly0021s0018' => 'mpo', 'Mapoly0041s0136' => 'mpo', 'Mapoly0041s0137' => 'mpo', 'Mapoly0041s0138' => 'mpo', 'Mapoly0041s0139' => 'mpo', 'Mapoly0041s0141' => 'mpo', 'Mapoly0041s0142' => 'mpo', 'Mapoly0041s0143' => 'mpo', 'Mapoly0041s0144' => 'mpo', 'Mapoly0041s0145' => 'mpo', 'Mapoly0047s0106' => 'mpo', 'Mapoly0047s0108' => 'mpo', 'Mapoly0050s0051' => 'mpo', 'Mapoly0050s0052' => 'mpo', 'Mapoly0050s0053' => 'mpo', 'Mapoly0058s0013' => 'mpo', 'Mapoly0091s0078' => 'mpo', 'Mapoly0091s0079' => 'mpo', 'Mapoly0091s0080' => 'mpo', 'Mapoly0091s0081' => 'mpo', 'Mapoly0278s0004' => 'mpo', 'Mapoly0278s0005' => 'mpo', 'Mapoly0278s0006' => 'mpo', 'MBI11_g30648_MAGBIO' => 'mbi', 'MCO03G194' => 'mco', 'MCO03G590' => 'mco', 'MCO07G312' => 'mco', 'MCO10G318' => 'mco', 'MCO12G244' => 'mco', 'MCO13G148' => 'mco', 'MCO13G194' => 'mco', 'MCO16G238' => 'mco', 'MD06G1134100' => 'mdo', 'MD13G1200100' => 'mdo', 'MD13G1200300' => 'mdo', 'MD13G1200600' => 'mdo', 'MD14G1150400' => 'mdo', 'MD16G1200000' => 'mdo', 'Medtr1g102570' => 'mtr', 'Medtr1g102780' => 'mtr', 'Medtr1g102800' => 'mtr', 'Medtr1g102810' => 'mtr', 'Medtr1g102830' => 'mtr', 'MELO3C006499.2' => 'cme', 'Migut.G00385' => 'egut', 'MSTRG.4063' => 'ama', 'Nitab4.5_0000090g0260' => 'nta', 'Nitab4.5_0000977g0030' => 'nta', 'Nitab4.5_0002541g0040' => 'nta', 'Nitab4.5_0007068g0040' => 'nta', 'Nn005s41408' => 'nnu', 'Nn005s41410' => 'nnu', 'Oeu010310.1' => 'oeu', 'Oeu010311.1' => 'oeu', 'Oeu043472.1' => 'oeu', 'Os01g0246400' => 'osa', 'Os04g0267950' => 'osa', 'Os07g0178700' => 'osa', 'Os07g0178800' => 'osa', 'Peaxi162Scf00316g00046' => 'pax', 'Peaxi162Scf00316g00049' => 'pax', 'Peaxi162Scf00316g00059' => 'pax', 'Peaxi162Scf00316g00328' => 'pax', 'Peaxi162Scf00316g00329' => 'pax', 'Peaxi162Scf00316g00411' => 'pax', 'Peaxi162Scf00316g00521' => 'pax', 'Peaxi162Scf00492g00068' => 'pax', 'Peaxi162Scf35631g00002' => 'pax', 'PGR142G3720' => 'pgr', 'PGSC0003DMG400006442' => 'stu', 'Phvul.007G062000' => 'pvu', 'Potri.008G157750' => 'ptr', 'Potri.008G157900' => 'ptr', 'Potri.008G158000' => 'ptr', 'Potri.008G158200' => 'ptr', 'Pp3c11_7280' => 'ppa', 'Pp3c11_7980' => 'ppa', 'Pp3c12_19450' => 'ppa', 'Pp3c14_1480' => 'ppa', 'Pp3c14_1501' => 'ppa', 'Pp3c16_4900' => 'ppa', 'Pp3c16_5010' => 'ppa', 'Pp3c16_5060' => 'ppa', 'Pp3c19_18250' => 'ppa', 'Pp3c23_8530' => 'ppa', 'Pp3c23_8550' => 'ppa', 'Pp3c24_9670' => 'ppa', 'Pp3c2_21390' => 'ppa', 'Pp3c2_31380' => 'ppa', 'Pp3c3_16620' => 'ppa', 'Pp3c3_8090' => 'ppa', 'Pp3c3_8110' => 'ppa', 'Pp3c3_8130' => 'ppa', 'Pp3c3_8150' => 'ppa', 'Pp3c4_14320' => 'ppa', 'Pp3c6_2560' => 'ppa', 'Pp3c9_16700' => 'ppa', 'PRCOL_00000234' => 'pco', 'PRCOL_00000235' => 'pco', 'PRCOL_00000777' => 'pco', 'PRCOL_00002344' => 'pco', 'PRCOL_00002372' => 'pco', 'PRCOL_00006120' => 'pco', 'Prupe.1G021400' => 'ppe', 'Prupe.1G021500' => 'ppe', 'Prupe.1G021600' => 'ppe', 'Prupe.1G021700' => 'ppe', 'Prupe.1G021800' => 'ppe', 'Prupe.5G145100' => 'ppe', 'Psat6g204040' => 'psa', 'Psat6g204800' => 'psa', 'Psat6g204920' => 'psa', 'Psat6g204960' => 'psa', 'Psat6g205080' => 'psa', 'PSO017G0271' => 'pso', 'PSO017G1276' => 'pso', 'PSO017G1429' => 'pso', 'PSO017G1861' => 'pso', 'PSO017G2787' => 'pso', 'PSO017G4466' => 'pso', 'PSO017G5118' => 'pso', 'PSO017G5420' => 'pso', 'PSO063G3678' => 'pso', 'PSO210G0546' => 'pso', 'PSO317G0001' => 'pso', 'PSO357G0512' => 'pso', 'PSO478G2682' => 'pso', 'PSO647G0001' => 'pso', 'PSO675G0001' => 'pso', 'PSO675G2699' => 'pso', 'PSO675G2849' => 'pso', 'PSO675G4991' => 'pso', 'PSO689G0001' => 'pso', 'QL06p000916' => 'qlo', 'QL06p000921' => 'qlo', 'QL06p001398' => 'qlo', 'QL06p001407' => 'qlo', 'QL06p002031' => 'qlo', 'RcHm_v2.0_Chr4g0387791' => 'rch', 'RcHm_v2.0_Chr4g0387801' => 'rch', 'RcHm_v2.0_Chr6g0286501' => 'rch', 'RcHm_v2.0_Chr6g0286511' => 'rch', 'RcHm_v2.0_Chr6g0286521' => 'rch', 'RcHm_v2.0_Chr6g0286531' => 'rch', 'RcHm_v2.0_Chr7g0189141' => 'rch', 'Rhsim02G0028700' => 'rsi', 'Rhsim02G0028800' => 'rsi', 'Rhsim02G0028900' => 'rsi', 'Rhsim02G0029000' => 'rsi', 'Rhsim02G0029100' => 'rsi', 'Rhsim02G0029200' => 'rsi', 'Rhsim02G0029300' => 'rsi', 'Rhsim02G0029400' => 'rsi', 'Rhsim02G0029500' => 'rsi', 'Rhsim02G0029600' => 'rsi', 'RhsimUnG0024000' => 'rsi', 'RhsimUnG0024100' => 'rsi', 'RhsimUnG0024200' => 'rsi', 'RhsimUnG0024300' => 'rsi', 'RhsimUnG0024400' => 'rsi', 'RhsimUnG0024500' => 'rsi', 'RhsimUnG0024700' => 'rsi', 'RhsimUnG0024800' => 'rsi', 'RhsimUnG0024900' => 'rsi', 'RhsimUnG0025100' => 'rsi', 'Sabra08G0120200' => 'sbr', 'Sabra08G0120300' => 'sbr', 'Sabra08G0120500' => 'sbr', 'Sabra08G0120600' => 'sbr', 'Sabra10G0158900' => 'sbr', 'SalBow2G3492' => 'sbo', 'Sc13g0004760' => 'sci', 'Sc13g0004770' => 'sci', 'Sed0003417' => 'sed', 'Sed0019750' => 'sed', 'SEGI_03419' => 'sgi', 'SEGI_05907' => 'sgi', 'SEGI_10682' => 'sgi', 'SEGI_13528' => 'sgi', 'SEGI_16081' => 'sgi', 'SEGI_19370' => 'sgi', 'SEGI_21015' => 'sgi', 'SEGI_21944' => 'sgi', 'SEGI_32906' => 'sgi', 'SEGI_33093' => 'sgi', 'SEGI_36110' => 'sgi', 'SEGI_40397' => 'sgi', 'SGA_v2.0_scaffold191G40426' => 'sas', 'SGA_v2.0_scaffold353G49717' => 'sas', 'SGA_v2.0_scaffold50G18550' => 'sas', 'SMO119G0173' => 'smo', 'SMO172G0002' => 'smo', 'Solyc09g082690.3' => 'sly', 'Solyc09g082700.2' => 'sly', 'Sopen09g031550' => 'spe', 'Sopen09g031560' => 'spe', 'Sp3g20540' => 'spa', 'Sp7g07580' => 'spa', 'TAR134G0002' => 'tar', 'TAR236G0001' => 'tar', 'TAR365G0892' => 'tar', 'TAR636G0166' => 'tar', 'TAR636G0646' => 'tar', 'TAR636G0869' => 'tar', 'TAR636G1317' => 'tar', 'TAR636G1744' => 'tar', 'TAR636G3358' => 'tar', 'TAR636G3436' => 'tar', 'THA.LOC104803047' => 'tha', 'Thecc.04G238900' => 'tca', 'Thhalv10021557m.g' => 'esa', 'Thhalv10026318m.g' => 'esa', 'Thhalv10026335m.g' => 'esa', 'TPR.G17433' => 'tpr', 'TPR.G18915' => 'tpr', 'TPR.G26125' => 'tpr', 'TWI09G0677' => 'twi', 'TWI73G0287' => 'twi', 'unitig_748.g8326' => 'ugi', 'vmacro15370' => 'vma', 'vmacro15371' => 'vma', 'vmacro15372' => 'vma', 'vmacro15373' => 'vma', 'vmacro15374' => 'vma', 'VMungo0720G2826' => 'vmu', 'Zm00001eb116960' => 'zma', 'Zm00001eb301260' => 'zma', 'Zm00001eb301270' => 'zma' ) $gf_id = 'HOM05D001460' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001460' ) $data_identifier = 'HOM05D001460' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 4, 'aag' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 2, 'aox' => (int) 2, 'arhy' => (int) 4, 'ath' => (int) 2, 'atr' => (int) 1, 'acertr' => (int) 10, 'cqu' => (int) 4, 'bca' => (int) 11, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 1, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 1, 'ccan' => (int) 1, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 1, 'col' => (int) 1, 'cpa' => (int) 1, 'cre' => (int) 7, 'csa' => (int) 1, 'camsi' => (int) 2, 'dca' => (int) 3, 'din' => (int) 2, 'dzi' => (int) 3, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 14, 'fve' => (int) 9, 'gma' => (int) 2, 'ghi' => (int) 4, 'gra' => (int) 2, 'vvi' => (int) 1, 'han' => (int) 13, 'cav' => (int) 1, 'hma' => (int) 2, 'sun' => (int) 2, 'lal' => (int) 2, 'lonja' => (int) 12, 'lja' => (int) 1, 'lsa' => (int) 7, 'mes' => (int) 1, 'mpo' => (int) 27, 'mbi' => (int) 1, 'mco' => (int) 8, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 1, 'egut' => (int) 1, 'ama' => (int) 1, 'nta' => (int) 4, 'nnu' => (int) 2, 'oeu' => (int) 3, 'osa' => (int) 4, 'pax' => (int) 9, 'pgr' => (int) 1, 'stu' => (int) 1, 'pvu' => (int) 1, 'ptr' => (int) 4, 'ppa' => (int) 22, 'pco' => (int) 6, 'ppe' => (int) 6, 'psa' => (int) 5, 'pso' => (int) 19, 'qlo' => (int) 5, 'rch' => (int) 7, 'rsi' => (int) 20, 'sbr' => (int) 5, 'sbo' => (int) 1, 'sci' => (int) 2, 'sed' => (int) 2, 'sgi' => (int) 12, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 2, 'tar' => (int) 10, 'tha' => (int) 1, 'tca' => (int) 1, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 2, 'ugi' => (int) 1, 'vma' => (int) 5, 'vmu' => (int) 1, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb301270' $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' => 'HOM05D001460', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '433', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p22980' => 'bna', 'A01p32340' => 'bna', 'A03p42970' => 'bna', 'A05p25880' => 'bna', 'Aa31LG8G9320' => 'aar', 'Aa31LG8G9330' => 'aar', 'Aa31LG8G9340' => 'aar', 'Aa31sc221G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1034' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1528' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.829' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2222' => 'aag', 'Ah.12g058830' => 'amhyb', 'Ah.12g058840' => 'amhyb', 'AL3G37160' => 'aly', 'AL7G41310' => 'aly', 'Aqoxy5G00395' => 'aox', 'Aqoxy5G00396' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0C8NZA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5185HY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JZ1PRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MD3LS0' => 'arhy', 'AT3G22840' => 'ath', 'AT4G14690' => 'ath', 'ATR0665G054' => 'atr', 'Atru.chr4.2344' => 'acertr', 'Atru.chr4.2346' => 'acertr', 'Atru.chr4.2347' => 'acertr', 'Atru.chr4.2348' => 'acertr', 'Atru.chr4.2355' => 'acertr', 'Atru.chr4.2356' => 'acertr', 'Atru.chr4.2358' => 'acertr', 'Atru.chr4.2359' => 'acertr', 'Atru.chr4.2360' => 'acertr', 'Atru.chr4.2361' => 'acertr', 'AUR62030476' => 'cqu', 'AUR62030478' => 'cqu', 'AUR62030819' => 'cqu', 'AUR62030820' => 'cqu', 'BcaB03g14648' => 'bca', 'BcaB04g20492' => 'bca', 'BcaB06g26399' => 'bca', 'BcaC01g03416' => 'bca', 'BcaC01g03419' => 'bca', 'BcaC01g03421' => 'bca', 'BcaC01g03424' => 'bca', 'BcaC05g28012' => 'bca', 'BcaC09g49212' => 'bca', 'BcaC09g50140' => 'bca', 'BcaNung00346' => 'bca', 'BolC1t02785H' => 'bol', 'BolC1t04095H' => 'bol', 'BolC3t17545H' => 'bol', 'BolC5t32769H' => 'bol', 'BraA01t02211Z' => 'bra', 'BraA01t03359Z' => 'bra', 'BraA03t13441Z' => 'bra', 'BraA05t21476Z' => 'bra', 'C01p28420' => 'bna', 'C01p41350' => 'bna', 'C03p52750' => 'bna', 'C03p52780' => 'bna', 'C05p40270' => 'bna', 'CAN.G1437.9' => 'can', 'CANSAT78G0035' => 'cansat', 'CANSAT78G1036' => 'cansat', 'CANSAT78G2272' => 'cansat', 'CANSAT78G2478' => 'cansat', 'CARHR098700' => 'chi', 'CARHR221120' => 'chi', 'CARHR221150' => 'chi', 'Carub.0003s2297' => 'cru', 'Carub.0007s2749' => 'cru', 'Carub.0007s2750' => 'cru', 'Carub.0007s2751' => 'cru', 'Ca_10849_v3' => 'car', 'Cc03_g04300' => 'ccan', 'CDE02G3648' => 'cde', 'CDE05G0060' => 'cde', 'CDE05G0692' => 'cde', 'CDE05G2285' => 'cde', 'CDE05G2884' => 'cde', 'CDE05G3072' => 'cde', 'Cfa008439' => 'cfa', 'Cfa008441' => 'cfa', 'Cfa008443' => 'cfa', 'Cfa008448' => 'cfa', 'Ciclev10005974m.g' => 'ccl', 'Ciclev10006006m.g' => 'ccl', 'Ciclev10006775m.g' => 'ccl', 'CiPaw.02G120400' => 'cil', 'CiPaw.02G120500' => 'cil', 'CiPaw.02G120600' => 'cil', 'ClCG05G004850' => 'cla', 'COL.COLO4_21566' => 'col', 'Cpa.g.sc44.124' => 'cpa', 'Cre07.g320400' => 'cre', 'Cre07.g320450' => 'cre', 'Cre08.g384650' => 'cre', 'Cre09.g393173' => 'cre', 'Cre09.g394325' => 'cre', 'Cre14.g626750' => 'cre', 'Cre16.g679250' => 'cre', 'CsaV3_3G012890' => 'csa', 'CSS0010865' => 'camsi', 'CSS0044338' => 'camsi', 'DCAR_002366' => 'dca', 'DCAR_030687' => 'dca', 'DCAR_030688' => 'dca', 'Dinv14047' => 'din', 'Dinv14048' => 'din', 'Duzib151G0105' => 'dzi', 'Duzib151G0114' => 'dzi', 'Duzib212G1029' => 'dzi', 'ECA232G3536' => 'eca', 'ECA240G0786' => 'eca', 'ECA240G1802' => 'eca', 'ECA240G3760' => 'eca', 'ECA240G3920' => 'eca', 'EL10Ac5g12536' => 'bvu', 'EL10Ac5g12537' => 'bvu', 'EL10Ac5g12538' => 'bvu', 'Eucgr.B01004' => 'egr', 'Eucgr.B01006' => 'egr', 'Eucgr.B01007' => 'egr', 'Eucgr.B01008' => 'egr', 'Eucgr.B01895' => 'egr', 'Eucgr.B01896' => 'egr', 'FAN04G1456' => 'fan', 'FAN08G1769' => 'fan', 'FAN08G2160' => 'fan', 'FAN13G2403' => 'fan', 'FAN13G3303' => 'fan', 'FAN15G2435' => 'fan', 'FAN17G0672' => 'fan', 'FAN17G2441' => 'fan', 'FAN18G1024' => 'fan', 'FAN22G1458' => 'fan', 'FAN24G0037' => 'fan', 'FAN24G0429' => 'fan', 'FAN24G2387' => 'fan', 'FAN27G2746' => 'fan', 'FvH4_2g20400' => 'fve', 'FvH4_2g20420' => 'fve', 'FvH4_2g20430' => 'fve', 'FvH4_4g01270' => 'fve', 'FvH4_4g01290' => 'fve', 'FvH4_4g01300' => 'fve', 'FvH4_4g01310' => 'fve', 'FvH4_4g01330' => 'fve', 'FvH4_5g09070' => 'fve', 'Glyma.10G243800' => 'gma', 'Glyma.20G150600' => 'gma', 'Gohir.A09G219200' => 'ghi', 'Gohir.A09G219300' => 'ghi', 'Gohir.D09G221400' => 'ghi', 'Gohir.D09G221500' => 'ghi', 'Gorai.006G242600' => 'gra', 'Gorai.006G242700' => 'gra', 'GSVIVG01018044001' => 'vvi', 'HanXRQChr03g0083821' => 'han', 'HanXRQChr03g0083841' => 'han', 'HanXRQChr03g0083881' => 'han', 'HanXRQChr03g0083901' => 'han', 'HanXRQChr03g0083921' => 'han', 'HanXRQChr03g0085331' => 'han', 'HanXRQChr03g0085361' => 'han', 'HanXRQChr03g0085411' => 'han', 'HanXRQChr03g0085421' => 'han', 'HanXRQChr03g0085431' => 'han', 'HanXRQChr08g0221991' => 'han', 'HanXRQChr11g0336061' => 'han', 'HanXRQChr11g0336411' => 'han', 'Haze_11234' => 'cav', 'Hma1.2p1_0549F.1_g177010' => 'hma', 'Hma1.2p1_0602F.1_g187630' => 'hma', 'Hund14876' => 'sun', 'Hund14879' => 'sun', 'Lalb_Chr06g0160741' => 'lal', 'Lalb_Chr21g0304781' => 'lal', 'Lj3A726G19' => 'lonja', 'Lj3A726T23' => 'lonja', 'Lj3A726T24' => 'lonja', 'Lj3A726T25' => 'lonja', 'Lj3A727T17' => 'lonja', 'Lj3C726T0' => 'lonja', 'Lj3C726T2' => 'lonja', 'Lj3P725T35' => 'lonja', 'Lj3P727T10' => 'lonja', 'Lj3P727T12' => 'lonja', 'Lj3P727T14' => 'lonja', 'Lj5g0023109' => 'lja', 'Lj6P646T44' => 'lonja', 'Lsat_1_v5_gn_6_75760' => 'lsa', 'Lsat_1_v5_gn_6_75800' => 'lsa', 'Lsat_1_v5_gn_6_75900' => 'lsa', 'Lsat_1_v5_gn_6_76240' => 'lsa', 'Lsat_1_v5_gn_6_76441' => 'lsa', 'Lsat_1_v5_gn_6_76700' => 'lsa', 'Lsat_1_v5_gn_6_76760' => 'lsa', 'Manes.15G033100' => 'mes', 'Mapoly0004s0074' => 'mpo', 'Mapoly0004s0075' => 'mpo', 'Mapoly0004s0163' => 'mpo', 'Mapoly0004s0164' => 'mpo', 'Mapoly0021s0018' => 'mpo', 'Mapoly0041s0136' => 'mpo', 'Mapoly0041s0137' => 'mpo', 'Mapoly0041s0138' => 'mpo', 'Mapoly0041s0139' => 'mpo', 'Mapoly0041s0141' => 'mpo', 'Mapoly0041s0142' => 'mpo', 'Mapoly0041s0143' => 'mpo', 'Mapoly0041s0144' => 'mpo', 'Mapoly0041s0145' => 'mpo', 'Mapoly0047s0106' => 'mpo', 'Mapoly0047s0108' => 'mpo', 'Mapoly0050s0051' => 'mpo', 'Mapoly0050s0052' => 'mpo', 'Mapoly0050s0053' => 'mpo', 'Mapoly0058s0013' => 'mpo', 'Mapoly0091s0078' => 'mpo', 'Mapoly0091s0079' => 'mpo', 'Mapoly0091s0080' => 'mpo', 'Mapoly0091s0081' => 'mpo', 'Mapoly0278s0004' => 'mpo', 'Mapoly0278s0005' => 'mpo', 'Mapoly0278s0006' => 'mpo', 'MBI11_g30648_MAGBIO' => 'mbi', 'MCO03G194' => 'mco', 'MCO03G590' => 'mco', 'MCO07G312' => 'mco', 'MCO10G318' => 'mco', 'MCO12G244' => 'mco', 'MCO13G148' => 'mco', 'MCO13G194' => 'mco', 'MCO16G238' => 'mco', 'MD06G1134100' => 'mdo', 'MD13G1200100' => 'mdo', 'MD13G1200300' => 'mdo', 'MD13G1200600' => 'mdo', 'MD14G1150400' => 'mdo', 'MD16G1200000' => 'mdo', 'Medtr1g102570' => 'mtr', 'Medtr1g102780' => 'mtr', 'Medtr1g102800' => 'mtr', 'Medtr1g102810' => 'mtr', 'Medtr1g102830' => 'mtr', 'MELO3C006499.2' => 'cme', 'Migut.G00385' => 'egut', 'MSTRG.4063' => 'ama', 'Nitab4.5_0000090g0260' => 'nta', 'Nitab4.5_0000977g0030' => 'nta', 'Nitab4.5_0002541g0040' => 'nta', 'Nitab4.5_0007068g0040' => 'nta', 'Nn005s41408' => 'nnu', 'Nn005s41410' => 'nnu', 'Oeu010310.1' => 'oeu', 'Oeu010311.1' => 'oeu', 'Oeu043472.1' => 'oeu', 'Os01g0246400' => 'osa', 'Os04g0267950' => 'osa', 'Os07g0178700' => 'osa', 'Os07g0178800' => 'osa', 'Peaxi162Scf00316g00046' => 'pax', 'Peaxi162Scf00316g00049' => 'pax', 'Peaxi162Scf00316g00059' => 'pax', 'Peaxi162Scf00316g00328' => 'pax', 'Peaxi162Scf00316g00329' => 'pax', 'Peaxi162Scf00316g00411' => 'pax', 'Peaxi162Scf00316g00521' => 'pax', 'Peaxi162Scf00492g00068' => 'pax', 'Peaxi162Scf35631g00002' => 'pax', 'PGR142G3720' => 'pgr', 'PGSC0003DMG400006442' => 'stu', 'Phvul.007G062000' => 'pvu', 'Potri.008G157750' => 'ptr', 'Potri.008G157900' => 'ptr', 'Potri.008G158000' => 'ptr', 'Potri.008G158200' => 'ptr', 'Pp3c11_7280' => 'ppa', 'Pp3c11_7980' => 'ppa', 'Pp3c12_19450' => 'ppa', 'Pp3c14_1480' => 'ppa', 'Pp3c14_1501' => 'ppa', 'Pp3c16_4900' => 'ppa', 'Pp3c16_5010' => 'ppa', 'Pp3c16_5060' => 'ppa', 'Pp3c19_18250' => 'ppa', 'Pp3c23_8530' => 'ppa', 'Pp3c23_8550' => 'ppa', 'Pp3c24_9670' => 'ppa', 'Pp3c2_21390' => 'ppa', 'Pp3c2_31380' => 'ppa', 'Pp3c3_16620' => 'ppa', 'Pp3c3_8090' => 'ppa', 'Pp3c3_8110' => 'ppa', 'Pp3c3_8130' => 'ppa', 'Pp3c3_8150' => 'ppa', 'Pp3c4_14320' => 'ppa', 'Pp3c6_2560' => 'ppa', 'Pp3c9_16700' => 'ppa', 'PRCOL_00000234' => 'pco', 'PRCOL_00000235' => 'pco', 'PRCOL_00000777' => 'pco', 'PRCOL_00002344' => 'pco', 'PRCOL_00002372' => 'pco', 'PRCOL_00006120' => 'pco', 'Prupe.1G021400' => 'ppe', 'Prupe.1G021500' => 'ppe', 'Prupe.1G021600' => 'ppe', 'Prupe.1G021700' => 'ppe', 'Prupe.1G021800' => 'ppe', 'Prupe.5G145100' => 'ppe', 'Psat6g204040' => 'psa', 'Psat6g204800' => 'psa', 'Psat6g204920' => 'psa', 'Psat6g204960' => 'psa', 'Psat6g205080' => 'psa', 'PSO017G0271' => 'pso', 'PSO017G1276' => 'pso', 'PSO017G1429' => 'pso', 'PSO017G1861' => 'pso', 'PSO017G2787' => 'pso', 'PSO017G4466' => 'pso', 'PSO017G5118' => 'pso', 'PSO017G5420' => 'pso', 'PSO063G3678' => 'pso', 'PSO210G0546' => 'pso', 'PSO317G0001' => 'pso', 'PSO357G0512' => 'pso', 'PSO478G2682' => 'pso', 'PSO647G0001' => 'pso', 'PSO675G0001' => 'pso', 'PSO675G2699' => 'pso', 'PSO675G2849' => 'pso', 'PSO675G4991' => 'pso', 'PSO689G0001' => 'pso', 'QL06p000916' => 'qlo', 'QL06p000921' => 'qlo', 'QL06p001398' => 'qlo', 'QL06p001407' => 'qlo', 'QL06p002031' => 'qlo', 'RcHm_v2.0_Chr4g0387791' => 'rch', 'RcHm_v2.0_Chr4g0387801' => 'rch', 'RcHm_v2.0_Chr6g0286501' => 'rch', 'RcHm_v2.0_Chr6g0286511' => 'rch', 'RcHm_v2.0_Chr6g0286521' => 'rch', 'RcHm_v2.0_Chr6g0286531' => 'rch', 'RcHm_v2.0_Chr7g0189141' => 'rch', 'Rhsim02G0028700' => 'rsi', 'Rhsim02G0028800' => 'rsi', 'Rhsim02G0028900' => 'rsi', 'Rhsim02G0029000' => 'rsi', 'Rhsim02G0029100' => 'rsi', 'Rhsim02G0029200' => 'rsi', 'Rhsim02G0029300' => 'rsi', 'Rhsim02G0029400' => 'rsi', 'Rhsim02G0029500' => 'rsi', 'Rhsim02G0029600' => 'rsi', 'RhsimUnG0024000' => 'rsi', 'RhsimUnG0024100' => 'rsi', 'RhsimUnG0024200' => 'rsi', 'RhsimUnG0024300' => 'rsi', 'RhsimUnG0024400' => 'rsi', 'RhsimUnG0024500' => 'rsi', 'RhsimUnG0024700' => 'rsi', 'RhsimUnG0024800' => 'rsi', 'RhsimUnG0024900' => 'rsi', 'RhsimUnG0025100' => 'rsi', 'Sabra08G0120200' => 'sbr', 'Sabra08G0120300' => 'sbr', 'Sabra08G0120500' => 'sbr', 'Sabra08G0120600' => 'sbr', 'Sabra10G0158900' => 'sbr', 'SalBow2G3492' => 'sbo', 'Sc13g0004760' => 'sci', 'Sc13g0004770' => 'sci', 'Sed0003417' => 'sed', 'Sed0019750' => 'sed', 'SEGI_03419' => 'sgi', 'SEGI_05907' => 'sgi', 'SEGI_10682' => 'sgi', 'SEGI_13528' => 'sgi', 'SEGI_16081' => 'sgi', 'SEGI_19370' => 'sgi', 'SEGI_21015' => 'sgi', 'SEGI_21944' => 'sgi', 'SEGI_32906' => 'sgi', 'SEGI_33093' => 'sgi', 'SEGI_36110' => 'sgi', 'SEGI_40397' => 'sgi', 'SGA_v2.0_scaffold191G40426' => 'sas', 'SGA_v2.0_scaffold353G49717' => 'sas', 'SGA_v2.0_scaffold50G18550' => 'sas', 'SMO119G0173' => 'smo', 'SMO172G0002' => 'smo', 'Solyc09g082690.3' => 'sly', 'Solyc09g082700.2' => 'sly', 'Sopen09g031550' => 'spe', 'Sopen09g031560' => 'spe', 'Sp3g20540' => 'spa', 'Sp7g07580' => 'spa', 'TAR134G0002' => 'tar', 'TAR236G0001' => 'tar', 'TAR365G0892' => 'tar', 'TAR636G0166' => 'tar', 'TAR636G0646' => 'tar', 'TAR636G0869' => 'tar', 'TAR636G1317' => 'tar', 'TAR636G1744' => 'tar', 'TAR636G3358' => 'tar', 'TAR636G3436' => 'tar', 'THA.LOC104803047' => 'tha', 'Thecc.04G238900' => 'tca', 'Thhalv10021557m.g' => 'esa', 'Thhalv10026318m.g' => 'esa', 'Thhalv10026335m.g' => 'esa', 'TPR.G17433' => 'tpr', 'TPR.G18915' => 'tpr', 'TPR.G26125' => 'tpr', 'TWI09G0677' => 'twi', 'TWI73G0287' => 'twi', 'unitig_748.g8326' => 'ugi', 'vmacro15370' => 'vma', 'vmacro15371' => 'vma', 'vmacro15372' => 'vma', 'vmacro15373' => 'vma', 'vmacro15374' => 'vma', 'VMungo0720G2826' => 'vmu', 'Zm00001eb116960' => 'zma', 'Zm00001eb301260' => 'zma', 'Zm00001eb301270' => 'zma' ), 'gf_id' => 'HOM05D001460', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001460' ), 'data_identifier' => 'HOM05D001460', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001460', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '433', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p22980' => 'bna', 'A01p32340' => 'bna', 'A03p42970' => 'bna', 'A05p25880' => 'bna', 'Aa31LG8G9320' => 'aar', 'Aa31LG8G9330' => 'aar', 'Aa31LG8G9340' => 'aar', 'Aa31sc221G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1034' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1528' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.829' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2222' => 'aag', 'Ah.12g058830' => 'amhyb', 'Ah.12g058840' => 'amhyb', 'AL3G37160' => 'aly', 'AL7G41310' => 'aly', 'Aqoxy5G00395' => 'aox', 'Aqoxy5G00396' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0C8NZA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5185HY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JZ1PRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MD3LS0' => 'arhy', 'AT3G22840' => 'ath', 'AT4G14690' => 'ath', 'ATR0665G054' => 'atr', 'Atru.chr4.2344' => 'acertr', 'Atru.chr4.2346' => 'acertr', 'Atru.chr4.2347' => 'acertr', 'Atru.chr4.2348' => 'acertr', 'Atru.chr4.2355' => 'acertr', 'Atru.chr4.2356' => 'acertr', 'Atru.chr4.2358' => 'acertr', 'Atru.chr4.2359' => 'acertr', 'Atru.chr4.2360' => 'acertr', 'Atru.chr4.2361' => 'acertr', 'AUR62030476' => 'cqu', 'AUR62030478' => 'cqu', 'AUR62030819' => 'cqu', 'AUR62030820' => 'cqu', 'BcaB03g14648' => 'bca', 'BcaB04g20492' => 'bca', 'BcaB06g26399' => 'bca', 'BcaC01g03416' => 'bca', 'BcaC01g03419' => 'bca', 'BcaC01g03421' => 'bca', 'BcaC01g03424' => 'bca', 'BcaC05g28012' => 'bca', 'BcaC09g49212' => 'bca', 'BcaC09g50140' => 'bca', 'BcaNung00346' => 'bca', 'BolC1t02785H' => 'bol', 'BolC1t04095H' => 'bol', 'BolC3t17545H' => 'bol', 'BolC5t32769H' => 'bol', 'BraA01t02211Z' => 'bra', 'BraA01t03359Z' => 'bra', 'BraA03t13441Z' => 'bra', 'BraA05t21476Z' => 'bra', 'C01p28420' => 'bna', 'C01p41350' => 'bna', 'C03p52750' => 'bna', 'C03p52780' => 'bna', 'C05p40270' => 'bna', 'CAN.G1437.9' => 'can', 'CANSAT78G0035' => 'cansat', 'CANSAT78G1036' => 'cansat', 'CANSAT78G2272' => 'cansat', 'CANSAT78G2478' => 'cansat', 'CARHR098700' => 'chi', 'CARHR221120' => 'chi', 'CARHR221150' => 'chi', 'Carub.0003s2297' => 'cru', 'Carub.0007s2749' => 'cru', 'Carub.0007s2750' => 'cru', 'Carub.0007s2751' => 'cru', 'Ca_10849_v3' => 'car', 'Cc03_g04300' => 'ccan', 'CDE02G3648' => 'cde', 'CDE05G0060' => 'cde', 'CDE05G0692' => 'cde', 'CDE05G2285' => 'cde', 'CDE05G2884' => 'cde', 'CDE05G3072' => 'cde', 'Cfa008439' => 'cfa', 'Cfa008441' => 'cfa', 'Cfa008443' => 'cfa', 'Cfa008448' => 'cfa', 'Ciclev10005974m.g' => 'ccl', 'Ciclev10006006m.g' => 'ccl', 'Ciclev10006775m.g' => 'ccl', 'CiPaw.02G120400' => 'cil', 'CiPaw.02G120500' => 'cil', 'CiPaw.02G120600' => 'cil', 'ClCG05G004850' => 'cla', 'COL.COLO4_21566' => 'col', 'Cpa.g.sc44.124' => 'cpa', 'Cre07.g320400' => 'cre', 'Cre07.g320450' => 'cre', 'Cre08.g384650' => 'cre', 'Cre09.g393173' => 'cre', 'Cre09.g394325' => 'cre', 'Cre14.g626750' => 'cre', 'Cre16.g679250' => 'cre', 'CsaV3_3G012890' => 'csa', 'CSS0010865' => 'camsi', 'CSS0044338' => 'camsi', 'DCAR_002366' => 'dca', 'DCAR_030687' => 'dca', 'DCAR_030688' => 'dca', 'Dinv14047' => 'din', 'Dinv14048' => 'din', 'Duzib151G0105' => 'dzi', 'Duzib151G0114' => 'dzi', 'Duzib212G1029' => 'dzi', 'ECA232G3536' => 'eca', 'ECA240G0786' => 'eca', 'ECA240G1802' => 'eca', 'ECA240G3760' => 'eca', 'ECA240G3920' => 'eca', 'EL10Ac5g12536' => 'bvu', 'EL10Ac5g12537' => 'bvu', 'EL10Ac5g12538' => 'bvu', 'Eucgr.B01004' => 'egr', 'Eucgr.B01006' => 'egr', 'Eucgr.B01007' => 'egr', 'Eucgr.B01008' => 'egr', 'Eucgr.B01895' => 'egr', 'Eucgr.B01896' => 'egr', 'FAN04G1456' => 'fan', 'FAN08G1769' => 'fan', 'FAN08G2160' => 'fan', 'FAN13G2403' => 'fan', 'FAN13G3303' => 'fan', 'FAN15G2435' => 'fan', 'FAN17G0672' => 'fan', 'FAN17G2441' => 'fan', 'FAN18G1024' => 'fan', 'FAN22G1458' => 'fan', 'FAN24G0037' => 'fan', 'FAN24G0429' => 'fan', 'FAN24G2387' => 'fan', 'FAN27G2746' => 'fan', 'FvH4_2g20400' => 'fve', 'FvH4_2g20420' => 'fve', 'FvH4_2g20430' => 'fve', 'FvH4_4g01270' => 'fve', 'FvH4_4g01290' => 'fve', 'FvH4_4g01300' => 'fve', 'FvH4_4g01310' => 'fve', 'FvH4_4g01330' => 'fve', 'FvH4_5g09070' => 'fve', 'Glyma.10G243800' => 'gma', 'Glyma.20G150600' => 'gma', 'Gohir.A09G219200' => 'ghi', 'Gohir.A09G219300' => 'ghi', 'Gohir.D09G221400' => 'ghi', 'Gohir.D09G221500' => 'ghi', 'Gorai.006G242600' => 'gra', 'Gorai.006G242700' => 'gra', 'GSVIVG01018044001' => 'vvi', 'HanXRQChr03g0083821' => 'han', 'HanXRQChr03g0083841' => 'han', 'HanXRQChr03g0083881' => 'han', 'HanXRQChr03g0083901' => 'han', 'HanXRQChr03g0083921' => 'han', 'HanXRQChr03g0085331' => 'han', 'HanXRQChr03g0085361' => 'han', 'HanXRQChr03g0085411' => 'han', 'HanXRQChr03g0085421' => 'han', 'HanXRQChr03g0085431' => 'han', 'HanXRQChr08g0221991' => 'han', 'HanXRQChr11g0336061' => 'han', 'HanXRQChr11g0336411' => 'han', 'Haze_11234' => 'cav', 'Hma1.2p1_0549F.1_g177010' => 'hma', 'Hma1.2p1_0602F.1_g187630' => 'hma', 'Hund14876' => 'sun', 'Hund14879' => 'sun', 'Lalb_Chr06g0160741' => 'lal', 'Lalb_Chr21g0304781' => 'lal', 'Lj3A726G19' => 'lonja', 'Lj3A726T23' => 'lonja', 'Lj3A726T24' => 'lonja', 'Lj3A726T25' => 'lonja', 'Lj3A727T17' => 'lonja', 'Lj3C726T0' => 'lonja', 'Lj3C726T2' => 'lonja', 'Lj3P725T35' => 'lonja', 'Lj3P727T10' => 'lonja', 'Lj3P727T12' => 'lonja', 'Lj3P727T14' => 'lonja', 'Lj5g0023109' => 'lja', 'Lj6P646T44' => 'lonja', 'Lsat_1_v5_gn_6_75760' => 'lsa', 'Lsat_1_v5_gn_6_75800' => 'lsa', 'Lsat_1_v5_gn_6_75900' => 'lsa', 'Lsat_1_v5_gn_6_76240' => 'lsa', 'Lsat_1_v5_gn_6_76441' => 'lsa', 'Lsat_1_v5_gn_6_76700' => 'lsa', 'Lsat_1_v5_gn_6_76760' => 'lsa', 'Manes.15G033100' => 'mes', 'Mapoly0004s0074' => 'mpo', 'Mapoly0004s0075' => 'mpo', 'Mapoly0004s0163' => 'mpo', 'Mapoly0004s0164' => 'mpo', 'Mapoly0021s0018' => 'mpo', 'Mapoly0041s0136' => 'mpo', 'Mapoly0041s0137' => 'mpo', 'Mapoly0041s0138' => 'mpo', 'Mapoly0041s0139' => 'mpo', 'Mapoly0041s0141' => 'mpo', 'Mapoly0041s0142' => 'mpo', 'Mapoly0041s0143' => 'mpo', 'Mapoly0041s0144' => 'mpo', 'Mapoly0041s0145' => 'mpo', 'Mapoly0047s0106' => 'mpo', 'Mapoly0047s0108' => 'mpo', 'Mapoly0050s0051' => 'mpo', 'Mapoly0050s0052' => 'mpo', 'Mapoly0050s0053' => 'mpo', 'Mapoly0058s0013' => 'mpo', 'Mapoly0091s0078' => 'mpo', 'Mapoly0091s0079' => 'mpo', 'Mapoly0091s0080' => 'mpo', 'Mapoly0091s0081' => 'mpo', 'Mapoly0278s0004' => 'mpo', 'Mapoly0278s0005' => 'mpo', 'Mapoly0278s0006' => 'mpo', 'MBI11_g30648_MAGBIO' => 'mbi', 'MCO03G194' => 'mco', 'MCO03G590' => 'mco', 'MCO07G312' => 'mco', 'MCO10G318' => 'mco', 'MCO12G244' => 'mco', 'MCO13G148' => 'mco', 'MCO13G194' => 'mco', 'MCO16G238' => 'mco', 'MD06G1134100' => 'mdo', 'MD13G1200100' => 'mdo', 'MD13G1200300' => 'mdo', 'MD13G1200600' => 'mdo', 'MD14G1150400' => 'mdo', 'MD16G1200000' => 'mdo', 'Medtr1g102570' => 'mtr', 'Medtr1g102780' => 'mtr', 'Medtr1g102800' => 'mtr', 'Medtr1g102810' => 'mtr', 'Medtr1g102830' => 'mtr', 'MELO3C006499.2' => 'cme', 'Migut.G00385' => 'egut', 'MSTRG.4063' => 'ama', 'Nitab4.5_0000090g0260' => 'nta', 'Nitab4.5_0000977g0030' => 'nta', 'Nitab4.5_0002541g0040' => 'nta', 'Nitab4.5_0007068g0040' => 'nta', 'Nn005s41408' => 'nnu', 'Nn005s41410' => 'nnu', 'Oeu010310.1' => 'oeu', 'Oeu010311.1' => 'oeu', 'Oeu043472.1' => 'oeu', 'Os01g0246400' => 'osa', 'Os04g0267950' => 'osa', 'Os07g0178700' => 'osa', 'Os07g0178800' => 'osa', 'Peaxi162Scf00316g00046' => 'pax', 'Peaxi162Scf00316g00049' => 'pax', 'Peaxi162Scf00316g00059' => 'pax', 'Peaxi162Scf00316g00328' => 'pax', 'Peaxi162Scf00316g00329' => 'pax', 'Peaxi162Scf00316g00411' => 'pax', 'Peaxi162Scf00316g00521' => 'pax', 'Peaxi162Scf00492g00068' => 'pax', 'Peaxi162Scf35631g00002' => 'pax', 'PGR142G3720' => 'pgr', 'PGSC0003DMG400006442' => 'stu', 'Phvul.007G062000' => 'pvu', 'Potri.008G157750' => 'ptr', 'Potri.008G157900' => 'ptr', 'Potri.008G158000' => 'ptr', 'Potri.008G158200' => 'ptr', 'Pp3c11_7280' => 'ppa', 'Pp3c11_7980' => 'ppa', 'Pp3c12_19450' => 'ppa', 'Pp3c14_1480' => 'ppa', 'Pp3c14_1501' => 'ppa', 'Pp3c16_4900' => 'ppa', 'Pp3c16_5010' => 'ppa', 'Pp3c16_5060' => 'ppa', 'Pp3c19_18250' => 'ppa', 'Pp3c23_8530' => 'ppa', 'Pp3c23_8550' => 'ppa', 'Pp3c24_9670' => 'ppa', 'Pp3c2_21390' => 'ppa', 'Pp3c2_31380' => 'ppa', 'Pp3c3_16620' => 'ppa', 'Pp3c3_8090' => 'ppa', 'Pp3c3_8110' => 'ppa', 'Pp3c3_8130' => 'ppa', 'Pp3c3_8150' => 'ppa', 'Pp3c4_14320' => 'ppa', 'Pp3c6_2560' => 'ppa', 'Pp3c9_16700' => 'ppa', 'PRCOL_00000234' => 'pco', 'PRCOL_00000235' => 'pco', 'PRCOL_00000777' => 'pco', 'PRCOL_00002344' => 'pco', 'PRCOL_00002372' => 'pco', 'PRCOL_00006120' => 'pco', 'Prupe.1G021400' => 'ppe', 'Prupe.1G021500' => 'ppe', 'Prupe.1G021600' => 'ppe', 'Prupe.1G021700' => 'ppe', 'Prupe.1G021800' => 'ppe', 'Prupe.5G145100' => 'ppe', 'Psat6g204040' => 'psa', 'Psat6g204800' => 'psa', 'Psat6g204920' => 'psa', 'Psat6g204960' => 'psa', 'Psat6g205080' => 'psa', 'PSO017G0271' => 'pso', 'PSO017G1276' => 'pso', 'PSO017G1429' => 'pso', 'PSO017G1861' => 'pso', 'PSO017G2787' => 'pso', 'PSO017G4466' => 'pso', 'PSO017G5118' => 'pso', 'PSO017G5420' => 'pso', 'PSO063G3678' => 'pso', 'PSO210G0546' => 'pso', 'PSO317G0001' => 'pso', 'PSO357G0512' => 'pso', 'PSO478G2682' => 'pso', 'PSO647G0001' => 'pso', 'PSO675G0001' => 'pso', 'PSO675G2699' => 'pso', 'PSO675G2849' => 'pso', 'PSO675G4991' => 'pso', 'PSO689G0001' => 'pso', 'QL06p000916' => 'qlo', 'QL06p000921' => 'qlo', 'QL06p001398' => 'qlo', 'QL06p001407' => 'qlo', 'QL06p002031' => 'qlo', 'RcHm_v2.0_Chr4g0387791' => 'rch', 'RcHm_v2.0_Chr4g0387801' => 'rch', 'RcHm_v2.0_Chr6g0286501' => 'rch', 'RcHm_v2.0_Chr6g0286511' => 'rch', 'RcHm_v2.0_Chr6g0286521' => 'rch', 'RcHm_v2.0_Chr6g0286531' => 'rch', 'RcHm_v2.0_Chr7g0189141' => 'rch', 'Rhsim02G0028700' => 'rsi', 'Rhsim02G0028800' => 'rsi', 'Rhsim02G0028900' => 'rsi', 'Rhsim02G0029000' => 'rsi', 'Rhsim02G0029100' => 'rsi', 'Rhsim02G0029200' => 'rsi', 'Rhsim02G0029300' => 'rsi', 'Rhsim02G0029400' => 'rsi', 'Rhsim02G0029500' => 'rsi', 'Rhsim02G0029600' => 'rsi', 'RhsimUnG0024000' => 'rsi', 'RhsimUnG0024100' => 'rsi', 'RhsimUnG0024200' => 'rsi', 'RhsimUnG0024300' => 'rsi', 'RhsimUnG0024400' => 'rsi', 'RhsimUnG0024500' => 'rsi', 'RhsimUnG0024700' => 'rsi', 'RhsimUnG0024800' => 'rsi', 'RhsimUnG0024900' => 'rsi', 'RhsimUnG0025100' => 'rsi', 'Sabra08G0120200' => 'sbr', 'Sabra08G0120300' => 'sbr', 'Sabra08G0120500' => 'sbr', 'Sabra08G0120600' => 'sbr', 'Sabra10G0158900' => 'sbr', 'SalBow2G3492' => 'sbo', 'Sc13g0004760' => 'sci', 'Sc13g0004770' => 'sci', 'Sed0003417' => 'sed', 'Sed0019750' => 'sed', 'SEGI_03419' => 'sgi', 'SEGI_05907' => 'sgi', 'SEGI_10682' => 'sgi', 'SEGI_13528' => 'sgi', 'SEGI_16081' => 'sgi', 'SEGI_19370' => 'sgi', 'SEGI_21015' => 'sgi', 'SEGI_21944' => 'sgi', 'SEGI_32906' => 'sgi', 'SEGI_33093' => 'sgi', 'SEGI_36110' => 'sgi', 'SEGI_40397' => 'sgi', 'SGA_v2.0_scaffold191G40426' => 'sas', 'SGA_v2.0_scaffold353G49717' => 'sas', 'SGA_v2.0_scaffold50G18550' => 'sas', 'SMO119G0173' => 'smo', 'SMO172G0002' => 'smo', 'Solyc09g082690.3' => 'sly', 'Solyc09g082700.2' => 'sly', 'Sopen09g031550' => 'spe', 'Sopen09g031560' => 'spe', 'Sp3g20540' => 'spa', 'Sp7g07580' => 'spa', 'TAR134G0002' => 'tar', 'TAR236G0001' => 'tar', 'TAR365G0892' => 'tar', 'TAR636G0166' => 'tar', 'TAR636G0646' => 'tar', 'TAR636G0869' => 'tar', 'TAR636G1317' => 'tar', 'TAR636G1744' => 'tar', 'TAR636G3358' => 'tar', 'TAR636G3436' => 'tar', 'THA.LOC104803047' => 'tha', 'Thecc.04G238900' => 'tca', 'Thhalv10021557m.g' => 'esa', 'Thhalv10026318m.g' => 'esa', 'Thhalv10026335m.g' => 'esa', 'TPR.G17433' => 'tpr', 'TPR.G18915' => 'tpr', 'TPR.G26125' => 'tpr', 'TWI09G0677' => 'twi', 'TWI73G0287' => 'twi', 'unitig_748.g8326' => 'ugi', 'vmacro15370' => 'vma', 'vmacro15371' => 'vma', 'vmacro15372' => 'vma', 'vmacro15373' => 'vma', 'vmacro15374' => 'vma', 'VMungo0720G2826' => 'vmu', 'Zm00001eb116960' => 'zma', 'Zm00001eb301260' => 'zma', 'Zm00001eb301270' => 'zma' ) $gf_id = 'HOM05D001460' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001460' ) $data_identifier = 'HOM05D001460' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 4, 'aag' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 2, 'aox' => (int) 2, 'arhy' => (int) 4, 'ath' => (int) 2, 'atr' => (int) 1, 'acertr' => (int) 10, 'cqu' => (int) 4, 'bca' => (int) 11, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 1, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 1, 'ccan' => (int) 1, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 1, 'col' => (int) 1, 'cpa' => (int) 1, 'cre' => (int) 7, 'csa' => (int) 1, 'camsi' => (int) 2, 'dca' => (int) 3, 'din' => (int) 2, 'dzi' => (int) 3, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 14, 'fve' => (int) 9, 'gma' => (int) 2, 'ghi' => (int) 4, 'gra' => (int) 2, 'vvi' => (int) 1, 'han' => (int) 13, 'cav' => (int) 1, 'hma' => (int) 2, 'sun' => (int) 2, 'lal' => (int) 2, 'lonja' => (int) 12, 'lja' => (int) 1, 'lsa' => (int) 7, 'mes' => (int) 1, 'mpo' => (int) 27, 'mbi' => (int) 1, 'mco' => (int) 8, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 1, 'egut' => (int) 1, 'ama' => (int) 1, 'nta' => (int) 4, 'nnu' => (int) 2, 'oeu' => (int) 3, 'osa' => (int) 4, 'pax' => (int) 9, 'pgr' => (int) 1, 'stu' => (int) 1, 'pvu' => (int) 1, 'ptr' => (int) 4, 'ppa' => (int) 22, 'pco' => (int) 6, 'ppe' => (int) 6, 'psa' => (int) 5, 'pso' => (int) 19, 'qlo' => (int) 5, 'rch' => (int) 7, 'rsi' => (int) 20, 'sbr' => (int) 5, 'sbo' => (int) 1, 'sci' => (int) 2, 'sed' => (int) 2, 'sgi' => (int) 12, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 2, 'tar' => (int) 10, 'tha' => (int) 1, 'tca' => (int) 1, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 2, 'ugi' => (int) 1, 'vma' => (int) 5, 'vmu' => (int) 1, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb301270' $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' => 'HOM05D001460', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '433', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p22980' => 'bna', 'A01p32340' => 'bna', 'A03p42970' => 'bna', 'A05p25880' => 'bna', 'Aa31LG8G9320' => 'aar', 'Aa31LG8G9330' => 'aar', 'Aa31LG8G9340' => 'aar', 'Aa31sc221G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1034' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1528' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.829' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2222' => 'aag', 'Ah.12g058830' => 'amhyb', 'Ah.12g058840' => 'amhyb', 'AL3G37160' => 'aly', 'AL7G41310' => 'aly', 'Aqoxy5G00395' => 'aox', 'Aqoxy5G00396' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0C8NZA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5185HY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JZ1PRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MD3LS0' => 'arhy', 'AT3G22840' => 'ath', 'AT4G14690' => 'ath', 'ATR0665G054' => 'atr', 'Atru.chr4.2344' => 'acertr', 'Atru.chr4.2346' => 'acertr', 'Atru.chr4.2347' => 'acertr', 'Atru.chr4.2348' => 'acertr', 'Atru.chr4.2355' => 'acertr', 'Atru.chr4.2356' => 'acertr', 'Atru.chr4.2358' => 'acertr', 'Atru.chr4.2359' => 'acertr', 'Atru.chr4.2360' => 'acertr', 'Atru.chr4.2361' => 'acertr', 'AUR62030476' => 'cqu', 'AUR62030478' => 'cqu', 'AUR62030819' => 'cqu', 'AUR62030820' => 'cqu', 'BcaB03g14648' => 'bca', 'BcaB04g20492' => 'bca', 'BcaB06g26399' => 'bca', 'BcaC01g03416' => 'bca', 'BcaC01g03419' => 'bca', 'BcaC01g03421' => 'bca', 'BcaC01g03424' => 'bca', 'BcaC05g28012' => 'bca', 'BcaC09g49212' => 'bca', 'BcaC09g50140' => 'bca', 'BcaNung00346' => 'bca', 'BolC1t02785H' => 'bol', 'BolC1t04095H' => 'bol', 'BolC3t17545H' => 'bol', 'BolC5t32769H' => 'bol', 'BraA01t02211Z' => 'bra', 'BraA01t03359Z' => 'bra', 'BraA03t13441Z' => 'bra', 'BraA05t21476Z' => 'bra', 'C01p28420' => 'bna', 'C01p41350' => 'bna', 'C03p52750' => 'bna', 'C03p52780' => 'bna', 'C05p40270' => 'bna', 'CAN.G1437.9' => 'can', 'CANSAT78G0035' => 'cansat', 'CANSAT78G1036' => 'cansat', 'CANSAT78G2272' => 'cansat', 'CANSAT78G2478' => 'cansat', 'CARHR098700' => 'chi', 'CARHR221120' => 'chi', 'CARHR221150' => 'chi', 'Carub.0003s2297' => 'cru', 'Carub.0007s2749' => 'cru', 'Carub.0007s2750' => 'cru', 'Carub.0007s2751' => 'cru', 'Ca_10849_v3' => 'car', 'Cc03_g04300' => 'ccan', 'CDE02G3648' => 'cde', 'CDE05G0060' => 'cde', 'CDE05G0692' => 'cde', 'CDE05G2285' => 'cde', 'CDE05G2884' => 'cde', 'CDE05G3072' => 'cde', 'Cfa008439' => 'cfa', 'Cfa008441' => 'cfa', 'Cfa008443' => 'cfa', 'Cfa008448' => 'cfa', 'Ciclev10005974m.g' => 'ccl', 'Ciclev10006006m.g' => 'ccl', 'Ciclev10006775m.g' => 'ccl', 'CiPaw.02G120400' => 'cil', 'CiPaw.02G120500' => 'cil', 'CiPaw.02G120600' => 'cil', 'ClCG05G004850' => 'cla', 'COL.COLO4_21566' => 'col', 'Cpa.g.sc44.124' => 'cpa', 'Cre07.g320400' => 'cre', 'Cre07.g320450' => 'cre', 'Cre08.g384650' => 'cre', 'Cre09.g393173' => 'cre', 'Cre09.g394325' => 'cre', 'Cre14.g626750' => 'cre', 'Cre16.g679250' => 'cre', 'CsaV3_3G012890' => 'csa', 'CSS0010865' => 'camsi', 'CSS0044338' => 'camsi', 'DCAR_002366' => 'dca', 'DCAR_030687' => 'dca', 'DCAR_030688' => 'dca', 'Dinv14047' => 'din', 'Dinv14048' => 'din', 'Duzib151G0105' => 'dzi', 'Duzib151G0114' => 'dzi', 'Duzib212G1029' => 'dzi', 'ECA232G3536' => 'eca', 'ECA240G0786' => 'eca', 'ECA240G1802' => 'eca', 'ECA240G3760' => 'eca', 'ECA240G3920' => 'eca', 'EL10Ac5g12536' => 'bvu', 'EL10Ac5g12537' => 'bvu', 'EL10Ac5g12538' => 'bvu', 'Eucgr.B01004' => 'egr', 'Eucgr.B01006' => 'egr', 'Eucgr.B01007' => 'egr', 'Eucgr.B01008' => 'egr', 'Eucgr.B01895' => 'egr', 'Eucgr.B01896' => 'egr', 'FAN04G1456' => 'fan', 'FAN08G1769' => 'fan', 'FAN08G2160' => 'fan', 'FAN13G2403' => 'fan', 'FAN13G3303' => 'fan', 'FAN15G2435' => 'fan', 'FAN17G0672' => 'fan', 'FAN17G2441' => 'fan', 'FAN18G1024' => 'fan', 'FAN22G1458' => 'fan', 'FAN24G0037' => 'fan', 'FAN24G0429' => 'fan', 'FAN24G2387' => 'fan', 'FAN27G2746' => 'fan', 'FvH4_2g20400' => 'fve', 'FvH4_2g20420' => 'fve', 'FvH4_2g20430' => 'fve', 'FvH4_4g01270' => 'fve', 'FvH4_4g01290' => 'fve', 'FvH4_4g01300' => 'fve', 'FvH4_4g01310' => 'fve', 'FvH4_4g01330' => 'fve', 'FvH4_5g09070' => 'fve', 'Glyma.10G243800' => 'gma', 'Glyma.20G150600' => 'gma', 'Gohir.A09G219200' => 'ghi', 'Gohir.A09G219300' => 'ghi', 'Gohir.D09G221400' => 'ghi', 'Gohir.D09G221500' => 'ghi', 'Gorai.006G242600' => 'gra', 'Gorai.006G242700' => 'gra', 'GSVIVG01018044001' => 'vvi', 'HanXRQChr03g0083821' => 'han', 'HanXRQChr03g0083841' => 'han', 'HanXRQChr03g0083881' => 'han', 'HanXRQChr03g0083901' => 'han', 'HanXRQChr03g0083921' => 'han', 'HanXRQChr03g0085331' => 'han', 'HanXRQChr03g0085361' => 'han', 'HanXRQChr03g0085411' => 'han', 'HanXRQChr03g0085421' => 'han', 'HanXRQChr03g0085431' => 'han', 'HanXRQChr08g0221991' => 'han', 'HanXRQChr11g0336061' => 'han', 'HanXRQChr11g0336411' => 'han', 'Haze_11234' => 'cav', 'Hma1.2p1_0549F.1_g177010' => 'hma', 'Hma1.2p1_0602F.1_g187630' => 'hma', 'Hund14876' => 'sun', 'Hund14879' => 'sun', 'Lalb_Chr06g0160741' => 'lal', 'Lalb_Chr21g0304781' => 'lal', 'Lj3A726G19' => 'lonja', 'Lj3A726T23' => 'lonja', 'Lj3A726T24' => 'lonja', 'Lj3A726T25' => 'lonja', 'Lj3A727T17' => 'lonja', 'Lj3C726T0' => 'lonja', 'Lj3C726T2' => 'lonja', 'Lj3P725T35' => 'lonja', 'Lj3P727T10' => 'lonja', 'Lj3P727T12' => 'lonja', 'Lj3P727T14' => 'lonja', 'Lj5g0023109' => 'lja', 'Lj6P646T44' => 'lonja', 'Lsat_1_v5_gn_6_75760' => 'lsa', 'Lsat_1_v5_gn_6_75800' => 'lsa', 'Lsat_1_v5_gn_6_75900' => 'lsa', 'Lsat_1_v5_gn_6_76240' => 'lsa', 'Lsat_1_v5_gn_6_76441' => 'lsa', 'Lsat_1_v5_gn_6_76700' => 'lsa', 'Lsat_1_v5_gn_6_76760' => 'lsa', 'Manes.15G033100' => 'mes', 'Mapoly0004s0074' => 'mpo', 'Mapoly0004s0075' => 'mpo', 'Mapoly0004s0163' => 'mpo', 'Mapoly0004s0164' => 'mpo', 'Mapoly0021s0018' => 'mpo', 'Mapoly0041s0136' => 'mpo', 'Mapoly0041s0137' => 'mpo', 'Mapoly0041s0138' => 'mpo', 'Mapoly0041s0139' => 'mpo', 'Mapoly0041s0141' => 'mpo', 'Mapoly0041s0142' => 'mpo', 'Mapoly0041s0143' => 'mpo', 'Mapoly0041s0144' => 'mpo', 'Mapoly0041s0145' => 'mpo', 'Mapoly0047s0106' => 'mpo', 'Mapoly0047s0108' => 'mpo', 'Mapoly0050s0051' => 'mpo', 'Mapoly0050s0052' => 'mpo', 'Mapoly0050s0053' => 'mpo', 'Mapoly0058s0013' => 'mpo', 'Mapoly0091s0078' => 'mpo', 'Mapoly0091s0079' => 'mpo', 'Mapoly0091s0080' => 'mpo', 'Mapoly0091s0081' => 'mpo', 'Mapoly0278s0004' => 'mpo', 'Mapoly0278s0005' => 'mpo', 'Mapoly0278s0006' => 'mpo', 'MBI11_g30648_MAGBIO' => 'mbi', 'MCO03G194' => 'mco', 'MCO03G590' => 'mco', 'MCO07G312' => 'mco', 'MCO10G318' => 'mco', 'MCO12G244' => 'mco', 'MCO13G148' => 'mco', 'MCO13G194' => 'mco', 'MCO16G238' => 'mco', 'MD06G1134100' => 'mdo', 'MD13G1200100' => 'mdo', 'MD13G1200300' => 'mdo', 'MD13G1200600' => 'mdo', 'MD14G1150400' => 'mdo', 'MD16G1200000' => 'mdo', 'Medtr1g102570' => 'mtr', 'Medtr1g102780' => 'mtr', 'Medtr1g102800' => 'mtr', 'Medtr1g102810' => 'mtr', 'Medtr1g102830' => 'mtr', 'MELO3C006499.2' => 'cme', 'Migut.G00385' => 'egut', 'MSTRG.4063' => 'ama', 'Nitab4.5_0000090g0260' => 'nta', 'Nitab4.5_0000977g0030' => 'nta', 'Nitab4.5_0002541g0040' => 'nta', 'Nitab4.5_0007068g0040' => 'nta', 'Nn005s41408' => 'nnu', 'Nn005s41410' => 'nnu', 'Oeu010310.1' => 'oeu', 'Oeu010311.1' => 'oeu', 'Oeu043472.1' => 'oeu', 'Os01g0246400' => 'osa', 'Os04g0267950' => 'osa', 'Os07g0178700' => 'osa', 'Os07g0178800' => 'osa', 'Peaxi162Scf00316g00046' => 'pax', 'Peaxi162Scf00316g00049' => 'pax', 'Peaxi162Scf00316g00059' => 'pax', 'Peaxi162Scf00316g00328' => 'pax', 'Peaxi162Scf00316g00329' => 'pax', 'Peaxi162Scf00316g00411' => 'pax', 'Peaxi162Scf00316g00521' => 'pax', 'Peaxi162Scf00492g00068' => 'pax', 'Peaxi162Scf35631g00002' => 'pax', 'PGR142G3720' => 'pgr', 'PGSC0003DMG400006442' => 'stu', 'Phvul.007G062000' => 'pvu', 'Potri.008G157750' => 'ptr', 'Potri.008G157900' => 'ptr', 'Potri.008G158000' => 'ptr', 'Potri.008G158200' => 'ptr', 'Pp3c11_7280' => 'ppa', 'Pp3c11_7980' => 'ppa', 'Pp3c12_19450' => 'ppa', 'Pp3c14_1480' => 'ppa', 'Pp3c14_1501' => 'ppa', 'Pp3c16_4900' => 'ppa', 'Pp3c16_5010' => 'ppa', 'Pp3c16_5060' => 'ppa', 'Pp3c19_18250' => 'ppa', 'Pp3c23_8530' => 'ppa', 'Pp3c23_8550' => 'ppa', 'Pp3c24_9670' => 'ppa', 'Pp3c2_21390' => 'ppa', 'Pp3c2_31380' => 'ppa', 'Pp3c3_16620' => 'ppa', 'Pp3c3_8090' => 'ppa', 'Pp3c3_8110' => 'ppa', 'Pp3c3_8130' => 'ppa', 'Pp3c3_8150' => 'ppa', 'Pp3c4_14320' => 'ppa', 'Pp3c6_2560' => 'ppa', 'Pp3c9_16700' => 'ppa', 'PRCOL_00000234' => 'pco', 'PRCOL_00000235' => 'pco', 'PRCOL_00000777' => 'pco', 'PRCOL_00002344' => 'pco', 'PRCOL_00002372' => 'pco', 'PRCOL_00006120' => 'pco', 'Prupe.1G021400' => 'ppe', 'Prupe.1G021500' => 'ppe', 'Prupe.1G021600' => 'ppe', 'Prupe.1G021700' => 'ppe', 'Prupe.1G021800' => 'ppe', 'Prupe.5G145100' => 'ppe', 'Psat6g204040' => 'psa', 'Psat6g204800' => 'psa', 'Psat6g204920' => 'psa', 'Psat6g204960' => 'psa', 'Psat6g205080' => 'psa', 'PSO017G0271' => 'pso', 'PSO017G1276' => 'pso', 'PSO017G1429' => 'pso', 'PSO017G1861' => 'pso', 'PSO017G2787' => 'pso', 'PSO017G4466' => 'pso', 'PSO017G5118' => 'pso', 'PSO017G5420' => 'pso', 'PSO063G3678' => 'pso', 'PSO210G0546' => 'pso', 'PSO317G0001' => 'pso', 'PSO357G0512' => 'pso', 'PSO478G2682' => 'pso', 'PSO647G0001' => 'pso', 'PSO675G0001' => 'pso', 'PSO675G2699' => 'pso', 'PSO675G2849' => 'pso', 'PSO675G4991' => 'pso', 'PSO689G0001' => 'pso', 'QL06p000916' => 'qlo', 'QL06p000921' => 'qlo', 'QL06p001398' => 'qlo', 'QL06p001407' => 'qlo', 'QL06p002031' => 'qlo', 'RcHm_v2.0_Chr4g0387791' => 'rch', 'RcHm_v2.0_Chr4g0387801' => 'rch', 'RcHm_v2.0_Chr6g0286501' => 'rch', 'RcHm_v2.0_Chr6g0286511' => 'rch', 'RcHm_v2.0_Chr6g0286521' => 'rch', 'RcHm_v2.0_Chr6g0286531' => 'rch', 'RcHm_v2.0_Chr7g0189141' => 'rch', 'Rhsim02G0028700' => 'rsi', 'Rhsim02G0028800' => 'rsi', 'Rhsim02G0028900' => 'rsi', 'Rhsim02G0029000' => 'rsi', 'Rhsim02G0029100' => 'rsi', 'Rhsim02G0029200' => 'rsi', 'Rhsim02G0029300' => 'rsi', 'Rhsim02G0029400' => 'rsi', 'Rhsim02G0029500' => 'rsi', 'Rhsim02G0029600' => 'rsi', 'RhsimUnG0024000' => 'rsi', 'RhsimUnG0024100' => 'rsi', 'RhsimUnG0024200' => 'rsi', 'RhsimUnG0024300' => 'rsi', 'RhsimUnG0024400' => 'rsi', 'RhsimUnG0024500' => 'rsi', 'RhsimUnG0024700' => 'rsi', 'RhsimUnG0024800' => 'rsi', 'RhsimUnG0024900' => 'rsi', 'RhsimUnG0025100' => 'rsi', 'Sabra08G0120200' => 'sbr', 'Sabra08G0120300' => 'sbr', 'Sabra08G0120500' => 'sbr', 'Sabra08G0120600' => 'sbr', 'Sabra10G0158900' => 'sbr', 'SalBow2G3492' => 'sbo', 'Sc13g0004760' => 'sci', 'Sc13g0004770' => 'sci', 'Sed0003417' => 'sed', 'Sed0019750' => 'sed', 'SEGI_03419' => 'sgi', 'SEGI_05907' => 'sgi', 'SEGI_10682' => 'sgi', 'SEGI_13528' => 'sgi', 'SEGI_16081' => 'sgi', 'SEGI_19370' => 'sgi', 'SEGI_21015' => 'sgi', 'SEGI_21944' => 'sgi', 'SEGI_32906' => 'sgi', 'SEGI_33093' => 'sgi', 'SEGI_36110' => 'sgi', 'SEGI_40397' => 'sgi', 'SGA_v2.0_scaffold191G40426' => 'sas', 'SGA_v2.0_scaffold353G49717' => 'sas', 'SGA_v2.0_scaffold50G18550' => 'sas', 'SMO119G0173' => 'smo', 'SMO172G0002' => 'smo', 'Solyc09g082690.3' => 'sly', 'Solyc09g082700.2' => 'sly', 'Sopen09g031550' => 'spe', 'Sopen09g031560' => 'spe', 'Sp3g20540' => 'spa', 'Sp7g07580' => 'spa', 'TAR134G0002' => 'tar', 'TAR236G0001' => 'tar', 'TAR365G0892' => 'tar', 'TAR636G0166' => 'tar', 'TAR636G0646' => 'tar', 'TAR636G0869' => 'tar', 'TAR636G1317' => 'tar', 'TAR636G1744' => 'tar', 'TAR636G3358' => 'tar', 'TAR636G3436' => 'tar', 'THA.LOC104803047' => 'tha', 'Thecc.04G238900' => 'tca', 'Thhalv10021557m.g' => 'esa', 'Thhalv10026318m.g' => 'esa', 'Thhalv10026335m.g' => 'esa', 'TPR.G17433' => 'tpr', 'TPR.G18915' => 'tpr', 'TPR.G26125' => 'tpr', 'TWI09G0677' => 'twi', 'TWI73G0287' => 'twi', 'unitig_748.g8326' => 'ugi', 'vmacro15370' => 'vma', 'vmacro15371' => 'vma', 'vmacro15372' => 'vma', 'vmacro15373' => 'vma', 'vmacro15374' => 'vma', 'VMungo0720G2826' => 'vmu', 'Zm00001eb116960' => 'zma', 'Zm00001eb301260' => 'zma', 'Zm00001eb301270' => 'zma' ), 'gf_id' => 'HOM05D001460', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001460' ), 'data_identifier' => 'HOM05D001460', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001460', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '433', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p22980' => 'bna', 'A01p32340' => 'bna', 'A03p42970' => 'bna', 'A05p25880' => 'bna', 'Aa31LG8G9320' => 'aar', 'Aa31LG8G9330' => 'aar', 'Aa31LG8G9340' => 'aar', 'Aa31sc221G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1034' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1528' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.829' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2222' => 'aag', 'Ah.12g058830' => 'amhyb', 'Ah.12g058840' => 'amhyb', 'AL3G37160' => 'aly', 'AL7G41310' => 'aly', 'Aqoxy5G00395' => 'aox', 'Aqoxy5G00396' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0C8NZA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5185HY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JZ1PRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MD3LS0' => 'arhy', 'AT3G22840' => 'ath', 'AT4G14690' => 'ath', 'ATR0665G054' => 'atr', 'Atru.chr4.2344' => 'acertr', 'Atru.chr4.2346' => 'acertr', 'Atru.chr4.2347' => 'acertr', 'Atru.chr4.2348' => 'acertr', 'Atru.chr4.2355' => 'acertr', 'Atru.chr4.2356' => 'acertr', 'Atru.chr4.2358' => 'acertr', 'Atru.chr4.2359' => 'acertr', 'Atru.chr4.2360' => 'acertr', 'Atru.chr4.2361' => 'acertr', 'AUR62030476' => 'cqu', 'AUR62030478' => 'cqu', 'AUR62030819' => 'cqu', 'AUR62030820' => 'cqu', 'BcaB03g14648' => 'bca', 'BcaB04g20492' => 'bca', 'BcaB06g26399' => 'bca', 'BcaC01g03416' => 'bca', 'BcaC01g03419' => 'bca', 'BcaC01g03421' => 'bca', 'BcaC01g03424' => 'bca', 'BcaC05g28012' => 'bca', 'BcaC09g49212' => 'bca', 'BcaC09g50140' => 'bca', 'BcaNung00346' => 'bca', 'BolC1t02785H' => 'bol', 'BolC1t04095H' => 'bol', 'BolC3t17545H' => 'bol', 'BolC5t32769H' => 'bol', 'BraA01t02211Z' => 'bra', 'BraA01t03359Z' => 'bra', 'BraA03t13441Z' => 'bra', 'BraA05t21476Z' => 'bra', 'C01p28420' => 'bna', 'C01p41350' => 'bna', 'C03p52750' => 'bna', 'C03p52780' => 'bna', 'C05p40270' => 'bna', 'CAN.G1437.9' => 'can', 'CANSAT78G0035' => 'cansat', 'CANSAT78G1036' => 'cansat', 'CANSAT78G2272' => 'cansat', 'CANSAT78G2478' => 'cansat', 'CARHR098700' => 'chi', 'CARHR221120' => 'chi', 'CARHR221150' => 'chi', 'Carub.0003s2297' => 'cru', 'Carub.0007s2749' => 'cru', 'Carub.0007s2750' => 'cru', 'Carub.0007s2751' => 'cru', 'Ca_10849_v3' => 'car', 'Cc03_g04300' => 'ccan', 'CDE02G3648' => 'cde', 'CDE05G0060' => 'cde', 'CDE05G0692' => 'cde', 'CDE05G2285' => 'cde', 'CDE05G2884' => 'cde', 'CDE05G3072' => 'cde', 'Cfa008439' => 'cfa', 'Cfa008441' => 'cfa', 'Cfa008443' => 'cfa', 'Cfa008448' => 'cfa', 'Ciclev10005974m.g' => 'ccl', 'Ciclev10006006m.g' => 'ccl', 'Ciclev10006775m.g' => 'ccl', 'CiPaw.02G120400' => 'cil', 'CiPaw.02G120500' => 'cil', 'CiPaw.02G120600' => 'cil', 'ClCG05G004850' => 'cla', 'COL.COLO4_21566' => 'col', 'Cpa.g.sc44.124' => 'cpa', 'Cre07.g320400' => 'cre', 'Cre07.g320450' => 'cre', 'Cre08.g384650' => 'cre', 'Cre09.g393173' => 'cre', 'Cre09.g394325' => 'cre', 'Cre14.g626750' => 'cre', 'Cre16.g679250' => 'cre', 'CsaV3_3G012890' => 'csa', 'CSS0010865' => 'camsi', 'CSS0044338' => 'camsi', 'DCAR_002366' => 'dca', 'DCAR_030687' => 'dca', 'DCAR_030688' => 'dca', 'Dinv14047' => 'din', 'Dinv14048' => 'din', 'Duzib151G0105' => 'dzi', 'Duzib151G0114' => 'dzi', 'Duzib212G1029' => 'dzi', 'ECA232G3536' => 'eca', 'ECA240G0786' => 'eca', 'ECA240G1802' => 'eca', 'ECA240G3760' => 'eca', 'ECA240G3920' => 'eca', 'EL10Ac5g12536' => 'bvu', 'EL10Ac5g12537' => 'bvu', 'EL10Ac5g12538' => 'bvu', 'Eucgr.B01004' => 'egr', 'Eucgr.B01006' => 'egr', 'Eucgr.B01007' => 'egr', 'Eucgr.B01008' => 'egr', 'Eucgr.B01895' => 'egr', 'Eucgr.B01896' => 'egr', 'FAN04G1456' => 'fan', 'FAN08G1769' => 'fan', 'FAN08G2160' => 'fan', 'FAN13G2403' => 'fan', 'FAN13G3303' => 'fan', 'FAN15G2435' => 'fan', 'FAN17G0672' => 'fan', 'FAN17G2441' => 'fan', 'FAN18G1024' => 'fan', 'FAN22G1458' => 'fan', 'FAN24G0037' => 'fan', 'FAN24G0429' => 'fan', 'FAN24G2387' => 'fan', 'FAN27G2746' => 'fan', 'FvH4_2g20400' => 'fve', 'FvH4_2g20420' => 'fve', 'FvH4_2g20430' => 'fve', 'FvH4_4g01270' => 'fve', 'FvH4_4g01290' => 'fve', 'FvH4_4g01300' => 'fve', 'FvH4_4g01310' => 'fve', 'FvH4_4g01330' => 'fve', 'FvH4_5g09070' => 'fve', 'Glyma.10G243800' => 'gma', 'Glyma.20G150600' => 'gma', 'Gohir.A09G219200' => 'ghi', 'Gohir.A09G219300' => 'ghi', 'Gohir.D09G221400' => 'ghi', 'Gohir.D09G221500' => 'ghi', 'Gorai.006G242600' => 'gra', 'Gorai.006G242700' => 'gra', 'GSVIVG01018044001' => 'vvi', 'HanXRQChr03g0083821' => 'han', 'HanXRQChr03g0083841' => 'han', 'HanXRQChr03g0083881' => 'han', 'HanXRQChr03g0083901' => 'han', 'HanXRQChr03g0083921' => 'han', 'HanXRQChr03g0085331' => 'han', 'HanXRQChr03g0085361' => 'han', 'HanXRQChr03g0085411' => 'han', 'HanXRQChr03g0085421' => 'han', 'HanXRQChr03g0085431' => 'han', 'HanXRQChr08g0221991' => 'han', 'HanXRQChr11g0336061' => 'han', 'HanXRQChr11g0336411' => 'han', 'Haze_11234' => 'cav', 'Hma1.2p1_0549F.1_g177010' => 'hma', 'Hma1.2p1_0602F.1_g187630' => 'hma', 'Hund14876' => 'sun', 'Hund14879' => 'sun', 'Lalb_Chr06g0160741' => 'lal', 'Lalb_Chr21g0304781' => 'lal', 'Lj3A726G19' => 'lonja', 'Lj3A726T23' => 'lonja', 'Lj3A726T24' => 'lonja', 'Lj3A726T25' => 'lonja', 'Lj3A727T17' => 'lonja', 'Lj3C726T0' => 'lonja', 'Lj3C726T2' => 'lonja', 'Lj3P725T35' => 'lonja', 'Lj3P727T10' => 'lonja', 'Lj3P727T12' => 'lonja', 'Lj3P727T14' => 'lonja', 'Lj5g0023109' => 'lja', 'Lj6P646T44' => 'lonja', 'Lsat_1_v5_gn_6_75760' => 'lsa', 'Lsat_1_v5_gn_6_75800' => 'lsa', 'Lsat_1_v5_gn_6_75900' => 'lsa', 'Lsat_1_v5_gn_6_76240' => 'lsa', 'Lsat_1_v5_gn_6_76441' => 'lsa', 'Lsat_1_v5_gn_6_76700' => 'lsa', 'Lsat_1_v5_gn_6_76760' => 'lsa', 'Manes.15G033100' => 'mes', 'Mapoly0004s0074' => 'mpo', 'Mapoly0004s0075' => 'mpo', 'Mapoly0004s0163' => 'mpo', 'Mapoly0004s0164' => 'mpo', 'Mapoly0021s0018' => 'mpo', 'Mapoly0041s0136' => 'mpo', 'Mapoly0041s0137' => 'mpo', 'Mapoly0041s0138' => 'mpo', 'Mapoly0041s0139' => 'mpo', 'Mapoly0041s0141' => 'mpo', 'Mapoly0041s0142' => 'mpo', 'Mapoly0041s0143' => 'mpo', 'Mapoly0041s0144' => 'mpo', 'Mapoly0041s0145' => 'mpo', 'Mapoly0047s0106' => 'mpo', 'Mapoly0047s0108' => 'mpo', 'Mapoly0050s0051' => 'mpo', 'Mapoly0050s0052' => 'mpo', 'Mapoly0050s0053' => 'mpo', 'Mapoly0058s0013' => 'mpo', 'Mapoly0091s0078' => 'mpo', 'Mapoly0091s0079' => 'mpo', 'Mapoly0091s0080' => 'mpo', 'Mapoly0091s0081' => 'mpo', 'Mapoly0278s0004' => 'mpo', 'Mapoly0278s0005' => 'mpo', 'Mapoly0278s0006' => 'mpo', 'MBI11_g30648_MAGBIO' => 'mbi', 'MCO03G194' => 'mco', 'MCO03G590' => 'mco', 'MCO07G312' => 'mco', 'MCO10G318' => 'mco', 'MCO12G244' => 'mco', 'MCO13G148' => 'mco', 'MCO13G194' => 'mco', 'MCO16G238' => 'mco', 'MD06G1134100' => 'mdo', 'MD13G1200100' => 'mdo', 'MD13G1200300' => 'mdo', 'MD13G1200600' => 'mdo', 'MD14G1150400' => 'mdo', 'MD16G1200000' => 'mdo', 'Medtr1g102570' => 'mtr', 'Medtr1g102780' => 'mtr', 'Medtr1g102800' => 'mtr', 'Medtr1g102810' => 'mtr', 'Medtr1g102830' => 'mtr', 'MELO3C006499.2' => 'cme', 'Migut.G00385' => 'egut', 'MSTRG.4063' => 'ama', 'Nitab4.5_0000090g0260' => 'nta', 'Nitab4.5_0000977g0030' => 'nta', 'Nitab4.5_0002541g0040' => 'nta', 'Nitab4.5_0007068g0040' => 'nta', 'Nn005s41408' => 'nnu', 'Nn005s41410' => 'nnu', 'Oeu010310.1' => 'oeu', 'Oeu010311.1' => 'oeu', 'Oeu043472.1' => 'oeu', 'Os01g0246400' => 'osa', 'Os04g0267950' => 'osa', 'Os07g0178700' => 'osa', 'Os07g0178800' => 'osa', 'Peaxi162Scf00316g00046' => 'pax', 'Peaxi162Scf00316g00049' => 'pax', 'Peaxi162Scf00316g00059' => 'pax', 'Peaxi162Scf00316g00328' => 'pax', 'Peaxi162Scf00316g00329' => 'pax', 'Peaxi162Scf00316g00411' => 'pax', 'Peaxi162Scf00316g00521' => 'pax', 'Peaxi162Scf00492g00068' => 'pax', 'Peaxi162Scf35631g00002' => 'pax', 'PGR142G3720' => 'pgr', 'PGSC0003DMG400006442' => 'stu', 'Phvul.007G062000' => 'pvu', 'Potri.008G157750' => 'ptr', 'Potri.008G157900' => 'ptr', 'Potri.008G158000' => 'ptr', 'Potri.008G158200' => 'ptr', 'Pp3c11_7280' => 'ppa', 'Pp3c11_7980' => 'ppa', 'Pp3c12_19450' => 'ppa', 'Pp3c14_1480' => 'ppa', 'Pp3c14_1501' => 'ppa', 'Pp3c16_4900' => 'ppa', 'Pp3c16_5010' => 'ppa', 'Pp3c16_5060' => 'ppa', 'Pp3c19_18250' => 'ppa', 'Pp3c23_8530' => 'ppa', 'Pp3c23_8550' => 'ppa', 'Pp3c24_9670' => 'ppa', 'Pp3c2_21390' => 'ppa', 'Pp3c2_31380' => 'ppa', 'Pp3c3_16620' => 'ppa', 'Pp3c3_8090' => 'ppa', 'Pp3c3_8110' => 'ppa', 'Pp3c3_8130' => 'ppa', 'Pp3c3_8150' => 'ppa', 'Pp3c4_14320' => 'ppa', 'Pp3c6_2560' => 'ppa', 'Pp3c9_16700' => 'ppa', 'PRCOL_00000234' => 'pco', 'PRCOL_00000235' => 'pco', 'PRCOL_00000777' => 'pco', 'PRCOL_00002344' => 'pco', 'PRCOL_00002372' => 'pco', 'PRCOL_00006120' => 'pco', 'Prupe.1G021400' => 'ppe', 'Prupe.1G021500' => 'ppe', 'Prupe.1G021600' => 'ppe', 'Prupe.1G021700' => 'ppe', 'Prupe.1G021800' => 'ppe', 'Prupe.5G145100' => 'ppe', 'Psat6g204040' => 'psa', 'Psat6g204800' => 'psa', 'Psat6g204920' => 'psa', 'Psat6g204960' => 'psa', 'Psat6g205080' => 'psa', 'PSO017G0271' => 'pso', 'PSO017G1276' => 'pso', 'PSO017G1429' => 'pso', 'PSO017G1861' => 'pso', 'PSO017G2787' => 'pso', 'PSO017G4466' => 'pso', 'PSO017G5118' => 'pso', 'PSO017G5420' => 'pso', 'PSO063G3678' => 'pso', 'PSO210G0546' => 'pso', 'PSO317G0001' => 'pso', 'PSO357G0512' => 'pso', 'PSO478G2682' => 'pso', 'PSO647G0001' => 'pso', 'PSO675G0001' => 'pso', 'PSO675G2699' => 'pso', 'PSO675G2849' => 'pso', 'PSO675G4991' => 'pso', 'PSO689G0001' => 'pso', 'QL06p000916' => 'qlo', 'QL06p000921' => 'qlo', 'QL06p001398' => 'qlo', 'QL06p001407' => 'qlo', 'QL06p002031' => 'qlo', 'RcHm_v2.0_Chr4g0387791' => 'rch', 'RcHm_v2.0_Chr4g0387801' => 'rch', 'RcHm_v2.0_Chr6g0286501' => 'rch', 'RcHm_v2.0_Chr6g0286511' => 'rch', 'RcHm_v2.0_Chr6g0286521' => 'rch', 'RcHm_v2.0_Chr6g0286531' => 'rch', 'RcHm_v2.0_Chr7g0189141' => 'rch', 'Rhsim02G0028700' => 'rsi', 'Rhsim02G0028800' => 'rsi', 'Rhsim02G0028900' => 'rsi', 'Rhsim02G0029000' => 'rsi', 'Rhsim02G0029100' => 'rsi', 'Rhsim02G0029200' => 'rsi', 'Rhsim02G0029300' => 'rsi', 'Rhsim02G0029400' => 'rsi', 'Rhsim02G0029500' => 'rsi', 'Rhsim02G0029600' => 'rsi', 'RhsimUnG0024000' => 'rsi', 'RhsimUnG0024100' => 'rsi', 'RhsimUnG0024200' => 'rsi', 'RhsimUnG0024300' => 'rsi', 'RhsimUnG0024400' => 'rsi', 'RhsimUnG0024500' => 'rsi', 'RhsimUnG0024700' => 'rsi', 'RhsimUnG0024800' => 'rsi', 'RhsimUnG0024900' => 'rsi', 'RhsimUnG0025100' => 'rsi', 'Sabra08G0120200' => 'sbr', 'Sabra08G0120300' => 'sbr', 'Sabra08G0120500' => 'sbr', 'Sabra08G0120600' => 'sbr', 'Sabra10G0158900' => 'sbr', 'SalBow2G3492' => 'sbo', 'Sc13g0004760' => 'sci', 'Sc13g0004770' => 'sci', 'Sed0003417' => 'sed', 'Sed0019750' => 'sed', 'SEGI_03419' => 'sgi', 'SEGI_05907' => 'sgi', 'SEGI_10682' => 'sgi', 'SEGI_13528' => 'sgi', 'SEGI_16081' => 'sgi', 'SEGI_19370' => 'sgi', 'SEGI_21015' => 'sgi', 'SEGI_21944' => 'sgi', 'SEGI_32906' => 'sgi', 'SEGI_33093' => 'sgi', 'SEGI_36110' => 'sgi', 'SEGI_40397' => 'sgi', 'SGA_v2.0_scaffold191G40426' => 'sas', 'SGA_v2.0_scaffold353G49717' => 'sas', 'SGA_v2.0_scaffold50G18550' => 'sas', 'SMO119G0173' => 'smo', 'SMO172G0002' => 'smo', 'Solyc09g082690.3' => 'sly', 'Solyc09g082700.2' => 'sly', 'Sopen09g031550' => 'spe', 'Sopen09g031560' => 'spe', 'Sp3g20540' => 'spa', 'Sp7g07580' => 'spa', 'TAR134G0002' => 'tar', 'TAR236G0001' => 'tar', 'TAR365G0892' => 'tar', 'TAR636G0166' => 'tar', 'TAR636G0646' => 'tar', 'TAR636G0869' => 'tar', 'TAR636G1317' => 'tar', 'TAR636G1744' => 'tar', 'TAR636G3358' => 'tar', 'TAR636G3436' => 'tar', 'THA.LOC104803047' => 'tha', 'Thecc.04G238900' => 'tca', 'Thhalv10021557m.g' => 'esa', 'Thhalv10026318m.g' => 'esa', 'Thhalv10026335m.g' => 'esa', 'TPR.G17433' => 'tpr', 'TPR.G18915' => 'tpr', 'TPR.G26125' => 'tpr', 'TWI09G0677' => 'twi', 'TWI73G0287' => 'twi', 'unitig_748.g8326' => 'ugi', 'vmacro15370' => 'vma', 'vmacro15371' => 'vma', 'vmacro15372' => 'vma', 'vmacro15373' => 'vma', 'vmacro15374' => 'vma', 'VMungo0720G2826' => 'vmu', 'Zm00001eb116960' => 'zma', 'Zm00001eb301260' => 'zma', 'Zm00001eb301270' => 'zma' ) $gf_id = 'HOM05D001460' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001460' ) $data_identifier = 'HOM05D001460' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 4, 'aag' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 2, 'aox' => (int) 2, 'arhy' => (int) 4, 'ath' => (int) 2, 'atr' => (int) 1, 'acertr' => (int) 10, 'cqu' => (int) 4, 'bca' => (int) 11, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 1, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 1, 'ccan' => (int) 1, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 1, 'col' => (int) 1, 'cpa' => (int) 1, 'cre' => (int) 7, 'csa' => (int) 1, 'camsi' => (int) 2, 'dca' => (int) 3, 'din' => (int) 2, 'dzi' => (int) 3, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 14, 'fve' => (int) 9, 'gma' => (int) 2, 'ghi' => (int) 4, 'gra' => (int) 2, 'vvi' => (int) 1, 'han' => (int) 13, 'cav' => (int) 1, 'hma' => (int) 2, 'sun' => (int) 2, 'lal' => (int) 2, 'lonja' => (int) 12, 'lja' => (int) 1, 'lsa' => (int) 7, 'mes' => (int) 1, 'mpo' => (int) 27, 'mbi' => (int) 1, 'mco' => (int) 8, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 1, 'egut' => (int) 1, 'ama' => (int) 1, 'nta' => (int) 4, 'nnu' => (int) 2, 'oeu' => (int) 3, 'osa' => (int) 4, 'pax' => (int) 9, 'pgr' => (int) 1, 'stu' => (int) 1, 'pvu' => (int) 1, 'ptr' => (int) 4, 'ppa' => (int) 22, 'pco' => (int) 6, 'ppe' => (int) 6, 'psa' => (int) 5, 'pso' => (int) 19, 'qlo' => (int) 5, 'rch' => (int) 7, 'rsi' => (int) 20, 'sbr' => (int) 5, 'sbo' => (int) 1, 'sci' => (int) 2, 'sed' => (int) 2, 'sgi' => (int) 12, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 2, 'tar' => (int) 10, 'tha' => (int) 1, 'tca' => (int) 1, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 2, 'ugi' => (int) 1, 'vma' => (int) 5, 'vmu' => (int) 1, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb301270' $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' => 'HOM05D001460', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '433', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p22980' => 'bna', 'A01p32340' => 'bna', 'A03p42970' => 'bna', 'A05p25880' => 'bna', 'Aa31LG8G9320' => 'aar', 'Aa31LG8G9330' => 'aar', 'Aa31LG8G9340' => 'aar', 'Aa31sc221G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1034' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1528' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.829' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2222' => 'aag', 'Ah.12g058830' => 'amhyb', 'Ah.12g058840' => 'amhyb', 'AL3G37160' => 'aly', 'AL7G41310' => 'aly', 'Aqoxy5G00395' => 'aox', 'Aqoxy5G00396' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0C8NZA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5185HY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JZ1PRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MD3LS0' => 'arhy', 'AT3G22840' => 'ath', 'AT4G14690' => 'ath', 'ATR0665G054' => 'atr', 'Atru.chr4.2344' => 'acertr', 'Atru.chr4.2346' => 'acertr', 'Atru.chr4.2347' => 'acertr', 'Atru.chr4.2348' => 'acertr', 'Atru.chr4.2355' => 'acertr', 'Atru.chr4.2356' => 'acertr', 'Atru.chr4.2358' => 'acertr', 'Atru.chr4.2359' => 'acertr', 'Atru.chr4.2360' => 'acertr', 'Atru.chr4.2361' => 'acertr', 'AUR62030476' => 'cqu', 'AUR62030478' => 'cqu', 'AUR62030819' => 'cqu', 'AUR62030820' => 'cqu', 'BcaB03g14648' => 'bca', 'BcaB04g20492' => 'bca', 'BcaB06g26399' => 'bca', 'BcaC01g03416' => 'bca', 'BcaC01g03419' => 'bca', 'BcaC01g03421' => 'bca', 'BcaC01g03424' => 'bca', 'BcaC05g28012' => 'bca', 'BcaC09g49212' => 'bca', 'BcaC09g50140' => 'bca', 'BcaNung00346' => 'bca', 'BolC1t02785H' => 'bol', 'BolC1t04095H' => 'bol', 'BolC3t17545H' => 'bol', 'BolC5t32769H' => 'bol', 'BraA01t02211Z' => 'bra', 'BraA01t03359Z' => 'bra', 'BraA03t13441Z' => 'bra', 'BraA05t21476Z' => 'bra', 'C01p28420' => 'bna', 'C01p41350' => 'bna', 'C03p52750' => 'bna', 'C03p52780' => 'bna', 'C05p40270' => 'bna', 'CAN.G1437.9' => 'can', 'CANSAT78G0035' => 'cansat', 'CANSAT78G1036' => 'cansat', 'CANSAT78G2272' => 'cansat', 'CANSAT78G2478' => 'cansat', 'CARHR098700' => 'chi', 'CARHR221120' => 'chi', 'CARHR221150' => 'chi', 'Carub.0003s2297' => 'cru', 'Carub.0007s2749' => 'cru', 'Carub.0007s2750' => 'cru', 'Carub.0007s2751' => 'cru', 'Ca_10849_v3' => 'car', 'Cc03_g04300' => 'ccan', 'CDE02G3648' => 'cde', 'CDE05G0060' => 'cde', 'CDE05G0692' => 'cde', 'CDE05G2285' => 'cde', 'CDE05G2884' => 'cde', 'CDE05G3072' => 'cde', 'Cfa008439' => 'cfa', 'Cfa008441' => 'cfa', 'Cfa008443' => 'cfa', 'Cfa008448' => 'cfa', 'Ciclev10005974m.g' => 'ccl', 'Ciclev10006006m.g' => 'ccl', 'Ciclev10006775m.g' => 'ccl', 'CiPaw.02G120400' => 'cil', 'CiPaw.02G120500' => 'cil', 'CiPaw.02G120600' => 'cil', 'ClCG05G004850' => 'cla', 'COL.COLO4_21566' => 'col', 'Cpa.g.sc44.124' => 'cpa', 'Cre07.g320400' => 'cre', 'Cre07.g320450' => 'cre', 'Cre08.g384650' => 'cre', 'Cre09.g393173' => 'cre', 'Cre09.g394325' => 'cre', 'Cre14.g626750' => 'cre', 'Cre16.g679250' => 'cre', 'CsaV3_3G012890' => 'csa', 'CSS0010865' => 'camsi', 'CSS0044338' => 'camsi', 'DCAR_002366' => 'dca', 'DCAR_030687' => 'dca', 'DCAR_030688' => 'dca', 'Dinv14047' => 'din', 'Dinv14048' => 'din', 'Duzib151G0105' => 'dzi', 'Duzib151G0114' => 'dzi', 'Duzib212G1029' => 'dzi', 'ECA232G3536' => 'eca', 'ECA240G0786' => 'eca', 'ECA240G1802' => 'eca', 'ECA240G3760' => 'eca', 'ECA240G3920' => 'eca', 'EL10Ac5g12536' => 'bvu', 'EL10Ac5g12537' => 'bvu', 'EL10Ac5g12538' => 'bvu', 'Eucgr.B01004' => 'egr', 'Eucgr.B01006' => 'egr', 'Eucgr.B01007' => 'egr', 'Eucgr.B01008' => 'egr', 'Eucgr.B01895' => 'egr', 'Eucgr.B01896' => 'egr', 'FAN04G1456' => 'fan', 'FAN08G1769' => 'fan', 'FAN08G2160' => 'fan', 'FAN13G2403' => 'fan', 'FAN13G3303' => 'fan', 'FAN15G2435' => 'fan', 'FAN17G0672' => 'fan', 'FAN17G2441' => 'fan', 'FAN18G1024' => 'fan', 'FAN22G1458' => 'fan', 'FAN24G0037' => 'fan', 'FAN24G0429' => 'fan', 'FAN24G2387' => 'fan', 'FAN27G2746' => 'fan', 'FvH4_2g20400' => 'fve', 'FvH4_2g20420' => 'fve', 'FvH4_2g20430' => 'fve', 'FvH4_4g01270' => 'fve', 'FvH4_4g01290' => 'fve', 'FvH4_4g01300' => 'fve', 'FvH4_4g01310' => 'fve', 'FvH4_4g01330' => 'fve', 'FvH4_5g09070' => 'fve', 'Glyma.10G243800' => 'gma', 'Glyma.20G150600' => 'gma', 'Gohir.A09G219200' => 'ghi', 'Gohir.A09G219300' => 'ghi', 'Gohir.D09G221400' => 'ghi', 'Gohir.D09G221500' => 'ghi', 'Gorai.006G242600' => 'gra', 'Gorai.006G242700' => 'gra', 'GSVIVG01018044001' => 'vvi', 'HanXRQChr03g0083821' => 'han', 'HanXRQChr03g0083841' => 'han', 'HanXRQChr03g0083881' => 'han', 'HanXRQChr03g0083901' => 'han', 'HanXRQChr03g0083921' => 'han', 'HanXRQChr03g0085331' => 'han', 'HanXRQChr03g0085361' => 'han', 'HanXRQChr03g0085411' => 'han', 'HanXRQChr03g0085421' => 'han', 'HanXRQChr03g0085431' => 'han', 'HanXRQChr08g0221991' => 'han', 'HanXRQChr11g0336061' => 'han', 'HanXRQChr11g0336411' => 'han', 'Haze_11234' => 'cav', 'Hma1.2p1_0549F.1_g177010' => 'hma', 'Hma1.2p1_0602F.1_g187630' => 'hma', 'Hund14876' => 'sun', 'Hund14879' => 'sun', 'Lalb_Chr06g0160741' => 'lal', 'Lalb_Chr21g0304781' => 'lal', 'Lj3A726G19' => 'lonja', 'Lj3A726T23' => 'lonja', 'Lj3A726T24' => 'lonja', 'Lj3A726T25' => 'lonja', 'Lj3A727T17' => 'lonja', 'Lj3C726T0' => 'lonja', 'Lj3C726T2' => 'lonja', 'Lj3P725T35' => 'lonja', 'Lj3P727T10' => 'lonja', 'Lj3P727T12' => 'lonja', 'Lj3P727T14' => 'lonja', 'Lj5g0023109' => 'lja', 'Lj6P646T44' => 'lonja', 'Lsat_1_v5_gn_6_75760' => 'lsa', 'Lsat_1_v5_gn_6_75800' => 'lsa', 'Lsat_1_v5_gn_6_75900' => 'lsa', 'Lsat_1_v5_gn_6_76240' => 'lsa', 'Lsat_1_v5_gn_6_76441' => 'lsa', 'Lsat_1_v5_gn_6_76700' => 'lsa', 'Lsat_1_v5_gn_6_76760' => 'lsa', 'Manes.15G033100' => 'mes', 'Mapoly0004s0074' => 'mpo', 'Mapoly0004s0075' => 'mpo', 'Mapoly0004s0163' => 'mpo', 'Mapoly0004s0164' => 'mpo', 'Mapoly0021s0018' => 'mpo', 'Mapoly0041s0136' => 'mpo', 'Mapoly0041s0137' => 'mpo', 'Mapoly0041s0138' => 'mpo', 'Mapoly0041s0139' => 'mpo', 'Mapoly0041s0141' => 'mpo', 'Mapoly0041s0142' => 'mpo', 'Mapoly0041s0143' => 'mpo', 'Mapoly0041s0144' => 'mpo', 'Mapoly0041s0145' => 'mpo', 'Mapoly0047s0106' => 'mpo', 'Mapoly0047s0108' => 'mpo', 'Mapoly0050s0051' => 'mpo', 'Mapoly0050s0052' => 'mpo', 'Mapoly0050s0053' => 'mpo', 'Mapoly0058s0013' => 'mpo', 'Mapoly0091s0078' => 'mpo', 'Mapoly0091s0079' => 'mpo', 'Mapoly0091s0080' => 'mpo', 'Mapoly0091s0081' => 'mpo', 'Mapoly0278s0004' => 'mpo', 'Mapoly0278s0005' => 'mpo', 'Mapoly0278s0006' => 'mpo', 'MBI11_g30648_MAGBIO' => 'mbi', 'MCO03G194' => 'mco', 'MCO03G590' => 'mco', 'MCO07G312' => 'mco', 'MCO10G318' => 'mco', 'MCO12G244' => 'mco', 'MCO13G148' => 'mco', 'MCO13G194' => 'mco', 'MCO16G238' => 'mco', 'MD06G1134100' => 'mdo', 'MD13G1200100' => 'mdo', 'MD13G1200300' => 'mdo', 'MD13G1200600' => 'mdo', 'MD14G1150400' => 'mdo', 'MD16G1200000' => 'mdo', 'Medtr1g102570' => 'mtr', 'Medtr1g102780' => 'mtr', 'Medtr1g102800' => 'mtr', 'Medtr1g102810' => 'mtr', 'Medtr1g102830' => 'mtr', 'MELO3C006499.2' => 'cme', 'Migut.G00385' => 'egut', 'MSTRG.4063' => 'ama', 'Nitab4.5_0000090g0260' => 'nta', 'Nitab4.5_0000977g0030' => 'nta', 'Nitab4.5_0002541g0040' => 'nta', 'Nitab4.5_0007068g0040' => 'nta', 'Nn005s41408' => 'nnu', 'Nn005s41410' => 'nnu', 'Oeu010310.1' => 'oeu', 'Oeu010311.1' => 'oeu', 'Oeu043472.1' => 'oeu', 'Os01g0246400' => 'osa', 'Os04g0267950' => 'osa', 'Os07g0178700' => 'osa', 'Os07g0178800' => 'osa', 'Peaxi162Scf00316g00046' => 'pax', 'Peaxi162Scf00316g00049' => 'pax', 'Peaxi162Scf00316g00059' => 'pax', 'Peaxi162Scf00316g00328' => 'pax', 'Peaxi162Scf00316g00329' => 'pax', 'Peaxi162Scf00316g00411' => 'pax', 'Peaxi162Scf00316g00521' => 'pax', 'Peaxi162Scf00492g00068' => 'pax', 'Peaxi162Scf35631g00002' => 'pax', 'PGR142G3720' => 'pgr', 'PGSC0003DMG400006442' => 'stu', 'Phvul.007G062000' => 'pvu', 'Potri.008G157750' => 'ptr', 'Potri.008G157900' => 'ptr', 'Potri.008G158000' => 'ptr', 'Potri.008G158200' => 'ptr', 'Pp3c11_7280' => 'ppa', 'Pp3c11_7980' => 'ppa', 'Pp3c12_19450' => 'ppa', 'Pp3c14_1480' => 'ppa', 'Pp3c14_1501' => 'ppa', 'Pp3c16_4900' => 'ppa', 'Pp3c16_5010' => 'ppa', 'Pp3c16_5060' => 'ppa', 'Pp3c19_18250' => 'ppa', 'Pp3c23_8530' => 'ppa', 'Pp3c23_8550' => 'ppa', 'Pp3c24_9670' => 'ppa', 'Pp3c2_21390' => 'ppa', 'Pp3c2_31380' => 'ppa', 'Pp3c3_16620' => 'ppa', 'Pp3c3_8090' => 'ppa', 'Pp3c3_8110' => 'ppa', 'Pp3c3_8130' => 'ppa', 'Pp3c3_8150' => 'ppa', 'Pp3c4_14320' => 'ppa', 'Pp3c6_2560' => 'ppa', 'Pp3c9_16700' => 'ppa', 'PRCOL_00000234' => 'pco', 'PRCOL_00000235' => 'pco', 'PRCOL_00000777' => 'pco', 'PRCOL_00002344' => 'pco', 'PRCOL_00002372' => 'pco', 'PRCOL_00006120' => 'pco', 'Prupe.1G021400' => 'ppe', 'Prupe.1G021500' => 'ppe', 'Prupe.1G021600' => 'ppe', 'Prupe.1G021700' => 'ppe', 'Prupe.1G021800' => 'ppe', 'Prupe.5G145100' => 'ppe', 'Psat6g204040' => 'psa', 'Psat6g204800' => 'psa', 'Psat6g204920' => 'psa', 'Psat6g204960' => 'psa', 'Psat6g205080' => 'psa', 'PSO017G0271' => 'pso', 'PSO017G1276' => 'pso', 'PSO017G1429' => 'pso', 'PSO017G1861' => 'pso', 'PSO017G2787' => 'pso', 'PSO017G4466' => 'pso', 'PSO017G5118' => 'pso', 'PSO017G5420' => 'pso', 'PSO063G3678' => 'pso', 'PSO210G0546' => 'pso', 'PSO317G0001' => 'pso', 'PSO357G0512' => 'pso', 'PSO478G2682' => 'pso', 'PSO647G0001' => 'pso', 'PSO675G0001' => 'pso', 'PSO675G2699' => 'pso', 'PSO675G2849' => 'pso', 'PSO675G4991' => 'pso', 'PSO689G0001' => 'pso', 'QL06p000916' => 'qlo', 'QL06p000921' => 'qlo', 'QL06p001398' => 'qlo', 'QL06p001407' => 'qlo', 'QL06p002031' => 'qlo', 'RcHm_v2.0_Chr4g0387791' => 'rch', 'RcHm_v2.0_Chr4g0387801' => 'rch', 'RcHm_v2.0_Chr6g0286501' => 'rch', 'RcHm_v2.0_Chr6g0286511' => 'rch', 'RcHm_v2.0_Chr6g0286521' => 'rch', 'RcHm_v2.0_Chr6g0286531' => 'rch', 'RcHm_v2.0_Chr7g0189141' => 'rch', 'Rhsim02G0028700' => 'rsi', 'Rhsim02G0028800' => 'rsi', 'Rhsim02G0028900' => 'rsi', 'Rhsim02G0029000' => 'rsi', 'Rhsim02G0029100' => 'rsi', 'Rhsim02G0029200' => 'rsi', 'Rhsim02G0029300' => 'rsi', 'Rhsim02G0029400' => 'rsi', 'Rhsim02G0029500' => 'rsi', 'Rhsim02G0029600' => 'rsi', 'RhsimUnG0024000' => 'rsi', 'RhsimUnG0024100' => 'rsi', 'RhsimUnG0024200' => 'rsi', 'RhsimUnG0024300' => 'rsi', 'RhsimUnG0024400' => 'rsi', 'RhsimUnG0024500' => 'rsi', 'RhsimUnG0024700' => 'rsi', 'RhsimUnG0024800' => 'rsi', 'RhsimUnG0024900' => 'rsi', 'RhsimUnG0025100' => 'rsi', 'Sabra08G0120200' => 'sbr', 'Sabra08G0120300' => 'sbr', 'Sabra08G0120500' => 'sbr', 'Sabra08G0120600' => 'sbr', 'Sabra10G0158900' => 'sbr', 'SalBow2G3492' => 'sbo', 'Sc13g0004760' => 'sci', 'Sc13g0004770' => 'sci', 'Sed0003417' => 'sed', 'Sed0019750' => 'sed', 'SEGI_03419' => 'sgi', 'SEGI_05907' => 'sgi', 'SEGI_10682' => 'sgi', 'SEGI_13528' => 'sgi', 'SEGI_16081' => 'sgi', 'SEGI_19370' => 'sgi', 'SEGI_21015' => 'sgi', 'SEGI_21944' => 'sgi', 'SEGI_32906' => 'sgi', 'SEGI_33093' => 'sgi', 'SEGI_36110' => 'sgi', 'SEGI_40397' => 'sgi', 'SGA_v2.0_scaffold191G40426' => 'sas', 'SGA_v2.0_scaffold353G49717' => 'sas', 'SGA_v2.0_scaffold50G18550' => 'sas', 'SMO119G0173' => 'smo', 'SMO172G0002' => 'smo', 'Solyc09g082690.3' => 'sly', 'Solyc09g082700.2' => 'sly', 'Sopen09g031550' => 'spe', 'Sopen09g031560' => 'spe', 'Sp3g20540' => 'spa', 'Sp7g07580' => 'spa', 'TAR134G0002' => 'tar', 'TAR236G0001' => 'tar', 'TAR365G0892' => 'tar', 'TAR636G0166' => 'tar', 'TAR636G0646' => 'tar', 'TAR636G0869' => 'tar', 'TAR636G1317' => 'tar', 'TAR636G1744' => 'tar', 'TAR636G3358' => 'tar', 'TAR636G3436' => 'tar', 'THA.LOC104803047' => 'tha', 'Thecc.04G238900' => 'tca', 'Thhalv10021557m.g' => 'esa', 'Thhalv10026318m.g' => 'esa', 'Thhalv10026335m.g' => 'esa', 'TPR.G17433' => 'tpr', 'TPR.G18915' => 'tpr', 'TPR.G26125' => 'tpr', 'TWI09G0677' => 'twi', 'TWI73G0287' => 'twi', 'unitig_748.g8326' => 'ugi', 'vmacro15370' => 'vma', 'vmacro15371' => 'vma', 'vmacro15372' => 'vma', 'vmacro15373' => 'vma', 'vmacro15374' => 'vma', 'VMungo0720G2826' => 'vmu', 'Zm00001eb116960' => 'zma', 'Zm00001eb301260' => 'zma', 'Zm00001eb301270' => 'zma' ), 'gf_id' => 'HOM05D001460', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001460' ), 'data_identifier' => 'HOM05D001460', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001460', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '433', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p22980' => 'bna', 'A01p32340' => 'bna', 'A03p42970' => 'bna', 'A05p25880' => 'bna', 'Aa31LG8G9320' => 'aar', 'Aa31LG8G9330' => 'aar', 'Aa31LG8G9340' => 'aar', 'Aa31sc221G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1034' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1528' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.829' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2222' => 'aag', 'Ah.12g058830' => 'amhyb', 'Ah.12g058840' => 'amhyb', 'AL3G37160' => 'aly', 'AL7G41310' => 'aly', 'Aqoxy5G00395' => 'aox', 'Aqoxy5G00396' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0C8NZA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5185HY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JZ1PRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MD3LS0' => 'arhy', 'AT3G22840' => 'ath', 'AT4G14690' => 'ath', 'ATR0665G054' => 'atr', 'Atru.chr4.2344' => 'acertr', 'Atru.chr4.2346' => 'acertr', 'Atru.chr4.2347' => 'acertr', 'Atru.chr4.2348' => 'acertr', 'Atru.chr4.2355' => 'acertr', 'Atru.chr4.2356' => 'acertr', 'Atru.chr4.2358' => 'acertr', 'Atru.chr4.2359' => 'acertr', 'Atru.chr4.2360' => 'acertr', 'Atru.chr4.2361' => 'acertr', 'AUR62030476' => 'cqu', 'AUR62030478' => 'cqu', 'AUR62030819' => 'cqu', 'AUR62030820' => 'cqu', 'BcaB03g14648' => 'bca', 'BcaB04g20492' => 'bca', 'BcaB06g26399' => 'bca', 'BcaC01g03416' => 'bca', 'BcaC01g03419' => 'bca', 'BcaC01g03421' => 'bca', 'BcaC01g03424' => 'bca', 'BcaC05g28012' => 'bca', 'BcaC09g49212' => 'bca', 'BcaC09g50140' => 'bca', 'BcaNung00346' => 'bca', 'BolC1t02785H' => 'bol', 'BolC1t04095H' => 'bol', 'BolC3t17545H' => 'bol', 'BolC5t32769H' => 'bol', 'BraA01t02211Z' => 'bra', 'BraA01t03359Z' => 'bra', 'BraA03t13441Z' => 'bra', 'BraA05t21476Z' => 'bra', 'C01p28420' => 'bna', 'C01p41350' => 'bna', 'C03p52750' => 'bna', 'C03p52780' => 'bna', 'C05p40270' => 'bna', 'CAN.G1437.9' => 'can', 'CANSAT78G0035' => 'cansat', 'CANSAT78G1036' => 'cansat', 'CANSAT78G2272' => 'cansat', 'CANSAT78G2478' => 'cansat', 'CARHR098700' => 'chi', 'CARHR221120' => 'chi', 'CARHR221150' => 'chi', 'Carub.0003s2297' => 'cru', 'Carub.0007s2749' => 'cru', 'Carub.0007s2750' => 'cru', 'Carub.0007s2751' => 'cru', 'Ca_10849_v3' => 'car', 'Cc03_g04300' => 'ccan', 'CDE02G3648' => 'cde', 'CDE05G0060' => 'cde', 'CDE05G0692' => 'cde', 'CDE05G2285' => 'cde', 'CDE05G2884' => 'cde', 'CDE05G3072' => 'cde', 'Cfa008439' => 'cfa', 'Cfa008441' => 'cfa', 'Cfa008443' => 'cfa', 'Cfa008448' => 'cfa', 'Ciclev10005974m.g' => 'ccl', 'Ciclev10006006m.g' => 'ccl', 'Ciclev10006775m.g' => 'ccl', 'CiPaw.02G120400' => 'cil', 'CiPaw.02G120500' => 'cil', 'CiPaw.02G120600' => 'cil', 'ClCG05G004850' => 'cla', 'COL.COLO4_21566' => 'col', 'Cpa.g.sc44.124' => 'cpa', 'Cre07.g320400' => 'cre', 'Cre07.g320450' => 'cre', 'Cre08.g384650' => 'cre', 'Cre09.g393173' => 'cre', 'Cre09.g394325' => 'cre', 'Cre14.g626750' => 'cre', 'Cre16.g679250' => 'cre', 'CsaV3_3G012890' => 'csa', 'CSS0010865' => 'camsi', 'CSS0044338' => 'camsi', 'DCAR_002366' => 'dca', 'DCAR_030687' => 'dca', 'DCAR_030688' => 'dca', 'Dinv14047' => 'din', 'Dinv14048' => 'din', 'Duzib151G0105' => 'dzi', 'Duzib151G0114' => 'dzi', 'Duzib212G1029' => 'dzi', 'ECA232G3536' => 'eca', 'ECA240G0786' => 'eca', 'ECA240G1802' => 'eca', 'ECA240G3760' => 'eca', 'ECA240G3920' => 'eca', 'EL10Ac5g12536' => 'bvu', 'EL10Ac5g12537' => 'bvu', 'EL10Ac5g12538' => 'bvu', 'Eucgr.B01004' => 'egr', 'Eucgr.B01006' => 'egr', 'Eucgr.B01007' => 'egr', 'Eucgr.B01008' => 'egr', 'Eucgr.B01895' => 'egr', 'Eucgr.B01896' => 'egr', 'FAN04G1456' => 'fan', 'FAN08G1769' => 'fan', 'FAN08G2160' => 'fan', 'FAN13G2403' => 'fan', 'FAN13G3303' => 'fan', 'FAN15G2435' => 'fan', 'FAN17G0672' => 'fan', 'FAN17G2441' => 'fan', 'FAN18G1024' => 'fan', 'FAN22G1458' => 'fan', 'FAN24G0037' => 'fan', 'FAN24G0429' => 'fan', 'FAN24G2387' => 'fan', 'FAN27G2746' => 'fan', 'FvH4_2g20400' => 'fve', 'FvH4_2g20420' => 'fve', 'FvH4_2g20430' => 'fve', 'FvH4_4g01270' => 'fve', 'FvH4_4g01290' => 'fve', 'FvH4_4g01300' => 'fve', 'FvH4_4g01310' => 'fve', 'FvH4_4g01330' => 'fve', 'FvH4_5g09070' => 'fve', 'Glyma.10G243800' => 'gma', 'Glyma.20G150600' => 'gma', 'Gohir.A09G219200' => 'ghi', 'Gohir.A09G219300' => 'ghi', 'Gohir.D09G221400' => 'ghi', 'Gohir.D09G221500' => 'ghi', 'Gorai.006G242600' => 'gra', 'Gorai.006G242700' => 'gra', 'GSVIVG01018044001' => 'vvi', 'HanXRQChr03g0083821' => 'han', 'HanXRQChr03g0083841' => 'han', 'HanXRQChr03g0083881' => 'han', 'HanXRQChr03g0083901' => 'han', 'HanXRQChr03g0083921' => 'han', 'HanXRQChr03g0085331' => 'han', 'HanXRQChr03g0085361' => 'han', 'HanXRQChr03g0085411' => 'han', 'HanXRQChr03g0085421' => 'han', 'HanXRQChr03g0085431' => 'han', 'HanXRQChr08g0221991' => 'han', 'HanXRQChr11g0336061' => 'han', 'HanXRQChr11g0336411' => 'han', 'Haze_11234' => 'cav', 'Hma1.2p1_0549F.1_g177010' => 'hma', 'Hma1.2p1_0602F.1_g187630' => 'hma', 'Hund14876' => 'sun', 'Hund14879' => 'sun', 'Lalb_Chr06g0160741' => 'lal', 'Lalb_Chr21g0304781' => 'lal', 'Lj3A726G19' => 'lonja', 'Lj3A726T23' => 'lonja', 'Lj3A726T24' => 'lonja', 'Lj3A726T25' => 'lonja', 'Lj3A727T17' => 'lonja', 'Lj3C726T0' => 'lonja', 'Lj3C726T2' => 'lonja', 'Lj3P725T35' => 'lonja', 'Lj3P727T10' => 'lonja', 'Lj3P727T12' => 'lonja', 'Lj3P727T14' => 'lonja', 'Lj5g0023109' => 'lja', 'Lj6P646T44' => 'lonja', 'Lsat_1_v5_gn_6_75760' => 'lsa', 'Lsat_1_v5_gn_6_75800' => 'lsa', 'Lsat_1_v5_gn_6_75900' => 'lsa', 'Lsat_1_v5_gn_6_76240' => 'lsa', 'Lsat_1_v5_gn_6_76441' => 'lsa', 'Lsat_1_v5_gn_6_76700' => 'lsa', 'Lsat_1_v5_gn_6_76760' => 'lsa', 'Manes.15G033100' => 'mes', 'Mapoly0004s0074' => 'mpo', 'Mapoly0004s0075' => 'mpo', 'Mapoly0004s0163' => 'mpo', 'Mapoly0004s0164' => 'mpo', 'Mapoly0021s0018' => 'mpo', 'Mapoly0041s0136' => 'mpo', 'Mapoly0041s0137' => 'mpo', 'Mapoly0041s0138' => 'mpo', 'Mapoly0041s0139' => 'mpo', 'Mapoly0041s0141' => 'mpo', 'Mapoly0041s0142' => 'mpo', 'Mapoly0041s0143' => 'mpo', 'Mapoly0041s0144' => 'mpo', 'Mapoly0041s0145' => 'mpo', 'Mapoly0047s0106' => 'mpo', 'Mapoly0047s0108' => 'mpo', 'Mapoly0050s0051' => 'mpo', 'Mapoly0050s0052' => 'mpo', 'Mapoly0050s0053' => 'mpo', 'Mapoly0058s0013' => 'mpo', 'Mapoly0091s0078' => 'mpo', 'Mapoly0091s0079' => 'mpo', 'Mapoly0091s0080' => 'mpo', 'Mapoly0091s0081' => 'mpo', 'Mapoly0278s0004' => 'mpo', 'Mapoly0278s0005' => 'mpo', 'Mapoly0278s0006' => 'mpo', 'MBI11_g30648_MAGBIO' => 'mbi', 'MCO03G194' => 'mco', 'MCO03G590' => 'mco', 'MCO07G312' => 'mco', 'MCO10G318' => 'mco', 'MCO12G244' => 'mco', 'MCO13G148' => 'mco', 'MCO13G194' => 'mco', 'MCO16G238' => 'mco', 'MD06G1134100' => 'mdo', 'MD13G1200100' => 'mdo', 'MD13G1200300' => 'mdo', 'MD13G1200600' => 'mdo', 'MD14G1150400' => 'mdo', 'MD16G1200000' => 'mdo', 'Medtr1g102570' => 'mtr', 'Medtr1g102780' => 'mtr', 'Medtr1g102800' => 'mtr', 'Medtr1g102810' => 'mtr', 'Medtr1g102830' => 'mtr', 'MELO3C006499.2' => 'cme', 'Migut.G00385' => 'egut', 'MSTRG.4063' => 'ama', 'Nitab4.5_0000090g0260' => 'nta', 'Nitab4.5_0000977g0030' => 'nta', 'Nitab4.5_0002541g0040' => 'nta', 'Nitab4.5_0007068g0040' => 'nta', 'Nn005s41408' => 'nnu', 'Nn005s41410' => 'nnu', 'Oeu010310.1' => 'oeu', 'Oeu010311.1' => 'oeu', 'Oeu043472.1' => 'oeu', 'Os01g0246400' => 'osa', 'Os04g0267950' => 'osa', 'Os07g0178700' => 'osa', 'Os07g0178800' => 'osa', 'Peaxi162Scf00316g00046' => 'pax', 'Peaxi162Scf00316g00049' => 'pax', 'Peaxi162Scf00316g00059' => 'pax', 'Peaxi162Scf00316g00328' => 'pax', 'Peaxi162Scf00316g00329' => 'pax', 'Peaxi162Scf00316g00411' => 'pax', 'Peaxi162Scf00316g00521' => 'pax', 'Peaxi162Scf00492g00068' => 'pax', 'Peaxi162Scf35631g00002' => 'pax', 'PGR142G3720' => 'pgr', 'PGSC0003DMG400006442' => 'stu', 'Phvul.007G062000' => 'pvu', 'Potri.008G157750' => 'ptr', 'Potri.008G157900' => 'ptr', 'Potri.008G158000' => 'ptr', 'Potri.008G158200' => 'ptr', 'Pp3c11_7280' => 'ppa', 'Pp3c11_7980' => 'ppa', 'Pp3c12_19450' => 'ppa', 'Pp3c14_1480' => 'ppa', 'Pp3c14_1501' => 'ppa', 'Pp3c16_4900' => 'ppa', 'Pp3c16_5010' => 'ppa', 'Pp3c16_5060' => 'ppa', 'Pp3c19_18250' => 'ppa', 'Pp3c23_8530' => 'ppa', 'Pp3c23_8550' => 'ppa', 'Pp3c24_9670' => 'ppa', 'Pp3c2_21390' => 'ppa', 'Pp3c2_31380' => 'ppa', 'Pp3c3_16620' => 'ppa', 'Pp3c3_8090' => 'ppa', 'Pp3c3_8110' => 'ppa', 'Pp3c3_8130' => 'ppa', 'Pp3c3_8150' => 'ppa', 'Pp3c4_14320' => 'ppa', 'Pp3c6_2560' => 'ppa', 'Pp3c9_16700' => 'ppa', 'PRCOL_00000234' => 'pco', 'PRCOL_00000235' => 'pco', 'PRCOL_00000777' => 'pco', 'PRCOL_00002344' => 'pco', 'PRCOL_00002372' => 'pco', 'PRCOL_00006120' => 'pco', 'Prupe.1G021400' => 'ppe', 'Prupe.1G021500' => 'ppe', 'Prupe.1G021600' => 'ppe', 'Prupe.1G021700' => 'ppe', 'Prupe.1G021800' => 'ppe', 'Prupe.5G145100' => 'ppe', 'Psat6g204040' => 'psa', 'Psat6g204800' => 'psa', 'Psat6g204920' => 'psa', 'Psat6g204960' => 'psa', 'Psat6g205080' => 'psa', 'PSO017G0271' => 'pso', 'PSO017G1276' => 'pso', 'PSO017G1429' => 'pso', 'PSO017G1861' => 'pso', 'PSO017G2787' => 'pso', 'PSO017G4466' => 'pso', 'PSO017G5118' => 'pso', 'PSO017G5420' => 'pso', 'PSO063G3678' => 'pso', 'PSO210G0546' => 'pso', 'PSO317G0001' => 'pso', 'PSO357G0512' => 'pso', 'PSO478G2682' => 'pso', 'PSO647G0001' => 'pso', 'PSO675G0001' => 'pso', 'PSO675G2699' => 'pso', 'PSO675G2849' => 'pso', 'PSO675G4991' => 'pso', 'PSO689G0001' => 'pso', 'QL06p000916' => 'qlo', 'QL06p000921' => 'qlo', 'QL06p001398' => 'qlo', 'QL06p001407' => 'qlo', 'QL06p002031' => 'qlo', 'RcHm_v2.0_Chr4g0387791' => 'rch', 'RcHm_v2.0_Chr4g0387801' => 'rch', 'RcHm_v2.0_Chr6g0286501' => 'rch', 'RcHm_v2.0_Chr6g0286511' => 'rch', 'RcHm_v2.0_Chr6g0286521' => 'rch', 'RcHm_v2.0_Chr6g0286531' => 'rch', 'RcHm_v2.0_Chr7g0189141' => 'rch', 'Rhsim02G0028700' => 'rsi', 'Rhsim02G0028800' => 'rsi', 'Rhsim02G0028900' => 'rsi', 'Rhsim02G0029000' => 'rsi', 'Rhsim02G0029100' => 'rsi', 'Rhsim02G0029200' => 'rsi', 'Rhsim02G0029300' => 'rsi', 'Rhsim02G0029400' => 'rsi', 'Rhsim02G0029500' => 'rsi', 'Rhsim02G0029600' => 'rsi', 'RhsimUnG0024000' => 'rsi', 'RhsimUnG0024100' => 'rsi', 'RhsimUnG0024200' => 'rsi', 'RhsimUnG0024300' => 'rsi', 'RhsimUnG0024400' => 'rsi', 'RhsimUnG0024500' => 'rsi', 'RhsimUnG0024700' => 'rsi', 'RhsimUnG0024800' => 'rsi', 'RhsimUnG0024900' => 'rsi', 'RhsimUnG0025100' => 'rsi', 'Sabra08G0120200' => 'sbr', 'Sabra08G0120300' => 'sbr', 'Sabra08G0120500' => 'sbr', 'Sabra08G0120600' => 'sbr', 'Sabra10G0158900' => 'sbr', 'SalBow2G3492' => 'sbo', 'Sc13g0004760' => 'sci', 'Sc13g0004770' => 'sci', 'Sed0003417' => 'sed', 'Sed0019750' => 'sed', 'SEGI_03419' => 'sgi', 'SEGI_05907' => 'sgi', 'SEGI_10682' => 'sgi', 'SEGI_13528' => 'sgi', 'SEGI_16081' => 'sgi', 'SEGI_19370' => 'sgi', 'SEGI_21015' => 'sgi', 'SEGI_21944' => 'sgi', 'SEGI_32906' => 'sgi', 'SEGI_33093' => 'sgi', 'SEGI_36110' => 'sgi', 'SEGI_40397' => 'sgi', 'SGA_v2.0_scaffold191G40426' => 'sas', 'SGA_v2.0_scaffold353G49717' => 'sas', 'SGA_v2.0_scaffold50G18550' => 'sas', 'SMO119G0173' => 'smo', 'SMO172G0002' => 'smo', 'Solyc09g082690.3' => 'sly', 'Solyc09g082700.2' => 'sly', 'Sopen09g031550' => 'spe', 'Sopen09g031560' => 'spe', 'Sp3g20540' => 'spa', 'Sp7g07580' => 'spa', 'TAR134G0002' => 'tar', 'TAR236G0001' => 'tar', 'TAR365G0892' => 'tar', 'TAR636G0166' => 'tar', 'TAR636G0646' => 'tar', 'TAR636G0869' => 'tar', 'TAR636G1317' => 'tar', 'TAR636G1744' => 'tar', 'TAR636G3358' => 'tar', 'TAR636G3436' => 'tar', 'THA.LOC104803047' => 'tha', 'Thecc.04G238900' => 'tca', 'Thhalv10021557m.g' => 'esa', 'Thhalv10026318m.g' => 'esa', 'Thhalv10026335m.g' => 'esa', 'TPR.G17433' => 'tpr', 'TPR.G18915' => 'tpr', 'TPR.G26125' => 'tpr', 'TWI09G0677' => 'twi', 'TWI73G0287' => 'twi', 'unitig_748.g8326' => 'ugi', 'vmacro15370' => 'vma', 'vmacro15371' => 'vma', 'vmacro15372' => 'vma', 'vmacro15373' => 'vma', 'vmacro15374' => 'vma', 'VMungo0720G2826' => 'vmu', 'Zm00001eb116960' => 'zma', 'Zm00001eb301260' => 'zma', 'Zm00001eb301270' => 'zma' ) $gf_id = 'HOM05D001460' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001460' ) $data_identifier = 'HOM05D001460' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 4, 'aag' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 2, 'aox' => (int) 2, 'arhy' => (int) 4, 'ath' => (int) 2, 'atr' => (int) 1, 'acertr' => (int) 10, 'cqu' => (int) 4, 'bca' => (int) 11, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 1, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 1, 'ccan' => (int) 1, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 1, 'col' => (int) 1, 'cpa' => (int) 1, 'cre' => (int) 7, 'csa' => (int) 1, 'camsi' => (int) 2, 'dca' => (int) 3, 'din' => (int) 2, 'dzi' => (int) 3, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 14, 'fve' => (int) 9, 'gma' => (int) 2, 'ghi' => (int) 4, 'gra' => (int) 2, 'vvi' => (int) 1, 'han' => (int) 13, 'cav' => (int) 1, 'hma' => (int) 2, 'sun' => (int) 2, 'lal' => (int) 2, 'lonja' => (int) 12, 'lja' => (int) 1, 'lsa' => (int) 7, 'mes' => (int) 1, 'mpo' => (int) 27, 'mbi' => (int) 1, 'mco' => (int) 8, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 1, 'egut' => (int) 1, 'ama' => (int) 1, 'nta' => (int) 4, 'nnu' => (int) 2, 'oeu' => (int) 3, 'osa' => (int) 4, 'pax' => (int) 9, 'pgr' => (int) 1, 'stu' => (int) 1, 'pvu' => (int) 1, 'ptr' => (int) 4, 'ppa' => (int) 22, 'pco' => (int) 6, 'ppe' => (int) 6, 'psa' => (int) 5, 'pso' => (int) 19, 'qlo' => (int) 5, 'rch' => (int) 7, 'rsi' => (int) 20, 'sbr' => (int) 5, 'sbo' => (int) 1, 'sci' => (int) 2, 'sed' => (int) 2, 'sgi' => (int) 12, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 2, 'tar' => (int) 10, 'tha' => (int) 1, 'tca' => (int) 1, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 2, 'ugi' => (int) 1, 'vma' => (int) 5, 'vmu' => (int) 1, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb301270' $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' => 'HOM05D001460', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '433', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p22980' => 'bna', 'A01p32340' => 'bna', 'A03p42970' => 'bna', 'A05p25880' => 'bna', 'Aa31LG8G9320' => 'aar', 'Aa31LG8G9330' => 'aar', 'Aa31LG8G9340' => 'aar', 'Aa31sc221G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1034' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1528' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.829' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2222' => 'aag', 'Ah.12g058830' => 'amhyb', 'Ah.12g058840' => 'amhyb', 'AL3G37160' => 'aly', 'AL7G41310' => 'aly', 'Aqoxy5G00395' => 'aox', 'Aqoxy5G00396' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0C8NZA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5185HY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JZ1PRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MD3LS0' => 'arhy', 'AT3G22840' => 'ath', 'AT4G14690' => 'ath', 'ATR0665G054' => 'atr', 'Atru.chr4.2344' => 'acertr', 'Atru.chr4.2346' => 'acertr', 'Atru.chr4.2347' => 'acertr', 'Atru.chr4.2348' => 'acertr', 'Atru.chr4.2355' => 'acertr', 'Atru.chr4.2356' => 'acertr', 'Atru.chr4.2358' => 'acertr', 'Atru.chr4.2359' => 'acertr', 'Atru.chr4.2360' => 'acertr', 'Atru.chr4.2361' => 'acertr', 'AUR62030476' => 'cqu', 'AUR62030478' => 'cqu', 'AUR62030819' => 'cqu', 'AUR62030820' => 'cqu', 'BcaB03g14648' => 'bca', 'BcaB04g20492' => 'bca', 'BcaB06g26399' => 'bca', 'BcaC01g03416' => 'bca', 'BcaC01g03419' => 'bca', 'BcaC01g03421' => 'bca', 'BcaC01g03424' => 'bca', 'BcaC05g28012' => 'bca', 'BcaC09g49212' => 'bca', 'BcaC09g50140' => 'bca', 'BcaNung00346' => 'bca', 'BolC1t02785H' => 'bol', 'BolC1t04095H' => 'bol', 'BolC3t17545H' => 'bol', 'BolC5t32769H' => 'bol', 'BraA01t02211Z' => 'bra', 'BraA01t03359Z' => 'bra', 'BraA03t13441Z' => 'bra', 'BraA05t21476Z' => 'bra', 'C01p28420' => 'bna', 'C01p41350' => 'bna', 'C03p52750' => 'bna', 'C03p52780' => 'bna', 'C05p40270' => 'bna', 'CAN.G1437.9' => 'can', 'CANSAT78G0035' => 'cansat', 'CANSAT78G1036' => 'cansat', 'CANSAT78G2272' => 'cansat', 'CANSAT78G2478' => 'cansat', 'CARHR098700' => 'chi', 'CARHR221120' => 'chi', 'CARHR221150' => 'chi', 'Carub.0003s2297' => 'cru', 'Carub.0007s2749' => 'cru', 'Carub.0007s2750' => 'cru', 'Carub.0007s2751' => 'cru', 'Ca_10849_v3' => 'car', 'Cc03_g04300' => 'ccan', 'CDE02G3648' => 'cde', 'CDE05G0060' => 'cde', 'CDE05G0692' => 'cde', 'CDE05G2285' => 'cde', 'CDE05G2884' => 'cde', 'CDE05G3072' => 'cde', 'Cfa008439' => 'cfa', 'Cfa008441' => 'cfa', 'Cfa008443' => 'cfa', 'Cfa008448' => 'cfa', 'Ciclev10005974m.g' => 'ccl', 'Ciclev10006006m.g' => 'ccl', 'Ciclev10006775m.g' => 'ccl', 'CiPaw.02G120400' => 'cil', 'CiPaw.02G120500' => 'cil', 'CiPaw.02G120600' => 'cil', 'ClCG05G004850' => 'cla', 'COL.COLO4_21566' => 'col', 'Cpa.g.sc44.124' => 'cpa', 'Cre07.g320400' => 'cre', 'Cre07.g320450' => 'cre', 'Cre08.g384650' => 'cre', 'Cre09.g393173' => 'cre', 'Cre09.g394325' => 'cre', 'Cre14.g626750' => 'cre', 'Cre16.g679250' => 'cre', 'CsaV3_3G012890' => 'csa', 'CSS0010865' => 'camsi', 'CSS0044338' => 'camsi', 'DCAR_002366' => 'dca', 'DCAR_030687' => 'dca', 'DCAR_030688' => 'dca', 'Dinv14047' => 'din', 'Dinv14048' => 'din', 'Duzib151G0105' => 'dzi', 'Duzib151G0114' => 'dzi', 'Duzib212G1029' => 'dzi', 'ECA232G3536' => 'eca', 'ECA240G0786' => 'eca', 'ECA240G1802' => 'eca', 'ECA240G3760' => 'eca', 'ECA240G3920' => 'eca', 'EL10Ac5g12536' => 'bvu', 'EL10Ac5g12537' => 'bvu', 'EL10Ac5g12538' => 'bvu', 'Eucgr.B01004' => 'egr', 'Eucgr.B01006' => 'egr', 'Eucgr.B01007' => 'egr', 'Eucgr.B01008' => 'egr', 'Eucgr.B01895' => 'egr', 'Eucgr.B01896' => 'egr', 'FAN04G1456' => 'fan', 'FAN08G1769' => 'fan', 'FAN08G2160' => 'fan', 'FAN13G2403' => 'fan', 'FAN13G3303' => 'fan', 'FAN15G2435' => 'fan', 'FAN17G0672' => 'fan', 'FAN17G2441' => 'fan', 'FAN18G1024' => 'fan', 'FAN22G1458' => 'fan', 'FAN24G0037' => 'fan', 'FAN24G0429' => 'fan', 'FAN24G2387' => 'fan', 'FAN27G2746' => 'fan', 'FvH4_2g20400' => 'fve', 'FvH4_2g20420' => 'fve', 'FvH4_2g20430' => 'fve', 'FvH4_4g01270' => 'fve', 'FvH4_4g01290' => 'fve', 'FvH4_4g01300' => 'fve', 'FvH4_4g01310' => 'fve', 'FvH4_4g01330' => 'fve', 'FvH4_5g09070' => 'fve', 'Glyma.10G243800' => 'gma', 'Glyma.20G150600' => 'gma', 'Gohir.A09G219200' => 'ghi', 'Gohir.A09G219300' => 'ghi', 'Gohir.D09G221400' => 'ghi', 'Gohir.D09G221500' => 'ghi', 'Gorai.006G242600' => 'gra', 'Gorai.006G242700' => 'gra', 'GSVIVG01018044001' => 'vvi', 'HanXRQChr03g0083821' => 'han', 'HanXRQChr03g0083841' => 'han', 'HanXRQChr03g0083881' => 'han', 'HanXRQChr03g0083901' => 'han', 'HanXRQChr03g0083921' => 'han', 'HanXRQChr03g0085331' => 'han', 'HanXRQChr03g0085361' => 'han', 'HanXRQChr03g0085411' => 'han', 'HanXRQChr03g0085421' => 'han', 'HanXRQChr03g0085431' => 'han', 'HanXRQChr08g0221991' => 'han', 'HanXRQChr11g0336061' => 'han', 'HanXRQChr11g0336411' => 'han', 'Haze_11234' => 'cav', 'Hma1.2p1_0549F.1_g177010' => 'hma', 'Hma1.2p1_0602F.1_g187630' => 'hma', 'Hund14876' => 'sun', 'Hund14879' => 'sun', 'Lalb_Chr06g0160741' => 'lal', 'Lalb_Chr21g0304781' => 'lal', 'Lj3A726G19' => 'lonja', 'Lj3A726T23' => 'lonja', 'Lj3A726T24' => 'lonja', 'Lj3A726T25' => 'lonja', 'Lj3A727T17' => 'lonja', 'Lj3C726T0' => 'lonja', 'Lj3C726T2' => 'lonja', 'Lj3P725T35' => 'lonja', 'Lj3P727T10' => 'lonja', 'Lj3P727T12' => 'lonja', 'Lj3P727T14' => 'lonja', 'Lj5g0023109' => 'lja', 'Lj6P646T44' => 'lonja', 'Lsat_1_v5_gn_6_75760' => 'lsa', 'Lsat_1_v5_gn_6_75800' => 'lsa', 'Lsat_1_v5_gn_6_75900' => 'lsa', 'Lsat_1_v5_gn_6_76240' => 'lsa', 'Lsat_1_v5_gn_6_76441' => 'lsa', 'Lsat_1_v5_gn_6_76700' => 'lsa', 'Lsat_1_v5_gn_6_76760' => 'lsa', 'Manes.15G033100' => 'mes', 'Mapoly0004s0074' => 'mpo', 'Mapoly0004s0075' => 'mpo', 'Mapoly0004s0163' => 'mpo', 'Mapoly0004s0164' => 'mpo', 'Mapoly0021s0018' => 'mpo', 'Mapoly0041s0136' => 'mpo', 'Mapoly0041s0137' => 'mpo', 'Mapoly0041s0138' => 'mpo', 'Mapoly0041s0139' => 'mpo', 'Mapoly0041s0141' => 'mpo', 'Mapoly0041s0142' => 'mpo', 'Mapoly0041s0143' => 'mpo', 'Mapoly0041s0144' => 'mpo', 'Mapoly0041s0145' => 'mpo', 'Mapoly0047s0106' => 'mpo', 'Mapoly0047s0108' => 'mpo', 'Mapoly0050s0051' => 'mpo', 'Mapoly0050s0052' => 'mpo', 'Mapoly0050s0053' => 'mpo', 'Mapoly0058s0013' => 'mpo', 'Mapoly0091s0078' => 'mpo', 'Mapoly0091s0079' => 'mpo', 'Mapoly0091s0080' => 'mpo', 'Mapoly0091s0081' => 'mpo', 'Mapoly0278s0004' => 'mpo', 'Mapoly0278s0005' => 'mpo', 'Mapoly0278s0006' => 'mpo', 'MBI11_g30648_MAGBIO' => 'mbi', 'MCO03G194' => 'mco', 'MCO03G590' => 'mco', 'MCO07G312' => 'mco', 'MCO10G318' => 'mco', 'MCO12G244' => 'mco', 'MCO13G148' => 'mco', 'MCO13G194' => 'mco', 'MCO16G238' => 'mco', 'MD06G1134100' => 'mdo', 'MD13G1200100' => 'mdo', 'MD13G1200300' => 'mdo', 'MD13G1200600' => 'mdo', 'MD14G1150400' => 'mdo', 'MD16G1200000' => 'mdo', 'Medtr1g102570' => 'mtr', 'Medtr1g102780' => 'mtr', 'Medtr1g102800' => 'mtr', 'Medtr1g102810' => 'mtr', 'Medtr1g102830' => 'mtr', 'MELO3C006499.2' => 'cme', 'Migut.G00385' => 'egut', 'MSTRG.4063' => 'ama', 'Nitab4.5_0000090g0260' => 'nta', 'Nitab4.5_0000977g0030' => 'nta', 'Nitab4.5_0002541g0040' => 'nta', 'Nitab4.5_0007068g0040' => 'nta', 'Nn005s41408' => 'nnu', 'Nn005s41410' => 'nnu', 'Oeu010310.1' => 'oeu', 'Oeu010311.1' => 'oeu', 'Oeu043472.1' => 'oeu', 'Os01g0246400' => 'osa', 'Os04g0267950' => 'osa', 'Os07g0178700' => 'osa', 'Os07g0178800' => 'osa', 'Peaxi162Scf00316g00046' => 'pax', 'Peaxi162Scf00316g00049' => 'pax', 'Peaxi162Scf00316g00059' => 'pax', 'Peaxi162Scf00316g00328' => 'pax', 'Peaxi162Scf00316g00329' => 'pax', 'Peaxi162Scf00316g00411' => 'pax', 'Peaxi162Scf00316g00521' => 'pax', 'Peaxi162Scf00492g00068' => 'pax', 'Peaxi162Scf35631g00002' => 'pax', 'PGR142G3720' => 'pgr', 'PGSC0003DMG400006442' => 'stu', 'Phvul.007G062000' => 'pvu', 'Potri.008G157750' => 'ptr', 'Potri.008G157900' => 'ptr', 'Potri.008G158000' => 'ptr', 'Potri.008G158200' => 'ptr', 'Pp3c11_7280' => 'ppa', 'Pp3c11_7980' => 'ppa', 'Pp3c12_19450' => 'ppa', 'Pp3c14_1480' => 'ppa', 'Pp3c14_1501' => 'ppa', 'Pp3c16_4900' => 'ppa', 'Pp3c16_5010' => 'ppa', 'Pp3c16_5060' => 'ppa', 'Pp3c19_18250' => 'ppa', 'Pp3c23_8530' => 'ppa', 'Pp3c23_8550' => 'ppa', 'Pp3c24_9670' => 'ppa', 'Pp3c2_21390' => 'ppa', 'Pp3c2_31380' => 'ppa', 'Pp3c3_16620' => 'ppa', 'Pp3c3_8090' => 'ppa', 'Pp3c3_8110' => 'ppa', 'Pp3c3_8130' => 'ppa', 'Pp3c3_8150' => 'ppa', 'Pp3c4_14320' => 'ppa', 'Pp3c6_2560' => 'ppa', 'Pp3c9_16700' => 'ppa', 'PRCOL_00000234' => 'pco', 'PRCOL_00000235' => 'pco', 'PRCOL_00000777' => 'pco', 'PRCOL_00002344' => 'pco', 'PRCOL_00002372' => 'pco', 'PRCOL_00006120' => 'pco', 'Prupe.1G021400' => 'ppe', 'Prupe.1G021500' => 'ppe', 'Prupe.1G021600' => 'ppe', 'Prupe.1G021700' => 'ppe', 'Prupe.1G021800' => 'ppe', 'Prupe.5G145100' => 'ppe', 'Psat6g204040' => 'psa', 'Psat6g204800' => 'psa', 'Psat6g204920' => 'psa', 'Psat6g204960' => 'psa', 'Psat6g205080' => 'psa', 'PSO017G0271' => 'pso', 'PSO017G1276' => 'pso', 'PSO017G1429' => 'pso', 'PSO017G1861' => 'pso', 'PSO017G2787' => 'pso', 'PSO017G4466' => 'pso', 'PSO017G5118' => 'pso', 'PSO017G5420' => 'pso', 'PSO063G3678' => 'pso', 'PSO210G0546' => 'pso', 'PSO317G0001' => 'pso', 'PSO357G0512' => 'pso', 'PSO478G2682' => 'pso', 'PSO647G0001' => 'pso', 'PSO675G0001' => 'pso', 'PSO675G2699' => 'pso', 'PSO675G2849' => 'pso', 'PSO675G4991' => 'pso', 'PSO689G0001' => 'pso', 'QL06p000916' => 'qlo', 'QL06p000921' => 'qlo', 'QL06p001398' => 'qlo', 'QL06p001407' => 'qlo', 'QL06p002031' => 'qlo', 'RcHm_v2.0_Chr4g0387791' => 'rch', 'RcHm_v2.0_Chr4g0387801' => 'rch', 'RcHm_v2.0_Chr6g0286501' => 'rch', 'RcHm_v2.0_Chr6g0286511' => 'rch', 'RcHm_v2.0_Chr6g0286521' => 'rch', 'RcHm_v2.0_Chr6g0286531' => 'rch', 'RcHm_v2.0_Chr7g0189141' => 'rch', 'Rhsim02G0028700' => 'rsi', 'Rhsim02G0028800' => 'rsi', 'Rhsim02G0028900' => 'rsi', 'Rhsim02G0029000' => 'rsi', 'Rhsim02G0029100' => 'rsi', 'Rhsim02G0029200' => 'rsi', 'Rhsim02G0029300' => 'rsi', 'Rhsim02G0029400' => 'rsi', 'Rhsim02G0029500' => 'rsi', 'Rhsim02G0029600' => 'rsi', 'RhsimUnG0024000' => 'rsi', 'RhsimUnG0024100' => 'rsi', 'RhsimUnG0024200' => 'rsi', 'RhsimUnG0024300' => 'rsi', 'RhsimUnG0024400' => 'rsi', 'RhsimUnG0024500' => 'rsi', 'RhsimUnG0024700' => 'rsi', 'RhsimUnG0024800' => 'rsi', 'RhsimUnG0024900' => 'rsi', 'RhsimUnG0025100' => 'rsi', 'Sabra08G0120200' => 'sbr', 'Sabra08G0120300' => 'sbr', 'Sabra08G0120500' => 'sbr', 'Sabra08G0120600' => 'sbr', 'Sabra10G0158900' => 'sbr', 'SalBow2G3492' => 'sbo', 'Sc13g0004760' => 'sci', 'Sc13g0004770' => 'sci', 'Sed0003417' => 'sed', 'Sed0019750' => 'sed', 'SEGI_03419' => 'sgi', 'SEGI_05907' => 'sgi', 'SEGI_10682' => 'sgi', 'SEGI_13528' => 'sgi', 'SEGI_16081' => 'sgi', 'SEGI_19370' => 'sgi', 'SEGI_21015' => 'sgi', 'SEGI_21944' => 'sgi', 'SEGI_32906' => 'sgi', 'SEGI_33093' => 'sgi', 'SEGI_36110' => 'sgi', 'SEGI_40397' => 'sgi', 'SGA_v2.0_scaffold191G40426' => 'sas', 'SGA_v2.0_scaffold353G49717' => 'sas', 'SGA_v2.0_scaffold50G18550' => 'sas', 'SMO119G0173' => 'smo', 'SMO172G0002' => 'smo', 'Solyc09g082690.3' => 'sly', 'Solyc09g082700.2' => 'sly', 'Sopen09g031550' => 'spe', 'Sopen09g031560' => 'spe', 'Sp3g20540' => 'spa', 'Sp7g07580' => 'spa', 'TAR134G0002' => 'tar', 'TAR236G0001' => 'tar', 'TAR365G0892' => 'tar', 'TAR636G0166' => 'tar', 'TAR636G0646' => 'tar', 'TAR636G0869' => 'tar', 'TAR636G1317' => 'tar', 'TAR636G1744' => 'tar', 'TAR636G3358' => 'tar', 'TAR636G3436' => 'tar', 'THA.LOC104803047' => 'tha', 'Thecc.04G238900' => 'tca', 'Thhalv10021557m.g' => 'esa', 'Thhalv10026318m.g' => 'esa', 'Thhalv10026335m.g' => 'esa', 'TPR.G17433' => 'tpr', 'TPR.G18915' => 'tpr', 'TPR.G26125' => 'tpr', 'TWI09G0677' => 'twi', 'TWI73G0287' => 'twi', 'unitig_748.g8326' => 'ugi', 'vmacro15370' => 'vma', 'vmacro15371' => 'vma', 'vmacro15372' => 'vma', 'vmacro15373' => 'vma', 'vmacro15374' => 'vma', 'VMungo0720G2826' => 'vmu', 'Zm00001eb116960' => 'zma', 'Zm00001eb301260' => 'zma', 'Zm00001eb301270' => 'zma' ), 'gf_id' => 'HOM05D001460', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001460' ), 'data_identifier' => 'HOM05D001460', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001460', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '433', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p22980' => 'bna', 'A01p32340' => 'bna', 'A03p42970' => 'bna', 'A05p25880' => 'bna', 'Aa31LG8G9320' => 'aar', 'Aa31LG8G9330' => 'aar', 'Aa31LG8G9340' => 'aar', 'Aa31sc221G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1034' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1528' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.829' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2222' => 'aag', 'Ah.12g058830' => 'amhyb', 'Ah.12g058840' => 'amhyb', 'AL3G37160' => 'aly', 'AL7G41310' => 'aly', 'Aqoxy5G00395' => 'aox', 'Aqoxy5G00396' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0C8NZA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5185HY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JZ1PRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MD3LS0' => 'arhy', 'AT3G22840' => 'ath', 'AT4G14690' => 'ath', 'ATR0665G054' => 'atr', 'Atru.chr4.2344' => 'acertr', 'Atru.chr4.2346' => 'acertr', 'Atru.chr4.2347' => 'acertr', 'Atru.chr4.2348' => 'acertr', 'Atru.chr4.2355' => 'acertr', 'Atru.chr4.2356' => 'acertr', 'Atru.chr4.2358' => 'acertr', 'Atru.chr4.2359' => 'acertr', 'Atru.chr4.2360' => 'acertr', 'Atru.chr4.2361' => 'acertr', 'AUR62030476' => 'cqu', 'AUR62030478' => 'cqu', 'AUR62030819' => 'cqu', 'AUR62030820' => 'cqu', 'BcaB03g14648' => 'bca', 'BcaB04g20492' => 'bca', 'BcaB06g26399' => 'bca', 'BcaC01g03416' => 'bca', 'BcaC01g03419' => 'bca', 'BcaC01g03421' => 'bca', 'BcaC01g03424' => 'bca', 'BcaC05g28012' => 'bca', 'BcaC09g49212' => 'bca', 'BcaC09g50140' => 'bca', 'BcaNung00346' => 'bca', 'BolC1t02785H' => 'bol', 'BolC1t04095H' => 'bol', 'BolC3t17545H' => 'bol', 'BolC5t32769H' => 'bol', 'BraA01t02211Z' => 'bra', 'BraA01t03359Z' => 'bra', 'BraA03t13441Z' => 'bra', 'BraA05t21476Z' => 'bra', 'C01p28420' => 'bna', 'C01p41350' => 'bna', 'C03p52750' => 'bna', 'C03p52780' => 'bna', 'C05p40270' => 'bna', 'CAN.G1437.9' => 'can', 'CANSAT78G0035' => 'cansat', 'CANSAT78G1036' => 'cansat', 'CANSAT78G2272' => 'cansat', 'CANSAT78G2478' => 'cansat', 'CARHR098700' => 'chi', 'CARHR221120' => 'chi', 'CARHR221150' => 'chi', 'Carub.0003s2297' => 'cru', 'Carub.0007s2749' => 'cru', 'Carub.0007s2750' => 'cru', 'Carub.0007s2751' => 'cru', 'Ca_10849_v3' => 'car', 'Cc03_g04300' => 'ccan', 'CDE02G3648' => 'cde', 'CDE05G0060' => 'cde', 'CDE05G0692' => 'cde', 'CDE05G2285' => 'cde', 'CDE05G2884' => 'cde', 'CDE05G3072' => 'cde', 'Cfa008439' => 'cfa', 'Cfa008441' => 'cfa', 'Cfa008443' => 'cfa', 'Cfa008448' => 'cfa', 'Ciclev10005974m.g' => 'ccl', 'Ciclev10006006m.g' => 'ccl', 'Ciclev10006775m.g' => 'ccl', 'CiPaw.02G120400' => 'cil', 'CiPaw.02G120500' => 'cil', 'CiPaw.02G120600' => 'cil', 'ClCG05G004850' => 'cla', 'COL.COLO4_21566' => 'col', 'Cpa.g.sc44.124' => 'cpa', 'Cre07.g320400' => 'cre', 'Cre07.g320450' => 'cre', 'Cre08.g384650' => 'cre', 'Cre09.g393173' => 'cre', 'Cre09.g394325' => 'cre', 'Cre14.g626750' => 'cre', 'Cre16.g679250' => 'cre', 'CsaV3_3G012890' => 'csa', 'CSS0010865' => 'camsi', 'CSS0044338' => 'camsi', 'DCAR_002366' => 'dca', 'DCAR_030687' => 'dca', 'DCAR_030688' => 'dca', 'Dinv14047' => 'din', 'Dinv14048' => 'din', 'Duzib151G0105' => 'dzi', 'Duzib151G0114' => 'dzi', 'Duzib212G1029' => 'dzi', 'ECA232G3536' => 'eca', 'ECA240G0786' => 'eca', 'ECA240G1802' => 'eca', 'ECA240G3760' => 'eca', 'ECA240G3920' => 'eca', 'EL10Ac5g12536' => 'bvu', 'EL10Ac5g12537' => 'bvu', 'EL10Ac5g12538' => 'bvu', 'Eucgr.B01004' => 'egr', 'Eucgr.B01006' => 'egr', 'Eucgr.B01007' => 'egr', 'Eucgr.B01008' => 'egr', 'Eucgr.B01895' => 'egr', 'Eucgr.B01896' => 'egr', 'FAN04G1456' => 'fan', 'FAN08G1769' => 'fan', 'FAN08G2160' => 'fan', 'FAN13G2403' => 'fan', 'FAN13G3303' => 'fan', 'FAN15G2435' => 'fan', 'FAN17G0672' => 'fan', 'FAN17G2441' => 'fan', 'FAN18G1024' => 'fan', 'FAN22G1458' => 'fan', 'FAN24G0037' => 'fan', 'FAN24G0429' => 'fan', 'FAN24G2387' => 'fan', 'FAN27G2746' => 'fan', 'FvH4_2g20400' => 'fve', 'FvH4_2g20420' => 'fve', 'FvH4_2g20430' => 'fve', 'FvH4_4g01270' => 'fve', 'FvH4_4g01290' => 'fve', 'FvH4_4g01300' => 'fve', 'FvH4_4g01310' => 'fve', 'FvH4_4g01330' => 'fve', 'FvH4_5g09070' => 'fve', 'Glyma.10G243800' => 'gma', 'Glyma.20G150600' => 'gma', 'Gohir.A09G219200' => 'ghi', 'Gohir.A09G219300' => 'ghi', 'Gohir.D09G221400' => 'ghi', 'Gohir.D09G221500' => 'ghi', 'Gorai.006G242600' => 'gra', 'Gorai.006G242700' => 'gra', 'GSVIVG01018044001' => 'vvi', 'HanXRQChr03g0083821' => 'han', 'HanXRQChr03g0083841' => 'han', 'HanXRQChr03g0083881' => 'han', 'HanXRQChr03g0083901' => 'han', 'HanXRQChr03g0083921' => 'han', 'HanXRQChr03g0085331' => 'han', 'HanXRQChr03g0085361' => 'han', 'HanXRQChr03g0085411' => 'han', 'HanXRQChr03g0085421' => 'han', 'HanXRQChr03g0085431' => 'han', 'HanXRQChr08g0221991' => 'han', 'HanXRQChr11g0336061' => 'han', 'HanXRQChr11g0336411' => 'han', 'Haze_11234' => 'cav', 'Hma1.2p1_0549F.1_g177010' => 'hma', 'Hma1.2p1_0602F.1_g187630' => 'hma', 'Hund14876' => 'sun', 'Hund14879' => 'sun', 'Lalb_Chr06g0160741' => 'lal', 'Lalb_Chr21g0304781' => 'lal', 'Lj3A726G19' => 'lonja', 'Lj3A726T23' => 'lonja', 'Lj3A726T24' => 'lonja', 'Lj3A726T25' => 'lonja', 'Lj3A727T17' => 'lonja', 'Lj3C726T0' => 'lonja', 'Lj3C726T2' => 'lonja', 'Lj3P725T35' => 'lonja', 'Lj3P727T10' => 'lonja', 'Lj3P727T12' => 'lonja', 'Lj3P727T14' => 'lonja', 'Lj5g0023109' => 'lja', 'Lj6P646T44' => 'lonja', 'Lsat_1_v5_gn_6_75760' => 'lsa', 'Lsat_1_v5_gn_6_75800' => 'lsa', 'Lsat_1_v5_gn_6_75900' => 'lsa', 'Lsat_1_v5_gn_6_76240' => 'lsa', 'Lsat_1_v5_gn_6_76441' => 'lsa', 'Lsat_1_v5_gn_6_76700' => 'lsa', 'Lsat_1_v5_gn_6_76760' => 'lsa', 'Manes.15G033100' => 'mes', 'Mapoly0004s0074' => 'mpo', 'Mapoly0004s0075' => 'mpo', 'Mapoly0004s0163' => 'mpo', 'Mapoly0004s0164' => 'mpo', 'Mapoly0021s0018' => 'mpo', 'Mapoly0041s0136' => 'mpo', 'Mapoly0041s0137' => 'mpo', 'Mapoly0041s0138' => 'mpo', 'Mapoly0041s0139' => 'mpo', 'Mapoly0041s0141' => 'mpo', 'Mapoly0041s0142' => 'mpo', 'Mapoly0041s0143' => 'mpo', 'Mapoly0041s0144' => 'mpo', 'Mapoly0041s0145' => 'mpo', 'Mapoly0047s0106' => 'mpo', 'Mapoly0047s0108' => 'mpo', 'Mapoly0050s0051' => 'mpo', 'Mapoly0050s0052' => 'mpo', 'Mapoly0050s0053' => 'mpo', 'Mapoly0058s0013' => 'mpo', 'Mapoly0091s0078' => 'mpo', 'Mapoly0091s0079' => 'mpo', 'Mapoly0091s0080' => 'mpo', 'Mapoly0091s0081' => 'mpo', 'Mapoly0278s0004' => 'mpo', 'Mapoly0278s0005' => 'mpo', 'Mapoly0278s0006' => 'mpo', 'MBI11_g30648_MAGBIO' => 'mbi', 'MCO03G194' => 'mco', 'MCO03G590' => 'mco', 'MCO07G312' => 'mco', 'MCO10G318' => 'mco', 'MCO12G244' => 'mco', 'MCO13G148' => 'mco', 'MCO13G194' => 'mco', 'MCO16G238' => 'mco', 'MD06G1134100' => 'mdo', 'MD13G1200100' => 'mdo', 'MD13G1200300' => 'mdo', 'MD13G1200600' => 'mdo', 'MD14G1150400' => 'mdo', 'MD16G1200000' => 'mdo', 'Medtr1g102570' => 'mtr', 'Medtr1g102780' => 'mtr', 'Medtr1g102800' => 'mtr', 'Medtr1g102810' => 'mtr', 'Medtr1g102830' => 'mtr', 'MELO3C006499.2' => 'cme', 'Migut.G00385' => 'egut', 'MSTRG.4063' => 'ama', 'Nitab4.5_0000090g0260' => 'nta', 'Nitab4.5_0000977g0030' => 'nta', 'Nitab4.5_0002541g0040' => 'nta', 'Nitab4.5_0007068g0040' => 'nta', 'Nn005s41408' => 'nnu', 'Nn005s41410' => 'nnu', 'Oeu010310.1' => 'oeu', 'Oeu010311.1' => 'oeu', 'Oeu043472.1' => 'oeu', 'Os01g0246400' => 'osa', 'Os04g0267950' => 'osa', 'Os07g0178700' => 'osa', 'Os07g0178800' => 'osa', 'Peaxi162Scf00316g00046' => 'pax', 'Peaxi162Scf00316g00049' => 'pax', 'Peaxi162Scf00316g00059' => 'pax', 'Peaxi162Scf00316g00328' => 'pax', 'Peaxi162Scf00316g00329' => 'pax', 'Peaxi162Scf00316g00411' => 'pax', 'Peaxi162Scf00316g00521' => 'pax', 'Peaxi162Scf00492g00068' => 'pax', 'Peaxi162Scf35631g00002' => 'pax', 'PGR142G3720' => 'pgr', 'PGSC0003DMG400006442' => 'stu', 'Phvul.007G062000' => 'pvu', 'Potri.008G157750' => 'ptr', 'Potri.008G157900' => 'ptr', 'Potri.008G158000' => 'ptr', 'Potri.008G158200' => 'ptr', 'Pp3c11_7280' => 'ppa', 'Pp3c11_7980' => 'ppa', 'Pp3c12_19450' => 'ppa', 'Pp3c14_1480' => 'ppa', 'Pp3c14_1501' => 'ppa', 'Pp3c16_4900' => 'ppa', 'Pp3c16_5010' => 'ppa', 'Pp3c16_5060' => 'ppa', 'Pp3c19_18250' => 'ppa', 'Pp3c23_8530' => 'ppa', 'Pp3c23_8550' => 'ppa', 'Pp3c24_9670' => 'ppa', 'Pp3c2_21390' => 'ppa', 'Pp3c2_31380' => 'ppa', 'Pp3c3_16620' => 'ppa', 'Pp3c3_8090' => 'ppa', 'Pp3c3_8110' => 'ppa', 'Pp3c3_8130' => 'ppa', 'Pp3c3_8150' => 'ppa', 'Pp3c4_14320' => 'ppa', 'Pp3c6_2560' => 'ppa', 'Pp3c9_16700' => 'ppa', 'PRCOL_00000234' => 'pco', 'PRCOL_00000235' => 'pco', 'PRCOL_00000777' => 'pco', 'PRCOL_00002344' => 'pco', 'PRCOL_00002372' => 'pco', 'PRCOL_00006120' => 'pco', 'Prupe.1G021400' => 'ppe', 'Prupe.1G021500' => 'ppe', 'Prupe.1G021600' => 'ppe', 'Prupe.1G021700' => 'ppe', 'Prupe.1G021800' => 'ppe', 'Prupe.5G145100' => 'ppe', 'Psat6g204040' => 'psa', 'Psat6g204800' => 'psa', 'Psat6g204920' => 'psa', 'Psat6g204960' => 'psa', 'Psat6g205080' => 'psa', 'PSO017G0271' => 'pso', 'PSO017G1276' => 'pso', 'PSO017G1429' => 'pso', 'PSO017G1861' => 'pso', 'PSO017G2787' => 'pso', 'PSO017G4466' => 'pso', 'PSO017G5118' => 'pso', 'PSO017G5420' => 'pso', 'PSO063G3678' => 'pso', 'PSO210G0546' => 'pso', 'PSO317G0001' => 'pso', 'PSO357G0512' => 'pso', 'PSO478G2682' => 'pso', 'PSO647G0001' => 'pso', 'PSO675G0001' => 'pso', 'PSO675G2699' => 'pso', 'PSO675G2849' => 'pso', 'PSO675G4991' => 'pso', 'PSO689G0001' => 'pso', 'QL06p000916' => 'qlo', 'QL06p000921' => 'qlo', 'QL06p001398' => 'qlo', 'QL06p001407' => 'qlo', 'QL06p002031' => 'qlo', 'RcHm_v2.0_Chr4g0387791' => 'rch', 'RcHm_v2.0_Chr4g0387801' => 'rch', 'RcHm_v2.0_Chr6g0286501' => 'rch', 'RcHm_v2.0_Chr6g0286511' => 'rch', 'RcHm_v2.0_Chr6g0286521' => 'rch', 'RcHm_v2.0_Chr6g0286531' => 'rch', 'RcHm_v2.0_Chr7g0189141' => 'rch', 'Rhsim02G0028700' => 'rsi', 'Rhsim02G0028800' => 'rsi', 'Rhsim02G0028900' => 'rsi', 'Rhsim02G0029000' => 'rsi', 'Rhsim02G0029100' => 'rsi', 'Rhsim02G0029200' => 'rsi', 'Rhsim02G0029300' => 'rsi', 'Rhsim02G0029400' => 'rsi', 'Rhsim02G0029500' => 'rsi', 'Rhsim02G0029600' => 'rsi', 'RhsimUnG0024000' => 'rsi', 'RhsimUnG0024100' => 'rsi', 'RhsimUnG0024200' => 'rsi', 'RhsimUnG0024300' => 'rsi', 'RhsimUnG0024400' => 'rsi', 'RhsimUnG0024500' => 'rsi', 'RhsimUnG0024700' => 'rsi', 'RhsimUnG0024800' => 'rsi', 'RhsimUnG0024900' => 'rsi', 'RhsimUnG0025100' => 'rsi', 'Sabra08G0120200' => 'sbr', 'Sabra08G0120300' => 'sbr', 'Sabra08G0120500' => 'sbr', 'Sabra08G0120600' => 'sbr', 'Sabra10G0158900' => 'sbr', 'SalBow2G3492' => 'sbo', 'Sc13g0004760' => 'sci', 'Sc13g0004770' => 'sci', 'Sed0003417' => 'sed', 'Sed0019750' => 'sed', 'SEGI_03419' => 'sgi', 'SEGI_05907' => 'sgi', 'SEGI_10682' => 'sgi', 'SEGI_13528' => 'sgi', 'SEGI_16081' => 'sgi', 'SEGI_19370' => 'sgi', 'SEGI_21015' => 'sgi', 'SEGI_21944' => 'sgi', 'SEGI_32906' => 'sgi', 'SEGI_33093' => 'sgi', 'SEGI_36110' => 'sgi', 'SEGI_40397' => 'sgi', 'SGA_v2.0_scaffold191G40426' => 'sas', 'SGA_v2.0_scaffold353G49717' => 'sas', 'SGA_v2.0_scaffold50G18550' => 'sas', 'SMO119G0173' => 'smo', 'SMO172G0002' => 'smo', 'Solyc09g082690.3' => 'sly', 'Solyc09g082700.2' => 'sly', 'Sopen09g031550' => 'spe', 'Sopen09g031560' => 'spe', 'Sp3g20540' => 'spa', 'Sp7g07580' => 'spa', 'TAR134G0002' => 'tar', 'TAR236G0001' => 'tar', 'TAR365G0892' => 'tar', 'TAR636G0166' => 'tar', 'TAR636G0646' => 'tar', 'TAR636G0869' => 'tar', 'TAR636G1317' => 'tar', 'TAR636G1744' => 'tar', 'TAR636G3358' => 'tar', 'TAR636G3436' => 'tar', 'THA.LOC104803047' => 'tha', 'Thecc.04G238900' => 'tca', 'Thhalv10021557m.g' => 'esa', 'Thhalv10026318m.g' => 'esa', 'Thhalv10026335m.g' => 'esa', 'TPR.G17433' => 'tpr', 'TPR.G18915' => 'tpr', 'TPR.G26125' => 'tpr', 'TWI09G0677' => 'twi', 'TWI73G0287' => 'twi', 'unitig_748.g8326' => 'ugi', 'vmacro15370' => 'vma', 'vmacro15371' => 'vma', 'vmacro15372' => 'vma', 'vmacro15373' => 'vma', 'vmacro15374' => 'vma', 'VMungo0720G2826' => 'vmu', 'Zm00001eb116960' => 'zma', 'Zm00001eb301260' => 'zma', 'Zm00001eb301270' => 'zma' ) $gf_id = 'HOM05D001460' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001460' ) $data_identifier = 'HOM05D001460' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 4, 'aag' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 2, 'aox' => (int) 2, 'arhy' => (int) 4, 'ath' => (int) 2, 'atr' => (int) 1, 'acertr' => (int) 10, 'cqu' => (int) 4, 'bca' => (int) 11, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 1, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 1, 'ccan' => (int) 1, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 1, 'col' => (int) 1, 'cpa' => (int) 1, 'cre' => (int) 7, 'csa' => (int) 1, 'camsi' => (int) 2, 'dca' => (int) 3, 'din' => (int) 2, 'dzi' => (int) 3, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 14, 'fve' => (int) 9, 'gma' => (int) 2, 'ghi' => (int) 4, 'gra' => (int) 2, 'vvi' => (int) 1, 'han' => (int) 13, 'cav' => (int) 1, 'hma' => (int) 2, 'sun' => (int) 2, 'lal' => (int) 2, 'lonja' => (int) 12, 'lja' => (int) 1, 'lsa' => (int) 7, 'mes' => (int) 1, 'mpo' => (int) 27, 'mbi' => (int) 1, 'mco' => (int) 8, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 1, 'egut' => (int) 1, 'ama' => (int) 1, 'nta' => (int) 4, 'nnu' => (int) 2, 'oeu' => (int) 3, 'osa' => (int) 4, 'pax' => (int) 9, 'pgr' => (int) 1, 'stu' => (int) 1, 'pvu' => (int) 1, 'ptr' => (int) 4, 'ppa' => (int) 22, 'pco' => (int) 6, 'ppe' => (int) 6, 'psa' => (int) 5, 'pso' => (int) 19, 'qlo' => (int) 5, 'rch' => (int) 7, 'rsi' => (int) 20, 'sbr' => (int) 5, 'sbo' => (int) 1, 'sci' => (int) 2, 'sed' => (int) 2, 'sgi' => (int) 12, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 2, 'tar' => (int) 10, 'tha' => (int) 1, 'tca' => (int) 1, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 2, 'ugi' => (int) 1, 'vma' => (int) 5, 'vmu' => (int) 1, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb301270' $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' => 'HOM05D001460', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '433', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p22980' => 'bna', 'A01p32340' => 'bna', 'A03p42970' => 'bna', 'A05p25880' => 'bna', 'Aa31LG8G9320' => 'aar', 'Aa31LG8G9330' => 'aar', 'Aa31LG8G9340' => 'aar', 'Aa31sc221G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1034' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1528' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.829' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2222' => 'aag', 'Ah.12g058830' => 'amhyb', 'Ah.12g058840' => 'amhyb', 'AL3G37160' => 'aly', 'AL7G41310' => 'aly', 'Aqoxy5G00395' => 'aox', 'Aqoxy5G00396' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0C8NZA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5185HY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JZ1PRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MD3LS0' => 'arhy', 'AT3G22840' => 'ath', 'AT4G14690' => 'ath', 'ATR0665G054' => 'atr', 'Atru.chr4.2344' => 'acertr', 'Atru.chr4.2346' => 'acertr', 'Atru.chr4.2347' => 'acertr', 'Atru.chr4.2348' => 'acertr', 'Atru.chr4.2355' => 'acertr', 'Atru.chr4.2356' => 'acertr', 'Atru.chr4.2358' => 'acertr', 'Atru.chr4.2359' => 'acertr', 'Atru.chr4.2360' => 'acertr', 'Atru.chr4.2361' => 'acertr', 'AUR62030476' => 'cqu', 'AUR62030478' => 'cqu', 'AUR62030819' => 'cqu', 'AUR62030820' => 'cqu', 'BcaB03g14648' => 'bca', 'BcaB04g20492' => 'bca', 'BcaB06g26399' => 'bca', 'BcaC01g03416' => 'bca', 'BcaC01g03419' => 'bca', 'BcaC01g03421' => 'bca', 'BcaC01g03424' => 'bca', 'BcaC05g28012' => 'bca', 'BcaC09g49212' => 'bca', 'BcaC09g50140' => 'bca', 'BcaNung00346' => 'bca', 'BolC1t02785H' => 'bol', 'BolC1t04095H' => 'bol', 'BolC3t17545H' => 'bol', 'BolC5t32769H' => 'bol', 'BraA01t02211Z' => 'bra', 'BraA01t03359Z' => 'bra', 'BraA03t13441Z' => 'bra', 'BraA05t21476Z' => 'bra', 'C01p28420' => 'bna', 'C01p41350' => 'bna', 'C03p52750' => 'bna', 'C03p52780' => 'bna', 'C05p40270' => 'bna', 'CAN.G1437.9' => 'can', 'CANSAT78G0035' => 'cansat', 'CANSAT78G1036' => 'cansat', 'CANSAT78G2272' => 'cansat', 'CANSAT78G2478' => 'cansat', 'CARHR098700' => 'chi', 'CARHR221120' => 'chi', 'CARHR221150' => 'chi', 'Carub.0003s2297' => 'cru', 'Carub.0007s2749' => 'cru', 'Carub.0007s2750' => 'cru', 'Carub.0007s2751' => 'cru', 'Ca_10849_v3' => 'car', 'Cc03_g04300' => 'ccan', 'CDE02G3648' => 'cde', 'CDE05G0060' => 'cde', 'CDE05G0692' => 'cde', 'CDE05G2285' => 'cde', 'CDE05G2884' => 'cde', 'CDE05G3072' => 'cde', 'Cfa008439' => 'cfa', 'Cfa008441' => 'cfa', 'Cfa008443' => 'cfa', 'Cfa008448' => 'cfa', 'Ciclev10005974m.g' => 'ccl', 'Ciclev10006006m.g' => 'ccl', 'Ciclev10006775m.g' => 'ccl', 'CiPaw.02G120400' => 'cil', 'CiPaw.02G120500' => 'cil', 'CiPaw.02G120600' => 'cil', 'ClCG05G004850' => 'cla', 'COL.COLO4_21566' => 'col', 'Cpa.g.sc44.124' => 'cpa', 'Cre07.g320400' => 'cre', 'Cre07.g320450' => 'cre', 'Cre08.g384650' => 'cre', 'Cre09.g393173' => 'cre', 'Cre09.g394325' => 'cre', 'Cre14.g626750' => 'cre', 'Cre16.g679250' => 'cre', 'CsaV3_3G012890' => 'csa', 'CSS0010865' => 'camsi', 'CSS0044338' => 'camsi', 'DCAR_002366' => 'dca', 'DCAR_030687' => 'dca', 'DCAR_030688' => 'dca', 'Dinv14047' => 'din', 'Dinv14048' => 'din', 'Duzib151G0105' => 'dzi', 'Duzib151G0114' => 'dzi', 'Duzib212G1029' => 'dzi', 'ECA232G3536' => 'eca', 'ECA240G0786' => 'eca', 'ECA240G1802' => 'eca', 'ECA240G3760' => 'eca', 'ECA240G3920' => 'eca', 'EL10Ac5g12536' => 'bvu', 'EL10Ac5g12537' => 'bvu', 'EL10Ac5g12538' => 'bvu', 'Eucgr.B01004' => 'egr', 'Eucgr.B01006' => 'egr', 'Eucgr.B01007' => 'egr', 'Eucgr.B01008' => 'egr', 'Eucgr.B01895' => 'egr', 'Eucgr.B01896' => 'egr', 'FAN04G1456' => 'fan', 'FAN08G1769' => 'fan', 'FAN08G2160' => 'fan', 'FAN13G2403' => 'fan', 'FAN13G3303' => 'fan', 'FAN15G2435' => 'fan', 'FAN17G0672' => 'fan', 'FAN17G2441' => 'fan', 'FAN18G1024' => 'fan', 'FAN22G1458' => 'fan', 'FAN24G0037' => 'fan', 'FAN24G0429' => 'fan', 'FAN24G2387' => 'fan', 'FAN27G2746' => 'fan', 'FvH4_2g20400' => 'fve', 'FvH4_2g20420' => 'fve', 'FvH4_2g20430' => 'fve', 'FvH4_4g01270' => 'fve', 'FvH4_4g01290' => 'fve', 'FvH4_4g01300' => 'fve', 'FvH4_4g01310' => 'fve', 'FvH4_4g01330' => 'fve', 'FvH4_5g09070' => 'fve', 'Glyma.10G243800' => 'gma', 'Glyma.20G150600' => 'gma', 'Gohir.A09G219200' => 'ghi', 'Gohir.A09G219300' => 'ghi', 'Gohir.D09G221400' => 'ghi', 'Gohir.D09G221500' => 'ghi', 'Gorai.006G242600' => 'gra', 'Gorai.006G242700' => 'gra', 'GSVIVG01018044001' => 'vvi', 'HanXRQChr03g0083821' => 'han', 'HanXRQChr03g0083841' => 'han', 'HanXRQChr03g0083881' => 'han', 'HanXRQChr03g0083901' => 'han', 'HanXRQChr03g0083921' => 'han', 'HanXRQChr03g0085331' => 'han', 'HanXRQChr03g0085361' => 'han', 'HanXRQChr03g0085411' => 'han', 'HanXRQChr03g0085421' => 'han', 'HanXRQChr03g0085431' => 'han', 'HanXRQChr08g0221991' => 'han', 'HanXRQChr11g0336061' => 'han', 'HanXRQChr11g0336411' => 'han', 'Haze_11234' => 'cav', 'Hma1.2p1_0549F.1_g177010' => 'hma', 'Hma1.2p1_0602F.1_g187630' => 'hma', 'Hund14876' => 'sun', 'Hund14879' => 'sun', 'Lalb_Chr06g0160741' => 'lal', 'Lalb_Chr21g0304781' => 'lal', 'Lj3A726G19' => 'lonja', 'Lj3A726T23' => 'lonja', 'Lj3A726T24' => 'lonja', 'Lj3A726T25' => 'lonja', 'Lj3A727T17' => 'lonja', 'Lj3C726T0' => 'lonja', 'Lj3C726T2' => 'lonja', 'Lj3P725T35' => 'lonja', 'Lj3P727T10' => 'lonja', 'Lj3P727T12' => 'lonja', 'Lj3P727T14' => 'lonja', 'Lj5g0023109' => 'lja', 'Lj6P646T44' => 'lonja', 'Lsat_1_v5_gn_6_75760' => 'lsa', 'Lsat_1_v5_gn_6_75800' => 'lsa', 'Lsat_1_v5_gn_6_75900' => 'lsa', 'Lsat_1_v5_gn_6_76240' => 'lsa', 'Lsat_1_v5_gn_6_76441' => 'lsa', 'Lsat_1_v5_gn_6_76700' => 'lsa', 'Lsat_1_v5_gn_6_76760' => 'lsa', 'Manes.15G033100' => 'mes', 'Mapoly0004s0074' => 'mpo', 'Mapoly0004s0075' => 'mpo', 'Mapoly0004s0163' => 'mpo', 'Mapoly0004s0164' => 'mpo', 'Mapoly0021s0018' => 'mpo', 'Mapoly0041s0136' => 'mpo', 'Mapoly0041s0137' => 'mpo', 'Mapoly0041s0138' => 'mpo', 'Mapoly0041s0139' => 'mpo', 'Mapoly0041s0141' => 'mpo', 'Mapoly0041s0142' => 'mpo', 'Mapoly0041s0143' => 'mpo', 'Mapoly0041s0144' => 'mpo', 'Mapoly0041s0145' => 'mpo', 'Mapoly0047s0106' => 'mpo', 'Mapoly0047s0108' => 'mpo', 'Mapoly0050s0051' => 'mpo', 'Mapoly0050s0052' => 'mpo', 'Mapoly0050s0053' => 'mpo', 'Mapoly0058s0013' => 'mpo', 'Mapoly0091s0078' => 'mpo', 'Mapoly0091s0079' => 'mpo', 'Mapoly0091s0080' => 'mpo', 'Mapoly0091s0081' => 'mpo', 'Mapoly0278s0004' => 'mpo', 'Mapoly0278s0005' => 'mpo', 'Mapoly0278s0006' => 'mpo', 'MBI11_g30648_MAGBIO' => 'mbi', 'MCO03G194' => 'mco', 'MCO03G590' => 'mco', 'MCO07G312' => 'mco', 'MCO10G318' => 'mco', 'MCO12G244' => 'mco', 'MCO13G148' => 'mco', 'MCO13G194' => 'mco', 'MCO16G238' => 'mco', 'MD06G1134100' => 'mdo', 'MD13G1200100' => 'mdo', 'MD13G1200300' => 'mdo', 'MD13G1200600' => 'mdo', 'MD14G1150400' => 'mdo', 'MD16G1200000' => 'mdo', 'Medtr1g102570' => 'mtr', 'Medtr1g102780' => 'mtr', 'Medtr1g102800' => 'mtr', 'Medtr1g102810' => 'mtr', 'Medtr1g102830' => 'mtr', 'MELO3C006499.2' => 'cme', 'Migut.G00385' => 'egut', 'MSTRG.4063' => 'ama', 'Nitab4.5_0000090g0260' => 'nta', 'Nitab4.5_0000977g0030' => 'nta', 'Nitab4.5_0002541g0040' => 'nta', 'Nitab4.5_0007068g0040' => 'nta', 'Nn005s41408' => 'nnu', 'Nn005s41410' => 'nnu', 'Oeu010310.1' => 'oeu', 'Oeu010311.1' => 'oeu', 'Oeu043472.1' => 'oeu', 'Os01g0246400' => 'osa', 'Os04g0267950' => 'osa', 'Os07g0178700' => 'osa', 'Os07g0178800' => 'osa', 'Peaxi162Scf00316g00046' => 'pax', 'Peaxi162Scf00316g00049' => 'pax', 'Peaxi162Scf00316g00059' => 'pax', 'Peaxi162Scf00316g00328' => 'pax', 'Peaxi162Scf00316g00329' => 'pax', 'Peaxi162Scf00316g00411' => 'pax', 'Peaxi162Scf00316g00521' => 'pax', 'Peaxi162Scf00492g00068' => 'pax', 'Peaxi162Scf35631g00002' => 'pax', 'PGR142G3720' => 'pgr', 'PGSC0003DMG400006442' => 'stu', 'Phvul.007G062000' => 'pvu', 'Potri.008G157750' => 'ptr', 'Potri.008G157900' => 'ptr', 'Potri.008G158000' => 'ptr', 'Potri.008G158200' => 'ptr', 'Pp3c11_7280' => 'ppa', 'Pp3c11_7980' => 'ppa', 'Pp3c12_19450' => 'ppa', 'Pp3c14_1480' => 'ppa', 'Pp3c14_1501' => 'ppa', 'Pp3c16_4900' => 'ppa', 'Pp3c16_5010' => 'ppa', 'Pp3c16_5060' => 'ppa', 'Pp3c19_18250' => 'ppa', 'Pp3c23_8530' => 'ppa', 'Pp3c23_8550' => 'ppa', 'Pp3c24_9670' => 'ppa', 'Pp3c2_21390' => 'ppa', 'Pp3c2_31380' => 'ppa', 'Pp3c3_16620' => 'ppa', 'Pp3c3_8090' => 'ppa', 'Pp3c3_8110' => 'ppa', 'Pp3c3_8130' => 'ppa', 'Pp3c3_8150' => 'ppa', 'Pp3c4_14320' => 'ppa', 'Pp3c6_2560' => 'ppa', 'Pp3c9_16700' => 'ppa', 'PRCOL_00000234' => 'pco', 'PRCOL_00000235' => 'pco', 'PRCOL_00000777' => 'pco', 'PRCOL_00002344' => 'pco', 'PRCOL_00002372' => 'pco', 'PRCOL_00006120' => 'pco', 'Prupe.1G021400' => 'ppe', 'Prupe.1G021500' => 'ppe', 'Prupe.1G021600' => 'ppe', 'Prupe.1G021700' => 'ppe', 'Prupe.1G021800' => 'ppe', 'Prupe.5G145100' => 'ppe', 'Psat6g204040' => 'psa', 'Psat6g204800' => 'psa', 'Psat6g204920' => 'psa', 'Psat6g204960' => 'psa', 'Psat6g205080' => 'psa', 'PSO017G0271' => 'pso', 'PSO017G1276' => 'pso', 'PSO017G1429' => 'pso', 'PSO017G1861' => 'pso', 'PSO017G2787' => 'pso', 'PSO017G4466' => 'pso', 'PSO017G5118' => 'pso', 'PSO017G5420' => 'pso', 'PSO063G3678' => 'pso', 'PSO210G0546' => 'pso', 'PSO317G0001' => 'pso', 'PSO357G0512' => 'pso', 'PSO478G2682' => 'pso', 'PSO647G0001' => 'pso', 'PSO675G0001' => 'pso', 'PSO675G2699' => 'pso', 'PSO675G2849' => 'pso', 'PSO675G4991' => 'pso', 'PSO689G0001' => 'pso', 'QL06p000916' => 'qlo', 'QL06p000921' => 'qlo', 'QL06p001398' => 'qlo', 'QL06p001407' => 'qlo', 'QL06p002031' => 'qlo', 'RcHm_v2.0_Chr4g0387791' => 'rch', 'RcHm_v2.0_Chr4g0387801' => 'rch', 'RcHm_v2.0_Chr6g0286501' => 'rch', 'RcHm_v2.0_Chr6g0286511' => 'rch', 'RcHm_v2.0_Chr6g0286521' => 'rch', 'RcHm_v2.0_Chr6g0286531' => 'rch', 'RcHm_v2.0_Chr7g0189141' => 'rch', 'Rhsim02G0028700' => 'rsi', 'Rhsim02G0028800' => 'rsi', 'Rhsim02G0028900' => 'rsi', 'Rhsim02G0029000' => 'rsi', 'Rhsim02G0029100' => 'rsi', 'Rhsim02G0029200' => 'rsi', 'Rhsim02G0029300' => 'rsi', 'Rhsim02G0029400' => 'rsi', 'Rhsim02G0029500' => 'rsi', 'Rhsim02G0029600' => 'rsi', 'RhsimUnG0024000' => 'rsi', 'RhsimUnG0024100' => 'rsi', 'RhsimUnG0024200' => 'rsi', 'RhsimUnG0024300' => 'rsi', 'RhsimUnG0024400' => 'rsi', 'RhsimUnG0024500' => 'rsi', 'RhsimUnG0024700' => 'rsi', 'RhsimUnG0024800' => 'rsi', 'RhsimUnG0024900' => 'rsi', 'RhsimUnG0025100' => 'rsi', 'Sabra08G0120200' => 'sbr', 'Sabra08G0120300' => 'sbr', 'Sabra08G0120500' => 'sbr', 'Sabra08G0120600' => 'sbr', 'Sabra10G0158900' => 'sbr', 'SalBow2G3492' => 'sbo', 'Sc13g0004760' => 'sci', 'Sc13g0004770' => 'sci', 'Sed0003417' => 'sed', 'Sed0019750' => 'sed', 'SEGI_03419' => 'sgi', 'SEGI_05907' => 'sgi', 'SEGI_10682' => 'sgi', 'SEGI_13528' => 'sgi', 'SEGI_16081' => 'sgi', 'SEGI_19370' => 'sgi', 'SEGI_21015' => 'sgi', 'SEGI_21944' => 'sgi', 'SEGI_32906' => 'sgi', 'SEGI_33093' => 'sgi', 'SEGI_36110' => 'sgi', 'SEGI_40397' => 'sgi', 'SGA_v2.0_scaffold191G40426' => 'sas', 'SGA_v2.0_scaffold353G49717' => 'sas', 'SGA_v2.0_scaffold50G18550' => 'sas', 'SMO119G0173' => 'smo', 'SMO172G0002' => 'smo', 'Solyc09g082690.3' => 'sly', 'Solyc09g082700.2' => 'sly', 'Sopen09g031550' => 'spe', 'Sopen09g031560' => 'spe', 'Sp3g20540' => 'spa', 'Sp7g07580' => 'spa', 'TAR134G0002' => 'tar', 'TAR236G0001' => 'tar', 'TAR365G0892' => 'tar', 'TAR636G0166' => 'tar', 'TAR636G0646' => 'tar', 'TAR636G0869' => 'tar', 'TAR636G1317' => 'tar', 'TAR636G1744' => 'tar', 'TAR636G3358' => 'tar', 'TAR636G3436' => 'tar', 'THA.LOC104803047' => 'tha', 'Thecc.04G238900' => 'tca', 'Thhalv10021557m.g' => 'esa', 'Thhalv10026318m.g' => 'esa', 'Thhalv10026335m.g' => 'esa', 'TPR.G17433' => 'tpr', 'TPR.G18915' => 'tpr', 'TPR.G26125' => 'tpr', 'TWI09G0677' => 'twi', 'TWI73G0287' => 'twi', 'unitig_748.g8326' => 'ugi', 'vmacro15370' => 'vma', 'vmacro15371' => 'vma', 'vmacro15372' => 'vma', 'vmacro15373' => 'vma', 'vmacro15374' => 'vma', 'VMungo0720G2826' => 'vmu', 'Zm00001eb116960' => 'zma', 'Zm00001eb301260' => 'zma', 'Zm00001eb301270' => 'zma' ), 'gf_id' => 'HOM05D001460', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001460' ), 'data_identifier' => 'HOM05D001460', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001460', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '433', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p22980' => 'bna', 'A01p32340' => 'bna', 'A03p42970' => 'bna', 'A05p25880' => 'bna', 'Aa31LG8G9320' => 'aar', 'Aa31LG8G9330' => 'aar', 'Aa31LG8G9340' => 'aar', 'Aa31sc221G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1034' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1528' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.829' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2222' => 'aag', 'Ah.12g058830' => 'amhyb', 'Ah.12g058840' => 'amhyb', 'AL3G37160' => 'aly', 'AL7G41310' => 'aly', 'Aqoxy5G00395' => 'aox', 'Aqoxy5G00396' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0C8NZA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5185HY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JZ1PRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MD3LS0' => 'arhy', 'AT3G22840' => 'ath', 'AT4G14690' => 'ath', 'ATR0665G054' => 'atr', 'Atru.chr4.2344' => 'acertr', 'Atru.chr4.2346' => 'acertr', 'Atru.chr4.2347' => 'acertr', 'Atru.chr4.2348' => 'acertr', 'Atru.chr4.2355' => 'acertr', 'Atru.chr4.2356' => 'acertr', 'Atru.chr4.2358' => 'acertr', 'Atru.chr4.2359' => 'acertr', 'Atru.chr4.2360' => 'acertr', 'Atru.chr4.2361' => 'acertr', 'AUR62030476' => 'cqu', 'AUR62030478' => 'cqu', 'AUR62030819' => 'cqu', 'AUR62030820' => 'cqu', 'BcaB03g14648' => 'bca', 'BcaB04g20492' => 'bca', 'BcaB06g26399' => 'bca', 'BcaC01g03416' => 'bca', 'BcaC01g03419' => 'bca', 'BcaC01g03421' => 'bca', 'BcaC01g03424' => 'bca', 'BcaC05g28012' => 'bca', 'BcaC09g49212' => 'bca', 'BcaC09g50140' => 'bca', 'BcaNung00346' => 'bca', 'BolC1t02785H' => 'bol', 'BolC1t04095H' => 'bol', 'BolC3t17545H' => 'bol', 'BolC5t32769H' => 'bol', 'BraA01t02211Z' => 'bra', 'BraA01t03359Z' => 'bra', 'BraA03t13441Z' => 'bra', 'BraA05t21476Z' => 'bra', 'C01p28420' => 'bna', 'C01p41350' => 'bna', 'C03p52750' => 'bna', 'C03p52780' => 'bna', 'C05p40270' => 'bna', 'CAN.G1437.9' => 'can', 'CANSAT78G0035' => 'cansat', 'CANSAT78G1036' => 'cansat', 'CANSAT78G2272' => 'cansat', 'CANSAT78G2478' => 'cansat', 'CARHR098700' => 'chi', 'CARHR221120' => 'chi', 'CARHR221150' => 'chi', 'Carub.0003s2297' => 'cru', 'Carub.0007s2749' => 'cru', 'Carub.0007s2750' => 'cru', 'Carub.0007s2751' => 'cru', 'Ca_10849_v3' => 'car', 'Cc03_g04300' => 'ccan', 'CDE02G3648' => 'cde', 'CDE05G0060' => 'cde', 'CDE05G0692' => 'cde', 'CDE05G2285' => 'cde', 'CDE05G2884' => 'cde', 'CDE05G3072' => 'cde', 'Cfa008439' => 'cfa', 'Cfa008441' => 'cfa', 'Cfa008443' => 'cfa', 'Cfa008448' => 'cfa', 'Ciclev10005974m.g' => 'ccl', 'Ciclev10006006m.g' => 'ccl', 'Ciclev10006775m.g' => 'ccl', 'CiPaw.02G120400' => 'cil', 'CiPaw.02G120500' => 'cil', 'CiPaw.02G120600' => 'cil', 'ClCG05G004850' => 'cla', 'COL.COLO4_21566' => 'col', 'Cpa.g.sc44.124' => 'cpa', 'Cre07.g320400' => 'cre', 'Cre07.g320450' => 'cre', 'Cre08.g384650' => 'cre', 'Cre09.g393173' => 'cre', 'Cre09.g394325' => 'cre', 'Cre14.g626750' => 'cre', 'Cre16.g679250' => 'cre', 'CsaV3_3G012890' => 'csa', 'CSS0010865' => 'camsi', 'CSS0044338' => 'camsi', 'DCAR_002366' => 'dca', 'DCAR_030687' => 'dca', 'DCAR_030688' => 'dca', 'Dinv14047' => 'din', 'Dinv14048' => 'din', 'Duzib151G0105' => 'dzi', 'Duzib151G0114' => 'dzi', 'Duzib212G1029' => 'dzi', 'ECA232G3536' => 'eca', 'ECA240G0786' => 'eca', 'ECA240G1802' => 'eca', 'ECA240G3760' => 'eca', 'ECA240G3920' => 'eca', 'EL10Ac5g12536' => 'bvu', 'EL10Ac5g12537' => 'bvu', 'EL10Ac5g12538' => 'bvu', 'Eucgr.B01004' => 'egr', 'Eucgr.B01006' => 'egr', 'Eucgr.B01007' => 'egr', 'Eucgr.B01008' => 'egr', 'Eucgr.B01895' => 'egr', 'Eucgr.B01896' => 'egr', 'FAN04G1456' => 'fan', 'FAN08G1769' => 'fan', 'FAN08G2160' => 'fan', 'FAN13G2403' => 'fan', 'FAN13G3303' => 'fan', 'FAN15G2435' => 'fan', 'FAN17G0672' => 'fan', 'FAN17G2441' => 'fan', 'FAN18G1024' => 'fan', 'FAN22G1458' => 'fan', 'FAN24G0037' => 'fan', 'FAN24G0429' => 'fan', 'FAN24G2387' => 'fan', 'FAN27G2746' => 'fan', 'FvH4_2g20400' => 'fve', 'FvH4_2g20420' => 'fve', 'FvH4_2g20430' => 'fve', 'FvH4_4g01270' => 'fve', 'FvH4_4g01290' => 'fve', 'FvH4_4g01300' => 'fve', 'FvH4_4g01310' => 'fve', 'FvH4_4g01330' => 'fve', 'FvH4_5g09070' => 'fve', 'Glyma.10G243800' => 'gma', 'Glyma.20G150600' => 'gma', 'Gohir.A09G219200' => 'ghi', 'Gohir.A09G219300' => 'ghi', 'Gohir.D09G221400' => 'ghi', 'Gohir.D09G221500' => 'ghi', 'Gorai.006G242600' => 'gra', 'Gorai.006G242700' => 'gra', 'GSVIVG01018044001' => 'vvi', 'HanXRQChr03g0083821' => 'han', 'HanXRQChr03g0083841' => 'han', 'HanXRQChr03g0083881' => 'han', 'HanXRQChr03g0083901' => 'han', 'HanXRQChr03g0083921' => 'han', 'HanXRQChr03g0085331' => 'han', 'HanXRQChr03g0085361' => 'han', 'HanXRQChr03g0085411' => 'han', 'HanXRQChr03g0085421' => 'han', 'HanXRQChr03g0085431' => 'han', 'HanXRQChr08g0221991' => 'han', 'HanXRQChr11g0336061' => 'han', 'HanXRQChr11g0336411' => 'han', 'Haze_11234' => 'cav', 'Hma1.2p1_0549F.1_g177010' => 'hma', 'Hma1.2p1_0602F.1_g187630' => 'hma', 'Hund14876' => 'sun', 'Hund14879' => 'sun', 'Lalb_Chr06g0160741' => 'lal', 'Lalb_Chr21g0304781' => 'lal', 'Lj3A726G19' => 'lonja', 'Lj3A726T23' => 'lonja', 'Lj3A726T24' => 'lonja', 'Lj3A726T25' => 'lonja', 'Lj3A727T17' => 'lonja', 'Lj3C726T0' => 'lonja', 'Lj3C726T2' => 'lonja', 'Lj3P725T35' => 'lonja', 'Lj3P727T10' => 'lonja', 'Lj3P727T12' => 'lonja', 'Lj3P727T14' => 'lonja', 'Lj5g0023109' => 'lja', 'Lj6P646T44' => 'lonja', 'Lsat_1_v5_gn_6_75760' => 'lsa', 'Lsat_1_v5_gn_6_75800' => 'lsa', 'Lsat_1_v5_gn_6_75900' => 'lsa', 'Lsat_1_v5_gn_6_76240' => 'lsa', 'Lsat_1_v5_gn_6_76441' => 'lsa', 'Lsat_1_v5_gn_6_76700' => 'lsa', 'Lsat_1_v5_gn_6_76760' => 'lsa', 'Manes.15G033100' => 'mes', 'Mapoly0004s0074' => 'mpo', 'Mapoly0004s0075' => 'mpo', 'Mapoly0004s0163' => 'mpo', 'Mapoly0004s0164' => 'mpo', 'Mapoly0021s0018' => 'mpo', 'Mapoly0041s0136' => 'mpo', 'Mapoly0041s0137' => 'mpo', 'Mapoly0041s0138' => 'mpo', 'Mapoly0041s0139' => 'mpo', 'Mapoly0041s0141' => 'mpo', 'Mapoly0041s0142' => 'mpo', 'Mapoly0041s0143' => 'mpo', 'Mapoly0041s0144' => 'mpo', 'Mapoly0041s0145' => 'mpo', 'Mapoly0047s0106' => 'mpo', 'Mapoly0047s0108' => 'mpo', 'Mapoly0050s0051' => 'mpo', 'Mapoly0050s0052' => 'mpo', 'Mapoly0050s0053' => 'mpo', 'Mapoly0058s0013' => 'mpo', 'Mapoly0091s0078' => 'mpo', 'Mapoly0091s0079' => 'mpo', 'Mapoly0091s0080' => 'mpo', 'Mapoly0091s0081' => 'mpo', 'Mapoly0278s0004' => 'mpo', 'Mapoly0278s0005' => 'mpo', 'Mapoly0278s0006' => 'mpo', 'MBI11_g30648_MAGBIO' => 'mbi', 'MCO03G194' => 'mco', 'MCO03G590' => 'mco', 'MCO07G312' => 'mco', 'MCO10G318' => 'mco', 'MCO12G244' => 'mco', 'MCO13G148' => 'mco', 'MCO13G194' => 'mco', 'MCO16G238' => 'mco', 'MD06G1134100' => 'mdo', 'MD13G1200100' => 'mdo', 'MD13G1200300' => 'mdo', 'MD13G1200600' => 'mdo', 'MD14G1150400' => 'mdo', 'MD16G1200000' => 'mdo', 'Medtr1g102570' => 'mtr', 'Medtr1g102780' => 'mtr', 'Medtr1g102800' => 'mtr', 'Medtr1g102810' => 'mtr', 'Medtr1g102830' => 'mtr', 'MELO3C006499.2' => 'cme', 'Migut.G00385' => 'egut', 'MSTRG.4063' => 'ama', 'Nitab4.5_0000090g0260' => 'nta', 'Nitab4.5_0000977g0030' => 'nta', 'Nitab4.5_0002541g0040' => 'nta', 'Nitab4.5_0007068g0040' => 'nta', 'Nn005s41408' => 'nnu', 'Nn005s41410' => 'nnu', 'Oeu010310.1' => 'oeu', 'Oeu010311.1' => 'oeu', 'Oeu043472.1' => 'oeu', 'Os01g0246400' => 'osa', 'Os04g0267950' => 'osa', 'Os07g0178700' => 'osa', 'Os07g0178800' => 'osa', 'Peaxi162Scf00316g00046' => 'pax', 'Peaxi162Scf00316g00049' => 'pax', 'Peaxi162Scf00316g00059' => 'pax', 'Peaxi162Scf00316g00328' => 'pax', 'Peaxi162Scf00316g00329' => 'pax', 'Peaxi162Scf00316g00411' => 'pax', 'Peaxi162Scf00316g00521' => 'pax', 'Peaxi162Scf00492g00068' => 'pax', 'Peaxi162Scf35631g00002' => 'pax', 'PGR142G3720' => 'pgr', 'PGSC0003DMG400006442' => 'stu', 'Phvul.007G062000' => 'pvu', 'Potri.008G157750' => 'ptr', 'Potri.008G157900' => 'ptr', 'Potri.008G158000' => 'ptr', 'Potri.008G158200' => 'ptr', 'Pp3c11_7280' => 'ppa', 'Pp3c11_7980' => 'ppa', 'Pp3c12_19450' => 'ppa', 'Pp3c14_1480' => 'ppa', 'Pp3c14_1501' => 'ppa', 'Pp3c16_4900' => 'ppa', 'Pp3c16_5010' => 'ppa', 'Pp3c16_5060' => 'ppa', 'Pp3c19_18250' => 'ppa', 'Pp3c23_8530' => 'ppa', 'Pp3c23_8550' => 'ppa', 'Pp3c24_9670' => 'ppa', 'Pp3c2_21390' => 'ppa', 'Pp3c2_31380' => 'ppa', 'Pp3c3_16620' => 'ppa', 'Pp3c3_8090' => 'ppa', 'Pp3c3_8110' => 'ppa', 'Pp3c3_8130' => 'ppa', 'Pp3c3_8150' => 'ppa', 'Pp3c4_14320' => 'ppa', 'Pp3c6_2560' => 'ppa', 'Pp3c9_16700' => 'ppa', 'PRCOL_00000234' => 'pco', 'PRCOL_00000235' => 'pco', 'PRCOL_00000777' => 'pco', 'PRCOL_00002344' => 'pco', 'PRCOL_00002372' => 'pco', 'PRCOL_00006120' => 'pco', 'Prupe.1G021400' => 'ppe', 'Prupe.1G021500' => 'ppe', 'Prupe.1G021600' => 'ppe', 'Prupe.1G021700' => 'ppe', 'Prupe.1G021800' => 'ppe', 'Prupe.5G145100' => 'ppe', 'Psat6g204040' => 'psa', 'Psat6g204800' => 'psa', 'Psat6g204920' => 'psa', 'Psat6g204960' => 'psa', 'Psat6g205080' => 'psa', 'PSO017G0271' => 'pso', 'PSO017G1276' => 'pso', 'PSO017G1429' => 'pso', 'PSO017G1861' => 'pso', 'PSO017G2787' => 'pso', 'PSO017G4466' => 'pso', 'PSO017G5118' => 'pso', 'PSO017G5420' => 'pso', 'PSO063G3678' => 'pso', 'PSO210G0546' => 'pso', 'PSO317G0001' => 'pso', 'PSO357G0512' => 'pso', 'PSO478G2682' => 'pso', 'PSO647G0001' => 'pso', 'PSO675G0001' => 'pso', 'PSO675G2699' => 'pso', 'PSO675G2849' => 'pso', 'PSO675G4991' => 'pso', 'PSO689G0001' => 'pso', 'QL06p000916' => 'qlo', 'QL06p000921' => 'qlo', 'QL06p001398' => 'qlo', 'QL06p001407' => 'qlo', 'QL06p002031' => 'qlo', 'RcHm_v2.0_Chr4g0387791' => 'rch', 'RcHm_v2.0_Chr4g0387801' => 'rch', 'RcHm_v2.0_Chr6g0286501' => 'rch', 'RcHm_v2.0_Chr6g0286511' => 'rch', 'RcHm_v2.0_Chr6g0286521' => 'rch', 'RcHm_v2.0_Chr6g0286531' => 'rch', 'RcHm_v2.0_Chr7g0189141' => 'rch', 'Rhsim02G0028700' => 'rsi', 'Rhsim02G0028800' => 'rsi', 'Rhsim02G0028900' => 'rsi', 'Rhsim02G0029000' => 'rsi', 'Rhsim02G0029100' => 'rsi', 'Rhsim02G0029200' => 'rsi', 'Rhsim02G0029300' => 'rsi', 'Rhsim02G0029400' => 'rsi', 'Rhsim02G0029500' => 'rsi', 'Rhsim02G0029600' => 'rsi', 'RhsimUnG0024000' => 'rsi', 'RhsimUnG0024100' => 'rsi', 'RhsimUnG0024200' => 'rsi', 'RhsimUnG0024300' => 'rsi', 'RhsimUnG0024400' => 'rsi', 'RhsimUnG0024500' => 'rsi', 'RhsimUnG0024700' => 'rsi', 'RhsimUnG0024800' => 'rsi', 'RhsimUnG0024900' => 'rsi', 'RhsimUnG0025100' => 'rsi', 'Sabra08G0120200' => 'sbr', 'Sabra08G0120300' => 'sbr', 'Sabra08G0120500' => 'sbr', 'Sabra08G0120600' => 'sbr', 'Sabra10G0158900' => 'sbr', 'SalBow2G3492' => 'sbo', 'Sc13g0004760' => 'sci', 'Sc13g0004770' => 'sci', 'Sed0003417' => 'sed', 'Sed0019750' => 'sed', 'SEGI_03419' => 'sgi', 'SEGI_05907' => 'sgi', 'SEGI_10682' => 'sgi', 'SEGI_13528' => 'sgi', 'SEGI_16081' => 'sgi', 'SEGI_19370' => 'sgi', 'SEGI_21015' => 'sgi', 'SEGI_21944' => 'sgi', 'SEGI_32906' => 'sgi', 'SEGI_33093' => 'sgi', 'SEGI_36110' => 'sgi', 'SEGI_40397' => 'sgi', 'SGA_v2.0_scaffold191G40426' => 'sas', 'SGA_v2.0_scaffold353G49717' => 'sas', 'SGA_v2.0_scaffold50G18550' => 'sas', 'SMO119G0173' => 'smo', 'SMO172G0002' => 'smo', 'Solyc09g082690.3' => 'sly', 'Solyc09g082700.2' => 'sly', 'Sopen09g031550' => 'spe', 'Sopen09g031560' => 'spe', 'Sp3g20540' => 'spa', 'Sp7g07580' => 'spa', 'TAR134G0002' => 'tar', 'TAR236G0001' => 'tar', 'TAR365G0892' => 'tar', 'TAR636G0166' => 'tar', 'TAR636G0646' => 'tar', 'TAR636G0869' => 'tar', 'TAR636G1317' => 'tar', 'TAR636G1744' => 'tar', 'TAR636G3358' => 'tar', 'TAR636G3436' => 'tar', 'THA.LOC104803047' => 'tha', 'Thecc.04G238900' => 'tca', 'Thhalv10021557m.g' => 'esa', 'Thhalv10026318m.g' => 'esa', 'Thhalv10026335m.g' => 'esa', 'TPR.G17433' => 'tpr', 'TPR.G18915' => 'tpr', 'TPR.G26125' => 'tpr', 'TWI09G0677' => 'twi', 'TWI73G0287' => 'twi', 'unitig_748.g8326' => 'ugi', 'vmacro15370' => 'vma', 'vmacro15371' => 'vma', 'vmacro15372' => 'vma', 'vmacro15373' => 'vma', 'vmacro15374' => 'vma', 'VMungo0720G2826' => 'vmu', 'Zm00001eb116960' => 'zma', 'Zm00001eb301260' => 'zma', 'Zm00001eb301270' => 'zma' ) $gf_id = 'HOM05D001460' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001460' ) $data_identifier = 'HOM05D001460' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 4, 'aag' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 2, 'aox' => (int) 2, 'arhy' => (int) 4, 'ath' => (int) 2, 'atr' => (int) 1, 'acertr' => (int) 10, 'cqu' => (int) 4, 'bca' => (int) 11, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 1, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 1, 'ccan' => (int) 1, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 1, 'col' => (int) 1, 'cpa' => (int) 1, 'cre' => (int) 7, 'csa' => (int) 1, 'camsi' => (int) 2, 'dca' => (int) 3, 'din' => (int) 2, 'dzi' => (int) 3, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 14, 'fve' => (int) 9, 'gma' => (int) 2, 'ghi' => (int) 4, 'gra' => (int) 2, 'vvi' => (int) 1, 'han' => (int) 13, 'cav' => (int) 1, 'hma' => (int) 2, 'sun' => (int) 2, 'lal' => (int) 2, 'lonja' => (int) 12, 'lja' => (int) 1, 'lsa' => (int) 7, 'mes' => (int) 1, 'mpo' => (int) 27, 'mbi' => (int) 1, 'mco' => (int) 8, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 1, 'egut' => (int) 1, 'ama' => (int) 1, 'nta' => (int) 4, 'nnu' => (int) 2, 'oeu' => (int) 3, 'osa' => (int) 4, 'pax' => (int) 9, 'pgr' => (int) 1, 'stu' => (int) 1, 'pvu' => (int) 1, 'ptr' => (int) 4, 'ppa' => (int) 22, 'pco' => (int) 6, 'ppe' => (int) 6, 'psa' => (int) 5, 'pso' => (int) 19, 'qlo' => (int) 5, 'rch' => (int) 7, 'rsi' => (int) 20, 'sbr' => (int) 5, 'sbo' => (int) 1, 'sci' => (int) 2, 'sed' => (int) 2, 'sgi' => (int) 12, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 2, 'tar' => (int) 10, 'tha' => (int) 1, 'tca' => (int) 1, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 2, 'ugi' => (int) 1, 'vma' => (int) 5, 'vmu' => (int) 1, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb301270' $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' => 'HOM05D001460', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '433', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p22980' => 'bna', 'A01p32340' => 'bna', 'A03p42970' => 'bna', 'A05p25880' => 'bna', 'Aa31LG8G9320' => 'aar', 'Aa31LG8G9330' => 'aar', 'Aa31LG8G9340' => 'aar', 'Aa31sc221G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1034' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1528' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.829' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2222' => 'aag', 'Ah.12g058830' => 'amhyb', 'Ah.12g058840' => 'amhyb', 'AL3G37160' => 'aly', 'AL7G41310' => 'aly', 'Aqoxy5G00395' => 'aox', 'Aqoxy5G00396' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0C8NZA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5185HY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JZ1PRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MD3LS0' => 'arhy', 'AT3G22840' => 'ath', 'AT4G14690' => 'ath', 'ATR0665G054' => 'atr', 'Atru.chr4.2344' => 'acertr', 'Atru.chr4.2346' => 'acertr', 'Atru.chr4.2347' => 'acertr', 'Atru.chr4.2348' => 'acertr', 'Atru.chr4.2355' => 'acertr', 'Atru.chr4.2356' => 'acertr', 'Atru.chr4.2358' => 'acertr', 'Atru.chr4.2359' => 'acertr', 'Atru.chr4.2360' => 'acertr', 'Atru.chr4.2361' => 'acertr', 'AUR62030476' => 'cqu', 'AUR62030478' => 'cqu', 'AUR62030819' => 'cqu', 'AUR62030820' => 'cqu', 'BcaB03g14648' => 'bca', 'BcaB04g20492' => 'bca', 'BcaB06g26399' => 'bca', 'BcaC01g03416' => 'bca', 'BcaC01g03419' => 'bca', 'BcaC01g03421' => 'bca', 'BcaC01g03424' => 'bca', 'BcaC05g28012' => 'bca', 'BcaC09g49212' => 'bca', 'BcaC09g50140' => 'bca', 'BcaNung00346' => 'bca', 'BolC1t02785H' => 'bol', 'BolC1t04095H' => 'bol', 'BolC3t17545H' => 'bol', 'BolC5t32769H' => 'bol', 'BraA01t02211Z' => 'bra', 'BraA01t03359Z' => 'bra', 'BraA03t13441Z' => 'bra', 'BraA05t21476Z' => 'bra', 'C01p28420' => 'bna', 'C01p41350' => 'bna', 'C03p52750' => 'bna', 'C03p52780' => 'bna', 'C05p40270' => 'bna', 'CAN.G1437.9' => 'can', 'CANSAT78G0035' => 'cansat', 'CANSAT78G1036' => 'cansat', 'CANSAT78G2272' => 'cansat', 'CANSAT78G2478' => 'cansat', 'CARHR098700' => 'chi', 'CARHR221120' => 'chi', 'CARHR221150' => 'chi', 'Carub.0003s2297' => 'cru', 'Carub.0007s2749' => 'cru', 'Carub.0007s2750' => 'cru', 'Carub.0007s2751' => 'cru', 'Ca_10849_v3' => 'car', 'Cc03_g04300' => 'ccan', 'CDE02G3648' => 'cde', 'CDE05G0060' => 'cde', 'CDE05G0692' => 'cde', 'CDE05G2285' => 'cde', 'CDE05G2884' => 'cde', 'CDE05G3072' => 'cde', 'Cfa008439' => 'cfa', 'Cfa008441' => 'cfa', 'Cfa008443' => 'cfa', 'Cfa008448' => 'cfa', 'Ciclev10005974m.g' => 'ccl', 'Ciclev10006006m.g' => 'ccl', 'Ciclev10006775m.g' => 'ccl', 'CiPaw.02G120400' => 'cil', 'CiPaw.02G120500' => 'cil', 'CiPaw.02G120600' => 'cil', 'ClCG05G004850' => 'cla', 'COL.COLO4_21566' => 'col', 'Cpa.g.sc44.124' => 'cpa', 'Cre07.g320400' => 'cre', 'Cre07.g320450' => 'cre', 'Cre08.g384650' => 'cre', 'Cre09.g393173' => 'cre', 'Cre09.g394325' => 'cre', 'Cre14.g626750' => 'cre', 'Cre16.g679250' => 'cre', 'CsaV3_3G012890' => 'csa', 'CSS0010865' => 'camsi', 'CSS0044338' => 'camsi', 'DCAR_002366' => 'dca', 'DCAR_030687' => 'dca', 'DCAR_030688' => 'dca', 'Dinv14047' => 'din', 'Dinv14048' => 'din', 'Duzib151G0105' => 'dzi', 'Duzib151G0114' => 'dzi', 'Duzib212G1029' => 'dzi', 'ECA232G3536' => 'eca', 'ECA240G0786' => 'eca', 'ECA240G1802' => 'eca', 'ECA240G3760' => 'eca', 'ECA240G3920' => 'eca', 'EL10Ac5g12536' => 'bvu', 'EL10Ac5g12537' => 'bvu', 'EL10Ac5g12538' => 'bvu', 'Eucgr.B01004' => 'egr', 'Eucgr.B01006' => 'egr', 'Eucgr.B01007' => 'egr', 'Eucgr.B01008' => 'egr', 'Eucgr.B01895' => 'egr', 'Eucgr.B01896' => 'egr', 'FAN04G1456' => 'fan', 'FAN08G1769' => 'fan', 'FAN08G2160' => 'fan', 'FAN13G2403' => 'fan', 'FAN13G3303' => 'fan', 'FAN15G2435' => 'fan', 'FAN17G0672' => 'fan', 'FAN17G2441' => 'fan', 'FAN18G1024' => 'fan', 'FAN22G1458' => 'fan', 'FAN24G0037' => 'fan', 'FAN24G0429' => 'fan', 'FAN24G2387' => 'fan', 'FAN27G2746' => 'fan', 'FvH4_2g20400' => 'fve', 'FvH4_2g20420' => 'fve', 'FvH4_2g20430' => 'fve', 'FvH4_4g01270' => 'fve', 'FvH4_4g01290' => 'fve', 'FvH4_4g01300' => 'fve', 'FvH4_4g01310' => 'fve', 'FvH4_4g01330' => 'fve', 'FvH4_5g09070' => 'fve', 'Glyma.10G243800' => 'gma', 'Glyma.20G150600' => 'gma', 'Gohir.A09G219200' => 'ghi', 'Gohir.A09G219300' => 'ghi', 'Gohir.D09G221400' => 'ghi', 'Gohir.D09G221500' => 'ghi', 'Gorai.006G242600' => 'gra', 'Gorai.006G242700' => 'gra', 'GSVIVG01018044001' => 'vvi', 'HanXRQChr03g0083821' => 'han', 'HanXRQChr03g0083841' => 'han', 'HanXRQChr03g0083881' => 'han', 'HanXRQChr03g0083901' => 'han', 'HanXRQChr03g0083921' => 'han', 'HanXRQChr03g0085331' => 'han', 'HanXRQChr03g0085361' => 'han', 'HanXRQChr03g0085411' => 'han', 'HanXRQChr03g0085421' => 'han', 'HanXRQChr03g0085431' => 'han', 'HanXRQChr08g0221991' => 'han', 'HanXRQChr11g0336061' => 'han', 'HanXRQChr11g0336411' => 'han', 'Haze_11234' => 'cav', 'Hma1.2p1_0549F.1_g177010' => 'hma', 'Hma1.2p1_0602F.1_g187630' => 'hma', 'Hund14876' => 'sun', 'Hund14879' => 'sun', 'Lalb_Chr06g0160741' => 'lal', 'Lalb_Chr21g0304781' => 'lal', 'Lj3A726G19' => 'lonja', 'Lj3A726T23' => 'lonja', 'Lj3A726T24' => 'lonja', 'Lj3A726T25' => 'lonja', 'Lj3A727T17' => 'lonja', 'Lj3C726T0' => 'lonja', 'Lj3C726T2' => 'lonja', 'Lj3P725T35' => 'lonja', 'Lj3P727T10' => 'lonja', 'Lj3P727T12' => 'lonja', 'Lj3P727T14' => 'lonja', 'Lj5g0023109' => 'lja', 'Lj6P646T44' => 'lonja', 'Lsat_1_v5_gn_6_75760' => 'lsa', 'Lsat_1_v5_gn_6_75800' => 'lsa', 'Lsat_1_v5_gn_6_75900' => 'lsa', 'Lsat_1_v5_gn_6_76240' => 'lsa', 'Lsat_1_v5_gn_6_76441' => 'lsa', 'Lsat_1_v5_gn_6_76700' => 'lsa', 'Lsat_1_v5_gn_6_76760' => 'lsa', 'Manes.15G033100' => 'mes', 'Mapoly0004s0074' => 'mpo', 'Mapoly0004s0075' => 'mpo', 'Mapoly0004s0163' => 'mpo', 'Mapoly0004s0164' => 'mpo', 'Mapoly0021s0018' => 'mpo', 'Mapoly0041s0136' => 'mpo', 'Mapoly0041s0137' => 'mpo', 'Mapoly0041s0138' => 'mpo', 'Mapoly0041s0139' => 'mpo', 'Mapoly0041s0141' => 'mpo', 'Mapoly0041s0142' => 'mpo', 'Mapoly0041s0143' => 'mpo', 'Mapoly0041s0144' => 'mpo', 'Mapoly0041s0145' => 'mpo', 'Mapoly0047s0106' => 'mpo', 'Mapoly0047s0108' => 'mpo', 'Mapoly0050s0051' => 'mpo', 'Mapoly0050s0052' => 'mpo', 'Mapoly0050s0053' => 'mpo', 'Mapoly0058s0013' => 'mpo', 'Mapoly0091s0078' => 'mpo', 'Mapoly0091s0079' => 'mpo', 'Mapoly0091s0080' => 'mpo', 'Mapoly0091s0081' => 'mpo', 'Mapoly0278s0004' => 'mpo', 'Mapoly0278s0005' => 'mpo', 'Mapoly0278s0006' => 'mpo', 'MBI11_g30648_MAGBIO' => 'mbi', 'MCO03G194' => 'mco', 'MCO03G590' => 'mco', 'MCO07G312' => 'mco', 'MCO10G318' => 'mco', 'MCO12G244' => 'mco', 'MCO13G148' => 'mco', 'MCO13G194' => 'mco', 'MCO16G238' => 'mco', 'MD06G1134100' => 'mdo', 'MD13G1200100' => 'mdo', 'MD13G1200300' => 'mdo', 'MD13G1200600' => 'mdo', 'MD14G1150400' => 'mdo', 'MD16G1200000' => 'mdo', 'Medtr1g102570' => 'mtr', 'Medtr1g102780' => 'mtr', 'Medtr1g102800' => 'mtr', 'Medtr1g102810' => 'mtr', 'Medtr1g102830' => 'mtr', 'MELO3C006499.2' => 'cme', 'Migut.G00385' => 'egut', 'MSTRG.4063' => 'ama', 'Nitab4.5_0000090g0260' => 'nta', 'Nitab4.5_0000977g0030' => 'nta', 'Nitab4.5_0002541g0040' => 'nta', 'Nitab4.5_0007068g0040' => 'nta', 'Nn005s41408' => 'nnu', 'Nn005s41410' => 'nnu', 'Oeu010310.1' => 'oeu', 'Oeu010311.1' => 'oeu', 'Oeu043472.1' => 'oeu', 'Os01g0246400' => 'osa', 'Os04g0267950' => 'osa', 'Os07g0178700' => 'osa', 'Os07g0178800' => 'osa', 'Peaxi162Scf00316g00046' => 'pax', 'Peaxi162Scf00316g00049' => 'pax', 'Peaxi162Scf00316g00059' => 'pax', 'Peaxi162Scf00316g00328' => 'pax', 'Peaxi162Scf00316g00329' => 'pax', 'Peaxi162Scf00316g00411' => 'pax', 'Peaxi162Scf00316g00521' => 'pax', 'Peaxi162Scf00492g00068' => 'pax', 'Peaxi162Scf35631g00002' => 'pax', 'PGR142G3720' => 'pgr', 'PGSC0003DMG400006442' => 'stu', 'Phvul.007G062000' => 'pvu', 'Potri.008G157750' => 'ptr', 'Potri.008G157900' => 'ptr', 'Potri.008G158000' => 'ptr', 'Potri.008G158200' => 'ptr', 'Pp3c11_7280' => 'ppa', 'Pp3c11_7980' => 'ppa', 'Pp3c12_19450' => 'ppa', 'Pp3c14_1480' => 'ppa', 'Pp3c14_1501' => 'ppa', 'Pp3c16_4900' => 'ppa', 'Pp3c16_5010' => 'ppa', 'Pp3c16_5060' => 'ppa', 'Pp3c19_18250' => 'ppa', 'Pp3c23_8530' => 'ppa', 'Pp3c23_8550' => 'ppa', 'Pp3c24_9670' => 'ppa', 'Pp3c2_21390' => 'ppa', 'Pp3c2_31380' => 'ppa', 'Pp3c3_16620' => 'ppa', 'Pp3c3_8090' => 'ppa', 'Pp3c3_8110' => 'ppa', 'Pp3c3_8130' => 'ppa', 'Pp3c3_8150' => 'ppa', 'Pp3c4_14320' => 'ppa', 'Pp3c6_2560' => 'ppa', 'Pp3c9_16700' => 'ppa', 'PRCOL_00000234' => 'pco', 'PRCOL_00000235' => 'pco', 'PRCOL_00000777' => 'pco', 'PRCOL_00002344' => 'pco', 'PRCOL_00002372' => 'pco', 'PRCOL_00006120' => 'pco', 'Prupe.1G021400' => 'ppe', 'Prupe.1G021500' => 'ppe', 'Prupe.1G021600' => 'ppe', 'Prupe.1G021700' => 'ppe', 'Prupe.1G021800' => 'ppe', 'Prupe.5G145100' => 'ppe', 'Psat6g204040' => 'psa', 'Psat6g204800' => 'psa', 'Psat6g204920' => 'psa', 'Psat6g204960' => 'psa', 'Psat6g205080' => 'psa', 'PSO017G0271' => 'pso', 'PSO017G1276' => 'pso', 'PSO017G1429' => 'pso', 'PSO017G1861' => 'pso', 'PSO017G2787' => 'pso', 'PSO017G4466' => 'pso', 'PSO017G5118' => 'pso', 'PSO017G5420' => 'pso', 'PSO063G3678' => 'pso', 'PSO210G0546' => 'pso', 'PSO317G0001' => 'pso', 'PSO357G0512' => 'pso', 'PSO478G2682' => 'pso', 'PSO647G0001' => 'pso', 'PSO675G0001' => 'pso', 'PSO675G2699' => 'pso', 'PSO675G2849' => 'pso', 'PSO675G4991' => 'pso', 'PSO689G0001' => 'pso', 'QL06p000916' => 'qlo', 'QL06p000921' => 'qlo', 'QL06p001398' => 'qlo', 'QL06p001407' => 'qlo', 'QL06p002031' => 'qlo', 'RcHm_v2.0_Chr4g0387791' => 'rch', 'RcHm_v2.0_Chr4g0387801' => 'rch', 'RcHm_v2.0_Chr6g0286501' => 'rch', 'RcHm_v2.0_Chr6g0286511' => 'rch', 'RcHm_v2.0_Chr6g0286521' => 'rch', 'RcHm_v2.0_Chr6g0286531' => 'rch', 'RcHm_v2.0_Chr7g0189141' => 'rch', 'Rhsim02G0028700' => 'rsi', 'Rhsim02G0028800' => 'rsi', 'Rhsim02G0028900' => 'rsi', 'Rhsim02G0029000' => 'rsi', 'Rhsim02G0029100' => 'rsi', 'Rhsim02G0029200' => 'rsi', 'Rhsim02G0029300' => 'rsi', 'Rhsim02G0029400' => 'rsi', 'Rhsim02G0029500' => 'rsi', 'Rhsim02G0029600' => 'rsi', 'RhsimUnG0024000' => 'rsi', 'RhsimUnG0024100' => 'rsi', 'RhsimUnG0024200' => 'rsi', 'RhsimUnG0024300' => 'rsi', 'RhsimUnG0024400' => 'rsi', 'RhsimUnG0024500' => 'rsi', 'RhsimUnG0024700' => 'rsi', 'RhsimUnG0024800' => 'rsi', 'RhsimUnG0024900' => 'rsi', 'RhsimUnG0025100' => 'rsi', 'Sabra08G0120200' => 'sbr', 'Sabra08G0120300' => 'sbr', 'Sabra08G0120500' => 'sbr', 'Sabra08G0120600' => 'sbr', 'Sabra10G0158900' => 'sbr', 'SalBow2G3492' => 'sbo', 'Sc13g0004760' => 'sci', 'Sc13g0004770' => 'sci', 'Sed0003417' => 'sed', 'Sed0019750' => 'sed', 'SEGI_03419' => 'sgi', 'SEGI_05907' => 'sgi', 'SEGI_10682' => 'sgi', 'SEGI_13528' => 'sgi', 'SEGI_16081' => 'sgi', 'SEGI_19370' => 'sgi', 'SEGI_21015' => 'sgi', 'SEGI_21944' => 'sgi', 'SEGI_32906' => 'sgi', 'SEGI_33093' => 'sgi', 'SEGI_36110' => 'sgi', 'SEGI_40397' => 'sgi', 'SGA_v2.0_scaffold191G40426' => 'sas', 'SGA_v2.0_scaffold353G49717' => 'sas', 'SGA_v2.0_scaffold50G18550' => 'sas', 'SMO119G0173' => 'smo', 'SMO172G0002' => 'smo', 'Solyc09g082690.3' => 'sly', 'Solyc09g082700.2' => 'sly', 'Sopen09g031550' => 'spe', 'Sopen09g031560' => 'spe', 'Sp3g20540' => 'spa', 'Sp7g07580' => 'spa', 'TAR134G0002' => 'tar', 'TAR236G0001' => 'tar', 'TAR365G0892' => 'tar', 'TAR636G0166' => 'tar', 'TAR636G0646' => 'tar', 'TAR636G0869' => 'tar', 'TAR636G1317' => 'tar', 'TAR636G1744' => 'tar', 'TAR636G3358' => 'tar', 'TAR636G3436' => 'tar', 'THA.LOC104803047' => 'tha', 'Thecc.04G238900' => 'tca', 'Thhalv10021557m.g' => 'esa', 'Thhalv10026318m.g' => 'esa', 'Thhalv10026335m.g' => 'esa', 'TPR.G17433' => 'tpr', 'TPR.G18915' => 'tpr', 'TPR.G26125' => 'tpr', 'TWI09G0677' => 'twi', 'TWI73G0287' => 'twi', 'unitig_748.g8326' => 'ugi', 'vmacro15370' => 'vma', 'vmacro15371' => 'vma', 'vmacro15372' => 'vma', 'vmacro15373' => 'vma', 'vmacro15374' => 'vma', 'VMungo0720G2826' => 'vmu', 'Zm00001eb116960' => 'zma', 'Zm00001eb301260' => 'zma', 'Zm00001eb301270' => 'zma' ), 'gf_id' => 'HOM05D001460', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001460' ), 'data_identifier' => 'HOM05D001460', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001460', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '433', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p22980' => 'bna', 'A01p32340' => 'bna', 'A03p42970' => 'bna', 'A05p25880' => 'bna', 'Aa31LG8G9320' => 'aar', 'Aa31LG8G9330' => 'aar', 'Aa31LG8G9340' => 'aar', 'Aa31sc221G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1034' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1528' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.829' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2222' => 'aag', 'Ah.12g058830' => 'amhyb', 'Ah.12g058840' => 'amhyb', 'AL3G37160' => 'aly', 'AL7G41310' => 'aly', 'Aqoxy5G00395' => 'aox', 'Aqoxy5G00396' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0C8NZA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5185HY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JZ1PRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MD3LS0' => 'arhy', 'AT3G22840' => 'ath', 'AT4G14690' => 'ath', 'ATR0665G054' => 'atr', 'Atru.chr4.2344' => 'acertr', 'Atru.chr4.2346' => 'acertr', 'Atru.chr4.2347' => 'acertr', 'Atru.chr4.2348' => 'acertr', 'Atru.chr4.2355' => 'acertr', 'Atru.chr4.2356' => 'acertr', 'Atru.chr4.2358' => 'acertr', 'Atru.chr4.2359' => 'acertr', 'Atru.chr4.2360' => 'acertr', 'Atru.chr4.2361' => 'acertr', 'AUR62030476' => 'cqu', 'AUR62030478' => 'cqu', 'AUR62030819' => 'cqu', 'AUR62030820' => 'cqu', 'BcaB03g14648' => 'bca', 'BcaB04g20492' => 'bca', 'BcaB06g26399' => 'bca', 'BcaC01g03416' => 'bca', 'BcaC01g03419' => 'bca', 'BcaC01g03421' => 'bca', 'BcaC01g03424' => 'bca', 'BcaC05g28012' => 'bca', 'BcaC09g49212' => 'bca', 'BcaC09g50140' => 'bca', 'BcaNung00346' => 'bca', 'BolC1t02785H' => 'bol', 'BolC1t04095H' => 'bol', 'BolC3t17545H' => 'bol', 'BolC5t32769H' => 'bol', 'BraA01t02211Z' => 'bra', 'BraA01t03359Z' => 'bra', 'BraA03t13441Z' => 'bra', 'BraA05t21476Z' => 'bra', 'C01p28420' => 'bna', 'C01p41350' => 'bna', 'C03p52750' => 'bna', 'C03p52780' => 'bna', 'C05p40270' => 'bna', 'CAN.G1437.9' => 'can', 'CANSAT78G0035' => 'cansat', 'CANSAT78G1036' => 'cansat', 'CANSAT78G2272' => 'cansat', 'CANSAT78G2478' => 'cansat', 'CARHR098700' => 'chi', 'CARHR221120' => 'chi', 'CARHR221150' => 'chi', 'Carub.0003s2297' => 'cru', 'Carub.0007s2749' => 'cru', 'Carub.0007s2750' => 'cru', 'Carub.0007s2751' => 'cru', 'Ca_10849_v3' => 'car', 'Cc03_g04300' => 'ccan', 'CDE02G3648' => 'cde', 'CDE05G0060' => 'cde', 'CDE05G0692' => 'cde', 'CDE05G2285' => 'cde', 'CDE05G2884' => 'cde', 'CDE05G3072' => 'cde', 'Cfa008439' => 'cfa', 'Cfa008441' => 'cfa', 'Cfa008443' => 'cfa', 'Cfa008448' => 'cfa', 'Ciclev10005974m.g' => 'ccl', 'Ciclev10006006m.g' => 'ccl', 'Ciclev10006775m.g' => 'ccl', 'CiPaw.02G120400' => 'cil', 'CiPaw.02G120500' => 'cil', 'CiPaw.02G120600' => 'cil', 'ClCG05G004850' => 'cla', 'COL.COLO4_21566' => 'col', 'Cpa.g.sc44.124' => 'cpa', 'Cre07.g320400' => 'cre', 'Cre07.g320450' => 'cre', 'Cre08.g384650' => 'cre', 'Cre09.g393173' => 'cre', 'Cre09.g394325' => 'cre', 'Cre14.g626750' => 'cre', 'Cre16.g679250' => 'cre', 'CsaV3_3G012890' => 'csa', 'CSS0010865' => 'camsi', 'CSS0044338' => 'camsi', 'DCAR_002366' => 'dca', 'DCAR_030687' => 'dca', 'DCAR_030688' => 'dca', 'Dinv14047' => 'din', 'Dinv14048' => 'din', 'Duzib151G0105' => 'dzi', 'Duzib151G0114' => 'dzi', 'Duzib212G1029' => 'dzi', 'ECA232G3536' => 'eca', 'ECA240G0786' => 'eca', 'ECA240G1802' => 'eca', 'ECA240G3760' => 'eca', 'ECA240G3920' => 'eca', 'EL10Ac5g12536' => 'bvu', 'EL10Ac5g12537' => 'bvu', 'EL10Ac5g12538' => 'bvu', 'Eucgr.B01004' => 'egr', 'Eucgr.B01006' => 'egr', 'Eucgr.B01007' => 'egr', 'Eucgr.B01008' => 'egr', 'Eucgr.B01895' => 'egr', 'Eucgr.B01896' => 'egr', 'FAN04G1456' => 'fan', 'FAN08G1769' => 'fan', 'FAN08G2160' => 'fan', 'FAN13G2403' => 'fan', 'FAN13G3303' => 'fan', 'FAN15G2435' => 'fan', 'FAN17G0672' => 'fan', 'FAN17G2441' => 'fan', 'FAN18G1024' => 'fan', 'FAN22G1458' => 'fan', 'FAN24G0037' => 'fan', 'FAN24G0429' => 'fan', 'FAN24G2387' => 'fan', 'FAN27G2746' => 'fan', 'FvH4_2g20400' => 'fve', 'FvH4_2g20420' => 'fve', 'FvH4_2g20430' => 'fve', 'FvH4_4g01270' => 'fve', 'FvH4_4g01290' => 'fve', 'FvH4_4g01300' => 'fve', 'FvH4_4g01310' => 'fve', 'FvH4_4g01330' => 'fve', 'FvH4_5g09070' => 'fve', 'Glyma.10G243800' => 'gma', 'Glyma.20G150600' => 'gma', 'Gohir.A09G219200' => 'ghi', 'Gohir.A09G219300' => 'ghi', 'Gohir.D09G221400' => 'ghi', 'Gohir.D09G221500' => 'ghi', 'Gorai.006G242600' => 'gra', 'Gorai.006G242700' => 'gra', 'GSVIVG01018044001' => 'vvi', 'HanXRQChr03g0083821' => 'han', 'HanXRQChr03g0083841' => 'han', 'HanXRQChr03g0083881' => 'han', 'HanXRQChr03g0083901' => 'han', 'HanXRQChr03g0083921' => 'han', 'HanXRQChr03g0085331' => 'han', 'HanXRQChr03g0085361' => 'han', 'HanXRQChr03g0085411' => 'han', 'HanXRQChr03g0085421' => 'han', 'HanXRQChr03g0085431' => 'han', 'HanXRQChr08g0221991' => 'han', 'HanXRQChr11g0336061' => 'han', 'HanXRQChr11g0336411' => 'han', 'Haze_11234' => 'cav', 'Hma1.2p1_0549F.1_g177010' => 'hma', 'Hma1.2p1_0602F.1_g187630' => 'hma', 'Hund14876' => 'sun', 'Hund14879' => 'sun', 'Lalb_Chr06g0160741' => 'lal', 'Lalb_Chr21g0304781' => 'lal', 'Lj3A726G19' => 'lonja', 'Lj3A726T23' => 'lonja', 'Lj3A726T24' => 'lonja', 'Lj3A726T25' => 'lonja', 'Lj3A727T17' => 'lonja', 'Lj3C726T0' => 'lonja', 'Lj3C726T2' => 'lonja', 'Lj3P725T35' => 'lonja', 'Lj3P727T10' => 'lonja', 'Lj3P727T12' => 'lonja', 'Lj3P727T14' => 'lonja', 'Lj5g0023109' => 'lja', 'Lj6P646T44' => 'lonja', 'Lsat_1_v5_gn_6_75760' => 'lsa', 'Lsat_1_v5_gn_6_75800' => 'lsa', 'Lsat_1_v5_gn_6_75900' => 'lsa', 'Lsat_1_v5_gn_6_76240' => 'lsa', 'Lsat_1_v5_gn_6_76441' => 'lsa', 'Lsat_1_v5_gn_6_76700' => 'lsa', 'Lsat_1_v5_gn_6_76760' => 'lsa', 'Manes.15G033100' => 'mes', 'Mapoly0004s0074' => 'mpo', 'Mapoly0004s0075' => 'mpo', 'Mapoly0004s0163' => 'mpo', 'Mapoly0004s0164' => 'mpo', 'Mapoly0021s0018' => 'mpo', 'Mapoly0041s0136' => 'mpo', 'Mapoly0041s0137' => 'mpo', 'Mapoly0041s0138' => 'mpo', 'Mapoly0041s0139' => 'mpo', 'Mapoly0041s0141' => 'mpo', 'Mapoly0041s0142' => 'mpo', 'Mapoly0041s0143' => 'mpo', 'Mapoly0041s0144' => 'mpo', 'Mapoly0041s0145' => 'mpo', 'Mapoly0047s0106' => 'mpo', 'Mapoly0047s0108' => 'mpo', 'Mapoly0050s0051' => 'mpo', 'Mapoly0050s0052' => 'mpo', 'Mapoly0050s0053' => 'mpo', 'Mapoly0058s0013' => 'mpo', 'Mapoly0091s0078' => 'mpo', 'Mapoly0091s0079' => 'mpo', 'Mapoly0091s0080' => 'mpo', 'Mapoly0091s0081' => 'mpo', 'Mapoly0278s0004' => 'mpo', 'Mapoly0278s0005' => 'mpo', 'Mapoly0278s0006' => 'mpo', 'MBI11_g30648_MAGBIO' => 'mbi', 'MCO03G194' => 'mco', 'MCO03G590' => 'mco', 'MCO07G312' => 'mco', 'MCO10G318' => 'mco', 'MCO12G244' => 'mco', 'MCO13G148' => 'mco', 'MCO13G194' => 'mco', 'MCO16G238' => 'mco', 'MD06G1134100' => 'mdo', 'MD13G1200100' => 'mdo', 'MD13G1200300' => 'mdo', 'MD13G1200600' => 'mdo', 'MD14G1150400' => 'mdo', 'MD16G1200000' => 'mdo', 'Medtr1g102570' => 'mtr', 'Medtr1g102780' => 'mtr', 'Medtr1g102800' => 'mtr', 'Medtr1g102810' => 'mtr', 'Medtr1g102830' => 'mtr', 'MELO3C006499.2' => 'cme', 'Migut.G00385' => 'egut', 'MSTRG.4063' => 'ama', 'Nitab4.5_0000090g0260' => 'nta', 'Nitab4.5_0000977g0030' => 'nta', 'Nitab4.5_0002541g0040' => 'nta', 'Nitab4.5_0007068g0040' => 'nta', 'Nn005s41408' => 'nnu', 'Nn005s41410' => 'nnu', 'Oeu010310.1' => 'oeu', 'Oeu010311.1' => 'oeu', 'Oeu043472.1' => 'oeu', 'Os01g0246400' => 'osa', 'Os04g0267950' => 'osa', 'Os07g0178700' => 'osa', 'Os07g0178800' => 'osa', 'Peaxi162Scf00316g00046' => 'pax', 'Peaxi162Scf00316g00049' => 'pax', 'Peaxi162Scf00316g00059' => 'pax', 'Peaxi162Scf00316g00328' => 'pax', 'Peaxi162Scf00316g00329' => 'pax', 'Peaxi162Scf00316g00411' => 'pax', 'Peaxi162Scf00316g00521' => 'pax', 'Peaxi162Scf00492g00068' => 'pax', 'Peaxi162Scf35631g00002' => 'pax', 'PGR142G3720' => 'pgr', 'PGSC0003DMG400006442' => 'stu', 'Phvul.007G062000' => 'pvu', 'Potri.008G157750' => 'ptr', 'Potri.008G157900' => 'ptr', 'Potri.008G158000' => 'ptr', 'Potri.008G158200' => 'ptr', 'Pp3c11_7280' => 'ppa', 'Pp3c11_7980' => 'ppa', 'Pp3c12_19450' => 'ppa', 'Pp3c14_1480' => 'ppa', 'Pp3c14_1501' => 'ppa', 'Pp3c16_4900' => 'ppa', 'Pp3c16_5010' => 'ppa', 'Pp3c16_5060' => 'ppa', 'Pp3c19_18250' => 'ppa', 'Pp3c23_8530' => 'ppa', 'Pp3c23_8550' => 'ppa', 'Pp3c24_9670' => 'ppa', 'Pp3c2_21390' => 'ppa', 'Pp3c2_31380' => 'ppa', 'Pp3c3_16620' => 'ppa', 'Pp3c3_8090' => 'ppa', 'Pp3c3_8110' => 'ppa', 'Pp3c3_8130' => 'ppa', 'Pp3c3_8150' => 'ppa', 'Pp3c4_14320' => 'ppa', 'Pp3c6_2560' => 'ppa', 'Pp3c9_16700' => 'ppa', 'PRCOL_00000234' => 'pco', 'PRCOL_00000235' => 'pco', 'PRCOL_00000777' => 'pco', 'PRCOL_00002344' => 'pco', 'PRCOL_00002372' => 'pco', 'PRCOL_00006120' => 'pco', 'Prupe.1G021400' => 'ppe', 'Prupe.1G021500' => 'ppe', 'Prupe.1G021600' => 'ppe', 'Prupe.1G021700' => 'ppe', 'Prupe.1G021800' => 'ppe', 'Prupe.5G145100' => 'ppe', 'Psat6g204040' => 'psa', 'Psat6g204800' => 'psa', 'Psat6g204920' => 'psa', 'Psat6g204960' => 'psa', 'Psat6g205080' => 'psa', 'PSO017G0271' => 'pso', 'PSO017G1276' => 'pso', 'PSO017G1429' => 'pso', 'PSO017G1861' => 'pso', 'PSO017G2787' => 'pso', 'PSO017G4466' => 'pso', 'PSO017G5118' => 'pso', 'PSO017G5420' => 'pso', 'PSO063G3678' => 'pso', 'PSO210G0546' => 'pso', 'PSO317G0001' => 'pso', 'PSO357G0512' => 'pso', 'PSO478G2682' => 'pso', 'PSO647G0001' => 'pso', 'PSO675G0001' => 'pso', 'PSO675G2699' => 'pso', 'PSO675G2849' => 'pso', 'PSO675G4991' => 'pso', 'PSO689G0001' => 'pso', 'QL06p000916' => 'qlo', 'QL06p000921' => 'qlo', 'QL06p001398' => 'qlo', 'QL06p001407' => 'qlo', 'QL06p002031' => 'qlo', 'RcHm_v2.0_Chr4g0387791' => 'rch', 'RcHm_v2.0_Chr4g0387801' => 'rch', 'RcHm_v2.0_Chr6g0286501' => 'rch', 'RcHm_v2.0_Chr6g0286511' => 'rch', 'RcHm_v2.0_Chr6g0286521' => 'rch', 'RcHm_v2.0_Chr6g0286531' => 'rch', 'RcHm_v2.0_Chr7g0189141' => 'rch', 'Rhsim02G0028700' => 'rsi', 'Rhsim02G0028800' => 'rsi', 'Rhsim02G0028900' => 'rsi', 'Rhsim02G0029000' => 'rsi', 'Rhsim02G0029100' => 'rsi', 'Rhsim02G0029200' => 'rsi', 'Rhsim02G0029300' => 'rsi', 'Rhsim02G0029400' => 'rsi', 'Rhsim02G0029500' => 'rsi', 'Rhsim02G0029600' => 'rsi', 'RhsimUnG0024000' => 'rsi', 'RhsimUnG0024100' => 'rsi', 'RhsimUnG0024200' => 'rsi', 'RhsimUnG0024300' => 'rsi', 'RhsimUnG0024400' => 'rsi', 'RhsimUnG0024500' => 'rsi', 'RhsimUnG0024700' => 'rsi', 'RhsimUnG0024800' => 'rsi', 'RhsimUnG0024900' => 'rsi', 'RhsimUnG0025100' => 'rsi', 'Sabra08G0120200' => 'sbr', 'Sabra08G0120300' => 'sbr', 'Sabra08G0120500' => 'sbr', 'Sabra08G0120600' => 'sbr', 'Sabra10G0158900' => 'sbr', 'SalBow2G3492' => 'sbo', 'Sc13g0004760' => 'sci', 'Sc13g0004770' => 'sci', 'Sed0003417' => 'sed', 'Sed0019750' => 'sed', 'SEGI_03419' => 'sgi', 'SEGI_05907' => 'sgi', 'SEGI_10682' => 'sgi', 'SEGI_13528' => 'sgi', 'SEGI_16081' => 'sgi', 'SEGI_19370' => 'sgi', 'SEGI_21015' => 'sgi', 'SEGI_21944' => 'sgi', 'SEGI_32906' => 'sgi', 'SEGI_33093' => 'sgi', 'SEGI_36110' => 'sgi', 'SEGI_40397' => 'sgi', 'SGA_v2.0_scaffold191G40426' => 'sas', 'SGA_v2.0_scaffold353G49717' => 'sas', 'SGA_v2.0_scaffold50G18550' => 'sas', 'SMO119G0173' => 'smo', 'SMO172G0002' => 'smo', 'Solyc09g082690.3' => 'sly', 'Solyc09g082700.2' => 'sly', 'Sopen09g031550' => 'spe', 'Sopen09g031560' => 'spe', 'Sp3g20540' => 'spa', 'Sp7g07580' => 'spa', 'TAR134G0002' => 'tar', 'TAR236G0001' => 'tar', 'TAR365G0892' => 'tar', 'TAR636G0166' => 'tar', 'TAR636G0646' => 'tar', 'TAR636G0869' => 'tar', 'TAR636G1317' => 'tar', 'TAR636G1744' => 'tar', 'TAR636G3358' => 'tar', 'TAR636G3436' => 'tar', 'THA.LOC104803047' => 'tha', 'Thecc.04G238900' => 'tca', 'Thhalv10021557m.g' => 'esa', 'Thhalv10026318m.g' => 'esa', 'Thhalv10026335m.g' => 'esa', 'TPR.G17433' => 'tpr', 'TPR.G18915' => 'tpr', 'TPR.G26125' => 'tpr', 'TWI09G0677' => 'twi', 'TWI73G0287' => 'twi', 'unitig_748.g8326' => 'ugi', 'vmacro15370' => 'vma', 'vmacro15371' => 'vma', 'vmacro15372' => 'vma', 'vmacro15373' => 'vma', 'vmacro15374' => 'vma', 'VMungo0720G2826' => 'vmu', 'Zm00001eb116960' => 'zma', 'Zm00001eb301260' => 'zma', 'Zm00001eb301270' => 'zma' ) $gf_id = 'HOM05D001460' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001460' ) $data_identifier = 'HOM05D001460' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 4, 'aag' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 2, 'aox' => (int) 2, 'arhy' => (int) 4, 'ath' => (int) 2, 'atr' => (int) 1, 'acertr' => (int) 10, 'cqu' => (int) 4, 'bca' => (int) 11, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 1, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 1, 'ccan' => (int) 1, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 1, 'col' => (int) 1, 'cpa' => (int) 1, 'cre' => (int) 7, 'csa' => (int) 1, 'camsi' => (int) 2, 'dca' => (int) 3, 'din' => (int) 2, 'dzi' => (int) 3, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 14, 'fve' => (int) 9, 'gma' => (int) 2, 'ghi' => (int) 4, 'gra' => (int) 2, 'vvi' => (int) 1, 'han' => (int) 13, 'cav' => (int) 1, 'hma' => (int) 2, 'sun' => (int) 2, 'lal' => (int) 2, 'lonja' => (int) 12, 'lja' => (int) 1, 'lsa' => (int) 7, 'mes' => (int) 1, 'mpo' => (int) 27, 'mbi' => (int) 1, 'mco' => (int) 8, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 1, 'egut' => (int) 1, 'ama' => (int) 1, 'nta' => (int) 4, 'nnu' => (int) 2, 'oeu' => (int) 3, 'osa' => (int) 4, 'pax' => (int) 9, 'pgr' => (int) 1, 'stu' => (int) 1, 'pvu' => (int) 1, 'ptr' => (int) 4, 'ppa' => (int) 22, 'pco' => (int) 6, 'ppe' => (int) 6, 'psa' => (int) 5, 'pso' => (int) 19, 'qlo' => (int) 5, 'rch' => (int) 7, 'rsi' => (int) 20, 'sbr' => (int) 5, 'sbo' => (int) 1, 'sci' => (int) 2, 'sed' => (int) 2, 'sgi' => (int) 12, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 2, 'tar' => (int) 10, 'tha' => (int) 1, 'tca' => (int) 1, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 2, 'ugi' => (int) 1, 'vma' => (int) 5, 'vmu' => (int) 1, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb301270' $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' => 'HOM05D001460', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '433', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p22980' => 'bna', 'A01p32340' => 'bna', 'A03p42970' => 'bna', 'A05p25880' => 'bna', 'Aa31LG8G9320' => 'aar', 'Aa31LG8G9330' => 'aar', 'Aa31LG8G9340' => 'aar', 'Aa31sc221G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1034' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1528' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.829' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2222' => 'aag', 'Ah.12g058830' => 'amhyb', 'Ah.12g058840' => 'amhyb', 'AL3G37160' => 'aly', 'AL7G41310' => 'aly', 'Aqoxy5G00395' => 'aox', 'Aqoxy5G00396' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0C8NZA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5185HY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JZ1PRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MD3LS0' => 'arhy', 'AT3G22840' => 'ath', 'AT4G14690' => 'ath', 'ATR0665G054' => 'atr', 'Atru.chr4.2344' => 'acertr', 'Atru.chr4.2346' => 'acertr', 'Atru.chr4.2347' => 'acertr', 'Atru.chr4.2348' => 'acertr', 'Atru.chr4.2355' => 'acertr', 'Atru.chr4.2356' => 'acertr', 'Atru.chr4.2358' => 'acertr', 'Atru.chr4.2359' => 'acertr', 'Atru.chr4.2360' => 'acertr', 'Atru.chr4.2361' => 'acertr', 'AUR62030476' => 'cqu', 'AUR62030478' => 'cqu', 'AUR62030819' => 'cqu', 'AUR62030820' => 'cqu', 'BcaB03g14648' => 'bca', 'BcaB04g20492' => 'bca', 'BcaB06g26399' => 'bca', 'BcaC01g03416' => 'bca', 'BcaC01g03419' => 'bca', 'BcaC01g03421' => 'bca', 'BcaC01g03424' => 'bca', 'BcaC05g28012' => 'bca', 'BcaC09g49212' => 'bca', 'BcaC09g50140' => 'bca', 'BcaNung00346' => 'bca', 'BolC1t02785H' => 'bol', 'BolC1t04095H' => 'bol', 'BolC3t17545H' => 'bol', 'BolC5t32769H' => 'bol', 'BraA01t02211Z' => 'bra', 'BraA01t03359Z' => 'bra', 'BraA03t13441Z' => 'bra', 'BraA05t21476Z' => 'bra', 'C01p28420' => 'bna', 'C01p41350' => 'bna', 'C03p52750' => 'bna', 'C03p52780' => 'bna', 'C05p40270' => 'bna', 'CAN.G1437.9' => 'can', 'CANSAT78G0035' => 'cansat', 'CANSAT78G1036' => 'cansat', 'CANSAT78G2272' => 'cansat', 'CANSAT78G2478' => 'cansat', 'CARHR098700' => 'chi', 'CARHR221120' => 'chi', 'CARHR221150' => 'chi', 'Carub.0003s2297' => 'cru', 'Carub.0007s2749' => 'cru', 'Carub.0007s2750' => 'cru', 'Carub.0007s2751' => 'cru', 'Ca_10849_v3' => 'car', 'Cc03_g04300' => 'ccan', 'CDE02G3648' => 'cde', 'CDE05G0060' => 'cde', 'CDE05G0692' => 'cde', 'CDE05G2285' => 'cde', 'CDE05G2884' => 'cde', 'CDE05G3072' => 'cde', 'Cfa008439' => 'cfa', 'Cfa008441' => 'cfa', 'Cfa008443' => 'cfa', 'Cfa008448' => 'cfa', 'Ciclev10005974m.g' => 'ccl', 'Ciclev10006006m.g' => 'ccl', 'Ciclev10006775m.g' => 'ccl', 'CiPaw.02G120400' => 'cil', 'CiPaw.02G120500' => 'cil', 'CiPaw.02G120600' => 'cil', 'ClCG05G004850' => 'cla', 'COL.COLO4_21566' => 'col', 'Cpa.g.sc44.124' => 'cpa', 'Cre07.g320400' => 'cre', 'Cre07.g320450' => 'cre', 'Cre08.g384650' => 'cre', 'Cre09.g393173' => 'cre', 'Cre09.g394325' => 'cre', 'Cre14.g626750' => 'cre', 'Cre16.g679250' => 'cre', 'CsaV3_3G012890' => 'csa', 'CSS0010865' => 'camsi', 'CSS0044338' => 'camsi', 'DCAR_002366' => 'dca', 'DCAR_030687' => 'dca', 'DCAR_030688' => 'dca', 'Dinv14047' => 'din', 'Dinv14048' => 'din', 'Duzib151G0105' => 'dzi', 'Duzib151G0114' => 'dzi', 'Duzib212G1029' => 'dzi', 'ECA232G3536' => 'eca', 'ECA240G0786' => 'eca', 'ECA240G1802' => 'eca', 'ECA240G3760' => 'eca', 'ECA240G3920' => 'eca', 'EL10Ac5g12536' => 'bvu', 'EL10Ac5g12537' => 'bvu', 'EL10Ac5g12538' => 'bvu', 'Eucgr.B01004' => 'egr', 'Eucgr.B01006' => 'egr', 'Eucgr.B01007' => 'egr', 'Eucgr.B01008' => 'egr', 'Eucgr.B01895' => 'egr', 'Eucgr.B01896' => 'egr', 'FAN04G1456' => 'fan', 'FAN08G1769' => 'fan', 'FAN08G2160' => 'fan', 'FAN13G2403' => 'fan', 'FAN13G3303' => 'fan', 'FAN15G2435' => 'fan', 'FAN17G0672' => 'fan', 'FAN17G2441' => 'fan', 'FAN18G1024' => 'fan', 'FAN22G1458' => 'fan', 'FAN24G0037' => 'fan', 'FAN24G0429' => 'fan', 'FAN24G2387' => 'fan', 'FAN27G2746' => 'fan', 'FvH4_2g20400' => 'fve', 'FvH4_2g20420' => 'fve', 'FvH4_2g20430' => 'fve', 'FvH4_4g01270' => 'fve', 'FvH4_4g01290' => 'fve', 'FvH4_4g01300' => 'fve', 'FvH4_4g01310' => 'fve', 'FvH4_4g01330' => 'fve', 'FvH4_5g09070' => 'fve', 'Glyma.10G243800' => 'gma', 'Glyma.20G150600' => 'gma', 'Gohir.A09G219200' => 'ghi', 'Gohir.A09G219300' => 'ghi', 'Gohir.D09G221400' => 'ghi', 'Gohir.D09G221500' => 'ghi', 'Gorai.006G242600' => 'gra', 'Gorai.006G242700' => 'gra', 'GSVIVG01018044001' => 'vvi', 'HanXRQChr03g0083821' => 'han', 'HanXRQChr03g0083841' => 'han', 'HanXRQChr03g0083881' => 'han', 'HanXRQChr03g0083901' => 'han', 'HanXRQChr03g0083921' => 'han', 'HanXRQChr03g0085331' => 'han', 'HanXRQChr03g0085361' => 'han', 'HanXRQChr03g0085411' => 'han', 'HanXRQChr03g0085421' => 'han', 'HanXRQChr03g0085431' => 'han', 'HanXRQChr08g0221991' => 'han', 'HanXRQChr11g0336061' => 'han', 'HanXRQChr11g0336411' => 'han', 'Haze_11234' => 'cav', 'Hma1.2p1_0549F.1_g177010' => 'hma', 'Hma1.2p1_0602F.1_g187630' => 'hma', 'Hund14876' => 'sun', 'Hund14879' => 'sun', 'Lalb_Chr06g0160741' => 'lal', 'Lalb_Chr21g0304781' => 'lal', 'Lj3A726G19' => 'lonja', 'Lj3A726T23' => 'lonja', 'Lj3A726T24' => 'lonja', 'Lj3A726T25' => 'lonja', 'Lj3A727T17' => 'lonja', 'Lj3C726T0' => 'lonja', 'Lj3C726T2' => 'lonja', 'Lj3P725T35' => 'lonja', 'Lj3P727T10' => 'lonja', 'Lj3P727T12' => 'lonja', 'Lj3P727T14' => 'lonja', 'Lj5g0023109' => 'lja', 'Lj6P646T44' => 'lonja', 'Lsat_1_v5_gn_6_75760' => 'lsa', 'Lsat_1_v5_gn_6_75800' => 'lsa', 'Lsat_1_v5_gn_6_75900' => 'lsa', 'Lsat_1_v5_gn_6_76240' => 'lsa', 'Lsat_1_v5_gn_6_76441' => 'lsa', 'Lsat_1_v5_gn_6_76700' => 'lsa', 'Lsat_1_v5_gn_6_76760' => 'lsa', 'Manes.15G033100' => 'mes', 'Mapoly0004s0074' => 'mpo', 'Mapoly0004s0075' => 'mpo', 'Mapoly0004s0163' => 'mpo', 'Mapoly0004s0164' => 'mpo', 'Mapoly0021s0018' => 'mpo', 'Mapoly0041s0136' => 'mpo', 'Mapoly0041s0137' => 'mpo', 'Mapoly0041s0138' => 'mpo', 'Mapoly0041s0139' => 'mpo', 'Mapoly0041s0141' => 'mpo', 'Mapoly0041s0142' => 'mpo', 'Mapoly0041s0143' => 'mpo', 'Mapoly0041s0144' => 'mpo', 'Mapoly0041s0145' => 'mpo', 'Mapoly0047s0106' => 'mpo', 'Mapoly0047s0108' => 'mpo', 'Mapoly0050s0051' => 'mpo', 'Mapoly0050s0052' => 'mpo', 'Mapoly0050s0053' => 'mpo', 'Mapoly0058s0013' => 'mpo', 'Mapoly0091s0078' => 'mpo', 'Mapoly0091s0079' => 'mpo', 'Mapoly0091s0080' => 'mpo', 'Mapoly0091s0081' => 'mpo', 'Mapoly0278s0004' => 'mpo', 'Mapoly0278s0005' => 'mpo', 'Mapoly0278s0006' => 'mpo', 'MBI11_g30648_MAGBIO' => 'mbi', 'MCO03G194' => 'mco', 'MCO03G590' => 'mco', 'MCO07G312' => 'mco', 'MCO10G318' => 'mco', 'MCO12G244' => 'mco', 'MCO13G148' => 'mco', 'MCO13G194' => 'mco', 'MCO16G238' => 'mco', 'MD06G1134100' => 'mdo', 'MD13G1200100' => 'mdo', 'MD13G1200300' => 'mdo', 'MD13G1200600' => 'mdo', 'MD14G1150400' => 'mdo', 'MD16G1200000' => 'mdo', 'Medtr1g102570' => 'mtr', 'Medtr1g102780' => 'mtr', 'Medtr1g102800' => 'mtr', 'Medtr1g102810' => 'mtr', 'Medtr1g102830' => 'mtr', 'MELO3C006499.2' => 'cme', 'Migut.G00385' => 'egut', 'MSTRG.4063' => 'ama', 'Nitab4.5_0000090g0260' => 'nta', 'Nitab4.5_0000977g0030' => 'nta', 'Nitab4.5_0002541g0040' => 'nta', 'Nitab4.5_0007068g0040' => 'nta', 'Nn005s41408' => 'nnu', 'Nn005s41410' => 'nnu', 'Oeu010310.1' => 'oeu', 'Oeu010311.1' => 'oeu', 'Oeu043472.1' => 'oeu', 'Os01g0246400' => 'osa', 'Os04g0267950' => 'osa', 'Os07g0178700' => 'osa', 'Os07g0178800' => 'osa', 'Peaxi162Scf00316g00046' => 'pax', 'Peaxi162Scf00316g00049' => 'pax', 'Peaxi162Scf00316g00059' => 'pax', 'Peaxi162Scf00316g00328' => 'pax', 'Peaxi162Scf00316g00329' => 'pax', 'Peaxi162Scf00316g00411' => 'pax', 'Peaxi162Scf00316g00521' => 'pax', 'Peaxi162Scf00492g00068' => 'pax', 'Peaxi162Scf35631g00002' => 'pax', 'PGR142G3720' => 'pgr', 'PGSC0003DMG400006442' => 'stu', 'Phvul.007G062000' => 'pvu', 'Potri.008G157750' => 'ptr', 'Potri.008G157900' => 'ptr', 'Potri.008G158000' => 'ptr', 'Potri.008G158200' => 'ptr', 'Pp3c11_7280' => 'ppa', 'Pp3c11_7980' => 'ppa', 'Pp3c12_19450' => 'ppa', 'Pp3c14_1480' => 'ppa', 'Pp3c14_1501' => 'ppa', 'Pp3c16_4900' => 'ppa', 'Pp3c16_5010' => 'ppa', 'Pp3c16_5060' => 'ppa', 'Pp3c19_18250' => 'ppa', 'Pp3c23_8530' => 'ppa', 'Pp3c23_8550' => 'ppa', 'Pp3c24_9670' => 'ppa', 'Pp3c2_21390' => 'ppa', 'Pp3c2_31380' => 'ppa', 'Pp3c3_16620' => 'ppa', 'Pp3c3_8090' => 'ppa', 'Pp3c3_8110' => 'ppa', 'Pp3c3_8130' => 'ppa', 'Pp3c3_8150' => 'ppa', 'Pp3c4_14320' => 'ppa', 'Pp3c6_2560' => 'ppa', 'Pp3c9_16700' => 'ppa', 'PRCOL_00000234' => 'pco', 'PRCOL_00000235' => 'pco', 'PRCOL_00000777' => 'pco', 'PRCOL_00002344' => 'pco', 'PRCOL_00002372' => 'pco', 'PRCOL_00006120' => 'pco', 'Prupe.1G021400' => 'ppe', 'Prupe.1G021500' => 'ppe', 'Prupe.1G021600' => 'ppe', 'Prupe.1G021700' => 'ppe', 'Prupe.1G021800' => 'ppe', 'Prupe.5G145100' => 'ppe', 'Psat6g204040' => 'psa', 'Psat6g204800' => 'psa', 'Psat6g204920' => 'psa', 'Psat6g204960' => 'psa', 'Psat6g205080' => 'psa', 'PSO017G0271' => 'pso', 'PSO017G1276' => 'pso', 'PSO017G1429' => 'pso', 'PSO017G1861' => 'pso', 'PSO017G2787' => 'pso', 'PSO017G4466' => 'pso', 'PSO017G5118' => 'pso', 'PSO017G5420' => 'pso', 'PSO063G3678' => 'pso', 'PSO210G0546' => 'pso', 'PSO317G0001' => 'pso', 'PSO357G0512' => 'pso', 'PSO478G2682' => 'pso', 'PSO647G0001' => 'pso', 'PSO675G0001' => 'pso', 'PSO675G2699' => 'pso', 'PSO675G2849' => 'pso', 'PSO675G4991' => 'pso', 'PSO689G0001' => 'pso', 'QL06p000916' => 'qlo', 'QL06p000921' => 'qlo', 'QL06p001398' => 'qlo', 'QL06p001407' => 'qlo', 'QL06p002031' => 'qlo', 'RcHm_v2.0_Chr4g0387791' => 'rch', 'RcHm_v2.0_Chr4g0387801' => 'rch', 'RcHm_v2.0_Chr6g0286501' => 'rch', 'RcHm_v2.0_Chr6g0286511' => 'rch', 'RcHm_v2.0_Chr6g0286521' => 'rch', 'RcHm_v2.0_Chr6g0286531' => 'rch', 'RcHm_v2.0_Chr7g0189141' => 'rch', 'Rhsim02G0028700' => 'rsi', 'Rhsim02G0028800' => 'rsi', 'Rhsim02G0028900' => 'rsi', 'Rhsim02G0029000' => 'rsi', 'Rhsim02G0029100' => 'rsi', 'Rhsim02G0029200' => 'rsi', 'Rhsim02G0029300' => 'rsi', 'Rhsim02G0029400' => 'rsi', 'Rhsim02G0029500' => 'rsi', 'Rhsim02G0029600' => 'rsi', 'RhsimUnG0024000' => 'rsi', 'RhsimUnG0024100' => 'rsi', 'RhsimUnG0024200' => 'rsi', 'RhsimUnG0024300' => 'rsi', 'RhsimUnG0024400' => 'rsi', 'RhsimUnG0024500' => 'rsi', 'RhsimUnG0024700' => 'rsi', 'RhsimUnG0024800' => 'rsi', 'RhsimUnG0024900' => 'rsi', 'RhsimUnG0025100' => 'rsi', 'Sabra08G0120200' => 'sbr', 'Sabra08G0120300' => 'sbr', 'Sabra08G0120500' => 'sbr', 'Sabra08G0120600' => 'sbr', 'Sabra10G0158900' => 'sbr', 'SalBow2G3492' => 'sbo', 'Sc13g0004760' => 'sci', 'Sc13g0004770' => 'sci', 'Sed0003417' => 'sed', 'Sed0019750' => 'sed', 'SEGI_03419' => 'sgi', 'SEGI_05907' => 'sgi', 'SEGI_10682' => 'sgi', 'SEGI_13528' => 'sgi', 'SEGI_16081' => 'sgi', 'SEGI_19370' => 'sgi', 'SEGI_21015' => 'sgi', 'SEGI_21944' => 'sgi', 'SEGI_32906' => 'sgi', 'SEGI_33093' => 'sgi', 'SEGI_36110' => 'sgi', 'SEGI_40397' => 'sgi', 'SGA_v2.0_scaffold191G40426' => 'sas', 'SGA_v2.0_scaffold353G49717' => 'sas', 'SGA_v2.0_scaffold50G18550' => 'sas', 'SMO119G0173' => 'smo', 'SMO172G0002' => 'smo', 'Solyc09g082690.3' => 'sly', 'Solyc09g082700.2' => 'sly', 'Sopen09g031550' => 'spe', 'Sopen09g031560' => 'spe', 'Sp3g20540' => 'spa', 'Sp7g07580' => 'spa', 'TAR134G0002' => 'tar', 'TAR236G0001' => 'tar', 'TAR365G0892' => 'tar', 'TAR636G0166' => 'tar', 'TAR636G0646' => 'tar', 'TAR636G0869' => 'tar', 'TAR636G1317' => 'tar', 'TAR636G1744' => 'tar', 'TAR636G3358' => 'tar', 'TAR636G3436' => 'tar', 'THA.LOC104803047' => 'tha', 'Thecc.04G238900' => 'tca', 'Thhalv10021557m.g' => 'esa', 'Thhalv10026318m.g' => 'esa', 'Thhalv10026335m.g' => 'esa', 'TPR.G17433' => 'tpr', 'TPR.G18915' => 'tpr', 'TPR.G26125' => 'tpr', 'TWI09G0677' => 'twi', 'TWI73G0287' => 'twi', 'unitig_748.g8326' => 'ugi', 'vmacro15370' => 'vma', 'vmacro15371' => 'vma', 'vmacro15372' => 'vma', 'vmacro15373' => 'vma', 'vmacro15374' => 'vma', 'VMungo0720G2826' => 'vmu', 'Zm00001eb116960' => 'zma', 'Zm00001eb301260' => 'zma', 'Zm00001eb301270' => 'zma' ), 'gf_id' => 'HOM05D001460', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001460' ), 'data_identifier' => 'HOM05D001460', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001460', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '433', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p22980' => 'bna', 'A01p32340' => 'bna', 'A03p42970' => 'bna', 'A05p25880' => 'bna', 'Aa31LG8G9320' => 'aar', 'Aa31LG8G9330' => 'aar', 'Aa31LG8G9340' => 'aar', 'Aa31sc221G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1034' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1528' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.829' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2222' => 'aag', 'Ah.12g058830' => 'amhyb', 'Ah.12g058840' => 'amhyb', 'AL3G37160' => 'aly', 'AL7G41310' => 'aly', 'Aqoxy5G00395' => 'aox', 'Aqoxy5G00396' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0C8NZA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5185HY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JZ1PRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MD3LS0' => 'arhy', 'AT3G22840' => 'ath', 'AT4G14690' => 'ath', 'ATR0665G054' => 'atr', 'Atru.chr4.2344' => 'acertr', 'Atru.chr4.2346' => 'acertr', 'Atru.chr4.2347' => 'acertr', 'Atru.chr4.2348' => 'acertr', 'Atru.chr4.2355' => 'acertr', 'Atru.chr4.2356' => 'acertr', 'Atru.chr4.2358' => 'acertr', 'Atru.chr4.2359' => 'acertr', 'Atru.chr4.2360' => 'acertr', 'Atru.chr4.2361' => 'acertr', 'AUR62030476' => 'cqu', 'AUR62030478' => 'cqu', 'AUR62030819' => 'cqu', 'AUR62030820' => 'cqu', 'BcaB03g14648' => 'bca', 'BcaB04g20492' => 'bca', 'BcaB06g26399' => 'bca', 'BcaC01g03416' => 'bca', 'BcaC01g03419' => 'bca', 'BcaC01g03421' => 'bca', 'BcaC01g03424' => 'bca', 'BcaC05g28012' => 'bca', 'BcaC09g49212' => 'bca', 'BcaC09g50140' => 'bca', 'BcaNung00346' => 'bca', 'BolC1t02785H' => 'bol', 'BolC1t04095H' => 'bol', 'BolC3t17545H' => 'bol', 'BolC5t32769H' => 'bol', 'BraA01t02211Z' => 'bra', 'BraA01t03359Z' => 'bra', 'BraA03t13441Z' => 'bra', 'BraA05t21476Z' => 'bra', 'C01p28420' => 'bna', 'C01p41350' => 'bna', 'C03p52750' => 'bna', 'C03p52780' => 'bna', 'C05p40270' => 'bna', 'CAN.G1437.9' => 'can', 'CANSAT78G0035' => 'cansat', 'CANSAT78G1036' => 'cansat', 'CANSAT78G2272' => 'cansat', 'CANSAT78G2478' => 'cansat', 'CARHR098700' => 'chi', 'CARHR221120' => 'chi', 'CARHR221150' => 'chi', 'Carub.0003s2297' => 'cru', 'Carub.0007s2749' => 'cru', 'Carub.0007s2750' => 'cru', 'Carub.0007s2751' => 'cru', 'Ca_10849_v3' => 'car', 'Cc03_g04300' => 'ccan', 'CDE02G3648' => 'cde', 'CDE05G0060' => 'cde', 'CDE05G0692' => 'cde', 'CDE05G2285' => 'cde', 'CDE05G2884' => 'cde', 'CDE05G3072' => 'cde', 'Cfa008439' => 'cfa', 'Cfa008441' => 'cfa', 'Cfa008443' => 'cfa', 'Cfa008448' => 'cfa', 'Ciclev10005974m.g' => 'ccl', 'Ciclev10006006m.g' => 'ccl', 'Ciclev10006775m.g' => 'ccl', 'CiPaw.02G120400' => 'cil', 'CiPaw.02G120500' => 'cil', 'CiPaw.02G120600' => 'cil', 'ClCG05G004850' => 'cla', 'COL.COLO4_21566' => 'col', 'Cpa.g.sc44.124' => 'cpa', 'Cre07.g320400' => 'cre', 'Cre07.g320450' => 'cre', 'Cre08.g384650' => 'cre', 'Cre09.g393173' => 'cre', 'Cre09.g394325' => 'cre', 'Cre14.g626750' => 'cre', 'Cre16.g679250' => 'cre', 'CsaV3_3G012890' => 'csa', 'CSS0010865' => 'camsi', 'CSS0044338' => 'camsi', 'DCAR_002366' => 'dca', 'DCAR_030687' => 'dca', 'DCAR_030688' => 'dca', 'Dinv14047' => 'din', 'Dinv14048' => 'din', 'Duzib151G0105' => 'dzi', 'Duzib151G0114' => 'dzi', 'Duzib212G1029' => 'dzi', 'ECA232G3536' => 'eca', 'ECA240G0786' => 'eca', 'ECA240G1802' => 'eca', 'ECA240G3760' => 'eca', 'ECA240G3920' => 'eca', 'EL10Ac5g12536' => 'bvu', 'EL10Ac5g12537' => 'bvu', 'EL10Ac5g12538' => 'bvu', 'Eucgr.B01004' => 'egr', 'Eucgr.B01006' => 'egr', 'Eucgr.B01007' => 'egr', 'Eucgr.B01008' => 'egr', 'Eucgr.B01895' => 'egr', 'Eucgr.B01896' => 'egr', 'FAN04G1456' => 'fan', 'FAN08G1769' => 'fan', 'FAN08G2160' => 'fan', 'FAN13G2403' => 'fan', 'FAN13G3303' => 'fan', 'FAN15G2435' => 'fan', 'FAN17G0672' => 'fan', 'FAN17G2441' => 'fan', 'FAN18G1024' => 'fan', 'FAN22G1458' => 'fan', 'FAN24G0037' => 'fan', 'FAN24G0429' => 'fan', 'FAN24G2387' => 'fan', 'FAN27G2746' => 'fan', 'FvH4_2g20400' => 'fve', 'FvH4_2g20420' => 'fve', 'FvH4_2g20430' => 'fve', 'FvH4_4g01270' => 'fve', 'FvH4_4g01290' => 'fve', 'FvH4_4g01300' => 'fve', 'FvH4_4g01310' => 'fve', 'FvH4_4g01330' => 'fve', 'FvH4_5g09070' => 'fve', 'Glyma.10G243800' => 'gma', 'Glyma.20G150600' => 'gma', 'Gohir.A09G219200' => 'ghi', 'Gohir.A09G219300' => 'ghi', 'Gohir.D09G221400' => 'ghi', 'Gohir.D09G221500' => 'ghi', 'Gorai.006G242600' => 'gra', 'Gorai.006G242700' => 'gra', 'GSVIVG01018044001' => 'vvi', 'HanXRQChr03g0083821' => 'han', 'HanXRQChr03g0083841' => 'han', 'HanXRQChr03g0083881' => 'han', 'HanXRQChr03g0083901' => 'han', 'HanXRQChr03g0083921' => 'han', 'HanXRQChr03g0085331' => 'han', 'HanXRQChr03g0085361' => 'han', 'HanXRQChr03g0085411' => 'han', 'HanXRQChr03g0085421' => 'han', 'HanXRQChr03g0085431' => 'han', 'HanXRQChr08g0221991' => 'han', 'HanXRQChr11g0336061' => 'han', 'HanXRQChr11g0336411' => 'han', 'Haze_11234' => 'cav', 'Hma1.2p1_0549F.1_g177010' => 'hma', 'Hma1.2p1_0602F.1_g187630' => 'hma', 'Hund14876' => 'sun', 'Hund14879' => 'sun', 'Lalb_Chr06g0160741' => 'lal', 'Lalb_Chr21g0304781' => 'lal', 'Lj3A726G19' => 'lonja', 'Lj3A726T23' => 'lonja', 'Lj3A726T24' => 'lonja', 'Lj3A726T25' => 'lonja', 'Lj3A727T17' => 'lonja', 'Lj3C726T0' => 'lonja', 'Lj3C726T2' => 'lonja', 'Lj3P725T35' => 'lonja', 'Lj3P727T10' => 'lonja', 'Lj3P727T12' => 'lonja', 'Lj3P727T14' => 'lonja', 'Lj5g0023109' => 'lja', 'Lj6P646T44' => 'lonja', 'Lsat_1_v5_gn_6_75760' => 'lsa', 'Lsat_1_v5_gn_6_75800' => 'lsa', 'Lsat_1_v5_gn_6_75900' => 'lsa', 'Lsat_1_v5_gn_6_76240' => 'lsa', 'Lsat_1_v5_gn_6_76441' => 'lsa', 'Lsat_1_v5_gn_6_76700' => 'lsa', 'Lsat_1_v5_gn_6_76760' => 'lsa', 'Manes.15G033100' => 'mes', 'Mapoly0004s0074' => 'mpo', 'Mapoly0004s0075' => 'mpo', 'Mapoly0004s0163' => 'mpo', 'Mapoly0004s0164' => 'mpo', 'Mapoly0021s0018' => 'mpo', 'Mapoly0041s0136' => 'mpo', 'Mapoly0041s0137' => 'mpo', 'Mapoly0041s0138' => 'mpo', 'Mapoly0041s0139' => 'mpo', 'Mapoly0041s0141' => 'mpo', 'Mapoly0041s0142' => 'mpo', 'Mapoly0041s0143' => 'mpo', 'Mapoly0041s0144' => 'mpo', 'Mapoly0041s0145' => 'mpo', 'Mapoly0047s0106' => 'mpo', 'Mapoly0047s0108' => 'mpo', 'Mapoly0050s0051' => 'mpo', 'Mapoly0050s0052' => 'mpo', 'Mapoly0050s0053' => 'mpo', 'Mapoly0058s0013' => 'mpo', 'Mapoly0091s0078' => 'mpo', 'Mapoly0091s0079' => 'mpo', 'Mapoly0091s0080' => 'mpo', 'Mapoly0091s0081' => 'mpo', 'Mapoly0278s0004' => 'mpo', 'Mapoly0278s0005' => 'mpo', 'Mapoly0278s0006' => 'mpo', 'MBI11_g30648_MAGBIO' => 'mbi', 'MCO03G194' => 'mco', 'MCO03G590' => 'mco', 'MCO07G312' => 'mco', 'MCO10G318' => 'mco', 'MCO12G244' => 'mco', 'MCO13G148' => 'mco', 'MCO13G194' => 'mco', 'MCO16G238' => 'mco', 'MD06G1134100' => 'mdo', 'MD13G1200100' => 'mdo', 'MD13G1200300' => 'mdo', 'MD13G1200600' => 'mdo', 'MD14G1150400' => 'mdo', 'MD16G1200000' => 'mdo', 'Medtr1g102570' => 'mtr', 'Medtr1g102780' => 'mtr', 'Medtr1g102800' => 'mtr', 'Medtr1g102810' => 'mtr', 'Medtr1g102830' => 'mtr', 'MELO3C006499.2' => 'cme', 'Migut.G00385' => 'egut', 'MSTRG.4063' => 'ama', 'Nitab4.5_0000090g0260' => 'nta', 'Nitab4.5_0000977g0030' => 'nta', 'Nitab4.5_0002541g0040' => 'nta', 'Nitab4.5_0007068g0040' => 'nta', 'Nn005s41408' => 'nnu', 'Nn005s41410' => 'nnu', 'Oeu010310.1' => 'oeu', 'Oeu010311.1' => 'oeu', 'Oeu043472.1' => 'oeu', 'Os01g0246400' => 'osa', 'Os04g0267950' => 'osa', 'Os07g0178700' => 'osa', 'Os07g0178800' => 'osa', 'Peaxi162Scf00316g00046' => 'pax', 'Peaxi162Scf00316g00049' => 'pax', 'Peaxi162Scf00316g00059' => 'pax', 'Peaxi162Scf00316g00328' => 'pax', 'Peaxi162Scf00316g00329' => 'pax', 'Peaxi162Scf00316g00411' => 'pax', 'Peaxi162Scf00316g00521' => 'pax', 'Peaxi162Scf00492g00068' => 'pax', 'Peaxi162Scf35631g00002' => 'pax', 'PGR142G3720' => 'pgr', 'PGSC0003DMG400006442' => 'stu', 'Phvul.007G062000' => 'pvu', 'Potri.008G157750' => 'ptr', 'Potri.008G157900' => 'ptr', 'Potri.008G158000' => 'ptr', 'Potri.008G158200' => 'ptr', 'Pp3c11_7280' => 'ppa', 'Pp3c11_7980' => 'ppa', 'Pp3c12_19450' => 'ppa', 'Pp3c14_1480' => 'ppa', 'Pp3c14_1501' => 'ppa', 'Pp3c16_4900' => 'ppa', 'Pp3c16_5010' => 'ppa', 'Pp3c16_5060' => 'ppa', 'Pp3c19_18250' => 'ppa', 'Pp3c23_8530' => 'ppa', 'Pp3c23_8550' => 'ppa', 'Pp3c24_9670' => 'ppa', 'Pp3c2_21390' => 'ppa', 'Pp3c2_31380' => 'ppa', 'Pp3c3_16620' => 'ppa', 'Pp3c3_8090' => 'ppa', 'Pp3c3_8110' => 'ppa', 'Pp3c3_8130' => 'ppa', 'Pp3c3_8150' => 'ppa', 'Pp3c4_14320' => 'ppa', 'Pp3c6_2560' => 'ppa', 'Pp3c9_16700' => 'ppa', 'PRCOL_00000234' => 'pco', 'PRCOL_00000235' => 'pco', 'PRCOL_00000777' => 'pco', 'PRCOL_00002344' => 'pco', 'PRCOL_00002372' => 'pco', 'PRCOL_00006120' => 'pco', 'Prupe.1G021400' => 'ppe', 'Prupe.1G021500' => 'ppe', 'Prupe.1G021600' => 'ppe', 'Prupe.1G021700' => 'ppe', 'Prupe.1G021800' => 'ppe', 'Prupe.5G145100' => 'ppe', 'Psat6g204040' => 'psa', 'Psat6g204800' => 'psa', 'Psat6g204920' => 'psa', 'Psat6g204960' => 'psa', 'Psat6g205080' => 'psa', 'PSO017G0271' => 'pso', 'PSO017G1276' => 'pso', 'PSO017G1429' => 'pso', 'PSO017G1861' => 'pso', 'PSO017G2787' => 'pso', 'PSO017G4466' => 'pso', 'PSO017G5118' => 'pso', 'PSO017G5420' => 'pso', 'PSO063G3678' => 'pso', 'PSO210G0546' => 'pso', 'PSO317G0001' => 'pso', 'PSO357G0512' => 'pso', 'PSO478G2682' => 'pso', 'PSO647G0001' => 'pso', 'PSO675G0001' => 'pso', 'PSO675G2699' => 'pso', 'PSO675G2849' => 'pso', 'PSO675G4991' => 'pso', 'PSO689G0001' => 'pso', 'QL06p000916' => 'qlo', 'QL06p000921' => 'qlo', 'QL06p001398' => 'qlo', 'QL06p001407' => 'qlo', 'QL06p002031' => 'qlo', 'RcHm_v2.0_Chr4g0387791' => 'rch', 'RcHm_v2.0_Chr4g0387801' => 'rch', 'RcHm_v2.0_Chr6g0286501' => 'rch', 'RcHm_v2.0_Chr6g0286511' => 'rch', 'RcHm_v2.0_Chr6g0286521' => 'rch', 'RcHm_v2.0_Chr6g0286531' => 'rch', 'RcHm_v2.0_Chr7g0189141' => 'rch', 'Rhsim02G0028700' => 'rsi', 'Rhsim02G0028800' => 'rsi', 'Rhsim02G0028900' => 'rsi', 'Rhsim02G0029000' => 'rsi', 'Rhsim02G0029100' => 'rsi', 'Rhsim02G0029200' => 'rsi', 'Rhsim02G0029300' => 'rsi', 'Rhsim02G0029400' => 'rsi', 'Rhsim02G0029500' => 'rsi', 'Rhsim02G0029600' => 'rsi', 'RhsimUnG0024000' => 'rsi', 'RhsimUnG0024100' => 'rsi', 'RhsimUnG0024200' => 'rsi', 'RhsimUnG0024300' => 'rsi', 'RhsimUnG0024400' => 'rsi', 'RhsimUnG0024500' => 'rsi', 'RhsimUnG0024700' => 'rsi', 'RhsimUnG0024800' => 'rsi', 'RhsimUnG0024900' => 'rsi', 'RhsimUnG0025100' => 'rsi', 'Sabra08G0120200' => 'sbr', 'Sabra08G0120300' => 'sbr', 'Sabra08G0120500' => 'sbr', 'Sabra08G0120600' => 'sbr', 'Sabra10G0158900' => 'sbr', 'SalBow2G3492' => 'sbo', 'Sc13g0004760' => 'sci', 'Sc13g0004770' => 'sci', 'Sed0003417' => 'sed', 'Sed0019750' => 'sed', 'SEGI_03419' => 'sgi', 'SEGI_05907' => 'sgi', 'SEGI_10682' => 'sgi', 'SEGI_13528' => 'sgi', 'SEGI_16081' => 'sgi', 'SEGI_19370' => 'sgi', 'SEGI_21015' => 'sgi', 'SEGI_21944' => 'sgi', 'SEGI_32906' => 'sgi', 'SEGI_33093' => 'sgi', 'SEGI_36110' => 'sgi', 'SEGI_40397' => 'sgi', 'SGA_v2.0_scaffold191G40426' => 'sas', 'SGA_v2.0_scaffold353G49717' => 'sas', 'SGA_v2.0_scaffold50G18550' => 'sas', 'SMO119G0173' => 'smo', 'SMO172G0002' => 'smo', 'Solyc09g082690.3' => 'sly', 'Solyc09g082700.2' => 'sly', 'Sopen09g031550' => 'spe', 'Sopen09g031560' => 'spe', 'Sp3g20540' => 'spa', 'Sp7g07580' => 'spa', 'TAR134G0002' => 'tar', 'TAR236G0001' => 'tar', 'TAR365G0892' => 'tar', 'TAR636G0166' => 'tar', 'TAR636G0646' => 'tar', 'TAR636G0869' => 'tar', 'TAR636G1317' => 'tar', 'TAR636G1744' => 'tar', 'TAR636G3358' => 'tar', 'TAR636G3436' => 'tar', 'THA.LOC104803047' => 'tha', 'Thecc.04G238900' => 'tca', 'Thhalv10021557m.g' => 'esa', 'Thhalv10026318m.g' => 'esa', 'Thhalv10026335m.g' => 'esa', 'TPR.G17433' => 'tpr', 'TPR.G18915' => 'tpr', 'TPR.G26125' => 'tpr', 'TWI09G0677' => 'twi', 'TWI73G0287' => 'twi', 'unitig_748.g8326' => 'ugi', 'vmacro15370' => 'vma', 'vmacro15371' => 'vma', 'vmacro15372' => 'vma', 'vmacro15373' => 'vma', 'vmacro15374' => 'vma', 'VMungo0720G2826' => 'vmu', 'Zm00001eb116960' => 'zma', 'Zm00001eb301260' => 'zma', 'Zm00001eb301270' => 'zma' ) $gf_id = 'HOM05D001460' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001460' ) $data_identifier = 'HOM05D001460' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 4, 'aag' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 2, 'aox' => (int) 2, 'arhy' => (int) 4, 'ath' => (int) 2, 'atr' => (int) 1, 'acertr' => (int) 10, 'cqu' => (int) 4, 'bca' => (int) 11, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 1, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 1, 'ccan' => (int) 1, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 1, 'col' => (int) 1, 'cpa' => (int) 1, 'cre' => (int) 7, 'csa' => (int) 1, 'camsi' => (int) 2, 'dca' => (int) 3, 'din' => (int) 2, 'dzi' => (int) 3, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 14, 'fve' => (int) 9, 'gma' => (int) 2, 'ghi' => (int) 4, 'gra' => (int) 2, 'vvi' => (int) 1, 'han' => (int) 13, 'cav' => (int) 1, 'hma' => (int) 2, 'sun' => (int) 2, 'lal' => (int) 2, 'lonja' => (int) 12, 'lja' => (int) 1, 'lsa' => (int) 7, 'mes' => (int) 1, 'mpo' => (int) 27, 'mbi' => (int) 1, 'mco' => (int) 8, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 1, 'egut' => (int) 1, 'ama' => (int) 1, 'nta' => (int) 4, 'nnu' => (int) 2, 'oeu' => (int) 3, 'osa' => (int) 4, 'pax' => (int) 9, 'pgr' => (int) 1, 'stu' => (int) 1, 'pvu' => (int) 1, 'ptr' => (int) 4, 'ppa' => (int) 22, 'pco' => (int) 6, 'ppe' => (int) 6, 'psa' => (int) 5, 'pso' => (int) 19, 'qlo' => (int) 5, 'rch' => (int) 7, 'rsi' => (int) 20, 'sbr' => (int) 5, 'sbo' => (int) 1, 'sci' => (int) 2, 'sed' => (int) 2, 'sgi' => (int) 12, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 2, 'tar' => (int) 10, 'tha' => (int) 1, 'tca' => (int) 1, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 2, 'ugi' => (int) 1, 'vma' => (int) 5, 'vmu' => (int) 1, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb301270' $species_info = array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ) $local_species = 'cqu' $disabled = '' $selected = '' $num_hits = (int) 0include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001460', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '433', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p22980' => 'bna', 'A01p32340' => 'bna', 'A03p42970' => 'bna', 'A05p25880' => 'bna', 'Aa31LG8G9320' => 'aar', 'Aa31LG8G9330' => 'aar', 'Aa31LG8G9340' => 'aar', 'Aa31sc221G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1034' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1528' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.829' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2222' => 'aag', 'Ah.12g058830' => 'amhyb', 'Ah.12g058840' => 'amhyb', 'AL3G37160' => 'aly', 'AL7G41310' => 'aly', 'Aqoxy5G00395' => 'aox', 'Aqoxy5G00396' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0C8NZA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5185HY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JZ1PRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MD3LS0' => 'arhy', 'AT3G22840' => 'ath', 'AT4G14690' => 'ath', 'ATR0665G054' => 'atr', 'Atru.chr4.2344' => 'acertr', 'Atru.chr4.2346' => 'acertr', 'Atru.chr4.2347' => 'acertr', 'Atru.chr4.2348' => 'acertr', 'Atru.chr4.2355' => 'acertr', 'Atru.chr4.2356' => 'acertr', 'Atru.chr4.2358' => 'acertr', 'Atru.chr4.2359' => 'acertr', 'Atru.chr4.2360' => 'acertr', 'Atru.chr4.2361' => 'acertr', 'AUR62030476' => 'cqu', 'AUR62030478' => 'cqu', 'AUR62030819' => 'cqu', 'AUR62030820' => 'cqu', 'BcaB03g14648' => 'bca', 'BcaB04g20492' => 'bca', 'BcaB06g26399' => 'bca', 'BcaC01g03416' => 'bca', 'BcaC01g03419' => 'bca', 'BcaC01g03421' => 'bca', 'BcaC01g03424' => 'bca', 'BcaC05g28012' => 'bca', 'BcaC09g49212' => 'bca', 'BcaC09g50140' => 'bca', 'BcaNung00346' => 'bca', 'BolC1t02785H' => 'bol', 'BolC1t04095H' => 'bol', 'BolC3t17545H' => 'bol', 'BolC5t32769H' => 'bol', 'BraA01t02211Z' => 'bra', 'BraA01t03359Z' => 'bra', 'BraA03t13441Z' => 'bra', 'BraA05t21476Z' => 'bra', 'C01p28420' => 'bna', 'C01p41350' => 'bna', 'C03p52750' => 'bna', 'C03p52780' => 'bna', 'C05p40270' => 'bna', 'CAN.G1437.9' => 'can', 'CANSAT78G0035' => 'cansat', 'CANSAT78G1036' => 'cansat', 'CANSAT78G2272' => 'cansat', 'CANSAT78G2478' => 'cansat', 'CARHR098700' => 'chi', 'CARHR221120' => 'chi', 'CARHR221150' => 'chi', 'Carub.0003s2297' => 'cru', 'Carub.0007s2749' => 'cru', 'Carub.0007s2750' => 'cru', 'Carub.0007s2751' => 'cru', 'Ca_10849_v3' => 'car', 'Cc03_g04300' => 'ccan', 'CDE02G3648' => 'cde', 'CDE05G0060' => 'cde', 'CDE05G0692' => 'cde', 'CDE05G2285' => 'cde', 'CDE05G2884' => 'cde', 'CDE05G3072' => 'cde', 'Cfa008439' => 'cfa', 'Cfa008441' => 'cfa', 'Cfa008443' => 'cfa', 'Cfa008448' => 'cfa', 'Ciclev10005974m.g' => 'ccl', 'Ciclev10006006m.g' => 'ccl', 'Ciclev10006775m.g' => 'ccl', 'CiPaw.02G120400' => 'cil', 'CiPaw.02G120500' => 'cil', 'CiPaw.02G120600' => 'cil', 'ClCG05G004850' => 'cla', 'COL.COLO4_21566' => 'col', 'Cpa.g.sc44.124' => 'cpa', 'Cre07.g320400' => 'cre', 'Cre07.g320450' => 'cre', 'Cre08.g384650' => 'cre', 'Cre09.g393173' => 'cre', 'Cre09.g394325' => 'cre', 'Cre14.g626750' => 'cre', 'Cre16.g679250' => 'cre', 'CsaV3_3G012890' => 'csa', 'CSS0010865' => 'camsi', 'CSS0044338' => 'camsi', 'DCAR_002366' => 'dca', 'DCAR_030687' => 'dca', 'DCAR_030688' => 'dca', 'Dinv14047' => 'din', 'Dinv14048' => 'din', 'Duzib151G0105' => 'dzi', 'Duzib151G0114' => 'dzi', 'Duzib212G1029' => 'dzi', 'ECA232G3536' => 'eca', 'ECA240G0786' => 'eca', 'ECA240G1802' => 'eca', 'ECA240G3760' => 'eca', 'ECA240G3920' => 'eca', 'EL10Ac5g12536' => 'bvu', 'EL10Ac5g12537' => 'bvu', 'EL10Ac5g12538' => 'bvu', 'Eucgr.B01004' => 'egr', 'Eucgr.B01006' => 'egr', 'Eucgr.B01007' => 'egr', 'Eucgr.B01008' => 'egr', 'Eucgr.B01895' => 'egr', 'Eucgr.B01896' => 'egr', 'FAN04G1456' => 'fan', 'FAN08G1769' => 'fan', 'FAN08G2160' => 'fan', 'FAN13G2403' => 'fan', 'FAN13G3303' => 'fan', 'FAN15G2435' => 'fan', 'FAN17G0672' => 'fan', 'FAN17G2441' => 'fan', 'FAN18G1024' => 'fan', 'FAN22G1458' => 'fan', 'FAN24G0037' => 'fan', 'FAN24G0429' => 'fan', 'FAN24G2387' => 'fan', 'FAN27G2746' => 'fan', 'FvH4_2g20400' => 'fve', 'FvH4_2g20420' => 'fve', 'FvH4_2g20430' => 'fve', 'FvH4_4g01270' => 'fve', 'FvH4_4g01290' => 'fve', 'FvH4_4g01300' => 'fve', 'FvH4_4g01310' => 'fve', 'FvH4_4g01330' => 'fve', 'FvH4_5g09070' => 'fve', 'Glyma.10G243800' => 'gma', 'Glyma.20G150600' => 'gma', 'Gohir.A09G219200' => 'ghi', 'Gohir.A09G219300' => 'ghi', 'Gohir.D09G221400' => 'ghi', 'Gohir.D09G221500' => 'ghi', 'Gorai.006G242600' => 'gra', 'Gorai.006G242700' => 'gra', 'GSVIVG01018044001' => 'vvi', 'HanXRQChr03g0083821' => 'han', 'HanXRQChr03g0083841' => 'han', 'HanXRQChr03g0083881' => 'han', 'HanXRQChr03g0083901' => 'han', 'HanXRQChr03g0083921' => 'han', 'HanXRQChr03g0085331' => 'han', 'HanXRQChr03g0085361' => 'han', 'HanXRQChr03g0085411' => 'han', 'HanXRQChr03g0085421' => 'han', 'HanXRQChr03g0085431' => 'han', 'HanXRQChr08g0221991' => 'han', 'HanXRQChr11g0336061' => 'han', 'HanXRQChr11g0336411' => 'han', 'Haze_11234' => 'cav', 'Hma1.2p1_0549F.1_g177010' => 'hma', 'Hma1.2p1_0602F.1_g187630' => 'hma', 'Hund14876' => 'sun', 'Hund14879' => 'sun', 'Lalb_Chr06g0160741' => 'lal', 'Lalb_Chr21g0304781' => 'lal', 'Lj3A726G19' => 'lonja', 'Lj3A726T23' => 'lonja', 'Lj3A726T24' => 'lonja', 'Lj3A726T25' => 'lonja', 'Lj3A727T17' => 'lonja', 'Lj3C726T0' => 'lonja', 'Lj3C726T2' => 'lonja', 'Lj3P725T35' => 'lonja', 'Lj3P727T10' => 'lonja', 'Lj3P727T12' => 'lonja', 'Lj3P727T14' => 'lonja', 'Lj5g0023109' => 'lja', 'Lj6P646T44' => 'lonja', 'Lsat_1_v5_gn_6_75760' => 'lsa', 'Lsat_1_v5_gn_6_75800' => 'lsa', 'Lsat_1_v5_gn_6_75900' => 'lsa', 'Lsat_1_v5_gn_6_76240' => 'lsa', 'Lsat_1_v5_gn_6_76441' => 'lsa', 'Lsat_1_v5_gn_6_76700' => 'lsa', 'Lsat_1_v5_gn_6_76760' => 'lsa', 'Manes.15G033100' => 'mes', 'Mapoly0004s0074' => 'mpo', 'Mapoly0004s0075' => 'mpo', 'Mapoly0004s0163' => 'mpo', 'Mapoly0004s0164' => 'mpo', 'Mapoly0021s0018' => 'mpo', 'Mapoly0041s0136' => 'mpo', 'Mapoly0041s0137' => 'mpo', 'Mapoly0041s0138' => 'mpo', 'Mapoly0041s0139' => 'mpo', 'Mapoly0041s0141' => 'mpo', 'Mapoly0041s0142' => 'mpo', 'Mapoly0041s0143' => 'mpo', 'Mapoly0041s0144' => 'mpo', 'Mapoly0041s0145' => 'mpo', 'Mapoly0047s0106' => 'mpo', 'Mapoly0047s0108' => 'mpo', 'Mapoly0050s0051' => 'mpo', 'Mapoly0050s0052' => 'mpo', 'Mapoly0050s0053' => 'mpo', 'Mapoly0058s0013' => 'mpo', 'Mapoly0091s0078' => 'mpo', 'Mapoly0091s0079' => 'mpo', 'Mapoly0091s0080' => 'mpo', 'Mapoly0091s0081' => 'mpo', 'Mapoly0278s0004' => 'mpo', 'Mapoly0278s0005' => 'mpo', 'Mapoly0278s0006' => 'mpo', 'MBI11_g30648_MAGBIO' => 'mbi', 'MCO03G194' => 'mco', 'MCO03G590' => 'mco', 'MCO07G312' => 'mco', 'MCO10G318' => 'mco', 'MCO12G244' => 'mco', 'MCO13G148' => 'mco', 'MCO13G194' => 'mco', 'MCO16G238' => 'mco', 'MD06G1134100' => 'mdo', 'MD13G1200100' => 'mdo', 'MD13G1200300' => 'mdo', 'MD13G1200600' => 'mdo', 'MD14G1150400' => 'mdo', 'MD16G1200000' => 'mdo', 'Medtr1g102570' => 'mtr', 'Medtr1g102780' => 'mtr', 'Medtr1g102800' => 'mtr', 'Medtr1g102810' => 'mtr', 'Medtr1g102830' => 'mtr', 'MELO3C006499.2' => 'cme', 'Migut.G00385' => 'egut', 'MSTRG.4063' => 'ama', 'Nitab4.5_0000090g0260' => 'nta', 'Nitab4.5_0000977g0030' => 'nta', 'Nitab4.5_0002541g0040' => 'nta', 'Nitab4.5_0007068g0040' => 'nta', 'Nn005s41408' => 'nnu', 'Nn005s41410' => 'nnu', 'Oeu010310.1' => 'oeu', 'Oeu010311.1' => 'oeu', 'Oeu043472.1' => 'oeu', 'Os01g0246400' => 'osa', 'Os04g0267950' => 'osa', 'Os07g0178700' => 'osa', 'Os07g0178800' => 'osa', 'Peaxi162Scf00316g00046' => 'pax', 'Peaxi162Scf00316g00049' => 'pax', 'Peaxi162Scf00316g00059' => 'pax', 'Peaxi162Scf00316g00328' => 'pax', 'Peaxi162Scf00316g00329' => 'pax', 'Peaxi162Scf00316g00411' => 'pax', 'Peaxi162Scf00316g00521' => 'pax', 'Peaxi162Scf00492g00068' => 'pax', 'Peaxi162Scf35631g00002' => 'pax', 'PGR142G3720' => 'pgr', 'PGSC0003DMG400006442' => 'stu', 'Phvul.007G062000' => 'pvu', 'Potri.008G157750' => 'ptr', 'Potri.008G157900' => 'ptr', 'Potri.008G158000' => 'ptr', 'Potri.008G158200' => 'ptr', 'Pp3c11_7280' => 'ppa', 'Pp3c11_7980' => 'ppa', 'Pp3c12_19450' => 'ppa', 'Pp3c14_1480' => 'ppa', 'Pp3c14_1501' => 'ppa', 'Pp3c16_4900' => 'ppa', 'Pp3c16_5010' => 'ppa', 'Pp3c16_5060' => 'ppa', 'Pp3c19_18250' => 'ppa', 'Pp3c23_8530' => 'ppa', 'Pp3c23_8550' => 'ppa', 'Pp3c24_9670' => 'ppa', 'Pp3c2_21390' => 'ppa', 'Pp3c2_31380' => 'ppa', 'Pp3c3_16620' => 'ppa', 'Pp3c3_8090' => 'ppa', 'Pp3c3_8110' => 'ppa', 'Pp3c3_8130' => 'ppa', 'Pp3c3_8150' => 'ppa', 'Pp3c4_14320' => 'ppa', 'Pp3c6_2560' => 'ppa', 'Pp3c9_16700' => 'ppa', 'PRCOL_00000234' => 'pco', 'PRCOL_00000235' => 'pco', 'PRCOL_00000777' => 'pco', 'PRCOL_00002344' => 'pco', 'PRCOL_00002372' => 'pco', 'PRCOL_00006120' => 'pco', 'Prupe.1G021400' => 'ppe', 'Prupe.1G021500' => 'ppe', 'Prupe.1G021600' => 'ppe', 'Prupe.1G021700' => 'ppe', 'Prupe.1G021800' => 'ppe', 'Prupe.5G145100' => 'ppe', 'Psat6g204040' => 'psa', 'Psat6g204800' => 'psa', 'Psat6g204920' => 'psa', 'Psat6g204960' => 'psa', 'Psat6g205080' => 'psa', 'PSO017G0271' => 'pso', 'PSO017G1276' => 'pso', 'PSO017G1429' => 'pso', 'PSO017G1861' => 'pso', 'PSO017G2787' => 'pso', 'PSO017G4466' => 'pso', 'PSO017G5118' => 'pso', 'PSO017G5420' => 'pso', 'PSO063G3678' => 'pso', 'PSO210G0546' => 'pso', 'PSO317G0001' => 'pso', 'PSO357G0512' => 'pso', 'PSO478G2682' => 'pso', 'PSO647G0001' => 'pso', 'PSO675G0001' => 'pso', 'PSO675G2699' => 'pso', 'PSO675G2849' => 'pso', 'PSO675G4991' => 'pso', 'PSO689G0001' => 'pso', 'QL06p000916' => 'qlo', 'QL06p000921' => 'qlo', 'QL06p001398' => 'qlo', 'QL06p001407' => 'qlo', 'QL06p002031' => 'qlo', 'RcHm_v2.0_Chr4g0387791' => 'rch', 'RcHm_v2.0_Chr4g0387801' => 'rch', 'RcHm_v2.0_Chr6g0286501' => 'rch', 'RcHm_v2.0_Chr6g0286511' => 'rch', 'RcHm_v2.0_Chr6g0286521' => 'rch', 'RcHm_v2.0_Chr6g0286531' => 'rch', 'RcHm_v2.0_Chr7g0189141' => 'rch', 'Rhsim02G0028700' => 'rsi', 'Rhsim02G0028800' => 'rsi', 'Rhsim02G0028900' => 'rsi', 'Rhsim02G0029000' => 'rsi', 'Rhsim02G0029100' => 'rsi', 'Rhsim02G0029200' => 'rsi', 'Rhsim02G0029300' => 'rsi', 'Rhsim02G0029400' => 'rsi', 'Rhsim02G0029500' => 'rsi', 'Rhsim02G0029600' => 'rsi', 'RhsimUnG0024000' => 'rsi', 'RhsimUnG0024100' => 'rsi', 'RhsimUnG0024200' => 'rsi', 'RhsimUnG0024300' => 'rsi', 'RhsimUnG0024400' => 'rsi', 'RhsimUnG0024500' => 'rsi', 'RhsimUnG0024700' => 'rsi', 'RhsimUnG0024800' => 'rsi', 'RhsimUnG0024900' => 'rsi', 'RhsimUnG0025100' => 'rsi', 'Sabra08G0120200' => 'sbr', 'Sabra08G0120300' => 'sbr', 'Sabra08G0120500' => 'sbr', 'Sabra08G0120600' => 'sbr', 'Sabra10G0158900' => 'sbr', 'SalBow2G3492' => 'sbo', 'Sc13g0004760' => 'sci', 'Sc13g0004770' => 'sci', 'Sed0003417' => 'sed', 'Sed0019750' => 'sed', 'SEGI_03419' => 'sgi', 'SEGI_05907' => 'sgi', 'SEGI_10682' => 'sgi', 'SEGI_13528' => 'sgi', 'SEGI_16081' => 'sgi', 'SEGI_19370' => 'sgi', 'SEGI_21015' => 'sgi', 'SEGI_21944' => 'sgi', 'SEGI_32906' => 'sgi', 'SEGI_33093' => 'sgi', 'SEGI_36110' => 'sgi', 'SEGI_40397' => 'sgi', 'SGA_v2.0_scaffold191G40426' => 'sas', 'SGA_v2.0_scaffold353G49717' => 'sas', 'SGA_v2.0_scaffold50G18550' => 'sas', 'SMO119G0173' => 'smo', 'SMO172G0002' => 'smo', 'Solyc09g082690.3' => 'sly', 'Solyc09g082700.2' => 'sly', 'Sopen09g031550' => 'spe', 'Sopen09g031560' => 'spe', 'Sp3g20540' => 'spa', 'Sp7g07580' => 'spa', 'TAR134G0002' => 'tar', 'TAR236G0001' => 'tar', 'TAR365G0892' => 'tar', 'TAR636G0166' => 'tar', 'TAR636G0646' => 'tar', 'TAR636G0869' => 'tar', 'TAR636G1317' => 'tar', 'TAR636G1744' => 'tar', 'TAR636G3358' => 'tar', 'TAR636G3436' => 'tar', 'THA.LOC104803047' => 'tha', 'Thecc.04G238900' => 'tca', 'Thhalv10021557m.g' => 'esa', 'Thhalv10026318m.g' => 'esa', 'Thhalv10026335m.g' => 'esa', 'TPR.G17433' => 'tpr', 'TPR.G18915' => 'tpr', 'TPR.G26125' => 'tpr', 'TWI09G0677' => 'twi', 'TWI73G0287' => 'twi', 'unitig_748.g8326' => 'ugi', 'vmacro15370' => 'vma', 'vmacro15371' => 'vma', 'vmacro15372' => 'vma', 'vmacro15373' => 'vma', 'vmacro15374' => 'vma', 'VMungo0720G2826' => 'vmu', 'Zm00001eb116960' => 'zma', 'Zm00001eb301260' => 'zma', 'Zm00001eb301270' => 'zma' ), 'gf_id' => 'HOM05D001460', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001460' ), 'data_identifier' => 'HOM05D001460', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001460', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '433', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p22980' => 'bna', 'A01p32340' => 'bna', 'A03p42970' => 'bna', 'A05p25880' => 'bna', 'Aa31LG8G9320' => 'aar', 'Aa31LG8G9330' => 'aar', 'Aa31LG8G9340' => 'aar', 'Aa31sc221G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1034' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1528' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.829' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2222' => 'aag', 'Ah.12g058830' => 'amhyb', 'Ah.12g058840' => 'amhyb', 'AL3G37160' => 'aly', 'AL7G41310' => 'aly', 'Aqoxy5G00395' => 'aox', 'Aqoxy5G00396' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0C8NZA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5185HY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JZ1PRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MD3LS0' => 'arhy', 'AT3G22840' => 'ath', 'AT4G14690' => 'ath', 'ATR0665G054' => 'atr', 'Atru.chr4.2344' => 'acertr', 'Atru.chr4.2346' => 'acertr', 'Atru.chr4.2347' => 'acertr', 'Atru.chr4.2348' => 'acertr', 'Atru.chr4.2355' => 'acertr', 'Atru.chr4.2356' => 'acertr', 'Atru.chr4.2358' => 'acertr', 'Atru.chr4.2359' => 'acertr', 'Atru.chr4.2360' => 'acertr', 'Atru.chr4.2361' => 'acertr', 'AUR62030476' => 'cqu', 'AUR62030478' => 'cqu', 'AUR62030819' => 'cqu', 'AUR62030820' => 'cqu', 'BcaB03g14648' => 'bca', 'BcaB04g20492' => 'bca', 'BcaB06g26399' => 'bca', 'BcaC01g03416' => 'bca', 'BcaC01g03419' => 'bca', 'BcaC01g03421' => 'bca', 'BcaC01g03424' => 'bca', 'BcaC05g28012' => 'bca', 'BcaC09g49212' => 'bca', 'BcaC09g50140' => 'bca', 'BcaNung00346' => 'bca', 'BolC1t02785H' => 'bol', 'BolC1t04095H' => 'bol', 'BolC3t17545H' => 'bol', 'BolC5t32769H' => 'bol', 'BraA01t02211Z' => 'bra', 'BraA01t03359Z' => 'bra', 'BraA03t13441Z' => 'bra', 'BraA05t21476Z' => 'bra', 'C01p28420' => 'bna', 'C01p41350' => 'bna', 'C03p52750' => 'bna', 'C03p52780' => 'bna', 'C05p40270' => 'bna', 'CAN.G1437.9' => 'can', 'CANSAT78G0035' => 'cansat', 'CANSAT78G1036' => 'cansat', 'CANSAT78G2272' => 'cansat', 'CANSAT78G2478' => 'cansat', 'CARHR098700' => 'chi', 'CARHR221120' => 'chi', 'CARHR221150' => 'chi', 'Carub.0003s2297' => 'cru', 'Carub.0007s2749' => 'cru', 'Carub.0007s2750' => 'cru', 'Carub.0007s2751' => 'cru', 'Ca_10849_v3' => 'car', 'Cc03_g04300' => 'ccan', 'CDE02G3648' => 'cde', 'CDE05G0060' => 'cde', 'CDE05G0692' => 'cde', 'CDE05G2285' => 'cde', 'CDE05G2884' => 'cde', 'CDE05G3072' => 'cde', 'Cfa008439' => 'cfa', 'Cfa008441' => 'cfa', 'Cfa008443' => 'cfa', 'Cfa008448' => 'cfa', 'Ciclev10005974m.g' => 'ccl', 'Ciclev10006006m.g' => 'ccl', 'Ciclev10006775m.g' => 'ccl', 'CiPaw.02G120400' => 'cil', 'CiPaw.02G120500' => 'cil', 'CiPaw.02G120600' => 'cil', 'ClCG05G004850' => 'cla', 'COL.COLO4_21566' => 'col', 'Cpa.g.sc44.124' => 'cpa', 'Cre07.g320400' => 'cre', 'Cre07.g320450' => 'cre', 'Cre08.g384650' => 'cre', 'Cre09.g393173' => 'cre', 'Cre09.g394325' => 'cre', 'Cre14.g626750' => 'cre', 'Cre16.g679250' => 'cre', 'CsaV3_3G012890' => 'csa', 'CSS0010865' => 'camsi', 'CSS0044338' => 'camsi', 'DCAR_002366' => 'dca', 'DCAR_030687' => 'dca', 'DCAR_030688' => 'dca', 'Dinv14047' => 'din', 'Dinv14048' => 'din', 'Duzib151G0105' => 'dzi', 'Duzib151G0114' => 'dzi', 'Duzib212G1029' => 'dzi', 'ECA232G3536' => 'eca', 'ECA240G0786' => 'eca', 'ECA240G1802' => 'eca', 'ECA240G3760' => 'eca', 'ECA240G3920' => 'eca', 'EL10Ac5g12536' => 'bvu', 'EL10Ac5g12537' => 'bvu', 'EL10Ac5g12538' => 'bvu', 'Eucgr.B01004' => 'egr', 'Eucgr.B01006' => 'egr', 'Eucgr.B01007' => 'egr', 'Eucgr.B01008' => 'egr', 'Eucgr.B01895' => 'egr', 'Eucgr.B01896' => 'egr', 'FAN04G1456' => 'fan', 'FAN08G1769' => 'fan', 'FAN08G2160' => 'fan', 'FAN13G2403' => 'fan', 'FAN13G3303' => 'fan', 'FAN15G2435' => 'fan', 'FAN17G0672' => 'fan', 'FAN17G2441' => 'fan', 'FAN18G1024' => 'fan', 'FAN22G1458' => 'fan', 'FAN24G0037' => 'fan', 'FAN24G0429' => 'fan', 'FAN24G2387' => 'fan', 'FAN27G2746' => 'fan', 'FvH4_2g20400' => 'fve', 'FvH4_2g20420' => 'fve', 'FvH4_2g20430' => 'fve', 'FvH4_4g01270' => 'fve', 'FvH4_4g01290' => 'fve', 'FvH4_4g01300' => 'fve', 'FvH4_4g01310' => 'fve', 'FvH4_4g01330' => 'fve', 'FvH4_5g09070' => 'fve', 'Glyma.10G243800' => 'gma', 'Glyma.20G150600' => 'gma', 'Gohir.A09G219200' => 'ghi', 'Gohir.A09G219300' => 'ghi', 'Gohir.D09G221400' => 'ghi', 'Gohir.D09G221500' => 'ghi', 'Gorai.006G242600' => 'gra', 'Gorai.006G242700' => 'gra', 'GSVIVG01018044001' => 'vvi', 'HanXRQChr03g0083821' => 'han', 'HanXRQChr03g0083841' => 'han', 'HanXRQChr03g0083881' => 'han', 'HanXRQChr03g0083901' => 'han', 'HanXRQChr03g0083921' => 'han', 'HanXRQChr03g0085331' => 'han', 'HanXRQChr03g0085361' => 'han', 'HanXRQChr03g0085411' => 'han', 'HanXRQChr03g0085421' => 'han', 'HanXRQChr03g0085431' => 'han', 'HanXRQChr08g0221991' => 'han', 'HanXRQChr11g0336061' => 'han', 'HanXRQChr11g0336411' => 'han', 'Haze_11234' => 'cav', 'Hma1.2p1_0549F.1_g177010' => 'hma', 'Hma1.2p1_0602F.1_g187630' => 'hma', 'Hund14876' => 'sun', 'Hund14879' => 'sun', 'Lalb_Chr06g0160741' => 'lal', 'Lalb_Chr21g0304781' => 'lal', 'Lj3A726G19' => 'lonja', 'Lj3A726T23' => 'lonja', 'Lj3A726T24' => 'lonja', 'Lj3A726T25' => 'lonja', 'Lj3A727T17' => 'lonja', 'Lj3C726T0' => 'lonja', 'Lj3C726T2' => 'lonja', 'Lj3P725T35' => 'lonja', 'Lj3P727T10' => 'lonja', 'Lj3P727T12' => 'lonja', 'Lj3P727T14' => 'lonja', 'Lj5g0023109' => 'lja', 'Lj6P646T44' => 'lonja', 'Lsat_1_v5_gn_6_75760' => 'lsa', 'Lsat_1_v5_gn_6_75800' => 'lsa', 'Lsat_1_v5_gn_6_75900' => 'lsa', 'Lsat_1_v5_gn_6_76240' => 'lsa', 'Lsat_1_v5_gn_6_76441' => 'lsa', 'Lsat_1_v5_gn_6_76700' => 'lsa', 'Lsat_1_v5_gn_6_76760' => 'lsa', 'Manes.15G033100' => 'mes', 'Mapoly0004s0074' => 'mpo', 'Mapoly0004s0075' => 'mpo', 'Mapoly0004s0163' => 'mpo', 'Mapoly0004s0164' => 'mpo', 'Mapoly0021s0018' => 'mpo', 'Mapoly0041s0136' => 'mpo', 'Mapoly0041s0137' => 'mpo', 'Mapoly0041s0138' => 'mpo', 'Mapoly0041s0139' => 'mpo', 'Mapoly0041s0141' => 'mpo', 'Mapoly0041s0142' => 'mpo', 'Mapoly0041s0143' => 'mpo', 'Mapoly0041s0144' => 'mpo', 'Mapoly0041s0145' => 'mpo', 'Mapoly0047s0106' => 'mpo', 'Mapoly0047s0108' => 'mpo', 'Mapoly0050s0051' => 'mpo', 'Mapoly0050s0052' => 'mpo', 'Mapoly0050s0053' => 'mpo', 'Mapoly0058s0013' => 'mpo', 'Mapoly0091s0078' => 'mpo', 'Mapoly0091s0079' => 'mpo', 'Mapoly0091s0080' => 'mpo', 'Mapoly0091s0081' => 'mpo', 'Mapoly0278s0004' => 'mpo', 'Mapoly0278s0005' => 'mpo', 'Mapoly0278s0006' => 'mpo', 'MBI11_g30648_MAGBIO' => 'mbi', 'MCO03G194' => 'mco', 'MCO03G590' => 'mco', 'MCO07G312' => 'mco', 'MCO10G318' => 'mco', 'MCO12G244' => 'mco', 'MCO13G148' => 'mco', 'MCO13G194' => 'mco', 'MCO16G238' => 'mco', 'MD06G1134100' => 'mdo', 'MD13G1200100' => 'mdo', 'MD13G1200300' => 'mdo', 'MD13G1200600' => 'mdo', 'MD14G1150400' => 'mdo', 'MD16G1200000' => 'mdo', 'Medtr1g102570' => 'mtr', 'Medtr1g102780' => 'mtr', 'Medtr1g102800' => 'mtr', 'Medtr1g102810' => 'mtr', 'Medtr1g102830' => 'mtr', 'MELO3C006499.2' => 'cme', 'Migut.G00385' => 'egut', 'MSTRG.4063' => 'ama', 'Nitab4.5_0000090g0260' => 'nta', 'Nitab4.5_0000977g0030' => 'nta', 'Nitab4.5_0002541g0040' => 'nta', 'Nitab4.5_0007068g0040' => 'nta', 'Nn005s41408' => 'nnu', 'Nn005s41410' => 'nnu', 'Oeu010310.1' => 'oeu', 'Oeu010311.1' => 'oeu', 'Oeu043472.1' => 'oeu', 'Os01g0246400' => 'osa', 'Os04g0267950' => 'osa', 'Os07g0178700' => 'osa', 'Os07g0178800' => 'osa', 'Peaxi162Scf00316g00046' => 'pax', 'Peaxi162Scf00316g00049' => 'pax', 'Peaxi162Scf00316g00059' => 'pax', 'Peaxi162Scf00316g00328' => 'pax', 'Peaxi162Scf00316g00329' => 'pax', 'Peaxi162Scf00316g00411' => 'pax', 'Peaxi162Scf00316g00521' => 'pax', 'Peaxi162Scf00492g00068' => 'pax', 'Peaxi162Scf35631g00002' => 'pax', 'PGR142G3720' => 'pgr', 'PGSC0003DMG400006442' => 'stu', 'Phvul.007G062000' => 'pvu', 'Potri.008G157750' => 'ptr', 'Potri.008G157900' => 'ptr', 'Potri.008G158000' => 'ptr', 'Potri.008G158200' => 'ptr', 'Pp3c11_7280' => 'ppa', 'Pp3c11_7980' => 'ppa', 'Pp3c12_19450' => 'ppa', 'Pp3c14_1480' => 'ppa', 'Pp3c14_1501' => 'ppa', 'Pp3c16_4900' => 'ppa', 'Pp3c16_5010' => 'ppa', 'Pp3c16_5060' => 'ppa', 'Pp3c19_18250' => 'ppa', 'Pp3c23_8530' => 'ppa', 'Pp3c23_8550' => 'ppa', 'Pp3c24_9670' => 'ppa', 'Pp3c2_21390' => 'ppa', 'Pp3c2_31380' => 'ppa', 'Pp3c3_16620' => 'ppa', 'Pp3c3_8090' => 'ppa', 'Pp3c3_8110' => 'ppa', 'Pp3c3_8130' => 'ppa', 'Pp3c3_8150' => 'ppa', 'Pp3c4_14320' => 'ppa', 'Pp3c6_2560' => 'ppa', 'Pp3c9_16700' => 'ppa', 'PRCOL_00000234' => 'pco', 'PRCOL_00000235' => 'pco', 'PRCOL_00000777' => 'pco', 'PRCOL_00002344' => 'pco', 'PRCOL_00002372' => 'pco', 'PRCOL_00006120' => 'pco', 'Prupe.1G021400' => 'ppe', 'Prupe.1G021500' => 'ppe', 'Prupe.1G021600' => 'ppe', 'Prupe.1G021700' => 'ppe', 'Prupe.1G021800' => 'ppe', 'Prupe.5G145100' => 'ppe', 'Psat6g204040' => 'psa', 'Psat6g204800' => 'psa', 'Psat6g204920' => 'psa', 'Psat6g204960' => 'psa', 'Psat6g205080' => 'psa', 'PSO017G0271' => 'pso', 'PSO017G1276' => 'pso', 'PSO017G1429' => 'pso', 'PSO017G1861' => 'pso', 'PSO017G2787' => 'pso', 'PSO017G4466' => 'pso', 'PSO017G5118' => 'pso', 'PSO017G5420' => 'pso', 'PSO063G3678' => 'pso', 'PSO210G0546' => 'pso', 'PSO317G0001' => 'pso', 'PSO357G0512' => 'pso', 'PSO478G2682' => 'pso', 'PSO647G0001' => 'pso', 'PSO675G0001' => 'pso', 'PSO675G2699' => 'pso', 'PSO675G2849' => 'pso', 'PSO675G4991' => 'pso', 'PSO689G0001' => 'pso', 'QL06p000916' => 'qlo', 'QL06p000921' => 'qlo', 'QL06p001398' => 'qlo', 'QL06p001407' => 'qlo', 'QL06p002031' => 'qlo', 'RcHm_v2.0_Chr4g0387791' => 'rch', 'RcHm_v2.0_Chr4g0387801' => 'rch', 'RcHm_v2.0_Chr6g0286501' => 'rch', 'RcHm_v2.0_Chr6g0286511' => 'rch', 'RcHm_v2.0_Chr6g0286521' => 'rch', 'RcHm_v2.0_Chr6g0286531' => 'rch', 'RcHm_v2.0_Chr7g0189141' => 'rch', 'Rhsim02G0028700' => 'rsi', 'Rhsim02G0028800' => 'rsi', 'Rhsim02G0028900' => 'rsi', 'Rhsim02G0029000' => 'rsi', 'Rhsim02G0029100' => 'rsi', 'Rhsim02G0029200' => 'rsi', 'Rhsim02G0029300' => 'rsi', 'Rhsim02G0029400' => 'rsi', 'Rhsim02G0029500' => 'rsi', 'Rhsim02G0029600' => 'rsi', 'RhsimUnG0024000' => 'rsi', 'RhsimUnG0024100' => 'rsi', 'RhsimUnG0024200' => 'rsi', 'RhsimUnG0024300' => 'rsi', 'RhsimUnG0024400' => 'rsi', 'RhsimUnG0024500' => 'rsi', 'RhsimUnG0024700' => 'rsi', 'RhsimUnG0024800' => 'rsi', 'RhsimUnG0024900' => 'rsi', 'RhsimUnG0025100' => 'rsi', 'Sabra08G0120200' => 'sbr', 'Sabra08G0120300' => 'sbr', 'Sabra08G0120500' => 'sbr', 'Sabra08G0120600' => 'sbr', 'Sabra10G0158900' => 'sbr', 'SalBow2G3492' => 'sbo', 'Sc13g0004760' => 'sci', 'Sc13g0004770' => 'sci', 'Sed0003417' => 'sed', 'Sed0019750' => 'sed', 'SEGI_03419' => 'sgi', 'SEGI_05907' => 'sgi', 'SEGI_10682' => 'sgi', 'SEGI_13528' => 'sgi', 'SEGI_16081' => 'sgi', 'SEGI_19370' => 'sgi', 'SEGI_21015' => 'sgi', 'SEGI_21944' => 'sgi', 'SEGI_32906' => 'sgi', 'SEGI_33093' => 'sgi', 'SEGI_36110' => 'sgi', 'SEGI_40397' => 'sgi', 'SGA_v2.0_scaffold191G40426' => 'sas', 'SGA_v2.0_scaffold353G49717' => 'sas', 'SGA_v2.0_scaffold50G18550' => 'sas', 'SMO119G0173' => 'smo', 'SMO172G0002' => 'smo', 'Solyc09g082690.3' => 'sly', 'Solyc09g082700.2' => 'sly', 'Sopen09g031550' => 'spe', 'Sopen09g031560' => 'spe', 'Sp3g20540' => 'spa', 'Sp7g07580' => 'spa', 'TAR134G0002' => 'tar', 'TAR236G0001' => 'tar', 'TAR365G0892' => 'tar', 'TAR636G0166' => 'tar', 'TAR636G0646' => 'tar', 'TAR636G0869' => 'tar', 'TAR636G1317' => 'tar', 'TAR636G1744' => 'tar', 'TAR636G3358' => 'tar', 'TAR636G3436' => 'tar', 'THA.LOC104803047' => 'tha', 'Thecc.04G238900' => 'tca', 'Thhalv10021557m.g' => 'esa', 'Thhalv10026318m.g' => 'esa', 'Thhalv10026335m.g' => 'esa', 'TPR.G17433' => 'tpr', 'TPR.G18915' => 'tpr', 'TPR.G26125' => 'tpr', 'TWI09G0677' => 'twi', 'TWI73G0287' => 'twi', 'unitig_748.g8326' => 'ugi', 'vmacro15370' => 'vma', 'vmacro15371' => 'vma', 'vmacro15372' => 'vma', 'vmacro15373' => 'vma', 'vmacro15374' => 'vma', 'VMungo0720G2826' => 'vmu', 'Zm00001eb116960' => 'zma', 'Zm00001eb301260' => 'zma', 'Zm00001eb301270' => 'zma' ) $gf_id = 'HOM05D001460' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001460' ) $data_identifier = 'HOM05D001460' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 4, 'aag' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 2, 'aox' => (int) 2, 'arhy' => (int) 4, 'ath' => (int) 2, 'atr' => (int) 1, 'acertr' => (int) 10, 'cqu' => (int) 4, 'bca' => (int) 11, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 1, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 1, 'ccan' => (int) 1, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 1, 'col' => (int) 1, 'cpa' => (int) 1, 'cre' => (int) 7, 'csa' => (int) 1, 'camsi' => (int) 2, 'dca' => (int) 3, 'din' => (int) 2, 'dzi' => (int) 3, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 14, 'fve' => (int) 9, 'gma' => (int) 2, 'ghi' => (int) 4, 'gra' => (int) 2, 'vvi' => (int) 1, 'han' => (int) 13, 'cav' => (int) 1, 'hma' => (int) 2, 'sun' => (int) 2, 'lal' => (int) 2, 'lonja' => (int) 12, 'lja' => (int) 1, 'lsa' => (int) 7, 'mes' => (int) 1, 'mpo' => (int) 27, 'mbi' => (int) 1, 'mco' => (int) 8, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 1, 'egut' => (int) 1, 'ama' => (int) 1, 'nta' => (int) 4, 'nnu' => (int) 2, 'oeu' => (int) 3, 'osa' => (int) 4, 'pax' => (int) 9, 'pgr' => (int) 1, 'stu' => (int) 1, 'pvu' => (int) 1, 'ptr' => (int) 4, 'ppa' => (int) 22, 'pco' => (int) 6, 'ppe' => (int) 6, 'psa' => (int) 5, 'pso' => (int) 19, 'qlo' => (int) 5, 'rch' => (int) 7, 'rsi' => (int) 20, 'sbr' => (int) 5, 'sbo' => (int) 1, 'sci' => (int) 2, 'sed' => (int) 2, 'sgi' => (int) 12, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 2, 'tar' => (int) 10, 'tha' => (int) 1, 'tca' => (int) 1, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 2, 'ugi' => (int) 1, 'vma' => (int) 5, 'vmu' => (int) 1, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb301270' $species_info = array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ) $local_species = 'cqu' $disabled = '' $selected = '' $num_hits = (int) 0
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001460', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '433', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p22980' => 'bna', 'A01p32340' => 'bna', 'A03p42970' => 'bna', 'A05p25880' => 'bna', 'Aa31LG8G9320' => 'aar', 'Aa31LG8G9330' => 'aar', 'Aa31LG8G9340' => 'aar', 'Aa31sc221G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1034' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1528' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.829' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2222' => 'aag', 'Ah.12g058830' => 'amhyb', 'Ah.12g058840' => 'amhyb', 'AL3G37160' => 'aly', 'AL7G41310' => 'aly', 'Aqoxy5G00395' => 'aox', 'Aqoxy5G00396' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0C8NZA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5185HY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JZ1PRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MD3LS0' => 'arhy', 'AT3G22840' => 'ath', 'AT4G14690' => 'ath', 'ATR0665G054' => 'atr', 'Atru.chr4.2344' => 'acertr', 'Atru.chr4.2346' => 'acertr', 'Atru.chr4.2347' => 'acertr', 'Atru.chr4.2348' => 'acertr', 'Atru.chr4.2355' => 'acertr', 'Atru.chr4.2356' => 'acertr', 'Atru.chr4.2358' => 'acertr', 'Atru.chr4.2359' => 'acertr', 'Atru.chr4.2360' => 'acertr', 'Atru.chr4.2361' => 'acertr', 'AUR62030476' => 'cqu', 'AUR62030478' => 'cqu', 'AUR62030819' => 'cqu', 'AUR62030820' => 'cqu', 'BcaB03g14648' => 'bca', 'BcaB04g20492' => 'bca', 'BcaB06g26399' => 'bca', 'BcaC01g03416' => 'bca', 'BcaC01g03419' => 'bca', 'BcaC01g03421' => 'bca', 'BcaC01g03424' => 'bca', 'BcaC05g28012' => 'bca', 'BcaC09g49212' => 'bca', 'BcaC09g50140' => 'bca', 'BcaNung00346' => 'bca', 'BolC1t02785H' => 'bol', 'BolC1t04095H' => 'bol', 'BolC3t17545H' => 'bol', 'BolC5t32769H' => 'bol', 'BraA01t02211Z' => 'bra', 'BraA01t03359Z' => 'bra', 'BraA03t13441Z' => 'bra', 'BraA05t21476Z' => 'bra', 'C01p28420' => 'bna', 'C01p41350' => 'bna', 'C03p52750' => 'bna', 'C03p52780' => 'bna', 'C05p40270' => 'bna', 'CAN.G1437.9' => 'can', 'CANSAT78G0035' => 'cansat', 'CANSAT78G1036' => 'cansat', 'CANSAT78G2272' => 'cansat', 'CANSAT78G2478' => 'cansat', 'CARHR098700' => 'chi', 'CARHR221120' => 'chi', 'CARHR221150' => 'chi', 'Carub.0003s2297' => 'cru', 'Carub.0007s2749' => 'cru', 'Carub.0007s2750' => 'cru', 'Carub.0007s2751' => 'cru', 'Ca_10849_v3' => 'car', 'Cc03_g04300' => 'ccan', 'CDE02G3648' => 'cde', 'CDE05G0060' => 'cde', 'CDE05G0692' => 'cde', 'CDE05G2285' => 'cde', 'CDE05G2884' => 'cde', 'CDE05G3072' => 'cde', 'Cfa008439' => 'cfa', 'Cfa008441' => 'cfa', 'Cfa008443' => 'cfa', 'Cfa008448' => 'cfa', 'Ciclev10005974m.g' => 'ccl', 'Ciclev10006006m.g' => 'ccl', 'Ciclev10006775m.g' => 'ccl', 'CiPaw.02G120400' => 'cil', 'CiPaw.02G120500' => 'cil', 'CiPaw.02G120600' => 'cil', 'ClCG05G004850' => 'cla', 'COL.COLO4_21566' => 'col', 'Cpa.g.sc44.124' => 'cpa', 'Cre07.g320400' => 'cre', 'Cre07.g320450' => 'cre', 'Cre08.g384650' => 'cre', 'Cre09.g393173' => 'cre', 'Cre09.g394325' => 'cre', 'Cre14.g626750' => 'cre', 'Cre16.g679250' => 'cre', 'CsaV3_3G012890' => 'csa', 'CSS0010865' => 'camsi', 'CSS0044338' => 'camsi', 'DCAR_002366' => 'dca', 'DCAR_030687' => 'dca', 'DCAR_030688' => 'dca', 'Dinv14047' => 'din', 'Dinv14048' => 'din', 'Duzib151G0105' => 'dzi', 'Duzib151G0114' => 'dzi', 'Duzib212G1029' => 'dzi', 'ECA232G3536' => 'eca', 'ECA240G0786' => 'eca', 'ECA240G1802' => 'eca', 'ECA240G3760' => 'eca', 'ECA240G3920' => 'eca', 'EL10Ac5g12536' => 'bvu', 'EL10Ac5g12537' => 'bvu', 'EL10Ac5g12538' => 'bvu', 'Eucgr.B01004' => 'egr', 'Eucgr.B01006' => 'egr', 'Eucgr.B01007' => 'egr', 'Eucgr.B01008' => 'egr', 'Eucgr.B01895' => 'egr', 'Eucgr.B01896' => 'egr', 'FAN04G1456' => 'fan', 'FAN08G1769' => 'fan', 'FAN08G2160' => 'fan', 'FAN13G2403' => 'fan', 'FAN13G3303' => 'fan', 'FAN15G2435' => 'fan', 'FAN17G0672' => 'fan', 'FAN17G2441' => 'fan', 'FAN18G1024' => 'fan', 'FAN22G1458' => 'fan', 'FAN24G0037' => 'fan', 'FAN24G0429' => 'fan', 'FAN24G2387' => 'fan', 'FAN27G2746' => 'fan', 'FvH4_2g20400' => 'fve', 'FvH4_2g20420' => 'fve', 'FvH4_2g20430' => 'fve', 'FvH4_4g01270' => 'fve', 'FvH4_4g01290' => 'fve', 'FvH4_4g01300' => 'fve', 'FvH4_4g01310' => 'fve', 'FvH4_4g01330' => 'fve', 'FvH4_5g09070' => 'fve', 'Glyma.10G243800' => 'gma', 'Glyma.20G150600' => 'gma', 'Gohir.A09G219200' => 'ghi', 'Gohir.A09G219300' => 'ghi', 'Gohir.D09G221400' => 'ghi', 'Gohir.D09G221500' => 'ghi', 'Gorai.006G242600' => 'gra', 'Gorai.006G242700' => 'gra', 'GSVIVG01018044001' => 'vvi', 'HanXRQChr03g0083821' => 'han', 'HanXRQChr03g0083841' => 'han', 'HanXRQChr03g0083881' => 'han', 'HanXRQChr03g0083901' => 'han', 'HanXRQChr03g0083921' => 'han', 'HanXRQChr03g0085331' => 'han', 'HanXRQChr03g0085361' => 'han', 'HanXRQChr03g0085411' => 'han', 'HanXRQChr03g0085421' => 'han', 'HanXRQChr03g0085431' => 'han', 'HanXRQChr08g0221991' => 'han', 'HanXRQChr11g0336061' => 'han', 'HanXRQChr11g0336411' => 'han', 'Haze_11234' => 'cav', 'Hma1.2p1_0549F.1_g177010' => 'hma', 'Hma1.2p1_0602F.1_g187630' => 'hma', 'Hund14876' => 'sun', 'Hund14879' => 'sun', 'Lalb_Chr06g0160741' => 'lal', 'Lalb_Chr21g0304781' => 'lal', 'Lj3A726G19' => 'lonja', 'Lj3A726T23' => 'lonja', 'Lj3A726T24' => 'lonja', 'Lj3A726T25' => 'lonja', 'Lj3A727T17' => 'lonja', 'Lj3C726T0' => 'lonja', 'Lj3C726T2' => 'lonja', 'Lj3P725T35' => 'lonja', 'Lj3P727T10' => 'lonja', 'Lj3P727T12' => 'lonja', 'Lj3P727T14' => 'lonja', 'Lj5g0023109' => 'lja', 'Lj6P646T44' => 'lonja', 'Lsat_1_v5_gn_6_75760' => 'lsa', 'Lsat_1_v5_gn_6_75800' => 'lsa', 'Lsat_1_v5_gn_6_75900' => 'lsa', 'Lsat_1_v5_gn_6_76240' => 'lsa', 'Lsat_1_v5_gn_6_76441' => 'lsa', 'Lsat_1_v5_gn_6_76700' => 'lsa', 'Lsat_1_v5_gn_6_76760' => 'lsa', 'Manes.15G033100' => 'mes', 'Mapoly0004s0074' => 'mpo', 'Mapoly0004s0075' => 'mpo', 'Mapoly0004s0163' => 'mpo', 'Mapoly0004s0164' => 'mpo', 'Mapoly0021s0018' => 'mpo', 'Mapoly0041s0136' => 'mpo', 'Mapoly0041s0137' => 'mpo', 'Mapoly0041s0138' => 'mpo', 'Mapoly0041s0139' => 'mpo', 'Mapoly0041s0141' => 'mpo', 'Mapoly0041s0142' => 'mpo', 'Mapoly0041s0143' => 'mpo', 'Mapoly0041s0144' => 'mpo', 'Mapoly0041s0145' => 'mpo', 'Mapoly0047s0106' => 'mpo', 'Mapoly0047s0108' => 'mpo', 'Mapoly0050s0051' => 'mpo', 'Mapoly0050s0052' => 'mpo', 'Mapoly0050s0053' => 'mpo', 'Mapoly0058s0013' => 'mpo', 'Mapoly0091s0078' => 'mpo', 'Mapoly0091s0079' => 'mpo', 'Mapoly0091s0080' => 'mpo', 'Mapoly0091s0081' => 'mpo', 'Mapoly0278s0004' => 'mpo', 'Mapoly0278s0005' => 'mpo', 'Mapoly0278s0006' => 'mpo', 'MBI11_g30648_MAGBIO' => 'mbi', 'MCO03G194' => 'mco', 'MCO03G590' => 'mco', 'MCO07G312' => 'mco', 'MCO10G318' => 'mco', 'MCO12G244' => 'mco', 'MCO13G148' => 'mco', 'MCO13G194' => 'mco', 'MCO16G238' => 'mco', 'MD06G1134100' => 'mdo', 'MD13G1200100' => 'mdo', 'MD13G1200300' => 'mdo', 'MD13G1200600' => 'mdo', 'MD14G1150400' => 'mdo', 'MD16G1200000' => 'mdo', 'Medtr1g102570' => 'mtr', 'Medtr1g102780' => 'mtr', 'Medtr1g102800' => 'mtr', 'Medtr1g102810' => 'mtr', 'Medtr1g102830' => 'mtr', 'MELO3C006499.2' => 'cme', 'Migut.G00385' => 'egut', 'MSTRG.4063' => 'ama', 'Nitab4.5_0000090g0260' => 'nta', 'Nitab4.5_0000977g0030' => 'nta', 'Nitab4.5_0002541g0040' => 'nta', 'Nitab4.5_0007068g0040' => 'nta', 'Nn005s41408' => 'nnu', 'Nn005s41410' => 'nnu', 'Oeu010310.1' => 'oeu', 'Oeu010311.1' => 'oeu', 'Oeu043472.1' => 'oeu', 'Os01g0246400' => 'osa', 'Os04g0267950' => 'osa', 'Os07g0178700' => 'osa', 'Os07g0178800' => 'osa', 'Peaxi162Scf00316g00046' => 'pax', 'Peaxi162Scf00316g00049' => 'pax', 'Peaxi162Scf00316g00059' => 'pax', 'Peaxi162Scf00316g00328' => 'pax', 'Peaxi162Scf00316g00329' => 'pax', 'Peaxi162Scf00316g00411' => 'pax', 'Peaxi162Scf00316g00521' => 'pax', 'Peaxi162Scf00492g00068' => 'pax', 'Peaxi162Scf35631g00002' => 'pax', 'PGR142G3720' => 'pgr', 'PGSC0003DMG400006442' => 'stu', 'Phvul.007G062000' => 'pvu', 'Potri.008G157750' => 'ptr', 'Potri.008G157900' => 'ptr', 'Potri.008G158000' => 'ptr', 'Potri.008G158200' => 'ptr', 'Pp3c11_7280' => 'ppa', 'Pp3c11_7980' => 'ppa', 'Pp3c12_19450' => 'ppa', 'Pp3c14_1480' => 'ppa', 'Pp3c14_1501' => 'ppa', 'Pp3c16_4900' => 'ppa', 'Pp3c16_5010' => 'ppa', 'Pp3c16_5060' => 'ppa', 'Pp3c19_18250' => 'ppa', 'Pp3c23_8530' => 'ppa', 'Pp3c23_8550' => 'ppa', 'Pp3c24_9670' => 'ppa', 'Pp3c2_21390' => 'ppa', 'Pp3c2_31380' => 'ppa', 'Pp3c3_16620' => 'ppa', 'Pp3c3_8090' => 'ppa', 'Pp3c3_8110' => 'ppa', 'Pp3c3_8130' => 'ppa', 'Pp3c3_8150' => 'ppa', 'Pp3c4_14320' => 'ppa', 'Pp3c6_2560' => 'ppa', 'Pp3c9_16700' => 'ppa', 'PRCOL_00000234' => 'pco', 'PRCOL_00000235' => 'pco', 'PRCOL_00000777' => 'pco', 'PRCOL_00002344' => 'pco', 'PRCOL_00002372' => 'pco', 'PRCOL_00006120' => 'pco', 'Prupe.1G021400' => 'ppe', 'Prupe.1G021500' => 'ppe', 'Prupe.1G021600' => 'ppe', 'Prupe.1G021700' => 'ppe', 'Prupe.1G021800' => 'ppe', 'Prupe.5G145100' => 'ppe', 'Psat6g204040' => 'psa', 'Psat6g204800' => 'psa', 'Psat6g204920' => 'psa', 'Psat6g204960' => 'psa', 'Psat6g205080' => 'psa', 'PSO017G0271' => 'pso', 'PSO017G1276' => 'pso', 'PSO017G1429' => 'pso', 'PSO017G1861' => 'pso', 'PSO017G2787' => 'pso', 'PSO017G4466' => 'pso', 'PSO017G5118' => 'pso', 'PSO017G5420' => 'pso', 'PSO063G3678' => 'pso', 'PSO210G0546' => 'pso', 'PSO317G0001' => 'pso', 'PSO357G0512' => 'pso', 'PSO478G2682' => 'pso', 'PSO647G0001' => 'pso', 'PSO675G0001' => 'pso', 'PSO675G2699' => 'pso', 'PSO675G2849' => 'pso', 'PSO675G4991' => 'pso', 'PSO689G0001' => 'pso', 'QL06p000916' => 'qlo', 'QL06p000921' => 'qlo', 'QL06p001398' => 'qlo', 'QL06p001407' => 'qlo', 'QL06p002031' => 'qlo', 'RcHm_v2.0_Chr4g0387791' => 'rch', 'RcHm_v2.0_Chr4g0387801' => 'rch', 'RcHm_v2.0_Chr6g0286501' => 'rch', 'RcHm_v2.0_Chr6g0286511' => 'rch', 'RcHm_v2.0_Chr6g0286521' => 'rch', 'RcHm_v2.0_Chr6g0286531' => 'rch', 'RcHm_v2.0_Chr7g0189141' => 'rch', 'Rhsim02G0028700' => 'rsi', 'Rhsim02G0028800' => 'rsi', 'Rhsim02G0028900' => 'rsi', 'Rhsim02G0029000' => 'rsi', 'Rhsim02G0029100' => 'rsi', 'Rhsim02G0029200' => 'rsi', 'Rhsim02G0029300' => 'rsi', 'Rhsim02G0029400' => 'rsi', 'Rhsim02G0029500' => 'rsi', 'Rhsim02G0029600' => 'rsi', 'RhsimUnG0024000' => 'rsi', 'RhsimUnG0024100' => 'rsi', 'RhsimUnG0024200' => 'rsi', 'RhsimUnG0024300' => 'rsi', 'RhsimUnG0024400' => 'rsi', 'RhsimUnG0024500' => 'rsi', 'RhsimUnG0024700' => 'rsi', 'RhsimUnG0024800' => 'rsi', 'RhsimUnG0024900' => 'rsi', 'RhsimUnG0025100' => 'rsi', 'Sabra08G0120200' => 'sbr', 'Sabra08G0120300' => 'sbr', 'Sabra08G0120500' => 'sbr', 'Sabra08G0120600' => 'sbr', 'Sabra10G0158900' => 'sbr', 'SalBow2G3492' => 'sbo', 'Sc13g0004760' => 'sci', 'Sc13g0004770' => 'sci', 'Sed0003417' => 'sed', 'Sed0019750' => 'sed', 'SEGI_03419' => 'sgi', 'SEGI_05907' => 'sgi', 'SEGI_10682' => 'sgi', 'SEGI_13528' => 'sgi', 'SEGI_16081' => 'sgi', 'SEGI_19370' => 'sgi', 'SEGI_21015' => 'sgi', 'SEGI_21944' => 'sgi', 'SEGI_32906' => 'sgi', 'SEGI_33093' => 'sgi', 'SEGI_36110' => 'sgi', 'SEGI_40397' => 'sgi', 'SGA_v2.0_scaffold191G40426' => 'sas', 'SGA_v2.0_scaffold353G49717' => 'sas', 'SGA_v2.0_scaffold50G18550' => 'sas', 'SMO119G0173' => 'smo', 'SMO172G0002' => 'smo', 'Solyc09g082690.3' => 'sly', 'Solyc09g082700.2' => 'sly', 'Sopen09g031550' => 'spe', 'Sopen09g031560' => 'spe', 'Sp3g20540' => 'spa', 'Sp7g07580' => 'spa', 'TAR134G0002' => 'tar', 'TAR236G0001' => 'tar', 'TAR365G0892' => 'tar', 'TAR636G0166' => 'tar', 'TAR636G0646' => 'tar', 'TAR636G0869' => 'tar', 'TAR636G1317' => 'tar', 'TAR636G1744' => 'tar', 'TAR636G3358' => 'tar', 'TAR636G3436' => 'tar', 'THA.LOC104803047' => 'tha', 'Thecc.04G238900' => 'tca', 'Thhalv10021557m.g' => 'esa', 'Thhalv10026318m.g' => 'esa', 'Thhalv10026335m.g' => 'esa', 'TPR.G17433' => 'tpr', 'TPR.G18915' => 'tpr', 'TPR.G26125' => 'tpr', 'TWI09G0677' => 'twi', 'TWI73G0287' => 'twi', 'unitig_748.g8326' => 'ugi', 'vmacro15370' => 'vma', 'vmacro15371' => 'vma', 'vmacro15372' => 'vma', 'vmacro15373' => 'vma', 'vmacro15374' => 'vma', 'VMungo0720G2826' => 'vmu', 'Zm00001eb116960' => 'zma', 'Zm00001eb301260' => 'zma', 'Zm00001eb301270' => 'zma' ), 'gf_id' => 'HOM05D001460', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001460' ), 'data_identifier' => 'HOM05D001460', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001460', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '433', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p22980' => 'bna', 'A01p32340' => 'bna', 'A03p42970' => 'bna', 'A05p25880' => 'bna', 'Aa31LG8G9320' => 'aar', 'Aa31LG8G9330' => 'aar', 'Aa31LG8G9340' => 'aar', 'Aa31sc221G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1034' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1528' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.829' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2222' => 'aag', 'Ah.12g058830' => 'amhyb', 'Ah.12g058840' => 'amhyb', 'AL3G37160' => 'aly', 'AL7G41310' => 'aly', 'Aqoxy5G00395' => 'aox', 'Aqoxy5G00396' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0C8NZA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5185HY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JZ1PRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MD3LS0' => 'arhy', 'AT3G22840' => 'ath', 'AT4G14690' => 'ath', 'ATR0665G054' => 'atr', 'Atru.chr4.2344' => 'acertr', 'Atru.chr4.2346' => 'acertr', 'Atru.chr4.2347' => 'acertr', 'Atru.chr4.2348' => 'acertr', 'Atru.chr4.2355' => 'acertr', 'Atru.chr4.2356' => 'acertr', 'Atru.chr4.2358' => 'acertr', 'Atru.chr4.2359' => 'acertr', 'Atru.chr4.2360' => 'acertr', 'Atru.chr4.2361' => 'acertr', 'AUR62030476' => 'cqu', 'AUR62030478' => 'cqu', 'AUR62030819' => 'cqu', 'AUR62030820' => 'cqu', 'BcaB03g14648' => 'bca', 'BcaB04g20492' => 'bca', 'BcaB06g26399' => 'bca', 'BcaC01g03416' => 'bca', 'BcaC01g03419' => 'bca', 'BcaC01g03421' => 'bca', 'BcaC01g03424' => 'bca', 'BcaC05g28012' => 'bca', 'BcaC09g49212' => 'bca', 'BcaC09g50140' => 'bca', 'BcaNung00346' => 'bca', 'BolC1t02785H' => 'bol', 'BolC1t04095H' => 'bol', 'BolC3t17545H' => 'bol', 'BolC5t32769H' => 'bol', 'BraA01t02211Z' => 'bra', 'BraA01t03359Z' => 'bra', 'BraA03t13441Z' => 'bra', 'BraA05t21476Z' => 'bra', 'C01p28420' => 'bna', 'C01p41350' => 'bna', 'C03p52750' => 'bna', 'C03p52780' => 'bna', 'C05p40270' => 'bna', 'CAN.G1437.9' => 'can', 'CANSAT78G0035' => 'cansat', 'CANSAT78G1036' => 'cansat', 'CANSAT78G2272' => 'cansat', 'CANSAT78G2478' => 'cansat', 'CARHR098700' => 'chi', 'CARHR221120' => 'chi', 'CARHR221150' => 'chi', 'Carub.0003s2297' => 'cru', 'Carub.0007s2749' => 'cru', 'Carub.0007s2750' => 'cru', 'Carub.0007s2751' => 'cru', 'Ca_10849_v3' => 'car', 'Cc03_g04300' => 'ccan', 'CDE02G3648' => 'cde', 'CDE05G0060' => 'cde', 'CDE05G0692' => 'cde', 'CDE05G2285' => 'cde', 'CDE05G2884' => 'cde', 'CDE05G3072' => 'cde', 'Cfa008439' => 'cfa', 'Cfa008441' => 'cfa', 'Cfa008443' => 'cfa', 'Cfa008448' => 'cfa', 'Ciclev10005974m.g' => 'ccl', 'Ciclev10006006m.g' => 'ccl', 'Ciclev10006775m.g' => 'ccl', 'CiPaw.02G120400' => 'cil', 'CiPaw.02G120500' => 'cil', 'CiPaw.02G120600' => 'cil', 'ClCG05G004850' => 'cla', 'COL.COLO4_21566' => 'col', 'Cpa.g.sc44.124' => 'cpa', 'Cre07.g320400' => 'cre', 'Cre07.g320450' => 'cre', 'Cre08.g384650' => 'cre', 'Cre09.g393173' => 'cre', 'Cre09.g394325' => 'cre', 'Cre14.g626750' => 'cre', 'Cre16.g679250' => 'cre', 'CsaV3_3G012890' => 'csa', 'CSS0010865' => 'camsi', 'CSS0044338' => 'camsi', 'DCAR_002366' => 'dca', 'DCAR_030687' => 'dca', 'DCAR_030688' => 'dca', 'Dinv14047' => 'din', 'Dinv14048' => 'din', 'Duzib151G0105' => 'dzi', 'Duzib151G0114' => 'dzi', 'Duzib212G1029' => 'dzi', 'ECA232G3536' => 'eca', 'ECA240G0786' => 'eca', 'ECA240G1802' => 'eca', 'ECA240G3760' => 'eca', 'ECA240G3920' => 'eca', 'EL10Ac5g12536' => 'bvu', 'EL10Ac5g12537' => 'bvu', 'EL10Ac5g12538' => 'bvu', 'Eucgr.B01004' => 'egr', 'Eucgr.B01006' => 'egr', 'Eucgr.B01007' => 'egr', 'Eucgr.B01008' => 'egr', 'Eucgr.B01895' => 'egr', 'Eucgr.B01896' => 'egr', 'FAN04G1456' => 'fan', 'FAN08G1769' => 'fan', 'FAN08G2160' => 'fan', 'FAN13G2403' => 'fan', 'FAN13G3303' => 'fan', 'FAN15G2435' => 'fan', 'FAN17G0672' => 'fan', 'FAN17G2441' => 'fan', 'FAN18G1024' => 'fan', 'FAN22G1458' => 'fan', 'FAN24G0037' => 'fan', 'FAN24G0429' => 'fan', 'FAN24G2387' => 'fan', 'FAN27G2746' => 'fan', 'FvH4_2g20400' => 'fve', 'FvH4_2g20420' => 'fve', 'FvH4_2g20430' => 'fve', 'FvH4_4g01270' => 'fve', 'FvH4_4g01290' => 'fve', 'FvH4_4g01300' => 'fve', 'FvH4_4g01310' => 'fve', 'FvH4_4g01330' => 'fve', 'FvH4_5g09070' => 'fve', 'Glyma.10G243800' => 'gma', 'Glyma.20G150600' => 'gma', 'Gohir.A09G219200' => 'ghi', 'Gohir.A09G219300' => 'ghi', 'Gohir.D09G221400' => 'ghi', 'Gohir.D09G221500' => 'ghi', 'Gorai.006G242600' => 'gra', 'Gorai.006G242700' => 'gra', 'GSVIVG01018044001' => 'vvi', 'HanXRQChr03g0083821' => 'han', 'HanXRQChr03g0083841' => 'han', 'HanXRQChr03g0083881' => 'han', 'HanXRQChr03g0083901' => 'han', 'HanXRQChr03g0083921' => 'han', 'HanXRQChr03g0085331' => 'han', 'HanXRQChr03g0085361' => 'han', 'HanXRQChr03g0085411' => 'han', 'HanXRQChr03g0085421' => 'han', 'HanXRQChr03g0085431' => 'han', 'HanXRQChr08g0221991' => 'han', 'HanXRQChr11g0336061' => 'han', 'HanXRQChr11g0336411' => 'han', 'Haze_11234' => 'cav', 'Hma1.2p1_0549F.1_g177010' => 'hma', 'Hma1.2p1_0602F.1_g187630' => 'hma', 'Hund14876' => 'sun', 'Hund14879' => 'sun', 'Lalb_Chr06g0160741' => 'lal', 'Lalb_Chr21g0304781' => 'lal', 'Lj3A726G19' => 'lonja', 'Lj3A726T23' => 'lonja', 'Lj3A726T24' => 'lonja', 'Lj3A726T25' => 'lonja', 'Lj3A727T17' => 'lonja', 'Lj3C726T0' => 'lonja', 'Lj3C726T2' => 'lonja', 'Lj3P725T35' => 'lonja', 'Lj3P727T10' => 'lonja', 'Lj3P727T12' => 'lonja', 'Lj3P727T14' => 'lonja', 'Lj5g0023109' => 'lja', 'Lj6P646T44' => 'lonja', 'Lsat_1_v5_gn_6_75760' => 'lsa', 'Lsat_1_v5_gn_6_75800' => 'lsa', 'Lsat_1_v5_gn_6_75900' => 'lsa', 'Lsat_1_v5_gn_6_76240' => 'lsa', 'Lsat_1_v5_gn_6_76441' => 'lsa', 'Lsat_1_v5_gn_6_76700' => 'lsa', 'Lsat_1_v5_gn_6_76760' => 'lsa', 'Manes.15G033100' => 'mes', 'Mapoly0004s0074' => 'mpo', 'Mapoly0004s0075' => 'mpo', 'Mapoly0004s0163' => 'mpo', 'Mapoly0004s0164' => 'mpo', 'Mapoly0021s0018' => 'mpo', 'Mapoly0041s0136' => 'mpo', 'Mapoly0041s0137' => 'mpo', 'Mapoly0041s0138' => 'mpo', 'Mapoly0041s0139' => 'mpo', 'Mapoly0041s0141' => 'mpo', 'Mapoly0041s0142' => 'mpo', 'Mapoly0041s0143' => 'mpo', 'Mapoly0041s0144' => 'mpo', 'Mapoly0041s0145' => 'mpo', 'Mapoly0047s0106' => 'mpo', 'Mapoly0047s0108' => 'mpo', 'Mapoly0050s0051' => 'mpo', 'Mapoly0050s0052' => 'mpo', 'Mapoly0050s0053' => 'mpo', 'Mapoly0058s0013' => 'mpo', 'Mapoly0091s0078' => 'mpo', 'Mapoly0091s0079' => 'mpo', 'Mapoly0091s0080' => 'mpo', 'Mapoly0091s0081' => 'mpo', 'Mapoly0278s0004' => 'mpo', 'Mapoly0278s0005' => 'mpo', 'Mapoly0278s0006' => 'mpo', 'MBI11_g30648_MAGBIO' => 'mbi', 'MCO03G194' => 'mco', 'MCO03G590' => 'mco', 'MCO07G312' => 'mco', 'MCO10G318' => 'mco', 'MCO12G244' => 'mco', 'MCO13G148' => 'mco', 'MCO13G194' => 'mco', 'MCO16G238' => 'mco', 'MD06G1134100' => 'mdo', 'MD13G1200100' => 'mdo', 'MD13G1200300' => 'mdo', 'MD13G1200600' => 'mdo', 'MD14G1150400' => 'mdo', 'MD16G1200000' => 'mdo', 'Medtr1g102570' => 'mtr', 'Medtr1g102780' => 'mtr', 'Medtr1g102800' => 'mtr', 'Medtr1g102810' => 'mtr', 'Medtr1g102830' => 'mtr', 'MELO3C006499.2' => 'cme', 'Migut.G00385' => 'egut', 'MSTRG.4063' => 'ama', 'Nitab4.5_0000090g0260' => 'nta', 'Nitab4.5_0000977g0030' => 'nta', 'Nitab4.5_0002541g0040' => 'nta', 'Nitab4.5_0007068g0040' => 'nta', 'Nn005s41408' => 'nnu', 'Nn005s41410' => 'nnu', 'Oeu010310.1' => 'oeu', 'Oeu010311.1' => 'oeu', 'Oeu043472.1' => 'oeu', 'Os01g0246400' => 'osa', 'Os04g0267950' => 'osa', 'Os07g0178700' => 'osa', 'Os07g0178800' => 'osa', 'Peaxi162Scf00316g00046' => 'pax', 'Peaxi162Scf00316g00049' => 'pax', 'Peaxi162Scf00316g00059' => 'pax', 'Peaxi162Scf00316g00328' => 'pax', 'Peaxi162Scf00316g00329' => 'pax', 'Peaxi162Scf00316g00411' => 'pax', 'Peaxi162Scf00316g00521' => 'pax', 'Peaxi162Scf00492g00068' => 'pax', 'Peaxi162Scf35631g00002' => 'pax', 'PGR142G3720' => 'pgr', 'PGSC0003DMG400006442' => 'stu', 'Phvul.007G062000' => 'pvu', 'Potri.008G157750' => 'ptr', 'Potri.008G157900' => 'ptr', 'Potri.008G158000' => 'ptr', 'Potri.008G158200' => 'ptr', 'Pp3c11_7280' => 'ppa', 'Pp3c11_7980' => 'ppa', 'Pp3c12_19450' => 'ppa', 'Pp3c14_1480' => 'ppa', 'Pp3c14_1501' => 'ppa', 'Pp3c16_4900' => 'ppa', 'Pp3c16_5010' => 'ppa', 'Pp3c16_5060' => 'ppa', 'Pp3c19_18250' => 'ppa', 'Pp3c23_8530' => 'ppa', 'Pp3c23_8550' => 'ppa', 'Pp3c24_9670' => 'ppa', 'Pp3c2_21390' => 'ppa', 'Pp3c2_31380' => 'ppa', 'Pp3c3_16620' => 'ppa', 'Pp3c3_8090' => 'ppa', 'Pp3c3_8110' => 'ppa', 'Pp3c3_8130' => 'ppa', 'Pp3c3_8150' => 'ppa', 'Pp3c4_14320' => 'ppa', 'Pp3c6_2560' => 'ppa', 'Pp3c9_16700' => 'ppa', 'PRCOL_00000234' => 'pco', 'PRCOL_00000235' => 'pco', 'PRCOL_00000777' => 'pco', 'PRCOL_00002344' => 'pco', 'PRCOL_00002372' => 'pco', 'PRCOL_00006120' => 'pco', 'Prupe.1G021400' => 'ppe', 'Prupe.1G021500' => 'ppe', 'Prupe.1G021600' => 'ppe', 'Prupe.1G021700' => 'ppe', 'Prupe.1G021800' => 'ppe', 'Prupe.5G145100' => 'ppe', 'Psat6g204040' => 'psa', 'Psat6g204800' => 'psa', 'Psat6g204920' => 'psa', 'Psat6g204960' => 'psa', 'Psat6g205080' => 'psa', 'PSO017G0271' => 'pso', 'PSO017G1276' => 'pso', 'PSO017G1429' => 'pso', 'PSO017G1861' => 'pso', 'PSO017G2787' => 'pso', 'PSO017G4466' => 'pso', 'PSO017G5118' => 'pso', 'PSO017G5420' => 'pso', 'PSO063G3678' => 'pso', 'PSO210G0546' => 'pso', 'PSO317G0001' => 'pso', 'PSO357G0512' => 'pso', 'PSO478G2682' => 'pso', 'PSO647G0001' => 'pso', 'PSO675G0001' => 'pso', 'PSO675G2699' => 'pso', 'PSO675G2849' => 'pso', 'PSO675G4991' => 'pso', 'PSO689G0001' => 'pso', 'QL06p000916' => 'qlo', 'QL06p000921' => 'qlo', 'QL06p001398' => 'qlo', 'QL06p001407' => 'qlo', 'QL06p002031' => 'qlo', 'RcHm_v2.0_Chr4g0387791' => 'rch', 'RcHm_v2.0_Chr4g0387801' => 'rch', 'RcHm_v2.0_Chr6g0286501' => 'rch', 'RcHm_v2.0_Chr6g0286511' => 'rch', 'RcHm_v2.0_Chr6g0286521' => 'rch', 'RcHm_v2.0_Chr6g0286531' => 'rch', 'RcHm_v2.0_Chr7g0189141' => 'rch', 'Rhsim02G0028700' => 'rsi', 'Rhsim02G0028800' => 'rsi', 'Rhsim02G0028900' => 'rsi', 'Rhsim02G0029000' => 'rsi', 'Rhsim02G0029100' => 'rsi', 'Rhsim02G0029200' => 'rsi', 'Rhsim02G0029300' => 'rsi', 'Rhsim02G0029400' => 'rsi', 'Rhsim02G0029500' => 'rsi', 'Rhsim02G0029600' => 'rsi', 'RhsimUnG0024000' => 'rsi', 'RhsimUnG0024100' => 'rsi', 'RhsimUnG0024200' => 'rsi', 'RhsimUnG0024300' => 'rsi', 'RhsimUnG0024400' => 'rsi', 'RhsimUnG0024500' => 'rsi', 'RhsimUnG0024700' => 'rsi', 'RhsimUnG0024800' => 'rsi', 'RhsimUnG0024900' => 'rsi', 'RhsimUnG0025100' => 'rsi', 'Sabra08G0120200' => 'sbr', 'Sabra08G0120300' => 'sbr', 'Sabra08G0120500' => 'sbr', 'Sabra08G0120600' => 'sbr', 'Sabra10G0158900' => 'sbr', 'SalBow2G3492' => 'sbo', 'Sc13g0004760' => 'sci', 'Sc13g0004770' => 'sci', 'Sed0003417' => 'sed', 'Sed0019750' => 'sed', 'SEGI_03419' => 'sgi', 'SEGI_05907' => 'sgi', 'SEGI_10682' => 'sgi', 'SEGI_13528' => 'sgi', 'SEGI_16081' => 'sgi', 'SEGI_19370' => 'sgi', 'SEGI_21015' => 'sgi', 'SEGI_21944' => 'sgi', 'SEGI_32906' => 'sgi', 'SEGI_33093' => 'sgi', 'SEGI_36110' => 'sgi', 'SEGI_40397' => 'sgi', 'SGA_v2.0_scaffold191G40426' => 'sas', 'SGA_v2.0_scaffold353G49717' => 'sas', 'SGA_v2.0_scaffold50G18550' => 'sas', 'SMO119G0173' => 'smo', 'SMO172G0002' => 'smo', 'Solyc09g082690.3' => 'sly', 'Solyc09g082700.2' => 'sly', 'Sopen09g031550' => 'spe', 'Sopen09g031560' => 'spe', 'Sp3g20540' => 'spa', 'Sp7g07580' => 'spa', 'TAR134G0002' => 'tar', 'TAR236G0001' => 'tar', 'TAR365G0892' => 'tar', 'TAR636G0166' => 'tar', 'TAR636G0646' => 'tar', 'TAR636G0869' => 'tar', 'TAR636G1317' => 'tar', 'TAR636G1744' => 'tar', 'TAR636G3358' => 'tar', 'TAR636G3436' => 'tar', 'THA.LOC104803047' => 'tha', 'Thecc.04G238900' => 'tca', 'Thhalv10021557m.g' => 'esa', 'Thhalv10026318m.g' => 'esa', 'Thhalv10026335m.g' => 'esa', 'TPR.G17433' => 'tpr', 'TPR.G18915' => 'tpr', 'TPR.G26125' => 'tpr', 'TWI09G0677' => 'twi', 'TWI73G0287' => 'twi', 'unitig_748.g8326' => 'ugi', 'vmacro15370' => 'vma', 'vmacro15371' => 'vma', 'vmacro15372' => 'vma', 'vmacro15373' => 'vma', 'vmacro15374' => 'vma', 'VMungo0720G2826' => 'vmu', 'Zm00001eb116960' => 'zma', 'Zm00001eb301260' => 'zma', 'Zm00001eb301270' => 'zma' ) $gf_id = 'HOM05D001460' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001460' ) $data_identifier = 'HOM05D001460' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 4, 'aag' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 2, 'aox' => (int) 2, 'arhy' => (int) 4, 'ath' => (int) 2, 'atr' => (int) 1, 'acertr' => (int) 10, 'cqu' => (int) 4, 'bca' => (int) 11, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 1, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 1, 'ccan' => (int) 1, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 1, 'col' => (int) 1, 'cpa' => (int) 1, 'cre' => (int) 7, 'csa' => (int) 1, 'camsi' => (int) 2, 'dca' => (int) 3, 'din' => (int) 2, 'dzi' => (int) 3, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 14, 'fve' => (int) 9, 'gma' => (int) 2, 'ghi' => (int) 4, 'gra' => (int) 2, 'vvi' => (int) 1, 'han' => (int) 13, 'cav' => (int) 1, 'hma' => (int) 2, 'sun' => (int) 2, 'lal' => (int) 2, 'lonja' => (int) 12, 'lja' => (int) 1, 'lsa' => (int) 7, 'mes' => (int) 1, 'mpo' => (int) 27, 'mbi' => (int) 1, 'mco' => (int) 8, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 1, 'egut' => (int) 1, 'ama' => (int) 1, 'nta' => (int) 4, 'nnu' => (int) 2, 'oeu' => (int) 3, 'osa' => (int) 4, 'pax' => (int) 9, 'pgr' => (int) 1, 'stu' => (int) 1, 'pvu' => (int) 1, 'ptr' => (int) 4, 'ppa' => (int) 22, 'pco' => (int) 6, 'ppe' => (int) 6, 'psa' => (int) 5, 'pso' => (int) 19, 'qlo' => (int) 5, 'rch' => (int) 7, 'rsi' => (int) 20, 'sbr' => (int) 5, 'sbo' => (int) 1, 'sci' => (int) 2, 'sed' => (int) 2, 'sgi' => (int) 12, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 2, 'tar' => (int) 10, 'tha' => (int) 1, 'tca' => (int) 1, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 2, 'ugi' => (int) 1, 'vma' => (int) 5, 'vmu' => (int) 1, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb301270' $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' => 'HOM05D001460', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '433', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p22980' => 'bna', 'A01p32340' => 'bna', 'A03p42970' => 'bna', 'A05p25880' => 'bna', 'Aa31LG8G9320' => 'aar', 'Aa31LG8G9330' => 'aar', 'Aa31LG8G9340' => 'aar', 'Aa31sc221G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1034' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1528' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.829' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2222' => 'aag', 'Ah.12g058830' => 'amhyb', 'Ah.12g058840' => 'amhyb', 'AL3G37160' => 'aly', 'AL7G41310' => 'aly', 'Aqoxy5G00395' => 'aox', 'Aqoxy5G00396' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0C8NZA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5185HY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JZ1PRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MD3LS0' => 'arhy', 'AT3G22840' => 'ath', 'AT4G14690' => 'ath', 'ATR0665G054' => 'atr', 'Atru.chr4.2344' => 'acertr', 'Atru.chr4.2346' => 'acertr', 'Atru.chr4.2347' => 'acertr', 'Atru.chr4.2348' => 'acertr', 'Atru.chr4.2355' => 'acertr', 'Atru.chr4.2356' => 'acertr', 'Atru.chr4.2358' => 'acertr', 'Atru.chr4.2359' => 'acertr', 'Atru.chr4.2360' => 'acertr', 'Atru.chr4.2361' => 'acertr', 'AUR62030476' => 'cqu', 'AUR62030478' => 'cqu', 'AUR62030819' => 'cqu', 'AUR62030820' => 'cqu', 'BcaB03g14648' => 'bca', 'BcaB04g20492' => 'bca', 'BcaB06g26399' => 'bca', 'BcaC01g03416' => 'bca', 'BcaC01g03419' => 'bca', 'BcaC01g03421' => 'bca', 'BcaC01g03424' => 'bca', 'BcaC05g28012' => 'bca', 'BcaC09g49212' => 'bca', 'BcaC09g50140' => 'bca', 'BcaNung00346' => 'bca', 'BolC1t02785H' => 'bol', 'BolC1t04095H' => 'bol', 'BolC3t17545H' => 'bol', 'BolC5t32769H' => 'bol', 'BraA01t02211Z' => 'bra', 'BraA01t03359Z' => 'bra', 'BraA03t13441Z' => 'bra', 'BraA05t21476Z' => 'bra', 'C01p28420' => 'bna', 'C01p41350' => 'bna', 'C03p52750' => 'bna', 'C03p52780' => 'bna', 'C05p40270' => 'bna', 'CAN.G1437.9' => 'can', 'CANSAT78G0035' => 'cansat', 'CANSAT78G1036' => 'cansat', 'CANSAT78G2272' => 'cansat', 'CANSAT78G2478' => 'cansat', 'CARHR098700' => 'chi', 'CARHR221120' => 'chi', 'CARHR221150' => 'chi', 'Carub.0003s2297' => 'cru', 'Carub.0007s2749' => 'cru', 'Carub.0007s2750' => 'cru', 'Carub.0007s2751' => 'cru', 'Ca_10849_v3' => 'car', 'Cc03_g04300' => 'ccan', 'CDE02G3648' => 'cde', 'CDE05G0060' => 'cde', 'CDE05G0692' => 'cde', 'CDE05G2285' => 'cde', 'CDE05G2884' => 'cde', 'CDE05G3072' => 'cde', 'Cfa008439' => 'cfa', 'Cfa008441' => 'cfa', 'Cfa008443' => 'cfa', 'Cfa008448' => 'cfa', 'Ciclev10005974m.g' => 'ccl', 'Ciclev10006006m.g' => 'ccl', 'Ciclev10006775m.g' => 'ccl', 'CiPaw.02G120400' => 'cil', 'CiPaw.02G120500' => 'cil', 'CiPaw.02G120600' => 'cil', 'ClCG05G004850' => 'cla', 'COL.COLO4_21566' => 'col', 'Cpa.g.sc44.124' => 'cpa', 'Cre07.g320400' => 'cre', 'Cre07.g320450' => 'cre', 'Cre08.g384650' => 'cre', 'Cre09.g393173' => 'cre', 'Cre09.g394325' => 'cre', 'Cre14.g626750' => 'cre', 'Cre16.g679250' => 'cre', 'CsaV3_3G012890' => 'csa', 'CSS0010865' => 'camsi', 'CSS0044338' => 'camsi', 'DCAR_002366' => 'dca', 'DCAR_030687' => 'dca', 'DCAR_030688' => 'dca', 'Dinv14047' => 'din', 'Dinv14048' => 'din', 'Duzib151G0105' => 'dzi', 'Duzib151G0114' => 'dzi', 'Duzib212G1029' => 'dzi', 'ECA232G3536' => 'eca', 'ECA240G0786' => 'eca', 'ECA240G1802' => 'eca', 'ECA240G3760' => 'eca', 'ECA240G3920' => 'eca', 'EL10Ac5g12536' => 'bvu', 'EL10Ac5g12537' => 'bvu', 'EL10Ac5g12538' => 'bvu', 'Eucgr.B01004' => 'egr', 'Eucgr.B01006' => 'egr', 'Eucgr.B01007' => 'egr', 'Eucgr.B01008' => 'egr', 'Eucgr.B01895' => 'egr', 'Eucgr.B01896' => 'egr', 'FAN04G1456' => 'fan', 'FAN08G1769' => 'fan', 'FAN08G2160' => 'fan', 'FAN13G2403' => 'fan', 'FAN13G3303' => 'fan', 'FAN15G2435' => 'fan', 'FAN17G0672' => 'fan', 'FAN17G2441' => 'fan', 'FAN18G1024' => 'fan', 'FAN22G1458' => 'fan', 'FAN24G0037' => 'fan', 'FAN24G0429' => 'fan', 'FAN24G2387' => 'fan', 'FAN27G2746' => 'fan', 'FvH4_2g20400' => 'fve', 'FvH4_2g20420' => 'fve', 'FvH4_2g20430' => 'fve', 'FvH4_4g01270' => 'fve', 'FvH4_4g01290' => 'fve', 'FvH4_4g01300' => 'fve', 'FvH4_4g01310' => 'fve', 'FvH4_4g01330' => 'fve', 'FvH4_5g09070' => 'fve', 'Glyma.10G243800' => 'gma', 'Glyma.20G150600' => 'gma', 'Gohir.A09G219200' => 'ghi', 'Gohir.A09G219300' => 'ghi', 'Gohir.D09G221400' => 'ghi', 'Gohir.D09G221500' => 'ghi', 'Gorai.006G242600' => 'gra', 'Gorai.006G242700' => 'gra', 'GSVIVG01018044001' => 'vvi', 'HanXRQChr03g0083821' => 'han', 'HanXRQChr03g0083841' => 'han', 'HanXRQChr03g0083881' => 'han', 'HanXRQChr03g0083901' => 'han', 'HanXRQChr03g0083921' => 'han', 'HanXRQChr03g0085331' => 'han', 'HanXRQChr03g0085361' => 'han', 'HanXRQChr03g0085411' => 'han', 'HanXRQChr03g0085421' => 'han', 'HanXRQChr03g0085431' => 'han', 'HanXRQChr08g0221991' => 'han', 'HanXRQChr11g0336061' => 'han', 'HanXRQChr11g0336411' => 'han', 'Haze_11234' => 'cav', 'Hma1.2p1_0549F.1_g177010' => 'hma', 'Hma1.2p1_0602F.1_g187630' => 'hma', 'Hund14876' => 'sun', 'Hund14879' => 'sun', 'Lalb_Chr06g0160741' => 'lal', 'Lalb_Chr21g0304781' => 'lal', 'Lj3A726G19' => 'lonja', 'Lj3A726T23' => 'lonja', 'Lj3A726T24' => 'lonja', 'Lj3A726T25' => 'lonja', 'Lj3A727T17' => 'lonja', 'Lj3C726T0' => 'lonja', 'Lj3C726T2' => 'lonja', 'Lj3P725T35' => 'lonja', 'Lj3P727T10' => 'lonja', 'Lj3P727T12' => 'lonja', 'Lj3P727T14' => 'lonja', 'Lj5g0023109' => 'lja', 'Lj6P646T44' => 'lonja', 'Lsat_1_v5_gn_6_75760' => 'lsa', 'Lsat_1_v5_gn_6_75800' => 'lsa', 'Lsat_1_v5_gn_6_75900' => 'lsa', 'Lsat_1_v5_gn_6_76240' => 'lsa', 'Lsat_1_v5_gn_6_76441' => 'lsa', 'Lsat_1_v5_gn_6_76700' => 'lsa', 'Lsat_1_v5_gn_6_76760' => 'lsa', 'Manes.15G033100' => 'mes', 'Mapoly0004s0074' => 'mpo', 'Mapoly0004s0075' => 'mpo', 'Mapoly0004s0163' => 'mpo', 'Mapoly0004s0164' => 'mpo', 'Mapoly0021s0018' => 'mpo', 'Mapoly0041s0136' => 'mpo', 'Mapoly0041s0137' => 'mpo', 'Mapoly0041s0138' => 'mpo', 'Mapoly0041s0139' => 'mpo', 'Mapoly0041s0141' => 'mpo', 'Mapoly0041s0142' => 'mpo', 'Mapoly0041s0143' => 'mpo', 'Mapoly0041s0144' => 'mpo', 'Mapoly0041s0145' => 'mpo', 'Mapoly0047s0106' => 'mpo', 'Mapoly0047s0108' => 'mpo', 'Mapoly0050s0051' => 'mpo', 'Mapoly0050s0052' => 'mpo', 'Mapoly0050s0053' => 'mpo', 'Mapoly0058s0013' => 'mpo', 'Mapoly0091s0078' => 'mpo', 'Mapoly0091s0079' => 'mpo', 'Mapoly0091s0080' => 'mpo', 'Mapoly0091s0081' => 'mpo', 'Mapoly0278s0004' => 'mpo', 'Mapoly0278s0005' => 'mpo', 'Mapoly0278s0006' => 'mpo', 'MBI11_g30648_MAGBIO' => 'mbi', 'MCO03G194' => 'mco', 'MCO03G590' => 'mco', 'MCO07G312' => 'mco', 'MCO10G318' => 'mco', 'MCO12G244' => 'mco', 'MCO13G148' => 'mco', 'MCO13G194' => 'mco', 'MCO16G238' => 'mco', 'MD06G1134100' => 'mdo', 'MD13G1200100' => 'mdo', 'MD13G1200300' => 'mdo', 'MD13G1200600' => 'mdo', 'MD14G1150400' => 'mdo', 'MD16G1200000' => 'mdo', 'Medtr1g102570' => 'mtr', 'Medtr1g102780' => 'mtr', 'Medtr1g102800' => 'mtr', 'Medtr1g102810' => 'mtr', 'Medtr1g102830' => 'mtr', 'MELO3C006499.2' => 'cme', 'Migut.G00385' => 'egut', 'MSTRG.4063' => 'ama', 'Nitab4.5_0000090g0260' => 'nta', 'Nitab4.5_0000977g0030' => 'nta', 'Nitab4.5_0002541g0040' => 'nta', 'Nitab4.5_0007068g0040' => 'nta', 'Nn005s41408' => 'nnu', 'Nn005s41410' => 'nnu', 'Oeu010310.1' => 'oeu', 'Oeu010311.1' => 'oeu', 'Oeu043472.1' => 'oeu', 'Os01g0246400' => 'osa', 'Os04g0267950' => 'osa', 'Os07g0178700' => 'osa', 'Os07g0178800' => 'osa', 'Peaxi162Scf00316g00046' => 'pax', 'Peaxi162Scf00316g00049' => 'pax', 'Peaxi162Scf00316g00059' => 'pax', 'Peaxi162Scf00316g00328' => 'pax', 'Peaxi162Scf00316g00329' => 'pax', 'Peaxi162Scf00316g00411' => 'pax', 'Peaxi162Scf00316g00521' => 'pax', 'Peaxi162Scf00492g00068' => 'pax', 'Peaxi162Scf35631g00002' => 'pax', 'PGR142G3720' => 'pgr', 'PGSC0003DMG400006442' => 'stu', 'Phvul.007G062000' => 'pvu', 'Potri.008G157750' => 'ptr', 'Potri.008G157900' => 'ptr', 'Potri.008G158000' => 'ptr', 'Potri.008G158200' => 'ptr', 'Pp3c11_7280' => 'ppa', 'Pp3c11_7980' => 'ppa', 'Pp3c12_19450' => 'ppa', 'Pp3c14_1480' => 'ppa', 'Pp3c14_1501' => 'ppa', 'Pp3c16_4900' => 'ppa', 'Pp3c16_5010' => 'ppa', 'Pp3c16_5060' => 'ppa', 'Pp3c19_18250' => 'ppa', 'Pp3c23_8530' => 'ppa', 'Pp3c23_8550' => 'ppa', 'Pp3c24_9670' => 'ppa', 'Pp3c2_21390' => 'ppa', 'Pp3c2_31380' => 'ppa', 'Pp3c3_16620' => 'ppa', 'Pp3c3_8090' => 'ppa', 'Pp3c3_8110' => 'ppa', 'Pp3c3_8130' => 'ppa', 'Pp3c3_8150' => 'ppa', 'Pp3c4_14320' => 'ppa', 'Pp3c6_2560' => 'ppa', 'Pp3c9_16700' => 'ppa', 'PRCOL_00000234' => 'pco', 'PRCOL_00000235' => 'pco', 'PRCOL_00000777' => 'pco', 'PRCOL_00002344' => 'pco', 'PRCOL_00002372' => 'pco', 'PRCOL_00006120' => 'pco', 'Prupe.1G021400' => 'ppe', 'Prupe.1G021500' => 'ppe', 'Prupe.1G021600' => 'ppe', 'Prupe.1G021700' => 'ppe', 'Prupe.1G021800' => 'ppe', 'Prupe.5G145100' => 'ppe', 'Psat6g204040' => 'psa', 'Psat6g204800' => 'psa', 'Psat6g204920' => 'psa', 'Psat6g204960' => 'psa', 'Psat6g205080' => 'psa', 'PSO017G0271' => 'pso', 'PSO017G1276' => 'pso', 'PSO017G1429' => 'pso', 'PSO017G1861' => 'pso', 'PSO017G2787' => 'pso', 'PSO017G4466' => 'pso', 'PSO017G5118' => 'pso', 'PSO017G5420' => 'pso', 'PSO063G3678' => 'pso', 'PSO210G0546' => 'pso', 'PSO317G0001' => 'pso', 'PSO357G0512' => 'pso', 'PSO478G2682' => 'pso', 'PSO647G0001' => 'pso', 'PSO675G0001' => 'pso', 'PSO675G2699' => 'pso', 'PSO675G2849' => 'pso', 'PSO675G4991' => 'pso', 'PSO689G0001' => 'pso', 'QL06p000916' => 'qlo', 'QL06p000921' => 'qlo', 'QL06p001398' => 'qlo', 'QL06p001407' => 'qlo', 'QL06p002031' => 'qlo', 'RcHm_v2.0_Chr4g0387791' => 'rch', 'RcHm_v2.0_Chr4g0387801' => 'rch', 'RcHm_v2.0_Chr6g0286501' => 'rch', 'RcHm_v2.0_Chr6g0286511' => 'rch', 'RcHm_v2.0_Chr6g0286521' => 'rch', 'RcHm_v2.0_Chr6g0286531' => 'rch', 'RcHm_v2.0_Chr7g0189141' => 'rch', 'Rhsim02G0028700' => 'rsi', 'Rhsim02G0028800' => 'rsi', 'Rhsim02G0028900' => 'rsi', 'Rhsim02G0029000' => 'rsi', 'Rhsim02G0029100' => 'rsi', 'Rhsim02G0029200' => 'rsi', 'Rhsim02G0029300' => 'rsi', 'Rhsim02G0029400' => 'rsi', 'Rhsim02G0029500' => 'rsi', 'Rhsim02G0029600' => 'rsi', 'RhsimUnG0024000' => 'rsi', 'RhsimUnG0024100' => 'rsi', 'RhsimUnG0024200' => 'rsi', 'RhsimUnG0024300' => 'rsi', 'RhsimUnG0024400' => 'rsi', 'RhsimUnG0024500' => 'rsi', 'RhsimUnG0024700' => 'rsi', 'RhsimUnG0024800' => 'rsi', 'RhsimUnG0024900' => 'rsi', 'RhsimUnG0025100' => 'rsi', 'Sabra08G0120200' => 'sbr', 'Sabra08G0120300' => 'sbr', 'Sabra08G0120500' => 'sbr', 'Sabra08G0120600' => 'sbr', 'Sabra10G0158900' => 'sbr', 'SalBow2G3492' => 'sbo', 'Sc13g0004760' => 'sci', 'Sc13g0004770' => 'sci', 'Sed0003417' => 'sed', 'Sed0019750' => 'sed', 'SEGI_03419' => 'sgi', 'SEGI_05907' => 'sgi', 'SEGI_10682' => 'sgi', 'SEGI_13528' => 'sgi', 'SEGI_16081' => 'sgi', 'SEGI_19370' => 'sgi', 'SEGI_21015' => 'sgi', 'SEGI_21944' => 'sgi', 'SEGI_32906' => 'sgi', 'SEGI_33093' => 'sgi', 'SEGI_36110' => 'sgi', 'SEGI_40397' => 'sgi', 'SGA_v2.0_scaffold191G40426' => 'sas', 'SGA_v2.0_scaffold353G49717' => 'sas', 'SGA_v2.0_scaffold50G18550' => 'sas', 'SMO119G0173' => 'smo', 'SMO172G0002' => 'smo', 'Solyc09g082690.3' => 'sly', 'Solyc09g082700.2' => 'sly', 'Sopen09g031550' => 'spe', 'Sopen09g031560' => 'spe', 'Sp3g20540' => 'spa', 'Sp7g07580' => 'spa', 'TAR134G0002' => 'tar', 'TAR236G0001' => 'tar', 'TAR365G0892' => 'tar', 'TAR636G0166' => 'tar', 'TAR636G0646' => 'tar', 'TAR636G0869' => 'tar', 'TAR636G1317' => 'tar', 'TAR636G1744' => 'tar', 'TAR636G3358' => 'tar', 'TAR636G3436' => 'tar', 'THA.LOC104803047' => 'tha', 'Thecc.04G238900' => 'tca', 'Thhalv10021557m.g' => 'esa', 'Thhalv10026318m.g' => 'esa', 'Thhalv10026335m.g' => 'esa', 'TPR.G17433' => 'tpr', 'TPR.G18915' => 'tpr', 'TPR.G26125' => 'tpr', 'TWI09G0677' => 'twi', 'TWI73G0287' => 'twi', 'unitig_748.g8326' => 'ugi', 'vmacro15370' => 'vma', 'vmacro15371' => 'vma', 'vmacro15372' => 'vma', 'vmacro15373' => 'vma', 'vmacro15374' => 'vma', 'VMungo0720G2826' => 'vmu', 'Zm00001eb116960' => 'zma', 'Zm00001eb301260' => 'zma', 'Zm00001eb301270' => 'zma' ), 'gf_id' => 'HOM05D001460', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001460' ), 'data_identifier' => 'HOM05D001460', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001460', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '433', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p22980' => 'bna', 'A01p32340' => 'bna', 'A03p42970' => 'bna', 'A05p25880' => 'bna', 'Aa31LG8G9320' => 'aar', 'Aa31LG8G9330' => 'aar', 'Aa31LG8G9340' => 'aar', 'Aa31sc221G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1034' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1528' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.829' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2222' => 'aag', 'Ah.12g058830' => 'amhyb', 'Ah.12g058840' => 'amhyb', 'AL3G37160' => 'aly', 'AL7G41310' => 'aly', 'Aqoxy5G00395' => 'aox', 'Aqoxy5G00396' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0C8NZA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5185HY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JZ1PRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MD3LS0' => 'arhy', 'AT3G22840' => 'ath', 'AT4G14690' => 'ath', 'ATR0665G054' => 'atr', 'Atru.chr4.2344' => 'acertr', 'Atru.chr4.2346' => 'acertr', 'Atru.chr4.2347' => 'acertr', 'Atru.chr4.2348' => 'acertr', 'Atru.chr4.2355' => 'acertr', 'Atru.chr4.2356' => 'acertr', 'Atru.chr4.2358' => 'acertr', 'Atru.chr4.2359' => 'acertr', 'Atru.chr4.2360' => 'acertr', 'Atru.chr4.2361' => 'acertr', 'AUR62030476' => 'cqu', 'AUR62030478' => 'cqu', 'AUR62030819' => 'cqu', 'AUR62030820' => 'cqu', 'BcaB03g14648' => 'bca', 'BcaB04g20492' => 'bca', 'BcaB06g26399' => 'bca', 'BcaC01g03416' => 'bca', 'BcaC01g03419' => 'bca', 'BcaC01g03421' => 'bca', 'BcaC01g03424' => 'bca', 'BcaC05g28012' => 'bca', 'BcaC09g49212' => 'bca', 'BcaC09g50140' => 'bca', 'BcaNung00346' => 'bca', 'BolC1t02785H' => 'bol', 'BolC1t04095H' => 'bol', 'BolC3t17545H' => 'bol', 'BolC5t32769H' => 'bol', 'BraA01t02211Z' => 'bra', 'BraA01t03359Z' => 'bra', 'BraA03t13441Z' => 'bra', 'BraA05t21476Z' => 'bra', 'C01p28420' => 'bna', 'C01p41350' => 'bna', 'C03p52750' => 'bna', 'C03p52780' => 'bna', 'C05p40270' => 'bna', 'CAN.G1437.9' => 'can', 'CANSAT78G0035' => 'cansat', 'CANSAT78G1036' => 'cansat', 'CANSAT78G2272' => 'cansat', 'CANSAT78G2478' => 'cansat', 'CARHR098700' => 'chi', 'CARHR221120' => 'chi', 'CARHR221150' => 'chi', 'Carub.0003s2297' => 'cru', 'Carub.0007s2749' => 'cru', 'Carub.0007s2750' => 'cru', 'Carub.0007s2751' => 'cru', 'Ca_10849_v3' => 'car', 'Cc03_g04300' => 'ccan', 'CDE02G3648' => 'cde', 'CDE05G0060' => 'cde', 'CDE05G0692' => 'cde', 'CDE05G2285' => 'cde', 'CDE05G2884' => 'cde', 'CDE05G3072' => 'cde', 'Cfa008439' => 'cfa', 'Cfa008441' => 'cfa', 'Cfa008443' => 'cfa', 'Cfa008448' => 'cfa', 'Ciclev10005974m.g' => 'ccl', 'Ciclev10006006m.g' => 'ccl', 'Ciclev10006775m.g' => 'ccl', 'CiPaw.02G120400' => 'cil', 'CiPaw.02G120500' => 'cil', 'CiPaw.02G120600' => 'cil', 'ClCG05G004850' => 'cla', 'COL.COLO4_21566' => 'col', 'Cpa.g.sc44.124' => 'cpa', 'Cre07.g320400' => 'cre', 'Cre07.g320450' => 'cre', 'Cre08.g384650' => 'cre', 'Cre09.g393173' => 'cre', 'Cre09.g394325' => 'cre', 'Cre14.g626750' => 'cre', 'Cre16.g679250' => 'cre', 'CsaV3_3G012890' => 'csa', 'CSS0010865' => 'camsi', 'CSS0044338' => 'camsi', 'DCAR_002366' => 'dca', 'DCAR_030687' => 'dca', 'DCAR_030688' => 'dca', 'Dinv14047' => 'din', 'Dinv14048' => 'din', 'Duzib151G0105' => 'dzi', 'Duzib151G0114' => 'dzi', 'Duzib212G1029' => 'dzi', 'ECA232G3536' => 'eca', 'ECA240G0786' => 'eca', 'ECA240G1802' => 'eca', 'ECA240G3760' => 'eca', 'ECA240G3920' => 'eca', 'EL10Ac5g12536' => 'bvu', 'EL10Ac5g12537' => 'bvu', 'EL10Ac5g12538' => 'bvu', 'Eucgr.B01004' => 'egr', 'Eucgr.B01006' => 'egr', 'Eucgr.B01007' => 'egr', 'Eucgr.B01008' => 'egr', 'Eucgr.B01895' => 'egr', 'Eucgr.B01896' => 'egr', 'FAN04G1456' => 'fan', 'FAN08G1769' => 'fan', 'FAN08G2160' => 'fan', 'FAN13G2403' => 'fan', 'FAN13G3303' => 'fan', 'FAN15G2435' => 'fan', 'FAN17G0672' => 'fan', 'FAN17G2441' => 'fan', 'FAN18G1024' => 'fan', 'FAN22G1458' => 'fan', 'FAN24G0037' => 'fan', 'FAN24G0429' => 'fan', 'FAN24G2387' => 'fan', 'FAN27G2746' => 'fan', 'FvH4_2g20400' => 'fve', 'FvH4_2g20420' => 'fve', 'FvH4_2g20430' => 'fve', 'FvH4_4g01270' => 'fve', 'FvH4_4g01290' => 'fve', 'FvH4_4g01300' => 'fve', 'FvH4_4g01310' => 'fve', 'FvH4_4g01330' => 'fve', 'FvH4_5g09070' => 'fve', 'Glyma.10G243800' => 'gma', 'Glyma.20G150600' => 'gma', 'Gohir.A09G219200' => 'ghi', 'Gohir.A09G219300' => 'ghi', 'Gohir.D09G221400' => 'ghi', 'Gohir.D09G221500' => 'ghi', 'Gorai.006G242600' => 'gra', 'Gorai.006G242700' => 'gra', 'GSVIVG01018044001' => 'vvi', 'HanXRQChr03g0083821' => 'han', 'HanXRQChr03g0083841' => 'han', 'HanXRQChr03g0083881' => 'han', 'HanXRQChr03g0083901' => 'han', 'HanXRQChr03g0083921' => 'han', 'HanXRQChr03g0085331' => 'han', 'HanXRQChr03g0085361' => 'han', 'HanXRQChr03g0085411' => 'han', 'HanXRQChr03g0085421' => 'han', 'HanXRQChr03g0085431' => 'han', 'HanXRQChr08g0221991' => 'han', 'HanXRQChr11g0336061' => 'han', 'HanXRQChr11g0336411' => 'han', 'Haze_11234' => 'cav', 'Hma1.2p1_0549F.1_g177010' => 'hma', 'Hma1.2p1_0602F.1_g187630' => 'hma', 'Hund14876' => 'sun', 'Hund14879' => 'sun', 'Lalb_Chr06g0160741' => 'lal', 'Lalb_Chr21g0304781' => 'lal', 'Lj3A726G19' => 'lonja', 'Lj3A726T23' => 'lonja', 'Lj3A726T24' => 'lonja', 'Lj3A726T25' => 'lonja', 'Lj3A727T17' => 'lonja', 'Lj3C726T0' => 'lonja', 'Lj3C726T2' => 'lonja', 'Lj3P725T35' => 'lonja', 'Lj3P727T10' => 'lonja', 'Lj3P727T12' => 'lonja', 'Lj3P727T14' => 'lonja', 'Lj5g0023109' => 'lja', 'Lj6P646T44' => 'lonja', 'Lsat_1_v5_gn_6_75760' => 'lsa', 'Lsat_1_v5_gn_6_75800' => 'lsa', 'Lsat_1_v5_gn_6_75900' => 'lsa', 'Lsat_1_v5_gn_6_76240' => 'lsa', 'Lsat_1_v5_gn_6_76441' => 'lsa', 'Lsat_1_v5_gn_6_76700' => 'lsa', 'Lsat_1_v5_gn_6_76760' => 'lsa', 'Manes.15G033100' => 'mes', 'Mapoly0004s0074' => 'mpo', 'Mapoly0004s0075' => 'mpo', 'Mapoly0004s0163' => 'mpo', 'Mapoly0004s0164' => 'mpo', 'Mapoly0021s0018' => 'mpo', 'Mapoly0041s0136' => 'mpo', 'Mapoly0041s0137' => 'mpo', 'Mapoly0041s0138' => 'mpo', 'Mapoly0041s0139' => 'mpo', 'Mapoly0041s0141' => 'mpo', 'Mapoly0041s0142' => 'mpo', 'Mapoly0041s0143' => 'mpo', 'Mapoly0041s0144' => 'mpo', 'Mapoly0041s0145' => 'mpo', 'Mapoly0047s0106' => 'mpo', 'Mapoly0047s0108' => 'mpo', 'Mapoly0050s0051' => 'mpo', 'Mapoly0050s0052' => 'mpo', 'Mapoly0050s0053' => 'mpo', 'Mapoly0058s0013' => 'mpo', 'Mapoly0091s0078' => 'mpo', 'Mapoly0091s0079' => 'mpo', 'Mapoly0091s0080' => 'mpo', 'Mapoly0091s0081' => 'mpo', 'Mapoly0278s0004' => 'mpo', 'Mapoly0278s0005' => 'mpo', 'Mapoly0278s0006' => 'mpo', 'MBI11_g30648_MAGBIO' => 'mbi', 'MCO03G194' => 'mco', 'MCO03G590' => 'mco', 'MCO07G312' => 'mco', 'MCO10G318' => 'mco', 'MCO12G244' => 'mco', 'MCO13G148' => 'mco', 'MCO13G194' => 'mco', 'MCO16G238' => 'mco', 'MD06G1134100' => 'mdo', 'MD13G1200100' => 'mdo', 'MD13G1200300' => 'mdo', 'MD13G1200600' => 'mdo', 'MD14G1150400' => 'mdo', 'MD16G1200000' => 'mdo', 'Medtr1g102570' => 'mtr', 'Medtr1g102780' => 'mtr', 'Medtr1g102800' => 'mtr', 'Medtr1g102810' => 'mtr', 'Medtr1g102830' => 'mtr', 'MELO3C006499.2' => 'cme', 'Migut.G00385' => 'egut', 'MSTRG.4063' => 'ama', 'Nitab4.5_0000090g0260' => 'nta', 'Nitab4.5_0000977g0030' => 'nta', 'Nitab4.5_0002541g0040' => 'nta', 'Nitab4.5_0007068g0040' => 'nta', 'Nn005s41408' => 'nnu', 'Nn005s41410' => 'nnu', 'Oeu010310.1' => 'oeu', 'Oeu010311.1' => 'oeu', 'Oeu043472.1' => 'oeu', 'Os01g0246400' => 'osa', 'Os04g0267950' => 'osa', 'Os07g0178700' => 'osa', 'Os07g0178800' => 'osa', 'Peaxi162Scf00316g00046' => 'pax', 'Peaxi162Scf00316g00049' => 'pax', 'Peaxi162Scf00316g00059' => 'pax', 'Peaxi162Scf00316g00328' => 'pax', 'Peaxi162Scf00316g00329' => 'pax', 'Peaxi162Scf00316g00411' => 'pax', 'Peaxi162Scf00316g00521' => 'pax', 'Peaxi162Scf00492g00068' => 'pax', 'Peaxi162Scf35631g00002' => 'pax', 'PGR142G3720' => 'pgr', 'PGSC0003DMG400006442' => 'stu', 'Phvul.007G062000' => 'pvu', 'Potri.008G157750' => 'ptr', 'Potri.008G157900' => 'ptr', 'Potri.008G158000' => 'ptr', 'Potri.008G158200' => 'ptr', 'Pp3c11_7280' => 'ppa', 'Pp3c11_7980' => 'ppa', 'Pp3c12_19450' => 'ppa', 'Pp3c14_1480' => 'ppa', 'Pp3c14_1501' => 'ppa', 'Pp3c16_4900' => 'ppa', 'Pp3c16_5010' => 'ppa', 'Pp3c16_5060' => 'ppa', 'Pp3c19_18250' => 'ppa', 'Pp3c23_8530' => 'ppa', 'Pp3c23_8550' => 'ppa', 'Pp3c24_9670' => 'ppa', 'Pp3c2_21390' => 'ppa', 'Pp3c2_31380' => 'ppa', 'Pp3c3_16620' => 'ppa', 'Pp3c3_8090' => 'ppa', 'Pp3c3_8110' => 'ppa', 'Pp3c3_8130' => 'ppa', 'Pp3c3_8150' => 'ppa', 'Pp3c4_14320' => 'ppa', 'Pp3c6_2560' => 'ppa', 'Pp3c9_16700' => 'ppa', 'PRCOL_00000234' => 'pco', 'PRCOL_00000235' => 'pco', 'PRCOL_00000777' => 'pco', 'PRCOL_00002344' => 'pco', 'PRCOL_00002372' => 'pco', 'PRCOL_00006120' => 'pco', 'Prupe.1G021400' => 'ppe', 'Prupe.1G021500' => 'ppe', 'Prupe.1G021600' => 'ppe', 'Prupe.1G021700' => 'ppe', 'Prupe.1G021800' => 'ppe', 'Prupe.5G145100' => 'ppe', 'Psat6g204040' => 'psa', 'Psat6g204800' => 'psa', 'Psat6g204920' => 'psa', 'Psat6g204960' => 'psa', 'Psat6g205080' => 'psa', 'PSO017G0271' => 'pso', 'PSO017G1276' => 'pso', 'PSO017G1429' => 'pso', 'PSO017G1861' => 'pso', 'PSO017G2787' => 'pso', 'PSO017G4466' => 'pso', 'PSO017G5118' => 'pso', 'PSO017G5420' => 'pso', 'PSO063G3678' => 'pso', 'PSO210G0546' => 'pso', 'PSO317G0001' => 'pso', 'PSO357G0512' => 'pso', 'PSO478G2682' => 'pso', 'PSO647G0001' => 'pso', 'PSO675G0001' => 'pso', 'PSO675G2699' => 'pso', 'PSO675G2849' => 'pso', 'PSO675G4991' => 'pso', 'PSO689G0001' => 'pso', 'QL06p000916' => 'qlo', 'QL06p000921' => 'qlo', 'QL06p001398' => 'qlo', 'QL06p001407' => 'qlo', 'QL06p002031' => 'qlo', 'RcHm_v2.0_Chr4g0387791' => 'rch', 'RcHm_v2.0_Chr4g0387801' => 'rch', 'RcHm_v2.0_Chr6g0286501' => 'rch', 'RcHm_v2.0_Chr6g0286511' => 'rch', 'RcHm_v2.0_Chr6g0286521' => 'rch', 'RcHm_v2.0_Chr6g0286531' => 'rch', 'RcHm_v2.0_Chr7g0189141' => 'rch', 'Rhsim02G0028700' => 'rsi', 'Rhsim02G0028800' => 'rsi', 'Rhsim02G0028900' => 'rsi', 'Rhsim02G0029000' => 'rsi', 'Rhsim02G0029100' => 'rsi', 'Rhsim02G0029200' => 'rsi', 'Rhsim02G0029300' => 'rsi', 'Rhsim02G0029400' => 'rsi', 'Rhsim02G0029500' => 'rsi', 'Rhsim02G0029600' => 'rsi', 'RhsimUnG0024000' => 'rsi', 'RhsimUnG0024100' => 'rsi', 'RhsimUnG0024200' => 'rsi', 'RhsimUnG0024300' => 'rsi', 'RhsimUnG0024400' => 'rsi', 'RhsimUnG0024500' => 'rsi', 'RhsimUnG0024700' => 'rsi', 'RhsimUnG0024800' => 'rsi', 'RhsimUnG0024900' => 'rsi', 'RhsimUnG0025100' => 'rsi', 'Sabra08G0120200' => 'sbr', 'Sabra08G0120300' => 'sbr', 'Sabra08G0120500' => 'sbr', 'Sabra08G0120600' => 'sbr', 'Sabra10G0158900' => 'sbr', 'SalBow2G3492' => 'sbo', 'Sc13g0004760' => 'sci', 'Sc13g0004770' => 'sci', 'Sed0003417' => 'sed', 'Sed0019750' => 'sed', 'SEGI_03419' => 'sgi', 'SEGI_05907' => 'sgi', 'SEGI_10682' => 'sgi', 'SEGI_13528' => 'sgi', 'SEGI_16081' => 'sgi', 'SEGI_19370' => 'sgi', 'SEGI_21015' => 'sgi', 'SEGI_21944' => 'sgi', 'SEGI_32906' => 'sgi', 'SEGI_33093' => 'sgi', 'SEGI_36110' => 'sgi', 'SEGI_40397' => 'sgi', 'SGA_v2.0_scaffold191G40426' => 'sas', 'SGA_v2.0_scaffold353G49717' => 'sas', 'SGA_v2.0_scaffold50G18550' => 'sas', 'SMO119G0173' => 'smo', 'SMO172G0002' => 'smo', 'Solyc09g082690.3' => 'sly', 'Solyc09g082700.2' => 'sly', 'Sopen09g031550' => 'spe', 'Sopen09g031560' => 'spe', 'Sp3g20540' => 'spa', 'Sp7g07580' => 'spa', 'TAR134G0002' => 'tar', 'TAR236G0001' => 'tar', 'TAR365G0892' => 'tar', 'TAR636G0166' => 'tar', 'TAR636G0646' => 'tar', 'TAR636G0869' => 'tar', 'TAR636G1317' => 'tar', 'TAR636G1744' => 'tar', 'TAR636G3358' => 'tar', 'TAR636G3436' => 'tar', 'THA.LOC104803047' => 'tha', 'Thecc.04G238900' => 'tca', 'Thhalv10021557m.g' => 'esa', 'Thhalv10026318m.g' => 'esa', 'Thhalv10026335m.g' => 'esa', 'TPR.G17433' => 'tpr', 'TPR.G18915' => 'tpr', 'TPR.G26125' => 'tpr', 'TWI09G0677' => 'twi', 'TWI73G0287' => 'twi', 'unitig_748.g8326' => 'ugi', 'vmacro15370' => 'vma', 'vmacro15371' => 'vma', 'vmacro15372' => 'vma', 'vmacro15373' => 'vma', 'vmacro15374' => 'vma', 'VMungo0720G2826' => 'vmu', 'Zm00001eb116960' => 'zma', 'Zm00001eb301260' => 'zma', 'Zm00001eb301270' => 'zma' ) $gf_id = 'HOM05D001460' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001460' ) $data_identifier = 'HOM05D001460' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 4, 'aag' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 2, 'aox' => (int) 2, 'arhy' => (int) 4, 'ath' => (int) 2, 'atr' => (int) 1, 'acertr' => (int) 10, 'cqu' => (int) 4, 'bca' => (int) 11, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 1, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 1, 'ccan' => (int) 1, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 1, 'col' => (int) 1, 'cpa' => (int) 1, 'cre' => (int) 7, 'csa' => (int) 1, 'camsi' => (int) 2, 'dca' => (int) 3, 'din' => (int) 2, 'dzi' => (int) 3, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 14, 'fve' => (int) 9, 'gma' => (int) 2, 'ghi' => (int) 4, 'gra' => (int) 2, 'vvi' => (int) 1, 'han' => (int) 13, 'cav' => (int) 1, 'hma' => (int) 2, 'sun' => (int) 2, 'lal' => (int) 2, 'lonja' => (int) 12, 'lja' => (int) 1, 'lsa' => (int) 7, 'mes' => (int) 1, 'mpo' => (int) 27, 'mbi' => (int) 1, 'mco' => (int) 8, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 1, 'egut' => (int) 1, 'ama' => (int) 1, 'nta' => (int) 4, 'nnu' => (int) 2, 'oeu' => (int) 3, 'osa' => (int) 4, 'pax' => (int) 9, 'pgr' => (int) 1, 'stu' => (int) 1, 'pvu' => (int) 1, 'ptr' => (int) 4, 'ppa' => (int) 22, 'pco' => (int) 6, 'ppe' => (int) 6, 'psa' => (int) 5, 'pso' => (int) 19, 'qlo' => (int) 5, 'rch' => (int) 7, 'rsi' => (int) 20, 'sbr' => (int) 5, 'sbo' => (int) 1, 'sci' => (int) 2, 'sed' => (int) 2, 'sgi' => (int) 12, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 2, 'tar' => (int) 10, 'tha' => (int) 1, 'tca' => (int) 1, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 2, 'ugi' => (int) 1, 'vma' => (int) 5, 'vmu' => (int) 1, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb301270' $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' => 'HOM05D001460', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '433', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p22980' => 'bna', 'A01p32340' => 'bna', 'A03p42970' => 'bna', 'A05p25880' => 'bna', 'Aa31LG8G9320' => 'aar', 'Aa31LG8G9330' => 'aar', 'Aa31LG8G9340' => 'aar', 'Aa31sc221G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1034' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1528' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.829' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2222' => 'aag', 'Ah.12g058830' => 'amhyb', 'Ah.12g058840' => 'amhyb', 'AL3G37160' => 'aly', 'AL7G41310' => 'aly', 'Aqoxy5G00395' => 'aox', 'Aqoxy5G00396' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0C8NZA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5185HY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JZ1PRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MD3LS0' => 'arhy', 'AT3G22840' => 'ath', 'AT4G14690' => 'ath', 'ATR0665G054' => 'atr', 'Atru.chr4.2344' => 'acertr', 'Atru.chr4.2346' => 'acertr', 'Atru.chr4.2347' => 'acertr', 'Atru.chr4.2348' => 'acertr', 'Atru.chr4.2355' => 'acertr', 'Atru.chr4.2356' => 'acertr', 'Atru.chr4.2358' => 'acertr', 'Atru.chr4.2359' => 'acertr', 'Atru.chr4.2360' => 'acertr', 'Atru.chr4.2361' => 'acertr', 'AUR62030476' => 'cqu', 'AUR62030478' => 'cqu', 'AUR62030819' => 'cqu', 'AUR62030820' => 'cqu', 'BcaB03g14648' => 'bca', 'BcaB04g20492' => 'bca', 'BcaB06g26399' => 'bca', 'BcaC01g03416' => 'bca', 'BcaC01g03419' => 'bca', 'BcaC01g03421' => 'bca', 'BcaC01g03424' => 'bca', 'BcaC05g28012' => 'bca', 'BcaC09g49212' => 'bca', 'BcaC09g50140' => 'bca', 'BcaNung00346' => 'bca', 'BolC1t02785H' => 'bol', 'BolC1t04095H' => 'bol', 'BolC3t17545H' => 'bol', 'BolC5t32769H' => 'bol', 'BraA01t02211Z' => 'bra', 'BraA01t03359Z' => 'bra', 'BraA03t13441Z' => 'bra', 'BraA05t21476Z' => 'bra', 'C01p28420' => 'bna', 'C01p41350' => 'bna', 'C03p52750' => 'bna', 'C03p52780' => 'bna', 'C05p40270' => 'bna', 'CAN.G1437.9' => 'can', 'CANSAT78G0035' => 'cansat', 'CANSAT78G1036' => 'cansat', 'CANSAT78G2272' => 'cansat', 'CANSAT78G2478' => 'cansat', 'CARHR098700' => 'chi', 'CARHR221120' => 'chi', 'CARHR221150' => 'chi', 'Carub.0003s2297' => 'cru', 'Carub.0007s2749' => 'cru', 'Carub.0007s2750' => 'cru', 'Carub.0007s2751' => 'cru', 'Ca_10849_v3' => 'car', 'Cc03_g04300' => 'ccan', 'CDE02G3648' => 'cde', 'CDE05G0060' => 'cde', 'CDE05G0692' => 'cde', 'CDE05G2285' => 'cde', 'CDE05G2884' => 'cde', 'CDE05G3072' => 'cde', 'Cfa008439' => 'cfa', 'Cfa008441' => 'cfa', 'Cfa008443' => 'cfa', 'Cfa008448' => 'cfa', 'Ciclev10005974m.g' => 'ccl', 'Ciclev10006006m.g' => 'ccl', 'Ciclev10006775m.g' => 'ccl', 'CiPaw.02G120400' => 'cil', 'CiPaw.02G120500' => 'cil', 'CiPaw.02G120600' => 'cil', 'ClCG05G004850' => 'cla', 'COL.COLO4_21566' => 'col', 'Cpa.g.sc44.124' => 'cpa', 'Cre07.g320400' => 'cre', 'Cre07.g320450' => 'cre', 'Cre08.g384650' => 'cre', 'Cre09.g393173' => 'cre', 'Cre09.g394325' => 'cre', 'Cre14.g626750' => 'cre', 'Cre16.g679250' => 'cre', 'CsaV3_3G012890' => 'csa', 'CSS0010865' => 'camsi', 'CSS0044338' => 'camsi', 'DCAR_002366' => 'dca', 'DCAR_030687' => 'dca', 'DCAR_030688' => 'dca', 'Dinv14047' => 'din', 'Dinv14048' => 'din', 'Duzib151G0105' => 'dzi', 'Duzib151G0114' => 'dzi', 'Duzib212G1029' => 'dzi', 'ECA232G3536' => 'eca', 'ECA240G0786' => 'eca', 'ECA240G1802' => 'eca', 'ECA240G3760' => 'eca', 'ECA240G3920' => 'eca', 'EL10Ac5g12536' => 'bvu', 'EL10Ac5g12537' => 'bvu', 'EL10Ac5g12538' => 'bvu', 'Eucgr.B01004' => 'egr', 'Eucgr.B01006' => 'egr', 'Eucgr.B01007' => 'egr', 'Eucgr.B01008' => 'egr', 'Eucgr.B01895' => 'egr', 'Eucgr.B01896' => 'egr', 'FAN04G1456' => 'fan', 'FAN08G1769' => 'fan', 'FAN08G2160' => 'fan', 'FAN13G2403' => 'fan', 'FAN13G3303' => 'fan', 'FAN15G2435' => 'fan', 'FAN17G0672' => 'fan', 'FAN17G2441' => 'fan', 'FAN18G1024' => 'fan', 'FAN22G1458' => 'fan', 'FAN24G0037' => 'fan', 'FAN24G0429' => 'fan', 'FAN24G2387' => 'fan', 'FAN27G2746' => 'fan', 'FvH4_2g20400' => 'fve', 'FvH4_2g20420' => 'fve', 'FvH4_2g20430' => 'fve', 'FvH4_4g01270' => 'fve', 'FvH4_4g01290' => 'fve', 'FvH4_4g01300' => 'fve', 'FvH4_4g01310' => 'fve', 'FvH4_4g01330' => 'fve', 'FvH4_5g09070' => 'fve', 'Glyma.10G243800' => 'gma', 'Glyma.20G150600' => 'gma', 'Gohir.A09G219200' => 'ghi', 'Gohir.A09G219300' => 'ghi', 'Gohir.D09G221400' => 'ghi', 'Gohir.D09G221500' => 'ghi', 'Gorai.006G242600' => 'gra', 'Gorai.006G242700' => 'gra', 'GSVIVG01018044001' => 'vvi', 'HanXRQChr03g0083821' => 'han', 'HanXRQChr03g0083841' => 'han', 'HanXRQChr03g0083881' => 'han', 'HanXRQChr03g0083901' => 'han', 'HanXRQChr03g0083921' => 'han', 'HanXRQChr03g0085331' => 'han', 'HanXRQChr03g0085361' => 'han', 'HanXRQChr03g0085411' => 'han', 'HanXRQChr03g0085421' => 'han', 'HanXRQChr03g0085431' => 'han', 'HanXRQChr08g0221991' => 'han', 'HanXRQChr11g0336061' => 'han', 'HanXRQChr11g0336411' => 'han', 'Haze_11234' => 'cav', 'Hma1.2p1_0549F.1_g177010' => 'hma', 'Hma1.2p1_0602F.1_g187630' => 'hma', 'Hund14876' => 'sun', 'Hund14879' => 'sun', 'Lalb_Chr06g0160741' => 'lal', 'Lalb_Chr21g0304781' => 'lal', 'Lj3A726G19' => 'lonja', 'Lj3A726T23' => 'lonja', 'Lj3A726T24' => 'lonja', 'Lj3A726T25' => 'lonja', 'Lj3A727T17' => 'lonja', 'Lj3C726T0' => 'lonja', 'Lj3C726T2' => 'lonja', 'Lj3P725T35' => 'lonja', 'Lj3P727T10' => 'lonja', 'Lj3P727T12' => 'lonja', 'Lj3P727T14' => 'lonja', 'Lj5g0023109' => 'lja', 'Lj6P646T44' => 'lonja', 'Lsat_1_v5_gn_6_75760' => 'lsa', 'Lsat_1_v5_gn_6_75800' => 'lsa', 'Lsat_1_v5_gn_6_75900' => 'lsa', 'Lsat_1_v5_gn_6_76240' => 'lsa', 'Lsat_1_v5_gn_6_76441' => 'lsa', 'Lsat_1_v5_gn_6_76700' => 'lsa', 'Lsat_1_v5_gn_6_76760' => 'lsa', 'Manes.15G033100' => 'mes', 'Mapoly0004s0074' => 'mpo', 'Mapoly0004s0075' => 'mpo', 'Mapoly0004s0163' => 'mpo', 'Mapoly0004s0164' => 'mpo', 'Mapoly0021s0018' => 'mpo', 'Mapoly0041s0136' => 'mpo', 'Mapoly0041s0137' => 'mpo', 'Mapoly0041s0138' => 'mpo', 'Mapoly0041s0139' => 'mpo', 'Mapoly0041s0141' => 'mpo', 'Mapoly0041s0142' => 'mpo', 'Mapoly0041s0143' => 'mpo', 'Mapoly0041s0144' => 'mpo', 'Mapoly0041s0145' => 'mpo', 'Mapoly0047s0106' => 'mpo', 'Mapoly0047s0108' => 'mpo', 'Mapoly0050s0051' => 'mpo', 'Mapoly0050s0052' => 'mpo', 'Mapoly0050s0053' => 'mpo', 'Mapoly0058s0013' => 'mpo', 'Mapoly0091s0078' => 'mpo', 'Mapoly0091s0079' => 'mpo', 'Mapoly0091s0080' => 'mpo', 'Mapoly0091s0081' => 'mpo', 'Mapoly0278s0004' => 'mpo', 'Mapoly0278s0005' => 'mpo', 'Mapoly0278s0006' => 'mpo', 'MBI11_g30648_MAGBIO' => 'mbi', 'MCO03G194' => 'mco', 'MCO03G590' => 'mco', 'MCO07G312' => 'mco', 'MCO10G318' => 'mco', 'MCO12G244' => 'mco', 'MCO13G148' => 'mco', 'MCO13G194' => 'mco', 'MCO16G238' => 'mco', 'MD06G1134100' => 'mdo', 'MD13G1200100' => 'mdo', 'MD13G1200300' => 'mdo', 'MD13G1200600' => 'mdo', 'MD14G1150400' => 'mdo', 'MD16G1200000' => 'mdo', 'Medtr1g102570' => 'mtr', 'Medtr1g102780' => 'mtr', 'Medtr1g102800' => 'mtr', 'Medtr1g102810' => 'mtr', 'Medtr1g102830' => 'mtr', 'MELO3C006499.2' => 'cme', 'Migut.G00385' => 'egut', 'MSTRG.4063' => 'ama', 'Nitab4.5_0000090g0260' => 'nta', 'Nitab4.5_0000977g0030' => 'nta', 'Nitab4.5_0002541g0040' => 'nta', 'Nitab4.5_0007068g0040' => 'nta', 'Nn005s41408' => 'nnu', 'Nn005s41410' => 'nnu', 'Oeu010310.1' => 'oeu', 'Oeu010311.1' => 'oeu', 'Oeu043472.1' => 'oeu', 'Os01g0246400' => 'osa', 'Os04g0267950' => 'osa', 'Os07g0178700' => 'osa', 'Os07g0178800' => 'osa', 'Peaxi162Scf00316g00046' => 'pax', 'Peaxi162Scf00316g00049' => 'pax', 'Peaxi162Scf00316g00059' => 'pax', 'Peaxi162Scf00316g00328' => 'pax', 'Peaxi162Scf00316g00329' => 'pax', 'Peaxi162Scf00316g00411' => 'pax', 'Peaxi162Scf00316g00521' => 'pax', 'Peaxi162Scf00492g00068' => 'pax', 'Peaxi162Scf35631g00002' => 'pax', 'PGR142G3720' => 'pgr', 'PGSC0003DMG400006442' => 'stu', 'Phvul.007G062000' => 'pvu', 'Potri.008G157750' => 'ptr', 'Potri.008G157900' => 'ptr', 'Potri.008G158000' => 'ptr', 'Potri.008G158200' => 'ptr', 'Pp3c11_7280' => 'ppa', 'Pp3c11_7980' => 'ppa', 'Pp3c12_19450' => 'ppa', 'Pp3c14_1480' => 'ppa', 'Pp3c14_1501' => 'ppa', 'Pp3c16_4900' => 'ppa', 'Pp3c16_5010' => 'ppa', 'Pp3c16_5060' => 'ppa', 'Pp3c19_18250' => 'ppa', 'Pp3c23_8530' => 'ppa', 'Pp3c23_8550' => 'ppa', 'Pp3c24_9670' => 'ppa', 'Pp3c2_21390' => 'ppa', 'Pp3c2_31380' => 'ppa', 'Pp3c3_16620' => 'ppa', 'Pp3c3_8090' => 'ppa', 'Pp3c3_8110' => 'ppa', 'Pp3c3_8130' => 'ppa', 'Pp3c3_8150' => 'ppa', 'Pp3c4_14320' => 'ppa', 'Pp3c6_2560' => 'ppa', 'Pp3c9_16700' => 'ppa', 'PRCOL_00000234' => 'pco', 'PRCOL_00000235' => 'pco', 'PRCOL_00000777' => 'pco', 'PRCOL_00002344' => 'pco', 'PRCOL_00002372' => 'pco', 'PRCOL_00006120' => 'pco', 'Prupe.1G021400' => 'ppe', 'Prupe.1G021500' => 'ppe', 'Prupe.1G021600' => 'ppe', 'Prupe.1G021700' => 'ppe', 'Prupe.1G021800' => 'ppe', 'Prupe.5G145100' => 'ppe', 'Psat6g204040' => 'psa', 'Psat6g204800' => 'psa', 'Psat6g204920' => 'psa', 'Psat6g204960' => 'psa', 'Psat6g205080' => 'psa', 'PSO017G0271' => 'pso', 'PSO017G1276' => 'pso', 'PSO017G1429' => 'pso', 'PSO017G1861' => 'pso', 'PSO017G2787' => 'pso', 'PSO017G4466' => 'pso', 'PSO017G5118' => 'pso', 'PSO017G5420' => 'pso', 'PSO063G3678' => 'pso', 'PSO210G0546' => 'pso', 'PSO317G0001' => 'pso', 'PSO357G0512' => 'pso', 'PSO478G2682' => 'pso', 'PSO647G0001' => 'pso', 'PSO675G0001' => 'pso', 'PSO675G2699' => 'pso', 'PSO675G2849' => 'pso', 'PSO675G4991' => 'pso', 'PSO689G0001' => 'pso', 'QL06p000916' => 'qlo', 'QL06p000921' => 'qlo', 'QL06p001398' => 'qlo', 'QL06p001407' => 'qlo', 'QL06p002031' => 'qlo', 'RcHm_v2.0_Chr4g0387791' => 'rch', 'RcHm_v2.0_Chr4g0387801' => 'rch', 'RcHm_v2.0_Chr6g0286501' => 'rch', 'RcHm_v2.0_Chr6g0286511' => 'rch', 'RcHm_v2.0_Chr6g0286521' => 'rch', 'RcHm_v2.0_Chr6g0286531' => 'rch', 'RcHm_v2.0_Chr7g0189141' => 'rch', 'Rhsim02G0028700' => 'rsi', 'Rhsim02G0028800' => 'rsi', 'Rhsim02G0028900' => 'rsi', 'Rhsim02G0029000' => 'rsi', 'Rhsim02G0029100' => 'rsi', 'Rhsim02G0029200' => 'rsi', 'Rhsim02G0029300' => 'rsi', 'Rhsim02G0029400' => 'rsi', 'Rhsim02G0029500' => 'rsi', 'Rhsim02G0029600' => 'rsi', 'RhsimUnG0024000' => 'rsi', 'RhsimUnG0024100' => 'rsi', 'RhsimUnG0024200' => 'rsi', 'RhsimUnG0024300' => 'rsi', 'RhsimUnG0024400' => 'rsi', 'RhsimUnG0024500' => 'rsi', 'RhsimUnG0024700' => 'rsi', 'RhsimUnG0024800' => 'rsi', 'RhsimUnG0024900' => 'rsi', 'RhsimUnG0025100' => 'rsi', 'Sabra08G0120200' => 'sbr', 'Sabra08G0120300' => 'sbr', 'Sabra08G0120500' => 'sbr', 'Sabra08G0120600' => 'sbr', 'Sabra10G0158900' => 'sbr', 'SalBow2G3492' => 'sbo', 'Sc13g0004760' => 'sci', 'Sc13g0004770' => 'sci', 'Sed0003417' => 'sed', 'Sed0019750' => 'sed', 'SEGI_03419' => 'sgi', 'SEGI_05907' => 'sgi', 'SEGI_10682' => 'sgi', 'SEGI_13528' => 'sgi', 'SEGI_16081' => 'sgi', 'SEGI_19370' => 'sgi', 'SEGI_21015' => 'sgi', 'SEGI_21944' => 'sgi', 'SEGI_32906' => 'sgi', 'SEGI_33093' => 'sgi', 'SEGI_36110' => 'sgi', 'SEGI_40397' => 'sgi', 'SGA_v2.0_scaffold191G40426' => 'sas', 'SGA_v2.0_scaffold353G49717' => 'sas', 'SGA_v2.0_scaffold50G18550' => 'sas', 'SMO119G0173' => 'smo', 'SMO172G0002' => 'smo', 'Solyc09g082690.3' => 'sly', 'Solyc09g082700.2' => 'sly', 'Sopen09g031550' => 'spe', 'Sopen09g031560' => 'spe', 'Sp3g20540' => 'spa', 'Sp7g07580' => 'spa', 'TAR134G0002' => 'tar', 'TAR236G0001' => 'tar', 'TAR365G0892' => 'tar', 'TAR636G0166' => 'tar', 'TAR636G0646' => 'tar', 'TAR636G0869' => 'tar', 'TAR636G1317' => 'tar', 'TAR636G1744' => 'tar', 'TAR636G3358' => 'tar', 'TAR636G3436' => 'tar', 'THA.LOC104803047' => 'tha', 'Thecc.04G238900' => 'tca', 'Thhalv10021557m.g' => 'esa', 'Thhalv10026318m.g' => 'esa', 'Thhalv10026335m.g' => 'esa', 'TPR.G17433' => 'tpr', 'TPR.G18915' => 'tpr', 'TPR.G26125' => 'tpr', 'TWI09G0677' => 'twi', 'TWI73G0287' => 'twi', 'unitig_748.g8326' => 'ugi', 'vmacro15370' => 'vma', 'vmacro15371' => 'vma', 'vmacro15372' => 'vma', 'vmacro15373' => 'vma', 'vmacro15374' => 'vma', 'VMungo0720G2826' => 'vmu', 'Zm00001eb116960' => 'zma', 'Zm00001eb301260' => 'zma', 'Zm00001eb301270' => 'zma' ), 'gf_id' => 'HOM05D001460', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001460' ), 'data_identifier' => 'HOM05D001460', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001460', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '433', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p22980' => 'bna', 'A01p32340' => 'bna', 'A03p42970' => 'bna', 'A05p25880' => 'bna', 'Aa31LG8G9320' => 'aar', 'Aa31LG8G9330' => 'aar', 'Aa31LG8G9340' => 'aar', 'Aa31sc221G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1034' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1528' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.829' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2222' => 'aag', 'Ah.12g058830' => 'amhyb', 'Ah.12g058840' => 'amhyb', 'AL3G37160' => 'aly', 'AL7G41310' => 'aly', 'Aqoxy5G00395' => 'aox', 'Aqoxy5G00396' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0C8NZA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5185HY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JZ1PRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MD3LS0' => 'arhy', 'AT3G22840' => 'ath', 'AT4G14690' => 'ath', 'ATR0665G054' => 'atr', 'Atru.chr4.2344' => 'acertr', 'Atru.chr4.2346' => 'acertr', 'Atru.chr4.2347' => 'acertr', 'Atru.chr4.2348' => 'acertr', 'Atru.chr4.2355' => 'acertr', 'Atru.chr4.2356' => 'acertr', 'Atru.chr4.2358' => 'acertr', 'Atru.chr4.2359' => 'acertr', 'Atru.chr4.2360' => 'acertr', 'Atru.chr4.2361' => 'acertr', 'AUR62030476' => 'cqu', 'AUR62030478' => 'cqu', 'AUR62030819' => 'cqu', 'AUR62030820' => 'cqu', 'BcaB03g14648' => 'bca', 'BcaB04g20492' => 'bca', 'BcaB06g26399' => 'bca', 'BcaC01g03416' => 'bca', 'BcaC01g03419' => 'bca', 'BcaC01g03421' => 'bca', 'BcaC01g03424' => 'bca', 'BcaC05g28012' => 'bca', 'BcaC09g49212' => 'bca', 'BcaC09g50140' => 'bca', 'BcaNung00346' => 'bca', 'BolC1t02785H' => 'bol', 'BolC1t04095H' => 'bol', 'BolC3t17545H' => 'bol', 'BolC5t32769H' => 'bol', 'BraA01t02211Z' => 'bra', 'BraA01t03359Z' => 'bra', 'BraA03t13441Z' => 'bra', 'BraA05t21476Z' => 'bra', 'C01p28420' => 'bna', 'C01p41350' => 'bna', 'C03p52750' => 'bna', 'C03p52780' => 'bna', 'C05p40270' => 'bna', 'CAN.G1437.9' => 'can', 'CANSAT78G0035' => 'cansat', 'CANSAT78G1036' => 'cansat', 'CANSAT78G2272' => 'cansat', 'CANSAT78G2478' => 'cansat', 'CARHR098700' => 'chi', 'CARHR221120' => 'chi', 'CARHR221150' => 'chi', 'Carub.0003s2297' => 'cru', 'Carub.0007s2749' => 'cru', 'Carub.0007s2750' => 'cru', 'Carub.0007s2751' => 'cru', 'Ca_10849_v3' => 'car', 'Cc03_g04300' => 'ccan', 'CDE02G3648' => 'cde', 'CDE05G0060' => 'cde', 'CDE05G0692' => 'cde', 'CDE05G2285' => 'cde', 'CDE05G2884' => 'cde', 'CDE05G3072' => 'cde', 'Cfa008439' => 'cfa', 'Cfa008441' => 'cfa', 'Cfa008443' => 'cfa', 'Cfa008448' => 'cfa', 'Ciclev10005974m.g' => 'ccl', 'Ciclev10006006m.g' => 'ccl', 'Ciclev10006775m.g' => 'ccl', 'CiPaw.02G120400' => 'cil', 'CiPaw.02G120500' => 'cil', 'CiPaw.02G120600' => 'cil', 'ClCG05G004850' => 'cla', 'COL.COLO4_21566' => 'col', 'Cpa.g.sc44.124' => 'cpa', 'Cre07.g320400' => 'cre', 'Cre07.g320450' => 'cre', 'Cre08.g384650' => 'cre', 'Cre09.g393173' => 'cre', 'Cre09.g394325' => 'cre', 'Cre14.g626750' => 'cre', 'Cre16.g679250' => 'cre', 'CsaV3_3G012890' => 'csa', 'CSS0010865' => 'camsi', 'CSS0044338' => 'camsi', 'DCAR_002366' => 'dca', 'DCAR_030687' => 'dca', 'DCAR_030688' => 'dca', 'Dinv14047' => 'din', 'Dinv14048' => 'din', 'Duzib151G0105' => 'dzi', 'Duzib151G0114' => 'dzi', 'Duzib212G1029' => 'dzi', 'ECA232G3536' => 'eca', 'ECA240G0786' => 'eca', 'ECA240G1802' => 'eca', 'ECA240G3760' => 'eca', 'ECA240G3920' => 'eca', 'EL10Ac5g12536' => 'bvu', 'EL10Ac5g12537' => 'bvu', 'EL10Ac5g12538' => 'bvu', 'Eucgr.B01004' => 'egr', 'Eucgr.B01006' => 'egr', 'Eucgr.B01007' => 'egr', 'Eucgr.B01008' => 'egr', 'Eucgr.B01895' => 'egr', 'Eucgr.B01896' => 'egr', 'FAN04G1456' => 'fan', 'FAN08G1769' => 'fan', 'FAN08G2160' => 'fan', 'FAN13G2403' => 'fan', 'FAN13G3303' => 'fan', 'FAN15G2435' => 'fan', 'FAN17G0672' => 'fan', 'FAN17G2441' => 'fan', 'FAN18G1024' => 'fan', 'FAN22G1458' => 'fan', 'FAN24G0037' => 'fan', 'FAN24G0429' => 'fan', 'FAN24G2387' => 'fan', 'FAN27G2746' => 'fan', 'FvH4_2g20400' => 'fve', 'FvH4_2g20420' => 'fve', 'FvH4_2g20430' => 'fve', 'FvH4_4g01270' => 'fve', 'FvH4_4g01290' => 'fve', 'FvH4_4g01300' => 'fve', 'FvH4_4g01310' => 'fve', 'FvH4_4g01330' => 'fve', 'FvH4_5g09070' => 'fve', 'Glyma.10G243800' => 'gma', 'Glyma.20G150600' => 'gma', 'Gohir.A09G219200' => 'ghi', 'Gohir.A09G219300' => 'ghi', 'Gohir.D09G221400' => 'ghi', 'Gohir.D09G221500' => 'ghi', 'Gorai.006G242600' => 'gra', 'Gorai.006G242700' => 'gra', 'GSVIVG01018044001' => 'vvi', 'HanXRQChr03g0083821' => 'han', 'HanXRQChr03g0083841' => 'han', 'HanXRQChr03g0083881' => 'han', 'HanXRQChr03g0083901' => 'han', 'HanXRQChr03g0083921' => 'han', 'HanXRQChr03g0085331' => 'han', 'HanXRQChr03g0085361' => 'han', 'HanXRQChr03g0085411' => 'han', 'HanXRQChr03g0085421' => 'han', 'HanXRQChr03g0085431' => 'han', 'HanXRQChr08g0221991' => 'han', 'HanXRQChr11g0336061' => 'han', 'HanXRQChr11g0336411' => 'han', 'Haze_11234' => 'cav', 'Hma1.2p1_0549F.1_g177010' => 'hma', 'Hma1.2p1_0602F.1_g187630' => 'hma', 'Hund14876' => 'sun', 'Hund14879' => 'sun', 'Lalb_Chr06g0160741' => 'lal', 'Lalb_Chr21g0304781' => 'lal', 'Lj3A726G19' => 'lonja', 'Lj3A726T23' => 'lonja', 'Lj3A726T24' => 'lonja', 'Lj3A726T25' => 'lonja', 'Lj3A727T17' => 'lonja', 'Lj3C726T0' => 'lonja', 'Lj3C726T2' => 'lonja', 'Lj3P725T35' => 'lonja', 'Lj3P727T10' => 'lonja', 'Lj3P727T12' => 'lonja', 'Lj3P727T14' => 'lonja', 'Lj5g0023109' => 'lja', 'Lj6P646T44' => 'lonja', 'Lsat_1_v5_gn_6_75760' => 'lsa', 'Lsat_1_v5_gn_6_75800' => 'lsa', 'Lsat_1_v5_gn_6_75900' => 'lsa', 'Lsat_1_v5_gn_6_76240' => 'lsa', 'Lsat_1_v5_gn_6_76441' => 'lsa', 'Lsat_1_v5_gn_6_76700' => 'lsa', 'Lsat_1_v5_gn_6_76760' => 'lsa', 'Manes.15G033100' => 'mes', 'Mapoly0004s0074' => 'mpo', 'Mapoly0004s0075' => 'mpo', 'Mapoly0004s0163' => 'mpo', 'Mapoly0004s0164' => 'mpo', 'Mapoly0021s0018' => 'mpo', 'Mapoly0041s0136' => 'mpo', 'Mapoly0041s0137' => 'mpo', 'Mapoly0041s0138' => 'mpo', 'Mapoly0041s0139' => 'mpo', 'Mapoly0041s0141' => 'mpo', 'Mapoly0041s0142' => 'mpo', 'Mapoly0041s0143' => 'mpo', 'Mapoly0041s0144' => 'mpo', 'Mapoly0041s0145' => 'mpo', 'Mapoly0047s0106' => 'mpo', 'Mapoly0047s0108' => 'mpo', 'Mapoly0050s0051' => 'mpo', 'Mapoly0050s0052' => 'mpo', 'Mapoly0050s0053' => 'mpo', 'Mapoly0058s0013' => 'mpo', 'Mapoly0091s0078' => 'mpo', 'Mapoly0091s0079' => 'mpo', 'Mapoly0091s0080' => 'mpo', 'Mapoly0091s0081' => 'mpo', 'Mapoly0278s0004' => 'mpo', 'Mapoly0278s0005' => 'mpo', 'Mapoly0278s0006' => 'mpo', 'MBI11_g30648_MAGBIO' => 'mbi', 'MCO03G194' => 'mco', 'MCO03G590' => 'mco', 'MCO07G312' => 'mco', 'MCO10G318' => 'mco', 'MCO12G244' => 'mco', 'MCO13G148' => 'mco', 'MCO13G194' => 'mco', 'MCO16G238' => 'mco', 'MD06G1134100' => 'mdo', 'MD13G1200100' => 'mdo', 'MD13G1200300' => 'mdo', 'MD13G1200600' => 'mdo', 'MD14G1150400' => 'mdo', 'MD16G1200000' => 'mdo', 'Medtr1g102570' => 'mtr', 'Medtr1g102780' => 'mtr', 'Medtr1g102800' => 'mtr', 'Medtr1g102810' => 'mtr', 'Medtr1g102830' => 'mtr', 'MELO3C006499.2' => 'cme', 'Migut.G00385' => 'egut', 'MSTRG.4063' => 'ama', 'Nitab4.5_0000090g0260' => 'nta', 'Nitab4.5_0000977g0030' => 'nta', 'Nitab4.5_0002541g0040' => 'nta', 'Nitab4.5_0007068g0040' => 'nta', 'Nn005s41408' => 'nnu', 'Nn005s41410' => 'nnu', 'Oeu010310.1' => 'oeu', 'Oeu010311.1' => 'oeu', 'Oeu043472.1' => 'oeu', 'Os01g0246400' => 'osa', 'Os04g0267950' => 'osa', 'Os07g0178700' => 'osa', 'Os07g0178800' => 'osa', 'Peaxi162Scf00316g00046' => 'pax', 'Peaxi162Scf00316g00049' => 'pax', 'Peaxi162Scf00316g00059' => 'pax', 'Peaxi162Scf00316g00328' => 'pax', 'Peaxi162Scf00316g00329' => 'pax', 'Peaxi162Scf00316g00411' => 'pax', 'Peaxi162Scf00316g00521' => 'pax', 'Peaxi162Scf00492g00068' => 'pax', 'Peaxi162Scf35631g00002' => 'pax', 'PGR142G3720' => 'pgr', 'PGSC0003DMG400006442' => 'stu', 'Phvul.007G062000' => 'pvu', 'Potri.008G157750' => 'ptr', 'Potri.008G157900' => 'ptr', 'Potri.008G158000' => 'ptr', 'Potri.008G158200' => 'ptr', 'Pp3c11_7280' => 'ppa', 'Pp3c11_7980' => 'ppa', 'Pp3c12_19450' => 'ppa', 'Pp3c14_1480' => 'ppa', 'Pp3c14_1501' => 'ppa', 'Pp3c16_4900' => 'ppa', 'Pp3c16_5010' => 'ppa', 'Pp3c16_5060' => 'ppa', 'Pp3c19_18250' => 'ppa', 'Pp3c23_8530' => 'ppa', 'Pp3c23_8550' => 'ppa', 'Pp3c24_9670' => 'ppa', 'Pp3c2_21390' => 'ppa', 'Pp3c2_31380' => 'ppa', 'Pp3c3_16620' => 'ppa', 'Pp3c3_8090' => 'ppa', 'Pp3c3_8110' => 'ppa', 'Pp3c3_8130' => 'ppa', 'Pp3c3_8150' => 'ppa', 'Pp3c4_14320' => 'ppa', 'Pp3c6_2560' => 'ppa', 'Pp3c9_16700' => 'ppa', 'PRCOL_00000234' => 'pco', 'PRCOL_00000235' => 'pco', 'PRCOL_00000777' => 'pco', 'PRCOL_00002344' => 'pco', 'PRCOL_00002372' => 'pco', 'PRCOL_00006120' => 'pco', 'Prupe.1G021400' => 'ppe', 'Prupe.1G021500' => 'ppe', 'Prupe.1G021600' => 'ppe', 'Prupe.1G021700' => 'ppe', 'Prupe.1G021800' => 'ppe', 'Prupe.5G145100' => 'ppe', 'Psat6g204040' => 'psa', 'Psat6g204800' => 'psa', 'Psat6g204920' => 'psa', 'Psat6g204960' => 'psa', 'Psat6g205080' => 'psa', 'PSO017G0271' => 'pso', 'PSO017G1276' => 'pso', 'PSO017G1429' => 'pso', 'PSO017G1861' => 'pso', 'PSO017G2787' => 'pso', 'PSO017G4466' => 'pso', 'PSO017G5118' => 'pso', 'PSO017G5420' => 'pso', 'PSO063G3678' => 'pso', 'PSO210G0546' => 'pso', 'PSO317G0001' => 'pso', 'PSO357G0512' => 'pso', 'PSO478G2682' => 'pso', 'PSO647G0001' => 'pso', 'PSO675G0001' => 'pso', 'PSO675G2699' => 'pso', 'PSO675G2849' => 'pso', 'PSO675G4991' => 'pso', 'PSO689G0001' => 'pso', 'QL06p000916' => 'qlo', 'QL06p000921' => 'qlo', 'QL06p001398' => 'qlo', 'QL06p001407' => 'qlo', 'QL06p002031' => 'qlo', 'RcHm_v2.0_Chr4g0387791' => 'rch', 'RcHm_v2.0_Chr4g0387801' => 'rch', 'RcHm_v2.0_Chr6g0286501' => 'rch', 'RcHm_v2.0_Chr6g0286511' => 'rch', 'RcHm_v2.0_Chr6g0286521' => 'rch', 'RcHm_v2.0_Chr6g0286531' => 'rch', 'RcHm_v2.0_Chr7g0189141' => 'rch', 'Rhsim02G0028700' => 'rsi', 'Rhsim02G0028800' => 'rsi', 'Rhsim02G0028900' => 'rsi', 'Rhsim02G0029000' => 'rsi', 'Rhsim02G0029100' => 'rsi', 'Rhsim02G0029200' => 'rsi', 'Rhsim02G0029300' => 'rsi', 'Rhsim02G0029400' => 'rsi', 'Rhsim02G0029500' => 'rsi', 'Rhsim02G0029600' => 'rsi', 'RhsimUnG0024000' => 'rsi', 'RhsimUnG0024100' => 'rsi', 'RhsimUnG0024200' => 'rsi', 'RhsimUnG0024300' => 'rsi', 'RhsimUnG0024400' => 'rsi', 'RhsimUnG0024500' => 'rsi', 'RhsimUnG0024700' => 'rsi', 'RhsimUnG0024800' => 'rsi', 'RhsimUnG0024900' => 'rsi', 'RhsimUnG0025100' => 'rsi', 'Sabra08G0120200' => 'sbr', 'Sabra08G0120300' => 'sbr', 'Sabra08G0120500' => 'sbr', 'Sabra08G0120600' => 'sbr', 'Sabra10G0158900' => 'sbr', 'SalBow2G3492' => 'sbo', 'Sc13g0004760' => 'sci', 'Sc13g0004770' => 'sci', 'Sed0003417' => 'sed', 'Sed0019750' => 'sed', 'SEGI_03419' => 'sgi', 'SEGI_05907' => 'sgi', 'SEGI_10682' => 'sgi', 'SEGI_13528' => 'sgi', 'SEGI_16081' => 'sgi', 'SEGI_19370' => 'sgi', 'SEGI_21015' => 'sgi', 'SEGI_21944' => 'sgi', 'SEGI_32906' => 'sgi', 'SEGI_33093' => 'sgi', 'SEGI_36110' => 'sgi', 'SEGI_40397' => 'sgi', 'SGA_v2.0_scaffold191G40426' => 'sas', 'SGA_v2.0_scaffold353G49717' => 'sas', 'SGA_v2.0_scaffold50G18550' => 'sas', 'SMO119G0173' => 'smo', 'SMO172G0002' => 'smo', 'Solyc09g082690.3' => 'sly', 'Solyc09g082700.2' => 'sly', 'Sopen09g031550' => 'spe', 'Sopen09g031560' => 'spe', 'Sp3g20540' => 'spa', 'Sp7g07580' => 'spa', 'TAR134G0002' => 'tar', 'TAR236G0001' => 'tar', 'TAR365G0892' => 'tar', 'TAR636G0166' => 'tar', 'TAR636G0646' => 'tar', 'TAR636G0869' => 'tar', 'TAR636G1317' => 'tar', 'TAR636G1744' => 'tar', 'TAR636G3358' => 'tar', 'TAR636G3436' => 'tar', 'THA.LOC104803047' => 'tha', 'Thecc.04G238900' => 'tca', 'Thhalv10021557m.g' => 'esa', 'Thhalv10026318m.g' => 'esa', 'Thhalv10026335m.g' => 'esa', 'TPR.G17433' => 'tpr', 'TPR.G18915' => 'tpr', 'TPR.G26125' => 'tpr', 'TWI09G0677' => 'twi', 'TWI73G0287' => 'twi', 'unitig_748.g8326' => 'ugi', 'vmacro15370' => 'vma', 'vmacro15371' => 'vma', 'vmacro15372' => 'vma', 'vmacro15373' => 'vma', 'vmacro15374' => 'vma', 'VMungo0720G2826' => 'vmu', 'Zm00001eb116960' => 'zma', 'Zm00001eb301260' => 'zma', 'Zm00001eb301270' => 'zma' ) $gf_id = 'HOM05D001460' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001460' ) $data_identifier = 'HOM05D001460' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 4, 'aag' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 2, 'aox' => (int) 2, 'arhy' => (int) 4, 'ath' => (int) 2, 'atr' => (int) 1, 'acertr' => (int) 10, 'cqu' => (int) 4, 'bca' => (int) 11, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 1, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 1, 'ccan' => (int) 1, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 1, 'col' => (int) 1, 'cpa' => (int) 1, 'cre' => (int) 7, 'csa' => (int) 1, 'camsi' => (int) 2, 'dca' => (int) 3, 'din' => (int) 2, 'dzi' => (int) 3, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 14, 'fve' => (int) 9, 'gma' => (int) 2, 'ghi' => (int) 4, 'gra' => (int) 2, 'vvi' => (int) 1, 'han' => (int) 13, 'cav' => (int) 1, 'hma' => (int) 2, 'sun' => (int) 2, 'lal' => (int) 2, 'lonja' => (int) 12, 'lja' => (int) 1, 'lsa' => (int) 7, 'mes' => (int) 1, 'mpo' => (int) 27, 'mbi' => (int) 1, 'mco' => (int) 8, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 1, 'egut' => (int) 1, 'ama' => (int) 1, 'nta' => (int) 4, 'nnu' => (int) 2, 'oeu' => (int) 3, 'osa' => (int) 4, 'pax' => (int) 9, 'pgr' => (int) 1, 'stu' => (int) 1, 'pvu' => (int) 1, 'ptr' => (int) 4, 'ppa' => (int) 22, 'pco' => (int) 6, 'ppe' => (int) 6, 'psa' => (int) 5, 'pso' => (int) 19, 'qlo' => (int) 5, 'rch' => (int) 7, 'rsi' => (int) 20, 'sbr' => (int) 5, 'sbo' => (int) 1, 'sci' => (int) 2, 'sed' => (int) 2, 'sgi' => (int) 12, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 2, 'tar' => (int) 10, 'tha' => (int) 1, 'tca' => (int) 1, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 2, 'ugi' => (int) 1, 'vma' => (int) 5, 'vmu' => (int) 1, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb301270' $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' => 'HOM05D001460', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '433', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p22980' => 'bna', 'A01p32340' => 'bna', 'A03p42970' => 'bna', 'A05p25880' => 'bna', 'Aa31LG8G9320' => 'aar', 'Aa31LG8G9330' => 'aar', 'Aa31LG8G9340' => 'aar', 'Aa31sc221G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1034' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1528' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.829' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2222' => 'aag', 'Ah.12g058830' => 'amhyb', 'Ah.12g058840' => 'amhyb', 'AL3G37160' => 'aly', 'AL7G41310' => 'aly', 'Aqoxy5G00395' => 'aox', 'Aqoxy5G00396' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0C8NZA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5185HY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JZ1PRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MD3LS0' => 'arhy', 'AT3G22840' => 'ath', 'AT4G14690' => 'ath', 'ATR0665G054' => 'atr', 'Atru.chr4.2344' => 'acertr', 'Atru.chr4.2346' => 'acertr', 'Atru.chr4.2347' => 'acertr', 'Atru.chr4.2348' => 'acertr', 'Atru.chr4.2355' => 'acertr', 'Atru.chr4.2356' => 'acertr', 'Atru.chr4.2358' => 'acertr', 'Atru.chr4.2359' => 'acertr', 'Atru.chr4.2360' => 'acertr', 'Atru.chr4.2361' => 'acertr', 'AUR62030476' => 'cqu', 'AUR62030478' => 'cqu', 'AUR62030819' => 'cqu', 'AUR62030820' => 'cqu', 'BcaB03g14648' => 'bca', 'BcaB04g20492' => 'bca', 'BcaB06g26399' => 'bca', 'BcaC01g03416' => 'bca', 'BcaC01g03419' => 'bca', 'BcaC01g03421' => 'bca', 'BcaC01g03424' => 'bca', 'BcaC05g28012' => 'bca', 'BcaC09g49212' => 'bca', 'BcaC09g50140' => 'bca', 'BcaNung00346' => 'bca', 'BolC1t02785H' => 'bol', 'BolC1t04095H' => 'bol', 'BolC3t17545H' => 'bol', 'BolC5t32769H' => 'bol', 'BraA01t02211Z' => 'bra', 'BraA01t03359Z' => 'bra', 'BraA03t13441Z' => 'bra', 'BraA05t21476Z' => 'bra', 'C01p28420' => 'bna', 'C01p41350' => 'bna', 'C03p52750' => 'bna', 'C03p52780' => 'bna', 'C05p40270' => 'bna', 'CAN.G1437.9' => 'can', 'CANSAT78G0035' => 'cansat', 'CANSAT78G1036' => 'cansat', 'CANSAT78G2272' => 'cansat', 'CANSAT78G2478' => 'cansat', 'CARHR098700' => 'chi', 'CARHR221120' => 'chi', 'CARHR221150' => 'chi', 'Carub.0003s2297' => 'cru', 'Carub.0007s2749' => 'cru', 'Carub.0007s2750' => 'cru', 'Carub.0007s2751' => 'cru', 'Ca_10849_v3' => 'car', 'Cc03_g04300' => 'ccan', 'CDE02G3648' => 'cde', 'CDE05G0060' => 'cde', 'CDE05G0692' => 'cde', 'CDE05G2285' => 'cde', 'CDE05G2884' => 'cde', 'CDE05G3072' => 'cde', 'Cfa008439' => 'cfa', 'Cfa008441' => 'cfa', 'Cfa008443' => 'cfa', 'Cfa008448' => 'cfa', 'Ciclev10005974m.g' => 'ccl', 'Ciclev10006006m.g' => 'ccl', 'Ciclev10006775m.g' => 'ccl', 'CiPaw.02G120400' => 'cil', 'CiPaw.02G120500' => 'cil', 'CiPaw.02G120600' => 'cil', 'ClCG05G004850' => 'cla', 'COL.COLO4_21566' => 'col', 'Cpa.g.sc44.124' => 'cpa', 'Cre07.g320400' => 'cre', 'Cre07.g320450' => 'cre', 'Cre08.g384650' => 'cre', 'Cre09.g393173' => 'cre', 'Cre09.g394325' => 'cre', 'Cre14.g626750' => 'cre', 'Cre16.g679250' => 'cre', 'CsaV3_3G012890' => 'csa', 'CSS0010865' => 'camsi', 'CSS0044338' => 'camsi', 'DCAR_002366' => 'dca', 'DCAR_030687' => 'dca', 'DCAR_030688' => 'dca', 'Dinv14047' => 'din', 'Dinv14048' => 'din', 'Duzib151G0105' => 'dzi', 'Duzib151G0114' => 'dzi', 'Duzib212G1029' => 'dzi', 'ECA232G3536' => 'eca', 'ECA240G0786' => 'eca', 'ECA240G1802' => 'eca', 'ECA240G3760' => 'eca', 'ECA240G3920' => 'eca', 'EL10Ac5g12536' => 'bvu', 'EL10Ac5g12537' => 'bvu', 'EL10Ac5g12538' => 'bvu', 'Eucgr.B01004' => 'egr', 'Eucgr.B01006' => 'egr', 'Eucgr.B01007' => 'egr', 'Eucgr.B01008' => 'egr', 'Eucgr.B01895' => 'egr', 'Eucgr.B01896' => 'egr', 'FAN04G1456' => 'fan', 'FAN08G1769' => 'fan', 'FAN08G2160' => 'fan', 'FAN13G2403' => 'fan', 'FAN13G3303' => 'fan', 'FAN15G2435' => 'fan', 'FAN17G0672' => 'fan', 'FAN17G2441' => 'fan', 'FAN18G1024' => 'fan', 'FAN22G1458' => 'fan', 'FAN24G0037' => 'fan', 'FAN24G0429' => 'fan', 'FAN24G2387' => 'fan', 'FAN27G2746' => 'fan', 'FvH4_2g20400' => 'fve', 'FvH4_2g20420' => 'fve', 'FvH4_2g20430' => 'fve', 'FvH4_4g01270' => 'fve', 'FvH4_4g01290' => 'fve', 'FvH4_4g01300' => 'fve', 'FvH4_4g01310' => 'fve', 'FvH4_4g01330' => 'fve', 'FvH4_5g09070' => 'fve', 'Glyma.10G243800' => 'gma', 'Glyma.20G150600' => 'gma', 'Gohir.A09G219200' => 'ghi', 'Gohir.A09G219300' => 'ghi', 'Gohir.D09G221400' => 'ghi', 'Gohir.D09G221500' => 'ghi', 'Gorai.006G242600' => 'gra', 'Gorai.006G242700' => 'gra', 'GSVIVG01018044001' => 'vvi', 'HanXRQChr03g0083821' => 'han', 'HanXRQChr03g0083841' => 'han', 'HanXRQChr03g0083881' => 'han', 'HanXRQChr03g0083901' => 'han', 'HanXRQChr03g0083921' => 'han', 'HanXRQChr03g0085331' => 'han', 'HanXRQChr03g0085361' => 'han', 'HanXRQChr03g0085411' => 'han', 'HanXRQChr03g0085421' => 'han', 'HanXRQChr03g0085431' => 'han', 'HanXRQChr08g0221991' => 'han', 'HanXRQChr11g0336061' => 'han', 'HanXRQChr11g0336411' => 'han', 'Haze_11234' => 'cav', 'Hma1.2p1_0549F.1_g177010' => 'hma', 'Hma1.2p1_0602F.1_g187630' => 'hma', 'Hund14876' => 'sun', 'Hund14879' => 'sun', 'Lalb_Chr06g0160741' => 'lal', 'Lalb_Chr21g0304781' => 'lal', 'Lj3A726G19' => 'lonja', 'Lj3A726T23' => 'lonja', 'Lj3A726T24' => 'lonja', 'Lj3A726T25' => 'lonja', 'Lj3A727T17' => 'lonja', 'Lj3C726T0' => 'lonja', 'Lj3C726T2' => 'lonja', 'Lj3P725T35' => 'lonja', 'Lj3P727T10' => 'lonja', 'Lj3P727T12' => 'lonja', 'Lj3P727T14' => 'lonja', 'Lj5g0023109' => 'lja', 'Lj6P646T44' => 'lonja', 'Lsat_1_v5_gn_6_75760' => 'lsa', 'Lsat_1_v5_gn_6_75800' => 'lsa', 'Lsat_1_v5_gn_6_75900' => 'lsa', 'Lsat_1_v5_gn_6_76240' => 'lsa', 'Lsat_1_v5_gn_6_76441' => 'lsa', 'Lsat_1_v5_gn_6_76700' => 'lsa', 'Lsat_1_v5_gn_6_76760' => 'lsa', 'Manes.15G033100' => 'mes', 'Mapoly0004s0074' => 'mpo', 'Mapoly0004s0075' => 'mpo', 'Mapoly0004s0163' => 'mpo', 'Mapoly0004s0164' => 'mpo', 'Mapoly0021s0018' => 'mpo', 'Mapoly0041s0136' => 'mpo', 'Mapoly0041s0137' => 'mpo', 'Mapoly0041s0138' => 'mpo', 'Mapoly0041s0139' => 'mpo', 'Mapoly0041s0141' => 'mpo', 'Mapoly0041s0142' => 'mpo', 'Mapoly0041s0143' => 'mpo', 'Mapoly0041s0144' => 'mpo', 'Mapoly0041s0145' => 'mpo', 'Mapoly0047s0106' => 'mpo', 'Mapoly0047s0108' => 'mpo', 'Mapoly0050s0051' => 'mpo', 'Mapoly0050s0052' => 'mpo', 'Mapoly0050s0053' => 'mpo', 'Mapoly0058s0013' => 'mpo', 'Mapoly0091s0078' => 'mpo', 'Mapoly0091s0079' => 'mpo', 'Mapoly0091s0080' => 'mpo', 'Mapoly0091s0081' => 'mpo', 'Mapoly0278s0004' => 'mpo', 'Mapoly0278s0005' => 'mpo', 'Mapoly0278s0006' => 'mpo', 'MBI11_g30648_MAGBIO' => 'mbi', 'MCO03G194' => 'mco', 'MCO03G590' => 'mco', 'MCO07G312' => 'mco', 'MCO10G318' => 'mco', 'MCO12G244' => 'mco', 'MCO13G148' => 'mco', 'MCO13G194' => 'mco', 'MCO16G238' => 'mco', 'MD06G1134100' => 'mdo', 'MD13G1200100' => 'mdo', 'MD13G1200300' => 'mdo', 'MD13G1200600' => 'mdo', 'MD14G1150400' => 'mdo', 'MD16G1200000' => 'mdo', 'Medtr1g102570' => 'mtr', 'Medtr1g102780' => 'mtr', 'Medtr1g102800' => 'mtr', 'Medtr1g102810' => 'mtr', 'Medtr1g102830' => 'mtr', 'MELO3C006499.2' => 'cme', 'Migut.G00385' => 'egut', 'MSTRG.4063' => 'ama', 'Nitab4.5_0000090g0260' => 'nta', 'Nitab4.5_0000977g0030' => 'nta', 'Nitab4.5_0002541g0040' => 'nta', 'Nitab4.5_0007068g0040' => 'nta', 'Nn005s41408' => 'nnu', 'Nn005s41410' => 'nnu', 'Oeu010310.1' => 'oeu', 'Oeu010311.1' => 'oeu', 'Oeu043472.1' => 'oeu', 'Os01g0246400' => 'osa', 'Os04g0267950' => 'osa', 'Os07g0178700' => 'osa', 'Os07g0178800' => 'osa', 'Peaxi162Scf00316g00046' => 'pax', 'Peaxi162Scf00316g00049' => 'pax', 'Peaxi162Scf00316g00059' => 'pax', 'Peaxi162Scf00316g00328' => 'pax', 'Peaxi162Scf00316g00329' => 'pax', 'Peaxi162Scf00316g00411' => 'pax', 'Peaxi162Scf00316g00521' => 'pax', 'Peaxi162Scf00492g00068' => 'pax', 'Peaxi162Scf35631g00002' => 'pax', 'PGR142G3720' => 'pgr', 'PGSC0003DMG400006442' => 'stu', 'Phvul.007G062000' => 'pvu', 'Potri.008G157750' => 'ptr', 'Potri.008G157900' => 'ptr', 'Potri.008G158000' => 'ptr', 'Potri.008G158200' => 'ptr', 'Pp3c11_7280' => 'ppa', 'Pp3c11_7980' => 'ppa', 'Pp3c12_19450' => 'ppa', 'Pp3c14_1480' => 'ppa', 'Pp3c14_1501' => 'ppa', 'Pp3c16_4900' => 'ppa', 'Pp3c16_5010' => 'ppa', 'Pp3c16_5060' => 'ppa', 'Pp3c19_18250' => 'ppa', 'Pp3c23_8530' => 'ppa', 'Pp3c23_8550' => 'ppa', 'Pp3c24_9670' => 'ppa', 'Pp3c2_21390' => 'ppa', 'Pp3c2_31380' => 'ppa', 'Pp3c3_16620' => 'ppa', 'Pp3c3_8090' => 'ppa', 'Pp3c3_8110' => 'ppa', 'Pp3c3_8130' => 'ppa', 'Pp3c3_8150' => 'ppa', 'Pp3c4_14320' => 'ppa', 'Pp3c6_2560' => 'ppa', 'Pp3c9_16700' => 'ppa', 'PRCOL_00000234' => 'pco', 'PRCOL_00000235' => 'pco', 'PRCOL_00000777' => 'pco', 'PRCOL_00002344' => 'pco', 'PRCOL_00002372' => 'pco', 'PRCOL_00006120' => 'pco', 'Prupe.1G021400' => 'ppe', 'Prupe.1G021500' => 'ppe', 'Prupe.1G021600' => 'ppe', 'Prupe.1G021700' => 'ppe', 'Prupe.1G021800' => 'ppe', 'Prupe.5G145100' => 'ppe', 'Psat6g204040' => 'psa', 'Psat6g204800' => 'psa', 'Psat6g204920' => 'psa', 'Psat6g204960' => 'psa', 'Psat6g205080' => 'psa', 'PSO017G0271' => 'pso', 'PSO017G1276' => 'pso', 'PSO017G1429' => 'pso', 'PSO017G1861' => 'pso', 'PSO017G2787' => 'pso', 'PSO017G4466' => 'pso', 'PSO017G5118' => 'pso', 'PSO017G5420' => 'pso', 'PSO063G3678' => 'pso', 'PSO210G0546' => 'pso', 'PSO317G0001' => 'pso', 'PSO357G0512' => 'pso', 'PSO478G2682' => 'pso', 'PSO647G0001' => 'pso', 'PSO675G0001' => 'pso', 'PSO675G2699' => 'pso', 'PSO675G2849' => 'pso', 'PSO675G4991' => 'pso', 'PSO689G0001' => 'pso', 'QL06p000916' => 'qlo', 'QL06p000921' => 'qlo', 'QL06p001398' => 'qlo', 'QL06p001407' => 'qlo', 'QL06p002031' => 'qlo', 'RcHm_v2.0_Chr4g0387791' => 'rch', 'RcHm_v2.0_Chr4g0387801' => 'rch', 'RcHm_v2.0_Chr6g0286501' => 'rch', 'RcHm_v2.0_Chr6g0286511' => 'rch', 'RcHm_v2.0_Chr6g0286521' => 'rch', 'RcHm_v2.0_Chr6g0286531' => 'rch', 'RcHm_v2.0_Chr7g0189141' => 'rch', 'Rhsim02G0028700' => 'rsi', 'Rhsim02G0028800' => 'rsi', 'Rhsim02G0028900' => 'rsi', 'Rhsim02G0029000' => 'rsi', 'Rhsim02G0029100' => 'rsi', 'Rhsim02G0029200' => 'rsi', 'Rhsim02G0029300' => 'rsi', 'Rhsim02G0029400' => 'rsi', 'Rhsim02G0029500' => 'rsi', 'Rhsim02G0029600' => 'rsi', 'RhsimUnG0024000' => 'rsi', 'RhsimUnG0024100' => 'rsi', 'RhsimUnG0024200' => 'rsi', 'RhsimUnG0024300' => 'rsi', 'RhsimUnG0024400' => 'rsi', 'RhsimUnG0024500' => 'rsi', 'RhsimUnG0024700' => 'rsi', 'RhsimUnG0024800' => 'rsi', 'RhsimUnG0024900' => 'rsi', 'RhsimUnG0025100' => 'rsi', 'Sabra08G0120200' => 'sbr', 'Sabra08G0120300' => 'sbr', 'Sabra08G0120500' => 'sbr', 'Sabra08G0120600' => 'sbr', 'Sabra10G0158900' => 'sbr', 'SalBow2G3492' => 'sbo', 'Sc13g0004760' => 'sci', 'Sc13g0004770' => 'sci', 'Sed0003417' => 'sed', 'Sed0019750' => 'sed', 'SEGI_03419' => 'sgi', 'SEGI_05907' => 'sgi', 'SEGI_10682' => 'sgi', 'SEGI_13528' => 'sgi', 'SEGI_16081' => 'sgi', 'SEGI_19370' => 'sgi', 'SEGI_21015' => 'sgi', 'SEGI_21944' => 'sgi', 'SEGI_32906' => 'sgi', 'SEGI_33093' => 'sgi', 'SEGI_36110' => 'sgi', 'SEGI_40397' => 'sgi', 'SGA_v2.0_scaffold191G40426' => 'sas', 'SGA_v2.0_scaffold353G49717' => 'sas', 'SGA_v2.0_scaffold50G18550' => 'sas', 'SMO119G0173' => 'smo', 'SMO172G0002' => 'smo', 'Solyc09g082690.3' => 'sly', 'Solyc09g082700.2' => 'sly', 'Sopen09g031550' => 'spe', 'Sopen09g031560' => 'spe', 'Sp3g20540' => 'spa', 'Sp7g07580' => 'spa', 'TAR134G0002' => 'tar', 'TAR236G0001' => 'tar', 'TAR365G0892' => 'tar', 'TAR636G0166' => 'tar', 'TAR636G0646' => 'tar', 'TAR636G0869' => 'tar', 'TAR636G1317' => 'tar', 'TAR636G1744' => 'tar', 'TAR636G3358' => 'tar', 'TAR636G3436' => 'tar', 'THA.LOC104803047' => 'tha', 'Thecc.04G238900' => 'tca', 'Thhalv10021557m.g' => 'esa', 'Thhalv10026318m.g' => 'esa', 'Thhalv10026335m.g' => 'esa', 'TPR.G17433' => 'tpr', 'TPR.G18915' => 'tpr', 'TPR.G26125' => 'tpr', 'TWI09G0677' => 'twi', 'TWI73G0287' => 'twi', 'unitig_748.g8326' => 'ugi', 'vmacro15370' => 'vma', 'vmacro15371' => 'vma', 'vmacro15372' => 'vma', 'vmacro15373' => 'vma', 'vmacro15374' => 'vma', 'VMungo0720G2826' => 'vmu', 'Zm00001eb116960' => 'zma', 'Zm00001eb301260' => 'zma', 'Zm00001eb301270' => 'zma' ), 'gf_id' => 'HOM05D001460', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001460' ), 'data_identifier' => 'HOM05D001460', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001460', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '433', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p22980' => 'bna', 'A01p32340' => 'bna', 'A03p42970' => 'bna', 'A05p25880' => 'bna', 'Aa31LG8G9320' => 'aar', 'Aa31LG8G9330' => 'aar', 'Aa31LG8G9340' => 'aar', 'Aa31sc221G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1034' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1528' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.829' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2222' => 'aag', 'Ah.12g058830' => 'amhyb', 'Ah.12g058840' => 'amhyb', 'AL3G37160' => 'aly', 'AL7G41310' => 'aly', 'Aqoxy5G00395' => 'aox', 'Aqoxy5G00396' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0C8NZA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5185HY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JZ1PRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MD3LS0' => 'arhy', 'AT3G22840' => 'ath', 'AT4G14690' => 'ath', 'ATR0665G054' => 'atr', 'Atru.chr4.2344' => 'acertr', 'Atru.chr4.2346' => 'acertr', 'Atru.chr4.2347' => 'acertr', 'Atru.chr4.2348' => 'acertr', 'Atru.chr4.2355' => 'acertr', 'Atru.chr4.2356' => 'acertr', 'Atru.chr4.2358' => 'acertr', 'Atru.chr4.2359' => 'acertr', 'Atru.chr4.2360' => 'acertr', 'Atru.chr4.2361' => 'acertr', 'AUR62030476' => 'cqu', 'AUR62030478' => 'cqu', 'AUR62030819' => 'cqu', 'AUR62030820' => 'cqu', 'BcaB03g14648' => 'bca', 'BcaB04g20492' => 'bca', 'BcaB06g26399' => 'bca', 'BcaC01g03416' => 'bca', 'BcaC01g03419' => 'bca', 'BcaC01g03421' => 'bca', 'BcaC01g03424' => 'bca', 'BcaC05g28012' => 'bca', 'BcaC09g49212' => 'bca', 'BcaC09g50140' => 'bca', 'BcaNung00346' => 'bca', 'BolC1t02785H' => 'bol', 'BolC1t04095H' => 'bol', 'BolC3t17545H' => 'bol', 'BolC5t32769H' => 'bol', 'BraA01t02211Z' => 'bra', 'BraA01t03359Z' => 'bra', 'BraA03t13441Z' => 'bra', 'BraA05t21476Z' => 'bra', 'C01p28420' => 'bna', 'C01p41350' => 'bna', 'C03p52750' => 'bna', 'C03p52780' => 'bna', 'C05p40270' => 'bna', 'CAN.G1437.9' => 'can', 'CANSAT78G0035' => 'cansat', 'CANSAT78G1036' => 'cansat', 'CANSAT78G2272' => 'cansat', 'CANSAT78G2478' => 'cansat', 'CARHR098700' => 'chi', 'CARHR221120' => 'chi', 'CARHR221150' => 'chi', 'Carub.0003s2297' => 'cru', 'Carub.0007s2749' => 'cru', 'Carub.0007s2750' => 'cru', 'Carub.0007s2751' => 'cru', 'Ca_10849_v3' => 'car', 'Cc03_g04300' => 'ccan', 'CDE02G3648' => 'cde', 'CDE05G0060' => 'cde', 'CDE05G0692' => 'cde', 'CDE05G2285' => 'cde', 'CDE05G2884' => 'cde', 'CDE05G3072' => 'cde', 'Cfa008439' => 'cfa', 'Cfa008441' => 'cfa', 'Cfa008443' => 'cfa', 'Cfa008448' => 'cfa', 'Ciclev10005974m.g' => 'ccl', 'Ciclev10006006m.g' => 'ccl', 'Ciclev10006775m.g' => 'ccl', 'CiPaw.02G120400' => 'cil', 'CiPaw.02G120500' => 'cil', 'CiPaw.02G120600' => 'cil', 'ClCG05G004850' => 'cla', 'COL.COLO4_21566' => 'col', 'Cpa.g.sc44.124' => 'cpa', 'Cre07.g320400' => 'cre', 'Cre07.g320450' => 'cre', 'Cre08.g384650' => 'cre', 'Cre09.g393173' => 'cre', 'Cre09.g394325' => 'cre', 'Cre14.g626750' => 'cre', 'Cre16.g679250' => 'cre', 'CsaV3_3G012890' => 'csa', 'CSS0010865' => 'camsi', 'CSS0044338' => 'camsi', 'DCAR_002366' => 'dca', 'DCAR_030687' => 'dca', 'DCAR_030688' => 'dca', 'Dinv14047' => 'din', 'Dinv14048' => 'din', 'Duzib151G0105' => 'dzi', 'Duzib151G0114' => 'dzi', 'Duzib212G1029' => 'dzi', 'ECA232G3536' => 'eca', 'ECA240G0786' => 'eca', 'ECA240G1802' => 'eca', 'ECA240G3760' => 'eca', 'ECA240G3920' => 'eca', 'EL10Ac5g12536' => 'bvu', 'EL10Ac5g12537' => 'bvu', 'EL10Ac5g12538' => 'bvu', 'Eucgr.B01004' => 'egr', 'Eucgr.B01006' => 'egr', 'Eucgr.B01007' => 'egr', 'Eucgr.B01008' => 'egr', 'Eucgr.B01895' => 'egr', 'Eucgr.B01896' => 'egr', 'FAN04G1456' => 'fan', 'FAN08G1769' => 'fan', 'FAN08G2160' => 'fan', 'FAN13G2403' => 'fan', 'FAN13G3303' => 'fan', 'FAN15G2435' => 'fan', 'FAN17G0672' => 'fan', 'FAN17G2441' => 'fan', 'FAN18G1024' => 'fan', 'FAN22G1458' => 'fan', 'FAN24G0037' => 'fan', 'FAN24G0429' => 'fan', 'FAN24G2387' => 'fan', 'FAN27G2746' => 'fan', 'FvH4_2g20400' => 'fve', 'FvH4_2g20420' => 'fve', 'FvH4_2g20430' => 'fve', 'FvH4_4g01270' => 'fve', 'FvH4_4g01290' => 'fve', 'FvH4_4g01300' => 'fve', 'FvH4_4g01310' => 'fve', 'FvH4_4g01330' => 'fve', 'FvH4_5g09070' => 'fve', 'Glyma.10G243800' => 'gma', 'Glyma.20G150600' => 'gma', 'Gohir.A09G219200' => 'ghi', 'Gohir.A09G219300' => 'ghi', 'Gohir.D09G221400' => 'ghi', 'Gohir.D09G221500' => 'ghi', 'Gorai.006G242600' => 'gra', 'Gorai.006G242700' => 'gra', 'GSVIVG01018044001' => 'vvi', 'HanXRQChr03g0083821' => 'han', 'HanXRQChr03g0083841' => 'han', 'HanXRQChr03g0083881' => 'han', 'HanXRQChr03g0083901' => 'han', 'HanXRQChr03g0083921' => 'han', 'HanXRQChr03g0085331' => 'han', 'HanXRQChr03g0085361' => 'han', 'HanXRQChr03g0085411' => 'han', 'HanXRQChr03g0085421' => 'han', 'HanXRQChr03g0085431' => 'han', 'HanXRQChr08g0221991' => 'han', 'HanXRQChr11g0336061' => 'han', 'HanXRQChr11g0336411' => 'han', 'Haze_11234' => 'cav', 'Hma1.2p1_0549F.1_g177010' => 'hma', 'Hma1.2p1_0602F.1_g187630' => 'hma', 'Hund14876' => 'sun', 'Hund14879' => 'sun', 'Lalb_Chr06g0160741' => 'lal', 'Lalb_Chr21g0304781' => 'lal', 'Lj3A726G19' => 'lonja', 'Lj3A726T23' => 'lonja', 'Lj3A726T24' => 'lonja', 'Lj3A726T25' => 'lonja', 'Lj3A727T17' => 'lonja', 'Lj3C726T0' => 'lonja', 'Lj3C726T2' => 'lonja', 'Lj3P725T35' => 'lonja', 'Lj3P727T10' => 'lonja', 'Lj3P727T12' => 'lonja', 'Lj3P727T14' => 'lonja', 'Lj5g0023109' => 'lja', 'Lj6P646T44' => 'lonja', 'Lsat_1_v5_gn_6_75760' => 'lsa', 'Lsat_1_v5_gn_6_75800' => 'lsa', 'Lsat_1_v5_gn_6_75900' => 'lsa', 'Lsat_1_v5_gn_6_76240' => 'lsa', 'Lsat_1_v5_gn_6_76441' => 'lsa', 'Lsat_1_v5_gn_6_76700' => 'lsa', 'Lsat_1_v5_gn_6_76760' => 'lsa', 'Manes.15G033100' => 'mes', 'Mapoly0004s0074' => 'mpo', 'Mapoly0004s0075' => 'mpo', 'Mapoly0004s0163' => 'mpo', 'Mapoly0004s0164' => 'mpo', 'Mapoly0021s0018' => 'mpo', 'Mapoly0041s0136' => 'mpo', 'Mapoly0041s0137' => 'mpo', 'Mapoly0041s0138' => 'mpo', 'Mapoly0041s0139' => 'mpo', 'Mapoly0041s0141' => 'mpo', 'Mapoly0041s0142' => 'mpo', 'Mapoly0041s0143' => 'mpo', 'Mapoly0041s0144' => 'mpo', 'Mapoly0041s0145' => 'mpo', 'Mapoly0047s0106' => 'mpo', 'Mapoly0047s0108' => 'mpo', 'Mapoly0050s0051' => 'mpo', 'Mapoly0050s0052' => 'mpo', 'Mapoly0050s0053' => 'mpo', 'Mapoly0058s0013' => 'mpo', 'Mapoly0091s0078' => 'mpo', 'Mapoly0091s0079' => 'mpo', 'Mapoly0091s0080' => 'mpo', 'Mapoly0091s0081' => 'mpo', 'Mapoly0278s0004' => 'mpo', 'Mapoly0278s0005' => 'mpo', 'Mapoly0278s0006' => 'mpo', 'MBI11_g30648_MAGBIO' => 'mbi', 'MCO03G194' => 'mco', 'MCO03G590' => 'mco', 'MCO07G312' => 'mco', 'MCO10G318' => 'mco', 'MCO12G244' => 'mco', 'MCO13G148' => 'mco', 'MCO13G194' => 'mco', 'MCO16G238' => 'mco', 'MD06G1134100' => 'mdo', 'MD13G1200100' => 'mdo', 'MD13G1200300' => 'mdo', 'MD13G1200600' => 'mdo', 'MD14G1150400' => 'mdo', 'MD16G1200000' => 'mdo', 'Medtr1g102570' => 'mtr', 'Medtr1g102780' => 'mtr', 'Medtr1g102800' => 'mtr', 'Medtr1g102810' => 'mtr', 'Medtr1g102830' => 'mtr', 'MELO3C006499.2' => 'cme', 'Migut.G00385' => 'egut', 'MSTRG.4063' => 'ama', 'Nitab4.5_0000090g0260' => 'nta', 'Nitab4.5_0000977g0030' => 'nta', 'Nitab4.5_0002541g0040' => 'nta', 'Nitab4.5_0007068g0040' => 'nta', 'Nn005s41408' => 'nnu', 'Nn005s41410' => 'nnu', 'Oeu010310.1' => 'oeu', 'Oeu010311.1' => 'oeu', 'Oeu043472.1' => 'oeu', 'Os01g0246400' => 'osa', 'Os04g0267950' => 'osa', 'Os07g0178700' => 'osa', 'Os07g0178800' => 'osa', 'Peaxi162Scf00316g00046' => 'pax', 'Peaxi162Scf00316g00049' => 'pax', 'Peaxi162Scf00316g00059' => 'pax', 'Peaxi162Scf00316g00328' => 'pax', 'Peaxi162Scf00316g00329' => 'pax', 'Peaxi162Scf00316g00411' => 'pax', 'Peaxi162Scf00316g00521' => 'pax', 'Peaxi162Scf00492g00068' => 'pax', 'Peaxi162Scf35631g00002' => 'pax', 'PGR142G3720' => 'pgr', 'PGSC0003DMG400006442' => 'stu', 'Phvul.007G062000' => 'pvu', 'Potri.008G157750' => 'ptr', 'Potri.008G157900' => 'ptr', 'Potri.008G158000' => 'ptr', 'Potri.008G158200' => 'ptr', 'Pp3c11_7280' => 'ppa', 'Pp3c11_7980' => 'ppa', 'Pp3c12_19450' => 'ppa', 'Pp3c14_1480' => 'ppa', 'Pp3c14_1501' => 'ppa', 'Pp3c16_4900' => 'ppa', 'Pp3c16_5010' => 'ppa', 'Pp3c16_5060' => 'ppa', 'Pp3c19_18250' => 'ppa', 'Pp3c23_8530' => 'ppa', 'Pp3c23_8550' => 'ppa', 'Pp3c24_9670' => 'ppa', 'Pp3c2_21390' => 'ppa', 'Pp3c2_31380' => 'ppa', 'Pp3c3_16620' => 'ppa', 'Pp3c3_8090' => 'ppa', 'Pp3c3_8110' => 'ppa', 'Pp3c3_8130' => 'ppa', 'Pp3c3_8150' => 'ppa', 'Pp3c4_14320' => 'ppa', 'Pp3c6_2560' => 'ppa', 'Pp3c9_16700' => 'ppa', 'PRCOL_00000234' => 'pco', 'PRCOL_00000235' => 'pco', 'PRCOL_00000777' => 'pco', 'PRCOL_00002344' => 'pco', 'PRCOL_00002372' => 'pco', 'PRCOL_00006120' => 'pco', 'Prupe.1G021400' => 'ppe', 'Prupe.1G021500' => 'ppe', 'Prupe.1G021600' => 'ppe', 'Prupe.1G021700' => 'ppe', 'Prupe.1G021800' => 'ppe', 'Prupe.5G145100' => 'ppe', 'Psat6g204040' => 'psa', 'Psat6g204800' => 'psa', 'Psat6g204920' => 'psa', 'Psat6g204960' => 'psa', 'Psat6g205080' => 'psa', 'PSO017G0271' => 'pso', 'PSO017G1276' => 'pso', 'PSO017G1429' => 'pso', 'PSO017G1861' => 'pso', 'PSO017G2787' => 'pso', 'PSO017G4466' => 'pso', 'PSO017G5118' => 'pso', 'PSO017G5420' => 'pso', 'PSO063G3678' => 'pso', 'PSO210G0546' => 'pso', 'PSO317G0001' => 'pso', 'PSO357G0512' => 'pso', 'PSO478G2682' => 'pso', 'PSO647G0001' => 'pso', 'PSO675G0001' => 'pso', 'PSO675G2699' => 'pso', 'PSO675G2849' => 'pso', 'PSO675G4991' => 'pso', 'PSO689G0001' => 'pso', 'QL06p000916' => 'qlo', 'QL06p000921' => 'qlo', 'QL06p001398' => 'qlo', 'QL06p001407' => 'qlo', 'QL06p002031' => 'qlo', 'RcHm_v2.0_Chr4g0387791' => 'rch', 'RcHm_v2.0_Chr4g0387801' => 'rch', 'RcHm_v2.0_Chr6g0286501' => 'rch', 'RcHm_v2.0_Chr6g0286511' => 'rch', 'RcHm_v2.0_Chr6g0286521' => 'rch', 'RcHm_v2.0_Chr6g0286531' => 'rch', 'RcHm_v2.0_Chr7g0189141' => 'rch', 'Rhsim02G0028700' => 'rsi', 'Rhsim02G0028800' => 'rsi', 'Rhsim02G0028900' => 'rsi', 'Rhsim02G0029000' => 'rsi', 'Rhsim02G0029100' => 'rsi', 'Rhsim02G0029200' => 'rsi', 'Rhsim02G0029300' => 'rsi', 'Rhsim02G0029400' => 'rsi', 'Rhsim02G0029500' => 'rsi', 'Rhsim02G0029600' => 'rsi', 'RhsimUnG0024000' => 'rsi', 'RhsimUnG0024100' => 'rsi', 'RhsimUnG0024200' => 'rsi', 'RhsimUnG0024300' => 'rsi', 'RhsimUnG0024400' => 'rsi', 'RhsimUnG0024500' => 'rsi', 'RhsimUnG0024700' => 'rsi', 'RhsimUnG0024800' => 'rsi', 'RhsimUnG0024900' => 'rsi', 'RhsimUnG0025100' => 'rsi', 'Sabra08G0120200' => 'sbr', 'Sabra08G0120300' => 'sbr', 'Sabra08G0120500' => 'sbr', 'Sabra08G0120600' => 'sbr', 'Sabra10G0158900' => 'sbr', 'SalBow2G3492' => 'sbo', 'Sc13g0004760' => 'sci', 'Sc13g0004770' => 'sci', 'Sed0003417' => 'sed', 'Sed0019750' => 'sed', 'SEGI_03419' => 'sgi', 'SEGI_05907' => 'sgi', 'SEGI_10682' => 'sgi', 'SEGI_13528' => 'sgi', 'SEGI_16081' => 'sgi', 'SEGI_19370' => 'sgi', 'SEGI_21015' => 'sgi', 'SEGI_21944' => 'sgi', 'SEGI_32906' => 'sgi', 'SEGI_33093' => 'sgi', 'SEGI_36110' => 'sgi', 'SEGI_40397' => 'sgi', 'SGA_v2.0_scaffold191G40426' => 'sas', 'SGA_v2.0_scaffold353G49717' => 'sas', 'SGA_v2.0_scaffold50G18550' => 'sas', 'SMO119G0173' => 'smo', 'SMO172G0002' => 'smo', 'Solyc09g082690.3' => 'sly', 'Solyc09g082700.2' => 'sly', 'Sopen09g031550' => 'spe', 'Sopen09g031560' => 'spe', 'Sp3g20540' => 'spa', 'Sp7g07580' => 'spa', 'TAR134G0002' => 'tar', 'TAR236G0001' => 'tar', 'TAR365G0892' => 'tar', 'TAR636G0166' => 'tar', 'TAR636G0646' => 'tar', 'TAR636G0869' => 'tar', 'TAR636G1317' => 'tar', 'TAR636G1744' => 'tar', 'TAR636G3358' => 'tar', 'TAR636G3436' => 'tar', 'THA.LOC104803047' => 'tha', 'Thecc.04G238900' => 'tca', 'Thhalv10021557m.g' => 'esa', 'Thhalv10026318m.g' => 'esa', 'Thhalv10026335m.g' => 'esa', 'TPR.G17433' => 'tpr', 'TPR.G18915' => 'tpr', 'TPR.G26125' => 'tpr', 'TWI09G0677' => 'twi', 'TWI73G0287' => 'twi', 'unitig_748.g8326' => 'ugi', 'vmacro15370' => 'vma', 'vmacro15371' => 'vma', 'vmacro15372' => 'vma', 'vmacro15373' => 'vma', 'vmacro15374' => 'vma', 'VMungo0720G2826' => 'vmu', 'Zm00001eb116960' => 'zma', 'Zm00001eb301260' => 'zma', 'Zm00001eb301270' => 'zma' ) $gf_id = 'HOM05D001460' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001460' ) $data_identifier = 'HOM05D001460' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 4, 'aag' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 2, 'aox' => (int) 2, 'arhy' => (int) 4, 'ath' => (int) 2, 'atr' => (int) 1, 'acertr' => (int) 10, 'cqu' => (int) 4, 'bca' => (int) 11, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 1, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 1, 'ccan' => (int) 1, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 1, 'col' => (int) 1, 'cpa' => (int) 1, 'cre' => (int) 7, 'csa' => (int) 1, 'camsi' => (int) 2, 'dca' => (int) 3, 'din' => (int) 2, 'dzi' => (int) 3, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 14, 'fve' => (int) 9, 'gma' => (int) 2, 'ghi' => (int) 4, 'gra' => (int) 2, 'vvi' => (int) 1, 'han' => (int) 13, 'cav' => (int) 1, 'hma' => (int) 2, 'sun' => (int) 2, 'lal' => (int) 2, 'lonja' => (int) 12, 'lja' => (int) 1, 'lsa' => (int) 7, 'mes' => (int) 1, 'mpo' => (int) 27, 'mbi' => (int) 1, 'mco' => (int) 8, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 1, 'egut' => (int) 1, 'ama' => (int) 1, 'nta' => (int) 4, 'nnu' => (int) 2, 'oeu' => (int) 3, 'osa' => (int) 4, 'pax' => (int) 9, 'pgr' => (int) 1, 'stu' => (int) 1, 'pvu' => (int) 1, 'ptr' => (int) 4, 'ppa' => (int) 22, 'pco' => (int) 6, 'ppe' => (int) 6, 'psa' => (int) 5, 'pso' => (int) 19, 'qlo' => (int) 5, 'rch' => (int) 7, 'rsi' => (int) 20, 'sbr' => (int) 5, 'sbo' => (int) 1, 'sci' => (int) 2, 'sed' => (int) 2, 'sgi' => (int) 12, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 2, 'tar' => (int) 10, 'tha' => (int) 1, 'tca' => (int) 1, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 2, 'ugi' => (int) 1, 'vma' => (int) 5, 'vmu' => (int) 1, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb301270' $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' => 'HOM05D001460', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '433', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p22980' => 'bna', 'A01p32340' => 'bna', 'A03p42970' => 'bna', 'A05p25880' => 'bna', 'Aa31LG8G9320' => 'aar', 'Aa31LG8G9330' => 'aar', 'Aa31LG8G9340' => 'aar', 'Aa31sc221G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1034' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1528' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.829' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2222' => 'aag', 'Ah.12g058830' => 'amhyb', 'Ah.12g058840' => 'amhyb', 'AL3G37160' => 'aly', 'AL7G41310' => 'aly', 'Aqoxy5G00395' => 'aox', 'Aqoxy5G00396' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0C8NZA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5185HY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JZ1PRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MD3LS0' => 'arhy', 'AT3G22840' => 'ath', 'AT4G14690' => 'ath', 'ATR0665G054' => 'atr', 'Atru.chr4.2344' => 'acertr', 'Atru.chr4.2346' => 'acertr', 'Atru.chr4.2347' => 'acertr', 'Atru.chr4.2348' => 'acertr', 'Atru.chr4.2355' => 'acertr', 'Atru.chr4.2356' => 'acertr', 'Atru.chr4.2358' => 'acertr', 'Atru.chr4.2359' => 'acertr', 'Atru.chr4.2360' => 'acertr', 'Atru.chr4.2361' => 'acertr', 'AUR62030476' => 'cqu', 'AUR62030478' => 'cqu', 'AUR62030819' => 'cqu', 'AUR62030820' => 'cqu', 'BcaB03g14648' => 'bca', 'BcaB04g20492' => 'bca', 'BcaB06g26399' => 'bca', 'BcaC01g03416' => 'bca', 'BcaC01g03419' => 'bca', 'BcaC01g03421' => 'bca', 'BcaC01g03424' => 'bca', 'BcaC05g28012' => 'bca', 'BcaC09g49212' => 'bca', 'BcaC09g50140' => 'bca', 'BcaNung00346' => 'bca', 'BolC1t02785H' => 'bol', 'BolC1t04095H' => 'bol', 'BolC3t17545H' => 'bol', 'BolC5t32769H' => 'bol', 'BraA01t02211Z' => 'bra', 'BraA01t03359Z' => 'bra', 'BraA03t13441Z' => 'bra', 'BraA05t21476Z' => 'bra', 'C01p28420' => 'bna', 'C01p41350' => 'bna', 'C03p52750' => 'bna', 'C03p52780' => 'bna', 'C05p40270' => 'bna', 'CAN.G1437.9' => 'can', 'CANSAT78G0035' => 'cansat', 'CANSAT78G1036' => 'cansat', 'CANSAT78G2272' => 'cansat', 'CANSAT78G2478' => 'cansat', 'CARHR098700' => 'chi', 'CARHR221120' => 'chi', 'CARHR221150' => 'chi', 'Carub.0003s2297' => 'cru', 'Carub.0007s2749' => 'cru', 'Carub.0007s2750' => 'cru', 'Carub.0007s2751' => 'cru', 'Ca_10849_v3' => 'car', 'Cc03_g04300' => 'ccan', 'CDE02G3648' => 'cde', 'CDE05G0060' => 'cde', 'CDE05G0692' => 'cde', 'CDE05G2285' => 'cde', 'CDE05G2884' => 'cde', 'CDE05G3072' => 'cde', 'Cfa008439' => 'cfa', 'Cfa008441' => 'cfa', 'Cfa008443' => 'cfa', 'Cfa008448' => 'cfa', 'Ciclev10005974m.g' => 'ccl', 'Ciclev10006006m.g' => 'ccl', 'Ciclev10006775m.g' => 'ccl', 'CiPaw.02G120400' => 'cil', 'CiPaw.02G120500' => 'cil', 'CiPaw.02G120600' => 'cil', 'ClCG05G004850' => 'cla', 'COL.COLO4_21566' => 'col', 'Cpa.g.sc44.124' => 'cpa', 'Cre07.g320400' => 'cre', 'Cre07.g320450' => 'cre', 'Cre08.g384650' => 'cre', 'Cre09.g393173' => 'cre', 'Cre09.g394325' => 'cre', 'Cre14.g626750' => 'cre', 'Cre16.g679250' => 'cre', 'CsaV3_3G012890' => 'csa', 'CSS0010865' => 'camsi', 'CSS0044338' => 'camsi', 'DCAR_002366' => 'dca', 'DCAR_030687' => 'dca', 'DCAR_030688' => 'dca', 'Dinv14047' => 'din', 'Dinv14048' => 'din', 'Duzib151G0105' => 'dzi', 'Duzib151G0114' => 'dzi', 'Duzib212G1029' => 'dzi', 'ECA232G3536' => 'eca', 'ECA240G0786' => 'eca', 'ECA240G1802' => 'eca', 'ECA240G3760' => 'eca', 'ECA240G3920' => 'eca', 'EL10Ac5g12536' => 'bvu', 'EL10Ac5g12537' => 'bvu', 'EL10Ac5g12538' => 'bvu', 'Eucgr.B01004' => 'egr', 'Eucgr.B01006' => 'egr', 'Eucgr.B01007' => 'egr', 'Eucgr.B01008' => 'egr', 'Eucgr.B01895' => 'egr', 'Eucgr.B01896' => 'egr', 'FAN04G1456' => 'fan', 'FAN08G1769' => 'fan', 'FAN08G2160' => 'fan', 'FAN13G2403' => 'fan', 'FAN13G3303' => 'fan', 'FAN15G2435' => 'fan', 'FAN17G0672' => 'fan', 'FAN17G2441' => 'fan', 'FAN18G1024' => 'fan', 'FAN22G1458' => 'fan', 'FAN24G0037' => 'fan', 'FAN24G0429' => 'fan', 'FAN24G2387' => 'fan', 'FAN27G2746' => 'fan', 'FvH4_2g20400' => 'fve', 'FvH4_2g20420' => 'fve', 'FvH4_2g20430' => 'fve', 'FvH4_4g01270' => 'fve', 'FvH4_4g01290' => 'fve', 'FvH4_4g01300' => 'fve', 'FvH4_4g01310' => 'fve', 'FvH4_4g01330' => 'fve', 'FvH4_5g09070' => 'fve', 'Glyma.10G243800' => 'gma', 'Glyma.20G150600' => 'gma', 'Gohir.A09G219200' => 'ghi', 'Gohir.A09G219300' => 'ghi', 'Gohir.D09G221400' => 'ghi', 'Gohir.D09G221500' => 'ghi', 'Gorai.006G242600' => 'gra', 'Gorai.006G242700' => 'gra', 'GSVIVG01018044001' => 'vvi', 'HanXRQChr03g0083821' => 'han', 'HanXRQChr03g0083841' => 'han', 'HanXRQChr03g0083881' => 'han', 'HanXRQChr03g0083901' => 'han', 'HanXRQChr03g0083921' => 'han', 'HanXRQChr03g0085331' => 'han', 'HanXRQChr03g0085361' => 'han', 'HanXRQChr03g0085411' => 'han', 'HanXRQChr03g0085421' => 'han', 'HanXRQChr03g0085431' => 'han', 'HanXRQChr08g0221991' => 'han', 'HanXRQChr11g0336061' => 'han', 'HanXRQChr11g0336411' => 'han', 'Haze_11234' => 'cav', 'Hma1.2p1_0549F.1_g177010' => 'hma', 'Hma1.2p1_0602F.1_g187630' => 'hma', 'Hund14876' => 'sun', 'Hund14879' => 'sun', 'Lalb_Chr06g0160741' => 'lal', 'Lalb_Chr21g0304781' => 'lal', 'Lj3A726G19' => 'lonja', 'Lj3A726T23' => 'lonja', 'Lj3A726T24' => 'lonja', 'Lj3A726T25' => 'lonja', 'Lj3A727T17' => 'lonja', 'Lj3C726T0' => 'lonja', 'Lj3C726T2' => 'lonja', 'Lj3P725T35' => 'lonja', 'Lj3P727T10' => 'lonja', 'Lj3P727T12' => 'lonja', 'Lj3P727T14' => 'lonja', 'Lj5g0023109' => 'lja', 'Lj6P646T44' => 'lonja', 'Lsat_1_v5_gn_6_75760' => 'lsa', 'Lsat_1_v5_gn_6_75800' => 'lsa', 'Lsat_1_v5_gn_6_75900' => 'lsa', 'Lsat_1_v5_gn_6_76240' => 'lsa', 'Lsat_1_v5_gn_6_76441' => 'lsa', 'Lsat_1_v5_gn_6_76700' => 'lsa', 'Lsat_1_v5_gn_6_76760' => 'lsa', 'Manes.15G033100' => 'mes', 'Mapoly0004s0074' => 'mpo', 'Mapoly0004s0075' => 'mpo', 'Mapoly0004s0163' => 'mpo', 'Mapoly0004s0164' => 'mpo', 'Mapoly0021s0018' => 'mpo', 'Mapoly0041s0136' => 'mpo', 'Mapoly0041s0137' => 'mpo', 'Mapoly0041s0138' => 'mpo', 'Mapoly0041s0139' => 'mpo', 'Mapoly0041s0141' => 'mpo', 'Mapoly0041s0142' => 'mpo', 'Mapoly0041s0143' => 'mpo', 'Mapoly0041s0144' => 'mpo', 'Mapoly0041s0145' => 'mpo', 'Mapoly0047s0106' => 'mpo', 'Mapoly0047s0108' => 'mpo', 'Mapoly0050s0051' => 'mpo', 'Mapoly0050s0052' => 'mpo', 'Mapoly0050s0053' => 'mpo', 'Mapoly0058s0013' => 'mpo', 'Mapoly0091s0078' => 'mpo', 'Mapoly0091s0079' => 'mpo', 'Mapoly0091s0080' => 'mpo', 'Mapoly0091s0081' => 'mpo', 'Mapoly0278s0004' => 'mpo', 'Mapoly0278s0005' => 'mpo', 'Mapoly0278s0006' => 'mpo', 'MBI11_g30648_MAGBIO' => 'mbi', 'MCO03G194' => 'mco', 'MCO03G590' => 'mco', 'MCO07G312' => 'mco', 'MCO10G318' => 'mco', 'MCO12G244' => 'mco', 'MCO13G148' => 'mco', 'MCO13G194' => 'mco', 'MCO16G238' => 'mco', 'MD06G1134100' => 'mdo', 'MD13G1200100' => 'mdo', 'MD13G1200300' => 'mdo', 'MD13G1200600' => 'mdo', 'MD14G1150400' => 'mdo', 'MD16G1200000' => 'mdo', 'Medtr1g102570' => 'mtr', 'Medtr1g102780' => 'mtr', 'Medtr1g102800' => 'mtr', 'Medtr1g102810' => 'mtr', 'Medtr1g102830' => 'mtr', 'MELO3C006499.2' => 'cme', 'Migut.G00385' => 'egut', 'MSTRG.4063' => 'ama', 'Nitab4.5_0000090g0260' => 'nta', 'Nitab4.5_0000977g0030' => 'nta', 'Nitab4.5_0002541g0040' => 'nta', 'Nitab4.5_0007068g0040' => 'nta', 'Nn005s41408' => 'nnu', 'Nn005s41410' => 'nnu', 'Oeu010310.1' => 'oeu', 'Oeu010311.1' => 'oeu', 'Oeu043472.1' => 'oeu', 'Os01g0246400' => 'osa', 'Os04g0267950' => 'osa', 'Os07g0178700' => 'osa', 'Os07g0178800' => 'osa', 'Peaxi162Scf00316g00046' => 'pax', 'Peaxi162Scf00316g00049' => 'pax', 'Peaxi162Scf00316g00059' => 'pax', 'Peaxi162Scf00316g00328' => 'pax', 'Peaxi162Scf00316g00329' => 'pax', 'Peaxi162Scf00316g00411' => 'pax', 'Peaxi162Scf00316g00521' => 'pax', 'Peaxi162Scf00492g00068' => 'pax', 'Peaxi162Scf35631g00002' => 'pax', 'PGR142G3720' => 'pgr', 'PGSC0003DMG400006442' => 'stu', 'Phvul.007G062000' => 'pvu', 'Potri.008G157750' => 'ptr', 'Potri.008G157900' => 'ptr', 'Potri.008G158000' => 'ptr', 'Potri.008G158200' => 'ptr', 'Pp3c11_7280' => 'ppa', 'Pp3c11_7980' => 'ppa', 'Pp3c12_19450' => 'ppa', 'Pp3c14_1480' => 'ppa', 'Pp3c14_1501' => 'ppa', 'Pp3c16_4900' => 'ppa', 'Pp3c16_5010' => 'ppa', 'Pp3c16_5060' => 'ppa', 'Pp3c19_18250' => 'ppa', 'Pp3c23_8530' => 'ppa', 'Pp3c23_8550' => 'ppa', 'Pp3c24_9670' => 'ppa', 'Pp3c2_21390' => 'ppa', 'Pp3c2_31380' => 'ppa', 'Pp3c3_16620' => 'ppa', 'Pp3c3_8090' => 'ppa', 'Pp3c3_8110' => 'ppa', 'Pp3c3_8130' => 'ppa', 'Pp3c3_8150' => 'ppa', 'Pp3c4_14320' => 'ppa', 'Pp3c6_2560' => 'ppa', 'Pp3c9_16700' => 'ppa', 'PRCOL_00000234' => 'pco', 'PRCOL_00000235' => 'pco', 'PRCOL_00000777' => 'pco', 'PRCOL_00002344' => 'pco', 'PRCOL_00002372' => 'pco', 'PRCOL_00006120' => 'pco', 'Prupe.1G021400' => 'ppe', 'Prupe.1G021500' => 'ppe', 'Prupe.1G021600' => 'ppe', 'Prupe.1G021700' => 'ppe', 'Prupe.1G021800' => 'ppe', 'Prupe.5G145100' => 'ppe', 'Psat6g204040' => 'psa', 'Psat6g204800' => 'psa', 'Psat6g204920' => 'psa', 'Psat6g204960' => 'psa', 'Psat6g205080' => 'psa', 'PSO017G0271' => 'pso', 'PSO017G1276' => 'pso', 'PSO017G1429' => 'pso', 'PSO017G1861' => 'pso', 'PSO017G2787' => 'pso', 'PSO017G4466' => 'pso', 'PSO017G5118' => 'pso', 'PSO017G5420' => 'pso', 'PSO063G3678' => 'pso', 'PSO210G0546' => 'pso', 'PSO317G0001' => 'pso', 'PSO357G0512' => 'pso', 'PSO478G2682' => 'pso', 'PSO647G0001' => 'pso', 'PSO675G0001' => 'pso', 'PSO675G2699' => 'pso', 'PSO675G2849' => 'pso', 'PSO675G4991' => 'pso', 'PSO689G0001' => 'pso', 'QL06p000916' => 'qlo', 'QL06p000921' => 'qlo', 'QL06p001398' => 'qlo', 'QL06p001407' => 'qlo', 'QL06p002031' => 'qlo', 'RcHm_v2.0_Chr4g0387791' => 'rch', 'RcHm_v2.0_Chr4g0387801' => 'rch', 'RcHm_v2.0_Chr6g0286501' => 'rch', 'RcHm_v2.0_Chr6g0286511' => 'rch', 'RcHm_v2.0_Chr6g0286521' => 'rch', 'RcHm_v2.0_Chr6g0286531' => 'rch', 'RcHm_v2.0_Chr7g0189141' => 'rch', 'Rhsim02G0028700' => 'rsi', 'Rhsim02G0028800' => 'rsi', 'Rhsim02G0028900' => 'rsi', 'Rhsim02G0029000' => 'rsi', 'Rhsim02G0029100' => 'rsi', 'Rhsim02G0029200' => 'rsi', 'Rhsim02G0029300' => 'rsi', 'Rhsim02G0029400' => 'rsi', 'Rhsim02G0029500' => 'rsi', 'Rhsim02G0029600' => 'rsi', 'RhsimUnG0024000' => 'rsi', 'RhsimUnG0024100' => 'rsi', 'RhsimUnG0024200' => 'rsi', 'RhsimUnG0024300' => 'rsi', 'RhsimUnG0024400' => 'rsi', 'RhsimUnG0024500' => 'rsi', 'RhsimUnG0024700' => 'rsi', 'RhsimUnG0024800' => 'rsi', 'RhsimUnG0024900' => 'rsi', 'RhsimUnG0025100' => 'rsi', 'Sabra08G0120200' => 'sbr', 'Sabra08G0120300' => 'sbr', 'Sabra08G0120500' => 'sbr', 'Sabra08G0120600' => 'sbr', 'Sabra10G0158900' => 'sbr', 'SalBow2G3492' => 'sbo', 'Sc13g0004760' => 'sci', 'Sc13g0004770' => 'sci', 'Sed0003417' => 'sed', 'Sed0019750' => 'sed', 'SEGI_03419' => 'sgi', 'SEGI_05907' => 'sgi', 'SEGI_10682' => 'sgi', 'SEGI_13528' => 'sgi', 'SEGI_16081' => 'sgi', 'SEGI_19370' => 'sgi', 'SEGI_21015' => 'sgi', 'SEGI_21944' => 'sgi', 'SEGI_32906' => 'sgi', 'SEGI_33093' => 'sgi', 'SEGI_36110' => 'sgi', 'SEGI_40397' => 'sgi', 'SGA_v2.0_scaffold191G40426' => 'sas', 'SGA_v2.0_scaffold353G49717' => 'sas', 'SGA_v2.0_scaffold50G18550' => 'sas', 'SMO119G0173' => 'smo', 'SMO172G0002' => 'smo', 'Solyc09g082690.3' => 'sly', 'Solyc09g082700.2' => 'sly', 'Sopen09g031550' => 'spe', 'Sopen09g031560' => 'spe', 'Sp3g20540' => 'spa', 'Sp7g07580' => 'spa', 'TAR134G0002' => 'tar', 'TAR236G0001' => 'tar', 'TAR365G0892' => 'tar', 'TAR636G0166' => 'tar', 'TAR636G0646' => 'tar', 'TAR636G0869' => 'tar', 'TAR636G1317' => 'tar', 'TAR636G1744' => 'tar', 'TAR636G3358' => 'tar', 'TAR636G3436' => 'tar', 'THA.LOC104803047' => 'tha', 'Thecc.04G238900' => 'tca', 'Thhalv10021557m.g' => 'esa', 'Thhalv10026318m.g' => 'esa', 'Thhalv10026335m.g' => 'esa', 'TPR.G17433' => 'tpr', 'TPR.G18915' => 'tpr', 'TPR.G26125' => 'tpr', 'TWI09G0677' => 'twi', 'TWI73G0287' => 'twi', 'unitig_748.g8326' => 'ugi', 'vmacro15370' => 'vma', 'vmacro15371' => 'vma', 'vmacro15372' => 'vma', 'vmacro15373' => 'vma', 'vmacro15374' => 'vma', 'VMungo0720G2826' => 'vmu', 'Zm00001eb116960' => 'zma', 'Zm00001eb301260' => 'zma', 'Zm00001eb301270' => 'zma' ), 'gf_id' => 'HOM05D001460', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001460' ), 'data_identifier' => 'HOM05D001460', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001460', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '433', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p22980' => 'bna', 'A01p32340' => 'bna', 'A03p42970' => 'bna', 'A05p25880' => 'bna', 'Aa31LG8G9320' => 'aar', 'Aa31LG8G9330' => 'aar', 'Aa31LG8G9340' => 'aar', 'Aa31sc221G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1034' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1528' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.829' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2222' => 'aag', 'Ah.12g058830' => 'amhyb', 'Ah.12g058840' => 'amhyb', 'AL3G37160' => 'aly', 'AL7G41310' => 'aly', 'Aqoxy5G00395' => 'aox', 'Aqoxy5G00396' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0C8NZA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5185HY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JZ1PRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MD3LS0' => 'arhy', 'AT3G22840' => 'ath', 'AT4G14690' => 'ath', 'ATR0665G054' => 'atr', 'Atru.chr4.2344' => 'acertr', 'Atru.chr4.2346' => 'acertr', 'Atru.chr4.2347' => 'acertr', 'Atru.chr4.2348' => 'acertr', 'Atru.chr4.2355' => 'acertr', 'Atru.chr4.2356' => 'acertr', 'Atru.chr4.2358' => 'acertr', 'Atru.chr4.2359' => 'acertr', 'Atru.chr4.2360' => 'acertr', 'Atru.chr4.2361' => 'acertr', 'AUR62030476' => 'cqu', 'AUR62030478' => 'cqu', 'AUR62030819' => 'cqu', 'AUR62030820' => 'cqu', 'BcaB03g14648' => 'bca', 'BcaB04g20492' => 'bca', 'BcaB06g26399' => 'bca', 'BcaC01g03416' => 'bca', 'BcaC01g03419' => 'bca', 'BcaC01g03421' => 'bca', 'BcaC01g03424' => 'bca', 'BcaC05g28012' => 'bca', 'BcaC09g49212' => 'bca', 'BcaC09g50140' => 'bca', 'BcaNung00346' => 'bca', 'BolC1t02785H' => 'bol', 'BolC1t04095H' => 'bol', 'BolC3t17545H' => 'bol', 'BolC5t32769H' => 'bol', 'BraA01t02211Z' => 'bra', 'BraA01t03359Z' => 'bra', 'BraA03t13441Z' => 'bra', 'BraA05t21476Z' => 'bra', 'C01p28420' => 'bna', 'C01p41350' => 'bna', 'C03p52750' => 'bna', 'C03p52780' => 'bna', 'C05p40270' => 'bna', 'CAN.G1437.9' => 'can', 'CANSAT78G0035' => 'cansat', 'CANSAT78G1036' => 'cansat', 'CANSAT78G2272' => 'cansat', 'CANSAT78G2478' => 'cansat', 'CARHR098700' => 'chi', 'CARHR221120' => 'chi', 'CARHR221150' => 'chi', 'Carub.0003s2297' => 'cru', 'Carub.0007s2749' => 'cru', 'Carub.0007s2750' => 'cru', 'Carub.0007s2751' => 'cru', 'Ca_10849_v3' => 'car', 'Cc03_g04300' => 'ccan', 'CDE02G3648' => 'cde', 'CDE05G0060' => 'cde', 'CDE05G0692' => 'cde', 'CDE05G2285' => 'cde', 'CDE05G2884' => 'cde', 'CDE05G3072' => 'cde', 'Cfa008439' => 'cfa', 'Cfa008441' => 'cfa', 'Cfa008443' => 'cfa', 'Cfa008448' => 'cfa', 'Ciclev10005974m.g' => 'ccl', 'Ciclev10006006m.g' => 'ccl', 'Ciclev10006775m.g' => 'ccl', 'CiPaw.02G120400' => 'cil', 'CiPaw.02G120500' => 'cil', 'CiPaw.02G120600' => 'cil', 'ClCG05G004850' => 'cla', 'COL.COLO4_21566' => 'col', 'Cpa.g.sc44.124' => 'cpa', 'Cre07.g320400' => 'cre', 'Cre07.g320450' => 'cre', 'Cre08.g384650' => 'cre', 'Cre09.g393173' => 'cre', 'Cre09.g394325' => 'cre', 'Cre14.g626750' => 'cre', 'Cre16.g679250' => 'cre', 'CsaV3_3G012890' => 'csa', 'CSS0010865' => 'camsi', 'CSS0044338' => 'camsi', 'DCAR_002366' => 'dca', 'DCAR_030687' => 'dca', 'DCAR_030688' => 'dca', 'Dinv14047' => 'din', 'Dinv14048' => 'din', 'Duzib151G0105' => 'dzi', 'Duzib151G0114' => 'dzi', 'Duzib212G1029' => 'dzi', 'ECA232G3536' => 'eca', 'ECA240G0786' => 'eca', 'ECA240G1802' => 'eca', 'ECA240G3760' => 'eca', 'ECA240G3920' => 'eca', 'EL10Ac5g12536' => 'bvu', 'EL10Ac5g12537' => 'bvu', 'EL10Ac5g12538' => 'bvu', 'Eucgr.B01004' => 'egr', 'Eucgr.B01006' => 'egr', 'Eucgr.B01007' => 'egr', 'Eucgr.B01008' => 'egr', 'Eucgr.B01895' => 'egr', 'Eucgr.B01896' => 'egr', 'FAN04G1456' => 'fan', 'FAN08G1769' => 'fan', 'FAN08G2160' => 'fan', 'FAN13G2403' => 'fan', 'FAN13G3303' => 'fan', 'FAN15G2435' => 'fan', 'FAN17G0672' => 'fan', 'FAN17G2441' => 'fan', 'FAN18G1024' => 'fan', 'FAN22G1458' => 'fan', 'FAN24G0037' => 'fan', 'FAN24G0429' => 'fan', 'FAN24G2387' => 'fan', 'FAN27G2746' => 'fan', 'FvH4_2g20400' => 'fve', 'FvH4_2g20420' => 'fve', 'FvH4_2g20430' => 'fve', 'FvH4_4g01270' => 'fve', 'FvH4_4g01290' => 'fve', 'FvH4_4g01300' => 'fve', 'FvH4_4g01310' => 'fve', 'FvH4_4g01330' => 'fve', 'FvH4_5g09070' => 'fve', 'Glyma.10G243800' => 'gma', 'Glyma.20G150600' => 'gma', 'Gohir.A09G219200' => 'ghi', 'Gohir.A09G219300' => 'ghi', 'Gohir.D09G221400' => 'ghi', 'Gohir.D09G221500' => 'ghi', 'Gorai.006G242600' => 'gra', 'Gorai.006G242700' => 'gra', 'GSVIVG01018044001' => 'vvi', 'HanXRQChr03g0083821' => 'han', 'HanXRQChr03g0083841' => 'han', 'HanXRQChr03g0083881' => 'han', 'HanXRQChr03g0083901' => 'han', 'HanXRQChr03g0083921' => 'han', 'HanXRQChr03g0085331' => 'han', 'HanXRQChr03g0085361' => 'han', 'HanXRQChr03g0085411' => 'han', 'HanXRQChr03g0085421' => 'han', 'HanXRQChr03g0085431' => 'han', 'HanXRQChr08g0221991' => 'han', 'HanXRQChr11g0336061' => 'han', 'HanXRQChr11g0336411' => 'han', 'Haze_11234' => 'cav', 'Hma1.2p1_0549F.1_g177010' => 'hma', 'Hma1.2p1_0602F.1_g187630' => 'hma', 'Hund14876' => 'sun', 'Hund14879' => 'sun', 'Lalb_Chr06g0160741' => 'lal', 'Lalb_Chr21g0304781' => 'lal', 'Lj3A726G19' => 'lonja', 'Lj3A726T23' => 'lonja', 'Lj3A726T24' => 'lonja', 'Lj3A726T25' => 'lonja', 'Lj3A727T17' => 'lonja', 'Lj3C726T0' => 'lonja', 'Lj3C726T2' => 'lonja', 'Lj3P725T35' => 'lonja', 'Lj3P727T10' => 'lonja', 'Lj3P727T12' => 'lonja', 'Lj3P727T14' => 'lonja', 'Lj5g0023109' => 'lja', 'Lj6P646T44' => 'lonja', 'Lsat_1_v5_gn_6_75760' => 'lsa', 'Lsat_1_v5_gn_6_75800' => 'lsa', 'Lsat_1_v5_gn_6_75900' => 'lsa', 'Lsat_1_v5_gn_6_76240' => 'lsa', 'Lsat_1_v5_gn_6_76441' => 'lsa', 'Lsat_1_v5_gn_6_76700' => 'lsa', 'Lsat_1_v5_gn_6_76760' => 'lsa', 'Manes.15G033100' => 'mes', 'Mapoly0004s0074' => 'mpo', 'Mapoly0004s0075' => 'mpo', 'Mapoly0004s0163' => 'mpo', 'Mapoly0004s0164' => 'mpo', 'Mapoly0021s0018' => 'mpo', 'Mapoly0041s0136' => 'mpo', 'Mapoly0041s0137' => 'mpo', 'Mapoly0041s0138' => 'mpo', 'Mapoly0041s0139' => 'mpo', 'Mapoly0041s0141' => 'mpo', 'Mapoly0041s0142' => 'mpo', 'Mapoly0041s0143' => 'mpo', 'Mapoly0041s0144' => 'mpo', 'Mapoly0041s0145' => 'mpo', 'Mapoly0047s0106' => 'mpo', 'Mapoly0047s0108' => 'mpo', 'Mapoly0050s0051' => 'mpo', 'Mapoly0050s0052' => 'mpo', 'Mapoly0050s0053' => 'mpo', 'Mapoly0058s0013' => 'mpo', 'Mapoly0091s0078' => 'mpo', 'Mapoly0091s0079' => 'mpo', 'Mapoly0091s0080' => 'mpo', 'Mapoly0091s0081' => 'mpo', 'Mapoly0278s0004' => 'mpo', 'Mapoly0278s0005' => 'mpo', 'Mapoly0278s0006' => 'mpo', 'MBI11_g30648_MAGBIO' => 'mbi', 'MCO03G194' => 'mco', 'MCO03G590' => 'mco', 'MCO07G312' => 'mco', 'MCO10G318' => 'mco', 'MCO12G244' => 'mco', 'MCO13G148' => 'mco', 'MCO13G194' => 'mco', 'MCO16G238' => 'mco', 'MD06G1134100' => 'mdo', 'MD13G1200100' => 'mdo', 'MD13G1200300' => 'mdo', 'MD13G1200600' => 'mdo', 'MD14G1150400' => 'mdo', 'MD16G1200000' => 'mdo', 'Medtr1g102570' => 'mtr', 'Medtr1g102780' => 'mtr', 'Medtr1g102800' => 'mtr', 'Medtr1g102810' => 'mtr', 'Medtr1g102830' => 'mtr', 'MELO3C006499.2' => 'cme', 'Migut.G00385' => 'egut', 'MSTRG.4063' => 'ama', 'Nitab4.5_0000090g0260' => 'nta', 'Nitab4.5_0000977g0030' => 'nta', 'Nitab4.5_0002541g0040' => 'nta', 'Nitab4.5_0007068g0040' => 'nta', 'Nn005s41408' => 'nnu', 'Nn005s41410' => 'nnu', 'Oeu010310.1' => 'oeu', 'Oeu010311.1' => 'oeu', 'Oeu043472.1' => 'oeu', 'Os01g0246400' => 'osa', 'Os04g0267950' => 'osa', 'Os07g0178700' => 'osa', 'Os07g0178800' => 'osa', 'Peaxi162Scf00316g00046' => 'pax', 'Peaxi162Scf00316g00049' => 'pax', 'Peaxi162Scf00316g00059' => 'pax', 'Peaxi162Scf00316g00328' => 'pax', 'Peaxi162Scf00316g00329' => 'pax', 'Peaxi162Scf00316g00411' => 'pax', 'Peaxi162Scf00316g00521' => 'pax', 'Peaxi162Scf00492g00068' => 'pax', 'Peaxi162Scf35631g00002' => 'pax', 'PGR142G3720' => 'pgr', 'PGSC0003DMG400006442' => 'stu', 'Phvul.007G062000' => 'pvu', 'Potri.008G157750' => 'ptr', 'Potri.008G157900' => 'ptr', 'Potri.008G158000' => 'ptr', 'Potri.008G158200' => 'ptr', 'Pp3c11_7280' => 'ppa', 'Pp3c11_7980' => 'ppa', 'Pp3c12_19450' => 'ppa', 'Pp3c14_1480' => 'ppa', 'Pp3c14_1501' => 'ppa', 'Pp3c16_4900' => 'ppa', 'Pp3c16_5010' => 'ppa', 'Pp3c16_5060' => 'ppa', 'Pp3c19_18250' => 'ppa', 'Pp3c23_8530' => 'ppa', 'Pp3c23_8550' => 'ppa', 'Pp3c24_9670' => 'ppa', 'Pp3c2_21390' => 'ppa', 'Pp3c2_31380' => 'ppa', 'Pp3c3_16620' => 'ppa', 'Pp3c3_8090' => 'ppa', 'Pp3c3_8110' => 'ppa', 'Pp3c3_8130' => 'ppa', 'Pp3c3_8150' => 'ppa', 'Pp3c4_14320' => 'ppa', 'Pp3c6_2560' => 'ppa', 'Pp3c9_16700' => 'ppa', 'PRCOL_00000234' => 'pco', 'PRCOL_00000235' => 'pco', 'PRCOL_00000777' => 'pco', 'PRCOL_00002344' => 'pco', 'PRCOL_00002372' => 'pco', 'PRCOL_00006120' => 'pco', 'Prupe.1G021400' => 'ppe', 'Prupe.1G021500' => 'ppe', 'Prupe.1G021600' => 'ppe', 'Prupe.1G021700' => 'ppe', 'Prupe.1G021800' => 'ppe', 'Prupe.5G145100' => 'ppe', 'Psat6g204040' => 'psa', 'Psat6g204800' => 'psa', 'Psat6g204920' => 'psa', 'Psat6g204960' => 'psa', 'Psat6g205080' => 'psa', 'PSO017G0271' => 'pso', 'PSO017G1276' => 'pso', 'PSO017G1429' => 'pso', 'PSO017G1861' => 'pso', 'PSO017G2787' => 'pso', 'PSO017G4466' => 'pso', 'PSO017G5118' => 'pso', 'PSO017G5420' => 'pso', 'PSO063G3678' => 'pso', 'PSO210G0546' => 'pso', 'PSO317G0001' => 'pso', 'PSO357G0512' => 'pso', 'PSO478G2682' => 'pso', 'PSO647G0001' => 'pso', 'PSO675G0001' => 'pso', 'PSO675G2699' => 'pso', 'PSO675G2849' => 'pso', 'PSO675G4991' => 'pso', 'PSO689G0001' => 'pso', 'QL06p000916' => 'qlo', 'QL06p000921' => 'qlo', 'QL06p001398' => 'qlo', 'QL06p001407' => 'qlo', 'QL06p002031' => 'qlo', 'RcHm_v2.0_Chr4g0387791' => 'rch', 'RcHm_v2.0_Chr4g0387801' => 'rch', 'RcHm_v2.0_Chr6g0286501' => 'rch', 'RcHm_v2.0_Chr6g0286511' => 'rch', 'RcHm_v2.0_Chr6g0286521' => 'rch', 'RcHm_v2.0_Chr6g0286531' => 'rch', 'RcHm_v2.0_Chr7g0189141' => 'rch', 'Rhsim02G0028700' => 'rsi', 'Rhsim02G0028800' => 'rsi', 'Rhsim02G0028900' => 'rsi', 'Rhsim02G0029000' => 'rsi', 'Rhsim02G0029100' => 'rsi', 'Rhsim02G0029200' => 'rsi', 'Rhsim02G0029300' => 'rsi', 'Rhsim02G0029400' => 'rsi', 'Rhsim02G0029500' => 'rsi', 'Rhsim02G0029600' => 'rsi', 'RhsimUnG0024000' => 'rsi', 'RhsimUnG0024100' => 'rsi', 'RhsimUnG0024200' => 'rsi', 'RhsimUnG0024300' => 'rsi', 'RhsimUnG0024400' => 'rsi', 'RhsimUnG0024500' => 'rsi', 'RhsimUnG0024700' => 'rsi', 'RhsimUnG0024800' => 'rsi', 'RhsimUnG0024900' => 'rsi', 'RhsimUnG0025100' => 'rsi', 'Sabra08G0120200' => 'sbr', 'Sabra08G0120300' => 'sbr', 'Sabra08G0120500' => 'sbr', 'Sabra08G0120600' => 'sbr', 'Sabra10G0158900' => 'sbr', 'SalBow2G3492' => 'sbo', 'Sc13g0004760' => 'sci', 'Sc13g0004770' => 'sci', 'Sed0003417' => 'sed', 'Sed0019750' => 'sed', 'SEGI_03419' => 'sgi', 'SEGI_05907' => 'sgi', 'SEGI_10682' => 'sgi', 'SEGI_13528' => 'sgi', 'SEGI_16081' => 'sgi', 'SEGI_19370' => 'sgi', 'SEGI_21015' => 'sgi', 'SEGI_21944' => 'sgi', 'SEGI_32906' => 'sgi', 'SEGI_33093' => 'sgi', 'SEGI_36110' => 'sgi', 'SEGI_40397' => 'sgi', 'SGA_v2.0_scaffold191G40426' => 'sas', 'SGA_v2.0_scaffold353G49717' => 'sas', 'SGA_v2.0_scaffold50G18550' => 'sas', 'SMO119G0173' => 'smo', 'SMO172G0002' => 'smo', 'Solyc09g082690.3' => 'sly', 'Solyc09g082700.2' => 'sly', 'Sopen09g031550' => 'spe', 'Sopen09g031560' => 'spe', 'Sp3g20540' => 'spa', 'Sp7g07580' => 'spa', 'TAR134G0002' => 'tar', 'TAR236G0001' => 'tar', 'TAR365G0892' => 'tar', 'TAR636G0166' => 'tar', 'TAR636G0646' => 'tar', 'TAR636G0869' => 'tar', 'TAR636G1317' => 'tar', 'TAR636G1744' => 'tar', 'TAR636G3358' => 'tar', 'TAR636G3436' => 'tar', 'THA.LOC104803047' => 'tha', 'Thecc.04G238900' => 'tca', 'Thhalv10021557m.g' => 'esa', 'Thhalv10026318m.g' => 'esa', 'Thhalv10026335m.g' => 'esa', 'TPR.G17433' => 'tpr', 'TPR.G18915' => 'tpr', 'TPR.G26125' => 'tpr', 'TWI09G0677' => 'twi', 'TWI73G0287' => 'twi', 'unitig_748.g8326' => 'ugi', 'vmacro15370' => 'vma', 'vmacro15371' => 'vma', 'vmacro15372' => 'vma', 'vmacro15373' => 'vma', 'vmacro15374' => 'vma', 'VMungo0720G2826' => 'vmu', 'Zm00001eb116960' => 'zma', 'Zm00001eb301260' => 'zma', 'Zm00001eb301270' => 'zma' ) $gf_id = 'HOM05D001460' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001460' ) $data_identifier = 'HOM05D001460' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 4, 'aag' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 2, 'aox' => (int) 2, 'arhy' => (int) 4, 'ath' => (int) 2, 'atr' => (int) 1, 'acertr' => (int) 10, 'cqu' => (int) 4, 'bca' => (int) 11, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 1, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 1, 'ccan' => (int) 1, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 1, 'col' => (int) 1, 'cpa' => (int) 1, 'cre' => (int) 7, 'csa' => (int) 1, 'camsi' => (int) 2, 'dca' => (int) 3, 'din' => (int) 2, 'dzi' => (int) 3, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 14, 'fve' => (int) 9, 'gma' => (int) 2, 'ghi' => (int) 4, 'gra' => (int) 2, 'vvi' => (int) 1, 'han' => (int) 13, 'cav' => (int) 1, 'hma' => (int) 2, 'sun' => (int) 2, 'lal' => (int) 2, 'lonja' => (int) 12, 'lja' => (int) 1, 'lsa' => (int) 7, 'mes' => (int) 1, 'mpo' => (int) 27, 'mbi' => (int) 1, 'mco' => (int) 8, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 1, 'egut' => (int) 1, 'ama' => (int) 1, 'nta' => (int) 4, 'nnu' => (int) 2, 'oeu' => (int) 3, 'osa' => (int) 4, 'pax' => (int) 9, 'pgr' => (int) 1, 'stu' => (int) 1, 'pvu' => (int) 1, 'ptr' => (int) 4, 'ppa' => (int) 22, 'pco' => (int) 6, 'ppe' => (int) 6, 'psa' => (int) 5, 'pso' => (int) 19, 'qlo' => (int) 5, 'rch' => (int) 7, 'rsi' => (int) 20, 'sbr' => (int) 5, 'sbo' => (int) 1, 'sci' => (int) 2, 'sed' => (int) 2, 'sgi' => (int) 12, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 2, 'tar' => (int) 10, 'tha' => (int) 1, 'tca' => (int) 1, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 2, 'ugi' => (int) 1, 'vma' => (int) 5, 'vmu' => (int) 1, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb301270' $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' => 'HOM05D001460', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '433', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p22980' => 'bna', 'A01p32340' => 'bna', 'A03p42970' => 'bna', 'A05p25880' => 'bna', 'Aa31LG8G9320' => 'aar', 'Aa31LG8G9330' => 'aar', 'Aa31LG8G9340' => 'aar', 'Aa31sc221G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1034' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1528' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.829' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2222' => 'aag', 'Ah.12g058830' => 'amhyb', 'Ah.12g058840' => 'amhyb', 'AL3G37160' => 'aly', 'AL7G41310' => 'aly', 'Aqoxy5G00395' => 'aox', 'Aqoxy5G00396' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0C8NZA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5185HY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JZ1PRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MD3LS0' => 'arhy', 'AT3G22840' => 'ath', 'AT4G14690' => 'ath', 'ATR0665G054' => 'atr', 'Atru.chr4.2344' => 'acertr', 'Atru.chr4.2346' => 'acertr', 'Atru.chr4.2347' => 'acertr', 'Atru.chr4.2348' => 'acertr', 'Atru.chr4.2355' => 'acertr', 'Atru.chr4.2356' => 'acertr', 'Atru.chr4.2358' => 'acertr', 'Atru.chr4.2359' => 'acertr', 'Atru.chr4.2360' => 'acertr', 'Atru.chr4.2361' => 'acertr', 'AUR62030476' => 'cqu', 'AUR62030478' => 'cqu', 'AUR62030819' => 'cqu', 'AUR62030820' => 'cqu', 'BcaB03g14648' => 'bca', 'BcaB04g20492' => 'bca', 'BcaB06g26399' => 'bca', 'BcaC01g03416' => 'bca', 'BcaC01g03419' => 'bca', 'BcaC01g03421' => 'bca', 'BcaC01g03424' => 'bca', 'BcaC05g28012' => 'bca', 'BcaC09g49212' => 'bca', 'BcaC09g50140' => 'bca', 'BcaNung00346' => 'bca', 'BolC1t02785H' => 'bol', 'BolC1t04095H' => 'bol', 'BolC3t17545H' => 'bol', 'BolC5t32769H' => 'bol', 'BraA01t02211Z' => 'bra', 'BraA01t03359Z' => 'bra', 'BraA03t13441Z' => 'bra', 'BraA05t21476Z' => 'bra', 'C01p28420' => 'bna', 'C01p41350' => 'bna', 'C03p52750' => 'bna', 'C03p52780' => 'bna', 'C05p40270' => 'bna', 'CAN.G1437.9' => 'can', 'CANSAT78G0035' => 'cansat', 'CANSAT78G1036' => 'cansat', 'CANSAT78G2272' => 'cansat', 'CANSAT78G2478' => 'cansat', 'CARHR098700' => 'chi', 'CARHR221120' => 'chi', 'CARHR221150' => 'chi', 'Carub.0003s2297' => 'cru', 'Carub.0007s2749' => 'cru', 'Carub.0007s2750' => 'cru', 'Carub.0007s2751' => 'cru', 'Ca_10849_v3' => 'car', 'Cc03_g04300' => 'ccan', 'CDE02G3648' => 'cde', 'CDE05G0060' => 'cde', 'CDE05G0692' => 'cde', 'CDE05G2285' => 'cde', 'CDE05G2884' => 'cde', 'CDE05G3072' => 'cde', 'Cfa008439' => 'cfa', 'Cfa008441' => 'cfa', 'Cfa008443' => 'cfa', 'Cfa008448' => 'cfa', 'Ciclev10005974m.g' => 'ccl', 'Ciclev10006006m.g' => 'ccl', 'Ciclev10006775m.g' => 'ccl', 'CiPaw.02G120400' => 'cil', 'CiPaw.02G120500' => 'cil', 'CiPaw.02G120600' => 'cil', 'ClCG05G004850' => 'cla', 'COL.COLO4_21566' => 'col', 'Cpa.g.sc44.124' => 'cpa', 'Cre07.g320400' => 'cre', 'Cre07.g320450' => 'cre', 'Cre08.g384650' => 'cre', 'Cre09.g393173' => 'cre', 'Cre09.g394325' => 'cre', 'Cre14.g626750' => 'cre', 'Cre16.g679250' => 'cre', 'CsaV3_3G012890' => 'csa', 'CSS0010865' => 'camsi', 'CSS0044338' => 'camsi', 'DCAR_002366' => 'dca', 'DCAR_030687' => 'dca', 'DCAR_030688' => 'dca', 'Dinv14047' => 'din', 'Dinv14048' => 'din', 'Duzib151G0105' => 'dzi', 'Duzib151G0114' => 'dzi', 'Duzib212G1029' => 'dzi', 'ECA232G3536' => 'eca', 'ECA240G0786' => 'eca', 'ECA240G1802' => 'eca', 'ECA240G3760' => 'eca', 'ECA240G3920' => 'eca', 'EL10Ac5g12536' => 'bvu', 'EL10Ac5g12537' => 'bvu', 'EL10Ac5g12538' => 'bvu', 'Eucgr.B01004' => 'egr', 'Eucgr.B01006' => 'egr', 'Eucgr.B01007' => 'egr', 'Eucgr.B01008' => 'egr', 'Eucgr.B01895' => 'egr', 'Eucgr.B01896' => 'egr', 'FAN04G1456' => 'fan', 'FAN08G1769' => 'fan', 'FAN08G2160' => 'fan', 'FAN13G2403' => 'fan', 'FAN13G3303' => 'fan', 'FAN15G2435' => 'fan', 'FAN17G0672' => 'fan', 'FAN17G2441' => 'fan', 'FAN18G1024' => 'fan', 'FAN22G1458' => 'fan', 'FAN24G0037' => 'fan', 'FAN24G0429' => 'fan', 'FAN24G2387' => 'fan', 'FAN27G2746' => 'fan', 'FvH4_2g20400' => 'fve', 'FvH4_2g20420' => 'fve', 'FvH4_2g20430' => 'fve', 'FvH4_4g01270' => 'fve', 'FvH4_4g01290' => 'fve', 'FvH4_4g01300' => 'fve', 'FvH4_4g01310' => 'fve', 'FvH4_4g01330' => 'fve', 'FvH4_5g09070' => 'fve', 'Glyma.10G243800' => 'gma', 'Glyma.20G150600' => 'gma', 'Gohir.A09G219200' => 'ghi', 'Gohir.A09G219300' => 'ghi', 'Gohir.D09G221400' => 'ghi', 'Gohir.D09G221500' => 'ghi', 'Gorai.006G242600' => 'gra', 'Gorai.006G242700' => 'gra', 'GSVIVG01018044001' => 'vvi', 'HanXRQChr03g0083821' => 'han', 'HanXRQChr03g0083841' => 'han', 'HanXRQChr03g0083881' => 'han', 'HanXRQChr03g0083901' => 'han', 'HanXRQChr03g0083921' => 'han', 'HanXRQChr03g0085331' => 'han', 'HanXRQChr03g0085361' => 'han', 'HanXRQChr03g0085411' => 'han', 'HanXRQChr03g0085421' => 'han', 'HanXRQChr03g0085431' => 'han', 'HanXRQChr08g0221991' => 'han', 'HanXRQChr11g0336061' => 'han', 'HanXRQChr11g0336411' => 'han', 'Haze_11234' => 'cav', 'Hma1.2p1_0549F.1_g177010' => 'hma', 'Hma1.2p1_0602F.1_g187630' => 'hma', 'Hund14876' => 'sun', 'Hund14879' => 'sun', 'Lalb_Chr06g0160741' => 'lal', 'Lalb_Chr21g0304781' => 'lal', 'Lj3A726G19' => 'lonja', 'Lj3A726T23' => 'lonja', 'Lj3A726T24' => 'lonja', 'Lj3A726T25' => 'lonja', 'Lj3A727T17' => 'lonja', 'Lj3C726T0' => 'lonja', 'Lj3C726T2' => 'lonja', 'Lj3P725T35' => 'lonja', 'Lj3P727T10' => 'lonja', 'Lj3P727T12' => 'lonja', 'Lj3P727T14' => 'lonja', 'Lj5g0023109' => 'lja', 'Lj6P646T44' => 'lonja', 'Lsat_1_v5_gn_6_75760' => 'lsa', 'Lsat_1_v5_gn_6_75800' => 'lsa', 'Lsat_1_v5_gn_6_75900' => 'lsa', 'Lsat_1_v5_gn_6_76240' => 'lsa', 'Lsat_1_v5_gn_6_76441' => 'lsa', 'Lsat_1_v5_gn_6_76700' => 'lsa', 'Lsat_1_v5_gn_6_76760' => 'lsa', 'Manes.15G033100' => 'mes', 'Mapoly0004s0074' => 'mpo', 'Mapoly0004s0075' => 'mpo', 'Mapoly0004s0163' => 'mpo', 'Mapoly0004s0164' => 'mpo', 'Mapoly0021s0018' => 'mpo', 'Mapoly0041s0136' => 'mpo', 'Mapoly0041s0137' => 'mpo', 'Mapoly0041s0138' => 'mpo', 'Mapoly0041s0139' => 'mpo', 'Mapoly0041s0141' => 'mpo', 'Mapoly0041s0142' => 'mpo', 'Mapoly0041s0143' => 'mpo', 'Mapoly0041s0144' => 'mpo', 'Mapoly0041s0145' => 'mpo', 'Mapoly0047s0106' => 'mpo', 'Mapoly0047s0108' => 'mpo', 'Mapoly0050s0051' => 'mpo', 'Mapoly0050s0052' => 'mpo', 'Mapoly0050s0053' => 'mpo', 'Mapoly0058s0013' => 'mpo', 'Mapoly0091s0078' => 'mpo', 'Mapoly0091s0079' => 'mpo', 'Mapoly0091s0080' => 'mpo', 'Mapoly0091s0081' => 'mpo', 'Mapoly0278s0004' => 'mpo', 'Mapoly0278s0005' => 'mpo', 'Mapoly0278s0006' => 'mpo', 'MBI11_g30648_MAGBIO' => 'mbi', 'MCO03G194' => 'mco', 'MCO03G590' => 'mco', 'MCO07G312' => 'mco', 'MCO10G318' => 'mco', 'MCO12G244' => 'mco', 'MCO13G148' => 'mco', 'MCO13G194' => 'mco', 'MCO16G238' => 'mco', 'MD06G1134100' => 'mdo', 'MD13G1200100' => 'mdo', 'MD13G1200300' => 'mdo', 'MD13G1200600' => 'mdo', 'MD14G1150400' => 'mdo', 'MD16G1200000' => 'mdo', 'Medtr1g102570' => 'mtr', 'Medtr1g102780' => 'mtr', 'Medtr1g102800' => 'mtr', 'Medtr1g102810' => 'mtr', 'Medtr1g102830' => 'mtr', 'MELO3C006499.2' => 'cme', 'Migut.G00385' => 'egut', 'MSTRG.4063' => 'ama', 'Nitab4.5_0000090g0260' => 'nta', 'Nitab4.5_0000977g0030' => 'nta', 'Nitab4.5_0002541g0040' => 'nta', 'Nitab4.5_0007068g0040' => 'nta', 'Nn005s41408' => 'nnu', 'Nn005s41410' => 'nnu', 'Oeu010310.1' => 'oeu', 'Oeu010311.1' => 'oeu', 'Oeu043472.1' => 'oeu', 'Os01g0246400' => 'osa', 'Os04g0267950' => 'osa', 'Os07g0178700' => 'osa', 'Os07g0178800' => 'osa', 'Peaxi162Scf00316g00046' => 'pax', 'Peaxi162Scf00316g00049' => 'pax', 'Peaxi162Scf00316g00059' => 'pax', 'Peaxi162Scf00316g00328' => 'pax', 'Peaxi162Scf00316g00329' => 'pax', 'Peaxi162Scf00316g00411' => 'pax', 'Peaxi162Scf00316g00521' => 'pax', 'Peaxi162Scf00492g00068' => 'pax', 'Peaxi162Scf35631g00002' => 'pax', 'PGR142G3720' => 'pgr', 'PGSC0003DMG400006442' => 'stu', 'Phvul.007G062000' => 'pvu', 'Potri.008G157750' => 'ptr', 'Potri.008G157900' => 'ptr', 'Potri.008G158000' => 'ptr', 'Potri.008G158200' => 'ptr', 'Pp3c11_7280' => 'ppa', 'Pp3c11_7980' => 'ppa', 'Pp3c12_19450' => 'ppa', 'Pp3c14_1480' => 'ppa', 'Pp3c14_1501' => 'ppa', 'Pp3c16_4900' => 'ppa', 'Pp3c16_5010' => 'ppa', 'Pp3c16_5060' => 'ppa', 'Pp3c19_18250' => 'ppa', 'Pp3c23_8530' => 'ppa', 'Pp3c23_8550' => 'ppa', 'Pp3c24_9670' => 'ppa', 'Pp3c2_21390' => 'ppa', 'Pp3c2_31380' => 'ppa', 'Pp3c3_16620' => 'ppa', 'Pp3c3_8090' => 'ppa', 'Pp3c3_8110' => 'ppa', 'Pp3c3_8130' => 'ppa', 'Pp3c3_8150' => 'ppa', 'Pp3c4_14320' => 'ppa', 'Pp3c6_2560' => 'ppa', 'Pp3c9_16700' => 'ppa', 'PRCOL_00000234' => 'pco', 'PRCOL_00000235' => 'pco', 'PRCOL_00000777' => 'pco', 'PRCOL_00002344' => 'pco', 'PRCOL_00002372' => 'pco', 'PRCOL_00006120' => 'pco', 'Prupe.1G021400' => 'ppe', 'Prupe.1G021500' => 'ppe', 'Prupe.1G021600' => 'ppe', 'Prupe.1G021700' => 'ppe', 'Prupe.1G021800' => 'ppe', 'Prupe.5G145100' => 'ppe', 'Psat6g204040' => 'psa', 'Psat6g204800' => 'psa', 'Psat6g204920' => 'psa', 'Psat6g204960' => 'psa', 'Psat6g205080' => 'psa', 'PSO017G0271' => 'pso', 'PSO017G1276' => 'pso', 'PSO017G1429' => 'pso', 'PSO017G1861' => 'pso', 'PSO017G2787' => 'pso', 'PSO017G4466' => 'pso', 'PSO017G5118' => 'pso', 'PSO017G5420' => 'pso', 'PSO063G3678' => 'pso', 'PSO210G0546' => 'pso', 'PSO317G0001' => 'pso', 'PSO357G0512' => 'pso', 'PSO478G2682' => 'pso', 'PSO647G0001' => 'pso', 'PSO675G0001' => 'pso', 'PSO675G2699' => 'pso', 'PSO675G2849' => 'pso', 'PSO675G4991' => 'pso', 'PSO689G0001' => 'pso', 'QL06p000916' => 'qlo', 'QL06p000921' => 'qlo', 'QL06p001398' => 'qlo', 'QL06p001407' => 'qlo', 'QL06p002031' => 'qlo', 'RcHm_v2.0_Chr4g0387791' => 'rch', 'RcHm_v2.0_Chr4g0387801' => 'rch', 'RcHm_v2.0_Chr6g0286501' => 'rch', 'RcHm_v2.0_Chr6g0286511' => 'rch', 'RcHm_v2.0_Chr6g0286521' => 'rch', 'RcHm_v2.0_Chr6g0286531' => 'rch', 'RcHm_v2.0_Chr7g0189141' => 'rch', 'Rhsim02G0028700' => 'rsi', 'Rhsim02G0028800' => 'rsi', 'Rhsim02G0028900' => 'rsi', 'Rhsim02G0029000' => 'rsi', 'Rhsim02G0029100' => 'rsi', 'Rhsim02G0029200' => 'rsi', 'Rhsim02G0029300' => 'rsi', 'Rhsim02G0029400' => 'rsi', 'Rhsim02G0029500' => 'rsi', 'Rhsim02G0029600' => 'rsi', 'RhsimUnG0024000' => 'rsi', 'RhsimUnG0024100' => 'rsi', 'RhsimUnG0024200' => 'rsi', 'RhsimUnG0024300' => 'rsi', 'RhsimUnG0024400' => 'rsi', 'RhsimUnG0024500' => 'rsi', 'RhsimUnG0024700' => 'rsi', 'RhsimUnG0024800' => 'rsi', 'RhsimUnG0024900' => 'rsi', 'RhsimUnG0025100' => 'rsi', 'Sabra08G0120200' => 'sbr', 'Sabra08G0120300' => 'sbr', 'Sabra08G0120500' => 'sbr', 'Sabra08G0120600' => 'sbr', 'Sabra10G0158900' => 'sbr', 'SalBow2G3492' => 'sbo', 'Sc13g0004760' => 'sci', 'Sc13g0004770' => 'sci', 'Sed0003417' => 'sed', 'Sed0019750' => 'sed', 'SEGI_03419' => 'sgi', 'SEGI_05907' => 'sgi', 'SEGI_10682' => 'sgi', 'SEGI_13528' => 'sgi', 'SEGI_16081' => 'sgi', 'SEGI_19370' => 'sgi', 'SEGI_21015' => 'sgi', 'SEGI_21944' => 'sgi', 'SEGI_32906' => 'sgi', 'SEGI_33093' => 'sgi', 'SEGI_36110' => 'sgi', 'SEGI_40397' => 'sgi', 'SGA_v2.0_scaffold191G40426' => 'sas', 'SGA_v2.0_scaffold353G49717' => 'sas', 'SGA_v2.0_scaffold50G18550' => 'sas', 'SMO119G0173' => 'smo', 'SMO172G0002' => 'smo', 'Solyc09g082690.3' => 'sly', 'Solyc09g082700.2' => 'sly', 'Sopen09g031550' => 'spe', 'Sopen09g031560' => 'spe', 'Sp3g20540' => 'spa', 'Sp7g07580' => 'spa', 'TAR134G0002' => 'tar', 'TAR236G0001' => 'tar', 'TAR365G0892' => 'tar', 'TAR636G0166' => 'tar', 'TAR636G0646' => 'tar', 'TAR636G0869' => 'tar', 'TAR636G1317' => 'tar', 'TAR636G1744' => 'tar', 'TAR636G3358' => 'tar', 'TAR636G3436' => 'tar', 'THA.LOC104803047' => 'tha', 'Thecc.04G238900' => 'tca', 'Thhalv10021557m.g' => 'esa', 'Thhalv10026318m.g' => 'esa', 'Thhalv10026335m.g' => 'esa', 'TPR.G17433' => 'tpr', 'TPR.G18915' => 'tpr', 'TPR.G26125' => 'tpr', 'TWI09G0677' => 'twi', 'TWI73G0287' => 'twi', 'unitig_748.g8326' => 'ugi', 'vmacro15370' => 'vma', 'vmacro15371' => 'vma', 'vmacro15372' => 'vma', 'vmacro15373' => 'vma', 'vmacro15374' => 'vma', 'VMungo0720G2826' => 'vmu', 'Zm00001eb116960' => 'zma', 'Zm00001eb301260' => 'zma', 'Zm00001eb301270' => 'zma' ), 'gf_id' => 'HOM05D001460', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001460' ), 'data_identifier' => 'HOM05D001460', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001460', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '433', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p22980' => 'bna', 'A01p32340' => 'bna', 'A03p42970' => 'bna', 'A05p25880' => 'bna', 'Aa31LG8G9320' => 'aar', 'Aa31LG8G9330' => 'aar', 'Aa31LG8G9340' => 'aar', 'Aa31sc221G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1034' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1528' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.829' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2222' => 'aag', 'Ah.12g058830' => 'amhyb', 'Ah.12g058840' => 'amhyb', 'AL3G37160' => 'aly', 'AL7G41310' => 'aly', 'Aqoxy5G00395' => 'aox', 'Aqoxy5G00396' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0C8NZA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5185HY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JZ1PRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MD3LS0' => 'arhy', 'AT3G22840' => 'ath', 'AT4G14690' => 'ath', 'ATR0665G054' => 'atr', 'Atru.chr4.2344' => 'acertr', 'Atru.chr4.2346' => 'acertr', 'Atru.chr4.2347' => 'acertr', 'Atru.chr4.2348' => 'acertr', 'Atru.chr4.2355' => 'acertr', 'Atru.chr4.2356' => 'acertr', 'Atru.chr4.2358' => 'acertr', 'Atru.chr4.2359' => 'acertr', 'Atru.chr4.2360' => 'acertr', 'Atru.chr4.2361' => 'acertr', 'AUR62030476' => 'cqu', 'AUR62030478' => 'cqu', 'AUR62030819' => 'cqu', 'AUR62030820' => 'cqu', 'BcaB03g14648' => 'bca', 'BcaB04g20492' => 'bca', 'BcaB06g26399' => 'bca', 'BcaC01g03416' => 'bca', 'BcaC01g03419' => 'bca', 'BcaC01g03421' => 'bca', 'BcaC01g03424' => 'bca', 'BcaC05g28012' => 'bca', 'BcaC09g49212' => 'bca', 'BcaC09g50140' => 'bca', 'BcaNung00346' => 'bca', 'BolC1t02785H' => 'bol', 'BolC1t04095H' => 'bol', 'BolC3t17545H' => 'bol', 'BolC5t32769H' => 'bol', 'BraA01t02211Z' => 'bra', 'BraA01t03359Z' => 'bra', 'BraA03t13441Z' => 'bra', 'BraA05t21476Z' => 'bra', 'C01p28420' => 'bna', 'C01p41350' => 'bna', 'C03p52750' => 'bna', 'C03p52780' => 'bna', 'C05p40270' => 'bna', 'CAN.G1437.9' => 'can', 'CANSAT78G0035' => 'cansat', 'CANSAT78G1036' => 'cansat', 'CANSAT78G2272' => 'cansat', 'CANSAT78G2478' => 'cansat', 'CARHR098700' => 'chi', 'CARHR221120' => 'chi', 'CARHR221150' => 'chi', 'Carub.0003s2297' => 'cru', 'Carub.0007s2749' => 'cru', 'Carub.0007s2750' => 'cru', 'Carub.0007s2751' => 'cru', 'Ca_10849_v3' => 'car', 'Cc03_g04300' => 'ccan', 'CDE02G3648' => 'cde', 'CDE05G0060' => 'cde', 'CDE05G0692' => 'cde', 'CDE05G2285' => 'cde', 'CDE05G2884' => 'cde', 'CDE05G3072' => 'cde', 'Cfa008439' => 'cfa', 'Cfa008441' => 'cfa', 'Cfa008443' => 'cfa', 'Cfa008448' => 'cfa', 'Ciclev10005974m.g' => 'ccl', 'Ciclev10006006m.g' => 'ccl', 'Ciclev10006775m.g' => 'ccl', 'CiPaw.02G120400' => 'cil', 'CiPaw.02G120500' => 'cil', 'CiPaw.02G120600' => 'cil', 'ClCG05G004850' => 'cla', 'COL.COLO4_21566' => 'col', 'Cpa.g.sc44.124' => 'cpa', 'Cre07.g320400' => 'cre', 'Cre07.g320450' => 'cre', 'Cre08.g384650' => 'cre', 'Cre09.g393173' => 'cre', 'Cre09.g394325' => 'cre', 'Cre14.g626750' => 'cre', 'Cre16.g679250' => 'cre', 'CsaV3_3G012890' => 'csa', 'CSS0010865' => 'camsi', 'CSS0044338' => 'camsi', 'DCAR_002366' => 'dca', 'DCAR_030687' => 'dca', 'DCAR_030688' => 'dca', 'Dinv14047' => 'din', 'Dinv14048' => 'din', 'Duzib151G0105' => 'dzi', 'Duzib151G0114' => 'dzi', 'Duzib212G1029' => 'dzi', 'ECA232G3536' => 'eca', 'ECA240G0786' => 'eca', 'ECA240G1802' => 'eca', 'ECA240G3760' => 'eca', 'ECA240G3920' => 'eca', 'EL10Ac5g12536' => 'bvu', 'EL10Ac5g12537' => 'bvu', 'EL10Ac5g12538' => 'bvu', 'Eucgr.B01004' => 'egr', 'Eucgr.B01006' => 'egr', 'Eucgr.B01007' => 'egr', 'Eucgr.B01008' => 'egr', 'Eucgr.B01895' => 'egr', 'Eucgr.B01896' => 'egr', 'FAN04G1456' => 'fan', 'FAN08G1769' => 'fan', 'FAN08G2160' => 'fan', 'FAN13G2403' => 'fan', 'FAN13G3303' => 'fan', 'FAN15G2435' => 'fan', 'FAN17G0672' => 'fan', 'FAN17G2441' => 'fan', 'FAN18G1024' => 'fan', 'FAN22G1458' => 'fan', 'FAN24G0037' => 'fan', 'FAN24G0429' => 'fan', 'FAN24G2387' => 'fan', 'FAN27G2746' => 'fan', 'FvH4_2g20400' => 'fve', 'FvH4_2g20420' => 'fve', 'FvH4_2g20430' => 'fve', 'FvH4_4g01270' => 'fve', 'FvH4_4g01290' => 'fve', 'FvH4_4g01300' => 'fve', 'FvH4_4g01310' => 'fve', 'FvH4_4g01330' => 'fve', 'FvH4_5g09070' => 'fve', 'Glyma.10G243800' => 'gma', 'Glyma.20G150600' => 'gma', 'Gohir.A09G219200' => 'ghi', 'Gohir.A09G219300' => 'ghi', 'Gohir.D09G221400' => 'ghi', 'Gohir.D09G221500' => 'ghi', 'Gorai.006G242600' => 'gra', 'Gorai.006G242700' => 'gra', 'GSVIVG01018044001' => 'vvi', 'HanXRQChr03g0083821' => 'han', 'HanXRQChr03g0083841' => 'han', 'HanXRQChr03g0083881' => 'han', 'HanXRQChr03g0083901' => 'han', 'HanXRQChr03g0083921' => 'han', 'HanXRQChr03g0085331' => 'han', 'HanXRQChr03g0085361' => 'han', 'HanXRQChr03g0085411' => 'han', 'HanXRQChr03g0085421' => 'han', 'HanXRQChr03g0085431' => 'han', 'HanXRQChr08g0221991' => 'han', 'HanXRQChr11g0336061' => 'han', 'HanXRQChr11g0336411' => 'han', 'Haze_11234' => 'cav', 'Hma1.2p1_0549F.1_g177010' => 'hma', 'Hma1.2p1_0602F.1_g187630' => 'hma', 'Hund14876' => 'sun', 'Hund14879' => 'sun', 'Lalb_Chr06g0160741' => 'lal', 'Lalb_Chr21g0304781' => 'lal', 'Lj3A726G19' => 'lonja', 'Lj3A726T23' => 'lonja', 'Lj3A726T24' => 'lonja', 'Lj3A726T25' => 'lonja', 'Lj3A727T17' => 'lonja', 'Lj3C726T0' => 'lonja', 'Lj3C726T2' => 'lonja', 'Lj3P725T35' => 'lonja', 'Lj3P727T10' => 'lonja', 'Lj3P727T12' => 'lonja', 'Lj3P727T14' => 'lonja', 'Lj5g0023109' => 'lja', 'Lj6P646T44' => 'lonja', 'Lsat_1_v5_gn_6_75760' => 'lsa', 'Lsat_1_v5_gn_6_75800' => 'lsa', 'Lsat_1_v5_gn_6_75900' => 'lsa', 'Lsat_1_v5_gn_6_76240' => 'lsa', 'Lsat_1_v5_gn_6_76441' => 'lsa', 'Lsat_1_v5_gn_6_76700' => 'lsa', 'Lsat_1_v5_gn_6_76760' => 'lsa', 'Manes.15G033100' => 'mes', 'Mapoly0004s0074' => 'mpo', 'Mapoly0004s0075' => 'mpo', 'Mapoly0004s0163' => 'mpo', 'Mapoly0004s0164' => 'mpo', 'Mapoly0021s0018' => 'mpo', 'Mapoly0041s0136' => 'mpo', 'Mapoly0041s0137' => 'mpo', 'Mapoly0041s0138' => 'mpo', 'Mapoly0041s0139' => 'mpo', 'Mapoly0041s0141' => 'mpo', 'Mapoly0041s0142' => 'mpo', 'Mapoly0041s0143' => 'mpo', 'Mapoly0041s0144' => 'mpo', 'Mapoly0041s0145' => 'mpo', 'Mapoly0047s0106' => 'mpo', 'Mapoly0047s0108' => 'mpo', 'Mapoly0050s0051' => 'mpo', 'Mapoly0050s0052' => 'mpo', 'Mapoly0050s0053' => 'mpo', 'Mapoly0058s0013' => 'mpo', 'Mapoly0091s0078' => 'mpo', 'Mapoly0091s0079' => 'mpo', 'Mapoly0091s0080' => 'mpo', 'Mapoly0091s0081' => 'mpo', 'Mapoly0278s0004' => 'mpo', 'Mapoly0278s0005' => 'mpo', 'Mapoly0278s0006' => 'mpo', 'MBI11_g30648_MAGBIO' => 'mbi', 'MCO03G194' => 'mco', 'MCO03G590' => 'mco', 'MCO07G312' => 'mco', 'MCO10G318' => 'mco', 'MCO12G244' => 'mco', 'MCO13G148' => 'mco', 'MCO13G194' => 'mco', 'MCO16G238' => 'mco', 'MD06G1134100' => 'mdo', 'MD13G1200100' => 'mdo', 'MD13G1200300' => 'mdo', 'MD13G1200600' => 'mdo', 'MD14G1150400' => 'mdo', 'MD16G1200000' => 'mdo', 'Medtr1g102570' => 'mtr', 'Medtr1g102780' => 'mtr', 'Medtr1g102800' => 'mtr', 'Medtr1g102810' => 'mtr', 'Medtr1g102830' => 'mtr', 'MELO3C006499.2' => 'cme', 'Migut.G00385' => 'egut', 'MSTRG.4063' => 'ama', 'Nitab4.5_0000090g0260' => 'nta', 'Nitab4.5_0000977g0030' => 'nta', 'Nitab4.5_0002541g0040' => 'nta', 'Nitab4.5_0007068g0040' => 'nta', 'Nn005s41408' => 'nnu', 'Nn005s41410' => 'nnu', 'Oeu010310.1' => 'oeu', 'Oeu010311.1' => 'oeu', 'Oeu043472.1' => 'oeu', 'Os01g0246400' => 'osa', 'Os04g0267950' => 'osa', 'Os07g0178700' => 'osa', 'Os07g0178800' => 'osa', 'Peaxi162Scf00316g00046' => 'pax', 'Peaxi162Scf00316g00049' => 'pax', 'Peaxi162Scf00316g00059' => 'pax', 'Peaxi162Scf00316g00328' => 'pax', 'Peaxi162Scf00316g00329' => 'pax', 'Peaxi162Scf00316g00411' => 'pax', 'Peaxi162Scf00316g00521' => 'pax', 'Peaxi162Scf00492g00068' => 'pax', 'Peaxi162Scf35631g00002' => 'pax', 'PGR142G3720' => 'pgr', 'PGSC0003DMG400006442' => 'stu', 'Phvul.007G062000' => 'pvu', 'Potri.008G157750' => 'ptr', 'Potri.008G157900' => 'ptr', 'Potri.008G158000' => 'ptr', 'Potri.008G158200' => 'ptr', 'Pp3c11_7280' => 'ppa', 'Pp3c11_7980' => 'ppa', 'Pp3c12_19450' => 'ppa', 'Pp3c14_1480' => 'ppa', 'Pp3c14_1501' => 'ppa', 'Pp3c16_4900' => 'ppa', 'Pp3c16_5010' => 'ppa', 'Pp3c16_5060' => 'ppa', 'Pp3c19_18250' => 'ppa', 'Pp3c23_8530' => 'ppa', 'Pp3c23_8550' => 'ppa', 'Pp3c24_9670' => 'ppa', 'Pp3c2_21390' => 'ppa', 'Pp3c2_31380' => 'ppa', 'Pp3c3_16620' => 'ppa', 'Pp3c3_8090' => 'ppa', 'Pp3c3_8110' => 'ppa', 'Pp3c3_8130' => 'ppa', 'Pp3c3_8150' => 'ppa', 'Pp3c4_14320' => 'ppa', 'Pp3c6_2560' => 'ppa', 'Pp3c9_16700' => 'ppa', 'PRCOL_00000234' => 'pco', 'PRCOL_00000235' => 'pco', 'PRCOL_00000777' => 'pco', 'PRCOL_00002344' => 'pco', 'PRCOL_00002372' => 'pco', 'PRCOL_00006120' => 'pco', 'Prupe.1G021400' => 'ppe', 'Prupe.1G021500' => 'ppe', 'Prupe.1G021600' => 'ppe', 'Prupe.1G021700' => 'ppe', 'Prupe.1G021800' => 'ppe', 'Prupe.5G145100' => 'ppe', 'Psat6g204040' => 'psa', 'Psat6g204800' => 'psa', 'Psat6g204920' => 'psa', 'Psat6g204960' => 'psa', 'Psat6g205080' => 'psa', 'PSO017G0271' => 'pso', 'PSO017G1276' => 'pso', 'PSO017G1429' => 'pso', 'PSO017G1861' => 'pso', 'PSO017G2787' => 'pso', 'PSO017G4466' => 'pso', 'PSO017G5118' => 'pso', 'PSO017G5420' => 'pso', 'PSO063G3678' => 'pso', 'PSO210G0546' => 'pso', 'PSO317G0001' => 'pso', 'PSO357G0512' => 'pso', 'PSO478G2682' => 'pso', 'PSO647G0001' => 'pso', 'PSO675G0001' => 'pso', 'PSO675G2699' => 'pso', 'PSO675G2849' => 'pso', 'PSO675G4991' => 'pso', 'PSO689G0001' => 'pso', 'QL06p000916' => 'qlo', 'QL06p000921' => 'qlo', 'QL06p001398' => 'qlo', 'QL06p001407' => 'qlo', 'QL06p002031' => 'qlo', 'RcHm_v2.0_Chr4g0387791' => 'rch', 'RcHm_v2.0_Chr4g0387801' => 'rch', 'RcHm_v2.0_Chr6g0286501' => 'rch', 'RcHm_v2.0_Chr6g0286511' => 'rch', 'RcHm_v2.0_Chr6g0286521' => 'rch', 'RcHm_v2.0_Chr6g0286531' => 'rch', 'RcHm_v2.0_Chr7g0189141' => 'rch', 'Rhsim02G0028700' => 'rsi', 'Rhsim02G0028800' => 'rsi', 'Rhsim02G0028900' => 'rsi', 'Rhsim02G0029000' => 'rsi', 'Rhsim02G0029100' => 'rsi', 'Rhsim02G0029200' => 'rsi', 'Rhsim02G0029300' => 'rsi', 'Rhsim02G0029400' => 'rsi', 'Rhsim02G0029500' => 'rsi', 'Rhsim02G0029600' => 'rsi', 'RhsimUnG0024000' => 'rsi', 'RhsimUnG0024100' => 'rsi', 'RhsimUnG0024200' => 'rsi', 'RhsimUnG0024300' => 'rsi', 'RhsimUnG0024400' => 'rsi', 'RhsimUnG0024500' => 'rsi', 'RhsimUnG0024700' => 'rsi', 'RhsimUnG0024800' => 'rsi', 'RhsimUnG0024900' => 'rsi', 'RhsimUnG0025100' => 'rsi', 'Sabra08G0120200' => 'sbr', 'Sabra08G0120300' => 'sbr', 'Sabra08G0120500' => 'sbr', 'Sabra08G0120600' => 'sbr', 'Sabra10G0158900' => 'sbr', 'SalBow2G3492' => 'sbo', 'Sc13g0004760' => 'sci', 'Sc13g0004770' => 'sci', 'Sed0003417' => 'sed', 'Sed0019750' => 'sed', 'SEGI_03419' => 'sgi', 'SEGI_05907' => 'sgi', 'SEGI_10682' => 'sgi', 'SEGI_13528' => 'sgi', 'SEGI_16081' => 'sgi', 'SEGI_19370' => 'sgi', 'SEGI_21015' => 'sgi', 'SEGI_21944' => 'sgi', 'SEGI_32906' => 'sgi', 'SEGI_33093' => 'sgi', 'SEGI_36110' => 'sgi', 'SEGI_40397' => 'sgi', 'SGA_v2.0_scaffold191G40426' => 'sas', 'SGA_v2.0_scaffold353G49717' => 'sas', 'SGA_v2.0_scaffold50G18550' => 'sas', 'SMO119G0173' => 'smo', 'SMO172G0002' => 'smo', 'Solyc09g082690.3' => 'sly', 'Solyc09g082700.2' => 'sly', 'Sopen09g031550' => 'spe', 'Sopen09g031560' => 'spe', 'Sp3g20540' => 'spa', 'Sp7g07580' => 'spa', 'TAR134G0002' => 'tar', 'TAR236G0001' => 'tar', 'TAR365G0892' => 'tar', 'TAR636G0166' => 'tar', 'TAR636G0646' => 'tar', 'TAR636G0869' => 'tar', 'TAR636G1317' => 'tar', 'TAR636G1744' => 'tar', 'TAR636G3358' => 'tar', 'TAR636G3436' => 'tar', 'THA.LOC104803047' => 'tha', 'Thecc.04G238900' => 'tca', 'Thhalv10021557m.g' => 'esa', 'Thhalv10026318m.g' => 'esa', 'Thhalv10026335m.g' => 'esa', 'TPR.G17433' => 'tpr', 'TPR.G18915' => 'tpr', 'TPR.G26125' => 'tpr', 'TWI09G0677' => 'twi', 'TWI73G0287' => 'twi', 'unitig_748.g8326' => 'ugi', 'vmacro15370' => 'vma', 'vmacro15371' => 'vma', 'vmacro15372' => 'vma', 'vmacro15373' => 'vma', 'vmacro15374' => 'vma', 'VMungo0720G2826' => 'vmu', 'Zm00001eb116960' => 'zma', 'Zm00001eb301260' => 'zma', 'Zm00001eb301270' => 'zma' ) $gf_id = 'HOM05D001460' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001460' ) $data_identifier = 'HOM05D001460' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 4, 'aag' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 2, 'aox' => (int) 2, 'arhy' => (int) 4, 'ath' => (int) 2, 'atr' => (int) 1, 'acertr' => (int) 10, 'cqu' => (int) 4, 'bca' => (int) 11, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 1, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 1, 'ccan' => (int) 1, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 1, 'col' => (int) 1, 'cpa' => (int) 1, 'cre' => (int) 7, 'csa' => (int) 1, 'camsi' => (int) 2, 'dca' => (int) 3, 'din' => (int) 2, 'dzi' => (int) 3, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 14, 'fve' => (int) 9, 'gma' => (int) 2, 'ghi' => (int) 4, 'gra' => (int) 2, 'vvi' => (int) 1, 'han' => (int) 13, 'cav' => (int) 1, 'hma' => (int) 2, 'sun' => (int) 2, 'lal' => (int) 2, 'lonja' => (int) 12, 'lja' => (int) 1, 'lsa' => (int) 7, 'mes' => (int) 1, 'mpo' => (int) 27, 'mbi' => (int) 1, 'mco' => (int) 8, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 1, 'egut' => (int) 1, 'ama' => (int) 1, 'nta' => (int) 4, 'nnu' => (int) 2, 'oeu' => (int) 3, 'osa' => (int) 4, 'pax' => (int) 9, 'pgr' => (int) 1, 'stu' => (int) 1, 'pvu' => (int) 1, 'ptr' => (int) 4, 'ppa' => (int) 22, 'pco' => (int) 6, 'ppe' => (int) 6, 'psa' => (int) 5, 'pso' => (int) 19, 'qlo' => (int) 5, 'rch' => (int) 7, 'rsi' => (int) 20, 'sbr' => (int) 5, 'sbo' => (int) 1, 'sci' => (int) 2, 'sed' => (int) 2, 'sgi' => (int) 12, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 2, 'tar' => (int) 10, 'tha' => (int) 1, 'tca' => (int) 1, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 2, 'ugi' => (int) 1, 'vma' => (int) 5, 'vmu' => (int) 1, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb301270' $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' => 'HOM05D001460', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '433', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p22980' => 'bna', 'A01p32340' => 'bna', 'A03p42970' => 'bna', 'A05p25880' => 'bna', 'Aa31LG8G9320' => 'aar', 'Aa31LG8G9330' => 'aar', 'Aa31LG8G9340' => 'aar', 'Aa31sc221G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1034' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1528' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.829' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2222' => 'aag', 'Ah.12g058830' => 'amhyb', 'Ah.12g058840' => 'amhyb', 'AL3G37160' => 'aly', 'AL7G41310' => 'aly', 'Aqoxy5G00395' => 'aox', 'Aqoxy5G00396' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0C8NZA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5185HY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JZ1PRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MD3LS0' => 'arhy', 'AT3G22840' => 'ath', 'AT4G14690' => 'ath', 'ATR0665G054' => 'atr', 'Atru.chr4.2344' => 'acertr', 'Atru.chr4.2346' => 'acertr', 'Atru.chr4.2347' => 'acertr', 'Atru.chr4.2348' => 'acertr', 'Atru.chr4.2355' => 'acertr', 'Atru.chr4.2356' => 'acertr', 'Atru.chr4.2358' => 'acertr', 'Atru.chr4.2359' => 'acertr', 'Atru.chr4.2360' => 'acertr', 'Atru.chr4.2361' => 'acertr', 'AUR62030476' => 'cqu', 'AUR62030478' => 'cqu', 'AUR62030819' => 'cqu', 'AUR62030820' => 'cqu', 'BcaB03g14648' => 'bca', 'BcaB04g20492' => 'bca', 'BcaB06g26399' => 'bca', 'BcaC01g03416' => 'bca', 'BcaC01g03419' => 'bca', 'BcaC01g03421' => 'bca', 'BcaC01g03424' => 'bca', 'BcaC05g28012' => 'bca', 'BcaC09g49212' => 'bca', 'BcaC09g50140' => 'bca', 'BcaNung00346' => 'bca', 'BolC1t02785H' => 'bol', 'BolC1t04095H' => 'bol', 'BolC3t17545H' => 'bol', 'BolC5t32769H' => 'bol', 'BraA01t02211Z' => 'bra', 'BraA01t03359Z' => 'bra', 'BraA03t13441Z' => 'bra', 'BraA05t21476Z' => 'bra', 'C01p28420' => 'bna', 'C01p41350' => 'bna', 'C03p52750' => 'bna', 'C03p52780' => 'bna', 'C05p40270' => 'bna', 'CAN.G1437.9' => 'can', 'CANSAT78G0035' => 'cansat', 'CANSAT78G1036' => 'cansat', 'CANSAT78G2272' => 'cansat', 'CANSAT78G2478' => 'cansat', 'CARHR098700' => 'chi', 'CARHR221120' => 'chi', 'CARHR221150' => 'chi', 'Carub.0003s2297' => 'cru', 'Carub.0007s2749' => 'cru', 'Carub.0007s2750' => 'cru', 'Carub.0007s2751' => 'cru', 'Ca_10849_v3' => 'car', 'Cc03_g04300' => 'ccan', 'CDE02G3648' => 'cde', 'CDE05G0060' => 'cde', 'CDE05G0692' => 'cde', 'CDE05G2285' => 'cde', 'CDE05G2884' => 'cde', 'CDE05G3072' => 'cde', 'Cfa008439' => 'cfa', 'Cfa008441' => 'cfa', 'Cfa008443' => 'cfa', 'Cfa008448' => 'cfa', 'Ciclev10005974m.g' => 'ccl', 'Ciclev10006006m.g' => 'ccl', 'Ciclev10006775m.g' => 'ccl', 'CiPaw.02G120400' => 'cil', 'CiPaw.02G120500' => 'cil', 'CiPaw.02G120600' => 'cil', 'ClCG05G004850' => 'cla', 'COL.COLO4_21566' => 'col', 'Cpa.g.sc44.124' => 'cpa', 'Cre07.g320400' => 'cre', 'Cre07.g320450' => 'cre', 'Cre08.g384650' => 'cre', 'Cre09.g393173' => 'cre', 'Cre09.g394325' => 'cre', 'Cre14.g626750' => 'cre', 'Cre16.g679250' => 'cre', 'CsaV3_3G012890' => 'csa', 'CSS0010865' => 'camsi', 'CSS0044338' => 'camsi', 'DCAR_002366' => 'dca', 'DCAR_030687' => 'dca', 'DCAR_030688' => 'dca', 'Dinv14047' => 'din', 'Dinv14048' => 'din', 'Duzib151G0105' => 'dzi', 'Duzib151G0114' => 'dzi', 'Duzib212G1029' => 'dzi', 'ECA232G3536' => 'eca', 'ECA240G0786' => 'eca', 'ECA240G1802' => 'eca', 'ECA240G3760' => 'eca', 'ECA240G3920' => 'eca', 'EL10Ac5g12536' => 'bvu', 'EL10Ac5g12537' => 'bvu', 'EL10Ac5g12538' => 'bvu', 'Eucgr.B01004' => 'egr', 'Eucgr.B01006' => 'egr', 'Eucgr.B01007' => 'egr', 'Eucgr.B01008' => 'egr', 'Eucgr.B01895' => 'egr', 'Eucgr.B01896' => 'egr', 'FAN04G1456' => 'fan', 'FAN08G1769' => 'fan', 'FAN08G2160' => 'fan', 'FAN13G2403' => 'fan', 'FAN13G3303' => 'fan', 'FAN15G2435' => 'fan', 'FAN17G0672' => 'fan', 'FAN17G2441' => 'fan', 'FAN18G1024' => 'fan', 'FAN22G1458' => 'fan', 'FAN24G0037' => 'fan', 'FAN24G0429' => 'fan', 'FAN24G2387' => 'fan', 'FAN27G2746' => 'fan', 'FvH4_2g20400' => 'fve', 'FvH4_2g20420' => 'fve', 'FvH4_2g20430' => 'fve', 'FvH4_4g01270' => 'fve', 'FvH4_4g01290' => 'fve', 'FvH4_4g01300' => 'fve', 'FvH4_4g01310' => 'fve', 'FvH4_4g01330' => 'fve', 'FvH4_5g09070' => 'fve', 'Glyma.10G243800' => 'gma', 'Glyma.20G150600' => 'gma', 'Gohir.A09G219200' => 'ghi', 'Gohir.A09G219300' => 'ghi', 'Gohir.D09G221400' => 'ghi', 'Gohir.D09G221500' => 'ghi', 'Gorai.006G242600' => 'gra', 'Gorai.006G242700' => 'gra', 'GSVIVG01018044001' => 'vvi', 'HanXRQChr03g0083821' => 'han', 'HanXRQChr03g0083841' => 'han', 'HanXRQChr03g0083881' => 'han', 'HanXRQChr03g0083901' => 'han', 'HanXRQChr03g0083921' => 'han', 'HanXRQChr03g0085331' => 'han', 'HanXRQChr03g0085361' => 'han', 'HanXRQChr03g0085411' => 'han', 'HanXRQChr03g0085421' => 'han', 'HanXRQChr03g0085431' => 'han', 'HanXRQChr08g0221991' => 'han', 'HanXRQChr11g0336061' => 'han', 'HanXRQChr11g0336411' => 'han', 'Haze_11234' => 'cav', 'Hma1.2p1_0549F.1_g177010' => 'hma', 'Hma1.2p1_0602F.1_g187630' => 'hma', 'Hund14876' => 'sun', 'Hund14879' => 'sun', 'Lalb_Chr06g0160741' => 'lal', 'Lalb_Chr21g0304781' => 'lal', 'Lj3A726G19' => 'lonja', 'Lj3A726T23' => 'lonja', 'Lj3A726T24' => 'lonja', 'Lj3A726T25' => 'lonja', 'Lj3A727T17' => 'lonja', 'Lj3C726T0' => 'lonja', 'Lj3C726T2' => 'lonja', 'Lj3P725T35' => 'lonja', 'Lj3P727T10' => 'lonja', 'Lj3P727T12' => 'lonja', 'Lj3P727T14' => 'lonja', 'Lj5g0023109' => 'lja', 'Lj6P646T44' => 'lonja', 'Lsat_1_v5_gn_6_75760' => 'lsa', 'Lsat_1_v5_gn_6_75800' => 'lsa', 'Lsat_1_v5_gn_6_75900' => 'lsa', 'Lsat_1_v5_gn_6_76240' => 'lsa', 'Lsat_1_v5_gn_6_76441' => 'lsa', 'Lsat_1_v5_gn_6_76700' => 'lsa', 'Lsat_1_v5_gn_6_76760' => 'lsa', 'Manes.15G033100' => 'mes', 'Mapoly0004s0074' => 'mpo', 'Mapoly0004s0075' => 'mpo', 'Mapoly0004s0163' => 'mpo', 'Mapoly0004s0164' => 'mpo', 'Mapoly0021s0018' => 'mpo', 'Mapoly0041s0136' => 'mpo', 'Mapoly0041s0137' => 'mpo', 'Mapoly0041s0138' => 'mpo', 'Mapoly0041s0139' => 'mpo', 'Mapoly0041s0141' => 'mpo', 'Mapoly0041s0142' => 'mpo', 'Mapoly0041s0143' => 'mpo', 'Mapoly0041s0144' => 'mpo', 'Mapoly0041s0145' => 'mpo', 'Mapoly0047s0106' => 'mpo', 'Mapoly0047s0108' => 'mpo', 'Mapoly0050s0051' => 'mpo', 'Mapoly0050s0052' => 'mpo', 'Mapoly0050s0053' => 'mpo', 'Mapoly0058s0013' => 'mpo', 'Mapoly0091s0078' => 'mpo', 'Mapoly0091s0079' => 'mpo', 'Mapoly0091s0080' => 'mpo', 'Mapoly0091s0081' => 'mpo', 'Mapoly0278s0004' => 'mpo', 'Mapoly0278s0005' => 'mpo', 'Mapoly0278s0006' => 'mpo', 'MBI11_g30648_MAGBIO' => 'mbi', 'MCO03G194' => 'mco', 'MCO03G590' => 'mco', 'MCO07G312' => 'mco', 'MCO10G318' => 'mco', 'MCO12G244' => 'mco', 'MCO13G148' => 'mco', 'MCO13G194' => 'mco', 'MCO16G238' => 'mco', 'MD06G1134100' => 'mdo', 'MD13G1200100' => 'mdo', 'MD13G1200300' => 'mdo', 'MD13G1200600' => 'mdo', 'MD14G1150400' => 'mdo', 'MD16G1200000' => 'mdo', 'Medtr1g102570' => 'mtr', 'Medtr1g102780' => 'mtr', 'Medtr1g102800' => 'mtr', 'Medtr1g102810' => 'mtr', 'Medtr1g102830' => 'mtr', 'MELO3C006499.2' => 'cme', 'Migut.G00385' => 'egut', 'MSTRG.4063' => 'ama', 'Nitab4.5_0000090g0260' => 'nta', 'Nitab4.5_0000977g0030' => 'nta', 'Nitab4.5_0002541g0040' => 'nta', 'Nitab4.5_0007068g0040' => 'nta', 'Nn005s41408' => 'nnu', 'Nn005s41410' => 'nnu', 'Oeu010310.1' => 'oeu', 'Oeu010311.1' => 'oeu', 'Oeu043472.1' => 'oeu', 'Os01g0246400' => 'osa', 'Os04g0267950' => 'osa', 'Os07g0178700' => 'osa', 'Os07g0178800' => 'osa', 'Peaxi162Scf00316g00046' => 'pax', 'Peaxi162Scf00316g00049' => 'pax', 'Peaxi162Scf00316g00059' => 'pax', 'Peaxi162Scf00316g00328' => 'pax', 'Peaxi162Scf00316g00329' => 'pax', 'Peaxi162Scf00316g00411' => 'pax', 'Peaxi162Scf00316g00521' => 'pax', 'Peaxi162Scf00492g00068' => 'pax', 'Peaxi162Scf35631g00002' => 'pax', 'PGR142G3720' => 'pgr', 'PGSC0003DMG400006442' => 'stu', 'Phvul.007G062000' => 'pvu', 'Potri.008G157750' => 'ptr', 'Potri.008G157900' => 'ptr', 'Potri.008G158000' => 'ptr', 'Potri.008G158200' => 'ptr', 'Pp3c11_7280' => 'ppa', 'Pp3c11_7980' => 'ppa', 'Pp3c12_19450' => 'ppa', 'Pp3c14_1480' => 'ppa', 'Pp3c14_1501' => 'ppa', 'Pp3c16_4900' => 'ppa', 'Pp3c16_5010' => 'ppa', 'Pp3c16_5060' => 'ppa', 'Pp3c19_18250' => 'ppa', 'Pp3c23_8530' => 'ppa', 'Pp3c23_8550' => 'ppa', 'Pp3c24_9670' => 'ppa', 'Pp3c2_21390' => 'ppa', 'Pp3c2_31380' => 'ppa', 'Pp3c3_16620' => 'ppa', 'Pp3c3_8090' => 'ppa', 'Pp3c3_8110' => 'ppa', 'Pp3c3_8130' => 'ppa', 'Pp3c3_8150' => 'ppa', 'Pp3c4_14320' => 'ppa', 'Pp3c6_2560' => 'ppa', 'Pp3c9_16700' => 'ppa', 'PRCOL_00000234' => 'pco', 'PRCOL_00000235' => 'pco', 'PRCOL_00000777' => 'pco', 'PRCOL_00002344' => 'pco', 'PRCOL_00002372' => 'pco', 'PRCOL_00006120' => 'pco', 'Prupe.1G021400' => 'ppe', 'Prupe.1G021500' => 'ppe', 'Prupe.1G021600' => 'ppe', 'Prupe.1G021700' => 'ppe', 'Prupe.1G021800' => 'ppe', 'Prupe.5G145100' => 'ppe', 'Psat6g204040' => 'psa', 'Psat6g204800' => 'psa', 'Psat6g204920' => 'psa', 'Psat6g204960' => 'psa', 'Psat6g205080' => 'psa', 'PSO017G0271' => 'pso', 'PSO017G1276' => 'pso', 'PSO017G1429' => 'pso', 'PSO017G1861' => 'pso', 'PSO017G2787' => 'pso', 'PSO017G4466' => 'pso', 'PSO017G5118' => 'pso', 'PSO017G5420' => 'pso', 'PSO063G3678' => 'pso', 'PSO210G0546' => 'pso', 'PSO317G0001' => 'pso', 'PSO357G0512' => 'pso', 'PSO478G2682' => 'pso', 'PSO647G0001' => 'pso', 'PSO675G0001' => 'pso', 'PSO675G2699' => 'pso', 'PSO675G2849' => 'pso', 'PSO675G4991' => 'pso', 'PSO689G0001' => 'pso', 'QL06p000916' => 'qlo', 'QL06p000921' => 'qlo', 'QL06p001398' => 'qlo', 'QL06p001407' => 'qlo', 'QL06p002031' => 'qlo', 'RcHm_v2.0_Chr4g0387791' => 'rch', 'RcHm_v2.0_Chr4g0387801' => 'rch', 'RcHm_v2.0_Chr6g0286501' => 'rch', 'RcHm_v2.0_Chr6g0286511' => 'rch', 'RcHm_v2.0_Chr6g0286521' => 'rch', 'RcHm_v2.0_Chr6g0286531' => 'rch', 'RcHm_v2.0_Chr7g0189141' => 'rch', 'Rhsim02G0028700' => 'rsi', 'Rhsim02G0028800' => 'rsi', 'Rhsim02G0028900' => 'rsi', 'Rhsim02G0029000' => 'rsi', 'Rhsim02G0029100' => 'rsi', 'Rhsim02G0029200' => 'rsi', 'Rhsim02G0029300' => 'rsi', 'Rhsim02G0029400' => 'rsi', 'Rhsim02G0029500' => 'rsi', 'Rhsim02G0029600' => 'rsi', 'RhsimUnG0024000' => 'rsi', 'RhsimUnG0024100' => 'rsi', 'RhsimUnG0024200' => 'rsi', 'RhsimUnG0024300' => 'rsi', 'RhsimUnG0024400' => 'rsi', 'RhsimUnG0024500' => 'rsi', 'RhsimUnG0024700' => 'rsi', 'RhsimUnG0024800' => 'rsi', 'RhsimUnG0024900' => 'rsi', 'RhsimUnG0025100' => 'rsi', 'Sabra08G0120200' => 'sbr', 'Sabra08G0120300' => 'sbr', 'Sabra08G0120500' => 'sbr', 'Sabra08G0120600' => 'sbr', 'Sabra10G0158900' => 'sbr', 'SalBow2G3492' => 'sbo', 'Sc13g0004760' => 'sci', 'Sc13g0004770' => 'sci', 'Sed0003417' => 'sed', 'Sed0019750' => 'sed', 'SEGI_03419' => 'sgi', 'SEGI_05907' => 'sgi', 'SEGI_10682' => 'sgi', 'SEGI_13528' => 'sgi', 'SEGI_16081' => 'sgi', 'SEGI_19370' => 'sgi', 'SEGI_21015' => 'sgi', 'SEGI_21944' => 'sgi', 'SEGI_32906' => 'sgi', 'SEGI_33093' => 'sgi', 'SEGI_36110' => 'sgi', 'SEGI_40397' => 'sgi', 'SGA_v2.0_scaffold191G40426' => 'sas', 'SGA_v2.0_scaffold353G49717' => 'sas', 'SGA_v2.0_scaffold50G18550' => 'sas', 'SMO119G0173' => 'smo', 'SMO172G0002' => 'smo', 'Solyc09g082690.3' => 'sly', 'Solyc09g082700.2' => 'sly', 'Sopen09g031550' => 'spe', 'Sopen09g031560' => 'spe', 'Sp3g20540' => 'spa', 'Sp7g07580' => 'spa', 'TAR134G0002' => 'tar', 'TAR236G0001' => 'tar', 'TAR365G0892' => 'tar', 'TAR636G0166' => 'tar', 'TAR636G0646' => 'tar', 'TAR636G0869' => 'tar', 'TAR636G1317' => 'tar', 'TAR636G1744' => 'tar', 'TAR636G3358' => 'tar', 'TAR636G3436' => 'tar', 'THA.LOC104803047' => 'tha', 'Thecc.04G238900' => 'tca', 'Thhalv10021557m.g' => 'esa', 'Thhalv10026318m.g' => 'esa', 'Thhalv10026335m.g' => 'esa', 'TPR.G17433' => 'tpr', 'TPR.G18915' => 'tpr', 'TPR.G26125' => 'tpr', 'TWI09G0677' => 'twi', 'TWI73G0287' => 'twi', 'unitig_748.g8326' => 'ugi', 'vmacro15370' => 'vma', 'vmacro15371' => 'vma', 'vmacro15372' => 'vma', 'vmacro15373' => 'vma', 'vmacro15374' => 'vma', 'VMungo0720G2826' => 'vmu', 'Zm00001eb116960' => 'zma', 'Zm00001eb301260' => 'zma', 'Zm00001eb301270' => 'zma' ), 'gf_id' => 'HOM05D001460', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001460' ), 'data_identifier' => 'HOM05D001460', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001460', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '433', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p22980' => 'bna', 'A01p32340' => 'bna', 'A03p42970' => 'bna', 'A05p25880' => 'bna', 'Aa31LG8G9320' => 'aar', 'Aa31LG8G9330' => 'aar', 'Aa31LG8G9340' => 'aar', 'Aa31sc221G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1034' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1528' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.829' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2222' => 'aag', 'Ah.12g058830' => 'amhyb', 'Ah.12g058840' => 'amhyb', 'AL3G37160' => 'aly', 'AL7G41310' => 'aly', 'Aqoxy5G00395' => 'aox', 'Aqoxy5G00396' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0C8NZA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5185HY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JZ1PRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MD3LS0' => 'arhy', 'AT3G22840' => 'ath', 'AT4G14690' => 'ath', 'ATR0665G054' => 'atr', 'Atru.chr4.2344' => 'acertr', 'Atru.chr4.2346' => 'acertr', 'Atru.chr4.2347' => 'acertr', 'Atru.chr4.2348' => 'acertr', 'Atru.chr4.2355' => 'acertr', 'Atru.chr4.2356' => 'acertr', 'Atru.chr4.2358' => 'acertr', 'Atru.chr4.2359' => 'acertr', 'Atru.chr4.2360' => 'acertr', 'Atru.chr4.2361' => 'acertr', 'AUR62030476' => 'cqu', 'AUR62030478' => 'cqu', 'AUR62030819' => 'cqu', 'AUR62030820' => 'cqu', 'BcaB03g14648' => 'bca', 'BcaB04g20492' => 'bca', 'BcaB06g26399' => 'bca', 'BcaC01g03416' => 'bca', 'BcaC01g03419' => 'bca', 'BcaC01g03421' => 'bca', 'BcaC01g03424' => 'bca', 'BcaC05g28012' => 'bca', 'BcaC09g49212' => 'bca', 'BcaC09g50140' => 'bca', 'BcaNung00346' => 'bca', 'BolC1t02785H' => 'bol', 'BolC1t04095H' => 'bol', 'BolC3t17545H' => 'bol', 'BolC5t32769H' => 'bol', 'BraA01t02211Z' => 'bra', 'BraA01t03359Z' => 'bra', 'BraA03t13441Z' => 'bra', 'BraA05t21476Z' => 'bra', 'C01p28420' => 'bna', 'C01p41350' => 'bna', 'C03p52750' => 'bna', 'C03p52780' => 'bna', 'C05p40270' => 'bna', 'CAN.G1437.9' => 'can', 'CANSAT78G0035' => 'cansat', 'CANSAT78G1036' => 'cansat', 'CANSAT78G2272' => 'cansat', 'CANSAT78G2478' => 'cansat', 'CARHR098700' => 'chi', 'CARHR221120' => 'chi', 'CARHR221150' => 'chi', 'Carub.0003s2297' => 'cru', 'Carub.0007s2749' => 'cru', 'Carub.0007s2750' => 'cru', 'Carub.0007s2751' => 'cru', 'Ca_10849_v3' => 'car', 'Cc03_g04300' => 'ccan', 'CDE02G3648' => 'cde', 'CDE05G0060' => 'cde', 'CDE05G0692' => 'cde', 'CDE05G2285' => 'cde', 'CDE05G2884' => 'cde', 'CDE05G3072' => 'cde', 'Cfa008439' => 'cfa', 'Cfa008441' => 'cfa', 'Cfa008443' => 'cfa', 'Cfa008448' => 'cfa', 'Ciclev10005974m.g' => 'ccl', 'Ciclev10006006m.g' => 'ccl', 'Ciclev10006775m.g' => 'ccl', 'CiPaw.02G120400' => 'cil', 'CiPaw.02G120500' => 'cil', 'CiPaw.02G120600' => 'cil', 'ClCG05G004850' => 'cla', 'COL.COLO4_21566' => 'col', 'Cpa.g.sc44.124' => 'cpa', 'Cre07.g320400' => 'cre', 'Cre07.g320450' => 'cre', 'Cre08.g384650' => 'cre', 'Cre09.g393173' => 'cre', 'Cre09.g394325' => 'cre', 'Cre14.g626750' => 'cre', 'Cre16.g679250' => 'cre', 'CsaV3_3G012890' => 'csa', 'CSS0010865' => 'camsi', 'CSS0044338' => 'camsi', 'DCAR_002366' => 'dca', 'DCAR_030687' => 'dca', 'DCAR_030688' => 'dca', 'Dinv14047' => 'din', 'Dinv14048' => 'din', 'Duzib151G0105' => 'dzi', 'Duzib151G0114' => 'dzi', 'Duzib212G1029' => 'dzi', 'ECA232G3536' => 'eca', 'ECA240G0786' => 'eca', 'ECA240G1802' => 'eca', 'ECA240G3760' => 'eca', 'ECA240G3920' => 'eca', 'EL10Ac5g12536' => 'bvu', 'EL10Ac5g12537' => 'bvu', 'EL10Ac5g12538' => 'bvu', 'Eucgr.B01004' => 'egr', 'Eucgr.B01006' => 'egr', 'Eucgr.B01007' => 'egr', 'Eucgr.B01008' => 'egr', 'Eucgr.B01895' => 'egr', 'Eucgr.B01896' => 'egr', 'FAN04G1456' => 'fan', 'FAN08G1769' => 'fan', 'FAN08G2160' => 'fan', 'FAN13G2403' => 'fan', 'FAN13G3303' => 'fan', 'FAN15G2435' => 'fan', 'FAN17G0672' => 'fan', 'FAN17G2441' => 'fan', 'FAN18G1024' => 'fan', 'FAN22G1458' => 'fan', 'FAN24G0037' => 'fan', 'FAN24G0429' => 'fan', 'FAN24G2387' => 'fan', 'FAN27G2746' => 'fan', 'FvH4_2g20400' => 'fve', 'FvH4_2g20420' => 'fve', 'FvH4_2g20430' => 'fve', 'FvH4_4g01270' => 'fve', 'FvH4_4g01290' => 'fve', 'FvH4_4g01300' => 'fve', 'FvH4_4g01310' => 'fve', 'FvH4_4g01330' => 'fve', 'FvH4_5g09070' => 'fve', 'Glyma.10G243800' => 'gma', 'Glyma.20G150600' => 'gma', 'Gohir.A09G219200' => 'ghi', 'Gohir.A09G219300' => 'ghi', 'Gohir.D09G221400' => 'ghi', 'Gohir.D09G221500' => 'ghi', 'Gorai.006G242600' => 'gra', 'Gorai.006G242700' => 'gra', 'GSVIVG01018044001' => 'vvi', 'HanXRQChr03g0083821' => 'han', 'HanXRQChr03g0083841' => 'han', 'HanXRQChr03g0083881' => 'han', 'HanXRQChr03g0083901' => 'han', 'HanXRQChr03g0083921' => 'han', 'HanXRQChr03g0085331' => 'han', 'HanXRQChr03g0085361' => 'han', 'HanXRQChr03g0085411' => 'han', 'HanXRQChr03g0085421' => 'han', 'HanXRQChr03g0085431' => 'han', 'HanXRQChr08g0221991' => 'han', 'HanXRQChr11g0336061' => 'han', 'HanXRQChr11g0336411' => 'han', 'Haze_11234' => 'cav', 'Hma1.2p1_0549F.1_g177010' => 'hma', 'Hma1.2p1_0602F.1_g187630' => 'hma', 'Hund14876' => 'sun', 'Hund14879' => 'sun', 'Lalb_Chr06g0160741' => 'lal', 'Lalb_Chr21g0304781' => 'lal', 'Lj3A726G19' => 'lonja', 'Lj3A726T23' => 'lonja', 'Lj3A726T24' => 'lonja', 'Lj3A726T25' => 'lonja', 'Lj3A727T17' => 'lonja', 'Lj3C726T0' => 'lonja', 'Lj3C726T2' => 'lonja', 'Lj3P725T35' => 'lonja', 'Lj3P727T10' => 'lonja', 'Lj3P727T12' => 'lonja', 'Lj3P727T14' => 'lonja', 'Lj5g0023109' => 'lja', 'Lj6P646T44' => 'lonja', 'Lsat_1_v5_gn_6_75760' => 'lsa', 'Lsat_1_v5_gn_6_75800' => 'lsa', 'Lsat_1_v5_gn_6_75900' => 'lsa', 'Lsat_1_v5_gn_6_76240' => 'lsa', 'Lsat_1_v5_gn_6_76441' => 'lsa', 'Lsat_1_v5_gn_6_76700' => 'lsa', 'Lsat_1_v5_gn_6_76760' => 'lsa', 'Manes.15G033100' => 'mes', 'Mapoly0004s0074' => 'mpo', 'Mapoly0004s0075' => 'mpo', 'Mapoly0004s0163' => 'mpo', 'Mapoly0004s0164' => 'mpo', 'Mapoly0021s0018' => 'mpo', 'Mapoly0041s0136' => 'mpo', 'Mapoly0041s0137' => 'mpo', 'Mapoly0041s0138' => 'mpo', 'Mapoly0041s0139' => 'mpo', 'Mapoly0041s0141' => 'mpo', 'Mapoly0041s0142' => 'mpo', 'Mapoly0041s0143' => 'mpo', 'Mapoly0041s0144' => 'mpo', 'Mapoly0041s0145' => 'mpo', 'Mapoly0047s0106' => 'mpo', 'Mapoly0047s0108' => 'mpo', 'Mapoly0050s0051' => 'mpo', 'Mapoly0050s0052' => 'mpo', 'Mapoly0050s0053' => 'mpo', 'Mapoly0058s0013' => 'mpo', 'Mapoly0091s0078' => 'mpo', 'Mapoly0091s0079' => 'mpo', 'Mapoly0091s0080' => 'mpo', 'Mapoly0091s0081' => 'mpo', 'Mapoly0278s0004' => 'mpo', 'Mapoly0278s0005' => 'mpo', 'Mapoly0278s0006' => 'mpo', 'MBI11_g30648_MAGBIO' => 'mbi', 'MCO03G194' => 'mco', 'MCO03G590' => 'mco', 'MCO07G312' => 'mco', 'MCO10G318' => 'mco', 'MCO12G244' => 'mco', 'MCO13G148' => 'mco', 'MCO13G194' => 'mco', 'MCO16G238' => 'mco', 'MD06G1134100' => 'mdo', 'MD13G1200100' => 'mdo', 'MD13G1200300' => 'mdo', 'MD13G1200600' => 'mdo', 'MD14G1150400' => 'mdo', 'MD16G1200000' => 'mdo', 'Medtr1g102570' => 'mtr', 'Medtr1g102780' => 'mtr', 'Medtr1g102800' => 'mtr', 'Medtr1g102810' => 'mtr', 'Medtr1g102830' => 'mtr', 'MELO3C006499.2' => 'cme', 'Migut.G00385' => 'egut', 'MSTRG.4063' => 'ama', 'Nitab4.5_0000090g0260' => 'nta', 'Nitab4.5_0000977g0030' => 'nta', 'Nitab4.5_0002541g0040' => 'nta', 'Nitab4.5_0007068g0040' => 'nta', 'Nn005s41408' => 'nnu', 'Nn005s41410' => 'nnu', 'Oeu010310.1' => 'oeu', 'Oeu010311.1' => 'oeu', 'Oeu043472.1' => 'oeu', 'Os01g0246400' => 'osa', 'Os04g0267950' => 'osa', 'Os07g0178700' => 'osa', 'Os07g0178800' => 'osa', 'Peaxi162Scf00316g00046' => 'pax', 'Peaxi162Scf00316g00049' => 'pax', 'Peaxi162Scf00316g00059' => 'pax', 'Peaxi162Scf00316g00328' => 'pax', 'Peaxi162Scf00316g00329' => 'pax', 'Peaxi162Scf00316g00411' => 'pax', 'Peaxi162Scf00316g00521' => 'pax', 'Peaxi162Scf00492g00068' => 'pax', 'Peaxi162Scf35631g00002' => 'pax', 'PGR142G3720' => 'pgr', 'PGSC0003DMG400006442' => 'stu', 'Phvul.007G062000' => 'pvu', 'Potri.008G157750' => 'ptr', 'Potri.008G157900' => 'ptr', 'Potri.008G158000' => 'ptr', 'Potri.008G158200' => 'ptr', 'Pp3c11_7280' => 'ppa', 'Pp3c11_7980' => 'ppa', 'Pp3c12_19450' => 'ppa', 'Pp3c14_1480' => 'ppa', 'Pp3c14_1501' => 'ppa', 'Pp3c16_4900' => 'ppa', 'Pp3c16_5010' => 'ppa', 'Pp3c16_5060' => 'ppa', 'Pp3c19_18250' => 'ppa', 'Pp3c23_8530' => 'ppa', 'Pp3c23_8550' => 'ppa', 'Pp3c24_9670' => 'ppa', 'Pp3c2_21390' => 'ppa', 'Pp3c2_31380' => 'ppa', 'Pp3c3_16620' => 'ppa', 'Pp3c3_8090' => 'ppa', 'Pp3c3_8110' => 'ppa', 'Pp3c3_8130' => 'ppa', 'Pp3c3_8150' => 'ppa', 'Pp3c4_14320' => 'ppa', 'Pp3c6_2560' => 'ppa', 'Pp3c9_16700' => 'ppa', 'PRCOL_00000234' => 'pco', 'PRCOL_00000235' => 'pco', 'PRCOL_00000777' => 'pco', 'PRCOL_00002344' => 'pco', 'PRCOL_00002372' => 'pco', 'PRCOL_00006120' => 'pco', 'Prupe.1G021400' => 'ppe', 'Prupe.1G021500' => 'ppe', 'Prupe.1G021600' => 'ppe', 'Prupe.1G021700' => 'ppe', 'Prupe.1G021800' => 'ppe', 'Prupe.5G145100' => 'ppe', 'Psat6g204040' => 'psa', 'Psat6g204800' => 'psa', 'Psat6g204920' => 'psa', 'Psat6g204960' => 'psa', 'Psat6g205080' => 'psa', 'PSO017G0271' => 'pso', 'PSO017G1276' => 'pso', 'PSO017G1429' => 'pso', 'PSO017G1861' => 'pso', 'PSO017G2787' => 'pso', 'PSO017G4466' => 'pso', 'PSO017G5118' => 'pso', 'PSO017G5420' => 'pso', 'PSO063G3678' => 'pso', 'PSO210G0546' => 'pso', 'PSO317G0001' => 'pso', 'PSO357G0512' => 'pso', 'PSO478G2682' => 'pso', 'PSO647G0001' => 'pso', 'PSO675G0001' => 'pso', 'PSO675G2699' => 'pso', 'PSO675G2849' => 'pso', 'PSO675G4991' => 'pso', 'PSO689G0001' => 'pso', 'QL06p000916' => 'qlo', 'QL06p000921' => 'qlo', 'QL06p001398' => 'qlo', 'QL06p001407' => 'qlo', 'QL06p002031' => 'qlo', 'RcHm_v2.0_Chr4g0387791' => 'rch', 'RcHm_v2.0_Chr4g0387801' => 'rch', 'RcHm_v2.0_Chr6g0286501' => 'rch', 'RcHm_v2.0_Chr6g0286511' => 'rch', 'RcHm_v2.0_Chr6g0286521' => 'rch', 'RcHm_v2.0_Chr6g0286531' => 'rch', 'RcHm_v2.0_Chr7g0189141' => 'rch', 'Rhsim02G0028700' => 'rsi', 'Rhsim02G0028800' => 'rsi', 'Rhsim02G0028900' => 'rsi', 'Rhsim02G0029000' => 'rsi', 'Rhsim02G0029100' => 'rsi', 'Rhsim02G0029200' => 'rsi', 'Rhsim02G0029300' => 'rsi', 'Rhsim02G0029400' => 'rsi', 'Rhsim02G0029500' => 'rsi', 'Rhsim02G0029600' => 'rsi', 'RhsimUnG0024000' => 'rsi', 'RhsimUnG0024100' => 'rsi', 'RhsimUnG0024200' => 'rsi', 'RhsimUnG0024300' => 'rsi', 'RhsimUnG0024400' => 'rsi', 'RhsimUnG0024500' => 'rsi', 'RhsimUnG0024700' => 'rsi', 'RhsimUnG0024800' => 'rsi', 'RhsimUnG0024900' => 'rsi', 'RhsimUnG0025100' => 'rsi', 'Sabra08G0120200' => 'sbr', 'Sabra08G0120300' => 'sbr', 'Sabra08G0120500' => 'sbr', 'Sabra08G0120600' => 'sbr', 'Sabra10G0158900' => 'sbr', 'SalBow2G3492' => 'sbo', 'Sc13g0004760' => 'sci', 'Sc13g0004770' => 'sci', 'Sed0003417' => 'sed', 'Sed0019750' => 'sed', 'SEGI_03419' => 'sgi', 'SEGI_05907' => 'sgi', 'SEGI_10682' => 'sgi', 'SEGI_13528' => 'sgi', 'SEGI_16081' => 'sgi', 'SEGI_19370' => 'sgi', 'SEGI_21015' => 'sgi', 'SEGI_21944' => 'sgi', 'SEGI_32906' => 'sgi', 'SEGI_33093' => 'sgi', 'SEGI_36110' => 'sgi', 'SEGI_40397' => 'sgi', 'SGA_v2.0_scaffold191G40426' => 'sas', 'SGA_v2.0_scaffold353G49717' => 'sas', 'SGA_v2.0_scaffold50G18550' => 'sas', 'SMO119G0173' => 'smo', 'SMO172G0002' => 'smo', 'Solyc09g082690.3' => 'sly', 'Solyc09g082700.2' => 'sly', 'Sopen09g031550' => 'spe', 'Sopen09g031560' => 'spe', 'Sp3g20540' => 'spa', 'Sp7g07580' => 'spa', 'TAR134G0002' => 'tar', 'TAR236G0001' => 'tar', 'TAR365G0892' => 'tar', 'TAR636G0166' => 'tar', 'TAR636G0646' => 'tar', 'TAR636G0869' => 'tar', 'TAR636G1317' => 'tar', 'TAR636G1744' => 'tar', 'TAR636G3358' => 'tar', 'TAR636G3436' => 'tar', 'THA.LOC104803047' => 'tha', 'Thecc.04G238900' => 'tca', 'Thhalv10021557m.g' => 'esa', 'Thhalv10026318m.g' => 'esa', 'Thhalv10026335m.g' => 'esa', 'TPR.G17433' => 'tpr', 'TPR.G18915' => 'tpr', 'TPR.G26125' => 'tpr', 'TWI09G0677' => 'twi', 'TWI73G0287' => 'twi', 'unitig_748.g8326' => 'ugi', 'vmacro15370' => 'vma', 'vmacro15371' => 'vma', 'vmacro15372' => 'vma', 'vmacro15373' => 'vma', 'vmacro15374' => 'vma', 'VMungo0720G2826' => 'vmu', 'Zm00001eb116960' => 'zma', 'Zm00001eb301260' => 'zma', 'Zm00001eb301270' => 'zma' ) $gf_id = 'HOM05D001460' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001460' ) $data_identifier = 'HOM05D001460' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 4, 'aag' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 2, 'aox' => (int) 2, 'arhy' => (int) 4, 'ath' => (int) 2, 'atr' => (int) 1, 'acertr' => (int) 10, 'cqu' => (int) 4, 'bca' => (int) 11, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 1, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 1, 'ccan' => (int) 1, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 1, 'col' => (int) 1, 'cpa' => (int) 1, 'cre' => (int) 7, 'csa' => (int) 1, 'camsi' => (int) 2, 'dca' => (int) 3, 'din' => (int) 2, 'dzi' => (int) 3, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 14, 'fve' => (int) 9, 'gma' => (int) 2, 'ghi' => (int) 4, 'gra' => (int) 2, 'vvi' => (int) 1, 'han' => (int) 13, 'cav' => (int) 1, 'hma' => (int) 2, 'sun' => (int) 2, 'lal' => (int) 2, 'lonja' => (int) 12, 'lja' => (int) 1, 'lsa' => (int) 7, 'mes' => (int) 1, 'mpo' => (int) 27, 'mbi' => (int) 1, 'mco' => (int) 8, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 1, 'egut' => (int) 1, 'ama' => (int) 1, 'nta' => (int) 4, 'nnu' => (int) 2, 'oeu' => (int) 3, 'osa' => (int) 4, 'pax' => (int) 9, 'pgr' => (int) 1, 'stu' => (int) 1, 'pvu' => (int) 1, 'ptr' => (int) 4, 'ppa' => (int) 22, 'pco' => (int) 6, 'ppe' => (int) 6, 'psa' => (int) 5, 'pso' => (int) 19, 'qlo' => (int) 5, 'rch' => (int) 7, 'rsi' => (int) 20, 'sbr' => (int) 5, 'sbo' => (int) 1, 'sci' => (int) 2, 'sed' => (int) 2, 'sgi' => (int) 12, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 2, 'tar' => (int) 10, 'tha' => (int) 1, 'tca' => (int) 1, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 2, 'ugi' => (int) 1, 'vma' => (int) 5, 'vmu' => (int) 1, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb301270' $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' => 'HOM05D001460', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '433', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p22980' => 'bna', 'A01p32340' => 'bna', 'A03p42970' => 'bna', 'A05p25880' => 'bna', 'Aa31LG8G9320' => 'aar', 'Aa31LG8G9330' => 'aar', 'Aa31LG8G9340' => 'aar', 'Aa31sc221G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1034' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1528' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.829' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2222' => 'aag', 'Ah.12g058830' => 'amhyb', 'Ah.12g058840' => 'amhyb', 'AL3G37160' => 'aly', 'AL7G41310' => 'aly', 'Aqoxy5G00395' => 'aox', 'Aqoxy5G00396' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0C8NZA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5185HY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JZ1PRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MD3LS0' => 'arhy', 'AT3G22840' => 'ath', 'AT4G14690' => 'ath', 'ATR0665G054' => 'atr', 'Atru.chr4.2344' => 'acertr', 'Atru.chr4.2346' => 'acertr', 'Atru.chr4.2347' => 'acertr', 'Atru.chr4.2348' => 'acertr', 'Atru.chr4.2355' => 'acertr', 'Atru.chr4.2356' => 'acertr', 'Atru.chr4.2358' => 'acertr', 'Atru.chr4.2359' => 'acertr', 'Atru.chr4.2360' => 'acertr', 'Atru.chr4.2361' => 'acertr', 'AUR62030476' => 'cqu', 'AUR62030478' => 'cqu', 'AUR62030819' => 'cqu', 'AUR62030820' => 'cqu', 'BcaB03g14648' => 'bca', 'BcaB04g20492' => 'bca', 'BcaB06g26399' => 'bca', 'BcaC01g03416' => 'bca', 'BcaC01g03419' => 'bca', 'BcaC01g03421' => 'bca', 'BcaC01g03424' => 'bca', 'BcaC05g28012' => 'bca', 'BcaC09g49212' => 'bca', 'BcaC09g50140' => 'bca', 'BcaNung00346' => 'bca', 'BolC1t02785H' => 'bol', 'BolC1t04095H' => 'bol', 'BolC3t17545H' => 'bol', 'BolC5t32769H' => 'bol', 'BraA01t02211Z' => 'bra', 'BraA01t03359Z' => 'bra', 'BraA03t13441Z' => 'bra', 'BraA05t21476Z' => 'bra', 'C01p28420' => 'bna', 'C01p41350' => 'bna', 'C03p52750' => 'bna', 'C03p52780' => 'bna', 'C05p40270' => 'bna', 'CAN.G1437.9' => 'can', 'CANSAT78G0035' => 'cansat', 'CANSAT78G1036' => 'cansat', 'CANSAT78G2272' => 'cansat', 'CANSAT78G2478' => 'cansat', 'CARHR098700' => 'chi', 'CARHR221120' => 'chi', 'CARHR221150' => 'chi', 'Carub.0003s2297' => 'cru', 'Carub.0007s2749' => 'cru', 'Carub.0007s2750' => 'cru', 'Carub.0007s2751' => 'cru', 'Ca_10849_v3' => 'car', 'Cc03_g04300' => 'ccan', 'CDE02G3648' => 'cde', 'CDE05G0060' => 'cde', 'CDE05G0692' => 'cde', 'CDE05G2285' => 'cde', 'CDE05G2884' => 'cde', 'CDE05G3072' => 'cde', 'Cfa008439' => 'cfa', 'Cfa008441' => 'cfa', 'Cfa008443' => 'cfa', 'Cfa008448' => 'cfa', 'Ciclev10005974m.g' => 'ccl', 'Ciclev10006006m.g' => 'ccl', 'Ciclev10006775m.g' => 'ccl', 'CiPaw.02G120400' => 'cil', 'CiPaw.02G120500' => 'cil', 'CiPaw.02G120600' => 'cil', 'ClCG05G004850' => 'cla', 'COL.COLO4_21566' => 'col', 'Cpa.g.sc44.124' => 'cpa', 'Cre07.g320400' => 'cre', 'Cre07.g320450' => 'cre', 'Cre08.g384650' => 'cre', 'Cre09.g393173' => 'cre', 'Cre09.g394325' => 'cre', 'Cre14.g626750' => 'cre', 'Cre16.g679250' => 'cre', 'CsaV3_3G012890' => 'csa', 'CSS0010865' => 'camsi', 'CSS0044338' => 'camsi', 'DCAR_002366' => 'dca', 'DCAR_030687' => 'dca', 'DCAR_030688' => 'dca', 'Dinv14047' => 'din', 'Dinv14048' => 'din', 'Duzib151G0105' => 'dzi', 'Duzib151G0114' => 'dzi', 'Duzib212G1029' => 'dzi', 'ECA232G3536' => 'eca', 'ECA240G0786' => 'eca', 'ECA240G1802' => 'eca', 'ECA240G3760' => 'eca', 'ECA240G3920' => 'eca', 'EL10Ac5g12536' => 'bvu', 'EL10Ac5g12537' => 'bvu', 'EL10Ac5g12538' => 'bvu', 'Eucgr.B01004' => 'egr', 'Eucgr.B01006' => 'egr', 'Eucgr.B01007' => 'egr', 'Eucgr.B01008' => 'egr', 'Eucgr.B01895' => 'egr', 'Eucgr.B01896' => 'egr', 'FAN04G1456' => 'fan', 'FAN08G1769' => 'fan', 'FAN08G2160' => 'fan', 'FAN13G2403' => 'fan', 'FAN13G3303' => 'fan', 'FAN15G2435' => 'fan', 'FAN17G0672' => 'fan', 'FAN17G2441' => 'fan', 'FAN18G1024' => 'fan', 'FAN22G1458' => 'fan', 'FAN24G0037' => 'fan', 'FAN24G0429' => 'fan', 'FAN24G2387' => 'fan', 'FAN27G2746' => 'fan', 'FvH4_2g20400' => 'fve', 'FvH4_2g20420' => 'fve', 'FvH4_2g20430' => 'fve', 'FvH4_4g01270' => 'fve', 'FvH4_4g01290' => 'fve', 'FvH4_4g01300' => 'fve', 'FvH4_4g01310' => 'fve', 'FvH4_4g01330' => 'fve', 'FvH4_5g09070' => 'fve', 'Glyma.10G243800' => 'gma', 'Glyma.20G150600' => 'gma', 'Gohir.A09G219200' => 'ghi', 'Gohir.A09G219300' => 'ghi', 'Gohir.D09G221400' => 'ghi', 'Gohir.D09G221500' => 'ghi', 'Gorai.006G242600' => 'gra', 'Gorai.006G242700' => 'gra', 'GSVIVG01018044001' => 'vvi', 'HanXRQChr03g0083821' => 'han', 'HanXRQChr03g0083841' => 'han', 'HanXRQChr03g0083881' => 'han', 'HanXRQChr03g0083901' => 'han', 'HanXRQChr03g0083921' => 'han', 'HanXRQChr03g0085331' => 'han', 'HanXRQChr03g0085361' => 'han', 'HanXRQChr03g0085411' => 'han', 'HanXRQChr03g0085421' => 'han', 'HanXRQChr03g0085431' => 'han', 'HanXRQChr08g0221991' => 'han', 'HanXRQChr11g0336061' => 'han', 'HanXRQChr11g0336411' => 'han', 'Haze_11234' => 'cav', 'Hma1.2p1_0549F.1_g177010' => 'hma', 'Hma1.2p1_0602F.1_g187630' => 'hma', 'Hund14876' => 'sun', 'Hund14879' => 'sun', 'Lalb_Chr06g0160741' => 'lal', 'Lalb_Chr21g0304781' => 'lal', 'Lj3A726G19' => 'lonja', 'Lj3A726T23' => 'lonja', 'Lj3A726T24' => 'lonja', 'Lj3A726T25' => 'lonja', 'Lj3A727T17' => 'lonja', 'Lj3C726T0' => 'lonja', 'Lj3C726T2' => 'lonja', 'Lj3P725T35' => 'lonja', 'Lj3P727T10' => 'lonja', 'Lj3P727T12' => 'lonja', 'Lj3P727T14' => 'lonja', 'Lj5g0023109' => 'lja', 'Lj6P646T44' => 'lonja', 'Lsat_1_v5_gn_6_75760' => 'lsa', 'Lsat_1_v5_gn_6_75800' => 'lsa', 'Lsat_1_v5_gn_6_75900' => 'lsa', 'Lsat_1_v5_gn_6_76240' => 'lsa', 'Lsat_1_v5_gn_6_76441' => 'lsa', 'Lsat_1_v5_gn_6_76700' => 'lsa', 'Lsat_1_v5_gn_6_76760' => 'lsa', 'Manes.15G033100' => 'mes', 'Mapoly0004s0074' => 'mpo', 'Mapoly0004s0075' => 'mpo', 'Mapoly0004s0163' => 'mpo', 'Mapoly0004s0164' => 'mpo', 'Mapoly0021s0018' => 'mpo', 'Mapoly0041s0136' => 'mpo', 'Mapoly0041s0137' => 'mpo', 'Mapoly0041s0138' => 'mpo', 'Mapoly0041s0139' => 'mpo', 'Mapoly0041s0141' => 'mpo', 'Mapoly0041s0142' => 'mpo', 'Mapoly0041s0143' => 'mpo', 'Mapoly0041s0144' => 'mpo', 'Mapoly0041s0145' => 'mpo', 'Mapoly0047s0106' => 'mpo', 'Mapoly0047s0108' => 'mpo', 'Mapoly0050s0051' => 'mpo', 'Mapoly0050s0052' => 'mpo', 'Mapoly0050s0053' => 'mpo', 'Mapoly0058s0013' => 'mpo', 'Mapoly0091s0078' => 'mpo', 'Mapoly0091s0079' => 'mpo', 'Mapoly0091s0080' => 'mpo', 'Mapoly0091s0081' => 'mpo', 'Mapoly0278s0004' => 'mpo', 'Mapoly0278s0005' => 'mpo', 'Mapoly0278s0006' => 'mpo', 'MBI11_g30648_MAGBIO' => 'mbi', 'MCO03G194' => 'mco', 'MCO03G590' => 'mco', 'MCO07G312' => 'mco', 'MCO10G318' => 'mco', 'MCO12G244' => 'mco', 'MCO13G148' => 'mco', 'MCO13G194' => 'mco', 'MCO16G238' => 'mco', 'MD06G1134100' => 'mdo', 'MD13G1200100' => 'mdo', 'MD13G1200300' => 'mdo', 'MD13G1200600' => 'mdo', 'MD14G1150400' => 'mdo', 'MD16G1200000' => 'mdo', 'Medtr1g102570' => 'mtr', 'Medtr1g102780' => 'mtr', 'Medtr1g102800' => 'mtr', 'Medtr1g102810' => 'mtr', 'Medtr1g102830' => 'mtr', 'MELO3C006499.2' => 'cme', 'Migut.G00385' => 'egut', 'MSTRG.4063' => 'ama', 'Nitab4.5_0000090g0260' => 'nta', 'Nitab4.5_0000977g0030' => 'nta', 'Nitab4.5_0002541g0040' => 'nta', 'Nitab4.5_0007068g0040' => 'nta', 'Nn005s41408' => 'nnu', 'Nn005s41410' => 'nnu', 'Oeu010310.1' => 'oeu', 'Oeu010311.1' => 'oeu', 'Oeu043472.1' => 'oeu', 'Os01g0246400' => 'osa', 'Os04g0267950' => 'osa', 'Os07g0178700' => 'osa', 'Os07g0178800' => 'osa', 'Peaxi162Scf00316g00046' => 'pax', 'Peaxi162Scf00316g00049' => 'pax', 'Peaxi162Scf00316g00059' => 'pax', 'Peaxi162Scf00316g00328' => 'pax', 'Peaxi162Scf00316g00329' => 'pax', 'Peaxi162Scf00316g00411' => 'pax', 'Peaxi162Scf00316g00521' => 'pax', 'Peaxi162Scf00492g00068' => 'pax', 'Peaxi162Scf35631g00002' => 'pax', 'PGR142G3720' => 'pgr', 'PGSC0003DMG400006442' => 'stu', 'Phvul.007G062000' => 'pvu', 'Potri.008G157750' => 'ptr', 'Potri.008G157900' => 'ptr', 'Potri.008G158000' => 'ptr', 'Potri.008G158200' => 'ptr', 'Pp3c11_7280' => 'ppa', 'Pp3c11_7980' => 'ppa', 'Pp3c12_19450' => 'ppa', 'Pp3c14_1480' => 'ppa', 'Pp3c14_1501' => 'ppa', 'Pp3c16_4900' => 'ppa', 'Pp3c16_5010' => 'ppa', 'Pp3c16_5060' => 'ppa', 'Pp3c19_18250' => 'ppa', 'Pp3c23_8530' => 'ppa', 'Pp3c23_8550' => 'ppa', 'Pp3c24_9670' => 'ppa', 'Pp3c2_21390' => 'ppa', 'Pp3c2_31380' => 'ppa', 'Pp3c3_16620' => 'ppa', 'Pp3c3_8090' => 'ppa', 'Pp3c3_8110' => 'ppa', 'Pp3c3_8130' => 'ppa', 'Pp3c3_8150' => 'ppa', 'Pp3c4_14320' => 'ppa', 'Pp3c6_2560' => 'ppa', 'Pp3c9_16700' => 'ppa', 'PRCOL_00000234' => 'pco', 'PRCOL_00000235' => 'pco', 'PRCOL_00000777' => 'pco', 'PRCOL_00002344' => 'pco', 'PRCOL_00002372' => 'pco', 'PRCOL_00006120' => 'pco', 'Prupe.1G021400' => 'ppe', 'Prupe.1G021500' => 'ppe', 'Prupe.1G021600' => 'ppe', 'Prupe.1G021700' => 'ppe', 'Prupe.1G021800' => 'ppe', 'Prupe.5G145100' => 'ppe', 'Psat6g204040' => 'psa', 'Psat6g204800' => 'psa', 'Psat6g204920' => 'psa', 'Psat6g204960' => 'psa', 'Psat6g205080' => 'psa', 'PSO017G0271' => 'pso', 'PSO017G1276' => 'pso', 'PSO017G1429' => 'pso', 'PSO017G1861' => 'pso', 'PSO017G2787' => 'pso', 'PSO017G4466' => 'pso', 'PSO017G5118' => 'pso', 'PSO017G5420' => 'pso', 'PSO063G3678' => 'pso', 'PSO210G0546' => 'pso', 'PSO317G0001' => 'pso', 'PSO357G0512' => 'pso', 'PSO478G2682' => 'pso', 'PSO647G0001' => 'pso', 'PSO675G0001' => 'pso', 'PSO675G2699' => 'pso', 'PSO675G2849' => 'pso', 'PSO675G4991' => 'pso', 'PSO689G0001' => 'pso', 'QL06p000916' => 'qlo', 'QL06p000921' => 'qlo', 'QL06p001398' => 'qlo', 'QL06p001407' => 'qlo', 'QL06p002031' => 'qlo', 'RcHm_v2.0_Chr4g0387791' => 'rch', 'RcHm_v2.0_Chr4g0387801' => 'rch', 'RcHm_v2.0_Chr6g0286501' => 'rch', 'RcHm_v2.0_Chr6g0286511' => 'rch', 'RcHm_v2.0_Chr6g0286521' => 'rch', 'RcHm_v2.0_Chr6g0286531' => 'rch', 'RcHm_v2.0_Chr7g0189141' => 'rch', 'Rhsim02G0028700' => 'rsi', 'Rhsim02G0028800' => 'rsi', 'Rhsim02G0028900' => 'rsi', 'Rhsim02G0029000' => 'rsi', 'Rhsim02G0029100' => 'rsi', 'Rhsim02G0029200' => 'rsi', 'Rhsim02G0029300' => 'rsi', 'Rhsim02G0029400' => 'rsi', 'Rhsim02G0029500' => 'rsi', 'Rhsim02G0029600' => 'rsi', 'RhsimUnG0024000' => 'rsi', 'RhsimUnG0024100' => 'rsi', 'RhsimUnG0024200' => 'rsi', 'RhsimUnG0024300' => 'rsi', 'RhsimUnG0024400' => 'rsi', 'RhsimUnG0024500' => 'rsi', 'RhsimUnG0024700' => 'rsi', 'RhsimUnG0024800' => 'rsi', 'RhsimUnG0024900' => 'rsi', 'RhsimUnG0025100' => 'rsi', 'Sabra08G0120200' => 'sbr', 'Sabra08G0120300' => 'sbr', 'Sabra08G0120500' => 'sbr', 'Sabra08G0120600' => 'sbr', 'Sabra10G0158900' => 'sbr', 'SalBow2G3492' => 'sbo', 'Sc13g0004760' => 'sci', 'Sc13g0004770' => 'sci', 'Sed0003417' => 'sed', 'Sed0019750' => 'sed', 'SEGI_03419' => 'sgi', 'SEGI_05907' => 'sgi', 'SEGI_10682' => 'sgi', 'SEGI_13528' => 'sgi', 'SEGI_16081' => 'sgi', 'SEGI_19370' => 'sgi', 'SEGI_21015' => 'sgi', 'SEGI_21944' => 'sgi', 'SEGI_32906' => 'sgi', 'SEGI_33093' => 'sgi', 'SEGI_36110' => 'sgi', 'SEGI_40397' => 'sgi', 'SGA_v2.0_scaffold191G40426' => 'sas', 'SGA_v2.0_scaffold353G49717' => 'sas', 'SGA_v2.0_scaffold50G18550' => 'sas', 'SMO119G0173' => 'smo', 'SMO172G0002' => 'smo', 'Solyc09g082690.3' => 'sly', 'Solyc09g082700.2' => 'sly', 'Sopen09g031550' => 'spe', 'Sopen09g031560' => 'spe', 'Sp3g20540' => 'spa', 'Sp7g07580' => 'spa', 'TAR134G0002' => 'tar', 'TAR236G0001' => 'tar', 'TAR365G0892' => 'tar', 'TAR636G0166' => 'tar', 'TAR636G0646' => 'tar', 'TAR636G0869' => 'tar', 'TAR636G1317' => 'tar', 'TAR636G1744' => 'tar', 'TAR636G3358' => 'tar', 'TAR636G3436' => 'tar', 'THA.LOC104803047' => 'tha', 'Thecc.04G238900' => 'tca', 'Thhalv10021557m.g' => 'esa', 'Thhalv10026318m.g' => 'esa', 'Thhalv10026335m.g' => 'esa', 'TPR.G17433' => 'tpr', 'TPR.G18915' => 'tpr', 'TPR.G26125' => 'tpr', 'TWI09G0677' => 'twi', 'TWI73G0287' => 'twi', 'unitig_748.g8326' => 'ugi', 'vmacro15370' => 'vma', 'vmacro15371' => 'vma', 'vmacro15372' => 'vma', 'vmacro15373' => 'vma', 'vmacro15374' => 'vma', 'VMungo0720G2826' => 'vmu', 'Zm00001eb116960' => 'zma', 'Zm00001eb301260' => 'zma', 'Zm00001eb301270' => 'zma' ), 'gf_id' => 'HOM05D001460', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001460' ), 'data_identifier' => 'HOM05D001460', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001460', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '433', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p22980' => 'bna', 'A01p32340' => 'bna', 'A03p42970' => 'bna', 'A05p25880' => 'bna', 'Aa31LG8G9320' => 'aar', 'Aa31LG8G9330' => 'aar', 'Aa31LG8G9340' => 'aar', 'Aa31sc221G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1034' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1528' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.829' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2222' => 'aag', 'Ah.12g058830' => 'amhyb', 'Ah.12g058840' => 'amhyb', 'AL3G37160' => 'aly', 'AL7G41310' => 'aly', 'Aqoxy5G00395' => 'aox', 'Aqoxy5G00396' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0C8NZA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5185HY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JZ1PRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MD3LS0' => 'arhy', 'AT3G22840' => 'ath', 'AT4G14690' => 'ath', 'ATR0665G054' => 'atr', 'Atru.chr4.2344' => 'acertr', 'Atru.chr4.2346' => 'acertr', 'Atru.chr4.2347' => 'acertr', 'Atru.chr4.2348' => 'acertr', 'Atru.chr4.2355' => 'acertr', 'Atru.chr4.2356' => 'acertr', 'Atru.chr4.2358' => 'acertr', 'Atru.chr4.2359' => 'acertr', 'Atru.chr4.2360' => 'acertr', 'Atru.chr4.2361' => 'acertr', 'AUR62030476' => 'cqu', 'AUR62030478' => 'cqu', 'AUR62030819' => 'cqu', 'AUR62030820' => 'cqu', 'BcaB03g14648' => 'bca', 'BcaB04g20492' => 'bca', 'BcaB06g26399' => 'bca', 'BcaC01g03416' => 'bca', 'BcaC01g03419' => 'bca', 'BcaC01g03421' => 'bca', 'BcaC01g03424' => 'bca', 'BcaC05g28012' => 'bca', 'BcaC09g49212' => 'bca', 'BcaC09g50140' => 'bca', 'BcaNung00346' => 'bca', 'BolC1t02785H' => 'bol', 'BolC1t04095H' => 'bol', 'BolC3t17545H' => 'bol', 'BolC5t32769H' => 'bol', 'BraA01t02211Z' => 'bra', 'BraA01t03359Z' => 'bra', 'BraA03t13441Z' => 'bra', 'BraA05t21476Z' => 'bra', 'C01p28420' => 'bna', 'C01p41350' => 'bna', 'C03p52750' => 'bna', 'C03p52780' => 'bna', 'C05p40270' => 'bna', 'CAN.G1437.9' => 'can', 'CANSAT78G0035' => 'cansat', 'CANSAT78G1036' => 'cansat', 'CANSAT78G2272' => 'cansat', 'CANSAT78G2478' => 'cansat', 'CARHR098700' => 'chi', 'CARHR221120' => 'chi', 'CARHR221150' => 'chi', 'Carub.0003s2297' => 'cru', 'Carub.0007s2749' => 'cru', 'Carub.0007s2750' => 'cru', 'Carub.0007s2751' => 'cru', 'Ca_10849_v3' => 'car', 'Cc03_g04300' => 'ccan', 'CDE02G3648' => 'cde', 'CDE05G0060' => 'cde', 'CDE05G0692' => 'cde', 'CDE05G2285' => 'cde', 'CDE05G2884' => 'cde', 'CDE05G3072' => 'cde', 'Cfa008439' => 'cfa', 'Cfa008441' => 'cfa', 'Cfa008443' => 'cfa', 'Cfa008448' => 'cfa', 'Ciclev10005974m.g' => 'ccl', 'Ciclev10006006m.g' => 'ccl', 'Ciclev10006775m.g' => 'ccl', 'CiPaw.02G120400' => 'cil', 'CiPaw.02G120500' => 'cil', 'CiPaw.02G120600' => 'cil', 'ClCG05G004850' => 'cla', 'COL.COLO4_21566' => 'col', 'Cpa.g.sc44.124' => 'cpa', 'Cre07.g320400' => 'cre', 'Cre07.g320450' => 'cre', 'Cre08.g384650' => 'cre', 'Cre09.g393173' => 'cre', 'Cre09.g394325' => 'cre', 'Cre14.g626750' => 'cre', 'Cre16.g679250' => 'cre', 'CsaV3_3G012890' => 'csa', 'CSS0010865' => 'camsi', 'CSS0044338' => 'camsi', 'DCAR_002366' => 'dca', 'DCAR_030687' => 'dca', 'DCAR_030688' => 'dca', 'Dinv14047' => 'din', 'Dinv14048' => 'din', 'Duzib151G0105' => 'dzi', 'Duzib151G0114' => 'dzi', 'Duzib212G1029' => 'dzi', 'ECA232G3536' => 'eca', 'ECA240G0786' => 'eca', 'ECA240G1802' => 'eca', 'ECA240G3760' => 'eca', 'ECA240G3920' => 'eca', 'EL10Ac5g12536' => 'bvu', 'EL10Ac5g12537' => 'bvu', 'EL10Ac5g12538' => 'bvu', 'Eucgr.B01004' => 'egr', 'Eucgr.B01006' => 'egr', 'Eucgr.B01007' => 'egr', 'Eucgr.B01008' => 'egr', 'Eucgr.B01895' => 'egr', 'Eucgr.B01896' => 'egr', 'FAN04G1456' => 'fan', 'FAN08G1769' => 'fan', 'FAN08G2160' => 'fan', 'FAN13G2403' => 'fan', 'FAN13G3303' => 'fan', 'FAN15G2435' => 'fan', 'FAN17G0672' => 'fan', 'FAN17G2441' => 'fan', 'FAN18G1024' => 'fan', 'FAN22G1458' => 'fan', 'FAN24G0037' => 'fan', 'FAN24G0429' => 'fan', 'FAN24G2387' => 'fan', 'FAN27G2746' => 'fan', 'FvH4_2g20400' => 'fve', 'FvH4_2g20420' => 'fve', 'FvH4_2g20430' => 'fve', 'FvH4_4g01270' => 'fve', 'FvH4_4g01290' => 'fve', 'FvH4_4g01300' => 'fve', 'FvH4_4g01310' => 'fve', 'FvH4_4g01330' => 'fve', 'FvH4_5g09070' => 'fve', 'Glyma.10G243800' => 'gma', 'Glyma.20G150600' => 'gma', 'Gohir.A09G219200' => 'ghi', 'Gohir.A09G219300' => 'ghi', 'Gohir.D09G221400' => 'ghi', 'Gohir.D09G221500' => 'ghi', 'Gorai.006G242600' => 'gra', 'Gorai.006G242700' => 'gra', 'GSVIVG01018044001' => 'vvi', 'HanXRQChr03g0083821' => 'han', 'HanXRQChr03g0083841' => 'han', 'HanXRQChr03g0083881' => 'han', 'HanXRQChr03g0083901' => 'han', 'HanXRQChr03g0083921' => 'han', 'HanXRQChr03g0085331' => 'han', 'HanXRQChr03g0085361' => 'han', 'HanXRQChr03g0085411' => 'han', 'HanXRQChr03g0085421' => 'han', 'HanXRQChr03g0085431' => 'han', 'HanXRQChr08g0221991' => 'han', 'HanXRQChr11g0336061' => 'han', 'HanXRQChr11g0336411' => 'han', 'Haze_11234' => 'cav', 'Hma1.2p1_0549F.1_g177010' => 'hma', 'Hma1.2p1_0602F.1_g187630' => 'hma', 'Hund14876' => 'sun', 'Hund14879' => 'sun', 'Lalb_Chr06g0160741' => 'lal', 'Lalb_Chr21g0304781' => 'lal', 'Lj3A726G19' => 'lonja', 'Lj3A726T23' => 'lonja', 'Lj3A726T24' => 'lonja', 'Lj3A726T25' => 'lonja', 'Lj3A727T17' => 'lonja', 'Lj3C726T0' => 'lonja', 'Lj3C726T2' => 'lonja', 'Lj3P725T35' => 'lonja', 'Lj3P727T10' => 'lonja', 'Lj3P727T12' => 'lonja', 'Lj3P727T14' => 'lonja', 'Lj5g0023109' => 'lja', 'Lj6P646T44' => 'lonja', 'Lsat_1_v5_gn_6_75760' => 'lsa', 'Lsat_1_v5_gn_6_75800' => 'lsa', 'Lsat_1_v5_gn_6_75900' => 'lsa', 'Lsat_1_v5_gn_6_76240' => 'lsa', 'Lsat_1_v5_gn_6_76441' => 'lsa', 'Lsat_1_v5_gn_6_76700' => 'lsa', 'Lsat_1_v5_gn_6_76760' => 'lsa', 'Manes.15G033100' => 'mes', 'Mapoly0004s0074' => 'mpo', 'Mapoly0004s0075' => 'mpo', 'Mapoly0004s0163' => 'mpo', 'Mapoly0004s0164' => 'mpo', 'Mapoly0021s0018' => 'mpo', 'Mapoly0041s0136' => 'mpo', 'Mapoly0041s0137' => 'mpo', 'Mapoly0041s0138' => 'mpo', 'Mapoly0041s0139' => 'mpo', 'Mapoly0041s0141' => 'mpo', 'Mapoly0041s0142' => 'mpo', 'Mapoly0041s0143' => 'mpo', 'Mapoly0041s0144' => 'mpo', 'Mapoly0041s0145' => 'mpo', 'Mapoly0047s0106' => 'mpo', 'Mapoly0047s0108' => 'mpo', 'Mapoly0050s0051' => 'mpo', 'Mapoly0050s0052' => 'mpo', 'Mapoly0050s0053' => 'mpo', 'Mapoly0058s0013' => 'mpo', 'Mapoly0091s0078' => 'mpo', 'Mapoly0091s0079' => 'mpo', 'Mapoly0091s0080' => 'mpo', 'Mapoly0091s0081' => 'mpo', 'Mapoly0278s0004' => 'mpo', 'Mapoly0278s0005' => 'mpo', 'Mapoly0278s0006' => 'mpo', 'MBI11_g30648_MAGBIO' => 'mbi', 'MCO03G194' => 'mco', 'MCO03G590' => 'mco', 'MCO07G312' => 'mco', 'MCO10G318' => 'mco', 'MCO12G244' => 'mco', 'MCO13G148' => 'mco', 'MCO13G194' => 'mco', 'MCO16G238' => 'mco', 'MD06G1134100' => 'mdo', 'MD13G1200100' => 'mdo', 'MD13G1200300' => 'mdo', 'MD13G1200600' => 'mdo', 'MD14G1150400' => 'mdo', 'MD16G1200000' => 'mdo', 'Medtr1g102570' => 'mtr', 'Medtr1g102780' => 'mtr', 'Medtr1g102800' => 'mtr', 'Medtr1g102810' => 'mtr', 'Medtr1g102830' => 'mtr', 'MELO3C006499.2' => 'cme', 'Migut.G00385' => 'egut', 'MSTRG.4063' => 'ama', 'Nitab4.5_0000090g0260' => 'nta', 'Nitab4.5_0000977g0030' => 'nta', 'Nitab4.5_0002541g0040' => 'nta', 'Nitab4.5_0007068g0040' => 'nta', 'Nn005s41408' => 'nnu', 'Nn005s41410' => 'nnu', 'Oeu010310.1' => 'oeu', 'Oeu010311.1' => 'oeu', 'Oeu043472.1' => 'oeu', 'Os01g0246400' => 'osa', 'Os04g0267950' => 'osa', 'Os07g0178700' => 'osa', 'Os07g0178800' => 'osa', 'Peaxi162Scf00316g00046' => 'pax', 'Peaxi162Scf00316g00049' => 'pax', 'Peaxi162Scf00316g00059' => 'pax', 'Peaxi162Scf00316g00328' => 'pax', 'Peaxi162Scf00316g00329' => 'pax', 'Peaxi162Scf00316g00411' => 'pax', 'Peaxi162Scf00316g00521' => 'pax', 'Peaxi162Scf00492g00068' => 'pax', 'Peaxi162Scf35631g00002' => 'pax', 'PGR142G3720' => 'pgr', 'PGSC0003DMG400006442' => 'stu', 'Phvul.007G062000' => 'pvu', 'Potri.008G157750' => 'ptr', 'Potri.008G157900' => 'ptr', 'Potri.008G158000' => 'ptr', 'Potri.008G158200' => 'ptr', 'Pp3c11_7280' => 'ppa', 'Pp3c11_7980' => 'ppa', 'Pp3c12_19450' => 'ppa', 'Pp3c14_1480' => 'ppa', 'Pp3c14_1501' => 'ppa', 'Pp3c16_4900' => 'ppa', 'Pp3c16_5010' => 'ppa', 'Pp3c16_5060' => 'ppa', 'Pp3c19_18250' => 'ppa', 'Pp3c23_8530' => 'ppa', 'Pp3c23_8550' => 'ppa', 'Pp3c24_9670' => 'ppa', 'Pp3c2_21390' => 'ppa', 'Pp3c2_31380' => 'ppa', 'Pp3c3_16620' => 'ppa', 'Pp3c3_8090' => 'ppa', 'Pp3c3_8110' => 'ppa', 'Pp3c3_8130' => 'ppa', 'Pp3c3_8150' => 'ppa', 'Pp3c4_14320' => 'ppa', 'Pp3c6_2560' => 'ppa', 'Pp3c9_16700' => 'ppa', 'PRCOL_00000234' => 'pco', 'PRCOL_00000235' => 'pco', 'PRCOL_00000777' => 'pco', 'PRCOL_00002344' => 'pco', 'PRCOL_00002372' => 'pco', 'PRCOL_00006120' => 'pco', 'Prupe.1G021400' => 'ppe', 'Prupe.1G021500' => 'ppe', 'Prupe.1G021600' => 'ppe', 'Prupe.1G021700' => 'ppe', 'Prupe.1G021800' => 'ppe', 'Prupe.5G145100' => 'ppe', 'Psat6g204040' => 'psa', 'Psat6g204800' => 'psa', 'Psat6g204920' => 'psa', 'Psat6g204960' => 'psa', 'Psat6g205080' => 'psa', 'PSO017G0271' => 'pso', 'PSO017G1276' => 'pso', 'PSO017G1429' => 'pso', 'PSO017G1861' => 'pso', 'PSO017G2787' => 'pso', 'PSO017G4466' => 'pso', 'PSO017G5118' => 'pso', 'PSO017G5420' => 'pso', 'PSO063G3678' => 'pso', 'PSO210G0546' => 'pso', 'PSO317G0001' => 'pso', 'PSO357G0512' => 'pso', 'PSO478G2682' => 'pso', 'PSO647G0001' => 'pso', 'PSO675G0001' => 'pso', 'PSO675G2699' => 'pso', 'PSO675G2849' => 'pso', 'PSO675G4991' => 'pso', 'PSO689G0001' => 'pso', 'QL06p000916' => 'qlo', 'QL06p000921' => 'qlo', 'QL06p001398' => 'qlo', 'QL06p001407' => 'qlo', 'QL06p002031' => 'qlo', 'RcHm_v2.0_Chr4g0387791' => 'rch', 'RcHm_v2.0_Chr4g0387801' => 'rch', 'RcHm_v2.0_Chr6g0286501' => 'rch', 'RcHm_v2.0_Chr6g0286511' => 'rch', 'RcHm_v2.0_Chr6g0286521' => 'rch', 'RcHm_v2.0_Chr6g0286531' => 'rch', 'RcHm_v2.0_Chr7g0189141' => 'rch', 'Rhsim02G0028700' => 'rsi', 'Rhsim02G0028800' => 'rsi', 'Rhsim02G0028900' => 'rsi', 'Rhsim02G0029000' => 'rsi', 'Rhsim02G0029100' => 'rsi', 'Rhsim02G0029200' => 'rsi', 'Rhsim02G0029300' => 'rsi', 'Rhsim02G0029400' => 'rsi', 'Rhsim02G0029500' => 'rsi', 'Rhsim02G0029600' => 'rsi', 'RhsimUnG0024000' => 'rsi', 'RhsimUnG0024100' => 'rsi', 'RhsimUnG0024200' => 'rsi', 'RhsimUnG0024300' => 'rsi', 'RhsimUnG0024400' => 'rsi', 'RhsimUnG0024500' => 'rsi', 'RhsimUnG0024700' => 'rsi', 'RhsimUnG0024800' => 'rsi', 'RhsimUnG0024900' => 'rsi', 'RhsimUnG0025100' => 'rsi', 'Sabra08G0120200' => 'sbr', 'Sabra08G0120300' => 'sbr', 'Sabra08G0120500' => 'sbr', 'Sabra08G0120600' => 'sbr', 'Sabra10G0158900' => 'sbr', 'SalBow2G3492' => 'sbo', 'Sc13g0004760' => 'sci', 'Sc13g0004770' => 'sci', 'Sed0003417' => 'sed', 'Sed0019750' => 'sed', 'SEGI_03419' => 'sgi', 'SEGI_05907' => 'sgi', 'SEGI_10682' => 'sgi', 'SEGI_13528' => 'sgi', 'SEGI_16081' => 'sgi', 'SEGI_19370' => 'sgi', 'SEGI_21015' => 'sgi', 'SEGI_21944' => 'sgi', 'SEGI_32906' => 'sgi', 'SEGI_33093' => 'sgi', 'SEGI_36110' => 'sgi', 'SEGI_40397' => 'sgi', 'SGA_v2.0_scaffold191G40426' => 'sas', 'SGA_v2.0_scaffold353G49717' => 'sas', 'SGA_v2.0_scaffold50G18550' => 'sas', 'SMO119G0173' => 'smo', 'SMO172G0002' => 'smo', 'Solyc09g082690.3' => 'sly', 'Solyc09g082700.2' => 'sly', 'Sopen09g031550' => 'spe', 'Sopen09g031560' => 'spe', 'Sp3g20540' => 'spa', 'Sp7g07580' => 'spa', 'TAR134G0002' => 'tar', 'TAR236G0001' => 'tar', 'TAR365G0892' => 'tar', 'TAR636G0166' => 'tar', 'TAR636G0646' => 'tar', 'TAR636G0869' => 'tar', 'TAR636G1317' => 'tar', 'TAR636G1744' => 'tar', 'TAR636G3358' => 'tar', 'TAR636G3436' => 'tar', 'THA.LOC104803047' => 'tha', 'Thecc.04G238900' => 'tca', 'Thhalv10021557m.g' => 'esa', 'Thhalv10026318m.g' => 'esa', 'Thhalv10026335m.g' => 'esa', 'TPR.G17433' => 'tpr', 'TPR.G18915' => 'tpr', 'TPR.G26125' => 'tpr', 'TWI09G0677' => 'twi', 'TWI73G0287' => 'twi', 'unitig_748.g8326' => 'ugi', 'vmacro15370' => 'vma', 'vmacro15371' => 'vma', 'vmacro15372' => 'vma', 'vmacro15373' => 'vma', 'vmacro15374' => 'vma', 'VMungo0720G2826' => 'vmu', 'Zm00001eb116960' => 'zma', 'Zm00001eb301260' => 'zma', 'Zm00001eb301270' => 'zma' ) $gf_id = 'HOM05D001460' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001460' ) $data_identifier = 'HOM05D001460' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 4, 'aag' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 2, 'aox' => (int) 2, 'arhy' => (int) 4, 'ath' => (int) 2, 'atr' => (int) 1, 'acertr' => (int) 10, 'cqu' => (int) 4, 'bca' => (int) 11, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 1, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 1, 'ccan' => (int) 1, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 1, 'col' => (int) 1, 'cpa' => (int) 1, 'cre' => (int) 7, 'csa' => (int) 1, 'camsi' => (int) 2, 'dca' => (int) 3, 'din' => (int) 2, 'dzi' => (int) 3, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 14, 'fve' => (int) 9, 'gma' => (int) 2, 'ghi' => (int) 4, 'gra' => (int) 2, 'vvi' => (int) 1, 'han' => (int) 13, 'cav' => (int) 1, 'hma' => (int) 2, 'sun' => (int) 2, 'lal' => (int) 2, 'lonja' => (int) 12, 'lja' => (int) 1, 'lsa' => (int) 7, 'mes' => (int) 1, 'mpo' => (int) 27, 'mbi' => (int) 1, 'mco' => (int) 8, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 1, 'egut' => (int) 1, 'ama' => (int) 1, 'nta' => (int) 4, 'nnu' => (int) 2, 'oeu' => (int) 3, 'osa' => (int) 4, 'pax' => (int) 9, 'pgr' => (int) 1, 'stu' => (int) 1, 'pvu' => (int) 1, 'ptr' => (int) 4, 'ppa' => (int) 22, 'pco' => (int) 6, 'ppe' => (int) 6, 'psa' => (int) 5, 'pso' => (int) 19, 'qlo' => (int) 5, 'rch' => (int) 7, 'rsi' => (int) 20, 'sbr' => (int) 5, 'sbo' => (int) 1, 'sci' => (int) 2, 'sed' => (int) 2, 'sgi' => (int) 12, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 2, 'tar' => (int) 10, 'tha' => (int) 1, 'tca' => (int) 1, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 2, 'ugi' => (int) 1, 'vma' => (int) 5, 'vmu' => (int) 1, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb301270' $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' => 'HOM05D001460', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '433', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p22980' => 'bna', 'A01p32340' => 'bna', 'A03p42970' => 'bna', 'A05p25880' => 'bna', 'Aa31LG8G9320' => 'aar', 'Aa31LG8G9330' => 'aar', 'Aa31LG8G9340' => 'aar', 'Aa31sc221G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1034' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1528' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.829' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2222' => 'aag', 'Ah.12g058830' => 'amhyb', 'Ah.12g058840' => 'amhyb', 'AL3G37160' => 'aly', 'AL7G41310' => 'aly', 'Aqoxy5G00395' => 'aox', 'Aqoxy5G00396' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0C8NZA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5185HY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JZ1PRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MD3LS0' => 'arhy', 'AT3G22840' => 'ath', 'AT4G14690' => 'ath', 'ATR0665G054' => 'atr', 'Atru.chr4.2344' => 'acertr', 'Atru.chr4.2346' => 'acertr', 'Atru.chr4.2347' => 'acertr', 'Atru.chr4.2348' => 'acertr', 'Atru.chr4.2355' => 'acertr', 'Atru.chr4.2356' => 'acertr', 'Atru.chr4.2358' => 'acertr', 'Atru.chr4.2359' => 'acertr', 'Atru.chr4.2360' => 'acertr', 'Atru.chr4.2361' => 'acertr', 'AUR62030476' => 'cqu', 'AUR62030478' => 'cqu', 'AUR62030819' => 'cqu', 'AUR62030820' => 'cqu', 'BcaB03g14648' => 'bca', 'BcaB04g20492' => 'bca', 'BcaB06g26399' => 'bca', 'BcaC01g03416' => 'bca', 'BcaC01g03419' => 'bca', 'BcaC01g03421' => 'bca', 'BcaC01g03424' => 'bca', 'BcaC05g28012' => 'bca', 'BcaC09g49212' => 'bca', 'BcaC09g50140' => 'bca', 'BcaNung00346' => 'bca', 'BolC1t02785H' => 'bol', 'BolC1t04095H' => 'bol', 'BolC3t17545H' => 'bol', 'BolC5t32769H' => 'bol', 'BraA01t02211Z' => 'bra', 'BraA01t03359Z' => 'bra', 'BraA03t13441Z' => 'bra', 'BraA05t21476Z' => 'bra', 'C01p28420' => 'bna', 'C01p41350' => 'bna', 'C03p52750' => 'bna', 'C03p52780' => 'bna', 'C05p40270' => 'bna', 'CAN.G1437.9' => 'can', 'CANSAT78G0035' => 'cansat', 'CANSAT78G1036' => 'cansat', 'CANSAT78G2272' => 'cansat', 'CANSAT78G2478' => 'cansat', 'CARHR098700' => 'chi', 'CARHR221120' => 'chi', 'CARHR221150' => 'chi', 'Carub.0003s2297' => 'cru', 'Carub.0007s2749' => 'cru', 'Carub.0007s2750' => 'cru', 'Carub.0007s2751' => 'cru', 'Ca_10849_v3' => 'car', 'Cc03_g04300' => 'ccan', 'CDE02G3648' => 'cde', 'CDE05G0060' => 'cde', 'CDE05G0692' => 'cde', 'CDE05G2285' => 'cde', 'CDE05G2884' => 'cde', 'CDE05G3072' => 'cde', 'Cfa008439' => 'cfa', 'Cfa008441' => 'cfa', 'Cfa008443' => 'cfa', 'Cfa008448' => 'cfa', 'Ciclev10005974m.g' => 'ccl', 'Ciclev10006006m.g' => 'ccl', 'Ciclev10006775m.g' => 'ccl', 'CiPaw.02G120400' => 'cil', 'CiPaw.02G120500' => 'cil', 'CiPaw.02G120600' => 'cil', 'ClCG05G004850' => 'cla', 'COL.COLO4_21566' => 'col', 'Cpa.g.sc44.124' => 'cpa', 'Cre07.g320400' => 'cre', 'Cre07.g320450' => 'cre', 'Cre08.g384650' => 'cre', 'Cre09.g393173' => 'cre', 'Cre09.g394325' => 'cre', 'Cre14.g626750' => 'cre', 'Cre16.g679250' => 'cre', 'CsaV3_3G012890' => 'csa', 'CSS0010865' => 'camsi', 'CSS0044338' => 'camsi', 'DCAR_002366' => 'dca', 'DCAR_030687' => 'dca', 'DCAR_030688' => 'dca', 'Dinv14047' => 'din', 'Dinv14048' => 'din', 'Duzib151G0105' => 'dzi', 'Duzib151G0114' => 'dzi', 'Duzib212G1029' => 'dzi', 'ECA232G3536' => 'eca', 'ECA240G0786' => 'eca', 'ECA240G1802' => 'eca', 'ECA240G3760' => 'eca', 'ECA240G3920' => 'eca', 'EL10Ac5g12536' => 'bvu', 'EL10Ac5g12537' => 'bvu', 'EL10Ac5g12538' => 'bvu', 'Eucgr.B01004' => 'egr', 'Eucgr.B01006' => 'egr', 'Eucgr.B01007' => 'egr', 'Eucgr.B01008' => 'egr', 'Eucgr.B01895' => 'egr', 'Eucgr.B01896' => 'egr', 'FAN04G1456' => 'fan', 'FAN08G1769' => 'fan', 'FAN08G2160' => 'fan', 'FAN13G2403' => 'fan', 'FAN13G3303' => 'fan', 'FAN15G2435' => 'fan', 'FAN17G0672' => 'fan', 'FAN17G2441' => 'fan', 'FAN18G1024' => 'fan', 'FAN22G1458' => 'fan', 'FAN24G0037' => 'fan', 'FAN24G0429' => 'fan', 'FAN24G2387' => 'fan', 'FAN27G2746' => 'fan', 'FvH4_2g20400' => 'fve', 'FvH4_2g20420' => 'fve', 'FvH4_2g20430' => 'fve', 'FvH4_4g01270' => 'fve', 'FvH4_4g01290' => 'fve', 'FvH4_4g01300' => 'fve', 'FvH4_4g01310' => 'fve', 'FvH4_4g01330' => 'fve', 'FvH4_5g09070' => 'fve', 'Glyma.10G243800' => 'gma', 'Glyma.20G150600' => 'gma', 'Gohir.A09G219200' => 'ghi', 'Gohir.A09G219300' => 'ghi', 'Gohir.D09G221400' => 'ghi', 'Gohir.D09G221500' => 'ghi', 'Gorai.006G242600' => 'gra', 'Gorai.006G242700' => 'gra', 'GSVIVG01018044001' => 'vvi', 'HanXRQChr03g0083821' => 'han', 'HanXRQChr03g0083841' => 'han', 'HanXRQChr03g0083881' => 'han', 'HanXRQChr03g0083901' => 'han', 'HanXRQChr03g0083921' => 'han', 'HanXRQChr03g0085331' => 'han', 'HanXRQChr03g0085361' => 'han', 'HanXRQChr03g0085411' => 'han', 'HanXRQChr03g0085421' => 'han', 'HanXRQChr03g0085431' => 'han', 'HanXRQChr08g0221991' => 'han', 'HanXRQChr11g0336061' => 'han', 'HanXRQChr11g0336411' => 'han', 'Haze_11234' => 'cav', 'Hma1.2p1_0549F.1_g177010' => 'hma', 'Hma1.2p1_0602F.1_g187630' => 'hma', 'Hund14876' => 'sun', 'Hund14879' => 'sun', 'Lalb_Chr06g0160741' => 'lal', 'Lalb_Chr21g0304781' => 'lal', 'Lj3A726G19' => 'lonja', 'Lj3A726T23' => 'lonja', 'Lj3A726T24' => 'lonja', 'Lj3A726T25' => 'lonja', 'Lj3A727T17' => 'lonja', 'Lj3C726T0' => 'lonja', 'Lj3C726T2' => 'lonja', 'Lj3P725T35' => 'lonja', 'Lj3P727T10' => 'lonja', 'Lj3P727T12' => 'lonja', 'Lj3P727T14' => 'lonja', 'Lj5g0023109' => 'lja', 'Lj6P646T44' => 'lonja', 'Lsat_1_v5_gn_6_75760' => 'lsa', 'Lsat_1_v5_gn_6_75800' => 'lsa', 'Lsat_1_v5_gn_6_75900' => 'lsa', 'Lsat_1_v5_gn_6_76240' => 'lsa', 'Lsat_1_v5_gn_6_76441' => 'lsa', 'Lsat_1_v5_gn_6_76700' => 'lsa', 'Lsat_1_v5_gn_6_76760' => 'lsa', 'Manes.15G033100' => 'mes', 'Mapoly0004s0074' => 'mpo', 'Mapoly0004s0075' => 'mpo', 'Mapoly0004s0163' => 'mpo', 'Mapoly0004s0164' => 'mpo', 'Mapoly0021s0018' => 'mpo', 'Mapoly0041s0136' => 'mpo', 'Mapoly0041s0137' => 'mpo', 'Mapoly0041s0138' => 'mpo', 'Mapoly0041s0139' => 'mpo', 'Mapoly0041s0141' => 'mpo', 'Mapoly0041s0142' => 'mpo', 'Mapoly0041s0143' => 'mpo', 'Mapoly0041s0144' => 'mpo', 'Mapoly0041s0145' => 'mpo', 'Mapoly0047s0106' => 'mpo', 'Mapoly0047s0108' => 'mpo', 'Mapoly0050s0051' => 'mpo', 'Mapoly0050s0052' => 'mpo', 'Mapoly0050s0053' => 'mpo', 'Mapoly0058s0013' => 'mpo', 'Mapoly0091s0078' => 'mpo', 'Mapoly0091s0079' => 'mpo', 'Mapoly0091s0080' => 'mpo', 'Mapoly0091s0081' => 'mpo', 'Mapoly0278s0004' => 'mpo', 'Mapoly0278s0005' => 'mpo', 'Mapoly0278s0006' => 'mpo', 'MBI11_g30648_MAGBIO' => 'mbi', 'MCO03G194' => 'mco', 'MCO03G590' => 'mco', 'MCO07G312' => 'mco', 'MCO10G318' => 'mco', 'MCO12G244' => 'mco', 'MCO13G148' => 'mco', 'MCO13G194' => 'mco', 'MCO16G238' => 'mco', 'MD06G1134100' => 'mdo', 'MD13G1200100' => 'mdo', 'MD13G1200300' => 'mdo', 'MD13G1200600' => 'mdo', 'MD14G1150400' => 'mdo', 'MD16G1200000' => 'mdo', 'Medtr1g102570' => 'mtr', 'Medtr1g102780' => 'mtr', 'Medtr1g102800' => 'mtr', 'Medtr1g102810' => 'mtr', 'Medtr1g102830' => 'mtr', 'MELO3C006499.2' => 'cme', 'Migut.G00385' => 'egut', 'MSTRG.4063' => 'ama', 'Nitab4.5_0000090g0260' => 'nta', 'Nitab4.5_0000977g0030' => 'nta', 'Nitab4.5_0002541g0040' => 'nta', 'Nitab4.5_0007068g0040' => 'nta', 'Nn005s41408' => 'nnu', 'Nn005s41410' => 'nnu', 'Oeu010310.1' => 'oeu', 'Oeu010311.1' => 'oeu', 'Oeu043472.1' => 'oeu', 'Os01g0246400' => 'osa', 'Os04g0267950' => 'osa', 'Os07g0178700' => 'osa', 'Os07g0178800' => 'osa', 'Peaxi162Scf00316g00046' => 'pax', 'Peaxi162Scf00316g00049' => 'pax', 'Peaxi162Scf00316g00059' => 'pax', 'Peaxi162Scf00316g00328' => 'pax', 'Peaxi162Scf00316g00329' => 'pax', 'Peaxi162Scf00316g00411' => 'pax', 'Peaxi162Scf00316g00521' => 'pax', 'Peaxi162Scf00492g00068' => 'pax', 'Peaxi162Scf35631g00002' => 'pax', 'PGR142G3720' => 'pgr', 'PGSC0003DMG400006442' => 'stu', 'Phvul.007G062000' => 'pvu', 'Potri.008G157750' => 'ptr', 'Potri.008G157900' => 'ptr', 'Potri.008G158000' => 'ptr', 'Potri.008G158200' => 'ptr', 'Pp3c11_7280' => 'ppa', 'Pp3c11_7980' => 'ppa', 'Pp3c12_19450' => 'ppa', 'Pp3c14_1480' => 'ppa', 'Pp3c14_1501' => 'ppa', 'Pp3c16_4900' => 'ppa', 'Pp3c16_5010' => 'ppa', 'Pp3c16_5060' => 'ppa', 'Pp3c19_18250' => 'ppa', 'Pp3c23_8530' => 'ppa', 'Pp3c23_8550' => 'ppa', 'Pp3c24_9670' => 'ppa', 'Pp3c2_21390' => 'ppa', 'Pp3c2_31380' => 'ppa', 'Pp3c3_16620' => 'ppa', 'Pp3c3_8090' => 'ppa', 'Pp3c3_8110' => 'ppa', 'Pp3c3_8130' => 'ppa', 'Pp3c3_8150' => 'ppa', 'Pp3c4_14320' => 'ppa', 'Pp3c6_2560' => 'ppa', 'Pp3c9_16700' => 'ppa', 'PRCOL_00000234' => 'pco', 'PRCOL_00000235' => 'pco', 'PRCOL_00000777' => 'pco', 'PRCOL_00002344' => 'pco', 'PRCOL_00002372' => 'pco', 'PRCOL_00006120' => 'pco', 'Prupe.1G021400' => 'ppe', 'Prupe.1G021500' => 'ppe', 'Prupe.1G021600' => 'ppe', 'Prupe.1G021700' => 'ppe', 'Prupe.1G021800' => 'ppe', 'Prupe.5G145100' => 'ppe', 'Psat6g204040' => 'psa', 'Psat6g204800' => 'psa', 'Psat6g204920' => 'psa', 'Psat6g204960' => 'psa', 'Psat6g205080' => 'psa', 'PSO017G0271' => 'pso', 'PSO017G1276' => 'pso', 'PSO017G1429' => 'pso', 'PSO017G1861' => 'pso', 'PSO017G2787' => 'pso', 'PSO017G4466' => 'pso', 'PSO017G5118' => 'pso', 'PSO017G5420' => 'pso', 'PSO063G3678' => 'pso', 'PSO210G0546' => 'pso', 'PSO317G0001' => 'pso', 'PSO357G0512' => 'pso', 'PSO478G2682' => 'pso', 'PSO647G0001' => 'pso', 'PSO675G0001' => 'pso', 'PSO675G2699' => 'pso', 'PSO675G2849' => 'pso', 'PSO675G4991' => 'pso', 'PSO689G0001' => 'pso', 'QL06p000916' => 'qlo', 'QL06p000921' => 'qlo', 'QL06p001398' => 'qlo', 'QL06p001407' => 'qlo', 'QL06p002031' => 'qlo', 'RcHm_v2.0_Chr4g0387791' => 'rch', 'RcHm_v2.0_Chr4g0387801' => 'rch', 'RcHm_v2.0_Chr6g0286501' => 'rch', 'RcHm_v2.0_Chr6g0286511' => 'rch', 'RcHm_v2.0_Chr6g0286521' => 'rch', 'RcHm_v2.0_Chr6g0286531' => 'rch', 'RcHm_v2.0_Chr7g0189141' => 'rch', 'Rhsim02G0028700' => 'rsi', 'Rhsim02G0028800' => 'rsi', 'Rhsim02G0028900' => 'rsi', 'Rhsim02G0029000' => 'rsi', 'Rhsim02G0029100' => 'rsi', 'Rhsim02G0029200' => 'rsi', 'Rhsim02G0029300' => 'rsi', 'Rhsim02G0029400' => 'rsi', 'Rhsim02G0029500' => 'rsi', 'Rhsim02G0029600' => 'rsi', 'RhsimUnG0024000' => 'rsi', 'RhsimUnG0024100' => 'rsi', 'RhsimUnG0024200' => 'rsi', 'RhsimUnG0024300' => 'rsi', 'RhsimUnG0024400' => 'rsi', 'RhsimUnG0024500' => 'rsi', 'RhsimUnG0024700' => 'rsi', 'RhsimUnG0024800' => 'rsi', 'RhsimUnG0024900' => 'rsi', 'RhsimUnG0025100' => 'rsi', 'Sabra08G0120200' => 'sbr', 'Sabra08G0120300' => 'sbr', 'Sabra08G0120500' => 'sbr', 'Sabra08G0120600' => 'sbr', 'Sabra10G0158900' => 'sbr', 'SalBow2G3492' => 'sbo', 'Sc13g0004760' => 'sci', 'Sc13g0004770' => 'sci', 'Sed0003417' => 'sed', 'Sed0019750' => 'sed', 'SEGI_03419' => 'sgi', 'SEGI_05907' => 'sgi', 'SEGI_10682' => 'sgi', 'SEGI_13528' => 'sgi', 'SEGI_16081' => 'sgi', 'SEGI_19370' => 'sgi', 'SEGI_21015' => 'sgi', 'SEGI_21944' => 'sgi', 'SEGI_32906' => 'sgi', 'SEGI_33093' => 'sgi', 'SEGI_36110' => 'sgi', 'SEGI_40397' => 'sgi', 'SGA_v2.0_scaffold191G40426' => 'sas', 'SGA_v2.0_scaffold353G49717' => 'sas', 'SGA_v2.0_scaffold50G18550' => 'sas', 'SMO119G0173' => 'smo', 'SMO172G0002' => 'smo', 'Solyc09g082690.3' => 'sly', 'Solyc09g082700.2' => 'sly', 'Sopen09g031550' => 'spe', 'Sopen09g031560' => 'spe', 'Sp3g20540' => 'spa', 'Sp7g07580' => 'spa', 'TAR134G0002' => 'tar', 'TAR236G0001' => 'tar', 'TAR365G0892' => 'tar', 'TAR636G0166' => 'tar', 'TAR636G0646' => 'tar', 'TAR636G0869' => 'tar', 'TAR636G1317' => 'tar', 'TAR636G1744' => 'tar', 'TAR636G3358' => 'tar', 'TAR636G3436' => 'tar', 'THA.LOC104803047' => 'tha', 'Thecc.04G238900' => 'tca', 'Thhalv10021557m.g' => 'esa', 'Thhalv10026318m.g' => 'esa', 'Thhalv10026335m.g' => 'esa', 'TPR.G17433' => 'tpr', 'TPR.G18915' => 'tpr', 'TPR.G26125' => 'tpr', 'TWI09G0677' => 'twi', 'TWI73G0287' => 'twi', 'unitig_748.g8326' => 'ugi', 'vmacro15370' => 'vma', 'vmacro15371' => 'vma', 'vmacro15372' => 'vma', 'vmacro15373' => 'vma', 'vmacro15374' => 'vma', 'VMungo0720G2826' => 'vmu', 'Zm00001eb116960' => 'zma', 'Zm00001eb301260' => 'zma', 'Zm00001eb301270' => 'zma' ), 'gf_id' => 'HOM05D001460', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001460' ), 'data_identifier' => 'HOM05D001460', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001460', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '433', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p22980' => 'bna', 'A01p32340' => 'bna', 'A03p42970' => 'bna', 'A05p25880' => 'bna', 'Aa31LG8G9320' => 'aar', 'Aa31LG8G9330' => 'aar', 'Aa31LG8G9340' => 'aar', 'Aa31sc221G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1034' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1528' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.829' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2222' => 'aag', 'Ah.12g058830' => 'amhyb', 'Ah.12g058840' => 'amhyb', 'AL3G37160' => 'aly', 'AL7G41310' => 'aly', 'Aqoxy5G00395' => 'aox', 'Aqoxy5G00396' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0C8NZA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5185HY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JZ1PRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MD3LS0' => 'arhy', 'AT3G22840' => 'ath', 'AT4G14690' => 'ath', 'ATR0665G054' => 'atr', 'Atru.chr4.2344' => 'acertr', 'Atru.chr4.2346' => 'acertr', 'Atru.chr4.2347' => 'acertr', 'Atru.chr4.2348' => 'acertr', 'Atru.chr4.2355' => 'acertr', 'Atru.chr4.2356' => 'acertr', 'Atru.chr4.2358' => 'acertr', 'Atru.chr4.2359' => 'acertr', 'Atru.chr4.2360' => 'acertr', 'Atru.chr4.2361' => 'acertr', 'AUR62030476' => 'cqu', 'AUR62030478' => 'cqu', 'AUR62030819' => 'cqu', 'AUR62030820' => 'cqu', 'BcaB03g14648' => 'bca', 'BcaB04g20492' => 'bca', 'BcaB06g26399' => 'bca', 'BcaC01g03416' => 'bca', 'BcaC01g03419' => 'bca', 'BcaC01g03421' => 'bca', 'BcaC01g03424' => 'bca', 'BcaC05g28012' => 'bca', 'BcaC09g49212' => 'bca', 'BcaC09g50140' => 'bca', 'BcaNung00346' => 'bca', 'BolC1t02785H' => 'bol', 'BolC1t04095H' => 'bol', 'BolC3t17545H' => 'bol', 'BolC5t32769H' => 'bol', 'BraA01t02211Z' => 'bra', 'BraA01t03359Z' => 'bra', 'BraA03t13441Z' => 'bra', 'BraA05t21476Z' => 'bra', 'C01p28420' => 'bna', 'C01p41350' => 'bna', 'C03p52750' => 'bna', 'C03p52780' => 'bna', 'C05p40270' => 'bna', 'CAN.G1437.9' => 'can', 'CANSAT78G0035' => 'cansat', 'CANSAT78G1036' => 'cansat', 'CANSAT78G2272' => 'cansat', 'CANSAT78G2478' => 'cansat', 'CARHR098700' => 'chi', 'CARHR221120' => 'chi', 'CARHR221150' => 'chi', 'Carub.0003s2297' => 'cru', 'Carub.0007s2749' => 'cru', 'Carub.0007s2750' => 'cru', 'Carub.0007s2751' => 'cru', 'Ca_10849_v3' => 'car', 'Cc03_g04300' => 'ccan', 'CDE02G3648' => 'cde', 'CDE05G0060' => 'cde', 'CDE05G0692' => 'cde', 'CDE05G2285' => 'cde', 'CDE05G2884' => 'cde', 'CDE05G3072' => 'cde', 'Cfa008439' => 'cfa', 'Cfa008441' => 'cfa', 'Cfa008443' => 'cfa', 'Cfa008448' => 'cfa', 'Ciclev10005974m.g' => 'ccl', 'Ciclev10006006m.g' => 'ccl', 'Ciclev10006775m.g' => 'ccl', 'CiPaw.02G120400' => 'cil', 'CiPaw.02G120500' => 'cil', 'CiPaw.02G120600' => 'cil', 'ClCG05G004850' => 'cla', 'COL.COLO4_21566' => 'col', 'Cpa.g.sc44.124' => 'cpa', 'Cre07.g320400' => 'cre', 'Cre07.g320450' => 'cre', 'Cre08.g384650' => 'cre', 'Cre09.g393173' => 'cre', 'Cre09.g394325' => 'cre', 'Cre14.g626750' => 'cre', 'Cre16.g679250' => 'cre', 'CsaV3_3G012890' => 'csa', 'CSS0010865' => 'camsi', 'CSS0044338' => 'camsi', 'DCAR_002366' => 'dca', 'DCAR_030687' => 'dca', 'DCAR_030688' => 'dca', 'Dinv14047' => 'din', 'Dinv14048' => 'din', 'Duzib151G0105' => 'dzi', 'Duzib151G0114' => 'dzi', 'Duzib212G1029' => 'dzi', 'ECA232G3536' => 'eca', 'ECA240G0786' => 'eca', 'ECA240G1802' => 'eca', 'ECA240G3760' => 'eca', 'ECA240G3920' => 'eca', 'EL10Ac5g12536' => 'bvu', 'EL10Ac5g12537' => 'bvu', 'EL10Ac5g12538' => 'bvu', 'Eucgr.B01004' => 'egr', 'Eucgr.B01006' => 'egr', 'Eucgr.B01007' => 'egr', 'Eucgr.B01008' => 'egr', 'Eucgr.B01895' => 'egr', 'Eucgr.B01896' => 'egr', 'FAN04G1456' => 'fan', 'FAN08G1769' => 'fan', 'FAN08G2160' => 'fan', 'FAN13G2403' => 'fan', 'FAN13G3303' => 'fan', 'FAN15G2435' => 'fan', 'FAN17G0672' => 'fan', 'FAN17G2441' => 'fan', 'FAN18G1024' => 'fan', 'FAN22G1458' => 'fan', 'FAN24G0037' => 'fan', 'FAN24G0429' => 'fan', 'FAN24G2387' => 'fan', 'FAN27G2746' => 'fan', 'FvH4_2g20400' => 'fve', 'FvH4_2g20420' => 'fve', 'FvH4_2g20430' => 'fve', 'FvH4_4g01270' => 'fve', 'FvH4_4g01290' => 'fve', 'FvH4_4g01300' => 'fve', 'FvH4_4g01310' => 'fve', 'FvH4_4g01330' => 'fve', 'FvH4_5g09070' => 'fve', 'Glyma.10G243800' => 'gma', 'Glyma.20G150600' => 'gma', 'Gohir.A09G219200' => 'ghi', 'Gohir.A09G219300' => 'ghi', 'Gohir.D09G221400' => 'ghi', 'Gohir.D09G221500' => 'ghi', 'Gorai.006G242600' => 'gra', 'Gorai.006G242700' => 'gra', 'GSVIVG01018044001' => 'vvi', 'HanXRQChr03g0083821' => 'han', 'HanXRQChr03g0083841' => 'han', 'HanXRQChr03g0083881' => 'han', 'HanXRQChr03g0083901' => 'han', 'HanXRQChr03g0083921' => 'han', 'HanXRQChr03g0085331' => 'han', 'HanXRQChr03g0085361' => 'han', 'HanXRQChr03g0085411' => 'han', 'HanXRQChr03g0085421' => 'han', 'HanXRQChr03g0085431' => 'han', 'HanXRQChr08g0221991' => 'han', 'HanXRQChr11g0336061' => 'han', 'HanXRQChr11g0336411' => 'han', 'Haze_11234' => 'cav', 'Hma1.2p1_0549F.1_g177010' => 'hma', 'Hma1.2p1_0602F.1_g187630' => 'hma', 'Hund14876' => 'sun', 'Hund14879' => 'sun', 'Lalb_Chr06g0160741' => 'lal', 'Lalb_Chr21g0304781' => 'lal', 'Lj3A726G19' => 'lonja', 'Lj3A726T23' => 'lonja', 'Lj3A726T24' => 'lonja', 'Lj3A726T25' => 'lonja', 'Lj3A727T17' => 'lonja', 'Lj3C726T0' => 'lonja', 'Lj3C726T2' => 'lonja', 'Lj3P725T35' => 'lonja', 'Lj3P727T10' => 'lonja', 'Lj3P727T12' => 'lonja', 'Lj3P727T14' => 'lonja', 'Lj5g0023109' => 'lja', 'Lj6P646T44' => 'lonja', 'Lsat_1_v5_gn_6_75760' => 'lsa', 'Lsat_1_v5_gn_6_75800' => 'lsa', 'Lsat_1_v5_gn_6_75900' => 'lsa', 'Lsat_1_v5_gn_6_76240' => 'lsa', 'Lsat_1_v5_gn_6_76441' => 'lsa', 'Lsat_1_v5_gn_6_76700' => 'lsa', 'Lsat_1_v5_gn_6_76760' => 'lsa', 'Manes.15G033100' => 'mes', 'Mapoly0004s0074' => 'mpo', 'Mapoly0004s0075' => 'mpo', 'Mapoly0004s0163' => 'mpo', 'Mapoly0004s0164' => 'mpo', 'Mapoly0021s0018' => 'mpo', 'Mapoly0041s0136' => 'mpo', 'Mapoly0041s0137' => 'mpo', 'Mapoly0041s0138' => 'mpo', 'Mapoly0041s0139' => 'mpo', 'Mapoly0041s0141' => 'mpo', 'Mapoly0041s0142' => 'mpo', 'Mapoly0041s0143' => 'mpo', 'Mapoly0041s0144' => 'mpo', 'Mapoly0041s0145' => 'mpo', 'Mapoly0047s0106' => 'mpo', 'Mapoly0047s0108' => 'mpo', 'Mapoly0050s0051' => 'mpo', 'Mapoly0050s0052' => 'mpo', 'Mapoly0050s0053' => 'mpo', 'Mapoly0058s0013' => 'mpo', 'Mapoly0091s0078' => 'mpo', 'Mapoly0091s0079' => 'mpo', 'Mapoly0091s0080' => 'mpo', 'Mapoly0091s0081' => 'mpo', 'Mapoly0278s0004' => 'mpo', 'Mapoly0278s0005' => 'mpo', 'Mapoly0278s0006' => 'mpo', 'MBI11_g30648_MAGBIO' => 'mbi', 'MCO03G194' => 'mco', 'MCO03G590' => 'mco', 'MCO07G312' => 'mco', 'MCO10G318' => 'mco', 'MCO12G244' => 'mco', 'MCO13G148' => 'mco', 'MCO13G194' => 'mco', 'MCO16G238' => 'mco', 'MD06G1134100' => 'mdo', 'MD13G1200100' => 'mdo', 'MD13G1200300' => 'mdo', 'MD13G1200600' => 'mdo', 'MD14G1150400' => 'mdo', 'MD16G1200000' => 'mdo', 'Medtr1g102570' => 'mtr', 'Medtr1g102780' => 'mtr', 'Medtr1g102800' => 'mtr', 'Medtr1g102810' => 'mtr', 'Medtr1g102830' => 'mtr', 'MELO3C006499.2' => 'cme', 'Migut.G00385' => 'egut', 'MSTRG.4063' => 'ama', 'Nitab4.5_0000090g0260' => 'nta', 'Nitab4.5_0000977g0030' => 'nta', 'Nitab4.5_0002541g0040' => 'nta', 'Nitab4.5_0007068g0040' => 'nta', 'Nn005s41408' => 'nnu', 'Nn005s41410' => 'nnu', 'Oeu010310.1' => 'oeu', 'Oeu010311.1' => 'oeu', 'Oeu043472.1' => 'oeu', 'Os01g0246400' => 'osa', 'Os04g0267950' => 'osa', 'Os07g0178700' => 'osa', 'Os07g0178800' => 'osa', 'Peaxi162Scf00316g00046' => 'pax', 'Peaxi162Scf00316g00049' => 'pax', 'Peaxi162Scf00316g00059' => 'pax', 'Peaxi162Scf00316g00328' => 'pax', 'Peaxi162Scf00316g00329' => 'pax', 'Peaxi162Scf00316g00411' => 'pax', 'Peaxi162Scf00316g00521' => 'pax', 'Peaxi162Scf00492g00068' => 'pax', 'Peaxi162Scf35631g00002' => 'pax', 'PGR142G3720' => 'pgr', 'PGSC0003DMG400006442' => 'stu', 'Phvul.007G062000' => 'pvu', 'Potri.008G157750' => 'ptr', 'Potri.008G157900' => 'ptr', 'Potri.008G158000' => 'ptr', 'Potri.008G158200' => 'ptr', 'Pp3c11_7280' => 'ppa', 'Pp3c11_7980' => 'ppa', 'Pp3c12_19450' => 'ppa', 'Pp3c14_1480' => 'ppa', 'Pp3c14_1501' => 'ppa', 'Pp3c16_4900' => 'ppa', 'Pp3c16_5010' => 'ppa', 'Pp3c16_5060' => 'ppa', 'Pp3c19_18250' => 'ppa', 'Pp3c23_8530' => 'ppa', 'Pp3c23_8550' => 'ppa', 'Pp3c24_9670' => 'ppa', 'Pp3c2_21390' => 'ppa', 'Pp3c2_31380' => 'ppa', 'Pp3c3_16620' => 'ppa', 'Pp3c3_8090' => 'ppa', 'Pp3c3_8110' => 'ppa', 'Pp3c3_8130' => 'ppa', 'Pp3c3_8150' => 'ppa', 'Pp3c4_14320' => 'ppa', 'Pp3c6_2560' => 'ppa', 'Pp3c9_16700' => 'ppa', 'PRCOL_00000234' => 'pco', 'PRCOL_00000235' => 'pco', 'PRCOL_00000777' => 'pco', 'PRCOL_00002344' => 'pco', 'PRCOL_00002372' => 'pco', 'PRCOL_00006120' => 'pco', 'Prupe.1G021400' => 'ppe', 'Prupe.1G021500' => 'ppe', 'Prupe.1G021600' => 'ppe', 'Prupe.1G021700' => 'ppe', 'Prupe.1G021800' => 'ppe', 'Prupe.5G145100' => 'ppe', 'Psat6g204040' => 'psa', 'Psat6g204800' => 'psa', 'Psat6g204920' => 'psa', 'Psat6g204960' => 'psa', 'Psat6g205080' => 'psa', 'PSO017G0271' => 'pso', 'PSO017G1276' => 'pso', 'PSO017G1429' => 'pso', 'PSO017G1861' => 'pso', 'PSO017G2787' => 'pso', 'PSO017G4466' => 'pso', 'PSO017G5118' => 'pso', 'PSO017G5420' => 'pso', 'PSO063G3678' => 'pso', 'PSO210G0546' => 'pso', 'PSO317G0001' => 'pso', 'PSO357G0512' => 'pso', 'PSO478G2682' => 'pso', 'PSO647G0001' => 'pso', 'PSO675G0001' => 'pso', 'PSO675G2699' => 'pso', 'PSO675G2849' => 'pso', 'PSO675G4991' => 'pso', 'PSO689G0001' => 'pso', 'QL06p000916' => 'qlo', 'QL06p000921' => 'qlo', 'QL06p001398' => 'qlo', 'QL06p001407' => 'qlo', 'QL06p002031' => 'qlo', 'RcHm_v2.0_Chr4g0387791' => 'rch', 'RcHm_v2.0_Chr4g0387801' => 'rch', 'RcHm_v2.0_Chr6g0286501' => 'rch', 'RcHm_v2.0_Chr6g0286511' => 'rch', 'RcHm_v2.0_Chr6g0286521' => 'rch', 'RcHm_v2.0_Chr6g0286531' => 'rch', 'RcHm_v2.0_Chr7g0189141' => 'rch', 'Rhsim02G0028700' => 'rsi', 'Rhsim02G0028800' => 'rsi', 'Rhsim02G0028900' => 'rsi', 'Rhsim02G0029000' => 'rsi', 'Rhsim02G0029100' => 'rsi', 'Rhsim02G0029200' => 'rsi', 'Rhsim02G0029300' => 'rsi', 'Rhsim02G0029400' => 'rsi', 'Rhsim02G0029500' => 'rsi', 'Rhsim02G0029600' => 'rsi', 'RhsimUnG0024000' => 'rsi', 'RhsimUnG0024100' => 'rsi', 'RhsimUnG0024200' => 'rsi', 'RhsimUnG0024300' => 'rsi', 'RhsimUnG0024400' => 'rsi', 'RhsimUnG0024500' => 'rsi', 'RhsimUnG0024700' => 'rsi', 'RhsimUnG0024800' => 'rsi', 'RhsimUnG0024900' => 'rsi', 'RhsimUnG0025100' => 'rsi', 'Sabra08G0120200' => 'sbr', 'Sabra08G0120300' => 'sbr', 'Sabra08G0120500' => 'sbr', 'Sabra08G0120600' => 'sbr', 'Sabra10G0158900' => 'sbr', 'SalBow2G3492' => 'sbo', 'Sc13g0004760' => 'sci', 'Sc13g0004770' => 'sci', 'Sed0003417' => 'sed', 'Sed0019750' => 'sed', 'SEGI_03419' => 'sgi', 'SEGI_05907' => 'sgi', 'SEGI_10682' => 'sgi', 'SEGI_13528' => 'sgi', 'SEGI_16081' => 'sgi', 'SEGI_19370' => 'sgi', 'SEGI_21015' => 'sgi', 'SEGI_21944' => 'sgi', 'SEGI_32906' => 'sgi', 'SEGI_33093' => 'sgi', 'SEGI_36110' => 'sgi', 'SEGI_40397' => 'sgi', 'SGA_v2.0_scaffold191G40426' => 'sas', 'SGA_v2.0_scaffold353G49717' => 'sas', 'SGA_v2.0_scaffold50G18550' => 'sas', 'SMO119G0173' => 'smo', 'SMO172G0002' => 'smo', 'Solyc09g082690.3' => 'sly', 'Solyc09g082700.2' => 'sly', 'Sopen09g031550' => 'spe', 'Sopen09g031560' => 'spe', 'Sp3g20540' => 'spa', 'Sp7g07580' => 'spa', 'TAR134G0002' => 'tar', 'TAR236G0001' => 'tar', 'TAR365G0892' => 'tar', 'TAR636G0166' => 'tar', 'TAR636G0646' => 'tar', 'TAR636G0869' => 'tar', 'TAR636G1317' => 'tar', 'TAR636G1744' => 'tar', 'TAR636G3358' => 'tar', 'TAR636G3436' => 'tar', 'THA.LOC104803047' => 'tha', 'Thecc.04G238900' => 'tca', 'Thhalv10021557m.g' => 'esa', 'Thhalv10026318m.g' => 'esa', 'Thhalv10026335m.g' => 'esa', 'TPR.G17433' => 'tpr', 'TPR.G18915' => 'tpr', 'TPR.G26125' => 'tpr', 'TWI09G0677' => 'twi', 'TWI73G0287' => 'twi', 'unitig_748.g8326' => 'ugi', 'vmacro15370' => 'vma', 'vmacro15371' => 'vma', 'vmacro15372' => 'vma', 'vmacro15373' => 'vma', 'vmacro15374' => 'vma', 'VMungo0720G2826' => 'vmu', 'Zm00001eb116960' => 'zma', 'Zm00001eb301260' => 'zma', 'Zm00001eb301270' => 'zma' ) $gf_id = 'HOM05D001460' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001460' ) $data_identifier = 'HOM05D001460' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 4, 'aag' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 2, 'aox' => (int) 2, 'arhy' => (int) 4, 'ath' => (int) 2, 'atr' => (int) 1, 'acertr' => (int) 10, 'cqu' => (int) 4, 'bca' => (int) 11, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 1, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 1, 'ccan' => (int) 1, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 1, 'col' => (int) 1, 'cpa' => (int) 1, 'cre' => (int) 7, 'csa' => (int) 1, 'camsi' => (int) 2, 'dca' => (int) 3, 'din' => (int) 2, 'dzi' => (int) 3, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 14, 'fve' => (int) 9, 'gma' => (int) 2, 'ghi' => (int) 4, 'gra' => (int) 2, 'vvi' => (int) 1, 'han' => (int) 13, 'cav' => (int) 1, 'hma' => (int) 2, 'sun' => (int) 2, 'lal' => (int) 2, 'lonja' => (int) 12, 'lja' => (int) 1, 'lsa' => (int) 7, 'mes' => (int) 1, 'mpo' => (int) 27, 'mbi' => (int) 1, 'mco' => (int) 8, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 1, 'egut' => (int) 1, 'ama' => (int) 1, 'nta' => (int) 4, 'nnu' => (int) 2, 'oeu' => (int) 3, 'osa' => (int) 4, 'pax' => (int) 9, 'pgr' => (int) 1, 'stu' => (int) 1, 'pvu' => (int) 1, 'ptr' => (int) 4, 'ppa' => (int) 22, 'pco' => (int) 6, 'ppe' => (int) 6, 'psa' => (int) 5, 'pso' => (int) 19, 'qlo' => (int) 5, 'rch' => (int) 7, 'rsi' => (int) 20, 'sbr' => (int) 5, 'sbo' => (int) 1, 'sci' => (int) 2, 'sed' => (int) 2, 'sgi' => (int) 12, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 2, 'tar' => (int) 10, 'tha' => (int) 1, 'tca' => (int) 1, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 2, 'ugi' => (int) 1, 'vma' => (int) 5, 'vmu' => (int) 1, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb301270' $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' => 'HOM05D001460', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '433', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p22980' => 'bna', 'A01p32340' => 'bna', 'A03p42970' => 'bna', 'A05p25880' => 'bna', 'Aa31LG8G9320' => 'aar', 'Aa31LG8G9330' => 'aar', 'Aa31LG8G9340' => 'aar', 'Aa31sc221G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1034' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1528' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.829' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2222' => 'aag', 'Ah.12g058830' => 'amhyb', 'Ah.12g058840' => 'amhyb', 'AL3G37160' => 'aly', 'AL7G41310' => 'aly', 'Aqoxy5G00395' => 'aox', 'Aqoxy5G00396' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0C8NZA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5185HY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JZ1PRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MD3LS0' => 'arhy', 'AT3G22840' => 'ath', 'AT4G14690' => 'ath', 'ATR0665G054' => 'atr', 'Atru.chr4.2344' => 'acertr', 'Atru.chr4.2346' => 'acertr', 'Atru.chr4.2347' => 'acertr', 'Atru.chr4.2348' => 'acertr', 'Atru.chr4.2355' => 'acertr', 'Atru.chr4.2356' => 'acertr', 'Atru.chr4.2358' => 'acertr', 'Atru.chr4.2359' => 'acertr', 'Atru.chr4.2360' => 'acertr', 'Atru.chr4.2361' => 'acertr', 'AUR62030476' => 'cqu', 'AUR62030478' => 'cqu', 'AUR62030819' => 'cqu', 'AUR62030820' => 'cqu', 'BcaB03g14648' => 'bca', 'BcaB04g20492' => 'bca', 'BcaB06g26399' => 'bca', 'BcaC01g03416' => 'bca', 'BcaC01g03419' => 'bca', 'BcaC01g03421' => 'bca', 'BcaC01g03424' => 'bca', 'BcaC05g28012' => 'bca', 'BcaC09g49212' => 'bca', 'BcaC09g50140' => 'bca', 'BcaNung00346' => 'bca', 'BolC1t02785H' => 'bol', 'BolC1t04095H' => 'bol', 'BolC3t17545H' => 'bol', 'BolC5t32769H' => 'bol', 'BraA01t02211Z' => 'bra', 'BraA01t03359Z' => 'bra', 'BraA03t13441Z' => 'bra', 'BraA05t21476Z' => 'bra', 'C01p28420' => 'bna', 'C01p41350' => 'bna', 'C03p52750' => 'bna', 'C03p52780' => 'bna', 'C05p40270' => 'bna', 'CAN.G1437.9' => 'can', 'CANSAT78G0035' => 'cansat', 'CANSAT78G1036' => 'cansat', 'CANSAT78G2272' => 'cansat', 'CANSAT78G2478' => 'cansat', 'CARHR098700' => 'chi', 'CARHR221120' => 'chi', 'CARHR221150' => 'chi', 'Carub.0003s2297' => 'cru', 'Carub.0007s2749' => 'cru', 'Carub.0007s2750' => 'cru', 'Carub.0007s2751' => 'cru', 'Ca_10849_v3' => 'car', 'Cc03_g04300' => 'ccan', 'CDE02G3648' => 'cde', 'CDE05G0060' => 'cde', 'CDE05G0692' => 'cde', 'CDE05G2285' => 'cde', 'CDE05G2884' => 'cde', 'CDE05G3072' => 'cde', 'Cfa008439' => 'cfa', 'Cfa008441' => 'cfa', 'Cfa008443' => 'cfa', 'Cfa008448' => 'cfa', 'Ciclev10005974m.g' => 'ccl', 'Ciclev10006006m.g' => 'ccl', 'Ciclev10006775m.g' => 'ccl', 'CiPaw.02G120400' => 'cil', 'CiPaw.02G120500' => 'cil', 'CiPaw.02G120600' => 'cil', 'ClCG05G004850' => 'cla', 'COL.COLO4_21566' => 'col', 'Cpa.g.sc44.124' => 'cpa', 'Cre07.g320400' => 'cre', 'Cre07.g320450' => 'cre', 'Cre08.g384650' => 'cre', 'Cre09.g393173' => 'cre', 'Cre09.g394325' => 'cre', 'Cre14.g626750' => 'cre', 'Cre16.g679250' => 'cre', 'CsaV3_3G012890' => 'csa', 'CSS0010865' => 'camsi', 'CSS0044338' => 'camsi', 'DCAR_002366' => 'dca', 'DCAR_030687' => 'dca', 'DCAR_030688' => 'dca', 'Dinv14047' => 'din', 'Dinv14048' => 'din', 'Duzib151G0105' => 'dzi', 'Duzib151G0114' => 'dzi', 'Duzib212G1029' => 'dzi', 'ECA232G3536' => 'eca', 'ECA240G0786' => 'eca', 'ECA240G1802' => 'eca', 'ECA240G3760' => 'eca', 'ECA240G3920' => 'eca', 'EL10Ac5g12536' => 'bvu', 'EL10Ac5g12537' => 'bvu', 'EL10Ac5g12538' => 'bvu', 'Eucgr.B01004' => 'egr', 'Eucgr.B01006' => 'egr', 'Eucgr.B01007' => 'egr', 'Eucgr.B01008' => 'egr', 'Eucgr.B01895' => 'egr', 'Eucgr.B01896' => 'egr', 'FAN04G1456' => 'fan', 'FAN08G1769' => 'fan', 'FAN08G2160' => 'fan', 'FAN13G2403' => 'fan', 'FAN13G3303' => 'fan', 'FAN15G2435' => 'fan', 'FAN17G0672' => 'fan', 'FAN17G2441' => 'fan', 'FAN18G1024' => 'fan', 'FAN22G1458' => 'fan', 'FAN24G0037' => 'fan', 'FAN24G0429' => 'fan', 'FAN24G2387' => 'fan', 'FAN27G2746' => 'fan', 'FvH4_2g20400' => 'fve', 'FvH4_2g20420' => 'fve', 'FvH4_2g20430' => 'fve', 'FvH4_4g01270' => 'fve', 'FvH4_4g01290' => 'fve', 'FvH4_4g01300' => 'fve', 'FvH4_4g01310' => 'fve', 'FvH4_4g01330' => 'fve', 'FvH4_5g09070' => 'fve', 'Glyma.10G243800' => 'gma', 'Glyma.20G150600' => 'gma', 'Gohir.A09G219200' => 'ghi', 'Gohir.A09G219300' => 'ghi', 'Gohir.D09G221400' => 'ghi', 'Gohir.D09G221500' => 'ghi', 'Gorai.006G242600' => 'gra', 'Gorai.006G242700' => 'gra', 'GSVIVG01018044001' => 'vvi', 'HanXRQChr03g0083821' => 'han', 'HanXRQChr03g0083841' => 'han', 'HanXRQChr03g0083881' => 'han', 'HanXRQChr03g0083901' => 'han', 'HanXRQChr03g0083921' => 'han', 'HanXRQChr03g0085331' => 'han', 'HanXRQChr03g0085361' => 'han', 'HanXRQChr03g0085411' => 'han', 'HanXRQChr03g0085421' => 'han', 'HanXRQChr03g0085431' => 'han', 'HanXRQChr08g0221991' => 'han', 'HanXRQChr11g0336061' => 'han', 'HanXRQChr11g0336411' => 'han', 'Haze_11234' => 'cav', 'Hma1.2p1_0549F.1_g177010' => 'hma', 'Hma1.2p1_0602F.1_g187630' => 'hma', 'Hund14876' => 'sun', 'Hund14879' => 'sun', 'Lalb_Chr06g0160741' => 'lal', 'Lalb_Chr21g0304781' => 'lal', 'Lj3A726G19' => 'lonja', 'Lj3A726T23' => 'lonja', 'Lj3A726T24' => 'lonja', 'Lj3A726T25' => 'lonja', 'Lj3A727T17' => 'lonja', 'Lj3C726T0' => 'lonja', 'Lj3C726T2' => 'lonja', 'Lj3P725T35' => 'lonja', 'Lj3P727T10' => 'lonja', 'Lj3P727T12' => 'lonja', 'Lj3P727T14' => 'lonja', 'Lj5g0023109' => 'lja', 'Lj6P646T44' => 'lonja', 'Lsat_1_v5_gn_6_75760' => 'lsa', 'Lsat_1_v5_gn_6_75800' => 'lsa', 'Lsat_1_v5_gn_6_75900' => 'lsa', 'Lsat_1_v5_gn_6_76240' => 'lsa', 'Lsat_1_v5_gn_6_76441' => 'lsa', 'Lsat_1_v5_gn_6_76700' => 'lsa', 'Lsat_1_v5_gn_6_76760' => 'lsa', 'Manes.15G033100' => 'mes', 'Mapoly0004s0074' => 'mpo', 'Mapoly0004s0075' => 'mpo', 'Mapoly0004s0163' => 'mpo', 'Mapoly0004s0164' => 'mpo', 'Mapoly0021s0018' => 'mpo', 'Mapoly0041s0136' => 'mpo', 'Mapoly0041s0137' => 'mpo', 'Mapoly0041s0138' => 'mpo', 'Mapoly0041s0139' => 'mpo', 'Mapoly0041s0141' => 'mpo', 'Mapoly0041s0142' => 'mpo', 'Mapoly0041s0143' => 'mpo', 'Mapoly0041s0144' => 'mpo', 'Mapoly0041s0145' => 'mpo', 'Mapoly0047s0106' => 'mpo', 'Mapoly0047s0108' => 'mpo', 'Mapoly0050s0051' => 'mpo', 'Mapoly0050s0052' => 'mpo', 'Mapoly0050s0053' => 'mpo', 'Mapoly0058s0013' => 'mpo', 'Mapoly0091s0078' => 'mpo', 'Mapoly0091s0079' => 'mpo', 'Mapoly0091s0080' => 'mpo', 'Mapoly0091s0081' => 'mpo', 'Mapoly0278s0004' => 'mpo', 'Mapoly0278s0005' => 'mpo', 'Mapoly0278s0006' => 'mpo', 'MBI11_g30648_MAGBIO' => 'mbi', 'MCO03G194' => 'mco', 'MCO03G590' => 'mco', 'MCO07G312' => 'mco', 'MCO10G318' => 'mco', 'MCO12G244' => 'mco', 'MCO13G148' => 'mco', 'MCO13G194' => 'mco', 'MCO16G238' => 'mco', 'MD06G1134100' => 'mdo', 'MD13G1200100' => 'mdo', 'MD13G1200300' => 'mdo', 'MD13G1200600' => 'mdo', 'MD14G1150400' => 'mdo', 'MD16G1200000' => 'mdo', 'Medtr1g102570' => 'mtr', 'Medtr1g102780' => 'mtr', 'Medtr1g102800' => 'mtr', 'Medtr1g102810' => 'mtr', 'Medtr1g102830' => 'mtr', 'MELO3C006499.2' => 'cme', 'Migut.G00385' => 'egut', 'MSTRG.4063' => 'ama', 'Nitab4.5_0000090g0260' => 'nta', 'Nitab4.5_0000977g0030' => 'nta', 'Nitab4.5_0002541g0040' => 'nta', 'Nitab4.5_0007068g0040' => 'nta', 'Nn005s41408' => 'nnu', 'Nn005s41410' => 'nnu', 'Oeu010310.1' => 'oeu', 'Oeu010311.1' => 'oeu', 'Oeu043472.1' => 'oeu', 'Os01g0246400' => 'osa', 'Os04g0267950' => 'osa', 'Os07g0178700' => 'osa', 'Os07g0178800' => 'osa', 'Peaxi162Scf00316g00046' => 'pax', 'Peaxi162Scf00316g00049' => 'pax', 'Peaxi162Scf00316g00059' => 'pax', 'Peaxi162Scf00316g00328' => 'pax', 'Peaxi162Scf00316g00329' => 'pax', 'Peaxi162Scf00316g00411' => 'pax', 'Peaxi162Scf00316g00521' => 'pax', 'Peaxi162Scf00492g00068' => 'pax', 'Peaxi162Scf35631g00002' => 'pax', 'PGR142G3720' => 'pgr', 'PGSC0003DMG400006442' => 'stu', 'Phvul.007G062000' => 'pvu', 'Potri.008G157750' => 'ptr', 'Potri.008G157900' => 'ptr', 'Potri.008G158000' => 'ptr', 'Potri.008G158200' => 'ptr', 'Pp3c11_7280' => 'ppa', 'Pp3c11_7980' => 'ppa', 'Pp3c12_19450' => 'ppa', 'Pp3c14_1480' => 'ppa', 'Pp3c14_1501' => 'ppa', 'Pp3c16_4900' => 'ppa', 'Pp3c16_5010' => 'ppa', 'Pp3c16_5060' => 'ppa', 'Pp3c19_18250' => 'ppa', 'Pp3c23_8530' => 'ppa', 'Pp3c23_8550' => 'ppa', 'Pp3c24_9670' => 'ppa', 'Pp3c2_21390' => 'ppa', 'Pp3c2_31380' => 'ppa', 'Pp3c3_16620' => 'ppa', 'Pp3c3_8090' => 'ppa', 'Pp3c3_8110' => 'ppa', 'Pp3c3_8130' => 'ppa', 'Pp3c3_8150' => 'ppa', 'Pp3c4_14320' => 'ppa', 'Pp3c6_2560' => 'ppa', 'Pp3c9_16700' => 'ppa', 'PRCOL_00000234' => 'pco', 'PRCOL_00000235' => 'pco', 'PRCOL_00000777' => 'pco', 'PRCOL_00002344' => 'pco', 'PRCOL_00002372' => 'pco', 'PRCOL_00006120' => 'pco', 'Prupe.1G021400' => 'ppe', 'Prupe.1G021500' => 'ppe', 'Prupe.1G021600' => 'ppe', 'Prupe.1G021700' => 'ppe', 'Prupe.1G021800' => 'ppe', 'Prupe.5G145100' => 'ppe', 'Psat6g204040' => 'psa', 'Psat6g204800' => 'psa', 'Psat6g204920' => 'psa', 'Psat6g204960' => 'psa', 'Psat6g205080' => 'psa', 'PSO017G0271' => 'pso', 'PSO017G1276' => 'pso', 'PSO017G1429' => 'pso', 'PSO017G1861' => 'pso', 'PSO017G2787' => 'pso', 'PSO017G4466' => 'pso', 'PSO017G5118' => 'pso', 'PSO017G5420' => 'pso', 'PSO063G3678' => 'pso', 'PSO210G0546' => 'pso', 'PSO317G0001' => 'pso', 'PSO357G0512' => 'pso', 'PSO478G2682' => 'pso', 'PSO647G0001' => 'pso', 'PSO675G0001' => 'pso', 'PSO675G2699' => 'pso', 'PSO675G2849' => 'pso', 'PSO675G4991' => 'pso', 'PSO689G0001' => 'pso', 'QL06p000916' => 'qlo', 'QL06p000921' => 'qlo', 'QL06p001398' => 'qlo', 'QL06p001407' => 'qlo', 'QL06p002031' => 'qlo', 'RcHm_v2.0_Chr4g0387791' => 'rch', 'RcHm_v2.0_Chr4g0387801' => 'rch', 'RcHm_v2.0_Chr6g0286501' => 'rch', 'RcHm_v2.0_Chr6g0286511' => 'rch', 'RcHm_v2.0_Chr6g0286521' => 'rch', 'RcHm_v2.0_Chr6g0286531' => 'rch', 'RcHm_v2.0_Chr7g0189141' => 'rch', 'Rhsim02G0028700' => 'rsi', 'Rhsim02G0028800' => 'rsi', 'Rhsim02G0028900' => 'rsi', 'Rhsim02G0029000' => 'rsi', 'Rhsim02G0029100' => 'rsi', 'Rhsim02G0029200' => 'rsi', 'Rhsim02G0029300' => 'rsi', 'Rhsim02G0029400' => 'rsi', 'Rhsim02G0029500' => 'rsi', 'Rhsim02G0029600' => 'rsi', 'RhsimUnG0024000' => 'rsi', 'RhsimUnG0024100' => 'rsi', 'RhsimUnG0024200' => 'rsi', 'RhsimUnG0024300' => 'rsi', 'RhsimUnG0024400' => 'rsi', 'RhsimUnG0024500' => 'rsi', 'RhsimUnG0024700' => 'rsi', 'RhsimUnG0024800' => 'rsi', 'RhsimUnG0024900' => 'rsi', 'RhsimUnG0025100' => 'rsi', 'Sabra08G0120200' => 'sbr', 'Sabra08G0120300' => 'sbr', 'Sabra08G0120500' => 'sbr', 'Sabra08G0120600' => 'sbr', 'Sabra10G0158900' => 'sbr', 'SalBow2G3492' => 'sbo', 'Sc13g0004760' => 'sci', 'Sc13g0004770' => 'sci', 'Sed0003417' => 'sed', 'Sed0019750' => 'sed', 'SEGI_03419' => 'sgi', 'SEGI_05907' => 'sgi', 'SEGI_10682' => 'sgi', 'SEGI_13528' => 'sgi', 'SEGI_16081' => 'sgi', 'SEGI_19370' => 'sgi', 'SEGI_21015' => 'sgi', 'SEGI_21944' => 'sgi', 'SEGI_32906' => 'sgi', 'SEGI_33093' => 'sgi', 'SEGI_36110' => 'sgi', 'SEGI_40397' => 'sgi', 'SGA_v2.0_scaffold191G40426' => 'sas', 'SGA_v2.0_scaffold353G49717' => 'sas', 'SGA_v2.0_scaffold50G18550' => 'sas', 'SMO119G0173' => 'smo', 'SMO172G0002' => 'smo', 'Solyc09g082690.3' => 'sly', 'Solyc09g082700.2' => 'sly', 'Sopen09g031550' => 'spe', 'Sopen09g031560' => 'spe', 'Sp3g20540' => 'spa', 'Sp7g07580' => 'spa', 'TAR134G0002' => 'tar', 'TAR236G0001' => 'tar', 'TAR365G0892' => 'tar', 'TAR636G0166' => 'tar', 'TAR636G0646' => 'tar', 'TAR636G0869' => 'tar', 'TAR636G1317' => 'tar', 'TAR636G1744' => 'tar', 'TAR636G3358' => 'tar', 'TAR636G3436' => 'tar', 'THA.LOC104803047' => 'tha', 'Thecc.04G238900' => 'tca', 'Thhalv10021557m.g' => 'esa', 'Thhalv10026318m.g' => 'esa', 'Thhalv10026335m.g' => 'esa', 'TPR.G17433' => 'tpr', 'TPR.G18915' => 'tpr', 'TPR.G26125' => 'tpr', 'TWI09G0677' => 'twi', 'TWI73G0287' => 'twi', 'unitig_748.g8326' => 'ugi', 'vmacro15370' => 'vma', 'vmacro15371' => 'vma', 'vmacro15372' => 'vma', 'vmacro15373' => 'vma', 'vmacro15374' => 'vma', 'VMungo0720G2826' => 'vmu', 'Zm00001eb116960' => 'zma', 'Zm00001eb301260' => 'zma', 'Zm00001eb301270' => 'zma' ), 'gf_id' => 'HOM05D001460', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001460' ), 'data_identifier' => 'HOM05D001460', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001460', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '433', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p22980' => 'bna', 'A01p32340' => 'bna', 'A03p42970' => 'bna', 'A05p25880' => 'bna', 'Aa31LG8G9320' => 'aar', 'Aa31LG8G9330' => 'aar', 'Aa31LG8G9340' => 'aar', 'Aa31sc221G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1034' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1528' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.829' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2222' => 'aag', 'Ah.12g058830' => 'amhyb', 'Ah.12g058840' => 'amhyb', 'AL3G37160' => 'aly', 'AL7G41310' => 'aly', 'Aqoxy5G00395' => 'aox', 'Aqoxy5G00396' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0C8NZA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5185HY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JZ1PRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MD3LS0' => 'arhy', 'AT3G22840' => 'ath', 'AT4G14690' => 'ath', 'ATR0665G054' => 'atr', 'Atru.chr4.2344' => 'acertr', 'Atru.chr4.2346' => 'acertr', 'Atru.chr4.2347' => 'acertr', 'Atru.chr4.2348' => 'acertr', 'Atru.chr4.2355' => 'acertr', 'Atru.chr4.2356' => 'acertr', 'Atru.chr4.2358' => 'acertr', 'Atru.chr4.2359' => 'acertr', 'Atru.chr4.2360' => 'acertr', 'Atru.chr4.2361' => 'acertr', 'AUR62030476' => 'cqu', 'AUR62030478' => 'cqu', 'AUR62030819' => 'cqu', 'AUR62030820' => 'cqu', 'BcaB03g14648' => 'bca', 'BcaB04g20492' => 'bca', 'BcaB06g26399' => 'bca', 'BcaC01g03416' => 'bca', 'BcaC01g03419' => 'bca', 'BcaC01g03421' => 'bca', 'BcaC01g03424' => 'bca', 'BcaC05g28012' => 'bca', 'BcaC09g49212' => 'bca', 'BcaC09g50140' => 'bca', 'BcaNung00346' => 'bca', 'BolC1t02785H' => 'bol', 'BolC1t04095H' => 'bol', 'BolC3t17545H' => 'bol', 'BolC5t32769H' => 'bol', 'BraA01t02211Z' => 'bra', 'BraA01t03359Z' => 'bra', 'BraA03t13441Z' => 'bra', 'BraA05t21476Z' => 'bra', 'C01p28420' => 'bna', 'C01p41350' => 'bna', 'C03p52750' => 'bna', 'C03p52780' => 'bna', 'C05p40270' => 'bna', 'CAN.G1437.9' => 'can', 'CANSAT78G0035' => 'cansat', 'CANSAT78G1036' => 'cansat', 'CANSAT78G2272' => 'cansat', 'CANSAT78G2478' => 'cansat', 'CARHR098700' => 'chi', 'CARHR221120' => 'chi', 'CARHR221150' => 'chi', 'Carub.0003s2297' => 'cru', 'Carub.0007s2749' => 'cru', 'Carub.0007s2750' => 'cru', 'Carub.0007s2751' => 'cru', 'Ca_10849_v3' => 'car', 'Cc03_g04300' => 'ccan', 'CDE02G3648' => 'cde', 'CDE05G0060' => 'cde', 'CDE05G0692' => 'cde', 'CDE05G2285' => 'cde', 'CDE05G2884' => 'cde', 'CDE05G3072' => 'cde', 'Cfa008439' => 'cfa', 'Cfa008441' => 'cfa', 'Cfa008443' => 'cfa', 'Cfa008448' => 'cfa', 'Ciclev10005974m.g' => 'ccl', 'Ciclev10006006m.g' => 'ccl', 'Ciclev10006775m.g' => 'ccl', 'CiPaw.02G120400' => 'cil', 'CiPaw.02G120500' => 'cil', 'CiPaw.02G120600' => 'cil', 'ClCG05G004850' => 'cla', 'COL.COLO4_21566' => 'col', 'Cpa.g.sc44.124' => 'cpa', 'Cre07.g320400' => 'cre', 'Cre07.g320450' => 'cre', 'Cre08.g384650' => 'cre', 'Cre09.g393173' => 'cre', 'Cre09.g394325' => 'cre', 'Cre14.g626750' => 'cre', 'Cre16.g679250' => 'cre', 'CsaV3_3G012890' => 'csa', 'CSS0010865' => 'camsi', 'CSS0044338' => 'camsi', 'DCAR_002366' => 'dca', 'DCAR_030687' => 'dca', 'DCAR_030688' => 'dca', 'Dinv14047' => 'din', 'Dinv14048' => 'din', 'Duzib151G0105' => 'dzi', 'Duzib151G0114' => 'dzi', 'Duzib212G1029' => 'dzi', 'ECA232G3536' => 'eca', 'ECA240G0786' => 'eca', 'ECA240G1802' => 'eca', 'ECA240G3760' => 'eca', 'ECA240G3920' => 'eca', 'EL10Ac5g12536' => 'bvu', 'EL10Ac5g12537' => 'bvu', 'EL10Ac5g12538' => 'bvu', 'Eucgr.B01004' => 'egr', 'Eucgr.B01006' => 'egr', 'Eucgr.B01007' => 'egr', 'Eucgr.B01008' => 'egr', 'Eucgr.B01895' => 'egr', 'Eucgr.B01896' => 'egr', 'FAN04G1456' => 'fan', 'FAN08G1769' => 'fan', 'FAN08G2160' => 'fan', 'FAN13G2403' => 'fan', 'FAN13G3303' => 'fan', 'FAN15G2435' => 'fan', 'FAN17G0672' => 'fan', 'FAN17G2441' => 'fan', 'FAN18G1024' => 'fan', 'FAN22G1458' => 'fan', 'FAN24G0037' => 'fan', 'FAN24G0429' => 'fan', 'FAN24G2387' => 'fan', 'FAN27G2746' => 'fan', 'FvH4_2g20400' => 'fve', 'FvH4_2g20420' => 'fve', 'FvH4_2g20430' => 'fve', 'FvH4_4g01270' => 'fve', 'FvH4_4g01290' => 'fve', 'FvH4_4g01300' => 'fve', 'FvH4_4g01310' => 'fve', 'FvH4_4g01330' => 'fve', 'FvH4_5g09070' => 'fve', 'Glyma.10G243800' => 'gma', 'Glyma.20G150600' => 'gma', 'Gohir.A09G219200' => 'ghi', 'Gohir.A09G219300' => 'ghi', 'Gohir.D09G221400' => 'ghi', 'Gohir.D09G221500' => 'ghi', 'Gorai.006G242600' => 'gra', 'Gorai.006G242700' => 'gra', 'GSVIVG01018044001' => 'vvi', 'HanXRQChr03g0083821' => 'han', 'HanXRQChr03g0083841' => 'han', 'HanXRQChr03g0083881' => 'han', 'HanXRQChr03g0083901' => 'han', 'HanXRQChr03g0083921' => 'han', 'HanXRQChr03g0085331' => 'han', 'HanXRQChr03g0085361' => 'han', 'HanXRQChr03g0085411' => 'han', 'HanXRQChr03g0085421' => 'han', 'HanXRQChr03g0085431' => 'han', 'HanXRQChr08g0221991' => 'han', 'HanXRQChr11g0336061' => 'han', 'HanXRQChr11g0336411' => 'han', 'Haze_11234' => 'cav', 'Hma1.2p1_0549F.1_g177010' => 'hma', 'Hma1.2p1_0602F.1_g187630' => 'hma', 'Hund14876' => 'sun', 'Hund14879' => 'sun', 'Lalb_Chr06g0160741' => 'lal', 'Lalb_Chr21g0304781' => 'lal', 'Lj3A726G19' => 'lonja', 'Lj3A726T23' => 'lonja', 'Lj3A726T24' => 'lonja', 'Lj3A726T25' => 'lonja', 'Lj3A727T17' => 'lonja', 'Lj3C726T0' => 'lonja', 'Lj3C726T2' => 'lonja', 'Lj3P725T35' => 'lonja', 'Lj3P727T10' => 'lonja', 'Lj3P727T12' => 'lonja', 'Lj3P727T14' => 'lonja', 'Lj5g0023109' => 'lja', 'Lj6P646T44' => 'lonja', 'Lsat_1_v5_gn_6_75760' => 'lsa', 'Lsat_1_v5_gn_6_75800' => 'lsa', 'Lsat_1_v5_gn_6_75900' => 'lsa', 'Lsat_1_v5_gn_6_76240' => 'lsa', 'Lsat_1_v5_gn_6_76441' => 'lsa', 'Lsat_1_v5_gn_6_76700' => 'lsa', 'Lsat_1_v5_gn_6_76760' => 'lsa', 'Manes.15G033100' => 'mes', 'Mapoly0004s0074' => 'mpo', 'Mapoly0004s0075' => 'mpo', 'Mapoly0004s0163' => 'mpo', 'Mapoly0004s0164' => 'mpo', 'Mapoly0021s0018' => 'mpo', 'Mapoly0041s0136' => 'mpo', 'Mapoly0041s0137' => 'mpo', 'Mapoly0041s0138' => 'mpo', 'Mapoly0041s0139' => 'mpo', 'Mapoly0041s0141' => 'mpo', 'Mapoly0041s0142' => 'mpo', 'Mapoly0041s0143' => 'mpo', 'Mapoly0041s0144' => 'mpo', 'Mapoly0041s0145' => 'mpo', 'Mapoly0047s0106' => 'mpo', 'Mapoly0047s0108' => 'mpo', 'Mapoly0050s0051' => 'mpo', 'Mapoly0050s0052' => 'mpo', 'Mapoly0050s0053' => 'mpo', 'Mapoly0058s0013' => 'mpo', 'Mapoly0091s0078' => 'mpo', 'Mapoly0091s0079' => 'mpo', 'Mapoly0091s0080' => 'mpo', 'Mapoly0091s0081' => 'mpo', 'Mapoly0278s0004' => 'mpo', 'Mapoly0278s0005' => 'mpo', 'Mapoly0278s0006' => 'mpo', 'MBI11_g30648_MAGBIO' => 'mbi', 'MCO03G194' => 'mco', 'MCO03G590' => 'mco', 'MCO07G312' => 'mco', 'MCO10G318' => 'mco', 'MCO12G244' => 'mco', 'MCO13G148' => 'mco', 'MCO13G194' => 'mco', 'MCO16G238' => 'mco', 'MD06G1134100' => 'mdo', 'MD13G1200100' => 'mdo', 'MD13G1200300' => 'mdo', 'MD13G1200600' => 'mdo', 'MD14G1150400' => 'mdo', 'MD16G1200000' => 'mdo', 'Medtr1g102570' => 'mtr', 'Medtr1g102780' => 'mtr', 'Medtr1g102800' => 'mtr', 'Medtr1g102810' => 'mtr', 'Medtr1g102830' => 'mtr', 'MELO3C006499.2' => 'cme', 'Migut.G00385' => 'egut', 'MSTRG.4063' => 'ama', 'Nitab4.5_0000090g0260' => 'nta', 'Nitab4.5_0000977g0030' => 'nta', 'Nitab4.5_0002541g0040' => 'nta', 'Nitab4.5_0007068g0040' => 'nta', 'Nn005s41408' => 'nnu', 'Nn005s41410' => 'nnu', 'Oeu010310.1' => 'oeu', 'Oeu010311.1' => 'oeu', 'Oeu043472.1' => 'oeu', 'Os01g0246400' => 'osa', 'Os04g0267950' => 'osa', 'Os07g0178700' => 'osa', 'Os07g0178800' => 'osa', 'Peaxi162Scf00316g00046' => 'pax', 'Peaxi162Scf00316g00049' => 'pax', 'Peaxi162Scf00316g00059' => 'pax', 'Peaxi162Scf00316g00328' => 'pax', 'Peaxi162Scf00316g00329' => 'pax', 'Peaxi162Scf00316g00411' => 'pax', 'Peaxi162Scf00316g00521' => 'pax', 'Peaxi162Scf00492g00068' => 'pax', 'Peaxi162Scf35631g00002' => 'pax', 'PGR142G3720' => 'pgr', 'PGSC0003DMG400006442' => 'stu', 'Phvul.007G062000' => 'pvu', 'Potri.008G157750' => 'ptr', 'Potri.008G157900' => 'ptr', 'Potri.008G158000' => 'ptr', 'Potri.008G158200' => 'ptr', 'Pp3c11_7280' => 'ppa', 'Pp3c11_7980' => 'ppa', 'Pp3c12_19450' => 'ppa', 'Pp3c14_1480' => 'ppa', 'Pp3c14_1501' => 'ppa', 'Pp3c16_4900' => 'ppa', 'Pp3c16_5010' => 'ppa', 'Pp3c16_5060' => 'ppa', 'Pp3c19_18250' => 'ppa', 'Pp3c23_8530' => 'ppa', 'Pp3c23_8550' => 'ppa', 'Pp3c24_9670' => 'ppa', 'Pp3c2_21390' => 'ppa', 'Pp3c2_31380' => 'ppa', 'Pp3c3_16620' => 'ppa', 'Pp3c3_8090' => 'ppa', 'Pp3c3_8110' => 'ppa', 'Pp3c3_8130' => 'ppa', 'Pp3c3_8150' => 'ppa', 'Pp3c4_14320' => 'ppa', 'Pp3c6_2560' => 'ppa', 'Pp3c9_16700' => 'ppa', 'PRCOL_00000234' => 'pco', 'PRCOL_00000235' => 'pco', 'PRCOL_00000777' => 'pco', 'PRCOL_00002344' => 'pco', 'PRCOL_00002372' => 'pco', 'PRCOL_00006120' => 'pco', 'Prupe.1G021400' => 'ppe', 'Prupe.1G021500' => 'ppe', 'Prupe.1G021600' => 'ppe', 'Prupe.1G021700' => 'ppe', 'Prupe.1G021800' => 'ppe', 'Prupe.5G145100' => 'ppe', 'Psat6g204040' => 'psa', 'Psat6g204800' => 'psa', 'Psat6g204920' => 'psa', 'Psat6g204960' => 'psa', 'Psat6g205080' => 'psa', 'PSO017G0271' => 'pso', 'PSO017G1276' => 'pso', 'PSO017G1429' => 'pso', 'PSO017G1861' => 'pso', 'PSO017G2787' => 'pso', 'PSO017G4466' => 'pso', 'PSO017G5118' => 'pso', 'PSO017G5420' => 'pso', 'PSO063G3678' => 'pso', 'PSO210G0546' => 'pso', 'PSO317G0001' => 'pso', 'PSO357G0512' => 'pso', 'PSO478G2682' => 'pso', 'PSO647G0001' => 'pso', 'PSO675G0001' => 'pso', 'PSO675G2699' => 'pso', 'PSO675G2849' => 'pso', 'PSO675G4991' => 'pso', 'PSO689G0001' => 'pso', 'QL06p000916' => 'qlo', 'QL06p000921' => 'qlo', 'QL06p001398' => 'qlo', 'QL06p001407' => 'qlo', 'QL06p002031' => 'qlo', 'RcHm_v2.0_Chr4g0387791' => 'rch', 'RcHm_v2.0_Chr4g0387801' => 'rch', 'RcHm_v2.0_Chr6g0286501' => 'rch', 'RcHm_v2.0_Chr6g0286511' => 'rch', 'RcHm_v2.0_Chr6g0286521' => 'rch', 'RcHm_v2.0_Chr6g0286531' => 'rch', 'RcHm_v2.0_Chr7g0189141' => 'rch', 'Rhsim02G0028700' => 'rsi', 'Rhsim02G0028800' => 'rsi', 'Rhsim02G0028900' => 'rsi', 'Rhsim02G0029000' => 'rsi', 'Rhsim02G0029100' => 'rsi', 'Rhsim02G0029200' => 'rsi', 'Rhsim02G0029300' => 'rsi', 'Rhsim02G0029400' => 'rsi', 'Rhsim02G0029500' => 'rsi', 'Rhsim02G0029600' => 'rsi', 'RhsimUnG0024000' => 'rsi', 'RhsimUnG0024100' => 'rsi', 'RhsimUnG0024200' => 'rsi', 'RhsimUnG0024300' => 'rsi', 'RhsimUnG0024400' => 'rsi', 'RhsimUnG0024500' => 'rsi', 'RhsimUnG0024700' => 'rsi', 'RhsimUnG0024800' => 'rsi', 'RhsimUnG0024900' => 'rsi', 'RhsimUnG0025100' => 'rsi', 'Sabra08G0120200' => 'sbr', 'Sabra08G0120300' => 'sbr', 'Sabra08G0120500' => 'sbr', 'Sabra08G0120600' => 'sbr', 'Sabra10G0158900' => 'sbr', 'SalBow2G3492' => 'sbo', 'Sc13g0004760' => 'sci', 'Sc13g0004770' => 'sci', 'Sed0003417' => 'sed', 'Sed0019750' => 'sed', 'SEGI_03419' => 'sgi', 'SEGI_05907' => 'sgi', 'SEGI_10682' => 'sgi', 'SEGI_13528' => 'sgi', 'SEGI_16081' => 'sgi', 'SEGI_19370' => 'sgi', 'SEGI_21015' => 'sgi', 'SEGI_21944' => 'sgi', 'SEGI_32906' => 'sgi', 'SEGI_33093' => 'sgi', 'SEGI_36110' => 'sgi', 'SEGI_40397' => 'sgi', 'SGA_v2.0_scaffold191G40426' => 'sas', 'SGA_v2.0_scaffold353G49717' => 'sas', 'SGA_v2.0_scaffold50G18550' => 'sas', 'SMO119G0173' => 'smo', 'SMO172G0002' => 'smo', 'Solyc09g082690.3' => 'sly', 'Solyc09g082700.2' => 'sly', 'Sopen09g031550' => 'spe', 'Sopen09g031560' => 'spe', 'Sp3g20540' => 'spa', 'Sp7g07580' => 'spa', 'TAR134G0002' => 'tar', 'TAR236G0001' => 'tar', 'TAR365G0892' => 'tar', 'TAR636G0166' => 'tar', 'TAR636G0646' => 'tar', 'TAR636G0869' => 'tar', 'TAR636G1317' => 'tar', 'TAR636G1744' => 'tar', 'TAR636G3358' => 'tar', 'TAR636G3436' => 'tar', 'THA.LOC104803047' => 'tha', 'Thecc.04G238900' => 'tca', 'Thhalv10021557m.g' => 'esa', 'Thhalv10026318m.g' => 'esa', 'Thhalv10026335m.g' => 'esa', 'TPR.G17433' => 'tpr', 'TPR.G18915' => 'tpr', 'TPR.G26125' => 'tpr', 'TWI09G0677' => 'twi', 'TWI73G0287' => 'twi', 'unitig_748.g8326' => 'ugi', 'vmacro15370' => 'vma', 'vmacro15371' => 'vma', 'vmacro15372' => 'vma', 'vmacro15373' => 'vma', 'vmacro15374' => 'vma', 'VMungo0720G2826' => 'vmu', 'Zm00001eb116960' => 'zma', 'Zm00001eb301260' => 'zma', 'Zm00001eb301270' => 'zma' ) $gf_id = 'HOM05D001460' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001460' ) $data_identifier = 'HOM05D001460' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 4, 'aag' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 2, 'aox' => (int) 2, 'arhy' => (int) 4, 'ath' => (int) 2, 'atr' => (int) 1, 'acertr' => (int) 10, 'cqu' => (int) 4, 'bca' => (int) 11, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 1, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 1, 'ccan' => (int) 1, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 1, 'col' => (int) 1, 'cpa' => (int) 1, 'cre' => (int) 7, 'csa' => (int) 1, 'camsi' => (int) 2, 'dca' => (int) 3, 'din' => (int) 2, 'dzi' => (int) 3, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 14, 'fve' => (int) 9, 'gma' => (int) 2, 'ghi' => (int) 4, 'gra' => (int) 2, 'vvi' => (int) 1, 'han' => (int) 13, 'cav' => (int) 1, 'hma' => (int) 2, 'sun' => (int) 2, 'lal' => (int) 2, 'lonja' => (int) 12, 'lja' => (int) 1, 'lsa' => (int) 7, 'mes' => (int) 1, 'mpo' => (int) 27, 'mbi' => (int) 1, 'mco' => (int) 8, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 1, 'egut' => (int) 1, 'ama' => (int) 1, 'nta' => (int) 4, 'nnu' => (int) 2, 'oeu' => (int) 3, 'osa' => (int) 4, 'pax' => (int) 9, 'pgr' => (int) 1, 'stu' => (int) 1, 'pvu' => (int) 1, 'ptr' => (int) 4, 'ppa' => (int) 22, 'pco' => (int) 6, 'ppe' => (int) 6, 'psa' => (int) 5, 'pso' => (int) 19, 'qlo' => (int) 5, 'rch' => (int) 7, 'rsi' => (int) 20, 'sbr' => (int) 5, 'sbo' => (int) 1, 'sci' => (int) 2, 'sed' => (int) 2, 'sgi' => (int) 12, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 2, 'tar' => (int) 10, 'tha' => (int) 1, 'tca' => (int) 1, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 2, 'ugi' => (int) 1, 'vma' => (int) 5, 'vmu' => (int) 1, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb301270' $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' => 'HOM05D001460', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '433', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p22980' => 'bna', 'A01p32340' => 'bna', 'A03p42970' => 'bna', 'A05p25880' => 'bna', 'Aa31LG8G9320' => 'aar', 'Aa31LG8G9330' => 'aar', 'Aa31LG8G9340' => 'aar', 'Aa31sc221G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1034' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1528' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.829' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2222' => 'aag', 'Ah.12g058830' => 'amhyb', 'Ah.12g058840' => 'amhyb', 'AL3G37160' => 'aly', 'AL7G41310' => 'aly', 'Aqoxy5G00395' => 'aox', 'Aqoxy5G00396' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0C8NZA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5185HY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JZ1PRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MD3LS0' => 'arhy', 'AT3G22840' => 'ath', 'AT4G14690' => 'ath', 'ATR0665G054' => 'atr', 'Atru.chr4.2344' => 'acertr', 'Atru.chr4.2346' => 'acertr', 'Atru.chr4.2347' => 'acertr', 'Atru.chr4.2348' => 'acertr', 'Atru.chr4.2355' => 'acertr', 'Atru.chr4.2356' => 'acertr', 'Atru.chr4.2358' => 'acertr', 'Atru.chr4.2359' => 'acertr', 'Atru.chr4.2360' => 'acertr', 'Atru.chr4.2361' => 'acertr', 'AUR62030476' => 'cqu', 'AUR62030478' => 'cqu', 'AUR62030819' => 'cqu', 'AUR62030820' => 'cqu', 'BcaB03g14648' => 'bca', 'BcaB04g20492' => 'bca', 'BcaB06g26399' => 'bca', 'BcaC01g03416' => 'bca', 'BcaC01g03419' => 'bca', 'BcaC01g03421' => 'bca', 'BcaC01g03424' => 'bca', 'BcaC05g28012' => 'bca', 'BcaC09g49212' => 'bca', 'BcaC09g50140' => 'bca', 'BcaNung00346' => 'bca', 'BolC1t02785H' => 'bol', 'BolC1t04095H' => 'bol', 'BolC3t17545H' => 'bol', 'BolC5t32769H' => 'bol', 'BraA01t02211Z' => 'bra', 'BraA01t03359Z' => 'bra', 'BraA03t13441Z' => 'bra', 'BraA05t21476Z' => 'bra', 'C01p28420' => 'bna', 'C01p41350' => 'bna', 'C03p52750' => 'bna', 'C03p52780' => 'bna', 'C05p40270' => 'bna', 'CAN.G1437.9' => 'can', 'CANSAT78G0035' => 'cansat', 'CANSAT78G1036' => 'cansat', 'CANSAT78G2272' => 'cansat', 'CANSAT78G2478' => 'cansat', 'CARHR098700' => 'chi', 'CARHR221120' => 'chi', 'CARHR221150' => 'chi', 'Carub.0003s2297' => 'cru', 'Carub.0007s2749' => 'cru', 'Carub.0007s2750' => 'cru', 'Carub.0007s2751' => 'cru', 'Ca_10849_v3' => 'car', 'Cc03_g04300' => 'ccan', 'CDE02G3648' => 'cde', 'CDE05G0060' => 'cde', 'CDE05G0692' => 'cde', 'CDE05G2285' => 'cde', 'CDE05G2884' => 'cde', 'CDE05G3072' => 'cde', 'Cfa008439' => 'cfa', 'Cfa008441' => 'cfa', 'Cfa008443' => 'cfa', 'Cfa008448' => 'cfa', 'Ciclev10005974m.g' => 'ccl', 'Ciclev10006006m.g' => 'ccl', 'Ciclev10006775m.g' => 'ccl', 'CiPaw.02G120400' => 'cil', 'CiPaw.02G120500' => 'cil', 'CiPaw.02G120600' => 'cil', 'ClCG05G004850' => 'cla', 'COL.COLO4_21566' => 'col', 'Cpa.g.sc44.124' => 'cpa', 'Cre07.g320400' => 'cre', 'Cre07.g320450' => 'cre', 'Cre08.g384650' => 'cre', 'Cre09.g393173' => 'cre', 'Cre09.g394325' => 'cre', 'Cre14.g626750' => 'cre', 'Cre16.g679250' => 'cre', 'CsaV3_3G012890' => 'csa', 'CSS0010865' => 'camsi', 'CSS0044338' => 'camsi', 'DCAR_002366' => 'dca', 'DCAR_030687' => 'dca', 'DCAR_030688' => 'dca', 'Dinv14047' => 'din', 'Dinv14048' => 'din', 'Duzib151G0105' => 'dzi', 'Duzib151G0114' => 'dzi', 'Duzib212G1029' => 'dzi', 'ECA232G3536' => 'eca', 'ECA240G0786' => 'eca', 'ECA240G1802' => 'eca', 'ECA240G3760' => 'eca', 'ECA240G3920' => 'eca', 'EL10Ac5g12536' => 'bvu', 'EL10Ac5g12537' => 'bvu', 'EL10Ac5g12538' => 'bvu', 'Eucgr.B01004' => 'egr', 'Eucgr.B01006' => 'egr', 'Eucgr.B01007' => 'egr', 'Eucgr.B01008' => 'egr', 'Eucgr.B01895' => 'egr', 'Eucgr.B01896' => 'egr', 'FAN04G1456' => 'fan', 'FAN08G1769' => 'fan', 'FAN08G2160' => 'fan', 'FAN13G2403' => 'fan', 'FAN13G3303' => 'fan', 'FAN15G2435' => 'fan', 'FAN17G0672' => 'fan', 'FAN17G2441' => 'fan', 'FAN18G1024' => 'fan', 'FAN22G1458' => 'fan', 'FAN24G0037' => 'fan', 'FAN24G0429' => 'fan', 'FAN24G2387' => 'fan', 'FAN27G2746' => 'fan', 'FvH4_2g20400' => 'fve', 'FvH4_2g20420' => 'fve', 'FvH4_2g20430' => 'fve', 'FvH4_4g01270' => 'fve', 'FvH4_4g01290' => 'fve', 'FvH4_4g01300' => 'fve', 'FvH4_4g01310' => 'fve', 'FvH4_4g01330' => 'fve', 'FvH4_5g09070' => 'fve', 'Glyma.10G243800' => 'gma', 'Glyma.20G150600' => 'gma', 'Gohir.A09G219200' => 'ghi', 'Gohir.A09G219300' => 'ghi', 'Gohir.D09G221400' => 'ghi', 'Gohir.D09G221500' => 'ghi', 'Gorai.006G242600' => 'gra', 'Gorai.006G242700' => 'gra', 'GSVIVG01018044001' => 'vvi', 'HanXRQChr03g0083821' => 'han', 'HanXRQChr03g0083841' => 'han', 'HanXRQChr03g0083881' => 'han', 'HanXRQChr03g0083901' => 'han', 'HanXRQChr03g0083921' => 'han', 'HanXRQChr03g0085331' => 'han', 'HanXRQChr03g0085361' => 'han', 'HanXRQChr03g0085411' => 'han', 'HanXRQChr03g0085421' => 'han', 'HanXRQChr03g0085431' => 'han', 'HanXRQChr08g0221991' => 'han', 'HanXRQChr11g0336061' => 'han', 'HanXRQChr11g0336411' => 'han', 'Haze_11234' => 'cav', 'Hma1.2p1_0549F.1_g177010' => 'hma', 'Hma1.2p1_0602F.1_g187630' => 'hma', 'Hund14876' => 'sun', 'Hund14879' => 'sun', 'Lalb_Chr06g0160741' => 'lal', 'Lalb_Chr21g0304781' => 'lal', 'Lj3A726G19' => 'lonja', 'Lj3A726T23' => 'lonja', 'Lj3A726T24' => 'lonja', 'Lj3A726T25' => 'lonja', 'Lj3A727T17' => 'lonja', 'Lj3C726T0' => 'lonja', 'Lj3C726T2' => 'lonja', 'Lj3P725T35' => 'lonja', 'Lj3P727T10' => 'lonja', 'Lj3P727T12' => 'lonja', 'Lj3P727T14' => 'lonja', 'Lj5g0023109' => 'lja', 'Lj6P646T44' => 'lonja', 'Lsat_1_v5_gn_6_75760' => 'lsa', 'Lsat_1_v5_gn_6_75800' => 'lsa', 'Lsat_1_v5_gn_6_75900' => 'lsa', 'Lsat_1_v5_gn_6_76240' => 'lsa', 'Lsat_1_v5_gn_6_76441' => 'lsa', 'Lsat_1_v5_gn_6_76700' => 'lsa', 'Lsat_1_v5_gn_6_76760' => 'lsa', 'Manes.15G033100' => 'mes', 'Mapoly0004s0074' => 'mpo', 'Mapoly0004s0075' => 'mpo', 'Mapoly0004s0163' => 'mpo', 'Mapoly0004s0164' => 'mpo', 'Mapoly0021s0018' => 'mpo', 'Mapoly0041s0136' => 'mpo', 'Mapoly0041s0137' => 'mpo', 'Mapoly0041s0138' => 'mpo', 'Mapoly0041s0139' => 'mpo', 'Mapoly0041s0141' => 'mpo', 'Mapoly0041s0142' => 'mpo', 'Mapoly0041s0143' => 'mpo', 'Mapoly0041s0144' => 'mpo', 'Mapoly0041s0145' => 'mpo', 'Mapoly0047s0106' => 'mpo', 'Mapoly0047s0108' => 'mpo', 'Mapoly0050s0051' => 'mpo', 'Mapoly0050s0052' => 'mpo', 'Mapoly0050s0053' => 'mpo', 'Mapoly0058s0013' => 'mpo', 'Mapoly0091s0078' => 'mpo', 'Mapoly0091s0079' => 'mpo', 'Mapoly0091s0080' => 'mpo', 'Mapoly0091s0081' => 'mpo', 'Mapoly0278s0004' => 'mpo', 'Mapoly0278s0005' => 'mpo', 'Mapoly0278s0006' => 'mpo', 'MBI11_g30648_MAGBIO' => 'mbi', 'MCO03G194' => 'mco', 'MCO03G590' => 'mco', 'MCO07G312' => 'mco', 'MCO10G318' => 'mco', 'MCO12G244' => 'mco', 'MCO13G148' => 'mco', 'MCO13G194' => 'mco', 'MCO16G238' => 'mco', 'MD06G1134100' => 'mdo', 'MD13G1200100' => 'mdo', 'MD13G1200300' => 'mdo', 'MD13G1200600' => 'mdo', 'MD14G1150400' => 'mdo', 'MD16G1200000' => 'mdo', 'Medtr1g102570' => 'mtr', 'Medtr1g102780' => 'mtr', 'Medtr1g102800' => 'mtr', 'Medtr1g102810' => 'mtr', 'Medtr1g102830' => 'mtr', 'MELO3C006499.2' => 'cme', 'Migut.G00385' => 'egut', 'MSTRG.4063' => 'ama', 'Nitab4.5_0000090g0260' => 'nta', 'Nitab4.5_0000977g0030' => 'nta', 'Nitab4.5_0002541g0040' => 'nta', 'Nitab4.5_0007068g0040' => 'nta', 'Nn005s41408' => 'nnu', 'Nn005s41410' => 'nnu', 'Oeu010310.1' => 'oeu', 'Oeu010311.1' => 'oeu', 'Oeu043472.1' => 'oeu', 'Os01g0246400' => 'osa', 'Os04g0267950' => 'osa', 'Os07g0178700' => 'osa', 'Os07g0178800' => 'osa', 'Peaxi162Scf00316g00046' => 'pax', 'Peaxi162Scf00316g00049' => 'pax', 'Peaxi162Scf00316g00059' => 'pax', 'Peaxi162Scf00316g00328' => 'pax', 'Peaxi162Scf00316g00329' => 'pax', 'Peaxi162Scf00316g00411' => 'pax', 'Peaxi162Scf00316g00521' => 'pax', 'Peaxi162Scf00492g00068' => 'pax', 'Peaxi162Scf35631g00002' => 'pax', 'PGR142G3720' => 'pgr', 'PGSC0003DMG400006442' => 'stu', 'Phvul.007G062000' => 'pvu', 'Potri.008G157750' => 'ptr', 'Potri.008G157900' => 'ptr', 'Potri.008G158000' => 'ptr', 'Potri.008G158200' => 'ptr', 'Pp3c11_7280' => 'ppa', 'Pp3c11_7980' => 'ppa', 'Pp3c12_19450' => 'ppa', 'Pp3c14_1480' => 'ppa', 'Pp3c14_1501' => 'ppa', 'Pp3c16_4900' => 'ppa', 'Pp3c16_5010' => 'ppa', 'Pp3c16_5060' => 'ppa', 'Pp3c19_18250' => 'ppa', 'Pp3c23_8530' => 'ppa', 'Pp3c23_8550' => 'ppa', 'Pp3c24_9670' => 'ppa', 'Pp3c2_21390' => 'ppa', 'Pp3c2_31380' => 'ppa', 'Pp3c3_16620' => 'ppa', 'Pp3c3_8090' => 'ppa', 'Pp3c3_8110' => 'ppa', 'Pp3c3_8130' => 'ppa', 'Pp3c3_8150' => 'ppa', 'Pp3c4_14320' => 'ppa', 'Pp3c6_2560' => 'ppa', 'Pp3c9_16700' => 'ppa', 'PRCOL_00000234' => 'pco', 'PRCOL_00000235' => 'pco', 'PRCOL_00000777' => 'pco', 'PRCOL_00002344' => 'pco', 'PRCOL_00002372' => 'pco', 'PRCOL_00006120' => 'pco', 'Prupe.1G021400' => 'ppe', 'Prupe.1G021500' => 'ppe', 'Prupe.1G021600' => 'ppe', 'Prupe.1G021700' => 'ppe', 'Prupe.1G021800' => 'ppe', 'Prupe.5G145100' => 'ppe', 'Psat6g204040' => 'psa', 'Psat6g204800' => 'psa', 'Psat6g204920' => 'psa', 'Psat6g204960' => 'psa', 'Psat6g205080' => 'psa', 'PSO017G0271' => 'pso', 'PSO017G1276' => 'pso', 'PSO017G1429' => 'pso', 'PSO017G1861' => 'pso', 'PSO017G2787' => 'pso', 'PSO017G4466' => 'pso', 'PSO017G5118' => 'pso', 'PSO017G5420' => 'pso', 'PSO063G3678' => 'pso', 'PSO210G0546' => 'pso', 'PSO317G0001' => 'pso', 'PSO357G0512' => 'pso', 'PSO478G2682' => 'pso', 'PSO647G0001' => 'pso', 'PSO675G0001' => 'pso', 'PSO675G2699' => 'pso', 'PSO675G2849' => 'pso', 'PSO675G4991' => 'pso', 'PSO689G0001' => 'pso', 'QL06p000916' => 'qlo', 'QL06p000921' => 'qlo', 'QL06p001398' => 'qlo', 'QL06p001407' => 'qlo', 'QL06p002031' => 'qlo', 'RcHm_v2.0_Chr4g0387791' => 'rch', 'RcHm_v2.0_Chr4g0387801' => 'rch', 'RcHm_v2.0_Chr6g0286501' => 'rch', 'RcHm_v2.0_Chr6g0286511' => 'rch', 'RcHm_v2.0_Chr6g0286521' => 'rch', 'RcHm_v2.0_Chr6g0286531' => 'rch', 'RcHm_v2.0_Chr7g0189141' => 'rch', 'Rhsim02G0028700' => 'rsi', 'Rhsim02G0028800' => 'rsi', 'Rhsim02G0028900' => 'rsi', 'Rhsim02G0029000' => 'rsi', 'Rhsim02G0029100' => 'rsi', 'Rhsim02G0029200' => 'rsi', 'Rhsim02G0029300' => 'rsi', 'Rhsim02G0029400' => 'rsi', 'Rhsim02G0029500' => 'rsi', 'Rhsim02G0029600' => 'rsi', 'RhsimUnG0024000' => 'rsi', 'RhsimUnG0024100' => 'rsi', 'RhsimUnG0024200' => 'rsi', 'RhsimUnG0024300' => 'rsi', 'RhsimUnG0024400' => 'rsi', 'RhsimUnG0024500' => 'rsi', 'RhsimUnG0024700' => 'rsi', 'RhsimUnG0024800' => 'rsi', 'RhsimUnG0024900' => 'rsi', 'RhsimUnG0025100' => 'rsi', 'Sabra08G0120200' => 'sbr', 'Sabra08G0120300' => 'sbr', 'Sabra08G0120500' => 'sbr', 'Sabra08G0120600' => 'sbr', 'Sabra10G0158900' => 'sbr', 'SalBow2G3492' => 'sbo', 'Sc13g0004760' => 'sci', 'Sc13g0004770' => 'sci', 'Sed0003417' => 'sed', 'Sed0019750' => 'sed', 'SEGI_03419' => 'sgi', 'SEGI_05907' => 'sgi', 'SEGI_10682' => 'sgi', 'SEGI_13528' => 'sgi', 'SEGI_16081' => 'sgi', 'SEGI_19370' => 'sgi', 'SEGI_21015' => 'sgi', 'SEGI_21944' => 'sgi', 'SEGI_32906' => 'sgi', 'SEGI_33093' => 'sgi', 'SEGI_36110' => 'sgi', 'SEGI_40397' => 'sgi', 'SGA_v2.0_scaffold191G40426' => 'sas', 'SGA_v2.0_scaffold353G49717' => 'sas', 'SGA_v2.0_scaffold50G18550' => 'sas', 'SMO119G0173' => 'smo', 'SMO172G0002' => 'smo', 'Solyc09g082690.3' => 'sly', 'Solyc09g082700.2' => 'sly', 'Sopen09g031550' => 'spe', 'Sopen09g031560' => 'spe', 'Sp3g20540' => 'spa', 'Sp7g07580' => 'spa', 'TAR134G0002' => 'tar', 'TAR236G0001' => 'tar', 'TAR365G0892' => 'tar', 'TAR636G0166' => 'tar', 'TAR636G0646' => 'tar', 'TAR636G0869' => 'tar', 'TAR636G1317' => 'tar', 'TAR636G1744' => 'tar', 'TAR636G3358' => 'tar', 'TAR636G3436' => 'tar', 'THA.LOC104803047' => 'tha', 'Thecc.04G238900' => 'tca', 'Thhalv10021557m.g' => 'esa', 'Thhalv10026318m.g' => 'esa', 'Thhalv10026335m.g' => 'esa', 'TPR.G17433' => 'tpr', 'TPR.G18915' => 'tpr', 'TPR.G26125' => 'tpr', 'TWI09G0677' => 'twi', 'TWI73G0287' => 'twi', 'unitig_748.g8326' => 'ugi', 'vmacro15370' => 'vma', 'vmacro15371' => 'vma', 'vmacro15372' => 'vma', 'vmacro15373' => 'vma', 'vmacro15374' => 'vma', 'VMungo0720G2826' => 'vmu', 'Zm00001eb116960' => 'zma', 'Zm00001eb301260' => 'zma', 'Zm00001eb301270' => 'zma' ), 'gf_id' => 'HOM05D001460', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001460' ), 'data_identifier' => 'HOM05D001460', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001460', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '433', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p22980' => 'bna', 'A01p32340' => 'bna', 'A03p42970' => 'bna', 'A05p25880' => 'bna', 'Aa31LG8G9320' => 'aar', 'Aa31LG8G9330' => 'aar', 'Aa31LG8G9340' => 'aar', 'Aa31sc221G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1034' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1528' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.829' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2222' => 'aag', 'Ah.12g058830' => 'amhyb', 'Ah.12g058840' => 'amhyb', 'AL3G37160' => 'aly', 'AL7G41310' => 'aly', 'Aqoxy5G00395' => 'aox', 'Aqoxy5G00396' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0C8NZA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5185HY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JZ1PRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MD3LS0' => 'arhy', 'AT3G22840' => 'ath', 'AT4G14690' => 'ath', 'ATR0665G054' => 'atr', 'Atru.chr4.2344' => 'acertr', 'Atru.chr4.2346' => 'acertr', 'Atru.chr4.2347' => 'acertr', 'Atru.chr4.2348' => 'acertr', 'Atru.chr4.2355' => 'acertr', 'Atru.chr4.2356' => 'acertr', 'Atru.chr4.2358' => 'acertr', 'Atru.chr4.2359' => 'acertr', 'Atru.chr4.2360' => 'acertr', 'Atru.chr4.2361' => 'acertr', 'AUR62030476' => 'cqu', 'AUR62030478' => 'cqu', 'AUR62030819' => 'cqu', 'AUR62030820' => 'cqu', 'BcaB03g14648' => 'bca', 'BcaB04g20492' => 'bca', 'BcaB06g26399' => 'bca', 'BcaC01g03416' => 'bca', 'BcaC01g03419' => 'bca', 'BcaC01g03421' => 'bca', 'BcaC01g03424' => 'bca', 'BcaC05g28012' => 'bca', 'BcaC09g49212' => 'bca', 'BcaC09g50140' => 'bca', 'BcaNung00346' => 'bca', 'BolC1t02785H' => 'bol', 'BolC1t04095H' => 'bol', 'BolC3t17545H' => 'bol', 'BolC5t32769H' => 'bol', 'BraA01t02211Z' => 'bra', 'BraA01t03359Z' => 'bra', 'BraA03t13441Z' => 'bra', 'BraA05t21476Z' => 'bra', 'C01p28420' => 'bna', 'C01p41350' => 'bna', 'C03p52750' => 'bna', 'C03p52780' => 'bna', 'C05p40270' => 'bna', 'CAN.G1437.9' => 'can', 'CANSAT78G0035' => 'cansat', 'CANSAT78G1036' => 'cansat', 'CANSAT78G2272' => 'cansat', 'CANSAT78G2478' => 'cansat', 'CARHR098700' => 'chi', 'CARHR221120' => 'chi', 'CARHR221150' => 'chi', 'Carub.0003s2297' => 'cru', 'Carub.0007s2749' => 'cru', 'Carub.0007s2750' => 'cru', 'Carub.0007s2751' => 'cru', 'Ca_10849_v3' => 'car', 'Cc03_g04300' => 'ccan', 'CDE02G3648' => 'cde', 'CDE05G0060' => 'cde', 'CDE05G0692' => 'cde', 'CDE05G2285' => 'cde', 'CDE05G2884' => 'cde', 'CDE05G3072' => 'cde', 'Cfa008439' => 'cfa', 'Cfa008441' => 'cfa', 'Cfa008443' => 'cfa', 'Cfa008448' => 'cfa', 'Ciclev10005974m.g' => 'ccl', 'Ciclev10006006m.g' => 'ccl', 'Ciclev10006775m.g' => 'ccl', 'CiPaw.02G120400' => 'cil', 'CiPaw.02G120500' => 'cil', 'CiPaw.02G120600' => 'cil', 'ClCG05G004850' => 'cla', 'COL.COLO4_21566' => 'col', 'Cpa.g.sc44.124' => 'cpa', 'Cre07.g320400' => 'cre', 'Cre07.g320450' => 'cre', 'Cre08.g384650' => 'cre', 'Cre09.g393173' => 'cre', 'Cre09.g394325' => 'cre', 'Cre14.g626750' => 'cre', 'Cre16.g679250' => 'cre', 'CsaV3_3G012890' => 'csa', 'CSS0010865' => 'camsi', 'CSS0044338' => 'camsi', 'DCAR_002366' => 'dca', 'DCAR_030687' => 'dca', 'DCAR_030688' => 'dca', 'Dinv14047' => 'din', 'Dinv14048' => 'din', 'Duzib151G0105' => 'dzi', 'Duzib151G0114' => 'dzi', 'Duzib212G1029' => 'dzi', 'ECA232G3536' => 'eca', 'ECA240G0786' => 'eca', 'ECA240G1802' => 'eca', 'ECA240G3760' => 'eca', 'ECA240G3920' => 'eca', 'EL10Ac5g12536' => 'bvu', 'EL10Ac5g12537' => 'bvu', 'EL10Ac5g12538' => 'bvu', 'Eucgr.B01004' => 'egr', 'Eucgr.B01006' => 'egr', 'Eucgr.B01007' => 'egr', 'Eucgr.B01008' => 'egr', 'Eucgr.B01895' => 'egr', 'Eucgr.B01896' => 'egr', 'FAN04G1456' => 'fan', 'FAN08G1769' => 'fan', 'FAN08G2160' => 'fan', 'FAN13G2403' => 'fan', 'FAN13G3303' => 'fan', 'FAN15G2435' => 'fan', 'FAN17G0672' => 'fan', 'FAN17G2441' => 'fan', 'FAN18G1024' => 'fan', 'FAN22G1458' => 'fan', 'FAN24G0037' => 'fan', 'FAN24G0429' => 'fan', 'FAN24G2387' => 'fan', 'FAN27G2746' => 'fan', 'FvH4_2g20400' => 'fve', 'FvH4_2g20420' => 'fve', 'FvH4_2g20430' => 'fve', 'FvH4_4g01270' => 'fve', 'FvH4_4g01290' => 'fve', 'FvH4_4g01300' => 'fve', 'FvH4_4g01310' => 'fve', 'FvH4_4g01330' => 'fve', 'FvH4_5g09070' => 'fve', 'Glyma.10G243800' => 'gma', 'Glyma.20G150600' => 'gma', 'Gohir.A09G219200' => 'ghi', 'Gohir.A09G219300' => 'ghi', 'Gohir.D09G221400' => 'ghi', 'Gohir.D09G221500' => 'ghi', 'Gorai.006G242600' => 'gra', 'Gorai.006G242700' => 'gra', 'GSVIVG01018044001' => 'vvi', 'HanXRQChr03g0083821' => 'han', 'HanXRQChr03g0083841' => 'han', 'HanXRQChr03g0083881' => 'han', 'HanXRQChr03g0083901' => 'han', 'HanXRQChr03g0083921' => 'han', 'HanXRQChr03g0085331' => 'han', 'HanXRQChr03g0085361' => 'han', 'HanXRQChr03g0085411' => 'han', 'HanXRQChr03g0085421' => 'han', 'HanXRQChr03g0085431' => 'han', 'HanXRQChr08g0221991' => 'han', 'HanXRQChr11g0336061' => 'han', 'HanXRQChr11g0336411' => 'han', 'Haze_11234' => 'cav', 'Hma1.2p1_0549F.1_g177010' => 'hma', 'Hma1.2p1_0602F.1_g187630' => 'hma', 'Hund14876' => 'sun', 'Hund14879' => 'sun', 'Lalb_Chr06g0160741' => 'lal', 'Lalb_Chr21g0304781' => 'lal', 'Lj3A726G19' => 'lonja', 'Lj3A726T23' => 'lonja', 'Lj3A726T24' => 'lonja', 'Lj3A726T25' => 'lonja', 'Lj3A727T17' => 'lonja', 'Lj3C726T0' => 'lonja', 'Lj3C726T2' => 'lonja', 'Lj3P725T35' => 'lonja', 'Lj3P727T10' => 'lonja', 'Lj3P727T12' => 'lonja', 'Lj3P727T14' => 'lonja', 'Lj5g0023109' => 'lja', 'Lj6P646T44' => 'lonja', 'Lsat_1_v5_gn_6_75760' => 'lsa', 'Lsat_1_v5_gn_6_75800' => 'lsa', 'Lsat_1_v5_gn_6_75900' => 'lsa', 'Lsat_1_v5_gn_6_76240' => 'lsa', 'Lsat_1_v5_gn_6_76441' => 'lsa', 'Lsat_1_v5_gn_6_76700' => 'lsa', 'Lsat_1_v5_gn_6_76760' => 'lsa', 'Manes.15G033100' => 'mes', 'Mapoly0004s0074' => 'mpo', 'Mapoly0004s0075' => 'mpo', 'Mapoly0004s0163' => 'mpo', 'Mapoly0004s0164' => 'mpo', 'Mapoly0021s0018' => 'mpo', 'Mapoly0041s0136' => 'mpo', 'Mapoly0041s0137' => 'mpo', 'Mapoly0041s0138' => 'mpo', 'Mapoly0041s0139' => 'mpo', 'Mapoly0041s0141' => 'mpo', 'Mapoly0041s0142' => 'mpo', 'Mapoly0041s0143' => 'mpo', 'Mapoly0041s0144' => 'mpo', 'Mapoly0041s0145' => 'mpo', 'Mapoly0047s0106' => 'mpo', 'Mapoly0047s0108' => 'mpo', 'Mapoly0050s0051' => 'mpo', 'Mapoly0050s0052' => 'mpo', 'Mapoly0050s0053' => 'mpo', 'Mapoly0058s0013' => 'mpo', 'Mapoly0091s0078' => 'mpo', 'Mapoly0091s0079' => 'mpo', 'Mapoly0091s0080' => 'mpo', 'Mapoly0091s0081' => 'mpo', 'Mapoly0278s0004' => 'mpo', 'Mapoly0278s0005' => 'mpo', 'Mapoly0278s0006' => 'mpo', 'MBI11_g30648_MAGBIO' => 'mbi', 'MCO03G194' => 'mco', 'MCO03G590' => 'mco', 'MCO07G312' => 'mco', 'MCO10G318' => 'mco', 'MCO12G244' => 'mco', 'MCO13G148' => 'mco', 'MCO13G194' => 'mco', 'MCO16G238' => 'mco', 'MD06G1134100' => 'mdo', 'MD13G1200100' => 'mdo', 'MD13G1200300' => 'mdo', 'MD13G1200600' => 'mdo', 'MD14G1150400' => 'mdo', 'MD16G1200000' => 'mdo', 'Medtr1g102570' => 'mtr', 'Medtr1g102780' => 'mtr', 'Medtr1g102800' => 'mtr', 'Medtr1g102810' => 'mtr', 'Medtr1g102830' => 'mtr', 'MELO3C006499.2' => 'cme', 'Migut.G00385' => 'egut', 'MSTRG.4063' => 'ama', 'Nitab4.5_0000090g0260' => 'nta', 'Nitab4.5_0000977g0030' => 'nta', 'Nitab4.5_0002541g0040' => 'nta', 'Nitab4.5_0007068g0040' => 'nta', 'Nn005s41408' => 'nnu', 'Nn005s41410' => 'nnu', 'Oeu010310.1' => 'oeu', 'Oeu010311.1' => 'oeu', 'Oeu043472.1' => 'oeu', 'Os01g0246400' => 'osa', 'Os04g0267950' => 'osa', 'Os07g0178700' => 'osa', 'Os07g0178800' => 'osa', 'Peaxi162Scf00316g00046' => 'pax', 'Peaxi162Scf00316g00049' => 'pax', 'Peaxi162Scf00316g00059' => 'pax', 'Peaxi162Scf00316g00328' => 'pax', 'Peaxi162Scf00316g00329' => 'pax', 'Peaxi162Scf00316g00411' => 'pax', 'Peaxi162Scf00316g00521' => 'pax', 'Peaxi162Scf00492g00068' => 'pax', 'Peaxi162Scf35631g00002' => 'pax', 'PGR142G3720' => 'pgr', 'PGSC0003DMG400006442' => 'stu', 'Phvul.007G062000' => 'pvu', 'Potri.008G157750' => 'ptr', 'Potri.008G157900' => 'ptr', 'Potri.008G158000' => 'ptr', 'Potri.008G158200' => 'ptr', 'Pp3c11_7280' => 'ppa', 'Pp3c11_7980' => 'ppa', 'Pp3c12_19450' => 'ppa', 'Pp3c14_1480' => 'ppa', 'Pp3c14_1501' => 'ppa', 'Pp3c16_4900' => 'ppa', 'Pp3c16_5010' => 'ppa', 'Pp3c16_5060' => 'ppa', 'Pp3c19_18250' => 'ppa', 'Pp3c23_8530' => 'ppa', 'Pp3c23_8550' => 'ppa', 'Pp3c24_9670' => 'ppa', 'Pp3c2_21390' => 'ppa', 'Pp3c2_31380' => 'ppa', 'Pp3c3_16620' => 'ppa', 'Pp3c3_8090' => 'ppa', 'Pp3c3_8110' => 'ppa', 'Pp3c3_8130' => 'ppa', 'Pp3c3_8150' => 'ppa', 'Pp3c4_14320' => 'ppa', 'Pp3c6_2560' => 'ppa', 'Pp3c9_16700' => 'ppa', 'PRCOL_00000234' => 'pco', 'PRCOL_00000235' => 'pco', 'PRCOL_00000777' => 'pco', 'PRCOL_00002344' => 'pco', 'PRCOL_00002372' => 'pco', 'PRCOL_00006120' => 'pco', 'Prupe.1G021400' => 'ppe', 'Prupe.1G021500' => 'ppe', 'Prupe.1G021600' => 'ppe', 'Prupe.1G021700' => 'ppe', 'Prupe.1G021800' => 'ppe', 'Prupe.5G145100' => 'ppe', 'Psat6g204040' => 'psa', 'Psat6g204800' => 'psa', 'Psat6g204920' => 'psa', 'Psat6g204960' => 'psa', 'Psat6g205080' => 'psa', 'PSO017G0271' => 'pso', 'PSO017G1276' => 'pso', 'PSO017G1429' => 'pso', 'PSO017G1861' => 'pso', 'PSO017G2787' => 'pso', 'PSO017G4466' => 'pso', 'PSO017G5118' => 'pso', 'PSO017G5420' => 'pso', 'PSO063G3678' => 'pso', 'PSO210G0546' => 'pso', 'PSO317G0001' => 'pso', 'PSO357G0512' => 'pso', 'PSO478G2682' => 'pso', 'PSO647G0001' => 'pso', 'PSO675G0001' => 'pso', 'PSO675G2699' => 'pso', 'PSO675G2849' => 'pso', 'PSO675G4991' => 'pso', 'PSO689G0001' => 'pso', 'QL06p000916' => 'qlo', 'QL06p000921' => 'qlo', 'QL06p001398' => 'qlo', 'QL06p001407' => 'qlo', 'QL06p002031' => 'qlo', 'RcHm_v2.0_Chr4g0387791' => 'rch', 'RcHm_v2.0_Chr4g0387801' => 'rch', 'RcHm_v2.0_Chr6g0286501' => 'rch', 'RcHm_v2.0_Chr6g0286511' => 'rch', 'RcHm_v2.0_Chr6g0286521' => 'rch', 'RcHm_v2.0_Chr6g0286531' => 'rch', 'RcHm_v2.0_Chr7g0189141' => 'rch', 'Rhsim02G0028700' => 'rsi', 'Rhsim02G0028800' => 'rsi', 'Rhsim02G0028900' => 'rsi', 'Rhsim02G0029000' => 'rsi', 'Rhsim02G0029100' => 'rsi', 'Rhsim02G0029200' => 'rsi', 'Rhsim02G0029300' => 'rsi', 'Rhsim02G0029400' => 'rsi', 'Rhsim02G0029500' => 'rsi', 'Rhsim02G0029600' => 'rsi', 'RhsimUnG0024000' => 'rsi', 'RhsimUnG0024100' => 'rsi', 'RhsimUnG0024200' => 'rsi', 'RhsimUnG0024300' => 'rsi', 'RhsimUnG0024400' => 'rsi', 'RhsimUnG0024500' => 'rsi', 'RhsimUnG0024700' => 'rsi', 'RhsimUnG0024800' => 'rsi', 'RhsimUnG0024900' => 'rsi', 'RhsimUnG0025100' => 'rsi', 'Sabra08G0120200' => 'sbr', 'Sabra08G0120300' => 'sbr', 'Sabra08G0120500' => 'sbr', 'Sabra08G0120600' => 'sbr', 'Sabra10G0158900' => 'sbr', 'SalBow2G3492' => 'sbo', 'Sc13g0004760' => 'sci', 'Sc13g0004770' => 'sci', 'Sed0003417' => 'sed', 'Sed0019750' => 'sed', 'SEGI_03419' => 'sgi', 'SEGI_05907' => 'sgi', 'SEGI_10682' => 'sgi', 'SEGI_13528' => 'sgi', 'SEGI_16081' => 'sgi', 'SEGI_19370' => 'sgi', 'SEGI_21015' => 'sgi', 'SEGI_21944' => 'sgi', 'SEGI_32906' => 'sgi', 'SEGI_33093' => 'sgi', 'SEGI_36110' => 'sgi', 'SEGI_40397' => 'sgi', 'SGA_v2.0_scaffold191G40426' => 'sas', 'SGA_v2.0_scaffold353G49717' => 'sas', 'SGA_v2.0_scaffold50G18550' => 'sas', 'SMO119G0173' => 'smo', 'SMO172G0002' => 'smo', 'Solyc09g082690.3' => 'sly', 'Solyc09g082700.2' => 'sly', 'Sopen09g031550' => 'spe', 'Sopen09g031560' => 'spe', 'Sp3g20540' => 'spa', 'Sp7g07580' => 'spa', 'TAR134G0002' => 'tar', 'TAR236G0001' => 'tar', 'TAR365G0892' => 'tar', 'TAR636G0166' => 'tar', 'TAR636G0646' => 'tar', 'TAR636G0869' => 'tar', 'TAR636G1317' => 'tar', 'TAR636G1744' => 'tar', 'TAR636G3358' => 'tar', 'TAR636G3436' => 'tar', 'THA.LOC104803047' => 'tha', 'Thecc.04G238900' => 'tca', 'Thhalv10021557m.g' => 'esa', 'Thhalv10026318m.g' => 'esa', 'Thhalv10026335m.g' => 'esa', 'TPR.G17433' => 'tpr', 'TPR.G18915' => 'tpr', 'TPR.G26125' => 'tpr', 'TWI09G0677' => 'twi', 'TWI73G0287' => 'twi', 'unitig_748.g8326' => 'ugi', 'vmacro15370' => 'vma', 'vmacro15371' => 'vma', 'vmacro15372' => 'vma', 'vmacro15373' => 'vma', 'vmacro15374' => 'vma', 'VMungo0720G2826' => 'vmu', 'Zm00001eb116960' => 'zma', 'Zm00001eb301260' => 'zma', 'Zm00001eb301270' => 'zma' ) $gf_id = 'HOM05D001460' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001460' ) $data_identifier = 'HOM05D001460' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 4, 'aag' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 2, 'aox' => (int) 2, 'arhy' => (int) 4, 'ath' => (int) 2, 'atr' => (int) 1, 'acertr' => (int) 10, 'cqu' => (int) 4, 'bca' => (int) 11, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 1, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 1, 'ccan' => (int) 1, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 1, 'col' => (int) 1, 'cpa' => (int) 1, 'cre' => (int) 7, 'csa' => (int) 1, 'camsi' => (int) 2, 'dca' => (int) 3, 'din' => (int) 2, 'dzi' => (int) 3, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 14, 'fve' => (int) 9, 'gma' => (int) 2, 'ghi' => (int) 4, 'gra' => (int) 2, 'vvi' => (int) 1, 'han' => (int) 13, 'cav' => (int) 1, 'hma' => (int) 2, 'sun' => (int) 2, 'lal' => (int) 2, 'lonja' => (int) 12, 'lja' => (int) 1, 'lsa' => (int) 7, 'mes' => (int) 1, 'mpo' => (int) 27, 'mbi' => (int) 1, 'mco' => (int) 8, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 1, 'egut' => (int) 1, 'ama' => (int) 1, 'nta' => (int) 4, 'nnu' => (int) 2, 'oeu' => (int) 3, 'osa' => (int) 4, 'pax' => (int) 9, 'pgr' => (int) 1, 'stu' => (int) 1, 'pvu' => (int) 1, 'ptr' => (int) 4, 'ppa' => (int) 22, 'pco' => (int) 6, 'ppe' => (int) 6, 'psa' => (int) 5, 'pso' => (int) 19, 'qlo' => (int) 5, 'rch' => (int) 7, 'rsi' => (int) 20, 'sbr' => (int) 5, 'sbo' => (int) 1, 'sci' => (int) 2, 'sed' => (int) 2, 'sgi' => (int) 12, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 2, 'tar' => (int) 10, 'tha' => (int) 1, 'tca' => (int) 1, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 2, 'ugi' => (int) 1, 'vma' => (int) 5, 'vmu' => (int) 1, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb301270' $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' => 'HOM05D001460', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '433', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p22980' => 'bna', 'A01p32340' => 'bna', 'A03p42970' => 'bna', 'A05p25880' => 'bna', 'Aa31LG8G9320' => 'aar', 'Aa31LG8G9330' => 'aar', 'Aa31LG8G9340' => 'aar', 'Aa31sc221G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1034' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1528' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.829' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2222' => 'aag', 'Ah.12g058830' => 'amhyb', 'Ah.12g058840' => 'amhyb', 'AL3G37160' => 'aly', 'AL7G41310' => 'aly', 'Aqoxy5G00395' => 'aox', 'Aqoxy5G00396' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0C8NZA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5185HY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JZ1PRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MD3LS0' => 'arhy', 'AT3G22840' => 'ath', 'AT4G14690' => 'ath', 'ATR0665G054' => 'atr', 'Atru.chr4.2344' => 'acertr', 'Atru.chr4.2346' => 'acertr', 'Atru.chr4.2347' => 'acertr', 'Atru.chr4.2348' => 'acertr', 'Atru.chr4.2355' => 'acertr', 'Atru.chr4.2356' => 'acertr', 'Atru.chr4.2358' => 'acertr', 'Atru.chr4.2359' => 'acertr', 'Atru.chr4.2360' => 'acertr', 'Atru.chr4.2361' => 'acertr', 'AUR62030476' => 'cqu', 'AUR62030478' => 'cqu', 'AUR62030819' => 'cqu', 'AUR62030820' => 'cqu', 'BcaB03g14648' => 'bca', 'BcaB04g20492' => 'bca', 'BcaB06g26399' => 'bca', 'BcaC01g03416' => 'bca', 'BcaC01g03419' => 'bca', 'BcaC01g03421' => 'bca', 'BcaC01g03424' => 'bca', 'BcaC05g28012' => 'bca', 'BcaC09g49212' => 'bca', 'BcaC09g50140' => 'bca', 'BcaNung00346' => 'bca', 'BolC1t02785H' => 'bol', 'BolC1t04095H' => 'bol', 'BolC3t17545H' => 'bol', 'BolC5t32769H' => 'bol', 'BraA01t02211Z' => 'bra', 'BraA01t03359Z' => 'bra', 'BraA03t13441Z' => 'bra', 'BraA05t21476Z' => 'bra', 'C01p28420' => 'bna', 'C01p41350' => 'bna', 'C03p52750' => 'bna', 'C03p52780' => 'bna', 'C05p40270' => 'bna', 'CAN.G1437.9' => 'can', 'CANSAT78G0035' => 'cansat', 'CANSAT78G1036' => 'cansat', 'CANSAT78G2272' => 'cansat', 'CANSAT78G2478' => 'cansat', 'CARHR098700' => 'chi', 'CARHR221120' => 'chi', 'CARHR221150' => 'chi', 'Carub.0003s2297' => 'cru', 'Carub.0007s2749' => 'cru', 'Carub.0007s2750' => 'cru', 'Carub.0007s2751' => 'cru', 'Ca_10849_v3' => 'car', 'Cc03_g04300' => 'ccan', 'CDE02G3648' => 'cde', 'CDE05G0060' => 'cde', 'CDE05G0692' => 'cde', 'CDE05G2285' => 'cde', 'CDE05G2884' => 'cde', 'CDE05G3072' => 'cde', 'Cfa008439' => 'cfa', 'Cfa008441' => 'cfa', 'Cfa008443' => 'cfa', 'Cfa008448' => 'cfa', 'Ciclev10005974m.g' => 'ccl', 'Ciclev10006006m.g' => 'ccl', 'Ciclev10006775m.g' => 'ccl', 'CiPaw.02G120400' => 'cil', 'CiPaw.02G120500' => 'cil', 'CiPaw.02G120600' => 'cil', 'ClCG05G004850' => 'cla', 'COL.COLO4_21566' => 'col', 'Cpa.g.sc44.124' => 'cpa', 'Cre07.g320400' => 'cre', 'Cre07.g320450' => 'cre', 'Cre08.g384650' => 'cre', 'Cre09.g393173' => 'cre', 'Cre09.g394325' => 'cre', 'Cre14.g626750' => 'cre', 'Cre16.g679250' => 'cre', 'CsaV3_3G012890' => 'csa', 'CSS0010865' => 'camsi', 'CSS0044338' => 'camsi', 'DCAR_002366' => 'dca', 'DCAR_030687' => 'dca', 'DCAR_030688' => 'dca', 'Dinv14047' => 'din', 'Dinv14048' => 'din', 'Duzib151G0105' => 'dzi', 'Duzib151G0114' => 'dzi', 'Duzib212G1029' => 'dzi', 'ECA232G3536' => 'eca', 'ECA240G0786' => 'eca', 'ECA240G1802' => 'eca', 'ECA240G3760' => 'eca', 'ECA240G3920' => 'eca', 'EL10Ac5g12536' => 'bvu', 'EL10Ac5g12537' => 'bvu', 'EL10Ac5g12538' => 'bvu', 'Eucgr.B01004' => 'egr', 'Eucgr.B01006' => 'egr', 'Eucgr.B01007' => 'egr', 'Eucgr.B01008' => 'egr', 'Eucgr.B01895' => 'egr', 'Eucgr.B01896' => 'egr', 'FAN04G1456' => 'fan', 'FAN08G1769' => 'fan', 'FAN08G2160' => 'fan', 'FAN13G2403' => 'fan', 'FAN13G3303' => 'fan', 'FAN15G2435' => 'fan', 'FAN17G0672' => 'fan', 'FAN17G2441' => 'fan', 'FAN18G1024' => 'fan', 'FAN22G1458' => 'fan', 'FAN24G0037' => 'fan', 'FAN24G0429' => 'fan', 'FAN24G2387' => 'fan', 'FAN27G2746' => 'fan', 'FvH4_2g20400' => 'fve', 'FvH4_2g20420' => 'fve', 'FvH4_2g20430' => 'fve', 'FvH4_4g01270' => 'fve', 'FvH4_4g01290' => 'fve', 'FvH4_4g01300' => 'fve', 'FvH4_4g01310' => 'fve', 'FvH4_4g01330' => 'fve', 'FvH4_5g09070' => 'fve', 'Glyma.10G243800' => 'gma', 'Glyma.20G150600' => 'gma', 'Gohir.A09G219200' => 'ghi', 'Gohir.A09G219300' => 'ghi', 'Gohir.D09G221400' => 'ghi', 'Gohir.D09G221500' => 'ghi', 'Gorai.006G242600' => 'gra', 'Gorai.006G242700' => 'gra', 'GSVIVG01018044001' => 'vvi', 'HanXRQChr03g0083821' => 'han', 'HanXRQChr03g0083841' => 'han', 'HanXRQChr03g0083881' => 'han', 'HanXRQChr03g0083901' => 'han', 'HanXRQChr03g0083921' => 'han', 'HanXRQChr03g0085331' => 'han', 'HanXRQChr03g0085361' => 'han', 'HanXRQChr03g0085411' => 'han', 'HanXRQChr03g0085421' => 'han', 'HanXRQChr03g0085431' => 'han', 'HanXRQChr08g0221991' => 'han', 'HanXRQChr11g0336061' => 'han', 'HanXRQChr11g0336411' => 'han', 'Haze_11234' => 'cav', 'Hma1.2p1_0549F.1_g177010' => 'hma', 'Hma1.2p1_0602F.1_g187630' => 'hma', 'Hund14876' => 'sun', 'Hund14879' => 'sun', 'Lalb_Chr06g0160741' => 'lal', 'Lalb_Chr21g0304781' => 'lal', 'Lj3A726G19' => 'lonja', 'Lj3A726T23' => 'lonja', 'Lj3A726T24' => 'lonja', 'Lj3A726T25' => 'lonja', 'Lj3A727T17' => 'lonja', 'Lj3C726T0' => 'lonja', 'Lj3C726T2' => 'lonja', 'Lj3P725T35' => 'lonja', 'Lj3P727T10' => 'lonja', 'Lj3P727T12' => 'lonja', 'Lj3P727T14' => 'lonja', 'Lj5g0023109' => 'lja', 'Lj6P646T44' => 'lonja', 'Lsat_1_v5_gn_6_75760' => 'lsa', 'Lsat_1_v5_gn_6_75800' => 'lsa', 'Lsat_1_v5_gn_6_75900' => 'lsa', 'Lsat_1_v5_gn_6_76240' => 'lsa', 'Lsat_1_v5_gn_6_76441' => 'lsa', 'Lsat_1_v5_gn_6_76700' => 'lsa', 'Lsat_1_v5_gn_6_76760' => 'lsa', 'Manes.15G033100' => 'mes', 'Mapoly0004s0074' => 'mpo', 'Mapoly0004s0075' => 'mpo', 'Mapoly0004s0163' => 'mpo', 'Mapoly0004s0164' => 'mpo', 'Mapoly0021s0018' => 'mpo', 'Mapoly0041s0136' => 'mpo', 'Mapoly0041s0137' => 'mpo', 'Mapoly0041s0138' => 'mpo', 'Mapoly0041s0139' => 'mpo', 'Mapoly0041s0141' => 'mpo', 'Mapoly0041s0142' => 'mpo', 'Mapoly0041s0143' => 'mpo', 'Mapoly0041s0144' => 'mpo', 'Mapoly0041s0145' => 'mpo', 'Mapoly0047s0106' => 'mpo', 'Mapoly0047s0108' => 'mpo', 'Mapoly0050s0051' => 'mpo', 'Mapoly0050s0052' => 'mpo', 'Mapoly0050s0053' => 'mpo', 'Mapoly0058s0013' => 'mpo', 'Mapoly0091s0078' => 'mpo', 'Mapoly0091s0079' => 'mpo', 'Mapoly0091s0080' => 'mpo', 'Mapoly0091s0081' => 'mpo', 'Mapoly0278s0004' => 'mpo', 'Mapoly0278s0005' => 'mpo', 'Mapoly0278s0006' => 'mpo', 'MBI11_g30648_MAGBIO' => 'mbi', 'MCO03G194' => 'mco', 'MCO03G590' => 'mco', 'MCO07G312' => 'mco', 'MCO10G318' => 'mco', 'MCO12G244' => 'mco', 'MCO13G148' => 'mco', 'MCO13G194' => 'mco', 'MCO16G238' => 'mco', 'MD06G1134100' => 'mdo', 'MD13G1200100' => 'mdo', 'MD13G1200300' => 'mdo', 'MD13G1200600' => 'mdo', 'MD14G1150400' => 'mdo', 'MD16G1200000' => 'mdo', 'Medtr1g102570' => 'mtr', 'Medtr1g102780' => 'mtr', 'Medtr1g102800' => 'mtr', 'Medtr1g102810' => 'mtr', 'Medtr1g102830' => 'mtr', 'MELO3C006499.2' => 'cme', 'Migut.G00385' => 'egut', 'MSTRG.4063' => 'ama', 'Nitab4.5_0000090g0260' => 'nta', 'Nitab4.5_0000977g0030' => 'nta', 'Nitab4.5_0002541g0040' => 'nta', 'Nitab4.5_0007068g0040' => 'nta', 'Nn005s41408' => 'nnu', 'Nn005s41410' => 'nnu', 'Oeu010310.1' => 'oeu', 'Oeu010311.1' => 'oeu', 'Oeu043472.1' => 'oeu', 'Os01g0246400' => 'osa', 'Os04g0267950' => 'osa', 'Os07g0178700' => 'osa', 'Os07g0178800' => 'osa', 'Peaxi162Scf00316g00046' => 'pax', 'Peaxi162Scf00316g00049' => 'pax', 'Peaxi162Scf00316g00059' => 'pax', 'Peaxi162Scf00316g00328' => 'pax', 'Peaxi162Scf00316g00329' => 'pax', 'Peaxi162Scf00316g00411' => 'pax', 'Peaxi162Scf00316g00521' => 'pax', 'Peaxi162Scf00492g00068' => 'pax', 'Peaxi162Scf35631g00002' => 'pax', 'PGR142G3720' => 'pgr', 'PGSC0003DMG400006442' => 'stu', 'Phvul.007G062000' => 'pvu', 'Potri.008G157750' => 'ptr', 'Potri.008G157900' => 'ptr', 'Potri.008G158000' => 'ptr', 'Potri.008G158200' => 'ptr', 'Pp3c11_7280' => 'ppa', 'Pp3c11_7980' => 'ppa', 'Pp3c12_19450' => 'ppa', 'Pp3c14_1480' => 'ppa', 'Pp3c14_1501' => 'ppa', 'Pp3c16_4900' => 'ppa', 'Pp3c16_5010' => 'ppa', 'Pp3c16_5060' => 'ppa', 'Pp3c19_18250' => 'ppa', 'Pp3c23_8530' => 'ppa', 'Pp3c23_8550' => 'ppa', 'Pp3c24_9670' => 'ppa', 'Pp3c2_21390' => 'ppa', 'Pp3c2_31380' => 'ppa', 'Pp3c3_16620' => 'ppa', 'Pp3c3_8090' => 'ppa', 'Pp3c3_8110' => 'ppa', 'Pp3c3_8130' => 'ppa', 'Pp3c3_8150' => 'ppa', 'Pp3c4_14320' => 'ppa', 'Pp3c6_2560' => 'ppa', 'Pp3c9_16700' => 'ppa', 'PRCOL_00000234' => 'pco', 'PRCOL_00000235' => 'pco', 'PRCOL_00000777' => 'pco', 'PRCOL_00002344' => 'pco', 'PRCOL_00002372' => 'pco', 'PRCOL_00006120' => 'pco', 'Prupe.1G021400' => 'ppe', 'Prupe.1G021500' => 'ppe', 'Prupe.1G021600' => 'ppe', 'Prupe.1G021700' => 'ppe', 'Prupe.1G021800' => 'ppe', 'Prupe.5G145100' => 'ppe', 'Psat6g204040' => 'psa', 'Psat6g204800' => 'psa', 'Psat6g204920' => 'psa', 'Psat6g204960' => 'psa', 'Psat6g205080' => 'psa', 'PSO017G0271' => 'pso', 'PSO017G1276' => 'pso', 'PSO017G1429' => 'pso', 'PSO017G1861' => 'pso', 'PSO017G2787' => 'pso', 'PSO017G4466' => 'pso', 'PSO017G5118' => 'pso', 'PSO017G5420' => 'pso', 'PSO063G3678' => 'pso', 'PSO210G0546' => 'pso', 'PSO317G0001' => 'pso', 'PSO357G0512' => 'pso', 'PSO478G2682' => 'pso', 'PSO647G0001' => 'pso', 'PSO675G0001' => 'pso', 'PSO675G2699' => 'pso', 'PSO675G2849' => 'pso', 'PSO675G4991' => 'pso', 'PSO689G0001' => 'pso', 'QL06p000916' => 'qlo', 'QL06p000921' => 'qlo', 'QL06p001398' => 'qlo', 'QL06p001407' => 'qlo', 'QL06p002031' => 'qlo', 'RcHm_v2.0_Chr4g0387791' => 'rch', 'RcHm_v2.0_Chr4g0387801' => 'rch', 'RcHm_v2.0_Chr6g0286501' => 'rch', 'RcHm_v2.0_Chr6g0286511' => 'rch', 'RcHm_v2.0_Chr6g0286521' => 'rch', 'RcHm_v2.0_Chr6g0286531' => 'rch', 'RcHm_v2.0_Chr7g0189141' => 'rch', 'Rhsim02G0028700' => 'rsi', 'Rhsim02G0028800' => 'rsi', 'Rhsim02G0028900' => 'rsi', 'Rhsim02G0029000' => 'rsi', 'Rhsim02G0029100' => 'rsi', 'Rhsim02G0029200' => 'rsi', 'Rhsim02G0029300' => 'rsi', 'Rhsim02G0029400' => 'rsi', 'Rhsim02G0029500' => 'rsi', 'Rhsim02G0029600' => 'rsi', 'RhsimUnG0024000' => 'rsi', 'RhsimUnG0024100' => 'rsi', 'RhsimUnG0024200' => 'rsi', 'RhsimUnG0024300' => 'rsi', 'RhsimUnG0024400' => 'rsi', 'RhsimUnG0024500' => 'rsi', 'RhsimUnG0024700' => 'rsi', 'RhsimUnG0024800' => 'rsi', 'RhsimUnG0024900' => 'rsi', 'RhsimUnG0025100' => 'rsi', 'Sabra08G0120200' => 'sbr', 'Sabra08G0120300' => 'sbr', 'Sabra08G0120500' => 'sbr', 'Sabra08G0120600' => 'sbr', 'Sabra10G0158900' => 'sbr', 'SalBow2G3492' => 'sbo', 'Sc13g0004760' => 'sci', 'Sc13g0004770' => 'sci', 'Sed0003417' => 'sed', 'Sed0019750' => 'sed', 'SEGI_03419' => 'sgi', 'SEGI_05907' => 'sgi', 'SEGI_10682' => 'sgi', 'SEGI_13528' => 'sgi', 'SEGI_16081' => 'sgi', 'SEGI_19370' => 'sgi', 'SEGI_21015' => 'sgi', 'SEGI_21944' => 'sgi', 'SEGI_32906' => 'sgi', 'SEGI_33093' => 'sgi', 'SEGI_36110' => 'sgi', 'SEGI_40397' => 'sgi', 'SGA_v2.0_scaffold191G40426' => 'sas', 'SGA_v2.0_scaffold353G49717' => 'sas', 'SGA_v2.0_scaffold50G18550' => 'sas', 'SMO119G0173' => 'smo', 'SMO172G0002' => 'smo', 'Solyc09g082690.3' => 'sly', 'Solyc09g082700.2' => 'sly', 'Sopen09g031550' => 'spe', 'Sopen09g031560' => 'spe', 'Sp3g20540' => 'spa', 'Sp7g07580' => 'spa', 'TAR134G0002' => 'tar', 'TAR236G0001' => 'tar', 'TAR365G0892' => 'tar', 'TAR636G0166' => 'tar', 'TAR636G0646' => 'tar', 'TAR636G0869' => 'tar', 'TAR636G1317' => 'tar', 'TAR636G1744' => 'tar', 'TAR636G3358' => 'tar', 'TAR636G3436' => 'tar', 'THA.LOC104803047' => 'tha', 'Thecc.04G238900' => 'tca', 'Thhalv10021557m.g' => 'esa', 'Thhalv10026318m.g' => 'esa', 'Thhalv10026335m.g' => 'esa', 'TPR.G17433' => 'tpr', 'TPR.G18915' => 'tpr', 'TPR.G26125' => 'tpr', 'TWI09G0677' => 'twi', 'TWI73G0287' => 'twi', 'unitig_748.g8326' => 'ugi', 'vmacro15370' => 'vma', 'vmacro15371' => 'vma', 'vmacro15372' => 'vma', 'vmacro15373' => 'vma', 'vmacro15374' => 'vma', 'VMungo0720G2826' => 'vmu', 'Zm00001eb116960' => 'zma', 'Zm00001eb301260' => 'zma', 'Zm00001eb301270' => 'zma' ), 'gf_id' => 'HOM05D001460', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001460' ), 'data_identifier' => 'HOM05D001460', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001460', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '433', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p22980' => 'bna', 'A01p32340' => 'bna', 'A03p42970' => 'bna', 'A05p25880' => 'bna', 'Aa31LG8G9320' => 'aar', 'Aa31LG8G9330' => 'aar', 'Aa31LG8G9340' => 'aar', 'Aa31sc221G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1034' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1528' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.829' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2222' => 'aag', 'Ah.12g058830' => 'amhyb', 'Ah.12g058840' => 'amhyb', 'AL3G37160' => 'aly', 'AL7G41310' => 'aly', 'Aqoxy5G00395' => 'aox', 'Aqoxy5G00396' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0C8NZA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5185HY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JZ1PRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MD3LS0' => 'arhy', 'AT3G22840' => 'ath', 'AT4G14690' => 'ath', 'ATR0665G054' => 'atr', 'Atru.chr4.2344' => 'acertr', 'Atru.chr4.2346' => 'acertr', 'Atru.chr4.2347' => 'acertr', 'Atru.chr4.2348' => 'acertr', 'Atru.chr4.2355' => 'acertr', 'Atru.chr4.2356' => 'acertr', 'Atru.chr4.2358' => 'acertr', 'Atru.chr4.2359' => 'acertr', 'Atru.chr4.2360' => 'acertr', 'Atru.chr4.2361' => 'acertr', 'AUR62030476' => 'cqu', 'AUR62030478' => 'cqu', 'AUR62030819' => 'cqu', 'AUR62030820' => 'cqu', 'BcaB03g14648' => 'bca', 'BcaB04g20492' => 'bca', 'BcaB06g26399' => 'bca', 'BcaC01g03416' => 'bca', 'BcaC01g03419' => 'bca', 'BcaC01g03421' => 'bca', 'BcaC01g03424' => 'bca', 'BcaC05g28012' => 'bca', 'BcaC09g49212' => 'bca', 'BcaC09g50140' => 'bca', 'BcaNung00346' => 'bca', 'BolC1t02785H' => 'bol', 'BolC1t04095H' => 'bol', 'BolC3t17545H' => 'bol', 'BolC5t32769H' => 'bol', 'BraA01t02211Z' => 'bra', 'BraA01t03359Z' => 'bra', 'BraA03t13441Z' => 'bra', 'BraA05t21476Z' => 'bra', 'C01p28420' => 'bna', 'C01p41350' => 'bna', 'C03p52750' => 'bna', 'C03p52780' => 'bna', 'C05p40270' => 'bna', 'CAN.G1437.9' => 'can', 'CANSAT78G0035' => 'cansat', 'CANSAT78G1036' => 'cansat', 'CANSAT78G2272' => 'cansat', 'CANSAT78G2478' => 'cansat', 'CARHR098700' => 'chi', 'CARHR221120' => 'chi', 'CARHR221150' => 'chi', 'Carub.0003s2297' => 'cru', 'Carub.0007s2749' => 'cru', 'Carub.0007s2750' => 'cru', 'Carub.0007s2751' => 'cru', 'Ca_10849_v3' => 'car', 'Cc03_g04300' => 'ccan', 'CDE02G3648' => 'cde', 'CDE05G0060' => 'cde', 'CDE05G0692' => 'cde', 'CDE05G2285' => 'cde', 'CDE05G2884' => 'cde', 'CDE05G3072' => 'cde', 'Cfa008439' => 'cfa', 'Cfa008441' => 'cfa', 'Cfa008443' => 'cfa', 'Cfa008448' => 'cfa', 'Ciclev10005974m.g' => 'ccl', 'Ciclev10006006m.g' => 'ccl', 'Ciclev10006775m.g' => 'ccl', 'CiPaw.02G120400' => 'cil', 'CiPaw.02G120500' => 'cil', 'CiPaw.02G120600' => 'cil', 'ClCG05G004850' => 'cla', 'COL.COLO4_21566' => 'col', 'Cpa.g.sc44.124' => 'cpa', 'Cre07.g320400' => 'cre', 'Cre07.g320450' => 'cre', 'Cre08.g384650' => 'cre', 'Cre09.g393173' => 'cre', 'Cre09.g394325' => 'cre', 'Cre14.g626750' => 'cre', 'Cre16.g679250' => 'cre', 'CsaV3_3G012890' => 'csa', 'CSS0010865' => 'camsi', 'CSS0044338' => 'camsi', 'DCAR_002366' => 'dca', 'DCAR_030687' => 'dca', 'DCAR_030688' => 'dca', 'Dinv14047' => 'din', 'Dinv14048' => 'din', 'Duzib151G0105' => 'dzi', 'Duzib151G0114' => 'dzi', 'Duzib212G1029' => 'dzi', 'ECA232G3536' => 'eca', 'ECA240G0786' => 'eca', 'ECA240G1802' => 'eca', 'ECA240G3760' => 'eca', 'ECA240G3920' => 'eca', 'EL10Ac5g12536' => 'bvu', 'EL10Ac5g12537' => 'bvu', 'EL10Ac5g12538' => 'bvu', 'Eucgr.B01004' => 'egr', 'Eucgr.B01006' => 'egr', 'Eucgr.B01007' => 'egr', 'Eucgr.B01008' => 'egr', 'Eucgr.B01895' => 'egr', 'Eucgr.B01896' => 'egr', 'FAN04G1456' => 'fan', 'FAN08G1769' => 'fan', 'FAN08G2160' => 'fan', 'FAN13G2403' => 'fan', 'FAN13G3303' => 'fan', 'FAN15G2435' => 'fan', 'FAN17G0672' => 'fan', 'FAN17G2441' => 'fan', 'FAN18G1024' => 'fan', 'FAN22G1458' => 'fan', 'FAN24G0037' => 'fan', 'FAN24G0429' => 'fan', 'FAN24G2387' => 'fan', 'FAN27G2746' => 'fan', 'FvH4_2g20400' => 'fve', 'FvH4_2g20420' => 'fve', 'FvH4_2g20430' => 'fve', 'FvH4_4g01270' => 'fve', 'FvH4_4g01290' => 'fve', 'FvH4_4g01300' => 'fve', 'FvH4_4g01310' => 'fve', 'FvH4_4g01330' => 'fve', 'FvH4_5g09070' => 'fve', 'Glyma.10G243800' => 'gma', 'Glyma.20G150600' => 'gma', 'Gohir.A09G219200' => 'ghi', 'Gohir.A09G219300' => 'ghi', 'Gohir.D09G221400' => 'ghi', 'Gohir.D09G221500' => 'ghi', 'Gorai.006G242600' => 'gra', 'Gorai.006G242700' => 'gra', 'GSVIVG01018044001' => 'vvi', 'HanXRQChr03g0083821' => 'han', 'HanXRQChr03g0083841' => 'han', 'HanXRQChr03g0083881' => 'han', 'HanXRQChr03g0083901' => 'han', 'HanXRQChr03g0083921' => 'han', 'HanXRQChr03g0085331' => 'han', 'HanXRQChr03g0085361' => 'han', 'HanXRQChr03g0085411' => 'han', 'HanXRQChr03g0085421' => 'han', 'HanXRQChr03g0085431' => 'han', 'HanXRQChr08g0221991' => 'han', 'HanXRQChr11g0336061' => 'han', 'HanXRQChr11g0336411' => 'han', 'Haze_11234' => 'cav', 'Hma1.2p1_0549F.1_g177010' => 'hma', 'Hma1.2p1_0602F.1_g187630' => 'hma', 'Hund14876' => 'sun', 'Hund14879' => 'sun', 'Lalb_Chr06g0160741' => 'lal', 'Lalb_Chr21g0304781' => 'lal', 'Lj3A726G19' => 'lonja', 'Lj3A726T23' => 'lonja', 'Lj3A726T24' => 'lonja', 'Lj3A726T25' => 'lonja', 'Lj3A727T17' => 'lonja', 'Lj3C726T0' => 'lonja', 'Lj3C726T2' => 'lonja', 'Lj3P725T35' => 'lonja', 'Lj3P727T10' => 'lonja', 'Lj3P727T12' => 'lonja', 'Lj3P727T14' => 'lonja', 'Lj5g0023109' => 'lja', 'Lj6P646T44' => 'lonja', 'Lsat_1_v5_gn_6_75760' => 'lsa', 'Lsat_1_v5_gn_6_75800' => 'lsa', 'Lsat_1_v5_gn_6_75900' => 'lsa', 'Lsat_1_v5_gn_6_76240' => 'lsa', 'Lsat_1_v5_gn_6_76441' => 'lsa', 'Lsat_1_v5_gn_6_76700' => 'lsa', 'Lsat_1_v5_gn_6_76760' => 'lsa', 'Manes.15G033100' => 'mes', 'Mapoly0004s0074' => 'mpo', 'Mapoly0004s0075' => 'mpo', 'Mapoly0004s0163' => 'mpo', 'Mapoly0004s0164' => 'mpo', 'Mapoly0021s0018' => 'mpo', 'Mapoly0041s0136' => 'mpo', 'Mapoly0041s0137' => 'mpo', 'Mapoly0041s0138' => 'mpo', 'Mapoly0041s0139' => 'mpo', 'Mapoly0041s0141' => 'mpo', 'Mapoly0041s0142' => 'mpo', 'Mapoly0041s0143' => 'mpo', 'Mapoly0041s0144' => 'mpo', 'Mapoly0041s0145' => 'mpo', 'Mapoly0047s0106' => 'mpo', 'Mapoly0047s0108' => 'mpo', 'Mapoly0050s0051' => 'mpo', 'Mapoly0050s0052' => 'mpo', 'Mapoly0050s0053' => 'mpo', 'Mapoly0058s0013' => 'mpo', 'Mapoly0091s0078' => 'mpo', 'Mapoly0091s0079' => 'mpo', 'Mapoly0091s0080' => 'mpo', 'Mapoly0091s0081' => 'mpo', 'Mapoly0278s0004' => 'mpo', 'Mapoly0278s0005' => 'mpo', 'Mapoly0278s0006' => 'mpo', 'MBI11_g30648_MAGBIO' => 'mbi', 'MCO03G194' => 'mco', 'MCO03G590' => 'mco', 'MCO07G312' => 'mco', 'MCO10G318' => 'mco', 'MCO12G244' => 'mco', 'MCO13G148' => 'mco', 'MCO13G194' => 'mco', 'MCO16G238' => 'mco', 'MD06G1134100' => 'mdo', 'MD13G1200100' => 'mdo', 'MD13G1200300' => 'mdo', 'MD13G1200600' => 'mdo', 'MD14G1150400' => 'mdo', 'MD16G1200000' => 'mdo', 'Medtr1g102570' => 'mtr', 'Medtr1g102780' => 'mtr', 'Medtr1g102800' => 'mtr', 'Medtr1g102810' => 'mtr', 'Medtr1g102830' => 'mtr', 'MELO3C006499.2' => 'cme', 'Migut.G00385' => 'egut', 'MSTRG.4063' => 'ama', 'Nitab4.5_0000090g0260' => 'nta', 'Nitab4.5_0000977g0030' => 'nta', 'Nitab4.5_0002541g0040' => 'nta', 'Nitab4.5_0007068g0040' => 'nta', 'Nn005s41408' => 'nnu', 'Nn005s41410' => 'nnu', 'Oeu010310.1' => 'oeu', 'Oeu010311.1' => 'oeu', 'Oeu043472.1' => 'oeu', 'Os01g0246400' => 'osa', 'Os04g0267950' => 'osa', 'Os07g0178700' => 'osa', 'Os07g0178800' => 'osa', 'Peaxi162Scf00316g00046' => 'pax', 'Peaxi162Scf00316g00049' => 'pax', 'Peaxi162Scf00316g00059' => 'pax', 'Peaxi162Scf00316g00328' => 'pax', 'Peaxi162Scf00316g00329' => 'pax', 'Peaxi162Scf00316g00411' => 'pax', 'Peaxi162Scf00316g00521' => 'pax', 'Peaxi162Scf00492g00068' => 'pax', 'Peaxi162Scf35631g00002' => 'pax', 'PGR142G3720' => 'pgr', 'PGSC0003DMG400006442' => 'stu', 'Phvul.007G062000' => 'pvu', 'Potri.008G157750' => 'ptr', 'Potri.008G157900' => 'ptr', 'Potri.008G158000' => 'ptr', 'Potri.008G158200' => 'ptr', 'Pp3c11_7280' => 'ppa', 'Pp3c11_7980' => 'ppa', 'Pp3c12_19450' => 'ppa', 'Pp3c14_1480' => 'ppa', 'Pp3c14_1501' => 'ppa', 'Pp3c16_4900' => 'ppa', 'Pp3c16_5010' => 'ppa', 'Pp3c16_5060' => 'ppa', 'Pp3c19_18250' => 'ppa', 'Pp3c23_8530' => 'ppa', 'Pp3c23_8550' => 'ppa', 'Pp3c24_9670' => 'ppa', 'Pp3c2_21390' => 'ppa', 'Pp3c2_31380' => 'ppa', 'Pp3c3_16620' => 'ppa', 'Pp3c3_8090' => 'ppa', 'Pp3c3_8110' => 'ppa', 'Pp3c3_8130' => 'ppa', 'Pp3c3_8150' => 'ppa', 'Pp3c4_14320' => 'ppa', 'Pp3c6_2560' => 'ppa', 'Pp3c9_16700' => 'ppa', 'PRCOL_00000234' => 'pco', 'PRCOL_00000235' => 'pco', 'PRCOL_00000777' => 'pco', 'PRCOL_00002344' => 'pco', 'PRCOL_00002372' => 'pco', 'PRCOL_00006120' => 'pco', 'Prupe.1G021400' => 'ppe', 'Prupe.1G021500' => 'ppe', 'Prupe.1G021600' => 'ppe', 'Prupe.1G021700' => 'ppe', 'Prupe.1G021800' => 'ppe', 'Prupe.5G145100' => 'ppe', 'Psat6g204040' => 'psa', 'Psat6g204800' => 'psa', 'Psat6g204920' => 'psa', 'Psat6g204960' => 'psa', 'Psat6g205080' => 'psa', 'PSO017G0271' => 'pso', 'PSO017G1276' => 'pso', 'PSO017G1429' => 'pso', 'PSO017G1861' => 'pso', 'PSO017G2787' => 'pso', 'PSO017G4466' => 'pso', 'PSO017G5118' => 'pso', 'PSO017G5420' => 'pso', 'PSO063G3678' => 'pso', 'PSO210G0546' => 'pso', 'PSO317G0001' => 'pso', 'PSO357G0512' => 'pso', 'PSO478G2682' => 'pso', 'PSO647G0001' => 'pso', 'PSO675G0001' => 'pso', 'PSO675G2699' => 'pso', 'PSO675G2849' => 'pso', 'PSO675G4991' => 'pso', 'PSO689G0001' => 'pso', 'QL06p000916' => 'qlo', 'QL06p000921' => 'qlo', 'QL06p001398' => 'qlo', 'QL06p001407' => 'qlo', 'QL06p002031' => 'qlo', 'RcHm_v2.0_Chr4g0387791' => 'rch', 'RcHm_v2.0_Chr4g0387801' => 'rch', 'RcHm_v2.0_Chr6g0286501' => 'rch', 'RcHm_v2.0_Chr6g0286511' => 'rch', 'RcHm_v2.0_Chr6g0286521' => 'rch', 'RcHm_v2.0_Chr6g0286531' => 'rch', 'RcHm_v2.0_Chr7g0189141' => 'rch', 'Rhsim02G0028700' => 'rsi', 'Rhsim02G0028800' => 'rsi', 'Rhsim02G0028900' => 'rsi', 'Rhsim02G0029000' => 'rsi', 'Rhsim02G0029100' => 'rsi', 'Rhsim02G0029200' => 'rsi', 'Rhsim02G0029300' => 'rsi', 'Rhsim02G0029400' => 'rsi', 'Rhsim02G0029500' => 'rsi', 'Rhsim02G0029600' => 'rsi', 'RhsimUnG0024000' => 'rsi', 'RhsimUnG0024100' => 'rsi', 'RhsimUnG0024200' => 'rsi', 'RhsimUnG0024300' => 'rsi', 'RhsimUnG0024400' => 'rsi', 'RhsimUnG0024500' => 'rsi', 'RhsimUnG0024700' => 'rsi', 'RhsimUnG0024800' => 'rsi', 'RhsimUnG0024900' => 'rsi', 'RhsimUnG0025100' => 'rsi', 'Sabra08G0120200' => 'sbr', 'Sabra08G0120300' => 'sbr', 'Sabra08G0120500' => 'sbr', 'Sabra08G0120600' => 'sbr', 'Sabra10G0158900' => 'sbr', 'SalBow2G3492' => 'sbo', 'Sc13g0004760' => 'sci', 'Sc13g0004770' => 'sci', 'Sed0003417' => 'sed', 'Sed0019750' => 'sed', 'SEGI_03419' => 'sgi', 'SEGI_05907' => 'sgi', 'SEGI_10682' => 'sgi', 'SEGI_13528' => 'sgi', 'SEGI_16081' => 'sgi', 'SEGI_19370' => 'sgi', 'SEGI_21015' => 'sgi', 'SEGI_21944' => 'sgi', 'SEGI_32906' => 'sgi', 'SEGI_33093' => 'sgi', 'SEGI_36110' => 'sgi', 'SEGI_40397' => 'sgi', 'SGA_v2.0_scaffold191G40426' => 'sas', 'SGA_v2.0_scaffold353G49717' => 'sas', 'SGA_v2.0_scaffold50G18550' => 'sas', 'SMO119G0173' => 'smo', 'SMO172G0002' => 'smo', 'Solyc09g082690.3' => 'sly', 'Solyc09g082700.2' => 'sly', 'Sopen09g031550' => 'spe', 'Sopen09g031560' => 'spe', 'Sp3g20540' => 'spa', 'Sp7g07580' => 'spa', 'TAR134G0002' => 'tar', 'TAR236G0001' => 'tar', 'TAR365G0892' => 'tar', 'TAR636G0166' => 'tar', 'TAR636G0646' => 'tar', 'TAR636G0869' => 'tar', 'TAR636G1317' => 'tar', 'TAR636G1744' => 'tar', 'TAR636G3358' => 'tar', 'TAR636G3436' => 'tar', 'THA.LOC104803047' => 'tha', 'Thecc.04G238900' => 'tca', 'Thhalv10021557m.g' => 'esa', 'Thhalv10026318m.g' => 'esa', 'Thhalv10026335m.g' => 'esa', 'TPR.G17433' => 'tpr', 'TPR.G18915' => 'tpr', 'TPR.G26125' => 'tpr', 'TWI09G0677' => 'twi', 'TWI73G0287' => 'twi', 'unitig_748.g8326' => 'ugi', 'vmacro15370' => 'vma', 'vmacro15371' => 'vma', 'vmacro15372' => 'vma', 'vmacro15373' => 'vma', 'vmacro15374' => 'vma', 'VMungo0720G2826' => 'vmu', 'Zm00001eb116960' => 'zma', 'Zm00001eb301260' => 'zma', 'Zm00001eb301270' => 'zma' ) $gf_id = 'HOM05D001460' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001460' ) $data_identifier = 'HOM05D001460' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 4, 'aag' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 2, 'aox' => (int) 2, 'arhy' => (int) 4, 'ath' => (int) 2, 'atr' => (int) 1, 'acertr' => (int) 10, 'cqu' => (int) 4, 'bca' => (int) 11, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 1, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 1, 'ccan' => (int) 1, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 1, 'col' => (int) 1, 'cpa' => (int) 1, 'cre' => (int) 7, 'csa' => (int) 1, 'camsi' => (int) 2, 'dca' => (int) 3, 'din' => (int) 2, 'dzi' => (int) 3, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 14, 'fve' => (int) 9, 'gma' => (int) 2, 'ghi' => (int) 4, 'gra' => (int) 2, 'vvi' => (int) 1, 'han' => (int) 13, 'cav' => (int) 1, 'hma' => (int) 2, 'sun' => (int) 2, 'lal' => (int) 2, 'lonja' => (int) 12, 'lja' => (int) 1, 'lsa' => (int) 7, 'mes' => (int) 1, 'mpo' => (int) 27, 'mbi' => (int) 1, 'mco' => (int) 8, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 1, 'egut' => (int) 1, 'ama' => (int) 1, 'nta' => (int) 4, 'nnu' => (int) 2, 'oeu' => (int) 3, 'osa' => (int) 4, 'pax' => (int) 9, 'pgr' => (int) 1, 'stu' => (int) 1, 'pvu' => (int) 1, 'ptr' => (int) 4, 'ppa' => (int) 22, 'pco' => (int) 6, 'ppe' => (int) 6, 'psa' => (int) 5, 'pso' => (int) 19, 'qlo' => (int) 5, 'rch' => (int) 7, 'rsi' => (int) 20, 'sbr' => (int) 5, 'sbo' => (int) 1, 'sci' => (int) 2, 'sed' => (int) 2, 'sgi' => (int) 12, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 2, 'tar' => (int) 10, 'tha' => (int) 1, 'tca' => (int) 1, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 2, 'ugi' => (int) 1, 'vma' => (int) 5, 'vmu' => (int) 1, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb301270' $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' => 'HOM05D001460', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '433', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p22980' => 'bna', 'A01p32340' => 'bna', 'A03p42970' => 'bna', 'A05p25880' => 'bna', 'Aa31LG8G9320' => 'aar', 'Aa31LG8G9330' => 'aar', 'Aa31LG8G9340' => 'aar', 'Aa31sc221G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1034' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1528' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.829' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2222' => 'aag', 'Ah.12g058830' => 'amhyb', 'Ah.12g058840' => 'amhyb', 'AL3G37160' => 'aly', 'AL7G41310' => 'aly', 'Aqoxy5G00395' => 'aox', 'Aqoxy5G00396' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0C8NZA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5185HY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JZ1PRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MD3LS0' => 'arhy', 'AT3G22840' => 'ath', 'AT4G14690' => 'ath', 'ATR0665G054' => 'atr', 'Atru.chr4.2344' => 'acertr', 'Atru.chr4.2346' => 'acertr', 'Atru.chr4.2347' => 'acertr', 'Atru.chr4.2348' => 'acertr', 'Atru.chr4.2355' => 'acertr', 'Atru.chr4.2356' => 'acertr', 'Atru.chr4.2358' => 'acertr', 'Atru.chr4.2359' => 'acertr', 'Atru.chr4.2360' => 'acertr', 'Atru.chr4.2361' => 'acertr', 'AUR62030476' => 'cqu', 'AUR62030478' => 'cqu', 'AUR62030819' => 'cqu', 'AUR62030820' => 'cqu', 'BcaB03g14648' => 'bca', 'BcaB04g20492' => 'bca', 'BcaB06g26399' => 'bca', 'BcaC01g03416' => 'bca', 'BcaC01g03419' => 'bca', 'BcaC01g03421' => 'bca', 'BcaC01g03424' => 'bca', 'BcaC05g28012' => 'bca', 'BcaC09g49212' => 'bca', 'BcaC09g50140' => 'bca', 'BcaNung00346' => 'bca', 'BolC1t02785H' => 'bol', 'BolC1t04095H' => 'bol', 'BolC3t17545H' => 'bol', 'BolC5t32769H' => 'bol', 'BraA01t02211Z' => 'bra', 'BraA01t03359Z' => 'bra', 'BraA03t13441Z' => 'bra', 'BraA05t21476Z' => 'bra', 'C01p28420' => 'bna', 'C01p41350' => 'bna', 'C03p52750' => 'bna', 'C03p52780' => 'bna', 'C05p40270' => 'bna', 'CAN.G1437.9' => 'can', 'CANSAT78G0035' => 'cansat', 'CANSAT78G1036' => 'cansat', 'CANSAT78G2272' => 'cansat', 'CANSAT78G2478' => 'cansat', 'CARHR098700' => 'chi', 'CARHR221120' => 'chi', 'CARHR221150' => 'chi', 'Carub.0003s2297' => 'cru', 'Carub.0007s2749' => 'cru', 'Carub.0007s2750' => 'cru', 'Carub.0007s2751' => 'cru', 'Ca_10849_v3' => 'car', 'Cc03_g04300' => 'ccan', 'CDE02G3648' => 'cde', 'CDE05G0060' => 'cde', 'CDE05G0692' => 'cde', 'CDE05G2285' => 'cde', 'CDE05G2884' => 'cde', 'CDE05G3072' => 'cde', 'Cfa008439' => 'cfa', 'Cfa008441' => 'cfa', 'Cfa008443' => 'cfa', 'Cfa008448' => 'cfa', 'Ciclev10005974m.g' => 'ccl', 'Ciclev10006006m.g' => 'ccl', 'Ciclev10006775m.g' => 'ccl', 'CiPaw.02G120400' => 'cil', 'CiPaw.02G120500' => 'cil', 'CiPaw.02G120600' => 'cil', 'ClCG05G004850' => 'cla', 'COL.COLO4_21566' => 'col', 'Cpa.g.sc44.124' => 'cpa', 'Cre07.g320400' => 'cre', 'Cre07.g320450' => 'cre', 'Cre08.g384650' => 'cre', 'Cre09.g393173' => 'cre', 'Cre09.g394325' => 'cre', 'Cre14.g626750' => 'cre', 'Cre16.g679250' => 'cre', 'CsaV3_3G012890' => 'csa', 'CSS0010865' => 'camsi', 'CSS0044338' => 'camsi', 'DCAR_002366' => 'dca', 'DCAR_030687' => 'dca', 'DCAR_030688' => 'dca', 'Dinv14047' => 'din', 'Dinv14048' => 'din', 'Duzib151G0105' => 'dzi', 'Duzib151G0114' => 'dzi', 'Duzib212G1029' => 'dzi', 'ECA232G3536' => 'eca', 'ECA240G0786' => 'eca', 'ECA240G1802' => 'eca', 'ECA240G3760' => 'eca', 'ECA240G3920' => 'eca', 'EL10Ac5g12536' => 'bvu', 'EL10Ac5g12537' => 'bvu', 'EL10Ac5g12538' => 'bvu', 'Eucgr.B01004' => 'egr', 'Eucgr.B01006' => 'egr', 'Eucgr.B01007' => 'egr', 'Eucgr.B01008' => 'egr', 'Eucgr.B01895' => 'egr', 'Eucgr.B01896' => 'egr', 'FAN04G1456' => 'fan', 'FAN08G1769' => 'fan', 'FAN08G2160' => 'fan', 'FAN13G2403' => 'fan', 'FAN13G3303' => 'fan', 'FAN15G2435' => 'fan', 'FAN17G0672' => 'fan', 'FAN17G2441' => 'fan', 'FAN18G1024' => 'fan', 'FAN22G1458' => 'fan', 'FAN24G0037' => 'fan', 'FAN24G0429' => 'fan', 'FAN24G2387' => 'fan', 'FAN27G2746' => 'fan', 'FvH4_2g20400' => 'fve', 'FvH4_2g20420' => 'fve', 'FvH4_2g20430' => 'fve', 'FvH4_4g01270' => 'fve', 'FvH4_4g01290' => 'fve', 'FvH4_4g01300' => 'fve', 'FvH4_4g01310' => 'fve', 'FvH4_4g01330' => 'fve', 'FvH4_5g09070' => 'fve', 'Glyma.10G243800' => 'gma', 'Glyma.20G150600' => 'gma', 'Gohir.A09G219200' => 'ghi', 'Gohir.A09G219300' => 'ghi', 'Gohir.D09G221400' => 'ghi', 'Gohir.D09G221500' => 'ghi', 'Gorai.006G242600' => 'gra', 'Gorai.006G242700' => 'gra', 'GSVIVG01018044001' => 'vvi', 'HanXRQChr03g0083821' => 'han', 'HanXRQChr03g0083841' => 'han', 'HanXRQChr03g0083881' => 'han', 'HanXRQChr03g0083901' => 'han', 'HanXRQChr03g0083921' => 'han', 'HanXRQChr03g0085331' => 'han', 'HanXRQChr03g0085361' => 'han', 'HanXRQChr03g0085411' => 'han', 'HanXRQChr03g0085421' => 'han', 'HanXRQChr03g0085431' => 'han', 'HanXRQChr08g0221991' => 'han', 'HanXRQChr11g0336061' => 'han', 'HanXRQChr11g0336411' => 'han', 'Haze_11234' => 'cav', 'Hma1.2p1_0549F.1_g177010' => 'hma', 'Hma1.2p1_0602F.1_g187630' => 'hma', 'Hund14876' => 'sun', 'Hund14879' => 'sun', 'Lalb_Chr06g0160741' => 'lal', 'Lalb_Chr21g0304781' => 'lal', 'Lj3A726G19' => 'lonja', 'Lj3A726T23' => 'lonja', 'Lj3A726T24' => 'lonja', 'Lj3A726T25' => 'lonja', 'Lj3A727T17' => 'lonja', 'Lj3C726T0' => 'lonja', 'Lj3C726T2' => 'lonja', 'Lj3P725T35' => 'lonja', 'Lj3P727T10' => 'lonja', 'Lj3P727T12' => 'lonja', 'Lj3P727T14' => 'lonja', 'Lj5g0023109' => 'lja', 'Lj6P646T44' => 'lonja', 'Lsat_1_v5_gn_6_75760' => 'lsa', 'Lsat_1_v5_gn_6_75800' => 'lsa', 'Lsat_1_v5_gn_6_75900' => 'lsa', 'Lsat_1_v5_gn_6_76240' => 'lsa', 'Lsat_1_v5_gn_6_76441' => 'lsa', 'Lsat_1_v5_gn_6_76700' => 'lsa', 'Lsat_1_v5_gn_6_76760' => 'lsa', 'Manes.15G033100' => 'mes', 'Mapoly0004s0074' => 'mpo', 'Mapoly0004s0075' => 'mpo', 'Mapoly0004s0163' => 'mpo', 'Mapoly0004s0164' => 'mpo', 'Mapoly0021s0018' => 'mpo', 'Mapoly0041s0136' => 'mpo', 'Mapoly0041s0137' => 'mpo', 'Mapoly0041s0138' => 'mpo', 'Mapoly0041s0139' => 'mpo', 'Mapoly0041s0141' => 'mpo', 'Mapoly0041s0142' => 'mpo', 'Mapoly0041s0143' => 'mpo', 'Mapoly0041s0144' => 'mpo', 'Mapoly0041s0145' => 'mpo', 'Mapoly0047s0106' => 'mpo', 'Mapoly0047s0108' => 'mpo', 'Mapoly0050s0051' => 'mpo', 'Mapoly0050s0052' => 'mpo', 'Mapoly0050s0053' => 'mpo', 'Mapoly0058s0013' => 'mpo', 'Mapoly0091s0078' => 'mpo', 'Mapoly0091s0079' => 'mpo', 'Mapoly0091s0080' => 'mpo', 'Mapoly0091s0081' => 'mpo', 'Mapoly0278s0004' => 'mpo', 'Mapoly0278s0005' => 'mpo', 'Mapoly0278s0006' => 'mpo', 'MBI11_g30648_MAGBIO' => 'mbi', 'MCO03G194' => 'mco', 'MCO03G590' => 'mco', 'MCO07G312' => 'mco', 'MCO10G318' => 'mco', 'MCO12G244' => 'mco', 'MCO13G148' => 'mco', 'MCO13G194' => 'mco', 'MCO16G238' => 'mco', 'MD06G1134100' => 'mdo', 'MD13G1200100' => 'mdo', 'MD13G1200300' => 'mdo', 'MD13G1200600' => 'mdo', 'MD14G1150400' => 'mdo', 'MD16G1200000' => 'mdo', 'Medtr1g102570' => 'mtr', 'Medtr1g102780' => 'mtr', 'Medtr1g102800' => 'mtr', 'Medtr1g102810' => 'mtr', 'Medtr1g102830' => 'mtr', 'MELO3C006499.2' => 'cme', 'Migut.G00385' => 'egut', 'MSTRG.4063' => 'ama', 'Nitab4.5_0000090g0260' => 'nta', 'Nitab4.5_0000977g0030' => 'nta', 'Nitab4.5_0002541g0040' => 'nta', 'Nitab4.5_0007068g0040' => 'nta', 'Nn005s41408' => 'nnu', 'Nn005s41410' => 'nnu', 'Oeu010310.1' => 'oeu', 'Oeu010311.1' => 'oeu', 'Oeu043472.1' => 'oeu', 'Os01g0246400' => 'osa', 'Os04g0267950' => 'osa', 'Os07g0178700' => 'osa', 'Os07g0178800' => 'osa', 'Peaxi162Scf00316g00046' => 'pax', 'Peaxi162Scf00316g00049' => 'pax', 'Peaxi162Scf00316g00059' => 'pax', 'Peaxi162Scf00316g00328' => 'pax', 'Peaxi162Scf00316g00329' => 'pax', 'Peaxi162Scf00316g00411' => 'pax', 'Peaxi162Scf00316g00521' => 'pax', 'Peaxi162Scf00492g00068' => 'pax', 'Peaxi162Scf35631g00002' => 'pax', 'PGR142G3720' => 'pgr', 'PGSC0003DMG400006442' => 'stu', 'Phvul.007G062000' => 'pvu', 'Potri.008G157750' => 'ptr', 'Potri.008G157900' => 'ptr', 'Potri.008G158000' => 'ptr', 'Potri.008G158200' => 'ptr', 'Pp3c11_7280' => 'ppa', 'Pp3c11_7980' => 'ppa', 'Pp3c12_19450' => 'ppa', 'Pp3c14_1480' => 'ppa', 'Pp3c14_1501' => 'ppa', 'Pp3c16_4900' => 'ppa', 'Pp3c16_5010' => 'ppa', 'Pp3c16_5060' => 'ppa', 'Pp3c19_18250' => 'ppa', 'Pp3c23_8530' => 'ppa', 'Pp3c23_8550' => 'ppa', 'Pp3c24_9670' => 'ppa', 'Pp3c2_21390' => 'ppa', 'Pp3c2_31380' => 'ppa', 'Pp3c3_16620' => 'ppa', 'Pp3c3_8090' => 'ppa', 'Pp3c3_8110' => 'ppa', 'Pp3c3_8130' => 'ppa', 'Pp3c3_8150' => 'ppa', 'Pp3c4_14320' => 'ppa', 'Pp3c6_2560' => 'ppa', 'Pp3c9_16700' => 'ppa', 'PRCOL_00000234' => 'pco', 'PRCOL_00000235' => 'pco', 'PRCOL_00000777' => 'pco', 'PRCOL_00002344' => 'pco', 'PRCOL_00002372' => 'pco', 'PRCOL_00006120' => 'pco', 'Prupe.1G021400' => 'ppe', 'Prupe.1G021500' => 'ppe', 'Prupe.1G021600' => 'ppe', 'Prupe.1G021700' => 'ppe', 'Prupe.1G021800' => 'ppe', 'Prupe.5G145100' => 'ppe', 'Psat6g204040' => 'psa', 'Psat6g204800' => 'psa', 'Psat6g204920' => 'psa', 'Psat6g204960' => 'psa', 'Psat6g205080' => 'psa', 'PSO017G0271' => 'pso', 'PSO017G1276' => 'pso', 'PSO017G1429' => 'pso', 'PSO017G1861' => 'pso', 'PSO017G2787' => 'pso', 'PSO017G4466' => 'pso', 'PSO017G5118' => 'pso', 'PSO017G5420' => 'pso', 'PSO063G3678' => 'pso', 'PSO210G0546' => 'pso', 'PSO317G0001' => 'pso', 'PSO357G0512' => 'pso', 'PSO478G2682' => 'pso', 'PSO647G0001' => 'pso', 'PSO675G0001' => 'pso', 'PSO675G2699' => 'pso', 'PSO675G2849' => 'pso', 'PSO675G4991' => 'pso', 'PSO689G0001' => 'pso', 'QL06p000916' => 'qlo', 'QL06p000921' => 'qlo', 'QL06p001398' => 'qlo', 'QL06p001407' => 'qlo', 'QL06p002031' => 'qlo', 'RcHm_v2.0_Chr4g0387791' => 'rch', 'RcHm_v2.0_Chr4g0387801' => 'rch', 'RcHm_v2.0_Chr6g0286501' => 'rch', 'RcHm_v2.0_Chr6g0286511' => 'rch', 'RcHm_v2.0_Chr6g0286521' => 'rch', 'RcHm_v2.0_Chr6g0286531' => 'rch', 'RcHm_v2.0_Chr7g0189141' => 'rch', 'Rhsim02G0028700' => 'rsi', 'Rhsim02G0028800' => 'rsi', 'Rhsim02G0028900' => 'rsi', 'Rhsim02G0029000' => 'rsi', 'Rhsim02G0029100' => 'rsi', 'Rhsim02G0029200' => 'rsi', 'Rhsim02G0029300' => 'rsi', 'Rhsim02G0029400' => 'rsi', 'Rhsim02G0029500' => 'rsi', 'Rhsim02G0029600' => 'rsi', 'RhsimUnG0024000' => 'rsi', 'RhsimUnG0024100' => 'rsi', 'RhsimUnG0024200' => 'rsi', 'RhsimUnG0024300' => 'rsi', 'RhsimUnG0024400' => 'rsi', 'RhsimUnG0024500' => 'rsi', 'RhsimUnG0024700' => 'rsi', 'RhsimUnG0024800' => 'rsi', 'RhsimUnG0024900' => 'rsi', 'RhsimUnG0025100' => 'rsi', 'Sabra08G0120200' => 'sbr', 'Sabra08G0120300' => 'sbr', 'Sabra08G0120500' => 'sbr', 'Sabra08G0120600' => 'sbr', 'Sabra10G0158900' => 'sbr', 'SalBow2G3492' => 'sbo', 'Sc13g0004760' => 'sci', 'Sc13g0004770' => 'sci', 'Sed0003417' => 'sed', 'Sed0019750' => 'sed', 'SEGI_03419' => 'sgi', 'SEGI_05907' => 'sgi', 'SEGI_10682' => 'sgi', 'SEGI_13528' => 'sgi', 'SEGI_16081' => 'sgi', 'SEGI_19370' => 'sgi', 'SEGI_21015' => 'sgi', 'SEGI_21944' => 'sgi', 'SEGI_32906' => 'sgi', 'SEGI_33093' => 'sgi', 'SEGI_36110' => 'sgi', 'SEGI_40397' => 'sgi', 'SGA_v2.0_scaffold191G40426' => 'sas', 'SGA_v2.0_scaffold353G49717' => 'sas', 'SGA_v2.0_scaffold50G18550' => 'sas', 'SMO119G0173' => 'smo', 'SMO172G0002' => 'smo', 'Solyc09g082690.3' => 'sly', 'Solyc09g082700.2' => 'sly', 'Sopen09g031550' => 'spe', 'Sopen09g031560' => 'spe', 'Sp3g20540' => 'spa', 'Sp7g07580' => 'spa', 'TAR134G0002' => 'tar', 'TAR236G0001' => 'tar', 'TAR365G0892' => 'tar', 'TAR636G0166' => 'tar', 'TAR636G0646' => 'tar', 'TAR636G0869' => 'tar', 'TAR636G1317' => 'tar', 'TAR636G1744' => 'tar', 'TAR636G3358' => 'tar', 'TAR636G3436' => 'tar', 'THA.LOC104803047' => 'tha', 'Thecc.04G238900' => 'tca', 'Thhalv10021557m.g' => 'esa', 'Thhalv10026318m.g' => 'esa', 'Thhalv10026335m.g' => 'esa', 'TPR.G17433' => 'tpr', 'TPR.G18915' => 'tpr', 'TPR.G26125' => 'tpr', 'TWI09G0677' => 'twi', 'TWI73G0287' => 'twi', 'unitig_748.g8326' => 'ugi', 'vmacro15370' => 'vma', 'vmacro15371' => 'vma', 'vmacro15372' => 'vma', 'vmacro15373' => 'vma', 'vmacro15374' => 'vma', 'VMungo0720G2826' => 'vmu', 'Zm00001eb116960' => 'zma', 'Zm00001eb301260' => 'zma', 'Zm00001eb301270' => 'zma' ), 'gf_id' => 'HOM05D001460', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001460' ), 'data_identifier' => 'HOM05D001460', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001460', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '433', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p22980' => 'bna', 'A01p32340' => 'bna', 'A03p42970' => 'bna', 'A05p25880' => 'bna', 'Aa31LG8G9320' => 'aar', 'Aa31LG8G9330' => 'aar', 'Aa31LG8G9340' => 'aar', 'Aa31sc221G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1034' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1528' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.829' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2222' => 'aag', 'Ah.12g058830' => 'amhyb', 'Ah.12g058840' => 'amhyb', 'AL3G37160' => 'aly', 'AL7G41310' => 'aly', 'Aqoxy5G00395' => 'aox', 'Aqoxy5G00396' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0C8NZA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5185HY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JZ1PRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MD3LS0' => 'arhy', 'AT3G22840' => 'ath', 'AT4G14690' => 'ath', 'ATR0665G054' => 'atr', 'Atru.chr4.2344' => 'acertr', 'Atru.chr4.2346' => 'acertr', 'Atru.chr4.2347' => 'acertr', 'Atru.chr4.2348' => 'acertr', 'Atru.chr4.2355' => 'acertr', 'Atru.chr4.2356' => 'acertr', 'Atru.chr4.2358' => 'acertr', 'Atru.chr4.2359' => 'acertr', 'Atru.chr4.2360' => 'acertr', 'Atru.chr4.2361' => 'acertr', 'AUR62030476' => 'cqu', 'AUR62030478' => 'cqu', 'AUR62030819' => 'cqu', 'AUR62030820' => 'cqu', 'BcaB03g14648' => 'bca', 'BcaB04g20492' => 'bca', 'BcaB06g26399' => 'bca', 'BcaC01g03416' => 'bca', 'BcaC01g03419' => 'bca', 'BcaC01g03421' => 'bca', 'BcaC01g03424' => 'bca', 'BcaC05g28012' => 'bca', 'BcaC09g49212' => 'bca', 'BcaC09g50140' => 'bca', 'BcaNung00346' => 'bca', 'BolC1t02785H' => 'bol', 'BolC1t04095H' => 'bol', 'BolC3t17545H' => 'bol', 'BolC5t32769H' => 'bol', 'BraA01t02211Z' => 'bra', 'BraA01t03359Z' => 'bra', 'BraA03t13441Z' => 'bra', 'BraA05t21476Z' => 'bra', 'C01p28420' => 'bna', 'C01p41350' => 'bna', 'C03p52750' => 'bna', 'C03p52780' => 'bna', 'C05p40270' => 'bna', 'CAN.G1437.9' => 'can', 'CANSAT78G0035' => 'cansat', 'CANSAT78G1036' => 'cansat', 'CANSAT78G2272' => 'cansat', 'CANSAT78G2478' => 'cansat', 'CARHR098700' => 'chi', 'CARHR221120' => 'chi', 'CARHR221150' => 'chi', 'Carub.0003s2297' => 'cru', 'Carub.0007s2749' => 'cru', 'Carub.0007s2750' => 'cru', 'Carub.0007s2751' => 'cru', 'Ca_10849_v3' => 'car', 'Cc03_g04300' => 'ccan', 'CDE02G3648' => 'cde', 'CDE05G0060' => 'cde', 'CDE05G0692' => 'cde', 'CDE05G2285' => 'cde', 'CDE05G2884' => 'cde', 'CDE05G3072' => 'cde', 'Cfa008439' => 'cfa', 'Cfa008441' => 'cfa', 'Cfa008443' => 'cfa', 'Cfa008448' => 'cfa', 'Ciclev10005974m.g' => 'ccl', 'Ciclev10006006m.g' => 'ccl', 'Ciclev10006775m.g' => 'ccl', 'CiPaw.02G120400' => 'cil', 'CiPaw.02G120500' => 'cil', 'CiPaw.02G120600' => 'cil', 'ClCG05G004850' => 'cla', 'COL.COLO4_21566' => 'col', 'Cpa.g.sc44.124' => 'cpa', 'Cre07.g320400' => 'cre', 'Cre07.g320450' => 'cre', 'Cre08.g384650' => 'cre', 'Cre09.g393173' => 'cre', 'Cre09.g394325' => 'cre', 'Cre14.g626750' => 'cre', 'Cre16.g679250' => 'cre', 'CsaV3_3G012890' => 'csa', 'CSS0010865' => 'camsi', 'CSS0044338' => 'camsi', 'DCAR_002366' => 'dca', 'DCAR_030687' => 'dca', 'DCAR_030688' => 'dca', 'Dinv14047' => 'din', 'Dinv14048' => 'din', 'Duzib151G0105' => 'dzi', 'Duzib151G0114' => 'dzi', 'Duzib212G1029' => 'dzi', 'ECA232G3536' => 'eca', 'ECA240G0786' => 'eca', 'ECA240G1802' => 'eca', 'ECA240G3760' => 'eca', 'ECA240G3920' => 'eca', 'EL10Ac5g12536' => 'bvu', 'EL10Ac5g12537' => 'bvu', 'EL10Ac5g12538' => 'bvu', 'Eucgr.B01004' => 'egr', 'Eucgr.B01006' => 'egr', 'Eucgr.B01007' => 'egr', 'Eucgr.B01008' => 'egr', 'Eucgr.B01895' => 'egr', 'Eucgr.B01896' => 'egr', 'FAN04G1456' => 'fan', 'FAN08G1769' => 'fan', 'FAN08G2160' => 'fan', 'FAN13G2403' => 'fan', 'FAN13G3303' => 'fan', 'FAN15G2435' => 'fan', 'FAN17G0672' => 'fan', 'FAN17G2441' => 'fan', 'FAN18G1024' => 'fan', 'FAN22G1458' => 'fan', 'FAN24G0037' => 'fan', 'FAN24G0429' => 'fan', 'FAN24G2387' => 'fan', 'FAN27G2746' => 'fan', 'FvH4_2g20400' => 'fve', 'FvH4_2g20420' => 'fve', 'FvH4_2g20430' => 'fve', 'FvH4_4g01270' => 'fve', 'FvH4_4g01290' => 'fve', 'FvH4_4g01300' => 'fve', 'FvH4_4g01310' => 'fve', 'FvH4_4g01330' => 'fve', 'FvH4_5g09070' => 'fve', 'Glyma.10G243800' => 'gma', 'Glyma.20G150600' => 'gma', 'Gohir.A09G219200' => 'ghi', 'Gohir.A09G219300' => 'ghi', 'Gohir.D09G221400' => 'ghi', 'Gohir.D09G221500' => 'ghi', 'Gorai.006G242600' => 'gra', 'Gorai.006G242700' => 'gra', 'GSVIVG01018044001' => 'vvi', 'HanXRQChr03g0083821' => 'han', 'HanXRQChr03g0083841' => 'han', 'HanXRQChr03g0083881' => 'han', 'HanXRQChr03g0083901' => 'han', 'HanXRQChr03g0083921' => 'han', 'HanXRQChr03g0085331' => 'han', 'HanXRQChr03g0085361' => 'han', 'HanXRQChr03g0085411' => 'han', 'HanXRQChr03g0085421' => 'han', 'HanXRQChr03g0085431' => 'han', 'HanXRQChr08g0221991' => 'han', 'HanXRQChr11g0336061' => 'han', 'HanXRQChr11g0336411' => 'han', 'Haze_11234' => 'cav', 'Hma1.2p1_0549F.1_g177010' => 'hma', 'Hma1.2p1_0602F.1_g187630' => 'hma', 'Hund14876' => 'sun', 'Hund14879' => 'sun', 'Lalb_Chr06g0160741' => 'lal', 'Lalb_Chr21g0304781' => 'lal', 'Lj3A726G19' => 'lonja', 'Lj3A726T23' => 'lonja', 'Lj3A726T24' => 'lonja', 'Lj3A726T25' => 'lonja', 'Lj3A727T17' => 'lonja', 'Lj3C726T0' => 'lonja', 'Lj3C726T2' => 'lonja', 'Lj3P725T35' => 'lonja', 'Lj3P727T10' => 'lonja', 'Lj3P727T12' => 'lonja', 'Lj3P727T14' => 'lonja', 'Lj5g0023109' => 'lja', 'Lj6P646T44' => 'lonja', 'Lsat_1_v5_gn_6_75760' => 'lsa', 'Lsat_1_v5_gn_6_75800' => 'lsa', 'Lsat_1_v5_gn_6_75900' => 'lsa', 'Lsat_1_v5_gn_6_76240' => 'lsa', 'Lsat_1_v5_gn_6_76441' => 'lsa', 'Lsat_1_v5_gn_6_76700' => 'lsa', 'Lsat_1_v5_gn_6_76760' => 'lsa', 'Manes.15G033100' => 'mes', 'Mapoly0004s0074' => 'mpo', 'Mapoly0004s0075' => 'mpo', 'Mapoly0004s0163' => 'mpo', 'Mapoly0004s0164' => 'mpo', 'Mapoly0021s0018' => 'mpo', 'Mapoly0041s0136' => 'mpo', 'Mapoly0041s0137' => 'mpo', 'Mapoly0041s0138' => 'mpo', 'Mapoly0041s0139' => 'mpo', 'Mapoly0041s0141' => 'mpo', 'Mapoly0041s0142' => 'mpo', 'Mapoly0041s0143' => 'mpo', 'Mapoly0041s0144' => 'mpo', 'Mapoly0041s0145' => 'mpo', 'Mapoly0047s0106' => 'mpo', 'Mapoly0047s0108' => 'mpo', 'Mapoly0050s0051' => 'mpo', 'Mapoly0050s0052' => 'mpo', 'Mapoly0050s0053' => 'mpo', 'Mapoly0058s0013' => 'mpo', 'Mapoly0091s0078' => 'mpo', 'Mapoly0091s0079' => 'mpo', 'Mapoly0091s0080' => 'mpo', 'Mapoly0091s0081' => 'mpo', 'Mapoly0278s0004' => 'mpo', 'Mapoly0278s0005' => 'mpo', 'Mapoly0278s0006' => 'mpo', 'MBI11_g30648_MAGBIO' => 'mbi', 'MCO03G194' => 'mco', 'MCO03G590' => 'mco', 'MCO07G312' => 'mco', 'MCO10G318' => 'mco', 'MCO12G244' => 'mco', 'MCO13G148' => 'mco', 'MCO13G194' => 'mco', 'MCO16G238' => 'mco', 'MD06G1134100' => 'mdo', 'MD13G1200100' => 'mdo', 'MD13G1200300' => 'mdo', 'MD13G1200600' => 'mdo', 'MD14G1150400' => 'mdo', 'MD16G1200000' => 'mdo', 'Medtr1g102570' => 'mtr', 'Medtr1g102780' => 'mtr', 'Medtr1g102800' => 'mtr', 'Medtr1g102810' => 'mtr', 'Medtr1g102830' => 'mtr', 'MELO3C006499.2' => 'cme', 'Migut.G00385' => 'egut', 'MSTRG.4063' => 'ama', 'Nitab4.5_0000090g0260' => 'nta', 'Nitab4.5_0000977g0030' => 'nta', 'Nitab4.5_0002541g0040' => 'nta', 'Nitab4.5_0007068g0040' => 'nta', 'Nn005s41408' => 'nnu', 'Nn005s41410' => 'nnu', 'Oeu010310.1' => 'oeu', 'Oeu010311.1' => 'oeu', 'Oeu043472.1' => 'oeu', 'Os01g0246400' => 'osa', 'Os04g0267950' => 'osa', 'Os07g0178700' => 'osa', 'Os07g0178800' => 'osa', 'Peaxi162Scf00316g00046' => 'pax', 'Peaxi162Scf00316g00049' => 'pax', 'Peaxi162Scf00316g00059' => 'pax', 'Peaxi162Scf00316g00328' => 'pax', 'Peaxi162Scf00316g00329' => 'pax', 'Peaxi162Scf00316g00411' => 'pax', 'Peaxi162Scf00316g00521' => 'pax', 'Peaxi162Scf00492g00068' => 'pax', 'Peaxi162Scf35631g00002' => 'pax', 'PGR142G3720' => 'pgr', 'PGSC0003DMG400006442' => 'stu', 'Phvul.007G062000' => 'pvu', 'Potri.008G157750' => 'ptr', 'Potri.008G157900' => 'ptr', 'Potri.008G158000' => 'ptr', 'Potri.008G158200' => 'ptr', 'Pp3c11_7280' => 'ppa', 'Pp3c11_7980' => 'ppa', 'Pp3c12_19450' => 'ppa', 'Pp3c14_1480' => 'ppa', 'Pp3c14_1501' => 'ppa', 'Pp3c16_4900' => 'ppa', 'Pp3c16_5010' => 'ppa', 'Pp3c16_5060' => 'ppa', 'Pp3c19_18250' => 'ppa', 'Pp3c23_8530' => 'ppa', 'Pp3c23_8550' => 'ppa', 'Pp3c24_9670' => 'ppa', 'Pp3c2_21390' => 'ppa', 'Pp3c2_31380' => 'ppa', 'Pp3c3_16620' => 'ppa', 'Pp3c3_8090' => 'ppa', 'Pp3c3_8110' => 'ppa', 'Pp3c3_8130' => 'ppa', 'Pp3c3_8150' => 'ppa', 'Pp3c4_14320' => 'ppa', 'Pp3c6_2560' => 'ppa', 'Pp3c9_16700' => 'ppa', 'PRCOL_00000234' => 'pco', 'PRCOL_00000235' => 'pco', 'PRCOL_00000777' => 'pco', 'PRCOL_00002344' => 'pco', 'PRCOL_00002372' => 'pco', 'PRCOL_00006120' => 'pco', 'Prupe.1G021400' => 'ppe', 'Prupe.1G021500' => 'ppe', 'Prupe.1G021600' => 'ppe', 'Prupe.1G021700' => 'ppe', 'Prupe.1G021800' => 'ppe', 'Prupe.5G145100' => 'ppe', 'Psat6g204040' => 'psa', 'Psat6g204800' => 'psa', 'Psat6g204920' => 'psa', 'Psat6g204960' => 'psa', 'Psat6g205080' => 'psa', 'PSO017G0271' => 'pso', 'PSO017G1276' => 'pso', 'PSO017G1429' => 'pso', 'PSO017G1861' => 'pso', 'PSO017G2787' => 'pso', 'PSO017G4466' => 'pso', 'PSO017G5118' => 'pso', 'PSO017G5420' => 'pso', 'PSO063G3678' => 'pso', 'PSO210G0546' => 'pso', 'PSO317G0001' => 'pso', 'PSO357G0512' => 'pso', 'PSO478G2682' => 'pso', 'PSO647G0001' => 'pso', 'PSO675G0001' => 'pso', 'PSO675G2699' => 'pso', 'PSO675G2849' => 'pso', 'PSO675G4991' => 'pso', 'PSO689G0001' => 'pso', 'QL06p000916' => 'qlo', 'QL06p000921' => 'qlo', 'QL06p001398' => 'qlo', 'QL06p001407' => 'qlo', 'QL06p002031' => 'qlo', 'RcHm_v2.0_Chr4g0387791' => 'rch', 'RcHm_v2.0_Chr4g0387801' => 'rch', 'RcHm_v2.0_Chr6g0286501' => 'rch', 'RcHm_v2.0_Chr6g0286511' => 'rch', 'RcHm_v2.0_Chr6g0286521' => 'rch', 'RcHm_v2.0_Chr6g0286531' => 'rch', 'RcHm_v2.0_Chr7g0189141' => 'rch', 'Rhsim02G0028700' => 'rsi', 'Rhsim02G0028800' => 'rsi', 'Rhsim02G0028900' => 'rsi', 'Rhsim02G0029000' => 'rsi', 'Rhsim02G0029100' => 'rsi', 'Rhsim02G0029200' => 'rsi', 'Rhsim02G0029300' => 'rsi', 'Rhsim02G0029400' => 'rsi', 'Rhsim02G0029500' => 'rsi', 'Rhsim02G0029600' => 'rsi', 'RhsimUnG0024000' => 'rsi', 'RhsimUnG0024100' => 'rsi', 'RhsimUnG0024200' => 'rsi', 'RhsimUnG0024300' => 'rsi', 'RhsimUnG0024400' => 'rsi', 'RhsimUnG0024500' => 'rsi', 'RhsimUnG0024700' => 'rsi', 'RhsimUnG0024800' => 'rsi', 'RhsimUnG0024900' => 'rsi', 'RhsimUnG0025100' => 'rsi', 'Sabra08G0120200' => 'sbr', 'Sabra08G0120300' => 'sbr', 'Sabra08G0120500' => 'sbr', 'Sabra08G0120600' => 'sbr', 'Sabra10G0158900' => 'sbr', 'SalBow2G3492' => 'sbo', 'Sc13g0004760' => 'sci', 'Sc13g0004770' => 'sci', 'Sed0003417' => 'sed', 'Sed0019750' => 'sed', 'SEGI_03419' => 'sgi', 'SEGI_05907' => 'sgi', 'SEGI_10682' => 'sgi', 'SEGI_13528' => 'sgi', 'SEGI_16081' => 'sgi', 'SEGI_19370' => 'sgi', 'SEGI_21015' => 'sgi', 'SEGI_21944' => 'sgi', 'SEGI_32906' => 'sgi', 'SEGI_33093' => 'sgi', 'SEGI_36110' => 'sgi', 'SEGI_40397' => 'sgi', 'SGA_v2.0_scaffold191G40426' => 'sas', 'SGA_v2.0_scaffold353G49717' => 'sas', 'SGA_v2.0_scaffold50G18550' => 'sas', 'SMO119G0173' => 'smo', 'SMO172G0002' => 'smo', 'Solyc09g082690.3' => 'sly', 'Solyc09g082700.2' => 'sly', 'Sopen09g031550' => 'spe', 'Sopen09g031560' => 'spe', 'Sp3g20540' => 'spa', 'Sp7g07580' => 'spa', 'TAR134G0002' => 'tar', 'TAR236G0001' => 'tar', 'TAR365G0892' => 'tar', 'TAR636G0166' => 'tar', 'TAR636G0646' => 'tar', 'TAR636G0869' => 'tar', 'TAR636G1317' => 'tar', 'TAR636G1744' => 'tar', 'TAR636G3358' => 'tar', 'TAR636G3436' => 'tar', 'THA.LOC104803047' => 'tha', 'Thecc.04G238900' => 'tca', 'Thhalv10021557m.g' => 'esa', 'Thhalv10026318m.g' => 'esa', 'Thhalv10026335m.g' => 'esa', 'TPR.G17433' => 'tpr', 'TPR.G18915' => 'tpr', 'TPR.G26125' => 'tpr', 'TWI09G0677' => 'twi', 'TWI73G0287' => 'twi', 'unitig_748.g8326' => 'ugi', 'vmacro15370' => 'vma', 'vmacro15371' => 'vma', 'vmacro15372' => 'vma', 'vmacro15373' => 'vma', 'vmacro15374' => 'vma', 'VMungo0720G2826' => 'vmu', 'Zm00001eb116960' => 'zma', 'Zm00001eb301260' => 'zma', 'Zm00001eb301270' => 'zma' ) $gf_id = 'HOM05D001460' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001460' ) $data_identifier = 'HOM05D001460' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 4, 'aag' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 2, 'aox' => (int) 2, 'arhy' => (int) 4, 'ath' => (int) 2, 'atr' => (int) 1, 'acertr' => (int) 10, 'cqu' => (int) 4, 'bca' => (int) 11, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 1, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 1, 'ccan' => (int) 1, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 1, 'col' => (int) 1, 'cpa' => (int) 1, 'cre' => (int) 7, 'csa' => (int) 1, 'camsi' => (int) 2, 'dca' => (int) 3, 'din' => (int) 2, 'dzi' => (int) 3, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 14, 'fve' => (int) 9, 'gma' => (int) 2, 'ghi' => (int) 4, 'gra' => (int) 2, 'vvi' => (int) 1, 'han' => (int) 13, 'cav' => (int) 1, 'hma' => (int) 2, 'sun' => (int) 2, 'lal' => (int) 2, 'lonja' => (int) 12, 'lja' => (int) 1, 'lsa' => (int) 7, 'mes' => (int) 1, 'mpo' => (int) 27, 'mbi' => (int) 1, 'mco' => (int) 8, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 1, 'egut' => (int) 1, 'ama' => (int) 1, 'nta' => (int) 4, 'nnu' => (int) 2, 'oeu' => (int) 3, 'osa' => (int) 4, 'pax' => (int) 9, 'pgr' => (int) 1, 'stu' => (int) 1, 'pvu' => (int) 1, 'ptr' => (int) 4, 'ppa' => (int) 22, 'pco' => (int) 6, 'ppe' => (int) 6, 'psa' => (int) 5, 'pso' => (int) 19, 'qlo' => (int) 5, 'rch' => (int) 7, 'rsi' => (int) 20, 'sbr' => (int) 5, 'sbo' => (int) 1, 'sci' => (int) 2, 'sed' => (int) 2, 'sgi' => (int) 12, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 2, 'tar' => (int) 10, 'tha' => (int) 1, 'tca' => (int) 1, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 2, 'ugi' => (int) 1, 'vma' => (int) 5, 'vmu' => (int) 1, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb301270' $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' => 'HOM05D001460', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '433', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p22980' => 'bna', 'A01p32340' => 'bna', 'A03p42970' => 'bna', 'A05p25880' => 'bna', 'Aa31LG8G9320' => 'aar', 'Aa31LG8G9330' => 'aar', 'Aa31LG8G9340' => 'aar', 'Aa31sc221G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1034' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1528' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.829' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2222' => 'aag', 'Ah.12g058830' => 'amhyb', 'Ah.12g058840' => 'amhyb', 'AL3G37160' => 'aly', 'AL7G41310' => 'aly', 'Aqoxy5G00395' => 'aox', 'Aqoxy5G00396' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0C8NZA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5185HY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JZ1PRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MD3LS0' => 'arhy', 'AT3G22840' => 'ath', 'AT4G14690' => 'ath', 'ATR0665G054' => 'atr', 'Atru.chr4.2344' => 'acertr', 'Atru.chr4.2346' => 'acertr', 'Atru.chr4.2347' => 'acertr', 'Atru.chr4.2348' => 'acertr', 'Atru.chr4.2355' => 'acertr', 'Atru.chr4.2356' => 'acertr', 'Atru.chr4.2358' => 'acertr', 'Atru.chr4.2359' => 'acertr', 'Atru.chr4.2360' => 'acertr', 'Atru.chr4.2361' => 'acertr', 'AUR62030476' => 'cqu', 'AUR62030478' => 'cqu', 'AUR62030819' => 'cqu', 'AUR62030820' => 'cqu', 'BcaB03g14648' => 'bca', 'BcaB04g20492' => 'bca', 'BcaB06g26399' => 'bca', 'BcaC01g03416' => 'bca', 'BcaC01g03419' => 'bca', 'BcaC01g03421' => 'bca', 'BcaC01g03424' => 'bca', 'BcaC05g28012' => 'bca', 'BcaC09g49212' => 'bca', 'BcaC09g50140' => 'bca', 'BcaNung00346' => 'bca', 'BolC1t02785H' => 'bol', 'BolC1t04095H' => 'bol', 'BolC3t17545H' => 'bol', 'BolC5t32769H' => 'bol', 'BraA01t02211Z' => 'bra', 'BraA01t03359Z' => 'bra', 'BraA03t13441Z' => 'bra', 'BraA05t21476Z' => 'bra', 'C01p28420' => 'bna', 'C01p41350' => 'bna', 'C03p52750' => 'bna', 'C03p52780' => 'bna', 'C05p40270' => 'bna', 'CAN.G1437.9' => 'can', 'CANSAT78G0035' => 'cansat', 'CANSAT78G1036' => 'cansat', 'CANSAT78G2272' => 'cansat', 'CANSAT78G2478' => 'cansat', 'CARHR098700' => 'chi', 'CARHR221120' => 'chi', 'CARHR221150' => 'chi', 'Carub.0003s2297' => 'cru', 'Carub.0007s2749' => 'cru', 'Carub.0007s2750' => 'cru', 'Carub.0007s2751' => 'cru', 'Ca_10849_v3' => 'car', 'Cc03_g04300' => 'ccan', 'CDE02G3648' => 'cde', 'CDE05G0060' => 'cde', 'CDE05G0692' => 'cde', 'CDE05G2285' => 'cde', 'CDE05G2884' => 'cde', 'CDE05G3072' => 'cde', 'Cfa008439' => 'cfa', 'Cfa008441' => 'cfa', 'Cfa008443' => 'cfa', 'Cfa008448' => 'cfa', 'Ciclev10005974m.g' => 'ccl', 'Ciclev10006006m.g' => 'ccl', 'Ciclev10006775m.g' => 'ccl', 'CiPaw.02G120400' => 'cil', 'CiPaw.02G120500' => 'cil', 'CiPaw.02G120600' => 'cil', 'ClCG05G004850' => 'cla', 'COL.COLO4_21566' => 'col', 'Cpa.g.sc44.124' => 'cpa', 'Cre07.g320400' => 'cre', 'Cre07.g320450' => 'cre', 'Cre08.g384650' => 'cre', 'Cre09.g393173' => 'cre', 'Cre09.g394325' => 'cre', 'Cre14.g626750' => 'cre', 'Cre16.g679250' => 'cre', 'CsaV3_3G012890' => 'csa', 'CSS0010865' => 'camsi', 'CSS0044338' => 'camsi', 'DCAR_002366' => 'dca', 'DCAR_030687' => 'dca', 'DCAR_030688' => 'dca', 'Dinv14047' => 'din', 'Dinv14048' => 'din', 'Duzib151G0105' => 'dzi', 'Duzib151G0114' => 'dzi', 'Duzib212G1029' => 'dzi', 'ECA232G3536' => 'eca', 'ECA240G0786' => 'eca', 'ECA240G1802' => 'eca', 'ECA240G3760' => 'eca', 'ECA240G3920' => 'eca', 'EL10Ac5g12536' => 'bvu', 'EL10Ac5g12537' => 'bvu', 'EL10Ac5g12538' => 'bvu', 'Eucgr.B01004' => 'egr', 'Eucgr.B01006' => 'egr', 'Eucgr.B01007' => 'egr', 'Eucgr.B01008' => 'egr', 'Eucgr.B01895' => 'egr', 'Eucgr.B01896' => 'egr', 'FAN04G1456' => 'fan', 'FAN08G1769' => 'fan', 'FAN08G2160' => 'fan', 'FAN13G2403' => 'fan', 'FAN13G3303' => 'fan', 'FAN15G2435' => 'fan', 'FAN17G0672' => 'fan', 'FAN17G2441' => 'fan', 'FAN18G1024' => 'fan', 'FAN22G1458' => 'fan', 'FAN24G0037' => 'fan', 'FAN24G0429' => 'fan', 'FAN24G2387' => 'fan', 'FAN27G2746' => 'fan', 'FvH4_2g20400' => 'fve', 'FvH4_2g20420' => 'fve', 'FvH4_2g20430' => 'fve', 'FvH4_4g01270' => 'fve', 'FvH4_4g01290' => 'fve', 'FvH4_4g01300' => 'fve', 'FvH4_4g01310' => 'fve', 'FvH4_4g01330' => 'fve', 'FvH4_5g09070' => 'fve', 'Glyma.10G243800' => 'gma', 'Glyma.20G150600' => 'gma', 'Gohir.A09G219200' => 'ghi', 'Gohir.A09G219300' => 'ghi', 'Gohir.D09G221400' => 'ghi', 'Gohir.D09G221500' => 'ghi', 'Gorai.006G242600' => 'gra', 'Gorai.006G242700' => 'gra', 'GSVIVG01018044001' => 'vvi', 'HanXRQChr03g0083821' => 'han', 'HanXRQChr03g0083841' => 'han', 'HanXRQChr03g0083881' => 'han', 'HanXRQChr03g0083901' => 'han', 'HanXRQChr03g0083921' => 'han', 'HanXRQChr03g0085331' => 'han', 'HanXRQChr03g0085361' => 'han', 'HanXRQChr03g0085411' => 'han', 'HanXRQChr03g0085421' => 'han', 'HanXRQChr03g0085431' => 'han', 'HanXRQChr08g0221991' => 'han', 'HanXRQChr11g0336061' => 'han', 'HanXRQChr11g0336411' => 'han', 'Haze_11234' => 'cav', 'Hma1.2p1_0549F.1_g177010' => 'hma', 'Hma1.2p1_0602F.1_g187630' => 'hma', 'Hund14876' => 'sun', 'Hund14879' => 'sun', 'Lalb_Chr06g0160741' => 'lal', 'Lalb_Chr21g0304781' => 'lal', 'Lj3A726G19' => 'lonja', 'Lj3A726T23' => 'lonja', 'Lj3A726T24' => 'lonja', 'Lj3A726T25' => 'lonja', 'Lj3A727T17' => 'lonja', 'Lj3C726T0' => 'lonja', 'Lj3C726T2' => 'lonja', 'Lj3P725T35' => 'lonja', 'Lj3P727T10' => 'lonja', 'Lj3P727T12' => 'lonja', 'Lj3P727T14' => 'lonja', 'Lj5g0023109' => 'lja', 'Lj6P646T44' => 'lonja', 'Lsat_1_v5_gn_6_75760' => 'lsa', 'Lsat_1_v5_gn_6_75800' => 'lsa', 'Lsat_1_v5_gn_6_75900' => 'lsa', 'Lsat_1_v5_gn_6_76240' => 'lsa', 'Lsat_1_v5_gn_6_76441' => 'lsa', 'Lsat_1_v5_gn_6_76700' => 'lsa', 'Lsat_1_v5_gn_6_76760' => 'lsa', 'Manes.15G033100' => 'mes', 'Mapoly0004s0074' => 'mpo', 'Mapoly0004s0075' => 'mpo', 'Mapoly0004s0163' => 'mpo', 'Mapoly0004s0164' => 'mpo', 'Mapoly0021s0018' => 'mpo', 'Mapoly0041s0136' => 'mpo', 'Mapoly0041s0137' => 'mpo', 'Mapoly0041s0138' => 'mpo', 'Mapoly0041s0139' => 'mpo', 'Mapoly0041s0141' => 'mpo', 'Mapoly0041s0142' => 'mpo', 'Mapoly0041s0143' => 'mpo', 'Mapoly0041s0144' => 'mpo', 'Mapoly0041s0145' => 'mpo', 'Mapoly0047s0106' => 'mpo', 'Mapoly0047s0108' => 'mpo', 'Mapoly0050s0051' => 'mpo', 'Mapoly0050s0052' => 'mpo', 'Mapoly0050s0053' => 'mpo', 'Mapoly0058s0013' => 'mpo', 'Mapoly0091s0078' => 'mpo', 'Mapoly0091s0079' => 'mpo', 'Mapoly0091s0080' => 'mpo', 'Mapoly0091s0081' => 'mpo', 'Mapoly0278s0004' => 'mpo', 'Mapoly0278s0005' => 'mpo', 'Mapoly0278s0006' => 'mpo', 'MBI11_g30648_MAGBIO' => 'mbi', 'MCO03G194' => 'mco', 'MCO03G590' => 'mco', 'MCO07G312' => 'mco', 'MCO10G318' => 'mco', 'MCO12G244' => 'mco', 'MCO13G148' => 'mco', 'MCO13G194' => 'mco', 'MCO16G238' => 'mco', 'MD06G1134100' => 'mdo', 'MD13G1200100' => 'mdo', 'MD13G1200300' => 'mdo', 'MD13G1200600' => 'mdo', 'MD14G1150400' => 'mdo', 'MD16G1200000' => 'mdo', 'Medtr1g102570' => 'mtr', 'Medtr1g102780' => 'mtr', 'Medtr1g102800' => 'mtr', 'Medtr1g102810' => 'mtr', 'Medtr1g102830' => 'mtr', 'MELO3C006499.2' => 'cme', 'Migut.G00385' => 'egut', 'MSTRG.4063' => 'ama', 'Nitab4.5_0000090g0260' => 'nta', 'Nitab4.5_0000977g0030' => 'nta', 'Nitab4.5_0002541g0040' => 'nta', 'Nitab4.5_0007068g0040' => 'nta', 'Nn005s41408' => 'nnu', 'Nn005s41410' => 'nnu', 'Oeu010310.1' => 'oeu', 'Oeu010311.1' => 'oeu', 'Oeu043472.1' => 'oeu', 'Os01g0246400' => 'osa', 'Os04g0267950' => 'osa', 'Os07g0178700' => 'osa', 'Os07g0178800' => 'osa', 'Peaxi162Scf00316g00046' => 'pax', 'Peaxi162Scf00316g00049' => 'pax', 'Peaxi162Scf00316g00059' => 'pax', 'Peaxi162Scf00316g00328' => 'pax', 'Peaxi162Scf00316g00329' => 'pax', 'Peaxi162Scf00316g00411' => 'pax', 'Peaxi162Scf00316g00521' => 'pax', 'Peaxi162Scf00492g00068' => 'pax', 'Peaxi162Scf35631g00002' => 'pax', 'PGR142G3720' => 'pgr', 'PGSC0003DMG400006442' => 'stu', 'Phvul.007G062000' => 'pvu', 'Potri.008G157750' => 'ptr', 'Potri.008G157900' => 'ptr', 'Potri.008G158000' => 'ptr', 'Potri.008G158200' => 'ptr', 'Pp3c11_7280' => 'ppa', 'Pp3c11_7980' => 'ppa', 'Pp3c12_19450' => 'ppa', 'Pp3c14_1480' => 'ppa', 'Pp3c14_1501' => 'ppa', 'Pp3c16_4900' => 'ppa', 'Pp3c16_5010' => 'ppa', 'Pp3c16_5060' => 'ppa', 'Pp3c19_18250' => 'ppa', 'Pp3c23_8530' => 'ppa', 'Pp3c23_8550' => 'ppa', 'Pp3c24_9670' => 'ppa', 'Pp3c2_21390' => 'ppa', 'Pp3c2_31380' => 'ppa', 'Pp3c3_16620' => 'ppa', 'Pp3c3_8090' => 'ppa', 'Pp3c3_8110' => 'ppa', 'Pp3c3_8130' => 'ppa', 'Pp3c3_8150' => 'ppa', 'Pp3c4_14320' => 'ppa', 'Pp3c6_2560' => 'ppa', 'Pp3c9_16700' => 'ppa', 'PRCOL_00000234' => 'pco', 'PRCOL_00000235' => 'pco', 'PRCOL_00000777' => 'pco', 'PRCOL_00002344' => 'pco', 'PRCOL_00002372' => 'pco', 'PRCOL_00006120' => 'pco', 'Prupe.1G021400' => 'ppe', 'Prupe.1G021500' => 'ppe', 'Prupe.1G021600' => 'ppe', 'Prupe.1G021700' => 'ppe', 'Prupe.1G021800' => 'ppe', 'Prupe.5G145100' => 'ppe', 'Psat6g204040' => 'psa', 'Psat6g204800' => 'psa', 'Psat6g204920' => 'psa', 'Psat6g204960' => 'psa', 'Psat6g205080' => 'psa', 'PSO017G0271' => 'pso', 'PSO017G1276' => 'pso', 'PSO017G1429' => 'pso', 'PSO017G1861' => 'pso', 'PSO017G2787' => 'pso', 'PSO017G4466' => 'pso', 'PSO017G5118' => 'pso', 'PSO017G5420' => 'pso', 'PSO063G3678' => 'pso', 'PSO210G0546' => 'pso', 'PSO317G0001' => 'pso', 'PSO357G0512' => 'pso', 'PSO478G2682' => 'pso', 'PSO647G0001' => 'pso', 'PSO675G0001' => 'pso', 'PSO675G2699' => 'pso', 'PSO675G2849' => 'pso', 'PSO675G4991' => 'pso', 'PSO689G0001' => 'pso', 'QL06p000916' => 'qlo', 'QL06p000921' => 'qlo', 'QL06p001398' => 'qlo', 'QL06p001407' => 'qlo', 'QL06p002031' => 'qlo', 'RcHm_v2.0_Chr4g0387791' => 'rch', 'RcHm_v2.0_Chr4g0387801' => 'rch', 'RcHm_v2.0_Chr6g0286501' => 'rch', 'RcHm_v2.0_Chr6g0286511' => 'rch', 'RcHm_v2.0_Chr6g0286521' => 'rch', 'RcHm_v2.0_Chr6g0286531' => 'rch', 'RcHm_v2.0_Chr7g0189141' => 'rch', 'Rhsim02G0028700' => 'rsi', 'Rhsim02G0028800' => 'rsi', 'Rhsim02G0028900' => 'rsi', 'Rhsim02G0029000' => 'rsi', 'Rhsim02G0029100' => 'rsi', 'Rhsim02G0029200' => 'rsi', 'Rhsim02G0029300' => 'rsi', 'Rhsim02G0029400' => 'rsi', 'Rhsim02G0029500' => 'rsi', 'Rhsim02G0029600' => 'rsi', 'RhsimUnG0024000' => 'rsi', 'RhsimUnG0024100' => 'rsi', 'RhsimUnG0024200' => 'rsi', 'RhsimUnG0024300' => 'rsi', 'RhsimUnG0024400' => 'rsi', 'RhsimUnG0024500' => 'rsi', 'RhsimUnG0024700' => 'rsi', 'RhsimUnG0024800' => 'rsi', 'RhsimUnG0024900' => 'rsi', 'RhsimUnG0025100' => 'rsi', 'Sabra08G0120200' => 'sbr', 'Sabra08G0120300' => 'sbr', 'Sabra08G0120500' => 'sbr', 'Sabra08G0120600' => 'sbr', 'Sabra10G0158900' => 'sbr', 'SalBow2G3492' => 'sbo', 'Sc13g0004760' => 'sci', 'Sc13g0004770' => 'sci', 'Sed0003417' => 'sed', 'Sed0019750' => 'sed', 'SEGI_03419' => 'sgi', 'SEGI_05907' => 'sgi', 'SEGI_10682' => 'sgi', 'SEGI_13528' => 'sgi', 'SEGI_16081' => 'sgi', 'SEGI_19370' => 'sgi', 'SEGI_21015' => 'sgi', 'SEGI_21944' => 'sgi', 'SEGI_32906' => 'sgi', 'SEGI_33093' => 'sgi', 'SEGI_36110' => 'sgi', 'SEGI_40397' => 'sgi', 'SGA_v2.0_scaffold191G40426' => 'sas', 'SGA_v2.0_scaffold353G49717' => 'sas', 'SGA_v2.0_scaffold50G18550' => 'sas', 'SMO119G0173' => 'smo', 'SMO172G0002' => 'smo', 'Solyc09g082690.3' => 'sly', 'Solyc09g082700.2' => 'sly', 'Sopen09g031550' => 'spe', 'Sopen09g031560' => 'spe', 'Sp3g20540' => 'spa', 'Sp7g07580' => 'spa', 'TAR134G0002' => 'tar', 'TAR236G0001' => 'tar', 'TAR365G0892' => 'tar', 'TAR636G0166' => 'tar', 'TAR636G0646' => 'tar', 'TAR636G0869' => 'tar', 'TAR636G1317' => 'tar', 'TAR636G1744' => 'tar', 'TAR636G3358' => 'tar', 'TAR636G3436' => 'tar', 'THA.LOC104803047' => 'tha', 'Thecc.04G238900' => 'tca', 'Thhalv10021557m.g' => 'esa', 'Thhalv10026318m.g' => 'esa', 'Thhalv10026335m.g' => 'esa', 'TPR.G17433' => 'tpr', 'TPR.G18915' => 'tpr', 'TPR.G26125' => 'tpr', 'TWI09G0677' => 'twi', 'TWI73G0287' => 'twi', 'unitig_748.g8326' => 'ugi', 'vmacro15370' => 'vma', 'vmacro15371' => 'vma', 'vmacro15372' => 'vma', 'vmacro15373' => 'vma', 'vmacro15374' => 'vma', 'VMungo0720G2826' => 'vmu', 'Zm00001eb116960' => 'zma', 'Zm00001eb301260' => 'zma', 'Zm00001eb301270' => 'zma' ), 'gf_id' => 'HOM05D001460', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001460' ), 'data_identifier' => 'HOM05D001460', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001460', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '433', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p22980' => 'bna', 'A01p32340' => 'bna', 'A03p42970' => 'bna', 'A05p25880' => 'bna', 'Aa31LG8G9320' => 'aar', 'Aa31LG8G9330' => 'aar', 'Aa31LG8G9340' => 'aar', 'Aa31sc221G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1034' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1528' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.829' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2222' => 'aag', 'Ah.12g058830' => 'amhyb', 'Ah.12g058840' => 'amhyb', 'AL3G37160' => 'aly', 'AL7G41310' => 'aly', 'Aqoxy5G00395' => 'aox', 'Aqoxy5G00396' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0C8NZA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5185HY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JZ1PRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MD3LS0' => 'arhy', 'AT3G22840' => 'ath', 'AT4G14690' => 'ath', 'ATR0665G054' => 'atr', 'Atru.chr4.2344' => 'acertr', 'Atru.chr4.2346' => 'acertr', 'Atru.chr4.2347' => 'acertr', 'Atru.chr4.2348' => 'acertr', 'Atru.chr4.2355' => 'acertr', 'Atru.chr4.2356' => 'acertr', 'Atru.chr4.2358' => 'acertr', 'Atru.chr4.2359' => 'acertr', 'Atru.chr4.2360' => 'acertr', 'Atru.chr4.2361' => 'acertr', 'AUR62030476' => 'cqu', 'AUR62030478' => 'cqu', 'AUR62030819' => 'cqu', 'AUR62030820' => 'cqu', 'BcaB03g14648' => 'bca', 'BcaB04g20492' => 'bca', 'BcaB06g26399' => 'bca', 'BcaC01g03416' => 'bca', 'BcaC01g03419' => 'bca', 'BcaC01g03421' => 'bca', 'BcaC01g03424' => 'bca', 'BcaC05g28012' => 'bca', 'BcaC09g49212' => 'bca', 'BcaC09g50140' => 'bca', 'BcaNung00346' => 'bca', 'BolC1t02785H' => 'bol', 'BolC1t04095H' => 'bol', 'BolC3t17545H' => 'bol', 'BolC5t32769H' => 'bol', 'BraA01t02211Z' => 'bra', 'BraA01t03359Z' => 'bra', 'BraA03t13441Z' => 'bra', 'BraA05t21476Z' => 'bra', 'C01p28420' => 'bna', 'C01p41350' => 'bna', 'C03p52750' => 'bna', 'C03p52780' => 'bna', 'C05p40270' => 'bna', 'CAN.G1437.9' => 'can', 'CANSAT78G0035' => 'cansat', 'CANSAT78G1036' => 'cansat', 'CANSAT78G2272' => 'cansat', 'CANSAT78G2478' => 'cansat', 'CARHR098700' => 'chi', 'CARHR221120' => 'chi', 'CARHR221150' => 'chi', 'Carub.0003s2297' => 'cru', 'Carub.0007s2749' => 'cru', 'Carub.0007s2750' => 'cru', 'Carub.0007s2751' => 'cru', 'Ca_10849_v3' => 'car', 'Cc03_g04300' => 'ccan', 'CDE02G3648' => 'cde', 'CDE05G0060' => 'cde', 'CDE05G0692' => 'cde', 'CDE05G2285' => 'cde', 'CDE05G2884' => 'cde', 'CDE05G3072' => 'cde', 'Cfa008439' => 'cfa', 'Cfa008441' => 'cfa', 'Cfa008443' => 'cfa', 'Cfa008448' => 'cfa', 'Ciclev10005974m.g' => 'ccl', 'Ciclev10006006m.g' => 'ccl', 'Ciclev10006775m.g' => 'ccl', 'CiPaw.02G120400' => 'cil', 'CiPaw.02G120500' => 'cil', 'CiPaw.02G120600' => 'cil', 'ClCG05G004850' => 'cla', 'COL.COLO4_21566' => 'col', 'Cpa.g.sc44.124' => 'cpa', 'Cre07.g320400' => 'cre', 'Cre07.g320450' => 'cre', 'Cre08.g384650' => 'cre', 'Cre09.g393173' => 'cre', 'Cre09.g394325' => 'cre', 'Cre14.g626750' => 'cre', 'Cre16.g679250' => 'cre', 'CsaV3_3G012890' => 'csa', 'CSS0010865' => 'camsi', 'CSS0044338' => 'camsi', 'DCAR_002366' => 'dca', 'DCAR_030687' => 'dca', 'DCAR_030688' => 'dca', 'Dinv14047' => 'din', 'Dinv14048' => 'din', 'Duzib151G0105' => 'dzi', 'Duzib151G0114' => 'dzi', 'Duzib212G1029' => 'dzi', 'ECA232G3536' => 'eca', 'ECA240G0786' => 'eca', 'ECA240G1802' => 'eca', 'ECA240G3760' => 'eca', 'ECA240G3920' => 'eca', 'EL10Ac5g12536' => 'bvu', 'EL10Ac5g12537' => 'bvu', 'EL10Ac5g12538' => 'bvu', 'Eucgr.B01004' => 'egr', 'Eucgr.B01006' => 'egr', 'Eucgr.B01007' => 'egr', 'Eucgr.B01008' => 'egr', 'Eucgr.B01895' => 'egr', 'Eucgr.B01896' => 'egr', 'FAN04G1456' => 'fan', 'FAN08G1769' => 'fan', 'FAN08G2160' => 'fan', 'FAN13G2403' => 'fan', 'FAN13G3303' => 'fan', 'FAN15G2435' => 'fan', 'FAN17G0672' => 'fan', 'FAN17G2441' => 'fan', 'FAN18G1024' => 'fan', 'FAN22G1458' => 'fan', 'FAN24G0037' => 'fan', 'FAN24G0429' => 'fan', 'FAN24G2387' => 'fan', 'FAN27G2746' => 'fan', 'FvH4_2g20400' => 'fve', 'FvH4_2g20420' => 'fve', 'FvH4_2g20430' => 'fve', 'FvH4_4g01270' => 'fve', 'FvH4_4g01290' => 'fve', 'FvH4_4g01300' => 'fve', 'FvH4_4g01310' => 'fve', 'FvH4_4g01330' => 'fve', 'FvH4_5g09070' => 'fve', 'Glyma.10G243800' => 'gma', 'Glyma.20G150600' => 'gma', 'Gohir.A09G219200' => 'ghi', 'Gohir.A09G219300' => 'ghi', 'Gohir.D09G221400' => 'ghi', 'Gohir.D09G221500' => 'ghi', 'Gorai.006G242600' => 'gra', 'Gorai.006G242700' => 'gra', 'GSVIVG01018044001' => 'vvi', 'HanXRQChr03g0083821' => 'han', 'HanXRQChr03g0083841' => 'han', 'HanXRQChr03g0083881' => 'han', 'HanXRQChr03g0083901' => 'han', 'HanXRQChr03g0083921' => 'han', 'HanXRQChr03g0085331' => 'han', 'HanXRQChr03g0085361' => 'han', 'HanXRQChr03g0085411' => 'han', 'HanXRQChr03g0085421' => 'han', 'HanXRQChr03g0085431' => 'han', 'HanXRQChr08g0221991' => 'han', 'HanXRQChr11g0336061' => 'han', 'HanXRQChr11g0336411' => 'han', 'Haze_11234' => 'cav', 'Hma1.2p1_0549F.1_g177010' => 'hma', 'Hma1.2p1_0602F.1_g187630' => 'hma', 'Hund14876' => 'sun', 'Hund14879' => 'sun', 'Lalb_Chr06g0160741' => 'lal', 'Lalb_Chr21g0304781' => 'lal', 'Lj3A726G19' => 'lonja', 'Lj3A726T23' => 'lonja', 'Lj3A726T24' => 'lonja', 'Lj3A726T25' => 'lonja', 'Lj3A727T17' => 'lonja', 'Lj3C726T0' => 'lonja', 'Lj3C726T2' => 'lonja', 'Lj3P725T35' => 'lonja', 'Lj3P727T10' => 'lonja', 'Lj3P727T12' => 'lonja', 'Lj3P727T14' => 'lonja', 'Lj5g0023109' => 'lja', 'Lj6P646T44' => 'lonja', 'Lsat_1_v5_gn_6_75760' => 'lsa', 'Lsat_1_v5_gn_6_75800' => 'lsa', 'Lsat_1_v5_gn_6_75900' => 'lsa', 'Lsat_1_v5_gn_6_76240' => 'lsa', 'Lsat_1_v5_gn_6_76441' => 'lsa', 'Lsat_1_v5_gn_6_76700' => 'lsa', 'Lsat_1_v5_gn_6_76760' => 'lsa', 'Manes.15G033100' => 'mes', 'Mapoly0004s0074' => 'mpo', 'Mapoly0004s0075' => 'mpo', 'Mapoly0004s0163' => 'mpo', 'Mapoly0004s0164' => 'mpo', 'Mapoly0021s0018' => 'mpo', 'Mapoly0041s0136' => 'mpo', 'Mapoly0041s0137' => 'mpo', 'Mapoly0041s0138' => 'mpo', 'Mapoly0041s0139' => 'mpo', 'Mapoly0041s0141' => 'mpo', 'Mapoly0041s0142' => 'mpo', 'Mapoly0041s0143' => 'mpo', 'Mapoly0041s0144' => 'mpo', 'Mapoly0041s0145' => 'mpo', 'Mapoly0047s0106' => 'mpo', 'Mapoly0047s0108' => 'mpo', 'Mapoly0050s0051' => 'mpo', 'Mapoly0050s0052' => 'mpo', 'Mapoly0050s0053' => 'mpo', 'Mapoly0058s0013' => 'mpo', 'Mapoly0091s0078' => 'mpo', 'Mapoly0091s0079' => 'mpo', 'Mapoly0091s0080' => 'mpo', 'Mapoly0091s0081' => 'mpo', 'Mapoly0278s0004' => 'mpo', 'Mapoly0278s0005' => 'mpo', 'Mapoly0278s0006' => 'mpo', 'MBI11_g30648_MAGBIO' => 'mbi', 'MCO03G194' => 'mco', 'MCO03G590' => 'mco', 'MCO07G312' => 'mco', 'MCO10G318' => 'mco', 'MCO12G244' => 'mco', 'MCO13G148' => 'mco', 'MCO13G194' => 'mco', 'MCO16G238' => 'mco', 'MD06G1134100' => 'mdo', 'MD13G1200100' => 'mdo', 'MD13G1200300' => 'mdo', 'MD13G1200600' => 'mdo', 'MD14G1150400' => 'mdo', 'MD16G1200000' => 'mdo', 'Medtr1g102570' => 'mtr', 'Medtr1g102780' => 'mtr', 'Medtr1g102800' => 'mtr', 'Medtr1g102810' => 'mtr', 'Medtr1g102830' => 'mtr', 'MELO3C006499.2' => 'cme', 'Migut.G00385' => 'egut', 'MSTRG.4063' => 'ama', 'Nitab4.5_0000090g0260' => 'nta', 'Nitab4.5_0000977g0030' => 'nta', 'Nitab4.5_0002541g0040' => 'nta', 'Nitab4.5_0007068g0040' => 'nta', 'Nn005s41408' => 'nnu', 'Nn005s41410' => 'nnu', 'Oeu010310.1' => 'oeu', 'Oeu010311.1' => 'oeu', 'Oeu043472.1' => 'oeu', 'Os01g0246400' => 'osa', 'Os04g0267950' => 'osa', 'Os07g0178700' => 'osa', 'Os07g0178800' => 'osa', 'Peaxi162Scf00316g00046' => 'pax', 'Peaxi162Scf00316g00049' => 'pax', 'Peaxi162Scf00316g00059' => 'pax', 'Peaxi162Scf00316g00328' => 'pax', 'Peaxi162Scf00316g00329' => 'pax', 'Peaxi162Scf00316g00411' => 'pax', 'Peaxi162Scf00316g00521' => 'pax', 'Peaxi162Scf00492g00068' => 'pax', 'Peaxi162Scf35631g00002' => 'pax', 'PGR142G3720' => 'pgr', 'PGSC0003DMG400006442' => 'stu', 'Phvul.007G062000' => 'pvu', 'Potri.008G157750' => 'ptr', 'Potri.008G157900' => 'ptr', 'Potri.008G158000' => 'ptr', 'Potri.008G158200' => 'ptr', 'Pp3c11_7280' => 'ppa', 'Pp3c11_7980' => 'ppa', 'Pp3c12_19450' => 'ppa', 'Pp3c14_1480' => 'ppa', 'Pp3c14_1501' => 'ppa', 'Pp3c16_4900' => 'ppa', 'Pp3c16_5010' => 'ppa', 'Pp3c16_5060' => 'ppa', 'Pp3c19_18250' => 'ppa', 'Pp3c23_8530' => 'ppa', 'Pp3c23_8550' => 'ppa', 'Pp3c24_9670' => 'ppa', 'Pp3c2_21390' => 'ppa', 'Pp3c2_31380' => 'ppa', 'Pp3c3_16620' => 'ppa', 'Pp3c3_8090' => 'ppa', 'Pp3c3_8110' => 'ppa', 'Pp3c3_8130' => 'ppa', 'Pp3c3_8150' => 'ppa', 'Pp3c4_14320' => 'ppa', 'Pp3c6_2560' => 'ppa', 'Pp3c9_16700' => 'ppa', 'PRCOL_00000234' => 'pco', 'PRCOL_00000235' => 'pco', 'PRCOL_00000777' => 'pco', 'PRCOL_00002344' => 'pco', 'PRCOL_00002372' => 'pco', 'PRCOL_00006120' => 'pco', 'Prupe.1G021400' => 'ppe', 'Prupe.1G021500' => 'ppe', 'Prupe.1G021600' => 'ppe', 'Prupe.1G021700' => 'ppe', 'Prupe.1G021800' => 'ppe', 'Prupe.5G145100' => 'ppe', 'Psat6g204040' => 'psa', 'Psat6g204800' => 'psa', 'Psat6g204920' => 'psa', 'Psat6g204960' => 'psa', 'Psat6g205080' => 'psa', 'PSO017G0271' => 'pso', 'PSO017G1276' => 'pso', 'PSO017G1429' => 'pso', 'PSO017G1861' => 'pso', 'PSO017G2787' => 'pso', 'PSO017G4466' => 'pso', 'PSO017G5118' => 'pso', 'PSO017G5420' => 'pso', 'PSO063G3678' => 'pso', 'PSO210G0546' => 'pso', 'PSO317G0001' => 'pso', 'PSO357G0512' => 'pso', 'PSO478G2682' => 'pso', 'PSO647G0001' => 'pso', 'PSO675G0001' => 'pso', 'PSO675G2699' => 'pso', 'PSO675G2849' => 'pso', 'PSO675G4991' => 'pso', 'PSO689G0001' => 'pso', 'QL06p000916' => 'qlo', 'QL06p000921' => 'qlo', 'QL06p001398' => 'qlo', 'QL06p001407' => 'qlo', 'QL06p002031' => 'qlo', 'RcHm_v2.0_Chr4g0387791' => 'rch', 'RcHm_v2.0_Chr4g0387801' => 'rch', 'RcHm_v2.0_Chr6g0286501' => 'rch', 'RcHm_v2.0_Chr6g0286511' => 'rch', 'RcHm_v2.0_Chr6g0286521' => 'rch', 'RcHm_v2.0_Chr6g0286531' => 'rch', 'RcHm_v2.0_Chr7g0189141' => 'rch', 'Rhsim02G0028700' => 'rsi', 'Rhsim02G0028800' => 'rsi', 'Rhsim02G0028900' => 'rsi', 'Rhsim02G0029000' => 'rsi', 'Rhsim02G0029100' => 'rsi', 'Rhsim02G0029200' => 'rsi', 'Rhsim02G0029300' => 'rsi', 'Rhsim02G0029400' => 'rsi', 'Rhsim02G0029500' => 'rsi', 'Rhsim02G0029600' => 'rsi', 'RhsimUnG0024000' => 'rsi', 'RhsimUnG0024100' => 'rsi', 'RhsimUnG0024200' => 'rsi', 'RhsimUnG0024300' => 'rsi', 'RhsimUnG0024400' => 'rsi', 'RhsimUnG0024500' => 'rsi', 'RhsimUnG0024700' => 'rsi', 'RhsimUnG0024800' => 'rsi', 'RhsimUnG0024900' => 'rsi', 'RhsimUnG0025100' => 'rsi', 'Sabra08G0120200' => 'sbr', 'Sabra08G0120300' => 'sbr', 'Sabra08G0120500' => 'sbr', 'Sabra08G0120600' => 'sbr', 'Sabra10G0158900' => 'sbr', 'SalBow2G3492' => 'sbo', 'Sc13g0004760' => 'sci', 'Sc13g0004770' => 'sci', 'Sed0003417' => 'sed', 'Sed0019750' => 'sed', 'SEGI_03419' => 'sgi', 'SEGI_05907' => 'sgi', 'SEGI_10682' => 'sgi', 'SEGI_13528' => 'sgi', 'SEGI_16081' => 'sgi', 'SEGI_19370' => 'sgi', 'SEGI_21015' => 'sgi', 'SEGI_21944' => 'sgi', 'SEGI_32906' => 'sgi', 'SEGI_33093' => 'sgi', 'SEGI_36110' => 'sgi', 'SEGI_40397' => 'sgi', 'SGA_v2.0_scaffold191G40426' => 'sas', 'SGA_v2.0_scaffold353G49717' => 'sas', 'SGA_v2.0_scaffold50G18550' => 'sas', 'SMO119G0173' => 'smo', 'SMO172G0002' => 'smo', 'Solyc09g082690.3' => 'sly', 'Solyc09g082700.2' => 'sly', 'Sopen09g031550' => 'spe', 'Sopen09g031560' => 'spe', 'Sp3g20540' => 'spa', 'Sp7g07580' => 'spa', 'TAR134G0002' => 'tar', 'TAR236G0001' => 'tar', 'TAR365G0892' => 'tar', 'TAR636G0166' => 'tar', 'TAR636G0646' => 'tar', 'TAR636G0869' => 'tar', 'TAR636G1317' => 'tar', 'TAR636G1744' => 'tar', 'TAR636G3358' => 'tar', 'TAR636G3436' => 'tar', 'THA.LOC104803047' => 'tha', 'Thecc.04G238900' => 'tca', 'Thhalv10021557m.g' => 'esa', 'Thhalv10026318m.g' => 'esa', 'Thhalv10026335m.g' => 'esa', 'TPR.G17433' => 'tpr', 'TPR.G18915' => 'tpr', 'TPR.G26125' => 'tpr', 'TWI09G0677' => 'twi', 'TWI73G0287' => 'twi', 'unitig_748.g8326' => 'ugi', 'vmacro15370' => 'vma', 'vmacro15371' => 'vma', 'vmacro15372' => 'vma', 'vmacro15373' => 'vma', 'vmacro15374' => 'vma', 'VMungo0720G2826' => 'vmu', 'Zm00001eb116960' => 'zma', 'Zm00001eb301260' => 'zma', 'Zm00001eb301270' => 'zma' ) $gf_id = 'HOM05D001460' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001460' ) $data_identifier = 'HOM05D001460' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 4, 'aag' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 2, 'aox' => (int) 2, 'arhy' => (int) 4, 'ath' => (int) 2, 'atr' => (int) 1, 'acertr' => (int) 10, 'cqu' => (int) 4, 'bca' => (int) 11, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 1, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 1, 'ccan' => (int) 1, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 1, 'col' => (int) 1, 'cpa' => (int) 1, 'cre' => (int) 7, 'csa' => (int) 1, 'camsi' => (int) 2, 'dca' => (int) 3, 'din' => (int) 2, 'dzi' => (int) 3, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 14, 'fve' => (int) 9, 'gma' => (int) 2, 'ghi' => (int) 4, 'gra' => (int) 2, 'vvi' => (int) 1, 'han' => (int) 13, 'cav' => (int) 1, 'hma' => (int) 2, 'sun' => (int) 2, 'lal' => (int) 2, 'lonja' => (int) 12, 'lja' => (int) 1, 'lsa' => (int) 7, 'mes' => (int) 1, 'mpo' => (int) 27, 'mbi' => (int) 1, 'mco' => (int) 8, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 1, 'egut' => (int) 1, 'ama' => (int) 1, 'nta' => (int) 4, 'nnu' => (int) 2, 'oeu' => (int) 3, 'osa' => (int) 4, 'pax' => (int) 9, 'pgr' => (int) 1, 'stu' => (int) 1, 'pvu' => (int) 1, 'ptr' => (int) 4, 'ppa' => (int) 22, 'pco' => (int) 6, 'ppe' => (int) 6, 'psa' => (int) 5, 'pso' => (int) 19, 'qlo' => (int) 5, 'rch' => (int) 7, 'rsi' => (int) 20, 'sbr' => (int) 5, 'sbo' => (int) 1, 'sci' => (int) 2, 'sed' => (int) 2, 'sgi' => (int) 12, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 2, 'tar' => (int) 10, 'tha' => (int) 1, 'tca' => (int) 1, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 2, 'ugi' => (int) 1, 'vma' => (int) 5, 'vmu' => (int) 1, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb301270' $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' => 'HOM05D001460', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '433', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p22980' => 'bna', 'A01p32340' => 'bna', 'A03p42970' => 'bna', 'A05p25880' => 'bna', 'Aa31LG8G9320' => 'aar', 'Aa31LG8G9330' => 'aar', 'Aa31LG8G9340' => 'aar', 'Aa31sc221G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1034' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1528' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.829' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2222' => 'aag', 'Ah.12g058830' => 'amhyb', 'Ah.12g058840' => 'amhyb', 'AL3G37160' => 'aly', 'AL7G41310' => 'aly', 'Aqoxy5G00395' => 'aox', 'Aqoxy5G00396' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0C8NZA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5185HY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JZ1PRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MD3LS0' => 'arhy', 'AT3G22840' => 'ath', 'AT4G14690' => 'ath', 'ATR0665G054' => 'atr', 'Atru.chr4.2344' => 'acertr', 'Atru.chr4.2346' => 'acertr', 'Atru.chr4.2347' => 'acertr', 'Atru.chr4.2348' => 'acertr', 'Atru.chr4.2355' => 'acertr', 'Atru.chr4.2356' => 'acertr', 'Atru.chr4.2358' => 'acertr', 'Atru.chr4.2359' => 'acertr', 'Atru.chr4.2360' => 'acertr', 'Atru.chr4.2361' => 'acertr', 'AUR62030476' => 'cqu', 'AUR62030478' => 'cqu', 'AUR62030819' => 'cqu', 'AUR62030820' => 'cqu', 'BcaB03g14648' => 'bca', 'BcaB04g20492' => 'bca', 'BcaB06g26399' => 'bca', 'BcaC01g03416' => 'bca', 'BcaC01g03419' => 'bca', 'BcaC01g03421' => 'bca', 'BcaC01g03424' => 'bca', 'BcaC05g28012' => 'bca', 'BcaC09g49212' => 'bca', 'BcaC09g50140' => 'bca', 'BcaNung00346' => 'bca', 'BolC1t02785H' => 'bol', 'BolC1t04095H' => 'bol', 'BolC3t17545H' => 'bol', 'BolC5t32769H' => 'bol', 'BraA01t02211Z' => 'bra', 'BraA01t03359Z' => 'bra', 'BraA03t13441Z' => 'bra', 'BraA05t21476Z' => 'bra', 'C01p28420' => 'bna', 'C01p41350' => 'bna', 'C03p52750' => 'bna', 'C03p52780' => 'bna', 'C05p40270' => 'bna', 'CAN.G1437.9' => 'can', 'CANSAT78G0035' => 'cansat', 'CANSAT78G1036' => 'cansat', 'CANSAT78G2272' => 'cansat', 'CANSAT78G2478' => 'cansat', 'CARHR098700' => 'chi', 'CARHR221120' => 'chi', 'CARHR221150' => 'chi', 'Carub.0003s2297' => 'cru', 'Carub.0007s2749' => 'cru', 'Carub.0007s2750' => 'cru', 'Carub.0007s2751' => 'cru', 'Ca_10849_v3' => 'car', 'Cc03_g04300' => 'ccan', 'CDE02G3648' => 'cde', 'CDE05G0060' => 'cde', 'CDE05G0692' => 'cde', 'CDE05G2285' => 'cde', 'CDE05G2884' => 'cde', 'CDE05G3072' => 'cde', 'Cfa008439' => 'cfa', 'Cfa008441' => 'cfa', 'Cfa008443' => 'cfa', 'Cfa008448' => 'cfa', 'Ciclev10005974m.g' => 'ccl', 'Ciclev10006006m.g' => 'ccl', 'Ciclev10006775m.g' => 'ccl', 'CiPaw.02G120400' => 'cil', 'CiPaw.02G120500' => 'cil', 'CiPaw.02G120600' => 'cil', 'ClCG05G004850' => 'cla', 'COL.COLO4_21566' => 'col', 'Cpa.g.sc44.124' => 'cpa', 'Cre07.g320400' => 'cre', 'Cre07.g320450' => 'cre', 'Cre08.g384650' => 'cre', 'Cre09.g393173' => 'cre', 'Cre09.g394325' => 'cre', 'Cre14.g626750' => 'cre', 'Cre16.g679250' => 'cre', 'CsaV3_3G012890' => 'csa', 'CSS0010865' => 'camsi', 'CSS0044338' => 'camsi', 'DCAR_002366' => 'dca', 'DCAR_030687' => 'dca', 'DCAR_030688' => 'dca', 'Dinv14047' => 'din', 'Dinv14048' => 'din', 'Duzib151G0105' => 'dzi', 'Duzib151G0114' => 'dzi', 'Duzib212G1029' => 'dzi', 'ECA232G3536' => 'eca', 'ECA240G0786' => 'eca', 'ECA240G1802' => 'eca', 'ECA240G3760' => 'eca', 'ECA240G3920' => 'eca', 'EL10Ac5g12536' => 'bvu', 'EL10Ac5g12537' => 'bvu', 'EL10Ac5g12538' => 'bvu', 'Eucgr.B01004' => 'egr', 'Eucgr.B01006' => 'egr', 'Eucgr.B01007' => 'egr', 'Eucgr.B01008' => 'egr', 'Eucgr.B01895' => 'egr', 'Eucgr.B01896' => 'egr', 'FAN04G1456' => 'fan', 'FAN08G1769' => 'fan', 'FAN08G2160' => 'fan', 'FAN13G2403' => 'fan', 'FAN13G3303' => 'fan', 'FAN15G2435' => 'fan', 'FAN17G0672' => 'fan', 'FAN17G2441' => 'fan', 'FAN18G1024' => 'fan', 'FAN22G1458' => 'fan', 'FAN24G0037' => 'fan', 'FAN24G0429' => 'fan', 'FAN24G2387' => 'fan', 'FAN27G2746' => 'fan', 'FvH4_2g20400' => 'fve', 'FvH4_2g20420' => 'fve', 'FvH4_2g20430' => 'fve', 'FvH4_4g01270' => 'fve', 'FvH4_4g01290' => 'fve', 'FvH4_4g01300' => 'fve', 'FvH4_4g01310' => 'fve', 'FvH4_4g01330' => 'fve', 'FvH4_5g09070' => 'fve', 'Glyma.10G243800' => 'gma', 'Glyma.20G150600' => 'gma', 'Gohir.A09G219200' => 'ghi', 'Gohir.A09G219300' => 'ghi', 'Gohir.D09G221400' => 'ghi', 'Gohir.D09G221500' => 'ghi', 'Gorai.006G242600' => 'gra', 'Gorai.006G242700' => 'gra', 'GSVIVG01018044001' => 'vvi', 'HanXRQChr03g0083821' => 'han', 'HanXRQChr03g0083841' => 'han', 'HanXRQChr03g0083881' => 'han', 'HanXRQChr03g0083901' => 'han', 'HanXRQChr03g0083921' => 'han', 'HanXRQChr03g0085331' => 'han', 'HanXRQChr03g0085361' => 'han', 'HanXRQChr03g0085411' => 'han', 'HanXRQChr03g0085421' => 'han', 'HanXRQChr03g0085431' => 'han', 'HanXRQChr08g0221991' => 'han', 'HanXRQChr11g0336061' => 'han', 'HanXRQChr11g0336411' => 'han', 'Haze_11234' => 'cav', 'Hma1.2p1_0549F.1_g177010' => 'hma', 'Hma1.2p1_0602F.1_g187630' => 'hma', 'Hund14876' => 'sun', 'Hund14879' => 'sun', 'Lalb_Chr06g0160741' => 'lal', 'Lalb_Chr21g0304781' => 'lal', 'Lj3A726G19' => 'lonja', 'Lj3A726T23' => 'lonja', 'Lj3A726T24' => 'lonja', 'Lj3A726T25' => 'lonja', 'Lj3A727T17' => 'lonja', 'Lj3C726T0' => 'lonja', 'Lj3C726T2' => 'lonja', 'Lj3P725T35' => 'lonja', 'Lj3P727T10' => 'lonja', 'Lj3P727T12' => 'lonja', 'Lj3P727T14' => 'lonja', 'Lj5g0023109' => 'lja', 'Lj6P646T44' => 'lonja', 'Lsat_1_v5_gn_6_75760' => 'lsa', 'Lsat_1_v5_gn_6_75800' => 'lsa', 'Lsat_1_v5_gn_6_75900' => 'lsa', 'Lsat_1_v5_gn_6_76240' => 'lsa', 'Lsat_1_v5_gn_6_76441' => 'lsa', 'Lsat_1_v5_gn_6_76700' => 'lsa', 'Lsat_1_v5_gn_6_76760' => 'lsa', 'Manes.15G033100' => 'mes', 'Mapoly0004s0074' => 'mpo', 'Mapoly0004s0075' => 'mpo', 'Mapoly0004s0163' => 'mpo', 'Mapoly0004s0164' => 'mpo', 'Mapoly0021s0018' => 'mpo', 'Mapoly0041s0136' => 'mpo', 'Mapoly0041s0137' => 'mpo', 'Mapoly0041s0138' => 'mpo', 'Mapoly0041s0139' => 'mpo', 'Mapoly0041s0141' => 'mpo', 'Mapoly0041s0142' => 'mpo', 'Mapoly0041s0143' => 'mpo', 'Mapoly0041s0144' => 'mpo', 'Mapoly0041s0145' => 'mpo', 'Mapoly0047s0106' => 'mpo', 'Mapoly0047s0108' => 'mpo', 'Mapoly0050s0051' => 'mpo', 'Mapoly0050s0052' => 'mpo', 'Mapoly0050s0053' => 'mpo', 'Mapoly0058s0013' => 'mpo', 'Mapoly0091s0078' => 'mpo', 'Mapoly0091s0079' => 'mpo', 'Mapoly0091s0080' => 'mpo', 'Mapoly0091s0081' => 'mpo', 'Mapoly0278s0004' => 'mpo', 'Mapoly0278s0005' => 'mpo', 'Mapoly0278s0006' => 'mpo', 'MBI11_g30648_MAGBIO' => 'mbi', 'MCO03G194' => 'mco', 'MCO03G590' => 'mco', 'MCO07G312' => 'mco', 'MCO10G318' => 'mco', 'MCO12G244' => 'mco', 'MCO13G148' => 'mco', 'MCO13G194' => 'mco', 'MCO16G238' => 'mco', 'MD06G1134100' => 'mdo', 'MD13G1200100' => 'mdo', 'MD13G1200300' => 'mdo', 'MD13G1200600' => 'mdo', 'MD14G1150400' => 'mdo', 'MD16G1200000' => 'mdo', 'Medtr1g102570' => 'mtr', 'Medtr1g102780' => 'mtr', 'Medtr1g102800' => 'mtr', 'Medtr1g102810' => 'mtr', 'Medtr1g102830' => 'mtr', 'MELO3C006499.2' => 'cme', 'Migut.G00385' => 'egut', 'MSTRG.4063' => 'ama', 'Nitab4.5_0000090g0260' => 'nta', 'Nitab4.5_0000977g0030' => 'nta', 'Nitab4.5_0002541g0040' => 'nta', 'Nitab4.5_0007068g0040' => 'nta', 'Nn005s41408' => 'nnu', 'Nn005s41410' => 'nnu', 'Oeu010310.1' => 'oeu', 'Oeu010311.1' => 'oeu', 'Oeu043472.1' => 'oeu', 'Os01g0246400' => 'osa', 'Os04g0267950' => 'osa', 'Os07g0178700' => 'osa', 'Os07g0178800' => 'osa', 'Peaxi162Scf00316g00046' => 'pax', 'Peaxi162Scf00316g00049' => 'pax', 'Peaxi162Scf00316g00059' => 'pax', 'Peaxi162Scf00316g00328' => 'pax', 'Peaxi162Scf00316g00329' => 'pax', 'Peaxi162Scf00316g00411' => 'pax', 'Peaxi162Scf00316g00521' => 'pax', 'Peaxi162Scf00492g00068' => 'pax', 'Peaxi162Scf35631g00002' => 'pax', 'PGR142G3720' => 'pgr', 'PGSC0003DMG400006442' => 'stu', 'Phvul.007G062000' => 'pvu', 'Potri.008G157750' => 'ptr', 'Potri.008G157900' => 'ptr', 'Potri.008G158000' => 'ptr', 'Potri.008G158200' => 'ptr', 'Pp3c11_7280' => 'ppa', 'Pp3c11_7980' => 'ppa', 'Pp3c12_19450' => 'ppa', 'Pp3c14_1480' => 'ppa', 'Pp3c14_1501' => 'ppa', 'Pp3c16_4900' => 'ppa', 'Pp3c16_5010' => 'ppa', 'Pp3c16_5060' => 'ppa', 'Pp3c19_18250' => 'ppa', 'Pp3c23_8530' => 'ppa', 'Pp3c23_8550' => 'ppa', 'Pp3c24_9670' => 'ppa', 'Pp3c2_21390' => 'ppa', 'Pp3c2_31380' => 'ppa', 'Pp3c3_16620' => 'ppa', 'Pp3c3_8090' => 'ppa', 'Pp3c3_8110' => 'ppa', 'Pp3c3_8130' => 'ppa', 'Pp3c3_8150' => 'ppa', 'Pp3c4_14320' => 'ppa', 'Pp3c6_2560' => 'ppa', 'Pp3c9_16700' => 'ppa', 'PRCOL_00000234' => 'pco', 'PRCOL_00000235' => 'pco', 'PRCOL_00000777' => 'pco', 'PRCOL_00002344' => 'pco', 'PRCOL_00002372' => 'pco', 'PRCOL_00006120' => 'pco', 'Prupe.1G021400' => 'ppe', 'Prupe.1G021500' => 'ppe', 'Prupe.1G021600' => 'ppe', 'Prupe.1G021700' => 'ppe', 'Prupe.1G021800' => 'ppe', 'Prupe.5G145100' => 'ppe', 'Psat6g204040' => 'psa', 'Psat6g204800' => 'psa', 'Psat6g204920' => 'psa', 'Psat6g204960' => 'psa', 'Psat6g205080' => 'psa', 'PSO017G0271' => 'pso', 'PSO017G1276' => 'pso', 'PSO017G1429' => 'pso', 'PSO017G1861' => 'pso', 'PSO017G2787' => 'pso', 'PSO017G4466' => 'pso', 'PSO017G5118' => 'pso', 'PSO017G5420' => 'pso', 'PSO063G3678' => 'pso', 'PSO210G0546' => 'pso', 'PSO317G0001' => 'pso', 'PSO357G0512' => 'pso', 'PSO478G2682' => 'pso', 'PSO647G0001' => 'pso', 'PSO675G0001' => 'pso', 'PSO675G2699' => 'pso', 'PSO675G2849' => 'pso', 'PSO675G4991' => 'pso', 'PSO689G0001' => 'pso', 'QL06p000916' => 'qlo', 'QL06p000921' => 'qlo', 'QL06p001398' => 'qlo', 'QL06p001407' => 'qlo', 'QL06p002031' => 'qlo', 'RcHm_v2.0_Chr4g0387791' => 'rch', 'RcHm_v2.0_Chr4g0387801' => 'rch', 'RcHm_v2.0_Chr6g0286501' => 'rch', 'RcHm_v2.0_Chr6g0286511' => 'rch', 'RcHm_v2.0_Chr6g0286521' => 'rch', 'RcHm_v2.0_Chr6g0286531' => 'rch', 'RcHm_v2.0_Chr7g0189141' => 'rch', 'Rhsim02G0028700' => 'rsi', 'Rhsim02G0028800' => 'rsi', 'Rhsim02G0028900' => 'rsi', 'Rhsim02G0029000' => 'rsi', 'Rhsim02G0029100' => 'rsi', 'Rhsim02G0029200' => 'rsi', 'Rhsim02G0029300' => 'rsi', 'Rhsim02G0029400' => 'rsi', 'Rhsim02G0029500' => 'rsi', 'Rhsim02G0029600' => 'rsi', 'RhsimUnG0024000' => 'rsi', 'RhsimUnG0024100' => 'rsi', 'RhsimUnG0024200' => 'rsi', 'RhsimUnG0024300' => 'rsi', 'RhsimUnG0024400' => 'rsi', 'RhsimUnG0024500' => 'rsi', 'RhsimUnG0024700' => 'rsi', 'RhsimUnG0024800' => 'rsi', 'RhsimUnG0024900' => 'rsi', 'RhsimUnG0025100' => 'rsi', 'Sabra08G0120200' => 'sbr', 'Sabra08G0120300' => 'sbr', 'Sabra08G0120500' => 'sbr', 'Sabra08G0120600' => 'sbr', 'Sabra10G0158900' => 'sbr', 'SalBow2G3492' => 'sbo', 'Sc13g0004760' => 'sci', 'Sc13g0004770' => 'sci', 'Sed0003417' => 'sed', 'Sed0019750' => 'sed', 'SEGI_03419' => 'sgi', 'SEGI_05907' => 'sgi', 'SEGI_10682' => 'sgi', 'SEGI_13528' => 'sgi', 'SEGI_16081' => 'sgi', 'SEGI_19370' => 'sgi', 'SEGI_21015' => 'sgi', 'SEGI_21944' => 'sgi', 'SEGI_32906' => 'sgi', 'SEGI_33093' => 'sgi', 'SEGI_36110' => 'sgi', 'SEGI_40397' => 'sgi', 'SGA_v2.0_scaffold191G40426' => 'sas', 'SGA_v2.0_scaffold353G49717' => 'sas', 'SGA_v2.0_scaffold50G18550' => 'sas', 'SMO119G0173' => 'smo', 'SMO172G0002' => 'smo', 'Solyc09g082690.3' => 'sly', 'Solyc09g082700.2' => 'sly', 'Sopen09g031550' => 'spe', 'Sopen09g031560' => 'spe', 'Sp3g20540' => 'spa', 'Sp7g07580' => 'spa', 'TAR134G0002' => 'tar', 'TAR236G0001' => 'tar', 'TAR365G0892' => 'tar', 'TAR636G0166' => 'tar', 'TAR636G0646' => 'tar', 'TAR636G0869' => 'tar', 'TAR636G1317' => 'tar', 'TAR636G1744' => 'tar', 'TAR636G3358' => 'tar', 'TAR636G3436' => 'tar', 'THA.LOC104803047' => 'tha', 'Thecc.04G238900' => 'tca', 'Thhalv10021557m.g' => 'esa', 'Thhalv10026318m.g' => 'esa', 'Thhalv10026335m.g' => 'esa', 'TPR.G17433' => 'tpr', 'TPR.G18915' => 'tpr', 'TPR.G26125' => 'tpr', 'TWI09G0677' => 'twi', 'TWI73G0287' => 'twi', 'unitig_748.g8326' => 'ugi', 'vmacro15370' => 'vma', 'vmacro15371' => 'vma', 'vmacro15372' => 'vma', 'vmacro15373' => 'vma', 'vmacro15374' => 'vma', 'VMungo0720G2826' => 'vmu', 'Zm00001eb116960' => 'zma', 'Zm00001eb301260' => 'zma', 'Zm00001eb301270' => 'zma' ), 'gf_id' => 'HOM05D001460', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001460' ), 'data_identifier' => 'HOM05D001460', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001460', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '433', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p22980' => 'bna', 'A01p32340' => 'bna', 'A03p42970' => 'bna', 'A05p25880' => 'bna', 'Aa31LG8G9320' => 'aar', 'Aa31LG8G9330' => 'aar', 'Aa31LG8G9340' => 'aar', 'Aa31sc221G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1034' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1528' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.829' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2222' => 'aag', 'Ah.12g058830' => 'amhyb', 'Ah.12g058840' => 'amhyb', 'AL3G37160' => 'aly', 'AL7G41310' => 'aly', 'Aqoxy5G00395' => 'aox', 'Aqoxy5G00396' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0C8NZA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5185HY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JZ1PRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MD3LS0' => 'arhy', 'AT3G22840' => 'ath', 'AT4G14690' => 'ath', 'ATR0665G054' => 'atr', 'Atru.chr4.2344' => 'acertr', 'Atru.chr4.2346' => 'acertr', 'Atru.chr4.2347' => 'acertr', 'Atru.chr4.2348' => 'acertr', 'Atru.chr4.2355' => 'acertr', 'Atru.chr4.2356' => 'acertr', 'Atru.chr4.2358' => 'acertr', 'Atru.chr4.2359' => 'acertr', 'Atru.chr4.2360' => 'acertr', 'Atru.chr4.2361' => 'acertr', 'AUR62030476' => 'cqu', 'AUR62030478' => 'cqu', 'AUR62030819' => 'cqu', 'AUR62030820' => 'cqu', 'BcaB03g14648' => 'bca', 'BcaB04g20492' => 'bca', 'BcaB06g26399' => 'bca', 'BcaC01g03416' => 'bca', 'BcaC01g03419' => 'bca', 'BcaC01g03421' => 'bca', 'BcaC01g03424' => 'bca', 'BcaC05g28012' => 'bca', 'BcaC09g49212' => 'bca', 'BcaC09g50140' => 'bca', 'BcaNung00346' => 'bca', 'BolC1t02785H' => 'bol', 'BolC1t04095H' => 'bol', 'BolC3t17545H' => 'bol', 'BolC5t32769H' => 'bol', 'BraA01t02211Z' => 'bra', 'BraA01t03359Z' => 'bra', 'BraA03t13441Z' => 'bra', 'BraA05t21476Z' => 'bra', 'C01p28420' => 'bna', 'C01p41350' => 'bna', 'C03p52750' => 'bna', 'C03p52780' => 'bna', 'C05p40270' => 'bna', 'CAN.G1437.9' => 'can', 'CANSAT78G0035' => 'cansat', 'CANSAT78G1036' => 'cansat', 'CANSAT78G2272' => 'cansat', 'CANSAT78G2478' => 'cansat', 'CARHR098700' => 'chi', 'CARHR221120' => 'chi', 'CARHR221150' => 'chi', 'Carub.0003s2297' => 'cru', 'Carub.0007s2749' => 'cru', 'Carub.0007s2750' => 'cru', 'Carub.0007s2751' => 'cru', 'Ca_10849_v3' => 'car', 'Cc03_g04300' => 'ccan', 'CDE02G3648' => 'cde', 'CDE05G0060' => 'cde', 'CDE05G0692' => 'cde', 'CDE05G2285' => 'cde', 'CDE05G2884' => 'cde', 'CDE05G3072' => 'cde', 'Cfa008439' => 'cfa', 'Cfa008441' => 'cfa', 'Cfa008443' => 'cfa', 'Cfa008448' => 'cfa', 'Ciclev10005974m.g' => 'ccl', 'Ciclev10006006m.g' => 'ccl', 'Ciclev10006775m.g' => 'ccl', 'CiPaw.02G120400' => 'cil', 'CiPaw.02G120500' => 'cil', 'CiPaw.02G120600' => 'cil', 'ClCG05G004850' => 'cla', 'COL.COLO4_21566' => 'col', 'Cpa.g.sc44.124' => 'cpa', 'Cre07.g320400' => 'cre', 'Cre07.g320450' => 'cre', 'Cre08.g384650' => 'cre', 'Cre09.g393173' => 'cre', 'Cre09.g394325' => 'cre', 'Cre14.g626750' => 'cre', 'Cre16.g679250' => 'cre', 'CsaV3_3G012890' => 'csa', 'CSS0010865' => 'camsi', 'CSS0044338' => 'camsi', 'DCAR_002366' => 'dca', 'DCAR_030687' => 'dca', 'DCAR_030688' => 'dca', 'Dinv14047' => 'din', 'Dinv14048' => 'din', 'Duzib151G0105' => 'dzi', 'Duzib151G0114' => 'dzi', 'Duzib212G1029' => 'dzi', 'ECA232G3536' => 'eca', 'ECA240G0786' => 'eca', 'ECA240G1802' => 'eca', 'ECA240G3760' => 'eca', 'ECA240G3920' => 'eca', 'EL10Ac5g12536' => 'bvu', 'EL10Ac5g12537' => 'bvu', 'EL10Ac5g12538' => 'bvu', 'Eucgr.B01004' => 'egr', 'Eucgr.B01006' => 'egr', 'Eucgr.B01007' => 'egr', 'Eucgr.B01008' => 'egr', 'Eucgr.B01895' => 'egr', 'Eucgr.B01896' => 'egr', 'FAN04G1456' => 'fan', 'FAN08G1769' => 'fan', 'FAN08G2160' => 'fan', 'FAN13G2403' => 'fan', 'FAN13G3303' => 'fan', 'FAN15G2435' => 'fan', 'FAN17G0672' => 'fan', 'FAN17G2441' => 'fan', 'FAN18G1024' => 'fan', 'FAN22G1458' => 'fan', 'FAN24G0037' => 'fan', 'FAN24G0429' => 'fan', 'FAN24G2387' => 'fan', 'FAN27G2746' => 'fan', 'FvH4_2g20400' => 'fve', 'FvH4_2g20420' => 'fve', 'FvH4_2g20430' => 'fve', 'FvH4_4g01270' => 'fve', 'FvH4_4g01290' => 'fve', 'FvH4_4g01300' => 'fve', 'FvH4_4g01310' => 'fve', 'FvH4_4g01330' => 'fve', 'FvH4_5g09070' => 'fve', 'Glyma.10G243800' => 'gma', 'Glyma.20G150600' => 'gma', 'Gohir.A09G219200' => 'ghi', 'Gohir.A09G219300' => 'ghi', 'Gohir.D09G221400' => 'ghi', 'Gohir.D09G221500' => 'ghi', 'Gorai.006G242600' => 'gra', 'Gorai.006G242700' => 'gra', 'GSVIVG01018044001' => 'vvi', 'HanXRQChr03g0083821' => 'han', 'HanXRQChr03g0083841' => 'han', 'HanXRQChr03g0083881' => 'han', 'HanXRQChr03g0083901' => 'han', 'HanXRQChr03g0083921' => 'han', 'HanXRQChr03g0085331' => 'han', 'HanXRQChr03g0085361' => 'han', 'HanXRQChr03g0085411' => 'han', 'HanXRQChr03g0085421' => 'han', 'HanXRQChr03g0085431' => 'han', 'HanXRQChr08g0221991' => 'han', 'HanXRQChr11g0336061' => 'han', 'HanXRQChr11g0336411' => 'han', 'Haze_11234' => 'cav', 'Hma1.2p1_0549F.1_g177010' => 'hma', 'Hma1.2p1_0602F.1_g187630' => 'hma', 'Hund14876' => 'sun', 'Hund14879' => 'sun', 'Lalb_Chr06g0160741' => 'lal', 'Lalb_Chr21g0304781' => 'lal', 'Lj3A726G19' => 'lonja', 'Lj3A726T23' => 'lonja', 'Lj3A726T24' => 'lonja', 'Lj3A726T25' => 'lonja', 'Lj3A727T17' => 'lonja', 'Lj3C726T0' => 'lonja', 'Lj3C726T2' => 'lonja', 'Lj3P725T35' => 'lonja', 'Lj3P727T10' => 'lonja', 'Lj3P727T12' => 'lonja', 'Lj3P727T14' => 'lonja', 'Lj5g0023109' => 'lja', 'Lj6P646T44' => 'lonja', 'Lsat_1_v5_gn_6_75760' => 'lsa', 'Lsat_1_v5_gn_6_75800' => 'lsa', 'Lsat_1_v5_gn_6_75900' => 'lsa', 'Lsat_1_v5_gn_6_76240' => 'lsa', 'Lsat_1_v5_gn_6_76441' => 'lsa', 'Lsat_1_v5_gn_6_76700' => 'lsa', 'Lsat_1_v5_gn_6_76760' => 'lsa', 'Manes.15G033100' => 'mes', 'Mapoly0004s0074' => 'mpo', 'Mapoly0004s0075' => 'mpo', 'Mapoly0004s0163' => 'mpo', 'Mapoly0004s0164' => 'mpo', 'Mapoly0021s0018' => 'mpo', 'Mapoly0041s0136' => 'mpo', 'Mapoly0041s0137' => 'mpo', 'Mapoly0041s0138' => 'mpo', 'Mapoly0041s0139' => 'mpo', 'Mapoly0041s0141' => 'mpo', 'Mapoly0041s0142' => 'mpo', 'Mapoly0041s0143' => 'mpo', 'Mapoly0041s0144' => 'mpo', 'Mapoly0041s0145' => 'mpo', 'Mapoly0047s0106' => 'mpo', 'Mapoly0047s0108' => 'mpo', 'Mapoly0050s0051' => 'mpo', 'Mapoly0050s0052' => 'mpo', 'Mapoly0050s0053' => 'mpo', 'Mapoly0058s0013' => 'mpo', 'Mapoly0091s0078' => 'mpo', 'Mapoly0091s0079' => 'mpo', 'Mapoly0091s0080' => 'mpo', 'Mapoly0091s0081' => 'mpo', 'Mapoly0278s0004' => 'mpo', 'Mapoly0278s0005' => 'mpo', 'Mapoly0278s0006' => 'mpo', 'MBI11_g30648_MAGBIO' => 'mbi', 'MCO03G194' => 'mco', 'MCO03G590' => 'mco', 'MCO07G312' => 'mco', 'MCO10G318' => 'mco', 'MCO12G244' => 'mco', 'MCO13G148' => 'mco', 'MCO13G194' => 'mco', 'MCO16G238' => 'mco', 'MD06G1134100' => 'mdo', 'MD13G1200100' => 'mdo', 'MD13G1200300' => 'mdo', 'MD13G1200600' => 'mdo', 'MD14G1150400' => 'mdo', 'MD16G1200000' => 'mdo', 'Medtr1g102570' => 'mtr', 'Medtr1g102780' => 'mtr', 'Medtr1g102800' => 'mtr', 'Medtr1g102810' => 'mtr', 'Medtr1g102830' => 'mtr', 'MELO3C006499.2' => 'cme', 'Migut.G00385' => 'egut', 'MSTRG.4063' => 'ama', 'Nitab4.5_0000090g0260' => 'nta', 'Nitab4.5_0000977g0030' => 'nta', 'Nitab4.5_0002541g0040' => 'nta', 'Nitab4.5_0007068g0040' => 'nta', 'Nn005s41408' => 'nnu', 'Nn005s41410' => 'nnu', 'Oeu010310.1' => 'oeu', 'Oeu010311.1' => 'oeu', 'Oeu043472.1' => 'oeu', 'Os01g0246400' => 'osa', 'Os04g0267950' => 'osa', 'Os07g0178700' => 'osa', 'Os07g0178800' => 'osa', 'Peaxi162Scf00316g00046' => 'pax', 'Peaxi162Scf00316g00049' => 'pax', 'Peaxi162Scf00316g00059' => 'pax', 'Peaxi162Scf00316g00328' => 'pax', 'Peaxi162Scf00316g00329' => 'pax', 'Peaxi162Scf00316g00411' => 'pax', 'Peaxi162Scf00316g00521' => 'pax', 'Peaxi162Scf00492g00068' => 'pax', 'Peaxi162Scf35631g00002' => 'pax', 'PGR142G3720' => 'pgr', 'PGSC0003DMG400006442' => 'stu', 'Phvul.007G062000' => 'pvu', 'Potri.008G157750' => 'ptr', 'Potri.008G157900' => 'ptr', 'Potri.008G158000' => 'ptr', 'Potri.008G158200' => 'ptr', 'Pp3c11_7280' => 'ppa', 'Pp3c11_7980' => 'ppa', 'Pp3c12_19450' => 'ppa', 'Pp3c14_1480' => 'ppa', 'Pp3c14_1501' => 'ppa', 'Pp3c16_4900' => 'ppa', 'Pp3c16_5010' => 'ppa', 'Pp3c16_5060' => 'ppa', 'Pp3c19_18250' => 'ppa', 'Pp3c23_8530' => 'ppa', 'Pp3c23_8550' => 'ppa', 'Pp3c24_9670' => 'ppa', 'Pp3c2_21390' => 'ppa', 'Pp3c2_31380' => 'ppa', 'Pp3c3_16620' => 'ppa', 'Pp3c3_8090' => 'ppa', 'Pp3c3_8110' => 'ppa', 'Pp3c3_8130' => 'ppa', 'Pp3c3_8150' => 'ppa', 'Pp3c4_14320' => 'ppa', 'Pp3c6_2560' => 'ppa', 'Pp3c9_16700' => 'ppa', 'PRCOL_00000234' => 'pco', 'PRCOL_00000235' => 'pco', 'PRCOL_00000777' => 'pco', 'PRCOL_00002344' => 'pco', 'PRCOL_00002372' => 'pco', 'PRCOL_00006120' => 'pco', 'Prupe.1G021400' => 'ppe', 'Prupe.1G021500' => 'ppe', 'Prupe.1G021600' => 'ppe', 'Prupe.1G021700' => 'ppe', 'Prupe.1G021800' => 'ppe', 'Prupe.5G145100' => 'ppe', 'Psat6g204040' => 'psa', 'Psat6g204800' => 'psa', 'Psat6g204920' => 'psa', 'Psat6g204960' => 'psa', 'Psat6g205080' => 'psa', 'PSO017G0271' => 'pso', 'PSO017G1276' => 'pso', 'PSO017G1429' => 'pso', 'PSO017G1861' => 'pso', 'PSO017G2787' => 'pso', 'PSO017G4466' => 'pso', 'PSO017G5118' => 'pso', 'PSO017G5420' => 'pso', 'PSO063G3678' => 'pso', 'PSO210G0546' => 'pso', 'PSO317G0001' => 'pso', 'PSO357G0512' => 'pso', 'PSO478G2682' => 'pso', 'PSO647G0001' => 'pso', 'PSO675G0001' => 'pso', 'PSO675G2699' => 'pso', 'PSO675G2849' => 'pso', 'PSO675G4991' => 'pso', 'PSO689G0001' => 'pso', 'QL06p000916' => 'qlo', 'QL06p000921' => 'qlo', 'QL06p001398' => 'qlo', 'QL06p001407' => 'qlo', 'QL06p002031' => 'qlo', 'RcHm_v2.0_Chr4g0387791' => 'rch', 'RcHm_v2.0_Chr4g0387801' => 'rch', 'RcHm_v2.0_Chr6g0286501' => 'rch', 'RcHm_v2.0_Chr6g0286511' => 'rch', 'RcHm_v2.0_Chr6g0286521' => 'rch', 'RcHm_v2.0_Chr6g0286531' => 'rch', 'RcHm_v2.0_Chr7g0189141' => 'rch', 'Rhsim02G0028700' => 'rsi', 'Rhsim02G0028800' => 'rsi', 'Rhsim02G0028900' => 'rsi', 'Rhsim02G0029000' => 'rsi', 'Rhsim02G0029100' => 'rsi', 'Rhsim02G0029200' => 'rsi', 'Rhsim02G0029300' => 'rsi', 'Rhsim02G0029400' => 'rsi', 'Rhsim02G0029500' => 'rsi', 'Rhsim02G0029600' => 'rsi', 'RhsimUnG0024000' => 'rsi', 'RhsimUnG0024100' => 'rsi', 'RhsimUnG0024200' => 'rsi', 'RhsimUnG0024300' => 'rsi', 'RhsimUnG0024400' => 'rsi', 'RhsimUnG0024500' => 'rsi', 'RhsimUnG0024700' => 'rsi', 'RhsimUnG0024800' => 'rsi', 'RhsimUnG0024900' => 'rsi', 'RhsimUnG0025100' => 'rsi', 'Sabra08G0120200' => 'sbr', 'Sabra08G0120300' => 'sbr', 'Sabra08G0120500' => 'sbr', 'Sabra08G0120600' => 'sbr', 'Sabra10G0158900' => 'sbr', 'SalBow2G3492' => 'sbo', 'Sc13g0004760' => 'sci', 'Sc13g0004770' => 'sci', 'Sed0003417' => 'sed', 'Sed0019750' => 'sed', 'SEGI_03419' => 'sgi', 'SEGI_05907' => 'sgi', 'SEGI_10682' => 'sgi', 'SEGI_13528' => 'sgi', 'SEGI_16081' => 'sgi', 'SEGI_19370' => 'sgi', 'SEGI_21015' => 'sgi', 'SEGI_21944' => 'sgi', 'SEGI_32906' => 'sgi', 'SEGI_33093' => 'sgi', 'SEGI_36110' => 'sgi', 'SEGI_40397' => 'sgi', 'SGA_v2.0_scaffold191G40426' => 'sas', 'SGA_v2.0_scaffold353G49717' => 'sas', 'SGA_v2.0_scaffold50G18550' => 'sas', 'SMO119G0173' => 'smo', 'SMO172G0002' => 'smo', 'Solyc09g082690.3' => 'sly', 'Solyc09g082700.2' => 'sly', 'Sopen09g031550' => 'spe', 'Sopen09g031560' => 'spe', 'Sp3g20540' => 'spa', 'Sp7g07580' => 'spa', 'TAR134G0002' => 'tar', 'TAR236G0001' => 'tar', 'TAR365G0892' => 'tar', 'TAR636G0166' => 'tar', 'TAR636G0646' => 'tar', 'TAR636G0869' => 'tar', 'TAR636G1317' => 'tar', 'TAR636G1744' => 'tar', 'TAR636G3358' => 'tar', 'TAR636G3436' => 'tar', 'THA.LOC104803047' => 'tha', 'Thecc.04G238900' => 'tca', 'Thhalv10021557m.g' => 'esa', 'Thhalv10026318m.g' => 'esa', 'Thhalv10026335m.g' => 'esa', 'TPR.G17433' => 'tpr', 'TPR.G18915' => 'tpr', 'TPR.G26125' => 'tpr', 'TWI09G0677' => 'twi', 'TWI73G0287' => 'twi', 'unitig_748.g8326' => 'ugi', 'vmacro15370' => 'vma', 'vmacro15371' => 'vma', 'vmacro15372' => 'vma', 'vmacro15373' => 'vma', 'vmacro15374' => 'vma', 'VMungo0720G2826' => 'vmu', 'Zm00001eb116960' => 'zma', 'Zm00001eb301260' => 'zma', 'Zm00001eb301270' => 'zma' ) $gf_id = 'HOM05D001460' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001460' ) $data_identifier = 'HOM05D001460' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 4, 'aag' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 2, 'aox' => (int) 2, 'arhy' => (int) 4, 'ath' => (int) 2, 'atr' => (int) 1, 'acertr' => (int) 10, 'cqu' => (int) 4, 'bca' => (int) 11, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 1, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 1, 'ccan' => (int) 1, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 1, 'col' => (int) 1, 'cpa' => (int) 1, 'cre' => (int) 7, 'csa' => (int) 1, 'camsi' => (int) 2, 'dca' => (int) 3, 'din' => (int) 2, 'dzi' => (int) 3, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 14, 'fve' => (int) 9, 'gma' => (int) 2, 'ghi' => (int) 4, 'gra' => (int) 2, 'vvi' => (int) 1, 'han' => (int) 13, 'cav' => (int) 1, 'hma' => (int) 2, 'sun' => (int) 2, 'lal' => (int) 2, 'lonja' => (int) 12, 'lja' => (int) 1, 'lsa' => (int) 7, 'mes' => (int) 1, 'mpo' => (int) 27, 'mbi' => (int) 1, 'mco' => (int) 8, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 1, 'egut' => (int) 1, 'ama' => (int) 1, 'nta' => (int) 4, 'nnu' => (int) 2, 'oeu' => (int) 3, 'osa' => (int) 4, 'pax' => (int) 9, 'pgr' => (int) 1, 'stu' => (int) 1, 'pvu' => (int) 1, 'ptr' => (int) 4, 'ppa' => (int) 22, 'pco' => (int) 6, 'ppe' => (int) 6, 'psa' => (int) 5, 'pso' => (int) 19, 'qlo' => (int) 5, 'rch' => (int) 7, 'rsi' => (int) 20, 'sbr' => (int) 5, 'sbo' => (int) 1, 'sci' => (int) 2, 'sed' => (int) 2, 'sgi' => (int) 12, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 2, 'tar' => (int) 10, 'tha' => (int) 1, 'tca' => (int) 1, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 2, 'ugi' => (int) 1, 'vma' => (int) 5, 'vmu' => (int) 1, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb301270' $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' => 'HOM05D001460', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '433', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p22980' => 'bna', 'A01p32340' => 'bna', 'A03p42970' => 'bna', 'A05p25880' => 'bna', 'Aa31LG8G9320' => 'aar', 'Aa31LG8G9330' => 'aar', 'Aa31LG8G9340' => 'aar', 'Aa31sc221G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1034' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1528' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.829' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2222' => 'aag', 'Ah.12g058830' => 'amhyb', 'Ah.12g058840' => 'amhyb', 'AL3G37160' => 'aly', 'AL7G41310' => 'aly', 'Aqoxy5G00395' => 'aox', 'Aqoxy5G00396' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0C8NZA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5185HY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JZ1PRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MD3LS0' => 'arhy', 'AT3G22840' => 'ath', 'AT4G14690' => 'ath', 'ATR0665G054' => 'atr', 'Atru.chr4.2344' => 'acertr', 'Atru.chr4.2346' => 'acertr', 'Atru.chr4.2347' => 'acertr', 'Atru.chr4.2348' => 'acertr', 'Atru.chr4.2355' => 'acertr', 'Atru.chr4.2356' => 'acertr', 'Atru.chr4.2358' => 'acertr', 'Atru.chr4.2359' => 'acertr', 'Atru.chr4.2360' => 'acertr', 'Atru.chr4.2361' => 'acertr', 'AUR62030476' => 'cqu', 'AUR62030478' => 'cqu', 'AUR62030819' => 'cqu', 'AUR62030820' => 'cqu', 'BcaB03g14648' => 'bca', 'BcaB04g20492' => 'bca', 'BcaB06g26399' => 'bca', 'BcaC01g03416' => 'bca', 'BcaC01g03419' => 'bca', 'BcaC01g03421' => 'bca', 'BcaC01g03424' => 'bca', 'BcaC05g28012' => 'bca', 'BcaC09g49212' => 'bca', 'BcaC09g50140' => 'bca', 'BcaNung00346' => 'bca', 'BolC1t02785H' => 'bol', 'BolC1t04095H' => 'bol', 'BolC3t17545H' => 'bol', 'BolC5t32769H' => 'bol', 'BraA01t02211Z' => 'bra', 'BraA01t03359Z' => 'bra', 'BraA03t13441Z' => 'bra', 'BraA05t21476Z' => 'bra', 'C01p28420' => 'bna', 'C01p41350' => 'bna', 'C03p52750' => 'bna', 'C03p52780' => 'bna', 'C05p40270' => 'bna', 'CAN.G1437.9' => 'can', 'CANSAT78G0035' => 'cansat', 'CANSAT78G1036' => 'cansat', 'CANSAT78G2272' => 'cansat', 'CANSAT78G2478' => 'cansat', 'CARHR098700' => 'chi', 'CARHR221120' => 'chi', 'CARHR221150' => 'chi', 'Carub.0003s2297' => 'cru', 'Carub.0007s2749' => 'cru', 'Carub.0007s2750' => 'cru', 'Carub.0007s2751' => 'cru', 'Ca_10849_v3' => 'car', 'Cc03_g04300' => 'ccan', 'CDE02G3648' => 'cde', 'CDE05G0060' => 'cde', 'CDE05G0692' => 'cde', 'CDE05G2285' => 'cde', 'CDE05G2884' => 'cde', 'CDE05G3072' => 'cde', 'Cfa008439' => 'cfa', 'Cfa008441' => 'cfa', 'Cfa008443' => 'cfa', 'Cfa008448' => 'cfa', 'Ciclev10005974m.g' => 'ccl', 'Ciclev10006006m.g' => 'ccl', 'Ciclev10006775m.g' => 'ccl', 'CiPaw.02G120400' => 'cil', 'CiPaw.02G120500' => 'cil', 'CiPaw.02G120600' => 'cil', 'ClCG05G004850' => 'cla', 'COL.COLO4_21566' => 'col', 'Cpa.g.sc44.124' => 'cpa', 'Cre07.g320400' => 'cre', 'Cre07.g320450' => 'cre', 'Cre08.g384650' => 'cre', 'Cre09.g393173' => 'cre', 'Cre09.g394325' => 'cre', 'Cre14.g626750' => 'cre', 'Cre16.g679250' => 'cre', 'CsaV3_3G012890' => 'csa', 'CSS0010865' => 'camsi', 'CSS0044338' => 'camsi', 'DCAR_002366' => 'dca', 'DCAR_030687' => 'dca', 'DCAR_030688' => 'dca', 'Dinv14047' => 'din', 'Dinv14048' => 'din', 'Duzib151G0105' => 'dzi', 'Duzib151G0114' => 'dzi', 'Duzib212G1029' => 'dzi', 'ECA232G3536' => 'eca', 'ECA240G0786' => 'eca', 'ECA240G1802' => 'eca', 'ECA240G3760' => 'eca', 'ECA240G3920' => 'eca', 'EL10Ac5g12536' => 'bvu', 'EL10Ac5g12537' => 'bvu', 'EL10Ac5g12538' => 'bvu', 'Eucgr.B01004' => 'egr', 'Eucgr.B01006' => 'egr', 'Eucgr.B01007' => 'egr', 'Eucgr.B01008' => 'egr', 'Eucgr.B01895' => 'egr', 'Eucgr.B01896' => 'egr', 'FAN04G1456' => 'fan', 'FAN08G1769' => 'fan', 'FAN08G2160' => 'fan', 'FAN13G2403' => 'fan', 'FAN13G3303' => 'fan', 'FAN15G2435' => 'fan', 'FAN17G0672' => 'fan', 'FAN17G2441' => 'fan', 'FAN18G1024' => 'fan', 'FAN22G1458' => 'fan', 'FAN24G0037' => 'fan', 'FAN24G0429' => 'fan', 'FAN24G2387' => 'fan', 'FAN27G2746' => 'fan', 'FvH4_2g20400' => 'fve', 'FvH4_2g20420' => 'fve', 'FvH4_2g20430' => 'fve', 'FvH4_4g01270' => 'fve', 'FvH4_4g01290' => 'fve', 'FvH4_4g01300' => 'fve', 'FvH4_4g01310' => 'fve', 'FvH4_4g01330' => 'fve', 'FvH4_5g09070' => 'fve', 'Glyma.10G243800' => 'gma', 'Glyma.20G150600' => 'gma', 'Gohir.A09G219200' => 'ghi', 'Gohir.A09G219300' => 'ghi', 'Gohir.D09G221400' => 'ghi', 'Gohir.D09G221500' => 'ghi', 'Gorai.006G242600' => 'gra', 'Gorai.006G242700' => 'gra', 'GSVIVG01018044001' => 'vvi', 'HanXRQChr03g0083821' => 'han', 'HanXRQChr03g0083841' => 'han', 'HanXRQChr03g0083881' => 'han', 'HanXRQChr03g0083901' => 'han', 'HanXRQChr03g0083921' => 'han', 'HanXRQChr03g0085331' => 'han', 'HanXRQChr03g0085361' => 'han', 'HanXRQChr03g0085411' => 'han', 'HanXRQChr03g0085421' => 'han', 'HanXRQChr03g0085431' => 'han', 'HanXRQChr08g0221991' => 'han', 'HanXRQChr11g0336061' => 'han', 'HanXRQChr11g0336411' => 'han', 'Haze_11234' => 'cav', 'Hma1.2p1_0549F.1_g177010' => 'hma', 'Hma1.2p1_0602F.1_g187630' => 'hma', 'Hund14876' => 'sun', 'Hund14879' => 'sun', 'Lalb_Chr06g0160741' => 'lal', 'Lalb_Chr21g0304781' => 'lal', 'Lj3A726G19' => 'lonja', 'Lj3A726T23' => 'lonja', 'Lj3A726T24' => 'lonja', 'Lj3A726T25' => 'lonja', 'Lj3A727T17' => 'lonja', 'Lj3C726T0' => 'lonja', 'Lj3C726T2' => 'lonja', 'Lj3P725T35' => 'lonja', 'Lj3P727T10' => 'lonja', 'Lj3P727T12' => 'lonja', 'Lj3P727T14' => 'lonja', 'Lj5g0023109' => 'lja', 'Lj6P646T44' => 'lonja', 'Lsat_1_v5_gn_6_75760' => 'lsa', 'Lsat_1_v5_gn_6_75800' => 'lsa', 'Lsat_1_v5_gn_6_75900' => 'lsa', 'Lsat_1_v5_gn_6_76240' => 'lsa', 'Lsat_1_v5_gn_6_76441' => 'lsa', 'Lsat_1_v5_gn_6_76700' => 'lsa', 'Lsat_1_v5_gn_6_76760' => 'lsa', 'Manes.15G033100' => 'mes', 'Mapoly0004s0074' => 'mpo', 'Mapoly0004s0075' => 'mpo', 'Mapoly0004s0163' => 'mpo', 'Mapoly0004s0164' => 'mpo', 'Mapoly0021s0018' => 'mpo', 'Mapoly0041s0136' => 'mpo', 'Mapoly0041s0137' => 'mpo', 'Mapoly0041s0138' => 'mpo', 'Mapoly0041s0139' => 'mpo', 'Mapoly0041s0141' => 'mpo', 'Mapoly0041s0142' => 'mpo', 'Mapoly0041s0143' => 'mpo', 'Mapoly0041s0144' => 'mpo', 'Mapoly0041s0145' => 'mpo', 'Mapoly0047s0106' => 'mpo', 'Mapoly0047s0108' => 'mpo', 'Mapoly0050s0051' => 'mpo', 'Mapoly0050s0052' => 'mpo', 'Mapoly0050s0053' => 'mpo', 'Mapoly0058s0013' => 'mpo', 'Mapoly0091s0078' => 'mpo', 'Mapoly0091s0079' => 'mpo', 'Mapoly0091s0080' => 'mpo', 'Mapoly0091s0081' => 'mpo', 'Mapoly0278s0004' => 'mpo', 'Mapoly0278s0005' => 'mpo', 'Mapoly0278s0006' => 'mpo', 'MBI11_g30648_MAGBIO' => 'mbi', 'MCO03G194' => 'mco', 'MCO03G590' => 'mco', 'MCO07G312' => 'mco', 'MCO10G318' => 'mco', 'MCO12G244' => 'mco', 'MCO13G148' => 'mco', 'MCO13G194' => 'mco', 'MCO16G238' => 'mco', 'MD06G1134100' => 'mdo', 'MD13G1200100' => 'mdo', 'MD13G1200300' => 'mdo', 'MD13G1200600' => 'mdo', 'MD14G1150400' => 'mdo', 'MD16G1200000' => 'mdo', 'Medtr1g102570' => 'mtr', 'Medtr1g102780' => 'mtr', 'Medtr1g102800' => 'mtr', 'Medtr1g102810' => 'mtr', 'Medtr1g102830' => 'mtr', 'MELO3C006499.2' => 'cme', 'Migut.G00385' => 'egut', 'MSTRG.4063' => 'ama', 'Nitab4.5_0000090g0260' => 'nta', 'Nitab4.5_0000977g0030' => 'nta', 'Nitab4.5_0002541g0040' => 'nta', 'Nitab4.5_0007068g0040' => 'nta', 'Nn005s41408' => 'nnu', 'Nn005s41410' => 'nnu', 'Oeu010310.1' => 'oeu', 'Oeu010311.1' => 'oeu', 'Oeu043472.1' => 'oeu', 'Os01g0246400' => 'osa', 'Os04g0267950' => 'osa', 'Os07g0178700' => 'osa', 'Os07g0178800' => 'osa', 'Peaxi162Scf00316g00046' => 'pax', 'Peaxi162Scf00316g00049' => 'pax', 'Peaxi162Scf00316g00059' => 'pax', 'Peaxi162Scf00316g00328' => 'pax', 'Peaxi162Scf00316g00329' => 'pax', 'Peaxi162Scf00316g00411' => 'pax', 'Peaxi162Scf00316g00521' => 'pax', 'Peaxi162Scf00492g00068' => 'pax', 'Peaxi162Scf35631g00002' => 'pax', 'PGR142G3720' => 'pgr', 'PGSC0003DMG400006442' => 'stu', 'Phvul.007G062000' => 'pvu', 'Potri.008G157750' => 'ptr', 'Potri.008G157900' => 'ptr', 'Potri.008G158000' => 'ptr', 'Potri.008G158200' => 'ptr', 'Pp3c11_7280' => 'ppa', 'Pp3c11_7980' => 'ppa', 'Pp3c12_19450' => 'ppa', 'Pp3c14_1480' => 'ppa', 'Pp3c14_1501' => 'ppa', 'Pp3c16_4900' => 'ppa', 'Pp3c16_5010' => 'ppa', 'Pp3c16_5060' => 'ppa', 'Pp3c19_18250' => 'ppa', 'Pp3c23_8530' => 'ppa', 'Pp3c23_8550' => 'ppa', 'Pp3c24_9670' => 'ppa', 'Pp3c2_21390' => 'ppa', 'Pp3c2_31380' => 'ppa', 'Pp3c3_16620' => 'ppa', 'Pp3c3_8090' => 'ppa', 'Pp3c3_8110' => 'ppa', 'Pp3c3_8130' => 'ppa', 'Pp3c3_8150' => 'ppa', 'Pp3c4_14320' => 'ppa', 'Pp3c6_2560' => 'ppa', 'Pp3c9_16700' => 'ppa', 'PRCOL_00000234' => 'pco', 'PRCOL_00000235' => 'pco', 'PRCOL_00000777' => 'pco', 'PRCOL_00002344' => 'pco', 'PRCOL_00002372' => 'pco', 'PRCOL_00006120' => 'pco', 'Prupe.1G021400' => 'ppe', 'Prupe.1G021500' => 'ppe', 'Prupe.1G021600' => 'ppe', 'Prupe.1G021700' => 'ppe', 'Prupe.1G021800' => 'ppe', 'Prupe.5G145100' => 'ppe', 'Psat6g204040' => 'psa', 'Psat6g204800' => 'psa', 'Psat6g204920' => 'psa', 'Psat6g204960' => 'psa', 'Psat6g205080' => 'psa', 'PSO017G0271' => 'pso', 'PSO017G1276' => 'pso', 'PSO017G1429' => 'pso', 'PSO017G1861' => 'pso', 'PSO017G2787' => 'pso', 'PSO017G4466' => 'pso', 'PSO017G5118' => 'pso', 'PSO017G5420' => 'pso', 'PSO063G3678' => 'pso', 'PSO210G0546' => 'pso', 'PSO317G0001' => 'pso', 'PSO357G0512' => 'pso', 'PSO478G2682' => 'pso', 'PSO647G0001' => 'pso', 'PSO675G0001' => 'pso', 'PSO675G2699' => 'pso', 'PSO675G2849' => 'pso', 'PSO675G4991' => 'pso', 'PSO689G0001' => 'pso', 'QL06p000916' => 'qlo', 'QL06p000921' => 'qlo', 'QL06p001398' => 'qlo', 'QL06p001407' => 'qlo', 'QL06p002031' => 'qlo', 'RcHm_v2.0_Chr4g0387791' => 'rch', 'RcHm_v2.0_Chr4g0387801' => 'rch', 'RcHm_v2.0_Chr6g0286501' => 'rch', 'RcHm_v2.0_Chr6g0286511' => 'rch', 'RcHm_v2.0_Chr6g0286521' => 'rch', 'RcHm_v2.0_Chr6g0286531' => 'rch', 'RcHm_v2.0_Chr7g0189141' => 'rch', 'Rhsim02G0028700' => 'rsi', 'Rhsim02G0028800' => 'rsi', 'Rhsim02G0028900' => 'rsi', 'Rhsim02G0029000' => 'rsi', 'Rhsim02G0029100' => 'rsi', 'Rhsim02G0029200' => 'rsi', 'Rhsim02G0029300' => 'rsi', 'Rhsim02G0029400' => 'rsi', 'Rhsim02G0029500' => 'rsi', 'Rhsim02G0029600' => 'rsi', 'RhsimUnG0024000' => 'rsi', 'RhsimUnG0024100' => 'rsi', 'RhsimUnG0024200' => 'rsi', 'RhsimUnG0024300' => 'rsi', 'RhsimUnG0024400' => 'rsi', 'RhsimUnG0024500' => 'rsi', 'RhsimUnG0024700' => 'rsi', 'RhsimUnG0024800' => 'rsi', 'RhsimUnG0024900' => 'rsi', 'RhsimUnG0025100' => 'rsi', 'Sabra08G0120200' => 'sbr', 'Sabra08G0120300' => 'sbr', 'Sabra08G0120500' => 'sbr', 'Sabra08G0120600' => 'sbr', 'Sabra10G0158900' => 'sbr', 'SalBow2G3492' => 'sbo', 'Sc13g0004760' => 'sci', 'Sc13g0004770' => 'sci', 'Sed0003417' => 'sed', 'Sed0019750' => 'sed', 'SEGI_03419' => 'sgi', 'SEGI_05907' => 'sgi', 'SEGI_10682' => 'sgi', 'SEGI_13528' => 'sgi', 'SEGI_16081' => 'sgi', 'SEGI_19370' => 'sgi', 'SEGI_21015' => 'sgi', 'SEGI_21944' => 'sgi', 'SEGI_32906' => 'sgi', 'SEGI_33093' => 'sgi', 'SEGI_36110' => 'sgi', 'SEGI_40397' => 'sgi', 'SGA_v2.0_scaffold191G40426' => 'sas', 'SGA_v2.0_scaffold353G49717' => 'sas', 'SGA_v2.0_scaffold50G18550' => 'sas', 'SMO119G0173' => 'smo', 'SMO172G0002' => 'smo', 'Solyc09g082690.3' => 'sly', 'Solyc09g082700.2' => 'sly', 'Sopen09g031550' => 'spe', 'Sopen09g031560' => 'spe', 'Sp3g20540' => 'spa', 'Sp7g07580' => 'spa', 'TAR134G0002' => 'tar', 'TAR236G0001' => 'tar', 'TAR365G0892' => 'tar', 'TAR636G0166' => 'tar', 'TAR636G0646' => 'tar', 'TAR636G0869' => 'tar', 'TAR636G1317' => 'tar', 'TAR636G1744' => 'tar', 'TAR636G3358' => 'tar', 'TAR636G3436' => 'tar', 'THA.LOC104803047' => 'tha', 'Thecc.04G238900' => 'tca', 'Thhalv10021557m.g' => 'esa', 'Thhalv10026318m.g' => 'esa', 'Thhalv10026335m.g' => 'esa', 'TPR.G17433' => 'tpr', 'TPR.G18915' => 'tpr', 'TPR.G26125' => 'tpr', 'TWI09G0677' => 'twi', 'TWI73G0287' => 'twi', 'unitig_748.g8326' => 'ugi', 'vmacro15370' => 'vma', 'vmacro15371' => 'vma', 'vmacro15372' => 'vma', 'vmacro15373' => 'vma', 'vmacro15374' => 'vma', 'VMungo0720G2826' => 'vmu', 'Zm00001eb116960' => 'zma', 'Zm00001eb301260' => 'zma', 'Zm00001eb301270' => 'zma' ), 'gf_id' => 'HOM05D001460', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001460' ), 'data_identifier' => 'HOM05D001460', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001460', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '433', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p22980' => 'bna', 'A01p32340' => 'bna', 'A03p42970' => 'bna', 'A05p25880' => 'bna', 'Aa31LG8G9320' => 'aar', 'Aa31LG8G9330' => 'aar', 'Aa31LG8G9340' => 'aar', 'Aa31sc221G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1034' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1528' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.829' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2222' => 'aag', 'Ah.12g058830' => 'amhyb', 'Ah.12g058840' => 'amhyb', 'AL3G37160' => 'aly', 'AL7G41310' => 'aly', 'Aqoxy5G00395' => 'aox', 'Aqoxy5G00396' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0C8NZA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5185HY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JZ1PRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MD3LS0' => 'arhy', 'AT3G22840' => 'ath', 'AT4G14690' => 'ath', 'ATR0665G054' => 'atr', 'Atru.chr4.2344' => 'acertr', 'Atru.chr4.2346' => 'acertr', 'Atru.chr4.2347' => 'acertr', 'Atru.chr4.2348' => 'acertr', 'Atru.chr4.2355' => 'acertr', 'Atru.chr4.2356' => 'acertr', 'Atru.chr4.2358' => 'acertr', 'Atru.chr4.2359' => 'acertr', 'Atru.chr4.2360' => 'acertr', 'Atru.chr4.2361' => 'acertr', 'AUR62030476' => 'cqu', 'AUR62030478' => 'cqu', 'AUR62030819' => 'cqu', 'AUR62030820' => 'cqu', 'BcaB03g14648' => 'bca', 'BcaB04g20492' => 'bca', 'BcaB06g26399' => 'bca', 'BcaC01g03416' => 'bca', 'BcaC01g03419' => 'bca', 'BcaC01g03421' => 'bca', 'BcaC01g03424' => 'bca', 'BcaC05g28012' => 'bca', 'BcaC09g49212' => 'bca', 'BcaC09g50140' => 'bca', 'BcaNung00346' => 'bca', 'BolC1t02785H' => 'bol', 'BolC1t04095H' => 'bol', 'BolC3t17545H' => 'bol', 'BolC5t32769H' => 'bol', 'BraA01t02211Z' => 'bra', 'BraA01t03359Z' => 'bra', 'BraA03t13441Z' => 'bra', 'BraA05t21476Z' => 'bra', 'C01p28420' => 'bna', 'C01p41350' => 'bna', 'C03p52750' => 'bna', 'C03p52780' => 'bna', 'C05p40270' => 'bna', 'CAN.G1437.9' => 'can', 'CANSAT78G0035' => 'cansat', 'CANSAT78G1036' => 'cansat', 'CANSAT78G2272' => 'cansat', 'CANSAT78G2478' => 'cansat', 'CARHR098700' => 'chi', 'CARHR221120' => 'chi', 'CARHR221150' => 'chi', 'Carub.0003s2297' => 'cru', 'Carub.0007s2749' => 'cru', 'Carub.0007s2750' => 'cru', 'Carub.0007s2751' => 'cru', 'Ca_10849_v3' => 'car', 'Cc03_g04300' => 'ccan', 'CDE02G3648' => 'cde', 'CDE05G0060' => 'cde', 'CDE05G0692' => 'cde', 'CDE05G2285' => 'cde', 'CDE05G2884' => 'cde', 'CDE05G3072' => 'cde', 'Cfa008439' => 'cfa', 'Cfa008441' => 'cfa', 'Cfa008443' => 'cfa', 'Cfa008448' => 'cfa', 'Ciclev10005974m.g' => 'ccl', 'Ciclev10006006m.g' => 'ccl', 'Ciclev10006775m.g' => 'ccl', 'CiPaw.02G120400' => 'cil', 'CiPaw.02G120500' => 'cil', 'CiPaw.02G120600' => 'cil', 'ClCG05G004850' => 'cla', 'COL.COLO4_21566' => 'col', 'Cpa.g.sc44.124' => 'cpa', 'Cre07.g320400' => 'cre', 'Cre07.g320450' => 'cre', 'Cre08.g384650' => 'cre', 'Cre09.g393173' => 'cre', 'Cre09.g394325' => 'cre', 'Cre14.g626750' => 'cre', 'Cre16.g679250' => 'cre', 'CsaV3_3G012890' => 'csa', 'CSS0010865' => 'camsi', 'CSS0044338' => 'camsi', 'DCAR_002366' => 'dca', 'DCAR_030687' => 'dca', 'DCAR_030688' => 'dca', 'Dinv14047' => 'din', 'Dinv14048' => 'din', 'Duzib151G0105' => 'dzi', 'Duzib151G0114' => 'dzi', 'Duzib212G1029' => 'dzi', 'ECA232G3536' => 'eca', 'ECA240G0786' => 'eca', 'ECA240G1802' => 'eca', 'ECA240G3760' => 'eca', 'ECA240G3920' => 'eca', 'EL10Ac5g12536' => 'bvu', 'EL10Ac5g12537' => 'bvu', 'EL10Ac5g12538' => 'bvu', 'Eucgr.B01004' => 'egr', 'Eucgr.B01006' => 'egr', 'Eucgr.B01007' => 'egr', 'Eucgr.B01008' => 'egr', 'Eucgr.B01895' => 'egr', 'Eucgr.B01896' => 'egr', 'FAN04G1456' => 'fan', 'FAN08G1769' => 'fan', 'FAN08G2160' => 'fan', 'FAN13G2403' => 'fan', 'FAN13G3303' => 'fan', 'FAN15G2435' => 'fan', 'FAN17G0672' => 'fan', 'FAN17G2441' => 'fan', 'FAN18G1024' => 'fan', 'FAN22G1458' => 'fan', 'FAN24G0037' => 'fan', 'FAN24G0429' => 'fan', 'FAN24G2387' => 'fan', 'FAN27G2746' => 'fan', 'FvH4_2g20400' => 'fve', 'FvH4_2g20420' => 'fve', 'FvH4_2g20430' => 'fve', 'FvH4_4g01270' => 'fve', 'FvH4_4g01290' => 'fve', 'FvH4_4g01300' => 'fve', 'FvH4_4g01310' => 'fve', 'FvH4_4g01330' => 'fve', 'FvH4_5g09070' => 'fve', 'Glyma.10G243800' => 'gma', 'Glyma.20G150600' => 'gma', 'Gohir.A09G219200' => 'ghi', 'Gohir.A09G219300' => 'ghi', 'Gohir.D09G221400' => 'ghi', 'Gohir.D09G221500' => 'ghi', 'Gorai.006G242600' => 'gra', 'Gorai.006G242700' => 'gra', 'GSVIVG01018044001' => 'vvi', 'HanXRQChr03g0083821' => 'han', 'HanXRQChr03g0083841' => 'han', 'HanXRQChr03g0083881' => 'han', 'HanXRQChr03g0083901' => 'han', 'HanXRQChr03g0083921' => 'han', 'HanXRQChr03g0085331' => 'han', 'HanXRQChr03g0085361' => 'han', 'HanXRQChr03g0085411' => 'han', 'HanXRQChr03g0085421' => 'han', 'HanXRQChr03g0085431' => 'han', 'HanXRQChr08g0221991' => 'han', 'HanXRQChr11g0336061' => 'han', 'HanXRQChr11g0336411' => 'han', 'Haze_11234' => 'cav', 'Hma1.2p1_0549F.1_g177010' => 'hma', 'Hma1.2p1_0602F.1_g187630' => 'hma', 'Hund14876' => 'sun', 'Hund14879' => 'sun', 'Lalb_Chr06g0160741' => 'lal', 'Lalb_Chr21g0304781' => 'lal', 'Lj3A726G19' => 'lonja', 'Lj3A726T23' => 'lonja', 'Lj3A726T24' => 'lonja', 'Lj3A726T25' => 'lonja', 'Lj3A727T17' => 'lonja', 'Lj3C726T0' => 'lonja', 'Lj3C726T2' => 'lonja', 'Lj3P725T35' => 'lonja', 'Lj3P727T10' => 'lonja', 'Lj3P727T12' => 'lonja', 'Lj3P727T14' => 'lonja', 'Lj5g0023109' => 'lja', 'Lj6P646T44' => 'lonja', 'Lsat_1_v5_gn_6_75760' => 'lsa', 'Lsat_1_v5_gn_6_75800' => 'lsa', 'Lsat_1_v5_gn_6_75900' => 'lsa', 'Lsat_1_v5_gn_6_76240' => 'lsa', 'Lsat_1_v5_gn_6_76441' => 'lsa', 'Lsat_1_v5_gn_6_76700' => 'lsa', 'Lsat_1_v5_gn_6_76760' => 'lsa', 'Manes.15G033100' => 'mes', 'Mapoly0004s0074' => 'mpo', 'Mapoly0004s0075' => 'mpo', 'Mapoly0004s0163' => 'mpo', 'Mapoly0004s0164' => 'mpo', 'Mapoly0021s0018' => 'mpo', 'Mapoly0041s0136' => 'mpo', 'Mapoly0041s0137' => 'mpo', 'Mapoly0041s0138' => 'mpo', 'Mapoly0041s0139' => 'mpo', 'Mapoly0041s0141' => 'mpo', 'Mapoly0041s0142' => 'mpo', 'Mapoly0041s0143' => 'mpo', 'Mapoly0041s0144' => 'mpo', 'Mapoly0041s0145' => 'mpo', 'Mapoly0047s0106' => 'mpo', 'Mapoly0047s0108' => 'mpo', 'Mapoly0050s0051' => 'mpo', 'Mapoly0050s0052' => 'mpo', 'Mapoly0050s0053' => 'mpo', 'Mapoly0058s0013' => 'mpo', 'Mapoly0091s0078' => 'mpo', 'Mapoly0091s0079' => 'mpo', 'Mapoly0091s0080' => 'mpo', 'Mapoly0091s0081' => 'mpo', 'Mapoly0278s0004' => 'mpo', 'Mapoly0278s0005' => 'mpo', 'Mapoly0278s0006' => 'mpo', 'MBI11_g30648_MAGBIO' => 'mbi', 'MCO03G194' => 'mco', 'MCO03G590' => 'mco', 'MCO07G312' => 'mco', 'MCO10G318' => 'mco', 'MCO12G244' => 'mco', 'MCO13G148' => 'mco', 'MCO13G194' => 'mco', 'MCO16G238' => 'mco', 'MD06G1134100' => 'mdo', 'MD13G1200100' => 'mdo', 'MD13G1200300' => 'mdo', 'MD13G1200600' => 'mdo', 'MD14G1150400' => 'mdo', 'MD16G1200000' => 'mdo', 'Medtr1g102570' => 'mtr', 'Medtr1g102780' => 'mtr', 'Medtr1g102800' => 'mtr', 'Medtr1g102810' => 'mtr', 'Medtr1g102830' => 'mtr', 'MELO3C006499.2' => 'cme', 'Migut.G00385' => 'egut', 'MSTRG.4063' => 'ama', 'Nitab4.5_0000090g0260' => 'nta', 'Nitab4.5_0000977g0030' => 'nta', 'Nitab4.5_0002541g0040' => 'nta', 'Nitab4.5_0007068g0040' => 'nta', 'Nn005s41408' => 'nnu', 'Nn005s41410' => 'nnu', 'Oeu010310.1' => 'oeu', 'Oeu010311.1' => 'oeu', 'Oeu043472.1' => 'oeu', 'Os01g0246400' => 'osa', 'Os04g0267950' => 'osa', 'Os07g0178700' => 'osa', 'Os07g0178800' => 'osa', 'Peaxi162Scf00316g00046' => 'pax', 'Peaxi162Scf00316g00049' => 'pax', 'Peaxi162Scf00316g00059' => 'pax', 'Peaxi162Scf00316g00328' => 'pax', 'Peaxi162Scf00316g00329' => 'pax', 'Peaxi162Scf00316g00411' => 'pax', 'Peaxi162Scf00316g00521' => 'pax', 'Peaxi162Scf00492g00068' => 'pax', 'Peaxi162Scf35631g00002' => 'pax', 'PGR142G3720' => 'pgr', 'PGSC0003DMG400006442' => 'stu', 'Phvul.007G062000' => 'pvu', 'Potri.008G157750' => 'ptr', 'Potri.008G157900' => 'ptr', 'Potri.008G158000' => 'ptr', 'Potri.008G158200' => 'ptr', 'Pp3c11_7280' => 'ppa', 'Pp3c11_7980' => 'ppa', 'Pp3c12_19450' => 'ppa', 'Pp3c14_1480' => 'ppa', 'Pp3c14_1501' => 'ppa', 'Pp3c16_4900' => 'ppa', 'Pp3c16_5010' => 'ppa', 'Pp3c16_5060' => 'ppa', 'Pp3c19_18250' => 'ppa', 'Pp3c23_8530' => 'ppa', 'Pp3c23_8550' => 'ppa', 'Pp3c24_9670' => 'ppa', 'Pp3c2_21390' => 'ppa', 'Pp3c2_31380' => 'ppa', 'Pp3c3_16620' => 'ppa', 'Pp3c3_8090' => 'ppa', 'Pp3c3_8110' => 'ppa', 'Pp3c3_8130' => 'ppa', 'Pp3c3_8150' => 'ppa', 'Pp3c4_14320' => 'ppa', 'Pp3c6_2560' => 'ppa', 'Pp3c9_16700' => 'ppa', 'PRCOL_00000234' => 'pco', 'PRCOL_00000235' => 'pco', 'PRCOL_00000777' => 'pco', 'PRCOL_00002344' => 'pco', 'PRCOL_00002372' => 'pco', 'PRCOL_00006120' => 'pco', 'Prupe.1G021400' => 'ppe', 'Prupe.1G021500' => 'ppe', 'Prupe.1G021600' => 'ppe', 'Prupe.1G021700' => 'ppe', 'Prupe.1G021800' => 'ppe', 'Prupe.5G145100' => 'ppe', 'Psat6g204040' => 'psa', 'Psat6g204800' => 'psa', 'Psat6g204920' => 'psa', 'Psat6g204960' => 'psa', 'Psat6g205080' => 'psa', 'PSO017G0271' => 'pso', 'PSO017G1276' => 'pso', 'PSO017G1429' => 'pso', 'PSO017G1861' => 'pso', 'PSO017G2787' => 'pso', 'PSO017G4466' => 'pso', 'PSO017G5118' => 'pso', 'PSO017G5420' => 'pso', 'PSO063G3678' => 'pso', 'PSO210G0546' => 'pso', 'PSO317G0001' => 'pso', 'PSO357G0512' => 'pso', 'PSO478G2682' => 'pso', 'PSO647G0001' => 'pso', 'PSO675G0001' => 'pso', 'PSO675G2699' => 'pso', 'PSO675G2849' => 'pso', 'PSO675G4991' => 'pso', 'PSO689G0001' => 'pso', 'QL06p000916' => 'qlo', 'QL06p000921' => 'qlo', 'QL06p001398' => 'qlo', 'QL06p001407' => 'qlo', 'QL06p002031' => 'qlo', 'RcHm_v2.0_Chr4g0387791' => 'rch', 'RcHm_v2.0_Chr4g0387801' => 'rch', 'RcHm_v2.0_Chr6g0286501' => 'rch', 'RcHm_v2.0_Chr6g0286511' => 'rch', 'RcHm_v2.0_Chr6g0286521' => 'rch', 'RcHm_v2.0_Chr6g0286531' => 'rch', 'RcHm_v2.0_Chr7g0189141' => 'rch', 'Rhsim02G0028700' => 'rsi', 'Rhsim02G0028800' => 'rsi', 'Rhsim02G0028900' => 'rsi', 'Rhsim02G0029000' => 'rsi', 'Rhsim02G0029100' => 'rsi', 'Rhsim02G0029200' => 'rsi', 'Rhsim02G0029300' => 'rsi', 'Rhsim02G0029400' => 'rsi', 'Rhsim02G0029500' => 'rsi', 'Rhsim02G0029600' => 'rsi', 'RhsimUnG0024000' => 'rsi', 'RhsimUnG0024100' => 'rsi', 'RhsimUnG0024200' => 'rsi', 'RhsimUnG0024300' => 'rsi', 'RhsimUnG0024400' => 'rsi', 'RhsimUnG0024500' => 'rsi', 'RhsimUnG0024700' => 'rsi', 'RhsimUnG0024800' => 'rsi', 'RhsimUnG0024900' => 'rsi', 'RhsimUnG0025100' => 'rsi', 'Sabra08G0120200' => 'sbr', 'Sabra08G0120300' => 'sbr', 'Sabra08G0120500' => 'sbr', 'Sabra08G0120600' => 'sbr', 'Sabra10G0158900' => 'sbr', 'SalBow2G3492' => 'sbo', 'Sc13g0004760' => 'sci', 'Sc13g0004770' => 'sci', 'Sed0003417' => 'sed', 'Sed0019750' => 'sed', 'SEGI_03419' => 'sgi', 'SEGI_05907' => 'sgi', 'SEGI_10682' => 'sgi', 'SEGI_13528' => 'sgi', 'SEGI_16081' => 'sgi', 'SEGI_19370' => 'sgi', 'SEGI_21015' => 'sgi', 'SEGI_21944' => 'sgi', 'SEGI_32906' => 'sgi', 'SEGI_33093' => 'sgi', 'SEGI_36110' => 'sgi', 'SEGI_40397' => 'sgi', 'SGA_v2.0_scaffold191G40426' => 'sas', 'SGA_v2.0_scaffold353G49717' => 'sas', 'SGA_v2.0_scaffold50G18550' => 'sas', 'SMO119G0173' => 'smo', 'SMO172G0002' => 'smo', 'Solyc09g082690.3' => 'sly', 'Solyc09g082700.2' => 'sly', 'Sopen09g031550' => 'spe', 'Sopen09g031560' => 'spe', 'Sp3g20540' => 'spa', 'Sp7g07580' => 'spa', 'TAR134G0002' => 'tar', 'TAR236G0001' => 'tar', 'TAR365G0892' => 'tar', 'TAR636G0166' => 'tar', 'TAR636G0646' => 'tar', 'TAR636G0869' => 'tar', 'TAR636G1317' => 'tar', 'TAR636G1744' => 'tar', 'TAR636G3358' => 'tar', 'TAR636G3436' => 'tar', 'THA.LOC104803047' => 'tha', 'Thecc.04G238900' => 'tca', 'Thhalv10021557m.g' => 'esa', 'Thhalv10026318m.g' => 'esa', 'Thhalv10026335m.g' => 'esa', 'TPR.G17433' => 'tpr', 'TPR.G18915' => 'tpr', 'TPR.G26125' => 'tpr', 'TWI09G0677' => 'twi', 'TWI73G0287' => 'twi', 'unitig_748.g8326' => 'ugi', 'vmacro15370' => 'vma', 'vmacro15371' => 'vma', 'vmacro15372' => 'vma', 'vmacro15373' => 'vma', 'vmacro15374' => 'vma', 'VMungo0720G2826' => 'vmu', 'Zm00001eb116960' => 'zma', 'Zm00001eb301260' => 'zma', 'Zm00001eb301270' => 'zma' ) $gf_id = 'HOM05D001460' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001460' ) $data_identifier = 'HOM05D001460' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 4, 'aag' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 2, 'aox' => (int) 2, 'arhy' => (int) 4, 'ath' => (int) 2, 'atr' => (int) 1, 'acertr' => (int) 10, 'cqu' => (int) 4, 'bca' => (int) 11, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 1, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 1, 'ccan' => (int) 1, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 1, 'col' => (int) 1, 'cpa' => (int) 1, 'cre' => (int) 7, 'csa' => (int) 1, 'camsi' => (int) 2, 'dca' => (int) 3, 'din' => (int) 2, 'dzi' => (int) 3, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 14, 'fve' => (int) 9, 'gma' => (int) 2, 'ghi' => (int) 4, 'gra' => (int) 2, 'vvi' => (int) 1, 'han' => (int) 13, 'cav' => (int) 1, 'hma' => (int) 2, 'sun' => (int) 2, 'lal' => (int) 2, 'lonja' => (int) 12, 'lja' => (int) 1, 'lsa' => (int) 7, 'mes' => (int) 1, 'mpo' => (int) 27, 'mbi' => (int) 1, 'mco' => (int) 8, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 1, 'egut' => (int) 1, 'ama' => (int) 1, 'nta' => (int) 4, 'nnu' => (int) 2, 'oeu' => (int) 3, 'osa' => (int) 4, 'pax' => (int) 9, 'pgr' => (int) 1, 'stu' => (int) 1, 'pvu' => (int) 1, 'ptr' => (int) 4, 'ppa' => (int) 22, 'pco' => (int) 6, 'ppe' => (int) 6, 'psa' => (int) 5, 'pso' => (int) 19, 'qlo' => (int) 5, 'rch' => (int) 7, 'rsi' => (int) 20, 'sbr' => (int) 5, 'sbo' => (int) 1, 'sci' => (int) 2, 'sed' => (int) 2, 'sgi' => (int) 12, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 2, 'tar' => (int) 10, 'tha' => (int) 1, 'tca' => (int) 1, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 2, 'ugi' => (int) 1, 'vma' => (int) 5, 'vmu' => (int) 1, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb301270' $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' => 'HOM05D001460', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '433', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p22980' => 'bna', 'A01p32340' => 'bna', 'A03p42970' => 'bna', 'A05p25880' => 'bna', 'Aa31LG8G9320' => 'aar', 'Aa31LG8G9330' => 'aar', 'Aa31LG8G9340' => 'aar', 'Aa31sc221G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1034' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1528' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.829' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2222' => 'aag', 'Ah.12g058830' => 'amhyb', 'Ah.12g058840' => 'amhyb', 'AL3G37160' => 'aly', 'AL7G41310' => 'aly', 'Aqoxy5G00395' => 'aox', 'Aqoxy5G00396' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0C8NZA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5185HY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JZ1PRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MD3LS0' => 'arhy', 'AT3G22840' => 'ath', 'AT4G14690' => 'ath', 'ATR0665G054' => 'atr', 'Atru.chr4.2344' => 'acertr', 'Atru.chr4.2346' => 'acertr', 'Atru.chr4.2347' => 'acertr', 'Atru.chr4.2348' => 'acertr', 'Atru.chr4.2355' => 'acertr', 'Atru.chr4.2356' => 'acertr', 'Atru.chr4.2358' => 'acertr', 'Atru.chr4.2359' => 'acertr', 'Atru.chr4.2360' => 'acertr', 'Atru.chr4.2361' => 'acertr', 'AUR62030476' => 'cqu', 'AUR62030478' => 'cqu', 'AUR62030819' => 'cqu', 'AUR62030820' => 'cqu', 'BcaB03g14648' => 'bca', 'BcaB04g20492' => 'bca', 'BcaB06g26399' => 'bca', 'BcaC01g03416' => 'bca', 'BcaC01g03419' => 'bca', 'BcaC01g03421' => 'bca', 'BcaC01g03424' => 'bca', 'BcaC05g28012' => 'bca', 'BcaC09g49212' => 'bca', 'BcaC09g50140' => 'bca', 'BcaNung00346' => 'bca', 'BolC1t02785H' => 'bol', 'BolC1t04095H' => 'bol', 'BolC3t17545H' => 'bol', 'BolC5t32769H' => 'bol', 'BraA01t02211Z' => 'bra', 'BraA01t03359Z' => 'bra', 'BraA03t13441Z' => 'bra', 'BraA05t21476Z' => 'bra', 'C01p28420' => 'bna', 'C01p41350' => 'bna', 'C03p52750' => 'bna', 'C03p52780' => 'bna', 'C05p40270' => 'bna', 'CAN.G1437.9' => 'can', 'CANSAT78G0035' => 'cansat', 'CANSAT78G1036' => 'cansat', 'CANSAT78G2272' => 'cansat', 'CANSAT78G2478' => 'cansat', 'CARHR098700' => 'chi', 'CARHR221120' => 'chi', 'CARHR221150' => 'chi', 'Carub.0003s2297' => 'cru', 'Carub.0007s2749' => 'cru', 'Carub.0007s2750' => 'cru', 'Carub.0007s2751' => 'cru', 'Ca_10849_v3' => 'car', 'Cc03_g04300' => 'ccan', 'CDE02G3648' => 'cde', 'CDE05G0060' => 'cde', 'CDE05G0692' => 'cde', 'CDE05G2285' => 'cde', 'CDE05G2884' => 'cde', 'CDE05G3072' => 'cde', 'Cfa008439' => 'cfa', 'Cfa008441' => 'cfa', 'Cfa008443' => 'cfa', 'Cfa008448' => 'cfa', 'Ciclev10005974m.g' => 'ccl', 'Ciclev10006006m.g' => 'ccl', 'Ciclev10006775m.g' => 'ccl', 'CiPaw.02G120400' => 'cil', 'CiPaw.02G120500' => 'cil', 'CiPaw.02G120600' => 'cil', 'ClCG05G004850' => 'cla', 'COL.COLO4_21566' => 'col', 'Cpa.g.sc44.124' => 'cpa', 'Cre07.g320400' => 'cre', 'Cre07.g320450' => 'cre', 'Cre08.g384650' => 'cre', 'Cre09.g393173' => 'cre', 'Cre09.g394325' => 'cre', 'Cre14.g626750' => 'cre', 'Cre16.g679250' => 'cre', 'CsaV3_3G012890' => 'csa', 'CSS0010865' => 'camsi', 'CSS0044338' => 'camsi', 'DCAR_002366' => 'dca', 'DCAR_030687' => 'dca', 'DCAR_030688' => 'dca', 'Dinv14047' => 'din', 'Dinv14048' => 'din', 'Duzib151G0105' => 'dzi', 'Duzib151G0114' => 'dzi', 'Duzib212G1029' => 'dzi', 'ECA232G3536' => 'eca', 'ECA240G0786' => 'eca', 'ECA240G1802' => 'eca', 'ECA240G3760' => 'eca', 'ECA240G3920' => 'eca', 'EL10Ac5g12536' => 'bvu', 'EL10Ac5g12537' => 'bvu', 'EL10Ac5g12538' => 'bvu', 'Eucgr.B01004' => 'egr', 'Eucgr.B01006' => 'egr', 'Eucgr.B01007' => 'egr', 'Eucgr.B01008' => 'egr', 'Eucgr.B01895' => 'egr', 'Eucgr.B01896' => 'egr', 'FAN04G1456' => 'fan', 'FAN08G1769' => 'fan', 'FAN08G2160' => 'fan', 'FAN13G2403' => 'fan', 'FAN13G3303' => 'fan', 'FAN15G2435' => 'fan', 'FAN17G0672' => 'fan', 'FAN17G2441' => 'fan', 'FAN18G1024' => 'fan', 'FAN22G1458' => 'fan', 'FAN24G0037' => 'fan', 'FAN24G0429' => 'fan', 'FAN24G2387' => 'fan', 'FAN27G2746' => 'fan', 'FvH4_2g20400' => 'fve', 'FvH4_2g20420' => 'fve', 'FvH4_2g20430' => 'fve', 'FvH4_4g01270' => 'fve', 'FvH4_4g01290' => 'fve', 'FvH4_4g01300' => 'fve', 'FvH4_4g01310' => 'fve', 'FvH4_4g01330' => 'fve', 'FvH4_5g09070' => 'fve', 'Glyma.10G243800' => 'gma', 'Glyma.20G150600' => 'gma', 'Gohir.A09G219200' => 'ghi', 'Gohir.A09G219300' => 'ghi', 'Gohir.D09G221400' => 'ghi', 'Gohir.D09G221500' => 'ghi', 'Gorai.006G242600' => 'gra', 'Gorai.006G242700' => 'gra', 'GSVIVG01018044001' => 'vvi', 'HanXRQChr03g0083821' => 'han', 'HanXRQChr03g0083841' => 'han', 'HanXRQChr03g0083881' => 'han', 'HanXRQChr03g0083901' => 'han', 'HanXRQChr03g0083921' => 'han', 'HanXRQChr03g0085331' => 'han', 'HanXRQChr03g0085361' => 'han', 'HanXRQChr03g0085411' => 'han', 'HanXRQChr03g0085421' => 'han', 'HanXRQChr03g0085431' => 'han', 'HanXRQChr08g0221991' => 'han', 'HanXRQChr11g0336061' => 'han', 'HanXRQChr11g0336411' => 'han', 'Haze_11234' => 'cav', 'Hma1.2p1_0549F.1_g177010' => 'hma', 'Hma1.2p1_0602F.1_g187630' => 'hma', 'Hund14876' => 'sun', 'Hund14879' => 'sun', 'Lalb_Chr06g0160741' => 'lal', 'Lalb_Chr21g0304781' => 'lal', 'Lj3A726G19' => 'lonja', 'Lj3A726T23' => 'lonja', 'Lj3A726T24' => 'lonja', 'Lj3A726T25' => 'lonja', 'Lj3A727T17' => 'lonja', 'Lj3C726T0' => 'lonja', 'Lj3C726T2' => 'lonja', 'Lj3P725T35' => 'lonja', 'Lj3P727T10' => 'lonja', 'Lj3P727T12' => 'lonja', 'Lj3P727T14' => 'lonja', 'Lj5g0023109' => 'lja', 'Lj6P646T44' => 'lonja', 'Lsat_1_v5_gn_6_75760' => 'lsa', 'Lsat_1_v5_gn_6_75800' => 'lsa', 'Lsat_1_v5_gn_6_75900' => 'lsa', 'Lsat_1_v5_gn_6_76240' => 'lsa', 'Lsat_1_v5_gn_6_76441' => 'lsa', 'Lsat_1_v5_gn_6_76700' => 'lsa', 'Lsat_1_v5_gn_6_76760' => 'lsa', 'Manes.15G033100' => 'mes', 'Mapoly0004s0074' => 'mpo', 'Mapoly0004s0075' => 'mpo', 'Mapoly0004s0163' => 'mpo', 'Mapoly0004s0164' => 'mpo', 'Mapoly0021s0018' => 'mpo', 'Mapoly0041s0136' => 'mpo', 'Mapoly0041s0137' => 'mpo', 'Mapoly0041s0138' => 'mpo', 'Mapoly0041s0139' => 'mpo', 'Mapoly0041s0141' => 'mpo', 'Mapoly0041s0142' => 'mpo', 'Mapoly0041s0143' => 'mpo', 'Mapoly0041s0144' => 'mpo', 'Mapoly0041s0145' => 'mpo', 'Mapoly0047s0106' => 'mpo', 'Mapoly0047s0108' => 'mpo', 'Mapoly0050s0051' => 'mpo', 'Mapoly0050s0052' => 'mpo', 'Mapoly0050s0053' => 'mpo', 'Mapoly0058s0013' => 'mpo', 'Mapoly0091s0078' => 'mpo', 'Mapoly0091s0079' => 'mpo', 'Mapoly0091s0080' => 'mpo', 'Mapoly0091s0081' => 'mpo', 'Mapoly0278s0004' => 'mpo', 'Mapoly0278s0005' => 'mpo', 'Mapoly0278s0006' => 'mpo', 'MBI11_g30648_MAGBIO' => 'mbi', 'MCO03G194' => 'mco', 'MCO03G590' => 'mco', 'MCO07G312' => 'mco', 'MCO10G318' => 'mco', 'MCO12G244' => 'mco', 'MCO13G148' => 'mco', 'MCO13G194' => 'mco', 'MCO16G238' => 'mco', 'MD06G1134100' => 'mdo', 'MD13G1200100' => 'mdo', 'MD13G1200300' => 'mdo', 'MD13G1200600' => 'mdo', 'MD14G1150400' => 'mdo', 'MD16G1200000' => 'mdo', 'Medtr1g102570' => 'mtr', 'Medtr1g102780' => 'mtr', 'Medtr1g102800' => 'mtr', 'Medtr1g102810' => 'mtr', 'Medtr1g102830' => 'mtr', 'MELO3C006499.2' => 'cme', 'Migut.G00385' => 'egut', 'MSTRG.4063' => 'ama', 'Nitab4.5_0000090g0260' => 'nta', 'Nitab4.5_0000977g0030' => 'nta', 'Nitab4.5_0002541g0040' => 'nta', 'Nitab4.5_0007068g0040' => 'nta', 'Nn005s41408' => 'nnu', 'Nn005s41410' => 'nnu', 'Oeu010310.1' => 'oeu', 'Oeu010311.1' => 'oeu', 'Oeu043472.1' => 'oeu', 'Os01g0246400' => 'osa', 'Os04g0267950' => 'osa', 'Os07g0178700' => 'osa', 'Os07g0178800' => 'osa', 'Peaxi162Scf00316g00046' => 'pax', 'Peaxi162Scf00316g00049' => 'pax', 'Peaxi162Scf00316g00059' => 'pax', 'Peaxi162Scf00316g00328' => 'pax', 'Peaxi162Scf00316g00329' => 'pax', 'Peaxi162Scf00316g00411' => 'pax', 'Peaxi162Scf00316g00521' => 'pax', 'Peaxi162Scf00492g00068' => 'pax', 'Peaxi162Scf35631g00002' => 'pax', 'PGR142G3720' => 'pgr', 'PGSC0003DMG400006442' => 'stu', 'Phvul.007G062000' => 'pvu', 'Potri.008G157750' => 'ptr', 'Potri.008G157900' => 'ptr', 'Potri.008G158000' => 'ptr', 'Potri.008G158200' => 'ptr', 'Pp3c11_7280' => 'ppa', 'Pp3c11_7980' => 'ppa', 'Pp3c12_19450' => 'ppa', 'Pp3c14_1480' => 'ppa', 'Pp3c14_1501' => 'ppa', 'Pp3c16_4900' => 'ppa', 'Pp3c16_5010' => 'ppa', 'Pp3c16_5060' => 'ppa', 'Pp3c19_18250' => 'ppa', 'Pp3c23_8530' => 'ppa', 'Pp3c23_8550' => 'ppa', 'Pp3c24_9670' => 'ppa', 'Pp3c2_21390' => 'ppa', 'Pp3c2_31380' => 'ppa', 'Pp3c3_16620' => 'ppa', 'Pp3c3_8090' => 'ppa', 'Pp3c3_8110' => 'ppa', 'Pp3c3_8130' => 'ppa', 'Pp3c3_8150' => 'ppa', 'Pp3c4_14320' => 'ppa', 'Pp3c6_2560' => 'ppa', 'Pp3c9_16700' => 'ppa', 'PRCOL_00000234' => 'pco', 'PRCOL_00000235' => 'pco', 'PRCOL_00000777' => 'pco', 'PRCOL_00002344' => 'pco', 'PRCOL_00002372' => 'pco', 'PRCOL_00006120' => 'pco', 'Prupe.1G021400' => 'ppe', 'Prupe.1G021500' => 'ppe', 'Prupe.1G021600' => 'ppe', 'Prupe.1G021700' => 'ppe', 'Prupe.1G021800' => 'ppe', 'Prupe.5G145100' => 'ppe', 'Psat6g204040' => 'psa', 'Psat6g204800' => 'psa', 'Psat6g204920' => 'psa', 'Psat6g204960' => 'psa', 'Psat6g205080' => 'psa', 'PSO017G0271' => 'pso', 'PSO017G1276' => 'pso', 'PSO017G1429' => 'pso', 'PSO017G1861' => 'pso', 'PSO017G2787' => 'pso', 'PSO017G4466' => 'pso', 'PSO017G5118' => 'pso', 'PSO017G5420' => 'pso', 'PSO063G3678' => 'pso', 'PSO210G0546' => 'pso', 'PSO317G0001' => 'pso', 'PSO357G0512' => 'pso', 'PSO478G2682' => 'pso', 'PSO647G0001' => 'pso', 'PSO675G0001' => 'pso', 'PSO675G2699' => 'pso', 'PSO675G2849' => 'pso', 'PSO675G4991' => 'pso', 'PSO689G0001' => 'pso', 'QL06p000916' => 'qlo', 'QL06p000921' => 'qlo', 'QL06p001398' => 'qlo', 'QL06p001407' => 'qlo', 'QL06p002031' => 'qlo', 'RcHm_v2.0_Chr4g0387791' => 'rch', 'RcHm_v2.0_Chr4g0387801' => 'rch', 'RcHm_v2.0_Chr6g0286501' => 'rch', 'RcHm_v2.0_Chr6g0286511' => 'rch', 'RcHm_v2.0_Chr6g0286521' => 'rch', 'RcHm_v2.0_Chr6g0286531' => 'rch', 'RcHm_v2.0_Chr7g0189141' => 'rch', 'Rhsim02G0028700' => 'rsi', 'Rhsim02G0028800' => 'rsi', 'Rhsim02G0028900' => 'rsi', 'Rhsim02G0029000' => 'rsi', 'Rhsim02G0029100' => 'rsi', 'Rhsim02G0029200' => 'rsi', 'Rhsim02G0029300' => 'rsi', 'Rhsim02G0029400' => 'rsi', 'Rhsim02G0029500' => 'rsi', 'Rhsim02G0029600' => 'rsi', 'RhsimUnG0024000' => 'rsi', 'RhsimUnG0024100' => 'rsi', 'RhsimUnG0024200' => 'rsi', 'RhsimUnG0024300' => 'rsi', 'RhsimUnG0024400' => 'rsi', 'RhsimUnG0024500' => 'rsi', 'RhsimUnG0024700' => 'rsi', 'RhsimUnG0024800' => 'rsi', 'RhsimUnG0024900' => 'rsi', 'RhsimUnG0025100' => 'rsi', 'Sabra08G0120200' => 'sbr', 'Sabra08G0120300' => 'sbr', 'Sabra08G0120500' => 'sbr', 'Sabra08G0120600' => 'sbr', 'Sabra10G0158900' => 'sbr', 'SalBow2G3492' => 'sbo', 'Sc13g0004760' => 'sci', 'Sc13g0004770' => 'sci', 'Sed0003417' => 'sed', 'Sed0019750' => 'sed', 'SEGI_03419' => 'sgi', 'SEGI_05907' => 'sgi', 'SEGI_10682' => 'sgi', 'SEGI_13528' => 'sgi', 'SEGI_16081' => 'sgi', 'SEGI_19370' => 'sgi', 'SEGI_21015' => 'sgi', 'SEGI_21944' => 'sgi', 'SEGI_32906' => 'sgi', 'SEGI_33093' => 'sgi', 'SEGI_36110' => 'sgi', 'SEGI_40397' => 'sgi', 'SGA_v2.0_scaffold191G40426' => 'sas', 'SGA_v2.0_scaffold353G49717' => 'sas', 'SGA_v2.0_scaffold50G18550' => 'sas', 'SMO119G0173' => 'smo', 'SMO172G0002' => 'smo', 'Solyc09g082690.3' => 'sly', 'Solyc09g082700.2' => 'sly', 'Sopen09g031550' => 'spe', 'Sopen09g031560' => 'spe', 'Sp3g20540' => 'spa', 'Sp7g07580' => 'spa', 'TAR134G0002' => 'tar', 'TAR236G0001' => 'tar', 'TAR365G0892' => 'tar', 'TAR636G0166' => 'tar', 'TAR636G0646' => 'tar', 'TAR636G0869' => 'tar', 'TAR636G1317' => 'tar', 'TAR636G1744' => 'tar', 'TAR636G3358' => 'tar', 'TAR636G3436' => 'tar', 'THA.LOC104803047' => 'tha', 'Thecc.04G238900' => 'tca', 'Thhalv10021557m.g' => 'esa', 'Thhalv10026318m.g' => 'esa', 'Thhalv10026335m.g' => 'esa', 'TPR.G17433' => 'tpr', 'TPR.G18915' => 'tpr', 'TPR.G26125' => 'tpr', 'TWI09G0677' => 'twi', 'TWI73G0287' => 'twi', 'unitig_748.g8326' => 'ugi', 'vmacro15370' => 'vma', 'vmacro15371' => 'vma', 'vmacro15372' => 'vma', 'vmacro15373' => 'vma', 'vmacro15374' => 'vma', 'VMungo0720G2826' => 'vmu', 'Zm00001eb116960' => 'zma', 'Zm00001eb301260' => 'zma', 'Zm00001eb301270' => 'zma' ), 'gf_id' => 'HOM05D001460', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001460' ), 'data_identifier' => 'HOM05D001460', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001460', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '433', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p22980' => 'bna', 'A01p32340' => 'bna', 'A03p42970' => 'bna', 'A05p25880' => 'bna', 'Aa31LG8G9320' => 'aar', 'Aa31LG8G9330' => 'aar', 'Aa31LG8G9340' => 'aar', 'Aa31sc221G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1034' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1528' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.829' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2222' => 'aag', 'Ah.12g058830' => 'amhyb', 'Ah.12g058840' => 'amhyb', 'AL3G37160' => 'aly', 'AL7G41310' => 'aly', 'Aqoxy5G00395' => 'aox', 'Aqoxy5G00396' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0C8NZA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5185HY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JZ1PRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MD3LS0' => 'arhy', 'AT3G22840' => 'ath', 'AT4G14690' => 'ath', 'ATR0665G054' => 'atr', 'Atru.chr4.2344' => 'acertr', 'Atru.chr4.2346' => 'acertr', 'Atru.chr4.2347' => 'acertr', 'Atru.chr4.2348' => 'acertr', 'Atru.chr4.2355' => 'acertr', 'Atru.chr4.2356' => 'acertr', 'Atru.chr4.2358' => 'acertr', 'Atru.chr4.2359' => 'acertr', 'Atru.chr4.2360' => 'acertr', 'Atru.chr4.2361' => 'acertr', 'AUR62030476' => 'cqu', 'AUR62030478' => 'cqu', 'AUR62030819' => 'cqu', 'AUR62030820' => 'cqu', 'BcaB03g14648' => 'bca', 'BcaB04g20492' => 'bca', 'BcaB06g26399' => 'bca', 'BcaC01g03416' => 'bca', 'BcaC01g03419' => 'bca', 'BcaC01g03421' => 'bca', 'BcaC01g03424' => 'bca', 'BcaC05g28012' => 'bca', 'BcaC09g49212' => 'bca', 'BcaC09g50140' => 'bca', 'BcaNung00346' => 'bca', 'BolC1t02785H' => 'bol', 'BolC1t04095H' => 'bol', 'BolC3t17545H' => 'bol', 'BolC5t32769H' => 'bol', 'BraA01t02211Z' => 'bra', 'BraA01t03359Z' => 'bra', 'BraA03t13441Z' => 'bra', 'BraA05t21476Z' => 'bra', 'C01p28420' => 'bna', 'C01p41350' => 'bna', 'C03p52750' => 'bna', 'C03p52780' => 'bna', 'C05p40270' => 'bna', 'CAN.G1437.9' => 'can', 'CANSAT78G0035' => 'cansat', 'CANSAT78G1036' => 'cansat', 'CANSAT78G2272' => 'cansat', 'CANSAT78G2478' => 'cansat', 'CARHR098700' => 'chi', 'CARHR221120' => 'chi', 'CARHR221150' => 'chi', 'Carub.0003s2297' => 'cru', 'Carub.0007s2749' => 'cru', 'Carub.0007s2750' => 'cru', 'Carub.0007s2751' => 'cru', 'Ca_10849_v3' => 'car', 'Cc03_g04300' => 'ccan', 'CDE02G3648' => 'cde', 'CDE05G0060' => 'cde', 'CDE05G0692' => 'cde', 'CDE05G2285' => 'cde', 'CDE05G2884' => 'cde', 'CDE05G3072' => 'cde', 'Cfa008439' => 'cfa', 'Cfa008441' => 'cfa', 'Cfa008443' => 'cfa', 'Cfa008448' => 'cfa', 'Ciclev10005974m.g' => 'ccl', 'Ciclev10006006m.g' => 'ccl', 'Ciclev10006775m.g' => 'ccl', 'CiPaw.02G120400' => 'cil', 'CiPaw.02G120500' => 'cil', 'CiPaw.02G120600' => 'cil', 'ClCG05G004850' => 'cla', 'COL.COLO4_21566' => 'col', 'Cpa.g.sc44.124' => 'cpa', 'Cre07.g320400' => 'cre', 'Cre07.g320450' => 'cre', 'Cre08.g384650' => 'cre', 'Cre09.g393173' => 'cre', 'Cre09.g394325' => 'cre', 'Cre14.g626750' => 'cre', 'Cre16.g679250' => 'cre', 'CsaV3_3G012890' => 'csa', 'CSS0010865' => 'camsi', 'CSS0044338' => 'camsi', 'DCAR_002366' => 'dca', 'DCAR_030687' => 'dca', 'DCAR_030688' => 'dca', 'Dinv14047' => 'din', 'Dinv14048' => 'din', 'Duzib151G0105' => 'dzi', 'Duzib151G0114' => 'dzi', 'Duzib212G1029' => 'dzi', 'ECA232G3536' => 'eca', 'ECA240G0786' => 'eca', 'ECA240G1802' => 'eca', 'ECA240G3760' => 'eca', 'ECA240G3920' => 'eca', 'EL10Ac5g12536' => 'bvu', 'EL10Ac5g12537' => 'bvu', 'EL10Ac5g12538' => 'bvu', 'Eucgr.B01004' => 'egr', 'Eucgr.B01006' => 'egr', 'Eucgr.B01007' => 'egr', 'Eucgr.B01008' => 'egr', 'Eucgr.B01895' => 'egr', 'Eucgr.B01896' => 'egr', 'FAN04G1456' => 'fan', 'FAN08G1769' => 'fan', 'FAN08G2160' => 'fan', 'FAN13G2403' => 'fan', 'FAN13G3303' => 'fan', 'FAN15G2435' => 'fan', 'FAN17G0672' => 'fan', 'FAN17G2441' => 'fan', 'FAN18G1024' => 'fan', 'FAN22G1458' => 'fan', 'FAN24G0037' => 'fan', 'FAN24G0429' => 'fan', 'FAN24G2387' => 'fan', 'FAN27G2746' => 'fan', 'FvH4_2g20400' => 'fve', 'FvH4_2g20420' => 'fve', 'FvH4_2g20430' => 'fve', 'FvH4_4g01270' => 'fve', 'FvH4_4g01290' => 'fve', 'FvH4_4g01300' => 'fve', 'FvH4_4g01310' => 'fve', 'FvH4_4g01330' => 'fve', 'FvH4_5g09070' => 'fve', 'Glyma.10G243800' => 'gma', 'Glyma.20G150600' => 'gma', 'Gohir.A09G219200' => 'ghi', 'Gohir.A09G219300' => 'ghi', 'Gohir.D09G221400' => 'ghi', 'Gohir.D09G221500' => 'ghi', 'Gorai.006G242600' => 'gra', 'Gorai.006G242700' => 'gra', 'GSVIVG01018044001' => 'vvi', 'HanXRQChr03g0083821' => 'han', 'HanXRQChr03g0083841' => 'han', 'HanXRQChr03g0083881' => 'han', 'HanXRQChr03g0083901' => 'han', 'HanXRQChr03g0083921' => 'han', 'HanXRQChr03g0085331' => 'han', 'HanXRQChr03g0085361' => 'han', 'HanXRQChr03g0085411' => 'han', 'HanXRQChr03g0085421' => 'han', 'HanXRQChr03g0085431' => 'han', 'HanXRQChr08g0221991' => 'han', 'HanXRQChr11g0336061' => 'han', 'HanXRQChr11g0336411' => 'han', 'Haze_11234' => 'cav', 'Hma1.2p1_0549F.1_g177010' => 'hma', 'Hma1.2p1_0602F.1_g187630' => 'hma', 'Hund14876' => 'sun', 'Hund14879' => 'sun', 'Lalb_Chr06g0160741' => 'lal', 'Lalb_Chr21g0304781' => 'lal', 'Lj3A726G19' => 'lonja', 'Lj3A726T23' => 'lonja', 'Lj3A726T24' => 'lonja', 'Lj3A726T25' => 'lonja', 'Lj3A727T17' => 'lonja', 'Lj3C726T0' => 'lonja', 'Lj3C726T2' => 'lonja', 'Lj3P725T35' => 'lonja', 'Lj3P727T10' => 'lonja', 'Lj3P727T12' => 'lonja', 'Lj3P727T14' => 'lonja', 'Lj5g0023109' => 'lja', 'Lj6P646T44' => 'lonja', 'Lsat_1_v5_gn_6_75760' => 'lsa', 'Lsat_1_v5_gn_6_75800' => 'lsa', 'Lsat_1_v5_gn_6_75900' => 'lsa', 'Lsat_1_v5_gn_6_76240' => 'lsa', 'Lsat_1_v5_gn_6_76441' => 'lsa', 'Lsat_1_v5_gn_6_76700' => 'lsa', 'Lsat_1_v5_gn_6_76760' => 'lsa', 'Manes.15G033100' => 'mes', 'Mapoly0004s0074' => 'mpo', 'Mapoly0004s0075' => 'mpo', 'Mapoly0004s0163' => 'mpo', 'Mapoly0004s0164' => 'mpo', 'Mapoly0021s0018' => 'mpo', 'Mapoly0041s0136' => 'mpo', 'Mapoly0041s0137' => 'mpo', 'Mapoly0041s0138' => 'mpo', 'Mapoly0041s0139' => 'mpo', 'Mapoly0041s0141' => 'mpo', 'Mapoly0041s0142' => 'mpo', 'Mapoly0041s0143' => 'mpo', 'Mapoly0041s0144' => 'mpo', 'Mapoly0041s0145' => 'mpo', 'Mapoly0047s0106' => 'mpo', 'Mapoly0047s0108' => 'mpo', 'Mapoly0050s0051' => 'mpo', 'Mapoly0050s0052' => 'mpo', 'Mapoly0050s0053' => 'mpo', 'Mapoly0058s0013' => 'mpo', 'Mapoly0091s0078' => 'mpo', 'Mapoly0091s0079' => 'mpo', 'Mapoly0091s0080' => 'mpo', 'Mapoly0091s0081' => 'mpo', 'Mapoly0278s0004' => 'mpo', 'Mapoly0278s0005' => 'mpo', 'Mapoly0278s0006' => 'mpo', 'MBI11_g30648_MAGBIO' => 'mbi', 'MCO03G194' => 'mco', 'MCO03G590' => 'mco', 'MCO07G312' => 'mco', 'MCO10G318' => 'mco', 'MCO12G244' => 'mco', 'MCO13G148' => 'mco', 'MCO13G194' => 'mco', 'MCO16G238' => 'mco', 'MD06G1134100' => 'mdo', 'MD13G1200100' => 'mdo', 'MD13G1200300' => 'mdo', 'MD13G1200600' => 'mdo', 'MD14G1150400' => 'mdo', 'MD16G1200000' => 'mdo', 'Medtr1g102570' => 'mtr', 'Medtr1g102780' => 'mtr', 'Medtr1g102800' => 'mtr', 'Medtr1g102810' => 'mtr', 'Medtr1g102830' => 'mtr', 'MELO3C006499.2' => 'cme', 'Migut.G00385' => 'egut', 'MSTRG.4063' => 'ama', 'Nitab4.5_0000090g0260' => 'nta', 'Nitab4.5_0000977g0030' => 'nta', 'Nitab4.5_0002541g0040' => 'nta', 'Nitab4.5_0007068g0040' => 'nta', 'Nn005s41408' => 'nnu', 'Nn005s41410' => 'nnu', 'Oeu010310.1' => 'oeu', 'Oeu010311.1' => 'oeu', 'Oeu043472.1' => 'oeu', 'Os01g0246400' => 'osa', 'Os04g0267950' => 'osa', 'Os07g0178700' => 'osa', 'Os07g0178800' => 'osa', 'Peaxi162Scf00316g00046' => 'pax', 'Peaxi162Scf00316g00049' => 'pax', 'Peaxi162Scf00316g00059' => 'pax', 'Peaxi162Scf00316g00328' => 'pax', 'Peaxi162Scf00316g00329' => 'pax', 'Peaxi162Scf00316g00411' => 'pax', 'Peaxi162Scf00316g00521' => 'pax', 'Peaxi162Scf00492g00068' => 'pax', 'Peaxi162Scf35631g00002' => 'pax', 'PGR142G3720' => 'pgr', 'PGSC0003DMG400006442' => 'stu', 'Phvul.007G062000' => 'pvu', 'Potri.008G157750' => 'ptr', 'Potri.008G157900' => 'ptr', 'Potri.008G158000' => 'ptr', 'Potri.008G158200' => 'ptr', 'Pp3c11_7280' => 'ppa', 'Pp3c11_7980' => 'ppa', 'Pp3c12_19450' => 'ppa', 'Pp3c14_1480' => 'ppa', 'Pp3c14_1501' => 'ppa', 'Pp3c16_4900' => 'ppa', 'Pp3c16_5010' => 'ppa', 'Pp3c16_5060' => 'ppa', 'Pp3c19_18250' => 'ppa', 'Pp3c23_8530' => 'ppa', 'Pp3c23_8550' => 'ppa', 'Pp3c24_9670' => 'ppa', 'Pp3c2_21390' => 'ppa', 'Pp3c2_31380' => 'ppa', 'Pp3c3_16620' => 'ppa', 'Pp3c3_8090' => 'ppa', 'Pp3c3_8110' => 'ppa', 'Pp3c3_8130' => 'ppa', 'Pp3c3_8150' => 'ppa', 'Pp3c4_14320' => 'ppa', 'Pp3c6_2560' => 'ppa', 'Pp3c9_16700' => 'ppa', 'PRCOL_00000234' => 'pco', 'PRCOL_00000235' => 'pco', 'PRCOL_00000777' => 'pco', 'PRCOL_00002344' => 'pco', 'PRCOL_00002372' => 'pco', 'PRCOL_00006120' => 'pco', 'Prupe.1G021400' => 'ppe', 'Prupe.1G021500' => 'ppe', 'Prupe.1G021600' => 'ppe', 'Prupe.1G021700' => 'ppe', 'Prupe.1G021800' => 'ppe', 'Prupe.5G145100' => 'ppe', 'Psat6g204040' => 'psa', 'Psat6g204800' => 'psa', 'Psat6g204920' => 'psa', 'Psat6g204960' => 'psa', 'Psat6g205080' => 'psa', 'PSO017G0271' => 'pso', 'PSO017G1276' => 'pso', 'PSO017G1429' => 'pso', 'PSO017G1861' => 'pso', 'PSO017G2787' => 'pso', 'PSO017G4466' => 'pso', 'PSO017G5118' => 'pso', 'PSO017G5420' => 'pso', 'PSO063G3678' => 'pso', 'PSO210G0546' => 'pso', 'PSO317G0001' => 'pso', 'PSO357G0512' => 'pso', 'PSO478G2682' => 'pso', 'PSO647G0001' => 'pso', 'PSO675G0001' => 'pso', 'PSO675G2699' => 'pso', 'PSO675G2849' => 'pso', 'PSO675G4991' => 'pso', 'PSO689G0001' => 'pso', 'QL06p000916' => 'qlo', 'QL06p000921' => 'qlo', 'QL06p001398' => 'qlo', 'QL06p001407' => 'qlo', 'QL06p002031' => 'qlo', 'RcHm_v2.0_Chr4g0387791' => 'rch', 'RcHm_v2.0_Chr4g0387801' => 'rch', 'RcHm_v2.0_Chr6g0286501' => 'rch', 'RcHm_v2.0_Chr6g0286511' => 'rch', 'RcHm_v2.0_Chr6g0286521' => 'rch', 'RcHm_v2.0_Chr6g0286531' => 'rch', 'RcHm_v2.0_Chr7g0189141' => 'rch', 'Rhsim02G0028700' => 'rsi', 'Rhsim02G0028800' => 'rsi', 'Rhsim02G0028900' => 'rsi', 'Rhsim02G0029000' => 'rsi', 'Rhsim02G0029100' => 'rsi', 'Rhsim02G0029200' => 'rsi', 'Rhsim02G0029300' => 'rsi', 'Rhsim02G0029400' => 'rsi', 'Rhsim02G0029500' => 'rsi', 'Rhsim02G0029600' => 'rsi', 'RhsimUnG0024000' => 'rsi', 'RhsimUnG0024100' => 'rsi', 'RhsimUnG0024200' => 'rsi', 'RhsimUnG0024300' => 'rsi', 'RhsimUnG0024400' => 'rsi', 'RhsimUnG0024500' => 'rsi', 'RhsimUnG0024700' => 'rsi', 'RhsimUnG0024800' => 'rsi', 'RhsimUnG0024900' => 'rsi', 'RhsimUnG0025100' => 'rsi', 'Sabra08G0120200' => 'sbr', 'Sabra08G0120300' => 'sbr', 'Sabra08G0120500' => 'sbr', 'Sabra08G0120600' => 'sbr', 'Sabra10G0158900' => 'sbr', 'SalBow2G3492' => 'sbo', 'Sc13g0004760' => 'sci', 'Sc13g0004770' => 'sci', 'Sed0003417' => 'sed', 'Sed0019750' => 'sed', 'SEGI_03419' => 'sgi', 'SEGI_05907' => 'sgi', 'SEGI_10682' => 'sgi', 'SEGI_13528' => 'sgi', 'SEGI_16081' => 'sgi', 'SEGI_19370' => 'sgi', 'SEGI_21015' => 'sgi', 'SEGI_21944' => 'sgi', 'SEGI_32906' => 'sgi', 'SEGI_33093' => 'sgi', 'SEGI_36110' => 'sgi', 'SEGI_40397' => 'sgi', 'SGA_v2.0_scaffold191G40426' => 'sas', 'SGA_v2.0_scaffold353G49717' => 'sas', 'SGA_v2.0_scaffold50G18550' => 'sas', 'SMO119G0173' => 'smo', 'SMO172G0002' => 'smo', 'Solyc09g082690.3' => 'sly', 'Solyc09g082700.2' => 'sly', 'Sopen09g031550' => 'spe', 'Sopen09g031560' => 'spe', 'Sp3g20540' => 'spa', 'Sp7g07580' => 'spa', 'TAR134G0002' => 'tar', 'TAR236G0001' => 'tar', 'TAR365G0892' => 'tar', 'TAR636G0166' => 'tar', 'TAR636G0646' => 'tar', 'TAR636G0869' => 'tar', 'TAR636G1317' => 'tar', 'TAR636G1744' => 'tar', 'TAR636G3358' => 'tar', 'TAR636G3436' => 'tar', 'THA.LOC104803047' => 'tha', 'Thecc.04G238900' => 'tca', 'Thhalv10021557m.g' => 'esa', 'Thhalv10026318m.g' => 'esa', 'Thhalv10026335m.g' => 'esa', 'TPR.G17433' => 'tpr', 'TPR.G18915' => 'tpr', 'TPR.G26125' => 'tpr', 'TWI09G0677' => 'twi', 'TWI73G0287' => 'twi', 'unitig_748.g8326' => 'ugi', 'vmacro15370' => 'vma', 'vmacro15371' => 'vma', 'vmacro15372' => 'vma', 'vmacro15373' => 'vma', 'vmacro15374' => 'vma', 'VMungo0720G2826' => 'vmu', 'Zm00001eb116960' => 'zma', 'Zm00001eb301260' => 'zma', 'Zm00001eb301270' => 'zma' ) $gf_id = 'HOM05D001460' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001460' ) $data_identifier = 'HOM05D001460' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 4, 'aag' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 2, 'aox' => (int) 2, 'arhy' => (int) 4, 'ath' => (int) 2, 'atr' => (int) 1, 'acertr' => (int) 10, 'cqu' => (int) 4, 'bca' => (int) 11, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 1, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 1, 'ccan' => (int) 1, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 1, 'col' => (int) 1, 'cpa' => (int) 1, 'cre' => (int) 7, 'csa' => (int) 1, 'camsi' => (int) 2, 'dca' => (int) 3, 'din' => (int) 2, 'dzi' => (int) 3, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 14, 'fve' => (int) 9, 'gma' => (int) 2, 'ghi' => (int) 4, 'gra' => (int) 2, 'vvi' => (int) 1, 'han' => (int) 13, 'cav' => (int) 1, 'hma' => (int) 2, 'sun' => (int) 2, 'lal' => (int) 2, 'lonja' => (int) 12, 'lja' => (int) 1, 'lsa' => (int) 7, 'mes' => (int) 1, 'mpo' => (int) 27, 'mbi' => (int) 1, 'mco' => (int) 8, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 1, 'egut' => (int) 1, 'ama' => (int) 1, 'nta' => (int) 4, 'nnu' => (int) 2, 'oeu' => (int) 3, 'osa' => (int) 4, 'pax' => (int) 9, 'pgr' => (int) 1, 'stu' => (int) 1, 'pvu' => (int) 1, 'ptr' => (int) 4, 'ppa' => (int) 22, 'pco' => (int) 6, 'ppe' => (int) 6, 'psa' => (int) 5, 'pso' => (int) 19, 'qlo' => (int) 5, 'rch' => (int) 7, 'rsi' => (int) 20, 'sbr' => (int) 5, 'sbo' => (int) 1, 'sci' => (int) 2, 'sed' => (int) 2, 'sgi' => (int) 12, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 2, 'tar' => (int) 10, 'tha' => (int) 1, 'tca' => (int) 1, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 2, 'ugi' => (int) 1, 'vma' => (int) 5, 'vmu' => (int) 1, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb301270' $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' => 'HOM05D001460', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '433', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p22980' => 'bna', 'A01p32340' => 'bna', 'A03p42970' => 'bna', 'A05p25880' => 'bna', 'Aa31LG8G9320' => 'aar', 'Aa31LG8G9330' => 'aar', 'Aa31LG8G9340' => 'aar', 'Aa31sc221G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1034' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1528' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.829' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2222' => 'aag', 'Ah.12g058830' => 'amhyb', 'Ah.12g058840' => 'amhyb', 'AL3G37160' => 'aly', 'AL7G41310' => 'aly', 'Aqoxy5G00395' => 'aox', 'Aqoxy5G00396' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0C8NZA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5185HY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JZ1PRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MD3LS0' => 'arhy', 'AT3G22840' => 'ath', 'AT4G14690' => 'ath', 'ATR0665G054' => 'atr', 'Atru.chr4.2344' => 'acertr', 'Atru.chr4.2346' => 'acertr', 'Atru.chr4.2347' => 'acertr', 'Atru.chr4.2348' => 'acertr', 'Atru.chr4.2355' => 'acertr', 'Atru.chr4.2356' => 'acertr', 'Atru.chr4.2358' => 'acertr', 'Atru.chr4.2359' => 'acertr', 'Atru.chr4.2360' => 'acertr', 'Atru.chr4.2361' => 'acertr', 'AUR62030476' => 'cqu', 'AUR62030478' => 'cqu', 'AUR62030819' => 'cqu', 'AUR62030820' => 'cqu', 'BcaB03g14648' => 'bca', 'BcaB04g20492' => 'bca', 'BcaB06g26399' => 'bca', 'BcaC01g03416' => 'bca', 'BcaC01g03419' => 'bca', 'BcaC01g03421' => 'bca', 'BcaC01g03424' => 'bca', 'BcaC05g28012' => 'bca', 'BcaC09g49212' => 'bca', 'BcaC09g50140' => 'bca', 'BcaNung00346' => 'bca', 'BolC1t02785H' => 'bol', 'BolC1t04095H' => 'bol', 'BolC3t17545H' => 'bol', 'BolC5t32769H' => 'bol', 'BraA01t02211Z' => 'bra', 'BraA01t03359Z' => 'bra', 'BraA03t13441Z' => 'bra', 'BraA05t21476Z' => 'bra', 'C01p28420' => 'bna', 'C01p41350' => 'bna', 'C03p52750' => 'bna', 'C03p52780' => 'bna', 'C05p40270' => 'bna', 'CAN.G1437.9' => 'can', 'CANSAT78G0035' => 'cansat', 'CANSAT78G1036' => 'cansat', 'CANSAT78G2272' => 'cansat', 'CANSAT78G2478' => 'cansat', 'CARHR098700' => 'chi', 'CARHR221120' => 'chi', 'CARHR221150' => 'chi', 'Carub.0003s2297' => 'cru', 'Carub.0007s2749' => 'cru', 'Carub.0007s2750' => 'cru', 'Carub.0007s2751' => 'cru', 'Ca_10849_v3' => 'car', 'Cc03_g04300' => 'ccan', 'CDE02G3648' => 'cde', 'CDE05G0060' => 'cde', 'CDE05G0692' => 'cde', 'CDE05G2285' => 'cde', 'CDE05G2884' => 'cde', 'CDE05G3072' => 'cde', 'Cfa008439' => 'cfa', 'Cfa008441' => 'cfa', 'Cfa008443' => 'cfa', 'Cfa008448' => 'cfa', 'Ciclev10005974m.g' => 'ccl', 'Ciclev10006006m.g' => 'ccl', 'Ciclev10006775m.g' => 'ccl', 'CiPaw.02G120400' => 'cil', 'CiPaw.02G120500' => 'cil', 'CiPaw.02G120600' => 'cil', 'ClCG05G004850' => 'cla', 'COL.COLO4_21566' => 'col', 'Cpa.g.sc44.124' => 'cpa', 'Cre07.g320400' => 'cre', 'Cre07.g320450' => 'cre', 'Cre08.g384650' => 'cre', 'Cre09.g393173' => 'cre', 'Cre09.g394325' => 'cre', 'Cre14.g626750' => 'cre', 'Cre16.g679250' => 'cre', 'CsaV3_3G012890' => 'csa', 'CSS0010865' => 'camsi', 'CSS0044338' => 'camsi', 'DCAR_002366' => 'dca', 'DCAR_030687' => 'dca', 'DCAR_030688' => 'dca', 'Dinv14047' => 'din', 'Dinv14048' => 'din', 'Duzib151G0105' => 'dzi', 'Duzib151G0114' => 'dzi', 'Duzib212G1029' => 'dzi', 'ECA232G3536' => 'eca', 'ECA240G0786' => 'eca', 'ECA240G1802' => 'eca', 'ECA240G3760' => 'eca', 'ECA240G3920' => 'eca', 'EL10Ac5g12536' => 'bvu', 'EL10Ac5g12537' => 'bvu', 'EL10Ac5g12538' => 'bvu', 'Eucgr.B01004' => 'egr', 'Eucgr.B01006' => 'egr', 'Eucgr.B01007' => 'egr', 'Eucgr.B01008' => 'egr', 'Eucgr.B01895' => 'egr', 'Eucgr.B01896' => 'egr', 'FAN04G1456' => 'fan', 'FAN08G1769' => 'fan', 'FAN08G2160' => 'fan', 'FAN13G2403' => 'fan', 'FAN13G3303' => 'fan', 'FAN15G2435' => 'fan', 'FAN17G0672' => 'fan', 'FAN17G2441' => 'fan', 'FAN18G1024' => 'fan', 'FAN22G1458' => 'fan', 'FAN24G0037' => 'fan', 'FAN24G0429' => 'fan', 'FAN24G2387' => 'fan', 'FAN27G2746' => 'fan', 'FvH4_2g20400' => 'fve', 'FvH4_2g20420' => 'fve', 'FvH4_2g20430' => 'fve', 'FvH4_4g01270' => 'fve', 'FvH4_4g01290' => 'fve', 'FvH4_4g01300' => 'fve', 'FvH4_4g01310' => 'fve', 'FvH4_4g01330' => 'fve', 'FvH4_5g09070' => 'fve', 'Glyma.10G243800' => 'gma', 'Glyma.20G150600' => 'gma', 'Gohir.A09G219200' => 'ghi', 'Gohir.A09G219300' => 'ghi', 'Gohir.D09G221400' => 'ghi', 'Gohir.D09G221500' => 'ghi', 'Gorai.006G242600' => 'gra', 'Gorai.006G242700' => 'gra', 'GSVIVG01018044001' => 'vvi', 'HanXRQChr03g0083821' => 'han', 'HanXRQChr03g0083841' => 'han', 'HanXRQChr03g0083881' => 'han', 'HanXRQChr03g0083901' => 'han', 'HanXRQChr03g0083921' => 'han', 'HanXRQChr03g0085331' => 'han', 'HanXRQChr03g0085361' => 'han', 'HanXRQChr03g0085411' => 'han', 'HanXRQChr03g0085421' => 'han', 'HanXRQChr03g0085431' => 'han', 'HanXRQChr08g0221991' => 'han', 'HanXRQChr11g0336061' => 'han', 'HanXRQChr11g0336411' => 'han', 'Haze_11234' => 'cav', 'Hma1.2p1_0549F.1_g177010' => 'hma', 'Hma1.2p1_0602F.1_g187630' => 'hma', 'Hund14876' => 'sun', 'Hund14879' => 'sun', 'Lalb_Chr06g0160741' => 'lal', 'Lalb_Chr21g0304781' => 'lal', 'Lj3A726G19' => 'lonja', 'Lj3A726T23' => 'lonja', 'Lj3A726T24' => 'lonja', 'Lj3A726T25' => 'lonja', 'Lj3A727T17' => 'lonja', 'Lj3C726T0' => 'lonja', 'Lj3C726T2' => 'lonja', 'Lj3P725T35' => 'lonja', 'Lj3P727T10' => 'lonja', 'Lj3P727T12' => 'lonja', 'Lj3P727T14' => 'lonja', 'Lj5g0023109' => 'lja', 'Lj6P646T44' => 'lonja', 'Lsat_1_v5_gn_6_75760' => 'lsa', 'Lsat_1_v5_gn_6_75800' => 'lsa', 'Lsat_1_v5_gn_6_75900' => 'lsa', 'Lsat_1_v5_gn_6_76240' => 'lsa', 'Lsat_1_v5_gn_6_76441' => 'lsa', 'Lsat_1_v5_gn_6_76700' => 'lsa', 'Lsat_1_v5_gn_6_76760' => 'lsa', 'Manes.15G033100' => 'mes', 'Mapoly0004s0074' => 'mpo', 'Mapoly0004s0075' => 'mpo', 'Mapoly0004s0163' => 'mpo', 'Mapoly0004s0164' => 'mpo', 'Mapoly0021s0018' => 'mpo', 'Mapoly0041s0136' => 'mpo', 'Mapoly0041s0137' => 'mpo', 'Mapoly0041s0138' => 'mpo', 'Mapoly0041s0139' => 'mpo', 'Mapoly0041s0141' => 'mpo', 'Mapoly0041s0142' => 'mpo', 'Mapoly0041s0143' => 'mpo', 'Mapoly0041s0144' => 'mpo', 'Mapoly0041s0145' => 'mpo', 'Mapoly0047s0106' => 'mpo', 'Mapoly0047s0108' => 'mpo', 'Mapoly0050s0051' => 'mpo', 'Mapoly0050s0052' => 'mpo', 'Mapoly0050s0053' => 'mpo', 'Mapoly0058s0013' => 'mpo', 'Mapoly0091s0078' => 'mpo', 'Mapoly0091s0079' => 'mpo', 'Mapoly0091s0080' => 'mpo', 'Mapoly0091s0081' => 'mpo', 'Mapoly0278s0004' => 'mpo', 'Mapoly0278s0005' => 'mpo', 'Mapoly0278s0006' => 'mpo', 'MBI11_g30648_MAGBIO' => 'mbi', 'MCO03G194' => 'mco', 'MCO03G590' => 'mco', 'MCO07G312' => 'mco', 'MCO10G318' => 'mco', 'MCO12G244' => 'mco', 'MCO13G148' => 'mco', 'MCO13G194' => 'mco', 'MCO16G238' => 'mco', 'MD06G1134100' => 'mdo', 'MD13G1200100' => 'mdo', 'MD13G1200300' => 'mdo', 'MD13G1200600' => 'mdo', 'MD14G1150400' => 'mdo', 'MD16G1200000' => 'mdo', 'Medtr1g102570' => 'mtr', 'Medtr1g102780' => 'mtr', 'Medtr1g102800' => 'mtr', 'Medtr1g102810' => 'mtr', 'Medtr1g102830' => 'mtr', 'MELO3C006499.2' => 'cme', 'Migut.G00385' => 'egut', 'MSTRG.4063' => 'ama', 'Nitab4.5_0000090g0260' => 'nta', 'Nitab4.5_0000977g0030' => 'nta', 'Nitab4.5_0002541g0040' => 'nta', 'Nitab4.5_0007068g0040' => 'nta', 'Nn005s41408' => 'nnu', 'Nn005s41410' => 'nnu', 'Oeu010310.1' => 'oeu', 'Oeu010311.1' => 'oeu', 'Oeu043472.1' => 'oeu', 'Os01g0246400' => 'osa', 'Os04g0267950' => 'osa', 'Os07g0178700' => 'osa', 'Os07g0178800' => 'osa', 'Peaxi162Scf00316g00046' => 'pax', 'Peaxi162Scf00316g00049' => 'pax', 'Peaxi162Scf00316g00059' => 'pax', 'Peaxi162Scf00316g00328' => 'pax', 'Peaxi162Scf00316g00329' => 'pax', 'Peaxi162Scf00316g00411' => 'pax', 'Peaxi162Scf00316g00521' => 'pax', 'Peaxi162Scf00492g00068' => 'pax', 'Peaxi162Scf35631g00002' => 'pax', 'PGR142G3720' => 'pgr', 'PGSC0003DMG400006442' => 'stu', 'Phvul.007G062000' => 'pvu', 'Potri.008G157750' => 'ptr', 'Potri.008G157900' => 'ptr', 'Potri.008G158000' => 'ptr', 'Potri.008G158200' => 'ptr', 'Pp3c11_7280' => 'ppa', 'Pp3c11_7980' => 'ppa', 'Pp3c12_19450' => 'ppa', 'Pp3c14_1480' => 'ppa', 'Pp3c14_1501' => 'ppa', 'Pp3c16_4900' => 'ppa', 'Pp3c16_5010' => 'ppa', 'Pp3c16_5060' => 'ppa', 'Pp3c19_18250' => 'ppa', 'Pp3c23_8530' => 'ppa', 'Pp3c23_8550' => 'ppa', 'Pp3c24_9670' => 'ppa', 'Pp3c2_21390' => 'ppa', 'Pp3c2_31380' => 'ppa', 'Pp3c3_16620' => 'ppa', 'Pp3c3_8090' => 'ppa', 'Pp3c3_8110' => 'ppa', 'Pp3c3_8130' => 'ppa', 'Pp3c3_8150' => 'ppa', 'Pp3c4_14320' => 'ppa', 'Pp3c6_2560' => 'ppa', 'Pp3c9_16700' => 'ppa', 'PRCOL_00000234' => 'pco', 'PRCOL_00000235' => 'pco', 'PRCOL_00000777' => 'pco', 'PRCOL_00002344' => 'pco', 'PRCOL_00002372' => 'pco', 'PRCOL_00006120' => 'pco', 'Prupe.1G021400' => 'ppe', 'Prupe.1G021500' => 'ppe', 'Prupe.1G021600' => 'ppe', 'Prupe.1G021700' => 'ppe', 'Prupe.1G021800' => 'ppe', 'Prupe.5G145100' => 'ppe', 'Psat6g204040' => 'psa', 'Psat6g204800' => 'psa', 'Psat6g204920' => 'psa', 'Psat6g204960' => 'psa', 'Psat6g205080' => 'psa', 'PSO017G0271' => 'pso', 'PSO017G1276' => 'pso', 'PSO017G1429' => 'pso', 'PSO017G1861' => 'pso', 'PSO017G2787' => 'pso', 'PSO017G4466' => 'pso', 'PSO017G5118' => 'pso', 'PSO017G5420' => 'pso', 'PSO063G3678' => 'pso', 'PSO210G0546' => 'pso', 'PSO317G0001' => 'pso', 'PSO357G0512' => 'pso', 'PSO478G2682' => 'pso', 'PSO647G0001' => 'pso', 'PSO675G0001' => 'pso', 'PSO675G2699' => 'pso', 'PSO675G2849' => 'pso', 'PSO675G4991' => 'pso', 'PSO689G0001' => 'pso', 'QL06p000916' => 'qlo', 'QL06p000921' => 'qlo', 'QL06p001398' => 'qlo', 'QL06p001407' => 'qlo', 'QL06p002031' => 'qlo', 'RcHm_v2.0_Chr4g0387791' => 'rch', 'RcHm_v2.0_Chr4g0387801' => 'rch', 'RcHm_v2.0_Chr6g0286501' => 'rch', 'RcHm_v2.0_Chr6g0286511' => 'rch', 'RcHm_v2.0_Chr6g0286521' => 'rch', 'RcHm_v2.0_Chr6g0286531' => 'rch', 'RcHm_v2.0_Chr7g0189141' => 'rch', 'Rhsim02G0028700' => 'rsi', 'Rhsim02G0028800' => 'rsi', 'Rhsim02G0028900' => 'rsi', 'Rhsim02G0029000' => 'rsi', 'Rhsim02G0029100' => 'rsi', 'Rhsim02G0029200' => 'rsi', 'Rhsim02G0029300' => 'rsi', 'Rhsim02G0029400' => 'rsi', 'Rhsim02G0029500' => 'rsi', 'Rhsim02G0029600' => 'rsi', 'RhsimUnG0024000' => 'rsi', 'RhsimUnG0024100' => 'rsi', 'RhsimUnG0024200' => 'rsi', 'RhsimUnG0024300' => 'rsi', 'RhsimUnG0024400' => 'rsi', 'RhsimUnG0024500' => 'rsi', 'RhsimUnG0024700' => 'rsi', 'RhsimUnG0024800' => 'rsi', 'RhsimUnG0024900' => 'rsi', 'RhsimUnG0025100' => 'rsi', 'Sabra08G0120200' => 'sbr', 'Sabra08G0120300' => 'sbr', 'Sabra08G0120500' => 'sbr', 'Sabra08G0120600' => 'sbr', 'Sabra10G0158900' => 'sbr', 'SalBow2G3492' => 'sbo', 'Sc13g0004760' => 'sci', 'Sc13g0004770' => 'sci', 'Sed0003417' => 'sed', 'Sed0019750' => 'sed', 'SEGI_03419' => 'sgi', 'SEGI_05907' => 'sgi', 'SEGI_10682' => 'sgi', 'SEGI_13528' => 'sgi', 'SEGI_16081' => 'sgi', 'SEGI_19370' => 'sgi', 'SEGI_21015' => 'sgi', 'SEGI_21944' => 'sgi', 'SEGI_32906' => 'sgi', 'SEGI_33093' => 'sgi', 'SEGI_36110' => 'sgi', 'SEGI_40397' => 'sgi', 'SGA_v2.0_scaffold191G40426' => 'sas', 'SGA_v2.0_scaffold353G49717' => 'sas', 'SGA_v2.0_scaffold50G18550' => 'sas', 'SMO119G0173' => 'smo', 'SMO172G0002' => 'smo', 'Solyc09g082690.3' => 'sly', 'Solyc09g082700.2' => 'sly', 'Sopen09g031550' => 'spe', 'Sopen09g031560' => 'spe', 'Sp3g20540' => 'spa', 'Sp7g07580' => 'spa', 'TAR134G0002' => 'tar', 'TAR236G0001' => 'tar', 'TAR365G0892' => 'tar', 'TAR636G0166' => 'tar', 'TAR636G0646' => 'tar', 'TAR636G0869' => 'tar', 'TAR636G1317' => 'tar', 'TAR636G1744' => 'tar', 'TAR636G3358' => 'tar', 'TAR636G3436' => 'tar', 'THA.LOC104803047' => 'tha', 'Thecc.04G238900' => 'tca', 'Thhalv10021557m.g' => 'esa', 'Thhalv10026318m.g' => 'esa', 'Thhalv10026335m.g' => 'esa', 'TPR.G17433' => 'tpr', 'TPR.G18915' => 'tpr', 'TPR.G26125' => 'tpr', 'TWI09G0677' => 'twi', 'TWI73G0287' => 'twi', 'unitig_748.g8326' => 'ugi', 'vmacro15370' => 'vma', 'vmacro15371' => 'vma', 'vmacro15372' => 'vma', 'vmacro15373' => 'vma', 'vmacro15374' => 'vma', 'VMungo0720G2826' => 'vmu', 'Zm00001eb116960' => 'zma', 'Zm00001eb301260' => 'zma', 'Zm00001eb301270' => 'zma' ), 'gf_id' => 'HOM05D001460', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001460' ), 'data_identifier' => 'HOM05D001460', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001460', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '433', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p22980' => 'bna', 'A01p32340' => 'bna', 'A03p42970' => 'bna', 'A05p25880' => 'bna', 'Aa31LG8G9320' => 'aar', 'Aa31LG8G9330' => 'aar', 'Aa31LG8G9340' => 'aar', 'Aa31sc221G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1034' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1528' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.829' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2222' => 'aag', 'Ah.12g058830' => 'amhyb', 'Ah.12g058840' => 'amhyb', 'AL3G37160' => 'aly', 'AL7G41310' => 'aly', 'Aqoxy5G00395' => 'aox', 'Aqoxy5G00396' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0C8NZA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5185HY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JZ1PRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MD3LS0' => 'arhy', 'AT3G22840' => 'ath', 'AT4G14690' => 'ath', 'ATR0665G054' => 'atr', 'Atru.chr4.2344' => 'acertr', 'Atru.chr4.2346' => 'acertr', 'Atru.chr4.2347' => 'acertr', 'Atru.chr4.2348' => 'acertr', 'Atru.chr4.2355' => 'acertr', 'Atru.chr4.2356' => 'acertr', 'Atru.chr4.2358' => 'acertr', 'Atru.chr4.2359' => 'acertr', 'Atru.chr4.2360' => 'acertr', 'Atru.chr4.2361' => 'acertr', 'AUR62030476' => 'cqu', 'AUR62030478' => 'cqu', 'AUR62030819' => 'cqu', 'AUR62030820' => 'cqu', 'BcaB03g14648' => 'bca', 'BcaB04g20492' => 'bca', 'BcaB06g26399' => 'bca', 'BcaC01g03416' => 'bca', 'BcaC01g03419' => 'bca', 'BcaC01g03421' => 'bca', 'BcaC01g03424' => 'bca', 'BcaC05g28012' => 'bca', 'BcaC09g49212' => 'bca', 'BcaC09g50140' => 'bca', 'BcaNung00346' => 'bca', 'BolC1t02785H' => 'bol', 'BolC1t04095H' => 'bol', 'BolC3t17545H' => 'bol', 'BolC5t32769H' => 'bol', 'BraA01t02211Z' => 'bra', 'BraA01t03359Z' => 'bra', 'BraA03t13441Z' => 'bra', 'BraA05t21476Z' => 'bra', 'C01p28420' => 'bna', 'C01p41350' => 'bna', 'C03p52750' => 'bna', 'C03p52780' => 'bna', 'C05p40270' => 'bna', 'CAN.G1437.9' => 'can', 'CANSAT78G0035' => 'cansat', 'CANSAT78G1036' => 'cansat', 'CANSAT78G2272' => 'cansat', 'CANSAT78G2478' => 'cansat', 'CARHR098700' => 'chi', 'CARHR221120' => 'chi', 'CARHR221150' => 'chi', 'Carub.0003s2297' => 'cru', 'Carub.0007s2749' => 'cru', 'Carub.0007s2750' => 'cru', 'Carub.0007s2751' => 'cru', 'Ca_10849_v3' => 'car', 'Cc03_g04300' => 'ccan', 'CDE02G3648' => 'cde', 'CDE05G0060' => 'cde', 'CDE05G0692' => 'cde', 'CDE05G2285' => 'cde', 'CDE05G2884' => 'cde', 'CDE05G3072' => 'cde', 'Cfa008439' => 'cfa', 'Cfa008441' => 'cfa', 'Cfa008443' => 'cfa', 'Cfa008448' => 'cfa', 'Ciclev10005974m.g' => 'ccl', 'Ciclev10006006m.g' => 'ccl', 'Ciclev10006775m.g' => 'ccl', 'CiPaw.02G120400' => 'cil', 'CiPaw.02G120500' => 'cil', 'CiPaw.02G120600' => 'cil', 'ClCG05G004850' => 'cla', 'COL.COLO4_21566' => 'col', 'Cpa.g.sc44.124' => 'cpa', 'Cre07.g320400' => 'cre', 'Cre07.g320450' => 'cre', 'Cre08.g384650' => 'cre', 'Cre09.g393173' => 'cre', 'Cre09.g394325' => 'cre', 'Cre14.g626750' => 'cre', 'Cre16.g679250' => 'cre', 'CsaV3_3G012890' => 'csa', 'CSS0010865' => 'camsi', 'CSS0044338' => 'camsi', 'DCAR_002366' => 'dca', 'DCAR_030687' => 'dca', 'DCAR_030688' => 'dca', 'Dinv14047' => 'din', 'Dinv14048' => 'din', 'Duzib151G0105' => 'dzi', 'Duzib151G0114' => 'dzi', 'Duzib212G1029' => 'dzi', 'ECA232G3536' => 'eca', 'ECA240G0786' => 'eca', 'ECA240G1802' => 'eca', 'ECA240G3760' => 'eca', 'ECA240G3920' => 'eca', 'EL10Ac5g12536' => 'bvu', 'EL10Ac5g12537' => 'bvu', 'EL10Ac5g12538' => 'bvu', 'Eucgr.B01004' => 'egr', 'Eucgr.B01006' => 'egr', 'Eucgr.B01007' => 'egr', 'Eucgr.B01008' => 'egr', 'Eucgr.B01895' => 'egr', 'Eucgr.B01896' => 'egr', 'FAN04G1456' => 'fan', 'FAN08G1769' => 'fan', 'FAN08G2160' => 'fan', 'FAN13G2403' => 'fan', 'FAN13G3303' => 'fan', 'FAN15G2435' => 'fan', 'FAN17G0672' => 'fan', 'FAN17G2441' => 'fan', 'FAN18G1024' => 'fan', 'FAN22G1458' => 'fan', 'FAN24G0037' => 'fan', 'FAN24G0429' => 'fan', 'FAN24G2387' => 'fan', 'FAN27G2746' => 'fan', 'FvH4_2g20400' => 'fve', 'FvH4_2g20420' => 'fve', 'FvH4_2g20430' => 'fve', 'FvH4_4g01270' => 'fve', 'FvH4_4g01290' => 'fve', 'FvH4_4g01300' => 'fve', 'FvH4_4g01310' => 'fve', 'FvH4_4g01330' => 'fve', 'FvH4_5g09070' => 'fve', 'Glyma.10G243800' => 'gma', 'Glyma.20G150600' => 'gma', 'Gohir.A09G219200' => 'ghi', 'Gohir.A09G219300' => 'ghi', 'Gohir.D09G221400' => 'ghi', 'Gohir.D09G221500' => 'ghi', 'Gorai.006G242600' => 'gra', 'Gorai.006G242700' => 'gra', 'GSVIVG01018044001' => 'vvi', 'HanXRQChr03g0083821' => 'han', 'HanXRQChr03g0083841' => 'han', 'HanXRQChr03g0083881' => 'han', 'HanXRQChr03g0083901' => 'han', 'HanXRQChr03g0083921' => 'han', 'HanXRQChr03g0085331' => 'han', 'HanXRQChr03g0085361' => 'han', 'HanXRQChr03g0085411' => 'han', 'HanXRQChr03g0085421' => 'han', 'HanXRQChr03g0085431' => 'han', 'HanXRQChr08g0221991' => 'han', 'HanXRQChr11g0336061' => 'han', 'HanXRQChr11g0336411' => 'han', 'Haze_11234' => 'cav', 'Hma1.2p1_0549F.1_g177010' => 'hma', 'Hma1.2p1_0602F.1_g187630' => 'hma', 'Hund14876' => 'sun', 'Hund14879' => 'sun', 'Lalb_Chr06g0160741' => 'lal', 'Lalb_Chr21g0304781' => 'lal', 'Lj3A726G19' => 'lonja', 'Lj3A726T23' => 'lonja', 'Lj3A726T24' => 'lonja', 'Lj3A726T25' => 'lonja', 'Lj3A727T17' => 'lonja', 'Lj3C726T0' => 'lonja', 'Lj3C726T2' => 'lonja', 'Lj3P725T35' => 'lonja', 'Lj3P727T10' => 'lonja', 'Lj3P727T12' => 'lonja', 'Lj3P727T14' => 'lonja', 'Lj5g0023109' => 'lja', 'Lj6P646T44' => 'lonja', 'Lsat_1_v5_gn_6_75760' => 'lsa', 'Lsat_1_v5_gn_6_75800' => 'lsa', 'Lsat_1_v5_gn_6_75900' => 'lsa', 'Lsat_1_v5_gn_6_76240' => 'lsa', 'Lsat_1_v5_gn_6_76441' => 'lsa', 'Lsat_1_v5_gn_6_76700' => 'lsa', 'Lsat_1_v5_gn_6_76760' => 'lsa', 'Manes.15G033100' => 'mes', 'Mapoly0004s0074' => 'mpo', 'Mapoly0004s0075' => 'mpo', 'Mapoly0004s0163' => 'mpo', 'Mapoly0004s0164' => 'mpo', 'Mapoly0021s0018' => 'mpo', 'Mapoly0041s0136' => 'mpo', 'Mapoly0041s0137' => 'mpo', 'Mapoly0041s0138' => 'mpo', 'Mapoly0041s0139' => 'mpo', 'Mapoly0041s0141' => 'mpo', 'Mapoly0041s0142' => 'mpo', 'Mapoly0041s0143' => 'mpo', 'Mapoly0041s0144' => 'mpo', 'Mapoly0041s0145' => 'mpo', 'Mapoly0047s0106' => 'mpo', 'Mapoly0047s0108' => 'mpo', 'Mapoly0050s0051' => 'mpo', 'Mapoly0050s0052' => 'mpo', 'Mapoly0050s0053' => 'mpo', 'Mapoly0058s0013' => 'mpo', 'Mapoly0091s0078' => 'mpo', 'Mapoly0091s0079' => 'mpo', 'Mapoly0091s0080' => 'mpo', 'Mapoly0091s0081' => 'mpo', 'Mapoly0278s0004' => 'mpo', 'Mapoly0278s0005' => 'mpo', 'Mapoly0278s0006' => 'mpo', 'MBI11_g30648_MAGBIO' => 'mbi', 'MCO03G194' => 'mco', 'MCO03G590' => 'mco', 'MCO07G312' => 'mco', 'MCO10G318' => 'mco', 'MCO12G244' => 'mco', 'MCO13G148' => 'mco', 'MCO13G194' => 'mco', 'MCO16G238' => 'mco', 'MD06G1134100' => 'mdo', 'MD13G1200100' => 'mdo', 'MD13G1200300' => 'mdo', 'MD13G1200600' => 'mdo', 'MD14G1150400' => 'mdo', 'MD16G1200000' => 'mdo', 'Medtr1g102570' => 'mtr', 'Medtr1g102780' => 'mtr', 'Medtr1g102800' => 'mtr', 'Medtr1g102810' => 'mtr', 'Medtr1g102830' => 'mtr', 'MELO3C006499.2' => 'cme', 'Migut.G00385' => 'egut', 'MSTRG.4063' => 'ama', 'Nitab4.5_0000090g0260' => 'nta', 'Nitab4.5_0000977g0030' => 'nta', 'Nitab4.5_0002541g0040' => 'nta', 'Nitab4.5_0007068g0040' => 'nta', 'Nn005s41408' => 'nnu', 'Nn005s41410' => 'nnu', 'Oeu010310.1' => 'oeu', 'Oeu010311.1' => 'oeu', 'Oeu043472.1' => 'oeu', 'Os01g0246400' => 'osa', 'Os04g0267950' => 'osa', 'Os07g0178700' => 'osa', 'Os07g0178800' => 'osa', 'Peaxi162Scf00316g00046' => 'pax', 'Peaxi162Scf00316g00049' => 'pax', 'Peaxi162Scf00316g00059' => 'pax', 'Peaxi162Scf00316g00328' => 'pax', 'Peaxi162Scf00316g00329' => 'pax', 'Peaxi162Scf00316g00411' => 'pax', 'Peaxi162Scf00316g00521' => 'pax', 'Peaxi162Scf00492g00068' => 'pax', 'Peaxi162Scf35631g00002' => 'pax', 'PGR142G3720' => 'pgr', 'PGSC0003DMG400006442' => 'stu', 'Phvul.007G062000' => 'pvu', 'Potri.008G157750' => 'ptr', 'Potri.008G157900' => 'ptr', 'Potri.008G158000' => 'ptr', 'Potri.008G158200' => 'ptr', 'Pp3c11_7280' => 'ppa', 'Pp3c11_7980' => 'ppa', 'Pp3c12_19450' => 'ppa', 'Pp3c14_1480' => 'ppa', 'Pp3c14_1501' => 'ppa', 'Pp3c16_4900' => 'ppa', 'Pp3c16_5010' => 'ppa', 'Pp3c16_5060' => 'ppa', 'Pp3c19_18250' => 'ppa', 'Pp3c23_8530' => 'ppa', 'Pp3c23_8550' => 'ppa', 'Pp3c24_9670' => 'ppa', 'Pp3c2_21390' => 'ppa', 'Pp3c2_31380' => 'ppa', 'Pp3c3_16620' => 'ppa', 'Pp3c3_8090' => 'ppa', 'Pp3c3_8110' => 'ppa', 'Pp3c3_8130' => 'ppa', 'Pp3c3_8150' => 'ppa', 'Pp3c4_14320' => 'ppa', 'Pp3c6_2560' => 'ppa', 'Pp3c9_16700' => 'ppa', 'PRCOL_00000234' => 'pco', 'PRCOL_00000235' => 'pco', 'PRCOL_00000777' => 'pco', 'PRCOL_00002344' => 'pco', 'PRCOL_00002372' => 'pco', 'PRCOL_00006120' => 'pco', 'Prupe.1G021400' => 'ppe', 'Prupe.1G021500' => 'ppe', 'Prupe.1G021600' => 'ppe', 'Prupe.1G021700' => 'ppe', 'Prupe.1G021800' => 'ppe', 'Prupe.5G145100' => 'ppe', 'Psat6g204040' => 'psa', 'Psat6g204800' => 'psa', 'Psat6g204920' => 'psa', 'Psat6g204960' => 'psa', 'Psat6g205080' => 'psa', 'PSO017G0271' => 'pso', 'PSO017G1276' => 'pso', 'PSO017G1429' => 'pso', 'PSO017G1861' => 'pso', 'PSO017G2787' => 'pso', 'PSO017G4466' => 'pso', 'PSO017G5118' => 'pso', 'PSO017G5420' => 'pso', 'PSO063G3678' => 'pso', 'PSO210G0546' => 'pso', 'PSO317G0001' => 'pso', 'PSO357G0512' => 'pso', 'PSO478G2682' => 'pso', 'PSO647G0001' => 'pso', 'PSO675G0001' => 'pso', 'PSO675G2699' => 'pso', 'PSO675G2849' => 'pso', 'PSO675G4991' => 'pso', 'PSO689G0001' => 'pso', 'QL06p000916' => 'qlo', 'QL06p000921' => 'qlo', 'QL06p001398' => 'qlo', 'QL06p001407' => 'qlo', 'QL06p002031' => 'qlo', 'RcHm_v2.0_Chr4g0387791' => 'rch', 'RcHm_v2.0_Chr4g0387801' => 'rch', 'RcHm_v2.0_Chr6g0286501' => 'rch', 'RcHm_v2.0_Chr6g0286511' => 'rch', 'RcHm_v2.0_Chr6g0286521' => 'rch', 'RcHm_v2.0_Chr6g0286531' => 'rch', 'RcHm_v2.0_Chr7g0189141' => 'rch', 'Rhsim02G0028700' => 'rsi', 'Rhsim02G0028800' => 'rsi', 'Rhsim02G0028900' => 'rsi', 'Rhsim02G0029000' => 'rsi', 'Rhsim02G0029100' => 'rsi', 'Rhsim02G0029200' => 'rsi', 'Rhsim02G0029300' => 'rsi', 'Rhsim02G0029400' => 'rsi', 'Rhsim02G0029500' => 'rsi', 'Rhsim02G0029600' => 'rsi', 'RhsimUnG0024000' => 'rsi', 'RhsimUnG0024100' => 'rsi', 'RhsimUnG0024200' => 'rsi', 'RhsimUnG0024300' => 'rsi', 'RhsimUnG0024400' => 'rsi', 'RhsimUnG0024500' => 'rsi', 'RhsimUnG0024700' => 'rsi', 'RhsimUnG0024800' => 'rsi', 'RhsimUnG0024900' => 'rsi', 'RhsimUnG0025100' => 'rsi', 'Sabra08G0120200' => 'sbr', 'Sabra08G0120300' => 'sbr', 'Sabra08G0120500' => 'sbr', 'Sabra08G0120600' => 'sbr', 'Sabra10G0158900' => 'sbr', 'SalBow2G3492' => 'sbo', 'Sc13g0004760' => 'sci', 'Sc13g0004770' => 'sci', 'Sed0003417' => 'sed', 'Sed0019750' => 'sed', 'SEGI_03419' => 'sgi', 'SEGI_05907' => 'sgi', 'SEGI_10682' => 'sgi', 'SEGI_13528' => 'sgi', 'SEGI_16081' => 'sgi', 'SEGI_19370' => 'sgi', 'SEGI_21015' => 'sgi', 'SEGI_21944' => 'sgi', 'SEGI_32906' => 'sgi', 'SEGI_33093' => 'sgi', 'SEGI_36110' => 'sgi', 'SEGI_40397' => 'sgi', 'SGA_v2.0_scaffold191G40426' => 'sas', 'SGA_v2.0_scaffold353G49717' => 'sas', 'SGA_v2.0_scaffold50G18550' => 'sas', 'SMO119G0173' => 'smo', 'SMO172G0002' => 'smo', 'Solyc09g082690.3' => 'sly', 'Solyc09g082700.2' => 'sly', 'Sopen09g031550' => 'spe', 'Sopen09g031560' => 'spe', 'Sp3g20540' => 'spa', 'Sp7g07580' => 'spa', 'TAR134G0002' => 'tar', 'TAR236G0001' => 'tar', 'TAR365G0892' => 'tar', 'TAR636G0166' => 'tar', 'TAR636G0646' => 'tar', 'TAR636G0869' => 'tar', 'TAR636G1317' => 'tar', 'TAR636G1744' => 'tar', 'TAR636G3358' => 'tar', 'TAR636G3436' => 'tar', 'THA.LOC104803047' => 'tha', 'Thecc.04G238900' => 'tca', 'Thhalv10021557m.g' => 'esa', 'Thhalv10026318m.g' => 'esa', 'Thhalv10026335m.g' => 'esa', 'TPR.G17433' => 'tpr', 'TPR.G18915' => 'tpr', 'TPR.G26125' => 'tpr', 'TWI09G0677' => 'twi', 'TWI73G0287' => 'twi', 'unitig_748.g8326' => 'ugi', 'vmacro15370' => 'vma', 'vmacro15371' => 'vma', 'vmacro15372' => 'vma', 'vmacro15373' => 'vma', 'vmacro15374' => 'vma', 'VMungo0720G2826' => 'vmu', 'Zm00001eb116960' => 'zma', 'Zm00001eb301260' => 'zma', 'Zm00001eb301270' => 'zma' ) $gf_id = 'HOM05D001460' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001460' ) $data_identifier = 'HOM05D001460' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 4, 'aag' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 2, 'aox' => (int) 2, 'arhy' => (int) 4, 'ath' => (int) 2, 'atr' => (int) 1, 'acertr' => (int) 10, 'cqu' => (int) 4, 'bca' => (int) 11, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 1, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 1, 'ccan' => (int) 1, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 1, 'col' => (int) 1, 'cpa' => (int) 1, 'cre' => (int) 7, 'csa' => (int) 1, 'camsi' => (int) 2, 'dca' => (int) 3, 'din' => (int) 2, 'dzi' => (int) 3, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 14, 'fve' => (int) 9, 'gma' => (int) 2, 'ghi' => (int) 4, 'gra' => (int) 2, 'vvi' => (int) 1, 'han' => (int) 13, 'cav' => (int) 1, 'hma' => (int) 2, 'sun' => (int) 2, 'lal' => (int) 2, 'lonja' => (int) 12, 'lja' => (int) 1, 'lsa' => (int) 7, 'mes' => (int) 1, 'mpo' => (int) 27, 'mbi' => (int) 1, 'mco' => (int) 8, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 1, 'egut' => (int) 1, 'ama' => (int) 1, 'nta' => (int) 4, 'nnu' => (int) 2, 'oeu' => (int) 3, 'osa' => (int) 4, 'pax' => (int) 9, 'pgr' => (int) 1, 'stu' => (int) 1, 'pvu' => (int) 1, 'ptr' => (int) 4, 'ppa' => (int) 22, 'pco' => (int) 6, 'ppe' => (int) 6, 'psa' => (int) 5, 'pso' => (int) 19, 'qlo' => (int) 5, 'rch' => (int) 7, 'rsi' => (int) 20, 'sbr' => (int) 5, 'sbo' => (int) 1, 'sci' => (int) 2, 'sed' => (int) 2, 'sgi' => (int) 12, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 2, 'tar' => (int) 10, 'tha' => (int) 1, 'tca' => (int) 1, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 2, 'ugi' => (int) 1, 'vma' => (int) 5, 'vmu' => (int) 1, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb301270' $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' => 'HOM05D001460', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '433', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p22980' => 'bna', 'A01p32340' => 'bna', 'A03p42970' => 'bna', 'A05p25880' => 'bna', 'Aa31LG8G9320' => 'aar', 'Aa31LG8G9330' => 'aar', 'Aa31LG8G9340' => 'aar', 'Aa31sc221G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1034' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1528' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.829' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2222' => 'aag', 'Ah.12g058830' => 'amhyb', 'Ah.12g058840' => 'amhyb', 'AL3G37160' => 'aly', 'AL7G41310' => 'aly', 'Aqoxy5G00395' => 'aox', 'Aqoxy5G00396' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0C8NZA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5185HY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JZ1PRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MD3LS0' => 'arhy', 'AT3G22840' => 'ath', 'AT4G14690' => 'ath', 'ATR0665G054' => 'atr', 'Atru.chr4.2344' => 'acertr', 'Atru.chr4.2346' => 'acertr', 'Atru.chr4.2347' => 'acertr', 'Atru.chr4.2348' => 'acertr', 'Atru.chr4.2355' => 'acertr', 'Atru.chr4.2356' => 'acertr', 'Atru.chr4.2358' => 'acertr', 'Atru.chr4.2359' => 'acertr', 'Atru.chr4.2360' => 'acertr', 'Atru.chr4.2361' => 'acertr', 'AUR62030476' => 'cqu', 'AUR62030478' => 'cqu', 'AUR62030819' => 'cqu', 'AUR62030820' => 'cqu', 'BcaB03g14648' => 'bca', 'BcaB04g20492' => 'bca', 'BcaB06g26399' => 'bca', 'BcaC01g03416' => 'bca', 'BcaC01g03419' => 'bca', 'BcaC01g03421' => 'bca', 'BcaC01g03424' => 'bca', 'BcaC05g28012' => 'bca', 'BcaC09g49212' => 'bca', 'BcaC09g50140' => 'bca', 'BcaNung00346' => 'bca', 'BolC1t02785H' => 'bol', 'BolC1t04095H' => 'bol', 'BolC3t17545H' => 'bol', 'BolC5t32769H' => 'bol', 'BraA01t02211Z' => 'bra', 'BraA01t03359Z' => 'bra', 'BraA03t13441Z' => 'bra', 'BraA05t21476Z' => 'bra', 'C01p28420' => 'bna', 'C01p41350' => 'bna', 'C03p52750' => 'bna', 'C03p52780' => 'bna', 'C05p40270' => 'bna', 'CAN.G1437.9' => 'can', 'CANSAT78G0035' => 'cansat', 'CANSAT78G1036' => 'cansat', 'CANSAT78G2272' => 'cansat', 'CANSAT78G2478' => 'cansat', 'CARHR098700' => 'chi', 'CARHR221120' => 'chi', 'CARHR221150' => 'chi', 'Carub.0003s2297' => 'cru', 'Carub.0007s2749' => 'cru', 'Carub.0007s2750' => 'cru', 'Carub.0007s2751' => 'cru', 'Ca_10849_v3' => 'car', 'Cc03_g04300' => 'ccan', 'CDE02G3648' => 'cde', 'CDE05G0060' => 'cde', 'CDE05G0692' => 'cde', 'CDE05G2285' => 'cde', 'CDE05G2884' => 'cde', 'CDE05G3072' => 'cde', 'Cfa008439' => 'cfa', 'Cfa008441' => 'cfa', 'Cfa008443' => 'cfa', 'Cfa008448' => 'cfa', 'Ciclev10005974m.g' => 'ccl', 'Ciclev10006006m.g' => 'ccl', 'Ciclev10006775m.g' => 'ccl', 'CiPaw.02G120400' => 'cil', 'CiPaw.02G120500' => 'cil', 'CiPaw.02G120600' => 'cil', 'ClCG05G004850' => 'cla', 'COL.COLO4_21566' => 'col', 'Cpa.g.sc44.124' => 'cpa', 'Cre07.g320400' => 'cre', 'Cre07.g320450' => 'cre', 'Cre08.g384650' => 'cre', 'Cre09.g393173' => 'cre', 'Cre09.g394325' => 'cre', 'Cre14.g626750' => 'cre', 'Cre16.g679250' => 'cre', 'CsaV3_3G012890' => 'csa', 'CSS0010865' => 'camsi', 'CSS0044338' => 'camsi', 'DCAR_002366' => 'dca', 'DCAR_030687' => 'dca', 'DCAR_030688' => 'dca', 'Dinv14047' => 'din', 'Dinv14048' => 'din', 'Duzib151G0105' => 'dzi', 'Duzib151G0114' => 'dzi', 'Duzib212G1029' => 'dzi', 'ECA232G3536' => 'eca', 'ECA240G0786' => 'eca', 'ECA240G1802' => 'eca', 'ECA240G3760' => 'eca', 'ECA240G3920' => 'eca', 'EL10Ac5g12536' => 'bvu', 'EL10Ac5g12537' => 'bvu', 'EL10Ac5g12538' => 'bvu', 'Eucgr.B01004' => 'egr', 'Eucgr.B01006' => 'egr', 'Eucgr.B01007' => 'egr', 'Eucgr.B01008' => 'egr', 'Eucgr.B01895' => 'egr', 'Eucgr.B01896' => 'egr', 'FAN04G1456' => 'fan', 'FAN08G1769' => 'fan', 'FAN08G2160' => 'fan', 'FAN13G2403' => 'fan', 'FAN13G3303' => 'fan', 'FAN15G2435' => 'fan', 'FAN17G0672' => 'fan', 'FAN17G2441' => 'fan', 'FAN18G1024' => 'fan', 'FAN22G1458' => 'fan', 'FAN24G0037' => 'fan', 'FAN24G0429' => 'fan', 'FAN24G2387' => 'fan', 'FAN27G2746' => 'fan', 'FvH4_2g20400' => 'fve', 'FvH4_2g20420' => 'fve', 'FvH4_2g20430' => 'fve', 'FvH4_4g01270' => 'fve', 'FvH4_4g01290' => 'fve', 'FvH4_4g01300' => 'fve', 'FvH4_4g01310' => 'fve', 'FvH4_4g01330' => 'fve', 'FvH4_5g09070' => 'fve', 'Glyma.10G243800' => 'gma', 'Glyma.20G150600' => 'gma', 'Gohir.A09G219200' => 'ghi', 'Gohir.A09G219300' => 'ghi', 'Gohir.D09G221400' => 'ghi', 'Gohir.D09G221500' => 'ghi', 'Gorai.006G242600' => 'gra', 'Gorai.006G242700' => 'gra', 'GSVIVG01018044001' => 'vvi', 'HanXRQChr03g0083821' => 'han', 'HanXRQChr03g0083841' => 'han', 'HanXRQChr03g0083881' => 'han', 'HanXRQChr03g0083901' => 'han', 'HanXRQChr03g0083921' => 'han', 'HanXRQChr03g0085331' => 'han', 'HanXRQChr03g0085361' => 'han', 'HanXRQChr03g0085411' => 'han', 'HanXRQChr03g0085421' => 'han', 'HanXRQChr03g0085431' => 'han', 'HanXRQChr08g0221991' => 'han', 'HanXRQChr11g0336061' => 'han', 'HanXRQChr11g0336411' => 'han', 'Haze_11234' => 'cav', 'Hma1.2p1_0549F.1_g177010' => 'hma', 'Hma1.2p1_0602F.1_g187630' => 'hma', 'Hund14876' => 'sun', 'Hund14879' => 'sun', 'Lalb_Chr06g0160741' => 'lal', 'Lalb_Chr21g0304781' => 'lal', 'Lj3A726G19' => 'lonja', 'Lj3A726T23' => 'lonja', 'Lj3A726T24' => 'lonja', 'Lj3A726T25' => 'lonja', 'Lj3A727T17' => 'lonja', 'Lj3C726T0' => 'lonja', 'Lj3C726T2' => 'lonja', 'Lj3P725T35' => 'lonja', 'Lj3P727T10' => 'lonja', 'Lj3P727T12' => 'lonja', 'Lj3P727T14' => 'lonja', 'Lj5g0023109' => 'lja', 'Lj6P646T44' => 'lonja', 'Lsat_1_v5_gn_6_75760' => 'lsa', 'Lsat_1_v5_gn_6_75800' => 'lsa', 'Lsat_1_v5_gn_6_75900' => 'lsa', 'Lsat_1_v5_gn_6_76240' => 'lsa', 'Lsat_1_v5_gn_6_76441' => 'lsa', 'Lsat_1_v5_gn_6_76700' => 'lsa', 'Lsat_1_v5_gn_6_76760' => 'lsa', 'Manes.15G033100' => 'mes', 'Mapoly0004s0074' => 'mpo', 'Mapoly0004s0075' => 'mpo', 'Mapoly0004s0163' => 'mpo', 'Mapoly0004s0164' => 'mpo', 'Mapoly0021s0018' => 'mpo', 'Mapoly0041s0136' => 'mpo', 'Mapoly0041s0137' => 'mpo', 'Mapoly0041s0138' => 'mpo', 'Mapoly0041s0139' => 'mpo', 'Mapoly0041s0141' => 'mpo', 'Mapoly0041s0142' => 'mpo', 'Mapoly0041s0143' => 'mpo', 'Mapoly0041s0144' => 'mpo', 'Mapoly0041s0145' => 'mpo', 'Mapoly0047s0106' => 'mpo', 'Mapoly0047s0108' => 'mpo', 'Mapoly0050s0051' => 'mpo', 'Mapoly0050s0052' => 'mpo', 'Mapoly0050s0053' => 'mpo', 'Mapoly0058s0013' => 'mpo', 'Mapoly0091s0078' => 'mpo', 'Mapoly0091s0079' => 'mpo', 'Mapoly0091s0080' => 'mpo', 'Mapoly0091s0081' => 'mpo', 'Mapoly0278s0004' => 'mpo', 'Mapoly0278s0005' => 'mpo', 'Mapoly0278s0006' => 'mpo', 'MBI11_g30648_MAGBIO' => 'mbi', 'MCO03G194' => 'mco', 'MCO03G590' => 'mco', 'MCO07G312' => 'mco', 'MCO10G318' => 'mco', 'MCO12G244' => 'mco', 'MCO13G148' => 'mco', 'MCO13G194' => 'mco', 'MCO16G238' => 'mco', 'MD06G1134100' => 'mdo', 'MD13G1200100' => 'mdo', 'MD13G1200300' => 'mdo', 'MD13G1200600' => 'mdo', 'MD14G1150400' => 'mdo', 'MD16G1200000' => 'mdo', 'Medtr1g102570' => 'mtr', 'Medtr1g102780' => 'mtr', 'Medtr1g102800' => 'mtr', 'Medtr1g102810' => 'mtr', 'Medtr1g102830' => 'mtr', 'MELO3C006499.2' => 'cme', 'Migut.G00385' => 'egut', 'MSTRG.4063' => 'ama', 'Nitab4.5_0000090g0260' => 'nta', 'Nitab4.5_0000977g0030' => 'nta', 'Nitab4.5_0002541g0040' => 'nta', 'Nitab4.5_0007068g0040' => 'nta', 'Nn005s41408' => 'nnu', 'Nn005s41410' => 'nnu', 'Oeu010310.1' => 'oeu', 'Oeu010311.1' => 'oeu', 'Oeu043472.1' => 'oeu', 'Os01g0246400' => 'osa', 'Os04g0267950' => 'osa', 'Os07g0178700' => 'osa', 'Os07g0178800' => 'osa', 'Peaxi162Scf00316g00046' => 'pax', 'Peaxi162Scf00316g00049' => 'pax', 'Peaxi162Scf00316g00059' => 'pax', 'Peaxi162Scf00316g00328' => 'pax', 'Peaxi162Scf00316g00329' => 'pax', 'Peaxi162Scf00316g00411' => 'pax', 'Peaxi162Scf00316g00521' => 'pax', 'Peaxi162Scf00492g00068' => 'pax', 'Peaxi162Scf35631g00002' => 'pax', 'PGR142G3720' => 'pgr', 'PGSC0003DMG400006442' => 'stu', 'Phvul.007G062000' => 'pvu', 'Potri.008G157750' => 'ptr', 'Potri.008G157900' => 'ptr', 'Potri.008G158000' => 'ptr', 'Potri.008G158200' => 'ptr', 'Pp3c11_7280' => 'ppa', 'Pp3c11_7980' => 'ppa', 'Pp3c12_19450' => 'ppa', 'Pp3c14_1480' => 'ppa', 'Pp3c14_1501' => 'ppa', 'Pp3c16_4900' => 'ppa', 'Pp3c16_5010' => 'ppa', 'Pp3c16_5060' => 'ppa', 'Pp3c19_18250' => 'ppa', 'Pp3c23_8530' => 'ppa', 'Pp3c23_8550' => 'ppa', 'Pp3c24_9670' => 'ppa', 'Pp3c2_21390' => 'ppa', 'Pp3c2_31380' => 'ppa', 'Pp3c3_16620' => 'ppa', 'Pp3c3_8090' => 'ppa', 'Pp3c3_8110' => 'ppa', 'Pp3c3_8130' => 'ppa', 'Pp3c3_8150' => 'ppa', 'Pp3c4_14320' => 'ppa', 'Pp3c6_2560' => 'ppa', 'Pp3c9_16700' => 'ppa', 'PRCOL_00000234' => 'pco', 'PRCOL_00000235' => 'pco', 'PRCOL_00000777' => 'pco', 'PRCOL_00002344' => 'pco', 'PRCOL_00002372' => 'pco', 'PRCOL_00006120' => 'pco', 'Prupe.1G021400' => 'ppe', 'Prupe.1G021500' => 'ppe', 'Prupe.1G021600' => 'ppe', 'Prupe.1G021700' => 'ppe', 'Prupe.1G021800' => 'ppe', 'Prupe.5G145100' => 'ppe', 'Psat6g204040' => 'psa', 'Psat6g204800' => 'psa', 'Psat6g204920' => 'psa', 'Psat6g204960' => 'psa', 'Psat6g205080' => 'psa', 'PSO017G0271' => 'pso', 'PSO017G1276' => 'pso', 'PSO017G1429' => 'pso', 'PSO017G1861' => 'pso', 'PSO017G2787' => 'pso', 'PSO017G4466' => 'pso', 'PSO017G5118' => 'pso', 'PSO017G5420' => 'pso', 'PSO063G3678' => 'pso', 'PSO210G0546' => 'pso', 'PSO317G0001' => 'pso', 'PSO357G0512' => 'pso', 'PSO478G2682' => 'pso', 'PSO647G0001' => 'pso', 'PSO675G0001' => 'pso', 'PSO675G2699' => 'pso', 'PSO675G2849' => 'pso', 'PSO675G4991' => 'pso', 'PSO689G0001' => 'pso', 'QL06p000916' => 'qlo', 'QL06p000921' => 'qlo', 'QL06p001398' => 'qlo', 'QL06p001407' => 'qlo', 'QL06p002031' => 'qlo', 'RcHm_v2.0_Chr4g0387791' => 'rch', 'RcHm_v2.0_Chr4g0387801' => 'rch', 'RcHm_v2.0_Chr6g0286501' => 'rch', 'RcHm_v2.0_Chr6g0286511' => 'rch', 'RcHm_v2.0_Chr6g0286521' => 'rch', 'RcHm_v2.0_Chr6g0286531' => 'rch', 'RcHm_v2.0_Chr7g0189141' => 'rch', 'Rhsim02G0028700' => 'rsi', 'Rhsim02G0028800' => 'rsi', 'Rhsim02G0028900' => 'rsi', 'Rhsim02G0029000' => 'rsi', 'Rhsim02G0029100' => 'rsi', 'Rhsim02G0029200' => 'rsi', 'Rhsim02G0029300' => 'rsi', 'Rhsim02G0029400' => 'rsi', 'Rhsim02G0029500' => 'rsi', 'Rhsim02G0029600' => 'rsi', 'RhsimUnG0024000' => 'rsi', 'RhsimUnG0024100' => 'rsi', 'RhsimUnG0024200' => 'rsi', 'RhsimUnG0024300' => 'rsi', 'RhsimUnG0024400' => 'rsi', 'RhsimUnG0024500' => 'rsi', 'RhsimUnG0024700' => 'rsi', 'RhsimUnG0024800' => 'rsi', 'RhsimUnG0024900' => 'rsi', 'RhsimUnG0025100' => 'rsi', 'Sabra08G0120200' => 'sbr', 'Sabra08G0120300' => 'sbr', 'Sabra08G0120500' => 'sbr', 'Sabra08G0120600' => 'sbr', 'Sabra10G0158900' => 'sbr', 'SalBow2G3492' => 'sbo', 'Sc13g0004760' => 'sci', 'Sc13g0004770' => 'sci', 'Sed0003417' => 'sed', 'Sed0019750' => 'sed', 'SEGI_03419' => 'sgi', 'SEGI_05907' => 'sgi', 'SEGI_10682' => 'sgi', 'SEGI_13528' => 'sgi', 'SEGI_16081' => 'sgi', 'SEGI_19370' => 'sgi', 'SEGI_21015' => 'sgi', 'SEGI_21944' => 'sgi', 'SEGI_32906' => 'sgi', 'SEGI_33093' => 'sgi', 'SEGI_36110' => 'sgi', 'SEGI_40397' => 'sgi', 'SGA_v2.0_scaffold191G40426' => 'sas', 'SGA_v2.0_scaffold353G49717' => 'sas', 'SGA_v2.0_scaffold50G18550' => 'sas', 'SMO119G0173' => 'smo', 'SMO172G0002' => 'smo', 'Solyc09g082690.3' => 'sly', 'Solyc09g082700.2' => 'sly', 'Sopen09g031550' => 'spe', 'Sopen09g031560' => 'spe', 'Sp3g20540' => 'spa', 'Sp7g07580' => 'spa', 'TAR134G0002' => 'tar', 'TAR236G0001' => 'tar', 'TAR365G0892' => 'tar', 'TAR636G0166' => 'tar', 'TAR636G0646' => 'tar', 'TAR636G0869' => 'tar', 'TAR636G1317' => 'tar', 'TAR636G1744' => 'tar', 'TAR636G3358' => 'tar', 'TAR636G3436' => 'tar', 'THA.LOC104803047' => 'tha', 'Thecc.04G238900' => 'tca', 'Thhalv10021557m.g' => 'esa', 'Thhalv10026318m.g' => 'esa', 'Thhalv10026335m.g' => 'esa', 'TPR.G17433' => 'tpr', 'TPR.G18915' => 'tpr', 'TPR.G26125' => 'tpr', 'TWI09G0677' => 'twi', 'TWI73G0287' => 'twi', 'unitig_748.g8326' => 'ugi', 'vmacro15370' => 'vma', 'vmacro15371' => 'vma', 'vmacro15372' => 'vma', 'vmacro15373' => 'vma', 'vmacro15374' => 'vma', 'VMungo0720G2826' => 'vmu', 'Zm00001eb116960' => 'zma', 'Zm00001eb301260' => 'zma', 'Zm00001eb301270' => 'zma' ), 'gf_id' => 'HOM05D001460', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001460' ), 'data_identifier' => 'HOM05D001460', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001460', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '433', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p22980' => 'bna', 'A01p32340' => 'bna', 'A03p42970' => 'bna', 'A05p25880' => 'bna', 'Aa31LG8G9320' => 'aar', 'Aa31LG8G9330' => 'aar', 'Aa31LG8G9340' => 'aar', 'Aa31sc221G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1034' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1528' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.829' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2222' => 'aag', 'Ah.12g058830' => 'amhyb', 'Ah.12g058840' => 'amhyb', 'AL3G37160' => 'aly', 'AL7G41310' => 'aly', 'Aqoxy5G00395' => 'aox', 'Aqoxy5G00396' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0C8NZA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5185HY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JZ1PRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MD3LS0' => 'arhy', 'AT3G22840' => 'ath', 'AT4G14690' => 'ath', 'ATR0665G054' => 'atr', 'Atru.chr4.2344' => 'acertr', 'Atru.chr4.2346' => 'acertr', 'Atru.chr4.2347' => 'acertr', 'Atru.chr4.2348' => 'acertr', 'Atru.chr4.2355' => 'acertr', 'Atru.chr4.2356' => 'acertr', 'Atru.chr4.2358' => 'acertr', 'Atru.chr4.2359' => 'acertr', 'Atru.chr4.2360' => 'acertr', 'Atru.chr4.2361' => 'acertr', 'AUR62030476' => 'cqu', 'AUR62030478' => 'cqu', 'AUR62030819' => 'cqu', 'AUR62030820' => 'cqu', 'BcaB03g14648' => 'bca', 'BcaB04g20492' => 'bca', 'BcaB06g26399' => 'bca', 'BcaC01g03416' => 'bca', 'BcaC01g03419' => 'bca', 'BcaC01g03421' => 'bca', 'BcaC01g03424' => 'bca', 'BcaC05g28012' => 'bca', 'BcaC09g49212' => 'bca', 'BcaC09g50140' => 'bca', 'BcaNung00346' => 'bca', 'BolC1t02785H' => 'bol', 'BolC1t04095H' => 'bol', 'BolC3t17545H' => 'bol', 'BolC5t32769H' => 'bol', 'BraA01t02211Z' => 'bra', 'BraA01t03359Z' => 'bra', 'BraA03t13441Z' => 'bra', 'BraA05t21476Z' => 'bra', 'C01p28420' => 'bna', 'C01p41350' => 'bna', 'C03p52750' => 'bna', 'C03p52780' => 'bna', 'C05p40270' => 'bna', 'CAN.G1437.9' => 'can', 'CANSAT78G0035' => 'cansat', 'CANSAT78G1036' => 'cansat', 'CANSAT78G2272' => 'cansat', 'CANSAT78G2478' => 'cansat', 'CARHR098700' => 'chi', 'CARHR221120' => 'chi', 'CARHR221150' => 'chi', 'Carub.0003s2297' => 'cru', 'Carub.0007s2749' => 'cru', 'Carub.0007s2750' => 'cru', 'Carub.0007s2751' => 'cru', 'Ca_10849_v3' => 'car', 'Cc03_g04300' => 'ccan', 'CDE02G3648' => 'cde', 'CDE05G0060' => 'cde', 'CDE05G0692' => 'cde', 'CDE05G2285' => 'cde', 'CDE05G2884' => 'cde', 'CDE05G3072' => 'cde', 'Cfa008439' => 'cfa', 'Cfa008441' => 'cfa', 'Cfa008443' => 'cfa', 'Cfa008448' => 'cfa', 'Ciclev10005974m.g' => 'ccl', 'Ciclev10006006m.g' => 'ccl', 'Ciclev10006775m.g' => 'ccl', 'CiPaw.02G120400' => 'cil', 'CiPaw.02G120500' => 'cil', 'CiPaw.02G120600' => 'cil', 'ClCG05G004850' => 'cla', 'COL.COLO4_21566' => 'col', 'Cpa.g.sc44.124' => 'cpa', 'Cre07.g320400' => 'cre', 'Cre07.g320450' => 'cre', 'Cre08.g384650' => 'cre', 'Cre09.g393173' => 'cre', 'Cre09.g394325' => 'cre', 'Cre14.g626750' => 'cre', 'Cre16.g679250' => 'cre', 'CsaV3_3G012890' => 'csa', 'CSS0010865' => 'camsi', 'CSS0044338' => 'camsi', 'DCAR_002366' => 'dca', 'DCAR_030687' => 'dca', 'DCAR_030688' => 'dca', 'Dinv14047' => 'din', 'Dinv14048' => 'din', 'Duzib151G0105' => 'dzi', 'Duzib151G0114' => 'dzi', 'Duzib212G1029' => 'dzi', 'ECA232G3536' => 'eca', 'ECA240G0786' => 'eca', 'ECA240G1802' => 'eca', 'ECA240G3760' => 'eca', 'ECA240G3920' => 'eca', 'EL10Ac5g12536' => 'bvu', 'EL10Ac5g12537' => 'bvu', 'EL10Ac5g12538' => 'bvu', 'Eucgr.B01004' => 'egr', 'Eucgr.B01006' => 'egr', 'Eucgr.B01007' => 'egr', 'Eucgr.B01008' => 'egr', 'Eucgr.B01895' => 'egr', 'Eucgr.B01896' => 'egr', 'FAN04G1456' => 'fan', 'FAN08G1769' => 'fan', 'FAN08G2160' => 'fan', 'FAN13G2403' => 'fan', 'FAN13G3303' => 'fan', 'FAN15G2435' => 'fan', 'FAN17G0672' => 'fan', 'FAN17G2441' => 'fan', 'FAN18G1024' => 'fan', 'FAN22G1458' => 'fan', 'FAN24G0037' => 'fan', 'FAN24G0429' => 'fan', 'FAN24G2387' => 'fan', 'FAN27G2746' => 'fan', 'FvH4_2g20400' => 'fve', 'FvH4_2g20420' => 'fve', 'FvH4_2g20430' => 'fve', 'FvH4_4g01270' => 'fve', 'FvH4_4g01290' => 'fve', 'FvH4_4g01300' => 'fve', 'FvH4_4g01310' => 'fve', 'FvH4_4g01330' => 'fve', 'FvH4_5g09070' => 'fve', 'Glyma.10G243800' => 'gma', 'Glyma.20G150600' => 'gma', 'Gohir.A09G219200' => 'ghi', 'Gohir.A09G219300' => 'ghi', 'Gohir.D09G221400' => 'ghi', 'Gohir.D09G221500' => 'ghi', 'Gorai.006G242600' => 'gra', 'Gorai.006G242700' => 'gra', 'GSVIVG01018044001' => 'vvi', 'HanXRQChr03g0083821' => 'han', 'HanXRQChr03g0083841' => 'han', 'HanXRQChr03g0083881' => 'han', 'HanXRQChr03g0083901' => 'han', 'HanXRQChr03g0083921' => 'han', 'HanXRQChr03g0085331' => 'han', 'HanXRQChr03g0085361' => 'han', 'HanXRQChr03g0085411' => 'han', 'HanXRQChr03g0085421' => 'han', 'HanXRQChr03g0085431' => 'han', 'HanXRQChr08g0221991' => 'han', 'HanXRQChr11g0336061' => 'han', 'HanXRQChr11g0336411' => 'han', 'Haze_11234' => 'cav', 'Hma1.2p1_0549F.1_g177010' => 'hma', 'Hma1.2p1_0602F.1_g187630' => 'hma', 'Hund14876' => 'sun', 'Hund14879' => 'sun', 'Lalb_Chr06g0160741' => 'lal', 'Lalb_Chr21g0304781' => 'lal', 'Lj3A726G19' => 'lonja', 'Lj3A726T23' => 'lonja', 'Lj3A726T24' => 'lonja', 'Lj3A726T25' => 'lonja', 'Lj3A727T17' => 'lonja', 'Lj3C726T0' => 'lonja', 'Lj3C726T2' => 'lonja', 'Lj3P725T35' => 'lonja', 'Lj3P727T10' => 'lonja', 'Lj3P727T12' => 'lonja', 'Lj3P727T14' => 'lonja', 'Lj5g0023109' => 'lja', 'Lj6P646T44' => 'lonja', 'Lsat_1_v5_gn_6_75760' => 'lsa', 'Lsat_1_v5_gn_6_75800' => 'lsa', 'Lsat_1_v5_gn_6_75900' => 'lsa', 'Lsat_1_v5_gn_6_76240' => 'lsa', 'Lsat_1_v5_gn_6_76441' => 'lsa', 'Lsat_1_v5_gn_6_76700' => 'lsa', 'Lsat_1_v5_gn_6_76760' => 'lsa', 'Manes.15G033100' => 'mes', 'Mapoly0004s0074' => 'mpo', 'Mapoly0004s0075' => 'mpo', 'Mapoly0004s0163' => 'mpo', 'Mapoly0004s0164' => 'mpo', 'Mapoly0021s0018' => 'mpo', 'Mapoly0041s0136' => 'mpo', 'Mapoly0041s0137' => 'mpo', 'Mapoly0041s0138' => 'mpo', 'Mapoly0041s0139' => 'mpo', 'Mapoly0041s0141' => 'mpo', 'Mapoly0041s0142' => 'mpo', 'Mapoly0041s0143' => 'mpo', 'Mapoly0041s0144' => 'mpo', 'Mapoly0041s0145' => 'mpo', 'Mapoly0047s0106' => 'mpo', 'Mapoly0047s0108' => 'mpo', 'Mapoly0050s0051' => 'mpo', 'Mapoly0050s0052' => 'mpo', 'Mapoly0050s0053' => 'mpo', 'Mapoly0058s0013' => 'mpo', 'Mapoly0091s0078' => 'mpo', 'Mapoly0091s0079' => 'mpo', 'Mapoly0091s0080' => 'mpo', 'Mapoly0091s0081' => 'mpo', 'Mapoly0278s0004' => 'mpo', 'Mapoly0278s0005' => 'mpo', 'Mapoly0278s0006' => 'mpo', 'MBI11_g30648_MAGBIO' => 'mbi', 'MCO03G194' => 'mco', 'MCO03G590' => 'mco', 'MCO07G312' => 'mco', 'MCO10G318' => 'mco', 'MCO12G244' => 'mco', 'MCO13G148' => 'mco', 'MCO13G194' => 'mco', 'MCO16G238' => 'mco', 'MD06G1134100' => 'mdo', 'MD13G1200100' => 'mdo', 'MD13G1200300' => 'mdo', 'MD13G1200600' => 'mdo', 'MD14G1150400' => 'mdo', 'MD16G1200000' => 'mdo', 'Medtr1g102570' => 'mtr', 'Medtr1g102780' => 'mtr', 'Medtr1g102800' => 'mtr', 'Medtr1g102810' => 'mtr', 'Medtr1g102830' => 'mtr', 'MELO3C006499.2' => 'cme', 'Migut.G00385' => 'egut', 'MSTRG.4063' => 'ama', 'Nitab4.5_0000090g0260' => 'nta', 'Nitab4.5_0000977g0030' => 'nta', 'Nitab4.5_0002541g0040' => 'nta', 'Nitab4.5_0007068g0040' => 'nta', 'Nn005s41408' => 'nnu', 'Nn005s41410' => 'nnu', 'Oeu010310.1' => 'oeu', 'Oeu010311.1' => 'oeu', 'Oeu043472.1' => 'oeu', 'Os01g0246400' => 'osa', 'Os04g0267950' => 'osa', 'Os07g0178700' => 'osa', 'Os07g0178800' => 'osa', 'Peaxi162Scf00316g00046' => 'pax', 'Peaxi162Scf00316g00049' => 'pax', 'Peaxi162Scf00316g00059' => 'pax', 'Peaxi162Scf00316g00328' => 'pax', 'Peaxi162Scf00316g00329' => 'pax', 'Peaxi162Scf00316g00411' => 'pax', 'Peaxi162Scf00316g00521' => 'pax', 'Peaxi162Scf00492g00068' => 'pax', 'Peaxi162Scf35631g00002' => 'pax', 'PGR142G3720' => 'pgr', 'PGSC0003DMG400006442' => 'stu', 'Phvul.007G062000' => 'pvu', 'Potri.008G157750' => 'ptr', 'Potri.008G157900' => 'ptr', 'Potri.008G158000' => 'ptr', 'Potri.008G158200' => 'ptr', 'Pp3c11_7280' => 'ppa', 'Pp3c11_7980' => 'ppa', 'Pp3c12_19450' => 'ppa', 'Pp3c14_1480' => 'ppa', 'Pp3c14_1501' => 'ppa', 'Pp3c16_4900' => 'ppa', 'Pp3c16_5010' => 'ppa', 'Pp3c16_5060' => 'ppa', 'Pp3c19_18250' => 'ppa', 'Pp3c23_8530' => 'ppa', 'Pp3c23_8550' => 'ppa', 'Pp3c24_9670' => 'ppa', 'Pp3c2_21390' => 'ppa', 'Pp3c2_31380' => 'ppa', 'Pp3c3_16620' => 'ppa', 'Pp3c3_8090' => 'ppa', 'Pp3c3_8110' => 'ppa', 'Pp3c3_8130' => 'ppa', 'Pp3c3_8150' => 'ppa', 'Pp3c4_14320' => 'ppa', 'Pp3c6_2560' => 'ppa', 'Pp3c9_16700' => 'ppa', 'PRCOL_00000234' => 'pco', 'PRCOL_00000235' => 'pco', 'PRCOL_00000777' => 'pco', 'PRCOL_00002344' => 'pco', 'PRCOL_00002372' => 'pco', 'PRCOL_00006120' => 'pco', 'Prupe.1G021400' => 'ppe', 'Prupe.1G021500' => 'ppe', 'Prupe.1G021600' => 'ppe', 'Prupe.1G021700' => 'ppe', 'Prupe.1G021800' => 'ppe', 'Prupe.5G145100' => 'ppe', 'Psat6g204040' => 'psa', 'Psat6g204800' => 'psa', 'Psat6g204920' => 'psa', 'Psat6g204960' => 'psa', 'Psat6g205080' => 'psa', 'PSO017G0271' => 'pso', 'PSO017G1276' => 'pso', 'PSO017G1429' => 'pso', 'PSO017G1861' => 'pso', 'PSO017G2787' => 'pso', 'PSO017G4466' => 'pso', 'PSO017G5118' => 'pso', 'PSO017G5420' => 'pso', 'PSO063G3678' => 'pso', 'PSO210G0546' => 'pso', 'PSO317G0001' => 'pso', 'PSO357G0512' => 'pso', 'PSO478G2682' => 'pso', 'PSO647G0001' => 'pso', 'PSO675G0001' => 'pso', 'PSO675G2699' => 'pso', 'PSO675G2849' => 'pso', 'PSO675G4991' => 'pso', 'PSO689G0001' => 'pso', 'QL06p000916' => 'qlo', 'QL06p000921' => 'qlo', 'QL06p001398' => 'qlo', 'QL06p001407' => 'qlo', 'QL06p002031' => 'qlo', 'RcHm_v2.0_Chr4g0387791' => 'rch', 'RcHm_v2.0_Chr4g0387801' => 'rch', 'RcHm_v2.0_Chr6g0286501' => 'rch', 'RcHm_v2.0_Chr6g0286511' => 'rch', 'RcHm_v2.0_Chr6g0286521' => 'rch', 'RcHm_v2.0_Chr6g0286531' => 'rch', 'RcHm_v2.0_Chr7g0189141' => 'rch', 'Rhsim02G0028700' => 'rsi', 'Rhsim02G0028800' => 'rsi', 'Rhsim02G0028900' => 'rsi', 'Rhsim02G0029000' => 'rsi', 'Rhsim02G0029100' => 'rsi', 'Rhsim02G0029200' => 'rsi', 'Rhsim02G0029300' => 'rsi', 'Rhsim02G0029400' => 'rsi', 'Rhsim02G0029500' => 'rsi', 'Rhsim02G0029600' => 'rsi', 'RhsimUnG0024000' => 'rsi', 'RhsimUnG0024100' => 'rsi', 'RhsimUnG0024200' => 'rsi', 'RhsimUnG0024300' => 'rsi', 'RhsimUnG0024400' => 'rsi', 'RhsimUnG0024500' => 'rsi', 'RhsimUnG0024700' => 'rsi', 'RhsimUnG0024800' => 'rsi', 'RhsimUnG0024900' => 'rsi', 'RhsimUnG0025100' => 'rsi', 'Sabra08G0120200' => 'sbr', 'Sabra08G0120300' => 'sbr', 'Sabra08G0120500' => 'sbr', 'Sabra08G0120600' => 'sbr', 'Sabra10G0158900' => 'sbr', 'SalBow2G3492' => 'sbo', 'Sc13g0004760' => 'sci', 'Sc13g0004770' => 'sci', 'Sed0003417' => 'sed', 'Sed0019750' => 'sed', 'SEGI_03419' => 'sgi', 'SEGI_05907' => 'sgi', 'SEGI_10682' => 'sgi', 'SEGI_13528' => 'sgi', 'SEGI_16081' => 'sgi', 'SEGI_19370' => 'sgi', 'SEGI_21015' => 'sgi', 'SEGI_21944' => 'sgi', 'SEGI_32906' => 'sgi', 'SEGI_33093' => 'sgi', 'SEGI_36110' => 'sgi', 'SEGI_40397' => 'sgi', 'SGA_v2.0_scaffold191G40426' => 'sas', 'SGA_v2.0_scaffold353G49717' => 'sas', 'SGA_v2.0_scaffold50G18550' => 'sas', 'SMO119G0173' => 'smo', 'SMO172G0002' => 'smo', 'Solyc09g082690.3' => 'sly', 'Solyc09g082700.2' => 'sly', 'Sopen09g031550' => 'spe', 'Sopen09g031560' => 'spe', 'Sp3g20540' => 'spa', 'Sp7g07580' => 'spa', 'TAR134G0002' => 'tar', 'TAR236G0001' => 'tar', 'TAR365G0892' => 'tar', 'TAR636G0166' => 'tar', 'TAR636G0646' => 'tar', 'TAR636G0869' => 'tar', 'TAR636G1317' => 'tar', 'TAR636G1744' => 'tar', 'TAR636G3358' => 'tar', 'TAR636G3436' => 'tar', 'THA.LOC104803047' => 'tha', 'Thecc.04G238900' => 'tca', 'Thhalv10021557m.g' => 'esa', 'Thhalv10026318m.g' => 'esa', 'Thhalv10026335m.g' => 'esa', 'TPR.G17433' => 'tpr', 'TPR.G18915' => 'tpr', 'TPR.G26125' => 'tpr', 'TWI09G0677' => 'twi', 'TWI73G0287' => 'twi', 'unitig_748.g8326' => 'ugi', 'vmacro15370' => 'vma', 'vmacro15371' => 'vma', 'vmacro15372' => 'vma', 'vmacro15373' => 'vma', 'vmacro15374' => 'vma', 'VMungo0720G2826' => 'vmu', 'Zm00001eb116960' => 'zma', 'Zm00001eb301260' => 'zma', 'Zm00001eb301270' => 'zma' ) $gf_id = 'HOM05D001460' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001460' ) $data_identifier = 'HOM05D001460' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 4, 'aag' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 2, 'aox' => (int) 2, 'arhy' => (int) 4, 'ath' => (int) 2, 'atr' => (int) 1, 'acertr' => (int) 10, 'cqu' => (int) 4, 'bca' => (int) 11, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 1, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 1, 'ccan' => (int) 1, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 1, 'col' => (int) 1, 'cpa' => (int) 1, 'cre' => (int) 7, 'csa' => (int) 1, 'camsi' => (int) 2, 'dca' => (int) 3, 'din' => (int) 2, 'dzi' => (int) 3, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 14, 'fve' => (int) 9, 'gma' => (int) 2, 'ghi' => (int) 4, 'gra' => (int) 2, 'vvi' => (int) 1, 'han' => (int) 13, 'cav' => (int) 1, 'hma' => (int) 2, 'sun' => (int) 2, 'lal' => (int) 2, 'lonja' => (int) 12, 'lja' => (int) 1, 'lsa' => (int) 7, 'mes' => (int) 1, 'mpo' => (int) 27, 'mbi' => (int) 1, 'mco' => (int) 8, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 1, 'egut' => (int) 1, 'ama' => (int) 1, 'nta' => (int) 4, 'nnu' => (int) 2, 'oeu' => (int) 3, 'osa' => (int) 4, 'pax' => (int) 9, 'pgr' => (int) 1, 'stu' => (int) 1, 'pvu' => (int) 1, 'ptr' => (int) 4, 'ppa' => (int) 22, 'pco' => (int) 6, 'ppe' => (int) 6, 'psa' => (int) 5, 'pso' => (int) 19, 'qlo' => (int) 5, 'rch' => (int) 7, 'rsi' => (int) 20, 'sbr' => (int) 5, 'sbo' => (int) 1, 'sci' => (int) 2, 'sed' => (int) 2, 'sgi' => (int) 12, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 2, 'tar' => (int) 10, 'tha' => (int) 1, 'tca' => (int) 1, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 2, 'ugi' => (int) 1, 'vma' => (int) 5, 'vmu' => (int) 1, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb301270' $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' => 'HOM05D001460', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '433', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p22980' => 'bna', 'A01p32340' => 'bna', 'A03p42970' => 'bna', 'A05p25880' => 'bna', 'Aa31LG8G9320' => 'aar', 'Aa31LG8G9330' => 'aar', 'Aa31LG8G9340' => 'aar', 'Aa31sc221G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1034' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1528' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.829' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2222' => 'aag', 'Ah.12g058830' => 'amhyb', 'Ah.12g058840' => 'amhyb', 'AL3G37160' => 'aly', 'AL7G41310' => 'aly', 'Aqoxy5G00395' => 'aox', 'Aqoxy5G00396' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0C8NZA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5185HY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JZ1PRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MD3LS0' => 'arhy', 'AT3G22840' => 'ath', 'AT4G14690' => 'ath', 'ATR0665G054' => 'atr', 'Atru.chr4.2344' => 'acertr', 'Atru.chr4.2346' => 'acertr', 'Atru.chr4.2347' => 'acertr', 'Atru.chr4.2348' => 'acertr', 'Atru.chr4.2355' => 'acertr', 'Atru.chr4.2356' => 'acertr', 'Atru.chr4.2358' => 'acertr', 'Atru.chr4.2359' => 'acertr', 'Atru.chr4.2360' => 'acertr', 'Atru.chr4.2361' => 'acertr', 'AUR62030476' => 'cqu', 'AUR62030478' => 'cqu', 'AUR62030819' => 'cqu', 'AUR62030820' => 'cqu', 'BcaB03g14648' => 'bca', 'BcaB04g20492' => 'bca', 'BcaB06g26399' => 'bca', 'BcaC01g03416' => 'bca', 'BcaC01g03419' => 'bca', 'BcaC01g03421' => 'bca', 'BcaC01g03424' => 'bca', 'BcaC05g28012' => 'bca', 'BcaC09g49212' => 'bca', 'BcaC09g50140' => 'bca', 'BcaNung00346' => 'bca', 'BolC1t02785H' => 'bol', 'BolC1t04095H' => 'bol', 'BolC3t17545H' => 'bol', 'BolC5t32769H' => 'bol', 'BraA01t02211Z' => 'bra', 'BraA01t03359Z' => 'bra', 'BraA03t13441Z' => 'bra', 'BraA05t21476Z' => 'bra', 'C01p28420' => 'bna', 'C01p41350' => 'bna', 'C03p52750' => 'bna', 'C03p52780' => 'bna', 'C05p40270' => 'bna', 'CAN.G1437.9' => 'can', 'CANSAT78G0035' => 'cansat', 'CANSAT78G1036' => 'cansat', 'CANSAT78G2272' => 'cansat', 'CANSAT78G2478' => 'cansat', 'CARHR098700' => 'chi', 'CARHR221120' => 'chi', 'CARHR221150' => 'chi', 'Carub.0003s2297' => 'cru', 'Carub.0007s2749' => 'cru', 'Carub.0007s2750' => 'cru', 'Carub.0007s2751' => 'cru', 'Ca_10849_v3' => 'car', 'Cc03_g04300' => 'ccan', 'CDE02G3648' => 'cde', 'CDE05G0060' => 'cde', 'CDE05G0692' => 'cde', 'CDE05G2285' => 'cde', 'CDE05G2884' => 'cde', 'CDE05G3072' => 'cde', 'Cfa008439' => 'cfa', 'Cfa008441' => 'cfa', 'Cfa008443' => 'cfa', 'Cfa008448' => 'cfa', 'Ciclev10005974m.g' => 'ccl', 'Ciclev10006006m.g' => 'ccl', 'Ciclev10006775m.g' => 'ccl', 'CiPaw.02G120400' => 'cil', 'CiPaw.02G120500' => 'cil', 'CiPaw.02G120600' => 'cil', 'ClCG05G004850' => 'cla', 'COL.COLO4_21566' => 'col', 'Cpa.g.sc44.124' => 'cpa', 'Cre07.g320400' => 'cre', 'Cre07.g320450' => 'cre', 'Cre08.g384650' => 'cre', 'Cre09.g393173' => 'cre', 'Cre09.g394325' => 'cre', 'Cre14.g626750' => 'cre', 'Cre16.g679250' => 'cre', 'CsaV3_3G012890' => 'csa', 'CSS0010865' => 'camsi', 'CSS0044338' => 'camsi', 'DCAR_002366' => 'dca', 'DCAR_030687' => 'dca', 'DCAR_030688' => 'dca', 'Dinv14047' => 'din', 'Dinv14048' => 'din', 'Duzib151G0105' => 'dzi', 'Duzib151G0114' => 'dzi', 'Duzib212G1029' => 'dzi', 'ECA232G3536' => 'eca', 'ECA240G0786' => 'eca', 'ECA240G1802' => 'eca', 'ECA240G3760' => 'eca', 'ECA240G3920' => 'eca', 'EL10Ac5g12536' => 'bvu', 'EL10Ac5g12537' => 'bvu', 'EL10Ac5g12538' => 'bvu', 'Eucgr.B01004' => 'egr', 'Eucgr.B01006' => 'egr', 'Eucgr.B01007' => 'egr', 'Eucgr.B01008' => 'egr', 'Eucgr.B01895' => 'egr', 'Eucgr.B01896' => 'egr', 'FAN04G1456' => 'fan', 'FAN08G1769' => 'fan', 'FAN08G2160' => 'fan', 'FAN13G2403' => 'fan', 'FAN13G3303' => 'fan', 'FAN15G2435' => 'fan', 'FAN17G0672' => 'fan', 'FAN17G2441' => 'fan', 'FAN18G1024' => 'fan', 'FAN22G1458' => 'fan', 'FAN24G0037' => 'fan', 'FAN24G0429' => 'fan', 'FAN24G2387' => 'fan', 'FAN27G2746' => 'fan', 'FvH4_2g20400' => 'fve', 'FvH4_2g20420' => 'fve', 'FvH4_2g20430' => 'fve', 'FvH4_4g01270' => 'fve', 'FvH4_4g01290' => 'fve', 'FvH4_4g01300' => 'fve', 'FvH4_4g01310' => 'fve', 'FvH4_4g01330' => 'fve', 'FvH4_5g09070' => 'fve', 'Glyma.10G243800' => 'gma', 'Glyma.20G150600' => 'gma', 'Gohir.A09G219200' => 'ghi', 'Gohir.A09G219300' => 'ghi', 'Gohir.D09G221400' => 'ghi', 'Gohir.D09G221500' => 'ghi', 'Gorai.006G242600' => 'gra', 'Gorai.006G242700' => 'gra', 'GSVIVG01018044001' => 'vvi', 'HanXRQChr03g0083821' => 'han', 'HanXRQChr03g0083841' => 'han', 'HanXRQChr03g0083881' => 'han', 'HanXRQChr03g0083901' => 'han', 'HanXRQChr03g0083921' => 'han', 'HanXRQChr03g0085331' => 'han', 'HanXRQChr03g0085361' => 'han', 'HanXRQChr03g0085411' => 'han', 'HanXRQChr03g0085421' => 'han', 'HanXRQChr03g0085431' => 'han', 'HanXRQChr08g0221991' => 'han', 'HanXRQChr11g0336061' => 'han', 'HanXRQChr11g0336411' => 'han', 'Haze_11234' => 'cav', 'Hma1.2p1_0549F.1_g177010' => 'hma', 'Hma1.2p1_0602F.1_g187630' => 'hma', 'Hund14876' => 'sun', 'Hund14879' => 'sun', 'Lalb_Chr06g0160741' => 'lal', 'Lalb_Chr21g0304781' => 'lal', 'Lj3A726G19' => 'lonja', 'Lj3A726T23' => 'lonja', 'Lj3A726T24' => 'lonja', 'Lj3A726T25' => 'lonja', 'Lj3A727T17' => 'lonja', 'Lj3C726T0' => 'lonja', 'Lj3C726T2' => 'lonja', 'Lj3P725T35' => 'lonja', 'Lj3P727T10' => 'lonja', 'Lj3P727T12' => 'lonja', 'Lj3P727T14' => 'lonja', 'Lj5g0023109' => 'lja', 'Lj6P646T44' => 'lonja', 'Lsat_1_v5_gn_6_75760' => 'lsa', 'Lsat_1_v5_gn_6_75800' => 'lsa', 'Lsat_1_v5_gn_6_75900' => 'lsa', 'Lsat_1_v5_gn_6_76240' => 'lsa', 'Lsat_1_v5_gn_6_76441' => 'lsa', 'Lsat_1_v5_gn_6_76700' => 'lsa', 'Lsat_1_v5_gn_6_76760' => 'lsa', 'Manes.15G033100' => 'mes', 'Mapoly0004s0074' => 'mpo', 'Mapoly0004s0075' => 'mpo', 'Mapoly0004s0163' => 'mpo', 'Mapoly0004s0164' => 'mpo', 'Mapoly0021s0018' => 'mpo', 'Mapoly0041s0136' => 'mpo', 'Mapoly0041s0137' => 'mpo', 'Mapoly0041s0138' => 'mpo', 'Mapoly0041s0139' => 'mpo', 'Mapoly0041s0141' => 'mpo', 'Mapoly0041s0142' => 'mpo', 'Mapoly0041s0143' => 'mpo', 'Mapoly0041s0144' => 'mpo', 'Mapoly0041s0145' => 'mpo', 'Mapoly0047s0106' => 'mpo', 'Mapoly0047s0108' => 'mpo', 'Mapoly0050s0051' => 'mpo', 'Mapoly0050s0052' => 'mpo', 'Mapoly0050s0053' => 'mpo', 'Mapoly0058s0013' => 'mpo', 'Mapoly0091s0078' => 'mpo', 'Mapoly0091s0079' => 'mpo', 'Mapoly0091s0080' => 'mpo', 'Mapoly0091s0081' => 'mpo', 'Mapoly0278s0004' => 'mpo', 'Mapoly0278s0005' => 'mpo', 'Mapoly0278s0006' => 'mpo', 'MBI11_g30648_MAGBIO' => 'mbi', 'MCO03G194' => 'mco', 'MCO03G590' => 'mco', 'MCO07G312' => 'mco', 'MCO10G318' => 'mco', 'MCO12G244' => 'mco', 'MCO13G148' => 'mco', 'MCO13G194' => 'mco', 'MCO16G238' => 'mco', 'MD06G1134100' => 'mdo', 'MD13G1200100' => 'mdo', 'MD13G1200300' => 'mdo', 'MD13G1200600' => 'mdo', 'MD14G1150400' => 'mdo', 'MD16G1200000' => 'mdo', 'Medtr1g102570' => 'mtr', 'Medtr1g102780' => 'mtr', 'Medtr1g102800' => 'mtr', 'Medtr1g102810' => 'mtr', 'Medtr1g102830' => 'mtr', 'MELO3C006499.2' => 'cme', 'Migut.G00385' => 'egut', 'MSTRG.4063' => 'ama', 'Nitab4.5_0000090g0260' => 'nta', 'Nitab4.5_0000977g0030' => 'nta', 'Nitab4.5_0002541g0040' => 'nta', 'Nitab4.5_0007068g0040' => 'nta', 'Nn005s41408' => 'nnu', 'Nn005s41410' => 'nnu', 'Oeu010310.1' => 'oeu', 'Oeu010311.1' => 'oeu', 'Oeu043472.1' => 'oeu', 'Os01g0246400' => 'osa', 'Os04g0267950' => 'osa', 'Os07g0178700' => 'osa', 'Os07g0178800' => 'osa', 'Peaxi162Scf00316g00046' => 'pax', 'Peaxi162Scf00316g00049' => 'pax', 'Peaxi162Scf00316g00059' => 'pax', 'Peaxi162Scf00316g00328' => 'pax', 'Peaxi162Scf00316g00329' => 'pax', 'Peaxi162Scf00316g00411' => 'pax', 'Peaxi162Scf00316g00521' => 'pax', 'Peaxi162Scf00492g00068' => 'pax', 'Peaxi162Scf35631g00002' => 'pax', 'PGR142G3720' => 'pgr', 'PGSC0003DMG400006442' => 'stu', 'Phvul.007G062000' => 'pvu', 'Potri.008G157750' => 'ptr', 'Potri.008G157900' => 'ptr', 'Potri.008G158000' => 'ptr', 'Potri.008G158200' => 'ptr', 'Pp3c11_7280' => 'ppa', 'Pp3c11_7980' => 'ppa', 'Pp3c12_19450' => 'ppa', 'Pp3c14_1480' => 'ppa', 'Pp3c14_1501' => 'ppa', 'Pp3c16_4900' => 'ppa', 'Pp3c16_5010' => 'ppa', 'Pp3c16_5060' => 'ppa', 'Pp3c19_18250' => 'ppa', 'Pp3c23_8530' => 'ppa', 'Pp3c23_8550' => 'ppa', 'Pp3c24_9670' => 'ppa', 'Pp3c2_21390' => 'ppa', 'Pp3c2_31380' => 'ppa', 'Pp3c3_16620' => 'ppa', 'Pp3c3_8090' => 'ppa', 'Pp3c3_8110' => 'ppa', 'Pp3c3_8130' => 'ppa', 'Pp3c3_8150' => 'ppa', 'Pp3c4_14320' => 'ppa', 'Pp3c6_2560' => 'ppa', 'Pp3c9_16700' => 'ppa', 'PRCOL_00000234' => 'pco', 'PRCOL_00000235' => 'pco', 'PRCOL_00000777' => 'pco', 'PRCOL_00002344' => 'pco', 'PRCOL_00002372' => 'pco', 'PRCOL_00006120' => 'pco', 'Prupe.1G021400' => 'ppe', 'Prupe.1G021500' => 'ppe', 'Prupe.1G021600' => 'ppe', 'Prupe.1G021700' => 'ppe', 'Prupe.1G021800' => 'ppe', 'Prupe.5G145100' => 'ppe', 'Psat6g204040' => 'psa', 'Psat6g204800' => 'psa', 'Psat6g204920' => 'psa', 'Psat6g204960' => 'psa', 'Psat6g205080' => 'psa', 'PSO017G0271' => 'pso', 'PSO017G1276' => 'pso', 'PSO017G1429' => 'pso', 'PSO017G1861' => 'pso', 'PSO017G2787' => 'pso', 'PSO017G4466' => 'pso', 'PSO017G5118' => 'pso', 'PSO017G5420' => 'pso', 'PSO063G3678' => 'pso', 'PSO210G0546' => 'pso', 'PSO317G0001' => 'pso', 'PSO357G0512' => 'pso', 'PSO478G2682' => 'pso', 'PSO647G0001' => 'pso', 'PSO675G0001' => 'pso', 'PSO675G2699' => 'pso', 'PSO675G2849' => 'pso', 'PSO675G4991' => 'pso', 'PSO689G0001' => 'pso', 'QL06p000916' => 'qlo', 'QL06p000921' => 'qlo', 'QL06p001398' => 'qlo', 'QL06p001407' => 'qlo', 'QL06p002031' => 'qlo', 'RcHm_v2.0_Chr4g0387791' => 'rch', 'RcHm_v2.0_Chr4g0387801' => 'rch', 'RcHm_v2.0_Chr6g0286501' => 'rch', 'RcHm_v2.0_Chr6g0286511' => 'rch', 'RcHm_v2.0_Chr6g0286521' => 'rch', 'RcHm_v2.0_Chr6g0286531' => 'rch', 'RcHm_v2.0_Chr7g0189141' => 'rch', 'Rhsim02G0028700' => 'rsi', 'Rhsim02G0028800' => 'rsi', 'Rhsim02G0028900' => 'rsi', 'Rhsim02G0029000' => 'rsi', 'Rhsim02G0029100' => 'rsi', 'Rhsim02G0029200' => 'rsi', 'Rhsim02G0029300' => 'rsi', 'Rhsim02G0029400' => 'rsi', 'Rhsim02G0029500' => 'rsi', 'Rhsim02G0029600' => 'rsi', 'RhsimUnG0024000' => 'rsi', 'RhsimUnG0024100' => 'rsi', 'RhsimUnG0024200' => 'rsi', 'RhsimUnG0024300' => 'rsi', 'RhsimUnG0024400' => 'rsi', 'RhsimUnG0024500' => 'rsi', 'RhsimUnG0024700' => 'rsi', 'RhsimUnG0024800' => 'rsi', 'RhsimUnG0024900' => 'rsi', 'RhsimUnG0025100' => 'rsi', 'Sabra08G0120200' => 'sbr', 'Sabra08G0120300' => 'sbr', 'Sabra08G0120500' => 'sbr', 'Sabra08G0120600' => 'sbr', 'Sabra10G0158900' => 'sbr', 'SalBow2G3492' => 'sbo', 'Sc13g0004760' => 'sci', 'Sc13g0004770' => 'sci', 'Sed0003417' => 'sed', 'Sed0019750' => 'sed', 'SEGI_03419' => 'sgi', 'SEGI_05907' => 'sgi', 'SEGI_10682' => 'sgi', 'SEGI_13528' => 'sgi', 'SEGI_16081' => 'sgi', 'SEGI_19370' => 'sgi', 'SEGI_21015' => 'sgi', 'SEGI_21944' => 'sgi', 'SEGI_32906' => 'sgi', 'SEGI_33093' => 'sgi', 'SEGI_36110' => 'sgi', 'SEGI_40397' => 'sgi', 'SGA_v2.0_scaffold191G40426' => 'sas', 'SGA_v2.0_scaffold353G49717' => 'sas', 'SGA_v2.0_scaffold50G18550' => 'sas', 'SMO119G0173' => 'smo', 'SMO172G0002' => 'smo', 'Solyc09g082690.3' => 'sly', 'Solyc09g082700.2' => 'sly', 'Sopen09g031550' => 'spe', 'Sopen09g031560' => 'spe', 'Sp3g20540' => 'spa', 'Sp7g07580' => 'spa', 'TAR134G0002' => 'tar', 'TAR236G0001' => 'tar', 'TAR365G0892' => 'tar', 'TAR636G0166' => 'tar', 'TAR636G0646' => 'tar', 'TAR636G0869' => 'tar', 'TAR636G1317' => 'tar', 'TAR636G1744' => 'tar', 'TAR636G3358' => 'tar', 'TAR636G3436' => 'tar', 'THA.LOC104803047' => 'tha', 'Thecc.04G238900' => 'tca', 'Thhalv10021557m.g' => 'esa', 'Thhalv10026318m.g' => 'esa', 'Thhalv10026335m.g' => 'esa', 'TPR.G17433' => 'tpr', 'TPR.G18915' => 'tpr', 'TPR.G26125' => 'tpr', 'TWI09G0677' => 'twi', 'TWI73G0287' => 'twi', 'unitig_748.g8326' => 'ugi', 'vmacro15370' => 'vma', 'vmacro15371' => 'vma', 'vmacro15372' => 'vma', 'vmacro15373' => 'vma', 'vmacro15374' => 'vma', 'VMungo0720G2826' => 'vmu', 'Zm00001eb116960' => 'zma', 'Zm00001eb301260' => 'zma', 'Zm00001eb301270' => 'zma' ), 'gf_id' => 'HOM05D001460', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001460' ), 'data_identifier' => 'HOM05D001460', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001460', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '433', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p22980' => 'bna', 'A01p32340' => 'bna', 'A03p42970' => 'bna', 'A05p25880' => 'bna', 'Aa31LG8G9320' => 'aar', 'Aa31LG8G9330' => 'aar', 'Aa31LG8G9340' => 'aar', 'Aa31sc221G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1034' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1528' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.829' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2222' => 'aag', 'Ah.12g058830' => 'amhyb', 'Ah.12g058840' => 'amhyb', 'AL3G37160' => 'aly', 'AL7G41310' => 'aly', 'Aqoxy5G00395' => 'aox', 'Aqoxy5G00396' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0C8NZA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5185HY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JZ1PRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MD3LS0' => 'arhy', 'AT3G22840' => 'ath', 'AT4G14690' => 'ath', 'ATR0665G054' => 'atr', 'Atru.chr4.2344' => 'acertr', 'Atru.chr4.2346' => 'acertr', 'Atru.chr4.2347' => 'acertr', 'Atru.chr4.2348' => 'acertr', 'Atru.chr4.2355' => 'acertr', 'Atru.chr4.2356' => 'acertr', 'Atru.chr4.2358' => 'acertr', 'Atru.chr4.2359' => 'acertr', 'Atru.chr4.2360' => 'acertr', 'Atru.chr4.2361' => 'acertr', 'AUR62030476' => 'cqu', 'AUR62030478' => 'cqu', 'AUR62030819' => 'cqu', 'AUR62030820' => 'cqu', 'BcaB03g14648' => 'bca', 'BcaB04g20492' => 'bca', 'BcaB06g26399' => 'bca', 'BcaC01g03416' => 'bca', 'BcaC01g03419' => 'bca', 'BcaC01g03421' => 'bca', 'BcaC01g03424' => 'bca', 'BcaC05g28012' => 'bca', 'BcaC09g49212' => 'bca', 'BcaC09g50140' => 'bca', 'BcaNung00346' => 'bca', 'BolC1t02785H' => 'bol', 'BolC1t04095H' => 'bol', 'BolC3t17545H' => 'bol', 'BolC5t32769H' => 'bol', 'BraA01t02211Z' => 'bra', 'BraA01t03359Z' => 'bra', 'BraA03t13441Z' => 'bra', 'BraA05t21476Z' => 'bra', 'C01p28420' => 'bna', 'C01p41350' => 'bna', 'C03p52750' => 'bna', 'C03p52780' => 'bna', 'C05p40270' => 'bna', 'CAN.G1437.9' => 'can', 'CANSAT78G0035' => 'cansat', 'CANSAT78G1036' => 'cansat', 'CANSAT78G2272' => 'cansat', 'CANSAT78G2478' => 'cansat', 'CARHR098700' => 'chi', 'CARHR221120' => 'chi', 'CARHR221150' => 'chi', 'Carub.0003s2297' => 'cru', 'Carub.0007s2749' => 'cru', 'Carub.0007s2750' => 'cru', 'Carub.0007s2751' => 'cru', 'Ca_10849_v3' => 'car', 'Cc03_g04300' => 'ccan', 'CDE02G3648' => 'cde', 'CDE05G0060' => 'cde', 'CDE05G0692' => 'cde', 'CDE05G2285' => 'cde', 'CDE05G2884' => 'cde', 'CDE05G3072' => 'cde', 'Cfa008439' => 'cfa', 'Cfa008441' => 'cfa', 'Cfa008443' => 'cfa', 'Cfa008448' => 'cfa', 'Ciclev10005974m.g' => 'ccl', 'Ciclev10006006m.g' => 'ccl', 'Ciclev10006775m.g' => 'ccl', 'CiPaw.02G120400' => 'cil', 'CiPaw.02G120500' => 'cil', 'CiPaw.02G120600' => 'cil', 'ClCG05G004850' => 'cla', 'COL.COLO4_21566' => 'col', 'Cpa.g.sc44.124' => 'cpa', 'Cre07.g320400' => 'cre', 'Cre07.g320450' => 'cre', 'Cre08.g384650' => 'cre', 'Cre09.g393173' => 'cre', 'Cre09.g394325' => 'cre', 'Cre14.g626750' => 'cre', 'Cre16.g679250' => 'cre', 'CsaV3_3G012890' => 'csa', 'CSS0010865' => 'camsi', 'CSS0044338' => 'camsi', 'DCAR_002366' => 'dca', 'DCAR_030687' => 'dca', 'DCAR_030688' => 'dca', 'Dinv14047' => 'din', 'Dinv14048' => 'din', 'Duzib151G0105' => 'dzi', 'Duzib151G0114' => 'dzi', 'Duzib212G1029' => 'dzi', 'ECA232G3536' => 'eca', 'ECA240G0786' => 'eca', 'ECA240G1802' => 'eca', 'ECA240G3760' => 'eca', 'ECA240G3920' => 'eca', 'EL10Ac5g12536' => 'bvu', 'EL10Ac5g12537' => 'bvu', 'EL10Ac5g12538' => 'bvu', 'Eucgr.B01004' => 'egr', 'Eucgr.B01006' => 'egr', 'Eucgr.B01007' => 'egr', 'Eucgr.B01008' => 'egr', 'Eucgr.B01895' => 'egr', 'Eucgr.B01896' => 'egr', 'FAN04G1456' => 'fan', 'FAN08G1769' => 'fan', 'FAN08G2160' => 'fan', 'FAN13G2403' => 'fan', 'FAN13G3303' => 'fan', 'FAN15G2435' => 'fan', 'FAN17G0672' => 'fan', 'FAN17G2441' => 'fan', 'FAN18G1024' => 'fan', 'FAN22G1458' => 'fan', 'FAN24G0037' => 'fan', 'FAN24G0429' => 'fan', 'FAN24G2387' => 'fan', 'FAN27G2746' => 'fan', 'FvH4_2g20400' => 'fve', 'FvH4_2g20420' => 'fve', 'FvH4_2g20430' => 'fve', 'FvH4_4g01270' => 'fve', 'FvH4_4g01290' => 'fve', 'FvH4_4g01300' => 'fve', 'FvH4_4g01310' => 'fve', 'FvH4_4g01330' => 'fve', 'FvH4_5g09070' => 'fve', 'Glyma.10G243800' => 'gma', 'Glyma.20G150600' => 'gma', 'Gohir.A09G219200' => 'ghi', 'Gohir.A09G219300' => 'ghi', 'Gohir.D09G221400' => 'ghi', 'Gohir.D09G221500' => 'ghi', 'Gorai.006G242600' => 'gra', 'Gorai.006G242700' => 'gra', 'GSVIVG01018044001' => 'vvi', 'HanXRQChr03g0083821' => 'han', 'HanXRQChr03g0083841' => 'han', 'HanXRQChr03g0083881' => 'han', 'HanXRQChr03g0083901' => 'han', 'HanXRQChr03g0083921' => 'han', 'HanXRQChr03g0085331' => 'han', 'HanXRQChr03g0085361' => 'han', 'HanXRQChr03g0085411' => 'han', 'HanXRQChr03g0085421' => 'han', 'HanXRQChr03g0085431' => 'han', 'HanXRQChr08g0221991' => 'han', 'HanXRQChr11g0336061' => 'han', 'HanXRQChr11g0336411' => 'han', 'Haze_11234' => 'cav', 'Hma1.2p1_0549F.1_g177010' => 'hma', 'Hma1.2p1_0602F.1_g187630' => 'hma', 'Hund14876' => 'sun', 'Hund14879' => 'sun', 'Lalb_Chr06g0160741' => 'lal', 'Lalb_Chr21g0304781' => 'lal', 'Lj3A726G19' => 'lonja', 'Lj3A726T23' => 'lonja', 'Lj3A726T24' => 'lonja', 'Lj3A726T25' => 'lonja', 'Lj3A727T17' => 'lonja', 'Lj3C726T0' => 'lonja', 'Lj3C726T2' => 'lonja', 'Lj3P725T35' => 'lonja', 'Lj3P727T10' => 'lonja', 'Lj3P727T12' => 'lonja', 'Lj3P727T14' => 'lonja', 'Lj5g0023109' => 'lja', 'Lj6P646T44' => 'lonja', 'Lsat_1_v5_gn_6_75760' => 'lsa', 'Lsat_1_v5_gn_6_75800' => 'lsa', 'Lsat_1_v5_gn_6_75900' => 'lsa', 'Lsat_1_v5_gn_6_76240' => 'lsa', 'Lsat_1_v5_gn_6_76441' => 'lsa', 'Lsat_1_v5_gn_6_76700' => 'lsa', 'Lsat_1_v5_gn_6_76760' => 'lsa', 'Manes.15G033100' => 'mes', 'Mapoly0004s0074' => 'mpo', 'Mapoly0004s0075' => 'mpo', 'Mapoly0004s0163' => 'mpo', 'Mapoly0004s0164' => 'mpo', 'Mapoly0021s0018' => 'mpo', 'Mapoly0041s0136' => 'mpo', 'Mapoly0041s0137' => 'mpo', 'Mapoly0041s0138' => 'mpo', 'Mapoly0041s0139' => 'mpo', 'Mapoly0041s0141' => 'mpo', 'Mapoly0041s0142' => 'mpo', 'Mapoly0041s0143' => 'mpo', 'Mapoly0041s0144' => 'mpo', 'Mapoly0041s0145' => 'mpo', 'Mapoly0047s0106' => 'mpo', 'Mapoly0047s0108' => 'mpo', 'Mapoly0050s0051' => 'mpo', 'Mapoly0050s0052' => 'mpo', 'Mapoly0050s0053' => 'mpo', 'Mapoly0058s0013' => 'mpo', 'Mapoly0091s0078' => 'mpo', 'Mapoly0091s0079' => 'mpo', 'Mapoly0091s0080' => 'mpo', 'Mapoly0091s0081' => 'mpo', 'Mapoly0278s0004' => 'mpo', 'Mapoly0278s0005' => 'mpo', 'Mapoly0278s0006' => 'mpo', 'MBI11_g30648_MAGBIO' => 'mbi', 'MCO03G194' => 'mco', 'MCO03G590' => 'mco', 'MCO07G312' => 'mco', 'MCO10G318' => 'mco', 'MCO12G244' => 'mco', 'MCO13G148' => 'mco', 'MCO13G194' => 'mco', 'MCO16G238' => 'mco', 'MD06G1134100' => 'mdo', 'MD13G1200100' => 'mdo', 'MD13G1200300' => 'mdo', 'MD13G1200600' => 'mdo', 'MD14G1150400' => 'mdo', 'MD16G1200000' => 'mdo', 'Medtr1g102570' => 'mtr', 'Medtr1g102780' => 'mtr', 'Medtr1g102800' => 'mtr', 'Medtr1g102810' => 'mtr', 'Medtr1g102830' => 'mtr', 'MELO3C006499.2' => 'cme', 'Migut.G00385' => 'egut', 'MSTRG.4063' => 'ama', 'Nitab4.5_0000090g0260' => 'nta', 'Nitab4.5_0000977g0030' => 'nta', 'Nitab4.5_0002541g0040' => 'nta', 'Nitab4.5_0007068g0040' => 'nta', 'Nn005s41408' => 'nnu', 'Nn005s41410' => 'nnu', 'Oeu010310.1' => 'oeu', 'Oeu010311.1' => 'oeu', 'Oeu043472.1' => 'oeu', 'Os01g0246400' => 'osa', 'Os04g0267950' => 'osa', 'Os07g0178700' => 'osa', 'Os07g0178800' => 'osa', 'Peaxi162Scf00316g00046' => 'pax', 'Peaxi162Scf00316g00049' => 'pax', 'Peaxi162Scf00316g00059' => 'pax', 'Peaxi162Scf00316g00328' => 'pax', 'Peaxi162Scf00316g00329' => 'pax', 'Peaxi162Scf00316g00411' => 'pax', 'Peaxi162Scf00316g00521' => 'pax', 'Peaxi162Scf00492g00068' => 'pax', 'Peaxi162Scf35631g00002' => 'pax', 'PGR142G3720' => 'pgr', 'PGSC0003DMG400006442' => 'stu', 'Phvul.007G062000' => 'pvu', 'Potri.008G157750' => 'ptr', 'Potri.008G157900' => 'ptr', 'Potri.008G158000' => 'ptr', 'Potri.008G158200' => 'ptr', 'Pp3c11_7280' => 'ppa', 'Pp3c11_7980' => 'ppa', 'Pp3c12_19450' => 'ppa', 'Pp3c14_1480' => 'ppa', 'Pp3c14_1501' => 'ppa', 'Pp3c16_4900' => 'ppa', 'Pp3c16_5010' => 'ppa', 'Pp3c16_5060' => 'ppa', 'Pp3c19_18250' => 'ppa', 'Pp3c23_8530' => 'ppa', 'Pp3c23_8550' => 'ppa', 'Pp3c24_9670' => 'ppa', 'Pp3c2_21390' => 'ppa', 'Pp3c2_31380' => 'ppa', 'Pp3c3_16620' => 'ppa', 'Pp3c3_8090' => 'ppa', 'Pp3c3_8110' => 'ppa', 'Pp3c3_8130' => 'ppa', 'Pp3c3_8150' => 'ppa', 'Pp3c4_14320' => 'ppa', 'Pp3c6_2560' => 'ppa', 'Pp3c9_16700' => 'ppa', 'PRCOL_00000234' => 'pco', 'PRCOL_00000235' => 'pco', 'PRCOL_00000777' => 'pco', 'PRCOL_00002344' => 'pco', 'PRCOL_00002372' => 'pco', 'PRCOL_00006120' => 'pco', 'Prupe.1G021400' => 'ppe', 'Prupe.1G021500' => 'ppe', 'Prupe.1G021600' => 'ppe', 'Prupe.1G021700' => 'ppe', 'Prupe.1G021800' => 'ppe', 'Prupe.5G145100' => 'ppe', 'Psat6g204040' => 'psa', 'Psat6g204800' => 'psa', 'Psat6g204920' => 'psa', 'Psat6g204960' => 'psa', 'Psat6g205080' => 'psa', 'PSO017G0271' => 'pso', 'PSO017G1276' => 'pso', 'PSO017G1429' => 'pso', 'PSO017G1861' => 'pso', 'PSO017G2787' => 'pso', 'PSO017G4466' => 'pso', 'PSO017G5118' => 'pso', 'PSO017G5420' => 'pso', 'PSO063G3678' => 'pso', 'PSO210G0546' => 'pso', 'PSO317G0001' => 'pso', 'PSO357G0512' => 'pso', 'PSO478G2682' => 'pso', 'PSO647G0001' => 'pso', 'PSO675G0001' => 'pso', 'PSO675G2699' => 'pso', 'PSO675G2849' => 'pso', 'PSO675G4991' => 'pso', 'PSO689G0001' => 'pso', 'QL06p000916' => 'qlo', 'QL06p000921' => 'qlo', 'QL06p001398' => 'qlo', 'QL06p001407' => 'qlo', 'QL06p002031' => 'qlo', 'RcHm_v2.0_Chr4g0387791' => 'rch', 'RcHm_v2.0_Chr4g0387801' => 'rch', 'RcHm_v2.0_Chr6g0286501' => 'rch', 'RcHm_v2.0_Chr6g0286511' => 'rch', 'RcHm_v2.0_Chr6g0286521' => 'rch', 'RcHm_v2.0_Chr6g0286531' => 'rch', 'RcHm_v2.0_Chr7g0189141' => 'rch', 'Rhsim02G0028700' => 'rsi', 'Rhsim02G0028800' => 'rsi', 'Rhsim02G0028900' => 'rsi', 'Rhsim02G0029000' => 'rsi', 'Rhsim02G0029100' => 'rsi', 'Rhsim02G0029200' => 'rsi', 'Rhsim02G0029300' => 'rsi', 'Rhsim02G0029400' => 'rsi', 'Rhsim02G0029500' => 'rsi', 'Rhsim02G0029600' => 'rsi', 'RhsimUnG0024000' => 'rsi', 'RhsimUnG0024100' => 'rsi', 'RhsimUnG0024200' => 'rsi', 'RhsimUnG0024300' => 'rsi', 'RhsimUnG0024400' => 'rsi', 'RhsimUnG0024500' => 'rsi', 'RhsimUnG0024700' => 'rsi', 'RhsimUnG0024800' => 'rsi', 'RhsimUnG0024900' => 'rsi', 'RhsimUnG0025100' => 'rsi', 'Sabra08G0120200' => 'sbr', 'Sabra08G0120300' => 'sbr', 'Sabra08G0120500' => 'sbr', 'Sabra08G0120600' => 'sbr', 'Sabra10G0158900' => 'sbr', 'SalBow2G3492' => 'sbo', 'Sc13g0004760' => 'sci', 'Sc13g0004770' => 'sci', 'Sed0003417' => 'sed', 'Sed0019750' => 'sed', 'SEGI_03419' => 'sgi', 'SEGI_05907' => 'sgi', 'SEGI_10682' => 'sgi', 'SEGI_13528' => 'sgi', 'SEGI_16081' => 'sgi', 'SEGI_19370' => 'sgi', 'SEGI_21015' => 'sgi', 'SEGI_21944' => 'sgi', 'SEGI_32906' => 'sgi', 'SEGI_33093' => 'sgi', 'SEGI_36110' => 'sgi', 'SEGI_40397' => 'sgi', 'SGA_v2.0_scaffold191G40426' => 'sas', 'SGA_v2.0_scaffold353G49717' => 'sas', 'SGA_v2.0_scaffold50G18550' => 'sas', 'SMO119G0173' => 'smo', 'SMO172G0002' => 'smo', 'Solyc09g082690.3' => 'sly', 'Solyc09g082700.2' => 'sly', 'Sopen09g031550' => 'spe', 'Sopen09g031560' => 'spe', 'Sp3g20540' => 'spa', 'Sp7g07580' => 'spa', 'TAR134G0002' => 'tar', 'TAR236G0001' => 'tar', 'TAR365G0892' => 'tar', 'TAR636G0166' => 'tar', 'TAR636G0646' => 'tar', 'TAR636G0869' => 'tar', 'TAR636G1317' => 'tar', 'TAR636G1744' => 'tar', 'TAR636G3358' => 'tar', 'TAR636G3436' => 'tar', 'THA.LOC104803047' => 'tha', 'Thecc.04G238900' => 'tca', 'Thhalv10021557m.g' => 'esa', 'Thhalv10026318m.g' => 'esa', 'Thhalv10026335m.g' => 'esa', 'TPR.G17433' => 'tpr', 'TPR.G18915' => 'tpr', 'TPR.G26125' => 'tpr', 'TWI09G0677' => 'twi', 'TWI73G0287' => 'twi', 'unitig_748.g8326' => 'ugi', 'vmacro15370' => 'vma', 'vmacro15371' => 'vma', 'vmacro15372' => 'vma', 'vmacro15373' => 'vma', 'vmacro15374' => 'vma', 'VMungo0720G2826' => 'vmu', 'Zm00001eb116960' => 'zma', 'Zm00001eb301260' => 'zma', 'Zm00001eb301270' => 'zma' ) $gf_id = 'HOM05D001460' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001460' ) $data_identifier = 'HOM05D001460' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 4, 'aag' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 2, 'aox' => (int) 2, 'arhy' => (int) 4, 'ath' => (int) 2, 'atr' => (int) 1, 'acertr' => (int) 10, 'cqu' => (int) 4, 'bca' => (int) 11, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 1, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 1, 'ccan' => (int) 1, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 1, 'col' => (int) 1, 'cpa' => (int) 1, 'cre' => (int) 7, 'csa' => (int) 1, 'camsi' => (int) 2, 'dca' => (int) 3, 'din' => (int) 2, 'dzi' => (int) 3, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 14, 'fve' => (int) 9, 'gma' => (int) 2, 'ghi' => (int) 4, 'gra' => (int) 2, 'vvi' => (int) 1, 'han' => (int) 13, 'cav' => (int) 1, 'hma' => (int) 2, 'sun' => (int) 2, 'lal' => (int) 2, 'lonja' => (int) 12, 'lja' => (int) 1, 'lsa' => (int) 7, 'mes' => (int) 1, 'mpo' => (int) 27, 'mbi' => (int) 1, 'mco' => (int) 8, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 1, 'egut' => (int) 1, 'ama' => (int) 1, 'nta' => (int) 4, 'nnu' => (int) 2, 'oeu' => (int) 3, 'osa' => (int) 4, 'pax' => (int) 9, 'pgr' => (int) 1, 'stu' => (int) 1, 'pvu' => (int) 1, 'ptr' => (int) 4, 'ppa' => (int) 22, 'pco' => (int) 6, 'ppe' => (int) 6, 'psa' => (int) 5, 'pso' => (int) 19, 'qlo' => (int) 5, 'rch' => (int) 7, 'rsi' => (int) 20, 'sbr' => (int) 5, 'sbo' => (int) 1, 'sci' => (int) 2, 'sed' => (int) 2, 'sgi' => (int) 12, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 2, 'tar' => (int) 10, 'tha' => (int) 1, 'tca' => (int) 1, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 2, 'ugi' => (int) 1, 'vma' => (int) 5, 'vmu' => (int) 1, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb301270' $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' => 'HOM05D001460', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '433', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p22980' => 'bna', 'A01p32340' => 'bna', 'A03p42970' => 'bna', 'A05p25880' => 'bna', 'Aa31LG8G9320' => 'aar', 'Aa31LG8G9330' => 'aar', 'Aa31LG8G9340' => 'aar', 'Aa31sc221G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1034' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1528' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.829' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2222' => 'aag', 'Ah.12g058830' => 'amhyb', 'Ah.12g058840' => 'amhyb', 'AL3G37160' => 'aly', 'AL7G41310' => 'aly', 'Aqoxy5G00395' => 'aox', 'Aqoxy5G00396' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0C8NZA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5185HY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JZ1PRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MD3LS0' => 'arhy', 'AT3G22840' => 'ath', 'AT4G14690' => 'ath', 'ATR0665G054' => 'atr', 'Atru.chr4.2344' => 'acertr', 'Atru.chr4.2346' => 'acertr', 'Atru.chr4.2347' => 'acertr', 'Atru.chr4.2348' => 'acertr', 'Atru.chr4.2355' => 'acertr', 'Atru.chr4.2356' => 'acertr', 'Atru.chr4.2358' => 'acertr', 'Atru.chr4.2359' => 'acertr', 'Atru.chr4.2360' => 'acertr', 'Atru.chr4.2361' => 'acertr', 'AUR62030476' => 'cqu', 'AUR62030478' => 'cqu', 'AUR62030819' => 'cqu', 'AUR62030820' => 'cqu', 'BcaB03g14648' => 'bca', 'BcaB04g20492' => 'bca', 'BcaB06g26399' => 'bca', 'BcaC01g03416' => 'bca', 'BcaC01g03419' => 'bca', 'BcaC01g03421' => 'bca', 'BcaC01g03424' => 'bca', 'BcaC05g28012' => 'bca', 'BcaC09g49212' => 'bca', 'BcaC09g50140' => 'bca', 'BcaNung00346' => 'bca', 'BolC1t02785H' => 'bol', 'BolC1t04095H' => 'bol', 'BolC3t17545H' => 'bol', 'BolC5t32769H' => 'bol', 'BraA01t02211Z' => 'bra', 'BraA01t03359Z' => 'bra', 'BraA03t13441Z' => 'bra', 'BraA05t21476Z' => 'bra', 'C01p28420' => 'bna', 'C01p41350' => 'bna', 'C03p52750' => 'bna', 'C03p52780' => 'bna', 'C05p40270' => 'bna', 'CAN.G1437.9' => 'can', 'CANSAT78G0035' => 'cansat', 'CANSAT78G1036' => 'cansat', 'CANSAT78G2272' => 'cansat', 'CANSAT78G2478' => 'cansat', 'CARHR098700' => 'chi', 'CARHR221120' => 'chi', 'CARHR221150' => 'chi', 'Carub.0003s2297' => 'cru', 'Carub.0007s2749' => 'cru', 'Carub.0007s2750' => 'cru', 'Carub.0007s2751' => 'cru', 'Ca_10849_v3' => 'car', 'Cc03_g04300' => 'ccan', 'CDE02G3648' => 'cde', 'CDE05G0060' => 'cde', 'CDE05G0692' => 'cde', 'CDE05G2285' => 'cde', 'CDE05G2884' => 'cde', 'CDE05G3072' => 'cde', 'Cfa008439' => 'cfa', 'Cfa008441' => 'cfa', 'Cfa008443' => 'cfa', 'Cfa008448' => 'cfa', 'Ciclev10005974m.g' => 'ccl', 'Ciclev10006006m.g' => 'ccl', 'Ciclev10006775m.g' => 'ccl', 'CiPaw.02G120400' => 'cil', 'CiPaw.02G120500' => 'cil', 'CiPaw.02G120600' => 'cil', 'ClCG05G004850' => 'cla', 'COL.COLO4_21566' => 'col', 'Cpa.g.sc44.124' => 'cpa', 'Cre07.g320400' => 'cre', 'Cre07.g320450' => 'cre', 'Cre08.g384650' => 'cre', 'Cre09.g393173' => 'cre', 'Cre09.g394325' => 'cre', 'Cre14.g626750' => 'cre', 'Cre16.g679250' => 'cre', 'CsaV3_3G012890' => 'csa', 'CSS0010865' => 'camsi', 'CSS0044338' => 'camsi', 'DCAR_002366' => 'dca', 'DCAR_030687' => 'dca', 'DCAR_030688' => 'dca', 'Dinv14047' => 'din', 'Dinv14048' => 'din', 'Duzib151G0105' => 'dzi', 'Duzib151G0114' => 'dzi', 'Duzib212G1029' => 'dzi', 'ECA232G3536' => 'eca', 'ECA240G0786' => 'eca', 'ECA240G1802' => 'eca', 'ECA240G3760' => 'eca', 'ECA240G3920' => 'eca', 'EL10Ac5g12536' => 'bvu', 'EL10Ac5g12537' => 'bvu', 'EL10Ac5g12538' => 'bvu', 'Eucgr.B01004' => 'egr', 'Eucgr.B01006' => 'egr', 'Eucgr.B01007' => 'egr', 'Eucgr.B01008' => 'egr', 'Eucgr.B01895' => 'egr', 'Eucgr.B01896' => 'egr', 'FAN04G1456' => 'fan', 'FAN08G1769' => 'fan', 'FAN08G2160' => 'fan', 'FAN13G2403' => 'fan', 'FAN13G3303' => 'fan', 'FAN15G2435' => 'fan', 'FAN17G0672' => 'fan', 'FAN17G2441' => 'fan', 'FAN18G1024' => 'fan', 'FAN22G1458' => 'fan', 'FAN24G0037' => 'fan', 'FAN24G0429' => 'fan', 'FAN24G2387' => 'fan', 'FAN27G2746' => 'fan', 'FvH4_2g20400' => 'fve', 'FvH4_2g20420' => 'fve', 'FvH4_2g20430' => 'fve', 'FvH4_4g01270' => 'fve', 'FvH4_4g01290' => 'fve', 'FvH4_4g01300' => 'fve', 'FvH4_4g01310' => 'fve', 'FvH4_4g01330' => 'fve', 'FvH4_5g09070' => 'fve', 'Glyma.10G243800' => 'gma', 'Glyma.20G150600' => 'gma', 'Gohir.A09G219200' => 'ghi', 'Gohir.A09G219300' => 'ghi', 'Gohir.D09G221400' => 'ghi', 'Gohir.D09G221500' => 'ghi', 'Gorai.006G242600' => 'gra', 'Gorai.006G242700' => 'gra', 'GSVIVG01018044001' => 'vvi', 'HanXRQChr03g0083821' => 'han', 'HanXRQChr03g0083841' => 'han', 'HanXRQChr03g0083881' => 'han', 'HanXRQChr03g0083901' => 'han', 'HanXRQChr03g0083921' => 'han', 'HanXRQChr03g0085331' => 'han', 'HanXRQChr03g0085361' => 'han', 'HanXRQChr03g0085411' => 'han', 'HanXRQChr03g0085421' => 'han', 'HanXRQChr03g0085431' => 'han', 'HanXRQChr08g0221991' => 'han', 'HanXRQChr11g0336061' => 'han', 'HanXRQChr11g0336411' => 'han', 'Haze_11234' => 'cav', 'Hma1.2p1_0549F.1_g177010' => 'hma', 'Hma1.2p1_0602F.1_g187630' => 'hma', 'Hund14876' => 'sun', 'Hund14879' => 'sun', 'Lalb_Chr06g0160741' => 'lal', 'Lalb_Chr21g0304781' => 'lal', 'Lj3A726G19' => 'lonja', 'Lj3A726T23' => 'lonja', 'Lj3A726T24' => 'lonja', 'Lj3A726T25' => 'lonja', 'Lj3A727T17' => 'lonja', 'Lj3C726T0' => 'lonja', 'Lj3C726T2' => 'lonja', 'Lj3P725T35' => 'lonja', 'Lj3P727T10' => 'lonja', 'Lj3P727T12' => 'lonja', 'Lj3P727T14' => 'lonja', 'Lj5g0023109' => 'lja', 'Lj6P646T44' => 'lonja', 'Lsat_1_v5_gn_6_75760' => 'lsa', 'Lsat_1_v5_gn_6_75800' => 'lsa', 'Lsat_1_v5_gn_6_75900' => 'lsa', 'Lsat_1_v5_gn_6_76240' => 'lsa', 'Lsat_1_v5_gn_6_76441' => 'lsa', 'Lsat_1_v5_gn_6_76700' => 'lsa', 'Lsat_1_v5_gn_6_76760' => 'lsa', 'Manes.15G033100' => 'mes', 'Mapoly0004s0074' => 'mpo', 'Mapoly0004s0075' => 'mpo', 'Mapoly0004s0163' => 'mpo', 'Mapoly0004s0164' => 'mpo', 'Mapoly0021s0018' => 'mpo', 'Mapoly0041s0136' => 'mpo', 'Mapoly0041s0137' => 'mpo', 'Mapoly0041s0138' => 'mpo', 'Mapoly0041s0139' => 'mpo', 'Mapoly0041s0141' => 'mpo', 'Mapoly0041s0142' => 'mpo', 'Mapoly0041s0143' => 'mpo', 'Mapoly0041s0144' => 'mpo', 'Mapoly0041s0145' => 'mpo', 'Mapoly0047s0106' => 'mpo', 'Mapoly0047s0108' => 'mpo', 'Mapoly0050s0051' => 'mpo', 'Mapoly0050s0052' => 'mpo', 'Mapoly0050s0053' => 'mpo', 'Mapoly0058s0013' => 'mpo', 'Mapoly0091s0078' => 'mpo', 'Mapoly0091s0079' => 'mpo', 'Mapoly0091s0080' => 'mpo', 'Mapoly0091s0081' => 'mpo', 'Mapoly0278s0004' => 'mpo', 'Mapoly0278s0005' => 'mpo', 'Mapoly0278s0006' => 'mpo', 'MBI11_g30648_MAGBIO' => 'mbi', 'MCO03G194' => 'mco', 'MCO03G590' => 'mco', 'MCO07G312' => 'mco', 'MCO10G318' => 'mco', 'MCO12G244' => 'mco', 'MCO13G148' => 'mco', 'MCO13G194' => 'mco', 'MCO16G238' => 'mco', 'MD06G1134100' => 'mdo', 'MD13G1200100' => 'mdo', 'MD13G1200300' => 'mdo', 'MD13G1200600' => 'mdo', 'MD14G1150400' => 'mdo', 'MD16G1200000' => 'mdo', 'Medtr1g102570' => 'mtr', 'Medtr1g102780' => 'mtr', 'Medtr1g102800' => 'mtr', 'Medtr1g102810' => 'mtr', 'Medtr1g102830' => 'mtr', 'MELO3C006499.2' => 'cme', 'Migut.G00385' => 'egut', 'MSTRG.4063' => 'ama', 'Nitab4.5_0000090g0260' => 'nta', 'Nitab4.5_0000977g0030' => 'nta', 'Nitab4.5_0002541g0040' => 'nta', 'Nitab4.5_0007068g0040' => 'nta', 'Nn005s41408' => 'nnu', 'Nn005s41410' => 'nnu', 'Oeu010310.1' => 'oeu', 'Oeu010311.1' => 'oeu', 'Oeu043472.1' => 'oeu', 'Os01g0246400' => 'osa', 'Os04g0267950' => 'osa', 'Os07g0178700' => 'osa', 'Os07g0178800' => 'osa', 'Peaxi162Scf00316g00046' => 'pax', 'Peaxi162Scf00316g00049' => 'pax', 'Peaxi162Scf00316g00059' => 'pax', 'Peaxi162Scf00316g00328' => 'pax', 'Peaxi162Scf00316g00329' => 'pax', 'Peaxi162Scf00316g00411' => 'pax', 'Peaxi162Scf00316g00521' => 'pax', 'Peaxi162Scf00492g00068' => 'pax', 'Peaxi162Scf35631g00002' => 'pax', 'PGR142G3720' => 'pgr', 'PGSC0003DMG400006442' => 'stu', 'Phvul.007G062000' => 'pvu', 'Potri.008G157750' => 'ptr', 'Potri.008G157900' => 'ptr', 'Potri.008G158000' => 'ptr', 'Potri.008G158200' => 'ptr', 'Pp3c11_7280' => 'ppa', 'Pp3c11_7980' => 'ppa', 'Pp3c12_19450' => 'ppa', 'Pp3c14_1480' => 'ppa', 'Pp3c14_1501' => 'ppa', 'Pp3c16_4900' => 'ppa', 'Pp3c16_5010' => 'ppa', 'Pp3c16_5060' => 'ppa', 'Pp3c19_18250' => 'ppa', 'Pp3c23_8530' => 'ppa', 'Pp3c23_8550' => 'ppa', 'Pp3c24_9670' => 'ppa', 'Pp3c2_21390' => 'ppa', 'Pp3c2_31380' => 'ppa', 'Pp3c3_16620' => 'ppa', 'Pp3c3_8090' => 'ppa', 'Pp3c3_8110' => 'ppa', 'Pp3c3_8130' => 'ppa', 'Pp3c3_8150' => 'ppa', 'Pp3c4_14320' => 'ppa', 'Pp3c6_2560' => 'ppa', 'Pp3c9_16700' => 'ppa', 'PRCOL_00000234' => 'pco', 'PRCOL_00000235' => 'pco', 'PRCOL_00000777' => 'pco', 'PRCOL_00002344' => 'pco', 'PRCOL_00002372' => 'pco', 'PRCOL_00006120' => 'pco', 'Prupe.1G021400' => 'ppe', 'Prupe.1G021500' => 'ppe', 'Prupe.1G021600' => 'ppe', 'Prupe.1G021700' => 'ppe', 'Prupe.1G021800' => 'ppe', 'Prupe.5G145100' => 'ppe', 'Psat6g204040' => 'psa', 'Psat6g204800' => 'psa', 'Psat6g204920' => 'psa', 'Psat6g204960' => 'psa', 'Psat6g205080' => 'psa', 'PSO017G0271' => 'pso', 'PSO017G1276' => 'pso', 'PSO017G1429' => 'pso', 'PSO017G1861' => 'pso', 'PSO017G2787' => 'pso', 'PSO017G4466' => 'pso', 'PSO017G5118' => 'pso', 'PSO017G5420' => 'pso', 'PSO063G3678' => 'pso', 'PSO210G0546' => 'pso', 'PSO317G0001' => 'pso', 'PSO357G0512' => 'pso', 'PSO478G2682' => 'pso', 'PSO647G0001' => 'pso', 'PSO675G0001' => 'pso', 'PSO675G2699' => 'pso', 'PSO675G2849' => 'pso', 'PSO675G4991' => 'pso', 'PSO689G0001' => 'pso', 'QL06p000916' => 'qlo', 'QL06p000921' => 'qlo', 'QL06p001398' => 'qlo', 'QL06p001407' => 'qlo', 'QL06p002031' => 'qlo', 'RcHm_v2.0_Chr4g0387791' => 'rch', 'RcHm_v2.0_Chr4g0387801' => 'rch', 'RcHm_v2.0_Chr6g0286501' => 'rch', 'RcHm_v2.0_Chr6g0286511' => 'rch', 'RcHm_v2.0_Chr6g0286521' => 'rch', 'RcHm_v2.0_Chr6g0286531' => 'rch', 'RcHm_v2.0_Chr7g0189141' => 'rch', 'Rhsim02G0028700' => 'rsi', 'Rhsim02G0028800' => 'rsi', 'Rhsim02G0028900' => 'rsi', 'Rhsim02G0029000' => 'rsi', 'Rhsim02G0029100' => 'rsi', 'Rhsim02G0029200' => 'rsi', 'Rhsim02G0029300' => 'rsi', 'Rhsim02G0029400' => 'rsi', 'Rhsim02G0029500' => 'rsi', 'Rhsim02G0029600' => 'rsi', 'RhsimUnG0024000' => 'rsi', 'RhsimUnG0024100' => 'rsi', 'RhsimUnG0024200' => 'rsi', 'RhsimUnG0024300' => 'rsi', 'RhsimUnG0024400' => 'rsi', 'RhsimUnG0024500' => 'rsi', 'RhsimUnG0024700' => 'rsi', 'RhsimUnG0024800' => 'rsi', 'RhsimUnG0024900' => 'rsi', 'RhsimUnG0025100' => 'rsi', 'Sabra08G0120200' => 'sbr', 'Sabra08G0120300' => 'sbr', 'Sabra08G0120500' => 'sbr', 'Sabra08G0120600' => 'sbr', 'Sabra10G0158900' => 'sbr', 'SalBow2G3492' => 'sbo', 'Sc13g0004760' => 'sci', 'Sc13g0004770' => 'sci', 'Sed0003417' => 'sed', 'Sed0019750' => 'sed', 'SEGI_03419' => 'sgi', 'SEGI_05907' => 'sgi', 'SEGI_10682' => 'sgi', 'SEGI_13528' => 'sgi', 'SEGI_16081' => 'sgi', 'SEGI_19370' => 'sgi', 'SEGI_21015' => 'sgi', 'SEGI_21944' => 'sgi', 'SEGI_32906' => 'sgi', 'SEGI_33093' => 'sgi', 'SEGI_36110' => 'sgi', 'SEGI_40397' => 'sgi', 'SGA_v2.0_scaffold191G40426' => 'sas', 'SGA_v2.0_scaffold353G49717' => 'sas', 'SGA_v2.0_scaffold50G18550' => 'sas', 'SMO119G0173' => 'smo', 'SMO172G0002' => 'smo', 'Solyc09g082690.3' => 'sly', 'Solyc09g082700.2' => 'sly', 'Sopen09g031550' => 'spe', 'Sopen09g031560' => 'spe', 'Sp3g20540' => 'spa', 'Sp7g07580' => 'spa', 'TAR134G0002' => 'tar', 'TAR236G0001' => 'tar', 'TAR365G0892' => 'tar', 'TAR636G0166' => 'tar', 'TAR636G0646' => 'tar', 'TAR636G0869' => 'tar', 'TAR636G1317' => 'tar', 'TAR636G1744' => 'tar', 'TAR636G3358' => 'tar', 'TAR636G3436' => 'tar', 'THA.LOC104803047' => 'tha', 'Thecc.04G238900' => 'tca', 'Thhalv10021557m.g' => 'esa', 'Thhalv10026318m.g' => 'esa', 'Thhalv10026335m.g' => 'esa', 'TPR.G17433' => 'tpr', 'TPR.G18915' => 'tpr', 'TPR.G26125' => 'tpr', 'TWI09G0677' => 'twi', 'TWI73G0287' => 'twi', 'unitig_748.g8326' => 'ugi', 'vmacro15370' => 'vma', 'vmacro15371' => 'vma', 'vmacro15372' => 'vma', 'vmacro15373' => 'vma', 'vmacro15374' => 'vma', 'VMungo0720G2826' => 'vmu', 'Zm00001eb116960' => 'zma', 'Zm00001eb301260' => 'zma', 'Zm00001eb301270' => 'zma' ), 'gf_id' => 'HOM05D001460', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001460' ), 'data_identifier' => 'HOM05D001460', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001460', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '433', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p22980' => 'bna', 'A01p32340' => 'bna', 'A03p42970' => 'bna', 'A05p25880' => 'bna', 'Aa31LG8G9320' => 'aar', 'Aa31LG8G9330' => 'aar', 'Aa31LG8G9340' => 'aar', 'Aa31sc221G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1034' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1528' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.829' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2222' => 'aag', 'Ah.12g058830' => 'amhyb', 'Ah.12g058840' => 'amhyb', 'AL3G37160' => 'aly', 'AL7G41310' => 'aly', 'Aqoxy5G00395' => 'aox', 'Aqoxy5G00396' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0C8NZA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5185HY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JZ1PRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MD3LS0' => 'arhy', 'AT3G22840' => 'ath', 'AT4G14690' => 'ath', 'ATR0665G054' => 'atr', 'Atru.chr4.2344' => 'acertr', 'Atru.chr4.2346' => 'acertr', 'Atru.chr4.2347' => 'acertr', 'Atru.chr4.2348' => 'acertr', 'Atru.chr4.2355' => 'acertr', 'Atru.chr4.2356' => 'acertr', 'Atru.chr4.2358' => 'acertr', 'Atru.chr4.2359' => 'acertr', 'Atru.chr4.2360' => 'acertr', 'Atru.chr4.2361' => 'acertr', 'AUR62030476' => 'cqu', 'AUR62030478' => 'cqu', 'AUR62030819' => 'cqu', 'AUR62030820' => 'cqu', 'BcaB03g14648' => 'bca', 'BcaB04g20492' => 'bca', 'BcaB06g26399' => 'bca', 'BcaC01g03416' => 'bca', 'BcaC01g03419' => 'bca', 'BcaC01g03421' => 'bca', 'BcaC01g03424' => 'bca', 'BcaC05g28012' => 'bca', 'BcaC09g49212' => 'bca', 'BcaC09g50140' => 'bca', 'BcaNung00346' => 'bca', 'BolC1t02785H' => 'bol', 'BolC1t04095H' => 'bol', 'BolC3t17545H' => 'bol', 'BolC5t32769H' => 'bol', 'BraA01t02211Z' => 'bra', 'BraA01t03359Z' => 'bra', 'BraA03t13441Z' => 'bra', 'BraA05t21476Z' => 'bra', 'C01p28420' => 'bna', 'C01p41350' => 'bna', 'C03p52750' => 'bna', 'C03p52780' => 'bna', 'C05p40270' => 'bna', 'CAN.G1437.9' => 'can', 'CANSAT78G0035' => 'cansat', 'CANSAT78G1036' => 'cansat', 'CANSAT78G2272' => 'cansat', 'CANSAT78G2478' => 'cansat', 'CARHR098700' => 'chi', 'CARHR221120' => 'chi', 'CARHR221150' => 'chi', 'Carub.0003s2297' => 'cru', 'Carub.0007s2749' => 'cru', 'Carub.0007s2750' => 'cru', 'Carub.0007s2751' => 'cru', 'Ca_10849_v3' => 'car', 'Cc03_g04300' => 'ccan', 'CDE02G3648' => 'cde', 'CDE05G0060' => 'cde', 'CDE05G0692' => 'cde', 'CDE05G2285' => 'cde', 'CDE05G2884' => 'cde', 'CDE05G3072' => 'cde', 'Cfa008439' => 'cfa', 'Cfa008441' => 'cfa', 'Cfa008443' => 'cfa', 'Cfa008448' => 'cfa', 'Ciclev10005974m.g' => 'ccl', 'Ciclev10006006m.g' => 'ccl', 'Ciclev10006775m.g' => 'ccl', 'CiPaw.02G120400' => 'cil', 'CiPaw.02G120500' => 'cil', 'CiPaw.02G120600' => 'cil', 'ClCG05G004850' => 'cla', 'COL.COLO4_21566' => 'col', 'Cpa.g.sc44.124' => 'cpa', 'Cre07.g320400' => 'cre', 'Cre07.g320450' => 'cre', 'Cre08.g384650' => 'cre', 'Cre09.g393173' => 'cre', 'Cre09.g394325' => 'cre', 'Cre14.g626750' => 'cre', 'Cre16.g679250' => 'cre', 'CsaV3_3G012890' => 'csa', 'CSS0010865' => 'camsi', 'CSS0044338' => 'camsi', 'DCAR_002366' => 'dca', 'DCAR_030687' => 'dca', 'DCAR_030688' => 'dca', 'Dinv14047' => 'din', 'Dinv14048' => 'din', 'Duzib151G0105' => 'dzi', 'Duzib151G0114' => 'dzi', 'Duzib212G1029' => 'dzi', 'ECA232G3536' => 'eca', 'ECA240G0786' => 'eca', 'ECA240G1802' => 'eca', 'ECA240G3760' => 'eca', 'ECA240G3920' => 'eca', 'EL10Ac5g12536' => 'bvu', 'EL10Ac5g12537' => 'bvu', 'EL10Ac5g12538' => 'bvu', 'Eucgr.B01004' => 'egr', 'Eucgr.B01006' => 'egr', 'Eucgr.B01007' => 'egr', 'Eucgr.B01008' => 'egr', 'Eucgr.B01895' => 'egr', 'Eucgr.B01896' => 'egr', 'FAN04G1456' => 'fan', 'FAN08G1769' => 'fan', 'FAN08G2160' => 'fan', 'FAN13G2403' => 'fan', 'FAN13G3303' => 'fan', 'FAN15G2435' => 'fan', 'FAN17G0672' => 'fan', 'FAN17G2441' => 'fan', 'FAN18G1024' => 'fan', 'FAN22G1458' => 'fan', 'FAN24G0037' => 'fan', 'FAN24G0429' => 'fan', 'FAN24G2387' => 'fan', 'FAN27G2746' => 'fan', 'FvH4_2g20400' => 'fve', 'FvH4_2g20420' => 'fve', 'FvH4_2g20430' => 'fve', 'FvH4_4g01270' => 'fve', 'FvH4_4g01290' => 'fve', 'FvH4_4g01300' => 'fve', 'FvH4_4g01310' => 'fve', 'FvH4_4g01330' => 'fve', 'FvH4_5g09070' => 'fve', 'Glyma.10G243800' => 'gma', 'Glyma.20G150600' => 'gma', 'Gohir.A09G219200' => 'ghi', 'Gohir.A09G219300' => 'ghi', 'Gohir.D09G221400' => 'ghi', 'Gohir.D09G221500' => 'ghi', 'Gorai.006G242600' => 'gra', 'Gorai.006G242700' => 'gra', 'GSVIVG01018044001' => 'vvi', 'HanXRQChr03g0083821' => 'han', 'HanXRQChr03g0083841' => 'han', 'HanXRQChr03g0083881' => 'han', 'HanXRQChr03g0083901' => 'han', 'HanXRQChr03g0083921' => 'han', 'HanXRQChr03g0085331' => 'han', 'HanXRQChr03g0085361' => 'han', 'HanXRQChr03g0085411' => 'han', 'HanXRQChr03g0085421' => 'han', 'HanXRQChr03g0085431' => 'han', 'HanXRQChr08g0221991' => 'han', 'HanXRQChr11g0336061' => 'han', 'HanXRQChr11g0336411' => 'han', 'Haze_11234' => 'cav', 'Hma1.2p1_0549F.1_g177010' => 'hma', 'Hma1.2p1_0602F.1_g187630' => 'hma', 'Hund14876' => 'sun', 'Hund14879' => 'sun', 'Lalb_Chr06g0160741' => 'lal', 'Lalb_Chr21g0304781' => 'lal', 'Lj3A726G19' => 'lonja', 'Lj3A726T23' => 'lonja', 'Lj3A726T24' => 'lonja', 'Lj3A726T25' => 'lonja', 'Lj3A727T17' => 'lonja', 'Lj3C726T0' => 'lonja', 'Lj3C726T2' => 'lonja', 'Lj3P725T35' => 'lonja', 'Lj3P727T10' => 'lonja', 'Lj3P727T12' => 'lonja', 'Lj3P727T14' => 'lonja', 'Lj5g0023109' => 'lja', 'Lj6P646T44' => 'lonja', 'Lsat_1_v5_gn_6_75760' => 'lsa', 'Lsat_1_v5_gn_6_75800' => 'lsa', 'Lsat_1_v5_gn_6_75900' => 'lsa', 'Lsat_1_v5_gn_6_76240' => 'lsa', 'Lsat_1_v5_gn_6_76441' => 'lsa', 'Lsat_1_v5_gn_6_76700' => 'lsa', 'Lsat_1_v5_gn_6_76760' => 'lsa', 'Manes.15G033100' => 'mes', 'Mapoly0004s0074' => 'mpo', 'Mapoly0004s0075' => 'mpo', 'Mapoly0004s0163' => 'mpo', 'Mapoly0004s0164' => 'mpo', 'Mapoly0021s0018' => 'mpo', 'Mapoly0041s0136' => 'mpo', 'Mapoly0041s0137' => 'mpo', 'Mapoly0041s0138' => 'mpo', 'Mapoly0041s0139' => 'mpo', 'Mapoly0041s0141' => 'mpo', 'Mapoly0041s0142' => 'mpo', 'Mapoly0041s0143' => 'mpo', 'Mapoly0041s0144' => 'mpo', 'Mapoly0041s0145' => 'mpo', 'Mapoly0047s0106' => 'mpo', 'Mapoly0047s0108' => 'mpo', 'Mapoly0050s0051' => 'mpo', 'Mapoly0050s0052' => 'mpo', 'Mapoly0050s0053' => 'mpo', 'Mapoly0058s0013' => 'mpo', 'Mapoly0091s0078' => 'mpo', 'Mapoly0091s0079' => 'mpo', 'Mapoly0091s0080' => 'mpo', 'Mapoly0091s0081' => 'mpo', 'Mapoly0278s0004' => 'mpo', 'Mapoly0278s0005' => 'mpo', 'Mapoly0278s0006' => 'mpo', 'MBI11_g30648_MAGBIO' => 'mbi', 'MCO03G194' => 'mco', 'MCO03G590' => 'mco', 'MCO07G312' => 'mco', 'MCO10G318' => 'mco', 'MCO12G244' => 'mco', 'MCO13G148' => 'mco', 'MCO13G194' => 'mco', 'MCO16G238' => 'mco', 'MD06G1134100' => 'mdo', 'MD13G1200100' => 'mdo', 'MD13G1200300' => 'mdo', 'MD13G1200600' => 'mdo', 'MD14G1150400' => 'mdo', 'MD16G1200000' => 'mdo', 'Medtr1g102570' => 'mtr', 'Medtr1g102780' => 'mtr', 'Medtr1g102800' => 'mtr', 'Medtr1g102810' => 'mtr', 'Medtr1g102830' => 'mtr', 'MELO3C006499.2' => 'cme', 'Migut.G00385' => 'egut', 'MSTRG.4063' => 'ama', 'Nitab4.5_0000090g0260' => 'nta', 'Nitab4.5_0000977g0030' => 'nta', 'Nitab4.5_0002541g0040' => 'nta', 'Nitab4.5_0007068g0040' => 'nta', 'Nn005s41408' => 'nnu', 'Nn005s41410' => 'nnu', 'Oeu010310.1' => 'oeu', 'Oeu010311.1' => 'oeu', 'Oeu043472.1' => 'oeu', 'Os01g0246400' => 'osa', 'Os04g0267950' => 'osa', 'Os07g0178700' => 'osa', 'Os07g0178800' => 'osa', 'Peaxi162Scf00316g00046' => 'pax', 'Peaxi162Scf00316g00049' => 'pax', 'Peaxi162Scf00316g00059' => 'pax', 'Peaxi162Scf00316g00328' => 'pax', 'Peaxi162Scf00316g00329' => 'pax', 'Peaxi162Scf00316g00411' => 'pax', 'Peaxi162Scf00316g00521' => 'pax', 'Peaxi162Scf00492g00068' => 'pax', 'Peaxi162Scf35631g00002' => 'pax', 'PGR142G3720' => 'pgr', 'PGSC0003DMG400006442' => 'stu', 'Phvul.007G062000' => 'pvu', 'Potri.008G157750' => 'ptr', 'Potri.008G157900' => 'ptr', 'Potri.008G158000' => 'ptr', 'Potri.008G158200' => 'ptr', 'Pp3c11_7280' => 'ppa', 'Pp3c11_7980' => 'ppa', 'Pp3c12_19450' => 'ppa', 'Pp3c14_1480' => 'ppa', 'Pp3c14_1501' => 'ppa', 'Pp3c16_4900' => 'ppa', 'Pp3c16_5010' => 'ppa', 'Pp3c16_5060' => 'ppa', 'Pp3c19_18250' => 'ppa', 'Pp3c23_8530' => 'ppa', 'Pp3c23_8550' => 'ppa', 'Pp3c24_9670' => 'ppa', 'Pp3c2_21390' => 'ppa', 'Pp3c2_31380' => 'ppa', 'Pp3c3_16620' => 'ppa', 'Pp3c3_8090' => 'ppa', 'Pp3c3_8110' => 'ppa', 'Pp3c3_8130' => 'ppa', 'Pp3c3_8150' => 'ppa', 'Pp3c4_14320' => 'ppa', 'Pp3c6_2560' => 'ppa', 'Pp3c9_16700' => 'ppa', 'PRCOL_00000234' => 'pco', 'PRCOL_00000235' => 'pco', 'PRCOL_00000777' => 'pco', 'PRCOL_00002344' => 'pco', 'PRCOL_00002372' => 'pco', 'PRCOL_00006120' => 'pco', 'Prupe.1G021400' => 'ppe', 'Prupe.1G021500' => 'ppe', 'Prupe.1G021600' => 'ppe', 'Prupe.1G021700' => 'ppe', 'Prupe.1G021800' => 'ppe', 'Prupe.5G145100' => 'ppe', 'Psat6g204040' => 'psa', 'Psat6g204800' => 'psa', 'Psat6g204920' => 'psa', 'Psat6g204960' => 'psa', 'Psat6g205080' => 'psa', 'PSO017G0271' => 'pso', 'PSO017G1276' => 'pso', 'PSO017G1429' => 'pso', 'PSO017G1861' => 'pso', 'PSO017G2787' => 'pso', 'PSO017G4466' => 'pso', 'PSO017G5118' => 'pso', 'PSO017G5420' => 'pso', 'PSO063G3678' => 'pso', 'PSO210G0546' => 'pso', 'PSO317G0001' => 'pso', 'PSO357G0512' => 'pso', 'PSO478G2682' => 'pso', 'PSO647G0001' => 'pso', 'PSO675G0001' => 'pso', 'PSO675G2699' => 'pso', 'PSO675G2849' => 'pso', 'PSO675G4991' => 'pso', 'PSO689G0001' => 'pso', 'QL06p000916' => 'qlo', 'QL06p000921' => 'qlo', 'QL06p001398' => 'qlo', 'QL06p001407' => 'qlo', 'QL06p002031' => 'qlo', 'RcHm_v2.0_Chr4g0387791' => 'rch', 'RcHm_v2.0_Chr4g0387801' => 'rch', 'RcHm_v2.0_Chr6g0286501' => 'rch', 'RcHm_v2.0_Chr6g0286511' => 'rch', 'RcHm_v2.0_Chr6g0286521' => 'rch', 'RcHm_v2.0_Chr6g0286531' => 'rch', 'RcHm_v2.0_Chr7g0189141' => 'rch', 'Rhsim02G0028700' => 'rsi', 'Rhsim02G0028800' => 'rsi', 'Rhsim02G0028900' => 'rsi', 'Rhsim02G0029000' => 'rsi', 'Rhsim02G0029100' => 'rsi', 'Rhsim02G0029200' => 'rsi', 'Rhsim02G0029300' => 'rsi', 'Rhsim02G0029400' => 'rsi', 'Rhsim02G0029500' => 'rsi', 'Rhsim02G0029600' => 'rsi', 'RhsimUnG0024000' => 'rsi', 'RhsimUnG0024100' => 'rsi', 'RhsimUnG0024200' => 'rsi', 'RhsimUnG0024300' => 'rsi', 'RhsimUnG0024400' => 'rsi', 'RhsimUnG0024500' => 'rsi', 'RhsimUnG0024700' => 'rsi', 'RhsimUnG0024800' => 'rsi', 'RhsimUnG0024900' => 'rsi', 'RhsimUnG0025100' => 'rsi', 'Sabra08G0120200' => 'sbr', 'Sabra08G0120300' => 'sbr', 'Sabra08G0120500' => 'sbr', 'Sabra08G0120600' => 'sbr', 'Sabra10G0158900' => 'sbr', 'SalBow2G3492' => 'sbo', 'Sc13g0004760' => 'sci', 'Sc13g0004770' => 'sci', 'Sed0003417' => 'sed', 'Sed0019750' => 'sed', 'SEGI_03419' => 'sgi', 'SEGI_05907' => 'sgi', 'SEGI_10682' => 'sgi', 'SEGI_13528' => 'sgi', 'SEGI_16081' => 'sgi', 'SEGI_19370' => 'sgi', 'SEGI_21015' => 'sgi', 'SEGI_21944' => 'sgi', 'SEGI_32906' => 'sgi', 'SEGI_33093' => 'sgi', 'SEGI_36110' => 'sgi', 'SEGI_40397' => 'sgi', 'SGA_v2.0_scaffold191G40426' => 'sas', 'SGA_v2.0_scaffold353G49717' => 'sas', 'SGA_v2.0_scaffold50G18550' => 'sas', 'SMO119G0173' => 'smo', 'SMO172G0002' => 'smo', 'Solyc09g082690.3' => 'sly', 'Solyc09g082700.2' => 'sly', 'Sopen09g031550' => 'spe', 'Sopen09g031560' => 'spe', 'Sp3g20540' => 'spa', 'Sp7g07580' => 'spa', 'TAR134G0002' => 'tar', 'TAR236G0001' => 'tar', 'TAR365G0892' => 'tar', 'TAR636G0166' => 'tar', 'TAR636G0646' => 'tar', 'TAR636G0869' => 'tar', 'TAR636G1317' => 'tar', 'TAR636G1744' => 'tar', 'TAR636G3358' => 'tar', 'TAR636G3436' => 'tar', 'THA.LOC104803047' => 'tha', 'Thecc.04G238900' => 'tca', 'Thhalv10021557m.g' => 'esa', 'Thhalv10026318m.g' => 'esa', 'Thhalv10026335m.g' => 'esa', 'TPR.G17433' => 'tpr', 'TPR.G18915' => 'tpr', 'TPR.G26125' => 'tpr', 'TWI09G0677' => 'twi', 'TWI73G0287' => 'twi', 'unitig_748.g8326' => 'ugi', 'vmacro15370' => 'vma', 'vmacro15371' => 'vma', 'vmacro15372' => 'vma', 'vmacro15373' => 'vma', 'vmacro15374' => 'vma', 'VMungo0720G2826' => 'vmu', 'Zm00001eb116960' => 'zma', 'Zm00001eb301260' => 'zma', 'Zm00001eb301270' => 'zma' ) $gf_id = 'HOM05D001460' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001460' ) $data_identifier = 'HOM05D001460' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 4, 'aag' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 2, 'aox' => (int) 2, 'arhy' => (int) 4, 'ath' => (int) 2, 'atr' => (int) 1, 'acertr' => (int) 10, 'cqu' => (int) 4, 'bca' => (int) 11, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 1, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 1, 'ccan' => (int) 1, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 1, 'col' => (int) 1, 'cpa' => (int) 1, 'cre' => (int) 7, 'csa' => (int) 1, 'camsi' => (int) 2, 'dca' => (int) 3, 'din' => (int) 2, 'dzi' => (int) 3, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 14, 'fve' => (int) 9, 'gma' => (int) 2, 'ghi' => (int) 4, 'gra' => (int) 2, 'vvi' => (int) 1, 'han' => (int) 13, 'cav' => (int) 1, 'hma' => (int) 2, 'sun' => (int) 2, 'lal' => (int) 2, 'lonja' => (int) 12, 'lja' => (int) 1, 'lsa' => (int) 7, 'mes' => (int) 1, 'mpo' => (int) 27, 'mbi' => (int) 1, 'mco' => (int) 8, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 1, 'egut' => (int) 1, 'ama' => (int) 1, 'nta' => (int) 4, 'nnu' => (int) 2, 'oeu' => (int) 3, 'osa' => (int) 4, 'pax' => (int) 9, 'pgr' => (int) 1, 'stu' => (int) 1, 'pvu' => (int) 1, 'ptr' => (int) 4, 'ppa' => (int) 22, 'pco' => (int) 6, 'ppe' => (int) 6, 'psa' => (int) 5, 'pso' => (int) 19, 'qlo' => (int) 5, 'rch' => (int) 7, 'rsi' => (int) 20, 'sbr' => (int) 5, 'sbo' => (int) 1, 'sci' => (int) 2, 'sed' => (int) 2, 'sgi' => (int) 12, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 2, 'tar' => (int) 10, 'tha' => (int) 1, 'tca' => (int) 1, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 2, 'ugi' => (int) 1, 'vma' => (int) 5, 'vmu' => (int) 1, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb301270' $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' => 'HOM05D001460', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '433', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p22980' => 'bna', 'A01p32340' => 'bna', 'A03p42970' => 'bna', 'A05p25880' => 'bna', 'Aa31LG8G9320' => 'aar', 'Aa31LG8G9330' => 'aar', 'Aa31LG8G9340' => 'aar', 'Aa31sc221G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1034' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1528' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.829' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2222' => 'aag', 'Ah.12g058830' => 'amhyb', 'Ah.12g058840' => 'amhyb', 'AL3G37160' => 'aly', 'AL7G41310' => 'aly', 'Aqoxy5G00395' => 'aox', 'Aqoxy5G00396' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0C8NZA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5185HY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JZ1PRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MD3LS0' => 'arhy', 'AT3G22840' => 'ath', 'AT4G14690' => 'ath', 'ATR0665G054' => 'atr', 'Atru.chr4.2344' => 'acertr', 'Atru.chr4.2346' => 'acertr', 'Atru.chr4.2347' => 'acertr', 'Atru.chr4.2348' => 'acertr', 'Atru.chr4.2355' => 'acertr', 'Atru.chr4.2356' => 'acertr', 'Atru.chr4.2358' => 'acertr', 'Atru.chr4.2359' => 'acertr', 'Atru.chr4.2360' => 'acertr', 'Atru.chr4.2361' => 'acertr', 'AUR62030476' => 'cqu', 'AUR62030478' => 'cqu', 'AUR62030819' => 'cqu', 'AUR62030820' => 'cqu', 'BcaB03g14648' => 'bca', 'BcaB04g20492' => 'bca', 'BcaB06g26399' => 'bca', 'BcaC01g03416' => 'bca', 'BcaC01g03419' => 'bca', 'BcaC01g03421' => 'bca', 'BcaC01g03424' => 'bca', 'BcaC05g28012' => 'bca', 'BcaC09g49212' => 'bca', 'BcaC09g50140' => 'bca', 'BcaNung00346' => 'bca', 'BolC1t02785H' => 'bol', 'BolC1t04095H' => 'bol', 'BolC3t17545H' => 'bol', 'BolC5t32769H' => 'bol', 'BraA01t02211Z' => 'bra', 'BraA01t03359Z' => 'bra', 'BraA03t13441Z' => 'bra', 'BraA05t21476Z' => 'bra', 'C01p28420' => 'bna', 'C01p41350' => 'bna', 'C03p52750' => 'bna', 'C03p52780' => 'bna', 'C05p40270' => 'bna', 'CAN.G1437.9' => 'can', 'CANSAT78G0035' => 'cansat', 'CANSAT78G1036' => 'cansat', 'CANSAT78G2272' => 'cansat', 'CANSAT78G2478' => 'cansat', 'CARHR098700' => 'chi', 'CARHR221120' => 'chi', 'CARHR221150' => 'chi', 'Carub.0003s2297' => 'cru', 'Carub.0007s2749' => 'cru', 'Carub.0007s2750' => 'cru', 'Carub.0007s2751' => 'cru', 'Ca_10849_v3' => 'car', 'Cc03_g04300' => 'ccan', 'CDE02G3648' => 'cde', 'CDE05G0060' => 'cde', 'CDE05G0692' => 'cde', 'CDE05G2285' => 'cde', 'CDE05G2884' => 'cde', 'CDE05G3072' => 'cde', 'Cfa008439' => 'cfa', 'Cfa008441' => 'cfa', 'Cfa008443' => 'cfa', 'Cfa008448' => 'cfa', 'Ciclev10005974m.g' => 'ccl', 'Ciclev10006006m.g' => 'ccl', 'Ciclev10006775m.g' => 'ccl', 'CiPaw.02G120400' => 'cil', 'CiPaw.02G120500' => 'cil', 'CiPaw.02G120600' => 'cil', 'ClCG05G004850' => 'cla', 'COL.COLO4_21566' => 'col', 'Cpa.g.sc44.124' => 'cpa', 'Cre07.g320400' => 'cre', 'Cre07.g320450' => 'cre', 'Cre08.g384650' => 'cre', 'Cre09.g393173' => 'cre', 'Cre09.g394325' => 'cre', 'Cre14.g626750' => 'cre', 'Cre16.g679250' => 'cre', 'CsaV3_3G012890' => 'csa', 'CSS0010865' => 'camsi', 'CSS0044338' => 'camsi', 'DCAR_002366' => 'dca', 'DCAR_030687' => 'dca', 'DCAR_030688' => 'dca', 'Dinv14047' => 'din', 'Dinv14048' => 'din', 'Duzib151G0105' => 'dzi', 'Duzib151G0114' => 'dzi', 'Duzib212G1029' => 'dzi', 'ECA232G3536' => 'eca', 'ECA240G0786' => 'eca', 'ECA240G1802' => 'eca', 'ECA240G3760' => 'eca', 'ECA240G3920' => 'eca', 'EL10Ac5g12536' => 'bvu', 'EL10Ac5g12537' => 'bvu', 'EL10Ac5g12538' => 'bvu', 'Eucgr.B01004' => 'egr', 'Eucgr.B01006' => 'egr', 'Eucgr.B01007' => 'egr', 'Eucgr.B01008' => 'egr', 'Eucgr.B01895' => 'egr', 'Eucgr.B01896' => 'egr', 'FAN04G1456' => 'fan', 'FAN08G1769' => 'fan', 'FAN08G2160' => 'fan', 'FAN13G2403' => 'fan', 'FAN13G3303' => 'fan', 'FAN15G2435' => 'fan', 'FAN17G0672' => 'fan', 'FAN17G2441' => 'fan', 'FAN18G1024' => 'fan', 'FAN22G1458' => 'fan', 'FAN24G0037' => 'fan', 'FAN24G0429' => 'fan', 'FAN24G2387' => 'fan', 'FAN27G2746' => 'fan', 'FvH4_2g20400' => 'fve', 'FvH4_2g20420' => 'fve', 'FvH4_2g20430' => 'fve', 'FvH4_4g01270' => 'fve', 'FvH4_4g01290' => 'fve', 'FvH4_4g01300' => 'fve', 'FvH4_4g01310' => 'fve', 'FvH4_4g01330' => 'fve', 'FvH4_5g09070' => 'fve', 'Glyma.10G243800' => 'gma', 'Glyma.20G150600' => 'gma', 'Gohir.A09G219200' => 'ghi', 'Gohir.A09G219300' => 'ghi', 'Gohir.D09G221400' => 'ghi', 'Gohir.D09G221500' => 'ghi', 'Gorai.006G242600' => 'gra', 'Gorai.006G242700' => 'gra', 'GSVIVG01018044001' => 'vvi', 'HanXRQChr03g0083821' => 'han', 'HanXRQChr03g0083841' => 'han', 'HanXRQChr03g0083881' => 'han', 'HanXRQChr03g0083901' => 'han', 'HanXRQChr03g0083921' => 'han', 'HanXRQChr03g0085331' => 'han', 'HanXRQChr03g0085361' => 'han', 'HanXRQChr03g0085411' => 'han', 'HanXRQChr03g0085421' => 'han', 'HanXRQChr03g0085431' => 'han', 'HanXRQChr08g0221991' => 'han', 'HanXRQChr11g0336061' => 'han', 'HanXRQChr11g0336411' => 'han', 'Haze_11234' => 'cav', 'Hma1.2p1_0549F.1_g177010' => 'hma', 'Hma1.2p1_0602F.1_g187630' => 'hma', 'Hund14876' => 'sun', 'Hund14879' => 'sun', 'Lalb_Chr06g0160741' => 'lal', 'Lalb_Chr21g0304781' => 'lal', 'Lj3A726G19' => 'lonja', 'Lj3A726T23' => 'lonja', 'Lj3A726T24' => 'lonja', 'Lj3A726T25' => 'lonja', 'Lj3A727T17' => 'lonja', 'Lj3C726T0' => 'lonja', 'Lj3C726T2' => 'lonja', 'Lj3P725T35' => 'lonja', 'Lj3P727T10' => 'lonja', 'Lj3P727T12' => 'lonja', 'Lj3P727T14' => 'lonja', 'Lj5g0023109' => 'lja', 'Lj6P646T44' => 'lonja', 'Lsat_1_v5_gn_6_75760' => 'lsa', 'Lsat_1_v5_gn_6_75800' => 'lsa', 'Lsat_1_v5_gn_6_75900' => 'lsa', 'Lsat_1_v5_gn_6_76240' => 'lsa', 'Lsat_1_v5_gn_6_76441' => 'lsa', 'Lsat_1_v5_gn_6_76700' => 'lsa', 'Lsat_1_v5_gn_6_76760' => 'lsa', 'Manes.15G033100' => 'mes', 'Mapoly0004s0074' => 'mpo', 'Mapoly0004s0075' => 'mpo', 'Mapoly0004s0163' => 'mpo', 'Mapoly0004s0164' => 'mpo', 'Mapoly0021s0018' => 'mpo', 'Mapoly0041s0136' => 'mpo', 'Mapoly0041s0137' => 'mpo', 'Mapoly0041s0138' => 'mpo', 'Mapoly0041s0139' => 'mpo', 'Mapoly0041s0141' => 'mpo', 'Mapoly0041s0142' => 'mpo', 'Mapoly0041s0143' => 'mpo', 'Mapoly0041s0144' => 'mpo', 'Mapoly0041s0145' => 'mpo', 'Mapoly0047s0106' => 'mpo', 'Mapoly0047s0108' => 'mpo', 'Mapoly0050s0051' => 'mpo', 'Mapoly0050s0052' => 'mpo', 'Mapoly0050s0053' => 'mpo', 'Mapoly0058s0013' => 'mpo', 'Mapoly0091s0078' => 'mpo', 'Mapoly0091s0079' => 'mpo', 'Mapoly0091s0080' => 'mpo', 'Mapoly0091s0081' => 'mpo', 'Mapoly0278s0004' => 'mpo', 'Mapoly0278s0005' => 'mpo', 'Mapoly0278s0006' => 'mpo', 'MBI11_g30648_MAGBIO' => 'mbi', 'MCO03G194' => 'mco', 'MCO03G590' => 'mco', 'MCO07G312' => 'mco', 'MCO10G318' => 'mco', 'MCO12G244' => 'mco', 'MCO13G148' => 'mco', 'MCO13G194' => 'mco', 'MCO16G238' => 'mco', 'MD06G1134100' => 'mdo', 'MD13G1200100' => 'mdo', 'MD13G1200300' => 'mdo', 'MD13G1200600' => 'mdo', 'MD14G1150400' => 'mdo', 'MD16G1200000' => 'mdo', 'Medtr1g102570' => 'mtr', 'Medtr1g102780' => 'mtr', 'Medtr1g102800' => 'mtr', 'Medtr1g102810' => 'mtr', 'Medtr1g102830' => 'mtr', 'MELO3C006499.2' => 'cme', 'Migut.G00385' => 'egut', 'MSTRG.4063' => 'ama', 'Nitab4.5_0000090g0260' => 'nta', 'Nitab4.5_0000977g0030' => 'nta', 'Nitab4.5_0002541g0040' => 'nta', 'Nitab4.5_0007068g0040' => 'nta', 'Nn005s41408' => 'nnu', 'Nn005s41410' => 'nnu', 'Oeu010310.1' => 'oeu', 'Oeu010311.1' => 'oeu', 'Oeu043472.1' => 'oeu', 'Os01g0246400' => 'osa', 'Os04g0267950' => 'osa', 'Os07g0178700' => 'osa', 'Os07g0178800' => 'osa', 'Peaxi162Scf00316g00046' => 'pax', 'Peaxi162Scf00316g00049' => 'pax', 'Peaxi162Scf00316g00059' => 'pax', 'Peaxi162Scf00316g00328' => 'pax', 'Peaxi162Scf00316g00329' => 'pax', 'Peaxi162Scf00316g00411' => 'pax', 'Peaxi162Scf00316g00521' => 'pax', 'Peaxi162Scf00492g00068' => 'pax', 'Peaxi162Scf35631g00002' => 'pax', 'PGR142G3720' => 'pgr', 'PGSC0003DMG400006442' => 'stu', 'Phvul.007G062000' => 'pvu', 'Potri.008G157750' => 'ptr', 'Potri.008G157900' => 'ptr', 'Potri.008G158000' => 'ptr', 'Potri.008G158200' => 'ptr', 'Pp3c11_7280' => 'ppa', 'Pp3c11_7980' => 'ppa', 'Pp3c12_19450' => 'ppa', 'Pp3c14_1480' => 'ppa', 'Pp3c14_1501' => 'ppa', 'Pp3c16_4900' => 'ppa', 'Pp3c16_5010' => 'ppa', 'Pp3c16_5060' => 'ppa', 'Pp3c19_18250' => 'ppa', 'Pp3c23_8530' => 'ppa', 'Pp3c23_8550' => 'ppa', 'Pp3c24_9670' => 'ppa', 'Pp3c2_21390' => 'ppa', 'Pp3c2_31380' => 'ppa', 'Pp3c3_16620' => 'ppa', 'Pp3c3_8090' => 'ppa', 'Pp3c3_8110' => 'ppa', 'Pp3c3_8130' => 'ppa', 'Pp3c3_8150' => 'ppa', 'Pp3c4_14320' => 'ppa', 'Pp3c6_2560' => 'ppa', 'Pp3c9_16700' => 'ppa', 'PRCOL_00000234' => 'pco', 'PRCOL_00000235' => 'pco', 'PRCOL_00000777' => 'pco', 'PRCOL_00002344' => 'pco', 'PRCOL_00002372' => 'pco', 'PRCOL_00006120' => 'pco', 'Prupe.1G021400' => 'ppe', 'Prupe.1G021500' => 'ppe', 'Prupe.1G021600' => 'ppe', 'Prupe.1G021700' => 'ppe', 'Prupe.1G021800' => 'ppe', 'Prupe.5G145100' => 'ppe', 'Psat6g204040' => 'psa', 'Psat6g204800' => 'psa', 'Psat6g204920' => 'psa', 'Psat6g204960' => 'psa', 'Psat6g205080' => 'psa', 'PSO017G0271' => 'pso', 'PSO017G1276' => 'pso', 'PSO017G1429' => 'pso', 'PSO017G1861' => 'pso', 'PSO017G2787' => 'pso', 'PSO017G4466' => 'pso', 'PSO017G5118' => 'pso', 'PSO017G5420' => 'pso', 'PSO063G3678' => 'pso', 'PSO210G0546' => 'pso', 'PSO317G0001' => 'pso', 'PSO357G0512' => 'pso', 'PSO478G2682' => 'pso', 'PSO647G0001' => 'pso', 'PSO675G0001' => 'pso', 'PSO675G2699' => 'pso', 'PSO675G2849' => 'pso', 'PSO675G4991' => 'pso', 'PSO689G0001' => 'pso', 'QL06p000916' => 'qlo', 'QL06p000921' => 'qlo', 'QL06p001398' => 'qlo', 'QL06p001407' => 'qlo', 'QL06p002031' => 'qlo', 'RcHm_v2.0_Chr4g0387791' => 'rch', 'RcHm_v2.0_Chr4g0387801' => 'rch', 'RcHm_v2.0_Chr6g0286501' => 'rch', 'RcHm_v2.0_Chr6g0286511' => 'rch', 'RcHm_v2.0_Chr6g0286521' => 'rch', 'RcHm_v2.0_Chr6g0286531' => 'rch', 'RcHm_v2.0_Chr7g0189141' => 'rch', 'Rhsim02G0028700' => 'rsi', 'Rhsim02G0028800' => 'rsi', 'Rhsim02G0028900' => 'rsi', 'Rhsim02G0029000' => 'rsi', 'Rhsim02G0029100' => 'rsi', 'Rhsim02G0029200' => 'rsi', 'Rhsim02G0029300' => 'rsi', 'Rhsim02G0029400' => 'rsi', 'Rhsim02G0029500' => 'rsi', 'Rhsim02G0029600' => 'rsi', 'RhsimUnG0024000' => 'rsi', 'RhsimUnG0024100' => 'rsi', 'RhsimUnG0024200' => 'rsi', 'RhsimUnG0024300' => 'rsi', 'RhsimUnG0024400' => 'rsi', 'RhsimUnG0024500' => 'rsi', 'RhsimUnG0024700' => 'rsi', 'RhsimUnG0024800' => 'rsi', 'RhsimUnG0024900' => 'rsi', 'RhsimUnG0025100' => 'rsi', 'Sabra08G0120200' => 'sbr', 'Sabra08G0120300' => 'sbr', 'Sabra08G0120500' => 'sbr', 'Sabra08G0120600' => 'sbr', 'Sabra10G0158900' => 'sbr', 'SalBow2G3492' => 'sbo', 'Sc13g0004760' => 'sci', 'Sc13g0004770' => 'sci', 'Sed0003417' => 'sed', 'Sed0019750' => 'sed', 'SEGI_03419' => 'sgi', 'SEGI_05907' => 'sgi', 'SEGI_10682' => 'sgi', 'SEGI_13528' => 'sgi', 'SEGI_16081' => 'sgi', 'SEGI_19370' => 'sgi', 'SEGI_21015' => 'sgi', 'SEGI_21944' => 'sgi', 'SEGI_32906' => 'sgi', 'SEGI_33093' => 'sgi', 'SEGI_36110' => 'sgi', 'SEGI_40397' => 'sgi', 'SGA_v2.0_scaffold191G40426' => 'sas', 'SGA_v2.0_scaffold353G49717' => 'sas', 'SGA_v2.0_scaffold50G18550' => 'sas', 'SMO119G0173' => 'smo', 'SMO172G0002' => 'smo', 'Solyc09g082690.3' => 'sly', 'Solyc09g082700.2' => 'sly', 'Sopen09g031550' => 'spe', 'Sopen09g031560' => 'spe', 'Sp3g20540' => 'spa', 'Sp7g07580' => 'spa', 'TAR134G0002' => 'tar', 'TAR236G0001' => 'tar', 'TAR365G0892' => 'tar', 'TAR636G0166' => 'tar', 'TAR636G0646' => 'tar', 'TAR636G0869' => 'tar', 'TAR636G1317' => 'tar', 'TAR636G1744' => 'tar', 'TAR636G3358' => 'tar', 'TAR636G3436' => 'tar', 'THA.LOC104803047' => 'tha', 'Thecc.04G238900' => 'tca', 'Thhalv10021557m.g' => 'esa', 'Thhalv10026318m.g' => 'esa', 'Thhalv10026335m.g' => 'esa', 'TPR.G17433' => 'tpr', 'TPR.G18915' => 'tpr', 'TPR.G26125' => 'tpr', 'TWI09G0677' => 'twi', 'TWI73G0287' => 'twi', 'unitig_748.g8326' => 'ugi', 'vmacro15370' => 'vma', 'vmacro15371' => 'vma', 'vmacro15372' => 'vma', 'vmacro15373' => 'vma', 'vmacro15374' => 'vma', 'VMungo0720G2826' => 'vmu', 'Zm00001eb116960' => 'zma', 'Zm00001eb301260' => 'zma', 'Zm00001eb301270' => 'zma' ), 'gf_id' => 'HOM05D001460', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001460' ), 'data_identifier' => 'HOM05D001460', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001460', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '433', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p22980' => 'bna', 'A01p32340' => 'bna', 'A03p42970' => 'bna', 'A05p25880' => 'bna', 'Aa31LG8G9320' => 'aar', 'Aa31LG8G9330' => 'aar', 'Aa31LG8G9340' => 'aar', 'Aa31sc221G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1034' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1528' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.829' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2222' => 'aag', 'Ah.12g058830' => 'amhyb', 'Ah.12g058840' => 'amhyb', 'AL3G37160' => 'aly', 'AL7G41310' => 'aly', 'Aqoxy5G00395' => 'aox', 'Aqoxy5G00396' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0C8NZA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5185HY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JZ1PRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MD3LS0' => 'arhy', 'AT3G22840' => 'ath', 'AT4G14690' => 'ath', 'ATR0665G054' => 'atr', 'Atru.chr4.2344' => 'acertr', 'Atru.chr4.2346' => 'acertr', 'Atru.chr4.2347' => 'acertr', 'Atru.chr4.2348' => 'acertr', 'Atru.chr4.2355' => 'acertr', 'Atru.chr4.2356' => 'acertr', 'Atru.chr4.2358' => 'acertr', 'Atru.chr4.2359' => 'acertr', 'Atru.chr4.2360' => 'acertr', 'Atru.chr4.2361' => 'acertr', 'AUR62030476' => 'cqu', 'AUR62030478' => 'cqu', 'AUR62030819' => 'cqu', 'AUR62030820' => 'cqu', 'BcaB03g14648' => 'bca', 'BcaB04g20492' => 'bca', 'BcaB06g26399' => 'bca', 'BcaC01g03416' => 'bca', 'BcaC01g03419' => 'bca', 'BcaC01g03421' => 'bca', 'BcaC01g03424' => 'bca', 'BcaC05g28012' => 'bca', 'BcaC09g49212' => 'bca', 'BcaC09g50140' => 'bca', 'BcaNung00346' => 'bca', 'BolC1t02785H' => 'bol', 'BolC1t04095H' => 'bol', 'BolC3t17545H' => 'bol', 'BolC5t32769H' => 'bol', 'BraA01t02211Z' => 'bra', 'BraA01t03359Z' => 'bra', 'BraA03t13441Z' => 'bra', 'BraA05t21476Z' => 'bra', 'C01p28420' => 'bna', 'C01p41350' => 'bna', 'C03p52750' => 'bna', 'C03p52780' => 'bna', 'C05p40270' => 'bna', 'CAN.G1437.9' => 'can', 'CANSAT78G0035' => 'cansat', 'CANSAT78G1036' => 'cansat', 'CANSAT78G2272' => 'cansat', 'CANSAT78G2478' => 'cansat', 'CARHR098700' => 'chi', 'CARHR221120' => 'chi', 'CARHR221150' => 'chi', 'Carub.0003s2297' => 'cru', 'Carub.0007s2749' => 'cru', 'Carub.0007s2750' => 'cru', 'Carub.0007s2751' => 'cru', 'Ca_10849_v3' => 'car', 'Cc03_g04300' => 'ccan', 'CDE02G3648' => 'cde', 'CDE05G0060' => 'cde', 'CDE05G0692' => 'cde', 'CDE05G2285' => 'cde', 'CDE05G2884' => 'cde', 'CDE05G3072' => 'cde', 'Cfa008439' => 'cfa', 'Cfa008441' => 'cfa', 'Cfa008443' => 'cfa', 'Cfa008448' => 'cfa', 'Ciclev10005974m.g' => 'ccl', 'Ciclev10006006m.g' => 'ccl', 'Ciclev10006775m.g' => 'ccl', 'CiPaw.02G120400' => 'cil', 'CiPaw.02G120500' => 'cil', 'CiPaw.02G120600' => 'cil', 'ClCG05G004850' => 'cla', 'COL.COLO4_21566' => 'col', 'Cpa.g.sc44.124' => 'cpa', 'Cre07.g320400' => 'cre', 'Cre07.g320450' => 'cre', 'Cre08.g384650' => 'cre', 'Cre09.g393173' => 'cre', 'Cre09.g394325' => 'cre', 'Cre14.g626750' => 'cre', 'Cre16.g679250' => 'cre', 'CsaV3_3G012890' => 'csa', 'CSS0010865' => 'camsi', 'CSS0044338' => 'camsi', 'DCAR_002366' => 'dca', 'DCAR_030687' => 'dca', 'DCAR_030688' => 'dca', 'Dinv14047' => 'din', 'Dinv14048' => 'din', 'Duzib151G0105' => 'dzi', 'Duzib151G0114' => 'dzi', 'Duzib212G1029' => 'dzi', 'ECA232G3536' => 'eca', 'ECA240G0786' => 'eca', 'ECA240G1802' => 'eca', 'ECA240G3760' => 'eca', 'ECA240G3920' => 'eca', 'EL10Ac5g12536' => 'bvu', 'EL10Ac5g12537' => 'bvu', 'EL10Ac5g12538' => 'bvu', 'Eucgr.B01004' => 'egr', 'Eucgr.B01006' => 'egr', 'Eucgr.B01007' => 'egr', 'Eucgr.B01008' => 'egr', 'Eucgr.B01895' => 'egr', 'Eucgr.B01896' => 'egr', 'FAN04G1456' => 'fan', 'FAN08G1769' => 'fan', 'FAN08G2160' => 'fan', 'FAN13G2403' => 'fan', 'FAN13G3303' => 'fan', 'FAN15G2435' => 'fan', 'FAN17G0672' => 'fan', 'FAN17G2441' => 'fan', 'FAN18G1024' => 'fan', 'FAN22G1458' => 'fan', 'FAN24G0037' => 'fan', 'FAN24G0429' => 'fan', 'FAN24G2387' => 'fan', 'FAN27G2746' => 'fan', 'FvH4_2g20400' => 'fve', 'FvH4_2g20420' => 'fve', 'FvH4_2g20430' => 'fve', 'FvH4_4g01270' => 'fve', 'FvH4_4g01290' => 'fve', 'FvH4_4g01300' => 'fve', 'FvH4_4g01310' => 'fve', 'FvH4_4g01330' => 'fve', 'FvH4_5g09070' => 'fve', 'Glyma.10G243800' => 'gma', 'Glyma.20G150600' => 'gma', 'Gohir.A09G219200' => 'ghi', 'Gohir.A09G219300' => 'ghi', 'Gohir.D09G221400' => 'ghi', 'Gohir.D09G221500' => 'ghi', 'Gorai.006G242600' => 'gra', 'Gorai.006G242700' => 'gra', 'GSVIVG01018044001' => 'vvi', 'HanXRQChr03g0083821' => 'han', 'HanXRQChr03g0083841' => 'han', 'HanXRQChr03g0083881' => 'han', 'HanXRQChr03g0083901' => 'han', 'HanXRQChr03g0083921' => 'han', 'HanXRQChr03g0085331' => 'han', 'HanXRQChr03g0085361' => 'han', 'HanXRQChr03g0085411' => 'han', 'HanXRQChr03g0085421' => 'han', 'HanXRQChr03g0085431' => 'han', 'HanXRQChr08g0221991' => 'han', 'HanXRQChr11g0336061' => 'han', 'HanXRQChr11g0336411' => 'han', 'Haze_11234' => 'cav', 'Hma1.2p1_0549F.1_g177010' => 'hma', 'Hma1.2p1_0602F.1_g187630' => 'hma', 'Hund14876' => 'sun', 'Hund14879' => 'sun', 'Lalb_Chr06g0160741' => 'lal', 'Lalb_Chr21g0304781' => 'lal', 'Lj3A726G19' => 'lonja', 'Lj3A726T23' => 'lonja', 'Lj3A726T24' => 'lonja', 'Lj3A726T25' => 'lonja', 'Lj3A727T17' => 'lonja', 'Lj3C726T0' => 'lonja', 'Lj3C726T2' => 'lonja', 'Lj3P725T35' => 'lonja', 'Lj3P727T10' => 'lonja', 'Lj3P727T12' => 'lonja', 'Lj3P727T14' => 'lonja', 'Lj5g0023109' => 'lja', 'Lj6P646T44' => 'lonja', 'Lsat_1_v5_gn_6_75760' => 'lsa', 'Lsat_1_v5_gn_6_75800' => 'lsa', 'Lsat_1_v5_gn_6_75900' => 'lsa', 'Lsat_1_v5_gn_6_76240' => 'lsa', 'Lsat_1_v5_gn_6_76441' => 'lsa', 'Lsat_1_v5_gn_6_76700' => 'lsa', 'Lsat_1_v5_gn_6_76760' => 'lsa', 'Manes.15G033100' => 'mes', 'Mapoly0004s0074' => 'mpo', 'Mapoly0004s0075' => 'mpo', 'Mapoly0004s0163' => 'mpo', 'Mapoly0004s0164' => 'mpo', 'Mapoly0021s0018' => 'mpo', 'Mapoly0041s0136' => 'mpo', 'Mapoly0041s0137' => 'mpo', 'Mapoly0041s0138' => 'mpo', 'Mapoly0041s0139' => 'mpo', 'Mapoly0041s0141' => 'mpo', 'Mapoly0041s0142' => 'mpo', 'Mapoly0041s0143' => 'mpo', 'Mapoly0041s0144' => 'mpo', 'Mapoly0041s0145' => 'mpo', 'Mapoly0047s0106' => 'mpo', 'Mapoly0047s0108' => 'mpo', 'Mapoly0050s0051' => 'mpo', 'Mapoly0050s0052' => 'mpo', 'Mapoly0050s0053' => 'mpo', 'Mapoly0058s0013' => 'mpo', 'Mapoly0091s0078' => 'mpo', 'Mapoly0091s0079' => 'mpo', 'Mapoly0091s0080' => 'mpo', 'Mapoly0091s0081' => 'mpo', 'Mapoly0278s0004' => 'mpo', 'Mapoly0278s0005' => 'mpo', 'Mapoly0278s0006' => 'mpo', 'MBI11_g30648_MAGBIO' => 'mbi', 'MCO03G194' => 'mco', 'MCO03G590' => 'mco', 'MCO07G312' => 'mco', 'MCO10G318' => 'mco', 'MCO12G244' => 'mco', 'MCO13G148' => 'mco', 'MCO13G194' => 'mco', 'MCO16G238' => 'mco', 'MD06G1134100' => 'mdo', 'MD13G1200100' => 'mdo', 'MD13G1200300' => 'mdo', 'MD13G1200600' => 'mdo', 'MD14G1150400' => 'mdo', 'MD16G1200000' => 'mdo', 'Medtr1g102570' => 'mtr', 'Medtr1g102780' => 'mtr', 'Medtr1g102800' => 'mtr', 'Medtr1g102810' => 'mtr', 'Medtr1g102830' => 'mtr', 'MELO3C006499.2' => 'cme', 'Migut.G00385' => 'egut', 'MSTRG.4063' => 'ama', 'Nitab4.5_0000090g0260' => 'nta', 'Nitab4.5_0000977g0030' => 'nta', 'Nitab4.5_0002541g0040' => 'nta', 'Nitab4.5_0007068g0040' => 'nta', 'Nn005s41408' => 'nnu', 'Nn005s41410' => 'nnu', 'Oeu010310.1' => 'oeu', 'Oeu010311.1' => 'oeu', 'Oeu043472.1' => 'oeu', 'Os01g0246400' => 'osa', 'Os04g0267950' => 'osa', 'Os07g0178700' => 'osa', 'Os07g0178800' => 'osa', 'Peaxi162Scf00316g00046' => 'pax', 'Peaxi162Scf00316g00049' => 'pax', 'Peaxi162Scf00316g00059' => 'pax', 'Peaxi162Scf00316g00328' => 'pax', 'Peaxi162Scf00316g00329' => 'pax', 'Peaxi162Scf00316g00411' => 'pax', 'Peaxi162Scf00316g00521' => 'pax', 'Peaxi162Scf00492g00068' => 'pax', 'Peaxi162Scf35631g00002' => 'pax', 'PGR142G3720' => 'pgr', 'PGSC0003DMG400006442' => 'stu', 'Phvul.007G062000' => 'pvu', 'Potri.008G157750' => 'ptr', 'Potri.008G157900' => 'ptr', 'Potri.008G158000' => 'ptr', 'Potri.008G158200' => 'ptr', 'Pp3c11_7280' => 'ppa', 'Pp3c11_7980' => 'ppa', 'Pp3c12_19450' => 'ppa', 'Pp3c14_1480' => 'ppa', 'Pp3c14_1501' => 'ppa', 'Pp3c16_4900' => 'ppa', 'Pp3c16_5010' => 'ppa', 'Pp3c16_5060' => 'ppa', 'Pp3c19_18250' => 'ppa', 'Pp3c23_8530' => 'ppa', 'Pp3c23_8550' => 'ppa', 'Pp3c24_9670' => 'ppa', 'Pp3c2_21390' => 'ppa', 'Pp3c2_31380' => 'ppa', 'Pp3c3_16620' => 'ppa', 'Pp3c3_8090' => 'ppa', 'Pp3c3_8110' => 'ppa', 'Pp3c3_8130' => 'ppa', 'Pp3c3_8150' => 'ppa', 'Pp3c4_14320' => 'ppa', 'Pp3c6_2560' => 'ppa', 'Pp3c9_16700' => 'ppa', 'PRCOL_00000234' => 'pco', 'PRCOL_00000235' => 'pco', 'PRCOL_00000777' => 'pco', 'PRCOL_00002344' => 'pco', 'PRCOL_00002372' => 'pco', 'PRCOL_00006120' => 'pco', 'Prupe.1G021400' => 'ppe', 'Prupe.1G021500' => 'ppe', 'Prupe.1G021600' => 'ppe', 'Prupe.1G021700' => 'ppe', 'Prupe.1G021800' => 'ppe', 'Prupe.5G145100' => 'ppe', 'Psat6g204040' => 'psa', 'Psat6g204800' => 'psa', 'Psat6g204920' => 'psa', 'Psat6g204960' => 'psa', 'Psat6g205080' => 'psa', 'PSO017G0271' => 'pso', 'PSO017G1276' => 'pso', 'PSO017G1429' => 'pso', 'PSO017G1861' => 'pso', 'PSO017G2787' => 'pso', 'PSO017G4466' => 'pso', 'PSO017G5118' => 'pso', 'PSO017G5420' => 'pso', 'PSO063G3678' => 'pso', 'PSO210G0546' => 'pso', 'PSO317G0001' => 'pso', 'PSO357G0512' => 'pso', 'PSO478G2682' => 'pso', 'PSO647G0001' => 'pso', 'PSO675G0001' => 'pso', 'PSO675G2699' => 'pso', 'PSO675G2849' => 'pso', 'PSO675G4991' => 'pso', 'PSO689G0001' => 'pso', 'QL06p000916' => 'qlo', 'QL06p000921' => 'qlo', 'QL06p001398' => 'qlo', 'QL06p001407' => 'qlo', 'QL06p002031' => 'qlo', 'RcHm_v2.0_Chr4g0387791' => 'rch', 'RcHm_v2.0_Chr4g0387801' => 'rch', 'RcHm_v2.0_Chr6g0286501' => 'rch', 'RcHm_v2.0_Chr6g0286511' => 'rch', 'RcHm_v2.0_Chr6g0286521' => 'rch', 'RcHm_v2.0_Chr6g0286531' => 'rch', 'RcHm_v2.0_Chr7g0189141' => 'rch', 'Rhsim02G0028700' => 'rsi', 'Rhsim02G0028800' => 'rsi', 'Rhsim02G0028900' => 'rsi', 'Rhsim02G0029000' => 'rsi', 'Rhsim02G0029100' => 'rsi', 'Rhsim02G0029200' => 'rsi', 'Rhsim02G0029300' => 'rsi', 'Rhsim02G0029400' => 'rsi', 'Rhsim02G0029500' => 'rsi', 'Rhsim02G0029600' => 'rsi', 'RhsimUnG0024000' => 'rsi', 'RhsimUnG0024100' => 'rsi', 'RhsimUnG0024200' => 'rsi', 'RhsimUnG0024300' => 'rsi', 'RhsimUnG0024400' => 'rsi', 'RhsimUnG0024500' => 'rsi', 'RhsimUnG0024700' => 'rsi', 'RhsimUnG0024800' => 'rsi', 'RhsimUnG0024900' => 'rsi', 'RhsimUnG0025100' => 'rsi', 'Sabra08G0120200' => 'sbr', 'Sabra08G0120300' => 'sbr', 'Sabra08G0120500' => 'sbr', 'Sabra08G0120600' => 'sbr', 'Sabra10G0158900' => 'sbr', 'SalBow2G3492' => 'sbo', 'Sc13g0004760' => 'sci', 'Sc13g0004770' => 'sci', 'Sed0003417' => 'sed', 'Sed0019750' => 'sed', 'SEGI_03419' => 'sgi', 'SEGI_05907' => 'sgi', 'SEGI_10682' => 'sgi', 'SEGI_13528' => 'sgi', 'SEGI_16081' => 'sgi', 'SEGI_19370' => 'sgi', 'SEGI_21015' => 'sgi', 'SEGI_21944' => 'sgi', 'SEGI_32906' => 'sgi', 'SEGI_33093' => 'sgi', 'SEGI_36110' => 'sgi', 'SEGI_40397' => 'sgi', 'SGA_v2.0_scaffold191G40426' => 'sas', 'SGA_v2.0_scaffold353G49717' => 'sas', 'SGA_v2.0_scaffold50G18550' => 'sas', 'SMO119G0173' => 'smo', 'SMO172G0002' => 'smo', 'Solyc09g082690.3' => 'sly', 'Solyc09g082700.2' => 'sly', 'Sopen09g031550' => 'spe', 'Sopen09g031560' => 'spe', 'Sp3g20540' => 'spa', 'Sp7g07580' => 'spa', 'TAR134G0002' => 'tar', 'TAR236G0001' => 'tar', 'TAR365G0892' => 'tar', 'TAR636G0166' => 'tar', 'TAR636G0646' => 'tar', 'TAR636G0869' => 'tar', 'TAR636G1317' => 'tar', 'TAR636G1744' => 'tar', 'TAR636G3358' => 'tar', 'TAR636G3436' => 'tar', 'THA.LOC104803047' => 'tha', 'Thecc.04G238900' => 'tca', 'Thhalv10021557m.g' => 'esa', 'Thhalv10026318m.g' => 'esa', 'Thhalv10026335m.g' => 'esa', 'TPR.G17433' => 'tpr', 'TPR.G18915' => 'tpr', 'TPR.G26125' => 'tpr', 'TWI09G0677' => 'twi', 'TWI73G0287' => 'twi', 'unitig_748.g8326' => 'ugi', 'vmacro15370' => 'vma', 'vmacro15371' => 'vma', 'vmacro15372' => 'vma', 'vmacro15373' => 'vma', 'vmacro15374' => 'vma', 'VMungo0720G2826' => 'vmu', 'Zm00001eb116960' => 'zma', 'Zm00001eb301260' => 'zma', 'Zm00001eb301270' => 'zma' ) $gf_id = 'HOM05D001460' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001460' ) $data_identifier = 'HOM05D001460' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 4, 'aag' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 2, 'aox' => (int) 2, 'arhy' => (int) 4, 'ath' => (int) 2, 'atr' => (int) 1, 'acertr' => (int) 10, 'cqu' => (int) 4, 'bca' => (int) 11, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 1, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 1, 'ccan' => (int) 1, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 1, 'col' => (int) 1, 'cpa' => (int) 1, 'cre' => (int) 7, 'csa' => (int) 1, 'camsi' => (int) 2, 'dca' => (int) 3, 'din' => (int) 2, 'dzi' => (int) 3, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 14, 'fve' => (int) 9, 'gma' => (int) 2, 'ghi' => (int) 4, 'gra' => (int) 2, 'vvi' => (int) 1, 'han' => (int) 13, 'cav' => (int) 1, 'hma' => (int) 2, 'sun' => (int) 2, 'lal' => (int) 2, 'lonja' => (int) 12, 'lja' => (int) 1, 'lsa' => (int) 7, 'mes' => (int) 1, 'mpo' => (int) 27, 'mbi' => (int) 1, 'mco' => (int) 8, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 1, 'egut' => (int) 1, 'ama' => (int) 1, 'nta' => (int) 4, 'nnu' => (int) 2, 'oeu' => (int) 3, 'osa' => (int) 4, 'pax' => (int) 9, 'pgr' => (int) 1, 'stu' => (int) 1, 'pvu' => (int) 1, 'ptr' => (int) 4, 'ppa' => (int) 22, 'pco' => (int) 6, 'ppe' => (int) 6, 'psa' => (int) 5, 'pso' => (int) 19, 'qlo' => (int) 5, 'rch' => (int) 7, 'rsi' => (int) 20, 'sbr' => (int) 5, 'sbo' => (int) 1, 'sci' => (int) 2, 'sed' => (int) 2, 'sgi' => (int) 12, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 2, 'tar' => (int) 10, 'tha' => (int) 1, 'tca' => (int) 1, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 2, 'ugi' => (int) 1, 'vma' => (int) 5, 'vmu' => (int) 1, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb301270' $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' => 'HOM05D001460', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '433', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p22980' => 'bna', 'A01p32340' => 'bna', 'A03p42970' => 'bna', 'A05p25880' => 'bna', 'Aa31LG8G9320' => 'aar', 'Aa31LG8G9330' => 'aar', 'Aa31LG8G9340' => 'aar', 'Aa31sc221G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1034' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1528' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.829' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2222' => 'aag', 'Ah.12g058830' => 'amhyb', 'Ah.12g058840' => 'amhyb', 'AL3G37160' => 'aly', 'AL7G41310' => 'aly', 'Aqoxy5G00395' => 'aox', 'Aqoxy5G00396' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0C8NZA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5185HY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JZ1PRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MD3LS0' => 'arhy', 'AT3G22840' => 'ath', 'AT4G14690' => 'ath', 'ATR0665G054' => 'atr', 'Atru.chr4.2344' => 'acertr', 'Atru.chr4.2346' => 'acertr', 'Atru.chr4.2347' => 'acertr', 'Atru.chr4.2348' => 'acertr', 'Atru.chr4.2355' => 'acertr', 'Atru.chr4.2356' => 'acertr', 'Atru.chr4.2358' => 'acertr', 'Atru.chr4.2359' => 'acertr', 'Atru.chr4.2360' => 'acertr', 'Atru.chr4.2361' => 'acertr', 'AUR62030476' => 'cqu', 'AUR62030478' => 'cqu', 'AUR62030819' => 'cqu', 'AUR62030820' => 'cqu', 'BcaB03g14648' => 'bca', 'BcaB04g20492' => 'bca', 'BcaB06g26399' => 'bca', 'BcaC01g03416' => 'bca', 'BcaC01g03419' => 'bca', 'BcaC01g03421' => 'bca', 'BcaC01g03424' => 'bca', 'BcaC05g28012' => 'bca', 'BcaC09g49212' => 'bca', 'BcaC09g50140' => 'bca', 'BcaNung00346' => 'bca', 'BolC1t02785H' => 'bol', 'BolC1t04095H' => 'bol', 'BolC3t17545H' => 'bol', 'BolC5t32769H' => 'bol', 'BraA01t02211Z' => 'bra', 'BraA01t03359Z' => 'bra', 'BraA03t13441Z' => 'bra', 'BraA05t21476Z' => 'bra', 'C01p28420' => 'bna', 'C01p41350' => 'bna', 'C03p52750' => 'bna', 'C03p52780' => 'bna', 'C05p40270' => 'bna', 'CAN.G1437.9' => 'can', 'CANSAT78G0035' => 'cansat', 'CANSAT78G1036' => 'cansat', 'CANSAT78G2272' => 'cansat', 'CANSAT78G2478' => 'cansat', 'CARHR098700' => 'chi', 'CARHR221120' => 'chi', 'CARHR221150' => 'chi', 'Carub.0003s2297' => 'cru', 'Carub.0007s2749' => 'cru', 'Carub.0007s2750' => 'cru', 'Carub.0007s2751' => 'cru', 'Ca_10849_v3' => 'car', 'Cc03_g04300' => 'ccan', 'CDE02G3648' => 'cde', 'CDE05G0060' => 'cde', 'CDE05G0692' => 'cde', 'CDE05G2285' => 'cde', 'CDE05G2884' => 'cde', 'CDE05G3072' => 'cde', 'Cfa008439' => 'cfa', 'Cfa008441' => 'cfa', 'Cfa008443' => 'cfa', 'Cfa008448' => 'cfa', 'Ciclev10005974m.g' => 'ccl', 'Ciclev10006006m.g' => 'ccl', 'Ciclev10006775m.g' => 'ccl', 'CiPaw.02G120400' => 'cil', 'CiPaw.02G120500' => 'cil', 'CiPaw.02G120600' => 'cil', 'ClCG05G004850' => 'cla', 'COL.COLO4_21566' => 'col', 'Cpa.g.sc44.124' => 'cpa', 'Cre07.g320400' => 'cre', 'Cre07.g320450' => 'cre', 'Cre08.g384650' => 'cre', 'Cre09.g393173' => 'cre', 'Cre09.g394325' => 'cre', 'Cre14.g626750' => 'cre', 'Cre16.g679250' => 'cre', 'CsaV3_3G012890' => 'csa', 'CSS0010865' => 'camsi', 'CSS0044338' => 'camsi', 'DCAR_002366' => 'dca', 'DCAR_030687' => 'dca', 'DCAR_030688' => 'dca', 'Dinv14047' => 'din', 'Dinv14048' => 'din', 'Duzib151G0105' => 'dzi', 'Duzib151G0114' => 'dzi', 'Duzib212G1029' => 'dzi', 'ECA232G3536' => 'eca', 'ECA240G0786' => 'eca', 'ECA240G1802' => 'eca', 'ECA240G3760' => 'eca', 'ECA240G3920' => 'eca', 'EL10Ac5g12536' => 'bvu', 'EL10Ac5g12537' => 'bvu', 'EL10Ac5g12538' => 'bvu', 'Eucgr.B01004' => 'egr', 'Eucgr.B01006' => 'egr', 'Eucgr.B01007' => 'egr', 'Eucgr.B01008' => 'egr', 'Eucgr.B01895' => 'egr', 'Eucgr.B01896' => 'egr', 'FAN04G1456' => 'fan', 'FAN08G1769' => 'fan', 'FAN08G2160' => 'fan', 'FAN13G2403' => 'fan', 'FAN13G3303' => 'fan', 'FAN15G2435' => 'fan', 'FAN17G0672' => 'fan', 'FAN17G2441' => 'fan', 'FAN18G1024' => 'fan', 'FAN22G1458' => 'fan', 'FAN24G0037' => 'fan', 'FAN24G0429' => 'fan', 'FAN24G2387' => 'fan', 'FAN27G2746' => 'fan', 'FvH4_2g20400' => 'fve', 'FvH4_2g20420' => 'fve', 'FvH4_2g20430' => 'fve', 'FvH4_4g01270' => 'fve', 'FvH4_4g01290' => 'fve', 'FvH4_4g01300' => 'fve', 'FvH4_4g01310' => 'fve', 'FvH4_4g01330' => 'fve', 'FvH4_5g09070' => 'fve', 'Glyma.10G243800' => 'gma', 'Glyma.20G150600' => 'gma', 'Gohir.A09G219200' => 'ghi', 'Gohir.A09G219300' => 'ghi', 'Gohir.D09G221400' => 'ghi', 'Gohir.D09G221500' => 'ghi', 'Gorai.006G242600' => 'gra', 'Gorai.006G242700' => 'gra', 'GSVIVG01018044001' => 'vvi', 'HanXRQChr03g0083821' => 'han', 'HanXRQChr03g0083841' => 'han', 'HanXRQChr03g0083881' => 'han', 'HanXRQChr03g0083901' => 'han', 'HanXRQChr03g0083921' => 'han', 'HanXRQChr03g0085331' => 'han', 'HanXRQChr03g0085361' => 'han', 'HanXRQChr03g0085411' => 'han', 'HanXRQChr03g0085421' => 'han', 'HanXRQChr03g0085431' => 'han', 'HanXRQChr08g0221991' => 'han', 'HanXRQChr11g0336061' => 'han', 'HanXRQChr11g0336411' => 'han', 'Haze_11234' => 'cav', 'Hma1.2p1_0549F.1_g177010' => 'hma', 'Hma1.2p1_0602F.1_g187630' => 'hma', 'Hund14876' => 'sun', 'Hund14879' => 'sun', 'Lalb_Chr06g0160741' => 'lal', 'Lalb_Chr21g0304781' => 'lal', 'Lj3A726G19' => 'lonja', 'Lj3A726T23' => 'lonja', 'Lj3A726T24' => 'lonja', 'Lj3A726T25' => 'lonja', 'Lj3A727T17' => 'lonja', 'Lj3C726T0' => 'lonja', 'Lj3C726T2' => 'lonja', 'Lj3P725T35' => 'lonja', 'Lj3P727T10' => 'lonja', 'Lj3P727T12' => 'lonja', 'Lj3P727T14' => 'lonja', 'Lj5g0023109' => 'lja', 'Lj6P646T44' => 'lonja', 'Lsat_1_v5_gn_6_75760' => 'lsa', 'Lsat_1_v5_gn_6_75800' => 'lsa', 'Lsat_1_v5_gn_6_75900' => 'lsa', 'Lsat_1_v5_gn_6_76240' => 'lsa', 'Lsat_1_v5_gn_6_76441' => 'lsa', 'Lsat_1_v5_gn_6_76700' => 'lsa', 'Lsat_1_v5_gn_6_76760' => 'lsa', 'Manes.15G033100' => 'mes', 'Mapoly0004s0074' => 'mpo', 'Mapoly0004s0075' => 'mpo', 'Mapoly0004s0163' => 'mpo', 'Mapoly0004s0164' => 'mpo', 'Mapoly0021s0018' => 'mpo', 'Mapoly0041s0136' => 'mpo', 'Mapoly0041s0137' => 'mpo', 'Mapoly0041s0138' => 'mpo', 'Mapoly0041s0139' => 'mpo', 'Mapoly0041s0141' => 'mpo', 'Mapoly0041s0142' => 'mpo', 'Mapoly0041s0143' => 'mpo', 'Mapoly0041s0144' => 'mpo', 'Mapoly0041s0145' => 'mpo', 'Mapoly0047s0106' => 'mpo', 'Mapoly0047s0108' => 'mpo', 'Mapoly0050s0051' => 'mpo', 'Mapoly0050s0052' => 'mpo', 'Mapoly0050s0053' => 'mpo', 'Mapoly0058s0013' => 'mpo', 'Mapoly0091s0078' => 'mpo', 'Mapoly0091s0079' => 'mpo', 'Mapoly0091s0080' => 'mpo', 'Mapoly0091s0081' => 'mpo', 'Mapoly0278s0004' => 'mpo', 'Mapoly0278s0005' => 'mpo', 'Mapoly0278s0006' => 'mpo', 'MBI11_g30648_MAGBIO' => 'mbi', 'MCO03G194' => 'mco', 'MCO03G590' => 'mco', 'MCO07G312' => 'mco', 'MCO10G318' => 'mco', 'MCO12G244' => 'mco', 'MCO13G148' => 'mco', 'MCO13G194' => 'mco', 'MCO16G238' => 'mco', 'MD06G1134100' => 'mdo', 'MD13G1200100' => 'mdo', 'MD13G1200300' => 'mdo', 'MD13G1200600' => 'mdo', 'MD14G1150400' => 'mdo', 'MD16G1200000' => 'mdo', 'Medtr1g102570' => 'mtr', 'Medtr1g102780' => 'mtr', 'Medtr1g102800' => 'mtr', 'Medtr1g102810' => 'mtr', 'Medtr1g102830' => 'mtr', 'MELO3C006499.2' => 'cme', 'Migut.G00385' => 'egut', 'MSTRG.4063' => 'ama', 'Nitab4.5_0000090g0260' => 'nta', 'Nitab4.5_0000977g0030' => 'nta', 'Nitab4.5_0002541g0040' => 'nta', 'Nitab4.5_0007068g0040' => 'nta', 'Nn005s41408' => 'nnu', 'Nn005s41410' => 'nnu', 'Oeu010310.1' => 'oeu', 'Oeu010311.1' => 'oeu', 'Oeu043472.1' => 'oeu', 'Os01g0246400' => 'osa', 'Os04g0267950' => 'osa', 'Os07g0178700' => 'osa', 'Os07g0178800' => 'osa', 'Peaxi162Scf00316g00046' => 'pax', 'Peaxi162Scf00316g00049' => 'pax', 'Peaxi162Scf00316g00059' => 'pax', 'Peaxi162Scf00316g00328' => 'pax', 'Peaxi162Scf00316g00329' => 'pax', 'Peaxi162Scf00316g00411' => 'pax', 'Peaxi162Scf00316g00521' => 'pax', 'Peaxi162Scf00492g00068' => 'pax', 'Peaxi162Scf35631g00002' => 'pax', 'PGR142G3720' => 'pgr', 'PGSC0003DMG400006442' => 'stu', 'Phvul.007G062000' => 'pvu', 'Potri.008G157750' => 'ptr', 'Potri.008G157900' => 'ptr', 'Potri.008G158000' => 'ptr', 'Potri.008G158200' => 'ptr', 'Pp3c11_7280' => 'ppa', 'Pp3c11_7980' => 'ppa', 'Pp3c12_19450' => 'ppa', 'Pp3c14_1480' => 'ppa', 'Pp3c14_1501' => 'ppa', 'Pp3c16_4900' => 'ppa', 'Pp3c16_5010' => 'ppa', 'Pp3c16_5060' => 'ppa', 'Pp3c19_18250' => 'ppa', 'Pp3c23_8530' => 'ppa', 'Pp3c23_8550' => 'ppa', 'Pp3c24_9670' => 'ppa', 'Pp3c2_21390' => 'ppa', 'Pp3c2_31380' => 'ppa', 'Pp3c3_16620' => 'ppa', 'Pp3c3_8090' => 'ppa', 'Pp3c3_8110' => 'ppa', 'Pp3c3_8130' => 'ppa', 'Pp3c3_8150' => 'ppa', 'Pp3c4_14320' => 'ppa', 'Pp3c6_2560' => 'ppa', 'Pp3c9_16700' => 'ppa', 'PRCOL_00000234' => 'pco', 'PRCOL_00000235' => 'pco', 'PRCOL_00000777' => 'pco', 'PRCOL_00002344' => 'pco', 'PRCOL_00002372' => 'pco', 'PRCOL_00006120' => 'pco', 'Prupe.1G021400' => 'ppe', 'Prupe.1G021500' => 'ppe', 'Prupe.1G021600' => 'ppe', 'Prupe.1G021700' => 'ppe', 'Prupe.1G021800' => 'ppe', 'Prupe.5G145100' => 'ppe', 'Psat6g204040' => 'psa', 'Psat6g204800' => 'psa', 'Psat6g204920' => 'psa', 'Psat6g204960' => 'psa', 'Psat6g205080' => 'psa', 'PSO017G0271' => 'pso', 'PSO017G1276' => 'pso', 'PSO017G1429' => 'pso', 'PSO017G1861' => 'pso', 'PSO017G2787' => 'pso', 'PSO017G4466' => 'pso', 'PSO017G5118' => 'pso', 'PSO017G5420' => 'pso', 'PSO063G3678' => 'pso', 'PSO210G0546' => 'pso', 'PSO317G0001' => 'pso', 'PSO357G0512' => 'pso', 'PSO478G2682' => 'pso', 'PSO647G0001' => 'pso', 'PSO675G0001' => 'pso', 'PSO675G2699' => 'pso', 'PSO675G2849' => 'pso', 'PSO675G4991' => 'pso', 'PSO689G0001' => 'pso', 'QL06p000916' => 'qlo', 'QL06p000921' => 'qlo', 'QL06p001398' => 'qlo', 'QL06p001407' => 'qlo', 'QL06p002031' => 'qlo', 'RcHm_v2.0_Chr4g0387791' => 'rch', 'RcHm_v2.0_Chr4g0387801' => 'rch', 'RcHm_v2.0_Chr6g0286501' => 'rch', 'RcHm_v2.0_Chr6g0286511' => 'rch', 'RcHm_v2.0_Chr6g0286521' => 'rch', 'RcHm_v2.0_Chr6g0286531' => 'rch', 'RcHm_v2.0_Chr7g0189141' => 'rch', 'Rhsim02G0028700' => 'rsi', 'Rhsim02G0028800' => 'rsi', 'Rhsim02G0028900' => 'rsi', 'Rhsim02G0029000' => 'rsi', 'Rhsim02G0029100' => 'rsi', 'Rhsim02G0029200' => 'rsi', 'Rhsim02G0029300' => 'rsi', 'Rhsim02G0029400' => 'rsi', 'Rhsim02G0029500' => 'rsi', 'Rhsim02G0029600' => 'rsi', 'RhsimUnG0024000' => 'rsi', 'RhsimUnG0024100' => 'rsi', 'RhsimUnG0024200' => 'rsi', 'RhsimUnG0024300' => 'rsi', 'RhsimUnG0024400' => 'rsi', 'RhsimUnG0024500' => 'rsi', 'RhsimUnG0024700' => 'rsi', 'RhsimUnG0024800' => 'rsi', 'RhsimUnG0024900' => 'rsi', 'RhsimUnG0025100' => 'rsi', 'Sabra08G0120200' => 'sbr', 'Sabra08G0120300' => 'sbr', 'Sabra08G0120500' => 'sbr', 'Sabra08G0120600' => 'sbr', 'Sabra10G0158900' => 'sbr', 'SalBow2G3492' => 'sbo', 'Sc13g0004760' => 'sci', 'Sc13g0004770' => 'sci', 'Sed0003417' => 'sed', 'Sed0019750' => 'sed', 'SEGI_03419' => 'sgi', 'SEGI_05907' => 'sgi', 'SEGI_10682' => 'sgi', 'SEGI_13528' => 'sgi', 'SEGI_16081' => 'sgi', 'SEGI_19370' => 'sgi', 'SEGI_21015' => 'sgi', 'SEGI_21944' => 'sgi', 'SEGI_32906' => 'sgi', 'SEGI_33093' => 'sgi', 'SEGI_36110' => 'sgi', 'SEGI_40397' => 'sgi', 'SGA_v2.0_scaffold191G40426' => 'sas', 'SGA_v2.0_scaffold353G49717' => 'sas', 'SGA_v2.0_scaffold50G18550' => 'sas', 'SMO119G0173' => 'smo', 'SMO172G0002' => 'smo', 'Solyc09g082690.3' => 'sly', 'Solyc09g082700.2' => 'sly', 'Sopen09g031550' => 'spe', 'Sopen09g031560' => 'spe', 'Sp3g20540' => 'spa', 'Sp7g07580' => 'spa', 'TAR134G0002' => 'tar', 'TAR236G0001' => 'tar', 'TAR365G0892' => 'tar', 'TAR636G0166' => 'tar', 'TAR636G0646' => 'tar', 'TAR636G0869' => 'tar', 'TAR636G1317' => 'tar', 'TAR636G1744' => 'tar', 'TAR636G3358' => 'tar', 'TAR636G3436' => 'tar', 'THA.LOC104803047' => 'tha', 'Thecc.04G238900' => 'tca', 'Thhalv10021557m.g' => 'esa', 'Thhalv10026318m.g' => 'esa', 'Thhalv10026335m.g' => 'esa', 'TPR.G17433' => 'tpr', 'TPR.G18915' => 'tpr', 'TPR.G26125' => 'tpr', 'TWI09G0677' => 'twi', 'TWI73G0287' => 'twi', 'unitig_748.g8326' => 'ugi', 'vmacro15370' => 'vma', 'vmacro15371' => 'vma', 'vmacro15372' => 'vma', 'vmacro15373' => 'vma', 'vmacro15374' => 'vma', 'VMungo0720G2826' => 'vmu', 'Zm00001eb116960' => 'zma', 'Zm00001eb301260' => 'zma', 'Zm00001eb301270' => 'zma' ), 'gf_id' => 'HOM05D001460', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001460' ), 'data_identifier' => 'HOM05D001460', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001460', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '433', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p22980' => 'bna', 'A01p32340' => 'bna', 'A03p42970' => 'bna', 'A05p25880' => 'bna', 'Aa31LG8G9320' => 'aar', 'Aa31LG8G9330' => 'aar', 'Aa31LG8G9340' => 'aar', 'Aa31sc221G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1034' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1528' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.829' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2222' => 'aag', 'Ah.12g058830' => 'amhyb', 'Ah.12g058840' => 'amhyb', 'AL3G37160' => 'aly', 'AL7G41310' => 'aly', 'Aqoxy5G00395' => 'aox', 'Aqoxy5G00396' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0C8NZA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5185HY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JZ1PRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MD3LS0' => 'arhy', 'AT3G22840' => 'ath', 'AT4G14690' => 'ath', 'ATR0665G054' => 'atr', 'Atru.chr4.2344' => 'acertr', 'Atru.chr4.2346' => 'acertr', 'Atru.chr4.2347' => 'acertr', 'Atru.chr4.2348' => 'acertr', 'Atru.chr4.2355' => 'acertr', 'Atru.chr4.2356' => 'acertr', 'Atru.chr4.2358' => 'acertr', 'Atru.chr4.2359' => 'acertr', 'Atru.chr4.2360' => 'acertr', 'Atru.chr4.2361' => 'acertr', 'AUR62030476' => 'cqu', 'AUR62030478' => 'cqu', 'AUR62030819' => 'cqu', 'AUR62030820' => 'cqu', 'BcaB03g14648' => 'bca', 'BcaB04g20492' => 'bca', 'BcaB06g26399' => 'bca', 'BcaC01g03416' => 'bca', 'BcaC01g03419' => 'bca', 'BcaC01g03421' => 'bca', 'BcaC01g03424' => 'bca', 'BcaC05g28012' => 'bca', 'BcaC09g49212' => 'bca', 'BcaC09g50140' => 'bca', 'BcaNung00346' => 'bca', 'BolC1t02785H' => 'bol', 'BolC1t04095H' => 'bol', 'BolC3t17545H' => 'bol', 'BolC5t32769H' => 'bol', 'BraA01t02211Z' => 'bra', 'BraA01t03359Z' => 'bra', 'BraA03t13441Z' => 'bra', 'BraA05t21476Z' => 'bra', 'C01p28420' => 'bna', 'C01p41350' => 'bna', 'C03p52750' => 'bna', 'C03p52780' => 'bna', 'C05p40270' => 'bna', 'CAN.G1437.9' => 'can', 'CANSAT78G0035' => 'cansat', 'CANSAT78G1036' => 'cansat', 'CANSAT78G2272' => 'cansat', 'CANSAT78G2478' => 'cansat', 'CARHR098700' => 'chi', 'CARHR221120' => 'chi', 'CARHR221150' => 'chi', 'Carub.0003s2297' => 'cru', 'Carub.0007s2749' => 'cru', 'Carub.0007s2750' => 'cru', 'Carub.0007s2751' => 'cru', 'Ca_10849_v3' => 'car', 'Cc03_g04300' => 'ccan', 'CDE02G3648' => 'cde', 'CDE05G0060' => 'cde', 'CDE05G0692' => 'cde', 'CDE05G2285' => 'cde', 'CDE05G2884' => 'cde', 'CDE05G3072' => 'cde', 'Cfa008439' => 'cfa', 'Cfa008441' => 'cfa', 'Cfa008443' => 'cfa', 'Cfa008448' => 'cfa', 'Ciclev10005974m.g' => 'ccl', 'Ciclev10006006m.g' => 'ccl', 'Ciclev10006775m.g' => 'ccl', 'CiPaw.02G120400' => 'cil', 'CiPaw.02G120500' => 'cil', 'CiPaw.02G120600' => 'cil', 'ClCG05G004850' => 'cla', 'COL.COLO4_21566' => 'col', 'Cpa.g.sc44.124' => 'cpa', 'Cre07.g320400' => 'cre', 'Cre07.g320450' => 'cre', 'Cre08.g384650' => 'cre', 'Cre09.g393173' => 'cre', 'Cre09.g394325' => 'cre', 'Cre14.g626750' => 'cre', 'Cre16.g679250' => 'cre', 'CsaV3_3G012890' => 'csa', 'CSS0010865' => 'camsi', 'CSS0044338' => 'camsi', 'DCAR_002366' => 'dca', 'DCAR_030687' => 'dca', 'DCAR_030688' => 'dca', 'Dinv14047' => 'din', 'Dinv14048' => 'din', 'Duzib151G0105' => 'dzi', 'Duzib151G0114' => 'dzi', 'Duzib212G1029' => 'dzi', 'ECA232G3536' => 'eca', 'ECA240G0786' => 'eca', 'ECA240G1802' => 'eca', 'ECA240G3760' => 'eca', 'ECA240G3920' => 'eca', 'EL10Ac5g12536' => 'bvu', 'EL10Ac5g12537' => 'bvu', 'EL10Ac5g12538' => 'bvu', 'Eucgr.B01004' => 'egr', 'Eucgr.B01006' => 'egr', 'Eucgr.B01007' => 'egr', 'Eucgr.B01008' => 'egr', 'Eucgr.B01895' => 'egr', 'Eucgr.B01896' => 'egr', 'FAN04G1456' => 'fan', 'FAN08G1769' => 'fan', 'FAN08G2160' => 'fan', 'FAN13G2403' => 'fan', 'FAN13G3303' => 'fan', 'FAN15G2435' => 'fan', 'FAN17G0672' => 'fan', 'FAN17G2441' => 'fan', 'FAN18G1024' => 'fan', 'FAN22G1458' => 'fan', 'FAN24G0037' => 'fan', 'FAN24G0429' => 'fan', 'FAN24G2387' => 'fan', 'FAN27G2746' => 'fan', 'FvH4_2g20400' => 'fve', 'FvH4_2g20420' => 'fve', 'FvH4_2g20430' => 'fve', 'FvH4_4g01270' => 'fve', 'FvH4_4g01290' => 'fve', 'FvH4_4g01300' => 'fve', 'FvH4_4g01310' => 'fve', 'FvH4_4g01330' => 'fve', 'FvH4_5g09070' => 'fve', 'Glyma.10G243800' => 'gma', 'Glyma.20G150600' => 'gma', 'Gohir.A09G219200' => 'ghi', 'Gohir.A09G219300' => 'ghi', 'Gohir.D09G221400' => 'ghi', 'Gohir.D09G221500' => 'ghi', 'Gorai.006G242600' => 'gra', 'Gorai.006G242700' => 'gra', 'GSVIVG01018044001' => 'vvi', 'HanXRQChr03g0083821' => 'han', 'HanXRQChr03g0083841' => 'han', 'HanXRQChr03g0083881' => 'han', 'HanXRQChr03g0083901' => 'han', 'HanXRQChr03g0083921' => 'han', 'HanXRQChr03g0085331' => 'han', 'HanXRQChr03g0085361' => 'han', 'HanXRQChr03g0085411' => 'han', 'HanXRQChr03g0085421' => 'han', 'HanXRQChr03g0085431' => 'han', 'HanXRQChr08g0221991' => 'han', 'HanXRQChr11g0336061' => 'han', 'HanXRQChr11g0336411' => 'han', 'Haze_11234' => 'cav', 'Hma1.2p1_0549F.1_g177010' => 'hma', 'Hma1.2p1_0602F.1_g187630' => 'hma', 'Hund14876' => 'sun', 'Hund14879' => 'sun', 'Lalb_Chr06g0160741' => 'lal', 'Lalb_Chr21g0304781' => 'lal', 'Lj3A726G19' => 'lonja', 'Lj3A726T23' => 'lonja', 'Lj3A726T24' => 'lonja', 'Lj3A726T25' => 'lonja', 'Lj3A727T17' => 'lonja', 'Lj3C726T0' => 'lonja', 'Lj3C726T2' => 'lonja', 'Lj3P725T35' => 'lonja', 'Lj3P727T10' => 'lonja', 'Lj3P727T12' => 'lonja', 'Lj3P727T14' => 'lonja', 'Lj5g0023109' => 'lja', 'Lj6P646T44' => 'lonja', 'Lsat_1_v5_gn_6_75760' => 'lsa', 'Lsat_1_v5_gn_6_75800' => 'lsa', 'Lsat_1_v5_gn_6_75900' => 'lsa', 'Lsat_1_v5_gn_6_76240' => 'lsa', 'Lsat_1_v5_gn_6_76441' => 'lsa', 'Lsat_1_v5_gn_6_76700' => 'lsa', 'Lsat_1_v5_gn_6_76760' => 'lsa', 'Manes.15G033100' => 'mes', 'Mapoly0004s0074' => 'mpo', 'Mapoly0004s0075' => 'mpo', 'Mapoly0004s0163' => 'mpo', 'Mapoly0004s0164' => 'mpo', 'Mapoly0021s0018' => 'mpo', 'Mapoly0041s0136' => 'mpo', 'Mapoly0041s0137' => 'mpo', 'Mapoly0041s0138' => 'mpo', 'Mapoly0041s0139' => 'mpo', 'Mapoly0041s0141' => 'mpo', 'Mapoly0041s0142' => 'mpo', 'Mapoly0041s0143' => 'mpo', 'Mapoly0041s0144' => 'mpo', 'Mapoly0041s0145' => 'mpo', 'Mapoly0047s0106' => 'mpo', 'Mapoly0047s0108' => 'mpo', 'Mapoly0050s0051' => 'mpo', 'Mapoly0050s0052' => 'mpo', 'Mapoly0050s0053' => 'mpo', 'Mapoly0058s0013' => 'mpo', 'Mapoly0091s0078' => 'mpo', 'Mapoly0091s0079' => 'mpo', 'Mapoly0091s0080' => 'mpo', 'Mapoly0091s0081' => 'mpo', 'Mapoly0278s0004' => 'mpo', 'Mapoly0278s0005' => 'mpo', 'Mapoly0278s0006' => 'mpo', 'MBI11_g30648_MAGBIO' => 'mbi', 'MCO03G194' => 'mco', 'MCO03G590' => 'mco', 'MCO07G312' => 'mco', 'MCO10G318' => 'mco', 'MCO12G244' => 'mco', 'MCO13G148' => 'mco', 'MCO13G194' => 'mco', 'MCO16G238' => 'mco', 'MD06G1134100' => 'mdo', 'MD13G1200100' => 'mdo', 'MD13G1200300' => 'mdo', 'MD13G1200600' => 'mdo', 'MD14G1150400' => 'mdo', 'MD16G1200000' => 'mdo', 'Medtr1g102570' => 'mtr', 'Medtr1g102780' => 'mtr', 'Medtr1g102800' => 'mtr', 'Medtr1g102810' => 'mtr', 'Medtr1g102830' => 'mtr', 'MELO3C006499.2' => 'cme', 'Migut.G00385' => 'egut', 'MSTRG.4063' => 'ama', 'Nitab4.5_0000090g0260' => 'nta', 'Nitab4.5_0000977g0030' => 'nta', 'Nitab4.5_0002541g0040' => 'nta', 'Nitab4.5_0007068g0040' => 'nta', 'Nn005s41408' => 'nnu', 'Nn005s41410' => 'nnu', 'Oeu010310.1' => 'oeu', 'Oeu010311.1' => 'oeu', 'Oeu043472.1' => 'oeu', 'Os01g0246400' => 'osa', 'Os04g0267950' => 'osa', 'Os07g0178700' => 'osa', 'Os07g0178800' => 'osa', 'Peaxi162Scf00316g00046' => 'pax', 'Peaxi162Scf00316g00049' => 'pax', 'Peaxi162Scf00316g00059' => 'pax', 'Peaxi162Scf00316g00328' => 'pax', 'Peaxi162Scf00316g00329' => 'pax', 'Peaxi162Scf00316g00411' => 'pax', 'Peaxi162Scf00316g00521' => 'pax', 'Peaxi162Scf00492g00068' => 'pax', 'Peaxi162Scf35631g00002' => 'pax', 'PGR142G3720' => 'pgr', 'PGSC0003DMG400006442' => 'stu', 'Phvul.007G062000' => 'pvu', 'Potri.008G157750' => 'ptr', 'Potri.008G157900' => 'ptr', 'Potri.008G158000' => 'ptr', 'Potri.008G158200' => 'ptr', 'Pp3c11_7280' => 'ppa', 'Pp3c11_7980' => 'ppa', 'Pp3c12_19450' => 'ppa', 'Pp3c14_1480' => 'ppa', 'Pp3c14_1501' => 'ppa', 'Pp3c16_4900' => 'ppa', 'Pp3c16_5010' => 'ppa', 'Pp3c16_5060' => 'ppa', 'Pp3c19_18250' => 'ppa', 'Pp3c23_8530' => 'ppa', 'Pp3c23_8550' => 'ppa', 'Pp3c24_9670' => 'ppa', 'Pp3c2_21390' => 'ppa', 'Pp3c2_31380' => 'ppa', 'Pp3c3_16620' => 'ppa', 'Pp3c3_8090' => 'ppa', 'Pp3c3_8110' => 'ppa', 'Pp3c3_8130' => 'ppa', 'Pp3c3_8150' => 'ppa', 'Pp3c4_14320' => 'ppa', 'Pp3c6_2560' => 'ppa', 'Pp3c9_16700' => 'ppa', 'PRCOL_00000234' => 'pco', 'PRCOL_00000235' => 'pco', 'PRCOL_00000777' => 'pco', 'PRCOL_00002344' => 'pco', 'PRCOL_00002372' => 'pco', 'PRCOL_00006120' => 'pco', 'Prupe.1G021400' => 'ppe', 'Prupe.1G021500' => 'ppe', 'Prupe.1G021600' => 'ppe', 'Prupe.1G021700' => 'ppe', 'Prupe.1G021800' => 'ppe', 'Prupe.5G145100' => 'ppe', 'Psat6g204040' => 'psa', 'Psat6g204800' => 'psa', 'Psat6g204920' => 'psa', 'Psat6g204960' => 'psa', 'Psat6g205080' => 'psa', 'PSO017G0271' => 'pso', 'PSO017G1276' => 'pso', 'PSO017G1429' => 'pso', 'PSO017G1861' => 'pso', 'PSO017G2787' => 'pso', 'PSO017G4466' => 'pso', 'PSO017G5118' => 'pso', 'PSO017G5420' => 'pso', 'PSO063G3678' => 'pso', 'PSO210G0546' => 'pso', 'PSO317G0001' => 'pso', 'PSO357G0512' => 'pso', 'PSO478G2682' => 'pso', 'PSO647G0001' => 'pso', 'PSO675G0001' => 'pso', 'PSO675G2699' => 'pso', 'PSO675G2849' => 'pso', 'PSO675G4991' => 'pso', 'PSO689G0001' => 'pso', 'QL06p000916' => 'qlo', 'QL06p000921' => 'qlo', 'QL06p001398' => 'qlo', 'QL06p001407' => 'qlo', 'QL06p002031' => 'qlo', 'RcHm_v2.0_Chr4g0387791' => 'rch', 'RcHm_v2.0_Chr4g0387801' => 'rch', 'RcHm_v2.0_Chr6g0286501' => 'rch', 'RcHm_v2.0_Chr6g0286511' => 'rch', 'RcHm_v2.0_Chr6g0286521' => 'rch', 'RcHm_v2.0_Chr6g0286531' => 'rch', 'RcHm_v2.0_Chr7g0189141' => 'rch', 'Rhsim02G0028700' => 'rsi', 'Rhsim02G0028800' => 'rsi', 'Rhsim02G0028900' => 'rsi', 'Rhsim02G0029000' => 'rsi', 'Rhsim02G0029100' => 'rsi', 'Rhsim02G0029200' => 'rsi', 'Rhsim02G0029300' => 'rsi', 'Rhsim02G0029400' => 'rsi', 'Rhsim02G0029500' => 'rsi', 'Rhsim02G0029600' => 'rsi', 'RhsimUnG0024000' => 'rsi', 'RhsimUnG0024100' => 'rsi', 'RhsimUnG0024200' => 'rsi', 'RhsimUnG0024300' => 'rsi', 'RhsimUnG0024400' => 'rsi', 'RhsimUnG0024500' => 'rsi', 'RhsimUnG0024700' => 'rsi', 'RhsimUnG0024800' => 'rsi', 'RhsimUnG0024900' => 'rsi', 'RhsimUnG0025100' => 'rsi', 'Sabra08G0120200' => 'sbr', 'Sabra08G0120300' => 'sbr', 'Sabra08G0120500' => 'sbr', 'Sabra08G0120600' => 'sbr', 'Sabra10G0158900' => 'sbr', 'SalBow2G3492' => 'sbo', 'Sc13g0004760' => 'sci', 'Sc13g0004770' => 'sci', 'Sed0003417' => 'sed', 'Sed0019750' => 'sed', 'SEGI_03419' => 'sgi', 'SEGI_05907' => 'sgi', 'SEGI_10682' => 'sgi', 'SEGI_13528' => 'sgi', 'SEGI_16081' => 'sgi', 'SEGI_19370' => 'sgi', 'SEGI_21015' => 'sgi', 'SEGI_21944' => 'sgi', 'SEGI_32906' => 'sgi', 'SEGI_33093' => 'sgi', 'SEGI_36110' => 'sgi', 'SEGI_40397' => 'sgi', 'SGA_v2.0_scaffold191G40426' => 'sas', 'SGA_v2.0_scaffold353G49717' => 'sas', 'SGA_v2.0_scaffold50G18550' => 'sas', 'SMO119G0173' => 'smo', 'SMO172G0002' => 'smo', 'Solyc09g082690.3' => 'sly', 'Solyc09g082700.2' => 'sly', 'Sopen09g031550' => 'spe', 'Sopen09g031560' => 'spe', 'Sp3g20540' => 'spa', 'Sp7g07580' => 'spa', 'TAR134G0002' => 'tar', 'TAR236G0001' => 'tar', 'TAR365G0892' => 'tar', 'TAR636G0166' => 'tar', 'TAR636G0646' => 'tar', 'TAR636G0869' => 'tar', 'TAR636G1317' => 'tar', 'TAR636G1744' => 'tar', 'TAR636G3358' => 'tar', 'TAR636G3436' => 'tar', 'THA.LOC104803047' => 'tha', 'Thecc.04G238900' => 'tca', 'Thhalv10021557m.g' => 'esa', 'Thhalv10026318m.g' => 'esa', 'Thhalv10026335m.g' => 'esa', 'TPR.G17433' => 'tpr', 'TPR.G18915' => 'tpr', 'TPR.G26125' => 'tpr', 'TWI09G0677' => 'twi', 'TWI73G0287' => 'twi', 'unitig_748.g8326' => 'ugi', 'vmacro15370' => 'vma', 'vmacro15371' => 'vma', 'vmacro15372' => 'vma', 'vmacro15373' => 'vma', 'vmacro15374' => 'vma', 'VMungo0720G2826' => 'vmu', 'Zm00001eb116960' => 'zma', 'Zm00001eb301260' => 'zma', 'Zm00001eb301270' => 'zma' ) $gf_id = 'HOM05D001460' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001460' ) $data_identifier = 'HOM05D001460' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 4, 'aag' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 2, 'aox' => (int) 2, 'arhy' => (int) 4, 'ath' => (int) 2, 'atr' => (int) 1, 'acertr' => (int) 10, 'cqu' => (int) 4, 'bca' => (int) 11, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 1, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 1, 'ccan' => (int) 1, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 1, 'col' => (int) 1, 'cpa' => (int) 1, 'cre' => (int) 7, 'csa' => (int) 1, 'camsi' => (int) 2, 'dca' => (int) 3, 'din' => (int) 2, 'dzi' => (int) 3, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 14, 'fve' => (int) 9, 'gma' => (int) 2, 'ghi' => (int) 4, 'gra' => (int) 2, 'vvi' => (int) 1, 'han' => (int) 13, 'cav' => (int) 1, 'hma' => (int) 2, 'sun' => (int) 2, 'lal' => (int) 2, 'lonja' => (int) 12, 'lja' => (int) 1, 'lsa' => (int) 7, 'mes' => (int) 1, 'mpo' => (int) 27, 'mbi' => (int) 1, 'mco' => (int) 8, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 1, 'egut' => (int) 1, 'ama' => (int) 1, 'nta' => (int) 4, 'nnu' => (int) 2, 'oeu' => (int) 3, 'osa' => (int) 4, 'pax' => (int) 9, 'pgr' => (int) 1, 'stu' => (int) 1, 'pvu' => (int) 1, 'ptr' => (int) 4, 'ppa' => (int) 22, 'pco' => (int) 6, 'ppe' => (int) 6, 'psa' => (int) 5, 'pso' => (int) 19, 'qlo' => (int) 5, 'rch' => (int) 7, 'rsi' => (int) 20, 'sbr' => (int) 5, 'sbo' => (int) 1, 'sci' => (int) 2, 'sed' => (int) 2, 'sgi' => (int) 12, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 2, 'tar' => (int) 10, 'tha' => (int) 1, 'tca' => (int) 1, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 2, 'ugi' => (int) 1, 'vma' => (int) 5, 'vmu' => (int) 1, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb301270' $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' => 'HOM05D001460', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '433', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p22980' => 'bna', 'A01p32340' => 'bna', 'A03p42970' => 'bna', 'A05p25880' => 'bna', 'Aa31LG8G9320' => 'aar', 'Aa31LG8G9330' => 'aar', 'Aa31LG8G9340' => 'aar', 'Aa31sc221G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1034' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1528' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.829' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2222' => 'aag', 'Ah.12g058830' => 'amhyb', 'Ah.12g058840' => 'amhyb', 'AL3G37160' => 'aly', 'AL7G41310' => 'aly', 'Aqoxy5G00395' => 'aox', 'Aqoxy5G00396' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0C8NZA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5185HY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JZ1PRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MD3LS0' => 'arhy', 'AT3G22840' => 'ath', 'AT4G14690' => 'ath', 'ATR0665G054' => 'atr', 'Atru.chr4.2344' => 'acertr', 'Atru.chr4.2346' => 'acertr', 'Atru.chr4.2347' => 'acertr', 'Atru.chr4.2348' => 'acertr', 'Atru.chr4.2355' => 'acertr', 'Atru.chr4.2356' => 'acertr', 'Atru.chr4.2358' => 'acertr', 'Atru.chr4.2359' => 'acertr', 'Atru.chr4.2360' => 'acertr', 'Atru.chr4.2361' => 'acertr', 'AUR62030476' => 'cqu', 'AUR62030478' => 'cqu', 'AUR62030819' => 'cqu', 'AUR62030820' => 'cqu', 'BcaB03g14648' => 'bca', 'BcaB04g20492' => 'bca', 'BcaB06g26399' => 'bca', 'BcaC01g03416' => 'bca', 'BcaC01g03419' => 'bca', 'BcaC01g03421' => 'bca', 'BcaC01g03424' => 'bca', 'BcaC05g28012' => 'bca', 'BcaC09g49212' => 'bca', 'BcaC09g50140' => 'bca', 'BcaNung00346' => 'bca', 'BolC1t02785H' => 'bol', 'BolC1t04095H' => 'bol', 'BolC3t17545H' => 'bol', 'BolC5t32769H' => 'bol', 'BraA01t02211Z' => 'bra', 'BraA01t03359Z' => 'bra', 'BraA03t13441Z' => 'bra', 'BraA05t21476Z' => 'bra', 'C01p28420' => 'bna', 'C01p41350' => 'bna', 'C03p52750' => 'bna', 'C03p52780' => 'bna', 'C05p40270' => 'bna', 'CAN.G1437.9' => 'can', 'CANSAT78G0035' => 'cansat', 'CANSAT78G1036' => 'cansat', 'CANSAT78G2272' => 'cansat', 'CANSAT78G2478' => 'cansat', 'CARHR098700' => 'chi', 'CARHR221120' => 'chi', 'CARHR221150' => 'chi', 'Carub.0003s2297' => 'cru', 'Carub.0007s2749' => 'cru', 'Carub.0007s2750' => 'cru', 'Carub.0007s2751' => 'cru', 'Ca_10849_v3' => 'car', 'Cc03_g04300' => 'ccan', 'CDE02G3648' => 'cde', 'CDE05G0060' => 'cde', 'CDE05G0692' => 'cde', 'CDE05G2285' => 'cde', 'CDE05G2884' => 'cde', 'CDE05G3072' => 'cde', 'Cfa008439' => 'cfa', 'Cfa008441' => 'cfa', 'Cfa008443' => 'cfa', 'Cfa008448' => 'cfa', 'Ciclev10005974m.g' => 'ccl', 'Ciclev10006006m.g' => 'ccl', 'Ciclev10006775m.g' => 'ccl', 'CiPaw.02G120400' => 'cil', 'CiPaw.02G120500' => 'cil', 'CiPaw.02G120600' => 'cil', 'ClCG05G004850' => 'cla', 'COL.COLO4_21566' => 'col', 'Cpa.g.sc44.124' => 'cpa', 'Cre07.g320400' => 'cre', 'Cre07.g320450' => 'cre', 'Cre08.g384650' => 'cre', 'Cre09.g393173' => 'cre', 'Cre09.g394325' => 'cre', 'Cre14.g626750' => 'cre', 'Cre16.g679250' => 'cre', 'CsaV3_3G012890' => 'csa', 'CSS0010865' => 'camsi', 'CSS0044338' => 'camsi', 'DCAR_002366' => 'dca', 'DCAR_030687' => 'dca', 'DCAR_030688' => 'dca', 'Dinv14047' => 'din', 'Dinv14048' => 'din', 'Duzib151G0105' => 'dzi', 'Duzib151G0114' => 'dzi', 'Duzib212G1029' => 'dzi', 'ECA232G3536' => 'eca', 'ECA240G0786' => 'eca', 'ECA240G1802' => 'eca', 'ECA240G3760' => 'eca', 'ECA240G3920' => 'eca', 'EL10Ac5g12536' => 'bvu', 'EL10Ac5g12537' => 'bvu', 'EL10Ac5g12538' => 'bvu', 'Eucgr.B01004' => 'egr', 'Eucgr.B01006' => 'egr', 'Eucgr.B01007' => 'egr', 'Eucgr.B01008' => 'egr', 'Eucgr.B01895' => 'egr', 'Eucgr.B01896' => 'egr', 'FAN04G1456' => 'fan', 'FAN08G1769' => 'fan', 'FAN08G2160' => 'fan', 'FAN13G2403' => 'fan', 'FAN13G3303' => 'fan', 'FAN15G2435' => 'fan', 'FAN17G0672' => 'fan', 'FAN17G2441' => 'fan', 'FAN18G1024' => 'fan', 'FAN22G1458' => 'fan', 'FAN24G0037' => 'fan', 'FAN24G0429' => 'fan', 'FAN24G2387' => 'fan', 'FAN27G2746' => 'fan', 'FvH4_2g20400' => 'fve', 'FvH4_2g20420' => 'fve', 'FvH4_2g20430' => 'fve', 'FvH4_4g01270' => 'fve', 'FvH4_4g01290' => 'fve', 'FvH4_4g01300' => 'fve', 'FvH4_4g01310' => 'fve', 'FvH4_4g01330' => 'fve', 'FvH4_5g09070' => 'fve', 'Glyma.10G243800' => 'gma', 'Glyma.20G150600' => 'gma', 'Gohir.A09G219200' => 'ghi', 'Gohir.A09G219300' => 'ghi', 'Gohir.D09G221400' => 'ghi', 'Gohir.D09G221500' => 'ghi', 'Gorai.006G242600' => 'gra', 'Gorai.006G242700' => 'gra', 'GSVIVG01018044001' => 'vvi', 'HanXRQChr03g0083821' => 'han', 'HanXRQChr03g0083841' => 'han', 'HanXRQChr03g0083881' => 'han', 'HanXRQChr03g0083901' => 'han', 'HanXRQChr03g0083921' => 'han', 'HanXRQChr03g0085331' => 'han', 'HanXRQChr03g0085361' => 'han', 'HanXRQChr03g0085411' => 'han', 'HanXRQChr03g0085421' => 'han', 'HanXRQChr03g0085431' => 'han', 'HanXRQChr08g0221991' => 'han', 'HanXRQChr11g0336061' => 'han', 'HanXRQChr11g0336411' => 'han', 'Haze_11234' => 'cav', 'Hma1.2p1_0549F.1_g177010' => 'hma', 'Hma1.2p1_0602F.1_g187630' => 'hma', 'Hund14876' => 'sun', 'Hund14879' => 'sun', 'Lalb_Chr06g0160741' => 'lal', 'Lalb_Chr21g0304781' => 'lal', 'Lj3A726G19' => 'lonja', 'Lj3A726T23' => 'lonja', 'Lj3A726T24' => 'lonja', 'Lj3A726T25' => 'lonja', 'Lj3A727T17' => 'lonja', 'Lj3C726T0' => 'lonja', 'Lj3C726T2' => 'lonja', 'Lj3P725T35' => 'lonja', 'Lj3P727T10' => 'lonja', 'Lj3P727T12' => 'lonja', 'Lj3P727T14' => 'lonja', 'Lj5g0023109' => 'lja', 'Lj6P646T44' => 'lonja', 'Lsat_1_v5_gn_6_75760' => 'lsa', 'Lsat_1_v5_gn_6_75800' => 'lsa', 'Lsat_1_v5_gn_6_75900' => 'lsa', 'Lsat_1_v5_gn_6_76240' => 'lsa', 'Lsat_1_v5_gn_6_76441' => 'lsa', 'Lsat_1_v5_gn_6_76700' => 'lsa', 'Lsat_1_v5_gn_6_76760' => 'lsa', 'Manes.15G033100' => 'mes', 'Mapoly0004s0074' => 'mpo', 'Mapoly0004s0075' => 'mpo', 'Mapoly0004s0163' => 'mpo', 'Mapoly0004s0164' => 'mpo', 'Mapoly0021s0018' => 'mpo', 'Mapoly0041s0136' => 'mpo', 'Mapoly0041s0137' => 'mpo', 'Mapoly0041s0138' => 'mpo', 'Mapoly0041s0139' => 'mpo', 'Mapoly0041s0141' => 'mpo', 'Mapoly0041s0142' => 'mpo', 'Mapoly0041s0143' => 'mpo', 'Mapoly0041s0144' => 'mpo', 'Mapoly0041s0145' => 'mpo', 'Mapoly0047s0106' => 'mpo', 'Mapoly0047s0108' => 'mpo', 'Mapoly0050s0051' => 'mpo', 'Mapoly0050s0052' => 'mpo', 'Mapoly0050s0053' => 'mpo', 'Mapoly0058s0013' => 'mpo', 'Mapoly0091s0078' => 'mpo', 'Mapoly0091s0079' => 'mpo', 'Mapoly0091s0080' => 'mpo', 'Mapoly0091s0081' => 'mpo', 'Mapoly0278s0004' => 'mpo', 'Mapoly0278s0005' => 'mpo', 'Mapoly0278s0006' => 'mpo', 'MBI11_g30648_MAGBIO' => 'mbi', 'MCO03G194' => 'mco', 'MCO03G590' => 'mco', 'MCO07G312' => 'mco', 'MCO10G318' => 'mco', 'MCO12G244' => 'mco', 'MCO13G148' => 'mco', 'MCO13G194' => 'mco', 'MCO16G238' => 'mco', 'MD06G1134100' => 'mdo', 'MD13G1200100' => 'mdo', 'MD13G1200300' => 'mdo', 'MD13G1200600' => 'mdo', 'MD14G1150400' => 'mdo', 'MD16G1200000' => 'mdo', 'Medtr1g102570' => 'mtr', 'Medtr1g102780' => 'mtr', 'Medtr1g102800' => 'mtr', 'Medtr1g102810' => 'mtr', 'Medtr1g102830' => 'mtr', 'MELO3C006499.2' => 'cme', 'Migut.G00385' => 'egut', 'MSTRG.4063' => 'ama', 'Nitab4.5_0000090g0260' => 'nta', 'Nitab4.5_0000977g0030' => 'nta', 'Nitab4.5_0002541g0040' => 'nta', 'Nitab4.5_0007068g0040' => 'nta', 'Nn005s41408' => 'nnu', 'Nn005s41410' => 'nnu', 'Oeu010310.1' => 'oeu', 'Oeu010311.1' => 'oeu', 'Oeu043472.1' => 'oeu', 'Os01g0246400' => 'osa', 'Os04g0267950' => 'osa', 'Os07g0178700' => 'osa', 'Os07g0178800' => 'osa', 'Peaxi162Scf00316g00046' => 'pax', 'Peaxi162Scf00316g00049' => 'pax', 'Peaxi162Scf00316g00059' => 'pax', 'Peaxi162Scf00316g00328' => 'pax', 'Peaxi162Scf00316g00329' => 'pax', 'Peaxi162Scf00316g00411' => 'pax', 'Peaxi162Scf00316g00521' => 'pax', 'Peaxi162Scf00492g00068' => 'pax', 'Peaxi162Scf35631g00002' => 'pax', 'PGR142G3720' => 'pgr', 'PGSC0003DMG400006442' => 'stu', 'Phvul.007G062000' => 'pvu', 'Potri.008G157750' => 'ptr', 'Potri.008G157900' => 'ptr', 'Potri.008G158000' => 'ptr', 'Potri.008G158200' => 'ptr', 'Pp3c11_7280' => 'ppa', 'Pp3c11_7980' => 'ppa', 'Pp3c12_19450' => 'ppa', 'Pp3c14_1480' => 'ppa', 'Pp3c14_1501' => 'ppa', 'Pp3c16_4900' => 'ppa', 'Pp3c16_5010' => 'ppa', 'Pp3c16_5060' => 'ppa', 'Pp3c19_18250' => 'ppa', 'Pp3c23_8530' => 'ppa', 'Pp3c23_8550' => 'ppa', 'Pp3c24_9670' => 'ppa', 'Pp3c2_21390' => 'ppa', 'Pp3c2_31380' => 'ppa', 'Pp3c3_16620' => 'ppa', 'Pp3c3_8090' => 'ppa', 'Pp3c3_8110' => 'ppa', 'Pp3c3_8130' => 'ppa', 'Pp3c3_8150' => 'ppa', 'Pp3c4_14320' => 'ppa', 'Pp3c6_2560' => 'ppa', 'Pp3c9_16700' => 'ppa', 'PRCOL_00000234' => 'pco', 'PRCOL_00000235' => 'pco', 'PRCOL_00000777' => 'pco', 'PRCOL_00002344' => 'pco', 'PRCOL_00002372' => 'pco', 'PRCOL_00006120' => 'pco', 'Prupe.1G021400' => 'ppe', 'Prupe.1G021500' => 'ppe', 'Prupe.1G021600' => 'ppe', 'Prupe.1G021700' => 'ppe', 'Prupe.1G021800' => 'ppe', 'Prupe.5G145100' => 'ppe', 'Psat6g204040' => 'psa', 'Psat6g204800' => 'psa', 'Psat6g204920' => 'psa', 'Psat6g204960' => 'psa', 'Psat6g205080' => 'psa', 'PSO017G0271' => 'pso', 'PSO017G1276' => 'pso', 'PSO017G1429' => 'pso', 'PSO017G1861' => 'pso', 'PSO017G2787' => 'pso', 'PSO017G4466' => 'pso', 'PSO017G5118' => 'pso', 'PSO017G5420' => 'pso', 'PSO063G3678' => 'pso', 'PSO210G0546' => 'pso', 'PSO317G0001' => 'pso', 'PSO357G0512' => 'pso', 'PSO478G2682' => 'pso', 'PSO647G0001' => 'pso', 'PSO675G0001' => 'pso', 'PSO675G2699' => 'pso', 'PSO675G2849' => 'pso', 'PSO675G4991' => 'pso', 'PSO689G0001' => 'pso', 'QL06p000916' => 'qlo', 'QL06p000921' => 'qlo', 'QL06p001398' => 'qlo', 'QL06p001407' => 'qlo', 'QL06p002031' => 'qlo', 'RcHm_v2.0_Chr4g0387791' => 'rch', 'RcHm_v2.0_Chr4g0387801' => 'rch', 'RcHm_v2.0_Chr6g0286501' => 'rch', 'RcHm_v2.0_Chr6g0286511' => 'rch', 'RcHm_v2.0_Chr6g0286521' => 'rch', 'RcHm_v2.0_Chr6g0286531' => 'rch', 'RcHm_v2.0_Chr7g0189141' => 'rch', 'Rhsim02G0028700' => 'rsi', 'Rhsim02G0028800' => 'rsi', 'Rhsim02G0028900' => 'rsi', 'Rhsim02G0029000' => 'rsi', 'Rhsim02G0029100' => 'rsi', 'Rhsim02G0029200' => 'rsi', 'Rhsim02G0029300' => 'rsi', 'Rhsim02G0029400' => 'rsi', 'Rhsim02G0029500' => 'rsi', 'Rhsim02G0029600' => 'rsi', 'RhsimUnG0024000' => 'rsi', 'RhsimUnG0024100' => 'rsi', 'RhsimUnG0024200' => 'rsi', 'RhsimUnG0024300' => 'rsi', 'RhsimUnG0024400' => 'rsi', 'RhsimUnG0024500' => 'rsi', 'RhsimUnG0024700' => 'rsi', 'RhsimUnG0024800' => 'rsi', 'RhsimUnG0024900' => 'rsi', 'RhsimUnG0025100' => 'rsi', 'Sabra08G0120200' => 'sbr', 'Sabra08G0120300' => 'sbr', 'Sabra08G0120500' => 'sbr', 'Sabra08G0120600' => 'sbr', 'Sabra10G0158900' => 'sbr', 'SalBow2G3492' => 'sbo', 'Sc13g0004760' => 'sci', 'Sc13g0004770' => 'sci', 'Sed0003417' => 'sed', 'Sed0019750' => 'sed', 'SEGI_03419' => 'sgi', 'SEGI_05907' => 'sgi', 'SEGI_10682' => 'sgi', 'SEGI_13528' => 'sgi', 'SEGI_16081' => 'sgi', 'SEGI_19370' => 'sgi', 'SEGI_21015' => 'sgi', 'SEGI_21944' => 'sgi', 'SEGI_32906' => 'sgi', 'SEGI_33093' => 'sgi', 'SEGI_36110' => 'sgi', 'SEGI_40397' => 'sgi', 'SGA_v2.0_scaffold191G40426' => 'sas', 'SGA_v2.0_scaffold353G49717' => 'sas', 'SGA_v2.0_scaffold50G18550' => 'sas', 'SMO119G0173' => 'smo', 'SMO172G0002' => 'smo', 'Solyc09g082690.3' => 'sly', 'Solyc09g082700.2' => 'sly', 'Sopen09g031550' => 'spe', 'Sopen09g031560' => 'spe', 'Sp3g20540' => 'spa', 'Sp7g07580' => 'spa', 'TAR134G0002' => 'tar', 'TAR236G0001' => 'tar', 'TAR365G0892' => 'tar', 'TAR636G0166' => 'tar', 'TAR636G0646' => 'tar', 'TAR636G0869' => 'tar', 'TAR636G1317' => 'tar', 'TAR636G1744' => 'tar', 'TAR636G3358' => 'tar', 'TAR636G3436' => 'tar', 'THA.LOC104803047' => 'tha', 'Thecc.04G238900' => 'tca', 'Thhalv10021557m.g' => 'esa', 'Thhalv10026318m.g' => 'esa', 'Thhalv10026335m.g' => 'esa', 'TPR.G17433' => 'tpr', 'TPR.G18915' => 'tpr', 'TPR.G26125' => 'tpr', 'TWI09G0677' => 'twi', 'TWI73G0287' => 'twi', 'unitig_748.g8326' => 'ugi', 'vmacro15370' => 'vma', 'vmacro15371' => 'vma', 'vmacro15372' => 'vma', 'vmacro15373' => 'vma', 'vmacro15374' => 'vma', 'VMungo0720G2826' => 'vmu', 'Zm00001eb116960' => 'zma', 'Zm00001eb301260' => 'zma', 'Zm00001eb301270' => 'zma' ), 'gf_id' => 'HOM05D001460', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001460' ), 'data_identifier' => 'HOM05D001460', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001460', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '433', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p22980' => 'bna', 'A01p32340' => 'bna', 'A03p42970' => 'bna', 'A05p25880' => 'bna', 'Aa31LG8G9320' => 'aar', 'Aa31LG8G9330' => 'aar', 'Aa31LG8G9340' => 'aar', 'Aa31sc221G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1034' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1528' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.829' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2222' => 'aag', 'Ah.12g058830' => 'amhyb', 'Ah.12g058840' => 'amhyb', 'AL3G37160' => 'aly', 'AL7G41310' => 'aly', 'Aqoxy5G00395' => 'aox', 'Aqoxy5G00396' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0C8NZA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5185HY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JZ1PRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MD3LS0' => 'arhy', 'AT3G22840' => 'ath', 'AT4G14690' => 'ath', 'ATR0665G054' => 'atr', 'Atru.chr4.2344' => 'acertr', 'Atru.chr4.2346' => 'acertr', 'Atru.chr4.2347' => 'acertr', 'Atru.chr4.2348' => 'acertr', 'Atru.chr4.2355' => 'acertr', 'Atru.chr4.2356' => 'acertr', 'Atru.chr4.2358' => 'acertr', 'Atru.chr4.2359' => 'acertr', 'Atru.chr4.2360' => 'acertr', 'Atru.chr4.2361' => 'acertr', 'AUR62030476' => 'cqu', 'AUR62030478' => 'cqu', 'AUR62030819' => 'cqu', 'AUR62030820' => 'cqu', 'BcaB03g14648' => 'bca', 'BcaB04g20492' => 'bca', 'BcaB06g26399' => 'bca', 'BcaC01g03416' => 'bca', 'BcaC01g03419' => 'bca', 'BcaC01g03421' => 'bca', 'BcaC01g03424' => 'bca', 'BcaC05g28012' => 'bca', 'BcaC09g49212' => 'bca', 'BcaC09g50140' => 'bca', 'BcaNung00346' => 'bca', 'BolC1t02785H' => 'bol', 'BolC1t04095H' => 'bol', 'BolC3t17545H' => 'bol', 'BolC5t32769H' => 'bol', 'BraA01t02211Z' => 'bra', 'BraA01t03359Z' => 'bra', 'BraA03t13441Z' => 'bra', 'BraA05t21476Z' => 'bra', 'C01p28420' => 'bna', 'C01p41350' => 'bna', 'C03p52750' => 'bna', 'C03p52780' => 'bna', 'C05p40270' => 'bna', 'CAN.G1437.9' => 'can', 'CANSAT78G0035' => 'cansat', 'CANSAT78G1036' => 'cansat', 'CANSAT78G2272' => 'cansat', 'CANSAT78G2478' => 'cansat', 'CARHR098700' => 'chi', 'CARHR221120' => 'chi', 'CARHR221150' => 'chi', 'Carub.0003s2297' => 'cru', 'Carub.0007s2749' => 'cru', 'Carub.0007s2750' => 'cru', 'Carub.0007s2751' => 'cru', 'Ca_10849_v3' => 'car', 'Cc03_g04300' => 'ccan', 'CDE02G3648' => 'cde', 'CDE05G0060' => 'cde', 'CDE05G0692' => 'cde', 'CDE05G2285' => 'cde', 'CDE05G2884' => 'cde', 'CDE05G3072' => 'cde', 'Cfa008439' => 'cfa', 'Cfa008441' => 'cfa', 'Cfa008443' => 'cfa', 'Cfa008448' => 'cfa', 'Ciclev10005974m.g' => 'ccl', 'Ciclev10006006m.g' => 'ccl', 'Ciclev10006775m.g' => 'ccl', 'CiPaw.02G120400' => 'cil', 'CiPaw.02G120500' => 'cil', 'CiPaw.02G120600' => 'cil', 'ClCG05G004850' => 'cla', 'COL.COLO4_21566' => 'col', 'Cpa.g.sc44.124' => 'cpa', 'Cre07.g320400' => 'cre', 'Cre07.g320450' => 'cre', 'Cre08.g384650' => 'cre', 'Cre09.g393173' => 'cre', 'Cre09.g394325' => 'cre', 'Cre14.g626750' => 'cre', 'Cre16.g679250' => 'cre', 'CsaV3_3G012890' => 'csa', 'CSS0010865' => 'camsi', 'CSS0044338' => 'camsi', 'DCAR_002366' => 'dca', 'DCAR_030687' => 'dca', 'DCAR_030688' => 'dca', 'Dinv14047' => 'din', 'Dinv14048' => 'din', 'Duzib151G0105' => 'dzi', 'Duzib151G0114' => 'dzi', 'Duzib212G1029' => 'dzi', 'ECA232G3536' => 'eca', 'ECA240G0786' => 'eca', 'ECA240G1802' => 'eca', 'ECA240G3760' => 'eca', 'ECA240G3920' => 'eca', 'EL10Ac5g12536' => 'bvu', 'EL10Ac5g12537' => 'bvu', 'EL10Ac5g12538' => 'bvu', 'Eucgr.B01004' => 'egr', 'Eucgr.B01006' => 'egr', 'Eucgr.B01007' => 'egr', 'Eucgr.B01008' => 'egr', 'Eucgr.B01895' => 'egr', 'Eucgr.B01896' => 'egr', 'FAN04G1456' => 'fan', 'FAN08G1769' => 'fan', 'FAN08G2160' => 'fan', 'FAN13G2403' => 'fan', 'FAN13G3303' => 'fan', 'FAN15G2435' => 'fan', 'FAN17G0672' => 'fan', 'FAN17G2441' => 'fan', 'FAN18G1024' => 'fan', 'FAN22G1458' => 'fan', 'FAN24G0037' => 'fan', 'FAN24G0429' => 'fan', 'FAN24G2387' => 'fan', 'FAN27G2746' => 'fan', 'FvH4_2g20400' => 'fve', 'FvH4_2g20420' => 'fve', 'FvH4_2g20430' => 'fve', 'FvH4_4g01270' => 'fve', 'FvH4_4g01290' => 'fve', 'FvH4_4g01300' => 'fve', 'FvH4_4g01310' => 'fve', 'FvH4_4g01330' => 'fve', 'FvH4_5g09070' => 'fve', 'Glyma.10G243800' => 'gma', 'Glyma.20G150600' => 'gma', 'Gohir.A09G219200' => 'ghi', 'Gohir.A09G219300' => 'ghi', 'Gohir.D09G221400' => 'ghi', 'Gohir.D09G221500' => 'ghi', 'Gorai.006G242600' => 'gra', 'Gorai.006G242700' => 'gra', 'GSVIVG01018044001' => 'vvi', 'HanXRQChr03g0083821' => 'han', 'HanXRQChr03g0083841' => 'han', 'HanXRQChr03g0083881' => 'han', 'HanXRQChr03g0083901' => 'han', 'HanXRQChr03g0083921' => 'han', 'HanXRQChr03g0085331' => 'han', 'HanXRQChr03g0085361' => 'han', 'HanXRQChr03g0085411' => 'han', 'HanXRQChr03g0085421' => 'han', 'HanXRQChr03g0085431' => 'han', 'HanXRQChr08g0221991' => 'han', 'HanXRQChr11g0336061' => 'han', 'HanXRQChr11g0336411' => 'han', 'Haze_11234' => 'cav', 'Hma1.2p1_0549F.1_g177010' => 'hma', 'Hma1.2p1_0602F.1_g187630' => 'hma', 'Hund14876' => 'sun', 'Hund14879' => 'sun', 'Lalb_Chr06g0160741' => 'lal', 'Lalb_Chr21g0304781' => 'lal', 'Lj3A726G19' => 'lonja', 'Lj3A726T23' => 'lonja', 'Lj3A726T24' => 'lonja', 'Lj3A726T25' => 'lonja', 'Lj3A727T17' => 'lonja', 'Lj3C726T0' => 'lonja', 'Lj3C726T2' => 'lonja', 'Lj3P725T35' => 'lonja', 'Lj3P727T10' => 'lonja', 'Lj3P727T12' => 'lonja', 'Lj3P727T14' => 'lonja', 'Lj5g0023109' => 'lja', 'Lj6P646T44' => 'lonja', 'Lsat_1_v5_gn_6_75760' => 'lsa', 'Lsat_1_v5_gn_6_75800' => 'lsa', 'Lsat_1_v5_gn_6_75900' => 'lsa', 'Lsat_1_v5_gn_6_76240' => 'lsa', 'Lsat_1_v5_gn_6_76441' => 'lsa', 'Lsat_1_v5_gn_6_76700' => 'lsa', 'Lsat_1_v5_gn_6_76760' => 'lsa', 'Manes.15G033100' => 'mes', 'Mapoly0004s0074' => 'mpo', 'Mapoly0004s0075' => 'mpo', 'Mapoly0004s0163' => 'mpo', 'Mapoly0004s0164' => 'mpo', 'Mapoly0021s0018' => 'mpo', 'Mapoly0041s0136' => 'mpo', 'Mapoly0041s0137' => 'mpo', 'Mapoly0041s0138' => 'mpo', 'Mapoly0041s0139' => 'mpo', 'Mapoly0041s0141' => 'mpo', 'Mapoly0041s0142' => 'mpo', 'Mapoly0041s0143' => 'mpo', 'Mapoly0041s0144' => 'mpo', 'Mapoly0041s0145' => 'mpo', 'Mapoly0047s0106' => 'mpo', 'Mapoly0047s0108' => 'mpo', 'Mapoly0050s0051' => 'mpo', 'Mapoly0050s0052' => 'mpo', 'Mapoly0050s0053' => 'mpo', 'Mapoly0058s0013' => 'mpo', 'Mapoly0091s0078' => 'mpo', 'Mapoly0091s0079' => 'mpo', 'Mapoly0091s0080' => 'mpo', 'Mapoly0091s0081' => 'mpo', 'Mapoly0278s0004' => 'mpo', 'Mapoly0278s0005' => 'mpo', 'Mapoly0278s0006' => 'mpo', 'MBI11_g30648_MAGBIO' => 'mbi', 'MCO03G194' => 'mco', 'MCO03G590' => 'mco', 'MCO07G312' => 'mco', 'MCO10G318' => 'mco', 'MCO12G244' => 'mco', 'MCO13G148' => 'mco', 'MCO13G194' => 'mco', 'MCO16G238' => 'mco', 'MD06G1134100' => 'mdo', 'MD13G1200100' => 'mdo', 'MD13G1200300' => 'mdo', 'MD13G1200600' => 'mdo', 'MD14G1150400' => 'mdo', 'MD16G1200000' => 'mdo', 'Medtr1g102570' => 'mtr', 'Medtr1g102780' => 'mtr', 'Medtr1g102800' => 'mtr', 'Medtr1g102810' => 'mtr', 'Medtr1g102830' => 'mtr', 'MELO3C006499.2' => 'cme', 'Migut.G00385' => 'egut', 'MSTRG.4063' => 'ama', 'Nitab4.5_0000090g0260' => 'nta', 'Nitab4.5_0000977g0030' => 'nta', 'Nitab4.5_0002541g0040' => 'nta', 'Nitab4.5_0007068g0040' => 'nta', 'Nn005s41408' => 'nnu', 'Nn005s41410' => 'nnu', 'Oeu010310.1' => 'oeu', 'Oeu010311.1' => 'oeu', 'Oeu043472.1' => 'oeu', 'Os01g0246400' => 'osa', 'Os04g0267950' => 'osa', 'Os07g0178700' => 'osa', 'Os07g0178800' => 'osa', 'Peaxi162Scf00316g00046' => 'pax', 'Peaxi162Scf00316g00049' => 'pax', 'Peaxi162Scf00316g00059' => 'pax', 'Peaxi162Scf00316g00328' => 'pax', 'Peaxi162Scf00316g00329' => 'pax', 'Peaxi162Scf00316g00411' => 'pax', 'Peaxi162Scf00316g00521' => 'pax', 'Peaxi162Scf00492g00068' => 'pax', 'Peaxi162Scf35631g00002' => 'pax', 'PGR142G3720' => 'pgr', 'PGSC0003DMG400006442' => 'stu', 'Phvul.007G062000' => 'pvu', 'Potri.008G157750' => 'ptr', 'Potri.008G157900' => 'ptr', 'Potri.008G158000' => 'ptr', 'Potri.008G158200' => 'ptr', 'Pp3c11_7280' => 'ppa', 'Pp3c11_7980' => 'ppa', 'Pp3c12_19450' => 'ppa', 'Pp3c14_1480' => 'ppa', 'Pp3c14_1501' => 'ppa', 'Pp3c16_4900' => 'ppa', 'Pp3c16_5010' => 'ppa', 'Pp3c16_5060' => 'ppa', 'Pp3c19_18250' => 'ppa', 'Pp3c23_8530' => 'ppa', 'Pp3c23_8550' => 'ppa', 'Pp3c24_9670' => 'ppa', 'Pp3c2_21390' => 'ppa', 'Pp3c2_31380' => 'ppa', 'Pp3c3_16620' => 'ppa', 'Pp3c3_8090' => 'ppa', 'Pp3c3_8110' => 'ppa', 'Pp3c3_8130' => 'ppa', 'Pp3c3_8150' => 'ppa', 'Pp3c4_14320' => 'ppa', 'Pp3c6_2560' => 'ppa', 'Pp3c9_16700' => 'ppa', 'PRCOL_00000234' => 'pco', 'PRCOL_00000235' => 'pco', 'PRCOL_00000777' => 'pco', 'PRCOL_00002344' => 'pco', 'PRCOL_00002372' => 'pco', 'PRCOL_00006120' => 'pco', 'Prupe.1G021400' => 'ppe', 'Prupe.1G021500' => 'ppe', 'Prupe.1G021600' => 'ppe', 'Prupe.1G021700' => 'ppe', 'Prupe.1G021800' => 'ppe', 'Prupe.5G145100' => 'ppe', 'Psat6g204040' => 'psa', 'Psat6g204800' => 'psa', 'Psat6g204920' => 'psa', 'Psat6g204960' => 'psa', 'Psat6g205080' => 'psa', 'PSO017G0271' => 'pso', 'PSO017G1276' => 'pso', 'PSO017G1429' => 'pso', 'PSO017G1861' => 'pso', 'PSO017G2787' => 'pso', 'PSO017G4466' => 'pso', 'PSO017G5118' => 'pso', 'PSO017G5420' => 'pso', 'PSO063G3678' => 'pso', 'PSO210G0546' => 'pso', 'PSO317G0001' => 'pso', 'PSO357G0512' => 'pso', 'PSO478G2682' => 'pso', 'PSO647G0001' => 'pso', 'PSO675G0001' => 'pso', 'PSO675G2699' => 'pso', 'PSO675G2849' => 'pso', 'PSO675G4991' => 'pso', 'PSO689G0001' => 'pso', 'QL06p000916' => 'qlo', 'QL06p000921' => 'qlo', 'QL06p001398' => 'qlo', 'QL06p001407' => 'qlo', 'QL06p002031' => 'qlo', 'RcHm_v2.0_Chr4g0387791' => 'rch', 'RcHm_v2.0_Chr4g0387801' => 'rch', 'RcHm_v2.0_Chr6g0286501' => 'rch', 'RcHm_v2.0_Chr6g0286511' => 'rch', 'RcHm_v2.0_Chr6g0286521' => 'rch', 'RcHm_v2.0_Chr6g0286531' => 'rch', 'RcHm_v2.0_Chr7g0189141' => 'rch', 'Rhsim02G0028700' => 'rsi', 'Rhsim02G0028800' => 'rsi', 'Rhsim02G0028900' => 'rsi', 'Rhsim02G0029000' => 'rsi', 'Rhsim02G0029100' => 'rsi', 'Rhsim02G0029200' => 'rsi', 'Rhsim02G0029300' => 'rsi', 'Rhsim02G0029400' => 'rsi', 'Rhsim02G0029500' => 'rsi', 'Rhsim02G0029600' => 'rsi', 'RhsimUnG0024000' => 'rsi', 'RhsimUnG0024100' => 'rsi', 'RhsimUnG0024200' => 'rsi', 'RhsimUnG0024300' => 'rsi', 'RhsimUnG0024400' => 'rsi', 'RhsimUnG0024500' => 'rsi', 'RhsimUnG0024700' => 'rsi', 'RhsimUnG0024800' => 'rsi', 'RhsimUnG0024900' => 'rsi', 'RhsimUnG0025100' => 'rsi', 'Sabra08G0120200' => 'sbr', 'Sabra08G0120300' => 'sbr', 'Sabra08G0120500' => 'sbr', 'Sabra08G0120600' => 'sbr', 'Sabra10G0158900' => 'sbr', 'SalBow2G3492' => 'sbo', 'Sc13g0004760' => 'sci', 'Sc13g0004770' => 'sci', 'Sed0003417' => 'sed', 'Sed0019750' => 'sed', 'SEGI_03419' => 'sgi', 'SEGI_05907' => 'sgi', 'SEGI_10682' => 'sgi', 'SEGI_13528' => 'sgi', 'SEGI_16081' => 'sgi', 'SEGI_19370' => 'sgi', 'SEGI_21015' => 'sgi', 'SEGI_21944' => 'sgi', 'SEGI_32906' => 'sgi', 'SEGI_33093' => 'sgi', 'SEGI_36110' => 'sgi', 'SEGI_40397' => 'sgi', 'SGA_v2.0_scaffold191G40426' => 'sas', 'SGA_v2.0_scaffold353G49717' => 'sas', 'SGA_v2.0_scaffold50G18550' => 'sas', 'SMO119G0173' => 'smo', 'SMO172G0002' => 'smo', 'Solyc09g082690.3' => 'sly', 'Solyc09g082700.2' => 'sly', 'Sopen09g031550' => 'spe', 'Sopen09g031560' => 'spe', 'Sp3g20540' => 'spa', 'Sp7g07580' => 'spa', 'TAR134G0002' => 'tar', 'TAR236G0001' => 'tar', 'TAR365G0892' => 'tar', 'TAR636G0166' => 'tar', 'TAR636G0646' => 'tar', 'TAR636G0869' => 'tar', 'TAR636G1317' => 'tar', 'TAR636G1744' => 'tar', 'TAR636G3358' => 'tar', 'TAR636G3436' => 'tar', 'THA.LOC104803047' => 'tha', 'Thecc.04G238900' => 'tca', 'Thhalv10021557m.g' => 'esa', 'Thhalv10026318m.g' => 'esa', 'Thhalv10026335m.g' => 'esa', 'TPR.G17433' => 'tpr', 'TPR.G18915' => 'tpr', 'TPR.G26125' => 'tpr', 'TWI09G0677' => 'twi', 'TWI73G0287' => 'twi', 'unitig_748.g8326' => 'ugi', 'vmacro15370' => 'vma', 'vmacro15371' => 'vma', 'vmacro15372' => 'vma', 'vmacro15373' => 'vma', 'vmacro15374' => 'vma', 'VMungo0720G2826' => 'vmu', 'Zm00001eb116960' => 'zma', 'Zm00001eb301260' => 'zma', 'Zm00001eb301270' => 'zma' ) $gf_id = 'HOM05D001460' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001460' ) $data_identifier = 'HOM05D001460' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 4, 'aag' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 2, 'aox' => (int) 2, 'arhy' => (int) 4, 'ath' => (int) 2, 'atr' => (int) 1, 'acertr' => (int) 10, 'cqu' => (int) 4, 'bca' => (int) 11, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 1, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 1, 'ccan' => (int) 1, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 1, 'col' => (int) 1, 'cpa' => (int) 1, 'cre' => (int) 7, 'csa' => (int) 1, 'camsi' => (int) 2, 'dca' => (int) 3, 'din' => (int) 2, 'dzi' => (int) 3, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 14, 'fve' => (int) 9, 'gma' => (int) 2, 'ghi' => (int) 4, 'gra' => (int) 2, 'vvi' => (int) 1, 'han' => (int) 13, 'cav' => (int) 1, 'hma' => (int) 2, 'sun' => (int) 2, 'lal' => (int) 2, 'lonja' => (int) 12, 'lja' => (int) 1, 'lsa' => (int) 7, 'mes' => (int) 1, 'mpo' => (int) 27, 'mbi' => (int) 1, 'mco' => (int) 8, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 1, 'egut' => (int) 1, 'ama' => (int) 1, 'nta' => (int) 4, 'nnu' => (int) 2, 'oeu' => (int) 3, 'osa' => (int) 4, 'pax' => (int) 9, 'pgr' => (int) 1, 'stu' => (int) 1, 'pvu' => (int) 1, 'ptr' => (int) 4, 'ppa' => (int) 22, 'pco' => (int) 6, 'ppe' => (int) 6, 'psa' => (int) 5, 'pso' => (int) 19, 'qlo' => (int) 5, 'rch' => (int) 7, 'rsi' => (int) 20, 'sbr' => (int) 5, 'sbo' => (int) 1, 'sci' => (int) 2, 'sed' => (int) 2, 'sgi' => (int) 12, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 2, 'tar' => (int) 10, 'tha' => (int) 1, 'tca' => (int) 1, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 2, 'ugi' => (int) 1, 'vma' => (int) 5, 'vmu' => (int) 1, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb301270' $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' => 'HOM05D001460', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '433', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p22980' => 'bna', 'A01p32340' => 'bna', 'A03p42970' => 'bna', 'A05p25880' => 'bna', 'Aa31LG8G9320' => 'aar', 'Aa31LG8G9330' => 'aar', 'Aa31LG8G9340' => 'aar', 'Aa31sc221G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1034' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1528' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.829' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2222' => 'aag', 'Ah.12g058830' => 'amhyb', 'Ah.12g058840' => 'amhyb', 'AL3G37160' => 'aly', 'AL7G41310' => 'aly', 'Aqoxy5G00395' => 'aox', 'Aqoxy5G00396' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0C8NZA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5185HY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JZ1PRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MD3LS0' => 'arhy', 'AT3G22840' => 'ath', 'AT4G14690' => 'ath', 'ATR0665G054' => 'atr', 'Atru.chr4.2344' => 'acertr', 'Atru.chr4.2346' => 'acertr', 'Atru.chr4.2347' => 'acertr', 'Atru.chr4.2348' => 'acertr', 'Atru.chr4.2355' => 'acertr', 'Atru.chr4.2356' => 'acertr', 'Atru.chr4.2358' => 'acertr', 'Atru.chr4.2359' => 'acertr', 'Atru.chr4.2360' => 'acertr', 'Atru.chr4.2361' => 'acertr', 'AUR62030476' => 'cqu', 'AUR62030478' => 'cqu', 'AUR62030819' => 'cqu', 'AUR62030820' => 'cqu', 'BcaB03g14648' => 'bca', 'BcaB04g20492' => 'bca', 'BcaB06g26399' => 'bca', 'BcaC01g03416' => 'bca', 'BcaC01g03419' => 'bca', 'BcaC01g03421' => 'bca', 'BcaC01g03424' => 'bca', 'BcaC05g28012' => 'bca', 'BcaC09g49212' => 'bca', 'BcaC09g50140' => 'bca', 'BcaNung00346' => 'bca', 'BolC1t02785H' => 'bol', 'BolC1t04095H' => 'bol', 'BolC3t17545H' => 'bol', 'BolC5t32769H' => 'bol', 'BraA01t02211Z' => 'bra', 'BraA01t03359Z' => 'bra', 'BraA03t13441Z' => 'bra', 'BraA05t21476Z' => 'bra', 'C01p28420' => 'bna', 'C01p41350' => 'bna', 'C03p52750' => 'bna', 'C03p52780' => 'bna', 'C05p40270' => 'bna', 'CAN.G1437.9' => 'can', 'CANSAT78G0035' => 'cansat', 'CANSAT78G1036' => 'cansat', 'CANSAT78G2272' => 'cansat', 'CANSAT78G2478' => 'cansat', 'CARHR098700' => 'chi', 'CARHR221120' => 'chi', 'CARHR221150' => 'chi', 'Carub.0003s2297' => 'cru', 'Carub.0007s2749' => 'cru', 'Carub.0007s2750' => 'cru', 'Carub.0007s2751' => 'cru', 'Ca_10849_v3' => 'car', 'Cc03_g04300' => 'ccan', 'CDE02G3648' => 'cde', 'CDE05G0060' => 'cde', 'CDE05G0692' => 'cde', 'CDE05G2285' => 'cde', 'CDE05G2884' => 'cde', 'CDE05G3072' => 'cde', 'Cfa008439' => 'cfa', 'Cfa008441' => 'cfa', 'Cfa008443' => 'cfa', 'Cfa008448' => 'cfa', 'Ciclev10005974m.g' => 'ccl', 'Ciclev10006006m.g' => 'ccl', 'Ciclev10006775m.g' => 'ccl', 'CiPaw.02G120400' => 'cil', 'CiPaw.02G120500' => 'cil', 'CiPaw.02G120600' => 'cil', 'ClCG05G004850' => 'cla', 'COL.COLO4_21566' => 'col', 'Cpa.g.sc44.124' => 'cpa', 'Cre07.g320400' => 'cre', 'Cre07.g320450' => 'cre', 'Cre08.g384650' => 'cre', 'Cre09.g393173' => 'cre', 'Cre09.g394325' => 'cre', 'Cre14.g626750' => 'cre', 'Cre16.g679250' => 'cre', 'CsaV3_3G012890' => 'csa', 'CSS0010865' => 'camsi', 'CSS0044338' => 'camsi', 'DCAR_002366' => 'dca', 'DCAR_030687' => 'dca', 'DCAR_030688' => 'dca', 'Dinv14047' => 'din', 'Dinv14048' => 'din', 'Duzib151G0105' => 'dzi', 'Duzib151G0114' => 'dzi', 'Duzib212G1029' => 'dzi', 'ECA232G3536' => 'eca', 'ECA240G0786' => 'eca', 'ECA240G1802' => 'eca', 'ECA240G3760' => 'eca', 'ECA240G3920' => 'eca', 'EL10Ac5g12536' => 'bvu', 'EL10Ac5g12537' => 'bvu', 'EL10Ac5g12538' => 'bvu', 'Eucgr.B01004' => 'egr', 'Eucgr.B01006' => 'egr', 'Eucgr.B01007' => 'egr', 'Eucgr.B01008' => 'egr', 'Eucgr.B01895' => 'egr', 'Eucgr.B01896' => 'egr', 'FAN04G1456' => 'fan', 'FAN08G1769' => 'fan', 'FAN08G2160' => 'fan', 'FAN13G2403' => 'fan', 'FAN13G3303' => 'fan', 'FAN15G2435' => 'fan', 'FAN17G0672' => 'fan', 'FAN17G2441' => 'fan', 'FAN18G1024' => 'fan', 'FAN22G1458' => 'fan', 'FAN24G0037' => 'fan', 'FAN24G0429' => 'fan', 'FAN24G2387' => 'fan', 'FAN27G2746' => 'fan', 'FvH4_2g20400' => 'fve', 'FvH4_2g20420' => 'fve', 'FvH4_2g20430' => 'fve', 'FvH4_4g01270' => 'fve', 'FvH4_4g01290' => 'fve', 'FvH4_4g01300' => 'fve', 'FvH4_4g01310' => 'fve', 'FvH4_4g01330' => 'fve', 'FvH4_5g09070' => 'fve', 'Glyma.10G243800' => 'gma', 'Glyma.20G150600' => 'gma', 'Gohir.A09G219200' => 'ghi', 'Gohir.A09G219300' => 'ghi', 'Gohir.D09G221400' => 'ghi', 'Gohir.D09G221500' => 'ghi', 'Gorai.006G242600' => 'gra', 'Gorai.006G242700' => 'gra', 'GSVIVG01018044001' => 'vvi', 'HanXRQChr03g0083821' => 'han', 'HanXRQChr03g0083841' => 'han', 'HanXRQChr03g0083881' => 'han', 'HanXRQChr03g0083901' => 'han', 'HanXRQChr03g0083921' => 'han', 'HanXRQChr03g0085331' => 'han', 'HanXRQChr03g0085361' => 'han', 'HanXRQChr03g0085411' => 'han', 'HanXRQChr03g0085421' => 'han', 'HanXRQChr03g0085431' => 'han', 'HanXRQChr08g0221991' => 'han', 'HanXRQChr11g0336061' => 'han', 'HanXRQChr11g0336411' => 'han', 'Haze_11234' => 'cav', 'Hma1.2p1_0549F.1_g177010' => 'hma', 'Hma1.2p1_0602F.1_g187630' => 'hma', 'Hund14876' => 'sun', 'Hund14879' => 'sun', 'Lalb_Chr06g0160741' => 'lal', 'Lalb_Chr21g0304781' => 'lal', 'Lj3A726G19' => 'lonja', 'Lj3A726T23' => 'lonja', 'Lj3A726T24' => 'lonja', 'Lj3A726T25' => 'lonja', 'Lj3A727T17' => 'lonja', 'Lj3C726T0' => 'lonja', 'Lj3C726T2' => 'lonja', 'Lj3P725T35' => 'lonja', 'Lj3P727T10' => 'lonja', 'Lj3P727T12' => 'lonja', 'Lj3P727T14' => 'lonja', 'Lj5g0023109' => 'lja', 'Lj6P646T44' => 'lonja', 'Lsat_1_v5_gn_6_75760' => 'lsa', 'Lsat_1_v5_gn_6_75800' => 'lsa', 'Lsat_1_v5_gn_6_75900' => 'lsa', 'Lsat_1_v5_gn_6_76240' => 'lsa', 'Lsat_1_v5_gn_6_76441' => 'lsa', 'Lsat_1_v5_gn_6_76700' => 'lsa', 'Lsat_1_v5_gn_6_76760' => 'lsa', 'Manes.15G033100' => 'mes', 'Mapoly0004s0074' => 'mpo', 'Mapoly0004s0075' => 'mpo', 'Mapoly0004s0163' => 'mpo', 'Mapoly0004s0164' => 'mpo', 'Mapoly0021s0018' => 'mpo', 'Mapoly0041s0136' => 'mpo', 'Mapoly0041s0137' => 'mpo', 'Mapoly0041s0138' => 'mpo', 'Mapoly0041s0139' => 'mpo', 'Mapoly0041s0141' => 'mpo', 'Mapoly0041s0142' => 'mpo', 'Mapoly0041s0143' => 'mpo', 'Mapoly0041s0144' => 'mpo', 'Mapoly0041s0145' => 'mpo', 'Mapoly0047s0106' => 'mpo', 'Mapoly0047s0108' => 'mpo', 'Mapoly0050s0051' => 'mpo', 'Mapoly0050s0052' => 'mpo', 'Mapoly0050s0053' => 'mpo', 'Mapoly0058s0013' => 'mpo', 'Mapoly0091s0078' => 'mpo', 'Mapoly0091s0079' => 'mpo', 'Mapoly0091s0080' => 'mpo', 'Mapoly0091s0081' => 'mpo', 'Mapoly0278s0004' => 'mpo', 'Mapoly0278s0005' => 'mpo', 'Mapoly0278s0006' => 'mpo', 'MBI11_g30648_MAGBIO' => 'mbi', 'MCO03G194' => 'mco', 'MCO03G590' => 'mco', 'MCO07G312' => 'mco', 'MCO10G318' => 'mco', 'MCO12G244' => 'mco', 'MCO13G148' => 'mco', 'MCO13G194' => 'mco', 'MCO16G238' => 'mco', 'MD06G1134100' => 'mdo', 'MD13G1200100' => 'mdo', 'MD13G1200300' => 'mdo', 'MD13G1200600' => 'mdo', 'MD14G1150400' => 'mdo', 'MD16G1200000' => 'mdo', 'Medtr1g102570' => 'mtr', 'Medtr1g102780' => 'mtr', 'Medtr1g102800' => 'mtr', 'Medtr1g102810' => 'mtr', 'Medtr1g102830' => 'mtr', 'MELO3C006499.2' => 'cme', 'Migut.G00385' => 'egut', 'MSTRG.4063' => 'ama', 'Nitab4.5_0000090g0260' => 'nta', 'Nitab4.5_0000977g0030' => 'nta', 'Nitab4.5_0002541g0040' => 'nta', 'Nitab4.5_0007068g0040' => 'nta', 'Nn005s41408' => 'nnu', 'Nn005s41410' => 'nnu', 'Oeu010310.1' => 'oeu', 'Oeu010311.1' => 'oeu', 'Oeu043472.1' => 'oeu', 'Os01g0246400' => 'osa', 'Os04g0267950' => 'osa', 'Os07g0178700' => 'osa', 'Os07g0178800' => 'osa', 'Peaxi162Scf00316g00046' => 'pax', 'Peaxi162Scf00316g00049' => 'pax', 'Peaxi162Scf00316g00059' => 'pax', 'Peaxi162Scf00316g00328' => 'pax', 'Peaxi162Scf00316g00329' => 'pax', 'Peaxi162Scf00316g00411' => 'pax', 'Peaxi162Scf00316g00521' => 'pax', 'Peaxi162Scf00492g00068' => 'pax', 'Peaxi162Scf35631g00002' => 'pax', 'PGR142G3720' => 'pgr', 'PGSC0003DMG400006442' => 'stu', 'Phvul.007G062000' => 'pvu', 'Potri.008G157750' => 'ptr', 'Potri.008G157900' => 'ptr', 'Potri.008G158000' => 'ptr', 'Potri.008G158200' => 'ptr', 'Pp3c11_7280' => 'ppa', 'Pp3c11_7980' => 'ppa', 'Pp3c12_19450' => 'ppa', 'Pp3c14_1480' => 'ppa', 'Pp3c14_1501' => 'ppa', 'Pp3c16_4900' => 'ppa', 'Pp3c16_5010' => 'ppa', 'Pp3c16_5060' => 'ppa', 'Pp3c19_18250' => 'ppa', 'Pp3c23_8530' => 'ppa', 'Pp3c23_8550' => 'ppa', 'Pp3c24_9670' => 'ppa', 'Pp3c2_21390' => 'ppa', 'Pp3c2_31380' => 'ppa', 'Pp3c3_16620' => 'ppa', 'Pp3c3_8090' => 'ppa', 'Pp3c3_8110' => 'ppa', 'Pp3c3_8130' => 'ppa', 'Pp3c3_8150' => 'ppa', 'Pp3c4_14320' => 'ppa', 'Pp3c6_2560' => 'ppa', 'Pp3c9_16700' => 'ppa', 'PRCOL_00000234' => 'pco', 'PRCOL_00000235' => 'pco', 'PRCOL_00000777' => 'pco', 'PRCOL_00002344' => 'pco', 'PRCOL_00002372' => 'pco', 'PRCOL_00006120' => 'pco', 'Prupe.1G021400' => 'ppe', 'Prupe.1G021500' => 'ppe', 'Prupe.1G021600' => 'ppe', 'Prupe.1G021700' => 'ppe', 'Prupe.1G021800' => 'ppe', 'Prupe.5G145100' => 'ppe', 'Psat6g204040' => 'psa', 'Psat6g204800' => 'psa', 'Psat6g204920' => 'psa', 'Psat6g204960' => 'psa', 'Psat6g205080' => 'psa', 'PSO017G0271' => 'pso', 'PSO017G1276' => 'pso', 'PSO017G1429' => 'pso', 'PSO017G1861' => 'pso', 'PSO017G2787' => 'pso', 'PSO017G4466' => 'pso', 'PSO017G5118' => 'pso', 'PSO017G5420' => 'pso', 'PSO063G3678' => 'pso', 'PSO210G0546' => 'pso', 'PSO317G0001' => 'pso', 'PSO357G0512' => 'pso', 'PSO478G2682' => 'pso', 'PSO647G0001' => 'pso', 'PSO675G0001' => 'pso', 'PSO675G2699' => 'pso', 'PSO675G2849' => 'pso', 'PSO675G4991' => 'pso', 'PSO689G0001' => 'pso', 'QL06p000916' => 'qlo', 'QL06p000921' => 'qlo', 'QL06p001398' => 'qlo', 'QL06p001407' => 'qlo', 'QL06p002031' => 'qlo', 'RcHm_v2.0_Chr4g0387791' => 'rch', 'RcHm_v2.0_Chr4g0387801' => 'rch', 'RcHm_v2.0_Chr6g0286501' => 'rch', 'RcHm_v2.0_Chr6g0286511' => 'rch', 'RcHm_v2.0_Chr6g0286521' => 'rch', 'RcHm_v2.0_Chr6g0286531' => 'rch', 'RcHm_v2.0_Chr7g0189141' => 'rch', 'Rhsim02G0028700' => 'rsi', 'Rhsim02G0028800' => 'rsi', 'Rhsim02G0028900' => 'rsi', 'Rhsim02G0029000' => 'rsi', 'Rhsim02G0029100' => 'rsi', 'Rhsim02G0029200' => 'rsi', 'Rhsim02G0029300' => 'rsi', 'Rhsim02G0029400' => 'rsi', 'Rhsim02G0029500' => 'rsi', 'Rhsim02G0029600' => 'rsi', 'RhsimUnG0024000' => 'rsi', 'RhsimUnG0024100' => 'rsi', 'RhsimUnG0024200' => 'rsi', 'RhsimUnG0024300' => 'rsi', 'RhsimUnG0024400' => 'rsi', 'RhsimUnG0024500' => 'rsi', 'RhsimUnG0024700' => 'rsi', 'RhsimUnG0024800' => 'rsi', 'RhsimUnG0024900' => 'rsi', 'RhsimUnG0025100' => 'rsi', 'Sabra08G0120200' => 'sbr', 'Sabra08G0120300' => 'sbr', 'Sabra08G0120500' => 'sbr', 'Sabra08G0120600' => 'sbr', 'Sabra10G0158900' => 'sbr', 'SalBow2G3492' => 'sbo', 'Sc13g0004760' => 'sci', 'Sc13g0004770' => 'sci', 'Sed0003417' => 'sed', 'Sed0019750' => 'sed', 'SEGI_03419' => 'sgi', 'SEGI_05907' => 'sgi', 'SEGI_10682' => 'sgi', 'SEGI_13528' => 'sgi', 'SEGI_16081' => 'sgi', 'SEGI_19370' => 'sgi', 'SEGI_21015' => 'sgi', 'SEGI_21944' => 'sgi', 'SEGI_32906' => 'sgi', 'SEGI_33093' => 'sgi', 'SEGI_36110' => 'sgi', 'SEGI_40397' => 'sgi', 'SGA_v2.0_scaffold191G40426' => 'sas', 'SGA_v2.0_scaffold353G49717' => 'sas', 'SGA_v2.0_scaffold50G18550' => 'sas', 'SMO119G0173' => 'smo', 'SMO172G0002' => 'smo', 'Solyc09g082690.3' => 'sly', 'Solyc09g082700.2' => 'sly', 'Sopen09g031550' => 'spe', 'Sopen09g031560' => 'spe', 'Sp3g20540' => 'spa', 'Sp7g07580' => 'spa', 'TAR134G0002' => 'tar', 'TAR236G0001' => 'tar', 'TAR365G0892' => 'tar', 'TAR636G0166' => 'tar', 'TAR636G0646' => 'tar', 'TAR636G0869' => 'tar', 'TAR636G1317' => 'tar', 'TAR636G1744' => 'tar', 'TAR636G3358' => 'tar', 'TAR636G3436' => 'tar', 'THA.LOC104803047' => 'tha', 'Thecc.04G238900' => 'tca', 'Thhalv10021557m.g' => 'esa', 'Thhalv10026318m.g' => 'esa', 'Thhalv10026335m.g' => 'esa', 'TPR.G17433' => 'tpr', 'TPR.G18915' => 'tpr', 'TPR.G26125' => 'tpr', 'TWI09G0677' => 'twi', 'TWI73G0287' => 'twi', 'unitig_748.g8326' => 'ugi', 'vmacro15370' => 'vma', 'vmacro15371' => 'vma', 'vmacro15372' => 'vma', 'vmacro15373' => 'vma', 'vmacro15374' => 'vma', 'VMungo0720G2826' => 'vmu', 'Zm00001eb116960' => 'zma', 'Zm00001eb301260' => 'zma', 'Zm00001eb301270' => 'zma' ), 'gf_id' => 'HOM05D001460', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001460' ), 'data_identifier' => 'HOM05D001460', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001460', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '433', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p22980' => 'bna', 'A01p32340' => 'bna', 'A03p42970' => 'bna', 'A05p25880' => 'bna', 'Aa31LG8G9320' => 'aar', 'Aa31LG8G9330' => 'aar', 'Aa31LG8G9340' => 'aar', 'Aa31sc221G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1034' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1528' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.829' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2222' => 'aag', 'Ah.12g058830' => 'amhyb', 'Ah.12g058840' => 'amhyb', 'AL3G37160' => 'aly', 'AL7G41310' => 'aly', 'Aqoxy5G00395' => 'aox', 'Aqoxy5G00396' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0C8NZA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5185HY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JZ1PRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MD3LS0' => 'arhy', 'AT3G22840' => 'ath', 'AT4G14690' => 'ath', 'ATR0665G054' => 'atr', 'Atru.chr4.2344' => 'acertr', 'Atru.chr4.2346' => 'acertr', 'Atru.chr4.2347' => 'acertr', 'Atru.chr4.2348' => 'acertr', 'Atru.chr4.2355' => 'acertr', 'Atru.chr4.2356' => 'acertr', 'Atru.chr4.2358' => 'acertr', 'Atru.chr4.2359' => 'acertr', 'Atru.chr4.2360' => 'acertr', 'Atru.chr4.2361' => 'acertr', 'AUR62030476' => 'cqu', 'AUR62030478' => 'cqu', 'AUR62030819' => 'cqu', 'AUR62030820' => 'cqu', 'BcaB03g14648' => 'bca', 'BcaB04g20492' => 'bca', 'BcaB06g26399' => 'bca', 'BcaC01g03416' => 'bca', 'BcaC01g03419' => 'bca', 'BcaC01g03421' => 'bca', 'BcaC01g03424' => 'bca', 'BcaC05g28012' => 'bca', 'BcaC09g49212' => 'bca', 'BcaC09g50140' => 'bca', 'BcaNung00346' => 'bca', 'BolC1t02785H' => 'bol', 'BolC1t04095H' => 'bol', 'BolC3t17545H' => 'bol', 'BolC5t32769H' => 'bol', 'BraA01t02211Z' => 'bra', 'BraA01t03359Z' => 'bra', 'BraA03t13441Z' => 'bra', 'BraA05t21476Z' => 'bra', 'C01p28420' => 'bna', 'C01p41350' => 'bna', 'C03p52750' => 'bna', 'C03p52780' => 'bna', 'C05p40270' => 'bna', 'CAN.G1437.9' => 'can', 'CANSAT78G0035' => 'cansat', 'CANSAT78G1036' => 'cansat', 'CANSAT78G2272' => 'cansat', 'CANSAT78G2478' => 'cansat', 'CARHR098700' => 'chi', 'CARHR221120' => 'chi', 'CARHR221150' => 'chi', 'Carub.0003s2297' => 'cru', 'Carub.0007s2749' => 'cru', 'Carub.0007s2750' => 'cru', 'Carub.0007s2751' => 'cru', 'Ca_10849_v3' => 'car', 'Cc03_g04300' => 'ccan', 'CDE02G3648' => 'cde', 'CDE05G0060' => 'cde', 'CDE05G0692' => 'cde', 'CDE05G2285' => 'cde', 'CDE05G2884' => 'cde', 'CDE05G3072' => 'cde', 'Cfa008439' => 'cfa', 'Cfa008441' => 'cfa', 'Cfa008443' => 'cfa', 'Cfa008448' => 'cfa', 'Ciclev10005974m.g' => 'ccl', 'Ciclev10006006m.g' => 'ccl', 'Ciclev10006775m.g' => 'ccl', 'CiPaw.02G120400' => 'cil', 'CiPaw.02G120500' => 'cil', 'CiPaw.02G120600' => 'cil', 'ClCG05G004850' => 'cla', 'COL.COLO4_21566' => 'col', 'Cpa.g.sc44.124' => 'cpa', 'Cre07.g320400' => 'cre', 'Cre07.g320450' => 'cre', 'Cre08.g384650' => 'cre', 'Cre09.g393173' => 'cre', 'Cre09.g394325' => 'cre', 'Cre14.g626750' => 'cre', 'Cre16.g679250' => 'cre', 'CsaV3_3G012890' => 'csa', 'CSS0010865' => 'camsi', 'CSS0044338' => 'camsi', 'DCAR_002366' => 'dca', 'DCAR_030687' => 'dca', 'DCAR_030688' => 'dca', 'Dinv14047' => 'din', 'Dinv14048' => 'din', 'Duzib151G0105' => 'dzi', 'Duzib151G0114' => 'dzi', 'Duzib212G1029' => 'dzi', 'ECA232G3536' => 'eca', 'ECA240G0786' => 'eca', 'ECA240G1802' => 'eca', 'ECA240G3760' => 'eca', 'ECA240G3920' => 'eca', 'EL10Ac5g12536' => 'bvu', 'EL10Ac5g12537' => 'bvu', 'EL10Ac5g12538' => 'bvu', 'Eucgr.B01004' => 'egr', 'Eucgr.B01006' => 'egr', 'Eucgr.B01007' => 'egr', 'Eucgr.B01008' => 'egr', 'Eucgr.B01895' => 'egr', 'Eucgr.B01896' => 'egr', 'FAN04G1456' => 'fan', 'FAN08G1769' => 'fan', 'FAN08G2160' => 'fan', 'FAN13G2403' => 'fan', 'FAN13G3303' => 'fan', 'FAN15G2435' => 'fan', 'FAN17G0672' => 'fan', 'FAN17G2441' => 'fan', 'FAN18G1024' => 'fan', 'FAN22G1458' => 'fan', 'FAN24G0037' => 'fan', 'FAN24G0429' => 'fan', 'FAN24G2387' => 'fan', 'FAN27G2746' => 'fan', 'FvH4_2g20400' => 'fve', 'FvH4_2g20420' => 'fve', 'FvH4_2g20430' => 'fve', 'FvH4_4g01270' => 'fve', 'FvH4_4g01290' => 'fve', 'FvH4_4g01300' => 'fve', 'FvH4_4g01310' => 'fve', 'FvH4_4g01330' => 'fve', 'FvH4_5g09070' => 'fve', 'Glyma.10G243800' => 'gma', 'Glyma.20G150600' => 'gma', 'Gohir.A09G219200' => 'ghi', 'Gohir.A09G219300' => 'ghi', 'Gohir.D09G221400' => 'ghi', 'Gohir.D09G221500' => 'ghi', 'Gorai.006G242600' => 'gra', 'Gorai.006G242700' => 'gra', 'GSVIVG01018044001' => 'vvi', 'HanXRQChr03g0083821' => 'han', 'HanXRQChr03g0083841' => 'han', 'HanXRQChr03g0083881' => 'han', 'HanXRQChr03g0083901' => 'han', 'HanXRQChr03g0083921' => 'han', 'HanXRQChr03g0085331' => 'han', 'HanXRQChr03g0085361' => 'han', 'HanXRQChr03g0085411' => 'han', 'HanXRQChr03g0085421' => 'han', 'HanXRQChr03g0085431' => 'han', 'HanXRQChr08g0221991' => 'han', 'HanXRQChr11g0336061' => 'han', 'HanXRQChr11g0336411' => 'han', 'Haze_11234' => 'cav', 'Hma1.2p1_0549F.1_g177010' => 'hma', 'Hma1.2p1_0602F.1_g187630' => 'hma', 'Hund14876' => 'sun', 'Hund14879' => 'sun', 'Lalb_Chr06g0160741' => 'lal', 'Lalb_Chr21g0304781' => 'lal', 'Lj3A726G19' => 'lonja', 'Lj3A726T23' => 'lonja', 'Lj3A726T24' => 'lonja', 'Lj3A726T25' => 'lonja', 'Lj3A727T17' => 'lonja', 'Lj3C726T0' => 'lonja', 'Lj3C726T2' => 'lonja', 'Lj3P725T35' => 'lonja', 'Lj3P727T10' => 'lonja', 'Lj3P727T12' => 'lonja', 'Lj3P727T14' => 'lonja', 'Lj5g0023109' => 'lja', 'Lj6P646T44' => 'lonja', 'Lsat_1_v5_gn_6_75760' => 'lsa', 'Lsat_1_v5_gn_6_75800' => 'lsa', 'Lsat_1_v5_gn_6_75900' => 'lsa', 'Lsat_1_v5_gn_6_76240' => 'lsa', 'Lsat_1_v5_gn_6_76441' => 'lsa', 'Lsat_1_v5_gn_6_76700' => 'lsa', 'Lsat_1_v5_gn_6_76760' => 'lsa', 'Manes.15G033100' => 'mes', 'Mapoly0004s0074' => 'mpo', 'Mapoly0004s0075' => 'mpo', 'Mapoly0004s0163' => 'mpo', 'Mapoly0004s0164' => 'mpo', 'Mapoly0021s0018' => 'mpo', 'Mapoly0041s0136' => 'mpo', 'Mapoly0041s0137' => 'mpo', 'Mapoly0041s0138' => 'mpo', 'Mapoly0041s0139' => 'mpo', 'Mapoly0041s0141' => 'mpo', 'Mapoly0041s0142' => 'mpo', 'Mapoly0041s0143' => 'mpo', 'Mapoly0041s0144' => 'mpo', 'Mapoly0041s0145' => 'mpo', 'Mapoly0047s0106' => 'mpo', 'Mapoly0047s0108' => 'mpo', 'Mapoly0050s0051' => 'mpo', 'Mapoly0050s0052' => 'mpo', 'Mapoly0050s0053' => 'mpo', 'Mapoly0058s0013' => 'mpo', 'Mapoly0091s0078' => 'mpo', 'Mapoly0091s0079' => 'mpo', 'Mapoly0091s0080' => 'mpo', 'Mapoly0091s0081' => 'mpo', 'Mapoly0278s0004' => 'mpo', 'Mapoly0278s0005' => 'mpo', 'Mapoly0278s0006' => 'mpo', 'MBI11_g30648_MAGBIO' => 'mbi', 'MCO03G194' => 'mco', 'MCO03G590' => 'mco', 'MCO07G312' => 'mco', 'MCO10G318' => 'mco', 'MCO12G244' => 'mco', 'MCO13G148' => 'mco', 'MCO13G194' => 'mco', 'MCO16G238' => 'mco', 'MD06G1134100' => 'mdo', 'MD13G1200100' => 'mdo', 'MD13G1200300' => 'mdo', 'MD13G1200600' => 'mdo', 'MD14G1150400' => 'mdo', 'MD16G1200000' => 'mdo', 'Medtr1g102570' => 'mtr', 'Medtr1g102780' => 'mtr', 'Medtr1g102800' => 'mtr', 'Medtr1g102810' => 'mtr', 'Medtr1g102830' => 'mtr', 'MELO3C006499.2' => 'cme', 'Migut.G00385' => 'egut', 'MSTRG.4063' => 'ama', 'Nitab4.5_0000090g0260' => 'nta', 'Nitab4.5_0000977g0030' => 'nta', 'Nitab4.5_0002541g0040' => 'nta', 'Nitab4.5_0007068g0040' => 'nta', 'Nn005s41408' => 'nnu', 'Nn005s41410' => 'nnu', 'Oeu010310.1' => 'oeu', 'Oeu010311.1' => 'oeu', 'Oeu043472.1' => 'oeu', 'Os01g0246400' => 'osa', 'Os04g0267950' => 'osa', 'Os07g0178700' => 'osa', 'Os07g0178800' => 'osa', 'Peaxi162Scf00316g00046' => 'pax', 'Peaxi162Scf00316g00049' => 'pax', 'Peaxi162Scf00316g00059' => 'pax', 'Peaxi162Scf00316g00328' => 'pax', 'Peaxi162Scf00316g00329' => 'pax', 'Peaxi162Scf00316g00411' => 'pax', 'Peaxi162Scf00316g00521' => 'pax', 'Peaxi162Scf00492g00068' => 'pax', 'Peaxi162Scf35631g00002' => 'pax', 'PGR142G3720' => 'pgr', 'PGSC0003DMG400006442' => 'stu', 'Phvul.007G062000' => 'pvu', 'Potri.008G157750' => 'ptr', 'Potri.008G157900' => 'ptr', 'Potri.008G158000' => 'ptr', 'Potri.008G158200' => 'ptr', 'Pp3c11_7280' => 'ppa', 'Pp3c11_7980' => 'ppa', 'Pp3c12_19450' => 'ppa', 'Pp3c14_1480' => 'ppa', 'Pp3c14_1501' => 'ppa', 'Pp3c16_4900' => 'ppa', 'Pp3c16_5010' => 'ppa', 'Pp3c16_5060' => 'ppa', 'Pp3c19_18250' => 'ppa', 'Pp3c23_8530' => 'ppa', 'Pp3c23_8550' => 'ppa', 'Pp3c24_9670' => 'ppa', 'Pp3c2_21390' => 'ppa', 'Pp3c2_31380' => 'ppa', 'Pp3c3_16620' => 'ppa', 'Pp3c3_8090' => 'ppa', 'Pp3c3_8110' => 'ppa', 'Pp3c3_8130' => 'ppa', 'Pp3c3_8150' => 'ppa', 'Pp3c4_14320' => 'ppa', 'Pp3c6_2560' => 'ppa', 'Pp3c9_16700' => 'ppa', 'PRCOL_00000234' => 'pco', 'PRCOL_00000235' => 'pco', 'PRCOL_00000777' => 'pco', 'PRCOL_00002344' => 'pco', 'PRCOL_00002372' => 'pco', 'PRCOL_00006120' => 'pco', 'Prupe.1G021400' => 'ppe', 'Prupe.1G021500' => 'ppe', 'Prupe.1G021600' => 'ppe', 'Prupe.1G021700' => 'ppe', 'Prupe.1G021800' => 'ppe', 'Prupe.5G145100' => 'ppe', 'Psat6g204040' => 'psa', 'Psat6g204800' => 'psa', 'Psat6g204920' => 'psa', 'Psat6g204960' => 'psa', 'Psat6g205080' => 'psa', 'PSO017G0271' => 'pso', 'PSO017G1276' => 'pso', 'PSO017G1429' => 'pso', 'PSO017G1861' => 'pso', 'PSO017G2787' => 'pso', 'PSO017G4466' => 'pso', 'PSO017G5118' => 'pso', 'PSO017G5420' => 'pso', 'PSO063G3678' => 'pso', 'PSO210G0546' => 'pso', 'PSO317G0001' => 'pso', 'PSO357G0512' => 'pso', 'PSO478G2682' => 'pso', 'PSO647G0001' => 'pso', 'PSO675G0001' => 'pso', 'PSO675G2699' => 'pso', 'PSO675G2849' => 'pso', 'PSO675G4991' => 'pso', 'PSO689G0001' => 'pso', 'QL06p000916' => 'qlo', 'QL06p000921' => 'qlo', 'QL06p001398' => 'qlo', 'QL06p001407' => 'qlo', 'QL06p002031' => 'qlo', 'RcHm_v2.0_Chr4g0387791' => 'rch', 'RcHm_v2.0_Chr4g0387801' => 'rch', 'RcHm_v2.0_Chr6g0286501' => 'rch', 'RcHm_v2.0_Chr6g0286511' => 'rch', 'RcHm_v2.0_Chr6g0286521' => 'rch', 'RcHm_v2.0_Chr6g0286531' => 'rch', 'RcHm_v2.0_Chr7g0189141' => 'rch', 'Rhsim02G0028700' => 'rsi', 'Rhsim02G0028800' => 'rsi', 'Rhsim02G0028900' => 'rsi', 'Rhsim02G0029000' => 'rsi', 'Rhsim02G0029100' => 'rsi', 'Rhsim02G0029200' => 'rsi', 'Rhsim02G0029300' => 'rsi', 'Rhsim02G0029400' => 'rsi', 'Rhsim02G0029500' => 'rsi', 'Rhsim02G0029600' => 'rsi', 'RhsimUnG0024000' => 'rsi', 'RhsimUnG0024100' => 'rsi', 'RhsimUnG0024200' => 'rsi', 'RhsimUnG0024300' => 'rsi', 'RhsimUnG0024400' => 'rsi', 'RhsimUnG0024500' => 'rsi', 'RhsimUnG0024700' => 'rsi', 'RhsimUnG0024800' => 'rsi', 'RhsimUnG0024900' => 'rsi', 'RhsimUnG0025100' => 'rsi', 'Sabra08G0120200' => 'sbr', 'Sabra08G0120300' => 'sbr', 'Sabra08G0120500' => 'sbr', 'Sabra08G0120600' => 'sbr', 'Sabra10G0158900' => 'sbr', 'SalBow2G3492' => 'sbo', 'Sc13g0004760' => 'sci', 'Sc13g0004770' => 'sci', 'Sed0003417' => 'sed', 'Sed0019750' => 'sed', 'SEGI_03419' => 'sgi', 'SEGI_05907' => 'sgi', 'SEGI_10682' => 'sgi', 'SEGI_13528' => 'sgi', 'SEGI_16081' => 'sgi', 'SEGI_19370' => 'sgi', 'SEGI_21015' => 'sgi', 'SEGI_21944' => 'sgi', 'SEGI_32906' => 'sgi', 'SEGI_33093' => 'sgi', 'SEGI_36110' => 'sgi', 'SEGI_40397' => 'sgi', 'SGA_v2.0_scaffold191G40426' => 'sas', 'SGA_v2.0_scaffold353G49717' => 'sas', 'SGA_v2.0_scaffold50G18550' => 'sas', 'SMO119G0173' => 'smo', 'SMO172G0002' => 'smo', 'Solyc09g082690.3' => 'sly', 'Solyc09g082700.2' => 'sly', 'Sopen09g031550' => 'spe', 'Sopen09g031560' => 'spe', 'Sp3g20540' => 'spa', 'Sp7g07580' => 'spa', 'TAR134G0002' => 'tar', 'TAR236G0001' => 'tar', 'TAR365G0892' => 'tar', 'TAR636G0166' => 'tar', 'TAR636G0646' => 'tar', 'TAR636G0869' => 'tar', 'TAR636G1317' => 'tar', 'TAR636G1744' => 'tar', 'TAR636G3358' => 'tar', 'TAR636G3436' => 'tar', 'THA.LOC104803047' => 'tha', 'Thecc.04G238900' => 'tca', 'Thhalv10021557m.g' => 'esa', 'Thhalv10026318m.g' => 'esa', 'Thhalv10026335m.g' => 'esa', 'TPR.G17433' => 'tpr', 'TPR.G18915' => 'tpr', 'TPR.G26125' => 'tpr', 'TWI09G0677' => 'twi', 'TWI73G0287' => 'twi', 'unitig_748.g8326' => 'ugi', 'vmacro15370' => 'vma', 'vmacro15371' => 'vma', 'vmacro15372' => 'vma', 'vmacro15373' => 'vma', 'vmacro15374' => 'vma', 'VMungo0720G2826' => 'vmu', 'Zm00001eb116960' => 'zma', 'Zm00001eb301260' => 'zma', 'Zm00001eb301270' => 'zma' ) $gf_id = 'HOM05D001460' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001460' ) $data_identifier = 'HOM05D001460' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 4, 'aag' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 2, 'aox' => (int) 2, 'arhy' => (int) 4, 'ath' => (int) 2, 'atr' => (int) 1, 'acertr' => (int) 10, 'cqu' => (int) 4, 'bca' => (int) 11, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 1, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 1, 'ccan' => (int) 1, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 1, 'col' => (int) 1, 'cpa' => (int) 1, 'cre' => (int) 7, 'csa' => (int) 1, 'camsi' => (int) 2, 'dca' => (int) 3, 'din' => (int) 2, 'dzi' => (int) 3, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 14, 'fve' => (int) 9, 'gma' => (int) 2, 'ghi' => (int) 4, 'gra' => (int) 2, 'vvi' => (int) 1, 'han' => (int) 13, 'cav' => (int) 1, 'hma' => (int) 2, 'sun' => (int) 2, 'lal' => (int) 2, 'lonja' => (int) 12, 'lja' => (int) 1, 'lsa' => (int) 7, 'mes' => (int) 1, 'mpo' => (int) 27, 'mbi' => (int) 1, 'mco' => (int) 8, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 1, 'egut' => (int) 1, 'ama' => (int) 1, 'nta' => (int) 4, 'nnu' => (int) 2, 'oeu' => (int) 3, 'osa' => (int) 4, 'pax' => (int) 9, 'pgr' => (int) 1, 'stu' => (int) 1, 'pvu' => (int) 1, 'ptr' => (int) 4, 'ppa' => (int) 22, 'pco' => (int) 6, 'ppe' => (int) 6, 'psa' => (int) 5, 'pso' => (int) 19, 'qlo' => (int) 5, 'rch' => (int) 7, 'rsi' => (int) 20, 'sbr' => (int) 5, 'sbo' => (int) 1, 'sci' => (int) 2, 'sed' => (int) 2, 'sgi' => (int) 12, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 2, 'tar' => (int) 10, 'tha' => (int) 1, 'tca' => (int) 1, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 2, 'ugi' => (int) 1, 'vma' => (int) 5, 'vmu' => (int) 1, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb301270' $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' => 'HOM05D001460', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '433', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p22980' => 'bna', 'A01p32340' => 'bna', 'A03p42970' => 'bna', 'A05p25880' => 'bna', 'Aa31LG8G9320' => 'aar', 'Aa31LG8G9330' => 'aar', 'Aa31LG8G9340' => 'aar', 'Aa31sc221G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1034' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1528' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.829' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2222' => 'aag', 'Ah.12g058830' => 'amhyb', 'Ah.12g058840' => 'amhyb', 'AL3G37160' => 'aly', 'AL7G41310' => 'aly', 'Aqoxy5G00395' => 'aox', 'Aqoxy5G00396' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0C8NZA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5185HY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JZ1PRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MD3LS0' => 'arhy', 'AT3G22840' => 'ath', 'AT4G14690' => 'ath', 'ATR0665G054' => 'atr', 'Atru.chr4.2344' => 'acertr', 'Atru.chr4.2346' => 'acertr', 'Atru.chr4.2347' => 'acertr', 'Atru.chr4.2348' => 'acertr', 'Atru.chr4.2355' => 'acertr', 'Atru.chr4.2356' => 'acertr', 'Atru.chr4.2358' => 'acertr', 'Atru.chr4.2359' => 'acertr', 'Atru.chr4.2360' => 'acertr', 'Atru.chr4.2361' => 'acertr', 'AUR62030476' => 'cqu', 'AUR62030478' => 'cqu', 'AUR62030819' => 'cqu', 'AUR62030820' => 'cqu', 'BcaB03g14648' => 'bca', 'BcaB04g20492' => 'bca', 'BcaB06g26399' => 'bca', 'BcaC01g03416' => 'bca', 'BcaC01g03419' => 'bca', 'BcaC01g03421' => 'bca', 'BcaC01g03424' => 'bca', 'BcaC05g28012' => 'bca', 'BcaC09g49212' => 'bca', 'BcaC09g50140' => 'bca', 'BcaNung00346' => 'bca', 'BolC1t02785H' => 'bol', 'BolC1t04095H' => 'bol', 'BolC3t17545H' => 'bol', 'BolC5t32769H' => 'bol', 'BraA01t02211Z' => 'bra', 'BraA01t03359Z' => 'bra', 'BraA03t13441Z' => 'bra', 'BraA05t21476Z' => 'bra', 'C01p28420' => 'bna', 'C01p41350' => 'bna', 'C03p52750' => 'bna', 'C03p52780' => 'bna', 'C05p40270' => 'bna', 'CAN.G1437.9' => 'can', 'CANSAT78G0035' => 'cansat', 'CANSAT78G1036' => 'cansat', 'CANSAT78G2272' => 'cansat', 'CANSAT78G2478' => 'cansat', 'CARHR098700' => 'chi', 'CARHR221120' => 'chi', 'CARHR221150' => 'chi', 'Carub.0003s2297' => 'cru', 'Carub.0007s2749' => 'cru', 'Carub.0007s2750' => 'cru', 'Carub.0007s2751' => 'cru', 'Ca_10849_v3' => 'car', 'Cc03_g04300' => 'ccan', 'CDE02G3648' => 'cde', 'CDE05G0060' => 'cde', 'CDE05G0692' => 'cde', 'CDE05G2285' => 'cde', 'CDE05G2884' => 'cde', 'CDE05G3072' => 'cde', 'Cfa008439' => 'cfa', 'Cfa008441' => 'cfa', 'Cfa008443' => 'cfa', 'Cfa008448' => 'cfa', 'Ciclev10005974m.g' => 'ccl', 'Ciclev10006006m.g' => 'ccl', 'Ciclev10006775m.g' => 'ccl', 'CiPaw.02G120400' => 'cil', 'CiPaw.02G120500' => 'cil', 'CiPaw.02G120600' => 'cil', 'ClCG05G004850' => 'cla', 'COL.COLO4_21566' => 'col', 'Cpa.g.sc44.124' => 'cpa', 'Cre07.g320400' => 'cre', 'Cre07.g320450' => 'cre', 'Cre08.g384650' => 'cre', 'Cre09.g393173' => 'cre', 'Cre09.g394325' => 'cre', 'Cre14.g626750' => 'cre', 'Cre16.g679250' => 'cre', 'CsaV3_3G012890' => 'csa', 'CSS0010865' => 'camsi', 'CSS0044338' => 'camsi', 'DCAR_002366' => 'dca', 'DCAR_030687' => 'dca', 'DCAR_030688' => 'dca', 'Dinv14047' => 'din', 'Dinv14048' => 'din', 'Duzib151G0105' => 'dzi', 'Duzib151G0114' => 'dzi', 'Duzib212G1029' => 'dzi', 'ECA232G3536' => 'eca', 'ECA240G0786' => 'eca', 'ECA240G1802' => 'eca', 'ECA240G3760' => 'eca', 'ECA240G3920' => 'eca', 'EL10Ac5g12536' => 'bvu', 'EL10Ac5g12537' => 'bvu', 'EL10Ac5g12538' => 'bvu', 'Eucgr.B01004' => 'egr', 'Eucgr.B01006' => 'egr', 'Eucgr.B01007' => 'egr', 'Eucgr.B01008' => 'egr', 'Eucgr.B01895' => 'egr', 'Eucgr.B01896' => 'egr', 'FAN04G1456' => 'fan', 'FAN08G1769' => 'fan', 'FAN08G2160' => 'fan', 'FAN13G2403' => 'fan', 'FAN13G3303' => 'fan', 'FAN15G2435' => 'fan', 'FAN17G0672' => 'fan', 'FAN17G2441' => 'fan', 'FAN18G1024' => 'fan', 'FAN22G1458' => 'fan', 'FAN24G0037' => 'fan', 'FAN24G0429' => 'fan', 'FAN24G2387' => 'fan', 'FAN27G2746' => 'fan', 'FvH4_2g20400' => 'fve', 'FvH4_2g20420' => 'fve', 'FvH4_2g20430' => 'fve', 'FvH4_4g01270' => 'fve', 'FvH4_4g01290' => 'fve', 'FvH4_4g01300' => 'fve', 'FvH4_4g01310' => 'fve', 'FvH4_4g01330' => 'fve', 'FvH4_5g09070' => 'fve', 'Glyma.10G243800' => 'gma', 'Glyma.20G150600' => 'gma', 'Gohir.A09G219200' => 'ghi', 'Gohir.A09G219300' => 'ghi', 'Gohir.D09G221400' => 'ghi', 'Gohir.D09G221500' => 'ghi', 'Gorai.006G242600' => 'gra', 'Gorai.006G242700' => 'gra', 'GSVIVG01018044001' => 'vvi', 'HanXRQChr03g0083821' => 'han', 'HanXRQChr03g0083841' => 'han', 'HanXRQChr03g0083881' => 'han', 'HanXRQChr03g0083901' => 'han', 'HanXRQChr03g0083921' => 'han', 'HanXRQChr03g0085331' => 'han', 'HanXRQChr03g0085361' => 'han', 'HanXRQChr03g0085411' => 'han', 'HanXRQChr03g0085421' => 'han', 'HanXRQChr03g0085431' => 'han', 'HanXRQChr08g0221991' => 'han', 'HanXRQChr11g0336061' => 'han', 'HanXRQChr11g0336411' => 'han', 'Haze_11234' => 'cav', 'Hma1.2p1_0549F.1_g177010' => 'hma', 'Hma1.2p1_0602F.1_g187630' => 'hma', 'Hund14876' => 'sun', 'Hund14879' => 'sun', 'Lalb_Chr06g0160741' => 'lal', 'Lalb_Chr21g0304781' => 'lal', 'Lj3A726G19' => 'lonja', 'Lj3A726T23' => 'lonja', 'Lj3A726T24' => 'lonja', 'Lj3A726T25' => 'lonja', 'Lj3A727T17' => 'lonja', 'Lj3C726T0' => 'lonja', 'Lj3C726T2' => 'lonja', 'Lj3P725T35' => 'lonja', 'Lj3P727T10' => 'lonja', 'Lj3P727T12' => 'lonja', 'Lj3P727T14' => 'lonja', 'Lj5g0023109' => 'lja', 'Lj6P646T44' => 'lonja', 'Lsat_1_v5_gn_6_75760' => 'lsa', 'Lsat_1_v5_gn_6_75800' => 'lsa', 'Lsat_1_v5_gn_6_75900' => 'lsa', 'Lsat_1_v5_gn_6_76240' => 'lsa', 'Lsat_1_v5_gn_6_76441' => 'lsa', 'Lsat_1_v5_gn_6_76700' => 'lsa', 'Lsat_1_v5_gn_6_76760' => 'lsa', 'Manes.15G033100' => 'mes', 'Mapoly0004s0074' => 'mpo', 'Mapoly0004s0075' => 'mpo', 'Mapoly0004s0163' => 'mpo', 'Mapoly0004s0164' => 'mpo', 'Mapoly0021s0018' => 'mpo', 'Mapoly0041s0136' => 'mpo', 'Mapoly0041s0137' => 'mpo', 'Mapoly0041s0138' => 'mpo', 'Mapoly0041s0139' => 'mpo', 'Mapoly0041s0141' => 'mpo', 'Mapoly0041s0142' => 'mpo', 'Mapoly0041s0143' => 'mpo', 'Mapoly0041s0144' => 'mpo', 'Mapoly0041s0145' => 'mpo', 'Mapoly0047s0106' => 'mpo', 'Mapoly0047s0108' => 'mpo', 'Mapoly0050s0051' => 'mpo', 'Mapoly0050s0052' => 'mpo', 'Mapoly0050s0053' => 'mpo', 'Mapoly0058s0013' => 'mpo', 'Mapoly0091s0078' => 'mpo', 'Mapoly0091s0079' => 'mpo', 'Mapoly0091s0080' => 'mpo', 'Mapoly0091s0081' => 'mpo', 'Mapoly0278s0004' => 'mpo', 'Mapoly0278s0005' => 'mpo', 'Mapoly0278s0006' => 'mpo', 'MBI11_g30648_MAGBIO' => 'mbi', 'MCO03G194' => 'mco', 'MCO03G590' => 'mco', 'MCO07G312' => 'mco', 'MCO10G318' => 'mco', 'MCO12G244' => 'mco', 'MCO13G148' => 'mco', 'MCO13G194' => 'mco', 'MCO16G238' => 'mco', 'MD06G1134100' => 'mdo', 'MD13G1200100' => 'mdo', 'MD13G1200300' => 'mdo', 'MD13G1200600' => 'mdo', 'MD14G1150400' => 'mdo', 'MD16G1200000' => 'mdo', 'Medtr1g102570' => 'mtr', 'Medtr1g102780' => 'mtr', 'Medtr1g102800' => 'mtr', 'Medtr1g102810' => 'mtr', 'Medtr1g102830' => 'mtr', 'MELO3C006499.2' => 'cme', 'Migut.G00385' => 'egut', 'MSTRG.4063' => 'ama', 'Nitab4.5_0000090g0260' => 'nta', 'Nitab4.5_0000977g0030' => 'nta', 'Nitab4.5_0002541g0040' => 'nta', 'Nitab4.5_0007068g0040' => 'nta', 'Nn005s41408' => 'nnu', 'Nn005s41410' => 'nnu', 'Oeu010310.1' => 'oeu', 'Oeu010311.1' => 'oeu', 'Oeu043472.1' => 'oeu', 'Os01g0246400' => 'osa', 'Os04g0267950' => 'osa', 'Os07g0178700' => 'osa', 'Os07g0178800' => 'osa', 'Peaxi162Scf00316g00046' => 'pax', 'Peaxi162Scf00316g00049' => 'pax', 'Peaxi162Scf00316g00059' => 'pax', 'Peaxi162Scf00316g00328' => 'pax', 'Peaxi162Scf00316g00329' => 'pax', 'Peaxi162Scf00316g00411' => 'pax', 'Peaxi162Scf00316g00521' => 'pax', 'Peaxi162Scf00492g00068' => 'pax', 'Peaxi162Scf35631g00002' => 'pax', 'PGR142G3720' => 'pgr', 'PGSC0003DMG400006442' => 'stu', 'Phvul.007G062000' => 'pvu', 'Potri.008G157750' => 'ptr', 'Potri.008G157900' => 'ptr', 'Potri.008G158000' => 'ptr', 'Potri.008G158200' => 'ptr', 'Pp3c11_7280' => 'ppa', 'Pp3c11_7980' => 'ppa', 'Pp3c12_19450' => 'ppa', 'Pp3c14_1480' => 'ppa', 'Pp3c14_1501' => 'ppa', 'Pp3c16_4900' => 'ppa', 'Pp3c16_5010' => 'ppa', 'Pp3c16_5060' => 'ppa', 'Pp3c19_18250' => 'ppa', 'Pp3c23_8530' => 'ppa', 'Pp3c23_8550' => 'ppa', 'Pp3c24_9670' => 'ppa', 'Pp3c2_21390' => 'ppa', 'Pp3c2_31380' => 'ppa', 'Pp3c3_16620' => 'ppa', 'Pp3c3_8090' => 'ppa', 'Pp3c3_8110' => 'ppa', 'Pp3c3_8130' => 'ppa', 'Pp3c3_8150' => 'ppa', 'Pp3c4_14320' => 'ppa', 'Pp3c6_2560' => 'ppa', 'Pp3c9_16700' => 'ppa', 'PRCOL_00000234' => 'pco', 'PRCOL_00000235' => 'pco', 'PRCOL_00000777' => 'pco', 'PRCOL_00002344' => 'pco', 'PRCOL_00002372' => 'pco', 'PRCOL_00006120' => 'pco', 'Prupe.1G021400' => 'ppe', 'Prupe.1G021500' => 'ppe', 'Prupe.1G021600' => 'ppe', 'Prupe.1G021700' => 'ppe', 'Prupe.1G021800' => 'ppe', 'Prupe.5G145100' => 'ppe', 'Psat6g204040' => 'psa', 'Psat6g204800' => 'psa', 'Psat6g204920' => 'psa', 'Psat6g204960' => 'psa', 'Psat6g205080' => 'psa', 'PSO017G0271' => 'pso', 'PSO017G1276' => 'pso', 'PSO017G1429' => 'pso', 'PSO017G1861' => 'pso', 'PSO017G2787' => 'pso', 'PSO017G4466' => 'pso', 'PSO017G5118' => 'pso', 'PSO017G5420' => 'pso', 'PSO063G3678' => 'pso', 'PSO210G0546' => 'pso', 'PSO317G0001' => 'pso', 'PSO357G0512' => 'pso', 'PSO478G2682' => 'pso', 'PSO647G0001' => 'pso', 'PSO675G0001' => 'pso', 'PSO675G2699' => 'pso', 'PSO675G2849' => 'pso', 'PSO675G4991' => 'pso', 'PSO689G0001' => 'pso', 'QL06p000916' => 'qlo', 'QL06p000921' => 'qlo', 'QL06p001398' => 'qlo', 'QL06p001407' => 'qlo', 'QL06p002031' => 'qlo', 'RcHm_v2.0_Chr4g0387791' => 'rch', 'RcHm_v2.0_Chr4g0387801' => 'rch', 'RcHm_v2.0_Chr6g0286501' => 'rch', 'RcHm_v2.0_Chr6g0286511' => 'rch', 'RcHm_v2.0_Chr6g0286521' => 'rch', 'RcHm_v2.0_Chr6g0286531' => 'rch', 'RcHm_v2.0_Chr7g0189141' => 'rch', 'Rhsim02G0028700' => 'rsi', 'Rhsim02G0028800' => 'rsi', 'Rhsim02G0028900' => 'rsi', 'Rhsim02G0029000' => 'rsi', 'Rhsim02G0029100' => 'rsi', 'Rhsim02G0029200' => 'rsi', 'Rhsim02G0029300' => 'rsi', 'Rhsim02G0029400' => 'rsi', 'Rhsim02G0029500' => 'rsi', 'Rhsim02G0029600' => 'rsi', 'RhsimUnG0024000' => 'rsi', 'RhsimUnG0024100' => 'rsi', 'RhsimUnG0024200' => 'rsi', 'RhsimUnG0024300' => 'rsi', 'RhsimUnG0024400' => 'rsi', 'RhsimUnG0024500' => 'rsi', 'RhsimUnG0024700' => 'rsi', 'RhsimUnG0024800' => 'rsi', 'RhsimUnG0024900' => 'rsi', 'RhsimUnG0025100' => 'rsi', 'Sabra08G0120200' => 'sbr', 'Sabra08G0120300' => 'sbr', 'Sabra08G0120500' => 'sbr', 'Sabra08G0120600' => 'sbr', 'Sabra10G0158900' => 'sbr', 'SalBow2G3492' => 'sbo', 'Sc13g0004760' => 'sci', 'Sc13g0004770' => 'sci', 'Sed0003417' => 'sed', 'Sed0019750' => 'sed', 'SEGI_03419' => 'sgi', 'SEGI_05907' => 'sgi', 'SEGI_10682' => 'sgi', 'SEGI_13528' => 'sgi', 'SEGI_16081' => 'sgi', 'SEGI_19370' => 'sgi', 'SEGI_21015' => 'sgi', 'SEGI_21944' => 'sgi', 'SEGI_32906' => 'sgi', 'SEGI_33093' => 'sgi', 'SEGI_36110' => 'sgi', 'SEGI_40397' => 'sgi', 'SGA_v2.0_scaffold191G40426' => 'sas', 'SGA_v2.0_scaffold353G49717' => 'sas', 'SGA_v2.0_scaffold50G18550' => 'sas', 'SMO119G0173' => 'smo', 'SMO172G0002' => 'smo', 'Solyc09g082690.3' => 'sly', 'Solyc09g082700.2' => 'sly', 'Sopen09g031550' => 'spe', 'Sopen09g031560' => 'spe', 'Sp3g20540' => 'spa', 'Sp7g07580' => 'spa', 'TAR134G0002' => 'tar', 'TAR236G0001' => 'tar', 'TAR365G0892' => 'tar', 'TAR636G0166' => 'tar', 'TAR636G0646' => 'tar', 'TAR636G0869' => 'tar', 'TAR636G1317' => 'tar', 'TAR636G1744' => 'tar', 'TAR636G3358' => 'tar', 'TAR636G3436' => 'tar', 'THA.LOC104803047' => 'tha', 'Thecc.04G238900' => 'tca', 'Thhalv10021557m.g' => 'esa', 'Thhalv10026318m.g' => 'esa', 'Thhalv10026335m.g' => 'esa', 'TPR.G17433' => 'tpr', 'TPR.G18915' => 'tpr', 'TPR.G26125' => 'tpr', 'TWI09G0677' => 'twi', 'TWI73G0287' => 'twi', 'unitig_748.g8326' => 'ugi', 'vmacro15370' => 'vma', 'vmacro15371' => 'vma', 'vmacro15372' => 'vma', 'vmacro15373' => 'vma', 'vmacro15374' => 'vma', 'VMungo0720G2826' => 'vmu', 'Zm00001eb116960' => 'zma', 'Zm00001eb301260' => 'zma', 'Zm00001eb301270' => 'zma' ), 'gf_id' => 'HOM05D001460', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001460' ), 'data_identifier' => 'HOM05D001460', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001460', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '433', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p22980' => 'bna', 'A01p32340' => 'bna', 'A03p42970' => 'bna', 'A05p25880' => 'bna', 'Aa31LG8G9320' => 'aar', 'Aa31LG8G9330' => 'aar', 'Aa31LG8G9340' => 'aar', 'Aa31sc221G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1034' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1528' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.829' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2222' => 'aag', 'Ah.12g058830' => 'amhyb', 'Ah.12g058840' => 'amhyb', 'AL3G37160' => 'aly', 'AL7G41310' => 'aly', 'Aqoxy5G00395' => 'aox', 'Aqoxy5G00396' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0C8NZA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5185HY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JZ1PRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MD3LS0' => 'arhy', 'AT3G22840' => 'ath', 'AT4G14690' => 'ath', 'ATR0665G054' => 'atr', 'Atru.chr4.2344' => 'acertr', 'Atru.chr4.2346' => 'acertr', 'Atru.chr4.2347' => 'acertr', 'Atru.chr4.2348' => 'acertr', 'Atru.chr4.2355' => 'acertr', 'Atru.chr4.2356' => 'acertr', 'Atru.chr4.2358' => 'acertr', 'Atru.chr4.2359' => 'acertr', 'Atru.chr4.2360' => 'acertr', 'Atru.chr4.2361' => 'acertr', 'AUR62030476' => 'cqu', 'AUR62030478' => 'cqu', 'AUR62030819' => 'cqu', 'AUR62030820' => 'cqu', 'BcaB03g14648' => 'bca', 'BcaB04g20492' => 'bca', 'BcaB06g26399' => 'bca', 'BcaC01g03416' => 'bca', 'BcaC01g03419' => 'bca', 'BcaC01g03421' => 'bca', 'BcaC01g03424' => 'bca', 'BcaC05g28012' => 'bca', 'BcaC09g49212' => 'bca', 'BcaC09g50140' => 'bca', 'BcaNung00346' => 'bca', 'BolC1t02785H' => 'bol', 'BolC1t04095H' => 'bol', 'BolC3t17545H' => 'bol', 'BolC5t32769H' => 'bol', 'BraA01t02211Z' => 'bra', 'BraA01t03359Z' => 'bra', 'BraA03t13441Z' => 'bra', 'BraA05t21476Z' => 'bra', 'C01p28420' => 'bna', 'C01p41350' => 'bna', 'C03p52750' => 'bna', 'C03p52780' => 'bna', 'C05p40270' => 'bna', 'CAN.G1437.9' => 'can', 'CANSAT78G0035' => 'cansat', 'CANSAT78G1036' => 'cansat', 'CANSAT78G2272' => 'cansat', 'CANSAT78G2478' => 'cansat', 'CARHR098700' => 'chi', 'CARHR221120' => 'chi', 'CARHR221150' => 'chi', 'Carub.0003s2297' => 'cru', 'Carub.0007s2749' => 'cru', 'Carub.0007s2750' => 'cru', 'Carub.0007s2751' => 'cru', 'Ca_10849_v3' => 'car', 'Cc03_g04300' => 'ccan', 'CDE02G3648' => 'cde', 'CDE05G0060' => 'cde', 'CDE05G0692' => 'cde', 'CDE05G2285' => 'cde', 'CDE05G2884' => 'cde', 'CDE05G3072' => 'cde', 'Cfa008439' => 'cfa', 'Cfa008441' => 'cfa', 'Cfa008443' => 'cfa', 'Cfa008448' => 'cfa', 'Ciclev10005974m.g' => 'ccl', 'Ciclev10006006m.g' => 'ccl', 'Ciclev10006775m.g' => 'ccl', 'CiPaw.02G120400' => 'cil', 'CiPaw.02G120500' => 'cil', 'CiPaw.02G120600' => 'cil', 'ClCG05G004850' => 'cla', 'COL.COLO4_21566' => 'col', 'Cpa.g.sc44.124' => 'cpa', 'Cre07.g320400' => 'cre', 'Cre07.g320450' => 'cre', 'Cre08.g384650' => 'cre', 'Cre09.g393173' => 'cre', 'Cre09.g394325' => 'cre', 'Cre14.g626750' => 'cre', 'Cre16.g679250' => 'cre', 'CsaV3_3G012890' => 'csa', 'CSS0010865' => 'camsi', 'CSS0044338' => 'camsi', 'DCAR_002366' => 'dca', 'DCAR_030687' => 'dca', 'DCAR_030688' => 'dca', 'Dinv14047' => 'din', 'Dinv14048' => 'din', 'Duzib151G0105' => 'dzi', 'Duzib151G0114' => 'dzi', 'Duzib212G1029' => 'dzi', 'ECA232G3536' => 'eca', 'ECA240G0786' => 'eca', 'ECA240G1802' => 'eca', 'ECA240G3760' => 'eca', 'ECA240G3920' => 'eca', 'EL10Ac5g12536' => 'bvu', 'EL10Ac5g12537' => 'bvu', 'EL10Ac5g12538' => 'bvu', 'Eucgr.B01004' => 'egr', 'Eucgr.B01006' => 'egr', 'Eucgr.B01007' => 'egr', 'Eucgr.B01008' => 'egr', 'Eucgr.B01895' => 'egr', 'Eucgr.B01896' => 'egr', 'FAN04G1456' => 'fan', 'FAN08G1769' => 'fan', 'FAN08G2160' => 'fan', 'FAN13G2403' => 'fan', 'FAN13G3303' => 'fan', 'FAN15G2435' => 'fan', 'FAN17G0672' => 'fan', 'FAN17G2441' => 'fan', 'FAN18G1024' => 'fan', 'FAN22G1458' => 'fan', 'FAN24G0037' => 'fan', 'FAN24G0429' => 'fan', 'FAN24G2387' => 'fan', 'FAN27G2746' => 'fan', 'FvH4_2g20400' => 'fve', 'FvH4_2g20420' => 'fve', 'FvH4_2g20430' => 'fve', 'FvH4_4g01270' => 'fve', 'FvH4_4g01290' => 'fve', 'FvH4_4g01300' => 'fve', 'FvH4_4g01310' => 'fve', 'FvH4_4g01330' => 'fve', 'FvH4_5g09070' => 'fve', 'Glyma.10G243800' => 'gma', 'Glyma.20G150600' => 'gma', 'Gohir.A09G219200' => 'ghi', 'Gohir.A09G219300' => 'ghi', 'Gohir.D09G221400' => 'ghi', 'Gohir.D09G221500' => 'ghi', 'Gorai.006G242600' => 'gra', 'Gorai.006G242700' => 'gra', 'GSVIVG01018044001' => 'vvi', 'HanXRQChr03g0083821' => 'han', 'HanXRQChr03g0083841' => 'han', 'HanXRQChr03g0083881' => 'han', 'HanXRQChr03g0083901' => 'han', 'HanXRQChr03g0083921' => 'han', 'HanXRQChr03g0085331' => 'han', 'HanXRQChr03g0085361' => 'han', 'HanXRQChr03g0085411' => 'han', 'HanXRQChr03g0085421' => 'han', 'HanXRQChr03g0085431' => 'han', 'HanXRQChr08g0221991' => 'han', 'HanXRQChr11g0336061' => 'han', 'HanXRQChr11g0336411' => 'han', 'Haze_11234' => 'cav', 'Hma1.2p1_0549F.1_g177010' => 'hma', 'Hma1.2p1_0602F.1_g187630' => 'hma', 'Hund14876' => 'sun', 'Hund14879' => 'sun', 'Lalb_Chr06g0160741' => 'lal', 'Lalb_Chr21g0304781' => 'lal', 'Lj3A726G19' => 'lonja', 'Lj3A726T23' => 'lonja', 'Lj3A726T24' => 'lonja', 'Lj3A726T25' => 'lonja', 'Lj3A727T17' => 'lonja', 'Lj3C726T0' => 'lonja', 'Lj3C726T2' => 'lonja', 'Lj3P725T35' => 'lonja', 'Lj3P727T10' => 'lonja', 'Lj3P727T12' => 'lonja', 'Lj3P727T14' => 'lonja', 'Lj5g0023109' => 'lja', 'Lj6P646T44' => 'lonja', 'Lsat_1_v5_gn_6_75760' => 'lsa', 'Lsat_1_v5_gn_6_75800' => 'lsa', 'Lsat_1_v5_gn_6_75900' => 'lsa', 'Lsat_1_v5_gn_6_76240' => 'lsa', 'Lsat_1_v5_gn_6_76441' => 'lsa', 'Lsat_1_v5_gn_6_76700' => 'lsa', 'Lsat_1_v5_gn_6_76760' => 'lsa', 'Manes.15G033100' => 'mes', 'Mapoly0004s0074' => 'mpo', 'Mapoly0004s0075' => 'mpo', 'Mapoly0004s0163' => 'mpo', 'Mapoly0004s0164' => 'mpo', 'Mapoly0021s0018' => 'mpo', 'Mapoly0041s0136' => 'mpo', 'Mapoly0041s0137' => 'mpo', 'Mapoly0041s0138' => 'mpo', 'Mapoly0041s0139' => 'mpo', 'Mapoly0041s0141' => 'mpo', 'Mapoly0041s0142' => 'mpo', 'Mapoly0041s0143' => 'mpo', 'Mapoly0041s0144' => 'mpo', 'Mapoly0041s0145' => 'mpo', 'Mapoly0047s0106' => 'mpo', 'Mapoly0047s0108' => 'mpo', 'Mapoly0050s0051' => 'mpo', 'Mapoly0050s0052' => 'mpo', 'Mapoly0050s0053' => 'mpo', 'Mapoly0058s0013' => 'mpo', 'Mapoly0091s0078' => 'mpo', 'Mapoly0091s0079' => 'mpo', 'Mapoly0091s0080' => 'mpo', 'Mapoly0091s0081' => 'mpo', 'Mapoly0278s0004' => 'mpo', 'Mapoly0278s0005' => 'mpo', 'Mapoly0278s0006' => 'mpo', 'MBI11_g30648_MAGBIO' => 'mbi', 'MCO03G194' => 'mco', 'MCO03G590' => 'mco', 'MCO07G312' => 'mco', 'MCO10G318' => 'mco', 'MCO12G244' => 'mco', 'MCO13G148' => 'mco', 'MCO13G194' => 'mco', 'MCO16G238' => 'mco', 'MD06G1134100' => 'mdo', 'MD13G1200100' => 'mdo', 'MD13G1200300' => 'mdo', 'MD13G1200600' => 'mdo', 'MD14G1150400' => 'mdo', 'MD16G1200000' => 'mdo', 'Medtr1g102570' => 'mtr', 'Medtr1g102780' => 'mtr', 'Medtr1g102800' => 'mtr', 'Medtr1g102810' => 'mtr', 'Medtr1g102830' => 'mtr', 'MELO3C006499.2' => 'cme', 'Migut.G00385' => 'egut', 'MSTRG.4063' => 'ama', 'Nitab4.5_0000090g0260' => 'nta', 'Nitab4.5_0000977g0030' => 'nta', 'Nitab4.5_0002541g0040' => 'nta', 'Nitab4.5_0007068g0040' => 'nta', 'Nn005s41408' => 'nnu', 'Nn005s41410' => 'nnu', 'Oeu010310.1' => 'oeu', 'Oeu010311.1' => 'oeu', 'Oeu043472.1' => 'oeu', 'Os01g0246400' => 'osa', 'Os04g0267950' => 'osa', 'Os07g0178700' => 'osa', 'Os07g0178800' => 'osa', 'Peaxi162Scf00316g00046' => 'pax', 'Peaxi162Scf00316g00049' => 'pax', 'Peaxi162Scf00316g00059' => 'pax', 'Peaxi162Scf00316g00328' => 'pax', 'Peaxi162Scf00316g00329' => 'pax', 'Peaxi162Scf00316g00411' => 'pax', 'Peaxi162Scf00316g00521' => 'pax', 'Peaxi162Scf00492g00068' => 'pax', 'Peaxi162Scf35631g00002' => 'pax', 'PGR142G3720' => 'pgr', 'PGSC0003DMG400006442' => 'stu', 'Phvul.007G062000' => 'pvu', 'Potri.008G157750' => 'ptr', 'Potri.008G157900' => 'ptr', 'Potri.008G158000' => 'ptr', 'Potri.008G158200' => 'ptr', 'Pp3c11_7280' => 'ppa', 'Pp3c11_7980' => 'ppa', 'Pp3c12_19450' => 'ppa', 'Pp3c14_1480' => 'ppa', 'Pp3c14_1501' => 'ppa', 'Pp3c16_4900' => 'ppa', 'Pp3c16_5010' => 'ppa', 'Pp3c16_5060' => 'ppa', 'Pp3c19_18250' => 'ppa', 'Pp3c23_8530' => 'ppa', 'Pp3c23_8550' => 'ppa', 'Pp3c24_9670' => 'ppa', 'Pp3c2_21390' => 'ppa', 'Pp3c2_31380' => 'ppa', 'Pp3c3_16620' => 'ppa', 'Pp3c3_8090' => 'ppa', 'Pp3c3_8110' => 'ppa', 'Pp3c3_8130' => 'ppa', 'Pp3c3_8150' => 'ppa', 'Pp3c4_14320' => 'ppa', 'Pp3c6_2560' => 'ppa', 'Pp3c9_16700' => 'ppa', 'PRCOL_00000234' => 'pco', 'PRCOL_00000235' => 'pco', 'PRCOL_00000777' => 'pco', 'PRCOL_00002344' => 'pco', 'PRCOL_00002372' => 'pco', 'PRCOL_00006120' => 'pco', 'Prupe.1G021400' => 'ppe', 'Prupe.1G021500' => 'ppe', 'Prupe.1G021600' => 'ppe', 'Prupe.1G021700' => 'ppe', 'Prupe.1G021800' => 'ppe', 'Prupe.5G145100' => 'ppe', 'Psat6g204040' => 'psa', 'Psat6g204800' => 'psa', 'Psat6g204920' => 'psa', 'Psat6g204960' => 'psa', 'Psat6g205080' => 'psa', 'PSO017G0271' => 'pso', 'PSO017G1276' => 'pso', 'PSO017G1429' => 'pso', 'PSO017G1861' => 'pso', 'PSO017G2787' => 'pso', 'PSO017G4466' => 'pso', 'PSO017G5118' => 'pso', 'PSO017G5420' => 'pso', 'PSO063G3678' => 'pso', 'PSO210G0546' => 'pso', 'PSO317G0001' => 'pso', 'PSO357G0512' => 'pso', 'PSO478G2682' => 'pso', 'PSO647G0001' => 'pso', 'PSO675G0001' => 'pso', 'PSO675G2699' => 'pso', 'PSO675G2849' => 'pso', 'PSO675G4991' => 'pso', 'PSO689G0001' => 'pso', 'QL06p000916' => 'qlo', 'QL06p000921' => 'qlo', 'QL06p001398' => 'qlo', 'QL06p001407' => 'qlo', 'QL06p002031' => 'qlo', 'RcHm_v2.0_Chr4g0387791' => 'rch', 'RcHm_v2.0_Chr4g0387801' => 'rch', 'RcHm_v2.0_Chr6g0286501' => 'rch', 'RcHm_v2.0_Chr6g0286511' => 'rch', 'RcHm_v2.0_Chr6g0286521' => 'rch', 'RcHm_v2.0_Chr6g0286531' => 'rch', 'RcHm_v2.0_Chr7g0189141' => 'rch', 'Rhsim02G0028700' => 'rsi', 'Rhsim02G0028800' => 'rsi', 'Rhsim02G0028900' => 'rsi', 'Rhsim02G0029000' => 'rsi', 'Rhsim02G0029100' => 'rsi', 'Rhsim02G0029200' => 'rsi', 'Rhsim02G0029300' => 'rsi', 'Rhsim02G0029400' => 'rsi', 'Rhsim02G0029500' => 'rsi', 'Rhsim02G0029600' => 'rsi', 'RhsimUnG0024000' => 'rsi', 'RhsimUnG0024100' => 'rsi', 'RhsimUnG0024200' => 'rsi', 'RhsimUnG0024300' => 'rsi', 'RhsimUnG0024400' => 'rsi', 'RhsimUnG0024500' => 'rsi', 'RhsimUnG0024700' => 'rsi', 'RhsimUnG0024800' => 'rsi', 'RhsimUnG0024900' => 'rsi', 'RhsimUnG0025100' => 'rsi', 'Sabra08G0120200' => 'sbr', 'Sabra08G0120300' => 'sbr', 'Sabra08G0120500' => 'sbr', 'Sabra08G0120600' => 'sbr', 'Sabra10G0158900' => 'sbr', 'SalBow2G3492' => 'sbo', 'Sc13g0004760' => 'sci', 'Sc13g0004770' => 'sci', 'Sed0003417' => 'sed', 'Sed0019750' => 'sed', 'SEGI_03419' => 'sgi', 'SEGI_05907' => 'sgi', 'SEGI_10682' => 'sgi', 'SEGI_13528' => 'sgi', 'SEGI_16081' => 'sgi', 'SEGI_19370' => 'sgi', 'SEGI_21015' => 'sgi', 'SEGI_21944' => 'sgi', 'SEGI_32906' => 'sgi', 'SEGI_33093' => 'sgi', 'SEGI_36110' => 'sgi', 'SEGI_40397' => 'sgi', 'SGA_v2.0_scaffold191G40426' => 'sas', 'SGA_v2.0_scaffold353G49717' => 'sas', 'SGA_v2.0_scaffold50G18550' => 'sas', 'SMO119G0173' => 'smo', 'SMO172G0002' => 'smo', 'Solyc09g082690.3' => 'sly', 'Solyc09g082700.2' => 'sly', 'Sopen09g031550' => 'spe', 'Sopen09g031560' => 'spe', 'Sp3g20540' => 'spa', 'Sp7g07580' => 'spa', 'TAR134G0002' => 'tar', 'TAR236G0001' => 'tar', 'TAR365G0892' => 'tar', 'TAR636G0166' => 'tar', 'TAR636G0646' => 'tar', 'TAR636G0869' => 'tar', 'TAR636G1317' => 'tar', 'TAR636G1744' => 'tar', 'TAR636G3358' => 'tar', 'TAR636G3436' => 'tar', 'THA.LOC104803047' => 'tha', 'Thecc.04G238900' => 'tca', 'Thhalv10021557m.g' => 'esa', 'Thhalv10026318m.g' => 'esa', 'Thhalv10026335m.g' => 'esa', 'TPR.G17433' => 'tpr', 'TPR.G18915' => 'tpr', 'TPR.G26125' => 'tpr', 'TWI09G0677' => 'twi', 'TWI73G0287' => 'twi', 'unitig_748.g8326' => 'ugi', 'vmacro15370' => 'vma', 'vmacro15371' => 'vma', 'vmacro15372' => 'vma', 'vmacro15373' => 'vma', 'vmacro15374' => 'vma', 'VMungo0720G2826' => 'vmu', 'Zm00001eb116960' => 'zma', 'Zm00001eb301260' => 'zma', 'Zm00001eb301270' => 'zma' ) $gf_id = 'HOM05D001460' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001460' ) $data_identifier = 'HOM05D001460' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 4, 'aag' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 2, 'aox' => (int) 2, 'arhy' => (int) 4, 'ath' => (int) 2, 'atr' => (int) 1, 'acertr' => (int) 10, 'cqu' => (int) 4, 'bca' => (int) 11, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 1, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 1, 'ccan' => (int) 1, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 1, 'col' => (int) 1, 'cpa' => (int) 1, 'cre' => (int) 7, 'csa' => (int) 1, 'camsi' => (int) 2, 'dca' => (int) 3, 'din' => (int) 2, 'dzi' => (int) 3, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 14, 'fve' => (int) 9, 'gma' => (int) 2, 'ghi' => (int) 4, 'gra' => (int) 2, 'vvi' => (int) 1, 'han' => (int) 13, 'cav' => (int) 1, 'hma' => (int) 2, 'sun' => (int) 2, 'lal' => (int) 2, 'lonja' => (int) 12, 'lja' => (int) 1, 'lsa' => (int) 7, 'mes' => (int) 1, 'mpo' => (int) 27, 'mbi' => (int) 1, 'mco' => (int) 8, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 1, 'egut' => (int) 1, 'ama' => (int) 1, 'nta' => (int) 4, 'nnu' => (int) 2, 'oeu' => (int) 3, 'osa' => (int) 4, 'pax' => (int) 9, 'pgr' => (int) 1, 'stu' => (int) 1, 'pvu' => (int) 1, 'ptr' => (int) 4, 'ppa' => (int) 22, 'pco' => (int) 6, 'ppe' => (int) 6, 'psa' => (int) 5, 'pso' => (int) 19, 'qlo' => (int) 5, 'rch' => (int) 7, 'rsi' => (int) 20, 'sbr' => (int) 5, 'sbo' => (int) 1, 'sci' => (int) 2, 'sed' => (int) 2, 'sgi' => (int) 12, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 2, 'tar' => (int) 10, 'tha' => (int) 1, 'tca' => (int) 1, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 2, 'ugi' => (int) 1, 'vma' => (int) 5, 'vmu' => (int) 1, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb301270' $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' => 'HOM05D001460', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '433', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p22980' => 'bna', 'A01p32340' => 'bna', 'A03p42970' => 'bna', 'A05p25880' => 'bna', 'Aa31LG8G9320' => 'aar', 'Aa31LG8G9330' => 'aar', 'Aa31LG8G9340' => 'aar', 'Aa31sc221G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1034' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1528' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.829' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2222' => 'aag', 'Ah.12g058830' => 'amhyb', 'Ah.12g058840' => 'amhyb', 'AL3G37160' => 'aly', 'AL7G41310' => 'aly', 'Aqoxy5G00395' => 'aox', 'Aqoxy5G00396' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0C8NZA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5185HY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JZ1PRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MD3LS0' => 'arhy', 'AT3G22840' => 'ath', 'AT4G14690' => 'ath', 'ATR0665G054' => 'atr', 'Atru.chr4.2344' => 'acertr', 'Atru.chr4.2346' => 'acertr', 'Atru.chr4.2347' => 'acertr', 'Atru.chr4.2348' => 'acertr', 'Atru.chr4.2355' => 'acertr', 'Atru.chr4.2356' => 'acertr', 'Atru.chr4.2358' => 'acertr', 'Atru.chr4.2359' => 'acertr', 'Atru.chr4.2360' => 'acertr', 'Atru.chr4.2361' => 'acertr', 'AUR62030476' => 'cqu', 'AUR62030478' => 'cqu', 'AUR62030819' => 'cqu', 'AUR62030820' => 'cqu', 'BcaB03g14648' => 'bca', 'BcaB04g20492' => 'bca', 'BcaB06g26399' => 'bca', 'BcaC01g03416' => 'bca', 'BcaC01g03419' => 'bca', 'BcaC01g03421' => 'bca', 'BcaC01g03424' => 'bca', 'BcaC05g28012' => 'bca', 'BcaC09g49212' => 'bca', 'BcaC09g50140' => 'bca', 'BcaNung00346' => 'bca', 'BolC1t02785H' => 'bol', 'BolC1t04095H' => 'bol', 'BolC3t17545H' => 'bol', 'BolC5t32769H' => 'bol', 'BraA01t02211Z' => 'bra', 'BraA01t03359Z' => 'bra', 'BraA03t13441Z' => 'bra', 'BraA05t21476Z' => 'bra', 'C01p28420' => 'bna', 'C01p41350' => 'bna', 'C03p52750' => 'bna', 'C03p52780' => 'bna', 'C05p40270' => 'bna', 'CAN.G1437.9' => 'can', 'CANSAT78G0035' => 'cansat', 'CANSAT78G1036' => 'cansat', 'CANSAT78G2272' => 'cansat', 'CANSAT78G2478' => 'cansat', 'CARHR098700' => 'chi', 'CARHR221120' => 'chi', 'CARHR221150' => 'chi', 'Carub.0003s2297' => 'cru', 'Carub.0007s2749' => 'cru', 'Carub.0007s2750' => 'cru', 'Carub.0007s2751' => 'cru', 'Ca_10849_v3' => 'car', 'Cc03_g04300' => 'ccan', 'CDE02G3648' => 'cde', 'CDE05G0060' => 'cde', 'CDE05G0692' => 'cde', 'CDE05G2285' => 'cde', 'CDE05G2884' => 'cde', 'CDE05G3072' => 'cde', 'Cfa008439' => 'cfa', 'Cfa008441' => 'cfa', 'Cfa008443' => 'cfa', 'Cfa008448' => 'cfa', 'Ciclev10005974m.g' => 'ccl', 'Ciclev10006006m.g' => 'ccl', 'Ciclev10006775m.g' => 'ccl', 'CiPaw.02G120400' => 'cil', 'CiPaw.02G120500' => 'cil', 'CiPaw.02G120600' => 'cil', 'ClCG05G004850' => 'cla', 'COL.COLO4_21566' => 'col', 'Cpa.g.sc44.124' => 'cpa', 'Cre07.g320400' => 'cre', 'Cre07.g320450' => 'cre', 'Cre08.g384650' => 'cre', 'Cre09.g393173' => 'cre', 'Cre09.g394325' => 'cre', 'Cre14.g626750' => 'cre', 'Cre16.g679250' => 'cre', 'CsaV3_3G012890' => 'csa', 'CSS0010865' => 'camsi', 'CSS0044338' => 'camsi', 'DCAR_002366' => 'dca', 'DCAR_030687' => 'dca', 'DCAR_030688' => 'dca', 'Dinv14047' => 'din', 'Dinv14048' => 'din', 'Duzib151G0105' => 'dzi', 'Duzib151G0114' => 'dzi', 'Duzib212G1029' => 'dzi', 'ECA232G3536' => 'eca', 'ECA240G0786' => 'eca', 'ECA240G1802' => 'eca', 'ECA240G3760' => 'eca', 'ECA240G3920' => 'eca', 'EL10Ac5g12536' => 'bvu', 'EL10Ac5g12537' => 'bvu', 'EL10Ac5g12538' => 'bvu', 'Eucgr.B01004' => 'egr', 'Eucgr.B01006' => 'egr', 'Eucgr.B01007' => 'egr', 'Eucgr.B01008' => 'egr', 'Eucgr.B01895' => 'egr', 'Eucgr.B01896' => 'egr', 'FAN04G1456' => 'fan', 'FAN08G1769' => 'fan', 'FAN08G2160' => 'fan', 'FAN13G2403' => 'fan', 'FAN13G3303' => 'fan', 'FAN15G2435' => 'fan', 'FAN17G0672' => 'fan', 'FAN17G2441' => 'fan', 'FAN18G1024' => 'fan', 'FAN22G1458' => 'fan', 'FAN24G0037' => 'fan', 'FAN24G0429' => 'fan', 'FAN24G2387' => 'fan', 'FAN27G2746' => 'fan', 'FvH4_2g20400' => 'fve', 'FvH4_2g20420' => 'fve', 'FvH4_2g20430' => 'fve', 'FvH4_4g01270' => 'fve', 'FvH4_4g01290' => 'fve', 'FvH4_4g01300' => 'fve', 'FvH4_4g01310' => 'fve', 'FvH4_4g01330' => 'fve', 'FvH4_5g09070' => 'fve', 'Glyma.10G243800' => 'gma', 'Glyma.20G150600' => 'gma', 'Gohir.A09G219200' => 'ghi', 'Gohir.A09G219300' => 'ghi', 'Gohir.D09G221400' => 'ghi', 'Gohir.D09G221500' => 'ghi', 'Gorai.006G242600' => 'gra', 'Gorai.006G242700' => 'gra', 'GSVIVG01018044001' => 'vvi', 'HanXRQChr03g0083821' => 'han', 'HanXRQChr03g0083841' => 'han', 'HanXRQChr03g0083881' => 'han', 'HanXRQChr03g0083901' => 'han', 'HanXRQChr03g0083921' => 'han', 'HanXRQChr03g0085331' => 'han', 'HanXRQChr03g0085361' => 'han', 'HanXRQChr03g0085411' => 'han', 'HanXRQChr03g0085421' => 'han', 'HanXRQChr03g0085431' => 'han', 'HanXRQChr08g0221991' => 'han', 'HanXRQChr11g0336061' => 'han', 'HanXRQChr11g0336411' => 'han', 'Haze_11234' => 'cav', 'Hma1.2p1_0549F.1_g177010' => 'hma', 'Hma1.2p1_0602F.1_g187630' => 'hma', 'Hund14876' => 'sun', 'Hund14879' => 'sun', 'Lalb_Chr06g0160741' => 'lal', 'Lalb_Chr21g0304781' => 'lal', 'Lj3A726G19' => 'lonja', 'Lj3A726T23' => 'lonja', 'Lj3A726T24' => 'lonja', 'Lj3A726T25' => 'lonja', 'Lj3A727T17' => 'lonja', 'Lj3C726T0' => 'lonja', 'Lj3C726T2' => 'lonja', 'Lj3P725T35' => 'lonja', 'Lj3P727T10' => 'lonja', 'Lj3P727T12' => 'lonja', 'Lj3P727T14' => 'lonja', 'Lj5g0023109' => 'lja', 'Lj6P646T44' => 'lonja', 'Lsat_1_v5_gn_6_75760' => 'lsa', 'Lsat_1_v5_gn_6_75800' => 'lsa', 'Lsat_1_v5_gn_6_75900' => 'lsa', 'Lsat_1_v5_gn_6_76240' => 'lsa', 'Lsat_1_v5_gn_6_76441' => 'lsa', 'Lsat_1_v5_gn_6_76700' => 'lsa', 'Lsat_1_v5_gn_6_76760' => 'lsa', 'Manes.15G033100' => 'mes', 'Mapoly0004s0074' => 'mpo', 'Mapoly0004s0075' => 'mpo', 'Mapoly0004s0163' => 'mpo', 'Mapoly0004s0164' => 'mpo', 'Mapoly0021s0018' => 'mpo', 'Mapoly0041s0136' => 'mpo', 'Mapoly0041s0137' => 'mpo', 'Mapoly0041s0138' => 'mpo', 'Mapoly0041s0139' => 'mpo', 'Mapoly0041s0141' => 'mpo', 'Mapoly0041s0142' => 'mpo', 'Mapoly0041s0143' => 'mpo', 'Mapoly0041s0144' => 'mpo', 'Mapoly0041s0145' => 'mpo', 'Mapoly0047s0106' => 'mpo', 'Mapoly0047s0108' => 'mpo', 'Mapoly0050s0051' => 'mpo', 'Mapoly0050s0052' => 'mpo', 'Mapoly0050s0053' => 'mpo', 'Mapoly0058s0013' => 'mpo', 'Mapoly0091s0078' => 'mpo', 'Mapoly0091s0079' => 'mpo', 'Mapoly0091s0080' => 'mpo', 'Mapoly0091s0081' => 'mpo', 'Mapoly0278s0004' => 'mpo', 'Mapoly0278s0005' => 'mpo', 'Mapoly0278s0006' => 'mpo', 'MBI11_g30648_MAGBIO' => 'mbi', 'MCO03G194' => 'mco', 'MCO03G590' => 'mco', 'MCO07G312' => 'mco', 'MCO10G318' => 'mco', 'MCO12G244' => 'mco', 'MCO13G148' => 'mco', 'MCO13G194' => 'mco', 'MCO16G238' => 'mco', 'MD06G1134100' => 'mdo', 'MD13G1200100' => 'mdo', 'MD13G1200300' => 'mdo', 'MD13G1200600' => 'mdo', 'MD14G1150400' => 'mdo', 'MD16G1200000' => 'mdo', 'Medtr1g102570' => 'mtr', 'Medtr1g102780' => 'mtr', 'Medtr1g102800' => 'mtr', 'Medtr1g102810' => 'mtr', 'Medtr1g102830' => 'mtr', 'MELO3C006499.2' => 'cme', 'Migut.G00385' => 'egut', 'MSTRG.4063' => 'ama', 'Nitab4.5_0000090g0260' => 'nta', 'Nitab4.5_0000977g0030' => 'nta', 'Nitab4.5_0002541g0040' => 'nta', 'Nitab4.5_0007068g0040' => 'nta', 'Nn005s41408' => 'nnu', 'Nn005s41410' => 'nnu', 'Oeu010310.1' => 'oeu', 'Oeu010311.1' => 'oeu', 'Oeu043472.1' => 'oeu', 'Os01g0246400' => 'osa', 'Os04g0267950' => 'osa', 'Os07g0178700' => 'osa', 'Os07g0178800' => 'osa', 'Peaxi162Scf00316g00046' => 'pax', 'Peaxi162Scf00316g00049' => 'pax', 'Peaxi162Scf00316g00059' => 'pax', 'Peaxi162Scf00316g00328' => 'pax', 'Peaxi162Scf00316g00329' => 'pax', 'Peaxi162Scf00316g00411' => 'pax', 'Peaxi162Scf00316g00521' => 'pax', 'Peaxi162Scf00492g00068' => 'pax', 'Peaxi162Scf35631g00002' => 'pax', 'PGR142G3720' => 'pgr', 'PGSC0003DMG400006442' => 'stu', 'Phvul.007G062000' => 'pvu', 'Potri.008G157750' => 'ptr', 'Potri.008G157900' => 'ptr', 'Potri.008G158000' => 'ptr', 'Potri.008G158200' => 'ptr', 'Pp3c11_7280' => 'ppa', 'Pp3c11_7980' => 'ppa', 'Pp3c12_19450' => 'ppa', 'Pp3c14_1480' => 'ppa', 'Pp3c14_1501' => 'ppa', 'Pp3c16_4900' => 'ppa', 'Pp3c16_5010' => 'ppa', 'Pp3c16_5060' => 'ppa', 'Pp3c19_18250' => 'ppa', 'Pp3c23_8530' => 'ppa', 'Pp3c23_8550' => 'ppa', 'Pp3c24_9670' => 'ppa', 'Pp3c2_21390' => 'ppa', 'Pp3c2_31380' => 'ppa', 'Pp3c3_16620' => 'ppa', 'Pp3c3_8090' => 'ppa', 'Pp3c3_8110' => 'ppa', 'Pp3c3_8130' => 'ppa', 'Pp3c3_8150' => 'ppa', 'Pp3c4_14320' => 'ppa', 'Pp3c6_2560' => 'ppa', 'Pp3c9_16700' => 'ppa', 'PRCOL_00000234' => 'pco', 'PRCOL_00000235' => 'pco', 'PRCOL_00000777' => 'pco', 'PRCOL_00002344' => 'pco', 'PRCOL_00002372' => 'pco', 'PRCOL_00006120' => 'pco', 'Prupe.1G021400' => 'ppe', 'Prupe.1G021500' => 'ppe', 'Prupe.1G021600' => 'ppe', 'Prupe.1G021700' => 'ppe', 'Prupe.1G021800' => 'ppe', 'Prupe.5G145100' => 'ppe', 'Psat6g204040' => 'psa', 'Psat6g204800' => 'psa', 'Psat6g204920' => 'psa', 'Psat6g204960' => 'psa', 'Psat6g205080' => 'psa', 'PSO017G0271' => 'pso', 'PSO017G1276' => 'pso', 'PSO017G1429' => 'pso', 'PSO017G1861' => 'pso', 'PSO017G2787' => 'pso', 'PSO017G4466' => 'pso', 'PSO017G5118' => 'pso', 'PSO017G5420' => 'pso', 'PSO063G3678' => 'pso', 'PSO210G0546' => 'pso', 'PSO317G0001' => 'pso', 'PSO357G0512' => 'pso', 'PSO478G2682' => 'pso', 'PSO647G0001' => 'pso', 'PSO675G0001' => 'pso', 'PSO675G2699' => 'pso', 'PSO675G2849' => 'pso', 'PSO675G4991' => 'pso', 'PSO689G0001' => 'pso', 'QL06p000916' => 'qlo', 'QL06p000921' => 'qlo', 'QL06p001398' => 'qlo', 'QL06p001407' => 'qlo', 'QL06p002031' => 'qlo', 'RcHm_v2.0_Chr4g0387791' => 'rch', 'RcHm_v2.0_Chr4g0387801' => 'rch', 'RcHm_v2.0_Chr6g0286501' => 'rch', 'RcHm_v2.0_Chr6g0286511' => 'rch', 'RcHm_v2.0_Chr6g0286521' => 'rch', 'RcHm_v2.0_Chr6g0286531' => 'rch', 'RcHm_v2.0_Chr7g0189141' => 'rch', 'Rhsim02G0028700' => 'rsi', 'Rhsim02G0028800' => 'rsi', 'Rhsim02G0028900' => 'rsi', 'Rhsim02G0029000' => 'rsi', 'Rhsim02G0029100' => 'rsi', 'Rhsim02G0029200' => 'rsi', 'Rhsim02G0029300' => 'rsi', 'Rhsim02G0029400' => 'rsi', 'Rhsim02G0029500' => 'rsi', 'Rhsim02G0029600' => 'rsi', 'RhsimUnG0024000' => 'rsi', 'RhsimUnG0024100' => 'rsi', 'RhsimUnG0024200' => 'rsi', 'RhsimUnG0024300' => 'rsi', 'RhsimUnG0024400' => 'rsi', 'RhsimUnG0024500' => 'rsi', 'RhsimUnG0024700' => 'rsi', 'RhsimUnG0024800' => 'rsi', 'RhsimUnG0024900' => 'rsi', 'RhsimUnG0025100' => 'rsi', 'Sabra08G0120200' => 'sbr', 'Sabra08G0120300' => 'sbr', 'Sabra08G0120500' => 'sbr', 'Sabra08G0120600' => 'sbr', 'Sabra10G0158900' => 'sbr', 'SalBow2G3492' => 'sbo', 'Sc13g0004760' => 'sci', 'Sc13g0004770' => 'sci', 'Sed0003417' => 'sed', 'Sed0019750' => 'sed', 'SEGI_03419' => 'sgi', 'SEGI_05907' => 'sgi', 'SEGI_10682' => 'sgi', 'SEGI_13528' => 'sgi', 'SEGI_16081' => 'sgi', 'SEGI_19370' => 'sgi', 'SEGI_21015' => 'sgi', 'SEGI_21944' => 'sgi', 'SEGI_32906' => 'sgi', 'SEGI_33093' => 'sgi', 'SEGI_36110' => 'sgi', 'SEGI_40397' => 'sgi', 'SGA_v2.0_scaffold191G40426' => 'sas', 'SGA_v2.0_scaffold353G49717' => 'sas', 'SGA_v2.0_scaffold50G18550' => 'sas', 'SMO119G0173' => 'smo', 'SMO172G0002' => 'smo', 'Solyc09g082690.3' => 'sly', 'Solyc09g082700.2' => 'sly', 'Sopen09g031550' => 'spe', 'Sopen09g031560' => 'spe', 'Sp3g20540' => 'spa', 'Sp7g07580' => 'spa', 'TAR134G0002' => 'tar', 'TAR236G0001' => 'tar', 'TAR365G0892' => 'tar', 'TAR636G0166' => 'tar', 'TAR636G0646' => 'tar', 'TAR636G0869' => 'tar', 'TAR636G1317' => 'tar', 'TAR636G1744' => 'tar', 'TAR636G3358' => 'tar', 'TAR636G3436' => 'tar', 'THA.LOC104803047' => 'tha', 'Thecc.04G238900' => 'tca', 'Thhalv10021557m.g' => 'esa', 'Thhalv10026318m.g' => 'esa', 'Thhalv10026335m.g' => 'esa', 'TPR.G17433' => 'tpr', 'TPR.G18915' => 'tpr', 'TPR.G26125' => 'tpr', 'TWI09G0677' => 'twi', 'TWI73G0287' => 'twi', 'unitig_748.g8326' => 'ugi', 'vmacro15370' => 'vma', 'vmacro15371' => 'vma', 'vmacro15372' => 'vma', 'vmacro15373' => 'vma', 'vmacro15374' => 'vma', 'VMungo0720G2826' => 'vmu', 'Zm00001eb116960' => 'zma', 'Zm00001eb301260' => 'zma', 'Zm00001eb301270' => 'zma' ), 'gf_id' => 'HOM05D001460', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001460' ), 'data_identifier' => 'HOM05D001460', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001460', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '433', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p22980' => 'bna', 'A01p32340' => 'bna', 'A03p42970' => 'bna', 'A05p25880' => 'bna', 'Aa31LG8G9320' => 'aar', 'Aa31LG8G9330' => 'aar', 'Aa31LG8G9340' => 'aar', 'Aa31sc221G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1034' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1528' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.829' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2222' => 'aag', 'Ah.12g058830' => 'amhyb', 'Ah.12g058840' => 'amhyb', 'AL3G37160' => 'aly', 'AL7G41310' => 'aly', 'Aqoxy5G00395' => 'aox', 'Aqoxy5G00396' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0C8NZA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5185HY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JZ1PRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MD3LS0' => 'arhy', 'AT3G22840' => 'ath', 'AT4G14690' => 'ath', 'ATR0665G054' => 'atr', 'Atru.chr4.2344' => 'acertr', 'Atru.chr4.2346' => 'acertr', 'Atru.chr4.2347' => 'acertr', 'Atru.chr4.2348' => 'acertr', 'Atru.chr4.2355' => 'acertr', 'Atru.chr4.2356' => 'acertr', 'Atru.chr4.2358' => 'acertr', 'Atru.chr4.2359' => 'acertr', 'Atru.chr4.2360' => 'acertr', 'Atru.chr4.2361' => 'acertr', 'AUR62030476' => 'cqu', 'AUR62030478' => 'cqu', 'AUR62030819' => 'cqu', 'AUR62030820' => 'cqu', 'BcaB03g14648' => 'bca', 'BcaB04g20492' => 'bca', 'BcaB06g26399' => 'bca', 'BcaC01g03416' => 'bca', 'BcaC01g03419' => 'bca', 'BcaC01g03421' => 'bca', 'BcaC01g03424' => 'bca', 'BcaC05g28012' => 'bca', 'BcaC09g49212' => 'bca', 'BcaC09g50140' => 'bca', 'BcaNung00346' => 'bca', 'BolC1t02785H' => 'bol', 'BolC1t04095H' => 'bol', 'BolC3t17545H' => 'bol', 'BolC5t32769H' => 'bol', 'BraA01t02211Z' => 'bra', 'BraA01t03359Z' => 'bra', 'BraA03t13441Z' => 'bra', 'BraA05t21476Z' => 'bra', 'C01p28420' => 'bna', 'C01p41350' => 'bna', 'C03p52750' => 'bna', 'C03p52780' => 'bna', 'C05p40270' => 'bna', 'CAN.G1437.9' => 'can', 'CANSAT78G0035' => 'cansat', 'CANSAT78G1036' => 'cansat', 'CANSAT78G2272' => 'cansat', 'CANSAT78G2478' => 'cansat', 'CARHR098700' => 'chi', 'CARHR221120' => 'chi', 'CARHR221150' => 'chi', 'Carub.0003s2297' => 'cru', 'Carub.0007s2749' => 'cru', 'Carub.0007s2750' => 'cru', 'Carub.0007s2751' => 'cru', 'Ca_10849_v3' => 'car', 'Cc03_g04300' => 'ccan', 'CDE02G3648' => 'cde', 'CDE05G0060' => 'cde', 'CDE05G0692' => 'cde', 'CDE05G2285' => 'cde', 'CDE05G2884' => 'cde', 'CDE05G3072' => 'cde', 'Cfa008439' => 'cfa', 'Cfa008441' => 'cfa', 'Cfa008443' => 'cfa', 'Cfa008448' => 'cfa', 'Ciclev10005974m.g' => 'ccl', 'Ciclev10006006m.g' => 'ccl', 'Ciclev10006775m.g' => 'ccl', 'CiPaw.02G120400' => 'cil', 'CiPaw.02G120500' => 'cil', 'CiPaw.02G120600' => 'cil', 'ClCG05G004850' => 'cla', 'COL.COLO4_21566' => 'col', 'Cpa.g.sc44.124' => 'cpa', 'Cre07.g320400' => 'cre', 'Cre07.g320450' => 'cre', 'Cre08.g384650' => 'cre', 'Cre09.g393173' => 'cre', 'Cre09.g394325' => 'cre', 'Cre14.g626750' => 'cre', 'Cre16.g679250' => 'cre', 'CsaV3_3G012890' => 'csa', 'CSS0010865' => 'camsi', 'CSS0044338' => 'camsi', 'DCAR_002366' => 'dca', 'DCAR_030687' => 'dca', 'DCAR_030688' => 'dca', 'Dinv14047' => 'din', 'Dinv14048' => 'din', 'Duzib151G0105' => 'dzi', 'Duzib151G0114' => 'dzi', 'Duzib212G1029' => 'dzi', 'ECA232G3536' => 'eca', 'ECA240G0786' => 'eca', 'ECA240G1802' => 'eca', 'ECA240G3760' => 'eca', 'ECA240G3920' => 'eca', 'EL10Ac5g12536' => 'bvu', 'EL10Ac5g12537' => 'bvu', 'EL10Ac5g12538' => 'bvu', 'Eucgr.B01004' => 'egr', 'Eucgr.B01006' => 'egr', 'Eucgr.B01007' => 'egr', 'Eucgr.B01008' => 'egr', 'Eucgr.B01895' => 'egr', 'Eucgr.B01896' => 'egr', 'FAN04G1456' => 'fan', 'FAN08G1769' => 'fan', 'FAN08G2160' => 'fan', 'FAN13G2403' => 'fan', 'FAN13G3303' => 'fan', 'FAN15G2435' => 'fan', 'FAN17G0672' => 'fan', 'FAN17G2441' => 'fan', 'FAN18G1024' => 'fan', 'FAN22G1458' => 'fan', 'FAN24G0037' => 'fan', 'FAN24G0429' => 'fan', 'FAN24G2387' => 'fan', 'FAN27G2746' => 'fan', 'FvH4_2g20400' => 'fve', 'FvH4_2g20420' => 'fve', 'FvH4_2g20430' => 'fve', 'FvH4_4g01270' => 'fve', 'FvH4_4g01290' => 'fve', 'FvH4_4g01300' => 'fve', 'FvH4_4g01310' => 'fve', 'FvH4_4g01330' => 'fve', 'FvH4_5g09070' => 'fve', 'Glyma.10G243800' => 'gma', 'Glyma.20G150600' => 'gma', 'Gohir.A09G219200' => 'ghi', 'Gohir.A09G219300' => 'ghi', 'Gohir.D09G221400' => 'ghi', 'Gohir.D09G221500' => 'ghi', 'Gorai.006G242600' => 'gra', 'Gorai.006G242700' => 'gra', 'GSVIVG01018044001' => 'vvi', 'HanXRQChr03g0083821' => 'han', 'HanXRQChr03g0083841' => 'han', 'HanXRQChr03g0083881' => 'han', 'HanXRQChr03g0083901' => 'han', 'HanXRQChr03g0083921' => 'han', 'HanXRQChr03g0085331' => 'han', 'HanXRQChr03g0085361' => 'han', 'HanXRQChr03g0085411' => 'han', 'HanXRQChr03g0085421' => 'han', 'HanXRQChr03g0085431' => 'han', 'HanXRQChr08g0221991' => 'han', 'HanXRQChr11g0336061' => 'han', 'HanXRQChr11g0336411' => 'han', 'Haze_11234' => 'cav', 'Hma1.2p1_0549F.1_g177010' => 'hma', 'Hma1.2p1_0602F.1_g187630' => 'hma', 'Hund14876' => 'sun', 'Hund14879' => 'sun', 'Lalb_Chr06g0160741' => 'lal', 'Lalb_Chr21g0304781' => 'lal', 'Lj3A726G19' => 'lonja', 'Lj3A726T23' => 'lonja', 'Lj3A726T24' => 'lonja', 'Lj3A726T25' => 'lonja', 'Lj3A727T17' => 'lonja', 'Lj3C726T0' => 'lonja', 'Lj3C726T2' => 'lonja', 'Lj3P725T35' => 'lonja', 'Lj3P727T10' => 'lonja', 'Lj3P727T12' => 'lonja', 'Lj3P727T14' => 'lonja', 'Lj5g0023109' => 'lja', 'Lj6P646T44' => 'lonja', 'Lsat_1_v5_gn_6_75760' => 'lsa', 'Lsat_1_v5_gn_6_75800' => 'lsa', 'Lsat_1_v5_gn_6_75900' => 'lsa', 'Lsat_1_v5_gn_6_76240' => 'lsa', 'Lsat_1_v5_gn_6_76441' => 'lsa', 'Lsat_1_v5_gn_6_76700' => 'lsa', 'Lsat_1_v5_gn_6_76760' => 'lsa', 'Manes.15G033100' => 'mes', 'Mapoly0004s0074' => 'mpo', 'Mapoly0004s0075' => 'mpo', 'Mapoly0004s0163' => 'mpo', 'Mapoly0004s0164' => 'mpo', 'Mapoly0021s0018' => 'mpo', 'Mapoly0041s0136' => 'mpo', 'Mapoly0041s0137' => 'mpo', 'Mapoly0041s0138' => 'mpo', 'Mapoly0041s0139' => 'mpo', 'Mapoly0041s0141' => 'mpo', 'Mapoly0041s0142' => 'mpo', 'Mapoly0041s0143' => 'mpo', 'Mapoly0041s0144' => 'mpo', 'Mapoly0041s0145' => 'mpo', 'Mapoly0047s0106' => 'mpo', 'Mapoly0047s0108' => 'mpo', 'Mapoly0050s0051' => 'mpo', 'Mapoly0050s0052' => 'mpo', 'Mapoly0050s0053' => 'mpo', 'Mapoly0058s0013' => 'mpo', 'Mapoly0091s0078' => 'mpo', 'Mapoly0091s0079' => 'mpo', 'Mapoly0091s0080' => 'mpo', 'Mapoly0091s0081' => 'mpo', 'Mapoly0278s0004' => 'mpo', 'Mapoly0278s0005' => 'mpo', 'Mapoly0278s0006' => 'mpo', 'MBI11_g30648_MAGBIO' => 'mbi', 'MCO03G194' => 'mco', 'MCO03G590' => 'mco', 'MCO07G312' => 'mco', 'MCO10G318' => 'mco', 'MCO12G244' => 'mco', 'MCO13G148' => 'mco', 'MCO13G194' => 'mco', 'MCO16G238' => 'mco', 'MD06G1134100' => 'mdo', 'MD13G1200100' => 'mdo', 'MD13G1200300' => 'mdo', 'MD13G1200600' => 'mdo', 'MD14G1150400' => 'mdo', 'MD16G1200000' => 'mdo', 'Medtr1g102570' => 'mtr', 'Medtr1g102780' => 'mtr', 'Medtr1g102800' => 'mtr', 'Medtr1g102810' => 'mtr', 'Medtr1g102830' => 'mtr', 'MELO3C006499.2' => 'cme', 'Migut.G00385' => 'egut', 'MSTRG.4063' => 'ama', 'Nitab4.5_0000090g0260' => 'nta', 'Nitab4.5_0000977g0030' => 'nta', 'Nitab4.5_0002541g0040' => 'nta', 'Nitab4.5_0007068g0040' => 'nta', 'Nn005s41408' => 'nnu', 'Nn005s41410' => 'nnu', 'Oeu010310.1' => 'oeu', 'Oeu010311.1' => 'oeu', 'Oeu043472.1' => 'oeu', 'Os01g0246400' => 'osa', 'Os04g0267950' => 'osa', 'Os07g0178700' => 'osa', 'Os07g0178800' => 'osa', 'Peaxi162Scf00316g00046' => 'pax', 'Peaxi162Scf00316g00049' => 'pax', 'Peaxi162Scf00316g00059' => 'pax', 'Peaxi162Scf00316g00328' => 'pax', 'Peaxi162Scf00316g00329' => 'pax', 'Peaxi162Scf00316g00411' => 'pax', 'Peaxi162Scf00316g00521' => 'pax', 'Peaxi162Scf00492g00068' => 'pax', 'Peaxi162Scf35631g00002' => 'pax', 'PGR142G3720' => 'pgr', 'PGSC0003DMG400006442' => 'stu', 'Phvul.007G062000' => 'pvu', 'Potri.008G157750' => 'ptr', 'Potri.008G157900' => 'ptr', 'Potri.008G158000' => 'ptr', 'Potri.008G158200' => 'ptr', 'Pp3c11_7280' => 'ppa', 'Pp3c11_7980' => 'ppa', 'Pp3c12_19450' => 'ppa', 'Pp3c14_1480' => 'ppa', 'Pp3c14_1501' => 'ppa', 'Pp3c16_4900' => 'ppa', 'Pp3c16_5010' => 'ppa', 'Pp3c16_5060' => 'ppa', 'Pp3c19_18250' => 'ppa', 'Pp3c23_8530' => 'ppa', 'Pp3c23_8550' => 'ppa', 'Pp3c24_9670' => 'ppa', 'Pp3c2_21390' => 'ppa', 'Pp3c2_31380' => 'ppa', 'Pp3c3_16620' => 'ppa', 'Pp3c3_8090' => 'ppa', 'Pp3c3_8110' => 'ppa', 'Pp3c3_8130' => 'ppa', 'Pp3c3_8150' => 'ppa', 'Pp3c4_14320' => 'ppa', 'Pp3c6_2560' => 'ppa', 'Pp3c9_16700' => 'ppa', 'PRCOL_00000234' => 'pco', 'PRCOL_00000235' => 'pco', 'PRCOL_00000777' => 'pco', 'PRCOL_00002344' => 'pco', 'PRCOL_00002372' => 'pco', 'PRCOL_00006120' => 'pco', 'Prupe.1G021400' => 'ppe', 'Prupe.1G021500' => 'ppe', 'Prupe.1G021600' => 'ppe', 'Prupe.1G021700' => 'ppe', 'Prupe.1G021800' => 'ppe', 'Prupe.5G145100' => 'ppe', 'Psat6g204040' => 'psa', 'Psat6g204800' => 'psa', 'Psat6g204920' => 'psa', 'Psat6g204960' => 'psa', 'Psat6g205080' => 'psa', 'PSO017G0271' => 'pso', 'PSO017G1276' => 'pso', 'PSO017G1429' => 'pso', 'PSO017G1861' => 'pso', 'PSO017G2787' => 'pso', 'PSO017G4466' => 'pso', 'PSO017G5118' => 'pso', 'PSO017G5420' => 'pso', 'PSO063G3678' => 'pso', 'PSO210G0546' => 'pso', 'PSO317G0001' => 'pso', 'PSO357G0512' => 'pso', 'PSO478G2682' => 'pso', 'PSO647G0001' => 'pso', 'PSO675G0001' => 'pso', 'PSO675G2699' => 'pso', 'PSO675G2849' => 'pso', 'PSO675G4991' => 'pso', 'PSO689G0001' => 'pso', 'QL06p000916' => 'qlo', 'QL06p000921' => 'qlo', 'QL06p001398' => 'qlo', 'QL06p001407' => 'qlo', 'QL06p002031' => 'qlo', 'RcHm_v2.0_Chr4g0387791' => 'rch', 'RcHm_v2.0_Chr4g0387801' => 'rch', 'RcHm_v2.0_Chr6g0286501' => 'rch', 'RcHm_v2.0_Chr6g0286511' => 'rch', 'RcHm_v2.0_Chr6g0286521' => 'rch', 'RcHm_v2.0_Chr6g0286531' => 'rch', 'RcHm_v2.0_Chr7g0189141' => 'rch', 'Rhsim02G0028700' => 'rsi', 'Rhsim02G0028800' => 'rsi', 'Rhsim02G0028900' => 'rsi', 'Rhsim02G0029000' => 'rsi', 'Rhsim02G0029100' => 'rsi', 'Rhsim02G0029200' => 'rsi', 'Rhsim02G0029300' => 'rsi', 'Rhsim02G0029400' => 'rsi', 'Rhsim02G0029500' => 'rsi', 'Rhsim02G0029600' => 'rsi', 'RhsimUnG0024000' => 'rsi', 'RhsimUnG0024100' => 'rsi', 'RhsimUnG0024200' => 'rsi', 'RhsimUnG0024300' => 'rsi', 'RhsimUnG0024400' => 'rsi', 'RhsimUnG0024500' => 'rsi', 'RhsimUnG0024700' => 'rsi', 'RhsimUnG0024800' => 'rsi', 'RhsimUnG0024900' => 'rsi', 'RhsimUnG0025100' => 'rsi', 'Sabra08G0120200' => 'sbr', 'Sabra08G0120300' => 'sbr', 'Sabra08G0120500' => 'sbr', 'Sabra08G0120600' => 'sbr', 'Sabra10G0158900' => 'sbr', 'SalBow2G3492' => 'sbo', 'Sc13g0004760' => 'sci', 'Sc13g0004770' => 'sci', 'Sed0003417' => 'sed', 'Sed0019750' => 'sed', 'SEGI_03419' => 'sgi', 'SEGI_05907' => 'sgi', 'SEGI_10682' => 'sgi', 'SEGI_13528' => 'sgi', 'SEGI_16081' => 'sgi', 'SEGI_19370' => 'sgi', 'SEGI_21015' => 'sgi', 'SEGI_21944' => 'sgi', 'SEGI_32906' => 'sgi', 'SEGI_33093' => 'sgi', 'SEGI_36110' => 'sgi', 'SEGI_40397' => 'sgi', 'SGA_v2.0_scaffold191G40426' => 'sas', 'SGA_v2.0_scaffold353G49717' => 'sas', 'SGA_v2.0_scaffold50G18550' => 'sas', 'SMO119G0173' => 'smo', 'SMO172G0002' => 'smo', 'Solyc09g082690.3' => 'sly', 'Solyc09g082700.2' => 'sly', 'Sopen09g031550' => 'spe', 'Sopen09g031560' => 'spe', 'Sp3g20540' => 'spa', 'Sp7g07580' => 'spa', 'TAR134G0002' => 'tar', 'TAR236G0001' => 'tar', 'TAR365G0892' => 'tar', 'TAR636G0166' => 'tar', 'TAR636G0646' => 'tar', 'TAR636G0869' => 'tar', 'TAR636G1317' => 'tar', 'TAR636G1744' => 'tar', 'TAR636G3358' => 'tar', 'TAR636G3436' => 'tar', 'THA.LOC104803047' => 'tha', 'Thecc.04G238900' => 'tca', 'Thhalv10021557m.g' => 'esa', 'Thhalv10026318m.g' => 'esa', 'Thhalv10026335m.g' => 'esa', 'TPR.G17433' => 'tpr', 'TPR.G18915' => 'tpr', 'TPR.G26125' => 'tpr', 'TWI09G0677' => 'twi', 'TWI73G0287' => 'twi', 'unitig_748.g8326' => 'ugi', 'vmacro15370' => 'vma', 'vmacro15371' => 'vma', 'vmacro15372' => 'vma', 'vmacro15373' => 'vma', 'vmacro15374' => 'vma', 'VMungo0720G2826' => 'vmu', 'Zm00001eb116960' => 'zma', 'Zm00001eb301260' => 'zma', 'Zm00001eb301270' => 'zma' ) $gf_id = 'HOM05D001460' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001460' ) $data_identifier = 'HOM05D001460' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 4, 'aag' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 2, 'aox' => (int) 2, 'arhy' => (int) 4, 'ath' => (int) 2, 'atr' => (int) 1, 'acertr' => (int) 10, 'cqu' => (int) 4, 'bca' => (int) 11, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 1, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 1, 'ccan' => (int) 1, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 1, 'col' => (int) 1, 'cpa' => (int) 1, 'cre' => (int) 7, 'csa' => (int) 1, 'camsi' => (int) 2, 'dca' => (int) 3, 'din' => (int) 2, 'dzi' => (int) 3, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 14, 'fve' => (int) 9, 'gma' => (int) 2, 'ghi' => (int) 4, 'gra' => (int) 2, 'vvi' => (int) 1, 'han' => (int) 13, 'cav' => (int) 1, 'hma' => (int) 2, 'sun' => (int) 2, 'lal' => (int) 2, 'lonja' => (int) 12, 'lja' => (int) 1, 'lsa' => (int) 7, 'mes' => (int) 1, 'mpo' => (int) 27, 'mbi' => (int) 1, 'mco' => (int) 8, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 1, 'egut' => (int) 1, 'ama' => (int) 1, 'nta' => (int) 4, 'nnu' => (int) 2, 'oeu' => (int) 3, 'osa' => (int) 4, 'pax' => (int) 9, 'pgr' => (int) 1, 'stu' => (int) 1, 'pvu' => (int) 1, 'ptr' => (int) 4, 'ppa' => (int) 22, 'pco' => (int) 6, 'ppe' => (int) 6, 'psa' => (int) 5, 'pso' => (int) 19, 'qlo' => (int) 5, 'rch' => (int) 7, 'rsi' => (int) 20, 'sbr' => (int) 5, 'sbo' => (int) 1, 'sci' => (int) 2, 'sed' => (int) 2, 'sgi' => (int) 12, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 2, 'tar' => (int) 10, 'tha' => (int) 1, 'tca' => (int) 1, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 2, 'ugi' => (int) 1, 'vma' => (int) 5, 'vmu' => (int) 1, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb301270' $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' => 'HOM05D001460', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '433', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p22980' => 'bna', 'A01p32340' => 'bna', 'A03p42970' => 'bna', 'A05p25880' => 'bna', 'Aa31LG8G9320' => 'aar', 'Aa31LG8G9330' => 'aar', 'Aa31LG8G9340' => 'aar', 'Aa31sc221G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1034' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1528' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.829' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2222' => 'aag', 'Ah.12g058830' => 'amhyb', 'Ah.12g058840' => 'amhyb', 'AL3G37160' => 'aly', 'AL7G41310' => 'aly', 'Aqoxy5G00395' => 'aox', 'Aqoxy5G00396' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0C8NZA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5185HY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JZ1PRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MD3LS0' => 'arhy', 'AT3G22840' => 'ath', 'AT4G14690' => 'ath', 'ATR0665G054' => 'atr', 'Atru.chr4.2344' => 'acertr', 'Atru.chr4.2346' => 'acertr', 'Atru.chr4.2347' => 'acertr', 'Atru.chr4.2348' => 'acertr', 'Atru.chr4.2355' => 'acertr', 'Atru.chr4.2356' => 'acertr', 'Atru.chr4.2358' => 'acertr', 'Atru.chr4.2359' => 'acertr', 'Atru.chr4.2360' => 'acertr', 'Atru.chr4.2361' => 'acertr', 'AUR62030476' => 'cqu', 'AUR62030478' => 'cqu', 'AUR62030819' => 'cqu', 'AUR62030820' => 'cqu', 'BcaB03g14648' => 'bca', 'BcaB04g20492' => 'bca', 'BcaB06g26399' => 'bca', 'BcaC01g03416' => 'bca', 'BcaC01g03419' => 'bca', 'BcaC01g03421' => 'bca', 'BcaC01g03424' => 'bca', 'BcaC05g28012' => 'bca', 'BcaC09g49212' => 'bca', 'BcaC09g50140' => 'bca', 'BcaNung00346' => 'bca', 'BolC1t02785H' => 'bol', 'BolC1t04095H' => 'bol', 'BolC3t17545H' => 'bol', 'BolC5t32769H' => 'bol', 'BraA01t02211Z' => 'bra', 'BraA01t03359Z' => 'bra', 'BraA03t13441Z' => 'bra', 'BraA05t21476Z' => 'bra', 'C01p28420' => 'bna', 'C01p41350' => 'bna', 'C03p52750' => 'bna', 'C03p52780' => 'bna', 'C05p40270' => 'bna', 'CAN.G1437.9' => 'can', 'CANSAT78G0035' => 'cansat', 'CANSAT78G1036' => 'cansat', 'CANSAT78G2272' => 'cansat', 'CANSAT78G2478' => 'cansat', 'CARHR098700' => 'chi', 'CARHR221120' => 'chi', 'CARHR221150' => 'chi', 'Carub.0003s2297' => 'cru', 'Carub.0007s2749' => 'cru', 'Carub.0007s2750' => 'cru', 'Carub.0007s2751' => 'cru', 'Ca_10849_v3' => 'car', 'Cc03_g04300' => 'ccan', 'CDE02G3648' => 'cde', 'CDE05G0060' => 'cde', 'CDE05G0692' => 'cde', 'CDE05G2285' => 'cde', 'CDE05G2884' => 'cde', 'CDE05G3072' => 'cde', 'Cfa008439' => 'cfa', 'Cfa008441' => 'cfa', 'Cfa008443' => 'cfa', 'Cfa008448' => 'cfa', 'Ciclev10005974m.g' => 'ccl', 'Ciclev10006006m.g' => 'ccl', 'Ciclev10006775m.g' => 'ccl', 'CiPaw.02G120400' => 'cil', 'CiPaw.02G120500' => 'cil', 'CiPaw.02G120600' => 'cil', 'ClCG05G004850' => 'cla', 'COL.COLO4_21566' => 'col', 'Cpa.g.sc44.124' => 'cpa', 'Cre07.g320400' => 'cre', 'Cre07.g320450' => 'cre', 'Cre08.g384650' => 'cre', 'Cre09.g393173' => 'cre', 'Cre09.g394325' => 'cre', 'Cre14.g626750' => 'cre', 'Cre16.g679250' => 'cre', 'CsaV3_3G012890' => 'csa', 'CSS0010865' => 'camsi', 'CSS0044338' => 'camsi', 'DCAR_002366' => 'dca', 'DCAR_030687' => 'dca', 'DCAR_030688' => 'dca', 'Dinv14047' => 'din', 'Dinv14048' => 'din', 'Duzib151G0105' => 'dzi', 'Duzib151G0114' => 'dzi', 'Duzib212G1029' => 'dzi', 'ECA232G3536' => 'eca', 'ECA240G0786' => 'eca', 'ECA240G1802' => 'eca', 'ECA240G3760' => 'eca', 'ECA240G3920' => 'eca', 'EL10Ac5g12536' => 'bvu', 'EL10Ac5g12537' => 'bvu', 'EL10Ac5g12538' => 'bvu', 'Eucgr.B01004' => 'egr', 'Eucgr.B01006' => 'egr', 'Eucgr.B01007' => 'egr', 'Eucgr.B01008' => 'egr', 'Eucgr.B01895' => 'egr', 'Eucgr.B01896' => 'egr', 'FAN04G1456' => 'fan', 'FAN08G1769' => 'fan', 'FAN08G2160' => 'fan', 'FAN13G2403' => 'fan', 'FAN13G3303' => 'fan', 'FAN15G2435' => 'fan', 'FAN17G0672' => 'fan', 'FAN17G2441' => 'fan', 'FAN18G1024' => 'fan', 'FAN22G1458' => 'fan', 'FAN24G0037' => 'fan', 'FAN24G0429' => 'fan', 'FAN24G2387' => 'fan', 'FAN27G2746' => 'fan', 'FvH4_2g20400' => 'fve', 'FvH4_2g20420' => 'fve', 'FvH4_2g20430' => 'fve', 'FvH4_4g01270' => 'fve', 'FvH4_4g01290' => 'fve', 'FvH4_4g01300' => 'fve', 'FvH4_4g01310' => 'fve', 'FvH4_4g01330' => 'fve', 'FvH4_5g09070' => 'fve', 'Glyma.10G243800' => 'gma', 'Glyma.20G150600' => 'gma', 'Gohir.A09G219200' => 'ghi', 'Gohir.A09G219300' => 'ghi', 'Gohir.D09G221400' => 'ghi', 'Gohir.D09G221500' => 'ghi', 'Gorai.006G242600' => 'gra', 'Gorai.006G242700' => 'gra', 'GSVIVG01018044001' => 'vvi', 'HanXRQChr03g0083821' => 'han', 'HanXRQChr03g0083841' => 'han', 'HanXRQChr03g0083881' => 'han', 'HanXRQChr03g0083901' => 'han', 'HanXRQChr03g0083921' => 'han', 'HanXRQChr03g0085331' => 'han', 'HanXRQChr03g0085361' => 'han', 'HanXRQChr03g0085411' => 'han', 'HanXRQChr03g0085421' => 'han', 'HanXRQChr03g0085431' => 'han', 'HanXRQChr08g0221991' => 'han', 'HanXRQChr11g0336061' => 'han', 'HanXRQChr11g0336411' => 'han', 'Haze_11234' => 'cav', 'Hma1.2p1_0549F.1_g177010' => 'hma', 'Hma1.2p1_0602F.1_g187630' => 'hma', 'Hund14876' => 'sun', 'Hund14879' => 'sun', 'Lalb_Chr06g0160741' => 'lal', 'Lalb_Chr21g0304781' => 'lal', 'Lj3A726G19' => 'lonja', 'Lj3A726T23' => 'lonja', 'Lj3A726T24' => 'lonja', 'Lj3A726T25' => 'lonja', 'Lj3A727T17' => 'lonja', 'Lj3C726T0' => 'lonja', 'Lj3C726T2' => 'lonja', 'Lj3P725T35' => 'lonja', 'Lj3P727T10' => 'lonja', 'Lj3P727T12' => 'lonja', 'Lj3P727T14' => 'lonja', 'Lj5g0023109' => 'lja', 'Lj6P646T44' => 'lonja', 'Lsat_1_v5_gn_6_75760' => 'lsa', 'Lsat_1_v5_gn_6_75800' => 'lsa', 'Lsat_1_v5_gn_6_75900' => 'lsa', 'Lsat_1_v5_gn_6_76240' => 'lsa', 'Lsat_1_v5_gn_6_76441' => 'lsa', 'Lsat_1_v5_gn_6_76700' => 'lsa', 'Lsat_1_v5_gn_6_76760' => 'lsa', 'Manes.15G033100' => 'mes', 'Mapoly0004s0074' => 'mpo', 'Mapoly0004s0075' => 'mpo', 'Mapoly0004s0163' => 'mpo', 'Mapoly0004s0164' => 'mpo', 'Mapoly0021s0018' => 'mpo', 'Mapoly0041s0136' => 'mpo', 'Mapoly0041s0137' => 'mpo', 'Mapoly0041s0138' => 'mpo', 'Mapoly0041s0139' => 'mpo', 'Mapoly0041s0141' => 'mpo', 'Mapoly0041s0142' => 'mpo', 'Mapoly0041s0143' => 'mpo', 'Mapoly0041s0144' => 'mpo', 'Mapoly0041s0145' => 'mpo', 'Mapoly0047s0106' => 'mpo', 'Mapoly0047s0108' => 'mpo', 'Mapoly0050s0051' => 'mpo', 'Mapoly0050s0052' => 'mpo', 'Mapoly0050s0053' => 'mpo', 'Mapoly0058s0013' => 'mpo', 'Mapoly0091s0078' => 'mpo', 'Mapoly0091s0079' => 'mpo', 'Mapoly0091s0080' => 'mpo', 'Mapoly0091s0081' => 'mpo', 'Mapoly0278s0004' => 'mpo', 'Mapoly0278s0005' => 'mpo', 'Mapoly0278s0006' => 'mpo', 'MBI11_g30648_MAGBIO' => 'mbi', 'MCO03G194' => 'mco', 'MCO03G590' => 'mco', 'MCO07G312' => 'mco', 'MCO10G318' => 'mco', 'MCO12G244' => 'mco', 'MCO13G148' => 'mco', 'MCO13G194' => 'mco', 'MCO16G238' => 'mco', 'MD06G1134100' => 'mdo', 'MD13G1200100' => 'mdo', 'MD13G1200300' => 'mdo', 'MD13G1200600' => 'mdo', 'MD14G1150400' => 'mdo', 'MD16G1200000' => 'mdo', 'Medtr1g102570' => 'mtr', 'Medtr1g102780' => 'mtr', 'Medtr1g102800' => 'mtr', 'Medtr1g102810' => 'mtr', 'Medtr1g102830' => 'mtr', 'MELO3C006499.2' => 'cme', 'Migut.G00385' => 'egut', 'MSTRG.4063' => 'ama', 'Nitab4.5_0000090g0260' => 'nta', 'Nitab4.5_0000977g0030' => 'nta', 'Nitab4.5_0002541g0040' => 'nta', 'Nitab4.5_0007068g0040' => 'nta', 'Nn005s41408' => 'nnu', 'Nn005s41410' => 'nnu', 'Oeu010310.1' => 'oeu', 'Oeu010311.1' => 'oeu', 'Oeu043472.1' => 'oeu', 'Os01g0246400' => 'osa', 'Os04g0267950' => 'osa', 'Os07g0178700' => 'osa', 'Os07g0178800' => 'osa', 'Peaxi162Scf00316g00046' => 'pax', 'Peaxi162Scf00316g00049' => 'pax', 'Peaxi162Scf00316g00059' => 'pax', 'Peaxi162Scf00316g00328' => 'pax', 'Peaxi162Scf00316g00329' => 'pax', 'Peaxi162Scf00316g00411' => 'pax', 'Peaxi162Scf00316g00521' => 'pax', 'Peaxi162Scf00492g00068' => 'pax', 'Peaxi162Scf35631g00002' => 'pax', 'PGR142G3720' => 'pgr', 'PGSC0003DMG400006442' => 'stu', 'Phvul.007G062000' => 'pvu', 'Potri.008G157750' => 'ptr', 'Potri.008G157900' => 'ptr', 'Potri.008G158000' => 'ptr', 'Potri.008G158200' => 'ptr', 'Pp3c11_7280' => 'ppa', 'Pp3c11_7980' => 'ppa', 'Pp3c12_19450' => 'ppa', 'Pp3c14_1480' => 'ppa', 'Pp3c14_1501' => 'ppa', 'Pp3c16_4900' => 'ppa', 'Pp3c16_5010' => 'ppa', 'Pp3c16_5060' => 'ppa', 'Pp3c19_18250' => 'ppa', 'Pp3c23_8530' => 'ppa', 'Pp3c23_8550' => 'ppa', 'Pp3c24_9670' => 'ppa', 'Pp3c2_21390' => 'ppa', 'Pp3c2_31380' => 'ppa', 'Pp3c3_16620' => 'ppa', 'Pp3c3_8090' => 'ppa', 'Pp3c3_8110' => 'ppa', 'Pp3c3_8130' => 'ppa', 'Pp3c3_8150' => 'ppa', 'Pp3c4_14320' => 'ppa', 'Pp3c6_2560' => 'ppa', 'Pp3c9_16700' => 'ppa', 'PRCOL_00000234' => 'pco', 'PRCOL_00000235' => 'pco', 'PRCOL_00000777' => 'pco', 'PRCOL_00002344' => 'pco', 'PRCOL_00002372' => 'pco', 'PRCOL_00006120' => 'pco', 'Prupe.1G021400' => 'ppe', 'Prupe.1G021500' => 'ppe', 'Prupe.1G021600' => 'ppe', 'Prupe.1G021700' => 'ppe', 'Prupe.1G021800' => 'ppe', 'Prupe.5G145100' => 'ppe', 'Psat6g204040' => 'psa', 'Psat6g204800' => 'psa', 'Psat6g204920' => 'psa', 'Psat6g204960' => 'psa', 'Psat6g205080' => 'psa', 'PSO017G0271' => 'pso', 'PSO017G1276' => 'pso', 'PSO017G1429' => 'pso', 'PSO017G1861' => 'pso', 'PSO017G2787' => 'pso', 'PSO017G4466' => 'pso', 'PSO017G5118' => 'pso', 'PSO017G5420' => 'pso', 'PSO063G3678' => 'pso', 'PSO210G0546' => 'pso', 'PSO317G0001' => 'pso', 'PSO357G0512' => 'pso', 'PSO478G2682' => 'pso', 'PSO647G0001' => 'pso', 'PSO675G0001' => 'pso', 'PSO675G2699' => 'pso', 'PSO675G2849' => 'pso', 'PSO675G4991' => 'pso', 'PSO689G0001' => 'pso', 'QL06p000916' => 'qlo', 'QL06p000921' => 'qlo', 'QL06p001398' => 'qlo', 'QL06p001407' => 'qlo', 'QL06p002031' => 'qlo', 'RcHm_v2.0_Chr4g0387791' => 'rch', 'RcHm_v2.0_Chr4g0387801' => 'rch', 'RcHm_v2.0_Chr6g0286501' => 'rch', 'RcHm_v2.0_Chr6g0286511' => 'rch', 'RcHm_v2.0_Chr6g0286521' => 'rch', 'RcHm_v2.0_Chr6g0286531' => 'rch', 'RcHm_v2.0_Chr7g0189141' => 'rch', 'Rhsim02G0028700' => 'rsi', 'Rhsim02G0028800' => 'rsi', 'Rhsim02G0028900' => 'rsi', 'Rhsim02G0029000' => 'rsi', 'Rhsim02G0029100' => 'rsi', 'Rhsim02G0029200' => 'rsi', 'Rhsim02G0029300' => 'rsi', 'Rhsim02G0029400' => 'rsi', 'Rhsim02G0029500' => 'rsi', 'Rhsim02G0029600' => 'rsi', 'RhsimUnG0024000' => 'rsi', 'RhsimUnG0024100' => 'rsi', 'RhsimUnG0024200' => 'rsi', 'RhsimUnG0024300' => 'rsi', 'RhsimUnG0024400' => 'rsi', 'RhsimUnG0024500' => 'rsi', 'RhsimUnG0024700' => 'rsi', 'RhsimUnG0024800' => 'rsi', 'RhsimUnG0024900' => 'rsi', 'RhsimUnG0025100' => 'rsi', 'Sabra08G0120200' => 'sbr', 'Sabra08G0120300' => 'sbr', 'Sabra08G0120500' => 'sbr', 'Sabra08G0120600' => 'sbr', 'Sabra10G0158900' => 'sbr', 'SalBow2G3492' => 'sbo', 'Sc13g0004760' => 'sci', 'Sc13g0004770' => 'sci', 'Sed0003417' => 'sed', 'Sed0019750' => 'sed', 'SEGI_03419' => 'sgi', 'SEGI_05907' => 'sgi', 'SEGI_10682' => 'sgi', 'SEGI_13528' => 'sgi', 'SEGI_16081' => 'sgi', 'SEGI_19370' => 'sgi', 'SEGI_21015' => 'sgi', 'SEGI_21944' => 'sgi', 'SEGI_32906' => 'sgi', 'SEGI_33093' => 'sgi', 'SEGI_36110' => 'sgi', 'SEGI_40397' => 'sgi', 'SGA_v2.0_scaffold191G40426' => 'sas', 'SGA_v2.0_scaffold353G49717' => 'sas', 'SGA_v2.0_scaffold50G18550' => 'sas', 'SMO119G0173' => 'smo', 'SMO172G0002' => 'smo', 'Solyc09g082690.3' => 'sly', 'Solyc09g082700.2' => 'sly', 'Sopen09g031550' => 'spe', 'Sopen09g031560' => 'spe', 'Sp3g20540' => 'spa', 'Sp7g07580' => 'spa', 'TAR134G0002' => 'tar', 'TAR236G0001' => 'tar', 'TAR365G0892' => 'tar', 'TAR636G0166' => 'tar', 'TAR636G0646' => 'tar', 'TAR636G0869' => 'tar', 'TAR636G1317' => 'tar', 'TAR636G1744' => 'tar', 'TAR636G3358' => 'tar', 'TAR636G3436' => 'tar', 'THA.LOC104803047' => 'tha', 'Thecc.04G238900' => 'tca', 'Thhalv10021557m.g' => 'esa', 'Thhalv10026318m.g' => 'esa', 'Thhalv10026335m.g' => 'esa', 'TPR.G17433' => 'tpr', 'TPR.G18915' => 'tpr', 'TPR.G26125' => 'tpr', 'TWI09G0677' => 'twi', 'TWI73G0287' => 'twi', 'unitig_748.g8326' => 'ugi', 'vmacro15370' => 'vma', 'vmacro15371' => 'vma', 'vmacro15372' => 'vma', 'vmacro15373' => 'vma', 'vmacro15374' => 'vma', 'VMungo0720G2826' => 'vmu', 'Zm00001eb116960' => 'zma', 'Zm00001eb301260' => 'zma', 'Zm00001eb301270' => 'zma' ), 'gf_id' => 'HOM05D001460', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001460' ), 'data_identifier' => 'HOM05D001460', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001460', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '433', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p22980' => 'bna', 'A01p32340' => 'bna', 'A03p42970' => 'bna', 'A05p25880' => 'bna', 'Aa31LG8G9320' => 'aar', 'Aa31LG8G9330' => 'aar', 'Aa31LG8G9340' => 'aar', 'Aa31sc221G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1034' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1528' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.829' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2222' => 'aag', 'Ah.12g058830' => 'amhyb', 'Ah.12g058840' => 'amhyb', 'AL3G37160' => 'aly', 'AL7G41310' => 'aly', 'Aqoxy5G00395' => 'aox', 'Aqoxy5G00396' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0C8NZA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5185HY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JZ1PRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MD3LS0' => 'arhy', 'AT3G22840' => 'ath', 'AT4G14690' => 'ath', 'ATR0665G054' => 'atr', 'Atru.chr4.2344' => 'acertr', 'Atru.chr4.2346' => 'acertr', 'Atru.chr4.2347' => 'acertr', 'Atru.chr4.2348' => 'acertr', 'Atru.chr4.2355' => 'acertr', 'Atru.chr4.2356' => 'acertr', 'Atru.chr4.2358' => 'acertr', 'Atru.chr4.2359' => 'acertr', 'Atru.chr4.2360' => 'acertr', 'Atru.chr4.2361' => 'acertr', 'AUR62030476' => 'cqu', 'AUR62030478' => 'cqu', 'AUR62030819' => 'cqu', 'AUR62030820' => 'cqu', 'BcaB03g14648' => 'bca', 'BcaB04g20492' => 'bca', 'BcaB06g26399' => 'bca', 'BcaC01g03416' => 'bca', 'BcaC01g03419' => 'bca', 'BcaC01g03421' => 'bca', 'BcaC01g03424' => 'bca', 'BcaC05g28012' => 'bca', 'BcaC09g49212' => 'bca', 'BcaC09g50140' => 'bca', 'BcaNung00346' => 'bca', 'BolC1t02785H' => 'bol', 'BolC1t04095H' => 'bol', 'BolC3t17545H' => 'bol', 'BolC5t32769H' => 'bol', 'BraA01t02211Z' => 'bra', 'BraA01t03359Z' => 'bra', 'BraA03t13441Z' => 'bra', 'BraA05t21476Z' => 'bra', 'C01p28420' => 'bna', 'C01p41350' => 'bna', 'C03p52750' => 'bna', 'C03p52780' => 'bna', 'C05p40270' => 'bna', 'CAN.G1437.9' => 'can', 'CANSAT78G0035' => 'cansat', 'CANSAT78G1036' => 'cansat', 'CANSAT78G2272' => 'cansat', 'CANSAT78G2478' => 'cansat', 'CARHR098700' => 'chi', 'CARHR221120' => 'chi', 'CARHR221150' => 'chi', 'Carub.0003s2297' => 'cru', 'Carub.0007s2749' => 'cru', 'Carub.0007s2750' => 'cru', 'Carub.0007s2751' => 'cru', 'Ca_10849_v3' => 'car', 'Cc03_g04300' => 'ccan', 'CDE02G3648' => 'cde', 'CDE05G0060' => 'cde', 'CDE05G0692' => 'cde', 'CDE05G2285' => 'cde', 'CDE05G2884' => 'cde', 'CDE05G3072' => 'cde', 'Cfa008439' => 'cfa', 'Cfa008441' => 'cfa', 'Cfa008443' => 'cfa', 'Cfa008448' => 'cfa', 'Ciclev10005974m.g' => 'ccl', 'Ciclev10006006m.g' => 'ccl', 'Ciclev10006775m.g' => 'ccl', 'CiPaw.02G120400' => 'cil', 'CiPaw.02G120500' => 'cil', 'CiPaw.02G120600' => 'cil', 'ClCG05G004850' => 'cla', 'COL.COLO4_21566' => 'col', 'Cpa.g.sc44.124' => 'cpa', 'Cre07.g320400' => 'cre', 'Cre07.g320450' => 'cre', 'Cre08.g384650' => 'cre', 'Cre09.g393173' => 'cre', 'Cre09.g394325' => 'cre', 'Cre14.g626750' => 'cre', 'Cre16.g679250' => 'cre', 'CsaV3_3G012890' => 'csa', 'CSS0010865' => 'camsi', 'CSS0044338' => 'camsi', 'DCAR_002366' => 'dca', 'DCAR_030687' => 'dca', 'DCAR_030688' => 'dca', 'Dinv14047' => 'din', 'Dinv14048' => 'din', 'Duzib151G0105' => 'dzi', 'Duzib151G0114' => 'dzi', 'Duzib212G1029' => 'dzi', 'ECA232G3536' => 'eca', 'ECA240G0786' => 'eca', 'ECA240G1802' => 'eca', 'ECA240G3760' => 'eca', 'ECA240G3920' => 'eca', 'EL10Ac5g12536' => 'bvu', 'EL10Ac5g12537' => 'bvu', 'EL10Ac5g12538' => 'bvu', 'Eucgr.B01004' => 'egr', 'Eucgr.B01006' => 'egr', 'Eucgr.B01007' => 'egr', 'Eucgr.B01008' => 'egr', 'Eucgr.B01895' => 'egr', 'Eucgr.B01896' => 'egr', 'FAN04G1456' => 'fan', 'FAN08G1769' => 'fan', 'FAN08G2160' => 'fan', 'FAN13G2403' => 'fan', 'FAN13G3303' => 'fan', 'FAN15G2435' => 'fan', 'FAN17G0672' => 'fan', 'FAN17G2441' => 'fan', 'FAN18G1024' => 'fan', 'FAN22G1458' => 'fan', 'FAN24G0037' => 'fan', 'FAN24G0429' => 'fan', 'FAN24G2387' => 'fan', 'FAN27G2746' => 'fan', 'FvH4_2g20400' => 'fve', 'FvH4_2g20420' => 'fve', 'FvH4_2g20430' => 'fve', 'FvH4_4g01270' => 'fve', 'FvH4_4g01290' => 'fve', 'FvH4_4g01300' => 'fve', 'FvH4_4g01310' => 'fve', 'FvH4_4g01330' => 'fve', 'FvH4_5g09070' => 'fve', 'Glyma.10G243800' => 'gma', 'Glyma.20G150600' => 'gma', 'Gohir.A09G219200' => 'ghi', 'Gohir.A09G219300' => 'ghi', 'Gohir.D09G221400' => 'ghi', 'Gohir.D09G221500' => 'ghi', 'Gorai.006G242600' => 'gra', 'Gorai.006G242700' => 'gra', 'GSVIVG01018044001' => 'vvi', 'HanXRQChr03g0083821' => 'han', 'HanXRQChr03g0083841' => 'han', 'HanXRQChr03g0083881' => 'han', 'HanXRQChr03g0083901' => 'han', 'HanXRQChr03g0083921' => 'han', 'HanXRQChr03g0085331' => 'han', 'HanXRQChr03g0085361' => 'han', 'HanXRQChr03g0085411' => 'han', 'HanXRQChr03g0085421' => 'han', 'HanXRQChr03g0085431' => 'han', 'HanXRQChr08g0221991' => 'han', 'HanXRQChr11g0336061' => 'han', 'HanXRQChr11g0336411' => 'han', 'Haze_11234' => 'cav', 'Hma1.2p1_0549F.1_g177010' => 'hma', 'Hma1.2p1_0602F.1_g187630' => 'hma', 'Hund14876' => 'sun', 'Hund14879' => 'sun', 'Lalb_Chr06g0160741' => 'lal', 'Lalb_Chr21g0304781' => 'lal', 'Lj3A726G19' => 'lonja', 'Lj3A726T23' => 'lonja', 'Lj3A726T24' => 'lonja', 'Lj3A726T25' => 'lonja', 'Lj3A727T17' => 'lonja', 'Lj3C726T0' => 'lonja', 'Lj3C726T2' => 'lonja', 'Lj3P725T35' => 'lonja', 'Lj3P727T10' => 'lonja', 'Lj3P727T12' => 'lonja', 'Lj3P727T14' => 'lonja', 'Lj5g0023109' => 'lja', 'Lj6P646T44' => 'lonja', 'Lsat_1_v5_gn_6_75760' => 'lsa', 'Lsat_1_v5_gn_6_75800' => 'lsa', 'Lsat_1_v5_gn_6_75900' => 'lsa', 'Lsat_1_v5_gn_6_76240' => 'lsa', 'Lsat_1_v5_gn_6_76441' => 'lsa', 'Lsat_1_v5_gn_6_76700' => 'lsa', 'Lsat_1_v5_gn_6_76760' => 'lsa', 'Manes.15G033100' => 'mes', 'Mapoly0004s0074' => 'mpo', 'Mapoly0004s0075' => 'mpo', 'Mapoly0004s0163' => 'mpo', 'Mapoly0004s0164' => 'mpo', 'Mapoly0021s0018' => 'mpo', 'Mapoly0041s0136' => 'mpo', 'Mapoly0041s0137' => 'mpo', 'Mapoly0041s0138' => 'mpo', 'Mapoly0041s0139' => 'mpo', 'Mapoly0041s0141' => 'mpo', 'Mapoly0041s0142' => 'mpo', 'Mapoly0041s0143' => 'mpo', 'Mapoly0041s0144' => 'mpo', 'Mapoly0041s0145' => 'mpo', 'Mapoly0047s0106' => 'mpo', 'Mapoly0047s0108' => 'mpo', 'Mapoly0050s0051' => 'mpo', 'Mapoly0050s0052' => 'mpo', 'Mapoly0050s0053' => 'mpo', 'Mapoly0058s0013' => 'mpo', 'Mapoly0091s0078' => 'mpo', 'Mapoly0091s0079' => 'mpo', 'Mapoly0091s0080' => 'mpo', 'Mapoly0091s0081' => 'mpo', 'Mapoly0278s0004' => 'mpo', 'Mapoly0278s0005' => 'mpo', 'Mapoly0278s0006' => 'mpo', 'MBI11_g30648_MAGBIO' => 'mbi', 'MCO03G194' => 'mco', 'MCO03G590' => 'mco', 'MCO07G312' => 'mco', 'MCO10G318' => 'mco', 'MCO12G244' => 'mco', 'MCO13G148' => 'mco', 'MCO13G194' => 'mco', 'MCO16G238' => 'mco', 'MD06G1134100' => 'mdo', 'MD13G1200100' => 'mdo', 'MD13G1200300' => 'mdo', 'MD13G1200600' => 'mdo', 'MD14G1150400' => 'mdo', 'MD16G1200000' => 'mdo', 'Medtr1g102570' => 'mtr', 'Medtr1g102780' => 'mtr', 'Medtr1g102800' => 'mtr', 'Medtr1g102810' => 'mtr', 'Medtr1g102830' => 'mtr', 'MELO3C006499.2' => 'cme', 'Migut.G00385' => 'egut', 'MSTRG.4063' => 'ama', 'Nitab4.5_0000090g0260' => 'nta', 'Nitab4.5_0000977g0030' => 'nta', 'Nitab4.5_0002541g0040' => 'nta', 'Nitab4.5_0007068g0040' => 'nta', 'Nn005s41408' => 'nnu', 'Nn005s41410' => 'nnu', 'Oeu010310.1' => 'oeu', 'Oeu010311.1' => 'oeu', 'Oeu043472.1' => 'oeu', 'Os01g0246400' => 'osa', 'Os04g0267950' => 'osa', 'Os07g0178700' => 'osa', 'Os07g0178800' => 'osa', 'Peaxi162Scf00316g00046' => 'pax', 'Peaxi162Scf00316g00049' => 'pax', 'Peaxi162Scf00316g00059' => 'pax', 'Peaxi162Scf00316g00328' => 'pax', 'Peaxi162Scf00316g00329' => 'pax', 'Peaxi162Scf00316g00411' => 'pax', 'Peaxi162Scf00316g00521' => 'pax', 'Peaxi162Scf00492g00068' => 'pax', 'Peaxi162Scf35631g00002' => 'pax', 'PGR142G3720' => 'pgr', 'PGSC0003DMG400006442' => 'stu', 'Phvul.007G062000' => 'pvu', 'Potri.008G157750' => 'ptr', 'Potri.008G157900' => 'ptr', 'Potri.008G158000' => 'ptr', 'Potri.008G158200' => 'ptr', 'Pp3c11_7280' => 'ppa', 'Pp3c11_7980' => 'ppa', 'Pp3c12_19450' => 'ppa', 'Pp3c14_1480' => 'ppa', 'Pp3c14_1501' => 'ppa', 'Pp3c16_4900' => 'ppa', 'Pp3c16_5010' => 'ppa', 'Pp3c16_5060' => 'ppa', 'Pp3c19_18250' => 'ppa', 'Pp3c23_8530' => 'ppa', 'Pp3c23_8550' => 'ppa', 'Pp3c24_9670' => 'ppa', 'Pp3c2_21390' => 'ppa', 'Pp3c2_31380' => 'ppa', 'Pp3c3_16620' => 'ppa', 'Pp3c3_8090' => 'ppa', 'Pp3c3_8110' => 'ppa', 'Pp3c3_8130' => 'ppa', 'Pp3c3_8150' => 'ppa', 'Pp3c4_14320' => 'ppa', 'Pp3c6_2560' => 'ppa', 'Pp3c9_16700' => 'ppa', 'PRCOL_00000234' => 'pco', 'PRCOL_00000235' => 'pco', 'PRCOL_00000777' => 'pco', 'PRCOL_00002344' => 'pco', 'PRCOL_00002372' => 'pco', 'PRCOL_00006120' => 'pco', 'Prupe.1G021400' => 'ppe', 'Prupe.1G021500' => 'ppe', 'Prupe.1G021600' => 'ppe', 'Prupe.1G021700' => 'ppe', 'Prupe.1G021800' => 'ppe', 'Prupe.5G145100' => 'ppe', 'Psat6g204040' => 'psa', 'Psat6g204800' => 'psa', 'Psat6g204920' => 'psa', 'Psat6g204960' => 'psa', 'Psat6g205080' => 'psa', 'PSO017G0271' => 'pso', 'PSO017G1276' => 'pso', 'PSO017G1429' => 'pso', 'PSO017G1861' => 'pso', 'PSO017G2787' => 'pso', 'PSO017G4466' => 'pso', 'PSO017G5118' => 'pso', 'PSO017G5420' => 'pso', 'PSO063G3678' => 'pso', 'PSO210G0546' => 'pso', 'PSO317G0001' => 'pso', 'PSO357G0512' => 'pso', 'PSO478G2682' => 'pso', 'PSO647G0001' => 'pso', 'PSO675G0001' => 'pso', 'PSO675G2699' => 'pso', 'PSO675G2849' => 'pso', 'PSO675G4991' => 'pso', 'PSO689G0001' => 'pso', 'QL06p000916' => 'qlo', 'QL06p000921' => 'qlo', 'QL06p001398' => 'qlo', 'QL06p001407' => 'qlo', 'QL06p002031' => 'qlo', 'RcHm_v2.0_Chr4g0387791' => 'rch', 'RcHm_v2.0_Chr4g0387801' => 'rch', 'RcHm_v2.0_Chr6g0286501' => 'rch', 'RcHm_v2.0_Chr6g0286511' => 'rch', 'RcHm_v2.0_Chr6g0286521' => 'rch', 'RcHm_v2.0_Chr6g0286531' => 'rch', 'RcHm_v2.0_Chr7g0189141' => 'rch', 'Rhsim02G0028700' => 'rsi', 'Rhsim02G0028800' => 'rsi', 'Rhsim02G0028900' => 'rsi', 'Rhsim02G0029000' => 'rsi', 'Rhsim02G0029100' => 'rsi', 'Rhsim02G0029200' => 'rsi', 'Rhsim02G0029300' => 'rsi', 'Rhsim02G0029400' => 'rsi', 'Rhsim02G0029500' => 'rsi', 'Rhsim02G0029600' => 'rsi', 'RhsimUnG0024000' => 'rsi', 'RhsimUnG0024100' => 'rsi', 'RhsimUnG0024200' => 'rsi', 'RhsimUnG0024300' => 'rsi', 'RhsimUnG0024400' => 'rsi', 'RhsimUnG0024500' => 'rsi', 'RhsimUnG0024700' => 'rsi', 'RhsimUnG0024800' => 'rsi', 'RhsimUnG0024900' => 'rsi', 'RhsimUnG0025100' => 'rsi', 'Sabra08G0120200' => 'sbr', 'Sabra08G0120300' => 'sbr', 'Sabra08G0120500' => 'sbr', 'Sabra08G0120600' => 'sbr', 'Sabra10G0158900' => 'sbr', 'SalBow2G3492' => 'sbo', 'Sc13g0004760' => 'sci', 'Sc13g0004770' => 'sci', 'Sed0003417' => 'sed', 'Sed0019750' => 'sed', 'SEGI_03419' => 'sgi', 'SEGI_05907' => 'sgi', 'SEGI_10682' => 'sgi', 'SEGI_13528' => 'sgi', 'SEGI_16081' => 'sgi', 'SEGI_19370' => 'sgi', 'SEGI_21015' => 'sgi', 'SEGI_21944' => 'sgi', 'SEGI_32906' => 'sgi', 'SEGI_33093' => 'sgi', 'SEGI_36110' => 'sgi', 'SEGI_40397' => 'sgi', 'SGA_v2.0_scaffold191G40426' => 'sas', 'SGA_v2.0_scaffold353G49717' => 'sas', 'SGA_v2.0_scaffold50G18550' => 'sas', 'SMO119G0173' => 'smo', 'SMO172G0002' => 'smo', 'Solyc09g082690.3' => 'sly', 'Solyc09g082700.2' => 'sly', 'Sopen09g031550' => 'spe', 'Sopen09g031560' => 'spe', 'Sp3g20540' => 'spa', 'Sp7g07580' => 'spa', 'TAR134G0002' => 'tar', 'TAR236G0001' => 'tar', 'TAR365G0892' => 'tar', 'TAR636G0166' => 'tar', 'TAR636G0646' => 'tar', 'TAR636G0869' => 'tar', 'TAR636G1317' => 'tar', 'TAR636G1744' => 'tar', 'TAR636G3358' => 'tar', 'TAR636G3436' => 'tar', 'THA.LOC104803047' => 'tha', 'Thecc.04G238900' => 'tca', 'Thhalv10021557m.g' => 'esa', 'Thhalv10026318m.g' => 'esa', 'Thhalv10026335m.g' => 'esa', 'TPR.G17433' => 'tpr', 'TPR.G18915' => 'tpr', 'TPR.G26125' => 'tpr', 'TWI09G0677' => 'twi', 'TWI73G0287' => 'twi', 'unitig_748.g8326' => 'ugi', 'vmacro15370' => 'vma', 'vmacro15371' => 'vma', 'vmacro15372' => 'vma', 'vmacro15373' => 'vma', 'vmacro15374' => 'vma', 'VMungo0720G2826' => 'vmu', 'Zm00001eb116960' => 'zma', 'Zm00001eb301260' => 'zma', 'Zm00001eb301270' => 'zma' ) $gf_id = 'HOM05D001460' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001460' ) $data_identifier = 'HOM05D001460' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 4, 'aag' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 2, 'aox' => (int) 2, 'arhy' => (int) 4, 'ath' => (int) 2, 'atr' => (int) 1, 'acertr' => (int) 10, 'cqu' => (int) 4, 'bca' => (int) 11, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 1, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 1, 'ccan' => (int) 1, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 1, 'col' => (int) 1, 'cpa' => (int) 1, 'cre' => (int) 7, 'csa' => (int) 1, 'camsi' => (int) 2, 'dca' => (int) 3, 'din' => (int) 2, 'dzi' => (int) 3, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 14, 'fve' => (int) 9, 'gma' => (int) 2, 'ghi' => (int) 4, 'gra' => (int) 2, 'vvi' => (int) 1, 'han' => (int) 13, 'cav' => (int) 1, 'hma' => (int) 2, 'sun' => (int) 2, 'lal' => (int) 2, 'lonja' => (int) 12, 'lja' => (int) 1, 'lsa' => (int) 7, 'mes' => (int) 1, 'mpo' => (int) 27, 'mbi' => (int) 1, 'mco' => (int) 8, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 1, 'egut' => (int) 1, 'ama' => (int) 1, 'nta' => (int) 4, 'nnu' => (int) 2, 'oeu' => (int) 3, 'osa' => (int) 4, 'pax' => (int) 9, 'pgr' => (int) 1, 'stu' => (int) 1, 'pvu' => (int) 1, 'ptr' => (int) 4, 'ppa' => (int) 22, 'pco' => (int) 6, 'ppe' => (int) 6, 'psa' => (int) 5, 'pso' => (int) 19, 'qlo' => (int) 5, 'rch' => (int) 7, 'rsi' => (int) 20, 'sbr' => (int) 5, 'sbo' => (int) 1, 'sci' => (int) 2, 'sed' => (int) 2, 'sgi' => (int) 12, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 2, 'tar' => (int) 10, 'tha' => (int) 1, 'tca' => (int) 1, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 2, 'ugi' => (int) 1, 'vma' => (int) 5, 'vmu' => (int) 1, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb301270' $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' => 'HOM05D001460', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '433', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p22980' => 'bna', 'A01p32340' => 'bna', 'A03p42970' => 'bna', 'A05p25880' => 'bna', 'Aa31LG8G9320' => 'aar', 'Aa31LG8G9330' => 'aar', 'Aa31LG8G9340' => 'aar', 'Aa31sc221G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1034' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1528' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.829' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2222' => 'aag', 'Ah.12g058830' => 'amhyb', 'Ah.12g058840' => 'amhyb', 'AL3G37160' => 'aly', 'AL7G41310' => 'aly', 'Aqoxy5G00395' => 'aox', 'Aqoxy5G00396' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0C8NZA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5185HY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JZ1PRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MD3LS0' => 'arhy', 'AT3G22840' => 'ath', 'AT4G14690' => 'ath', 'ATR0665G054' => 'atr', 'Atru.chr4.2344' => 'acertr', 'Atru.chr4.2346' => 'acertr', 'Atru.chr4.2347' => 'acertr', 'Atru.chr4.2348' => 'acertr', 'Atru.chr4.2355' => 'acertr', 'Atru.chr4.2356' => 'acertr', 'Atru.chr4.2358' => 'acertr', 'Atru.chr4.2359' => 'acertr', 'Atru.chr4.2360' => 'acertr', 'Atru.chr4.2361' => 'acertr', 'AUR62030476' => 'cqu', 'AUR62030478' => 'cqu', 'AUR62030819' => 'cqu', 'AUR62030820' => 'cqu', 'BcaB03g14648' => 'bca', 'BcaB04g20492' => 'bca', 'BcaB06g26399' => 'bca', 'BcaC01g03416' => 'bca', 'BcaC01g03419' => 'bca', 'BcaC01g03421' => 'bca', 'BcaC01g03424' => 'bca', 'BcaC05g28012' => 'bca', 'BcaC09g49212' => 'bca', 'BcaC09g50140' => 'bca', 'BcaNung00346' => 'bca', 'BolC1t02785H' => 'bol', 'BolC1t04095H' => 'bol', 'BolC3t17545H' => 'bol', 'BolC5t32769H' => 'bol', 'BraA01t02211Z' => 'bra', 'BraA01t03359Z' => 'bra', 'BraA03t13441Z' => 'bra', 'BraA05t21476Z' => 'bra', 'C01p28420' => 'bna', 'C01p41350' => 'bna', 'C03p52750' => 'bna', 'C03p52780' => 'bna', 'C05p40270' => 'bna', 'CAN.G1437.9' => 'can', 'CANSAT78G0035' => 'cansat', 'CANSAT78G1036' => 'cansat', 'CANSAT78G2272' => 'cansat', 'CANSAT78G2478' => 'cansat', 'CARHR098700' => 'chi', 'CARHR221120' => 'chi', 'CARHR221150' => 'chi', 'Carub.0003s2297' => 'cru', 'Carub.0007s2749' => 'cru', 'Carub.0007s2750' => 'cru', 'Carub.0007s2751' => 'cru', 'Ca_10849_v3' => 'car', 'Cc03_g04300' => 'ccan', 'CDE02G3648' => 'cde', 'CDE05G0060' => 'cde', 'CDE05G0692' => 'cde', 'CDE05G2285' => 'cde', 'CDE05G2884' => 'cde', 'CDE05G3072' => 'cde', 'Cfa008439' => 'cfa', 'Cfa008441' => 'cfa', 'Cfa008443' => 'cfa', 'Cfa008448' => 'cfa', 'Ciclev10005974m.g' => 'ccl', 'Ciclev10006006m.g' => 'ccl', 'Ciclev10006775m.g' => 'ccl', 'CiPaw.02G120400' => 'cil', 'CiPaw.02G120500' => 'cil', 'CiPaw.02G120600' => 'cil', 'ClCG05G004850' => 'cla', 'COL.COLO4_21566' => 'col', 'Cpa.g.sc44.124' => 'cpa', 'Cre07.g320400' => 'cre', 'Cre07.g320450' => 'cre', 'Cre08.g384650' => 'cre', 'Cre09.g393173' => 'cre', 'Cre09.g394325' => 'cre', 'Cre14.g626750' => 'cre', 'Cre16.g679250' => 'cre', 'CsaV3_3G012890' => 'csa', 'CSS0010865' => 'camsi', 'CSS0044338' => 'camsi', 'DCAR_002366' => 'dca', 'DCAR_030687' => 'dca', 'DCAR_030688' => 'dca', 'Dinv14047' => 'din', 'Dinv14048' => 'din', 'Duzib151G0105' => 'dzi', 'Duzib151G0114' => 'dzi', 'Duzib212G1029' => 'dzi', 'ECA232G3536' => 'eca', 'ECA240G0786' => 'eca', 'ECA240G1802' => 'eca', 'ECA240G3760' => 'eca', 'ECA240G3920' => 'eca', 'EL10Ac5g12536' => 'bvu', 'EL10Ac5g12537' => 'bvu', 'EL10Ac5g12538' => 'bvu', 'Eucgr.B01004' => 'egr', 'Eucgr.B01006' => 'egr', 'Eucgr.B01007' => 'egr', 'Eucgr.B01008' => 'egr', 'Eucgr.B01895' => 'egr', 'Eucgr.B01896' => 'egr', 'FAN04G1456' => 'fan', 'FAN08G1769' => 'fan', 'FAN08G2160' => 'fan', 'FAN13G2403' => 'fan', 'FAN13G3303' => 'fan', 'FAN15G2435' => 'fan', 'FAN17G0672' => 'fan', 'FAN17G2441' => 'fan', 'FAN18G1024' => 'fan', 'FAN22G1458' => 'fan', 'FAN24G0037' => 'fan', 'FAN24G0429' => 'fan', 'FAN24G2387' => 'fan', 'FAN27G2746' => 'fan', 'FvH4_2g20400' => 'fve', 'FvH4_2g20420' => 'fve', 'FvH4_2g20430' => 'fve', 'FvH4_4g01270' => 'fve', 'FvH4_4g01290' => 'fve', 'FvH4_4g01300' => 'fve', 'FvH4_4g01310' => 'fve', 'FvH4_4g01330' => 'fve', 'FvH4_5g09070' => 'fve', 'Glyma.10G243800' => 'gma', 'Glyma.20G150600' => 'gma', 'Gohir.A09G219200' => 'ghi', 'Gohir.A09G219300' => 'ghi', 'Gohir.D09G221400' => 'ghi', 'Gohir.D09G221500' => 'ghi', 'Gorai.006G242600' => 'gra', 'Gorai.006G242700' => 'gra', 'GSVIVG01018044001' => 'vvi', 'HanXRQChr03g0083821' => 'han', 'HanXRQChr03g0083841' => 'han', 'HanXRQChr03g0083881' => 'han', 'HanXRQChr03g0083901' => 'han', 'HanXRQChr03g0083921' => 'han', 'HanXRQChr03g0085331' => 'han', 'HanXRQChr03g0085361' => 'han', 'HanXRQChr03g0085411' => 'han', 'HanXRQChr03g0085421' => 'han', 'HanXRQChr03g0085431' => 'han', 'HanXRQChr08g0221991' => 'han', 'HanXRQChr11g0336061' => 'han', 'HanXRQChr11g0336411' => 'han', 'Haze_11234' => 'cav', 'Hma1.2p1_0549F.1_g177010' => 'hma', 'Hma1.2p1_0602F.1_g187630' => 'hma', 'Hund14876' => 'sun', 'Hund14879' => 'sun', 'Lalb_Chr06g0160741' => 'lal', 'Lalb_Chr21g0304781' => 'lal', 'Lj3A726G19' => 'lonja', 'Lj3A726T23' => 'lonja', 'Lj3A726T24' => 'lonja', 'Lj3A726T25' => 'lonja', 'Lj3A727T17' => 'lonja', 'Lj3C726T0' => 'lonja', 'Lj3C726T2' => 'lonja', 'Lj3P725T35' => 'lonja', 'Lj3P727T10' => 'lonja', 'Lj3P727T12' => 'lonja', 'Lj3P727T14' => 'lonja', 'Lj5g0023109' => 'lja', 'Lj6P646T44' => 'lonja', 'Lsat_1_v5_gn_6_75760' => 'lsa', 'Lsat_1_v5_gn_6_75800' => 'lsa', 'Lsat_1_v5_gn_6_75900' => 'lsa', 'Lsat_1_v5_gn_6_76240' => 'lsa', 'Lsat_1_v5_gn_6_76441' => 'lsa', 'Lsat_1_v5_gn_6_76700' => 'lsa', 'Lsat_1_v5_gn_6_76760' => 'lsa', 'Manes.15G033100' => 'mes', 'Mapoly0004s0074' => 'mpo', 'Mapoly0004s0075' => 'mpo', 'Mapoly0004s0163' => 'mpo', 'Mapoly0004s0164' => 'mpo', 'Mapoly0021s0018' => 'mpo', 'Mapoly0041s0136' => 'mpo', 'Mapoly0041s0137' => 'mpo', 'Mapoly0041s0138' => 'mpo', 'Mapoly0041s0139' => 'mpo', 'Mapoly0041s0141' => 'mpo', 'Mapoly0041s0142' => 'mpo', 'Mapoly0041s0143' => 'mpo', 'Mapoly0041s0144' => 'mpo', 'Mapoly0041s0145' => 'mpo', 'Mapoly0047s0106' => 'mpo', 'Mapoly0047s0108' => 'mpo', 'Mapoly0050s0051' => 'mpo', 'Mapoly0050s0052' => 'mpo', 'Mapoly0050s0053' => 'mpo', 'Mapoly0058s0013' => 'mpo', 'Mapoly0091s0078' => 'mpo', 'Mapoly0091s0079' => 'mpo', 'Mapoly0091s0080' => 'mpo', 'Mapoly0091s0081' => 'mpo', 'Mapoly0278s0004' => 'mpo', 'Mapoly0278s0005' => 'mpo', 'Mapoly0278s0006' => 'mpo', 'MBI11_g30648_MAGBIO' => 'mbi', 'MCO03G194' => 'mco', 'MCO03G590' => 'mco', 'MCO07G312' => 'mco', 'MCO10G318' => 'mco', 'MCO12G244' => 'mco', 'MCO13G148' => 'mco', 'MCO13G194' => 'mco', 'MCO16G238' => 'mco', 'MD06G1134100' => 'mdo', 'MD13G1200100' => 'mdo', 'MD13G1200300' => 'mdo', 'MD13G1200600' => 'mdo', 'MD14G1150400' => 'mdo', 'MD16G1200000' => 'mdo', 'Medtr1g102570' => 'mtr', 'Medtr1g102780' => 'mtr', 'Medtr1g102800' => 'mtr', 'Medtr1g102810' => 'mtr', 'Medtr1g102830' => 'mtr', 'MELO3C006499.2' => 'cme', 'Migut.G00385' => 'egut', 'MSTRG.4063' => 'ama', 'Nitab4.5_0000090g0260' => 'nta', 'Nitab4.5_0000977g0030' => 'nta', 'Nitab4.5_0002541g0040' => 'nta', 'Nitab4.5_0007068g0040' => 'nta', 'Nn005s41408' => 'nnu', 'Nn005s41410' => 'nnu', 'Oeu010310.1' => 'oeu', 'Oeu010311.1' => 'oeu', 'Oeu043472.1' => 'oeu', 'Os01g0246400' => 'osa', 'Os04g0267950' => 'osa', 'Os07g0178700' => 'osa', 'Os07g0178800' => 'osa', 'Peaxi162Scf00316g00046' => 'pax', 'Peaxi162Scf00316g00049' => 'pax', 'Peaxi162Scf00316g00059' => 'pax', 'Peaxi162Scf00316g00328' => 'pax', 'Peaxi162Scf00316g00329' => 'pax', 'Peaxi162Scf00316g00411' => 'pax', 'Peaxi162Scf00316g00521' => 'pax', 'Peaxi162Scf00492g00068' => 'pax', 'Peaxi162Scf35631g00002' => 'pax', 'PGR142G3720' => 'pgr', 'PGSC0003DMG400006442' => 'stu', 'Phvul.007G062000' => 'pvu', 'Potri.008G157750' => 'ptr', 'Potri.008G157900' => 'ptr', 'Potri.008G158000' => 'ptr', 'Potri.008G158200' => 'ptr', 'Pp3c11_7280' => 'ppa', 'Pp3c11_7980' => 'ppa', 'Pp3c12_19450' => 'ppa', 'Pp3c14_1480' => 'ppa', 'Pp3c14_1501' => 'ppa', 'Pp3c16_4900' => 'ppa', 'Pp3c16_5010' => 'ppa', 'Pp3c16_5060' => 'ppa', 'Pp3c19_18250' => 'ppa', 'Pp3c23_8530' => 'ppa', 'Pp3c23_8550' => 'ppa', 'Pp3c24_9670' => 'ppa', 'Pp3c2_21390' => 'ppa', 'Pp3c2_31380' => 'ppa', 'Pp3c3_16620' => 'ppa', 'Pp3c3_8090' => 'ppa', 'Pp3c3_8110' => 'ppa', 'Pp3c3_8130' => 'ppa', 'Pp3c3_8150' => 'ppa', 'Pp3c4_14320' => 'ppa', 'Pp3c6_2560' => 'ppa', 'Pp3c9_16700' => 'ppa', 'PRCOL_00000234' => 'pco', 'PRCOL_00000235' => 'pco', 'PRCOL_00000777' => 'pco', 'PRCOL_00002344' => 'pco', 'PRCOL_00002372' => 'pco', 'PRCOL_00006120' => 'pco', 'Prupe.1G021400' => 'ppe', 'Prupe.1G021500' => 'ppe', 'Prupe.1G021600' => 'ppe', 'Prupe.1G021700' => 'ppe', 'Prupe.1G021800' => 'ppe', 'Prupe.5G145100' => 'ppe', 'Psat6g204040' => 'psa', 'Psat6g204800' => 'psa', 'Psat6g204920' => 'psa', 'Psat6g204960' => 'psa', 'Psat6g205080' => 'psa', 'PSO017G0271' => 'pso', 'PSO017G1276' => 'pso', 'PSO017G1429' => 'pso', 'PSO017G1861' => 'pso', 'PSO017G2787' => 'pso', 'PSO017G4466' => 'pso', 'PSO017G5118' => 'pso', 'PSO017G5420' => 'pso', 'PSO063G3678' => 'pso', 'PSO210G0546' => 'pso', 'PSO317G0001' => 'pso', 'PSO357G0512' => 'pso', 'PSO478G2682' => 'pso', 'PSO647G0001' => 'pso', 'PSO675G0001' => 'pso', 'PSO675G2699' => 'pso', 'PSO675G2849' => 'pso', 'PSO675G4991' => 'pso', 'PSO689G0001' => 'pso', 'QL06p000916' => 'qlo', 'QL06p000921' => 'qlo', 'QL06p001398' => 'qlo', 'QL06p001407' => 'qlo', 'QL06p002031' => 'qlo', 'RcHm_v2.0_Chr4g0387791' => 'rch', 'RcHm_v2.0_Chr4g0387801' => 'rch', 'RcHm_v2.0_Chr6g0286501' => 'rch', 'RcHm_v2.0_Chr6g0286511' => 'rch', 'RcHm_v2.0_Chr6g0286521' => 'rch', 'RcHm_v2.0_Chr6g0286531' => 'rch', 'RcHm_v2.0_Chr7g0189141' => 'rch', 'Rhsim02G0028700' => 'rsi', 'Rhsim02G0028800' => 'rsi', 'Rhsim02G0028900' => 'rsi', 'Rhsim02G0029000' => 'rsi', 'Rhsim02G0029100' => 'rsi', 'Rhsim02G0029200' => 'rsi', 'Rhsim02G0029300' => 'rsi', 'Rhsim02G0029400' => 'rsi', 'Rhsim02G0029500' => 'rsi', 'Rhsim02G0029600' => 'rsi', 'RhsimUnG0024000' => 'rsi', 'RhsimUnG0024100' => 'rsi', 'RhsimUnG0024200' => 'rsi', 'RhsimUnG0024300' => 'rsi', 'RhsimUnG0024400' => 'rsi', 'RhsimUnG0024500' => 'rsi', 'RhsimUnG0024700' => 'rsi', 'RhsimUnG0024800' => 'rsi', 'RhsimUnG0024900' => 'rsi', 'RhsimUnG0025100' => 'rsi', 'Sabra08G0120200' => 'sbr', 'Sabra08G0120300' => 'sbr', 'Sabra08G0120500' => 'sbr', 'Sabra08G0120600' => 'sbr', 'Sabra10G0158900' => 'sbr', 'SalBow2G3492' => 'sbo', 'Sc13g0004760' => 'sci', 'Sc13g0004770' => 'sci', 'Sed0003417' => 'sed', 'Sed0019750' => 'sed', 'SEGI_03419' => 'sgi', 'SEGI_05907' => 'sgi', 'SEGI_10682' => 'sgi', 'SEGI_13528' => 'sgi', 'SEGI_16081' => 'sgi', 'SEGI_19370' => 'sgi', 'SEGI_21015' => 'sgi', 'SEGI_21944' => 'sgi', 'SEGI_32906' => 'sgi', 'SEGI_33093' => 'sgi', 'SEGI_36110' => 'sgi', 'SEGI_40397' => 'sgi', 'SGA_v2.0_scaffold191G40426' => 'sas', 'SGA_v2.0_scaffold353G49717' => 'sas', 'SGA_v2.0_scaffold50G18550' => 'sas', 'SMO119G0173' => 'smo', 'SMO172G0002' => 'smo', 'Solyc09g082690.3' => 'sly', 'Solyc09g082700.2' => 'sly', 'Sopen09g031550' => 'spe', 'Sopen09g031560' => 'spe', 'Sp3g20540' => 'spa', 'Sp7g07580' => 'spa', 'TAR134G0002' => 'tar', 'TAR236G0001' => 'tar', 'TAR365G0892' => 'tar', 'TAR636G0166' => 'tar', 'TAR636G0646' => 'tar', 'TAR636G0869' => 'tar', 'TAR636G1317' => 'tar', 'TAR636G1744' => 'tar', 'TAR636G3358' => 'tar', 'TAR636G3436' => 'tar', 'THA.LOC104803047' => 'tha', 'Thecc.04G238900' => 'tca', 'Thhalv10021557m.g' => 'esa', 'Thhalv10026318m.g' => 'esa', 'Thhalv10026335m.g' => 'esa', 'TPR.G17433' => 'tpr', 'TPR.G18915' => 'tpr', 'TPR.G26125' => 'tpr', 'TWI09G0677' => 'twi', 'TWI73G0287' => 'twi', 'unitig_748.g8326' => 'ugi', 'vmacro15370' => 'vma', 'vmacro15371' => 'vma', 'vmacro15372' => 'vma', 'vmacro15373' => 'vma', 'vmacro15374' => 'vma', 'VMungo0720G2826' => 'vmu', 'Zm00001eb116960' => 'zma', 'Zm00001eb301260' => 'zma', 'Zm00001eb301270' => 'zma' ), 'gf_id' => 'HOM05D001460', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001460' ), 'data_identifier' => 'HOM05D001460', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001460', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '433', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p22980' => 'bna', 'A01p32340' => 'bna', 'A03p42970' => 'bna', 'A05p25880' => 'bna', 'Aa31LG8G9320' => 'aar', 'Aa31LG8G9330' => 'aar', 'Aa31LG8G9340' => 'aar', 'Aa31sc221G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1034' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1528' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.829' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2222' => 'aag', 'Ah.12g058830' => 'amhyb', 'Ah.12g058840' => 'amhyb', 'AL3G37160' => 'aly', 'AL7G41310' => 'aly', 'Aqoxy5G00395' => 'aox', 'Aqoxy5G00396' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0C8NZA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5185HY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JZ1PRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MD3LS0' => 'arhy', 'AT3G22840' => 'ath', 'AT4G14690' => 'ath', 'ATR0665G054' => 'atr', 'Atru.chr4.2344' => 'acertr', 'Atru.chr4.2346' => 'acertr', 'Atru.chr4.2347' => 'acertr', 'Atru.chr4.2348' => 'acertr', 'Atru.chr4.2355' => 'acertr', 'Atru.chr4.2356' => 'acertr', 'Atru.chr4.2358' => 'acertr', 'Atru.chr4.2359' => 'acertr', 'Atru.chr4.2360' => 'acertr', 'Atru.chr4.2361' => 'acertr', 'AUR62030476' => 'cqu', 'AUR62030478' => 'cqu', 'AUR62030819' => 'cqu', 'AUR62030820' => 'cqu', 'BcaB03g14648' => 'bca', 'BcaB04g20492' => 'bca', 'BcaB06g26399' => 'bca', 'BcaC01g03416' => 'bca', 'BcaC01g03419' => 'bca', 'BcaC01g03421' => 'bca', 'BcaC01g03424' => 'bca', 'BcaC05g28012' => 'bca', 'BcaC09g49212' => 'bca', 'BcaC09g50140' => 'bca', 'BcaNung00346' => 'bca', 'BolC1t02785H' => 'bol', 'BolC1t04095H' => 'bol', 'BolC3t17545H' => 'bol', 'BolC5t32769H' => 'bol', 'BraA01t02211Z' => 'bra', 'BraA01t03359Z' => 'bra', 'BraA03t13441Z' => 'bra', 'BraA05t21476Z' => 'bra', 'C01p28420' => 'bna', 'C01p41350' => 'bna', 'C03p52750' => 'bna', 'C03p52780' => 'bna', 'C05p40270' => 'bna', 'CAN.G1437.9' => 'can', 'CANSAT78G0035' => 'cansat', 'CANSAT78G1036' => 'cansat', 'CANSAT78G2272' => 'cansat', 'CANSAT78G2478' => 'cansat', 'CARHR098700' => 'chi', 'CARHR221120' => 'chi', 'CARHR221150' => 'chi', 'Carub.0003s2297' => 'cru', 'Carub.0007s2749' => 'cru', 'Carub.0007s2750' => 'cru', 'Carub.0007s2751' => 'cru', 'Ca_10849_v3' => 'car', 'Cc03_g04300' => 'ccan', 'CDE02G3648' => 'cde', 'CDE05G0060' => 'cde', 'CDE05G0692' => 'cde', 'CDE05G2285' => 'cde', 'CDE05G2884' => 'cde', 'CDE05G3072' => 'cde', 'Cfa008439' => 'cfa', 'Cfa008441' => 'cfa', 'Cfa008443' => 'cfa', 'Cfa008448' => 'cfa', 'Ciclev10005974m.g' => 'ccl', 'Ciclev10006006m.g' => 'ccl', 'Ciclev10006775m.g' => 'ccl', 'CiPaw.02G120400' => 'cil', 'CiPaw.02G120500' => 'cil', 'CiPaw.02G120600' => 'cil', 'ClCG05G004850' => 'cla', 'COL.COLO4_21566' => 'col', 'Cpa.g.sc44.124' => 'cpa', 'Cre07.g320400' => 'cre', 'Cre07.g320450' => 'cre', 'Cre08.g384650' => 'cre', 'Cre09.g393173' => 'cre', 'Cre09.g394325' => 'cre', 'Cre14.g626750' => 'cre', 'Cre16.g679250' => 'cre', 'CsaV3_3G012890' => 'csa', 'CSS0010865' => 'camsi', 'CSS0044338' => 'camsi', 'DCAR_002366' => 'dca', 'DCAR_030687' => 'dca', 'DCAR_030688' => 'dca', 'Dinv14047' => 'din', 'Dinv14048' => 'din', 'Duzib151G0105' => 'dzi', 'Duzib151G0114' => 'dzi', 'Duzib212G1029' => 'dzi', 'ECA232G3536' => 'eca', 'ECA240G0786' => 'eca', 'ECA240G1802' => 'eca', 'ECA240G3760' => 'eca', 'ECA240G3920' => 'eca', 'EL10Ac5g12536' => 'bvu', 'EL10Ac5g12537' => 'bvu', 'EL10Ac5g12538' => 'bvu', 'Eucgr.B01004' => 'egr', 'Eucgr.B01006' => 'egr', 'Eucgr.B01007' => 'egr', 'Eucgr.B01008' => 'egr', 'Eucgr.B01895' => 'egr', 'Eucgr.B01896' => 'egr', 'FAN04G1456' => 'fan', 'FAN08G1769' => 'fan', 'FAN08G2160' => 'fan', 'FAN13G2403' => 'fan', 'FAN13G3303' => 'fan', 'FAN15G2435' => 'fan', 'FAN17G0672' => 'fan', 'FAN17G2441' => 'fan', 'FAN18G1024' => 'fan', 'FAN22G1458' => 'fan', 'FAN24G0037' => 'fan', 'FAN24G0429' => 'fan', 'FAN24G2387' => 'fan', 'FAN27G2746' => 'fan', 'FvH4_2g20400' => 'fve', 'FvH4_2g20420' => 'fve', 'FvH4_2g20430' => 'fve', 'FvH4_4g01270' => 'fve', 'FvH4_4g01290' => 'fve', 'FvH4_4g01300' => 'fve', 'FvH4_4g01310' => 'fve', 'FvH4_4g01330' => 'fve', 'FvH4_5g09070' => 'fve', 'Glyma.10G243800' => 'gma', 'Glyma.20G150600' => 'gma', 'Gohir.A09G219200' => 'ghi', 'Gohir.A09G219300' => 'ghi', 'Gohir.D09G221400' => 'ghi', 'Gohir.D09G221500' => 'ghi', 'Gorai.006G242600' => 'gra', 'Gorai.006G242700' => 'gra', 'GSVIVG01018044001' => 'vvi', 'HanXRQChr03g0083821' => 'han', 'HanXRQChr03g0083841' => 'han', 'HanXRQChr03g0083881' => 'han', 'HanXRQChr03g0083901' => 'han', 'HanXRQChr03g0083921' => 'han', 'HanXRQChr03g0085331' => 'han', 'HanXRQChr03g0085361' => 'han', 'HanXRQChr03g0085411' => 'han', 'HanXRQChr03g0085421' => 'han', 'HanXRQChr03g0085431' => 'han', 'HanXRQChr08g0221991' => 'han', 'HanXRQChr11g0336061' => 'han', 'HanXRQChr11g0336411' => 'han', 'Haze_11234' => 'cav', 'Hma1.2p1_0549F.1_g177010' => 'hma', 'Hma1.2p1_0602F.1_g187630' => 'hma', 'Hund14876' => 'sun', 'Hund14879' => 'sun', 'Lalb_Chr06g0160741' => 'lal', 'Lalb_Chr21g0304781' => 'lal', 'Lj3A726G19' => 'lonja', 'Lj3A726T23' => 'lonja', 'Lj3A726T24' => 'lonja', 'Lj3A726T25' => 'lonja', 'Lj3A727T17' => 'lonja', 'Lj3C726T0' => 'lonja', 'Lj3C726T2' => 'lonja', 'Lj3P725T35' => 'lonja', 'Lj3P727T10' => 'lonja', 'Lj3P727T12' => 'lonja', 'Lj3P727T14' => 'lonja', 'Lj5g0023109' => 'lja', 'Lj6P646T44' => 'lonja', 'Lsat_1_v5_gn_6_75760' => 'lsa', 'Lsat_1_v5_gn_6_75800' => 'lsa', 'Lsat_1_v5_gn_6_75900' => 'lsa', 'Lsat_1_v5_gn_6_76240' => 'lsa', 'Lsat_1_v5_gn_6_76441' => 'lsa', 'Lsat_1_v5_gn_6_76700' => 'lsa', 'Lsat_1_v5_gn_6_76760' => 'lsa', 'Manes.15G033100' => 'mes', 'Mapoly0004s0074' => 'mpo', 'Mapoly0004s0075' => 'mpo', 'Mapoly0004s0163' => 'mpo', 'Mapoly0004s0164' => 'mpo', 'Mapoly0021s0018' => 'mpo', 'Mapoly0041s0136' => 'mpo', 'Mapoly0041s0137' => 'mpo', 'Mapoly0041s0138' => 'mpo', 'Mapoly0041s0139' => 'mpo', 'Mapoly0041s0141' => 'mpo', 'Mapoly0041s0142' => 'mpo', 'Mapoly0041s0143' => 'mpo', 'Mapoly0041s0144' => 'mpo', 'Mapoly0041s0145' => 'mpo', 'Mapoly0047s0106' => 'mpo', 'Mapoly0047s0108' => 'mpo', 'Mapoly0050s0051' => 'mpo', 'Mapoly0050s0052' => 'mpo', 'Mapoly0050s0053' => 'mpo', 'Mapoly0058s0013' => 'mpo', 'Mapoly0091s0078' => 'mpo', 'Mapoly0091s0079' => 'mpo', 'Mapoly0091s0080' => 'mpo', 'Mapoly0091s0081' => 'mpo', 'Mapoly0278s0004' => 'mpo', 'Mapoly0278s0005' => 'mpo', 'Mapoly0278s0006' => 'mpo', 'MBI11_g30648_MAGBIO' => 'mbi', 'MCO03G194' => 'mco', 'MCO03G590' => 'mco', 'MCO07G312' => 'mco', 'MCO10G318' => 'mco', 'MCO12G244' => 'mco', 'MCO13G148' => 'mco', 'MCO13G194' => 'mco', 'MCO16G238' => 'mco', 'MD06G1134100' => 'mdo', 'MD13G1200100' => 'mdo', 'MD13G1200300' => 'mdo', 'MD13G1200600' => 'mdo', 'MD14G1150400' => 'mdo', 'MD16G1200000' => 'mdo', 'Medtr1g102570' => 'mtr', 'Medtr1g102780' => 'mtr', 'Medtr1g102800' => 'mtr', 'Medtr1g102810' => 'mtr', 'Medtr1g102830' => 'mtr', 'MELO3C006499.2' => 'cme', 'Migut.G00385' => 'egut', 'MSTRG.4063' => 'ama', 'Nitab4.5_0000090g0260' => 'nta', 'Nitab4.5_0000977g0030' => 'nta', 'Nitab4.5_0002541g0040' => 'nta', 'Nitab4.5_0007068g0040' => 'nta', 'Nn005s41408' => 'nnu', 'Nn005s41410' => 'nnu', 'Oeu010310.1' => 'oeu', 'Oeu010311.1' => 'oeu', 'Oeu043472.1' => 'oeu', 'Os01g0246400' => 'osa', 'Os04g0267950' => 'osa', 'Os07g0178700' => 'osa', 'Os07g0178800' => 'osa', 'Peaxi162Scf00316g00046' => 'pax', 'Peaxi162Scf00316g00049' => 'pax', 'Peaxi162Scf00316g00059' => 'pax', 'Peaxi162Scf00316g00328' => 'pax', 'Peaxi162Scf00316g00329' => 'pax', 'Peaxi162Scf00316g00411' => 'pax', 'Peaxi162Scf00316g00521' => 'pax', 'Peaxi162Scf00492g00068' => 'pax', 'Peaxi162Scf35631g00002' => 'pax', 'PGR142G3720' => 'pgr', 'PGSC0003DMG400006442' => 'stu', 'Phvul.007G062000' => 'pvu', 'Potri.008G157750' => 'ptr', 'Potri.008G157900' => 'ptr', 'Potri.008G158000' => 'ptr', 'Potri.008G158200' => 'ptr', 'Pp3c11_7280' => 'ppa', 'Pp3c11_7980' => 'ppa', 'Pp3c12_19450' => 'ppa', 'Pp3c14_1480' => 'ppa', 'Pp3c14_1501' => 'ppa', 'Pp3c16_4900' => 'ppa', 'Pp3c16_5010' => 'ppa', 'Pp3c16_5060' => 'ppa', 'Pp3c19_18250' => 'ppa', 'Pp3c23_8530' => 'ppa', 'Pp3c23_8550' => 'ppa', 'Pp3c24_9670' => 'ppa', 'Pp3c2_21390' => 'ppa', 'Pp3c2_31380' => 'ppa', 'Pp3c3_16620' => 'ppa', 'Pp3c3_8090' => 'ppa', 'Pp3c3_8110' => 'ppa', 'Pp3c3_8130' => 'ppa', 'Pp3c3_8150' => 'ppa', 'Pp3c4_14320' => 'ppa', 'Pp3c6_2560' => 'ppa', 'Pp3c9_16700' => 'ppa', 'PRCOL_00000234' => 'pco', 'PRCOL_00000235' => 'pco', 'PRCOL_00000777' => 'pco', 'PRCOL_00002344' => 'pco', 'PRCOL_00002372' => 'pco', 'PRCOL_00006120' => 'pco', 'Prupe.1G021400' => 'ppe', 'Prupe.1G021500' => 'ppe', 'Prupe.1G021600' => 'ppe', 'Prupe.1G021700' => 'ppe', 'Prupe.1G021800' => 'ppe', 'Prupe.5G145100' => 'ppe', 'Psat6g204040' => 'psa', 'Psat6g204800' => 'psa', 'Psat6g204920' => 'psa', 'Psat6g204960' => 'psa', 'Psat6g205080' => 'psa', 'PSO017G0271' => 'pso', 'PSO017G1276' => 'pso', 'PSO017G1429' => 'pso', 'PSO017G1861' => 'pso', 'PSO017G2787' => 'pso', 'PSO017G4466' => 'pso', 'PSO017G5118' => 'pso', 'PSO017G5420' => 'pso', 'PSO063G3678' => 'pso', 'PSO210G0546' => 'pso', 'PSO317G0001' => 'pso', 'PSO357G0512' => 'pso', 'PSO478G2682' => 'pso', 'PSO647G0001' => 'pso', 'PSO675G0001' => 'pso', 'PSO675G2699' => 'pso', 'PSO675G2849' => 'pso', 'PSO675G4991' => 'pso', 'PSO689G0001' => 'pso', 'QL06p000916' => 'qlo', 'QL06p000921' => 'qlo', 'QL06p001398' => 'qlo', 'QL06p001407' => 'qlo', 'QL06p002031' => 'qlo', 'RcHm_v2.0_Chr4g0387791' => 'rch', 'RcHm_v2.0_Chr4g0387801' => 'rch', 'RcHm_v2.0_Chr6g0286501' => 'rch', 'RcHm_v2.0_Chr6g0286511' => 'rch', 'RcHm_v2.0_Chr6g0286521' => 'rch', 'RcHm_v2.0_Chr6g0286531' => 'rch', 'RcHm_v2.0_Chr7g0189141' => 'rch', 'Rhsim02G0028700' => 'rsi', 'Rhsim02G0028800' => 'rsi', 'Rhsim02G0028900' => 'rsi', 'Rhsim02G0029000' => 'rsi', 'Rhsim02G0029100' => 'rsi', 'Rhsim02G0029200' => 'rsi', 'Rhsim02G0029300' => 'rsi', 'Rhsim02G0029400' => 'rsi', 'Rhsim02G0029500' => 'rsi', 'Rhsim02G0029600' => 'rsi', 'RhsimUnG0024000' => 'rsi', 'RhsimUnG0024100' => 'rsi', 'RhsimUnG0024200' => 'rsi', 'RhsimUnG0024300' => 'rsi', 'RhsimUnG0024400' => 'rsi', 'RhsimUnG0024500' => 'rsi', 'RhsimUnG0024700' => 'rsi', 'RhsimUnG0024800' => 'rsi', 'RhsimUnG0024900' => 'rsi', 'RhsimUnG0025100' => 'rsi', 'Sabra08G0120200' => 'sbr', 'Sabra08G0120300' => 'sbr', 'Sabra08G0120500' => 'sbr', 'Sabra08G0120600' => 'sbr', 'Sabra10G0158900' => 'sbr', 'SalBow2G3492' => 'sbo', 'Sc13g0004760' => 'sci', 'Sc13g0004770' => 'sci', 'Sed0003417' => 'sed', 'Sed0019750' => 'sed', 'SEGI_03419' => 'sgi', 'SEGI_05907' => 'sgi', 'SEGI_10682' => 'sgi', 'SEGI_13528' => 'sgi', 'SEGI_16081' => 'sgi', 'SEGI_19370' => 'sgi', 'SEGI_21015' => 'sgi', 'SEGI_21944' => 'sgi', 'SEGI_32906' => 'sgi', 'SEGI_33093' => 'sgi', 'SEGI_36110' => 'sgi', 'SEGI_40397' => 'sgi', 'SGA_v2.0_scaffold191G40426' => 'sas', 'SGA_v2.0_scaffold353G49717' => 'sas', 'SGA_v2.0_scaffold50G18550' => 'sas', 'SMO119G0173' => 'smo', 'SMO172G0002' => 'smo', 'Solyc09g082690.3' => 'sly', 'Solyc09g082700.2' => 'sly', 'Sopen09g031550' => 'spe', 'Sopen09g031560' => 'spe', 'Sp3g20540' => 'spa', 'Sp7g07580' => 'spa', 'TAR134G0002' => 'tar', 'TAR236G0001' => 'tar', 'TAR365G0892' => 'tar', 'TAR636G0166' => 'tar', 'TAR636G0646' => 'tar', 'TAR636G0869' => 'tar', 'TAR636G1317' => 'tar', 'TAR636G1744' => 'tar', 'TAR636G3358' => 'tar', 'TAR636G3436' => 'tar', 'THA.LOC104803047' => 'tha', 'Thecc.04G238900' => 'tca', 'Thhalv10021557m.g' => 'esa', 'Thhalv10026318m.g' => 'esa', 'Thhalv10026335m.g' => 'esa', 'TPR.G17433' => 'tpr', 'TPR.G18915' => 'tpr', 'TPR.G26125' => 'tpr', 'TWI09G0677' => 'twi', 'TWI73G0287' => 'twi', 'unitig_748.g8326' => 'ugi', 'vmacro15370' => 'vma', 'vmacro15371' => 'vma', 'vmacro15372' => 'vma', 'vmacro15373' => 'vma', 'vmacro15374' => 'vma', 'VMungo0720G2826' => 'vmu', 'Zm00001eb116960' => 'zma', 'Zm00001eb301260' => 'zma', 'Zm00001eb301270' => 'zma' ) $gf_id = 'HOM05D001460' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001460' ) $data_identifier = 'HOM05D001460' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 4, 'aag' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 2, 'aox' => (int) 2, 'arhy' => (int) 4, 'ath' => (int) 2, 'atr' => (int) 1, 'acertr' => (int) 10, 'cqu' => (int) 4, 'bca' => (int) 11, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 1, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 1, 'ccan' => (int) 1, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 1, 'col' => (int) 1, 'cpa' => (int) 1, 'cre' => (int) 7, 'csa' => (int) 1, 'camsi' => (int) 2, 'dca' => (int) 3, 'din' => (int) 2, 'dzi' => (int) 3, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 14, 'fve' => (int) 9, 'gma' => (int) 2, 'ghi' => (int) 4, 'gra' => (int) 2, 'vvi' => (int) 1, 'han' => (int) 13, 'cav' => (int) 1, 'hma' => (int) 2, 'sun' => (int) 2, 'lal' => (int) 2, 'lonja' => (int) 12, 'lja' => (int) 1, 'lsa' => (int) 7, 'mes' => (int) 1, 'mpo' => (int) 27, 'mbi' => (int) 1, 'mco' => (int) 8, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 1, 'egut' => (int) 1, 'ama' => (int) 1, 'nta' => (int) 4, 'nnu' => (int) 2, 'oeu' => (int) 3, 'osa' => (int) 4, 'pax' => (int) 9, 'pgr' => (int) 1, 'stu' => (int) 1, 'pvu' => (int) 1, 'ptr' => (int) 4, 'ppa' => (int) 22, 'pco' => (int) 6, 'ppe' => (int) 6, 'psa' => (int) 5, 'pso' => (int) 19, 'qlo' => (int) 5, 'rch' => (int) 7, 'rsi' => (int) 20, 'sbr' => (int) 5, 'sbo' => (int) 1, 'sci' => (int) 2, 'sed' => (int) 2, 'sgi' => (int) 12, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 2, 'tar' => (int) 10, 'tha' => (int) 1, 'tca' => (int) 1, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 2, 'ugi' => (int) 1, 'vma' => (int) 5, 'vmu' => (int) 1, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb301270' $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' => 'HOM05D001460', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '433', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p22980' => 'bna', 'A01p32340' => 'bna', 'A03p42970' => 'bna', 'A05p25880' => 'bna', 'Aa31LG8G9320' => 'aar', 'Aa31LG8G9330' => 'aar', 'Aa31LG8G9340' => 'aar', 'Aa31sc221G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1034' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1528' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.829' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2222' => 'aag', 'Ah.12g058830' => 'amhyb', 'Ah.12g058840' => 'amhyb', 'AL3G37160' => 'aly', 'AL7G41310' => 'aly', 'Aqoxy5G00395' => 'aox', 'Aqoxy5G00396' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0C8NZA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5185HY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JZ1PRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MD3LS0' => 'arhy', 'AT3G22840' => 'ath', 'AT4G14690' => 'ath', 'ATR0665G054' => 'atr', 'Atru.chr4.2344' => 'acertr', 'Atru.chr4.2346' => 'acertr', 'Atru.chr4.2347' => 'acertr', 'Atru.chr4.2348' => 'acertr', 'Atru.chr4.2355' => 'acertr', 'Atru.chr4.2356' => 'acertr', 'Atru.chr4.2358' => 'acertr', 'Atru.chr4.2359' => 'acertr', 'Atru.chr4.2360' => 'acertr', 'Atru.chr4.2361' => 'acertr', 'AUR62030476' => 'cqu', 'AUR62030478' => 'cqu', 'AUR62030819' => 'cqu', 'AUR62030820' => 'cqu', 'BcaB03g14648' => 'bca', 'BcaB04g20492' => 'bca', 'BcaB06g26399' => 'bca', 'BcaC01g03416' => 'bca', 'BcaC01g03419' => 'bca', 'BcaC01g03421' => 'bca', 'BcaC01g03424' => 'bca', 'BcaC05g28012' => 'bca', 'BcaC09g49212' => 'bca', 'BcaC09g50140' => 'bca', 'BcaNung00346' => 'bca', 'BolC1t02785H' => 'bol', 'BolC1t04095H' => 'bol', 'BolC3t17545H' => 'bol', 'BolC5t32769H' => 'bol', 'BraA01t02211Z' => 'bra', 'BraA01t03359Z' => 'bra', 'BraA03t13441Z' => 'bra', 'BraA05t21476Z' => 'bra', 'C01p28420' => 'bna', 'C01p41350' => 'bna', 'C03p52750' => 'bna', 'C03p52780' => 'bna', 'C05p40270' => 'bna', 'CAN.G1437.9' => 'can', 'CANSAT78G0035' => 'cansat', 'CANSAT78G1036' => 'cansat', 'CANSAT78G2272' => 'cansat', 'CANSAT78G2478' => 'cansat', 'CARHR098700' => 'chi', 'CARHR221120' => 'chi', 'CARHR221150' => 'chi', 'Carub.0003s2297' => 'cru', 'Carub.0007s2749' => 'cru', 'Carub.0007s2750' => 'cru', 'Carub.0007s2751' => 'cru', 'Ca_10849_v3' => 'car', 'Cc03_g04300' => 'ccan', 'CDE02G3648' => 'cde', 'CDE05G0060' => 'cde', 'CDE05G0692' => 'cde', 'CDE05G2285' => 'cde', 'CDE05G2884' => 'cde', 'CDE05G3072' => 'cde', 'Cfa008439' => 'cfa', 'Cfa008441' => 'cfa', 'Cfa008443' => 'cfa', 'Cfa008448' => 'cfa', 'Ciclev10005974m.g' => 'ccl', 'Ciclev10006006m.g' => 'ccl', 'Ciclev10006775m.g' => 'ccl', 'CiPaw.02G120400' => 'cil', 'CiPaw.02G120500' => 'cil', 'CiPaw.02G120600' => 'cil', 'ClCG05G004850' => 'cla', 'COL.COLO4_21566' => 'col', 'Cpa.g.sc44.124' => 'cpa', 'Cre07.g320400' => 'cre', 'Cre07.g320450' => 'cre', 'Cre08.g384650' => 'cre', 'Cre09.g393173' => 'cre', 'Cre09.g394325' => 'cre', 'Cre14.g626750' => 'cre', 'Cre16.g679250' => 'cre', 'CsaV3_3G012890' => 'csa', 'CSS0010865' => 'camsi', 'CSS0044338' => 'camsi', 'DCAR_002366' => 'dca', 'DCAR_030687' => 'dca', 'DCAR_030688' => 'dca', 'Dinv14047' => 'din', 'Dinv14048' => 'din', 'Duzib151G0105' => 'dzi', 'Duzib151G0114' => 'dzi', 'Duzib212G1029' => 'dzi', 'ECA232G3536' => 'eca', 'ECA240G0786' => 'eca', 'ECA240G1802' => 'eca', 'ECA240G3760' => 'eca', 'ECA240G3920' => 'eca', 'EL10Ac5g12536' => 'bvu', 'EL10Ac5g12537' => 'bvu', 'EL10Ac5g12538' => 'bvu', 'Eucgr.B01004' => 'egr', 'Eucgr.B01006' => 'egr', 'Eucgr.B01007' => 'egr', 'Eucgr.B01008' => 'egr', 'Eucgr.B01895' => 'egr', 'Eucgr.B01896' => 'egr', 'FAN04G1456' => 'fan', 'FAN08G1769' => 'fan', 'FAN08G2160' => 'fan', 'FAN13G2403' => 'fan', 'FAN13G3303' => 'fan', 'FAN15G2435' => 'fan', 'FAN17G0672' => 'fan', 'FAN17G2441' => 'fan', 'FAN18G1024' => 'fan', 'FAN22G1458' => 'fan', 'FAN24G0037' => 'fan', 'FAN24G0429' => 'fan', 'FAN24G2387' => 'fan', 'FAN27G2746' => 'fan', 'FvH4_2g20400' => 'fve', 'FvH4_2g20420' => 'fve', 'FvH4_2g20430' => 'fve', 'FvH4_4g01270' => 'fve', 'FvH4_4g01290' => 'fve', 'FvH4_4g01300' => 'fve', 'FvH4_4g01310' => 'fve', 'FvH4_4g01330' => 'fve', 'FvH4_5g09070' => 'fve', 'Glyma.10G243800' => 'gma', 'Glyma.20G150600' => 'gma', 'Gohir.A09G219200' => 'ghi', 'Gohir.A09G219300' => 'ghi', 'Gohir.D09G221400' => 'ghi', 'Gohir.D09G221500' => 'ghi', 'Gorai.006G242600' => 'gra', 'Gorai.006G242700' => 'gra', 'GSVIVG01018044001' => 'vvi', 'HanXRQChr03g0083821' => 'han', 'HanXRQChr03g0083841' => 'han', 'HanXRQChr03g0083881' => 'han', 'HanXRQChr03g0083901' => 'han', 'HanXRQChr03g0083921' => 'han', 'HanXRQChr03g0085331' => 'han', 'HanXRQChr03g0085361' => 'han', 'HanXRQChr03g0085411' => 'han', 'HanXRQChr03g0085421' => 'han', 'HanXRQChr03g0085431' => 'han', 'HanXRQChr08g0221991' => 'han', 'HanXRQChr11g0336061' => 'han', 'HanXRQChr11g0336411' => 'han', 'Haze_11234' => 'cav', 'Hma1.2p1_0549F.1_g177010' => 'hma', 'Hma1.2p1_0602F.1_g187630' => 'hma', 'Hund14876' => 'sun', 'Hund14879' => 'sun', 'Lalb_Chr06g0160741' => 'lal', 'Lalb_Chr21g0304781' => 'lal', 'Lj3A726G19' => 'lonja', 'Lj3A726T23' => 'lonja', 'Lj3A726T24' => 'lonja', 'Lj3A726T25' => 'lonja', 'Lj3A727T17' => 'lonja', 'Lj3C726T0' => 'lonja', 'Lj3C726T2' => 'lonja', 'Lj3P725T35' => 'lonja', 'Lj3P727T10' => 'lonja', 'Lj3P727T12' => 'lonja', 'Lj3P727T14' => 'lonja', 'Lj5g0023109' => 'lja', 'Lj6P646T44' => 'lonja', 'Lsat_1_v5_gn_6_75760' => 'lsa', 'Lsat_1_v5_gn_6_75800' => 'lsa', 'Lsat_1_v5_gn_6_75900' => 'lsa', 'Lsat_1_v5_gn_6_76240' => 'lsa', 'Lsat_1_v5_gn_6_76441' => 'lsa', 'Lsat_1_v5_gn_6_76700' => 'lsa', 'Lsat_1_v5_gn_6_76760' => 'lsa', 'Manes.15G033100' => 'mes', 'Mapoly0004s0074' => 'mpo', 'Mapoly0004s0075' => 'mpo', 'Mapoly0004s0163' => 'mpo', 'Mapoly0004s0164' => 'mpo', 'Mapoly0021s0018' => 'mpo', 'Mapoly0041s0136' => 'mpo', 'Mapoly0041s0137' => 'mpo', 'Mapoly0041s0138' => 'mpo', 'Mapoly0041s0139' => 'mpo', 'Mapoly0041s0141' => 'mpo', 'Mapoly0041s0142' => 'mpo', 'Mapoly0041s0143' => 'mpo', 'Mapoly0041s0144' => 'mpo', 'Mapoly0041s0145' => 'mpo', 'Mapoly0047s0106' => 'mpo', 'Mapoly0047s0108' => 'mpo', 'Mapoly0050s0051' => 'mpo', 'Mapoly0050s0052' => 'mpo', 'Mapoly0050s0053' => 'mpo', 'Mapoly0058s0013' => 'mpo', 'Mapoly0091s0078' => 'mpo', 'Mapoly0091s0079' => 'mpo', 'Mapoly0091s0080' => 'mpo', 'Mapoly0091s0081' => 'mpo', 'Mapoly0278s0004' => 'mpo', 'Mapoly0278s0005' => 'mpo', 'Mapoly0278s0006' => 'mpo', 'MBI11_g30648_MAGBIO' => 'mbi', 'MCO03G194' => 'mco', 'MCO03G590' => 'mco', 'MCO07G312' => 'mco', 'MCO10G318' => 'mco', 'MCO12G244' => 'mco', 'MCO13G148' => 'mco', 'MCO13G194' => 'mco', 'MCO16G238' => 'mco', 'MD06G1134100' => 'mdo', 'MD13G1200100' => 'mdo', 'MD13G1200300' => 'mdo', 'MD13G1200600' => 'mdo', 'MD14G1150400' => 'mdo', 'MD16G1200000' => 'mdo', 'Medtr1g102570' => 'mtr', 'Medtr1g102780' => 'mtr', 'Medtr1g102800' => 'mtr', 'Medtr1g102810' => 'mtr', 'Medtr1g102830' => 'mtr', 'MELO3C006499.2' => 'cme', 'Migut.G00385' => 'egut', 'MSTRG.4063' => 'ama', 'Nitab4.5_0000090g0260' => 'nta', 'Nitab4.5_0000977g0030' => 'nta', 'Nitab4.5_0002541g0040' => 'nta', 'Nitab4.5_0007068g0040' => 'nta', 'Nn005s41408' => 'nnu', 'Nn005s41410' => 'nnu', 'Oeu010310.1' => 'oeu', 'Oeu010311.1' => 'oeu', 'Oeu043472.1' => 'oeu', 'Os01g0246400' => 'osa', 'Os04g0267950' => 'osa', 'Os07g0178700' => 'osa', 'Os07g0178800' => 'osa', 'Peaxi162Scf00316g00046' => 'pax', 'Peaxi162Scf00316g00049' => 'pax', 'Peaxi162Scf00316g00059' => 'pax', 'Peaxi162Scf00316g00328' => 'pax', 'Peaxi162Scf00316g00329' => 'pax', 'Peaxi162Scf00316g00411' => 'pax', 'Peaxi162Scf00316g00521' => 'pax', 'Peaxi162Scf00492g00068' => 'pax', 'Peaxi162Scf35631g00002' => 'pax', 'PGR142G3720' => 'pgr', 'PGSC0003DMG400006442' => 'stu', 'Phvul.007G062000' => 'pvu', 'Potri.008G157750' => 'ptr', 'Potri.008G157900' => 'ptr', 'Potri.008G158000' => 'ptr', 'Potri.008G158200' => 'ptr', 'Pp3c11_7280' => 'ppa', 'Pp3c11_7980' => 'ppa', 'Pp3c12_19450' => 'ppa', 'Pp3c14_1480' => 'ppa', 'Pp3c14_1501' => 'ppa', 'Pp3c16_4900' => 'ppa', 'Pp3c16_5010' => 'ppa', 'Pp3c16_5060' => 'ppa', 'Pp3c19_18250' => 'ppa', 'Pp3c23_8530' => 'ppa', 'Pp3c23_8550' => 'ppa', 'Pp3c24_9670' => 'ppa', 'Pp3c2_21390' => 'ppa', 'Pp3c2_31380' => 'ppa', 'Pp3c3_16620' => 'ppa', 'Pp3c3_8090' => 'ppa', 'Pp3c3_8110' => 'ppa', 'Pp3c3_8130' => 'ppa', 'Pp3c3_8150' => 'ppa', 'Pp3c4_14320' => 'ppa', 'Pp3c6_2560' => 'ppa', 'Pp3c9_16700' => 'ppa', 'PRCOL_00000234' => 'pco', 'PRCOL_00000235' => 'pco', 'PRCOL_00000777' => 'pco', 'PRCOL_00002344' => 'pco', 'PRCOL_00002372' => 'pco', 'PRCOL_00006120' => 'pco', 'Prupe.1G021400' => 'ppe', 'Prupe.1G021500' => 'ppe', 'Prupe.1G021600' => 'ppe', 'Prupe.1G021700' => 'ppe', 'Prupe.1G021800' => 'ppe', 'Prupe.5G145100' => 'ppe', 'Psat6g204040' => 'psa', 'Psat6g204800' => 'psa', 'Psat6g204920' => 'psa', 'Psat6g204960' => 'psa', 'Psat6g205080' => 'psa', 'PSO017G0271' => 'pso', 'PSO017G1276' => 'pso', 'PSO017G1429' => 'pso', 'PSO017G1861' => 'pso', 'PSO017G2787' => 'pso', 'PSO017G4466' => 'pso', 'PSO017G5118' => 'pso', 'PSO017G5420' => 'pso', 'PSO063G3678' => 'pso', 'PSO210G0546' => 'pso', 'PSO317G0001' => 'pso', 'PSO357G0512' => 'pso', 'PSO478G2682' => 'pso', 'PSO647G0001' => 'pso', 'PSO675G0001' => 'pso', 'PSO675G2699' => 'pso', 'PSO675G2849' => 'pso', 'PSO675G4991' => 'pso', 'PSO689G0001' => 'pso', 'QL06p000916' => 'qlo', 'QL06p000921' => 'qlo', 'QL06p001398' => 'qlo', 'QL06p001407' => 'qlo', 'QL06p002031' => 'qlo', 'RcHm_v2.0_Chr4g0387791' => 'rch', 'RcHm_v2.0_Chr4g0387801' => 'rch', 'RcHm_v2.0_Chr6g0286501' => 'rch', 'RcHm_v2.0_Chr6g0286511' => 'rch', 'RcHm_v2.0_Chr6g0286521' => 'rch', 'RcHm_v2.0_Chr6g0286531' => 'rch', 'RcHm_v2.0_Chr7g0189141' => 'rch', 'Rhsim02G0028700' => 'rsi', 'Rhsim02G0028800' => 'rsi', 'Rhsim02G0028900' => 'rsi', 'Rhsim02G0029000' => 'rsi', 'Rhsim02G0029100' => 'rsi', 'Rhsim02G0029200' => 'rsi', 'Rhsim02G0029300' => 'rsi', 'Rhsim02G0029400' => 'rsi', 'Rhsim02G0029500' => 'rsi', 'Rhsim02G0029600' => 'rsi', 'RhsimUnG0024000' => 'rsi', 'RhsimUnG0024100' => 'rsi', 'RhsimUnG0024200' => 'rsi', 'RhsimUnG0024300' => 'rsi', 'RhsimUnG0024400' => 'rsi', 'RhsimUnG0024500' => 'rsi', 'RhsimUnG0024700' => 'rsi', 'RhsimUnG0024800' => 'rsi', 'RhsimUnG0024900' => 'rsi', 'RhsimUnG0025100' => 'rsi', 'Sabra08G0120200' => 'sbr', 'Sabra08G0120300' => 'sbr', 'Sabra08G0120500' => 'sbr', 'Sabra08G0120600' => 'sbr', 'Sabra10G0158900' => 'sbr', 'SalBow2G3492' => 'sbo', 'Sc13g0004760' => 'sci', 'Sc13g0004770' => 'sci', 'Sed0003417' => 'sed', 'Sed0019750' => 'sed', 'SEGI_03419' => 'sgi', 'SEGI_05907' => 'sgi', 'SEGI_10682' => 'sgi', 'SEGI_13528' => 'sgi', 'SEGI_16081' => 'sgi', 'SEGI_19370' => 'sgi', 'SEGI_21015' => 'sgi', 'SEGI_21944' => 'sgi', 'SEGI_32906' => 'sgi', 'SEGI_33093' => 'sgi', 'SEGI_36110' => 'sgi', 'SEGI_40397' => 'sgi', 'SGA_v2.0_scaffold191G40426' => 'sas', 'SGA_v2.0_scaffold353G49717' => 'sas', 'SGA_v2.0_scaffold50G18550' => 'sas', 'SMO119G0173' => 'smo', 'SMO172G0002' => 'smo', 'Solyc09g082690.3' => 'sly', 'Solyc09g082700.2' => 'sly', 'Sopen09g031550' => 'spe', 'Sopen09g031560' => 'spe', 'Sp3g20540' => 'spa', 'Sp7g07580' => 'spa', 'TAR134G0002' => 'tar', 'TAR236G0001' => 'tar', 'TAR365G0892' => 'tar', 'TAR636G0166' => 'tar', 'TAR636G0646' => 'tar', 'TAR636G0869' => 'tar', 'TAR636G1317' => 'tar', 'TAR636G1744' => 'tar', 'TAR636G3358' => 'tar', 'TAR636G3436' => 'tar', 'THA.LOC104803047' => 'tha', 'Thecc.04G238900' => 'tca', 'Thhalv10021557m.g' => 'esa', 'Thhalv10026318m.g' => 'esa', 'Thhalv10026335m.g' => 'esa', 'TPR.G17433' => 'tpr', 'TPR.G18915' => 'tpr', 'TPR.G26125' => 'tpr', 'TWI09G0677' => 'twi', 'TWI73G0287' => 'twi', 'unitig_748.g8326' => 'ugi', 'vmacro15370' => 'vma', 'vmacro15371' => 'vma', 'vmacro15372' => 'vma', 'vmacro15373' => 'vma', 'vmacro15374' => 'vma', 'VMungo0720G2826' => 'vmu', 'Zm00001eb116960' => 'zma', 'Zm00001eb301260' => 'zma', 'Zm00001eb301270' => 'zma' ), 'gf_id' => 'HOM05D001460', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001460' ), 'data_identifier' => 'HOM05D001460', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001460', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '433', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p22980' => 'bna', 'A01p32340' => 'bna', 'A03p42970' => 'bna', 'A05p25880' => 'bna', 'Aa31LG8G9320' => 'aar', 'Aa31LG8G9330' => 'aar', 'Aa31LG8G9340' => 'aar', 'Aa31sc221G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1034' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1528' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.829' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2222' => 'aag', 'Ah.12g058830' => 'amhyb', 'Ah.12g058840' => 'amhyb', 'AL3G37160' => 'aly', 'AL7G41310' => 'aly', 'Aqoxy5G00395' => 'aox', 'Aqoxy5G00396' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0C8NZA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5185HY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JZ1PRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MD3LS0' => 'arhy', 'AT3G22840' => 'ath', 'AT4G14690' => 'ath', 'ATR0665G054' => 'atr', 'Atru.chr4.2344' => 'acertr', 'Atru.chr4.2346' => 'acertr', 'Atru.chr4.2347' => 'acertr', 'Atru.chr4.2348' => 'acertr', 'Atru.chr4.2355' => 'acertr', 'Atru.chr4.2356' => 'acertr', 'Atru.chr4.2358' => 'acertr', 'Atru.chr4.2359' => 'acertr', 'Atru.chr4.2360' => 'acertr', 'Atru.chr4.2361' => 'acertr', 'AUR62030476' => 'cqu', 'AUR62030478' => 'cqu', 'AUR62030819' => 'cqu', 'AUR62030820' => 'cqu', 'BcaB03g14648' => 'bca', 'BcaB04g20492' => 'bca', 'BcaB06g26399' => 'bca', 'BcaC01g03416' => 'bca', 'BcaC01g03419' => 'bca', 'BcaC01g03421' => 'bca', 'BcaC01g03424' => 'bca', 'BcaC05g28012' => 'bca', 'BcaC09g49212' => 'bca', 'BcaC09g50140' => 'bca', 'BcaNung00346' => 'bca', 'BolC1t02785H' => 'bol', 'BolC1t04095H' => 'bol', 'BolC3t17545H' => 'bol', 'BolC5t32769H' => 'bol', 'BraA01t02211Z' => 'bra', 'BraA01t03359Z' => 'bra', 'BraA03t13441Z' => 'bra', 'BraA05t21476Z' => 'bra', 'C01p28420' => 'bna', 'C01p41350' => 'bna', 'C03p52750' => 'bna', 'C03p52780' => 'bna', 'C05p40270' => 'bna', 'CAN.G1437.9' => 'can', 'CANSAT78G0035' => 'cansat', 'CANSAT78G1036' => 'cansat', 'CANSAT78G2272' => 'cansat', 'CANSAT78G2478' => 'cansat', 'CARHR098700' => 'chi', 'CARHR221120' => 'chi', 'CARHR221150' => 'chi', 'Carub.0003s2297' => 'cru', 'Carub.0007s2749' => 'cru', 'Carub.0007s2750' => 'cru', 'Carub.0007s2751' => 'cru', 'Ca_10849_v3' => 'car', 'Cc03_g04300' => 'ccan', 'CDE02G3648' => 'cde', 'CDE05G0060' => 'cde', 'CDE05G0692' => 'cde', 'CDE05G2285' => 'cde', 'CDE05G2884' => 'cde', 'CDE05G3072' => 'cde', 'Cfa008439' => 'cfa', 'Cfa008441' => 'cfa', 'Cfa008443' => 'cfa', 'Cfa008448' => 'cfa', 'Ciclev10005974m.g' => 'ccl', 'Ciclev10006006m.g' => 'ccl', 'Ciclev10006775m.g' => 'ccl', 'CiPaw.02G120400' => 'cil', 'CiPaw.02G120500' => 'cil', 'CiPaw.02G120600' => 'cil', 'ClCG05G004850' => 'cla', 'COL.COLO4_21566' => 'col', 'Cpa.g.sc44.124' => 'cpa', 'Cre07.g320400' => 'cre', 'Cre07.g320450' => 'cre', 'Cre08.g384650' => 'cre', 'Cre09.g393173' => 'cre', 'Cre09.g394325' => 'cre', 'Cre14.g626750' => 'cre', 'Cre16.g679250' => 'cre', 'CsaV3_3G012890' => 'csa', 'CSS0010865' => 'camsi', 'CSS0044338' => 'camsi', 'DCAR_002366' => 'dca', 'DCAR_030687' => 'dca', 'DCAR_030688' => 'dca', 'Dinv14047' => 'din', 'Dinv14048' => 'din', 'Duzib151G0105' => 'dzi', 'Duzib151G0114' => 'dzi', 'Duzib212G1029' => 'dzi', 'ECA232G3536' => 'eca', 'ECA240G0786' => 'eca', 'ECA240G1802' => 'eca', 'ECA240G3760' => 'eca', 'ECA240G3920' => 'eca', 'EL10Ac5g12536' => 'bvu', 'EL10Ac5g12537' => 'bvu', 'EL10Ac5g12538' => 'bvu', 'Eucgr.B01004' => 'egr', 'Eucgr.B01006' => 'egr', 'Eucgr.B01007' => 'egr', 'Eucgr.B01008' => 'egr', 'Eucgr.B01895' => 'egr', 'Eucgr.B01896' => 'egr', 'FAN04G1456' => 'fan', 'FAN08G1769' => 'fan', 'FAN08G2160' => 'fan', 'FAN13G2403' => 'fan', 'FAN13G3303' => 'fan', 'FAN15G2435' => 'fan', 'FAN17G0672' => 'fan', 'FAN17G2441' => 'fan', 'FAN18G1024' => 'fan', 'FAN22G1458' => 'fan', 'FAN24G0037' => 'fan', 'FAN24G0429' => 'fan', 'FAN24G2387' => 'fan', 'FAN27G2746' => 'fan', 'FvH4_2g20400' => 'fve', 'FvH4_2g20420' => 'fve', 'FvH4_2g20430' => 'fve', 'FvH4_4g01270' => 'fve', 'FvH4_4g01290' => 'fve', 'FvH4_4g01300' => 'fve', 'FvH4_4g01310' => 'fve', 'FvH4_4g01330' => 'fve', 'FvH4_5g09070' => 'fve', 'Glyma.10G243800' => 'gma', 'Glyma.20G150600' => 'gma', 'Gohir.A09G219200' => 'ghi', 'Gohir.A09G219300' => 'ghi', 'Gohir.D09G221400' => 'ghi', 'Gohir.D09G221500' => 'ghi', 'Gorai.006G242600' => 'gra', 'Gorai.006G242700' => 'gra', 'GSVIVG01018044001' => 'vvi', 'HanXRQChr03g0083821' => 'han', 'HanXRQChr03g0083841' => 'han', 'HanXRQChr03g0083881' => 'han', 'HanXRQChr03g0083901' => 'han', 'HanXRQChr03g0083921' => 'han', 'HanXRQChr03g0085331' => 'han', 'HanXRQChr03g0085361' => 'han', 'HanXRQChr03g0085411' => 'han', 'HanXRQChr03g0085421' => 'han', 'HanXRQChr03g0085431' => 'han', 'HanXRQChr08g0221991' => 'han', 'HanXRQChr11g0336061' => 'han', 'HanXRQChr11g0336411' => 'han', 'Haze_11234' => 'cav', 'Hma1.2p1_0549F.1_g177010' => 'hma', 'Hma1.2p1_0602F.1_g187630' => 'hma', 'Hund14876' => 'sun', 'Hund14879' => 'sun', 'Lalb_Chr06g0160741' => 'lal', 'Lalb_Chr21g0304781' => 'lal', 'Lj3A726G19' => 'lonja', 'Lj3A726T23' => 'lonja', 'Lj3A726T24' => 'lonja', 'Lj3A726T25' => 'lonja', 'Lj3A727T17' => 'lonja', 'Lj3C726T0' => 'lonja', 'Lj3C726T2' => 'lonja', 'Lj3P725T35' => 'lonja', 'Lj3P727T10' => 'lonja', 'Lj3P727T12' => 'lonja', 'Lj3P727T14' => 'lonja', 'Lj5g0023109' => 'lja', 'Lj6P646T44' => 'lonja', 'Lsat_1_v5_gn_6_75760' => 'lsa', 'Lsat_1_v5_gn_6_75800' => 'lsa', 'Lsat_1_v5_gn_6_75900' => 'lsa', 'Lsat_1_v5_gn_6_76240' => 'lsa', 'Lsat_1_v5_gn_6_76441' => 'lsa', 'Lsat_1_v5_gn_6_76700' => 'lsa', 'Lsat_1_v5_gn_6_76760' => 'lsa', 'Manes.15G033100' => 'mes', 'Mapoly0004s0074' => 'mpo', 'Mapoly0004s0075' => 'mpo', 'Mapoly0004s0163' => 'mpo', 'Mapoly0004s0164' => 'mpo', 'Mapoly0021s0018' => 'mpo', 'Mapoly0041s0136' => 'mpo', 'Mapoly0041s0137' => 'mpo', 'Mapoly0041s0138' => 'mpo', 'Mapoly0041s0139' => 'mpo', 'Mapoly0041s0141' => 'mpo', 'Mapoly0041s0142' => 'mpo', 'Mapoly0041s0143' => 'mpo', 'Mapoly0041s0144' => 'mpo', 'Mapoly0041s0145' => 'mpo', 'Mapoly0047s0106' => 'mpo', 'Mapoly0047s0108' => 'mpo', 'Mapoly0050s0051' => 'mpo', 'Mapoly0050s0052' => 'mpo', 'Mapoly0050s0053' => 'mpo', 'Mapoly0058s0013' => 'mpo', 'Mapoly0091s0078' => 'mpo', 'Mapoly0091s0079' => 'mpo', 'Mapoly0091s0080' => 'mpo', 'Mapoly0091s0081' => 'mpo', 'Mapoly0278s0004' => 'mpo', 'Mapoly0278s0005' => 'mpo', 'Mapoly0278s0006' => 'mpo', 'MBI11_g30648_MAGBIO' => 'mbi', 'MCO03G194' => 'mco', 'MCO03G590' => 'mco', 'MCO07G312' => 'mco', 'MCO10G318' => 'mco', 'MCO12G244' => 'mco', 'MCO13G148' => 'mco', 'MCO13G194' => 'mco', 'MCO16G238' => 'mco', 'MD06G1134100' => 'mdo', 'MD13G1200100' => 'mdo', 'MD13G1200300' => 'mdo', 'MD13G1200600' => 'mdo', 'MD14G1150400' => 'mdo', 'MD16G1200000' => 'mdo', 'Medtr1g102570' => 'mtr', 'Medtr1g102780' => 'mtr', 'Medtr1g102800' => 'mtr', 'Medtr1g102810' => 'mtr', 'Medtr1g102830' => 'mtr', 'MELO3C006499.2' => 'cme', 'Migut.G00385' => 'egut', 'MSTRG.4063' => 'ama', 'Nitab4.5_0000090g0260' => 'nta', 'Nitab4.5_0000977g0030' => 'nta', 'Nitab4.5_0002541g0040' => 'nta', 'Nitab4.5_0007068g0040' => 'nta', 'Nn005s41408' => 'nnu', 'Nn005s41410' => 'nnu', 'Oeu010310.1' => 'oeu', 'Oeu010311.1' => 'oeu', 'Oeu043472.1' => 'oeu', 'Os01g0246400' => 'osa', 'Os04g0267950' => 'osa', 'Os07g0178700' => 'osa', 'Os07g0178800' => 'osa', 'Peaxi162Scf00316g00046' => 'pax', 'Peaxi162Scf00316g00049' => 'pax', 'Peaxi162Scf00316g00059' => 'pax', 'Peaxi162Scf00316g00328' => 'pax', 'Peaxi162Scf00316g00329' => 'pax', 'Peaxi162Scf00316g00411' => 'pax', 'Peaxi162Scf00316g00521' => 'pax', 'Peaxi162Scf00492g00068' => 'pax', 'Peaxi162Scf35631g00002' => 'pax', 'PGR142G3720' => 'pgr', 'PGSC0003DMG400006442' => 'stu', 'Phvul.007G062000' => 'pvu', 'Potri.008G157750' => 'ptr', 'Potri.008G157900' => 'ptr', 'Potri.008G158000' => 'ptr', 'Potri.008G158200' => 'ptr', 'Pp3c11_7280' => 'ppa', 'Pp3c11_7980' => 'ppa', 'Pp3c12_19450' => 'ppa', 'Pp3c14_1480' => 'ppa', 'Pp3c14_1501' => 'ppa', 'Pp3c16_4900' => 'ppa', 'Pp3c16_5010' => 'ppa', 'Pp3c16_5060' => 'ppa', 'Pp3c19_18250' => 'ppa', 'Pp3c23_8530' => 'ppa', 'Pp3c23_8550' => 'ppa', 'Pp3c24_9670' => 'ppa', 'Pp3c2_21390' => 'ppa', 'Pp3c2_31380' => 'ppa', 'Pp3c3_16620' => 'ppa', 'Pp3c3_8090' => 'ppa', 'Pp3c3_8110' => 'ppa', 'Pp3c3_8130' => 'ppa', 'Pp3c3_8150' => 'ppa', 'Pp3c4_14320' => 'ppa', 'Pp3c6_2560' => 'ppa', 'Pp3c9_16700' => 'ppa', 'PRCOL_00000234' => 'pco', 'PRCOL_00000235' => 'pco', 'PRCOL_00000777' => 'pco', 'PRCOL_00002344' => 'pco', 'PRCOL_00002372' => 'pco', 'PRCOL_00006120' => 'pco', 'Prupe.1G021400' => 'ppe', 'Prupe.1G021500' => 'ppe', 'Prupe.1G021600' => 'ppe', 'Prupe.1G021700' => 'ppe', 'Prupe.1G021800' => 'ppe', 'Prupe.5G145100' => 'ppe', 'Psat6g204040' => 'psa', 'Psat6g204800' => 'psa', 'Psat6g204920' => 'psa', 'Psat6g204960' => 'psa', 'Psat6g205080' => 'psa', 'PSO017G0271' => 'pso', 'PSO017G1276' => 'pso', 'PSO017G1429' => 'pso', 'PSO017G1861' => 'pso', 'PSO017G2787' => 'pso', 'PSO017G4466' => 'pso', 'PSO017G5118' => 'pso', 'PSO017G5420' => 'pso', 'PSO063G3678' => 'pso', 'PSO210G0546' => 'pso', 'PSO317G0001' => 'pso', 'PSO357G0512' => 'pso', 'PSO478G2682' => 'pso', 'PSO647G0001' => 'pso', 'PSO675G0001' => 'pso', 'PSO675G2699' => 'pso', 'PSO675G2849' => 'pso', 'PSO675G4991' => 'pso', 'PSO689G0001' => 'pso', 'QL06p000916' => 'qlo', 'QL06p000921' => 'qlo', 'QL06p001398' => 'qlo', 'QL06p001407' => 'qlo', 'QL06p002031' => 'qlo', 'RcHm_v2.0_Chr4g0387791' => 'rch', 'RcHm_v2.0_Chr4g0387801' => 'rch', 'RcHm_v2.0_Chr6g0286501' => 'rch', 'RcHm_v2.0_Chr6g0286511' => 'rch', 'RcHm_v2.0_Chr6g0286521' => 'rch', 'RcHm_v2.0_Chr6g0286531' => 'rch', 'RcHm_v2.0_Chr7g0189141' => 'rch', 'Rhsim02G0028700' => 'rsi', 'Rhsim02G0028800' => 'rsi', 'Rhsim02G0028900' => 'rsi', 'Rhsim02G0029000' => 'rsi', 'Rhsim02G0029100' => 'rsi', 'Rhsim02G0029200' => 'rsi', 'Rhsim02G0029300' => 'rsi', 'Rhsim02G0029400' => 'rsi', 'Rhsim02G0029500' => 'rsi', 'Rhsim02G0029600' => 'rsi', 'RhsimUnG0024000' => 'rsi', 'RhsimUnG0024100' => 'rsi', 'RhsimUnG0024200' => 'rsi', 'RhsimUnG0024300' => 'rsi', 'RhsimUnG0024400' => 'rsi', 'RhsimUnG0024500' => 'rsi', 'RhsimUnG0024700' => 'rsi', 'RhsimUnG0024800' => 'rsi', 'RhsimUnG0024900' => 'rsi', 'RhsimUnG0025100' => 'rsi', 'Sabra08G0120200' => 'sbr', 'Sabra08G0120300' => 'sbr', 'Sabra08G0120500' => 'sbr', 'Sabra08G0120600' => 'sbr', 'Sabra10G0158900' => 'sbr', 'SalBow2G3492' => 'sbo', 'Sc13g0004760' => 'sci', 'Sc13g0004770' => 'sci', 'Sed0003417' => 'sed', 'Sed0019750' => 'sed', 'SEGI_03419' => 'sgi', 'SEGI_05907' => 'sgi', 'SEGI_10682' => 'sgi', 'SEGI_13528' => 'sgi', 'SEGI_16081' => 'sgi', 'SEGI_19370' => 'sgi', 'SEGI_21015' => 'sgi', 'SEGI_21944' => 'sgi', 'SEGI_32906' => 'sgi', 'SEGI_33093' => 'sgi', 'SEGI_36110' => 'sgi', 'SEGI_40397' => 'sgi', 'SGA_v2.0_scaffold191G40426' => 'sas', 'SGA_v2.0_scaffold353G49717' => 'sas', 'SGA_v2.0_scaffold50G18550' => 'sas', 'SMO119G0173' => 'smo', 'SMO172G0002' => 'smo', 'Solyc09g082690.3' => 'sly', 'Solyc09g082700.2' => 'sly', 'Sopen09g031550' => 'spe', 'Sopen09g031560' => 'spe', 'Sp3g20540' => 'spa', 'Sp7g07580' => 'spa', 'TAR134G0002' => 'tar', 'TAR236G0001' => 'tar', 'TAR365G0892' => 'tar', 'TAR636G0166' => 'tar', 'TAR636G0646' => 'tar', 'TAR636G0869' => 'tar', 'TAR636G1317' => 'tar', 'TAR636G1744' => 'tar', 'TAR636G3358' => 'tar', 'TAR636G3436' => 'tar', 'THA.LOC104803047' => 'tha', 'Thecc.04G238900' => 'tca', 'Thhalv10021557m.g' => 'esa', 'Thhalv10026318m.g' => 'esa', 'Thhalv10026335m.g' => 'esa', 'TPR.G17433' => 'tpr', 'TPR.G18915' => 'tpr', 'TPR.G26125' => 'tpr', 'TWI09G0677' => 'twi', 'TWI73G0287' => 'twi', 'unitig_748.g8326' => 'ugi', 'vmacro15370' => 'vma', 'vmacro15371' => 'vma', 'vmacro15372' => 'vma', 'vmacro15373' => 'vma', 'vmacro15374' => 'vma', 'VMungo0720G2826' => 'vmu', 'Zm00001eb116960' => 'zma', 'Zm00001eb301260' => 'zma', 'Zm00001eb301270' => 'zma' ) $gf_id = 'HOM05D001460' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001460' ) $data_identifier = 'HOM05D001460' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 4, 'aag' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 2, 'aox' => (int) 2, 'arhy' => (int) 4, 'ath' => (int) 2, 'atr' => (int) 1, 'acertr' => (int) 10, 'cqu' => (int) 4, 'bca' => (int) 11, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 1, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 1, 'ccan' => (int) 1, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 1, 'col' => (int) 1, 'cpa' => (int) 1, 'cre' => (int) 7, 'csa' => (int) 1, 'camsi' => (int) 2, 'dca' => (int) 3, 'din' => (int) 2, 'dzi' => (int) 3, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 14, 'fve' => (int) 9, 'gma' => (int) 2, 'ghi' => (int) 4, 'gra' => (int) 2, 'vvi' => (int) 1, 'han' => (int) 13, 'cav' => (int) 1, 'hma' => (int) 2, 'sun' => (int) 2, 'lal' => (int) 2, 'lonja' => (int) 12, 'lja' => (int) 1, 'lsa' => (int) 7, 'mes' => (int) 1, 'mpo' => (int) 27, 'mbi' => (int) 1, 'mco' => (int) 8, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 1, 'egut' => (int) 1, 'ama' => (int) 1, 'nta' => (int) 4, 'nnu' => (int) 2, 'oeu' => (int) 3, 'osa' => (int) 4, 'pax' => (int) 9, 'pgr' => (int) 1, 'stu' => (int) 1, 'pvu' => (int) 1, 'ptr' => (int) 4, 'ppa' => (int) 22, 'pco' => (int) 6, 'ppe' => (int) 6, 'psa' => (int) 5, 'pso' => (int) 19, 'qlo' => (int) 5, 'rch' => (int) 7, 'rsi' => (int) 20, 'sbr' => (int) 5, 'sbo' => (int) 1, 'sci' => (int) 2, 'sed' => (int) 2, 'sgi' => (int) 12, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 2, 'tar' => (int) 10, 'tha' => (int) 1, 'tca' => (int) 1, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 2, 'ugi' => (int) 1, 'vma' => (int) 5, 'vmu' => (int) 1, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb301270' $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' => 'HOM05D001460', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '433', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p22980' => 'bna', 'A01p32340' => 'bna', 'A03p42970' => 'bna', 'A05p25880' => 'bna', 'Aa31LG8G9320' => 'aar', 'Aa31LG8G9330' => 'aar', 'Aa31LG8G9340' => 'aar', 'Aa31sc221G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1034' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1528' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.829' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2222' => 'aag', 'Ah.12g058830' => 'amhyb', 'Ah.12g058840' => 'amhyb', 'AL3G37160' => 'aly', 'AL7G41310' => 'aly', 'Aqoxy5G00395' => 'aox', 'Aqoxy5G00396' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0C8NZA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5185HY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JZ1PRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MD3LS0' => 'arhy', 'AT3G22840' => 'ath', 'AT4G14690' => 'ath', 'ATR0665G054' => 'atr', 'Atru.chr4.2344' => 'acertr', 'Atru.chr4.2346' => 'acertr', 'Atru.chr4.2347' => 'acertr', 'Atru.chr4.2348' => 'acertr', 'Atru.chr4.2355' => 'acertr', 'Atru.chr4.2356' => 'acertr', 'Atru.chr4.2358' => 'acertr', 'Atru.chr4.2359' => 'acertr', 'Atru.chr4.2360' => 'acertr', 'Atru.chr4.2361' => 'acertr', 'AUR62030476' => 'cqu', 'AUR62030478' => 'cqu', 'AUR62030819' => 'cqu', 'AUR62030820' => 'cqu', 'BcaB03g14648' => 'bca', 'BcaB04g20492' => 'bca', 'BcaB06g26399' => 'bca', 'BcaC01g03416' => 'bca', 'BcaC01g03419' => 'bca', 'BcaC01g03421' => 'bca', 'BcaC01g03424' => 'bca', 'BcaC05g28012' => 'bca', 'BcaC09g49212' => 'bca', 'BcaC09g50140' => 'bca', 'BcaNung00346' => 'bca', 'BolC1t02785H' => 'bol', 'BolC1t04095H' => 'bol', 'BolC3t17545H' => 'bol', 'BolC5t32769H' => 'bol', 'BraA01t02211Z' => 'bra', 'BraA01t03359Z' => 'bra', 'BraA03t13441Z' => 'bra', 'BraA05t21476Z' => 'bra', 'C01p28420' => 'bna', 'C01p41350' => 'bna', 'C03p52750' => 'bna', 'C03p52780' => 'bna', 'C05p40270' => 'bna', 'CAN.G1437.9' => 'can', 'CANSAT78G0035' => 'cansat', 'CANSAT78G1036' => 'cansat', 'CANSAT78G2272' => 'cansat', 'CANSAT78G2478' => 'cansat', 'CARHR098700' => 'chi', 'CARHR221120' => 'chi', 'CARHR221150' => 'chi', 'Carub.0003s2297' => 'cru', 'Carub.0007s2749' => 'cru', 'Carub.0007s2750' => 'cru', 'Carub.0007s2751' => 'cru', 'Ca_10849_v3' => 'car', 'Cc03_g04300' => 'ccan', 'CDE02G3648' => 'cde', 'CDE05G0060' => 'cde', 'CDE05G0692' => 'cde', 'CDE05G2285' => 'cde', 'CDE05G2884' => 'cde', 'CDE05G3072' => 'cde', 'Cfa008439' => 'cfa', 'Cfa008441' => 'cfa', 'Cfa008443' => 'cfa', 'Cfa008448' => 'cfa', 'Ciclev10005974m.g' => 'ccl', 'Ciclev10006006m.g' => 'ccl', 'Ciclev10006775m.g' => 'ccl', 'CiPaw.02G120400' => 'cil', 'CiPaw.02G120500' => 'cil', 'CiPaw.02G120600' => 'cil', 'ClCG05G004850' => 'cla', 'COL.COLO4_21566' => 'col', 'Cpa.g.sc44.124' => 'cpa', 'Cre07.g320400' => 'cre', 'Cre07.g320450' => 'cre', 'Cre08.g384650' => 'cre', 'Cre09.g393173' => 'cre', 'Cre09.g394325' => 'cre', 'Cre14.g626750' => 'cre', 'Cre16.g679250' => 'cre', 'CsaV3_3G012890' => 'csa', 'CSS0010865' => 'camsi', 'CSS0044338' => 'camsi', 'DCAR_002366' => 'dca', 'DCAR_030687' => 'dca', 'DCAR_030688' => 'dca', 'Dinv14047' => 'din', 'Dinv14048' => 'din', 'Duzib151G0105' => 'dzi', 'Duzib151G0114' => 'dzi', 'Duzib212G1029' => 'dzi', 'ECA232G3536' => 'eca', 'ECA240G0786' => 'eca', 'ECA240G1802' => 'eca', 'ECA240G3760' => 'eca', 'ECA240G3920' => 'eca', 'EL10Ac5g12536' => 'bvu', 'EL10Ac5g12537' => 'bvu', 'EL10Ac5g12538' => 'bvu', 'Eucgr.B01004' => 'egr', 'Eucgr.B01006' => 'egr', 'Eucgr.B01007' => 'egr', 'Eucgr.B01008' => 'egr', 'Eucgr.B01895' => 'egr', 'Eucgr.B01896' => 'egr', 'FAN04G1456' => 'fan', 'FAN08G1769' => 'fan', 'FAN08G2160' => 'fan', 'FAN13G2403' => 'fan', 'FAN13G3303' => 'fan', 'FAN15G2435' => 'fan', 'FAN17G0672' => 'fan', 'FAN17G2441' => 'fan', 'FAN18G1024' => 'fan', 'FAN22G1458' => 'fan', 'FAN24G0037' => 'fan', 'FAN24G0429' => 'fan', 'FAN24G2387' => 'fan', 'FAN27G2746' => 'fan', 'FvH4_2g20400' => 'fve', 'FvH4_2g20420' => 'fve', 'FvH4_2g20430' => 'fve', 'FvH4_4g01270' => 'fve', 'FvH4_4g01290' => 'fve', 'FvH4_4g01300' => 'fve', 'FvH4_4g01310' => 'fve', 'FvH4_4g01330' => 'fve', 'FvH4_5g09070' => 'fve', 'Glyma.10G243800' => 'gma', 'Glyma.20G150600' => 'gma', 'Gohir.A09G219200' => 'ghi', 'Gohir.A09G219300' => 'ghi', 'Gohir.D09G221400' => 'ghi', 'Gohir.D09G221500' => 'ghi', 'Gorai.006G242600' => 'gra', 'Gorai.006G242700' => 'gra', 'GSVIVG01018044001' => 'vvi', 'HanXRQChr03g0083821' => 'han', 'HanXRQChr03g0083841' => 'han', 'HanXRQChr03g0083881' => 'han', 'HanXRQChr03g0083901' => 'han', 'HanXRQChr03g0083921' => 'han', 'HanXRQChr03g0085331' => 'han', 'HanXRQChr03g0085361' => 'han', 'HanXRQChr03g0085411' => 'han', 'HanXRQChr03g0085421' => 'han', 'HanXRQChr03g0085431' => 'han', 'HanXRQChr08g0221991' => 'han', 'HanXRQChr11g0336061' => 'han', 'HanXRQChr11g0336411' => 'han', 'Haze_11234' => 'cav', 'Hma1.2p1_0549F.1_g177010' => 'hma', 'Hma1.2p1_0602F.1_g187630' => 'hma', 'Hund14876' => 'sun', 'Hund14879' => 'sun', 'Lalb_Chr06g0160741' => 'lal', 'Lalb_Chr21g0304781' => 'lal', 'Lj3A726G19' => 'lonja', 'Lj3A726T23' => 'lonja', 'Lj3A726T24' => 'lonja', 'Lj3A726T25' => 'lonja', 'Lj3A727T17' => 'lonja', 'Lj3C726T0' => 'lonja', 'Lj3C726T2' => 'lonja', 'Lj3P725T35' => 'lonja', 'Lj3P727T10' => 'lonja', 'Lj3P727T12' => 'lonja', 'Lj3P727T14' => 'lonja', 'Lj5g0023109' => 'lja', 'Lj6P646T44' => 'lonja', 'Lsat_1_v5_gn_6_75760' => 'lsa', 'Lsat_1_v5_gn_6_75800' => 'lsa', 'Lsat_1_v5_gn_6_75900' => 'lsa', 'Lsat_1_v5_gn_6_76240' => 'lsa', 'Lsat_1_v5_gn_6_76441' => 'lsa', 'Lsat_1_v5_gn_6_76700' => 'lsa', 'Lsat_1_v5_gn_6_76760' => 'lsa', 'Manes.15G033100' => 'mes', 'Mapoly0004s0074' => 'mpo', 'Mapoly0004s0075' => 'mpo', 'Mapoly0004s0163' => 'mpo', 'Mapoly0004s0164' => 'mpo', 'Mapoly0021s0018' => 'mpo', 'Mapoly0041s0136' => 'mpo', 'Mapoly0041s0137' => 'mpo', 'Mapoly0041s0138' => 'mpo', 'Mapoly0041s0139' => 'mpo', 'Mapoly0041s0141' => 'mpo', 'Mapoly0041s0142' => 'mpo', 'Mapoly0041s0143' => 'mpo', 'Mapoly0041s0144' => 'mpo', 'Mapoly0041s0145' => 'mpo', 'Mapoly0047s0106' => 'mpo', 'Mapoly0047s0108' => 'mpo', 'Mapoly0050s0051' => 'mpo', 'Mapoly0050s0052' => 'mpo', 'Mapoly0050s0053' => 'mpo', 'Mapoly0058s0013' => 'mpo', 'Mapoly0091s0078' => 'mpo', 'Mapoly0091s0079' => 'mpo', 'Mapoly0091s0080' => 'mpo', 'Mapoly0091s0081' => 'mpo', 'Mapoly0278s0004' => 'mpo', 'Mapoly0278s0005' => 'mpo', 'Mapoly0278s0006' => 'mpo', 'MBI11_g30648_MAGBIO' => 'mbi', 'MCO03G194' => 'mco', 'MCO03G590' => 'mco', 'MCO07G312' => 'mco', 'MCO10G318' => 'mco', 'MCO12G244' => 'mco', 'MCO13G148' => 'mco', 'MCO13G194' => 'mco', 'MCO16G238' => 'mco', 'MD06G1134100' => 'mdo', 'MD13G1200100' => 'mdo', 'MD13G1200300' => 'mdo', 'MD13G1200600' => 'mdo', 'MD14G1150400' => 'mdo', 'MD16G1200000' => 'mdo', 'Medtr1g102570' => 'mtr', 'Medtr1g102780' => 'mtr', 'Medtr1g102800' => 'mtr', 'Medtr1g102810' => 'mtr', 'Medtr1g102830' => 'mtr', 'MELO3C006499.2' => 'cme', 'Migut.G00385' => 'egut', 'MSTRG.4063' => 'ama', 'Nitab4.5_0000090g0260' => 'nta', 'Nitab4.5_0000977g0030' => 'nta', 'Nitab4.5_0002541g0040' => 'nta', 'Nitab4.5_0007068g0040' => 'nta', 'Nn005s41408' => 'nnu', 'Nn005s41410' => 'nnu', 'Oeu010310.1' => 'oeu', 'Oeu010311.1' => 'oeu', 'Oeu043472.1' => 'oeu', 'Os01g0246400' => 'osa', 'Os04g0267950' => 'osa', 'Os07g0178700' => 'osa', 'Os07g0178800' => 'osa', 'Peaxi162Scf00316g00046' => 'pax', 'Peaxi162Scf00316g00049' => 'pax', 'Peaxi162Scf00316g00059' => 'pax', 'Peaxi162Scf00316g00328' => 'pax', 'Peaxi162Scf00316g00329' => 'pax', 'Peaxi162Scf00316g00411' => 'pax', 'Peaxi162Scf00316g00521' => 'pax', 'Peaxi162Scf00492g00068' => 'pax', 'Peaxi162Scf35631g00002' => 'pax', 'PGR142G3720' => 'pgr', 'PGSC0003DMG400006442' => 'stu', 'Phvul.007G062000' => 'pvu', 'Potri.008G157750' => 'ptr', 'Potri.008G157900' => 'ptr', 'Potri.008G158000' => 'ptr', 'Potri.008G158200' => 'ptr', 'Pp3c11_7280' => 'ppa', 'Pp3c11_7980' => 'ppa', 'Pp3c12_19450' => 'ppa', 'Pp3c14_1480' => 'ppa', 'Pp3c14_1501' => 'ppa', 'Pp3c16_4900' => 'ppa', 'Pp3c16_5010' => 'ppa', 'Pp3c16_5060' => 'ppa', 'Pp3c19_18250' => 'ppa', 'Pp3c23_8530' => 'ppa', 'Pp3c23_8550' => 'ppa', 'Pp3c24_9670' => 'ppa', 'Pp3c2_21390' => 'ppa', 'Pp3c2_31380' => 'ppa', 'Pp3c3_16620' => 'ppa', 'Pp3c3_8090' => 'ppa', 'Pp3c3_8110' => 'ppa', 'Pp3c3_8130' => 'ppa', 'Pp3c3_8150' => 'ppa', 'Pp3c4_14320' => 'ppa', 'Pp3c6_2560' => 'ppa', 'Pp3c9_16700' => 'ppa', 'PRCOL_00000234' => 'pco', 'PRCOL_00000235' => 'pco', 'PRCOL_00000777' => 'pco', 'PRCOL_00002344' => 'pco', 'PRCOL_00002372' => 'pco', 'PRCOL_00006120' => 'pco', 'Prupe.1G021400' => 'ppe', 'Prupe.1G021500' => 'ppe', 'Prupe.1G021600' => 'ppe', 'Prupe.1G021700' => 'ppe', 'Prupe.1G021800' => 'ppe', 'Prupe.5G145100' => 'ppe', 'Psat6g204040' => 'psa', 'Psat6g204800' => 'psa', 'Psat6g204920' => 'psa', 'Psat6g204960' => 'psa', 'Psat6g205080' => 'psa', 'PSO017G0271' => 'pso', 'PSO017G1276' => 'pso', 'PSO017G1429' => 'pso', 'PSO017G1861' => 'pso', 'PSO017G2787' => 'pso', 'PSO017G4466' => 'pso', 'PSO017G5118' => 'pso', 'PSO017G5420' => 'pso', 'PSO063G3678' => 'pso', 'PSO210G0546' => 'pso', 'PSO317G0001' => 'pso', 'PSO357G0512' => 'pso', 'PSO478G2682' => 'pso', 'PSO647G0001' => 'pso', 'PSO675G0001' => 'pso', 'PSO675G2699' => 'pso', 'PSO675G2849' => 'pso', 'PSO675G4991' => 'pso', 'PSO689G0001' => 'pso', 'QL06p000916' => 'qlo', 'QL06p000921' => 'qlo', 'QL06p001398' => 'qlo', 'QL06p001407' => 'qlo', 'QL06p002031' => 'qlo', 'RcHm_v2.0_Chr4g0387791' => 'rch', 'RcHm_v2.0_Chr4g0387801' => 'rch', 'RcHm_v2.0_Chr6g0286501' => 'rch', 'RcHm_v2.0_Chr6g0286511' => 'rch', 'RcHm_v2.0_Chr6g0286521' => 'rch', 'RcHm_v2.0_Chr6g0286531' => 'rch', 'RcHm_v2.0_Chr7g0189141' => 'rch', 'Rhsim02G0028700' => 'rsi', 'Rhsim02G0028800' => 'rsi', 'Rhsim02G0028900' => 'rsi', 'Rhsim02G0029000' => 'rsi', 'Rhsim02G0029100' => 'rsi', 'Rhsim02G0029200' => 'rsi', 'Rhsim02G0029300' => 'rsi', 'Rhsim02G0029400' => 'rsi', 'Rhsim02G0029500' => 'rsi', 'Rhsim02G0029600' => 'rsi', 'RhsimUnG0024000' => 'rsi', 'RhsimUnG0024100' => 'rsi', 'RhsimUnG0024200' => 'rsi', 'RhsimUnG0024300' => 'rsi', 'RhsimUnG0024400' => 'rsi', 'RhsimUnG0024500' => 'rsi', 'RhsimUnG0024700' => 'rsi', 'RhsimUnG0024800' => 'rsi', 'RhsimUnG0024900' => 'rsi', 'RhsimUnG0025100' => 'rsi', 'Sabra08G0120200' => 'sbr', 'Sabra08G0120300' => 'sbr', 'Sabra08G0120500' => 'sbr', 'Sabra08G0120600' => 'sbr', 'Sabra10G0158900' => 'sbr', 'SalBow2G3492' => 'sbo', 'Sc13g0004760' => 'sci', 'Sc13g0004770' => 'sci', 'Sed0003417' => 'sed', 'Sed0019750' => 'sed', 'SEGI_03419' => 'sgi', 'SEGI_05907' => 'sgi', 'SEGI_10682' => 'sgi', 'SEGI_13528' => 'sgi', 'SEGI_16081' => 'sgi', 'SEGI_19370' => 'sgi', 'SEGI_21015' => 'sgi', 'SEGI_21944' => 'sgi', 'SEGI_32906' => 'sgi', 'SEGI_33093' => 'sgi', 'SEGI_36110' => 'sgi', 'SEGI_40397' => 'sgi', 'SGA_v2.0_scaffold191G40426' => 'sas', 'SGA_v2.0_scaffold353G49717' => 'sas', 'SGA_v2.0_scaffold50G18550' => 'sas', 'SMO119G0173' => 'smo', 'SMO172G0002' => 'smo', 'Solyc09g082690.3' => 'sly', 'Solyc09g082700.2' => 'sly', 'Sopen09g031550' => 'spe', 'Sopen09g031560' => 'spe', 'Sp3g20540' => 'spa', 'Sp7g07580' => 'spa', 'TAR134G0002' => 'tar', 'TAR236G0001' => 'tar', 'TAR365G0892' => 'tar', 'TAR636G0166' => 'tar', 'TAR636G0646' => 'tar', 'TAR636G0869' => 'tar', 'TAR636G1317' => 'tar', 'TAR636G1744' => 'tar', 'TAR636G3358' => 'tar', 'TAR636G3436' => 'tar', 'THA.LOC104803047' => 'tha', 'Thecc.04G238900' => 'tca', 'Thhalv10021557m.g' => 'esa', 'Thhalv10026318m.g' => 'esa', 'Thhalv10026335m.g' => 'esa', 'TPR.G17433' => 'tpr', 'TPR.G18915' => 'tpr', 'TPR.G26125' => 'tpr', 'TWI09G0677' => 'twi', 'TWI73G0287' => 'twi', 'unitig_748.g8326' => 'ugi', 'vmacro15370' => 'vma', 'vmacro15371' => 'vma', 'vmacro15372' => 'vma', 'vmacro15373' => 'vma', 'vmacro15374' => 'vma', 'VMungo0720G2826' => 'vmu', 'Zm00001eb116960' => 'zma', 'Zm00001eb301260' => 'zma', 'Zm00001eb301270' => 'zma' ), 'gf_id' => 'HOM05D001460', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001460' ), 'data_identifier' => 'HOM05D001460', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001460', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '433', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p22980' => 'bna', 'A01p32340' => 'bna', 'A03p42970' => 'bna', 'A05p25880' => 'bna', 'Aa31LG8G9320' => 'aar', 'Aa31LG8G9330' => 'aar', 'Aa31LG8G9340' => 'aar', 'Aa31sc221G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1034' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1528' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.829' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2222' => 'aag', 'Ah.12g058830' => 'amhyb', 'Ah.12g058840' => 'amhyb', 'AL3G37160' => 'aly', 'AL7G41310' => 'aly', 'Aqoxy5G00395' => 'aox', 'Aqoxy5G00396' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0C8NZA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5185HY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JZ1PRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MD3LS0' => 'arhy', 'AT3G22840' => 'ath', 'AT4G14690' => 'ath', 'ATR0665G054' => 'atr', 'Atru.chr4.2344' => 'acertr', 'Atru.chr4.2346' => 'acertr', 'Atru.chr4.2347' => 'acertr', 'Atru.chr4.2348' => 'acertr', 'Atru.chr4.2355' => 'acertr', 'Atru.chr4.2356' => 'acertr', 'Atru.chr4.2358' => 'acertr', 'Atru.chr4.2359' => 'acertr', 'Atru.chr4.2360' => 'acertr', 'Atru.chr4.2361' => 'acertr', 'AUR62030476' => 'cqu', 'AUR62030478' => 'cqu', 'AUR62030819' => 'cqu', 'AUR62030820' => 'cqu', 'BcaB03g14648' => 'bca', 'BcaB04g20492' => 'bca', 'BcaB06g26399' => 'bca', 'BcaC01g03416' => 'bca', 'BcaC01g03419' => 'bca', 'BcaC01g03421' => 'bca', 'BcaC01g03424' => 'bca', 'BcaC05g28012' => 'bca', 'BcaC09g49212' => 'bca', 'BcaC09g50140' => 'bca', 'BcaNung00346' => 'bca', 'BolC1t02785H' => 'bol', 'BolC1t04095H' => 'bol', 'BolC3t17545H' => 'bol', 'BolC5t32769H' => 'bol', 'BraA01t02211Z' => 'bra', 'BraA01t03359Z' => 'bra', 'BraA03t13441Z' => 'bra', 'BraA05t21476Z' => 'bra', 'C01p28420' => 'bna', 'C01p41350' => 'bna', 'C03p52750' => 'bna', 'C03p52780' => 'bna', 'C05p40270' => 'bna', 'CAN.G1437.9' => 'can', 'CANSAT78G0035' => 'cansat', 'CANSAT78G1036' => 'cansat', 'CANSAT78G2272' => 'cansat', 'CANSAT78G2478' => 'cansat', 'CARHR098700' => 'chi', 'CARHR221120' => 'chi', 'CARHR221150' => 'chi', 'Carub.0003s2297' => 'cru', 'Carub.0007s2749' => 'cru', 'Carub.0007s2750' => 'cru', 'Carub.0007s2751' => 'cru', 'Ca_10849_v3' => 'car', 'Cc03_g04300' => 'ccan', 'CDE02G3648' => 'cde', 'CDE05G0060' => 'cde', 'CDE05G0692' => 'cde', 'CDE05G2285' => 'cde', 'CDE05G2884' => 'cde', 'CDE05G3072' => 'cde', 'Cfa008439' => 'cfa', 'Cfa008441' => 'cfa', 'Cfa008443' => 'cfa', 'Cfa008448' => 'cfa', 'Ciclev10005974m.g' => 'ccl', 'Ciclev10006006m.g' => 'ccl', 'Ciclev10006775m.g' => 'ccl', 'CiPaw.02G120400' => 'cil', 'CiPaw.02G120500' => 'cil', 'CiPaw.02G120600' => 'cil', 'ClCG05G004850' => 'cla', 'COL.COLO4_21566' => 'col', 'Cpa.g.sc44.124' => 'cpa', 'Cre07.g320400' => 'cre', 'Cre07.g320450' => 'cre', 'Cre08.g384650' => 'cre', 'Cre09.g393173' => 'cre', 'Cre09.g394325' => 'cre', 'Cre14.g626750' => 'cre', 'Cre16.g679250' => 'cre', 'CsaV3_3G012890' => 'csa', 'CSS0010865' => 'camsi', 'CSS0044338' => 'camsi', 'DCAR_002366' => 'dca', 'DCAR_030687' => 'dca', 'DCAR_030688' => 'dca', 'Dinv14047' => 'din', 'Dinv14048' => 'din', 'Duzib151G0105' => 'dzi', 'Duzib151G0114' => 'dzi', 'Duzib212G1029' => 'dzi', 'ECA232G3536' => 'eca', 'ECA240G0786' => 'eca', 'ECA240G1802' => 'eca', 'ECA240G3760' => 'eca', 'ECA240G3920' => 'eca', 'EL10Ac5g12536' => 'bvu', 'EL10Ac5g12537' => 'bvu', 'EL10Ac5g12538' => 'bvu', 'Eucgr.B01004' => 'egr', 'Eucgr.B01006' => 'egr', 'Eucgr.B01007' => 'egr', 'Eucgr.B01008' => 'egr', 'Eucgr.B01895' => 'egr', 'Eucgr.B01896' => 'egr', 'FAN04G1456' => 'fan', 'FAN08G1769' => 'fan', 'FAN08G2160' => 'fan', 'FAN13G2403' => 'fan', 'FAN13G3303' => 'fan', 'FAN15G2435' => 'fan', 'FAN17G0672' => 'fan', 'FAN17G2441' => 'fan', 'FAN18G1024' => 'fan', 'FAN22G1458' => 'fan', 'FAN24G0037' => 'fan', 'FAN24G0429' => 'fan', 'FAN24G2387' => 'fan', 'FAN27G2746' => 'fan', 'FvH4_2g20400' => 'fve', 'FvH4_2g20420' => 'fve', 'FvH4_2g20430' => 'fve', 'FvH4_4g01270' => 'fve', 'FvH4_4g01290' => 'fve', 'FvH4_4g01300' => 'fve', 'FvH4_4g01310' => 'fve', 'FvH4_4g01330' => 'fve', 'FvH4_5g09070' => 'fve', 'Glyma.10G243800' => 'gma', 'Glyma.20G150600' => 'gma', 'Gohir.A09G219200' => 'ghi', 'Gohir.A09G219300' => 'ghi', 'Gohir.D09G221400' => 'ghi', 'Gohir.D09G221500' => 'ghi', 'Gorai.006G242600' => 'gra', 'Gorai.006G242700' => 'gra', 'GSVIVG01018044001' => 'vvi', 'HanXRQChr03g0083821' => 'han', 'HanXRQChr03g0083841' => 'han', 'HanXRQChr03g0083881' => 'han', 'HanXRQChr03g0083901' => 'han', 'HanXRQChr03g0083921' => 'han', 'HanXRQChr03g0085331' => 'han', 'HanXRQChr03g0085361' => 'han', 'HanXRQChr03g0085411' => 'han', 'HanXRQChr03g0085421' => 'han', 'HanXRQChr03g0085431' => 'han', 'HanXRQChr08g0221991' => 'han', 'HanXRQChr11g0336061' => 'han', 'HanXRQChr11g0336411' => 'han', 'Haze_11234' => 'cav', 'Hma1.2p1_0549F.1_g177010' => 'hma', 'Hma1.2p1_0602F.1_g187630' => 'hma', 'Hund14876' => 'sun', 'Hund14879' => 'sun', 'Lalb_Chr06g0160741' => 'lal', 'Lalb_Chr21g0304781' => 'lal', 'Lj3A726G19' => 'lonja', 'Lj3A726T23' => 'lonja', 'Lj3A726T24' => 'lonja', 'Lj3A726T25' => 'lonja', 'Lj3A727T17' => 'lonja', 'Lj3C726T0' => 'lonja', 'Lj3C726T2' => 'lonja', 'Lj3P725T35' => 'lonja', 'Lj3P727T10' => 'lonja', 'Lj3P727T12' => 'lonja', 'Lj3P727T14' => 'lonja', 'Lj5g0023109' => 'lja', 'Lj6P646T44' => 'lonja', 'Lsat_1_v5_gn_6_75760' => 'lsa', 'Lsat_1_v5_gn_6_75800' => 'lsa', 'Lsat_1_v5_gn_6_75900' => 'lsa', 'Lsat_1_v5_gn_6_76240' => 'lsa', 'Lsat_1_v5_gn_6_76441' => 'lsa', 'Lsat_1_v5_gn_6_76700' => 'lsa', 'Lsat_1_v5_gn_6_76760' => 'lsa', 'Manes.15G033100' => 'mes', 'Mapoly0004s0074' => 'mpo', 'Mapoly0004s0075' => 'mpo', 'Mapoly0004s0163' => 'mpo', 'Mapoly0004s0164' => 'mpo', 'Mapoly0021s0018' => 'mpo', 'Mapoly0041s0136' => 'mpo', 'Mapoly0041s0137' => 'mpo', 'Mapoly0041s0138' => 'mpo', 'Mapoly0041s0139' => 'mpo', 'Mapoly0041s0141' => 'mpo', 'Mapoly0041s0142' => 'mpo', 'Mapoly0041s0143' => 'mpo', 'Mapoly0041s0144' => 'mpo', 'Mapoly0041s0145' => 'mpo', 'Mapoly0047s0106' => 'mpo', 'Mapoly0047s0108' => 'mpo', 'Mapoly0050s0051' => 'mpo', 'Mapoly0050s0052' => 'mpo', 'Mapoly0050s0053' => 'mpo', 'Mapoly0058s0013' => 'mpo', 'Mapoly0091s0078' => 'mpo', 'Mapoly0091s0079' => 'mpo', 'Mapoly0091s0080' => 'mpo', 'Mapoly0091s0081' => 'mpo', 'Mapoly0278s0004' => 'mpo', 'Mapoly0278s0005' => 'mpo', 'Mapoly0278s0006' => 'mpo', 'MBI11_g30648_MAGBIO' => 'mbi', 'MCO03G194' => 'mco', 'MCO03G590' => 'mco', 'MCO07G312' => 'mco', 'MCO10G318' => 'mco', 'MCO12G244' => 'mco', 'MCO13G148' => 'mco', 'MCO13G194' => 'mco', 'MCO16G238' => 'mco', 'MD06G1134100' => 'mdo', 'MD13G1200100' => 'mdo', 'MD13G1200300' => 'mdo', 'MD13G1200600' => 'mdo', 'MD14G1150400' => 'mdo', 'MD16G1200000' => 'mdo', 'Medtr1g102570' => 'mtr', 'Medtr1g102780' => 'mtr', 'Medtr1g102800' => 'mtr', 'Medtr1g102810' => 'mtr', 'Medtr1g102830' => 'mtr', 'MELO3C006499.2' => 'cme', 'Migut.G00385' => 'egut', 'MSTRG.4063' => 'ama', 'Nitab4.5_0000090g0260' => 'nta', 'Nitab4.5_0000977g0030' => 'nta', 'Nitab4.5_0002541g0040' => 'nta', 'Nitab4.5_0007068g0040' => 'nta', 'Nn005s41408' => 'nnu', 'Nn005s41410' => 'nnu', 'Oeu010310.1' => 'oeu', 'Oeu010311.1' => 'oeu', 'Oeu043472.1' => 'oeu', 'Os01g0246400' => 'osa', 'Os04g0267950' => 'osa', 'Os07g0178700' => 'osa', 'Os07g0178800' => 'osa', 'Peaxi162Scf00316g00046' => 'pax', 'Peaxi162Scf00316g00049' => 'pax', 'Peaxi162Scf00316g00059' => 'pax', 'Peaxi162Scf00316g00328' => 'pax', 'Peaxi162Scf00316g00329' => 'pax', 'Peaxi162Scf00316g00411' => 'pax', 'Peaxi162Scf00316g00521' => 'pax', 'Peaxi162Scf00492g00068' => 'pax', 'Peaxi162Scf35631g00002' => 'pax', 'PGR142G3720' => 'pgr', 'PGSC0003DMG400006442' => 'stu', 'Phvul.007G062000' => 'pvu', 'Potri.008G157750' => 'ptr', 'Potri.008G157900' => 'ptr', 'Potri.008G158000' => 'ptr', 'Potri.008G158200' => 'ptr', 'Pp3c11_7280' => 'ppa', 'Pp3c11_7980' => 'ppa', 'Pp3c12_19450' => 'ppa', 'Pp3c14_1480' => 'ppa', 'Pp3c14_1501' => 'ppa', 'Pp3c16_4900' => 'ppa', 'Pp3c16_5010' => 'ppa', 'Pp3c16_5060' => 'ppa', 'Pp3c19_18250' => 'ppa', 'Pp3c23_8530' => 'ppa', 'Pp3c23_8550' => 'ppa', 'Pp3c24_9670' => 'ppa', 'Pp3c2_21390' => 'ppa', 'Pp3c2_31380' => 'ppa', 'Pp3c3_16620' => 'ppa', 'Pp3c3_8090' => 'ppa', 'Pp3c3_8110' => 'ppa', 'Pp3c3_8130' => 'ppa', 'Pp3c3_8150' => 'ppa', 'Pp3c4_14320' => 'ppa', 'Pp3c6_2560' => 'ppa', 'Pp3c9_16700' => 'ppa', 'PRCOL_00000234' => 'pco', 'PRCOL_00000235' => 'pco', 'PRCOL_00000777' => 'pco', 'PRCOL_00002344' => 'pco', 'PRCOL_00002372' => 'pco', 'PRCOL_00006120' => 'pco', 'Prupe.1G021400' => 'ppe', 'Prupe.1G021500' => 'ppe', 'Prupe.1G021600' => 'ppe', 'Prupe.1G021700' => 'ppe', 'Prupe.1G021800' => 'ppe', 'Prupe.5G145100' => 'ppe', 'Psat6g204040' => 'psa', 'Psat6g204800' => 'psa', 'Psat6g204920' => 'psa', 'Psat6g204960' => 'psa', 'Psat6g205080' => 'psa', 'PSO017G0271' => 'pso', 'PSO017G1276' => 'pso', 'PSO017G1429' => 'pso', 'PSO017G1861' => 'pso', 'PSO017G2787' => 'pso', 'PSO017G4466' => 'pso', 'PSO017G5118' => 'pso', 'PSO017G5420' => 'pso', 'PSO063G3678' => 'pso', 'PSO210G0546' => 'pso', 'PSO317G0001' => 'pso', 'PSO357G0512' => 'pso', 'PSO478G2682' => 'pso', 'PSO647G0001' => 'pso', 'PSO675G0001' => 'pso', 'PSO675G2699' => 'pso', 'PSO675G2849' => 'pso', 'PSO675G4991' => 'pso', 'PSO689G0001' => 'pso', 'QL06p000916' => 'qlo', 'QL06p000921' => 'qlo', 'QL06p001398' => 'qlo', 'QL06p001407' => 'qlo', 'QL06p002031' => 'qlo', 'RcHm_v2.0_Chr4g0387791' => 'rch', 'RcHm_v2.0_Chr4g0387801' => 'rch', 'RcHm_v2.0_Chr6g0286501' => 'rch', 'RcHm_v2.0_Chr6g0286511' => 'rch', 'RcHm_v2.0_Chr6g0286521' => 'rch', 'RcHm_v2.0_Chr6g0286531' => 'rch', 'RcHm_v2.0_Chr7g0189141' => 'rch', 'Rhsim02G0028700' => 'rsi', 'Rhsim02G0028800' => 'rsi', 'Rhsim02G0028900' => 'rsi', 'Rhsim02G0029000' => 'rsi', 'Rhsim02G0029100' => 'rsi', 'Rhsim02G0029200' => 'rsi', 'Rhsim02G0029300' => 'rsi', 'Rhsim02G0029400' => 'rsi', 'Rhsim02G0029500' => 'rsi', 'Rhsim02G0029600' => 'rsi', 'RhsimUnG0024000' => 'rsi', 'RhsimUnG0024100' => 'rsi', 'RhsimUnG0024200' => 'rsi', 'RhsimUnG0024300' => 'rsi', 'RhsimUnG0024400' => 'rsi', 'RhsimUnG0024500' => 'rsi', 'RhsimUnG0024700' => 'rsi', 'RhsimUnG0024800' => 'rsi', 'RhsimUnG0024900' => 'rsi', 'RhsimUnG0025100' => 'rsi', 'Sabra08G0120200' => 'sbr', 'Sabra08G0120300' => 'sbr', 'Sabra08G0120500' => 'sbr', 'Sabra08G0120600' => 'sbr', 'Sabra10G0158900' => 'sbr', 'SalBow2G3492' => 'sbo', 'Sc13g0004760' => 'sci', 'Sc13g0004770' => 'sci', 'Sed0003417' => 'sed', 'Sed0019750' => 'sed', 'SEGI_03419' => 'sgi', 'SEGI_05907' => 'sgi', 'SEGI_10682' => 'sgi', 'SEGI_13528' => 'sgi', 'SEGI_16081' => 'sgi', 'SEGI_19370' => 'sgi', 'SEGI_21015' => 'sgi', 'SEGI_21944' => 'sgi', 'SEGI_32906' => 'sgi', 'SEGI_33093' => 'sgi', 'SEGI_36110' => 'sgi', 'SEGI_40397' => 'sgi', 'SGA_v2.0_scaffold191G40426' => 'sas', 'SGA_v2.0_scaffold353G49717' => 'sas', 'SGA_v2.0_scaffold50G18550' => 'sas', 'SMO119G0173' => 'smo', 'SMO172G0002' => 'smo', 'Solyc09g082690.3' => 'sly', 'Solyc09g082700.2' => 'sly', 'Sopen09g031550' => 'spe', 'Sopen09g031560' => 'spe', 'Sp3g20540' => 'spa', 'Sp7g07580' => 'spa', 'TAR134G0002' => 'tar', 'TAR236G0001' => 'tar', 'TAR365G0892' => 'tar', 'TAR636G0166' => 'tar', 'TAR636G0646' => 'tar', 'TAR636G0869' => 'tar', 'TAR636G1317' => 'tar', 'TAR636G1744' => 'tar', 'TAR636G3358' => 'tar', 'TAR636G3436' => 'tar', 'THA.LOC104803047' => 'tha', 'Thecc.04G238900' => 'tca', 'Thhalv10021557m.g' => 'esa', 'Thhalv10026318m.g' => 'esa', 'Thhalv10026335m.g' => 'esa', 'TPR.G17433' => 'tpr', 'TPR.G18915' => 'tpr', 'TPR.G26125' => 'tpr', 'TWI09G0677' => 'twi', 'TWI73G0287' => 'twi', 'unitig_748.g8326' => 'ugi', 'vmacro15370' => 'vma', 'vmacro15371' => 'vma', 'vmacro15372' => 'vma', 'vmacro15373' => 'vma', 'vmacro15374' => 'vma', 'VMungo0720G2826' => 'vmu', 'Zm00001eb116960' => 'zma', 'Zm00001eb301260' => 'zma', 'Zm00001eb301270' => 'zma' ) $gf_id = 'HOM05D001460' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001460' ) $data_identifier = 'HOM05D001460' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 4, 'aag' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 2, 'aox' => (int) 2, 'arhy' => (int) 4, 'ath' => (int) 2, 'atr' => (int) 1, 'acertr' => (int) 10, 'cqu' => (int) 4, 'bca' => (int) 11, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 1, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 1, 'ccan' => (int) 1, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 1, 'col' => (int) 1, 'cpa' => (int) 1, 'cre' => (int) 7, 'csa' => (int) 1, 'camsi' => (int) 2, 'dca' => (int) 3, 'din' => (int) 2, 'dzi' => (int) 3, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 14, 'fve' => (int) 9, 'gma' => (int) 2, 'ghi' => (int) 4, 'gra' => (int) 2, 'vvi' => (int) 1, 'han' => (int) 13, 'cav' => (int) 1, 'hma' => (int) 2, 'sun' => (int) 2, 'lal' => (int) 2, 'lonja' => (int) 12, 'lja' => (int) 1, 'lsa' => (int) 7, 'mes' => (int) 1, 'mpo' => (int) 27, 'mbi' => (int) 1, 'mco' => (int) 8, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 1, 'egut' => (int) 1, 'ama' => (int) 1, 'nta' => (int) 4, 'nnu' => (int) 2, 'oeu' => (int) 3, 'osa' => (int) 4, 'pax' => (int) 9, 'pgr' => (int) 1, 'stu' => (int) 1, 'pvu' => (int) 1, 'ptr' => (int) 4, 'ppa' => (int) 22, 'pco' => (int) 6, 'ppe' => (int) 6, 'psa' => (int) 5, 'pso' => (int) 19, 'qlo' => (int) 5, 'rch' => (int) 7, 'rsi' => (int) 20, 'sbr' => (int) 5, 'sbo' => (int) 1, 'sci' => (int) 2, 'sed' => (int) 2, 'sgi' => (int) 12, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 2, 'tar' => (int) 10, 'tha' => (int) 1, 'tca' => (int) 1, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 2, 'ugi' => (int) 1, 'vma' => (int) 5, 'vmu' => (int) 1, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb301270' $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' => 'HOM05D001460', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '433', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p22980' => 'bna', 'A01p32340' => 'bna', 'A03p42970' => 'bna', 'A05p25880' => 'bna', 'Aa31LG8G9320' => 'aar', 'Aa31LG8G9330' => 'aar', 'Aa31LG8G9340' => 'aar', 'Aa31sc221G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1034' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1528' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.829' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2222' => 'aag', 'Ah.12g058830' => 'amhyb', 'Ah.12g058840' => 'amhyb', 'AL3G37160' => 'aly', 'AL7G41310' => 'aly', 'Aqoxy5G00395' => 'aox', 'Aqoxy5G00396' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0C8NZA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5185HY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JZ1PRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MD3LS0' => 'arhy', 'AT3G22840' => 'ath', 'AT4G14690' => 'ath', 'ATR0665G054' => 'atr', 'Atru.chr4.2344' => 'acertr', 'Atru.chr4.2346' => 'acertr', 'Atru.chr4.2347' => 'acertr', 'Atru.chr4.2348' => 'acertr', 'Atru.chr4.2355' => 'acertr', 'Atru.chr4.2356' => 'acertr', 'Atru.chr4.2358' => 'acertr', 'Atru.chr4.2359' => 'acertr', 'Atru.chr4.2360' => 'acertr', 'Atru.chr4.2361' => 'acertr', 'AUR62030476' => 'cqu', 'AUR62030478' => 'cqu', 'AUR62030819' => 'cqu', 'AUR62030820' => 'cqu', 'BcaB03g14648' => 'bca', 'BcaB04g20492' => 'bca', 'BcaB06g26399' => 'bca', 'BcaC01g03416' => 'bca', 'BcaC01g03419' => 'bca', 'BcaC01g03421' => 'bca', 'BcaC01g03424' => 'bca', 'BcaC05g28012' => 'bca', 'BcaC09g49212' => 'bca', 'BcaC09g50140' => 'bca', 'BcaNung00346' => 'bca', 'BolC1t02785H' => 'bol', 'BolC1t04095H' => 'bol', 'BolC3t17545H' => 'bol', 'BolC5t32769H' => 'bol', 'BraA01t02211Z' => 'bra', 'BraA01t03359Z' => 'bra', 'BraA03t13441Z' => 'bra', 'BraA05t21476Z' => 'bra', 'C01p28420' => 'bna', 'C01p41350' => 'bna', 'C03p52750' => 'bna', 'C03p52780' => 'bna', 'C05p40270' => 'bna', 'CAN.G1437.9' => 'can', 'CANSAT78G0035' => 'cansat', 'CANSAT78G1036' => 'cansat', 'CANSAT78G2272' => 'cansat', 'CANSAT78G2478' => 'cansat', 'CARHR098700' => 'chi', 'CARHR221120' => 'chi', 'CARHR221150' => 'chi', 'Carub.0003s2297' => 'cru', 'Carub.0007s2749' => 'cru', 'Carub.0007s2750' => 'cru', 'Carub.0007s2751' => 'cru', 'Ca_10849_v3' => 'car', 'Cc03_g04300' => 'ccan', 'CDE02G3648' => 'cde', 'CDE05G0060' => 'cde', 'CDE05G0692' => 'cde', 'CDE05G2285' => 'cde', 'CDE05G2884' => 'cde', 'CDE05G3072' => 'cde', 'Cfa008439' => 'cfa', 'Cfa008441' => 'cfa', 'Cfa008443' => 'cfa', 'Cfa008448' => 'cfa', 'Ciclev10005974m.g' => 'ccl', 'Ciclev10006006m.g' => 'ccl', 'Ciclev10006775m.g' => 'ccl', 'CiPaw.02G120400' => 'cil', 'CiPaw.02G120500' => 'cil', 'CiPaw.02G120600' => 'cil', 'ClCG05G004850' => 'cla', 'COL.COLO4_21566' => 'col', 'Cpa.g.sc44.124' => 'cpa', 'Cre07.g320400' => 'cre', 'Cre07.g320450' => 'cre', 'Cre08.g384650' => 'cre', 'Cre09.g393173' => 'cre', 'Cre09.g394325' => 'cre', 'Cre14.g626750' => 'cre', 'Cre16.g679250' => 'cre', 'CsaV3_3G012890' => 'csa', 'CSS0010865' => 'camsi', 'CSS0044338' => 'camsi', 'DCAR_002366' => 'dca', 'DCAR_030687' => 'dca', 'DCAR_030688' => 'dca', 'Dinv14047' => 'din', 'Dinv14048' => 'din', 'Duzib151G0105' => 'dzi', 'Duzib151G0114' => 'dzi', 'Duzib212G1029' => 'dzi', 'ECA232G3536' => 'eca', 'ECA240G0786' => 'eca', 'ECA240G1802' => 'eca', 'ECA240G3760' => 'eca', 'ECA240G3920' => 'eca', 'EL10Ac5g12536' => 'bvu', 'EL10Ac5g12537' => 'bvu', 'EL10Ac5g12538' => 'bvu', 'Eucgr.B01004' => 'egr', 'Eucgr.B01006' => 'egr', 'Eucgr.B01007' => 'egr', 'Eucgr.B01008' => 'egr', 'Eucgr.B01895' => 'egr', 'Eucgr.B01896' => 'egr', 'FAN04G1456' => 'fan', 'FAN08G1769' => 'fan', 'FAN08G2160' => 'fan', 'FAN13G2403' => 'fan', 'FAN13G3303' => 'fan', 'FAN15G2435' => 'fan', 'FAN17G0672' => 'fan', 'FAN17G2441' => 'fan', 'FAN18G1024' => 'fan', 'FAN22G1458' => 'fan', 'FAN24G0037' => 'fan', 'FAN24G0429' => 'fan', 'FAN24G2387' => 'fan', 'FAN27G2746' => 'fan', 'FvH4_2g20400' => 'fve', 'FvH4_2g20420' => 'fve', 'FvH4_2g20430' => 'fve', 'FvH4_4g01270' => 'fve', 'FvH4_4g01290' => 'fve', 'FvH4_4g01300' => 'fve', 'FvH4_4g01310' => 'fve', 'FvH4_4g01330' => 'fve', 'FvH4_5g09070' => 'fve', 'Glyma.10G243800' => 'gma', 'Glyma.20G150600' => 'gma', 'Gohir.A09G219200' => 'ghi', 'Gohir.A09G219300' => 'ghi', 'Gohir.D09G221400' => 'ghi', 'Gohir.D09G221500' => 'ghi', 'Gorai.006G242600' => 'gra', 'Gorai.006G242700' => 'gra', 'GSVIVG01018044001' => 'vvi', 'HanXRQChr03g0083821' => 'han', 'HanXRQChr03g0083841' => 'han', 'HanXRQChr03g0083881' => 'han', 'HanXRQChr03g0083901' => 'han', 'HanXRQChr03g0083921' => 'han', 'HanXRQChr03g0085331' => 'han', 'HanXRQChr03g0085361' => 'han', 'HanXRQChr03g0085411' => 'han', 'HanXRQChr03g0085421' => 'han', 'HanXRQChr03g0085431' => 'han', 'HanXRQChr08g0221991' => 'han', 'HanXRQChr11g0336061' => 'han', 'HanXRQChr11g0336411' => 'han', 'Haze_11234' => 'cav', 'Hma1.2p1_0549F.1_g177010' => 'hma', 'Hma1.2p1_0602F.1_g187630' => 'hma', 'Hund14876' => 'sun', 'Hund14879' => 'sun', 'Lalb_Chr06g0160741' => 'lal', 'Lalb_Chr21g0304781' => 'lal', 'Lj3A726G19' => 'lonja', 'Lj3A726T23' => 'lonja', 'Lj3A726T24' => 'lonja', 'Lj3A726T25' => 'lonja', 'Lj3A727T17' => 'lonja', 'Lj3C726T0' => 'lonja', 'Lj3C726T2' => 'lonja', 'Lj3P725T35' => 'lonja', 'Lj3P727T10' => 'lonja', 'Lj3P727T12' => 'lonja', 'Lj3P727T14' => 'lonja', 'Lj5g0023109' => 'lja', 'Lj6P646T44' => 'lonja', 'Lsat_1_v5_gn_6_75760' => 'lsa', 'Lsat_1_v5_gn_6_75800' => 'lsa', 'Lsat_1_v5_gn_6_75900' => 'lsa', 'Lsat_1_v5_gn_6_76240' => 'lsa', 'Lsat_1_v5_gn_6_76441' => 'lsa', 'Lsat_1_v5_gn_6_76700' => 'lsa', 'Lsat_1_v5_gn_6_76760' => 'lsa', 'Manes.15G033100' => 'mes', 'Mapoly0004s0074' => 'mpo', 'Mapoly0004s0075' => 'mpo', 'Mapoly0004s0163' => 'mpo', 'Mapoly0004s0164' => 'mpo', 'Mapoly0021s0018' => 'mpo', 'Mapoly0041s0136' => 'mpo', 'Mapoly0041s0137' => 'mpo', 'Mapoly0041s0138' => 'mpo', 'Mapoly0041s0139' => 'mpo', 'Mapoly0041s0141' => 'mpo', 'Mapoly0041s0142' => 'mpo', 'Mapoly0041s0143' => 'mpo', 'Mapoly0041s0144' => 'mpo', 'Mapoly0041s0145' => 'mpo', 'Mapoly0047s0106' => 'mpo', 'Mapoly0047s0108' => 'mpo', 'Mapoly0050s0051' => 'mpo', 'Mapoly0050s0052' => 'mpo', 'Mapoly0050s0053' => 'mpo', 'Mapoly0058s0013' => 'mpo', 'Mapoly0091s0078' => 'mpo', 'Mapoly0091s0079' => 'mpo', 'Mapoly0091s0080' => 'mpo', 'Mapoly0091s0081' => 'mpo', 'Mapoly0278s0004' => 'mpo', 'Mapoly0278s0005' => 'mpo', 'Mapoly0278s0006' => 'mpo', 'MBI11_g30648_MAGBIO' => 'mbi', 'MCO03G194' => 'mco', 'MCO03G590' => 'mco', 'MCO07G312' => 'mco', 'MCO10G318' => 'mco', 'MCO12G244' => 'mco', 'MCO13G148' => 'mco', 'MCO13G194' => 'mco', 'MCO16G238' => 'mco', 'MD06G1134100' => 'mdo', 'MD13G1200100' => 'mdo', 'MD13G1200300' => 'mdo', 'MD13G1200600' => 'mdo', 'MD14G1150400' => 'mdo', 'MD16G1200000' => 'mdo', 'Medtr1g102570' => 'mtr', 'Medtr1g102780' => 'mtr', 'Medtr1g102800' => 'mtr', 'Medtr1g102810' => 'mtr', 'Medtr1g102830' => 'mtr', 'MELO3C006499.2' => 'cme', 'Migut.G00385' => 'egut', 'MSTRG.4063' => 'ama', 'Nitab4.5_0000090g0260' => 'nta', 'Nitab4.5_0000977g0030' => 'nta', 'Nitab4.5_0002541g0040' => 'nta', 'Nitab4.5_0007068g0040' => 'nta', 'Nn005s41408' => 'nnu', 'Nn005s41410' => 'nnu', 'Oeu010310.1' => 'oeu', 'Oeu010311.1' => 'oeu', 'Oeu043472.1' => 'oeu', 'Os01g0246400' => 'osa', 'Os04g0267950' => 'osa', 'Os07g0178700' => 'osa', 'Os07g0178800' => 'osa', 'Peaxi162Scf00316g00046' => 'pax', 'Peaxi162Scf00316g00049' => 'pax', 'Peaxi162Scf00316g00059' => 'pax', 'Peaxi162Scf00316g00328' => 'pax', 'Peaxi162Scf00316g00329' => 'pax', 'Peaxi162Scf00316g00411' => 'pax', 'Peaxi162Scf00316g00521' => 'pax', 'Peaxi162Scf00492g00068' => 'pax', 'Peaxi162Scf35631g00002' => 'pax', 'PGR142G3720' => 'pgr', 'PGSC0003DMG400006442' => 'stu', 'Phvul.007G062000' => 'pvu', 'Potri.008G157750' => 'ptr', 'Potri.008G157900' => 'ptr', 'Potri.008G158000' => 'ptr', 'Potri.008G158200' => 'ptr', 'Pp3c11_7280' => 'ppa', 'Pp3c11_7980' => 'ppa', 'Pp3c12_19450' => 'ppa', 'Pp3c14_1480' => 'ppa', 'Pp3c14_1501' => 'ppa', 'Pp3c16_4900' => 'ppa', 'Pp3c16_5010' => 'ppa', 'Pp3c16_5060' => 'ppa', 'Pp3c19_18250' => 'ppa', 'Pp3c23_8530' => 'ppa', 'Pp3c23_8550' => 'ppa', 'Pp3c24_9670' => 'ppa', 'Pp3c2_21390' => 'ppa', 'Pp3c2_31380' => 'ppa', 'Pp3c3_16620' => 'ppa', 'Pp3c3_8090' => 'ppa', 'Pp3c3_8110' => 'ppa', 'Pp3c3_8130' => 'ppa', 'Pp3c3_8150' => 'ppa', 'Pp3c4_14320' => 'ppa', 'Pp3c6_2560' => 'ppa', 'Pp3c9_16700' => 'ppa', 'PRCOL_00000234' => 'pco', 'PRCOL_00000235' => 'pco', 'PRCOL_00000777' => 'pco', 'PRCOL_00002344' => 'pco', 'PRCOL_00002372' => 'pco', 'PRCOL_00006120' => 'pco', 'Prupe.1G021400' => 'ppe', 'Prupe.1G021500' => 'ppe', 'Prupe.1G021600' => 'ppe', 'Prupe.1G021700' => 'ppe', 'Prupe.1G021800' => 'ppe', 'Prupe.5G145100' => 'ppe', 'Psat6g204040' => 'psa', 'Psat6g204800' => 'psa', 'Psat6g204920' => 'psa', 'Psat6g204960' => 'psa', 'Psat6g205080' => 'psa', 'PSO017G0271' => 'pso', 'PSO017G1276' => 'pso', 'PSO017G1429' => 'pso', 'PSO017G1861' => 'pso', 'PSO017G2787' => 'pso', 'PSO017G4466' => 'pso', 'PSO017G5118' => 'pso', 'PSO017G5420' => 'pso', 'PSO063G3678' => 'pso', 'PSO210G0546' => 'pso', 'PSO317G0001' => 'pso', 'PSO357G0512' => 'pso', 'PSO478G2682' => 'pso', 'PSO647G0001' => 'pso', 'PSO675G0001' => 'pso', 'PSO675G2699' => 'pso', 'PSO675G2849' => 'pso', 'PSO675G4991' => 'pso', 'PSO689G0001' => 'pso', 'QL06p000916' => 'qlo', 'QL06p000921' => 'qlo', 'QL06p001398' => 'qlo', 'QL06p001407' => 'qlo', 'QL06p002031' => 'qlo', 'RcHm_v2.0_Chr4g0387791' => 'rch', 'RcHm_v2.0_Chr4g0387801' => 'rch', 'RcHm_v2.0_Chr6g0286501' => 'rch', 'RcHm_v2.0_Chr6g0286511' => 'rch', 'RcHm_v2.0_Chr6g0286521' => 'rch', 'RcHm_v2.0_Chr6g0286531' => 'rch', 'RcHm_v2.0_Chr7g0189141' => 'rch', 'Rhsim02G0028700' => 'rsi', 'Rhsim02G0028800' => 'rsi', 'Rhsim02G0028900' => 'rsi', 'Rhsim02G0029000' => 'rsi', 'Rhsim02G0029100' => 'rsi', 'Rhsim02G0029200' => 'rsi', 'Rhsim02G0029300' => 'rsi', 'Rhsim02G0029400' => 'rsi', 'Rhsim02G0029500' => 'rsi', 'Rhsim02G0029600' => 'rsi', 'RhsimUnG0024000' => 'rsi', 'RhsimUnG0024100' => 'rsi', 'RhsimUnG0024200' => 'rsi', 'RhsimUnG0024300' => 'rsi', 'RhsimUnG0024400' => 'rsi', 'RhsimUnG0024500' => 'rsi', 'RhsimUnG0024700' => 'rsi', 'RhsimUnG0024800' => 'rsi', 'RhsimUnG0024900' => 'rsi', 'RhsimUnG0025100' => 'rsi', 'Sabra08G0120200' => 'sbr', 'Sabra08G0120300' => 'sbr', 'Sabra08G0120500' => 'sbr', 'Sabra08G0120600' => 'sbr', 'Sabra10G0158900' => 'sbr', 'SalBow2G3492' => 'sbo', 'Sc13g0004760' => 'sci', 'Sc13g0004770' => 'sci', 'Sed0003417' => 'sed', 'Sed0019750' => 'sed', 'SEGI_03419' => 'sgi', 'SEGI_05907' => 'sgi', 'SEGI_10682' => 'sgi', 'SEGI_13528' => 'sgi', 'SEGI_16081' => 'sgi', 'SEGI_19370' => 'sgi', 'SEGI_21015' => 'sgi', 'SEGI_21944' => 'sgi', 'SEGI_32906' => 'sgi', 'SEGI_33093' => 'sgi', 'SEGI_36110' => 'sgi', 'SEGI_40397' => 'sgi', 'SGA_v2.0_scaffold191G40426' => 'sas', 'SGA_v2.0_scaffold353G49717' => 'sas', 'SGA_v2.0_scaffold50G18550' => 'sas', 'SMO119G0173' => 'smo', 'SMO172G0002' => 'smo', 'Solyc09g082690.3' => 'sly', 'Solyc09g082700.2' => 'sly', 'Sopen09g031550' => 'spe', 'Sopen09g031560' => 'spe', 'Sp3g20540' => 'spa', 'Sp7g07580' => 'spa', 'TAR134G0002' => 'tar', 'TAR236G0001' => 'tar', 'TAR365G0892' => 'tar', 'TAR636G0166' => 'tar', 'TAR636G0646' => 'tar', 'TAR636G0869' => 'tar', 'TAR636G1317' => 'tar', 'TAR636G1744' => 'tar', 'TAR636G3358' => 'tar', 'TAR636G3436' => 'tar', 'THA.LOC104803047' => 'tha', 'Thecc.04G238900' => 'tca', 'Thhalv10021557m.g' => 'esa', 'Thhalv10026318m.g' => 'esa', 'Thhalv10026335m.g' => 'esa', 'TPR.G17433' => 'tpr', 'TPR.G18915' => 'tpr', 'TPR.G26125' => 'tpr', 'TWI09G0677' => 'twi', 'TWI73G0287' => 'twi', 'unitig_748.g8326' => 'ugi', 'vmacro15370' => 'vma', 'vmacro15371' => 'vma', 'vmacro15372' => 'vma', 'vmacro15373' => 'vma', 'vmacro15374' => 'vma', 'VMungo0720G2826' => 'vmu', 'Zm00001eb116960' => 'zma', 'Zm00001eb301260' => 'zma', 'Zm00001eb301270' => 'zma' ), 'gf_id' => 'HOM05D001460', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001460' ), 'data_identifier' => 'HOM05D001460', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001460', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '433', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p22980' => 'bna', 'A01p32340' => 'bna', 'A03p42970' => 'bna', 'A05p25880' => 'bna', 'Aa31LG8G9320' => 'aar', 'Aa31LG8G9330' => 'aar', 'Aa31LG8G9340' => 'aar', 'Aa31sc221G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1034' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1528' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.829' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2222' => 'aag', 'Ah.12g058830' => 'amhyb', 'Ah.12g058840' => 'amhyb', 'AL3G37160' => 'aly', 'AL7G41310' => 'aly', 'Aqoxy5G00395' => 'aox', 'Aqoxy5G00396' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0C8NZA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5185HY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JZ1PRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MD3LS0' => 'arhy', 'AT3G22840' => 'ath', 'AT4G14690' => 'ath', 'ATR0665G054' => 'atr', 'Atru.chr4.2344' => 'acertr', 'Atru.chr4.2346' => 'acertr', 'Atru.chr4.2347' => 'acertr', 'Atru.chr4.2348' => 'acertr', 'Atru.chr4.2355' => 'acertr', 'Atru.chr4.2356' => 'acertr', 'Atru.chr4.2358' => 'acertr', 'Atru.chr4.2359' => 'acertr', 'Atru.chr4.2360' => 'acertr', 'Atru.chr4.2361' => 'acertr', 'AUR62030476' => 'cqu', 'AUR62030478' => 'cqu', 'AUR62030819' => 'cqu', 'AUR62030820' => 'cqu', 'BcaB03g14648' => 'bca', 'BcaB04g20492' => 'bca', 'BcaB06g26399' => 'bca', 'BcaC01g03416' => 'bca', 'BcaC01g03419' => 'bca', 'BcaC01g03421' => 'bca', 'BcaC01g03424' => 'bca', 'BcaC05g28012' => 'bca', 'BcaC09g49212' => 'bca', 'BcaC09g50140' => 'bca', 'BcaNung00346' => 'bca', 'BolC1t02785H' => 'bol', 'BolC1t04095H' => 'bol', 'BolC3t17545H' => 'bol', 'BolC5t32769H' => 'bol', 'BraA01t02211Z' => 'bra', 'BraA01t03359Z' => 'bra', 'BraA03t13441Z' => 'bra', 'BraA05t21476Z' => 'bra', 'C01p28420' => 'bna', 'C01p41350' => 'bna', 'C03p52750' => 'bna', 'C03p52780' => 'bna', 'C05p40270' => 'bna', 'CAN.G1437.9' => 'can', 'CANSAT78G0035' => 'cansat', 'CANSAT78G1036' => 'cansat', 'CANSAT78G2272' => 'cansat', 'CANSAT78G2478' => 'cansat', 'CARHR098700' => 'chi', 'CARHR221120' => 'chi', 'CARHR221150' => 'chi', 'Carub.0003s2297' => 'cru', 'Carub.0007s2749' => 'cru', 'Carub.0007s2750' => 'cru', 'Carub.0007s2751' => 'cru', 'Ca_10849_v3' => 'car', 'Cc03_g04300' => 'ccan', 'CDE02G3648' => 'cde', 'CDE05G0060' => 'cde', 'CDE05G0692' => 'cde', 'CDE05G2285' => 'cde', 'CDE05G2884' => 'cde', 'CDE05G3072' => 'cde', 'Cfa008439' => 'cfa', 'Cfa008441' => 'cfa', 'Cfa008443' => 'cfa', 'Cfa008448' => 'cfa', 'Ciclev10005974m.g' => 'ccl', 'Ciclev10006006m.g' => 'ccl', 'Ciclev10006775m.g' => 'ccl', 'CiPaw.02G120400' => 'cil', 'CiPaw.02G120500' => 'cil', 'CiPaw.02G120600' => 'cil', 'ClCG05G004850' => 'cla', 'COL.COLO4_21566' => 'col', 'Cpa.g.sc44.124' => 'cpa', 'Cre07.g320400' => 'cre', 'Cre07.g320450' => 'cre', 'Cre08.g384650' => 'cre', 'Cre09.g393173' => 'cre', 'Cre09.g394325' => 'cre', 'Cre14.g626750' => 'cre', 'Cre16.g679250' => 'cre', 'CsaV3_3G012890' => 'csa', 'CSS0010865' => 'camsi', 'CSS0044338' => 'camsi', 'DCAR_002366' => 'dca', 'DCAR_030687' => 'dca', 'DCAR_030688' => 'dca', 'Dinv14047' => 'din', 'Dinv14048' => 'din', 'Duzib151G0105' => 'dzi', 'Duzib151G0114' => 'dzi', 'Duzib212G1029' => 'dzi', 'ECA232G3536' => 'eca', 'ECA240G0786' => 'eca', 'ECA240G1802' => 'eca', 'ECA240G3760' => 'eca', 'ECA240G3920' => 'eca', 'EL10Ac5g12536' => 'bvu', 'EL10Ac5g12537' => 'bvu', 'EL10Ac5g12538' => 'bvu', 'Eucgr.B01004' => 'egr', 'Eucgr.B01006' => 'egr', 'Eucgr.B01007' => 'egr', 'Eucgr.B01008' => 'egr', 'Eucgr.B01895' => 'egr', 'Eucgr.B01896' => 'egr', 'FAN04G1456' => 'fan', 'FAN08G1769' => 'fan', 'FAN08G2160' => 'fan', 'FAN13G2403' => 'fan', 'FAN13G3303' => 'fan', 'FAN15G2435' => 'fan', 'FAN17G0672' => 'fan', 'FAN17G2441' => 'fan', 'FAN18G1024' => 'fan', 'FAN22G1458' => 'fan', 'FAN24G0037' => 'fan', 'FAN24G0429' => 'fan', 'FAN24G2387' => 'fan', 'FAN27G2746' => 'fan', 'FvH4_2g20400' => 'fve', 'FvH4_2g20420' => 'fve', 'FvH4_2g20430' => 'fve', 'FvH4_4g01270' => 'fve', 'FvH4_4g01290' => 'fve', 'FvH4_4g01300' => 'fve', 'FvH4_4g01310' => 'fve', 'FvH4_4g01330' => 'fve', 'FvH4_5g09070' => 'fve', 'Glyma.10G243800' => 'gma', 'Glyma.20G150600' => 'gma', 'Gohir.A09G219200' => 'ghi', 'Gohir.A09G219300' => 'ghi', 'Gohir.D09G221400' => 'ghi', 'Gohir.D09G221500' => 'ghi', 'Gorai.006G242600' => 'gra', 'Gorai.006G242700' => 'gra', 'GSVIVG01018044001' => 'vvi', 'HanXRQChr03g0083821' => 'han', 'HanXRQChr03g0083841' => 'han', 'HanXRQChr03g0083881' => 'han', 'HanXRQChr03g0083901' => 'han', 'HanXRQChr03g0083921' => 'han', 'HanXRQChr03g0085331' => 'han', 'HanXRQChr03g0085361' => 'han', 'HanXRQChr03g0085411' => 'han', 'HanXRQChr03g0085421' => 'han', 'HanXRQChr03g0085431' => 'han', 'HanXRQChr08g0221991' => 'han', 'HanXRQChr11g0336061' => 'han', 'HanXRQChr11g0336411' => 'han', 'Haze_11234' => 'cav', 'Hma1.2p1_0549F.1_g177010' => 'hma', 'Hma1.2p1_0602F.1_g187630' => 'hma', 'Hund14876' => 'sun', 'Hund14879' => 'sun', 'Lalb_Chr06g0160741' => 'lal', 'Lalb_Chr21g0304781' => 'lal', 'Lj3A726G19' => 'lonja', 'Lj3A726T23' => 'lonja', 'Lj3A726T24' => 'lonja', 'Lj3A726T25' => 'lonja', 'Lj3A727T17' => 'lonja', 'Lj3C726T0' => 'lonja', 'Lj3C726T2' => 'lonja', 'Lj3P725T35' => 'lonja', 'Lj3P727T10' => 'lonja', 'Lj3P727T12' => 'lonja', 'Lj3P727T14' => 'lonja', 'Lj5g0023109' => 'lja', 'Lj6P646T44' => 'lonja', 'Lsat_1_v5_gn_6_75760' => 'lsa', 'Lsat_1_v5_gn_6_75800' => 'lsa', 'Lsat_1_v5_gn_6_75900' => 'lsa', 'Lsat_1_v5_gn_6_76240' => 'lsa', 'Lsat_1_v5_gn_6_76441' => 'lsa', 'Lsat_1_v5_gn_6_76700' => 'lsa', 'Lsat_1_v5_gn_6_76760' => 'lsa', 'Manes.15G033100' => 'mes', 'Mapoly0004s0074' => 'mpo', 'Mapoly0004s0075' => 'mpo', 'Mapoly0004s0163' => 'mpo', 'Mapoly0004s0164' => 'mpo', 'Mapoly0021s0018' => 'mpo', 'Mapoly0041s0136' => 'mpo', 'Mapoly0041s0137' => 'mpo', 'Mapoly0041s0138' => 'mpo', 'Mapoly0041s0139' => 'mpo', 'Mapoly0041s0141' => 'mpo', 'Mapoly0041s0142' => 'mpo', 'Mapoly0041s0143' => 'mpo', 'Mapoly0041s0144' => 'mpo', 'Mapoly0041s0145' => 'mpo', 'Mapoly0047s0106' => 'mpo', 'Mapoly0047s0108' => 'mpo', 'Mapoly0050s0051' => 'mpo', 'Mapoly0050s0052' => 'mpo', 'Mapoly0050s0053' => 'mpo', 'Mapoly0058s0013' => 'mpo', 'Mapoly0091s0078' => 'mpo', 'Mapoly0091s0079' => 'mpo', 'Mapoly0091s0080' => 'mpo', 'Mapoly0091s0081' => 'mpo', 'Mapoly0278s0004' => 'mpo', 'Mapoly0278s0005' => 'mpo', 'Mapoly0278s0006' => 'mpo', 'MBI11_g30648_MAGBIO' => 'mbi', 'MCO03G194' => 'mco', 'MCO03G590' => 'mco', 'MCO07G312' => 'mco', 'MCO10G318' => 'mco', 'MCO12G244' => 'mco', 'MCO13G148' => 'mco', 'MCO13G194' => 'mco', 'MCO16G238' => 'mco', 'MD06G1134100' => 'mdo', 'MD13G1200100' => 'mdo', 'MD13G1200300' => 'mdo', 'MD13G1200600' => 'mdo', 'MD14G1150400' => 'mdo', 'MD16G1200000' => 'mdo', 'Medtr1g102570' => 'mtr', 'Medtr1g102780' => 'mtr', 'Medtr1g102800' => 'mtr', 'Medtr1g102810' => 'mtr', 'Medtr1g102830' => 'mtr', 'MELO3C006499.2' => 'cme', 'Migut.G00385' => 'egut', 'MSTRG.4063' => 'ama', 'Nitab4.5_0000090g0260' => 'nta', 'Nitab4.5_0000977g0030' => 'nta', 'Nitab4.5_0002541g0040' => 'nta', 'Nitab4.5_0007068g0040' => 'nta', 'Nn005s41408' => 'nnu', 'Nn005s41410' => 'nnu', 'Oeu010310.1' => 'oeu', 'Oeu010311.1' => 'oeu', 'Oeu043472.1' => 'oeu', 'Os01g0246400' => 'osa', 'Os04g0267950' => 'osa', 'Os07g0178700' => 'osa', 'Os07g0178800' => 'osa', 'Peaxi162Scf00316g00046' => 'pax', 'Peaxi162Scf00316g00049' => 'pax', 'Peaxi162Scf00316g00059' => 'pax', 'Peaxi162Scf00316g00328' => 'pax', 'Peaxi162Scf00316g00329' => 'pax', 'Peaxi162Scf00316g00411' => 'pax', 'Peaxi162Scf00316g00521' => 'pax', 'Peaxi162Scf00492g00068' => 'pax', 'Peaxi162Scf35631g00002' => 'pax', 'PGR142G3720' => 'pgr', 'PGSC0003DMG400006442' => 'stu', 'Phvul.007G062000' => 'pvu', 'Potri.008G157750' => 'ptr', 'Potri.008G157900' => 'ptr', 'Potri.008G158000' => 'ptr', 'Potri.008G158200' => 'ptr', 'Pp3c11_7280' => 'ppa', 'Pp3c11_7980' => 'ppa', 'Pp3c12_19450' => 'ppa', 'Pp3c14_1480' => 'ppa', 'Pp3c14_1501' => 'ppa', 'Pp3c16_4900' => 'ppa', 'Pp3c16_5010' => 'ppa', 'Pp3c16_5060' => 'ppa', 'Pp3c19_18250' => 'ppa', 'Pp3c23_8530' => 'ppa', 'Pp3c23_8550' => 'ppa', 'Pp3c24_9670' => 'ppa', 'Pp3c2_21390' => 'ppa', 'Pp3c2_31380' => 'ppa', 'Pp3c3_16620' => 'ppa', 'Pp3c3_8090' => 'ppa', 'Pp3c3_8110' => 'ppa', 'Pp3c3_8130' => 'ppa', 'Pp3c3_8150' => 'ppa', 'Pp3c4_14320' => 'ppa', 'Pp3c6_2560' => 'ppa', 'Pp3c9_16700' => 'ppa', 'PRCOL_00000234' => 'pco', 'PRCOL_00000235' => 'pco', 'PRCOL_00000777' => 'pco', 'PRCOL_00002344' => 'pco', 'PRCOL_00002372' => 'pco', 'PRCOL_00006120' => 'pco', 'Prupe.1G021400' => 'ppe', 'Prupe.1G021500' => 'ppe', 'Prupe.1G021600' => 'ppe', 'Prupe.1G021700' => 'ppe', 'Prupe.1G021800' => 'ppe', 'Prupe.5G145100' => 'ppe', 'Psat6g204040' => 'psa', 'Psat6g204800' => 'psa', 'Psat6g204920' => 'psa', 'Psat6g204960' => 'psa', 'Psat6g205080' => 'psa', 'PSO017G0271' => 'pso', 'PSO017G1276' => 'pso', 'PSO017G1429' => 'pso', 'PSO017G1861' => 'pso', 'PSO017G2787' => 'pso', 'PSO017G4466' => 'pso', 'PSO017G5118' => 'pso', 'PSO017G5420' => 'pso', 'PSO063G3678' => 'pso', 'PSO210G0546' => 'pso', 'PSO317G0001' => 'pso', 'PSO357G0512' => 'pso', 'PSO478G2682' => 'pso', 'PSO647G0001' => 'pso', 'PSO675G0001' => 'pso', 'PSO675G2699' => 'pso', 'PSO675G2849' => 'pso', 'PSO675G4991' => 'pso', 'PSO689G0001' => 'pso', 'QL06p000916' => 'qlo', 'QL06p000921' => 'qlo', 'QL06p001398' => 'qlo', 'QL06p001407' => 'qlo', 'QL06p002031' => 'qlo', 'RcHm_v2.0_Chr4g0387791' => 'rch', 'RcHm_v2.0_Chr4g0387801' => 'rch', 'RcHm_v2.0_Chr6g0286501' => 'rch', 'RcHm_v2.0_Chr6g0286511' => 'rch', 'RcHm_v2.0_Chr6g0286521' => 'rch', 'RcHm_v2.0_Chr6g0286531' => 'rch', 'RcHm_v2.0_Chr7g0189141' => 'rch', 'Rhsim02G0028700' => 'rsi', 'Rhsim02G0028800' => 'rsi', 'Rhsim02G0028900' => 'rsi', 'Rhsim02G0029000' => 'rsi', 'Rhsim02G0029100' => 'rsi', 'Rhsim02G0029200' => 'rsi', 'Rhsim02G0029300' => 'rsi', 'Rhsim02G0029400' => 'rsi', 'Rhsim02G0029500' => 'rsi', 'Rhsim02G0029600' => 'rsi', 'RhsimUnG0024000' => 'rsi', 'RhsimUnG0024100' => 'rsi', 'RhsimUnG0024200' => 'rsi', 'RhsimUnG0024300' => 'rsi', 'RhsimUnG0024400' => 'rsi', 'RhsimUnG0024500' => 'rsi', 'RhsimUnG0024700' => 'rsi', 'RhsimUnG0024800' => 'rsi', 'RhsimUnG0024900' => 'rsi', 'RhsimUnG0025100' => 'rsi', 'Sabra08G0120200' => 'sbr', 'Sabra08G0120300' => 'sbr', 'Sabra08G0120500' => 'sbr', 'Sabra08G0120600' => 'sbr', 'Sabra10G0158900' => 'sbr', 'SalBow2G3492' => 'sbo', 'Sc13g0004760' => 'sci', 'Sc13g0004770' => 'sci', 'Sed0003417' => 'sed', 'Sed0019750' => 'sed', 'SEGI_03419' => 'sgi', 'SEGI_05907' => 'sgi', 'SEGI_10682' => 'sgi', 'SEGI_13528' => 'sgi', 'SEGI_16081' => 'sgi', 'SEGI_19370' => 'sgi', 'SEGI_21015' => 'sgi', 'SEGI_21944' => 'sgi', 'SEGI_32906' => 'sgi', 'SEGI_33093' => 'sgi', 'SEGI_36110' => 'sgi', 'SEGI_40397' => 'sgi', 'SGA_v2.0_scaffold191G40426' => 'sas', 'SGA_v2.0_scaffold353G49717' => 'sas', 'SGA_v2.0_scaffold50G18550' => 'sas', 'SMO119G0173' => 'smo', 'SMO172G0002' => 'smo', 'Solyc09g082690.3' => 'sly', 'Solyc09g082700.2' => 'sly', 'Sopen09g031550' => 'spe', 'Sopen09g031560' => 'spe', 'Sp3g20540' => 'spa', 'Sp7g07580' => 'spa', 'TAR134G0002' => 'tar', 'TAR236G0001' => 'tar', 'TAR365G0892' => 'tar', 'TAR636G0166' => 'tar', 'TAR636G0646' => 'tar', 'TAR636G0869' => 'tar', 'TAR636G1317' => 'tar', 'TAR636G1744' => 'tar', 'TAR636G3358' => 'tar', 'TAR636G3436' => 'tar', 'THA.LOC104803047' => 'tha', 'Thecc.04G238900' => 'tca', 'Thhalv10021557m.g' => 'esa', 'Thhalv10026318m.g' => 'esa', 'Thhalv10026335m.g' => 'esa', 'TPR.G17433' => 'tpr', 'TPR.G18915' => 'tpr', 'TPR.G26125' => 'tpr', 'TWI09G0677' => 'twi', 'TWI73G0287' => 'twi', 'unitig_748.g8326' => 'ugi', 'vmacro15370' => 'vma', 'vmacro15371' => 'vma', 'vmacro15372' => 'vma', 'vmacro15373' => 'vma', 'vmacro15374' => 'vma', 'VMungo0720G2826' => 'vmu', 'Zm00001eb116960' => 'zma', 'Zm00001eb301260' => 'zma', 'Zm00001eb301270' => 'zma' ) $gf_id = 'HOM05D001460' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001460' ) $data_identifier = 'HOM05D001460' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 4, 'aag' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 2, 'aox' => (int) 2, 'arhy' => (int) 4, 'ath' => (int) 2, 'atr' => (int) 1, 'acertr' => (int) 10, 'cqu' => (int) 4, 'bca' => (int) 11, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 1, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 1, 'ccan' => (int) 1, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 1, 'col' => (int) 1, 'cpa' => (int) 1, 'cre' => (int) 7, 'csa' => (int) 1, 'camsi' => (int) 2, 'dca' => (int) 3, 'din' => (int) 2, 'dzi' => (int) 3, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 14, 'fve' => (int) 9, 'gma' => (int) 2, 'ghi' => (int) 4, 'gra' => (int) 2, 'vvi' => (int) 1, 'han' => (int) 13, 'cav' => (int) 1, 'hma' => (int) 2, 'sun' => (int) 2, 'lal' => (int) 2, 'lonja' => (int) 12, 'lja' => (int) 1, 'lsa' => (int) 7, 'mes' => (int) 1, 'mpo' => (int) 27, 'mbi' => (int) 1, 'mco' => (int) 8, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 1, 'egut' => (int) 1, 'ama' => (int) 1, 'nta' => (int) 4, 'nnu' => (int) 2, 'oeu' => (int) 3, 'osa' => (int) 4, 'pax' => (int) 9, 'pgr' => (int) 1, 'stu' => (int) 1, 'pvu' => (int) 1, 'ptr' => (int) 4, 'ppa' => (int) 22, 'pco' => (int) 6, 'ppe' => (int) 6, 'psa' => (int) 5, 'pso' => (int) 19, 'qlo' => (int) 5, 'rch' => (int) 7, 'rsi' => (int) 20, 'sbr' => (int) 5, 'sbo' => (int) 1, 'sci' => (int) 2, 'sed' => (int) 2, 'sgi' => (int) 12, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 2, 'tar' => (int) 10, 'tha' => (int) 1, 'tca' => (int) 1, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 2, 'ugi' => (int) 1, 'vma' => (int) 5, 'vmu' => (int) 1, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb301270' $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' => 'HOM05D001460', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '433', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p22980' => 'bna', 'A01p32340' => 'bna', 'A03p42970' => 'bna', 'A05p25880' => 'bna', 'Aa31LG8G9320' => 'aar', 'Aa31LG8G9330' => 'aar', 'Aa31LG8G9340' => 'aar', 'Aa31sc221G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1034' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1528' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.829' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2222' => 'aag', 'Ah.12g058830' => 'amhyb', 'Ah.12g058840' => 'amhyb', 'AL3G37160' => 'aly', 'AL7G41310' => 'aly', 'Aqoxy5G00395' => 'aox', 'Aqoxy5G00396' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0C8NZA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5185HY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JZ1PRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MD3LS0' => 'arhy', 'AT3G22840' => 'ath', 'AT4G14690' => 'ath', 'ATR0665G054' => 'atr', 'Atru.chr4.2344' => 'acertr', 'Atru.chr4.2346' => 'acertr', 'Atru.chr4.2347' => 'acertr', 'Atru.chr4.2348' => 'acertr', 'Atru.chr4.2355' => 'acertr', 'Atru.chr4.2356' => 'acertr', 'Atru.chr4.2358' => 'acertr', 'Atru.chr4.2359' => 'acertr', 'Atru.chr4.2360' => 'acertr', 'Atru.chr4.2361' => 'acertr', 'AUR62030476' => 'cqu', 'AUR62030478' => 'cqu', 'AUR62030819' => 'cqu', 'AUR62030820' => 'cqu', 'BcaB03g14648' => 'bca', 'BcaB04g20492' => 'bca', 'BcaB06g26399' => 'bca', 'BcaC01g03416' => 'bca', 'BcaC01g03419' => 'bca', 'BcaC01g03421' => 'bca', 'BcaC01g03424' => 'bca', 'BcaC05g28012' => 'bca', 'BcaC09g49212' => 'bca', 'BcaC09g50140' => 'bca', 'BcaNung00346' => 'bca', 'BolC1t02785H' => 'bol', 'BolC1t04095H' => 'bol', 'BolC3t17545H' => 'bol', 'BolC5t32769H' => 'bol', 'BraA01t02211Z' => 'bra', 'BraA01t03359Z' => 'bra', 'BraA03t13441Z' => 'bra', 'BraA05t21476Z' => 'bra', 'C01p28420' => 'bna', 'C01p41350' => 'bna', 'C03p52750' => 'bna', 'C03p52780' => 'bna', 'C05p40270' => 'bna', 'CAN.G1437.9' => 'can', 'CANSAT78G0035' => 'cansat', 'CANSAT78G1036' => 'cansat', 'CANSAT78G2272' => 'cansat', 'CANSAT78G2478' => 'cansat', 'CARHR098700' => 'chi', 'CARHR221120' => 'chi', 'CARHR221150' => 'chi', 'Carub.0003s2297' => 'cru', 'Carub.0007s2749' => 'cru', 'Carub.0007s2750' => 'cru', 'Carub.0007s2751' => 'cru', 'Ca_10849_v3' => 'car', 'Cc03_g04300' => 'ccan', 'CDE02G3648' => 'cde', 'CDE05G0060' => 'cde', 'CDE05G0692' => 'cde', 'CDE05G2285' => 'cde', 'CDE05G2884' => 'cde', 'CDE05G3072' => 'cde', 'Cfa008439' => 'cfa', 'Cfa008441' => 'cfa', 'Cfa008443' => 'cfa', 'Cfa008448' => 'cfa', 'Ciclev10005974m.g' => 'ccl', 'Ciclev10006006m.g' => 'ccl', 'Ciclev10006775m.g' => 'ccl', 'CiPaw.02G120400' => 'cil', 'CiPaw.02G120500' => 'cil', 'CiPaw.02G120600' => 'cil', 'ClCG05G004850' => 'cla', 'COL.COLO4_21566' => 'col', 'Cpa.g.sc44.124' => 'cpa', 'Cre07.g320400' => 'cre', 'Cre07.g320450' => 'cre', 'Cre08.g384650' => 'cre', 'Cre09.g393173' => 'cre', 'Cre09.g394325' => 'cre', 'Cre14.g626750' => 'cre', 'Cre16.g679250' => 'cre', 'CsaV3_3G012890' => 'csa', 'CSS0010865' => 'camsi', 'CSS0044338' => 'camsi', 'DCAR_002366' => 'dca', 'DCAR_030687' => 'dca', 'DCAR_030688' => 'dca', 'Dinv14047' => 'din', 'Dinv14048' => 'din', 'Duzib151G0105' => 'dzi', 'Duzib151G0114' => 'dzi', 'Duzib212G1029' => 'dzi', 'ECA232G3536' => 'eca', 'ECA240G0786' => 'eca', 'ECA240G1802' => 'eca', 'ECA240G3760' => 'eca', 'ECA240G3920' => 'eca', 'EL10Ac5g12536' => 'bvu', 'EL10Ac5g12537' => 'bvu', 'EL10Ac5g12538' => 'bvu', 'Eucgr.B01004' => 'egr', 'Eucgr.B01006' => 'egr', 'Eucgr.B01007' => 'egr', 'Eucgr.B01008' => 'egr', 'Eucgr.B01895' => 'egr', 'Eucgr.B01896' => 'egr', 'FAN04G1456' => 'fan', 'FAN08G1769' => 'fan', 'FAN08G2160' => 'fan', 'FAN13G2403' => 'fan', 'FAN13G3303' => 'fan', 'FAN15G2435' => 'fan', 'FAN17G0672' => 'fan', 'FAN17G2441' => 'fan', 'FAN18G1024' => 'fan', 'FAN22G1458' => 'fan', 'FAN24G0037' => 'fan', 'FAN24G0429' => 'fan', 'FAN24G2387' => 'fan', 'FAN27G2746' => 'fan', 'FvH4_2g20400' => 'fve', 'FvH4_2g20420' => 'fve', 'FvH4_2g20430' => 'fve', 'FvH4_4g01270' => 'fve', 'FvH4_4g01290' => 'fve', 'FvH4_4g01300' => 'fve', 'FvH4_4g01310' => 'fve', 'FvH4_4g01330' => 'fve', 'FvH4_5g09070' => 'fve', 'Glyma.10G243800' => 'gma', 'Glyma.20G150600' => 'gma', 'Gohir.A09G219200' => 'ghi', 'Gohir.A09G219300' => 'ghi', 'Gohir.D09G221400' => 'ghi', 'Gohir.D09G221500' => 'ghi', 'Gorai.006G242600' => 'gra', 'Gorai.006G242700' => 'gra', 'GSVIVG01018044001' => 'vvi', 'HanXRQChr03g0083821' => 'han', 'HanXRQChr03g0083841' => 'han', 'HanXRQChr03g0083881' => 'han', 'HanXRQChr03g0083901' => 'han', 'HanXRQChr03g0083921' => 'han', 'HanXRQChr03g0085331' => 'han', 'HanXRQChr03g0085361' => 'han', 'HanXRQChr03g0085411' => 'han', 'HanXRQChr03g0085421' => 'han', 'HanXRQChr03g0085431' => 'han', 'HanXRQChr08g0221991' => 'han', 'HanXRQChr11g0336061' => 'han', 'HanXRQChr11g0336411' => 'han', 'Haze_11234' => 'cav', 'Hma1.2p1_0549F.1_g177010' => 'hma', 'Hma1.2p1_0602F.1_g187630' => 'hma', 'Hund14876' => 'sun', 'Hund14879' => 'sun', 'Lalb_Chr06g0160741' => 'lal', 'Lalb_Chr21g0304781' => 'lal', 'Lj3A726G19' => 'lonja', 'Lj3A726T23' => 'lonja', 'Lj3A726T24' => 'lonja', 'Lj3A726T25' => 'lonja', 'Lj3A727T17' => 'lonja', 'Lj3C726T0' => 'lonja', 'Lj3C726T2' => 'lonja', 'Lj3P725T35' => 'lonja', 'Lj3P727T10' => 'lonja', 'Lj3P727T12' => 'lonja', 'Lj3P727T14' => 'lonja', 'Lj5g0023109' => 'lja', 'Lj6P646T44' => 'lonja', 'Lsat_1_v5_gn_6_75760' => 'lsa', 'Lsat_1_v5_gn_6_75800' => 'lsa', 'Lsat_1_v5_gn_6_75900' => 'lsa', 'Lsat_1_v5_gn_6_76240' => 'lsa', 'Lsat_1_v5_gn_6_76441' => 'lsa', 'Lsat_1_v5_gn_6_76700' => 'lsa', 'Lsat_1_v5_gn_6_76760' => 'lsa', 'Manes.15G033100' => 'mes', 'Mapoly0004s0074' => 'mpo', 'Mapoly0004s0075' => 'mpo', 'Mapoly0004s0163' => 'mpo', 'Mapoly0004s0164' => 'mpo', 'Mapoly0021s0018' => 'mpo', 'Mapoly0041s0136' => 'mpo', 'Mapoly0041s0137' => 'mpo', 'Mapoly0041s0138' => 'mpo', 'Mapoly0041s0139' => 'mpo', 'Mapoly0041s0141' => 'mpo', 'Mapoly0041s0142' => 'mpo', 'Mapoly0041s0143' => 'mpo', 'Mapoly0041s0144' => 'mpo', 'Mapoly0041s0145' => 'mpo', 'Mapoly0047s0106' => 'mpo', 'Mapoly0047s0108' => 'mpo', 'Mapoly0050s0051' => 'mpo', 'Mapoly0050s0052' => 'mpo', 'Mapoly0050s0053' => 'mpo', 'Mapoly0058s0013' => 'mpo', 'Mapoly0091s0078' => 'mpo', 'Mapoly0091s0079' => 'mpo', 'Mapoly0091s0080' => 'mpo', 'Mapoly0091s0081' => 'mpo', 'Mapoly0278s0004' => 'mpo', 'Mapoly0278s0005' => 'mpo', 'Mapoly0278s0006' => 'mpo', 'MBI11_g30648_MAGBIO' => 'mbi', 'MCO03G194' => 'mco', 'MCO03G590' => 'mco', 'MCO07G312' => 'mco', 'MCO10G318' => 'mco', 'MCO12G244' => 'mco', 'MCO13G148' => 'mco', 'MCO13G194' => 'mco', 'MCO16G238' => 'mco', 'MD06G1134100' => 'mdo', 'MD13G1200100' => 'mdo', 'MD13G1200300' => 'mdo', 'MD13G1200600' => 'mdo', 'MD14G1150400' => 'mdo', 'MD16G1200000' => 'mdo', 'Medtr1g102570' => 'mtr', 'Medtr1g102780' => 'mtr', 'Medtr1g102800' => 'mtr', 'Medtr1g102810' => 'mtr', 'Medtr1g102830' => 'mtr', 'MELO3C006499.2' => 'cme', 'Migut.G00385' => 'egut', 'MSTRG.4063' => 'ama', 'Nitab4.5_0000090g0260' => 'nta', 'Nitab4.5_0000977g0030' => 'nta', 'Nitab4.5_0002541g0040' => 'nta', 'Nitab4.5_0007068g0040' => 'nta', 'Nn005s41408' => 'nnu', 'Nn005s41410' => 'nnu', 'Oeu010310.1' => 'oeu', 'Oeu010311.1' => 'oeu', 'Oeu043472.1' => 'oeu', 'Os01g0246400' => 'osa', 'Os04g0267950' => 'osa', 'Os07g0178700' => 'osa', 'Os07g0178800' => 'osa', 'Peaxi162Scf00316g00046' => 'pax', 'Peaxi162Scf00316g00049' => 'pax', 'Peaxi162Scf00316g00059' => 'pax', 'Peaxi162Scf00316g00328' => 'pax', 'Peaxi162Scf00316g00329' => 'pax', 'Peaxi162Scf00316g00411' => 'pax', 'Peaxi162Scf00316g00521' => 'pax', 'Peaxi162Scf00492g00068' => 'pax', 'Peaxi162Scf35631g00002' => 'pax', 'PGR142G3720' => 'pgr', 'PGSC0003DMG400006442' => 'stu', 'Phvul.007G062000' => 'pvu', 'Potri.008G157750' => 'ptr', 'Potri.008G157900' => 'ptr', 'Potri.008G158000' => 'ptr', 'Potri.008G158200' => 'ptr', 'Pp3c11_7280' => 'ppa', 'Pp3c11_7980' => 'ppa', 'Pp3c12_19450' => 'ppa', 'Pp3c14_1480' => 'ppa', 'Pp3c14_1501' => 'ppa', 'Pp3c16_4900' => 'ppa', 'Pp3c16_5010' => 'ppa', 'Pp3c16_5060' => 'ppa', 'Pp3c19_18250' => 'ppa', 'Pp3c23_8530' => 'ppa', 'Pp3c23_8550' => 'ppa', 'Pp3c24_9670' => 'ppa', 'Pp3c2_21390' => 'ppa', 'Pp3c2_31380' => 'ppa', 'Pp3c3_16620' => 'ppa', 'Pp3c3_8090' => 'ppa', 'Pp3c3_8110' => 'ppa', 'Pp3c3_8130' => 'ppa', 'Pp3c3_8150' => 'ppa', 'Pp3c4_14320' => 'ppa', 'Pp3c6_2560' => 'ppa', 'Pp3c9_16700' => 'ppa', 'PRCOL_00000234' => 'pco', 'PRCOL_00000235' => 'pco', 'PRCOL_00000777' => 'pco', 'PRCOL_00002344' => 'pco', 'PRCOL_00002372' => 'pco', 'PRCOL_00006120' => 'pco', 'Prupe.1G021400' => 'ppe', 'Prupe.1G021500' => 'ppe', 'Prupe.1G021600' => 'ppe', 'Prupe.1G021700' => 'ppe', 'Prupe.1G021800' => 'ppe', 'Prupe.5G145100' => 'ppe', 'Psat6g204040' => 'psa', 'Psat6g204800' => 'psa', 'Psat6g204920' => 'psa', 'Psat6g204960' => 'psa', 'Psat6g205080' => 'psa', 'PSO017G0271' => 'pso', 'PSO017G1276' => 'pso', 'PSO017G1429' => 'pso', 'PSO017G1861' => 'pso', 'PSO017G2787' => 'pso', 'PSO017G4466' => 'pso', 'PSO017G5118' => 'pso', 'PSO017G5420' => 'pso', 'PSO063G3678' => 'pso', 'PSO210G0546' => 'pso', 'PSO317G0001' => 'pso', 'PSO357G0512' => 'pso', 'PSO478G2682' => 'pso', 'PSO647G0001' => 'pso', 'PSO675G0001' => 'pso', 'PSO675G2699' => 'pso', 'PSO675G2849' => 'pso', 'PSO675G4991' => 'pso', 'PSO689G0001' => 'pso', 'QL06p000916' => 'qlo', 'QL06p000921' => 'qlo', 'QL06p001398' => 'qlo', 'QL06p001407' => 'qlo', 'QL06p002031' => 'qlo', 'RcHm_v2.0_Chr4g0387791' => 'rch', 'RcHm_v2.0_Chr4g0387801' => 'rch', 'RcHm_v2.0_Chr6g0286501' => 'rch', 'RcHm_v2.0_Chr6g0286511' => 'rch', 'RcHm_v2.0_Chr6g0286521' => 'rch', 'RcHm_v2.0_Chr6g0286531' => 'rch', 'RcHm_v2.0_Chr7g0189141' => 'rch', 'Rhsim02G0028700' => 'rsi', 'Rhsim02G0028800' => 'rsi', 'Rhsim02G0028900' => 'rsi', 'Rhsim02G0029000' => 'rsi', 'Rhsim02G0029100' => 'rsi', 'Rhsim02G0029200' => 'rsi', 'Rhsim02G0029300' => 'rsi', 'Rhsim02G0029400' => 'rsi', 'Rhsim02G0029500' => 'rsi', 'Rhsim02G0029600' => 'rsi', 'RhsimUnG0024000' => 'rsi', 'RhsimUnG0024100' => 'rsi', 'RhsimUnG0024200' => 'rsi', 'RhsimUnG0024300' => 'rsi', 'RhsimUnG0024400' => 'rsi', 'RhsimUnG0024500' => 'rsi', 'RhsimUnG0024700' => 'rsi', 'RhsimUnG0024800' => 'rsi', 'RhsimUnG0024900' => 'rsi', 'RhsimUnG0025100' => 'rsi', 'Sabra08G0120200' => 'sbr', 'Sabra08G0120300' => 'sbr', 'Sabra08G0120500' => 'sbr', 'Sabra08G0120600' => 'sbr', 'Sabra10G0158900' => 'sbr', 'SalBow2G3492' => 'sbo', 'Sc13g0004760' => 'sci', 'Sc13g0004770' => 'sci', 'Sed0003417' => 'sed', 'Sed0019750' => 'sed', 'SEGI_03419' => 'sgi', 'SEGI_05907' => 'sgi', 'SEGI_10682' => 'sgi', 'SEGI_13528' => 'sgi', 'SEGI_16081' => 'sgi', 'SEGI_19370' => 'sgi', 'SEGI_21015' => 'sgi', 'SEGI_21944' => 'sgi', 'SEGI_32906' => 'sgi', 'SEGI_33093' => 'sgi', 'SEGI_36110' => 'sgi', 'SEGI_40397' => 'sgi', 'SGA_v2.0_scaffold191G40426' => 'sas', 'SGA_v2.0_scaffold353G49717' => 'sas', 'SGA_v2.0_scaffold50G18550' => 'sas', 'SMO119G0173' => 'smo', 'SMO172G0002' => 'smo', 'Solyc09g082690.3' => 'sly', 'Solyc09g082700.2' => 'sly', 'Sopen09g031550' => 'spe', 'Sopen09g031560' => 'spe', 'Sp3g20540' => 'spa', 'Sp7g07580' => 'spa', 'TAR134G0002' => 'tar', 'TAR236G0001' => 'tar', 'TAR365G0892' => 'tar', 'TAR636G0166' => 'tar', 'TAR636G0646' => 'tar', 'TAR636G0869' => 'tar', 'TAR636G1317' => 'tar', 'TAR636G1744' => 'tar', 'TAR636G3358' => 'tar', 'TAR636G3436' => 'tar', 'THA.LOC104803047' => 'tha', 'Thecc.04G238900' => 'tca', 'Thhalv10021557m.g' => 'esa', 'Thhalv10026318m.g' => 'esa', 'Thhalv10026335m.g' => 'esa', 'TPR.G17433' => 'tpr', 'TPR.G18915' => 'tpr', 'TPR.G26125' => 'tpr', 'TWI09G0677' => 'twi', 'TWI73G0287' => 'twi', 'unitig_748.g8326' => 'ugi', 'vmacro15370' => 'vma', 'vmacro15371' => 'vma', 'vmacro15372' => 'vma', 'vmacro15373' => 'vma', 'vmacro15374' => 'vma', 'VMungo0720G2826' => 'vmu', 'Zm00001eb116960' => 'zma', 'Zm00001eb301260' => 'zma', 'Zm00001eb301270' => 'zma' ), 'gf_id' => 'HOM05D001460', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001460' ), 'data_identifier' => 'HOM05D001460', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001460', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '433', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p22980' => 'bna', 'A01p32340' => 'bna', 'A03p42970' => 'bna', 'A05p25880' => 'bna', 'Aa31LG8G9320' => 'aar', 'Aa31LG8G9330' => 'aar', 'Aa31LG8G9340' => 'aar', 'Aa31sc221G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1034' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1528' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.829' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2222' => 'aag', 'Ah.12g058830' => 'amhyb', 'Ah.12g058840' => 'amhyb', 'AL3G37160' => 'aly', 'AL7G41310' => 'aly', 'Aqoxy5G00395' => 'aox', 'Aqoxy5G00396' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0C8NZA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5185HY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JZ1PRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MD3LS0' => 'arhy', 'AT3G22840' => 'ath', 'AT4G14690' => 'ath', 'ATR0665G054' => 'atr', 'Atru.chr4.2344' => 'acertr', 'Atru.chr4.2346' => 'acertr', 'Atru.chr4.2347' => 'acertr', 'Atru.chr4.2348' => 'acertr', 'Atru.chr4.2355' => 'acertr', 'Atru.chr4.2356' => 'acertr', 'Atru.chr4.2358' => 'acertr', 'Atru.chr4.2359' => 'acertr', 'Atru.chr4.2360' => 'acertr', 'Atru.chr4.2361' => 'acertr', 'AUR62030476' => 'cqu', 'AUR62030478' => 'cqu', 'AUR62030819' => 'cqu', 'AUR62030820' => 'cqu', 'BcaB03g14648' => 'bca', 'BcaB04g20492' => 'bca', 'BcaB06g26399' => 'bca', 'BcaC01g03416' => 'bca', 'BcaC01g03419' => 'bca', 'BcaC01g03421' => 'bca', 'BcaC01g03424' => 'bca', 'BcaC05g28012' => 'bca', 'BcaC09g49212' => 'bca', 'BcaC09g50140' => 'bca', 'BcaNung00346' => 'bca', 'BolC1t02785H' => 'bol', 'BolC1t04095H' => 'bol', 'BolC3t17545H' => 'bol', 'BolC5t32769H' => 'bol', 'BraA01t02211Z' => 'bra', 'BraA01t03359Z' => 'bra', 'BraA03t13441Z' => 'bra', 'BraA05t21476Z' => 'bra', 'C01p28420' => 'bna', 'C01p41350' => 'bna', 'C03p52750' => 'bna', 'C03p52780' => 'bna', 'C05p40270' => 'bna', 'CAN.G1437.9' => 'can', 'CANSAT78G0035' => 'cansat', 'CANSAT78G1036' => 'cansat', 'CANSAT78G2272' => 'cansat', 'CANSAT78G2478' => 'cansat', 'CARHR098700' => 'chi', 'CARHR221120' => 'chi', 'CARHR221150' => 'chi', 'Carub.0003s2297' => 'cru', 'Carub.0007s2749' => 'cru', 'Carub.0007s2750' => 'cru', 'Carub.0007s2751' => 'cru', 'Ca_10849_v3' => 'car', 'Cc03_g04300' => 'ccan', 'CDE02G3648' => 'cde', 'CDE05G0060' => 'cde', 'CDE05G0692' => 'cde', 'CDE05G2285' => 'cde', 'CDE05G2884' => 'cde', 'CDE05G3072' => 'cde', 'Cfa008439' => 'cfa', 'Cfa008441' => 'cfa', 'Cfa008443' => 'cfa', 'Cfa008448' => 'cfa', 'Ciclev10005974m.g' => 'ccl', 'Ciclev10006006m.g' => 'ccl', 'Ciclev10006775m.g' => 'ccl', 'CiPaw.02G120400' => 'cil', 'CiPaw.02G120500' => 'cil', 'CiPaw.02G120600' => 'cil', 'ClCG05G004850' => 'cla', 'COL.COLO4_21566' => 'col', 'Cpa.g.sc44.124' => 'cpa', 'Cre07.g320400' => 'cre', 'Cre07.g320450' => 'cre', 'Cre08.g384650' => 'cre', 'Cre09.g393173' => 'cre', 'Cre09.g394325' => 'cre', 'Cre14.g626750' => 'cre', 'Cre16.g679250' => 'cre', 'CsaV3_3G012890' => 'csa', 'CSS0010865' => 'camsi', 'CSS0044338' => 'camsi', 'DCAR_002366' => 'dca', 'DCAR_030687' => 'dca', 'DCAR_030688' => 'dca', 'Dinv14047' => 'din', 'Dinv14048' => 'din', 'Duzib151G0105' => 'dzi', 'Duzib151G0114' => 'dzi', 'Duzib212G1029' => 'dzi', 'ECA232G3536' => 'eca', 'ECA240G0786' => 'eca', 'ECA240G1802' => 'eca', 'ECA240G3760' => 'eca', 'ECA240G3920' => 'eca', 'EL10Ac5g12536' => 'bvu', 'EL10Ac5g12537' => 'bvu', 'EL10Ac5g12538' => 'bvu', 'Eucgr.B01004' => 'egr', 'Eucgr.B01006' => 'egr', 'Eucgr.B01007' => 'egr', 'Eucgr.B01008' => 'egr', 'Eucgr.B01895' => 'egr', 'Eucgr.B01896' => 'egr', 'FAN04G1456' => 'fan', 'FAN08G1769' => 'fan', 'FAN08G2160' => 'fan', 'FAN13G2403' => 'fan', 'FAN13G3303' => 'fan', 'FAN15G2435' => 'fan', 'FAN17G0672' => 'fan', 'FAN17G2441' => 'fan', 'FAN18G1024' => 'fan', 'FAN22G1458' => 'fan', 'FAN24G0037' => 'fan', 'FAN24G0429' => 'fan', 'FAN24G2387' => 'fan', 'FAN27G2746' => 'fan', 'FvH4_2g20400' => 'fve', 'FvH4_2g20420' => 'fve', 'FvH4_2g20430' => 'fve', 'FvH4_4g01270' => 'fve', 'FvH4_4g01290' => 'fve', 'FvH4_4g01300' => 'fve', 'FvH4_4g01310' => 'fve', 'FvH4_4g01330' => 'fve', 'FvH4_5g09070' => 'fve', 'Glyma.10G243800' => 'gma', 'Glyma.20G150600' => 'gma', 'Gohir.A09G219200' => 'ghi', 'Gohir.A09G219300' => 'ghi', 'Gohir.D09G221400' => 'ghi', 'Gohir.D09G221500' => 'ghi', 'Gorai.006G242600' => 'gra', 'Gorai.006G242700' => 'gra', 'GSVIVG01018044001' => 'vvi', 'HanXRQChr03g0083821' => 'han', 'HanXRQChr03g0083841' => 'han', 'HanXRQChr03g0083881' => 'han', 'HanXRQChr03g0083901' => 'han', 'HanXRQChr03g0083921' => 'han', 'HanXRQChr03g0085331' => 'han', 'HanXRQChr03g0085361' => 'han', 'HanXRQChr03g0085411' => 'han', 'HanXRQChr03g0085421' => 'han', 'HanXRQChr03g0085431' => 'han', 'HanXRQChr08g0221991' => 'han', 'HanXRQChr11g0336061' => 'han', 'HanXRQChr11g0336411' => 'han', 'Haze_11234' => 'cav', 'Hma1.2p1_0549F.1_g177010' => 'hma', 'Hma1.2p1_0602F.1_g187630' => 'hma', 'Hund14876' => 'sun', 'Hund14879' => 'sun', 'Lalb_Chr06g0160741' => 'lal', 'Lalb_Chr21g0304781' => 'lal', 'Lj3A726G19' => 'lonja', 'Lj3A726T23' => 'lonja', 'Lj3A726T24' => 'lonja', 'Lj3A726T25' => 'lonja', 'Lj3A727T17' => 'lonja', 'Lj3C726T0' => 'lonja', 'Lj3C726T2' => 'lonja', 'Lj3P725T35' => 'lonja', 'Lj3P727T10' => 'lonja', 'Lj3P727T12' => 'lonja', 'Lj3P727T14' => 'lonja', 'Lj5g0023109' => 'lja', 'Lj6P646T44' => 'lonja', 'Lsat_1_v5_gn_6_75760' => 'lsa', 'Lsat_1_v5_gn_6_75800' => 'lsa', 'Lsat_1_v5_gn_6_75900' => 'lsa', 'Lsat_1_v5_gn_6_76240' => 'lsa', 'Lsat_1_v5_gn_6_76441' => 'lsa', 'Lsat_1_v5_gn_6_76700' => 'lsa', 'Lsat_1_v5_gn_6_76760' => 'lsa', 'Manes.15G033100' => 'mes', 'Mapoly0004s0074' => 'mpo', 'Mapoly0004s0075' => 'mpo', 'Mapoly0004s0163' => 'mpo', 'Mapoly0004s0164' => 'mpo', 'Mapoly0021s0018' => 'mpo', 'Mapoly0041s0136' => 'mpo', 'Mapoly0041s0137' => 'mpo', 'Mapoly0041s0138' => 'mpo', 'Mapoly0041s0139' => 'mpo', 'Mapoly0041s0141' => 'mpo', 'Mapoly0041s0142' => 'mpo', 'Mapoly0041s0143' => 'mpo', 'Mapoly0041s0144' => 'mpo', 'Mapoly0041s0145' => 'mpo', 'Mapoly0047s0106' => 'mpo', 'Mapoly0047s0108' => 'mpo', 'Mapoly0050s0051' => 'mpo', 'Mapoly0050s0052' => 'mpo', 'Mapoly0050s0053' => 'mpo', 'Mapoly0058s0013' => 'mpo', 'Mapoly0091s0078' => 'mpo', 'Mapoly0091s0079' => 'mpo', 'Mapoly0091s0080' => 'mpo', 'Mapoly0091s0081' => 'mpo', 'Mapoly0278s0004' => 'mpo', 'Mapoly0278s0005' => 'mpo', 'Mapoly0278s0006' => 'mpo', 'MBI11_g30648_MAGBIO' => 'mbi', 'MCO03G194' => 'mco', 'MCO03G590' => 'mco', 'MCO07G312' => 'mco', 'MCO10G318' => 'mco', 'MCO12G244' => 'mco', 'MCO13G148' => 'mco', 'MCO13G194' => 'mco', 'MCO16G238' => 'mco', 'MD06G1134100' => 'mdo', 'MD13G1200100' => 'mdo', 'MD13G1200300' => 'mdo', 'MD13G1200600' => 'mdo', 'MD14G1150400' => 'mdo', 'MD16G1200000' => 'mdo', 'Medtr1g102570' => 'mtr', 'Medtr1g102780' => 'mtr', 'Medtr1g102800' => 'mtr', 'Medtr1g102810' => 'mtr', 'Medtr1g102830' => 'mtr', 'MELO3C006499.2' => 'cme', 'Migut.G00385' => 'egut', 'MSTRG.4063' => 'ama', 'Nitab4.5_0000090g0260' => 'nta', 'Nitab4.5_0000977g0030' => 'nta', 'Nitab4.5_0002541g0040' => 'nta', 'Nitab4.5_0007068g0040' => 'nta', 'Nn005s41408' => 'nnu', 'Nn005s41410' => 'nnu', 'Oeu010310.1' => 'oeu', 'Oeu010311.1' => 'oeu', 'Oeu043472.1' => 'oeu', 'Os01g0246400' => 'osa', 'Os04g0267950' => 'osa', 'Os07g0178700' => 'osa', 'Os07g0178800' => 'osa', 'Peaxi162Scf00316g00046' => 'pax', 'Peaxi162Scf00316g00049' => 'pax', 'Peaxi162Scf00316g00059' => 'pax', 'Peaxi162Scf00316g00328' => 'pax', 'Peaxi162Scf00316g00329' => 'pax', 'Peaxi162Scf00316g00411' => 'pax', 'Peaxi162Scf00316g00521' => 'pax', 'Peaxi162Scf00492g00068' => 'pax', 'Peaxi162Scf35631g00002' => 'pax', 'PGR142G3720' => 'pgr', 'PGSC0003DMG400006442' => 'stu', 'Phvul.007G062000' => 'pvu', 'Potri.008G157750' => 'ptr', 'Potri.008G157900' => 'ptr', 'Potri.008G158000' => 'ptr', 'Potri.008G158200' => 'ptr', 'Pp3c11_7280' => 'ppa', 'Pp3c11_7980' => 'ppa', 'Pp3c12_19450' => 'ppa', 'Pp3c14_1480' => 'ppa', 'Pp3c14_1501' => 'ppa', 'Pp3c16_4900' => 'ppa', 'Pp3c16_5010' => 'ppa', 'Pp3c16_5060' => 'ppa', 'Pp3c19_18250' => 'ppa', 'Pp3c23_8530' => 'ppa', 'Pp3c23_8550' => 'ppa', 'Pp3c24_9670' => 'ppa', 'Pp3c2_21390' => 'ppa', 'Pp3c2_31380' => 'ppa', 'Pp3c3_16620' => 'ppa', 'Pp3c3_8090' => 'ppa', 'Pp3c3_8110' => 'ppa', 'Pp3c3_8130' => 'ppa', 'Pp3c3_8150' => 'ppa', 'Pp3c4_14320' => 'ppa', 'Pp3c6_2560' => 'ppa', 'Pp3c9_16700' => 'ppa', 'PRCOL_00000234' => 'pco', 'PRCOL_00000235' => 'pco', 'PRCOL_00000777' => 'pco', 'PRCOL_00002344' => 'pco', 'PRCOL_00002372' => 'pco', 'PRCOL_00006120' => 'pco', 'Prupe.1G021400' => 'ppe', 'Prupe.1G021500' => 'ppe', 'Prupe.1G021600' => 'ppe', 'Prupe.1G021700' => 'ppe', 'Prupe.1G021800' => 'ppe', 'Prupe.5G145100' => 'ppe', 'Psat6g204040' => 'psa', 'Psat6g204800' => 'psa', 'Psat6g204920' => 'psa', 'Psat6g204960' => 'psa', 'Psat6g205080' => 'psa', 'PSO017G0271' => 'pso', 'PSO017G1276' => 'pso', 'PSO017G1429' => 'pso', 'PSO017G1861' => 'pso', 'PSO017G2787' => 'pso', 'PSO017G4466' => 'pso', 'PSO017G5118' => 'pso', 'PSO017G5420' => 'pso', 'PSO063G3678' => 'pso', 'PSO210G0546' => 'pso', 'PSO317G0001' => 'pso', 'PSO357G0512' => 'pso', 'PSO478G2682' => 'pso', 'PSO647G0001' => 'pso', 'PSO675G0001' => 'pso', 'PSO675G2699' => 'pso', 'PSO675G2849' => 'pso', 'PSO675G4991' => 'pso', 'PSO689G0001' => 'pso', 'QL06p000916' => 'qlo', 'QL06p000921' => 'qlo', 'QL06p001398' => 'qlo', 'QL06p001407' => 'qlo', 'QL06p002031' => 'qlo', 'RcHm_v2.0_Chr4g0387791' => 'rch', 'RcHm_v2.0_Chr4g0387801' => 'rch', 'RcHm_v2.0_Chr6g0286501' => 'rch', 'RcHm_v2.0_Chr6g0286511' => 'rch', 'RcHm_v2.0_Chr6g0286521' => 'rch', 'RcHm_v2.0_Chr6g0286531' => 'rch', 'RcHm_v2.0_Chr7g0189141' => 'rch', 'Rhsim02G0028700' => 'rsi', 'Rhsim02G0028800' => 'rsi', 'Rhsim02G0028900' => 'rsi', 'Rhsim02G0029000' => 'rsi', 'Rhsim02G0029100' => 'rsi', 'Rhsim02G0029200' => 'rsi', 'Rhsim02G0029300' => 'rsi', 'Rhsim02G0029400' => 'rsi', 'Rhsim02G0029500' => 'rsi', 'Rhsim02G0029600' => 'rsi', 'RhsimUnG0024000' => 'rsi', 'RhsimUnG0024100' => 'rsi', 'RhsimUnG0024200' => 'rsi', 'RhsimUnG0024300' => 'rsi', 'RhsimUnG0024400' => 'rsi', 'RhsimUnG0024500' => 'rsi', 'RhsimUnG0024700' => 'rsi', 'RhsimUnG0024800' => 'rsi', 'RhsimUnG0024900' => 'rsi', 'RhsimUnG0025100' => 'rsi', 'Sabra08G0120200' => 'sbr', 'Sabra08G0120300' => 'sbr', 'Sabra08G0120500' => 'sbr', 'Sabra08G0120600' => 'sbr', 'Sabra10G0158900' => 'sbr', 'SalBow2G3492' => 'sbo', 'Sc13g0004760' => 'sci', 'Sc13g0004770' => 'sci', 'Sed0003417' => 'sed', 'Sed0019750' => 'sed', 'SEGI_03419' => 'sgi', 'SEGI_05907' => 'sgi', 'SEGI_10682' => 'sgi', 'SEGI_13528' => 'sgi', 'SEGI_16081' => 'sgi', 'SEGI_19370' => 'sgi', 'SEGI_21015' => 'sgi', 'SEGI_21944' => 'sgi', 'SEGI_32906' => 'sgi', 'SEGI_33093' => 'sgi', 'SEGI_36110' => 'sgi', 'SEGI_40397' => 'sgi', 'SGA_v2.0_scaffold191G40426' => 'sas', 'SGA_v2.0_scaffold353G49717' => 'sas', 'SGA_v2.0_scaffold50G18550' => 'sas', 'SMO119G0173' => 'smo', 'SMO172G0002' => 'smo', 'Solyc09g082690.3' => 'sly', 'Solyc09g082700.2' => 'sly', 'Sopen09g031550' => 'spe', 'Sopen09g031560' => 'spe', 'Sp3g20540' => 'spa', 'Sp7g07580' => 'spa', 'TAR134G0002' => 'tar', 'TAR236G0001' => 'tar', 'TAR365G0892' => 'tar', 'TAR636G0166' => 'tar', 'TAR636G0646' => 'tar', 'TAR636G0869' => 'tar', 'TAR636G1317' => 'tar', 'TAR636G1744' => 'tar', 'TAR636G3358' => 'tar', 'TAR636G3436' => 'tar', 'THA.LOC104803047' => 'tha', 'Thecc.04G238900' => 'tca', 'Thhalv10021557m.g' => 'esa', 'Thhalv10026318m.g' => 'esa', 'Thhalv10026335m.g' => 'esa', 'TPR.G17433' => 'tpr', 'TPR.G18915' => 'tpr', 'TPR.G26125' => 'tpr', 'TWI09G0677' => 'twi', 'TWI73G0287' => 'twi', 'unitig_748.g8326' => 'ugi', 'vmacro15370' => 'vma', 'vmacro15371' => 'vma', 'vmacro15372' => 'vma', 'vmacro15373' => 'vma', 'vmacro15374' => 'vma', 'VMungo0720G2826' => 'vmu', 'Zm00001eb116960' => 'zma', 'Zm00001eb301260' => 'zma', 'Zm00001eb301270' => 'zma' ) $gf_id = 'HOM05D001460' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001460' ) $data_identifier = 'HOM05D001460' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 4, 'aag' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 2, 'aox' => (int) 2, 'arhy' => (int) 4, 'ath' => (int) 2, 'atr' => (int) 1, 'acertr' => (int) 10, 'cqu' => (int) 4, 'bca' => (int) 11, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 1, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 1, 'ccan' => (int) 1, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 1, 'col' => (int) 1, 'cpa' => (int) 1, 'cre' => (int) 7, 'csa' => (int) 1, 'camsi' => (int) 2, 'dca' => (int) 3, 'din' => (int) 2, 'dzi' => (int) 3, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 14, 'fve' => (int) 9, 'gma' => (int) 2, 'ghi' => (int) 4, 'gra' => (int) 2, 'vvi' => (int) 1, 'han' => (int) 13, 'cav' => (int) 1, 'hma' => (int) 2, 'sun' => (int) 2, 'lal' => (int) 2, 'lonja' => (int) 12, 'lja' => (int) 1, 'lsa' => (int) 7, 'mes' => (int) 1, 'mpo' => (int) 27, 'mbi' => (int) 1, 'mco' => (int) 8, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 1, 'egut' => (int) 1, 'ama' => (int) 1, 'nta' => (int) 4, 'nnu' => (int) 2, 'oeu' => (int) 3, 'osa' => (int) 4, 'pax' => (int) 9, 'pgr' => (int) 1, 'stu' => (int) 1, 'pvu' => (int) 1, 'ptr' => (int) 4, 'ppa' => (int) 22, 'pco' => (int) 6, 'ppe' => (int) 6, 'psa' => (int) 5, 'pso' => (int) 19, 'qlo' => (int) 5, 'rch' => (int) 7, 'rsi' => (int) 20, 'sbr' => (int) 5, 'sbo' => (int) 1, 'sci' => (int) 2, 'sed' => (int) 2, 'sgi' => (int) 12, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 2, 'tar' => (int) 10, 'tha' => (int) 1, 'tca' => (int) 1, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 2, 'ugi' => (int) 1, 'vma' => (int) 5, 'vmu' => (int) 1, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb301270' $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' => 'HOM05D001460', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '433', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p22980' => 'bna', 'A01p32340' => 'bna', 'A03p42970' => 'bna', 'A05p25880' => 'bna', 'Aa31LG8G9320' => 'aar', 'Aa31LG8G9330' => 'aar', 'Aa31LG8G9340' => 'aar', 'Aa31sc221G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1034' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1528' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.829' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2222' => 'aag', 'Ah.12g058830' => 'amhyb', 'Ah.12g058840' => 'amhyb', 'AL3G37160' => 'aly', 'AL7G41310' => 'aly', 'Aqoxy5G00395' => 'aox', 'Aqoxy5G00396' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0C8NZA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5185HY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JZ1PRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MD3LS0' => 'arhy', 'AT3G22840' => 'ath', 'AT4G14690' => 'ath', 'ATR0665G054' => 'atr', 'Atru.chr4.2344' => 'acertr', 'Atru.chr4.2346' => 'acertr', 'Atru.chr4.2347' => 'acertr', 'Atru.chr4.2348' => 'acertr', 'Atru.chr4.2355' => 'acertr', 'Atru.chr4.2356' => 'acertr', 'Atru.chr4.2358' => 'acertr', 'Atru.chr4.2359' => 'acertr', 'Atru.chr4.2360' => 'acertr', 'Atru.chr4.2361' => 'acertr', 'AUR62030476' => 'cqu', 'AUR62030478' => 'cqu', 'AUR62030819' => 'cqu', 'AUR62030820' => 'cqu', 'BcaB03g14648' => 'bca', 'BcaB04g20492' => 'bca', 'BcaB06g26399' => 'bca', 'BcaC01g03416' => 'bca', 'BcaC01g03419' => 'bca', 'BcaC01g03421' => 'bca', 'BcaC01g03424' => 'bca', 'BcaC05g28012' => 'bca', 'BcaC09g49212' => 'bca', 'BcaC09g50140' => 'bca', 'BcaNung00346' => 'bca', 'BolC1t02785H' => 'bol', 'BolC1t04095H' => 'bol', 'BolC3t17545H' => 'bol', 'BolC5t32769H' => 'bol', 'BraA01t02211Z' => 'bra', 'BraA01t03359Z' => 'bra', 'BraA03t13441Z' => 'bra', 'BraA05t21476Z' => 'bra', 'C01p28420' => 'bna', 'C01p41350' => 'bna', 'C03p52750' => 'bna', 'C03p52780' => 'bna', 'C05p40270' => 'bna', 'CAN.G1437.9' => 'can', 'CANSAT78G0035' => 'cansat', 'CANSAT78G1036' => 'cansat', 'CANSAT78G2272' => 'cansat', 'CANSAT78G2478' => 'cansat', 'CARHR098700' => 'chi', 'CARHR221120' => 'chi', 'CARHR221150' => 'chi', 'Carub.0003s2297' => 'cru', 'Carub.0007s2749' => 'cru', 'Carub.0007s2750' => 'cru', 'Carub.0007s2751' => 'cru', 'Ca_10849_v3' => 'car', 'Cc03_g04300' => 'ccan', 'CDE02G3648' => 'cde', 'CDE05G0060' => 'cde', 'CDE05G0692' => 'cde', 'CDE05G2285' => 'cde', 'CDE05G2884' => 'cde', 'CDE05G3072' => 'cde', 'Cfa008439' => 'cfa', 'Cfa008441' => 'cfa', 'Cfa008443' => 'cfa', 'Cfa008448' => 'cfa', 'Ciclev10005974m.g' => 'ccl', 'Ciclev10006006m.g' => 'ccl', 'Ciclev10006775m.g' => 'ccl', 'CiPaw.02G120400' => 'cil', 'CiPaw.02G120500' => 'cil', 'CiPaw.02G120600' => 'cil', 'ClCG05G004850' => 'cla', 'COL.COLO4_21566' => 'col', 'Cpa.g.sc44.124' => 'cpa', 'Cre07.g320400' => 'cre', 'Cre07.g320450' => 'cre', 'Cre08.g384650' => 'cre', 'Cre09.g393173' => 'cre', 'Cre09.g394325' => 'cre', 'Cre14.g626750' => 'cre', 'Cre16.g679250' => 'cre', 'CsaV3_3G012890' => 'csa', 'CSS0010865' => 'camsi', 'CSS0044338' => 'camsi', 'DCAR_002366' => 'dca', 'DCAR_030687' => 'dca', 'DCAR_030688' => 'dca', 'Dinv14047' => 'din', 'Dinv14048' => 'din', 'Duzib151G0105' => 'dzi', 'Duzib151G0114' => 'dzi', 'Duzib212G1029' => 'dzi', 'ECA232G3536' => 'eca', 'ECA240G0786' => 'eca', 'ECA240G1802' => 'eca', 'ECA240G3760' => 'eca', 'ECA240G3920' => 'eca', 'EL10Ac5g12536' => 'bvu', 'EL10Ac5g12537' => 'bvu', 'EL10Ac5g12538' => 'bvu', 'Eucgr.B01004' => 'egr', 'Eucgr.B01006' => 'egr', 'Eucgr.B01007' => 'egr', 'Eucgr.B01008' => 'egr', 'Eucgr.B01895' => 'egr', 'Eucgr.B01896' => 'egr', 'FAN04G1456' => 'fan', 'FAN08G1769' => 'fan', 'FAN08G2160' => 'fan', 'FAN13G2403' => 'fan', 'FAN13G3303' => 'fan', 'FAN15G2435' => 'fan', 'FAN17G0672' => 'fan', 'FAN17G2441' => 'fan', 'FAN18G1024' => 'fan', 'FAN22G1458' => 'fan', 'FAN24G0037' => 'fan', 'FAN24G0429' => 'fan', 'FAN24G2387' => 'fan', 'FAN27G2746' => 'fan', 'FvH4_2g20400' => 'fve', 'FvH4_2g20420' => 'fve', 'FvH4_2g20430' => 'fve', 'FvH4_4g01270' => 'fve', 'FvH4_4g01290' => 'fve', 'FvH4_4g01300' => 'fve', 'FvH4_4g01310' => 'fve', 'FvH4_4g01330' => 'fve', 'FvH4_5g09070' => 'fve', 'Glyma.10G243800' => 'gma', 'Glyma.20G150600' => 'gma', 'Gohir.A09G219200' => 'ghi', 'Gohir.A09G219300' => 'ghi', 'Gohir.D09G221400' => 'ghi', 'Gohir.D09G221500' => 'ghi', 'Gorai.006G242600' => 'gra', 'Gorai.006G242700' => 'gra', 'GSVIVG01018044001' => 'vvi', 'HanXRQChr03g0083821' => 'han', 'HanXRQChr03g0083841' => 'han', 'HanXRQChr03g0083881' => 'han', 'HanXRQChr03g0083901' => 'han', 'HanXRQChr03g0083921' => 'han', 'HanXRQChr03g0085331' => 'han', 'HanXRQChr03g0085361' => 'han', 'HanXRQChr03g0085411' => 'han', 'HanXRQChr03g0085421' => 'han', 'HanXRQChr03g0085431' => 'han', 'HanXRQChr08g0221991' => 'han', 'HanXRQChr11g0336061' => 'han', 'HanXRQChr11g0336411' => 'han', 'Haze_11234' => 'cav', 'Hma1.2p1_0549F.1_g177010' => 'hma', 'Hma1.2p1_0602F.1_g187630' => 'hma', 'Hund14876' => 'sun', 'Hund14879' => 'sun', 'Lalb_Chr06g0160741' => 'lal', 'Lalb_Chr21g0304781' => 'lal', 'Lj3A726G19' => 'lonja', 'Lj3A726T23' => 'lonja', 'Lj3A726T24' => 'lonja', 'Lj3A726T25' => 'lonja', 'Lj3A727T17' => 'lonja', 'Lj3C726T0' => 'lonja', 'Lj3C726T2' => 'lonja', 'Lj3P725T35' => 'lonja', 'Lj3P727T10' => 'lonja', 'Lj3P727T12' => 'lonja', 'Lj3P727T14' => 'lonja', 'Lj5g0023109' => 'lja', 'Lj6P646T44' => 'lonja', 'Lsat_1_v5_gn_6_75760' => 'lsa', 'Lsat_1_v5_gn_6_75800' => 'lsa', 'Lsat_1_v5_gn_6_75900' => 'lsa', 'Lsat_1_v5_gn_6_76240' => 'lsa', 'Lsat_1_v5_gn_6_76441' => 'lsa', 'Lsat_1_v5_gn_6_76700' => 'lsa', 'Lsat_1_v5_gn_6_76760' => 'lsa', 'Manes.15G033100' => 'mes', 'Mapoly0004s0074' => 'mpo', 'Mapoly0004s0075' => 'mpo', 'Mapoly0004s0163' => 'mpo', 'Mapoly0004s0164' => 'mpo', 'Mapoly0021s0018' => 'mpo', 'Mapoly0041s0136' => 'mpo', 'Mapoly0041s0137' => 'mpo', 'Mapoly0041s0138' => 'mpo', 'Mapoly0041s0139' => 'mpo', 'Mapoly0041s0141' => 'mpo', 'Mapoly0041s0142' => 'mpo', 'Mapoly0041s0143' => 'mpo', 'Mapoly0041s0144' => 'mpo', 'Mapoly0041s0145' => 'mpo', 'Mapoly0047s0106' => 'mpo', 'Mapoly0047s0108' => 'mpo', 'Mapoly0050s0051' => 'mpo', 'Mapoly0050s0052' => 'mpo', 'Mapoly0050s0053' => 'mpo', 'Mapoly0058s0013' => 'mpo', 'Mapoly0091s0078' => 'mpo', 'Mapoly0091s0079' => 'mpo', 'Mapoly0091s0080' => 'mpo', 'Mapoly0091s0081' => 'mpo', 'Mapoly0278s0004' => 'mpo', 'Mapoly0278s0005' => 'mpo', 'Mapoly0278s0006' => 'mpo', 'MBI11_g30648_MAGBIO' => 'mbi', 'MCO03G194' => 'mco', 'MCO03G590' => 'mco', 'MCO07G312' => 'mco', 'MCO10G318' => 'mco', 'MCO12G244' => 'mco', 'MCO13G148' => 'mco', 'MCO13G194' => 'mco', 'MCO16G238' => 'mco', 'MD06G1134100' => 'mdo', 'MD13G1200100' => 'mdo', 'MD13G1200300' => 'mdo', 'MD13G1200600' => 'mdo', 'MD14G1150400' => 'mdo', 'MD16G1200000' => 'mdo', 'Medtr1g102570' => 'mtr', 'Medtr1g102780' => 'mtr', 'Medtr1g102800' => 'mtr', 'Medtr1g102810' => 'mtr', 'Medtr1g102830' => 'mtr', 'MELO3C006499.2' => 'cme', 'Migut.G00385' => 'egut', 'MSTRG.4063' => 'ama', 'Nitab4.5_0000090g0260' => 'nta', 'Nitab4.5_0000977g0030' => 'nta', 'Nitab4.5_0002541g0040' => 'nta', 'Nitab4.5_0007068g0040' => 'nta', 'Nn005s41408' => 'nnu', 'Nn005s41410' => 'nnu', 'Oeu010310.1' => 'oeu', 'Oeu010311.1' => 'oeu', 'Oeu043472.1' => 'oeu', 'Os01g0246400' => 'osa', 'Os04g0267950' => 'osa', 'Os07g0178700' => 'osa', 'Os07g0178800' => 'osa', 'Peaxi162Scf00316g00046' => 'pax', 'Peaxi162Scf00316g00049' => 'pax', 'Peaxi162Scf00316g00059' => 'pax', 'Peaxi162Scf00316g00328' => 'pax', 'Peaxi162Scf00316g00329' => 'pax', 'Peaxi162Scf00316g00411' => 'pax', 'Peaxi162Scf00316g00521' => 'pax', 'Peaxi162Scf00492g00068' => 'pax', 'Peaxi162Scf35631g00002' => 'pax', 'PGR142G3720' => 'pgr', 'PGSC0003DMG400006442' => 'stu', 'Phvul.007G062000' => 'pvu', 'Potri.008G157750' => 'ptr', 'Potri.008G157900' => 'ptr', 'Potri.008G158000' => 'ptr', 'Potri.008G158200' => 'ptr', 'Pp3c11_7280' => 'ppa', 'Pp3c11_7980' => 'ppa', 'Pp3c12_19450' => 'ppa', 'Pp3c14_1480' => 'ppa', 'Pp3c14_1501' => 'ppa', 'Pp3c16_4900' => 'ppa', 'Pp3c16_5010' => 'ppa', 'Pp3c16_5060' => 'ppa', 'Pp3c19_18250' => 'ppa', 'Pp3c23_8530' => 'ppa', 'Pp3c23_8550' => 'ppa', 'Pp3c24_9670' => 'ppa', 'Pp3c2_21390' => 'ppa', 'Pp3c2_31380' => 'ppa', 'Pp3c3_16620' => 'ppa', 'Pp3c3_8090' => 'ppa', 'Pp3c3_8110' => 'ppa', 'Pp3c3_8130' => 'ppa', 'Pp3c3_8150' => 'ppa', 'Pp3c4_14320' => 'ppa', 'Pp3c6_2560' => 'ppa', 'Pp3c9_16700' => 'ppa', 'PRCOL_00000234' => 'pco', 'PRCOL_00000235' => 'pco', 'PRCOL_00000777' => 'pco', 'PRCOL_00002344' => 'pco', 'PRCOL_00002372' => 'pco', 'PRCOL_00006120' => 'pco', 'Prupe.1G021400' => 'ppe', 'Prupe.1G021500' => 'ppe', 'Prupe.1G021600' => 'ppe', 'Prupe.1G021700' => 'ppe', 'Prupe.1G021800' => 'ppe', 'Prupe.5G145100' => 'ppe', 'Psat6g204040' => 'psa', 'Psat6g204800' => 'psa', 'Psat6g204920' => 'psa', 'Psat6g204960' => 'psa', 'Psat6g205080' => 'psa', 'PSO017G0271' => 'pso', 'PSO017G1276' => 'pso', 'PSO017G1429' => 'pso', 'PSO017G1861' => 'pso', 'PSO017G2787' => 'pso', 'PSO017G4466' => 'pso', 'PSO017G5118' => 'pso', 'PSO017G5420' => 'pso', 'PSO063G3678' => 'pso', 'PSO210G0546' => 'pso', 'PSO317G0001' => 'pso', 'PSO357G0512' => 'pso', 'PSO478G2682' => 'pso', 'PSO647G0001' => 'pso', 'PSO675G0001' => 'pso', 'PSO675G2699' => 'pso', 'PSO675G2849' => 'pso', 'PSO675G4991' => 'pso', 'PSO689G0001' => 'pso', 'QL06p000916' => 'qlo', 'QL06p000921' => 'qlo', 'QL06p001398' => 'qlo', 'QL06p001407' => 'qlo', 'QL06p002031' => 'qlo', 'RcHm_v2.0_Chr4g0387791' => 'rch', 'RcHm_v2.0_Chr4g0387801' => 'rch', 'RcHm_v2.0_Chr6g0286501' => 'rch', 'RcHm_v2.0_Chr6g0286511' => 'rch', 'RcHm_v2.0_Chr6g0286521' => 'rch', 'RcHm_v2.0_Chr6g0286531' => 'rch', 'RcHm_v2.0_Chr7g0189141' => 'rch', 'Rhsim02G0028700' => 'rsi', 'Rhsim02G0028800' => 'rsi', 'Rhsim02G0028900' => 'rsi', 'Rhsim02G0029000' => 'rsi', 'Rhsim02G0029100' => 'rsi', 'Rhsim02G0029200' => 'rsi', 'Rhsim02G0029300' => 'rsi', 'Rhsim02G0029400' => 'rsi', 'Rhsim02G0029500' => 'rsi', 'Rhsim02G0029600' => 'rsi', 'RhsimUnG0024000' => 'rsi', 'RhsimUnG0024100' => 'rsi', 'RhsimUnG0024200' => 'rsi', 'RhsimUnG0024300' => 'rsi', 'RhsimUnG0024400' => 'rsi', 'RhsimUnG0024500' => 'rsi', 'RhsimUnG0024700' => 'rsi', 'RhsimUnG0024800' => 'rsi', 'RhsimUnG0024900' => 'rsi', 'RhsimUnG0025100' => 'rsi', 'Sabra08G0120200' => 'sbr', 'Sabra08G0120300' => 'sbr', 'Sabra08G0120500' => 'sbr', 'Sabra08G0120600' => 'sbr', 'Sabra10G0158900' => 'sbr', 'SalBow2G3492' => 'sbo', 'Sc13g0004760' => 'sci', 'Sc13g0004770' => 'sci', 'Sed0003417' => 'sed', 'Sed0019750' => 'sed', 'SEGI_03419' => 'sgi', 'SEGI_05907' => 'sgi', 'SEGI_10682' => 'sgi', 'SEGI_13528' => 'sgi', 'SEGI_16081' => 'sgi', 'SEGI_19370' => 'sgi', 'SEGI_21015' => 'sgi', 'SEGI_21944' => 'sgi', 'SEGI_32906' => 'sgi', 'SEGI_33093' => 'sgi', 'SEGI_36110' => 'sgi', 'SEGI_40397' => 'sgi', 'SGA_v2.0_scaffold191G40426' => 'sas', 'SGA_v2.0_scaffold353G49717' => 'sas', 'SGA_v2.0_scaffold50G18550' => 'sas', 'SMO119G0173' => 'smo', 'SMO172G0002' => 'smo', 'Solyc09g082690.3' => 'sly', 'Solyc09g082700.2' => 'sly', 'Sopen09g031550' => 'spe', 'Sopen09g031560' => 'spe', 'Sp3g20540' => 'spa', 'Sp7g07580' => 'spa', 'TAR134G0002' => 'tar', 'TAR236G0001' => 'tar', 'TAR365G0892' => 'tar', 'TAR636G0166' => 'tar', 'TAR636G0646' => 'tar', 'TAR636G0869' => 'tar', 'TAR636G1317' => 'tar', 'TAR636G1744' => 'tar', 'TAR636G3358' => 'tar', 'TAR636G3436' => 'tar', 'THA.LOC104803047' => 'tha', 'Thecc.04G238900' => 'tca', 'Thhalv10021557m.g' => 'esa', 'Thhalv10026318m.g' => 'esa', 'Thhalv10026335m.g' => 'esa', 'TPR.G17433' => 'tpr', 'TPR.G18915' => 'tpr', 'TPR.G26125' => 'tpr', 'TWI09G0677' => 'twi', 'TWI73G0287' => 'twi', 'unitig_748.g8326' => 'ugi', 'vmacro15370' => 'vma', 'vmacro15371' => 'vma', 'vmacro15372' => 'vma', 'vmacro15373' => 'vma', 'vmacro15374' => 'vma', 'VMungo0720G2826' => 'vmu', 'Zm00001eb116960' => 'zma', 'Zm00001eb301260' => 'zma', 'Zm00001eb301270' => 'zma' ), 'gf_id' => 'HOM05D001460', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001460' ), 'data_identifier' => 'HOM05D001460', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001460', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '433', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p22980' => 'bna', 'A01p32340' => 'bna', 'A03p42970' => 'bna', 'A05p25880' => 'bna', 'Aa31LG8G9320' => 'aar', 'Aa31LG8G9330' => 'aar', 'Aa31LG8G9340' => 'aar', 'Aa31sc221G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1034' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1528' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.829' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2222' => 'aag', 'Ah.12g058830' => 'amhyb', 'Ah.12g058840' => 'amhyb', 'AL3G37160' => 'aly', 'AL7G41310' => 'aly', 'Aqoxy5G00395' => 'aox', 'Aqoxy5G00396' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0C8NZA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5185HY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JZ1PRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MD3LS0' => 'arhy', 'AT3G22840' => 'ath', 'AT4G14690' => 'ath', 'ATR0665G054' => 'atr', 'Atru.chr4.2344' => 'acertr', 'Atru.chr4.2346' => 'acertr', 'Atru.chr4.2347' => 'acertr', 'Atru.chr4.2348' => 'acertr', 'Atru.chr4.2355' => 'acertr', 'Atru.chr4.2356' => 'acertr', 'Atru.chr4.2358' => 'acertr', 'Atru.chr4.2359' => 'acertr', 'Atru.chr4.2360' => 'acertr', 'Atru.chr4.2361' => 'acertr', 'AUR62030476' => 'cqu', 'AUR62030478' => 'cqu', 'AUR62030819' => 'cqu', 'AUR62030820' => 'cqu', 'BcaB03g14648' => 'bca', 'BcaB04g20492' => 'bca', 'BcaB06g26399' => 'bca', 'BcaC01g03416' => 'bca', 'BcaC01g03419' => 'bca', 'BcaC01g03421' => 'bca', 'BcaC01g03424' => 'bca', 'BcaC05g28012' => 'bca', 'BcaC09g49212' => 'bca', 'BcaC09g50140' => 'bca', 'BcaNung00346' => 'bca', 'BolC1t02785H' => 'bol', 'BolC1t04095H' => 'bol', 'BolC3t17545H' => 'bol', 'BolC5t32769H' => 'bol', 'BraA01t02211Z' => 'bra', 'BraA01t03359Z' => 'bra', 'BraA03t13441Z' => 'bra', 'BraA05t21476Z' => 'bra', 'C01p28420' => 'bna', 'C01p41350' => 'bna', 'C03p52750' => 'bna', 'C03p52780' => 'bna', 'C05p40270' => 'bna', 'CAN.G1437.9' => 'can', 'CANSAT78G0035' => 'cansat', 'CANSAT78G1036' => 'cansat', 'CANSAT78G2272' => 'cansat', 'CANSAT78G2478' => 'cansat', 'CARHR098700' => 'chi', 'CARHR221120' => 'chi', 'CARHR221150' => 'chi', 'Carub.0003s2297' => 'cru', 'Carub.0007s2749' => 'cru', 'Carub.0007s2750' => 'cru', 'Carub.0007s2751' => 'cru', 'Ca_10849_v3' => 'car', 'Cc03_g04300' => 'ccan', 'CDE02G3648' => 'cde', 'CDE05G0060' => 'cde', 'CDE05G0692' => 'cde', 'CDE05G2285' => 'cde', 'CDE05G2884' => 'cde', 'CDE05G3072' => 'cde', 'Cfa008439' => 'cfa', 'Cfa008441' => 'cfa', 'Cfa008443' => 'cfa', 'Cfa008448' => 'cfa', 'Ciclev10005974m.g' => 'ccl', 'Ciclev10006006m.g' => 'ccl', 'Ciclev10006775m.g' => 'ccl', 'CiPaw.02G120400' => 'cil', 'CiPaw.02G120500' => 'cil', 'CiPaw.02G120600' => 'cil', 'ClCG05G004850' => 'cla', 'COL.COLO4_21566' => 'col', 'Cpa.g.sc44.124' => 'cpa', 'Cre07.g320400' => 'cre', 'Cre07.g320450' => 'cre', 'Cre08.g384650' => 'cre', 'Cre09.g393173' => 'cre', 'Cre09.g394325' => 'cre', 'Cre14.g626750' => 'cre', 'Cre16.g679250' => 'cre', 'CsaV3_3G012890' => 'csa', 'CSS0010865' => 'camsi', 'CSS0044338' => 'camsi', 'DCAR_002366' => 'dca', 'DCAR_030687' => 'dca', 'DCAR_030688' => 'dca', 'Dinv14047' => 'din', 'Dinv14048' => 'din', 'Duzib151G0105' => 'dzi', 'Duzib151G0114' => 'dzi', 'Duzib212G1029' => 'dzi', 'ECA232G3536' => 'eca', 'ECA240G0786' => 'eca', 'ECA240G1802' => 'eca', 'ECA240G3760' => 'eca', 'ECA240G3920' => 'eca', 'EL10Ac5g12536' => 'bvu', 'EL10Ac5g12537' => 'bvu', 'EL10Ac5g12538' => 'bvu', 'Eucgr.B01004' => 'egr', 'Eucgr.B01006' => 'egr', 'Eucgr.B01007' => 'egr', 'Eucgr.B01008' => 'egr', 'Eucgr.B01895' => 'egr', 'Eucgr.B01896' => 'egr', 'FAN04G1456' => 'fan', 'FAN08G1769' => 'fan', 'FAN08G2160' => 'fan', 'FAN13G2403' => 'fan', 'FAN13G3303' => 'fan', 'FAN15G2435' => 'fan', 'FAN17G0672' => 'fan', 'FAN17G2441' => 'fan', 'FAN18G1024' => 'fan', 'FAN22G1458' => 'fan', 'FAN24G0037' => 'fan', 'FAN24G0429' => 'fan', 'FAN24G2387' => 'fan', 'FAN27G2746' => 'fan', 'FvH4_2g20400' => 'fve', 'FvH4_2g20420' => 'fve', 'FvH4_2g20430' => 'fve', 'FvH4_4g01270' => 'fve', 'FvH4_4g01290' => 'fve', 'FvH4_4g01300' => 'fve', 'FvH4_4g01310' => 'fve', 'FvH4_4g01330' => 'fve', 'FvH4_5g09070' => 'fve', 'Glyma.10G243800' => 'gma', 'Glyma.20G150600' => 'gma', 'Gohir.A09G219200' => 'ghi', 'Gohir.A09G219300' => 'ghi', 'Gohir.D09G221400' => 'ghi', 'Gohir.D09G221500' => 'ghi', 'Gorai.006G242600' => 'gra', 'Gorai.006G242700' => 'gra', 'GSVIVG01018044001' => 'vvi', 'HanXRQChr03g0083821' => 'han', 'HanXRQChr03g0083841' => 'han', 'HanXRQChr03g0083881' => 'han', 'HanXRQChr03g0083901' => 'han', 'HanXRQChr03g0083921' => 'han', 'HanXRQChr03g0085331' => 'han', 'HanXRQChr03g0085361' => 'han', 'HanXRQChr03g0085411' => 'han', 'HanXRQChr03g0085421' => 'han', 'HanXRQChr03g0085431' => 'han', 'HanXRQChr08g0221991' => 'han', 'HanXRQChr11g0336061' => 'han', 'HanXRQChr11g0336411' => 'han', 'Haze_11234' => 'cav', 'Hma1.2p1_0549F.1_g177010' => 'hma', 'Hma1.2p1_0602F.1_g187630' => 'hma', 'Hund14876' => 'sun', 'Hund14879' => 'sun', 'Lalb_Chr06g0160741' => 'lal', 'Lalb_Chr21g0304781' => 'lal', 'Lj3A726G19' => 'lonja', 'Lj3A726T23' => 'lonja', 'Lj3A726T24' => 'lonja', 'Lj3A726T25' => 'lonja', 'Lj3A727T17' => 'lonja', 'Lj3C726T0' => 'lonja', 'Lj3C726T2' => 'lonja', 'Lj3P725T35' => 'lonja', 'Lj3P727T10' => 'lonja', 'Lj3P727T12' => 'lonja', 'Lj3P727T14' => 'lonja', 'Lj5g0023109' => 'lja', 'Lj6P646T44' => 'lonja', 'Lsat_1_v5_gn_6_75760' => 'lsa', 'Lsat_1_v5_gn_6_75800' => 'lsa', 'Lsat_1_v5_gn_6_75900' => 'lsa', 'Lsat_1_v5_gn_6_76240' => 'lsa', 'Lsat_1_v5_gn_6_76441' => 'lsa', 'Lsat_1_v5_gn_6_76700' => 'lsa', 'Lsat_1_v5_gn_6_76760' => 'lsa', 'Manes.15G033100' => 'mes', 'Mapoly0004s0074' => 'mpo', 'Mapoly0004s0075' => 'mpo', 'Mapoly0004s0163' => 'mpo', 'Mapoly0004s0164' => 'mpo', 'Mapoly0021s0018' => 'mpo', 'Mapoly0041s0136' => 'mpo', 'Mapoly0041s0137' => 'mpo', 'Mapoly0041s0138' => 'mpo', 'Mapoly0041s0139' => 'mpo', 'Mapoly0041s0141' => 'mpo', 'Mapoly0041s0142' => 'mpo', 'Mapoly0041s0143' => 'mpo', 'Mapoly0041s0144' => 'mpo', 'Mapoly0041s0145' => 'mpo', 'Mapoly0047s0106' => 'mpo', 'Mapoly0047s0108' => 'mpo', 'Mapoly0050s0051' => 'mpo', 'Mapoly0050s0052' => 'mpo', 'Mapoly0050s0053' => 'mpo', 'Mapoly0058s0013' => 'mpo', 'Mapoly0091s0078' => 'mpo', 'Mapoly0091s0079' => 'mpo', 'Mapoly0091s0080' => 'mpo', 'Mapoly0091s0081' => 'mpo', 'Mapoly0278s0004' => 'mpo', 'Mapoly0278s0005' => 'mpo', 'Mapoly0278s0006' => 'mpo', 'MBI11_g30648_MAGBIO' => 'mbi', 'MCO03G194' => 'mco', 'MCO03G590' => 'mco', 'MCO07G312' => 'mco', 'MCO10G318' => 'mco', 'MCO12G244' => 'mco', 'MCO13G148' => 'mco', 'MCO13G194' => 'mco', 'MCO16G238' => 'mco', 'MD06G1134100' => 'mdo', 'MD13G1200100' => 'mdo', 'MD13G1200300' => 'mdo', 'MD13G1200600' => 'mdo', 'MD14G1150400' => 'mdo', 'MD16G1200000' => 'mdo', 'Medtr1g102570' => 'mtr', 'Medtr1g102780' => 'mtr', 'Medtr1g102800' => 'mtr', 'Medtr1g102810' => 'mtr', 'Medtr1g102830' => 'mtr', 'MELO3C006499.2' => 'cme', 'Migut.G00385' => 'egut', 'MSTRG.4063' => 'ama', 'Nitab4.5_0000090g0260' => 'nta', 'Nitab4.5_0000977g0030' => 'nta', 'Nitab4.5_0002541g0040' => 'nta', 'Nitab4.5_0007068g0040' => 'nta', 'Nn005s41408' => 'nnu', 'Nn005s41410' => 'nnu', 'Oeu010310.1' => 'oeu', 'Oeu010311.1' => 'oeu', 'Oeu043472.1' => 'oeu', 'Os01g0246400' => 'osa', 'Os04g0267950' => 'osa', 'Os07g0178700' => 'osa', 'Os07g0178800' => 'osa', 'Peaxi162Scf00316g00046' => 'pax', 'Peaxi162Scf00316g00049' => 'pax', 'Peaxi162Scf00316g00059' => 'pax', 'Peaxi162Scf00316g00328' => 'pax', 'Peaxi162Scf00316g00329' => 'pax', 'Peaxi162Scf00316g00411' => 'pax', 'Peaxi162Scf00316g00521' => 'pax', 'Peaxi162Scf00492g00068' => 'pax', 'Peaxi162Scf35631g00002' => 'pax', 'PGR142G3720' => 'pgr', 'PGSC0003DMG400006442' => 'stu', 'Phvul.007G062000' => 'pvu', 'Potri.008G157750' => 'ptr', 'Potri.008G157900' => 'ptr', 'Potri.008G158000' => 'ptr', 'Potri.008G158200' => 'ptr', 'Pp3c11_7280' => 'ppa', 'Pp3c11_7980' => 'ppa', 'Pp3c12_19450' => 'ppa', 'Pp3c14_1480' => 'ppa', 'Pp3c14_1501' => 'ppa', 'Pp3c16_4900' => 'ppa', 'Pp3c16_5010' => 'ppa', 'Pp3c16_5060' => 'ppa', 'Pp3c19_18250' => 'ppa', 'Pp3c23_8530' => 'ppa', 'Pp3c23_8550' => 'ppa', 'Pp3c24_9670' => 'ppa', 'Pp3c2_21390' => 'ppa', 'Pp3c2_31380' => 'ppa', 'Pp3c3_16620' => 'ppa', 'Pp3c3_8090' => 'ppa', 'Pp3c3_8110' => 'ppa', 'Pp3c3_8130' => 'ppa', 'Pp3c3_8150' => 'ppa', 'Pp3c4_14320' => 'ppa', 'Pp3c6_2560' => 'ppa', 'Pp3c9_16700' => 'ppa', 'PRCOL_00000234' => 'pco', 'PRCOL_00000235' => 'pco', 'PRCOL_00000777' => 'pco', 'PRCOL_00002344' => 'pco', 'PRCOL_00002372' => 'pco', 'PRCOL_00006120' => 'pco', 'Prupe.1G021400' => 'ppe', 'Prupe.1G021500' => 'ppe', 'Prupe.1G021600' => 'ppe', 'Prupe.1G021700' => 'ppe', 'Prupe.1G021800' => 'ppe', 'Prupe.5G145100' => 'ppe', 'Psat6g204040' => 'psa', 'Psat6g204800' => 'psa', 'Psat6g204920' => 'psa', 'Psat6g204960' => 'psa', 'Psat6g205080' => 'psa', 'PSO017G0271' => 'pso', 'PSO017G1276' => 'pso', 'PSO017G1429' => 'pso', 'PSO017G1861' => 'pso', 'PSO017G2787' => 'pso', 'PSO017G4466' => 'pso', 'PSO017G5118' => 'pso', 'PSO017G5420' => 'pso', 'PSO063G3678' => 'pso', 'PSO210G0546' => 'pso', 'PSO317G0001' => 'pso', 'PSO357G0512' => 'pso', 'PSO478G2682' => 'pso', 'PSO647G0001' => 'pso', 'PSO675G0001' => 'pso', 'PSO675G2699' => 'pso', 'PSO675G2849' => 'pso', 'PSO675G4991' => 'pso', 'PSO689G0001' => 'pso', 'QL06p000916' => 'qlo', 'QL06p000921' => 'qlo', 'QL06p001398' => 'qlo', 'QL06p001407' => 'qlo', 'QL06p002031' => 'qlo', 'RcHm_v2.0_Chr4g0387791' => 'rch', 'RcHm_v2.0_Chr4g0387801' => 'rch', 'RcHm_v2.0_Chr6g0286501' => 'rch', 'RcHm_v2.0_Chr6g0286511' => 'rch', 'RcHm_v2.0_Chr6g0286521' => 'rch', 'RcHm_v2.0_Chr6g0286531' => 'rch', 'RcHm_v2.0_Chr7g0189141' => 'rch', 'Rhsim02G0028700' => 'rsi', 'Rhsim02G0028800' => 'rsi', 'Rhsim02G0028900' => 'rsi', 'Rhsim02G0029000' => 'rsi', 'Rhsim02G0029100' => 'rsi', 'Rhsim02G0029200' => 'rsi', 'Rhsim02G0029300' => 'rsi', 'Rhsim02G0029400' => 'rsi', 'Rhsim02G0029500' => 'rsi', 'Rhsim02G0029600' => 'rsi', 'RhsimUnG0024000' => 'rsi', 'RhsimUnG0024100' => 'rsi', 'RhsimUnG0024200' => 'rsi', 'RhsimUnG0024300' => 'rsi', 'RhsimUnG0024400' => 'rsi', 'RhsimUnG0024500' => 'rsi', 'RhsimUnG0024700' => 'rsi', 'RhsimUnG0024800' => 'rsi', 'RhsimUnG0024900' => 'rsi', 'RhsimUnG0025100' => 'rsi', 'Sabra08G0120200' => 'sbr', 'Sabra08G0120300' => 'sbr', 'Sabra08G0120500' => 'sbr', 'Sabra08G0120600' => 'sbr', 'Sabra10G0158900' => 'sbr', 'SalBow2G3492' => 'sbo', 'Sc13g0004760' => 'sci', 'Sc13g0004770' => 'sci', 'Sed0003417' => 'sed', 'Sed0019750' => 'sed', 'SEGI_03419' => 'sgi', 'SEGI_05907' => 'sgi', 'SEGI_10682' => 'sgi', 'SEGI_13528' => 'sgi', 'SEGI_16081' => 'sgi', 'SEGI_19370' => 'sgi', 'SEGI_21015' => 'sgi', 'SEGI_21944' => 'sgi', 'SEGI_32906' => 'sgi', 'SEGI_33093' => 'sgi', 'SEGI_36110' => 'sgi', 'SEGI_40397' => 'sgi', 'SGA_v2.0_scaffold191G40426' => 'sas', 'SGA_v2.0_scaffold353G49717' => 'sas', 'SGA_v2.0_scaffold50G18550' => 'sas', 'SMO119G0173' => 'smo', 'SMO172G0002' => 'smo', 'Solyc09g082690.3' => 'sly', 'Solyc09g082700.2' => 'sly', 'Sopen09g031550' => 'spe', 'Sopen09g031560' => 'spe', 'Sp3g20540' => 'spa', 'Sp7g07580' => 'spa', 'TAR134G0002' => 'tar', 'TAR236G0001' => 'tar', 'TAR365G0892' => 'tar', 'TAR636G0166' => 'tar', 'TAR636G0646' => 'tar', 'TAR636G0869' => 'tar', 'TAR636G1317' => 'tar', 'TAR636G1744' => 'tar', 'TAR636G3358' => 'tar', 'TAR636G3436' => 'tar', 'THA.LOC104803047' => 'tha', 'Thecc.04G238900' => 'tca', 'Thhalv10021557m.g' => 'esa', 'Thhalv10026318m.g' => 'esa', 'Thhalv10026335m.g' => 'esa', 'TPR.G17433' => 'tpr', 'TPR.G18915' => 'tpr', 'TPR.G26125' => 'tpr', 'TWI09G0677' => 'twi', 'TWI73G0287' => 'twi', 'unitig_748.g8326' => 'ugi', 'vmacro15370' => 'vma', 'vmacro15371' => 'vma', 'vmacro15372' => 'vma', 'vmacro15373' => 'vma', 'vmacro15374' => 'vma', 'VMungo0720G2826' => 'vmu', 'Zm00001eb116960' => 'zma', 'Zm00001eb301260' => 'zma', 'Zm00001eb301270' => 'zma' ) $gf_id = 'HOM05D001460' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001460' ) $data_identifier = 'HOM05D001460' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 4, 'aag' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 2, 'aox' => (int) 2, 'arhy' => (int) 4, 'ath' => (int) 2, 'atr' => (int) 1, 'acertr' => (int) 10, 'cqu' => (int) 4, 'bca' => (int) 11, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 1, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 1, 'ccan' => (int) 1, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 1, 'col' => (int) 1, 'cpa' => (int) 1, 'cre' => (int) 7, 'csa' => (int) 1, 'camsi' => (int) 2, 'dca' => (int) 3, 'din' => (int) 2, 'dzi' => (int) 3, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 14, 'fve' => (int) 9, 'gma' => (int) 2, 'ghi' => (int) 4, 'gra' => (int) 2, 'vvi' => (int) 1, 'han' => (int) 13, 'cav' => (int) 1, 'hma' => (int) 2, 'sun' => (int) 2, 'lal' => (int) 2, 'lonja' => (int) 12, 'lja' => (int) 1, 'lsa' => (int) 7, 'mes' => (int) 1, 'mpo' => (int) 27, 'mbi' => (int) 1, 'mco' => (int) 8, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 1, 'egut' => (int) 1, 'ama' => (int) 1, 'nta' => (int) 4, 'nnu' => (int) 2, 'oeu' => (int) 3, 'osa' => (int) 4, 'pax' => (int) 9, 'pgr' => (int) 1, 'stu' => (int) 1, 'pvu' => (int) 1, 'ptr' => (int) 4, 'ppa' => (int) 22, 'pco' => (int) 6, 'ppe' => (int) 6, 'psa' => (int) 5, 'pso' => (int) 19, 'qlo' => (int) 5, 'rch' => (int) 7, 'rsi' => (int) 20, 'sbr' => (int) 5, 'sbo' => (int) 1, 'sci' => (int) 2, 'sed' => (int) 2, 'sgi' => (int) 12, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 2, 'tar' => (int) 10, 'tha' => (int) 1, 'tca' => (int) 1, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 2, 'ugi' => (int) 1, 'vma' => (int) 5, 'vmu' => (int) 1, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb301270' $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' => 'HOM05D001460', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '433', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p22980' => 'bna', 'A01p32340' => 'bna', 'A03p42970' => 'bna', 'A05p25880' => 'bna', 'Aa31LG8G9320' => 'aar', 'Aa31LG8G9330' => 'aar', 'Aa31LG8G9340' => 'aar', 'Aa31sc221G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1034' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1528' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.829' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2222' => 'aag', 'Ah.12g058830' => 'amhyb', 'Ah.12g058840' => 'amhyb', 'AL3G37160' => 'aly', 'AL7G41310' => 'aly', 'Aqoxy5G00395' => 'aox', 'Aqoxy5G00396' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0C8NZA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5185HY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JZ1PRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MD3LS0' => 'arhy', 'AT3G22840' => 'ath', 'AT4G14690' => 'ath', 'ATR0665G054' => 'atr', 'Atru.chr4.2344' => 'acertr', 'Atru.chr4.2346' => 'acertr', 'Atru.chr4.2347' => 'acertr', 'Atru.chr4.2348' => 'acertr', 'Atru.chr4.2355' => 'acertr', 'Atru.chr4.2356' => 'acertr', 'Atru.chr4.2358' => 'acertr', 'Atru.chr4.2359' => 'acertr', 'Atru.chr4.2360' => 'acertr', 'Atru.chr4.2361' => 'acertr', 'AUR62030476' => 'cqu', 'AUR62030478' => 'cqu', 'AUR62030819' => 'cqu', 'AUR62030820' => 'cqu', 'BcaB03g14648' => 'bca', 'BcaB04g20492' => 'bca', 'BcaB06g26399' => 'bca', 'BcaC01g03416' => 'bca', 'BcaC01g03419' => 'bca', 'BcaC01g03421' => 'bca', 'BcaC01g03424' => 'bca', 'BcaC05g28012' => 'bca', 'BcaC09g49212' => 'bca', 'BcaC09g50140' => 'bca', 'BcaNung00346' => 'bca', 'BolC1t02785H' => 'bol', 'BolC1t04095H' => 'bol', 'BolC3t17545H' => 'bol', 'BolC5t32769H' => 'bol', 'BraA01t02211Z' => 'bra', 'BraA01t03359Z' => 'bra', 'BraA03t13441Z' => 'bra', 'BraA05t21476Z' => 'bra', 'C01p28420' => 'bna', 'C01p41350' => 'bna', 'C03p52750' => 'bna', 'C03p52780' => 'bna', 'C05p40270' => 'bna', 'CAN.G1437.9' => 'can', 'CANSAT78G0035' => 'cansat', 'CANSAT78G1036' => 'cansat', 'CANSAT78G2272' => 'cansat', 'CANSAT78G2478' => 'cansat', 'CARHR098700' => 'chi', 'CARHR221120' => 'chi', 'CARHR221150' => 'chi', 'Carub.0003s2297' => 'cru', 'Carub.0007s2749' => 'cru', 'Carub.0007s2750' => 'cru', 'Carub.0007s2751' => 'cru', 'Ca_10849_v3' => 'car', 'Cc03_g04300' => 'ccan', 'CDE02G3648' => 'cde', 'CDE05G0060' => 'cde', 'CDE05G0692' => 'cde', 'CDE05G2285' => 'cde', 'CDE05G2884' => 'cde', 'CDE05G3072' => 'cde', 'Cfa008439' => 'cfa', 'Cfa008441' => 'cfa', 'Cfa008443' => 'cfa', 'Cfa008448' => 'cfa', 'Ciclev10005974m.g' => 'ccl', 'Ciclev10006006m.g' => 'ccl', 'Ciclev10006775m.g' => 'ccl', 'CiPaw.02G120400' => 'cil', 'CiPaw.02G120500' => 'cil', 'CiPaw.02G120600' => 'cil', 'ClCG05G004850' => 'cla', 'COL.COLO4_21566' => 'col', 'Cpa.g.sc44.124' => 'cpa', 'Cre07.g320400' => 'cre', 'Cre07.g320450' => 'cre', 'Cre08.g384650' => 'cre', 'Cre09.g393173' => 'cre', 'Cre09.g394325' => 'cre', 'Cre14.g626750' => 'cre', 'Cre16.g679250' => 'cre', 'CsaV3_3G012890' => 'csa', 'CSS0010865' => 'camsi', 'CSS0044338' => 'camsi', 'DCAR_002366' => 'dca', 'DCAR_030687' => 'dca', 'DCAR_030688' => 'dca', 'Dinv14047' => 'din', 'Dinv14048' => 'din', 'Duzib151G0105' => 'dzi', 'Duzib151G0114' => 'dzi', 'Duzib212G1029' => 'dzi', 'ECA232G3536' => 'eca', 'ECA240G0786' => 'eca', 'ECA240G1802' => 'eca', 'ECA240G3760' => 'eca', 'ECA240G3920' => 'eca', 'EL10Ac5g12536' => 'bvu', 'EL10Ac5g12537' => 'bvu', 'EL10Ac5g12538' => 'bvu', 'Eucgr.B01004' => 'egr', 'Eucgr.B01006' => 'egr', 'Eucgr.B01007' => 'egr', 'Eucgr.B01008' => 'egr', 'Eucgr.B01895' => 'egr', 'Eucgr.B01896' => 'egr', 'FAN04G1456' => 'fan', 'FAN08G1769' => 'fan', 'FAN08G2160' => 'fan', 'FAN13G2403' => 'fan', 'FAN13G3303' => 'fan', 'FAN15G2435' => 'fan', 'FAN17G0672' => 'fan', 'FAN17G2441' => 'fan', 'FAN18G1024' => 'fan', 'FAN22G1458' => 'fan', 'FAN24G0037' => 'fan', 'FAN24G0429' => 'fan', 'FAN24G2387' => 'fan', 'FAN27G2746' => 'fan', 'FvH4_2g20400' => 'fve', 'FvH4_2g20420' => 'fve', 'FvH4_2g20430' => 'fve', 'FvH4_4g01270' => 'fve', 'FvH4_4g01290' => 'fve', 'FvH4_4g01300' => 'fve', 'FvH4_4g01310' => 'fve', 'FvH4_4g01330' => 'fve', 'FvH4_5g09070' => 'fve', 'Glyma.10G243800' => 'gma', 'Glyma.20G150600' => 'gma', 'Gohir.A09G219200' => 'ghi', 'Gohir.A09G219300' => 'ghi', 'Gohir.D09G221400' => 'ghi', 'Gohir.D09G221500' => 'ghi', 'Gorai.006G242600' => 'gra', 'Gorai.006G242700' => 'gra', 'GSVIVG01018044001' => 'vvi', 'HanXRQChr03g0083821' => 'han', 'HanXRQChr03g0083841' => 'han', 'HanXRQChr03g0083881' => 'han', 'HanXRQChr03g0083901' => 'han', 'HanXRQChr03g0083921' => 'han', 'HanXRQChr03g0085331' => 'han', 'HanXRQChr03g0085361' => 'han', 'HanXRQChr03g0085411' => 'han', 'HanXRQChr03g0085421' => 'han', 'HanXRQChr03g0085431' => 'han', 'HanXRQChr08g0221991' => 'han', 'HanXRQChr11g0336061' => 'han', 'HanXRQChr11g0336411' => 'han', 'Haze_11234' => 'cav', 'Hma1.2p1_0549F.1_g177010' => 'hma', 'Hma1.2p1_0602F.1_g187630' => 'hma', 'Hund14876' => 'sun', 'Hund14879' => 'sun', 'Lalb_Chr06g0160741' => 'lal', 'Lalb_Chr21g0304781' => 'lal', 'Lj3A726G19' => 'lonja', 'Lj3A726T23' => 'lonja', 'Lj3A726T24' => 'lonja', 'Lj3A726T25' => 'lonja', 'Lj3A727T17' => 'lonja', 'Lj3C726T0' => 'lonja', 'Lj3C726T2' => 'lonja', 'Lj3P725T35' => 'lonja', 'Lj3P727T10' => 'lonja', 'Lj3P727T12' => 'lonja', 'Lj3P727T14' => 'lonja', 'Lj5g0023109' => 'lja', 'Lj6P646T44' => 'lonja', 'Lsat_1_v5_gn_6_75760' => 'lsa', 'Lsat_1_v5_gn_6_75800' => 'lsa', 'Lsat_1_v5_gn_6_75900' => 'lsa', 'Lsat_1_v5_gn_6_76240' => 'lsa', 'Lsat_1_v5_gn_6_76441' => 'lsa', 'Lsat_1_v5_gn_6_76700' => 'lsa', 'Lsat_1_v5_gn_6_76760' => 'lsa', 'Manes.15G033100' => 'mes', 'Mapoly0004s0074' => 'mpo', 'Mapoly0004s0075' => 'mpo', 'Mapoly0004s0163' => 'mpo', 'Mapoly0004s0164' => 'mpo', 'Mapoly0021s0018' => 'mpo', 'Mapoly0041s0136' => 'mpo', 'Mapoly0041s0137' => 'mpo', 'Mapoly0041s0138' => 'mpo', 'Mapoly0041s0139' => 'mpo', 'Mapoly0041s0141' => 'mpo', 'Mapoly0041s0142' => 'mpo', 'Mapoly0041s0143' => 'mpo', 'Mapoly0041s0144' => 'mpo', 'Mapoly0041s0145' => 'mpo', 'Mapoly0047s0106' => 'mpo', 'Mapoly0047s0108' => 'mpo', 'Mapoly0050s0051' => 'mpo', 'Mapoly0050s0052' => 'mpo', 'Mapoly0050s0053' => 'mpo', 'Mapoly0058s0013' => 'mpo', 'Mapoly0091s0078' => 'mpo', 'Mapoly0091s0079' => 'mpo', 'Mapoly0091s0080' => 'mpo', 'Mapoly0091s0081' => 'mpo', 'Mapoly0278s0004' => 'mpo', 'Mapoly0278s0005' => 'mpo', 'Mapoly0278s0006' => 'mpo', 'MBI11_g30648_MAGBIO' => 'mbi', 'MCO03G194' => 'mco', 'MCO03G590' => 'mco', 'MCO07G312' => 'mco', 'MCO10G318' => 'mco', 'MCO12G244' => 'mco', 'MCO13G148' => 'mco', 'MCO13G194' => 'mco', 'MCO16G238' => 'mco', 'MD06G1134100' => 'mdo', 'MD13G1200100' => 'mdo', 'MD13G1200300' => 'mdo', 'MD13G1200600' => 'mdo', 'MD14G1150400' => 'mdo', 'MD16G1200000' => 'mdo', 'Medtr1g102570' => 'mtr', 'Medtr1g102780' => 'mtr', 'Medtr1g102800' => 'mtr', 'Medtr1g102810' => 'mtr', 'Medtr1g102830' => 'mtr', 'MELO3C006499.2' => 'cme', 'Migut.G00385' => 'egut', 'MSTRG.4063' => 'ama', 'Nitab4.5_0000090g0260' => 'nta', 'Nitab4.5_0000977g0030' => 'nta', 'Nitab4.5_0002541g0040' => 'nta', 'Nitab4.5_0007068g0040' => 'nta', 'Nn005s41408' => 'nnu', 'Nn005s41410' => 'nnu', 'Oeu010310.1' => 'oeu', 'Oeu010311.1' => 'oeu', 'Oeu043472.1' => 'oeu', 'Os01g0246400' => 'osa', 'Os04g0267950' => 'osa', 'Os07g0178700' => 'osa', 'Os07g0178800' => 'osa', 'Peaxi162Scf00316g00046' => 'pax', 'Peaxi162Scf00316g00049' => 'pax', 'Peaxi162Scf00316g00059' => 'pax', 'Peaxi162Scf00316g00328' => 'pax', 'Peaxi162Scf00316g00329' => 'pax', 'Peaxi162Scf00316g00411' => 'pax', 'Peaxi162Scf00316g00521' => 'pax', 'Peaxi162Scf00492g00068' => 'pax', 'Peaxi162Scf35631g00002' => 'pax', 'PGR142G3720' => 'pgr', 'PGSC0003DMG400006442' => 'stu', 'Phvul.007G062000' => 'pvu', 'Potri.008G157750' => 'ptr', 'Potri.008G157900' => 'ptr', 'Potri.008G158000' => 'ptr', 'Potri.008G158200' => 'ptr', 'Pp3c11_7280' => 'ppa', 'Pp3c11_7980' => 'ppa', 'Pp3c12_19450' => 'ppa', 'Pp3c14_1480' => 'ppa', 'Pp3c14_1501' => 'ppa', 'Pp3c16_4900' => 'ppa', 'Pp3c16_5010' => 'ppa', 'Pp3c16_5060' => 'ppa', 'Pp3c19_18250' => 'ppa', 'Pp3c23_8530' => 'ppa', 'Pp3c23_8550' => 'ppa', 'Pp3c24_9670' => 'ppa', 'Pp3c2_21390' => 'ppa', 'Pp3c2_31380' => 'ppa', 'Pp3c3_16620' => 'ppa', 'Pp3c3_8090' => 'ppa', 'Pp3c3_8110' => 'ppa', 'Pp3c3_8130' => 'ppa', 'Pp3c3_8150' => 'ppa', 'Pp3c4_14320' => 'ppa', 'Pp3c6_2560' => 'ppa', 'Pp3c9_16700' => 'ppa', 'PRCOL_00000234' => 'pco', 'PRCOL_00000235' => 'pco', 'PRCOL_00000777' => 'pco', 'PRCOL_00002344' => 'pco', 'PRCOL_00002372' => 'pco', 'PRCOL_00006120' => 'pco', 'Prupe.1G021400' => 'ppe', 'Prupe.1G021500' => 'ppe', 'Prupe.1G021600' => 'ppe', 'Prupe.1G021700' => 'ppe', 'Prupe.1G021800' => 'ppe', 'Prupe.5G145100' => 'ppe', 'Psat6g204040' => 'psa', 'Psat6g204800' => 'psa', 'Psat6g204920' => 'psa', 'Psat6g204960' => 'psa', 'Psat6g205080' => 'psa', 'PSO017G0271' => 'pso', 'PSO017G1276' => 'pso', 'PSO017G1429' => 'pso', 'PSO017G1861' => 'pso', 'PSO017G2787' => 'pso', 'PSO017G4466' => 'pso', 'PSO017G5118' => 'pso', 'PSO017G5420' => 'pso', 'PSO063G3678' => 'pso', 'PSO210G0546' => 'pso', 'PSO317G0001' => 'pso', 'PSO357G0512' => 'pso', 'PSO478G2682' => 'pso', 'PSO647G0001' => 'pso', 'PSO675G0001' => 'pso', 'PSO675G2699' => 'pso', 'PSO675G2849' => 'pso', 'PSO675G4991' => 'pso', 'PSO689G0001' => 'pso', 'QL06p000916' => 'qlo', 'QL06p000921' => 'qlo', 'QL06p001398' => 'qlo', 'QL06p001407' => 'qlo', 'QL06p002031' => 'qlo', 'RcHm_v2.0_Chr4g0387791' => 'rch', 'RcHm_v2.0_Chr4g0387801' => 'rch', 'RcHm_v2.0_Chr6g0286501' => 'rch', 'RcHm_v2.0_Chr6g0286511' => 'rch', 'RcHm_v2.0_Chr6g0286521' => 'rch', 'RcHm_v2.0_Chr6g0286531' => 'rch', 'RcHm_v2.0_Chr7g0189141' => 'rch', 'Rhsim02G0028700' => 'rsi', 'Rhsim02G0028800' => 'rsi', 'Rhsim02G0028900' => 'rsi', 'Rhsim02G0029000' => 'rsi', 'Rhsim02G0029100' => 'rsi', 'Rhsim02G0029200' => 'rsi', 'Rhsim02G0029300' => 'rsi', 'Rhsim02G0029400' => 'rsi', 'Rhsim02G0029500' => 'rsi', 'Rhsim02G0029600' => 'rsi', 'RhsimUnG0024000' => 'rsi', 'RhsimUnG0024100' => 'rsi', 'RhsimUnG0024200' => 'rsi', 'RhsimUnG0024300' => 'rsi', 'RhsimUnG0024400' => 'rsi', 'RhsimUnG0024500' => 'rsi', 'RhsimUnG0024700' => 'rsi', 'RhsimUnG0024800' => 'rsi', 'RhsimUnG0024900' => 'rsi', 'RhsimUnG0025100' => 'rsi', 'Sabra08G0120200' => 'sbr', 'Sabra08G0120300' => 'sbr', 'Sabra08G0120500' => 'sbr', 'Sabra08G0120600' => 'sbr', 'Sabra10G0158900' => 'sbr', 'SalBow2G3492' => 'sbo', 'Sc13g0004760' => 'sci', 'Sc13g0004770' => 'sci', 'Sed0003417' => 'sed', 'Sed0019750' => 'sed', 'SEGI_03419' => 'sgi', 'SEGI_05907' => 'sgi', 'SEGI_10682' => 'sgi', 'SEGI_13528' => 'sgi', 'SEGI_16081' => 'sgi', 'SEGI_19370' => 'sgi', 'SEGI_21015' => 'sgi', 'SEGI_21944' => 'sgi', 'SEGI_32906' => 'sgi', 'SEGI_33093' => 'sgi', 'SEGI_36110' => 'sgi', 'SEGI_40397' => 'sgi', 'SGA_v2.0_scaffold191G40426' => 'sas', 'SGA_v2.0_scaffold353G49717' => 'sas', 'SGA_v2.0_scaffold50G18550' => 'sas', 'SMO119G0173' => 'smo', 'SMO172G0002' => 'smo', 'Solyc09g082690.3' => 'sly', 'Solyc09g082700.2' => 'sly', 'Sopen09g031550' => 'spe', 'Sopen09g031560' => 'spe', 'Sp3g20540' => 'spa', 'Sp7g07580' => 'spa', 'TAR134G0002' => 'tar', 'TAR236G0001' => 'tar', 'TAR365G0892' => 'tar', 'TAR636G0166' => 'tar', 'TAR636G0646' => 'tar', 'TAR636G0869' => 'tar', 'TAR636G1317' => 'tar', 'TAR636G1744' => 'tar', 'TAR636G3358' => 'tar', 'TAR636G3436' => 'tar', 'THA.LOC104803047' => 'tha', 'Thecc.04G238900' => 'tca', 'Thhalv10021557m.g' => 'esa', 'Thhalv10026318m.g' => 'esa', 'Thhalv10026335m.g' => 'esa', 'TPR.G17433' => 'tpr', 'TPR.G18915' => 'tpr', 'TPR.G26125' => 'tpr', 'TWI09G0677' => 'twi', 'TWI73G0287' => 'twi', 'unitig_748.g8326' => 'ugi', 'vmacro15370' => 'vma', 'vmacro15371' => 'vma', 'vmacro15372' => 'vma', 'vmacro15373' => 'vma', 'vmacro15374' => 'vma', 'VMungo0720G2826' => 'vmu', 'Zm00001eb116960' => 'zma', 'Zm00001eb301260' => 'zma', 'Zm00001eb301270' => 'zma' ), 'gf_id' => 'HOM05D001460', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001460' ), 'data_identifier' => 'HOM05D001460', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001460', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '433', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p22980' => 'bna', 'A01p32340' => 'bna', 'A03p42970' => 'bna', 'A05p25880' => 'bna', 'Aa31LG8G9320' => 'aar', 'Aa31LG8G9330' => 'aar', 'Aa31LG8G9340' => 'aar', 'Aa31sc221G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1034' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1528' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.829' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2222' => 'aag', 'Ah.12g058830' => 'amhyb', 'Ah.12g058840' => 'amhyb', 'AL3G37160' => 'aly', 'AL7G41310' => 'aly', 'Aqoxy5G00395' => 'aox', 'Aqoxy5G00396' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0C8NZA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5185HY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JZ1PRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MD3LS0' => 'arhy', 'AT3G22840' => 'ath', 'AT4G14690' => 'ath', 'ATR0665G054' => 'atr', 'Atru.chr4.2344' => 'acertr', 'Atru.chr4.2346' => 'acertr', 'Atru.chr4.2347' => 'acertr', 'Atru.chr4.2348' => 'acertr', 'Atru.chr4.2355' => 'acertr', 'Atru.chr4.2356' => 'acertr', 'Atru.chr4.2358' => 'acertr', 'Atru.chr4.2359' => 'acertr', 'Atru.chr4.2360' => 'acertr', 'Atru.chr4.2361' => 'acertr', 'AUR62030476' => 'cqu', 'AUR62030478' => 'cqu', 'AUR62030819' => 'cqu', 'AUR62030820' => 'cqu', 'BcaB03g14648' => 'bca', 'BcaB04g20492' => 'bca', 'BcaB06g26399' => 'bca', 'BcaC01g03416' => 'bca', 'BcaC01g03419' => 'bca', 'BcaC01g03421' => 'bca', 'BcaC01g03424' => 'bca', 'BcaC05g28012' => 'bca', 'BcaC09g49212' => 'bca', 'BcaC09g50140' => 'bca', 'BcaNung00346' => 'bca', 'BolC1t02785H' => 'bol', 'BolC1t04095H' => 'bol', 'BolC3t17545H' => 'bol', 'BolC5t32769H' => 'bol', 'BraA01t02211Z' => 'bra', 'BraA01t03359Z' => 'bra', 'BraA03t13441Z' => 'bra', 'BraA05t21476Z' => 'bra', 'C01p28420' => 'bna', 'C01p41350' => 'bna', 'C03p52750' => 'bna', 'C03p52780' => 'bna', 'C05p40270' => 'bna', 'CAN.G1437.9' => 'can', 'CANSAT78G0035' => 'cansat', 'CANSAT78G1036' => 'cansat', 'CANSAT78G2272' => 'cansat', 'CANSAT78G2478' => 'cansat', 'CARHR098700' => 'chi', 'CARHR221120' => 'chi', 'CARHR221150' => 'chi', 'Carub.0003s2297' => 'cru', 'Carub.0007s2749' => 'cru', 'Carub.0007s2750' => 'cru', 'Carub.0007s2751' => 'cru', 'Ca_10849_v3' => 'car', 'Cc03_g04300' => 'ccan', 'CDE02G3648' => 'cde', 'CDE05G0060' => 'cde', 'CDE05G0692' => 'cde', 'CDE05G2285' => 'cde', 'CDE05G2884' => 'cde', 'CDE05G3072' => 'cde', 'Cfa008439' => 'cfa', 'Cfa008441' => 'cfa', 'Cfa008443' => 'cfa', 'Cfa008448' => 'cfa', 'Ciclev10005974m.g' => 'ccl', 'Ciclev10006006m.g' => 'ccl', 'Ciclev10006775m.g' => 'ccl', 'CiPaw.02G120400' => 'cil', 'CiPaw.02G120500' => 'cil', 'CiPaw.02G120600' => 'cil', 'ClCG05G004850' => 'cla', 'COL.COLO4_21566' => 'col', 'Cpa.g.sc44.124' => 'cpa', 'Cre07.g320400' => 'cre', 'Cre07.g320450' => 'cre', 'Cre08.g384650' => 'cre', 'Cre09.g393173' => 'cre', 'Cre09.g394325' => 'cre', 'Cre14.g626750' => 'cre', 'Cre16.g679250' => 'cre', 'CsaV3_3G012890' => 'csa', 'CSS0010865' => 'camsi', 'CSS0044338' => 'camsi', 'DCAR_002366' => 'dca', 'DCAR_030687' => 'dca', 'DCAR_030688' => 'dca', 'Dinv14047' => 'din', 'Dinv14048' => 'din', 'Duzib151G0105' => 'dzi', 'Duzib151G0114' => 'dzi', 'Duzib212G1029' => 'dzi', 'ECA232G3536' => 'eca', 'ECA240G0786' => 'eca', 'ECA240G1802' => 'eca', 'ECA240G3760' => 'eca', 'ECA240G3920' => 'eca', 'EL10Ac5g12536' => 'bvu', 'EL10Ac5g12537' => 'bvu', 'EL10Ac5g12538' => 'bvu', 'Eucgr.B01004' => 'egr', 'Eucgr.B01006' => 'egr', 'Eucgr.B01007' => 'egr', 'Eucgr.B01008' => 'egr', 'Eucgr.B01895' => 'egr', 'Eucgr.B01896' => 'egr', 'FAN04G1456' => 'fan', 'FAN08G1769' => 'fan', 'FAN08G2160' => 'fan', 'FAN13G2403' => 'fan', 'FAN13G3303' => 'fan', 'FAN15G2435' => 'fan', 'FAN17G0672' => 'fan', 'FAN17G2441' => 'fan', 'FAN18G1024' => 'fan', 'FAN22G1458' => 'fan', 'FAN24G0037' => 'fan', 'FAN24G0429' => 'fan', 'FAN24G2387' => 'fan', 'FAN27G2746' => 'fan', 'FvH4_2g20400' => 'fve', 'FvH4_2g20420' => 'fve', 'FvH4_2g20430' => 'fve', 'FvH4_4g01270' => 'fve', 'FvH4_4g01290' => 'fve', 'FvH4_4g01300' => 'fve', 'FvH4_4g01310' => 'fve', 'FvH4_4g01330' => 'fve', 'FvH4_5g09070' => 'fve', 'Glyma.10G243800' => 'gma', 'Glyma.20G150600' => 'gma', 'Gohir.A09G219200' => 'ghi', 'Gohir.A09G219300' => 'ghi', 'Gohir.D09G221400' => 'ghi', 'Gohir.D09G221500' => 'ghi', 'Gorai.006G242600' => 'gra', 'Gorai.006G242700' => 'gra', 'GSVIVG01018044001' => 'vvi', 'HanXRQChr03g0083821' => 'han', 'HanXRQChr03g0083841' => 'han', 'HanXRQChr03g0083881' => 'han', 'HanXRQChr03g0083901' => 'han', 'HanXRQChr03g0083921' => 'han', 'HanXRQChr03g0085331' => 'han', 'HanXRQChr03g0085361' => 'han', 'HanXRQChr03g0085411' => 'han', 'HanXRQChr03g0085421' => 'han', 'HanXRQChr03g0085431' => 'han', 'HanXRQChr08g0221991' => 'han', 'HanXRQChr11g0336061' => 'han', 'HanXRQChr11g0336411' => 'han', 'Haze_11234' => 'cav', 'Hma1.2p1_0549F.1_g177010' => 'hma', 'Hma1.2p1_0602F.1_g187630' => 'hma', 'Hund14876' => 'sun', 'Hund14879' => 'sun', 'Lalb_Chr06g0160741' => 'lal', 'Lalb_Chr21g0304781' => 'lal', 'Lj3A726G19' => 'lonja', 'Lj3A726T23' => 'lonja', 'Lj3A726T24' => 'lonja', 'Lj3A726T25' => 'lonja', 'Lj3A727T17' => 'lonja', 'Lj3C726T0' => 'lonja', 'Lj3C726T2' => 'lonja', 'Lj3P725T35' => 'lonja', 'Lj3P727T10' => 'lonja', 'Lj3P727T12' => 'lonja', 'Lj3P727T14' => 'lonja', 'Lj5g0023109' => 'lja', 'Lj6P646T44' => 'lonja', 'Lsat_1_v5_gn_6_75760' => 'lsa', 'Lsat_1_v5_gn_6_75800' => 'lsa', 'Lsat_1_v5_gn_6_75900' => 'lsa', 'Lsat_1_v5_gn_6_76240' => 'lsa', 'Lsat_1_v5_gn_6_76441' => 'lsa', 'Lsat_1_v5_gn_6_76700' => 'lsa', 'Lsat_1_v5_gn_6_76760' => 'lsa', 'Manes.15G033100' => 'mes', 'Mapoly0004s0074' => 'mpo', 'Mapoly0004s0075' => 'mpo', 'Mapoly0004s0163' => 'mpo', 'Mapoly0004s0164' => 'mpo', 'Mapoly0021s0018' => 'mpo', 'Mapoly0041s0136' => 'mpo', 'Mapoly0041s0137' => 'mpo', 'Mapoly0041s0138' => 'mpo', 'Mapoly0041s0139' => 'mpo', 'Mapoly0041s0141' => 'mpo', 'Mapoly0041s0142' => 'mpo', 'Mapoly0041s0143' => 'mpo', 'Mapoly0041s0144' => 'mpo', 'Mapoly0041s0145' => 'mpo', 'Mapoly0047s0106' => 'mpo', 'Mapoly0047s0108' => 'mpo', 'Mapoly0050s0051' => 'mpo', 'Mapoly0050s0052' => 'mpo', 'Mapoly0050s0053' => 'mpo', 'Mapoly0058s0013' => 'mpo', 'Mapoly0091s0078' => 'mpo', 'Mapoly0091s0079' => 'mpo', 'Mapoly0091s0080' => 'mpo', 'Mapoly0091s0081' => 'mpo', 'Mapoly0278s0004' => 'mpo', 'Mapoly0278s0005' => 'mpo', 'Mapoly0278s0006' => 'mpo', 'MBI11_g30648_MAGBIO' => 'mbi', 'MCO03G194' => 'mco', 'MCO03G590' => 'mco', 'MCO07G312' => 'mco', 'MCO10G318' => 'mco', 'MCO12G244' => 'mco', 'MCO13G148' => 'mco', 'MCO13G194' => 'mco', 'MCO16G238' => 'mco', 'MD06G1134100' => 'mdo', 'MD13G1200100' => 'mdo', 'MD13G1200300' => 'mdo', 'MD13G1200600' => 'mdo', 'MD14G1150400' => 'mdo', 'MD16G1200000' => 'mdo', 'Medtr1g102570' => 'mtr', 'Medtr1g102780' => 'mtr', 'Medtr1g102800' => 'mtr', 'Medtr1g102810' => 'mtr', 'Medtr1g102830' => 'mtr', 'MELO3C006499.2' => 'cme', 'Migut.G00385' => 'egut', 'MSTRG.4063' => 'ama', 'Nitab4.5_0000090g0260' => 'nta', 'Nitab4.5_0000977g0030' => 'nta', 'Nitab4.5_0002541g0040' => 'nta', 'Nitab4.5_0007068g0040' => 'nta', 'Nn005s41408' => 'nnu', 'Nn005s41410' => 'nnu', 'Oeu010310.1' => 'oeu', 'Oeu010311.1' => 'oeu', 'Oeu043472.1' => 'oeu', 'Os01g0246400' => 'osa', 'Os04g0267950' => 'osa', 'Os07g0178700' => 'osa', 'Os07g0178800' => 'osa', 'Peaxi162Scf00316g00046' => 'pax', 'Peaxi162Scf00316g00049' => 'pax', 'Peaxi162Scf00316g00059' => 'pax', 'Peaxi162Scf00316g00328' => 'pax', 'Peaxi162Scf00316g00329' => 'pax', 'Peaxi162Scf00316g00411' => 'pax', 'Peaxi162Scf00316g00521' => 'pax', 'Peaxi162Scf00492g00068' => 'pax', 'Peaxi162Scf35631g00002' => 'pax', 'PGR142G3720' => 'pgr', 'PGSC0003DMG400006442' => 'stu', 'Phvul.007G062000' => 'pvu', 'Potri.008G157750' => 'ptr', 'Potri.008G157900' => 'ptr', 'Potri.008G158000' => 'ptr', 'Potri.008G158200' => 'ptr', 'Pp3c11_7280' => 'ppa', 'Pp3c11_7980' => 'ppa', 'Pp3c12_19450' => 'ppa', 'Pp3c14_1480' => 'ppa', 'Pp3c14_1501' => 'ppa', 'Pp3c16_4900' => 'ppa', 'Pp3c16_5010' => 'ppa', 'Pp3c16_5060' => 'ppa', 'Pp3c19_18250' => 'ppa', 'Pp3c23_8530' => 'ppa', 'Pp3c23_8550' => 'ppa', 'Pp3c24_9670' => 'ppa', 'Pp3c2_21390' => 'ppa', 'Pp3c2_31380' => 'ppa', 'Pp3c3_16620' => 'ppa', 'Pp3c3_8090' => 'ppa', 'Pp3c3_8110' => 'ppa', 'Pp3c3_8130' => 'ppa', 'Pp3c3_8150' => 'ppa', 'Pp3c4_14320' => 'ppa', 'Pp3c6_2560' => 'ppa', 'Pp3c9_16700' => 'ppa', 'PRCOL_00000234' => 'pco', 'PRCOL_00000235' => 'pco', 'PRCOL_00000777' => 'pco', 'PRCOL_00002344' => 'pco', 'PRCOL_00002372' => 'pco', 'PRCOL_00006120' => 'pco', 'Prupe.1G021400' => 'ppe', 'Prupe.1G021500' => 'ppe', 'Prupe.1G021600' => 'ppe', 'Prupe.1G021700' => 'ppe', 'Prupe.1G021800' => 'ppe', 'Prupe.5G145100' => 'ppe', 'Psat6g204040' => 'psa', 'Psat6g204800' => 'psa', 'Psat6g204920' => 'psa', 'Psat6g204960' => 'psa', 'Psat6g205080' => 'psa', 'PSO017G0271' => 'pso', 'PSO017G1276' => 'pso', 'PSO017G1429' => 'pso', 'PSO017G1861' => 'pso', 'PSO017G2787' => 'pso', 'PSO017G4466' => 'pso', 'PSO017G5118' => 'pso', 'PSO017G5420' => 'pso', 'PSO063G3678' => 'pso', 'PSO210G0546' => 'pso', 'PSO317G0001' => 'pso', 'PSO357G0512' => 'pso', 'PSO478G2682' => 'pso', 'PSO647G0001' => 'pso', 'PSO675G0001' => 'pso', 'PSO675G2699' => 'pso', 'PSO675G2849' => 'pso', 'PSO675G4991' => 'pso', 'PSO689G0001' => 'pso', 'QL06p000916' => 'qlo', 'QL06p000921' => 'qlo', 'QL06p001398' => 'qlo', 'QL06p001407' => 'qlo', 'QL06p002031' => 'qlo', 'RcHm_v2.0_Chr4g0387791' => 'rch', 'RcHm_v2.0_Chr4g0387801' => 'rch', 'RcHm_v2.0_Chr6g0286501' => 'rch', 'RcHm_v2.0_Chr6g0286511' => 'rch', 'RcHm_v2.0_Chr6g0286521' => 'rch', 'RcHm_v2.0_Chr6g0286531' => 'rch', 'RcHm_v2.0_Chr7g0189141' => 'rch', 'Rhsim02G0028700' => 'rsi', 'Rhsim02G0028800' => 'rsi', 'Rhsim02G0028900' => 'rsi', 'Rhsim02G0029000' => 'rsi', 'Rhsim02G0029100' => 'rsi', 'Rhsim02G0029200' => 'rsi', 'Rhsim02G0029300' => 'rsi', 'Rhsim02G0029400' => 'rsi', 'Rhsim02G0029500' => 'rsi', 'Rhsim02G0029600' => 'rsi', 'RhsimUnG0024000' => 'rsi', 'RhsimUnG0024100' => 'rsi', 'RhsimUnG0024200' => 'rsi', 'RhsimUnG0024300' => 'rsi', 'RhsimUnG0024400' => 'rsi', 'RhsimUnG0024500' => 'rsi', 'RhsimUnG0024700' => 'rsi', 'RhsimUnG0024800' => 'rsi', 'RhsimUnG0024900' => 'rsi', 'RhsimUnG0025100' => 'rsi', 'Sabra08G0120200' => 'sbr', 'Sabra08G0120300' => 'sbr', 'Sabra08G0120500' => 'sbr', 'Sabra08G0120600' => 'sbr', 'Sabra10G0158900' => 'sbr', 'SalBow2G3492' => 'sbo', 'Sc13g0004760' => 'sci', 'Sc13g0004770' => 'sci', 'Sed0003417' => 'sed', 'Sed0019750' => 'sed', 'SEGI_03419' => 'sgi', 'SEGI_05907' => 'sgi', 'SEGI_10682' => 'sgi', 'SEGI_13528' => 'sgi', 'SEGI_16081' => 'sgi', 'SEGI_19370' => 'sgi', 'SEGI_21015' => 'sgi', 'SEGI_21944' => 'sgi', 'SEGI_32906' => 'sgi', 'SEGI_33093' => 'sgi', 'SEGI_36110' => 'sgi', 'SEGI_40397' => 'sgi', 'SGA_v2.0_scaffold191G40426' => 'sas', 'SGA_v2.0_scaffold353G49717' => 'sas', 'SGA_v2.0_scaffold50G18550' => 'sas', 'SMO119G0173' => 'smo', 'SMO172G0002' => 'smo', 'Solyc09g082690.3' => 'sly', 'Solyc09g082700.2' => 'sly', 'Sopen09g031550' => 'spe', 'Sopen09g031560' => 'spe', 'Sp3g20540' => 'spa', 'Sp7g07580' => 'spa', 'TAR134G0002' => 'tar', 'TAR236G0001' => 'tar', 'TAR365G0892' => 'tar', 'TAR636G0166' => 'tar', 'TAR636G0646' => 'tar', 'TAR636G0869' => 'tar', 'TAR636G1317' => 'tar', 'TAR636G1744' => 'tar', 'TAR636G3358' => 'tar', 'TAR636G3436' => 'tar', 'THA.LOC104803047' => 'tha', 'Thecc.04G238900' => 'tca', 'Thhalv10021557m.g' => 'esa', 'Thhalv10026318m.g' => 'esa', 'Thhalv10026335m.g' => 'esa', 'TPR.G17433' => 'tpr', 'TPR.G18915' => 'tpr', 'TPR.G26125' => 'tpr', 'TWI09G0677' => 'twi', 'TWI73G0287' => 'twi', 'unitig_748.g8326' => 'ugi', 'vmacro15370' => 'vma', 'vmacro15371' => 'vma', 'vmacro15372' => 'vma', 'vmacro15373' => 'vma', 'vmacro15374' => 'vma', 'VMungo0720G2826' => 'vmu', 'Zm00001eb116960' => 'zma', 'Zm00001eb301260' => 'zma', 'Zm00001eb301270' => 'zma' ) $gf_id = 'HOM05D001460' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001460' ) $data_identifier = 'HOM05D001460' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 4, 'aag' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 2, 'aox' => (int) 2, 'arhy' => (int) 4, 'ath' => (int) 2, 'atr' => (int) 1, 'acertr' => (int) 10, 'cqu' => (int) 4, 'bca' => (int) 11, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 1, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 1, 'ccan' => (int) 1, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 1, 'col' => (int) 1, 'cpa' => (int) 1, 'cre' => (int) 7, 'csa' => (int) 1, 'camsi' => (int) 2, 'dca' => (int) 3, 'din' => (int) 2, 'dzi' => (int) 3, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 14, 'fve' => (int) 9, 'gma' => (int) 2, 'ghi' => (int) 4, 'gra' => (int) 2, 'vvi' => (int) 1, 'han' => (int) 13, 'cav' => (int) 1, 'hma' => (int) 2, 'sun' => (int) 2, 'lal' => (int) 2, 'lonja' => (int) 12, 'lja' => (int) 1, 'lsa' => (int) 7, 'mes' => (int) 1, 'mpo' => (int) 27, 'mbi' => (int) 1, 'mco' => (int) 8, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 1, 'egut' => (int) 1, 'ama' => (int) 1, 'nta' => (int) 4, 'nnu' => (int) 2, 'oeu' => (int) 3, 'osa' => (int) 4, 'pax' => (int) 9, 'pgr' => (int) 1, 'stu' => (int) 1, 'pvu' => (int) 1, 'ptr' => (int) 4, 'ppa' => (int) 22, 'pco' => (int) 6, 'ppe' => (int) 6, 'psa' => (int) 5, 'pso' => (int) 19, 'qlo' => (int) 5, 'rch' => (int) 7, 'rsi' => (int) 20, 'sbr' => (int) 5, 'sbo' => (int) 1, 'sci' => (int) 2, 'sed' => (int) 2, 'sgi' => (int) 12, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 2, 'tar' => (int) 10, 'tha' => (int) 1, 'tca' => (int) 1, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 2, 'ugi' => (int) 1, 'vma' => (int) 5, 'vmu' => (int) 1, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb301270' $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' => 'HOM05D001460', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '433', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p22980' => 'bna', 'A01p32340' => 'bna', 'A03p42970' => 'bna', 'A05p25880' => 'bna', 'Aa31LG8G9320' => 'aar', 'Aa31LG8G9330' => 'aar', 'Aa31LG8G9340' => 'aar', 'Aa31sc221G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1034' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1528' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.829' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2222' => 'aag', 'Ah.12g058830' => 'amhyb', 'Ah.12g058840' => 'amhyb', 'AL3G37160' => 'aly', 'AL7G41310' => 'aly', 'Aqoxy5G00395' => 'aox', 'Aqoxy5G00396' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0C8NZA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5185HY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JZ1PRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MD3LS0' => 'arhy', 'AT3G22840' => 'ath', 'AT4G14690' => 'ath', 'ATR0665G054' => 'atr', 'Atru.chr4.2344' => 'acertr', 'Atru.chr4.2346' => 'acertr', 'Atru.chr4.2347' => 'acertr', 'Atru.chr4.2348' => 'acertr', 'Atru.chr4.2355' => 'acertr', 'Atru.chr4.2356' => 'acertr', 'Atru.chr4.2358' => 'acertr', 'Atru.chr4.2359' => 'acertr', 'Atru.chr4.2360' => 'acertr', 'Atru.chr4.2361' => 'acertr', 'AUR62030476' => 'cqu', 'AUR62030478' => 'cqu', 'AUR62030819' => 'cqu', 'AUR62030820' => 'cqu', 'BcaB03g14648' => 'bca', 'BcaB04g20492' => 'bca', 'BcaB06g26399' => 'bca', 'BcaC01g03416' => 'bca', 'BcaC01g03419' => 'bca', 'BcaC01g03421' => 'bca', 'BcaC01g03424' => 'bca', 'BcaC05g28012' => 'bca', 'BcaC09g49212' => 'bca', 'BcaC09g50140' => 'bca', 'BcaNung00346' => 'bca', 'BolC1t02785H' => 'bol', 'BolC1t04095H' => 'bol', 'BolC3t17545H' => 'bol', 'BolC5t32769H' => 'bol', 'BraA01t02211Z' => 'bra', 'BraA01t03359Z' => 'bra', 'BraA03t13441Z' => 'bra', 'BraA05t21476Z' => 'bra', 'C01p28420' => 'bna', 'C01p41350' => 'bna', 'C03p52750' => 'bna', 'C03p52780' => 'bna', 'C05p40270' => 'bna', 'CAN.G1437.9' => 'can', 'CANSAT78G0035' => 'cansat', 'CANSAT78G1036' => 'cansat', 'CANSAT78G2272' => 'cansat', 'CANSAT78G2478' => 'cansat', 'CARHR098700' => 'chi', 'CARHR221120' => 'chi', 'CARHR221150' => 'chi', 'Carub.0003s2297' => 'cru', 'Carub.0007s2749' => 'cru', 'Carub.0007s2750' => 'cru', 'Carub.0007s2751' => 'cru', 'Ca_10849_v3' => 'car', 'Cc03_g04300' => 'ccan', 'CDE02G3648' => 'cde', 'CDE05G0060' => 'cde', 'CDE05G0692' => 'cde', 'CDE05G2285' => 'cde', 'CDE05G2884' => 'cde', 'CDE05G3072' => 'cde', 'Cfa008439' => 'cfa', 'Cfa008441' => 'cfa', 'Cfa008443' => 'cfa', 'Cfa008448' => 'cfa', 'Ciclev10005974m.g' => 'ccl', 'Ciclev10006006m.g' => 'ccl', 'Ciclev10006775m.g' => 'ccl', 'CiPaw.02G120400' => 'cil', 'CiPaw.02G120500' => 'cil', 'CiPaw.02G120600' => 'cil', 'ClCG05G004850' => 'cla', 'COL.COLO4_21566' => 'col', 'Cpa.g.sc44.124' => 'cpa', 'Cre07.g320400' => 'cre', 'Cre07.g320450' => 'cre', 'Cre08.g384650' => 'cre', 'Cre09.g393173' => 'cre', 'Cre09.g394325' => 'cre', 'Cre14.g626750' => 'cre', 'Cre16.g679250' => 'cre', 'CsaV3_3G012890' => 'csa', 'CSS0010865' => 'camsi', 'CSS0044338' => 'camsi', 'DCAR_002366' => 'dca', 'DCAR_030687' => 'dca', 'DCAR_030688' => 'dca', 'Dinv14047' => 'din', 'Dinv14048' => 'din', 'Duzib151G0105' => 'dzi', 'Duzib151G0114' => 'dzi', 'Duzib212G1029' => 'dzi', 'ECA232G3536' => 'eca', 'ECA240G0786' => 'eca', 'ECA240G1802' => 'eca', 'ECA240G3760' => 'eca', 'ECA240G3920' => 'eca', 'EL10Ac5g12536' => 'bvu', 'EL10Ac5g12537' => 'bvu', 'EL10Ac5g12538' => 'bvu', 'Eucgr.B01004' => 'egr', 'Eucgr.B01006' => 'egr', 'Eucgr.B01007' => 'egr', 'Eucgr.B01008' => 'egr', 'Eucgr.B01895' => 'egr', 'Eucgr.B01896' => 'egr', 'FAN04G1456' => 'fan', 'FAN08G1769' => 'fan', 'FAN08G2160' => 'fan', 'FAN13G2403' => 'fan', 'FAN13G3303' => 'fan', 'FAN15G2435' => 'fan', 'FAN17G0672' => 'fan', 'FAN17G2441' => 'fan', 'FAN18G1024' => 'fan', 'FAN22G1458' => 'fan', 'FAN24G0037' => 'fan', 'FAN24G0429' => 'fan', 'FAN24G2387' => 'fan', 'FAN27G2746' => 'fan', 'FvH4_2g20400' => 'fve', 'FvH4_2g20420' => 'fve', 'FvH4_2g20430' => 'fve', 'FvH4_4g01270' => 'fve', 'FvH4_4g01290' => 'fve', 'FvH4_4g01300' => 'fve', 'FvH4_4g01310' => 'fve', 'FvH4_4g01330' => 'fve', 'FvH4_5g09070' => 'fve', 'Glyma.10G243800' => 'gma', 'Glyma.20G150600' => 'gma', 'Gohir.A09G219200' => 'ghi', 'Gohir.A09G219300' => 'ghi', 'Gohir.D09G221400' => 'ghi', 'Gohir.D09G221500' => 'ghi', 'Gorai.006G242600' => 'gra', 'Gorai.006G242700' => 'gra', 'GSVIVG01018044001' => 'vvi', 'HanXRQChr03g0083821' => 'han', 'HanXRQChr03g0083841' => 'han', 'HanXRQChr03g0083881' => 'han', 'HanXRQChr03g0083901' => 'han', 'HanXRQChr03g0083921' => 'han', 'HanXRQChr03g0085331' => 'han', 'HanXRQChr03g0085361' => 'han', 'HanXRQChr03g0085411' => 'han', 'HanXRQChr03g0085421' => 'han', 'HanXRQChr03g0085431' => 'han', 'HanXRQChr08g0221991' => 'han', 'HanXRQChr11g0336061' => 'han', 'HanXRQChr11g0336411' => 'han', 'Haze_11234' => 'cav', 'Hma1.2p1_0549F.1_g177010' => 'hma', 'Hma1.2p1_0602F.1_g187630' => 'hma', 'Hund14876' => 'sun', 'Hund14879' => 'sun', 'Lalb_Chr06g0160741' => 'lal', 'Lalb_Chr21g0304781' => 'lal', 'Lj3A726G19' => 'lonja', 'Lj3A726T23' => 'lonja', 'Lj3A726T24' => 'lonja', 'Lj3A726T25' => 'lonja', 'Lj3A727T17' => 'lonja', 'Lj3C726T0' => 'lonja', 'Lj3C726T2' => 'lonja', 'Lj3P725T35' => 'lonja', 'Lj3P727T10' => 'lonja', 'Lj3P727T12' => 'lonja', 'Lj3P727T14' => 'lonja', 'Lj5g0023109' => 'lja', 'Lj6P646T44' => 'lonja', 'Lsat_1_v5_gn_6_75760' => 'lsa', 'Lsat_1_v5_gn_6_75800' => 'lsa', 'Lsat_1_v5_gn_6_75900' => 'lsa', 'Lsat_1_v5_gn_6_76240' => 'lsa', 'Lsat_1_v5_gn_6_76441' => 'lsa', 'Lsat_1_v5_gn_6_76700' => 'lsa', 'Lsat_1_v5_gn_6_76760' => 'lsa', 'Manes.15G033100' => 'mes', 'Mapoly0004s0074' => 'mpo', 'Mapoly0004s0075' => 'mpo', 'Mapoly0004s0163' => 'mpo', 'Mapoly0004s0164' => 'mpo', 'Mapoly0021s0018' => 'mpo', 'Mapoly0041s0136' => 'mpo', 'Mapoly0041s0137' => 'mpo', 'Mapoly0041s0138' => 'mpo', 'Mapoly0041s0139' => 'mpo', 'Mapoly0041s0141' => 'mpo', 'Mapoly0041s0142' => 'mpo', 'Mapoly0041s0143' => 'mpo', 'Mapoly0041s0144' => 'mpo', 'Mapoly0041s0145' => 'mpo', 'Mapoly0047s0106' => 'mpo', 'Mapoly0047s0108' => 'mpo', 'Mapoly0050s0051' => 'mpo', 'Mapoly0050s0052' => 'mpo', 'Mapoly0050s0053' => 'mpo', 'Mapoly0058s0013' => 'mpo', 'Mapoly0091s0078' => 'mpo', 'Mapoly0091s0079' => 'mpo', 'Mapoly0091s0080' => 'mpo', 'Mapoly0091s0081' => 'mpo', 'Mapoly0278s0004' => 'mpo', 'Mapoly0278s0005' => 'mpo', 'Mapoly0278s0006' => 'mpo', 'MBI11_g30648_MAGBIO' => 'mbi', 'MCO03G194' => 'mco', 'MCO03G590' => 'mco', 'MCO07G312' => 'mco', 'MCO10G318' => 'mco', 'MCO12G244' => 'mco', 'MCO13G148' => 'mco', 'MCO13G194' => 'mco', 'MCO16G238' => 'mco', 'MD06G1134100' => 'mdo', 'MD13G1200100' => 'mdo', 'MD13G1200300' => 'mdo', 'MD13G1200600' => 'mdo', 'MD14G1150400' => 'mdo', 'MD16G1200000' => 'mdo', 'Medtr1g102570' => 'mtr', 'Medtr1g102780' => 'mtr', 'Medtr1g102800' => 'mtr', 'Medtr1g102810' => 'mtr', 'Medtr1g102830' => 'mtr', 'MELO3C006499.2' => 'cme', 'Migut.G00385' => 'egut', 'MSTRG.4063' => 'ama', 'Nitab4.5_0000090g0260' => 'nta', 'Nitab4.5_0000977g0030' => 'nta', 'Nitab4.5_0002541g0040' => 'nta', 'Nitab4.5_0007068g0040' => 'nta', 'Nn005s41408' => 'nnu', 'Nn005s41410' => 'nnu', 'Oeu010310.1' => 'oeu', 'Oeu010311.1' => 'oeu', 'Oeu043472.1' => 'oeu', 'Os01g0246400' => 'osa', 'Os04g0267950' => 'osa', 'Os07g0178700' => 'osa', 'Os07g0178800' => 'osa', 'Peaxi162Scf00316g00046' => 'pax', 'Peaxi162Scf00316g00049' => 'pax', 'Peaxi162Scf00316g00059' => 'pax', 'Peaxi162Scf00316g00328' => 'pax', 'Peaxi162Scf00316g00329' => 'pax', 'Peaxi162Scf00316g00411' => 'pax', 'Peaxi162Scf00316g00521' => 'pax', 'Peaxi162Scf00492g00068' => 'pax', 'Peaxi162Scf35631g00002' => 'pax', 'PGR142G3720' => 'pgr', 'PGSC0003DMG400006442' => 'stu', 'Phvul.007G062000' => 'pvu', 'Potri.008G157750' => 'ptr', 'Potri.008G157900' => 'ptr', 'Potri.008G158000' => 'ptr', 'Potri.008G158200' => 'ptr', 'Pp3c11_7280' => 'ppa', 'Pp3c11_7980' => 'ppa', 'Pp3c12_19450' => 'ppa', 'Pp3c14_1480' => 'ppa', 'Pp3c14_1501' => 'ppa', 'Pp3c16_4900' => 'ppa', 'Pp3c16_5010' => 'ppa', 'Pp3c16_5060' => 'ppa', 'Pp3c19_18250' => 'ppa', 'Pp3c23_8530' => 'ppa', 'Pp3c23_8550' => 'ppa', 'Pp3c24_9670' => 'ppa', 'Pp3c2_21390' => 'ppa', 'Pp3c2_31380' => 'ppa', 'Pp3c3_16620' => 'ppa', 'Pp3c3_8090' => 'ppa', 'Pp3c3_8110' => 'ppa', 'Pp3c3_8130' => 'ppa', 'Pp3c3_8150' => 'ppa', 'Pp3c4_14320' => 'ppa', 'Pp3c6_2560' => 'ppa', 'Pp3c9_16700' => 'ppa', 'PRCOL_00000234' => 'pco', 'PRCOL_00000235' => 'pco', 'PRCOL_00000777' => 'pco', 'PRCOL_00002344' => 'pco', 'PRCOL_00002372' => 'pco', 'PRCOL_00006120' => 'pco', 'Prupe.1G021400' => 'ppe', 'Prupe.1G021500' => 'ppe', 'Prupe.1G021600' => 'ppe', 'Prupe.1G021700' => 'ppe', 'Prupe.1G021800' => 'ppe', 'Prupe.5G145100' => 'ppe', 'Psat6g204040' => 'psa', 'Psat6g204800' => 'psa', 'Psat6g204920' => 'psa', 'Psat6g204960' => 'psa', 'Psat6g205080' => 'psa', 'PSO017G0271' => 'pso', 'PSO017G1276' => 'pso', 'PSO017G1429' => 'pso', 'PSO017G1861' => 'pso', 'PSO017G2787' => 'pso', 'PSO017G4466' => 'pso', 'PSO017G5118' => 'pso', 'PSO017G5420' => 'pso', 'PSO063G3678' => 'pso', 'PSO210G0546' => 'pso', 'PSO317G0001' => 'pso', 'PSO357G0512' => 'pso', 'PSO478G2682' => 'pso', 'PSO647G0001' => 'pso', 'PSO675G0001' => 'pso', 'PSO675G2699' => 'pso', 'PSO675G2849' => 'pso', 'PSO675G4991' => 'pso', 'PSO689G0001' => 'pso', 'QL06p000916' => 'qlo', 'QL06p000921' => 'qlo', 'QL06p001398' => 'qlo', 'QL06p001407' => 'qlo', 'QL06p002031' => 'qlo', 'RcHm_v2.0_Chr4g0387791' => 'rch', 'RcHm_v2.0_Chr4g0387801' => 'rch', 'RcHm_v2.0_Chr6g0286501' => 'rch', 'RcHm_v2.0_Chr6g0286511' => 'rch', 'RcHm_v2.0_Chr6g0286521' => 'rch', 'RcHm_v2.0_Chr6g0286531' => 'rch', 'RcHm_v2.0_Chr7g0189141' => 'rch', 'Rhsim02G0028700' => 'rsi', 'Rhsim02G0028800' => 'rsi', 'Rhsim02G0028900' => 'rsi', 'Rhsim02G0029000' => 'rsi', 'Rhsim02G0029100' => 'rsi', 'Rhsim02G0029200' => 'rsi', 'Rhsim02G0029300' => 'rsi', 'Rhsim02G0029400' => 'rsi', 'Rhsim02G0029500' => 'rsi', 'Rhsim02G0029600' => 'rsi', 'RhsimUnG0024000' => 'rsi', 'RhsimUnG0024100' => 'rsi', 'RhsimUnG0024200' => 'rsi', 'RhsimUnG0024300' => 'rsi', 'RhsimUnG0024400' => 'rsi', 'RhsimUnG0024500' => 'rsi', 'RhsimUnG0024700' => 'rsi', 'RhsimUnG0024800' => 'rsi', 'RhsimUnG0024900' => 'rsi', 'RhsimUnG0025100' => 'rsi', 'Sabra08G0120200' => 'sbr', 'Sabra08G0120300' => 'sbr', 'Sabra08G0120500' => 'sbr', 'Sabra08G0120600' => 'sbr', 'Sabra10G0158900' => 'sbr', 'SalBow2G3492' => 'sbo', 'Sc13g0004760' => 'sci', 'Sc13g0004770' => 'sci', 'Sed0003417' => 'sed', 'Sed0019750' => 'sed', 'SEGI_03419' => 'sgi', 'SEGI_05907' => 'sgi', 'SEGI_10682' => 'sgi', 'SEGI_13528' => 'sgi', 'SEGI_16081' => 'sgi', 'SEGI_19370' => 'sgi', 'SEGI_21015' => 'sgi', 'SEGI_21944' => 'sgi', 'SEGI_32906' => 'sgi', 'SEGI_33093' => 'sgi', 'SEGI_36110' => 'sgi', 'SEGI_40397' => 'sgi', 'SGA_v2.0_scaffold191G40426' => 'sas', 'SGA_v2.0_scaffold353G49717' => 'sas', 'SGA_v2.0_scaffold50G18550' => 'sas', 'SMO119G0173' => 'smo', 'SMO172G0002' => 'smo', 'Solyc09g082690.3' => 'sly', 'Solyc09g082700.2' => 'sly', 'Sopen09g031550' => 'spe', 'Sopen09g031560' => 'spe', 'Sp3g20540' => 'spa', 'Sp7g07580' => 'spa', 'TAR134G0002' => 'tar', 'TAR236G0001' => 'tar', 'TAR365G0892' => 'tar', 'TAR636G0166' => 'tar', 'TAR636G0646' => 'tar', 'TAR636G0869' => 'tar', 'TAR636G1317' => 'tar', 'TAR636G1744' => 'tar', 'TAR636G3358' => 'tar', 'TAR636G3436' => 'tar', 'THA.LOC104803047' => 'tha', 'Thecc.04G238900' => 'tca', 'Thhalv10021557m.g' => 'esa', 'Thhalv10026318m.g' => 'esa', 'Thhalv10026335m.g' => 'esa', 'TPR.G17433' => 'tpr', 'TPR.G18915' => 'tpr', 'TPR.G26125' => 'tpr', 'TWI09G0677' => 'twi', 'TWI73G0287' => 'twi', 'unitig_748.g8326' => 'ugi', 'vmacro15370' => 'vma', 'vmacro15371' => 'vma', 'vmacro15372' => 'vma', 'vmacro15373' => 'vma', 'vmacro15374' => 'vma', 'VMungo0720G2826' => 'vmu', 'Zm00001eb116960' => 'zma', 'Zm00001eb301260' => 'zma', 'Zm00001eb301270' => 'zma' ), 'gf_id' => 'HOM05D001460', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001460' ), 'data_identifier' => 'HOM05D001460', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001460', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '433', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p22980' => 'bna', 'A01p32340' => 'bna', 'A03p42970' => 'bna', 'A05p25880' => 'bna', 'Aa31LG8G9320' => 'aar', 'Aa31LG8G9330' => 'aar', 'Aa31LG8G9340' => 'aar', 'Aa31sc221G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1034' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1528' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.829' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2222' => 'aag', 'Ah.12g058830' => 'amhyb', 'Ah.12g058840' => 'amhyb', 'AL3G37160' => 'aly', 'AL7G41310' => 'aly', 'Aqoxy5G00395' => 'aox', 'Aqoxy5G00396' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0C8NZA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5185HY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JZ1PRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MD3LS0' => 'arhy', 'AT3G22840' => 'ath', 'AT4G14690' => 'ath', 'ATR0665G054' => 'atr', 'Atru.chr4.2344' => 'acertr', 'Atru.chr4.2346' => 'acertr', 'Atru.chr4.2347' => 'acertr', 'Atru.chr4.2348' => 'acertr', 'Atru.chr4.2355' => 'acertr', 'Atru.chr4.2356' => 'acertr', 'Atru.chr4.2358' => 'acertr', 'Atru.chr4.2359' => 'acertr', 'Atru.chr4.2360' => 'acertr', 'Atru.chr4.2361' => 'acertr', 'AUR62030476' => 'cqu', 'AUR62030478' => 'cqu', 'AUR62030819' => 'cqu', 'AUR62030820' => 'cqu', 'BcaB03g14648' => 'bca', 'BcaB04g20492' => 'bca', 'BcaB06g26399' => 'bca', 'BcaC01g03416' => 'bca', 'BcaC01g03419' => 'bca', 'BcaC01g03421' => 'bca', 'BcaC01g03424' => 'bca', 'BcaC05g28012' => 'bca', 'BcaC09g49212' => 'bca', 'BcaC09g50140' => 'bca', 'BcaNung00346' => 'bca', 'BolC1t02785H' => 'bol', 'BolC1t04095H' => 'bol', 'BolC3t17545H' => 'bol', 'BolC5t32769H' => 'bol', 'BraA01t02211Z' => 'bra', 'BraA01t03359Z' => 'bra', 'BraA03t13441Z' => 'bra', 'BraA05t21476Z' => 'bra', 'C01p28420' => 'bna', 'C01p41350' => 'bna', 'C03p52750' => 'bna', 'C03p52780' => 'bna', 'C05p40270' => 'bna', 'CAN.G1437.9' => 'can', 'CANSAT78G0035' => 'cansat', 'CANSAT78G1036' => 'cansat', 'CANSAT78G2272' => 'cansat', 'CANSAT78G2478' => 'cansat', 'CARHR098700' => 'chi', 'CARHR221120' => 'chi', 'CARHR221150' => 'chi', 'Carub.0003s2297' => 'cru', 'Carub.0007s2749' => 'cru', 'Carub.0007s2750' => 'cru', 'Carub.0007s2751' => 'cru', 'Ca_10849_v3' => 'car', 'Cc03_g04300' => 'ccan', 'CDE02G3648' => 'cde', 'CDE05G0060' => 'cde', 'CDE05G0692' => 'cde', 'CDE05G2285' => 'cde', 'CDE05G2884' => 'cde', 'CDE05G3072' => 'cde', 'Cfa008439' => 'cfa', 'Cfa008441' => 'cfa', 'Cfa008443' => 'cfa', 'Cfa008448' => 'cfa', 'Ciclev10005974m.g' => 'ccl', 'Ciclev10006006m.g' => 'ccl', 'Ciclev10006775m.g' => 'ccl', 'CiPaw.02G120400' => 'cil', 'CiPaw.02G120500' => 'cil', 'CiPaw.02G120600' => 'cil', 'ClCG05G004850' => 'cla', 'COL.COLO4_21566' => 'col', 'Cpa.g.sc44.124' => 'cpa', 'Cre07.g320400' => 'cre', 'Cre07.g320450' => 'cre', 'Cre08.g384650' => 'cre', 'Cre09.g393173' => 'cre', 'Cre09.g394325' => 'cre', 'Cre14.g626750' => 'cre', 'Cre16.g679250' => 'cre', 'CsaV3_3G012890' => 'csa', 'CSS0010865' => 'camsi', 'CSS0044338' => 'camsi', 'DCAR_002366' => 'dca', 'DCAR_030687' => 'dca', 'DCAR_030688' => 'dca', 'Dinv14047' => 'din', 'Dinv14048' => 'din', 'Duzib151G0105' => 'dzi', 'Duzib151G0114' => 'dzi', 'Duzib212G1029' => 'dzi', 'ECA232G3536' => 'eca', 'ECA240G0786' => 'eca', 'ECA240G1802' => 'eca', 'ECA240G3760' => 'eca', 'ECA240G3920' => 'eca', 'EL10Ac5g12536' => 'bvu', 'EL10Ac5g12537' => 'bvu', 'EL10Ac5g12538' => 'bvu', 'Eucgr.B01004' => 'egr', 'Eucgr.B01006' => 'egr', 'Eucgr.B01007' => 'egr', 'Eucgr.B01008' => 'egr', 'Eucgr.B01895' => 'egr', 'Eucgr.B01896' => 'egr', 'FAN04G1456' => 'fan', 'FAN08G1769' => 'fan', 'FAN08G2160' => 'fan', 'FAN13G2403' => 'fan', 'FAN13G3303' => 'fan', 'FAN15G2435' => 'fan', 'FAN17G0672' => 'fan', 'FAN17G2441' => 'fan', 'FAN18G1024' => 'fan', 'FAN22G1458' => 'fan', 'FAN24G0037' => 'fan', 'FAN24G0429' => 'fan', 'FAN24G2387' => 'fan', 'FAN27G2746' => 'fan', 'FvH4_2g20400' => 'fve', 'FvH4_2g20420' => 'fve', 'FvH4_2g20430' => 'fve', 'FvH4_4g01270' => 'fve', 'FvH4_4g01290' => 'fve', 'FvH4_4g01300' => 'fve', 'FvH4_4g01310' => 'fve', 'FvH4_4g01330' => 'fve', 'FvH4_5g09070' => 'fve', 'Glyma.10G243800' => 'gma', 'Glyma.20G150600' => 'gma', 'Gohir.A09G219200' => 'ghi', 'Gohir.A09G219300' => 'ghi', 'Gohir.D09G221400' => 'ghi', 'Gohir.D09G221500' => 'ghi', 'Gorai.006G242600' => 'gra', 'Gorai.006G242700' => 'gra', 'GSVIVG01018044001' => 'vvi', 'HanXRQChr03g0083821' => 'han', 'HanXRQChr03g0083841' => 'han', 'HanXRQChr03g0083881' => 'han', 'HanXRQChr03g0083901' => 'han', 'HanXRQChr03g0083921' => 'han', 'HanXRQChr03g0085331' => 'han', 'HanXRQChr03g0085361' => 'han', 'HanXRQChr03g0085411' => 'han', 'HanXRQChr03g0085421' => 'han', 'HanXRQChr03g0085431' => 'han', 'HanXRQChr08g0221991' => 'han', 'HanXRQChr11g0336061' => 'han', 'HanXRQChr11g0336411' => 'han', 'Haze_11234' => 'cav', 'Hma1.2p1_0549F.1_g177010' => 'hma', 'Hma1.2p1_0602F.1_g187630' => 'hma', 'Hund14876' => 'sun', 'Hund14879' => 'sun', 'Lalb_Chr06g0160741' => 'lal', 'Lalb_Chr21g0304781' => 'lal', 'Lj3A726G19' => 'lonja', 'Lj3A726T23' => 'lonja', 'Lj3A726T24' => 'lonja', 'Lj3A726T25' => 'lonja', 'Lj3A727T17' => 'lonja', 'Lj3C726T0' => 'lonja', 'Lj3C726T2' => 'lonja', 'Lj3P725T35' => 'lonja', 'Lj3P727T10' => 'lonja', 'Lj3P727T12' => 'lonja', 'Lj3P727T14' => 'lonja', 'Lj5g0023109' => 'lja', 'Lj6P646T44' => 'lonja', 'Lsat_1_v5_gn_6_75760' => 'lsa', 'Lsat_1_v5_gn_6_75800' => 'lsa', 'Lsat_1_v5_gn_6_75900' => 'lsa', 'Lsat_1_v5_gn_6_76240' => 'lsa', 'Lsat_1_v5_gn_6_76441' => 'lsa', 'Lsat_1_v5_gn_6_76700' => 'lsa', 'Lsat_1_v5_gn_6_76760' => 'lsa', 'Manes.15G033100' => 'mes', 'Mapoly0004s0074' => 'mpo', 'Mapoly0004s0075' => 'mpo', 'Mapoly0004s0163' => 'mpo', 'Mapoly0004s0164' => 'mpo', 'Mapoly0021s0018' => 'mpo', 'Mapoly0041s0136' => 'mpo', 'Mapoly0041s0137' => 'mpo', 'Mapoly0041s0138' => 'mpo', 'Mapoly0041s0139' => 'mpo', 'Mapoly0041s0141' => 'mpo', 'Mapoly0041s0142' => 'mpo', 'Mapoly0041s0143' => 'mpo', 'Mapoly0041s0144' => 'mpo', 'Mapoly0041s0145' => 'mpo', 'Mapoly0047s0106' => 'mpo', 'Mapoly0047s0108' => 'mpo', 'Mapoly0050s0051' => 'mpo', 'Mapoly0050s0052' => 'mpo', 'Mapoly0050s0053' => 'mpo', 'Mapoly0058s0013' => 'mpo', 'Mapoly0091s0078' => 'mpo', 'Mapoly0091s0079' => 'mpo', 'Mapoly0091s0080' => 'mpo', 'Mapoly0091s0081' => 'mpo', 'Mapoly0278s0004' => 'mpo', 'Mapoly0278s0005' => 'mpo', 'Mapoly0278s0006' => 'mpo', 'MBI11_g30648_MAGBIO' => 'mbi', 'MCO03G194' => 'mco', 'MCO03G590' => 'mco', 'MCO07G312' => 'mco', 'MCO10G318' => 'mco', 'MCO12G244' => 'mco', 'MCO13G148' => 'mco', 'MCO13G194' => 'mco', 'MCO16G238' => 'mco', 'MD06G1134100' => 'mdo', 'MD13G1200100' => 'mdo', 'MD13G1200300' => 'mdo', 'MD13G1200600' => 'mdo', 'MD14G1150400' => 'mdo', 'MD16G1200000' => 'mdo', 'Medtr1g102570' => 'mtr', 'Medtr1g102780' => 'mtr', 'Medtr1g102800' => 'mtr', 'Medtr1g102810' => 'mtr', 'Medtr1g102830' => 'mtr', 'MELO3C006499.2' => 'cme', 'Migut.G00385' => 'egut', 'MSTRG.4063' => 'ama', 'Nitab4.5_0000090g0260' => 'nta', 'Nitab4.5_0000977g0030' => 'nta', 'Nitab4.5_0002541g0040' => 'nta', 'Nitab4.5_0007068g0040' => 'nta', 'Nn005s41408' => 'nnu', 'Nn005s41410' => 'nnu', 'Oeu010310.1' => 'oeu', 'Oeu010311.1' => 'oeu', 'Oeu043472.1' => 'oeu', 'Os01g0246400' => 'osa', 'Os04g0267950' => 'osa', 'Os07g0178700' => 'osa', 'Os07g0178800' => 'osa', 'Peaxi162Scf00316g00046' => 'pax', 'Peaxi162Scf00316g00049' => 'pax', 'Peaxi162Scf00316g00059' => 'pax', 'Peaxi162Scf00316g00328' => 'pax', 'Peaxi162Scf00316g00329' => 'pax', 'Peaxi162Scf00316g00411' => 'pax', 'Peaxi162Scf00316g00521' => 'pax', 'Peaxi162Scf00492g00068' => 'pax', 'Peaxi162Scf35631g00002' => 'pax', 'PGR142G3720' => 'pgr', 'PGSC0003DMG400006442' => 'stu', 'Phvul.007G062000' => 'pvu', 'Potri.008G157750' => 'ptr', 'Potri.008G157900' => 'ptr', 'Potri.008G158000' => 'ptr', 'Potri.008G158200' => 'ptr', 'Pp3c11_7280' => 'ppa', 'Pp3c11_7980' => 'ppa', 'Pp3c12_19450' => 'ppa', 'Pp3c14_1480' => 'ppa', 'Pp3c14_1501' => 'ppa', 'Pp3c16_4900' => 'ppa', 'Pp3c16_5010' => 'ppa', 'Pp3c16_5060' => 'ppa', 'Pp3c19_18250' => 'ppa', 'Pp3c23_8530' => 'ppa', 'Pp3c23_8550' => 'ppa', 'Pp3c24_9670' => 'ppa', 'Pp3c2_21390' => 'ppa', 'Pp3c2_31380' => 'ppa', 'Pp3c3_16620' => 'ppa', 'Pp3c3_8090' => 'ppa', 'Pp3c3_8110' => 'ppa', 'Pp3c3_8130' => 'ppa', 'Pp3c3_8150' => 'ppa', 'Pp3c4_14320' => 'ppa', 'Pp3c6_2560' => 'ppa', 'Pp3c9_16700' => 'ppa', 'PRCOL_00000234' => 'pco', 'PRCOL_00000235' => 'pco', 'PRCOL_00000777' => 'pco', 'PRCOL_00002344' => 'pco', 'PRCOL_00002372' => 'pco', 'PRCOL_00006120' => 'pco', 'Prupe.1G021400' => 'ppe', 'Prupe.1G021500' => 'ppe', 'Prupe.1G021600' => 'ppe', 'Prupe.1G021700' => 'ppe', 'Prupe.1G021800' => 'ppe', 'Prupe.5G145100' => 'ppe', 'Psat6g204040' => 'psa', 'Psat6g204800' => 'psa', 'Psat6g204920' => 'psa', 'Psat6g204960' => 'psa', 'Psat6g205080' => 'psa', 'PSO017G0271' => 'pso', 'PSO017G1276' => 'pso', 'PSO017G1429' => 'pso', 'PSO017G1861' => 'pso', 'PSO017G2787' => 'pso', 'PSO017G4466' => 'pso', 'PSO017G5118' => 'pso', 'PSO017G5420' => 'pso', 'PSO063G3678' => 'pso', 'PSO210G0546' => 'pso', 'PSO317G0001' => 'pso', 'PSO357G0512' => 'pso', 'PSO478G2682' => 'pso', 'PSO647G0001' => 'pso', 'PSO675G0001' => 'pso', 'PSO675G2699' => 'pso', 'PSO675G2849' => 'pso', 'PSO675G4991' => 'pso', 'PSO689G0001' => 'pso', 'QL06p000916' => 'qlo', 'QL06p000921' => 'qlo', 'QL06p001398' => 'qlo', 'QL06p001407' => 'qlo', 'QL06p002031' => 'qlo', 'RcHm_v2.0_Chr4g0387791' => 'rch', 'RcHm_v2.0_Chr4g0387801' => 'rch', 'RcHm_v2.0_Chr6g0286501' => 'rch', 'RcHm_v2.0_Chr6g0286511' => 'rch', 'RcHm_v2.0_Chr6g0286521' => 'rch', 'RcHm_v2.0_Chr6g0286531' => 'rch', 'RcHm_v2.0_Chr7g0189141' => 'rch', 'Rhsim02G0028700' => 'rsi', 'Rhsim02G0028800' => 'rsi', 'Rhsim02G0028900' => 'rsi', 'Rhsim02G0029000' => 'rsi', 'Rhsim02G0029100' => 'rsi', 'Rhsim02G0029200' => 'rsi', 'Rhsim02G0029300' => 'rsi', 'Rhsim02G0029400' => 'rsi', 'Rhsim02G0029500' => 'rsi', 'Rhsim02G0029600' => 'rsi', 'RhsimUnG0024000' => 'rsi', 'RhsimUnG0024100' => 'rsi', 'RhsimUnG0024200' => 'rsi', 'RhsimUnG0024300' => 'rsi', 'RhsimUnG0024400' => 'rsi', 'RhsimUnG0024500' => 'rsi', 'RhsimUnG0024700' => 'rsi', 'RhsimUnG0024800' => 'rsi', 'RhsimUnG0024900' => 'rsi', 'RhsimUnG0025100' => 'rsi', 'Sabra08G0120200' => 'sbr', 'Sabra08G0120300' => 'sbr', 'Sabra08G0120500' => 'sbr', 'Sabra08G0120600' => 'sbr', 'Sabra10G0158900' => 'sbr', 'SalBow2G3492' => 'sbo', 'Sc13g0004760' => 'sci', 'Sc13g0004770' => 'sci', 'Sed0003417' => 'sed', 'Sed0019750' => 'sed', 'SEGI_03419' => 'sgi', 'SEGI_05907' => 'sgi', 'SEGI_10682' => 'sgi', 'SEGI_13528' => 'sgi', 'SEGI_16081' => 'sgi', 'SEGI_19370' => 'sgi', 'SEGI_21015' => 'sgi', 'SEGI_21944' => 'sgi', 'SEGI_32906' => 'sgi', 'SEGI_33093' => 'sgi', 'SEGI_36110' => 'sgi', 'SEGI_40397' => 'sgi', 'SGA_v2.0_scaffold191G40426' => 'sas', 'SGA_v2.0_scaffold353G49717' => 'sas', 'SGA_v2.0_scaffold50G18550' => 'sas', 'SMO119G0173' => 'smo', 'SMO172G0002' => 'smo', 'Solyc09g082690.3' => 'sly', 'Solyc09g082700.2' => 'sly', 'Sopen09g031550' => 'spe', 'Sopen09g031560' => 'spe', 'Sp3g20540' => 'spa', 'Sp7g07580' => 'spa', 'TAR134G0002' => 'tar', 'TAR236G0001' => 'tar', 'TAR365G0892' => 'tar', 'TAR636G0166' => 'tar', 'TAR636G0646' => 'tar', 'TAR636G0869' => 'tar', 'TAR636G1317' => 'tar', 'TAR636G1744' => 'tar', 'TAR636G3358' => 'tar', 'TAR636G3436' => 'tar', 'THA.LOC104803047' => 'tha', 'Thecc.04G238900' => 'tca', 'Thhalv10021557m.g' => 'esa', 'Thhalv10026318m.g' => 'esa', 'Thhalv10026335m.g' => 'esa', 'TPR.G17433' => 'tpr', 'TPR.G18915' => 'tpr', 'TPR.G26125' => 'tpr', 'TWI09G0677' => 'twi', 'TWI73G0287' => 'twi', 'unitig_748.g8326' => 'ugi', 'vmacro15370' => 'vma', 'vmacro15371' => 'vma', 'vmacro15372' => 'vma', 'vmacro15373' => 'vma', 'vmacro15374' => 'vma', 'VMungo0720G2826' => 'vmu', 'Zm00001eb116960' => 'zma', 'Zm00001eb301260' => 'zma', 'Zm00001eb301270' => 'zma' ) $gf_id = 'HOM05D001460' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001460' ) $data_identifier = 'HOM05D001460' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 4, 'aag' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 2, 'aox' => (int) 2, 'arhy' => (int) 4, 'ath' => (int) 2, 'atr' => (int) 1, 'acertr' => (int) 10, 'cqu' => (int) 4, 'bca' => (int) 11, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 1, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 1, 'ccan' => (int) 1, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 1, 'col' => (int) 1, 'cpa' => (int) 1, 'cre' => (int) 7, 'csa' => (int) 1, 'camsi' => (int) 2, 'dca' => (int) 3, 'din' => (int) 2, 'dzi' => (int) 3, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 14, 'fve' => (int) 9, 'gma' => (int) 2, 'ghi' => (int) 4, 'gra' => (int) 2, 'vvi' => (int) 1, 'han' => (int) 13, 'cav' => (int) 1, 'hma' => (int) 2, 'sun' => (int) 2, 'lal' => (int) 2, 'lonja' => (int) 12, 'lja' => (int) 1, 'lsa' => (int) 7, 'mes' => (int) 1, 'mpo' => (int) 27, 'mbi' => (int) 1, 'mco' => (int) 8, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 1, 'egut' => (int) 1, 'ama' => (int) 1, 'nta' => (int) 4, 'nnu' => (int) 2, 'oeu' => (int) 3, 'osa' => (int) 4, 'pax' => (int) 9, 'pgr' => (int) 1, 'stu' => (int) 1, 'pvu' => (int) 1, 'ptr' => (int) 4, 'ppa' => (int) 22, 'pco' => (int) 6, 'ppe' => (int) 6, 'psa' => (int) 5, 'pso' => (int) 19, 'qlo' => (int) 5, 'rch' => (int) 7, 'rsi' => (int) 20, 'sbr' => (int) 5, 'sbo' => (int) 1, 'sci' => (int) 2, 'sed' => (int) 2, 'sgi' => (int) 12, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 2, 'tar' => (int) 10, 'tha' => (int) 1, 'tca' => (int) 1, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 2, 'ugi' => (int) 1, 'vma' => (int) 5, 'vmu' => (int) 1, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb301270' $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' => 'HOM05D001460', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '433', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p22980' => 'bna', 'A01p32340' => 'bna', 'A03p42970' => 'bna', 'A05p25880' => 'bna', 'Aa31LG8G9320' => 'aar', 'Aa31LG8G9330' => 'aar', 'Aa31LG8G9340' => 'aar', 'Aa31sc221G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1034' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1528' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.829' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2222' => 'aag', 'Ah.12g058830' => 'amhyb', 'Ah.12g058840' => 'amhyb', 'AL3G37160' => 'aly', 'AL7G41310' => 'aly', 'Aqoxy5G00395' => 'aox', 'Aqoxy5G00396' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0C8NZA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5185HY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JZ1PRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MD3LS0' => 'arhy', 'AT3G22840' => 'ath', 'AT4G14690' => 'ath', 'ATR0665G054' => 'atr', 'Atru.chr4.2344' => 'acertr', 'Atru.chr4.2346' => 'acertr', 'Atru.chr4.2347' => 'acertr', 'Atru.chr4.2348' => 'acertr', 'Atru.chr4.2355' => 'acertr', 'Atru.chr4.2356' => 'acertr', 'Atru.chr4.2358' => 'acertr', 'Atru.chr4.2359' => 'acertr', 'Atru.chr4.2360' => 'acertr', 'Atru.chr4.2361' => 'acertr', 'AUR62030476' => 'cqu', 'AUR62030478' => 'cqu', 'AUR62030819' => 'cqu', 'AUR62030820' => 'cqu', 'BcaB03g14648' => 'bca', 'BcaB04g20492' => 'bca', 'BcaB06g26399' => 'bca', 'BcaC01g03416' => 'bca', 'BcaC01g03419' => 'bca', 'BcaC01g03421' => 'bca', 'BcaC01g03424' => 'bca', 'BcaC05g28012' => 'bca', 'BcaC09g49212' => 'bca', 'BcaC09g50140' => 'bca', 'BcaNung00346' => 'bca', 'BolC1t02785H' => 'bol', 'BolC1t04095H' => 'bol', 'BolC3t17545H' => 'bol', 'BolC5t32769H' => 'bol', 'BraA01t02211Z' => 'bra', 'BraA01t03359Z' => 'bra', 'BraA03t13441Z' => 'bra', 'BraA05t21476Z' => 'bra', 'C01p28420' => 'bna', 'C01p41350' => 'bna', 'C03p52750' => 'bna', 'C03p52780' => 'bna', 'C05p40270' => 'bna', 'CAN.G1437.9' => 'can', 'CANSAT78G0035' => 'cansat', 'CANSAT78G1036' => 'cansat', 'CANSAT78G2272' => 'cansat', 'CANSAT78G2478' => 'cansat', 'CARHR098700' => 'chi', 'CARHR221120' => 'chi', 'CARHR221150' => 'chi', 'Carub.0003s2297' => 'cru', 'Carub.0007s2749' => 'cru', 'Carub.0007s2750' => 'cru', 'Carub.0007s2751' => 'cru', 'Ca_10849_v3' => 'car', 'Cc03_g04300' => 'ccan', 'CDE02G3648' => 'cde', 'CDE05G0060' => 'cde', 'CDE05G0692' => 'cde', 'CDE05G2285' => 'cde', 'CDE05G2884' => 'cde', 'CDE05G3072' => 'cde', 'Cfa008439' => 'cfa', 'Cfa008441' => 'cfa', 'Cfa008443' => 'cfa', 'Cfa008448' => 'cfa', 'Ciclev10005974m.g' => 'ccl', 'Ciclev10006006m.g' => 'ccl', 'Ciclev10006775m.g' => 'ccl', 'CiPaw.02G120400' => 'cil', 'CiPaw.02G120500' => 'cil', 'CiPaw.02G120600' => 'cil', 'ClCG05G004850' => 'cla', 'COL.COLO4_21566' => 'col', 'Cpa.g.sc44.124' => 'cpa', 'Cre07.g320400' => 'cre', 'Cre07.g320450' => 'cre', 'Cre08.g384650' => 'cre', 'Cre09.g393173' => 'cre', 'Cre09.g394325' => 'cre', 'Cre14.g626750' => 'cre', 'Cre16.g679250' => 'cre', 'CsaV3_3G012890' => 'csa', 'CSS0010865' => 'camsi', 'CSS0044338' => 'camsi', 'DCAR_002366' => 'dca', 'DCAR_030687' => 'dca', 'DCAR_030688' => 'dca', 'Dinv14047' => 'din', 'Dinv14048' => 'din', 'Duzib151G0105' => 'dzi', 'Duzib151G0114' => 'dzi', 'Duzib212G1029' => 'dzi', 'ECA232G3536' => 'eca', 'ECA240G0786' => 'eca', 'ECA240G1802' => 'eca', 'ECA240G3760' => 'eca', 'ECA240G3920' => 'eca', 'EL10Ac5g12536' => 'bvu', 'EL10Ac5g12537' => 'bvu', 'EL10Ac5g12538' => 'bvu', 'Eucgr.B01004' => 'egr', 'Eucgr.B01006' => 'egr', 'Eucgr.B01007' => 'egr', 'Eucgr.B01008' => 'egr', 'Eucgr.B01895' => 'egr', 'Eucgr.B01896' => 'egr', 'FAN04G1456' => 'fan', 'FAN08G1769' => 'fan', 'FAN08G2160' => 'fan', 'FAN13G2403' => 'fan', 'FAN13G3303' => 'fan', 'FAN15G2435' => 'fan', 'FAN17G0672' => 'fan', 'FAN17G2441' => 'fan', 'FAN18G1024' => 'fan', 'FAN22G1458' => 'fan', 'FAN24G0037' => 'fan', 'FAN24G0429' => 'fan', 'FAN24G2387' => 'fan', 'FAN27G2746' => 'fan', 'FvH4_2g20400' => 'fve', 'FvH4_2g20420' => 'fve', 'FvH4_2g20430' => 'fve', 'FvH4_4g01270' => 'fve', 'FvH4_4g01290' => 'fve', 'FvH4_4g01300' => 'fve', 'FvH4_4g01310' => 'fve', 'FvH4_4g01330' => 'fve', 'FvH4_5g09070' => 'fve', 'Glyma.10G243800' => 'gma', 'Glyma.20G150600' => 'gma', 'Gohir.A09G219200' => 'ghi', 'Gohir.A09G219300' => 'ghi', 'Gohir.D09G221400' => 'ghi', 'Gohir.D09G221500' => 'ghi', 'Gorai.006G242600' => 'gra', 'Gorai.006G242700' => 'gra', 'GSVIVG01018044001' => 'vvi', 'HanXRQChr03g0083821' => 'han', 'HanXRQChr03g0083841' => 'han', 'HanXRQChr03g0083881' => 'han', 'HanXRQChr03g0083901' => 'han', 'HanXRQChr03g0083921' => 'han', 'HanXRQChr03g0085331' => 'han', 'HanXRQChr03g0085361' => 'han', 'HanXRQChr03g0085411' => 'han', 'HanXRQChr03g0085421' => 'han', 'HanXRQChr03g0085431' => 'han', 'HanXRQChr08g0221991' => 'han', 'HanXRQChr11g0336061' => 'han', 'HanXRQChr11g0336411' => 'han', 'Haze_11234' => 'cav', 'Hma1.2p1_0549F.1_g177010' => 'hma', 'Hma1.2p1_0602F.1_g187630' => 'hma', 'Hund14876' => 'sun', 'Hund14879' => 'sun', 'Lalb_Chr06g0160741' => 'lal', 'Lalb_Chr21g0304781' => 'lal', 'Lj3A726G19' => 'lonja', 'Lj3A726T23' => 'lonja', 'Lj3A726T24' => 'lonja', 'Lj3A726T25' => 'lonja', 'Lj3A727T17' => 'lonja', 'Lj3C726T0' => 'lonja', 'Lj3C726T2' => 'lonja', 'Lj3P725T35' => 'lonja', 'Lj3P727T10' => 'lonja', 'Lj3P727T12' => 'lonja', 'Lj3P727T14' => 'lonja', 'Lj5g0023109' => 'lja', 'Lj6P646T44' => 'lonja', 'Lsat_1_v5_gn_6_75760' => 'lsa', 'Lsat_1_v5_gn_6_75800' => 'lsa', 'Lsat_1_v5_gn_6_75900' => 'lsa', 'Lsat_1_v5_gn_6_76240' => 'lsa', 'Lsat_1_v5_gn_6_76441' => 'lsa', 'Lsat_1_v5_gn_6_76700' => 'lsa', 'Lsat_1_v5_gn_6_76760' => 'lsa', 'Manes.15G033100' => 'mes', 'Mapoly0004s0074' => 'mpo', 'Mapoly0004s0075' => 'mpo', 'Mapoly0004s0163' => 'mpo', 'Mapoly0004s0164' => 'mpo', 'Mapoly0021s0018' => 'mpo', 'Mapoly0041s0136' => 'mpo', 'Mapoly0041s0137' => 'mpo', 'Mapoly0041s0138' => 'mpo', 'Mapoly0041s0139' => 'mpo', 'Mapoly0041s0141' => 'mpo', 'Mapoly0041s0142' => 'mpo', 'Mapoly0041s0143' => 'mpo', 'Mapoly0041s0144' => 'mpo', 'Mapoly0041s0145' => 'mpo', 'Mapoly0047s0106' => 'mpo', 'Mapoly0047s0108' => 'mpo', 'Mapoly0050s0051' => 'mpo', 'Mapoly0050s0052' => 'mpo', 'Mapoly0050s0053' => 'mpo', 'Mapoly0058s0013' => 'mpo', 'Mapoly0091s0078' => 'mpo', 'Mapoly0091s0079' => 'mpo', 'Mapoly0091s0080' => 'mpo', 'Mapoly0091s0081' => 'mpo', 'Mapoly0278s0004' => 'mpo', 'Mapoly0278s0005' => 'mpo', 'Mapoly0278s0006' => 'mpo', 'MBI11_g30648_MAGBIO' => 'mbi', 'MCO03G194' => 'mco', 'MCO03G590' => 'mco', 'MCO07G312' => 'mco', 'MCO10G318' => 'mco', 'MCO12G244' => 'mco', 'MCO13G148' => 'mco', 'MCO13G194' => 'mco', 'MCO16G238' => 'mco', 'MD06G1134100' => 'mdo', 'MD13G1200100' => 'mdo', 'MD13G1200300' => 'mdo', 'MD13G1200600' => 'mdo', 'MD14G1150400' => 'mdo', 'MD16G1200000' => 'mdo', 'Medtr1g102570' => 'mtr', 'Medtr1g102780' => 'mtr', 'Medtr1g102800' => 'mtr', 'Medtr1g102810' => 'mtr', 'Medtr1g102830' => 'mtr', 'MELO3C006499.2' => 'cme', 'Migut.G00385' => 'egut', 'MSTRG.4063' => 'ama', 'Nitab4.5_0000090g0260' => 'nta', 'Nitab4.5_0000977g0030' => 'nta', 'Nitab4.5_0002541g0040' => 'nta', 'Nitab4.5_0007068g0040' => 'nta', 'Nn005s41408' => 'nnu', 'Nn005s41410' => 'nnu', 'Oeu010310.1' => 'oeu', 'Oeu010311.1' => 'oeu', 'Oeu043472.1' => 'oeu', 'Os01g0246400' => 'osa', 'Os04g0267950' => 'osa', 'Os07g0178700' => 'osa', 'Os07g0178800' => 'osa', 'Peaxi162Scf00316g00046' => 'pax', 'Peaxi162Scf00316g00049' => 'pax', 'Peaxi162Scf00316g00059' => 'pax', 'Peaxi162Scf00316g00328' => 'pax', 'Peaxi162Scf00316g00329' => 'pax', 'Peaxi162Scf00316g00411' => 'pax', 'Peaxi162Scf00316g00521' => 'pax', 'Peaxi162Scf00492g00068' => 'pax', 'Peaxi162Scf35631g00002' => 'pax', 'PGR142G3720' => 'pgr', 'PGSC0003DMG400006442' => 'stu', 'Phvul.007G062000' => 'pvu', 'Potri.008G157750' => 'ptr', 'Potri.008G157900' => 'ptr', 'Potri.008G158000' => 'ptr', 'Potri.008G158200' => 'ptr', 'Pp3c11_7280' => 'ppa', 'Pp3c11_7980' => 'ppa', 'Pp3c12_19450' => 'ppa', 'Pp3c14_1480' => 'ppa', 'Pp3c14_1501' => 'ppa', 'Pp3c16_4900' => 'ppa', 'Pp3c16_5010' => 'ppa', 'Pp3c16_5060' => 'ppa', 'Pp3c19_18250' => 'ppa', 'Pp3c23_8530' => 'ppa', 'Pp3c23_8550' => 'ppa', 'Pp3c24_9670' => 'ppa', 'Pp3c2_21390' => 'ppa', 'Pp3c2_31380' => 'ppa', 'Pp3c3_16620' => 'ppa', 'Pp3c3_8090' => 'ppa', 'Pp3c3_8110' => 'ppa', 'Pp3c3_8130' => 'ppa', 'Pp3c3_8150' => 'ppa', 'Pp3c4_14320' => 'ppa', 'Pp3c6_2560' => 'ppa', 'Pp3c9_16700' => 'ppa', 'PRCOL_00000234' => 'pco', 'PRCOL_00000235' => 'pco', 'PRCOL_00000777' => 'pco', 'PRCOL_00002344' => 'pco', 'PRCOL_00002372' => 'pco', 'PRCOL_00006120' => 'pco', 'Prupe.1G021400' => 'ppe', 'Prupe.1G021500' => 'ppe', 'Prupe.1G021600' => 'ppe', 'Prupe.1G021700' => 'ppe', 'Prupe.1G021800' => 'ppe', 'Prupe.5G145100' => 'ppe', 'Psat6g204040' => 'psa', 'Psat6g204800' => 'psa', 'Psat6g204920' => 'psa', 'Psat6g204960' => 'psa', 'Psat6g205080' => 'psa', 'PSO017G0271' => 'pso', 'PSO017G1276' => 'pso', 'PSO017G1429' => 'pso', 'PSO017G1861' => 'pso', 'PSO017G2787' => 'pso', 'PSO017G4466' => 'pso', 'PSO017G5118' => 'pso', 'PSO017G5420' => 'pso', 'PSO063G3678' => 'pso', 'PSO210G0546' => 'pso', 'PSO317G0001' => 'pso', 'PSO357G0512' => 'pso', 'PSO478G2682' => 'pso', 'PSO647G0001' => 'pso', 'PSO675G0001' => 'pso', 'PSO675G2699' => 'pso', 'PSO675G2849' => 'pso', 'PSO675G4991' => 'pso', 'PSO689G0001' => 'pso', 'QL06p000916' => 'qlo', 'QL06p000921' => 'qlo', 'QL06p001398' => 'qlo', 'QL06p001407' => 'qlo', 'QL06p002031' => 'qlo', 'RcHm_v2.0_Chr4g0387791' => 'rch', 'RcHm_v2.0_Chr4g0387801' => 'rch', 'RcHm_v2.0_Chr6g0286501' => 'rch', 'RcHm_v2.0_Chr6g0286511' => 'rch', 'RcHm_v2.0_Chr6g0286521' => 'rch', 'RcHm_v2.0_Chr6g0286531' => 'rch', 'RcHm_v2.0_Chr7g0189141' => 'rch', 'Rhsim02G0028700' => 'rsi', 'Rhsim02G0028800' => 'rsi', 'Rhsim02G0028900' => 'rsi', 'Rhsim02G0029000' => 'rsi', 'Rhsim02G0029100' => 'rsi', 'Rhsim02G0029200' => 'rsi', 'Rhsim02G0029300' => 'rsi', 'Rhsim02G0029400' => 'rsi', 'Rhsim02G0029500' => 'rsi', 'Rhsim02G0029600' => 'rsi', 'RhsimUnG0024000' => 'rsi', 'RhsimUnG0024100' => 'rsi', 'RhsimUnG0024200' => 'rsi', 'RhsimUnG0024300' => 'rsi', 'RhsimUnG0024400' => 'rsi', 'RhsimUnG0024500' => 'rsi', 'RhsimUnG0024700' => 'rsi', 'RhsimUnG0024800' => 'rsi', 'RhsimUnG0024900' => 'rsi', 'RhsimUnG0025100' => 'rsi', 'Sabra08G0120200' => 'sbr', 'Sabra08G0120300' => 'sbr', 'Sabra08G0120500' => 'sbr', 'Sabra08G0120600' => 'sbr', 'Sabra10G0158900' => 'sbr', 'SalBow2G3492' => 'sbo', 'Sc13g0004760' => 'sci', 'Sc13g0004770' => 'sci', 'Sed0003417' => 'sed', 'Sed0019750' => 'sed', 'SEGI_03419' => 'sgi', 'SEGI_05907' => 'sgi', 'SEGI_10682' => 'sgi', 'SEGI_13528' => 'sgi', 'SEGI_16081' => 'sgi', 'SEGI_19370' => 'sgi', 'SEGI_21015' => 'sgi', 'SEGI_21944' => 'sgi', 'SEGI_32906' => 'sgi', 'SEGI_33093' => 'sgi', 'SEGI_36110' => 'sgi', 'SEGI_40397' => 'sgi', 'SGA_v2.0_scaffold191G40426' => 'sas', 'SGA_v2.0_scaffold353G49717' => 'sas', 'SGA_v2.0_scaffold50G18550' => 'sas', 'SMO119G0173' => 'smo', 'SMO172G0002' => 'smo', 'Solyc09g082690.3' => 'sly', 'Solyc09g082700.2' => 'sly', 'Sopen09g031550' => 'spe', 'Sopen09g031560' => 'spe', 'Sp3g20540' => 'spa', 'Sp7g07580' => 'spa', 'TAR134G0002' => 'tar', 'TAR236G0001' => 'tar', 'TAR365G0892' => 'tar', 'TAR636G0166' => 'tar', 'TAR636G0646' => 'tar', 'TAR636G0869' => 'tar', 'TAR636G1317' => 'tar', 'TAR636G1744' => 'tar', 'TAR636G3358' => 'tar', 'TAR636G3436' => 'tar', 'THA.LOC104803047' => 'tha', 'Thecc.04G238900' => 'tca', 'Thhalv10021557m.g' => 'esa', 'Thhalv10026318m.g' => 'esa', 'Thhalv10026335m.g' => 'esa', 'TPR.G17433' => 'tpr', 'TPR.G18915' => 'tpr', 'TPR.G26125' => 'tpr', 'TWI09G0677' => 'twi', 'TWI73G0287' => 'twi', 'unitig_748.g8326' => 'ugi', 'vmacro15370' => 'vma', 'vmacro15371' => 'vma', 'vmacro15372' => 'vma', 'vmacro15373' => 'vma', 'vmacro15374' => 'vma', 'VMungo0720G2826' => 'vmu', 'Zm00001eb116960' => 'zma', 'Zm00001eb301260' => 'zma', 'Zm00001eb301270' => 'zma' ), 'gf_id' => 'HOM05D001460', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001460' ), 'data_identifier' => 'HOM05D001460', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001460', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '433', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p22980' => 'bna', 'A01p32340' => 'bna', 'A03p42970' => 'bna', 'A05p25880' => 'bna', 'Aa31LG8G9320' => 'aar', 'Aa31LG8G9330' => 'aar', 'Aa31LG8G9340' => 'aar', 'Aa31sc221G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1034' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1528' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.829' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2222' => 'aag', 'Ah.12g058830' => 'amhyb', 'Ah.12g058840' => 'amhyb', 'AL3G37160' => 'aly', 'AL7G41310' => 'aly', 'Aqoxy5G00395' => 'aox', 'Aqoxy5G00396' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0C8NZA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5185HY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JZ1PRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MD3LS0' => 'arhy', 'AT3G22840' => 'ath', 'AT4G14690' => 'ath', 'ATR0665G054' => 'atr', 'Atru.chr4.2344' => 'acertr', 'Atru.chr4.2346' => 'acertr', 'Atru.chr4.2347' => 'acertr', 'Atru.chr4.2348' => 'acertr', 'Atru.chr4.2355' => 'acertr', 'Atru.chr4.2356' => 'acertr', 'Atru.chr4.2358' => 'acertr', 'Atru.chr4.2359' => 'acertr', 'Atru.chr4.2360' => 'acertr', 'Atru.chr4.2361' => 'acertr', 'AUR62030476' => 'cqu', 'AUR62030478' => 'cqu', 'AUR62030819' => 'cqu', 'AUR62030820' => 'cqu', 'BcaB03g14648' => 'bca', 'BcaB04g20492' => 'bca', 'BcaB06g26399' => 'bca', 'BcaC01g03416' => 'bca', 'BcaC01g03419' => 'bca', 'BcaC01g03421' => 'bca', 'BcaC01g03424' => 'bca', 'BcaC05g28012' => 'bca', 'BcaC09g49212' => 'bca', 'BcaC09g50140' => 'bca', 'BcaNung00346' => 'bca', 'BolC1t02785H' => 'bol', 'BolC1t04095H' => 'bol', 'BolC3t17545H' => 'bol', 'BolC5t32769H' => 'bol', 'BraA01t02211Z' => 'bra', 'BraA01t03359Z' => 'bra', 'BraA03t13441Z' => 'bra', 'BraA05t21476Z' => 'bra', 'C01p28420' => 'bna', 'C01p41350' => 'bna', 'C03p52750' => 'bna', 'C03p52780' => 'bna', 'C05p40270' => 'bna', 'CAN.G1437.9' => 'can', 'CANSAT78G0035' => 'cansat', 'CANSAT78G1036' => 'cansat', 'CANSAT78G2272' => 'cansat', 'CANSAT78G2478' => 'cansat', 'CARHR098700' => 'chi', 'CARHR221120' => 'chi', 'CARHR221150' => 'chi', 'Carub.0003s2297' => 'cru', 'Carub.0007s2749' => 'cru', 'Carub.0007s2750' => 'cru', 'Carub.0007s2751' => 'cru', 'Ca_10849_v3' => 'car', 'Cc03_g04300' => 'ccan', 'CDE02G3648' => 'cde', 'CDE05G0060' => 'cde', 'CDE05G0692' => 'cde', 'CDE05G2285' => 'cde', 'CDE05G2884' => 'cde', 'CDE05G3072' => 'cde', 'Cfa008439' => 'cfa', 'Cfa008441' => 'cfa', 'Cfa008443' => 'cfa', 'Cfa008448' => 'cfa', 'Ciclev10005974m.g' => 'ccl', 'Ciclev10006006m.g' => 'ccl', 'Ciclev10006775m.g' => 'ccl', 'CiPaw.02G120400' => 'cil', 'CiPaw.02G120500' => 'cil', 'CiPaw.02G120600' => 'cil', 'ClCG05G004850' => 'cla', 'COL.COLO4_21566' => 'col', 'Cpa.g.sc44.124' => 'cpa', 'Cre07.g320400' => 'cre', 'Cre07.g320450' => 'cre', 'Cre08.g384650' => 'cre', 'Cre09.g393173' => 'cre', 'Cre09.g394325' => 'cre', 'Cre14.g626750' => 'cre', 'Cre16.g679250' => 'cre', 'CsaV3_3G012890' => 'csa', 'CSS0010865' => 'camsi', 'CSS0044338' => 'camsi', 'DCAR_002366' => 'dca', 'DCAR_030687' => 'dca', 'DCAR_030688' => 'dca', 'Dinv14047' => 'din', 'Dinv14048' => 'din', 'Duzib151G0105' => 'dzi', 'Duzib151G0114' => 'dzi', 'Duzib212G1029' => 'dzi', 'ECA232G3536' => 'eca', 'ECA240G0786' => 'eca', 'ECA240G1802' => 'eca', 'ECA240G3760' => 'eca', 'ECA240G3920' => 'eca', 'EL10Ac5g12536' => 'bvu', 'EL10Ac5g12537' => 'bvu', 'EL10Ac5g12538' => 'bvu', 'Eucgr.B01004' => 'egr', 'Eucgr.B01006' => 'egr', 'Eucgr.B01007' => 'egr', 'Eucgr.B01008' => 'egr', 'Eucgr.B01895' => 'egr', 'Eucgr.B01896' => 'egr', 'FAN04G1456' => 'fan', 'FAN08G1769' => 'fan', 'FAN08G2160' => 'fan', 'FAN13G2403' => 'fan', 'FAN13G3303' => 'fan', 'FAN15G2435' => 'fan', 'FAN17G0672' => 'fan', 'FAN17G2441' => 'fan', 'FAN18G1024' => 'fan', 'FAN22G1458' => 'fan', 'FAN24G0037' => 'fan', 'FAN24G0429' => 'fan', 'FAN24G2387' => 'fan', 'FAN27G2746' => 'fan', 'FvH4_2g20400' => 'fve', 'FvH4_2g20420' => 'fve', 'FvH4_2g20430' => 'fve', 'FvH4_4g01270' => 'fve', 'FvH4_4g01290' => 'fve', 'FvH4_4g01300' => 'fve', 'FvH4_4g01310' => 'fve', 'FvH4_4g01330' => 'fve', 'FvH4_5g09070' => 'fve', 'Glyma.10G243800' => 'gma', 'Glyma.20G150600' => 'gma', 'Gohir.A09G219200' => 'ghi', 'Gohir.A09G219300' => 'ghi', 'Gohir.D09G221400' => 'ghi', 'Gohir.D09G221500' => 'ghi', 'Gorai.006G242600' => 'gra', 'Gorai.006G242700' => 'gra', 'GSVIVG01018044001' => 'vvi', 'HanXRQChr03g0083821' => 'han', 'HanXRQChr03g0083841' => 'han', 'HanXRQChr03g0083881' => 'han', 'HanXRQChr03g0083901' => 'han', 'HanXRQChr03g0083921' => 'han', 'HanXRQChr03g0085331' => 'han', 'HanXRQChr03g0085361' => 'han', 'HanXRQChr03g0085411' => 'han', 'HanXRQChr03g0085421' => 'han', 'HanXRQChr03g0085431' => 'han', 'HanXRQChr08g0221991' => 'han', 'HanXRQChr11g0336061' => 'han', 'HanXRQChr11g0336411' => 'han', 'Haze_11234' => 'cav', 'Hma1.2p1_0549F.1_g177010' => 'hma', 'Hma1.2p1_0602F.1_g187630' => 'hma', 'Hund14876' => 'sun', 'Hund14879' => 'sun', 'Lalb_Chr06g0160741' => 'lal', 'Lalb_Chr21g0304781' => 'lal', 'Lj3A726G19' => 'lonja', 'Lj3A726T23' => 'lonja', 'Lj3A726T24' => 'lonja', 'Lj3A726T25' => 'lonja', 'Lj3A727T17' => 'lonja', 'Lj3C726T0' => 'lonja', 'Lj3C726T2' => 'lonja', 'Lj3P725T35' => 'lonja', 'Lj3P727T10' => 'lonja', 'Lj3P727T12' => 'lonja', 'Lj3P727T14' => 'lonja', 'Lj5g0023109' => 'lja', 'Lj6P646T44' => 'lonja', 'Lsat_1_v5_gn_6_75760' => 'lsa', 'Lsat_1_v5_gn_6_75800' => 'lsa', 'Lsat_1_v5_gn_6_75900' => 'lsa', 'Lsat_1_v5_gn_6_76240' => 'lsa', 'Lsat_1_v5_gn_6_76441' => 'lsa', 'Lsat_1_v5_gn_6_76700' => 'lsa', 'Lsat_1_v5_gn_6_76760' => 'lsa', 'Manes.15G033100' => 'mes', 'Mapoly0004s0074' => 'mpo', 'Mapoly0004s0075' => 'mpo', 'Mapoly0004s0163' => 'mpo', 'Mapoly0004s0164' => 'mpo', 'Mapoly0021s0018' => 'mpo', 'Mapoly0041s0136' => 'mpo', 'Mapoly0041s0137' => 'mpo', 'Mapoly0041s0138' => 'mpo', 'Mapoly0041s0139' => 'mpo', 'Mapoly0041s0141' => 'mpo', 'Mapoly0041s0142' => 'mpo', 'Mapoly0041s0143' => 'mpo', 'Mapoly0041s0144' => 'mpo', 'Mapoly0041s0145' => 'mpo', 'Mapoly0047s0106' => 'mpo', 'Mapoly0047s0108' => 'mpo', 'Mapoly0050s0051' => 'mpo', 'Mapoly0050s0052' => 'mpo', 'Mapoly0050s0053' => 'mpo', 'Mapoly0058s0013' => 'mpo', 'Mapoly0091s0078' => 'mpo', 'Mapoly0091s0079' => 'mpo', 'Mapoly0091s0080' => 'mpo', 'Mapoly0091s0081' => 'mpo', 'Mapoly0278s0004' => 'mpo', 'Mapoly0278s0005' => 'mpo', 'Mapoly0278s0006' => 'mpo', 'MBI11_g30648_MAGBIO' => 'mbi', 'MCO03G194' => 'mco', 'MCO03G590' => 'mco', 'MCO07G312' => 'mco', 'MCO10G318' => 'mco', 'MCO12G244' => 'mco', 'MCO13G148' => 'mco', 'MCO13G194' => 'mco', 'MCO16G238' => 'mco', 'MD06G1134100' => 'mdo', 'MD13G1200100' => 'mdo', 'MD13G1200300' => 'mdo', 'MD13G1200600' => 'mdo', 'MD14G1150400' => 'mdo', 'MD16G1200000' => 'mdo', 'Medtr1g102570' => 'mtr', 'Medtr1g102780' => 'mtr', 'Medtr1g102800' => 'mtr', 'Medtr1g102810' => 'mtr', 'Medtr1g102830' => 'mtr', 'MELO3C006499.2' => 'cme', 'Migut.G00385' => 'egut', 'MSTRG.4063' => 'ama', 'Nitab4.5_0000090g0260' => 'nta', 'Nitab4.5_0000977g0030' => 'nta', 'Nitab4.5_0002541g0040' => 'nta', 'Nitab4.5_0007068g0040' => 'nta', 'Nn005s41408' => 'nnu', 'Nn005s41410' => 'nnu', 'Oeu010310.1' => 'oeu', 'Oeu010311.1' => 'oeu', 'Oeu043472.1' => 'oeu', 'Os01g0246400' => 'osa', 'Os04g0267950' => 'osa', 'Os07g0178700' => 'osa', 'Os07g0178800' => 'osa', 'Peaxi162Scf00316g00046' => 'pax', 'Peaxi162Scf00316g00049' => 'pax', 'Peaxi162Scf00316g00059' => 'pax', 'Peaxi162Scf00316g00328' => 'pax', 'Peaxi162Scf00316g00329' => 'pax', 'Peaxi162Scf00316g00411' => 'pax', 'Peaxi162Scf00316g00521' => 'pax', 'Peaxi162Scf00492g00068' => 'pax', 'Peaxi162Scf35631g00002' => 'pax', 'PGR142G3720' => 'pgr', 'PGSC0003DMG400006442' => 'stu', 'Phvul.007G062000' => 'pvu', 'Potri.008G157750' => 'ptr', 'Potri.008G157900' => 'ptr', 'Potri.008G158000' => 'ptr', 'Potri.008G158200' => 'ptr', 'Pp3c11_7280' => 'ppa', 'Pp3c11_7980' => 'ppa', 'Pp3c12_19450' => 'ppa', 'Pp3c14_1480' => 'ppa', 'Pp3c14_1501' => 'ppa', 'Pp3c16_4900' => 'ppa', 'Pp3c16_5010' => 'ppa', 'Pp3c16_5060' => 'ppa', 'Pp3c19_18250' => 'ppa', 'Pp3c23_8530' => 'ppa', 'Pp3c23_8550' => 'ppa', 'Pp3c24_9670' => 'ppa', 'Pp3c2_21390' => 'ppa', 'Pp3c2_31380' => 'ppa', 'Pp3c3_16620' => 'ppa', 'Pp3c3_8090' => 'ppa', 'Pp3c3_8110' => 'ppa', 'Pp3c3_8130' => 'ppa', 'Pp3c3_8150' => 'ppa', 'Pp3c4_14320' => 'ppa', 'Pp3c6_2560' => 'ppa', 'Pp3c9_16700' => 'ppa', 'PRCOL_00000234' => 'pco', 'PRCOL_00000235' => 'pco', 'PRCOL_00000777' => 'pco', 'PRCOL_00002344' => 'pco', 'PRCOL_00002372' => 'pco', 'PRCOL_00006120' => 'pco', 'Prupe.1G021400' => 'ppe', 'Prupe.1G021500' => 'ppe', 'Prupe.1G021600' => 'ppe', 'Prupe.1G021700' => 'ppe', 'Prupe.1G021800' => 'ppe', 'Prupe.5G145100' => 'ppe', 'Psat6g204040' => 'psa', 'Psat6g204800' => 'psa', 'Psat6g204920' => 'psa', 'Psat6g204960' => 'psa', 'Psat6g205080' => 'psa', 'PSO017G0271' => 'pso', 'PSO017G1276' => 'pso', 'PSO017G1429' => 'pso', 'PSO017G1861' => 'pso', 'PSO017G2787' => 'pso', 'PSO017G4466' => 'pso', 'PSO017G5118' => 'pso', 'PSO017G5420' => 'pso', 'PSO063G3678' => 'pso', 'PSO210G0546' => 'pso', 'PSO317G0001' => 'pso', 'PSO357G0512' => 'pso', 'PSO478G2682' => 'pso', 'PSO647G0001' => 'pso', 'PSO675G0001' => 'pso', 'PSO675G2699' => 'pso', 'PSO675G2849' => 'pso', 'PSO675G4991' => 'pso', 'PSO689G0001' => 'pso', 'QL06p000916' => 'qlo', 'QL06p000921' => 'qlo', 'QL06p001398' => 'qlo', 'QL06p001407' => 'qlo', 'QL06p002031' => 'qlo', 'RcHm_v2.0_Chr4g0387791' => 'rch', 'RcHm_v2.0_Chr4g0387801' => 'rch', 'RcHm_v2.0_Chr6g0286501' => 'rch', 'RcHm_v2.0_Chr6g0286511' => 'rch', 'RcHm_v2.0_Chr6g0286521' => 'rch', 'RcHm_v2.0_Chr6g0286531' => 'rch', 'RcHm_v2.0_Chr7g0189141' => 'rch', 'Rhsim02G0028700' => 'rsi', 'Rhsim02G0028800' => 'rsi', 'Rhsim02G0028900' => 'rsi', 'Rhsim02G0029000' => 'rsi', 'Rhsim02G0029100' => 'rsi', 'Rhsim02G0029200' => 'rsi', 'Rhsim02G0029300' => 'rsi', 'Rhsim02G0029400' => 'rsi', 'Rhsim02G0029500' => 'rsi', 'Rhsim02G0029600' => 'rsi', 'RhsimUnG0024000' => 'rsi', 'RhsimUnG0024100' => 'rsi', 'RhsimUnG0024200' => 'rsi', 'RhsimUnG0024300' => 'rsi', 'RhsimUnG0024400' => 'rsi', 'RhsimUnG0024500' => 'rsi', 'RhsimUnG0024700' => 'rsi', 'RhsimUnG0024800' => 'rsi', 'RhsimUnG0024900' => 'rsi', 'RhsimUnG0025100' => 'rsi', 'Sabra08G0120200' => 'sbr', 'Sabra08G0120300' => 'sbr', 'Sabra08G0120500' => 'sbr', 'Sabra08G0120600' => 'sbr', 'Sabra10G0158900' => 'sbr', 'SalBow2G3492' => 'sbo', 'Sc13g0004760' => 'sci', 'Sc13g0004770' => 'sci', 'Sed0003417' => 'sed', 'Sed0019750' => 'sed', 'SEGI_03419' => 'sgi', 'SEGI_05907' => 'sgi', 'SEGI_10682' => 'sgi', 'SEGI_13528' => 'sgi', 'SEGI_16081' => 'sgi', 'SEGI_19370' => 'sgi', 'SEGI_21015' => 'sgi', 'SEGI_21944' => 'sgi', 'SEGI_32906' => 'sgi', 'SEGI_33093' => 'sgi', 'SEGI_36110' => 'sgi', 'SEGI_40397' => 'sgi', 'SGA_v2.0_scaffold191G40426' => 'sas', 'SGA_v2.0_scaffold353G49717' => 'sas', 'SGA_v2.0_scaffold50G18550' => 'sas', 'SMO119G0173' => 'smo', 'SMO172G0002' => 'smo', 'Solyc09g082690.3' => 'sly', 'Solyc09g082700.2' => 'sly', 'Sopen09g031550' => 'spe', 'Sopen09g031560' => 'spe', 'Sp3g20540' => 'spa', 'Sp7g07580' => 'spa', 'TAR134G0002' => 'tar', 'TAR236G0001' => 'tar', 'TAR365G0892' => 'tar', 'TAR636G0166' => 'tar', 'TAR636G0646' => 'tar', 'TAR636G0869' => 'tar', 'TAR636G1317' => 'tar', 'TAR636G1744' => 'tar', 'TAR636G3358' => 'tar', 'TAR636G3436' => 'tar', 'THA.LOC104803047' => 'tha', 'Thecc.04G238900' => 'tca', 'Thhalv10021557m.g' => 'esa', 'Thhalv10026318m.g' => 'esa', 'Thhalv10026335m.g' => 'esa', 'TPR.G17433' => 'tpr', 'TPR.G18915' => 'tpr', 'TPR.G26125' => 'tpr', 'TWI09G0677' => 'twi', 'TWI73G0287' => 'twi', 'unitig_748.g8326' => 'ugi', 'vmacro15370' => 'vma', 'vmacro15371' => 'vma', 'vmacro15372' => 'vma', 'vmacro15373' => 'vma', 'vmacro15374' => 'vma', 'VMungo0720G2826' => 'vmu', 'Zm00001eb116960' => 'zma', 'Zm00001eb301260' => 'zma', 'Zm00001eb301270' => 'zma' ) $gf_id = 'HOM05D001460' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001460' ) $data_identifier = 'HOM05D001460' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 4, 'aag' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 2, 'aox' => (int) 2, 'arhy' => (int) 4, 'ath' => (int) 2, 'atr' => (int) 1, 'acertr' => (int) 10, 'cqu' => (int) 4, 'bca' => (int) 11, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 1, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 1, 'ccan' => (int) 1, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 1, 'col' => (int) 1, 'cpa' => (int) 1, 'cre' => (int) 7, 'csa' => (int) 1, 'camsi' => (int) 2, 'dca' => (int) 3, 'din' => (int) 2, 'dzi' => (int) 3, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 14, 'fve' => (int) 9, 'gma' => (int) 2, 'ghi' => (int) 4, 'gra' => (int) 2, 'vvi' => (int) 1, 'han' => (int) 13, 'cav' => (int) 1, 'hma' => (int) 2, 'sun' => (int) 2, 'lal' => (int) 2, 'lonja' => (int) 12, 'lja' => (int) 1, 'lsa' => (int) 7, 'mes' => (int) 1, 'mpo' => (int) 27, 'mbi' => (int) 1, 'mco' => (int) 8, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 1, 'egut' => (int) 1, 'ama' => (int) 1, 'nta' => (int) 4, 'nnu' => (int) 2, 'oeu' => (int) 3, 'osa' => (int) 4, 'pax' => (int) 9, 'pgr' => (int) 1, 'stu' => (int) 1, 'pvu' => (int) 1, 'ptr' => (int) 4, 'ppa' => (int) 22, 'pco' => (int) 6, 'ppe' => (int) 6, 'psa' => (int) 5, 'pso' => (int) 19, 'qlo' => (int) 5, 'rch' => (int) 7, 'rsi' => (int) 20, 'sbr' => (int) 5, 'sbo' => (int) 1, 'sci' => (int) 2, 'sed' => (int) 2, 'sgi' => (int) 12, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 2, 'tar' => (int) 10, 'tha' => (int) 1, 'tca' => (int) 1, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 2, 'ugi' => (int) 1, 'vma' => (int) 5, 'vmu' => (int) 1, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb301270' $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' => 'HOM05D001460', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '433', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p22980' => 'bna', 'A01p32340' => 'bna', 'A03p42970' => 'bna', 'A05p25880' => 'bna', 'Aa31LG8G9320' => 'aar', 'Aa31LG8G9330' => 'aar', 'Aa31LG8G9340' => 'aar', 'Aa31sc221G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1034' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1528' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.829' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2222' => 'aag', 'Ah.12g058830' => 'amhyb', 'Ah.12g058840' => 'amhyb', 'AL3G37160' => 'aly', 'AL7G41310' => 'aly', 'Aqoxy5G00395' => 'aox', 'Aqoxy5G00396' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0C8NZA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5185HY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JZ1PRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MD3LS0' => 'arhy', 'AT3G22840' => 'ath', 'AT4G14690' => 'ath', 'ATR0665G054' => 'atr', 'Atru.chr4.2344' => 'acertr', 'Atru.chr4.2346' => 'acertr', 'Atru.chr4.2347' => 'acertr', 'Atru.chr4.2348' => 'acertr', 'Atru.chr4.2355' => 'acertr', 'Atru.chr4.2356' => 'acertr', 'Atru.chr4.2358' => 'acertr', 'Atru.chr4.2359' => 'acertr', 'Atru.chr4.2360' => 'acertr', 'Atru.chr4.2361' => 'acertr', 'AUR62030476' => 'cqu', 'AUR62030478' => 'cqu', 'AUR62030819' => 'cqu', 'AUR62030820' => 'cqu', 'BcaB03g14648' => 'bca', 'BcaB04g20492' => 'bca', 'BcaB06g26399' => 'bca', 'BcaC01g03416' => 'bca', 'BcaC01g03419' => 'bca', 'BcaC01g03421' => 'bca', 'BcaC01g03424' => 'bca', 'BcaC05g28012' => 'bca', 'BcaC09g49212' => 'bca', 'BcaC09g50140' => 'bca', 'BcaNung00346' => 'bca', 'BolC1t02785H' => 'bol', 'BolC1t04095H' => 'bol', 'BolC3t17545H' => 'bol', 'BolC5t32769H' => 'bol', 'BraA01t02211Z' => 'bra', 'BraA01t03359Z' => 'bra', 'BraA03t13441Z' => 'bra', 'BraA05t21476Z' => 'bra', 'C01p28420' => 'bna', 'C01p41350' => 'bna', 'C03p52750' => 'bna', 'C03p52780' => 'bna', 'C05p40270' => 'bna', 'CAN.G1437.9' => 'can', 'CANSAT78G0035' => 'cansat', 'CANSAT78G1036' => 'cansat', 'CANSAT78G2272' => 'cansat', 'CANSAT78G2478' => 'cansat', 'CARHR098700' => 'chi', 'CARHR221120' => 'chi', 'CARHR221150' => 'chi', 'Carub.0003s2297' => 'cru', 'Carub.0007s2749' => 'cru', 'Carub.0007s2750' => 'cru', 'Carub.0007s2751' => 'cru', 'Ca_10849_v3' => 'car', 'Cc03_g04300' => 'ccan', 'CDE02G3648' => 'cde', 'CDE05G0060' => 'cde', 'CDE05G0692' => 'cde', 'CDE05G2285' => 'cde', 'CDE05G2884' => 'cde', 'CDE05G3072' => 'cde', 'Cfa008439' => 'cfa', 'Cfa008441' => 'cfa', 'Cfa008443' => 'cfa', 'Cfa008448' => 'cfa', 'Ciclev10005974m.g' => 'ccl', 'Ciclev10006006m.g' => 'ccl', 'Ciclev10006775m.g' => 'ccl', 'CiPaw.02G120400' => 'cil', 'CiPaw.02G120500' => 'cil', 'CiPaw.02G120600' => 'cil', 'ClCG05G004850' => 'cla', 'COL.COLO4_21566' => 'col', 'Cpa.g.sc44.124' => 'cpa', 'Cre07.g320400' => 'cre', 'Cre07.g320450' => 'cre', 'Cre08.g384650' => 'cre', 'Cre09.g393173' => 'cre', 'Cre09.g394325' => 'cre', 'Cre14.g626750' => 'cre', 'Cre16.g679250' => 'cre', 'CsaV3_3G012890' => 'csa', 'CSS0010865' => 'camsi', 'CSS0044338' => 'camsi', 'DCAR_002366' => 'dca', 'DCAR_030687' => 'dca', 'DCAR_030688' => 'dca', 'Dinv14047' => 'din', 'Dinv14048' => 'din', 'Duzib151G0105' => 'dzi', 'Duzib151G0114' => 'dzi', 'Duzib212G1029' => 'dzi', 'ECA232G3536' => 'eca', 'ECA240G0786' => 'eca', 'ECA240G1802' => 'eca', 'ECA240G3760' => 'eca', 'ECA240G3920' => 'eca', 'EL10Ac5g12536' => 'bvu', 'EL10Ac5g12537' => 'bvu', 'EL10Ac5g12538' => 'bvu', 'Eucgr.B01004' => 'egr', 'Eucgr.B01006' => 'egr', 'Eucgr.B01007' => 'egr', 'Eucgr.B01008' => 'egr', 'Eucgr.B01895' => 'egr', 'Eucgr.B01896' => 'egr', 'FAN04G1456' => 'fan', 'FAN08G1769' => 'fan', 'FAN08G2160' => 'fan', 'FAN13G2403' => 'fan', 'FAN13G3303' => 'fan', 'FAN15G2435' => 'fan', 'FAN17G0672' => 'fan', 'FAN17G2441' => 'fan', 'FAN18G1024' => 'fan', 'FAN22G1458' => 'fan', 'FAN24G0037' => 'fan', 'FAN24G0429' => 'fan', 'FAN24G2387' => 'fan', 'FAN27G2746' => 'fan', 'FvH4_2g20400' => 'fve', 'FvH4_2g20420' => 'fve', 'FvH4_2g20430' => 'fve', 'FvH4_4g01270' => 'fve', 'FvH4_4g01290' => 'fve', 'FvH4_4g01300' => 'fve', 'FvH4_4g01310' => 'fve', 'FvH4_4g01330' => 'fve', 'FvH4_5g09070' => 'fve', 'Glyma.10G243800' => 'gma', 'Glyma.20G150600' => 'gma', 'Gohir.A09G219200' => 'ghi', 'Gohir.A09G219300' => 'ghi', 'Gohir.D09G221400' => 'ghi', 'Gohir.D09G221500' => 'ghi', 'Gorai.006G242600' => 'gra', 'Gorai.006G242700' => 'gra', 'GSVIVG01018044001' => 'vvi', 'HanXRQChr03g0083821' => 'han', 'HanXRQChr03g0083841' => 'han', 'HanXRQChr03g0083881' => 'han', 'HanXRQChr03g0083901' => 'han', 'HanXRQChr03g0083921' => 'han', 'HanXRQChr03g0085331' => 'han', 'HanXRQChr03g0085361' => 'han', 'HanXRQChr03g0085411' => 'han', 'HanXRQChr03g0085421' => 'han', 'HanXRQChr03g0085431' => 'han', 'HanXRQChr08g0221991' => 'han', 'HanXRQChr11g0336061' => 'han', 'HanXRQChr11g0336411' => 'han', 'Haze_11234' => 'cav', 'Hma1.2p1_0549F.1_g177010' => 'hma', 'Hma1.2p1_0602F.1_g187630' => 'hma', 'Hund14876' => 'sun', 'Hund14879' => 'sun', 'Lalb_Chr06g0160741' => 'lal', 'Lalb_Chr21g0304781' => 'lal', 'Lj3A726G19' => 'lonja', 'Lj3A726T23' => 'lonja', 'Lj3A726T24' => 'lonja', 'Lj3A726T25' => 'lonja', 'Lj3A727T17' => 'lonja', 'Lj3C726T0' => 'lonja', 'Lj3C726T2' => 'lonja', 'Lj3P725T35' => 'lonja', 'Lj3P727T10' => 'lonja', 'Lj3P727T12' => 'lonja', 'Lj3P727T14' => 'lonja', 'Lj5g0023109' => 'lja', 'Lj6P646T44' => 'lonja', 'Lsat_1_v5_gn_6_75760' => 'lsa', 'Lsat_1_v5_gn_6_75800' => 'lsa', 'Lsat_1_v5_gn_6_75900' => 'lsa', 'Lsat_1_v5_gn_6_76240' => 'lsa', 'Lsat_1_v5_gn_6_76441' => 'lsa', 'Lsat_1_v5_gn_6_76700' => 'lsa', 'Lsat_1_v5_gn_6_76760' => 'lsa', 'Manes.15G033100' => 'mes', 'Mapoly0004s0074' => 'mpo', 'Mapoly0004s0075' => 'mpo', 'Mapoly0004s0163' => 'mpo', 'Mapoly0004s0164' => 'mpo', 'Mapoly0021s0018' => 'mpo', 'Mapoly0041s0136' => 'mpo', 'Mapoly0041s0137' => 'mpo', 'Mapoly0041s0138' => 'mpo', 'Mapoly0041s0139' => 'mpo', 'Mapoly0041s0141' => 'mpo', 'Mapoly0041s0142' => 'mpo', 'Mapoly0041s0143' => 'mpo', 'Mapoly0041s0144' => 'mpo', 'Mapoly0041s0145' => 'mpo', 'Mapoly0047s0106' => 'mpo', 'Mapoly0047s0108' => 'mpo', 'Mapoly0050s0051' => 'mpo', 'Mapoly0050s0052' => 'mpo', 'Mapoly0050s0053' => 'mpo', 'Mapoly0058s0013' => 'mpo', 'Mapoly0091s0078' => 'mpo', 'Mapoly0091s0079' => 'mpo', 'Mapoly0091s0080' => 'mpo', 'Mapoly0091s0081' => 'mpo', 'Mapoly0278s0004' => 'mpo', 'Mapoly0278s0005' => 'mpo', 'Mapoly0278s0006' => 'mpo', 'MBI11_g30648_MAGBIO' => 'mbi', 'MCO03G194' => 'mco', 'MCO03G590' => 'mco', 'MCO07G312' => 'mco', 'MCO10G318' => 'mco', 'MCO12G244' => 'mco', 'MCO13G148' => 'mco', 'MCO13G194' => 'mco', 'MCO16G238' => 'mco', 'MD06G1134100' => 'mdo', 'MD13G1200100' => 'mdo', 'MD13G1200300' => 'mdo', 'MD13G1200600' => 'mdo', 'MD14G1150400' => 'mdo', 'MD16G1200000' => 'mdo', 'Medtr1g102570' => 'mtr', 'Medtr1g102780' => 'mtr', 'Medtr1g102800' => 'mtr', 'Medtr1g102810' => 'mtr', 'Medtr1g102830' => 'mtr', 'MELO3C006499.2' => 'cme', 'Migut.G00385' => 'egut', 'MSTRG.4063' => 'ama', 'Nitab4.5_0000090g0260' => 'nta', 'Nitab4.5_0000977g0030' => 'nta', 'Nitab4.5_0002541g0040' => 'nta', 'Nitab4.5_0007068g0040' => 'nta', 'Nn005s41408' => 'nnu', 'Nn005s41410' => 'nnu', 'Oeu010310.1' => 'oeu', 'Oeu010311.1' => 'oeu', 'Oeu043472.1' => 'oeu', 'Os01g0246400' => 'osa', 'Os04g0267950' => 'osa', 'Os07g0178700' => 'osa', 'Os07g0178800' => 'osa', 'Peaxi162Scf00316g00046' => 'pax', 'Peaxi162Scf00316g00049' => 'pax', 'Peaxi162Scf00316g00059' => 'pax', 'Peaxi162Scf00316g00328' => 'pax', 'Peaxi162Scf00316g00329' => 'pax', 'Peaxi162Scf00316g00411' => 'pax', 'Peaxi162Scf00316g00521' => 'pax', 'Peaxi162Scf00492g00068' => 'pax', 'Peaxi162Scf35631g00002' => 'pax', 'PGR142G3720' => 'pgr', 'PGSC0003DMG400006442' => 'stu', 'Phvul.007G062000' => 'pvu', 'Potri.008G157750' => 'ptr', 'Potri.008G157900' => 'ptr', 'Potri.008G158000' => 'ptr', 'Potri.008G158200' => 'ptr', 'Pp3c11_7280' => 'ppa', 'Pp3c11_7980' => 'ppa', 'Pp3c12_19450' => 'ppa', 'Pp3c14_1480' => 'ppa', 'Pp3c14_1501' => 'ppa', 'Pp3c16_4900' => 'ppa', 'Pp3c16_5010' => 'ppa', 'Pp3c16_5060' => 'ppa', 'Pp3c19_18250' => 'ppa', 'Pp3c23_8530' => 'ppa', 'Pp3c23_8550' => 'ppa', 'Pp3c24_9670' => 'ppa', 'Pp3c2_21390' => 'ppa', 'Pp3c2_31380' => 'ppa', 'Pp3c3_16620' => 'ppa', 'Pp3c3_8090' => 'ppa', 'Pp3c3_8110' => 'ppa', 'Pp3c3_8130' => 'ppa', 'Pp3c3_8150' => 'ppa', 'Pp3c4_14320' => 'ppa', 'Pp3c6_2560' => 'ppa', 'Pp3c9_16700' => 'ppa', 'PRCOL_00000234' => 'pco', 'PRCOL_00000235' => 'pco', 'PRCOL_00000777' => 'pco', 'PRCOL_00002344' => 'pco', 'PRCOL_00002372' => 'pco', 'PRCOL_00006120' => 'pco', 'Prupe.1G021400' => 'ppe', 'Prupe.1G021500' => 'ppe', 'Prupe.1G021600' => 'ppe', 'Prupe.1G021700' => 'ppe', 'Prupe.1G021800' => 'ppe', 'Prupe.5G145100' => 'ppe', 'Psat6g204040' => 'psa', 'Psat6g204800' => 'psa', 'Psat6g204920' => 'psa', 'Psat6g204960' => 'psa', 'Psat6g205080' => 'psa', 'PSO017G0271' => 'pso', 'PSO017G1276' => 'pso', 'PSO017G1429' => 'pso', 'PSO017G1861' => 'pso', 'PSO017G2787' => 'pso', 'PSO017G4466' => 'pso', 'PSO017G5118' => 'pso', 'PSO017G5420' => 'pso', 'PSO063G3678' => 'pso', 'PSO210G0546' => 'pso', 'PSO317G0001' => 'pso', 'PSO357G0512' => 'pso', 'PSO478G2682' => 'pso', 'PSO647G0001' => 'pso', 'PSO675G0001' => 'pso', 'PSO675G2699' => 'pso', 'PSO675G2849' => 'pso', 'PSO675G4991' => 'pso', 'PSO689G0001' => 'pso', 'QL06p000916' => 'qlo', 'QL06p000921' => 'qlo', 'QL06p001398' => 'qlo', 'QL06p001407' => 'qlo', 'QL06p002031' => 'qlo', 'RcHm_v2.0_Chr4g0387791' => 'rch', 'RcHm_v2.0_Chr4g0387801' => 'rch', 'RcHm_v2.0_Chr6g0286501' => 'rch', 'RcHm_v2.0_Chr6g0286511' => 'rch', 'RcHm_v2.0_Chr6g0286521' => 'rch', 'RcHm_v2.0_Chr6g0286531' => 'rch', 'RcHm_v2.0_Chr7g0189141' => 'rch', 'Rhsim02G0028700' => 'rsi', 'Rhsim02G0028800' => 'rsi', 'Rhsim02G0028900' => 'rsi', 'Rhsim02G0029000' => 'rsi', 'Rhsim02G0029100' => 'rsi', 'Rhsim02G0029200' => 'rsi', 'Rhsim02G0029300' => 'rsi', 'Rhsim02G0029400' => 'rsi', 'Rhsim02G0029500' => 'rsi', 'Rhsim02G0029600' => 'rsi', 'RhsimUnG0024000' => 'rsi', 'RhsimUnG0024100' => 'rsi', 'RhsimUnG0024200' => 'rsi', 'RhsimUnG0024300' => 'rsi', 'RhsimUnG0024400' => 'rsi', 'RhsimUnG0024500' => 'rsi', 'RhsimUnG0024700' => 'rsi', 'RhsimUnG0024800' => 'rsi', 'RhsimUnG0024900' => 'rsi', 'RhsimUnG0025100' => 'rsi', 'Sabra08G0120200' => 'sbr', 'Sabra08G0120300' => 'sbr', 'Sabra08G0120500' => 'sbr', 'Sabra08G0120600' => 'sbr', 'Sabra10G0158900' => 'sbr', 'SalBow2G3492' => 'sbo', 'Sc13g0004760' => 'sci', 'Sc13g0004770' => 'sci', 'Sed0003417' => 'sed', 'Sed0019750' => 'sed', 'SEGI_03419' => 'sgi', 'SEGI_05907' => 'sgi', 'SEGI_10682' => 'sgi', 'SEGI_13528' => 'sgi', 'SEGI_16081' => 'sgi', 'SEGI_19370' => 'sgi', 'SEGI_21015' => 'sgi', 'SEGI_21944' => 'sgi', 'SEGI_32906' => 'sgi', 'SEGI_33093' => 'sgi', 'SEGI_36110' => 'sgi', 'SEGI_40397' => 'sgi', 'SGA_v2.0_scaffold191G40426' => 'sas', 'SGA_v2.0_scaffold353G49717' => 'sas', 'SGA_v2.0_scaffold50G18550' => 'sas', 'SMO119G0173' => 'smo', 'SMO172G0002' => 'smo', 'Solyc09g082690.3' => 'sly', 'Solyc09g082700.2' => 'sly', 'Sopen09g031550' => 'spe', 'Sopen09g031560' => 'spe', 'Sp3g20540' => 'spa', 'Sp7g07580' => 'spa', 'TAR134G0002' => 'tar', 'TAR236G0001' => 'tar', 'TAR365G0892' => 'tar', 'TAR636G0166' => 'tar', 'TAR636G0646' => 'tar', 'TAR636G0869' => 'tar', 'TAR636G1317' => 'tar', 'TAR636G1744' => 'tar', 'TAR636G3358' => 'tar', 'TAR636G3436' => 'tar', 'THA.LOC104803047' => 'tha', 'Thecc.04G238900' => 'tca', 'Thhalv10021557m.g' => 'esa', 'Thhalv10026318m.g' => 'esa', 'Thhalv10026335m.g' => 'esa', 'TPR.G17433' => 'tpr', 'TPR.G18915' => 'tpr', 'TPR.G26125' => 'tpr', 'TWI09G0677' => 'twi', 'TWI73G0287' => 'twi', 'unitig_748.g8326' => 'ugi', 'vmacro15370' => 'vma', 'vmacro15371' => 'vma', 'vmacro15372' => 'vma', 'vmacro15373' => 'vma', 'vmacro15374' => 'vma', 'VMungo0720G2826' => 'vmu', 'Zm00001eb116960' => 'zma', 'Zm00001eb301260' => 'zma', 'Zm00001eb301270' => 'zma' ), 'gf_id' => 'HOM05D001460', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001460' ), 'data_identifier' => 'HOM05D001460', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001460', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '433', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p22980' => 'bna', 'A01p32340' => 'bna', 'A03p42970' => 'bna', 'A05p25880' => 'bna', 'Aa31LG8G9320' => 'aar', 'Aa31LG8G9330' => 'aar', 'Aa31LG8G9340' => 'aar', 'Aa31sc221G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1034' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1528' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.829' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2222' => 'aag', 'Ah.12g058830' => 'amhyb', 'Ah.12g058840' => 'amhyb', 'AL3G37160' => 'aly', 'AL7G41310' => 'aly', 'Aqoxy5G00395' => 'aox', 'Aqoxy5G00396' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0C8NZA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5185HY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JZ1PRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MD3LS0' => 'arhy', 'AT3G22840' => 'ath', 'AT4G14690' => 'ath', 'ATR0665G054' => 'atr', 'Atru.chr4.2344' => 'acertr', 'Atru.chr4.2346' => 'acertr', 'Atru.chr4.2347' => 'acertr', 'Atru.chr4.2348' => 'acertr', 'Atru.chr4.2355' => 'acertr', 'Atru.chr4.2356' => 'acertr', 'Atru.chr4.2358' => 'acertr', 'Atru.chr4.2359' => 'acertr', 'Atru.chr4.2360' => 'acertr', 'Atru.chr4.2361' => 'acertr', 'AUR62030476' => 'cqu', 'AUR62030478' => 'cqu', 'AUR62030819' => 'cqu', 'AUR62030820' => 'cqu', 'BcaB03g14648' => 'bca', 'BcaB04g20492' => 'bca', 'BcaB06g26399' => 'bca', 'BcaC01g03416' => 'bca', 'BcaC01g03419' => 'bca', 'BcaC01g03421' => 'bca', 'BcaC01g03424' => 'bca', 'BcaC05g28012' => 'bca', 'BcaC09g49212' => 'bca', 'BcaC09g50140' => 'bca', 'BcaNung00346' => 'bca', 'BolC1t02785H' => 'bol', 'BolC1t04095H' => 'bol', 'BolC3t17545H' => 'bol', 'BolC5t32769H' => 'bol', 'BraA01t02211Z' => 'bra', 'BraA01t03359Z' => 'bra', 'BraA03t13441Z' => 'bra', 'BraA05t21476Z' => 'bra', 'C01p28420' => 'bna', 'C01p41350' => 'bna', 'C03p52750' => 'bna', 'C03p52780' => 'bna', 'C05p40270' => 'bna', 'CAN.G1437.9' => 'can', 'CANSAT78G0035' => 'cansat', 'CANSAT78G1036' => 'cansat', 'CANSAT78G2272' => 'cansat', 'CANSAT78G2478' => 'cansat', 'CARHR098700' => 'chi', 'CARHR221120' => 'chi', 'CARHR221150' => 'chi', 'Carub.0003s2297' => 'cru', 'Carub.0007s2749' => 'cru', 'Carub.0007s2750' => 'cru', 'Carub.0007s2751' => 'cru', 'Ca_10849_v3' => 'car', 'Cc03_g04300' => 'ccan', 'CDE02G3648' => 'cde', 'CDE05G0060' => 'cde', 'CDE05G0692' => 'cde', 'CDE05G2285' => 'cde', 'CDE05G2884' => 'cde', 'CDE05G3072' => 'cde', 'Cfa008439' => 'cfa', 'Cfa008441' => 'cfa', 'Cfa008443' => 'cfa', 'Cfa008448' => 'cfa', 'Ciclev10005974m.g' => 'ccl', 'Ciclev10006006m.g' => 'ccl', 'Ciclev10006775m.g' => 'ccl', 'CiPaw.02G120400' => 'cil', 'CiPaw.02G120500' => 'cil', 'CiPaw.02G120600' => 'cil', 'ClCG05G004850' => 'cla', 'COL.COLO4_21566' => 'col', 'Cpa.g.sc44.124' => 'cpa', 'Cre07.g320400' => 'cre', 'Cre07.g320450' => 'cre', 'Cre08.g384650' => 'cre', 'Cre09.g393173' => 'cre', 'Cre09.g394325' => 'cre', 'Cre14.g626750' => 'cre', 'Cre16.g679250' => 'cre', 'CsaV3_3G012890' => 'csa', 'CSS0010865' => 'camsi', 'CSS0044338' => 'camsi', 'DCAR_002366' => 'dca', 'DCAR_030687' => 'dca', 'DCAR_030688' => 'dca', 'Dinv14047' => 'din', 'Dinv14048' => 'din', 'Duzib151G0105' => 'dzi', 'Duzib151G0114' => 'dzi', 'Duzib212G1029' => 'dzi', 'ECA232G3536' => 'eca', 'ECA240G0786' => 'eca', 'ECA240G1802' => 'eca', 'ECA240G3760' => 'eca', 'ECA240G3920' => 'eca', 'EL10Ac5g12536' => 'bvu', 'EL10Ac5g12537' => 'bvu', 'EL10Ac5g12538' => 'bvu', 'Eucgr.B01004' => 'egr', 'Eucgr.B01006' => 'egr', 'Eucgr.B01007' => 'egr', 'Eucgr.B01008' => 'egr', 'Eucgr.B01895' => 'egr', 'Eucgr.B01896' => 'egr', 'FAN04G1456' => 'fan', 'FAN08G1769' => 'fan', 'FAN08G2160' => 'fan', 'FAN13G2403' => 'fan', 'FAN13G3303' => 'fan', 'FAN15G2435' => 'fan', 'FAN17G0672' => 'fan', 'FAN17G2441' => 'fan', 'FAN18G1024' => 'fan', 'FAN22G1458' => 'fan', 'FAN24G0037' => 'fan', 'FAN24G0429' => 'fan', 'FAN24G2387' => 'fan', 'FAN27G2746' => 'fan', 'FvH4_2g20400' => 'fve', 'FvH4_2g20420' => 'fve', 'FvH4_2g20430' => 'fve', 'FvH4_4g01270' => 'fve', 'FvH4_4g01290' => 'fve', 'FvH4_4g01300' => 'fve', 'FvH4_4g01310' => 'fve', 'FvH4_4g01330' => 'fve', 'FvH4_5g09070' => 'fve', 'Glyma.10G243800' => 'gma', 'Glyma.20G150600' => 'gma', 'Gohir.A09G219200' => 'ghi', 'Gohir.A09G219300' => 'ghi', 'Gohir.D09G221400' => 'ghi', 'Gohir.D09G221500' => 'ghi', 'Gorai.006G242600' => 'gra', 'Gorai.006G242700' => 'gra', 'GSVIVG01018044001' => 'vvi', 'HanXRQChr03g0083821' => 'han', 'HanXRQChr03g0083841' => 'han', 'HanXRQChr03g0083881' => 'han', 'HanXRQChr03g0083901' => 'han', 'HanXRQChr03g0083921' => 'han', 'HanXRQChr03g0085331' => 'han', 'HanXRQChr03g0085361' => 'han', 'HanXRQChr03g0085411' => 'han', 'HanXRQChr03g0085421' => 'han', 'HanXRQChr03g0085431' => 'han', 'HanXRQChr08g0221991' => 'han', 'HanXRQChr11g0336061' => 'han', 'HanXRQChr11g0336411' => 'han', 'Haze_11234' => 'cav', 'Hma1.2p1_0549F.1_g177010' => 'hma', 'Hma1.2p1_0602F.1_g187630' => 'hma', 'Hund14876' => 'sun', 'Hund14879' => 'sun', 'Lalb_Chr06g0160741' => 'lal', 'Lalb_Chr21g0304781' => 'lal', 'Lj3A726G19' => 'lonja', 'Lj3A726T23' => 'lonja', 'Lj3A726T24' => 'lonja', 'Lj3A726T25' => 'lonja', 'Lj3A727T17' => 'lonja', 'Lj3C726T0' => 'lonja', 'Lj3C726T2' => 'lonja', 'Lj3P725T35' => 'lonja', 'Lj3P727T10' => 'lonja', 'Lj3P727T12' => 'lonja', 'Lj3P727T14' => 'lonja', 'Lj5g0023109' => 'lja', 'Lj6P646T44' => 'lonja', 'Lsat_1_v5_gn_6_75760' => 'lsa', 'Lsat_1_v5_gn_6_75800' => 'lsa', 'Lsat_1_v5_gn_6_75900' => 'lsa', 'Lsat_1_v5_gn_6_76240' => 'lsa', 'Lsat_1_v5_gn_6_76441' => 'lsa', 'Lsat_1_v5_gn_6_76700' => 'lsa', 'Lsat_1_v5_gn_6_76760' => 'lsa', 'Manes.15G033100' => 'mes', 'Mapoly0004s0074' => 'mpo', 'Mapoly0004s0075' => 'mpo', 'Mapoly0004s0163' => 'mpo', 'Mapoly0004s0164' => 'mpo', 'Mapoly0021s0018' => 'mpo', 'Mapoly0041s0136' => 'mpo', 'Mapoly0041s0137' => 'mpo', 'Mapoly0041s0138' => 'mpo', 'Mapoly0041s0139' => 'mpo', 'Mapoly0041s0141' => 'mpo', 'Mapoly0041s0142' => 'mpo', 'Mapoly0041s0143' => 'mpo', 'Mapoly0041s0144' => 'mpo', 'Mapoly0041s0145' => 'mpo', 'Mapoly0047s0106' => 'mpo', 'Mapoly0047s0108' => 'mpo', 'Mapoly0050s0051' => 'mpo', 'Mapoly0050s0052' => 'mpo', 'Mapoly0050s0053' => 'mpo', 'Mapoly0058s0013' => 'mpo', 'Mapoly0091s0078' => 'mpo', 'Mapoly0091s0079' => 'mpo', 'Mapoly0091s0080' => 'mpo', 'Mapoly0091s0081' => 'mpo', 'Mapoly0278s0004' => 'mpo', 'Mapoly0278s0005' => 'mpo', 'Mapoly0278s0006' => 'mpo', 'MBI11_g30648_MAGBIO' => 'mbi', 'MCO03G194' => 'mco', 'MCO03G590' => 'mco', 'MCO07G312' => 'mco', 'MCO10G318' => 'mco', 'MCO12G244' => 'mco', 'MCO13G148' => 'mco', 'MCO13G194' => 'mco', 'MCO16G238' => 'mco', 'MD06G1134100' => 'mdo', 'MD13G1200100' => 'mdo', 'MD13G1200300' => 'mdo', 'MD13G1200600' => 'mdo', 'MD14G1150400' => 'mdo', 'MD16G1200000' => 'mdo', 'Medtr1g102570' => 'mtr', 'Medtr1g102780' => 'mtr', 'Medtr1g102800' => 'mtr', 'Medtr1g102810' => 'mtr', 'Medtr1g102830' => 'mtr', 'MELO3C006499.2' => 'cme', 'Migut.G00385' => 'egut', 'MSTRG.4063' => 'ama', 'Nitab4.5_0000090g0260' => 'nta', 'Nitab4.5_0000977g0030' => 'nta', 'Nitab4.5_0002541g0040' => 'nta', 'Nitab4.5_0007068g0040' => 'nta', 'Nn005s41408' => 'nnu', 'Nn005s41410' => 'nnu', 'Oeu010310.1' => 'oeu', 'Oeu010311.1' => 'oeu', 'Oeu043472.1' => 'oeu', 'Os01g0246400' => 'osa', 'Os04g0267950' => 'osa', 'Os07g0178700' => 'osa', 'Os07g0178800' => 'osa', 'Peaxi162Scf00316g00046' => 'pax', 'Peaxi162Scf00316g00049' => 'pax', 'Peaxi162Scf00316g00059' => 'pax', 'Peaxi162Scf00316g00328' => 'pax', 'Peaxi162Scf00316g00329' => 'pax', 'Peaxi162Scf00316g00411' => 'pax', 'Peaxi162Scf00316g00521' => 'pax', 'Peaxi162Scf00492g00068' => 'pax', 'Peaxi162Scf35631g00002' => 'pax', 'PGR142G3720' => 'pgr', 'PGSC0003DMG400006442' => 'stu', 'Phvul.007G062000' => 'pvu', 'Potri.008G157750' => 'ptr', 'Potri.008G157900' => 'ptr', 'Potri.008G158000' => 'ptr', 'Potri.008G158200' => 'ptr', 'Pp3c11_7280' => 'ppa', 'Pp3c11_7980' => 'ppa', 'Pp3c12_19450' => 'ppa', 'Pp3c14_1480' => 'ppa', 'Pp3c14_1501' => 'ppa', 'Pp3c16_4900' => 'ppa', 'Pp3c16_5010' => 'ppa', 'Pp3c16_5060' => 'ppa', 'Pp3c19_18250' => 'ppa', 'Pp3c23_8530' => 'ppa', 'Pp3c23_8550' => 'ppa', 'Pp3c24_9670' => 'ppa', 'Pp3c2_21390' => 'ppa', 'Pp3c2_31380' => 'ppa', 'Pp3c3_16620' => 'ppa', 'Pp3c3_8090' => 'ppa', 'Pp3c3_8110' => 'ppa', 'Pp3c3_8130' => 'ppa', 'Pp3c3_8150' => 'ppa', 'Pp3c4_14320' => 'ppa', 'Pp3c6_2560' => 'ppa', 'Pp3c9_16700' => 'ppa', 'PRCOL_00000234' => 'pco', 'PRCOL_00000235' => 'pco', 'PRCOL_00000777' => 'pco', 'PRCOL_00002344' => 'pco', 'PRCOL_00002372' => 'pco', 'PRCOL_00006120' => 'pco', 'Prupe.1G021400' => 'ppe', 'Prupe.1G021500' => 'ppe', 'Prupe.1G021600' => 'ppe', 'Prupe.1G021700' => 'ppe', 'Prupe.1G021800' => 'ppe', 'Prupe.5G145100' => 'ppe', 'Psat6g204040' => 'psa', 'Psat6g204800' => 'psa', 'Psat6g204920' => 'psa', 'Psat6g204960' => 'psa', 'Psat6g205080' => 'psa', 'PSO017G0271' => 'pso', 'PSO017G1276' => 'pso', 'PSO017G1429' => 'pso', 'PSO017G1861' => 'pso', 'PSO017G2787' => 'pso', 'PSO017G4466' => 'pso', 'PSO017G5118' => 'pso', 'PSO017G5420' => 'pso', 'PSO063G3678' => 'pso', 'PSO210G0546' => 'pso', 'PSO317G0001' => 'pso', 'PSO357G0512' => 'pso', 'PSO478G2682' => 'pso', 'PSO647G0001' => 'pso', 'PSO675G0001' => 'pso', 'PSO675G2699' => 'pso', 'PSO675G2849' => 'pso', 'PSO675G4991' => 'pso', 'PSO689G0001' => 'pso', 'QL06p000916' => 'qlo', 'QL06p000921' => 'qlo', 'QL06p001398' => 'qlo', 'QL06p001407' => 'qlo', 'QL06p002031' => 'qlo', 'RcHm_v2.0_Chr4g0387791' => 'rch', 'RcHm_v2.0_Chr4g0387801' => 'rch', 'RcHm_v2.0_Chr6g0286501' => 'rch', 'RcHm_v2.0_Chr6g0286511' => 'rch', 'RcHm_v2.0_Chr6g0286521' => 'rch', 'RcHm_v2.0_Chr6g0286531' => 'rch', 'RcHm_v2.0_Chr7g0189141' => 'rch', 'Rhsim02G0028700' => 'rsi', 'Rhsim02G0028800' => 'rsi', 'Rhsim02G0028900' => 'rsi', 'Rhsim02G0029000' => 'rsi', 'Rhsim02G0029100' => 'rsi', 'Rhsim02G0029200' => 'rsi', 'Rhsim02G0029300' => 'rsi', 'Rhsim02G0029400' => 'rsi', 'Rhsim02G0029500' => 'rsi', 'Rhsim02G0029600' => 'rsi', 'RhsimUnG0024000' => 'rsi', 'RhsimUnG0024100' => 'rsi', 'RhsimUnG0024200' => 'rsi', 'RhsimUnG0024300' => 'rsi', 'RhsimUnG0024400' => 'rsi', 'RhsimUnG0024500' => 'rsi', 'RhsimUnG0024700' => 'rsi', 'RhsimUnG0024800' => 'rsi', 'RhsimUnG0024900' => 'rsi', 'RhsimUnG0025100' => 'rsi', 'Sabra08G0120200' => 'sbr', 'Sabra08G0120300' => 'sbr', 'Sabra08G0120500' => 'sbr', 'Sabra08G0120600' => 'sbr', 'Sabra10G0158900' => 'sbr', 'SalBow2G3492' => 'sbo', 'Sc13g0004760' => 'sci', 'Sc13g0004770' => 'sci', 'Sed0003417' => 'sed', 'Sed0019750' => 'sed', 'SEGI_03419' => 'sgi', 'SEGI_05907' => 'sgi', 'SEGI_10682' => 'sgi', 'SEGI_13528' => 'sgi', 'SEGI_16081' => 'sgi', 'SEGI_19370' => 'sgi', 'SEGI_21015' => 'sgi', 'SEGI_21944' => 'sgi', 'SEGI_32906' => 'sgi', 'SEGI_33093' => 'sgi', 'SEGI_36110' => 'sgi', 'SEGI_40397' => 'sgi', 'SGA_v2.0_scaffold191G40426' => 'sas', 'SGA_v2.0_scaffold353G49717' => 'sas', 'SGA_v2.0_scaffold50G18550' => 'sas', 'SMO119G0173' => 'smo', 'SMO172G0002' => 'smo', 'Solyc09g082690.3' => 'sly', 'Solyc09g082700.2' => 'sly', 'Sopen09g031550' => 'spe', 'Sopen09g031560' => 'spe', 'Sp3g20540' => 'spa', 'Sp7g07580' => 'spa', 'TAR134G0002' => 'tar', 'TAR236G0001' => 'tar', 'TAR365G0892' => 'tar', 'TAR636G0166' => 'tar', 'TAR636G0646' => 'tar', 'TAR636G0869' => 'tar', 'TAR636G1317' => 'tar', 'TAR636G1744' => 'tar', 'TAR636G3358' => 'tar', 'TAR636G3436' => 'tar', 'THA.LOC104803047' => 'tha', 'Thecc.04G238900' => 'tca', 'Thhalv10021557m.g' => 'esa', 'Thhalv10026318m.g' => 'esa', 'Thhalv10026335m.g' => 'esa', 'TPR.G17433' => 'tpr', 'TPR.G18915' => 'tpr', 'TPR.G26125' => 'tpr', 'TWI09G0677' => 'twi', 'TWI73G0287' => 'twi', 'unitig_748.g8326' => 'ugi', 'vmacro15370' => 'vma', 'vmacro15371' => 'vma', 'vmacro15372' => 'vma', 'vmacro15373' => 'vma', 'vmacro15374' => 'vma', 'VMungo0720G2826' => 'vmu', 'Zm00001eb116960' => 'zma', 'Zm00001eb301260' => 'zma', 'Zm00001eb301270' => 'zma' ) $gf_id = 'HOM05D001460' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001460' ) $data_identifier = 'HOM05D001460' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 4, 'aag' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 2, 'aox' => (int) 2, 'arhy' => (int) 4, 'ath' => (int) 2, 'atr' => (int) 1, 'acertr' => (int) 10, 'cqu' => (int) 4, 'bca' => (int) 11, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 1, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 1, 'ccan' => (int) 1, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 1, 'col' => (int) 1, 'cpa' => (int) 1, 'cre' => (int) 7, 'csa' => (int) 1, 'camsi' => (int) 2, 'dca' => (int) 3, 'din' => (int) 2, 'dzi' => (int) 3, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 14, 'fve' => (int) 9, 'gma' => (int) 2, 'ghi' => (int) 4, 'gra' => (int) 2, 'vvi' => (int) 1, 'han' => (int) 13, 'cav' => (int) 1, 'hma' => (int) 2, 'sun' => (int) 2, 'lal' => (int) 2, 'lonja' => (int) 12, 'lja' => (int) 1, 'lsa' => (int) 7, 'mes' => (int) 1, 'mpo' => (int) 27, 'mbi' => (int) 1, 'mco' => (int) 8, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 1, 'egut' => (int) 1, 'ama' => (int) 1, 'nta' => (int) 4, 'nnu' => (int) 2, 'oeu' => (int) 3, 'osa' => (int) 4, 'pax' => (int) 9, 'pgr' => (int) 1, 'stu' => (int) 1, 'pvu' => (int) 1, 'ptr' => (int) 4, 'ppa' => (int) 22, 'pco' => (int) 6, 'ppe' => (int) 6, 'psa' => (int) 5, 'pso' => (int) 19, 'qlo' => (int) 5, 'rch' => (int) 7, 'rsi' => (int) 20, 'sbr' => (int) 5, 'sbo' => (int) 1, 'sci' => (int) 2, 'sed' => (int) 2, 'sgi' => (int) 12, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 2, 'tar' => (int) 10, 'tha' => (int) 1, 'tca' => (int) 1, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 2, 'ugi' => (int) 1, 'vma' => (int) 5, 'vmu' => (int) 1, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb301270' $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' => 'HOM05D001460', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '433', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p22980' => 'bna', 'A01p32340' => 'bna', 'A03p42970' => 'bna', 'A05p25880' => 'bna', 'Aa31LG8G9320' => 'aar', 'Aa31LG8G9330' => 'aar', 'Aa31LG8G9340' => 'aar', 'Aa31sc221G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1034' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1528' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.829' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2222' => 'aag', 'Ah.12g058830' => 'amhyb', 'Ah.12g058840' => 'amhyb', 'AL3G37160' => 'aly', 'AL7G41310' => 'aly', 'Aqoxy5G00395' => 'aox', 'Aqoxy5G00396' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0C8NZA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5185HY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JZ1PRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MD3LS0' => 'arhy', 'AT3G22840' => 'ath', 'AT4G14690' => 'ath', 'ATR0665G054' => 'atr', 'Atru.chr4.2344' => 'acertr', 'Atru.chr4.2346' => 'acertr', 'Atru.chr4.2347' => 'acertr', 'Atru.chr4.2348' => 'acertr', 'Atru.chr4.2355' => 'acertr', 'Atru.chr4.2356' => 'acertr', 'Atru.chr4.2358' => 'acertr', 'Atru.chr4.2359' => 'acertr', 'Atru.chr4.2360' => 'acertr', 'Atru.chr4.2361' => 'acertr', 'AUR62030476' => 'cqu', 'AUR62030478' => 'cqu', 'AUR62030819' => 'cqu', 'AUR62030820' => 'cqu', 'BcaB03g14648' => 'bca', 'BcaB04g20492' => 'bca', 'BcaB06g26399' => 'bca', 'BcaC01g03416' => 'bca', 'BcaC01g03419' => 'bca', 'BcaC01g03421' => 'bca', 'BcaC01g03424' => 'bca', 'BcaC05g28012' => 'bca', 'BcaC09g49212' => 'bca', 'BcaC09g50140' => 'bca', 'BcaNung00346' => 'bca', 'BolC1t02785H' => 'bol', 'BolC1t04095H' => 'bol', 'BolC3t17545H' => 'bol', 'BolC5t32769H' => 'bol', 'BraA01t02211Z' => 'bra', 'BraA01t03359Z' => 'bra', 'BraA03t13441Z' => 'bra', 'BraA05t21476Z' => 'bra', 'C01p28420' => 'bna', 'C01p41350' => 'bna', 'C03p52750' => 'bna', 'C03p52780' => 'bna', 'C05p40270' => 'bna', 'CAN.G1437.9' => 'can', 'CANSAT78G0035' => 'cansat', 'CANSAT78G1036' => 'cansat', 'CANSAT78G2272' => 'cansat', 'CANSAT78G2478' => 'cansat', 'CARHR098700' => 'chi', 'CARHR221120' => 'chi', 'CARHR221150' => 'chi', 'Carub.0003s2297' => 'cru', 'Carub.0007s2749' => 'cru', 'Carub.0007s2750' => 'cru', 'Carub.0007s2751' => 'cru', 'Ca_10849_v3' => 'car', 'Cc03_g04300' => 'ccan', 'CDE02G3648' => 'cde', 'CDE05G0060' => 'cde', 'CDE05G0692' => 'cde', 'CDE05G2285' => 'cde', 'CDE05G2884' => 'cde', 'CDE05G3072' => 'cde', 'Cfa008439' => 'cfa', 'Cfa008441' => 'cfa', 'Cfa008443' => 'cfa', 'Cfa008448' => 'cfa', 'Ciclev10005974m.g' => 'ccl', 'Ciclev10006006m.g' => 'ccl', 'Ciclev10006775m.g' => 'ccl', 'CiPaw.02G120400' => 'cil', 'CiPaw.02G120500' => 'cil', 'CiPaw.02G120600' => 'cil', 'ClCG05G004850' => 'cla', 'COL.COLO4_21566' => 'col', 'Cpa.g.sc44.124' => 'cpa', 'Cre07.g320400' => 'cre', 'Cre07.g320450' => 'cre', 'Cre08.g384650' => 'cre', 'Cre09.g393173' => 'cre', 'Cre09.g394325' => 'cre', 'Cre14.g626750' => 'cre', 'Cre16.g679250' => 'cre', 'CsaV3_3G012890' => 'csa', 'CSS0010865' => 'camsi', 'CSS0044338' => 'camsi', 'DCAR_002366' => 'dca', 'DCAR_030687' => 'dca', 'DCAR_030688' => 'dca', 'Dinv14047' => 'din', 'Dinv14048' => 'din', 'Duzib151G0105' => 'dzi', 'Duzib151G0114' => 'dzi', 'Duzib212G1029' => 'dzi', 'ECA232G3536' => 'eca', 'ECA240G0786' => 'eca', 'ECA240G1802' => 'eca', 'ECA240G3760' => 'eca', 'ECA240G3920' => 'eca', 'EL10Ac5g12536' => 'bvu', 'EL10Ac5g12537' => 'bvu', 'EL10Ac5g12538' => 'bvu', 'Eucgr.B01004' => 'egr', 'Eucgr.B01006' => 'egr', 'Eucgr.B01007' => 'egr', 'Eucgr.B01008' => 'egr', 'Eucgr.B01895' => 'egr', 'Eucgr.B01896' => 'egr', 'FAN04G1456' => 'fan', 'FAN08G1769' => 'fan', 'FAN08G2160' => 'fan', 'FAN13G2403' => 'fan', 'FAN13G3303' => 'fan', 'FAN15G2435' => 'fan', 'FAN17G0672' => 'fan', 'FAN17G2441' => 'fan', 'FAN18G1024' => 'fan', 'FAN22G1458' => 'fan', 'FAN24G0037' => 'fan', 'FAN24G0429' => 'fan', 'FAN24G2387' => 'fan', 'FAN27G2746' => 'fan', 'FvH4_2g20400' => 'fve', 'FvH4_2g20420' => 'fve', 'FvH4_2g20430' => 'fve', 'FvH4_4g01270' => 'fve', 'FvH4_4g01290' => 'fve', 'FvH4_4g01300' => 'fve', 'FvH4_4g01310' => 'fve', 'FvH4_4g01330' => 'fve', 'FvH4_5g09070' => 'fve', 'Glyma.10G243800' => 'gma', 'Glyma.20G150600' => 'gma', 'Gohir.A09G219200' => 'ghi', 'Gohir.A09G219300' => 'ghi', 'Gohir.D09G221400' => 'ghi', 'Gohir.D09G221500' => 'ghi', 'Gorai.006G242600' => 'gra', 'Gorai.006G242700' => 'gra', 'GSVIVG01018044001' => 'vvi', 'HanXRQChr03g0083821' => 'han', 'HanXRQChr03g0083841' => 'han', 'HanXRQChr03g0083881' => 'han', 'HanXRQChr03g0083901' => 'han', 'HanXRQChr03g0083921' => 'han', 'HanXRQChr03g0085331' => 'han', 'HanXRQChr03g0085361' => 'han', 'HanXRQChr03g0085411' => 'han', 'HanXRQChr03g0085421' => 'han', 'HanXRQChr03g0085431' => 'han', 'HanXRQChr08g0221991' => 'han', 'HanXRQChr11g0336061' => 'han', 'HanXRQChr11g0336411' => 'han', 'Haze_11234' => 'cav', 'Hma1.2p1_0549F.1_g177010' => 'hma', 'Hma1.2p1_0602F.1_g187630' => 'hma', 'Hund14876' => 'sun', 'Hund14879' => 'sun', 'Lalb_Chr06g0160741' => 'lal', 'Lalb_Chr21g0304781' => 'lal', 'Lj3A726G19' => 'lonja', 'Lj3A726T23' => 'lonja', 'Lj3A726T24' => 'lonja', 'Lj3A726T25' => 'lonja', 'Lj3A727T17' => 'lonja', 'Lj3C726T0' => 'lonja', 'Lj3C726T2' => 'lonja', 'Lj3P725T35' => 'lonja', 'Lj3P727T10' => 'lonja', 'Lj3P727T12' => 'lonja', 'Lj3P727T14' => 'lonja', 'Lj5g0023109' => 'lja', 'Lj6P646T44' => 'lonja', 'Lsat_1_v5_gn_6_75760' => 'lsa', 'Lsat_1_v5_gn_6_75800' => 'lsa', 'Lsat_1_v5_gn_6_75900' => 'lsa', 'Lsat_1_v5_gn_6_76240' => 'lsa', 'Lsat_1_v5_gn_6_76441' => 'lsa', 'Lsat_1_v5_gn_6_76700' => 'lsa', 'Lsat_1_v5_gn_6_76760' => 'lsa', 'Manes.15G033100' => 'mes', 'Mapoly0004s0074' => 'mpo', 'Mapoly0004s0075' => 'mpo', 'Mapoly0004s0163' => 'mpo', 'Mapoly0004s0164' => 'mpo', 'Mapoly0021s0018' => 'mpo', 'Mapoly0041s0136' => 'mpo', 'Mapoly0041s0137' => 'mpo', 'Mapoly0041s0138' => 'mpo', 'Mapoly0041s0139' => 'mpo', 'Mapoly0041s0141' => 'mpo', 'Mapoly0041s0142' => 'mpo', 'Mapoly0041s0143' => 'mpo', 'Mapoly0041s0144' => 'mpo', 'Mapoly0041s0145' => 'mpo', 'Mapoly0047s0106' => 'mpo', 'Mapoly0047s0108' => 'mpo', 'Mapoly0050s0051' => 'mpo', 'Mapoly0050s0052' => 'mpo', 'Mapoly0050s0053' => 'mpo', 'Mapoly0058s0013' => 'mpo', 'Mapoly0091s0078' => 'mpo', 'Mapoly0091s0079' => 'mpo', 'Mapoly0091s0080' => 'mpo', 'Mapoly0091s0081' => 'mpo', 'Mapoly0278s0004' => 'mpo', 'Mapoly0278s0005' => 'mpo', 'Mapoly0278s0006' => 'mpo', 'MBI11_g30648_MAGBIO' => 'mbi', 'MCO03G194' => 'mco', 'MCO03G590' => 'mco', 'MCO07G312' => 'mco', 'MCO10G318' => 'mco', 'MCO12G244' => 'mco', 'MCO13G148' => 'mco', 'MCO13G194' => 'mco', 'MCO16G238' => 'mco', 'MD06G1134100' => 'mdo', 'MD13G1200100' => 'mdo', 'MD13G1200300' => 'mdo', 'MD13G1200600' => 'mdo', 'MD14G1150400' => 'mdo', 'MD16G1200000' => 'mdo', 'Medtr1g102570' => 'mtr', 'Medtr1g102780' => 'mtr', 'Medtr1g102800' => 'mtr', 'Medtr1g102810' => 'mtr', 'Medtr1g102830' => 'mtr', 'MELO3C006499.2' => 'cme', 'Migut.G00385' => 'egut', 'MSTRG.4063' => 'ama', 'Nitab4.5_0000090g0260' => 'nta', 'Nitab4.5_0000977g0030' => 'nta', 'Nitab4.5_0002541g0040' => 'nta', 'Nitab4.5_0007068g0040' => 'nta', 'Nn005s41408' => 'nnu', 'Nn005s41410' => 'nnu', 'Oeu010310.1' => 'oeu', 'Oeu010311.1' => 'oeu', 'Oeu043472.1' => 'oeu', 'Os01g0246400' => 'osa', 'Os04g0267950' => 'osa', 'Os07g0178700' => 'osa', 'Os07g0178800' => 'osa', 'Peaxi162Scf00316g00046' => 'pax', 'Peaxi162Scf00316g00049' => 'pax', 'Peaxi162Scf00316g00059' => 'pax', 'Peaxi162Scf00316g00328' => 'pax', 'Peaxi162Scf00316g00329' => 'pax', 'Peaxi162Scf00316g00411' => 'pax', 'Peaxi162Scf00316g00521' => 'pax', 'Peaxi162Scf00492g00068' => 'pax', 'Peaxi162Scf35631g00002' => 'pax', 'PGR142G3720' => 'pgr', 'PGSC0003DMG400006442' => 'stu', 'Phvul.007G062000' => 'pvu', 'Potri.008G157750' => 'ptr', 'Potri.008G157900' => 'ptr', 'Potri.008G158000' => 'ptr', 'Potri.008G158200' => 'ptr', 'Pp3c11_7280' => 'ppa', 'Pp3c11_7980' => 'ppa', 'Pp3c12_19450' => 'ppa', 'Pp3c14_1480' => 'ppa', 'Pp3c14_1501' => 'ppa', 'Pp3c16_4900' => 'ppa', 'Pp3c16_5010' => 'ppa', 'Pp3c16_5060' => 'ppa', 'Pp3c19_18250' => 'ppa', 'Pp3c23_8530' => 'ppa', 'Pp3c23_8550' => 'ppa', 'Pp3c24_9670' => 'ppa', 'Pp3c2_21390' => 'ppa', 'Pp3c2_31380' => 'ppa', 'Pp3c3_16620' => 'ppa', 'Pp3c3_8090' => 'ppa', 'Pp3c3_8110' => 'ppa', 'Pp3c3_8130' => 'ppa', 'Pp3c3_8150' => 'ppa', 'Pp3c4_14320' => 'ppa', 'Pp3c6_2560' => 'ppa', 'Pp3c9_16700' => 'ppa', 'PRCOL_00000234' => 'pco', 'PRCOL_00000235' => 'pco', 'PRCOL_00000777' => 'pco', 'PRCOL_00002344' => 'pco', 'PRCOL_00002372' => 'pco', 'PRCOL_00006120' => 'pco', 'Prupe.1G021400' => 'ppe', 'Prupe.1G021500' => 'ppe', 'Prupe.1G021600' => 'ppe', 'Prupe.1G021700' => 'ppe', 'Prupe.1G021800' => 'ppe', 'Prupe.5G145100' => 'ppe', 'Psat6g204040' => 'psa', 'Psat6g204800' => 'psa', 'Psat6g204920' => 'psa', 'Psat6g204960' => 'psa', 'Psat6g205080' => 'psa', 'PSO017G0271' => 'pso', 'PSO017G1276' => 'pso', 'PSO017G1429' => 'pso', 'PSO017G1861' => 'pso', 'PSO017G2787' => 'pso', 'PSO017G4466' => 'pso', 'PSO017G5118' => 'pso', 'PSO017G5420' => 'pso', 'PSO063G3678' => 'pso', 'PSO210G0546' => 'pso', 'PSO317G0001' => 'pso', 'PSO357G0512' => 'pso', 'PSO478G2682' => 'pso', 'PSO647G0001' => 'pso', 'PSO675G0001' => 'pso', 'PSO675G2699' => 'pso', 'PSO675G2849' => 'pso', 'PSO675G4991' => 'pso', 'PSO689G0001' => 'pso', 'QL06p000916' => 'qlo', 'QL06p000921' => 'qlo', 'QL06p001398' => 'qlo', 'QL06p001407' => 'qlo', 'QL06p002031' => 'qlo', 'RcHm_v2.0_Chr4g0387791' => 'rch', 'RcHm_v2.0_Chr4g0387801' => 'rch', 'RcHm_v2.0_Chr6g0286501' => 'rch', 'RcHm_v2.0_Chr6g0286511' => 'rch', 'RcHm_v2.0_Chr6g0286521' => 'rch', 'RcHm_v2.0_Chr6g0286531' => 'rch', 'RcHm_v2.0_Chr7g0189141' => 'rch', 'Rhsim02G0028700' => 'rsi', 'Rhsim02G0028800' => 'rsi', 'Rhsim02G0028900' => 'rsi', 'Rhsim02G0029000' => 'rsi', 'Rhsim02G0029100' => 'rsi', 'Rhsim02G0029200' => 'rsi', 'Rhsim02G0029300' => 'rsi', 'Rhsim02G0029400' => 'rsi', 'Rhsim02G0029500' => 'rsi', 'Rhsim02G0029600' => 'rsi', 'RhsimUnG0024000' => 'rsi', 'RhsimUnG0024100' => 'rsi', 'RhsimUnG0024200' => 'rsi', 'RhsimUnG0024300' => 'rsi', 'RhsimUnG0024400' => 'rsi', 'RhsimUnG0024500' => 'rsi', 'RhsimUnG0024700' => 'rsi', 'RhsimUnG0024800' => 'rsi', 'RhsimUnG0024900' => 'rsi', 'RhsimUnG0025100' => 'rsi', 'Sabra08G0120200' => 'sbr', 'Sabra08G0120300' => 'sbr', 'Sabra08G0120500' => 'sbr', 'Sabra08G0120600' => 'sbr', 'Sabra10G0158900' => 'sbr', 'SalBow2G3492' => 'sbo', 'Sc13g0004760' => 'sci', 'Sc13g0004770' => 'sci', 'Sed0003417' => 'sed', 'Sed0019750' => 'sed', 'SEGI_03419' => 'sgi', 'SEGI_05907' => 'sgi', 'SEGI_10682' => 'sgi', 'SEGI_13528' => 'sgi', 'SEGI_16081' => 'sgi', 'SEGI_19370' => 'sgi', 'SEGI_21015' => 'sgi', 'SEGI_21944' => 'sgi', 'SEGI_32906' => 'sgi', 'SEGI_33093' => 'sgi', 'SEGI_36110' => 'sgi', 'SEGI_40397' => 'sgi', 'SGA_v2.0_scaffold191G40426' => 'sas', 'SGA_v2.0_scaffold353G49717' => 'sas', 'SGA_v2.0_scaffold50G18550' => 'sas', 'SMO119G0173' => 'smo', 'SMO172G0002' => 'smo', 'Solyc09g082690.3' => 'sly', 'Solyc09g082700.2' => 'sly', 'Sopen09g031550' => 'spe', 'Sopen09g031560' => 'spe', 'Sp3g20540' => 'spa', 'Sp7g07580' => 'spa', 'TAR134G0002' => 'tar', 'TAR236G0001' => 'tar', 'TAR365G0892' => 'tar', 'TAR636G0166' => 'tar', 'TAR636G0646' => 'tar', 'TAR636G0869' => 'tar', 'TAR636G1317' => 'tar', 'TAR636G1744' => 'tar', 'TAR636G3358' => 'tar', 'TAR636G3436' => 'tar', 'THA.LOC104803047' => 'tha', 'Thecc.04G238900' => 'tca', 'Thhalv10021557m.g' => 'esa', 'Thhalv10026318m.g' => 'esa', 'Thhalv10026335m.g' => 'esa', 'TPR.G17433' => 'tpr', 'TPR.G18915' => 'tpr', 'TPR.G26125' => 'tpr', 'TWI09G0677' => 'twi', 'TWI73G0287' => 'twi', 'unitig_748.g8326' => 'ugi', 'vmacro15370' => 'vma', 'vmacro15371' => 'vma', 'vmacro15372' => 'vma', 'vmacro15373' => 'vma', 'vmacro15374' => 'vma', 'VMungo0720G2826' => 'vmu', 'Zm00001eb116960' => 'zma', 'Zm00001eb301260' => 'zma', 'Zm00001eb301270' => 'zma' ), 'gf_id' => 'HOM05D001460', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001460' ), 'data_identifier' => 'HOM05D001460', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001460', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '433', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p22980' => 'bna', 'A01p32340' => 'bna', 'A03p42970' => 'bna', 'A05p25880' => 'bna', 'Aa31LG8G9320' => 'aar', 'Aa31LG8G9330' => 'aar', 'Aa31LG8G9340' => 'aar', 'Aa31sc221G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1034' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1528' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.829' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2222' => 'aag', 'Ah.12g058830' => 'amhyb', 'Ah.12g058840' => 'amhyb', 'AL3G37160' => 'aly', 'AL7G41310' => 'aly', 'Aqoxy5G00395' => 'aox', 'Aqoxy5G00396' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0C8NZA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5185HY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JZ1PRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MD3LS0' => 'arhy', 'AT3G22840' => 'ath', 'AT4G14690' => 'ath', 'ATR0665G054' => 'atr', 'Atru.chr4.2344' => 'acertr', 'Atru.chr4.2346' => 'acertr', 'Atru.chr4.2347' => 'acertr', 'Atru.chr4.2348' => 'acertr', 'Atru.chr4.2355' => 'acertr', 'Atru.chr4.2356' => 'acertr', 'Atru.chr4.2358' => 'acertr', 'Atru.chr4.2359' => 'acertr', 'Atru.chr4.2360' => 'acertr', 'Atru.chr4.2361' => 'acertr', 'AUR62030476' => 'cqu', 'AUR62030478' => 'cqu', 'AUR62030819' => 'cqu', 'AUR62030820' => 'cqu', 'BcaB03g14648' => 'bca', 'BcaB04g20492' => 'bca', 'BcaB06g26399' => 'bca', 'BcaC01g03416' => 'bca', 'BcaC01g03419' => 'bca', 'BcaC01g03421' => 'bca', 'BcaC01g03424' => 'bca', 'BcaC05g28012' => 'bca', 'BcaC09g49212' => 'bca', 'BcaC09g50140' => 'bca', 'BcaNung00346' => 'bca', 'BolC1t02785H' => 'bol', 'BolC1t04095H' => 'bol', 'BolC3t17545H' => 'bol', 'BolC5t32769H' => 'bol', 'BraA01t02211Z' => 'bra', 'BraA01t03359Z' => 'bra', 'BraA03t13441Z' => 'bra', 'BraA05t21476Z' => 'bra', 'C01p28420' => 'bna', 'C01p41350' => 'bna', 'C03p52750' => 'bna', 'C03p52780' => 'bna', 'C05p40270' => 'bna', 'CAN.G1437.9' => 'can', 'CANSAT78G0035' => 'cansat', 'CANSAT78G1036' => 'cansat', 'CANSAT78G2272' => 'cansat', 'CANSAT78G2478' => 'cansat', 'CARHR098700' => 'chi', 'CARHR221120' => 'chi', 'CARHR221150' => 'chi', 'Carub.0003s2297' => 'cru', 'Carub.0007s2749' => 'cru', 'Carub.0007s2750' => 'cru', 'Carub.0007s2751' => 'cru', 'Ca_10849_v3' => 'car', 'Cc03_g04300' => 'ccan', 'CDE02G3648' => 'cde', 'CDE05G0060' => 'cde', 'CDE05G0692' => 'cde', 'CDE05G2285' => 'cde', 'CDE05G2884' => 'cde', 'CDE05G3072' => 'cde', 'Cfa008439' => 'cfa', 'Cfa008441' => 'cfa', 'Cfa008443' => 'cfa', 'Cfa008448' => 'cfa', 'Ciclev10005974m.g' => 'ccl', 'Ciclev10006006m.g' => 'ccl', 'Ciclev10006775m.g' => 'ccl', 'CiPaw.02G120400' => 'cil', 'CiPaw.02G120500' => 'cil', 'CiPaw.02G120600' => 'cil', 'ClCG05G004850' => 'cla', 'COL.COLO4_21566' => 'col', 'Cpa.g.sc44.124' => 'cpa', 'Cre07.g320400' => 'cre', 'Cre07.g320450' => 'cre', 'Cre08.g384650' => 'cre', 'Cre09.g393173' => 'cre', 'Cre09.g394325' => 'cre', 'Cre14.g626750' => 'cre', 'Cre16.g679250' => 'cre', 'CsaV3_3G012890' => 'csa', 'CSS0010865' => 'camsi', 'CSS0044338' => 'camsi', 'DCAR_002366' => 'dca', 'DCAR_030687' => 'dca', 'DCAR_030688' => 'dca', 'Dinv14047' => 'din', 'Dinv14048' => 'din', 'Duzib151G0105' => 'dzi', 'Duzib151G0114' => 'dzi', 'Duzib212G1029' => 'dzi', 'ECA232G3536' => 'eca', 'ECA240G0786' => 'eca', 'ECA240G1802' => 'eca', 'ECA240G3760' => 'eca', 'ECA240G3920' => 'eca', 'EL10Ac5g12536' => 'bvu', 'EL10Ac5g12537' => 'bvu', 'EL10Ac5g12538' => 'bvu', 'Eucgr.B01004' => 'egr', 'Eucgr.B01006' => 'egr', 'Eucgr.B01007' => 'egr', 'Eucgr.B01008' => 'egr', 'Eucgr.B01895' => 'egr', 'Eucgr.B01896' => 'egr', 'FAN04G1456' => 'fan', 'FAN08G1769' => 'fan', 'FAN08G2160' => 'fan', 'FAN13G2403' => 'fan', 'FAN13G3303' => 'fan', 'FAN15G2435' => 'fan', 'FAN17G0672' => 'fan', 'FAN17G2441' => 'fan', 'FAN18G1024' => 'fan', 'FAN22G1458' => 'fan', 'FAN24G0037' => 'fan', 'FAN24G0429' => 'fan', 'FAN24G2387' => 'fan', 'FAN27G2746' => 'fan', 'FvH4_2g20400' => 'fve', 'FvH4_2g20420' => 'fve', 'FvH4_2g20430' => 'fve', 'FvH4_4g01270' => 'fve', 'FvH4_4g01290' => 'fve', 'FvH4_4g01300' => 'fve', 'FvH4_4g01310' => 'fve', 'FvH4_4g01330' => 'fve', 'FvH4_5g09070' => 'fve', 'Glyma.10G243800' => 'gma', 'Glyma.20G150600' => 'gma', 'Gohir.A09G219200' => 'ghi', 'Gohir.A09G219300' => 'ghi', 'Gohir.D09G221400' => 'ghi', 'Gohir.D09G221500' => 'ghi', 'Gorai.006G242600' => 'gra', 'Gorai.006G242700' => 'gra', 'GSVIVG01018044001' => 'vvi', 'HanXRQChr03g0083821' => 'han', 'HanXRQChr03g0083841' => 'han', 'HanXRQChr03g0083881' => 'han', 'HanXRQChr03g0083901' => 'han', 'HanXRQChr03g0083921' => 'han', 'HanXRQChr03g0085331' => 'han', 'HanXRQChr03g0085361' => 'han', 'HanXRQChr03g0085411' => 'han', 'HanXRQChr03g0085421' => 'han', 'HanXRQChr03g0085431' => 'han', 'HanXRQChr08g0221991' => 'han', 'HanXRQChr11g0336061' => 'han', 'HanXRQChr11g0336411' => 'han', 'Haze_11234' => 'cav', 'Hma1.2p1_0549F.1_g177010' => 'hma', 'Hma1.2p1_0602F.1_g187630' => 'hma', 'Hund14876' => 'sun', 'Hund14879' => 'sun', 'Lalb_Chr06g0160741' => 'lal', 'Lalb_Chr21g0304781' => 'lal', 'Lj3A726G19' => 'lonja', 'Lj3A726T23' => 'lonja', 'Lj3A726T24' => 'lonja', 'Lj3A726T25' => 'lonja', 'Lj3A727T17' => 'lonja', 'Lj3C726T0' => 'lonja', 'Lj3C726T2' => 'lonja', 'Lj3P725T35' => 'lonja', 'Lj3P727T10' => 'lonja', 'Lj3P727T12' => 'lonja', 'Lj3P727T14' => 'lonja', 'Lj5g0023109' => 'lja', 'Lj6P646T44' => 'lonja', 'Lsat_1_v5_gn_6_75760' => 'lsa', 'Lsat_1_v5_gn_6_75800' => 'lsa', 'Lsat_1_v5_gn_6_75900' => 'lsa', 'Lsat_1_v5_gn_6_76240' => 'lsa', 'Lsat_1_v5_gn_6_76441' => 'lsa', 'Lsat_1_v5_gn_6_76700' => 'lsa', 'Lsat_1_v5_gn_6_76760' => 'lsa', 'Manes.15G033100' => 'mes', 'Mapoly0004s0074' => 'mpo', 'Mapoly0004s0075' => 'mpo', 'Mapoly0004s0163' => 'mpo', 'Mapoly0004s0164' => 'mpo', 'Mapoly0021s0018' => 'mpo', 'Mapoly0041s0136' => 'mpo', 'Mapoly0041s0137' => 'mpo', 'Mapoly0041s0138' => 'mpo', 'Mapoly0041s0139' => 'mpo', 'Mapoly0041s0141' => 'mpo', 'Mapoly0041s0142' => 'mpo', 'Mapoly0041s0143' => 'mpo', 'Mapoly0041s0144' => 'mpo', 'Mapoly0041s0145' => 'mpo', 'Mapoly0047s0106' => 'mpo', 'Mapoly0047s0108' => 'mpo', 'Mapoly0050s0051' => 'mpo', 'Mapoly0050s0052' => 'mpo', 'Mapoly0050s0053' => 'mpo', 'Mapoly0058s0013' => 'mpo', 'Mapoly0091s0078' => 'mpo', 'Mapoly0091s0079' => 'mpo', 'Mapoly0091s0080' => 'mpo', 'Mapoly0091s0081' => 'mpo', 'Mapoly0278s0004' => 'mpo', 'Mapoly0278s0005' => 'mpo', 'Mapoly0278s0006' => 'mpo', 'MBI11_g30648_MAGBIO' => 'mbi', 'MCO03G194' => 'mco', 'MCO03G590' => 'mco', 'MCO07G312' => 'mco', 'MCO10G318' => 'mco', 'MCO12G244' => 'mco', 'MCO13G148' => 'mco', 'MCO13G194' => 'mco', 'MCO16G238' => 'mco', 'MD06G1134100' => 'mdo', 'MD13G1200100' => 'mdo', 'MD13G1200300' => 'mdo', 'MD13G1200600' => 'mdo', 'MD14G1150400' => 'mdo', 'MD16G1200000' => 'mdo', 'Medtr1g102570' => 'mtr', 'Medtr1g102780' => 'mtr', 'Medtr1g102800' => 'mtr', 'Medtr1g102810' => 'mtr', 'Medtr1g102830' => 'mtr', 'MELO3C006499.2' => 'cme', 'Migut.G00385' => 'egut', 'MSTRG.4063' => 'ama', 'Nitab4.5_0000090g0260' => 'nta', 'Nitab4.5_0000977g0030' => 'nta', 'Nitab4.5_0002541g0040' => 'nta', 'Nitab4.5_0007068g0040' => 'nta', 'Nn005s41408' => 'nnu', 'Nn005s41410' => 'nnu', 'Oeu010310.1' => 'oeu', 'Oeu010311.1' => 'oeu', 'Oeu043472.1' => 'oeu', 'Os01g0246400' => 'osa', 'Os04g0267950' => 'osa', 'Os07g0178700' => 'osa', 'Os07g0178800' => 'osa', 'Peaxi162Scf00316g00046' => 'pax', 'Peaxi162Scf00316g00049' => 'pax', 'Peaxi162Scf00316g00059' => 'pax', 'Peaxi162Scf00316g00328' => 'pax', 'Peaxi162Scf00316g00329' => 'pax', 'Peaxi162Scf00316g00411' => 'pax', 'Peaxi162Scf00316g00521' => 'pax', 'Peaxi162Scf00492g00068' => 'pax', 'Peaxi162Scf35631g00002' => 'pax', 'PGR142G3720' => 'pgr', 'PGSC0003DMG400006442' => 'stu', 'Phvul.007G062000' => 'pvu', 'Potri.008G157750' => 'ptr', 'Potri.008G157900' => 'ptr', 'Potri.008G158000' => 'ptr', 'Potri.008G158200' => 'ptr', 'Pp3c11_7280' => 'ppa', 'Pp3c11_7980' => 'ppa', 'Pp3c12_19450' => 'ppa', 'Pp3c14_1480' => 'ppa', 'Pp3c14_1501' => 'ppa', 'Pp3c16_4900' => 'ppa', 'Pp3c16_5010' => 'ppa', 'Pp3c16_5060' => 'ppa', 'Pp3c19_18250' => 'ppa', 'Pp3c23_8530' => 'ppa', 'Pp3c23_8550' => 'ppa', 'Pp3c24_9670' => 'ppa', 'Pp3c2_21390' => 'ppa', 'Pp3c2_31380' => 'ppa', 'Pp3c3_16620' => 'ppa', 'Pp3c3_8090' => 'ppa', 'Pp3c3_8110' => 'ppa', 'Pp3c3_8130' => 'ppa', 'Pp3c3_8150' => 'ppa', 'Pp3c4_14320' => 'ppa', 'Pp3c6_2560' => 'ppa', 'Pp3c9_16700' => 'ppa', 'PRCOL_00000234' => 'pco', 'PRCOL_00000235' => 'pco', 'PRCOL_00000777' => 'pco', 'PRCOL_00002344' => 'pco', 'PRCOL_00002372' => 'pco', 'PRCOL_00006120' => 'pco', 'Prupe.1G021400' => 'ppe', 'Prupe.1G021500' => 'ppe', 'Prupe.1G021600' => 'ppe', 'Prupe.1G021700' => 'ppe', 'Prupe.1G021800' => 'ppe', 'Prupe.5G145100' => 'ppe', 'Psat6g204040' => 'psa', 'Psat6g204800' => 'psa', 'Psat6g204920' => 'psa', 'Psat6g204960' => 'psa', 'Psat6g205080' => 'psa', 'PSO017G0271' => 'pso', 'PSO017G1276' => 'pso', 'PSO017G1429' => 'pso', 'PSO017G1861' => 'pso', 'PSO017G2787' => 'pso', 'PSO017G4466' => 'pso', 'PSO017G5118' => 'pso', 'PSO017G5420' => 'pso', 'PSO063G3678' => 'pso', 'PSO210G0546' => 'pso', 'PSO317G0001' => 'pso', 'PSO357G0512' => 'pso', 'PSO478G2682' => 'pso', 'PSO647G0001' => 'pso', 'PSO675G0001' => 'pso', 'PSO675G2699' => 'pso', 'PSO675G2849' => 'pso', 'PSO675G4991' => 'pso', 'PSO689G0001' => 'pso', 'QL06p000916' => 'qlo', 'QL06p000921' => 'qlo', 'QL06p001398' => 'qlo', 'QL06p001407' => 'qlo', 'QL06p002031' => 'qlo', 'RcHm_v2.0_Chr4g0387791' => 'rch', 'RcHm_v2.0_Chr4g0387801' => 'rch', 'RcHm_v2.0_Chr6g0286501' => 'rch', 'RcHm_v2.0_Chr6g0286511' => 'rch', 'RcHm_v2.0_Chr6g0286521' => 'rch', 'RcHm_v2.0_Chr6g0286531' => 'rch', 'RcHm_v2.0_Chr7g0189141' => 'rch', 'Rhsim02G0028700' => 'rsi', 'Rhsim02G0028800' => 'rsi', 'Rhsim02G0028900' => 'rsi', 'Rhsim02G0029000' => 'rsi', 'Rhsim02G0029100' => 'rsi', 'Rhsim02G0029200' => 'rsi', 'Rhsim02G0029300' => 'rsi', 'Rhsim02G0029400' => 'rsi', 'Rhsim02G0029500' => 'rsi', 'Rhsim02G0029600' => 'rsi', 'RhsimUnG0024000' => 'rsi', 'RhsimUnG0024100' => 'rsi', 'RhsimUnG0024200' => 'rsi', 'RhsimUnG0024300' => 'rsi', 'RhsimUnG0024400' => 'rsi', 'RhsimUnG0024500' => 'rsi', 'RhsimUnG0024700' => 'rsi', 'RhsimUnG0024800' => 'rsi', 'RhsimUnG0024900' => 'rsi', 'RhsimUnG0025100' => 'rsi', 'Sabra08G0120200' => 'sbr', 'Sabra08G0120300' => 'sbr', 'Sabra08G0120500' => 'sbr', 'Sabra08G0120600' => 'sbr', 'Sabra10G0158900' => 'sbr', 'SalBow2G3492' => 'sbo', 'Sc13g0004760' => 'sci', 'Sc13g0004770' => 'sci', 'Sed0003417' => 'sed', 'Sed0019750' => 'sed', 'SEGI_03419' => 'sgi', 'SEGI_05907' => 'sgi', 'SEGI_10682' => 'sgi', 'SEGI_13528' => 'sgi', 'SEGI_16081' => 'sgi', 'SEGI_19370' => 'sgi', 'SEGI_21015' => 'sgi', 'SEGI_21944' => 'sgi', 'SEGI_32906' => 'sgi', 'SEGI_33093' => 'sgi', 'SEGI_36110' => 'sgi', 'SEGI_40397' => 'sgi', 'SGA_v2.0_scaffold191G40426' => 'sas', 'SGA_v2.0_scaffold353G49717' => 'sas', 'SGA_v2.0_scaffold50G18550' => 'sas', 'SMO119G0173' => 'smo', 'SMO172G0002' => 'smo', 'Solyc09g082690.3' => 'sly', 'Solyc09g082700.2' => 'sly', 'Sopen09g031550' => 'spe', 'Sopen09g031560' => 'spe', 'Sp3g20540' => 'spa', 'Sp7g07580' => 'spa', 'TAR134G0002' => 'tar', 'TAR236G0001' => 'tar', 'TAR365G0892' => 'tar', 'TAR636G0166' => 'tar', 'TAR636G0646' => 'tar', 'TAR636G0869' => 'tar', 'TAR636G1317' => 'tar', 'TAR636G1744' => 'tar', 'TAR636G3358' => 'tar', 'TAR636G3436' => 'tar', 'THA.LOC104803047' => 'tha', 'Thecc.04G238900' => 'tca', 'Thhalv10021557m.g' => 'esa', 'Thhalv10026318m.g' => 'esa', 'Thhalv10026335m.g' => 'esa', 'TPR.G17433' => 'tpr', 'TPR.G18915' => 'tpr', 'TPR.G26125' => 'tpr', 'TWI09G0677' => 'twi', 'TWI73G0287' => 'twi', 'unitig_748.g8326' => 'ugi', 'vmacro15370' => 'vma', 'vmacro15371' => 'vma', 'vmacro15372' => 'vma', 'vmacro15373' => 'vma', 'vmacro15374' => 'vma', 'VMungo0720G2826' => 'vmu', 'Zm00001eb116960' => 'zma', 'Zm00001eb301260' => 'zma', 'Zm00001eb301270' => 'zma' ) $gf_id = 'HOM05D001460' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001460' ) $data_identifier = 'HOM05D001460' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 4, 'aag' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 2, 'aox' => (int) 2, 'arhy' => (int) 4, 'ath' => (int) 2, 'atr' => (int) 1, 'acertr' => (int) 10, 'cqu' => (int) 4, 'bca' => (int) 11, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 1, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 1, 'ccan' => (int) 1, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 1, 'col' => (int) 1, 'cpa' => (int) 1, 'cre' => (int) 7, 'csa' => (int) 1, 'camsi' => (int) 2, 'dca' => (int) 3, 'din' => (int) 2, 'dzi' => (int) 3, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 14, 'fve' => (int) 9, 'gma' => (int) 2, 'ghi' => (int) 4, 'gra' => (int) 2, 'vvi' => (int) 1, 'han' => (int) 13, 'cav' => (int) 1, 'hma' => (int) 2, 'sun' => (int) 2, 'lal' => (int) 2, 'lonja' => (int) 12, 'lja' => (int) 1, 'lsa' => (int) 7, 'mes' => (int) 1, 'mpo' => (int) 27, 'mbi' => (int) 1, 'mco' => (int) 8, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 1, 'egut' => (int) 1, 'ama' => (int) 1, 'nta' => (int) 4, 'nnu' => (int) 2, 'oeu' => (int) 3, 'osa' => (int) 4, 'pax' => (int) 9, 'pgr' => (int) 1, 'stu' => (int) 1, 'pvu' => (int) 1, 'ptr' => (int) 4, 'ppa' => (int) 22, 'pco' => (int) 6, 'ppe' => (int) 6, 'psa' => (int) 5, 'pso' => (int) 19, 'qlo' => (int) 5, 'rch' => (int) 7, 'rsi' => (int) 20, 'sbr' => (int) 5, 'sbo' => (int) 1, 'sci' => (int) 2, 'sed' => (int) 2, 'sgi' => (int) 12, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 2, 'tar' => (int) 10, 'tha' => (int) 1, 'tca' => (int) 1, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 2, 'ugi' => (int) 1, 'vma' => (int) 5, 'vmu' => (int) 1, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb301270' $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' => 'HOM05D001460', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '433', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p22980' => 'bna', 'A01p32340' => 'bna', 'A03p42970' => 'bna', 'A05p25880' => 'bna', 'Aa31LG8G9320' => 'aar', 'Aa31LG8G9330' => 'aar', 'Aa31LG8G9340' => 'aar', 'Aa31sc221G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1034' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1528' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.829' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2222' => 'aag', 'Ah.12g058830' => 'amhyb', 'Ah.12g058840' => 'amhyb', 'AL3G37160' => 'aly', 'AL7G41310' => 'aly', 'Aqoxy5G00395' => 'aox', 'Aqoxy5G00396' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0C8NZA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5185HY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JZ1PRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MD3LS0' => 'arhy', 'AT3G22840' => 'ath', 'AT4G14690' => 'ath', 'ATR0665G054' => 'atr', 'Atru.chr4.2344' => 'acertr', 'Atru.chr4.2346' => 'acertr', 'Atru.chr4.2347' => 'acertr', 'Atru.chr4.2348' => 'acertr', 'Atru.chr4.2355' => 'acertr', 'Atru.chr4.2356' => 'acertr', 'Atru.chr4.2358' => 'acertr', 'Atru.chr4.2359' => 'acertr', 'Atru.chr4.2360' => 'acertr', 'Atru.chr4.2361' => 'acertr', 'AUR62030476' => 'cqu', 'AUR62030478' => 'cqu', 'AUR62030819' => 'cqu', 'AUR62030820' => 'cqu', 'BcaB03g14648' => 'bca', 'BcaB04g20492' => 'bca', 'BcaB06g26399' => 'bca', 'BcaC01g03416' => 'bca', 'BcaC01g03419' => 'bca', 'BcaC01g03421' => 'bca', 'BcaC01g03424' => 'bca', 'BcaC05g28012' => 'bca', 'BcaC09g49212' => 'bca', 'BcaC09g50140' => 'bca', 'BcaNung00346' => 'bca', 'BolC1t02785H' => 'bol', 'BolC1t04095H' => 'bol', 'BolC3t17545H' => 'bol', 'BolC5t32769H' => 'bol', 'BraA01t02211Z' => 'bra', 'BraA01t03359Z' => 'bra', 'BraA03t13441Z' => 'bra', 'BraA05t21476Z' => 'bra', 'C01p28420' => 'bna', 'C01p41350' => 'bna', 'C03p52750' => 'bna', 'C03p52780' => 'bna', 'C05p40270' => 'bna', 'CAN.G1437.9' => 'can', 'CANSAT78G0035' => 'cansat', 'CANSAT78G1036' => 'cansat', 'CANSAT78G2272' => 'cansat', 'CANSAT78G2478' => 'cansat', 'CARHR098700' => 'chi', 'CARHR221120' => 'chi', 'CARHR221150' => 'chi', 'Carub.0003s2297' => 'cru', 'Carub.0007s2749' => 'cru', 'Carub.0007s2750' => 'cru', 'Carub.0007s2751' => 'cru', 'Ca_10849_v3' => 'car', 'Cc03_g04300' => 'ccan', 'CDE02G3648' => 'cde', 'CDE05G0060' => 'cde', 'CDE05G0692' => 'cde', 'CDE05G2285' => 'cde', 'CDE05G2884' => 'cde', 'CDE05G3072' => 'cde', 'Cfa008439' => 'cfa', 'Cfa008441' => 'cfa', 'Cfa008443' => 'cfa', 'Cfa008448' => 'cfa', 'Ciclev10005974m.g' => 'ccl', 'Ciclev10006006m.g' => 'ccl', 'Ciclev10006775m.g' => 'ccl', 'CiPaw.02G120400' => 'cil', 'CiPaw.02G120500' => 'cil', 'CiPaw.02G120600' => 'cil', 'ClCG05G004850' => 'cla', 'COL.COLO4_21566' => 'col', 'Cpa.g.sc44.124' => 'cpa', 'Cre07.g320400' => 'cre', 'Cre07.g320450' => 'cre', 'Cre08.g384650' => 'cre', 'Cre09.g393173' => 'cre', 'Cre09.g394325' => 'cre', 'Cre14.g626750' => 'cre', 'Cre16.g679250' => 'cre', 'CsaV3_3G012890' => 'csa', 'CSS0010865' => 'camsi', 'CSS0044338' => 'camsi', 'DCAR_002366' => 'dca', 'DCAR_030687' => 'dca', 'DCAR_030688' => 'dca', 'Dinv14047' => 'din', 'Dinv14048' => 'din', 'Duzib151G0105' => 'dzi', 'Duzib151G0114' => 'dzi', 'Duzib212G1029' => 'dzi', 'ECA232G3536' => 'eca', 'ECA240G0786' => 'eca', 'ECA240G1802' => 'eca', 'ECA240G3760' => 'eca', 'ECA240G3920' => 'eca', 'EL10Ac5g12536' => 'bvu', 'EL10Ac5g12537' => 'bvu', 'EL10Ac5g12538' => 'bvu', 'Eucgr.B01004' => 'egr', 'Eucgr.B01006' => 'egr', 'Eucgr.B01007' => 'egr', 'Eucgr.B01008' => 'egr', 'Eucgr.B01895' => 'egr', 'Eucgr.B01896' => 'egr', 'FAN04G1456' => 'fan', 'FAN08G1769' => 'fan', 'FAN08G2160' => 'fan', 'FAN13G2403' => 'fan', 'FAN13G3303' => 'fan', 'FAN15G2435' => 'fan', 'FAN17G0672' => 'fan', 'FAN17G2441' => 'fan', 'FAN18G1024' => 'fan', 'FAN22G1458' => 'fan', 'FAN24G0037' => 'fan', 'FAN24G0429' => 'fan', 'FAN24G2387' => 'fan', 'FAN27G2746' => 'fan', 'FvH4_2g20400' => 'fve', 'FvH4_2g20420' => 'fve', 'FvH4_2g20430' => 'fve', 'FvH4_4g01270' => 'fve', 'FvH4_4g01290' => 'fve', 'FvH4_4g01300' => 'fve', 'FvH4_4g01310' => 'fve', 'FvH4_4g01330' => 'fve', 'FvH4_5g09070' => 'fve', 'Glyma.10G243800' => 'gma', 'Glyma.20G150600' => 'gma', 'Gohir.A09G219200' => 'ghi', 'Gohir.A09G219300' => 'ghi', 'Gohir.D09G221400' => 'ghi', 'Gohir.D09G221500' => 'ghi', 'Gorai.006G242600' => 'gra', 'Gorai.006G242700' => 'gra', 'GSVIVG01018044001' => 'vvi', 'HanXRQChr03g0083821' => 'han', 'HanXRQChr03g0083841' => 'han', 'HanXRQChr03g0083881' => 'han', 'HanXRQChr03g0083901' => 'han', 'HanXRQChr03g0083921' => 'han', 'HanXRQChr03g0085331' => 'han', 'HanXRQChr03g0085361' => 'han', 'HanXRQChr03g0085411' => 'han', 'HanXRQChr03g0085421' => 'han', 'HanXRQChr03g0085431' => 'han', 'HanXRQChr08g0221991' => 'han', 'HanXRQChr11g0336061' => 'han', 'HanXRQChr11g0336411' => 'han', 'Haze_11234' => 'cav', 'Hma1.2p1_0549F.1_g177010' => 'hma', 'Hma1.2p1_0602F.1_g187630' => 'hma', 'Hund14876' => 'sun', 'Hund14879' => 'sun', 'Lalb_Chr06g0160741' => 'lal', 'Lalb_Chr21g0304781' => 'lal', 'Lj3A726G19' => 'lonja', 'Lj3A726T23' => 'lonja', 'Lj3A726T24' => 'lonja', 'Lj3A726T25' => 'lonja', 'Lj3A727T17' => 'lonja', 'Lj3C726T0' => 'lonja', 'Lj3C726T2' => 'lonja', 'Lj3P725T35' => 'lonja', 'Lj3P727T10' => 'lonja', 'Lj3P727T12' => 'lonja', 'Lj3P727T14' => 'lonja', 'Lj5g0023109' => 'lja', 'Lj6P646T44' => 'lonja', 'Lsat_1_v5_gn_6_75760' => 'lsa', 'Lsat_1_v5_gn_6_75800' => 'lsa', 'Lsat_1_v5_gn_6_75900' => 'lsa', 'Lsat_1_v5_gn_6_76240' => 'lsa', 'Lsat_1_v5_gn_6_76441' => 'lsa', 'Lsat_1_v5_gn_6_76700' => 'lsa', 'Lsat_1_v5_gn_6_76760' => 'lsa', 'Manes.15G033100' => 'mes', 'Mapoly0004s0074' => 'mpo', 'Mapoly0004s0075' => 'mpo', 'Mapoly0004s0163' => 'mpo', 'Mapoly0004s0164' => 'mpo', 'Mapoly0021s0018' => 'mpo', 'Mapoly0041s0136' => 'mpo', 'Mapoly0041s0137' => 'mpo', 'Mapoly0041s0138' => 'mpo', 'Mapoly0041s0139' => 'mpo', 'Mapoly0041s0141' => 'mpo', 'Mapoly0041s0142' => 'mpo', 'Mapoly0041s0143' => 'mpo', 'Mapoly0041s0144' => 'mpo', 'Mapoly0041s0145' => 'mpo', 'Mapoly0047s0106' => 'mpo', 'Mapoly0047s0108' => 'mpo', 'Mapoly0050s0051' => 'mpo', 'Mapoly0050s0052' => 'mpo', 'Mapoly0050s0053' => 'mpo', 'Mapoly0058s0013' => 'mpo', 'Mapoly0091s0078' => 'mpo', 'Mapoly0091s0079' => 'mpo', 'Mapoly0091s0080' => 'mpo', 'Mapoly0091s0081' => 'mpo', 'Mapoly0278s0004' => 'mpo', 'Mapoly0278s0005' => 'mpo', 'Mapoly0278s0006' => 'mpo', 'MBI11_g30648_MAGBIO' => 'mbi', 'MCO03G194' => 'mco', 'MCO03G590' => 'mco', 'MCO07G312' => 'mco', 'MCO10G318' => 'mco', 'MCO12G244' => 'mco', 'MCO13G148' => 'mco', 'MCO13G194' => 'mco', 'MCO16G238' => 'mco', 'MD06G1134100' => 'mdo', 'MD13G1200100' => 'mdo', 'MD13G1200300' => 'mdo', 'MD13G1200600' => 'mdo', 'MD14G1150400' => 'mdo', 'MD16G1200000' => 'mdo', 'Medtr1g102570' => 'mtr', 'Medtr1g102780' => 'mtr', 'Medtr1g102800' => 'mtr', 'Medtr1g102810' => 'mtr', 'Medtr1g102830' => 'mtr', 'MELO3C006499.2' => 'cme', 'Migut.G00385' => 'egut', 'MSTRG.4063' => 'ama', 'Nitab4.5_0000090g0260' => 'nta', 'Nitab4.5_0000977g0030' => 'nta', 'Nitab4.5_0002541g0040' => 'nta', 'Nitab4.5_0007068g0040' => 'nta', 'Nn005s41408' => 'nnu', 'Nn005s41410' => 'nnu', 'Oeu010310.1' => 'oeu', 'Oeu010311.1' => 'oeu', 'Oeu043472.1' => 'oeu', 'Os01g0246400' => 'osa', 'Os04g0267950' => 'osa', 'Os07g0178700' => 'osa', 'Os07g0178800' => 'osa', 'Peaxi162Scf00316g00046' => 'pax', 'Peaxi162Scf00316g00049' => 'pax', 'Peaxi162Scf00316g00059' => 'pax', 'Peaxi162Scf00316g00328' => 'pax', 'Peaxi162Scf00316g00329' => 'pax', 'Peaxi162Scf00316g00411' => 'pax', 'Peaxi162Scf00316g00521' => 'pax', 'Peaxi162Scf00492g00068' => 'pax', 'Peaxi162Scf35631g00002' => 'pax', 'PGR142G3720' => 'pgr', 'PGSC0003DMG400006442' => 'stu', 'Phvul.007G062000' => 'pvu', 'Potri.008G157750' => 'ptr', 'Potri.008G157900' => 'ptr', 'Potri.008G158000' => 'ptr', 'Potri.008G158200' => 'ptr', 'Pp3c11_7280' => 'ppa', 'Pp3c11_7980' => 'ppa', 'Pp3c12_19450' => 'ppa', 'Pp3c14_1480' => 'ppa', 'Pp3c14_1501' => 'ppa', 'Pp3c16_4900' => 'ppa', 'Pp3c16_5010' => 'ppa', 'Pp3c16_5060' => 'ppa', 'Pp3c19_18250' => 'ppa', 'Pp3c23_8530' => 'ppa', 'Pp3c23_8550' => 'ppa', 'Pp3c24_9670' => 'ppa', 'Pp3c2_21390' => 'ppa', 'Pp3c2_31380' => 'ppa', 'Pp3c3_16620' => 'ppa', 'Pp3c3_8090' => 'ppa', 'Pp3c3_8110' => 'ppa', 'Pp3c3_8130' => 'ppa', 'Pp3c3_8150' => 'ppa', 'Pp3c4_14320' => 'ppa', 'Pp3c6_2560' => 'ppa', 'Pp3c9_16700' => 'ppa', 'PRCOL_00000234' => 'pco', 'PRCOL_00000235' => 'pco', 'PRCOL_00000777' => 'pco', 'PRCOL_00002344' => 'pco', 'PRCOL_00002372' => 'pco', 'PRCOL_00006120' => 'pco', 'Prupe.1G021400' => 'ppe', 'Prupe.1G021500' => 'ppe', 'Prupe.1G021600' => 'ppe', 'Prupe.1G021700' => 'ppe', 'Prupe.1G021800' => 'ppe', 'Prupe.5G145100' => 'ppe', 'Psat6g204040' => 'psa', 'Psat6g204800' => 'psa', 'Psat6g204920' => 'psa', 'Psat6g204960' => 'psa', 'Psat6g205080' => 'psa', 'PSO017G0271' => 'pso', 'PSO017G1276' => 'pso', 'PSO017G1429' => 'pso', 'PSO017G1861' => 'pso', 'PSO017G2787' => 'pso', 'PSO017G4466' => 'pso', 'PSO017G5118' => 'pso', 'PSO017G5420' => 'pso', 'PSO063G3678' => 'pso', 'PSO210G0546' => 'pso', 'PSO317G0001' => 'pso', 'PSO357G0512' => 'pso', 'PSO478G2682' => 'pso', 'PSO647G0001' => 'pso', 'PSO675G0001' => 'pso', 'PSO675G2699' => 'pso', 'PSO675G2849' => 'pso', 'PSO675G4991' => 'pso', 'PSO689G0001' => 'pso', 'QL06p000916' => 'qlo', 'QL06p000921' => 'qlo', 'QL06p001398' => 'qlo', 'QL06p001407' => 'qlo', 'QL06p002031' => 'qlo', 'RcHm_v2.0_Chr4g0387791' => 'rch', 'RcHm_v2.0_Chr4g0387801' => 'rch', 'RcHm_v2.0_Chr6g0286501' => 'rch', 'RcHm_v2.0_Chr6g0286511' => 'rch', 'RcHm_v2.0_Chr6g0286521' => 'rch', 'RcHm_v2.0_Chr6g0286531' => 'rch', 'RcHm_v2.0_Chr7g0189141' => 'rch', 'Rhsim02G0028700' => 'rsi', 'Rhsim02G0028800' => 'rsi', 'Rhsim02G0028900' => 'rsi', 'Rhsim02G0029000' => 'rsi', 'Rhsim02G0029100' => 'rsi', 'Rhsim02G0029200' => 'rsi', 'Rhsim02G0029300' => 'rsi', 'Rhsim02G0029400' => 'rsi', 'Rhsim02G0029500' => 'rsi', 'Rhsim02G0029600' => 'rsi', 'RhsimUnG0024000' => 'rsi', 'RhsimUnG0024100' => 'rsi', 'RhsimUnG0024200' => 'rsi', 'RhsimUnG0024300' => 'rsi', 'RhsimUnG0024400' => 'rsi', 'RhsimUnG0024500' => 'rsi', 'RhsimUnG0024700' => 'rsi', 'RhsimUnG0024800' => 'rsi', 'RhsimUnG0024900' => 'rsi', 'RhsimUnG0025100' => 'rsi', 'Sabra08G0120200' => 'sbr', 'Sabra08G0120300' => 'sbr', 'Sabra08G0120500' => 'sbr', 'Sabra08G0120600' => 'sbr', 'Sabra10G0158900' => 'sbr', 'SalBow2G3492' => 'sbo', 'Sc13g0004760' => 'sci', 'Sc13g0004770' => 'sci', 'Sed0003417' => 'sed', 'Sed0019750' => 'sed', 'SEGI_03419' => 'sgi', 'SEGI_05907' => 'sgi', 'SEGI_10682' => 'sgi', 'SEGI_13528' => 'sgi', 'SEGI_16081' => 'sgi', 'SEGI_19370' => 'sgi', 'SEGI_21015' => 'sgi', 'SEGI_21944' => 'sgi', 'SEGI_32906' => 'sgi', 'SEGI_33093' => 'sgi', 'SEGI_36110' => 'sgi', 'SEGI_40397' => 'sgi', 'SGA_v2.0_scaffold191G40426' => 'sas', 'SGA_v2.0_scaffold353G49717' => 'sas', 'SGA_v2.0_scaffold50G18550' => 'sas', 'SMO119G0173' => 'smo', 'SMO172G0002' => 'smo', 'Solyc09g082690.3' => 'sly', 'Solyc09g082700.2' => 'sly', 'Sopen09g031550' => 'spe', 'Sopen09g031560' => 'spe', 'Sp3g20540' => 'spa', 'Sp7g07580' => 'spa', 'TAR134G0002' => 'tar', 'TAR236G0001' => 'tar', 'TAR365G0892' => 'tar', 'TAR636G0166' => 'tar', 'TAR636G0646' => 'tar', 'TAR636G0869' => 'tar', 'TAR636G1317' => 'tar', 'TAR636G1744' => 'tar', 'TAR636G3358' => 'tar', 'TAR636G3436' => 'tar', 'THA.LOC104803047' => 'tha', 'Thecc.04G238900' => 'tca', 'Thhalv10021557m.g' => 'esa', 'Thhalv10026318m.g' => 'esa', 'Thhalv10026335m.g' => 'esa', 'TPR.G17433' => 'tpr', 'TPR.G18915' => 'tpr', 'TPR.G26125' => 'tpr', 'TWI09G0677' => 'twi', 'TWI73G0287' => 'twi', 'unitig_748.g8326' => 'ugi', 'vmacro15370' => 'vma', 'vmacro15371' => 'vma', 'vmacro15372' => 'vma', 'vmacro15373' => 'vma', 'vmacro15374' => 'vma', 'VMungo0720G2826' => 'vmu', 'Zm00001eb116960' => 'zma', 'Zm00001eb301260' => 'zma', 'Zm00001eb301270' => 'zma' ), 'gf_id' => 'HOM05D001460', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001460' ), 'data_identifier' => 'HOM05D001460', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001460', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '433', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p22980' => 'bna', 'A01p32340' => 'bna', 'A03p42970' => 'bna', 'A05p25880' => 'bna', 'Aa31LG8G9320' => 'aar', 'Aa31LG8G9330' => 'aar', 'Aa31LG8G9340' => 'aar', 'Aa31sc221G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1034' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1528' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.829' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2222' => 'aag', 'Ah.12g058830' => 'amhyb', 'Ah.12g058840' => 'amhyb', 'AL3G37160' => 'aly', 'AL7G41310' => 'aly', 'Aqoxy5G00395' => 'aox', 'Aqoxy5G00396' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0C8NZA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5185HY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JZ1PRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MD3LS0' => 'arhy', 'AT3G22840' => 'ath', 'AT4G14690' => 'ath', 'ATR0665G054' => 'atr', 'Atru.chr4.2344' => 'acertr', 'Atru.chr4.2346' => 'acertr', 'Atru.chr4.2347' => 'acertr', 'Atru.chr4.2348' => 'acertr', 'Atru.chr4.2355' => 'acertr', 'Atru.chr4.2356' => 'acertr', 'Atru.chr4.2358' => 'acertr', 'Atru.chr4.2359' => 'acertr', 'Atru.chr4.2360' => 'acertr', 'Atru.chr4.2361' => 'acertr', 'AUR62030476' => 'cqu', 'AUR62030478' => 'cqu', 'AUR62030819' => 'cqu', 'AUR62030820' => 'cqu', 'BcaB03g14648' => 'bca', 'BcaB04g20492' => 'bca', 'BcaB06g26399' => 'bca', 'BcaC01g03416' => 'bca', 'BcaC01g03419' => 'bca', 'BcaC01g03421' => 'bca', 'BcaC01g03424' => 'bca', 'BcaC05g28012' => 'bca', 'BcaC09g49212' => 'bca', 'BcaC09g50140' => 'bca', 'BcaNung00346' => 'bca', 'BolC1t02785H' => 'bol', 'BolC1t04095H' => 'bol', 'BolC3t17545H' => 'bol', 'BolC5t32769H' => 'bol', 'BraA01t02211Z' => 'bra', 'BraA01t03359Z' => 'bra', 'BraA03t13441Z' => 'bra', 'BraA05t21476Z' => 'bra', 'C01p28420' => 'bna', 'C01p41350' => 'bna', 'C03p52750' => 'bna', 'C03p52780' => 'bna', 'C05p40270' => 'bna', 'CAN.G1437.9' => 'can', 'CANSAT78G0035' => 'cansat', 'CANSAT78G1036' => 'cansat', 'CANSAT78G2272' => 'cansat', 'CANSAT78G2478' => 'cansat', 'CARHR098700' => 'chi', 'CARHR221120' => 'chi', 'CARHR221150' => 'chi', 'Carub.0003s2297' => 'cru', 'Carub.0007s2749' => 'cru', 'Carub.0007s2750' => 'cru', 'Carub.0007s2751' => 'cru', 'Ca_10849_v3' => 'car', 'Cc03_g04300' => 'ccan', 'CDE02G3648' => 'cde', 'CDE05G0060' => 'cde', 'CDE05G0692' => 'cde', 'CDE05G2285' => 'cde', 'CDE05G2884' => 'cde', 'CDE05G3072' => 'cde', 'Cfa008439' => 'cfa', 'Cfa008441' => 'cfa', 'Cfa008443' => 'cfa', 'Cfa008448' => 'cfa', 'Ciclev10005974m.g' => 'ccl', 'Ciclev10006006m.g' => 'ccl', 'Ciclev10006775m.g' => 'ccl', 'CiPaw.02G120400' => 'cil', 'CiPaw.02G120500' => 'cil', 'CiPaw.02G120600' => 'cil', 'ClCG05G004850' => 'cla', 'COL.COLO4_21566' => 'col', 'Cpa.g.sc44.124' => 'cpa', 'Cre07.g320400' => 'cre', 'Cre07.g320450' => 'cre', 'Cre08.g384650' => 'cre', 'Cre09.g393173' => 'cre', 'Cre09.g394325' => 'cre', 'Cre14.g626750' => 'cre', 'Cre16.g679250' => 'cre', 'CsaV3_3G012890' => 'csa', 'CSS0010865' => 'camsi', 'CSS0044338' => 'camsi', 'DCAR_002366' => 'dca', 'DCAR_030687' => 'dca', 'DCAR_030688' => 'dca', 'Dinv14047' => 'din', 'Dinv14048' => 'din', 'Duzib151G0105' => 'dzi', 'Duzib151G0114' => 'dzi', 'Duzib212G1029' => 'dzi', 'ECA232G3536' => 'eca', 'ECA240G0786' => 'eca', 'ECA240G1802' => 'eca', 'ECA240G3760' => 'eca', 'ECA240G3920' => 'eca', 'EL10Ac5g12536' => 'bvu', 'EL10Ac5g12537' => 'bvu', 'EL10Ac5g12538' => 'bvu', 'Eucgr.B01004' => 'egr', 'Eucgr.B01006' => 'egr', 'Eucgr.B01007' => 'egr', 'Eucgr.B01008' => 'egr', 'Eucgr.B01895' => 'egr', 'Eucgr.B01896' => 'egr', 'FAN04G1456' => 'fan', 'FAN08G1769' => 'fan', 'FAN08G2160' => 'fan', 'FAN13G2403' => 'fan', 'FAN13G3303' => 'fan', 'FAN15G2435' => 'fan', 'FAN17G0672' => 'fan', 'FAN17G2441' => 'fan', 'FAN18G1024' => 'fan', 'FAN22G1458' => 'fan', 'FAN24G0037' => 'fan', 'FAN24G0429' => 'fan', 'FAN24G2387' => 'fan', 'FAN27G2746' => 'fan', 'FvH4_2g20400' => 'fve', 'FvH4_2g20420' => 'fve', 'FvH4_2g20430' => 'fve', 'FvH4_4g01270' => 'fve', 'FvH4_4g01290' => 'fve', 'FvH4_4g01300' => 'fve', 'FvH4_4g01310' => 'fve', 'FvH4_4g01330' => 'fve', 'FvH4_5g09070' => 'fve', 'Glyma.10G243800' => 'gma', 'Glyma.20G150600' => 'gma', 'Gohir.A09G219200' => 'ghi', 'Gohir.A09G219300' => 'ghi', 'Gohir.D09G221400' => 'ghi', 'Gohir.D09G221500' => 'ghi', 'Gorai.006G242600' => 'gra', 'Gorai.006G242700' => 'gra', 'GSVIVG01018044001' => 'vvi', 'HanXRQChr03g0083821' => 'han', 'HanXRQChr03g0083841' => 'han', 'HanXRQChr03g0083881' => 'han', 'HanXRQChr03g0083901' => 'han', 'HanXRQChr03g0083921' => 'han', 'HanXRQChr03g0085331' => 'han', 'HanXRQChr03g0085361' => 'han', 'HanXRQChr03g0085411' => 'han', 'HanXRQChr03g0085421' => 'han', 'HanXRQChr03g0085431' => 'han', 'HanXRQChr08g0221991' => 'han', 'HanXRQChr11g0336061' => 'han', 'HanXRQChr11g0336411' => 'han', 'Haze_11234' => 'cav', 'Hma1.2p1_0549F.1_g177010' => 'hma', 'Hma1.2p1_0602F.1_g187630' => 'hma', 'Hund14876' => 'sun', 'Hund14879' => 'sun', 'Lalb_Chr06g0160741' => 'lal', 'Lalb_Chr21g0304781' => 'lal', 'Lj3A726G19' => 'lonja', 'Lj3A726T23' => 'lonja', 'Lj3A726T24' => 'lonja', 'Lj3A726T25' => 'lonja', 'Lj3A727T17' => 'lonja', 'Lj3C726T0' => 'lonja', 'Lj3C726T2' => 'lonja', 'Lj3P725T35' => 'lonja', 'Lj3P727T10' => 'lonja', 'Lj3P727T12' => 'lonja', 'Lj3P727T14' => 'lonja', 'Lj5g0023109' => 'lja', 'Lj6P646T44' => 'lonja', 'Lsat_1_v5_gn_6_75760' => 'lsa', 'Lsat_1_v5_gn_6_75800' => 'lsa', 'Lsat_1_v5_gn_6_75900' => 'lsa', 'Lsat_1_v5_gn_6_76240' => 'lsa', 'Lsat_1_v5_gn_6_76441' => 'lsa', 'Lsat_1_v5_gn_6_76700' => 'lsa', 'Lsat_1_v5_gn_6_76760' => 'lsa', 'Manes.15G033100' => 'mes', 'Mapoly0004s0074' => 'mpo', 'Mapoly0004s0075' => 'mpo', 'Mapoly0004s0163' => 'mpo', 'Mapoly0004s0164' => 'mpo', 'Mapoly0021s0018' => 'mpo', 'Mapoly0041s0136' => 'mpo', 'Mapoly0041s0137' => 'mpo', 'Mapoly0041s0138' => 'mpo', 'Mapoly0041s0139' => 'mpo', 'Mapoly0041s0141' => 'mpo', 'Mapoly0041s0142' => 'mpo', 'Mapoly0041s0143' => 'mpo', 'Mapoly0041s0144' => 'mpo', 'Mapoly0041s0145' => 'mpo', 'Mapoly0047s0106' => 'mpo', 'Mapoly0047s0108' => 'mpo', 'Mapoly0050s0051' => 'mpo', 'Mapoly0050s0052' => 'mpo', 'Mapoly0050s0053' => 'mpo', 'Mapoly0058s0013' => 'mpo', 'Mapoly0091s0078' => 'mpo', 'Mapoly0091s0079' => 'mpo', 'Mapoly0091s0080' => 'mpo', 'Mapoly0091s0081' => 'mpo', 'Mapoly0278s0004' => 'mpo', 'Mapoly0278s0005' => 'mpo', 'Mapoly0278s0006' => 'mpo', 'MBI11_g30648_MAGBIO' => 'mbi', 'MCO03G194' => 'mco', 'MCO03G590' => 'mco', 'MCO07G312' => 'mco', 'MCO10G318' => 'mco', 'MCO12G244' => 'mco', 'MCO13G148' => 'mco', 'MCO13G194' => 'mco', 'MCO16G238' => 'mco', 'MD06G1134100' => 'mdo', 'MD13G1200100' => 'mdo', 'MD13G1200300' => 'mdo', 'MD13G1200600' => 'mdo', 'MD14G1150400' => 'mdo', 'MD16G1200000' => 'mdo', 'Medtr1g102570' => 'mtr', 'Medtr1g102780' => 'mtr', 'Medtr1g102800' => 'mtr', 'Medtr1g102810' => 'mtr', 'Medtr1g102830' => 'mtr', 'MELO3C006499.2' => 'cme', 'Migut.G00385' => 'egut', 'MSTRG.4063' => 'ama', 'Nitab4.5_0000090g0260' => 'nta', 'Nitab4.5_0000977g0030' => 'nta', 'Nitab4.5_0002541g0040' => 'nta', 'Nitab4.5_0007068g0040' => 'nta', 'Nn005s41408' => 'nnu', 'Nn005s41410' => 'nnu', 'Oeu010310.1' => 'oeu', 'Oeu010311.1' => 'oeu', 'Oeu043472.1' => 'oeu', 'Os01g0246400' => 'osa', 'Os04g0267950' => 'osa', 'Os07g0178700' => 'osa', 'Os07g0178800' => 'osa', 'Peaxi162Scf00316g00046' => 'pax', 'Peaxi162Scf00316g00049' => 'pax', 'Peaxi162Scf00316g00059' => 'pax', 'Peaxi162Scf00316g00328' => 'pax', 'Peaxi162Scf00316g00329' => 'pax', 'Peaxi162Scf00316g00411' => 'pax', 'Peaxi162Scf00316g00521' => 'pax', 'Peaxi162Scf00492g00068' => 'pax', 'Peaxi162Scf35631g00002' => 'pax', 'PGR142G3720' => 'pgr', 'PGSC0003DMG400006442' => 'stu', 'Phvul.007G062000' => 'pvu', 'Potri.008G157750' => 'ptr', 'Potri.008G157900' => 'ptr', 'Potri.008G158000' => 'ptr', 'Potri.008G158200' => 'ptr', 'Pp3c11_7280' => 'ppa', 'Pp3c11_7980' => 'ppa', 'Pp3c12_19450' => 'ppa', 'Pp3c14_1480' => 'ppa', 'Pp3c14_1501' => 'ppa', 'Pp3c16_4900' => 'ppa', 'Pp3c16_5010' => 'ppa', 'Pp3c16_5060' => 'ppa', 'Pp3c19_18250' => 'ppa', 'Pp3c23_8530' => 'ppa', 'Pp3c23_8550' => 'ppa', 'Pp3c24_9670' => 'ppa', 'Pp3c2_21390' => 'ppa', 'Pp3c2_31380' => 'ppa', 'Pp3c3_16620' => 'ppa', 'Pp3c3_8090' => 'ppa', 'Pp3c3_8110' => 'ppa', 'Pp3c3_8130' => 'ppa', 'Pp3c3_8150' => 'ppa', 'Pp3c4_14320' => 'ppa', 'Pp3c6_2560' => 'ppa', 'Pp3c9_16700' => 'ppa', 'PRCOL_00000234' => 'pco', 'PRCOL_00000235' => 'pco', 'PRCOL_00000777' => 'pco', 'PRCOL_00002344' => 'pco', 'PRCOL_00002372' => 'pco', 'PRCOL_00006120' => 'pco', 'Prupe.1G021400' => 'ppe', 'Prupe.1G021500' => 'ppe', 'Prupe.1G021600' => 'ppe', 'Prupe.1G021700' => 'ppe', 'Prupe.1G021800' => 'ppe', 'Prupe.5G145100' => 'ppe', 'Psat6g204040' => 'psa', 'Psat6g204800' => 'psa', 'Psat6g204920' => 'psa', 'Psat6g204960' => 'psa', 'Psat6g205080' => 'psa', 'PSO017G0271' => 'pso', 'PSO017G1276' => 'pso', 'PSO017G1429' => 'pso', 'PSO017G1861' => 'pso', 'PSO017G2787' => 'pso', 'PSO017G4466' => 'pso', 'PSO017G5118' => 'pso', 'PSO017G5420' => 'pso', 'PSO063G3678' => 'pso', 'PSO210G0546' => 'pso', 'PSO317G0001' => 'pso', 'PSO357G0512' => 'pso', 'PSO478G2682' => 'pso', 'PSO647G0001' => 'pso', 'PSO675G0001' => 'pso', 'PSO675G2699' => 'pso', 'PSO675G2849' => 'pso', 'PSO675G4991' => 'pso', 'PSO689G0001' => 'pso', 'QL06p000916' => 'qlo', 'QL06p000921' => 'qlo', 'QL06p001398' => 'qlo', 'QL06p001407' => 'qlo', 'QL06p002031' => 'qlo', 'RcHm_v2.0_Chr4g0387791' => 'rch', 'RcHm_v2.0_Chr4g0387801' => 'rch', 'RcHm_v2.0_Chr6g0286501' => 'rch', 'RcHm_v2.0_Chr6g0286511' => 'rch', 'RcHm_v2.0_Chr6g0286521' => 'rch', 'RcHm_v2.0_Chr6g0286531' => 'rch', 'RcHm_v2.0_Chr7g0189141' => 'rch', 'Rhsim02G0028700' => 'rsi', 'Rhsim02G0028800' => 'rsi', 'Rhsim02G0028900' => 'rsi', 'Rhsim02G0029000' => 'rsi', 'Rhsim02G0029100' => 'rsi', 'Rhsim02G0029200' => 'rsi', 'Rhsim02G0029300' => 'rsi', 'Rhsim02G0029400' => 'rsi', 'Rhsim02G0029500' => 'rsi', 'Rhsim02G0029600' => 'rsi', 'RhsimUnG0024000' => 'rsi', 'RhsimUnG0024100' => 'rsi', 'RhsimUnG0024200' => 'rsi', 'RhsimUnG0024300' => 'rsi', 'RhsimUnG0024400' => 'rsi', 'RhsimUnG0024500' => 'rsi', 'RhsimUnG0024700' => 'rsi', 'RhsimUnG0024800' => 'rsi', 'RhsimUnG0024900' => 'rsi', 'RhsimUnG0025100' => 'rsi', 'Sabra08G0120200' => 'sbr', 'Sabra08G0120300' => 'sbr', 'Sabra08G0120500' => 'sbr', 'Sabra08G0120600' => 'sbr', 'Sabra10G0158900' => 'sbr', 'SalBow2G3492' => 'sbo', 'Sc13g0004760' => 'sci', 'Sc13g0004770' => 'sci', 'Sed0003417' => 'sed', 'Sed0019750' => 'sed', 'SEGI_03419' => 'sgi', 'SEGI_05907' => 'sgi', 'SEGI_10682' => 'sgi', 'SEGI_13528' => 'sgi', 'SEGI_16081' => 'sgi', 'SEGI_19370' => 'sgi', 'SEGI_21015' => 'sgi', 'SEGI_21944' => 'sgi', 'SEGI_32906' => 'sgi', 'SEGI_33093' => 'sgi', 'SEGI_36110' => 'sgi', 'SEGI_40397' => 'sgi', 'SGA_v2.0_scaffold191G40426' => 'sas', 'SGA_v2.0_scaffold353G49717' => 'sas', 'SGA_v2.0_scaffold50G18550' => 'sas', 'SMO119G0173' => 'smo', 'SMO172G0002' => 'smo', 'Solyc09g082690.3' => 'sly', 'Solyc09g082700.2' => 'sly', 'Sopen09g031550' => 'spe', 'Sopen09g031560' => 'spe', 'Sp3g20540' => 'spa', 'Sp7g07580' => 'spa', 'TAR134G0002' => 'tar', 'TAR236G0001' => 'tar', 'TAR365G0892' => 'tar', 'TAR636G0166' => 'tar', 'TAR636G0646' => 'tar', 'TAR636G0869' => 'tar', 'TAR636G1317' => 'tar', 'TAR636G1744' => 'tar', 'TAR636G3358' => 'tar', 'TAR636G3436' => 'tar', 'THA.LOC104803047' => 'tha', 'Thecc.04G238900' => 'tca', 'Thhalv10021557m.g' => 'esa', 'Thhalv10026318m.g' => 'esa', 'Thhalv10026335m.g' => 'esa', 'TPR.G17433' => 'tpr', 'TPR.G18915' => 'tpr', 'TPR.G26125' => 'tpr', 'TWI09G0677' => 'twi', 'TWI73G0287' => 'twi', 'unitig_748.g8326' => 'ugi', 'vmacro15370' => 'vma', 'vmacro15371' => 'vma', 'vmacro15372' => 'vma', 'vmacro15373' => 'vma', 'vmacro15374' => 'vma', 'VMungo0720G2826' => 'vmu', 'Zm00001eb116960' => 'zma', 'Zm00001eb301260' => 'zma', 'Zm00001eb301270' => 'zma' ) $gf_id = 'HOM05D001460' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001460' ) $data_identifier = 'HOM05D001460' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 4, 'aag' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 2, 'aox' => (int) 2, 'arhy' => (int) 4, 'ath' => (int) 2, 'atr' => (int) 1, 'acertr' => (int) 10, 'cqu' => (int) 4, 'bca' => (int) 11, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 1, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 1, 'ccan' => (int) 1, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 1, 'col' => (int) 1, 'cpa' => (int) 1, 'cre' => (int) 7, 'csa' => (int) 1, 'camsi' => (int) 2, 'dca' => (int) 3, 'din' => (int) 2, 'dzi' => (int) 3, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 14, 'fve' => (int) 9, 'gma' => (int) 2, 'ghi' => (int) 4, 'gra' => (int) 2, 'vvi' => (int) 1, 'han' => (int) 13, 'cav' => (int) 1, 'hma' => (int) 2, 'sun' => (int) 2, 'lal' => (int) 2, 'lonja' => (int) 12, 'lja' => (int) 1, 'lsa' => (int) 7, 'mes' => (int) 1, 'mpo' => (int) 27, 'mbi' => (int) 1, 'mco' => (int) 8, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 1, 'egut' => (int) 1, 'ama' => (int) 1, 'nta' => (int) 4, 'nnu' => (int) 2, 'oeu' => (int) 3, 'osa' => (int) 4, 'pax' => (int) 9, 'pgr' => (int) 1, 'stu' => (int) 1, 'pvu' => (int) 1, 'ptr' => (int) 4, 'ppa' => (int) 22, 'pco' => (int) 6, 'ppe' => (int) 6, 'psa' => (int) 5, 'pso' => (int) 19, 'qlo' => (int) 5, 'rch' => (int) 7, 'rsi' => (int) 20, 'sbr' => (int) 5, 'sbo' => (int) 1, 'sci' => (int) 2, 'sed' => (int) 2, 'sgi' => (int) 12, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 2, 'tar' => (int) 10, 'tha' => (int) 1, 'tca' => (int) 1, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 2, 'ugi' => (int) 1, 'vma' => (int) 5, 'vmu' => (int) 1, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb301270' $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' => 'HOM05D001460', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '433', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p22980' => 'bna', 'A01p32340' => 'bna', 'A03p42970' => 'bna', 'A05p25880' => 'bna', 'Aa31LG8G9320' => 'aar', 'Aa31LG8G9330' => 'aar', 'Aa31LG8G9340' => 'aar', 'Aa31sc221G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1034' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1528' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.829' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2222' => 'aag', 'Ah.12g058830' => 'amhyb', 'Ah.12g058840' => 'amhyb', 'AL3G37160' => 'aly', 'AL7G41310' => 'aly', 'Aqoxy5G00395' => 'aox', 'Aqoxy5G00396' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0C8NZA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5185HY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JZ1PRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MD3LS0' => 'arhy', 'AT3G22840' => 'ath', 'AT4G14690' => 'ath', 'ATR0665G054' => 'atr', 'Atru.chr4.2344' => 'acertr', 'Atru.chr4.2346' => 'acertr', 'Atru.chr4.2347' => 'acertr', 'Atru.chr4.2348' => 'acertr', 'Atru.chr4.2355' => 'acertr', 'Atru.chr4.2356' => 'acertr', 'Atru.chr4.2358' => 'acertr', 'Atru.chr4.2359' => 'acertr', 'Atru.chr4.2360' => 'acertr', 'Atru.chr4.2361' => 'acertr', 'AUR62030476' => 'cqu', 'AUR62030478' => 'cqu', 'AUR62030819' => 'cqu', 'AUR62030820' => 'cqu', 'BcaB03g14648' => 'bca', 'BcaB04g20492' => 'bca', 'BcaB06g26399' => 'bca', 'BcaC01g03416' => 'bca', 'BcaC01g03419' => 'bca', 'BcaC01g03421' => 'bca', 'BcaC01g03424' => 'bca', 'BcaC05g28012' => 'bca', 'BcaC09g49212' => 'bca', 'BcaC09g50140' => 'bca', 'BcaNung00346' => 'bca', 'BolC1t02785H' => 'bol', 'BolC1t04095H' => 'bol', 'BolC3t17545H' => 'bol', 'BolC5t32769H' => 'bol', 'BraA01t02211Z' => 'bra', 'BraA01t03359Z' => 'bra', 'BraA03t13441Z' => 'bra', 'BraA05t21476Z' => 'bra', 'C01p28420' => 'bna', 'C01p41350' => 'bna', 'C03p52750' => 'bna', 'C03p52780' => 'bna', 'C05p40270' => 'bna', 'CAN.G1437.9' => 'can', 'CANSAT78G0035' => 'cansat', 'CANSAT78G1036' => 'cansat', 'CANSAT78G2272' => 'cansat', 'CANSAT78G2478' => 'cansat', 'CARHR098700' => 'chi', 'CARHR221120' => 'chi', 'CARHR221150' => 'chi', 'Carub.0003s2297' => 'cru', 'Carub.0007s2749' => 'cru', 'Carub.0007s2750' => 'cru', 'Carub.0007s2751' => 'cru', 'Ca_10849_v3' => 'car', 'Cc03_g04300' => 'ccan', 'CDE02G3648' => 'cde', 'CDE05G0060' => 'cde', 'CDE05G0692' => 'cde', 'CDE05G2285' => 'cde', 'CDE05G2884' => 'cde', 'CDE05G3072' => 'cde', 'Cfa008439' => 'cfa', 'Cfa008441' => 'cfa', 'Cfa008443' => 'cfa', 'Cfa008448' => 'cfa', 'Ciclev10005974m.g' => 'ccl', 'Ciclev10006006m.g' => 'ccl', 'Ciclev10006775m.g' => 'ccl', 'CiPaw.02G120400' => 'cil', 'CiPaw.02G120500' => 'cil', 'CiPaw.02G120600' => 'cil', 'ClCG05G004850' => 'cla', 'COL.COLO4_21566' => 'col', 'Cpa.g.sc44.124' => 'cpa', 'Cre07.g320400' => 'cre', 'Cre07.g320450' => 'cre', 'Cre08.g384650' => 'cre', 'Cre09.g393173' => 'cre', 'Cre09.g394325' => 'cre', 'Cre14.g626750' => 'cre', 'Cre16.g679250' => 'cre', 'CsaV3_3G012890' => 'csa', 'CSS0010865' => 'camsi', 'CSS0044338' => 'camsi', 'DCAR_002366' => 'dca', 'DCAR_030687' => 'dca', 'DCAR_030688' => 'dca', 'Dinv14047' => 'din', 'Dinv14048' => 'din', 'Duzib151G0105' => 'dzi', 'Duzib151G0114' => 'dzi', 'Duzib212G1029' => 'dzi', 'ECA232G3536' => 'eca', 'ECA240G0786' => 'eca', 'ECA240G1802' => 'eca', 'ECA240G3760' => 'eca', 'ECA240G3920' => 'eca', 'EL10Ac5g12536' => 'bvu', 'EL10Ac5g12537' => 'bvu', 'EL10Ac5g12538' => 'bvu', 'Eucgr.B01004' => 'egr', 'Eucgr.B01006' => 'egr', 'Eucgr.B01007' => 'egr', 'Eucgr.B01008' => 'egr', 'Eucgr.B01895' => 'egr', 'Eucgr.B01896' => 'egr', 'FAN04G1456' => 'fan', 'FAN08G1769' => 'fan', 'FAN08G2160' => 'fan', 'FAN13G2403' => 'fan', 'FAN13G3303' => 'fan', 'FAN15G2435' => 'fan', 'FAN17G0672' => 'fan', 'FAN17G2441' => 'fan', 'FAN18G1024' => 'fan', 'FAN22G1458' => 'fan', 'FAN24G0037' => 'fan', 'FAN24G0429' => 'fan', 'FAN24G2387' => 'fan', 'FAN27G2746' => 'fan', 'FvH4_2g20400' => 'fve', 'FvH4_2g20420' => 'fve', 'FvH4_2g20430' => 'fve', 'FvH4_4g01270' => 'fve', 'FvH4_4g01290' => 'fve', 'FvH4_4g01300' => 'fve', 'FvH4_4g01310' => 'fve', 'FvH4_4g01330' => 'fve', 'FvH4_5g09070' => 'fve', 'Glyma.10G243800' => 'gma', 'Glyma.20G150600' => 'gma', 'Gohir.A09G219200' => 'ghi', 'Gohir.A09G219300' => 'ghi', 'Gohir.D09G221400' => 'ghi', 'Gohir.D09G221500' => 'ghi', 'Gorai.006G242600' => 'gra', 'Gorai.006G242700' => 'gra', 'GSVIVG01018044001' => 'vvi', 'HanXRQChr03g0083821' => 'han', 'HanXRQChr03g0083841' => 'han', 'HanXRQChr03g0083881' => 'han', 'HanXRQChr03g0083901' => 'han', 'HanXRQChr03g0083921' => 'han', 'HanXRQChr03g0085331' => 'han', 'HanXRQChr03g0085361' => 'han', 'HanXRQChr03g0085411' => 'han', 'HanXRQChr03g0085421' => 'han', 'HanXRQChr03g0085431' => 'han', 'HanXRQChr08g0221991' => 'han', 'HanXRQChr11g0336061' => 'han', 'HanXRQChr11g0336411' => 'han', 'Haze_11234' => 'cav', 'Hma1.2p1_0549F.1_g177010' => 'hma', 'Hma1.2p1_0602F.1_g187630' => 'hma', 'Hund14876' => 'sun', 'Hund14879' => 'sun', 'Lalb_Chr06g0160741' => 'lal', 'Lalb_Chr21g0304781' => 'lal', 'Lj3A726G19' => 'lonja', 'Lj3A726T23' => 'lonja', 'Lj3A726T24' => 'lonja', 'Lj3A726T25' => 'lonja', 'Lj3A727T17' => 'lonja', 'Lj3C726T0' => 'lonja', 'Lj3C726T2' => 'lonja', 'Lj3P725T35' => 'lonja', 'Lj3P727T10' => 'lonja', 'Lj3P727T12' => 'lonja', 'Lj3P727T14' => 'lonja', 'Lj5g0023109' => 'lja', 'Lj6P646T44' => 'lonja', 'Lsat_1_v5_gn_6_75760' => 'lsa', 'Lsat_1_v5_gn_6_75800' => 'lsa', 'Lsat_1_v5_gn_6_75900' => 'lsa', 'Lsat_1_v5_gn_6_76240' => 'lsa', 'Lsat_1_v5_gn_6_76441' => 'lsa', 'Lsat_1_v5_gn_6_76700' => 'lsa', 'Lsat_1_v5_gn_6_76760' => 'lsa', 'Manes.15G033100' => 'mes', 'Mapoly0004s0074' => 'mpo', 'Mapoly0004s0075' => 'mpo', 'Mapoly0004s0163' => 'mpo', 'Mapoly0004s0164' => 'mpo', 'Mapoly0021s0018' => 'mpo', 'Mapoly0041s0136' => 'mpo', 'Mapoly0041s0137' => 'mpo', 'Mapoly0041s0138' => 'mpo', 'Mapoly0041s0139' => 'mpo', 'Mapoly0041s0141' => 'mpo', 'Mapoly0041s0142' => 'mpo', 'Mapoly0041s0143' => 'mpo', 'Mapoly0041s0144' => 'mpo', 'Mapoly0041s0145' => 'mpo', 'Mapoly0047s0106' => 'mpo', 'Mapoly0047s0108' => 'mpo', 'Mapoly0050s0051' => 'mpo', 'Mapoly0050s0052' => 'mpo', 'Mapoly0050s0053' => 'mpo', 'Mapoly0058s0013' => 'mpo', 'Mapoly0091s0078' => 'mpo', 'Mapoly0091s0079' => 'mpo', 'Mapoly0091s0080' => 'mpo', 'Mapoly0091s0081' => 'mpo', 'Mapoly0278s0004' => 'mpo', 'Mapoly0278s0005' => 'mpo', 'Mapoly0278s0006' => 'mpo', 'MBI11_g30648_MAGBIO' => 'mbi', 'MCO03G194' => 'mco', 'MCO03G590' => 'mco', 'MCO07G312' => 'mco', 'MCO10G318' => 'mco', 'MCO12G244' => 'mco', 'MCO13G148' => 'mco', 'MCO13G194' => 'mco', 'MCO16G238' => 'mco', 'MD06G1134100' => 'mdo', 'MD13G1200100' => 'mdo', 'MD13G1200300' => 'mdo', 'MD13G1200600' => 'mdo', 'MD14G1150400' => 'mdo', 'MD16G1200000' => 'mdo', 'Medtr1g102570' => 'mtr', 'Medtr1g102780' => 'mtr', 'Medtr1g102800' => 'mtr', 'Medtr1g102810' => 'mtr', 'Medtr1g102830' => 'mtr', 'MELO3C006499.2' => 'cme', 'Migut.G00385' => 'egut', 'MSTRG.4063' => 'ama', 'Nitab4.5_0000090g0260' => 'nta', 'Nitab4.5_0000977g0030' => 'nta', 'Nitab4.5_0002541g0040' => 'nta', 'Nitab4.5_0007068g0040' => 'nta', 'Nn005s41408' => 'nnu', 'Nn005s41410' => 'nnu', 'Oeu010310.1' => 'oeu', 'Oeu010311.1' => 'oeu', 'Oeu043472.1' => 'oeu', 'Os01g0246400' => 'osa', 'Os04g0267950' => 'osa', 'Os07g0178700' => 'osa', 'Os07g0178800' => 'osa', 'Peaxi162Scf00316g00046' => 'pax', 'Peaxi162Scf00316g00049' => 'pax', 'Peaxi162Scf00316g00059' => 'pax', 'Peaxi162Scf00316g00328' => 'pax', 'Peaxi162Scf00316g00329' => 'pax', 'Peaxi162Scf00316g00411' => 'pax', 'Peaxi162Scf00316g00521' => 'pax', 'Peaxi162Scf00492g00068' => 'pax', 'Peaxi162Scf35631g00002' => 'pax', 'PGR142G3720' => 'pgr', 'PGSC0003DMG400006442' => 'stu', 'Phvul.007G062000' => 'pvu', 'Potri.008G157750' => 'ptr', 'Potri.008G157900' => 'ptr', 'Potri.008G158000' => 'ptr', 'Potri.008G158200' => 'ptr', 'Pp3c11_7280' => 'ppa', 'Pp3c11_7980' => 'ppa', 'Pp3c12_19450' => 'ppa', 'Pp3c14_1480' => 'ppa', 'Pp3c14_1501' => 'ppa', 'Pp3c16_4900' => 'ppa', 'Pp3c16_5010' => 'ppa', 'Pp3c16_5060' => 'ppa', 'Pp3c19_18250' => 'ppa', 'Pp3c23_8530' => 'ppa', 'Pp3c23_8550' => 'ppa', 'Pp3c24_9670' => 'ppa', 'Pp3c2_21390' => 'ppa', 'Pp3c2_31380' => 'ppa', 'Pp3c3_16620' => 'ppa', 'Pp3c3_8090' => 'ppa', 'Pp3c3_8110' => 'ppa', 'Pp3c3_8130' => 'ppa', 'Pp3c3_8150' => 'ppa', 'Pp3c4_14320' => 'ppa', 'Pp3c6_2560' => 'ppa', 'Pp3c9_16700' => 'ppa', 'PRCOL_00000234' => 'pco', 'PRCOL_00000235' => 'pco', 'PRCOL_00000777' => 'pco', 'PRCOL_00002344' => 'pco', 'PRCOL_00002372' => 'pco', 'PRCOL_00006120' => 'pco', 'Prupe.1G021400' => 'ppe', 'Prupe.1G021500' => 'ppe', 'Prupe.1G021600' => 'ppe', 'Prupe.1G021700' => 'ppe', 'Prupe.1G021800' => 'ppe', 'Prupe.5G145100' => 'ppe', 'Psat6g204040' => 'psa', 'Psat6g204800' => 'psa', 'Psat6g204920' => 'psa', 'Psat6g204960' => 'psa', 'Psat6g205080' => 'psa', 'PSO017G0271' => 'pso', 'PSO017G1276' => 'pso', 'PSO017G1429' => 'pso', 'PSO017G1861' => 'pso', 'PSO017G2787' => 'pso', 'PSO017G4466' => 'pso', 'PSO017G5118' => 'pso', 'PSO017G5420' => 'pso', 'PSO063G3678' => 'pso', 'PSO210G0546' => 'pso', 'PSO317G0001' => 'pso', 'PSO357G0512' => 'pso', 'PSO478G2682' => 'pso', 'PSO647G0001' => 'pso', 'PSO675G0001' => 'pso', 'PSO675G2699' => 'pso', 'PSO675G2849' => 'pso', 'PSO675G4991' => 'pso', 'PSO689G0001' => 'pso', 'QL06p000916' => 'qlo', 'QL06p000921' => 'qlo', 'QL06p001398' => 'qlo', 'QL06p001407' => 'qlo', 'QL06p002031' => 'qlo', 'RcHm_v2.0_Chr4g0387791' => 'rch', 'RcHm_v2.0_Chr4g0387801' => 'rch', 'RcHm_v2.0_Chr6g0286501' => 'rch', 'RcHm_v2.0_Chr6g0286511' => 'rch', 'RcHm_v2.0_Chr6g0286521' => 'rch', 'RcHm_v2.0_Chr6g0286531' => 'rch', 'RcHm_v2.0_Chr7g0189141' => 'rch', 'Rhsim02G0028700' => 'rsi', 'Rhsim02G0028800' => 'rsi', 'Rhsim02G0028900' => 'rsi', 'Rhsim02G0029000' => 'rsi', 'Rhsim02G0029100' => 'rsi', 'Rhsim02G0029200' => 'rsi', 'Rhsim02G0029300' => 'rsi', 'Rhsim02G0029400' => 'rsi', 'Rhsim02G0029500' => 'rsi', 'Rhsim02G0029600' => 'rsi', 'RhsimUnG0024000' => 'rsi', 'RhsimUnG0024100' => 'rsi', 'RhsimUnG0024200' => 'rsi', 'RhsimUnG0024300' => 'rsi', 'RhsimUnG0024400' => 'rsi', 'RhsimUnG0024500' => 'rsi', 'RhsimUnG0024700' => 'rsi', 'RhsimUnG0024800' => 'rsi', 'RhsimUnG0024900' => 'rsi', 'RhsimUnG0025100' => 'rsi', 'Sabra08G0120200' => 'sbr', 'Sabra08G0120300' => 'sbr', 'Sabra08G0120500' => 'sbr', 'Sabra08G0120600' => 'sbr', 'Sabra10G0158900' => 'sbr', 'SalBow2G3492' => 'sbo', 'Sc13g0004760' => 'sci', 'Sc13g0004770' => 'sci', 'Sed0003417' => 'sed', 'Sed0019750' => 'sed', 'SEGI_03419' => 'sgi', 'SEGI_05907' => 'sgi', 'SEGI_10682' => 'sgi', 'SEGI_13528' => 'sgi', 'SEGI_16081' => 'sgi', 'SEGI_19370' => 'sgi', 'SEGI_21015' => 'sgi', 'SEGI_21944' => 'sgi', 'SEGI_32906' => 'sgi', 'SEGI_33093' => 'sgi', 'SEGI_36110' => 'sgi', 'SEGI_40397' => 'sgi', 'SGA_v2.0_scaffold191G40426' => 'sas', 'SGA_v2.0_scaffold353G49717' => 'sas', 'SGA_v2.0_scaffold50G18550' => 'sas', 'SMO119G0173' => 'smo', 'SMO172G0002' => 'smo', 'Solyc09g082690.3' => 'sly', 'Solyc09g082700.2' => 'sly', 'Sopen09g031550' => 'spe', 'Sopen09g031560' => 'spe', 'Sp3g20540' => 'spa', 'Sp7g07580' => 'spa', 'TAR134G0002' => 'tar', 'TAR236G0001' => 'tar', 'TAR365G0892' => 'tar', 'TAR636G0166' => 'tar', 'TAR636G0646' => 'tar', 'TAR636G0869' => 'tar', 'TAR636G1317' => 'tar', 'TAR636G1744' => 'tar', 'TAR636G3358' => 'tar', 'TAR636G3436' => 'tar', 'THA.LOC104803047' => 'tha', 'Thecc.04G238900' => 'tca', 'Thhalv10021557m.g' => 'esa', 'Thhalv10026318m.g' => 'esa', 'Thhalv10026335m.g' => 'esa', 'TPR.G17433' => 'tpr', 'TPR.G18915' => 'tpr', 'TPR.G26125' => 'tpr', 'TWI09G0677' => 'twi', 'TWI73G0287' => 'twi', 'unitig_748.g8326' => 'ugi', 'vmacro15370' => 'vma', 'vmacro15371' => 'vma', 'vmacro15372' => 'vma', 'vmacro15373' => 'vma', 'vmacro15374' => 'vma', 'VMungo0720G2826' => 'vmu', 'Zm00001eb116960' => 'zma', 'Zm00001eb301260' => 'zma', 'Zm00001eb301270' => 'zma' ), 'gf_id' => 'HOM05D001460', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001460' ), 'data_identifier' => 'HOM05D001460', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001460', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '433', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p22980' => 'bna', 'A01p32340' => 'bna', 'A03p42970' => 'bna', 'A05p25880' => 'bna', 'Aa31LG8G9320' => 'aar', 'Aa31LG8G9330' => 'aar', 'Aa31LG8G9340' => 'aar', 'Aa31sc221G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1034' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1528' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.829' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2222' => 'aag', 'Ah.12g058830' => 'amhyb', 'Ah.12g058840' => 'amhyb', 'AL3G37160' => 'aly', 'AL7G41310' => 'aly', 'Aqoxy5G00395' => 'aox', 'Aqoxy5G00396' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0C8NZA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5185HY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JZ1PRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MD3LS0' => 'arhy', 'AT3G22840' => 'ath', 'AT4G14690' => 'ath', 'ATR0665G054' => 'atr', 'Atru.chr4.2344' => 'acertr', 'Atru.chr4.2346' => 'acertr', 'Atru.chr4.2347' => 'acertr', 'Atru.chr4.2348' => 'acertr', 'Atru.chr4.2355' => 'acertr', 'Atru.chr4.2356' => 'acertr', 'Atru.chr4.2358' => 'acertr', 'Atru.chr4.2359' => 'acertr', 'Atru.chr4.2360' => 'acertr', 'Atru.chr4.2361' => 'acertr', 'AUR62030476' => 'cqu', 'AUR62030478' => 'cqu', 'AUR62030819' => 'cqu', 'AUR62030820' => 'cqu', 'BcaB03g14648' => 'bca', 'BcaB04g20492' => 'bca', 'BcaB06g26399' => 'bca', 'BcaC01g03416' => 'bca', 'BcaC01g03419' => 'bca', 'BcaC01g03421' => 'bca', 'BcaC01g03424' => 'bca', 'BcaC05g28012' => 'bca', 'BcaC09g49212' => 'bca', 'BcaC09g50140' => 'bca', 'BcaNung00346' => 'bca', 'BolC1t02785H' => 'bol', 'BolC1t04095H' => 'bol', 'BolC3t17545H' => 'bol', 'BolC5t32769H' => 'bol', 'BraA01t02211Z' => 'bra', 'BraA01t03359Z' => 'bra', 'BraA03t13441Z' => 'bra', 'BraA05t21476Z' => 'bra', 'C01p28420' => 'bna', 'C01p41350' => 'bna', 'C03p52750' => 'bna', 'C03p52780' => 'bna', 'C05p40270' => 'bna', 'CAN.G1437.9' => 'can', 'CANSAT78G0035' => 'cansat', 'CANSAT78G1036' => 'cansat', 'CANSAT78G2272' => 'cansat', 'CANSAT78G2478' => 'cansat', 'CARHR098700' => 'chi', 'CARHR221120' => 'chi', 'CARHR221150' => 'chi', 'Carub.0003s2297' => 'cru', 'Carub.0007s2749' => 'cru', 'Carub.0007s2750' => 'cru', 'Carub.0007s2751' => 'cru', 'Ca_10849_v3' => 'car', 'Cc03_g04300' => 'ccan', 'CDE02G3648' => 'cde', 'CDE05G0060' => 'cde', 'CDE05G0692' => 'cde', 'CDE05G2285' => 'cde', 'CDE05G2884' => 'cde', 'CDE05G3072' => 'cde', 'Cfa008439' => 'cfa', 'Cfa008441' => 'cfa', 'Cfa008443' => 'cfa', 'Cfa008448' => 'cfa', 'Ciclev10005974m.g' => 'ccl', 'Ciclev10006006m.g' => 'ccl', 'Ciclev10006775m.g' => 'ccl', 'CiPaw.02G120400' => 'cil', 'CiPaw.02G120500' => 'cil', 'CiPaw.02G120600' => 'cil', 'ClCG05G004850' => 'cla', 'COL.COLO4_21566' => 'col', 'Cpa.g.sc44.124' => 'cpa', 'Cre07.g320400' => 'cre', 'Cre07.g320450' => 'cre', 'Cre08.g384650' => 'cre', 'Cre09.g393173' => 'cre', 'Cre09.g394325' => 'cre', 'Cre14.g626750' => 'cre', 'Cre16.g679250' => 'cre', 'CsaV3_3G012890' => 'csa', 'CSS0010865' => 'camsi', 'CSS0044338' => 'camsi', 'DCAR_002366' => 'dca', 'DCAR_030687' => 'dca', 'DCAR_030688' => 'dca', 'Dinv14047' => 'din', 'Dinv14048' => 'din', 'Duzib151G0105' => 'dzi', 'Duzib151G0114' => 'dzi', 'Duzib212G1029' => 'dzi', 'ECA232G3536' => 'eca', 'ECA240G0786' => 'eca', 'ECA240G1802' => 'eca', 'ECA240G3760' => 'eca', 'ECA240G3920' => 'eca', 'EL10Ac5g12536' => 'bvu', 'EL10Ac5g12537' => 'bvu', 'EL10Ac5g12538' => 'bvu', 'Eucgr.B01004' => 'egr', 'Eucgr.B01006' => 'egr', 'Eucgr.B01007' => 'egr', 'Eucgr.B01008' => 'egr', 'Eucgr.B01895' => 'egr', 'Eucgr.B01896' => 'egr', 'FAN04G1456' => 'fan', 'FAN08G1769' => 'fan', 'FAN08G2160' => 'fan', 'FAN13G2403' => 'fan', 'FAN13G3303' => 'fan', 'FAN15G2435' => 'fan', 'FAN17G0672' => 'fan', 'FAN17G2441' => 'fan', 'FAN18G1024' => 'fan', 'FAN22G1458' => 'fan', 'FAN24G0037' => 'fan', 'FAN24G0429' => 'fan', 'FAN24G2387' => 'fan', 'FAN27G2746' => 'fan', 'FvH4_2g20400' => 'fve', 'FvH4_2g20420' => 'fve', 'FvH4_2g20430' => 'fve', 'FvH4_4g01270' => 'fve', 'FvH4_4g01290' => 'fve', 'FvH4_4g01300' => 'fve', 'FvH4_4g01310' => 'fve', 'FvH4_4g01330' => 'fve', 'FvH4_5g09070' => 'fve', 'Glyma.10G243800' => 'gma', 'Glyma.20G150600' => 'gma', 'Gohir.A09G219200' => 'ghi', 'Gohir.A09G219300' => 'ghi', 'Gohir.D09G221400' => 'ghi', 'Gohir.D09G221500' => 'ghi', 'Gorai.006G242600' => 'gra', 'Gorai.006G242700' => 'gra', 'GSVIVG01018044001' => 'vvi', 'HanXRQChr03g0083821' => 'han', 'HanXRQChr03g0083841' => 'han', 'HanXRQChr03g0083881' => 'han', 'HanXRQChr03g0083901' => 'han', 'HanXRQChr03g0083921' => 'han', 'HanXRQChr03g0085331' => 'han', 'HanXRQChr03g0085361' => 'han', 'HanXRQChr03g0085411' => 'han', 'HanXRQChr03g0085421' => 'han', 'HanXRQChr03g0085431' => 'han', 'HanXRQChr08g0221991' => 'han', 'HanXRQChr11g0336061' => 'han', 'HanXRQChr11g0336411' => 'han', 'Haze_11234' => 'cav', 'Hma1.2p1_0549F.1_g177010' => 'hma', 'Hma1.2p1_0602F.1_g187630' => 'hma', 'Hund14876' => 'sun', 'Hund14879' => 'sun', 'Lalb_Chr06g0160741' => 'lal', 'Lalb_Chr21g0304781' => 'lal', 'Lj3A726G19' => 'lonja', 'Lj3A726T23' => 'lonja', 'Lj3A726T24' => 'lonja', 'Lj3A726T25' => 'lonja', 'Lj3A727T17' => 'lonja', 'Lj3C726T0' => 'lonja', 'Lj3C726T2' => 'lonja', 'Lj3P725T35' => 'lonja', 'Lj3P727T10' => 'lonja', 'Lj3P727T12' => 'lonja', 'Lj3P727T14' => 'lonja', 'Lj5g0023109' => 'lja', 'Lj6P646T44' => 'lonja', 'Lsat_1_v5_gn_6_75760' => 'lsa', 'Lsat_1_v5_gn_6_75800' => 'lsa', 'Lsat_1_v5_gn_6_75900' => 'lsa', 'Lsat_1_v5_gn_6_76240' => 'lsa', 'Lsat_1_v5_gn_6_76441' => 'lsa', 'Lsat_1_v5_gn_6_76700' => 'lsa', 'Lsat_1_v5_gn_6_76760' => 'lsa', 'Manes.15G033100' => 'mes', 'Mapoly0004s0074' => 'mpo', 'Mapoly0004s0075' => 'mpo', 'Mapoly0004s0163' => 'mpo', 'Mapoly0004s0164' => 'mpo', 'Mapoly0021s0018' => 'mpo', 'Mapoly0041s0136' => 'mpo', 'Mapoly0041s0137' => 'mpo', 'Mapoly0041s0138' => 'mpo', 'Mapoly0041s0139' => 'mpo', 'Mapoly0041s0141' => 'mpo', 'Mapoly0041s0142' => 'mpo', 'Mapoly0041s0143' => 'mpo', 'Mapoly0041s0144' => 'mpo', 'Mapoly0041s0145' => 'mpo', 'Mapoly0047s0106' => 'mpo', 'Mapoly0047s0108' => 'mpo', 'Mapoly0050s0051' => 'mpo', 'Mapoly0050s0052' => 'mpo', 'Mapoly0050s0053' => 'mpo', 'Mapoly0058s0013' => 'mpo', 'Mapoly0091s0078' => 'mpo', 'Mapoly0091s0079' => 'mpo', 'Mapoly0091s0080' => 'mpo', 'Mapoly0091s0081' => 'mpo', 'Mapoly0278s0004' => 'mpo', 'Mapoly0278s0005' => 'mpo', 'Mapoly0278s0006' => 'mpo', 'MBI11_g30648_MAGBIO' => 'mbi', 'MCO03G194' => 'mco', 'MCO03G590' => 'mco', 'MCO07G312' => 'mco', 'MCO10G318' => 'mco', 'MCO12G244' => 'mco', 'MCO13G148' => 'mco', 'MCO13G194' => 'mco', 'MCO16G238' => 'mco', 'MD06G1134100' => 'mdo', 'MD13G1200100' => 'mdo', 'MD13G1200300' => 'mdo', 'MD13G1200600' => 'mdo', 'MD14G1150400' => 'mdo', 'MD16G1200000' => 'mdo', 'Medtr1g102570' => 'mtr', 'Medtr1g102780' => 'mtr', 'Medtr1g102800' => 'mtr', 'Medtr1g102810' => 'mtr', 'Medtr1g102830' => 'mtr', 'MELO3C006499.2' => 'cme', 'Migut.G00385' => 'egut', 'MSTRG.4063' => 'ama', 'Nitab4.5_0000090g0260' => 'nta', 'Nitab4.5_0000977g0030' => 'nta', 'Nitab4.5_0002541g0040' => 'nta', 'Nitab4.5_0007068g0040' => 'nta', 'Nn005s41408' => 'nnu', 'Nn005s41410' => 'nnu', 'Oeu010310.1' => 'oeu', 'Oeu010311.1' => 'oeu', 'Oeu043472.1' => 'oeu', 'Os01g0246400' => 'osa', 'Os04g0267950' => 'osa', 'Os07g0178700' => 'osa', 'Os07g0178800' => 'osa', 'Peaxi162Scf00316g00046' => 'pax', 'Peaxi162Scf00316g00049' => 'pax', 'Peaxi162Scf00316g00059' => 'pax', 'Peaxi162Scf00316g00328' => 'pax', 'Peaxi162Scf00316g00329' => 'pax', 'Peaxi162Scf00316g00411' => 'pax', 'Peaxi162Scf00316g00521' => 'pax', 'Peaxi162Scf00492g00068' => 'pax', 'Peaxi162Scf35631g00002' => 'pax', 'PGR142G3720' => 'pgr', 'PGSC0003DMG400006442' => 'stu', 'Phvul.007G062000' => 'pvu', 'Potri.008G157750' => 'ptr', 'Potri.008G157900' => 'ptr', 'Potri.008G158000' => 'ptr', 'Potri.008G158200' => 'ptr', 'Pp3c11_7280' => 'ppa', 'Pp3c11_7980' => 'ppa', 'Pp3c12_19450' => 'ppa', 'Pp3c14_1480' => 'ppa', 'Pp3c14_1501' => 'ppa', 'Pp3c16_4900' => 'ppa', 'Pp3c16_5010' => 'ppa', 'Pp3c16_5060' => 'ppa', 'Pp3c19_18250' => 'ppa', 'Pp3c23_8530' => 'ppa', 'Pp3c23_8550' => 'ppa', 'Pp3c24_9670' => 'ppa', 'Pp3c2_21390' => 'ppa', 'Pp3c2_31380' => 'ppa', 'Pp3c3_16620' => 'ppa', 'Pp3c3_8090' => 'ppa', 'Pp3c3_8110' => 'ppa', 'Pp3c3_8130' => 'ppa', 'Pp3c3_8150' => 'ppa', 'Pp3c4_14320' => 'ppa', 'Pp3c6_2560' => 'ppa', 'Pp3c9_16700' => 'ppa', 'PRCOL_00000234' => 'pco', 'PRCOL_00000235' => 'pco', 'PRCOL_00000777' => 'pco', 'PRCOL_00002344' => 'pco', 'PRCOL_00002372' => 'pco', 'PRCOL_00006120' => 'pco', 'Prupe.1G021400' => 'ppe', 'Prupe.1G021500' => 'ppe', 'Prupe.1G021600' => 'ppe', 'Prupe.1G021700' => 'ppe', 'Prupe.1G021800' => 'ppe', 'Prupe.5G145100' => 'ppe', 'Psat6g204040' => 'psa', 'Psat6g204800' => 'psa', 'Psat6g204920' => 'psa', 'Psat6g204960' => 'psa', 'Psat6g205080' => 'psa', 'PSO017G0271' => 'pso', 'PSO017G1276' => 'pso', 'PSO017G1429' => 'pso', 'PSO017G1861' => 'pso', 'PSO017G2787' => 'pso', 'PSO017G4466' => 'pso', 'PSO017G5118' => 'pso', 'PSO017G5420' => 'pso', 'PSO063G3678' => 'pso', 'PSO210G0546' => 'pso', 'PSO317G0001' => 'pso', 'PSO357G0512' => 'pso', 'PSO478G2682' => 'pso', 'PSO647G0001' => 'pso', 'PSO675G0001' => 'pso', 'PSO675G2699' => 'pso', 'PSO675G2849' => 'pso', 'PSO675G4991' => 'pso', 'PSO689G0001' => 'pso', 'QL06p000916' => 'qlo', 'QL06p000921' => 'qlo', 'QL06p001398' => 'qlo', 'QL06p001407' => 'qlo', 'QL06p002031' => 'qlo', 'RcHm_v2.0_Chr4g0387791' => 'rch', 'RcHm_v2.0_Chr4g0387801' => 'rch', 'RcHm_v2.0_Chr6g0286501' => 'rch', 'RcHm_v2.0_Chr6g0286511' => 'rch', 'RcHm_v2.0_Chr6g0286521' => 'rch', 'RcHm_v2.0_Chr6g0286531' => 'rch', 'RcHm_v2.0_Chr7g0189141' => 'rch', 'Rhsim02G0028700' => 'rsi', 'Rhsim02G0028800' => 'rsi', 'Rhsim02G0028900' => 'rsi', 'Rhsim02G0029000' => 'rsi', 'Rhsim02G0029100' => 'rsi', 'Rhsim02G0029200' => 'rsi', 'Rhsim02G0029300' => 'rsi', 'Rhsim02G0029400' => 'rsi', 'Rhsim02G0029500' => 'rsi', 'Rhsim02G0029600' => 'rsi', 'RhsimUnG0024000' => 'rsi', 'RhsimUnG0024100' => 'rsi', 'RhsimUnG0024200' => 'rsi', 'RhsimUnG0024300' => 'rsi', 'RhsimUnG0024400' => 'rsi', 'RhsimUnG0024500' => 'rsi', 'RhsimUnG0024700' => 'rsi', 'RhsimUnG0024800' => 'rsi', 'RhsimUnG0024900' => 'rsi', 'RhsimUnG0025100' => 'rsi', 'Sabra08G0120200' => 'sbr', 'Sabra08G0120300' => 'sbr', 'Sabra08G0120500' => 'sbr', 'Sabra08G0120600' => 'sbr', 'Sabra10G0158900' => 'sbr', 'SalBow2G3492' => 'sbo', 'Sc13g0004760' => 'sci', 'Sc13g0004770' => 'sci', 'Sed0003417' => 'sed', 'Sed0019750' => 'sed', 'SEGI_03419' => 'sgi', 'SEGI_05907' => 'sgi', 'SEGI_10682' => 'sgi', 'SEGI_13528' => 'sgi', 'SEGI_16081' => 'sgi', 'SEGI_19370' => 'sgi', 'SEGI_21015' => 'sgi', 'SEGI_21944' => 'sgi', 'SEGI_32906' => 'sgi', 'SEGI_33093' => 'sgi', 'SEGI_36110' => 'sgi', 'SEGI_40397' => 'sgi', 'SGA_v2.0_scaffold191G40426' => 'sas', 'SGA_v2.0_scaffold353G49717' => 'sas', 'SGA_v2.0_scaffold50G18550' => 'sas', 'SMO119G0173' => 'smo', 'SMO172G0002' => 'smo', 'Solyc09g082690.3' => 'sly', 'Solyc09g082700.2' => 'sly', 'Sopen09g031550' => 'spe', 'Sopen09g031560' => 'spe', 'Sp3g20540' => 'spa', 'Sp7g07580' => 'spa', 'TAR134G0002' => 'tar', 'TAR236G0001' => 'tar', 'TAR365G0892' => 'tar', 'TAR636G0166' => 'tar', 'TAR636G0646' => 'tar', 'TAR636G0869' => 'tar', 'TAR636G1317' => 'tar', 'TAR636G1744' => 'tar', 'TAR636G3358' => 'tar', 'TAR636G3436' => 'tar', 'THA.LOC104803047' => 'tha', 'Thecc.04G238900' => 'tca', 'Thhalv10021557m.g' => 'esa', 'Thhalv10026318m.g' => 'esa', 'Thhalv10026335m.g' => 'esa', 'TPR.G17433' => 'tpr', 'TPR.G18915' => 'tpr', 'TPR.G26125' => 'tpr', 'TWI09G0677' => 'twi', 'TWI73G0287' => 'twi', 'unitig_748.g8326' => 'ugi', 'vmacro15370' => 'vma', 'vmacro15371' => 'vma', 'vmacro15372' => 'vma', 'vmacro15373' => 'vma', 'vmacro15374' => 'vma', 'VMungo0720G2826' => 'vmu', 'Zm00001eb116960' => 'zma', 'Zm00001eb301260' => 'zma', 'Zm00001eb301270' => 'zma' ) $gf_id = 'HOM05D001460' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001460' ) $data_identifier = 'HOM05D001460' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 4, 'aag' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 2, 'aox' => (int) 2, 'arhy' => (int) 4, 'ath' => (int) 2, 'atr' => (int) 1, 'acertr' => (int) 10, 'cqu' => (int) 4, 'bca' => (int) 11, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 1, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 1, 'ccan' => (int) 1, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 1, 'col' => (int) 1, 'cpa' => (int) 1, 'cre' => (int) 7, 'csa' => (int) 1, 'camsi' => (int) 2, 'dca' => (int) 3, 'din' => (int) 2, 'dzi' => (int) 3, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 14, 'fve' => (int) 9, 'gma' => (int) 2, 'ghi' => (int) 4, 'gra' => (int) 2, 'vvi' => (int) 1, 'han' => (int) 13, 'cav' => (int) 1, 'hma' => (int) 2, 'sun' => (int) 2, 'lal' => (int) 2, 'lonja' => (int) 12, 'lja' => (int) 1, 'lsa' => (int) 7, 'mes' => (int) 1, 'mpo' => (int) 27, 'mbi' => (int) 1, 'mco' => (int) 8, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 1, 'egut' => (int) 1, 'ama' => (int) 1, 'nta' => (int) 4, 'nnu' => (int) 2, 'oeu' => (int) 3, 'osa' => (int) 4, 'pax' => (int) 9, 'pgr' => (int) 1, 'stu' => (int) 1, 'pvu' => (int) 1, 'ptr' => (int) 4, 'ppa' => (int) 22, 'pco' => (int) 6, 'ppe' => (int) 6, 'psa' => (int) 5, 'pso' => (int) 19, 'qlo' => (int) 5, 'rch' => (int) 7, 'rsi' => (int) 20, 'sbr' => (int) 5, 'sbo' => (int) 1, 'sci' => (int) 2, 'sed' => (int) 2, 'sgi' => (int) 12, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 2, 'tar' => (int) 10, 'tha' => (int) 1, 'tca' => (int) 1, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 2, 'ugi' => (int) 1, 'vma' => (int) 5, 'vmu' => (int) 1, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb301270' $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' => 'HOM05D001460', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '433', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p22980' => 'bna', 'A01p32340' => 'bna', 'A03p42970' => 'bna', 'A05p25880' => 'bna', 'Aa31LG8G9320' => 'aar', 'Aa31LG8G9330' => 'aar', 'Aa31LG8G9340' => 'aar', 'Aa31sc221G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1034' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1528' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.829' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2222' => 'aag', 'Ah.12g058830' => 'amhyb', 'Ah.12g058840' => 'amhyb', 'AL3G37160' => 'aly', 'AL7G41310' => 'aly', 'Aqoxy5G00395' => 'aox', 'Aqoxy5G00396' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0C8NZA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5185HY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JZ1PRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MD3LS0' => 'arhy', 'AT3G22840' => 'ath', 'AT4G14690' => 'ath', 'ATR0665G054' => 'atr', 'Atru.chr4.2344' => 'acertr', 'Atru.chr4.2346' => 'acertr', 'Atru.chr4.2347' => 'acertr', 'Atru.chr4.2348' => 'acertr', 'Atru.chr4.2355' => 'acertr', 'Atru.chr4.2356' => 'acertr', 'Atru.chr4.2358' => 'acertr', 'Atru.chr4.2359' => 'acertr', 'Atru.chr4.2360' => 'acertr', 'Atru.chr4.2361' => 'acertr', 'AUR62030476' => 'cqu', 'AUR62030478' => 'cqu', 'AUR62030819' => 'cqu', 'AUR62030820' => 'cqu', 'BcaB03g14648' => 'bca', 'BcaB04g20492' => 'bca', 'BcaB06g26399' => 'bca', 'BcaC01g03416' => 'bca', 'BcaC01g03419' => 'bca', 'BcaC01g03421' => 'bca', 'BcaC01g03424' => 'bca', 'BcaC05g28012' => 'bca', 'BcaC09g49212' => 'bca', 'BcaC09g50140' => 'bca', 'BcaNung00346' => 'bca', 'BolC1t02785H' => 'bol', 'BolC1t04095H' => 'bol', 'BolC3t17545H' => 'bol', 'BolC5t32769H' => 'bol', 'BraA01t02211Z' => 'bra', 'BraA01t03359Z' => 'bra', 'BraA03t13441Z' => 'bra', 'BraA05t21476Z' => 'bra', 'C01p28420' => 'bna', 'C01p41350' => 'bna', 'C03p52750' => 'bna', 'C03p52780' => 'bna', 'C05p40270' => 'bna', 'CAN.G1437.9' => 'can', 'CANSAT78G0035' => 'cansat', 'CANSAT78G1036' => 'cansat', 'CANSAT78G2272' => 'cansat', 'CANSAT78G2478' => 'cansat', 'CARHR098700' => 'chi', 'CARHR221120' => 'chi', 'CARHR221150' => 'chi', 'Carub.0003s2297' => 'cru', 'Carub.0007s2749' => 'cru', 'Carub.0007s2750' => 'cru', 'Carub.0007s2751' => 'cru', 'Ca_10849_v3' => 'car', 'Cc03_g04300' => 'ccan', 'CDE02G3648' => 'cde', 'CDE05G0060' => 'cde', 'CDE05G0692' => 'cde', 'CDE05G2285' => 'cde', 'CDE05G2884' => 'cde', 'CDE05G3072' => 'cde', 'Cfa008439' => 'cfa', 'Cfa008441' => 'cfa', 'Cfa008443' => 'cfa', 'Cfa008448' => 'cfa', 'Ciclev10005974m.g' => 'ccl', 'Ciclev10006006m.g' => 'ccl', 'Ciclev10006775m.g' => 'ccl', 'CiPaw.02G120400' => 'cil', 'CiPaw.02G120500' => 'cil', 'CiPaw.02G120600' => 'cil', 'ClCG05G004850' => 'cla', 'COL.COLO4_21566' => 'col', 'Cpa.g.sc44.124' => 'cpa', 'Cre07.g320400' => 'cre', 'Cre07.g320450' => 'cre', 'Cre08.g384650' => 'cre', 'Cre09.g393173' => 'cre', 'Cre09.g394325' => 'cre', 'Cre14.g626750' => 'cre', 'Cre16.g679250' => 'cre', 'CsaV3_3G012890' => 'csa', 'CSS0010865' => 'camsi', 'CSS0044338' => 'camsi', 'DCAR_002366' => 'dca', 'DCAR_030687' => 'dca', 'DCAR_030688' => 'dca', 'Dinv14047' => 'din', 'Dinv14048' => 'din', 'Duzib151G0105' => 'dzi', 'Duzib151G0114' => 'dzi', 'Duzib212G1029' => 'dzi', 'ECA232G3536' => 'eca', 'ECA240G0786' => 'eca', 'ECA240G1802' => 'eca', 'ECA240G3760' => 'eca', 'ECA240G3920' => 'eca', 'EL10Ac5g12536' => 'bvu', 'EL10Ac5g12537' => 'bvu', 'EL10Ac5g12538' => 'bvu', 'Eucgr.B01004' => 'egr', 'Eucgr.B01006' => 'egr', 'Eucgr.B01007' => 'egr', 'Eucgr.B01008' => 'egr', 'Eucgr.B01895' => 'egr', 'Eucgr.B01896' => 'egr', 'FAN04G1456' => 'fan', 'FAN08G1769' => 'fan', 'FAN08G2160' => 'fan', 'FAN13G2403' => 'fan', 'FAN13G3303' => 'fan', 'FAN15G2435' => 'fan', 'FAN17G0672' => 'fan', 'FAN17G2441' => 'fan', 'FAN18G1024' => 'fan', 'FAN22G1458' => 'fan', 'FAN24G0037' => 'fan', 'FAN24G0429' => 'fan', 'FAN24G2387' => 'fan', 'FAN27G2746' => 'fan', 'FvH4_2g20400' => 'fve', 'FvH4_2g20420' => 'fve', 'FvH4_2g20430' => 'fve', 'FvH4_4g01270' => 'fve', 'FvH4_4g01290' => 'fve', 'FvH4_4g01300' => 'fve', 'FvH4_4g01310' => 'fve', 'FvH4_4g01330' => 'fve', 'FvH4_5g09070' => 'fve', 'Glyma.10G243800' => 'gma', 'Glyma.20G150600' => 'gma', 'Gohir.A09G219200' => 'ghi', 'Gohir.A09G219300' => 'ghi', 'Gohir.D09G221400' => 'ghi', 'Gohir.D09G221500' => 'ghi', 'Gorai.006G242600' => 'gra', 'Gorai.006G242700' => 'gra', 'GSVIVG01018044001' => 'vvi', 'HanXRQChr03g0083821' => 'han', 'HanXRQChr03g0083841' => 'han', 'HanXRQChr03g0083881' => 'han', 'HanXRQChr03g0083901' => 'han', 'HanXRQChr03g0083921' => 'han', 'HanXRQChr03g0085331' => 'han', 'HanXRQChr03g0085361' => 'han', 'HanXRQChr03g0085411' => 'han', 'HanXRQChr03g0085421' => 'han', 'HanXRQChr03g0085431' => 'han', 'HanXRQChr08g0221991' => 'han', 'HanXRQChr11g0336061' => 'han', 'HanXRQChr11g0336411' => 'han', 'Haze_11234' => 'cav', 'Hma1.2p1_0549F.1_g177010' => 'hma', 'Hma1.2p1_0602F.1_g187630' => 'hma', 'Hund14876' => 'sun', 'Hund14879' => 'sun', 'Lalb_Chr06g0160741' => 'lal', 'Lalb_Chr21g0304781' => 'lal', 'Lj3A726G19' => 'lonja', 'Lj3A726T23' => 'lonja', 'Lj3A726T24' => 'lonja', 'Lj3A726T25' => 'lonja', 'Lj3A727T17' => 'lonja', 'Lj3C726T0' => 'lonja', 'Lj3C726T2' => 'lonja', 'Lj3P725T35' => 'lonja', 'Lj3P727T10' => 'lonja', 'Lj3P727T12' => 'lonja', 'Lj3P727T14' => 'lonja', 'Lj5g0023109' => 'lja', 'Lj6P646T44' => 'lonja', 'Lsat_1_v5_gn_6_75760' => 'lsa', 'Lsat_1_v5_gn_6_75800' => 'lsa', 'Lsat_1_v5_gn_6_75900' => 'lsa', 'Lsat_1_v5_gn_6_76240' => 'lsa', 'Lsat_1_v5_gn_6_76441' => 'lsa', 'Lsat_1_v5_gn_6_76700' => 'lsa', 'Lsat_1_v5_gn_6_76760' => 'lsa', 'Manes.15G033100' => 'mes', 'Mapoly0004s0074' => 'mpo', 'Mapoly0004s0075' => 'mpo', 'Mapoly0004s0163' => 'mpo', 'Mapoly0004s0164' => 'mpo', 'Mapoly0021s0018' => 'mpo', 'Mapoly0041s0136' => 'mpo', 'Mapoly0041s0137' => 'mpo', 'Mapoly0041s0138' => 'mpo', 'Mapoly0041s0139' => 'mpo', 'Mapoly0041s0141' => 'mpo', 'Mapoly0041s0142' => 'mpo', 'Mapoly0041s0143' => 'mpo', 'Mapoly0041s0144' => 'mpo', 'Mapoly0041s0145' => 'mpo', 'Mapoly0047s0106' => 'mpo', 'Mapoly0047s0108' => 'mpo', 'Mapoly0050s0051' => 'mpo', 'Mapoly0050s0052' => 'mpo', 'Mapoly0050s0053' => 'mpo', 'Mapoly0058s0013' => 'mpo', 'Mapoly0091s0078' => 'mpo', 'Mapoly0091s0079' => 'mpo', 'Mapoly0091s0080' => 'mpo', 'Mapoly0091s0081' => 'mpo', 'Mapoly0278s0004' => 'mpo', 'Mapoly0278s0005' => 'mpo', 'Mapoly0278s0006' => 'mpo', 'MBI11_g30648_MAGBIO' => 'mbi', 'MCO03G194' => 'mco', 'MCO03G590' => 'mco', 'MCO07G312' => 'mco', 'MCO10G318' => 'mco', 'MCO12G244' => 'mco', 'MCO13G148' => 'mco', 'MCO13G194' => 'mco', 'MCO16G238' => 'mco', 'MD06G1134100' => 'mdo', 'MD13G1200100' => 'mdo', 'MD13G1200300' => 'mdo', 'MD13G1200600' => 'mdo', 'MD14G1150400' => 'mdo', 'MD16G1200000' => 'mdo', 'Medtr1g102570' => 'mtr', 'Medtr1g102780' => 'mtr', 'Medtr1g102800' => 'mtr', 'Medtr1g102810' => 'mtr', 'Medtr1g102830' => 'mtr', 'MELO3C006499.2' => 'cme', 'Migut.G00385' => 'egut', 'MSTRG.4063' => 'ama', 'Nitab4.5_0000090g0260' => 'nta', 'Nitab4.5_0000977g0030' => 'nta', 'Nitab4.5_0002541g0040' => 'nta', 'Nitab4.5_0007068g0040' => 'nta', 'Nn005s41408' => 'nnu', 'Nn005s41410' => 'nnu', 'Oeu010310.1' => 'oeu', 'Oeu010311.1' => 'oeu', 'Oeu043472.1' => 'oeu', 'Os01g0246400' => 'osa', 'Os04g0267950' => 'osa', 'Os07g0178700' => 'osa', 'Os07g0178800' => 'osa', 'Peaxi162Scf00316g00046' => 'pax', 'Peaxi162Scf00316g00049' => 'pax', 'Peaxi162Scf00316g00059' => 'pax', 'Peaxi162Scf00316g00328' => 'pax', 'Peaxi162Scf00316g00329' => 'pax', 'Peaxi162Scf00316g00411' => 'pax', 'Peaxi162Scf00316g00521' => 'pax', 'Peaxi162Scf00492g00068' => 'pax', 'Peaxi162Scf35631g00002' => 'pax', 'PGR142G3720' => 'pgr', 'PGSC0003DMG400006442' => 'stu', 'Phvul.007G062000' => 'pvu', 'Potri.008G157750' => 'ptr', 'Potri.008G157900' => 'ptr', 'Potri.008G158000' => 'ptr', 'Potri.008G158200' => 'ptr', 'Pp3c11_7280' => 'ppa', 'Pp3c11_7980' => 'ppa', 'Pp3c12_19450' => 'ppa', 'Pp3c14_1480' => 'ppa', 'Pp3c14_1501' => 'ppa', 'Pp3c16_4900' => 'ppa', 'Pp3c16_5010' => 'ppa', 'Pp3c16_5060' => 'ppa', 'Pp3c19_18250' => 'ppa', 'Pp3c23_8530' => 'ppa', 'Pp3c23_8550' => 'ppa', 'Pp3c24_9670' => 'ppa', 'Pp3c2_21390' => 'ppa', 'Pp3c2_31380' => 'ppa', 'Pp3c3_16620' => 'ppa', 'Pp3c3_8090' => 'ppa', 'Pp3c3_8110' => 'ppa', 'Pp3c3_8130' => 'ppa', 'Pp3c3_8150' => 'ppa', 'Pp3c4_14320' => 'ppa', 'Pp3c6_2560' => 'ppa', 'Pp3c9_16700' => 'ppa', 'PRCOL_00000234' => 'pco', 'PRCOL_00000235' => 'pco', 'PRCOL_00000777' => 'pco', 'PRCOL_00002344' => 'pco', 'PRCOL_00002372' => 'pco', 'PRCOL_00006120' => 'pco', 'Prupe.1G021400' => 'ppe', 'Prupe.1G021500' => 'ppe', 'Prupe.1G021600' => 'ppe', 'Prupe.1G021700' => 'ppe', 'Prupe.1G021800' => 'ppe', 'Prupe.5G145100' => 'ppe', 'Psat6g204040' => 'psa', 'Psat6g204800' => 'psa', 'Psat6g204920' => 'psa', 'Psat6g204960' => 'psa', 'Psat6g205080' => 'psa', 'PSO017G0271' => 'pso', 'PSO017G1276' => 'pso', 'PSO017G1429' => 'pso', 'PSO017G1861' => 'pso', 'PSO017G2787' => 'pso', 'PSO017G4466' => 'pso', 'PSO017G5118' => 'pso', 'PSO017G5420' => 'pso', 'PSO063G3678' => 'pso', 'PSO210G0546' => 'pso', 'PSO317G0001' => 'pso', 'PSO357G0512' => 'pso', 'PSO478G2682' => 'pso', 'PSO647G0001' => 'pso', 'PSO675G0001' => 'pso', 'PSO675G2699' => 'pso', 'PSO675G2849' => 'pso', 'PSO675G4991' => 'pso', 'PSO689G0001' => 'pso', 'QL06p000916' => 'qlo', 'QL06p000921' => 'qlo', 'QL06p001398' => 'qlo', 'QL06p001407' => 'qlo', 'QL06p002031' => 'qlo', 'RcHm_v2.0_Chr4g0387791' => 'rch', 'RcHm_v2.0_Chr4g0387801' => 'rch', 'RcHm_v2.0_Chr6g0286501' => 'rch', 'RcHm_v2.0_Chr6g0286511' => 'rch', 'RcHm_v2.0_Chr6g0286521' => 'rch', 'RcHm_v2.0_Chr6g0286531' => 'rch', 'RcHm_v2.0_Chr7g0189141' => 'rch', 'Rhsim02G0028700' => 'rsi', 'Rhsim02G0028800' => 'rsi', 'Rhsim02G0028900' => 'rsi', 'Rhsim02G0029000' => 'rsi', 'Rhsim02G0029100' => 'rsi', 'Rhsim02G0029200' => 'rsi', 'Rhsim02G0029300' => 'rsi', 'Rhsim02G0029400' => 'rsi', 'Rhsim02G0029500' => 'rsi', 'Rhsim02G0029600' => 'rsi', 'RhsimUnG0024000' => 'rsi', 'RhsimUnG0024100' => 'rsi', 'RhsimUnG0024200' => 'rsi', 'RhsimUnG0024300' => 'rsi', 'RhsimUnG0024400' => 'rsi', 'RhsimUnG0024500' => 'rsi', 'RhsimUnG0024700' => 'rsi', 'RhsimUnG0024800' => 'rsi', 'RhsimUnG0024900' => 'rsi', 'RhsimUnG0025100' => 'rsi', 'Sabra08G0120200' => 'sbr', 'Sabra08G0120300' => 'sbr', 'Sabra08G0120500' => 'sbr', 'Sabra08G0120600' => 'sbr', 'Sabra10G0158900' => 'sbr', 'SalBow2G3492' => 'sbo', 'Sc13g0004760' => 'sci', 'Sc13g0004770' => 'sci', 'Sed0003417' => 'sed', 'Sed0019750' => 'sed', 'SEGI_03419' => 'sgi', 'SEGI_05907' => 'sgi', 'SEGI_10682' => 'sgi', 'SEGI_13528' => 'sgi', 'SEGI_16081' => 'sgi', 'SEGI_19370' => 'sgi', 'SEGI_21015' => 'sgi', 'SEGI_21944' => 'sgi', 'SEGI_32906' => 'sgi', 'SEGI_33093' => 'sgi', 'SEGI_36110' => 'sgi', 'SEGI_40397' => 'sgi', 'SGA_v2.0_scaffold191G40426' => 'sas', 'SGA_v2.0_scaffold353G49717' => 'sas', 'SGA_v2.0_scaffold50G18550' => 'sas', 'SMO119G0173' => 'smo', 'SMO172G0002' => 'smo', 'Solyc09g082690.3' => 'sly', 'Solyc09g082700.2' => 'sly', 'Sopen09g031550' => 'spe', 'Sopen09g031560' => 'spe', 'Sp3g20540' => 'spa', 'Sp7g07580' => 'spa', 'TAR134G0002' => 'tar', 'TAR236G0001' => 'tar', 'TAR365G0892' => 'tar', 'TAR636G0166' => 'tar', 'TAR636G0646' => 'tar', 'TAR636G0869' => 'tar', 'TAR636G1317' => 'tar', 'TAR636G1744' => 'tar', 'TAR636G3358' => 'tar', 'TAR636G3436' => 'tar', 'THA.LOC104803047' => 'tha', 'Thecc.04G238900' => 'tca', 'Thhalv10021557m.g' => 'esa', 'Thhalv10026318m.g' => 'esa', 'Thhalv10026335m.g' => 'esa', 'TPR.G17433' => 'tpr', 'TPR.G18915' => 'tpr', 'TPR.G26125' => 'tpr', 'TWI09G0677' => 'twi', 'TWI73G0287' => 'twi', 'unitig_748.g8326' => 'ugi', 'vmacro15370' => 'vma', 'vmacro15371' => 'vma', 'vmacro15372' => 'vma', 'vmacro15373' => 'vma', 'vmacro15374' => 'vma', 'VMungo0720G2826' => 'vmu', 'Zm00001eb116960' => 'zma', 'Zm00001eb301260' => 'zma', 'Zm00001eb301270' => 'zma' ), 'gf_id' => 'HOM05D001460', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001460' ), 'data_identifier' => 'HOM05D001460', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001460', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '433', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p22980' => 'bna', 'A01p32340' => 'bna', 'A03p42970' => 'bna', 'A05p25880' => 'bna', 'Aa31LG8G9320' => 'aar', 'Aa31LG8G9330' => 'aar', 'Aa31LG8G9340' => 'aar', 'Aa31sc221G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1034' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1528' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.829' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2222' => 'aag', 'Ah.12g058830' => 'amhyb', 'Ah.12g058840' => 'amhyb', 'AL3G37160' => 'aly', 'AL7G41310' => 'aly', 'Aqoxy5G00395' => 'aox', 'Aqoxy5G00396' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0C8NZA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5185HY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JZ1PRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MD3LS0' => 'arhy', 'AT3G22840' => 'ath', 'AT4G14690' => 'ath', 'ATR0665G054' => 'atr', 'Atru.chr4.2344' => 'acertr', 'Atru.chr4.2346' => 'acertr', 'Atru.chr4.2347' => 'acertr', 'Atru.chr4.2348' => 'acertr', 'Atru.chr4.2355' => 'acertr', 'Atru.chr4.2356' => 'acertr', 'Atru.chr4.2358' => 'acertr', 'Atru.chr4.2359' => 'acertr', 'Atru.chr4.2360' => 'acertr', 'Atru.chr4.2361' => 'acertr', 'AUR62030476' => 'cqu', 'AUR62030478' => 'cqu', 'AUR62030819' => 'cqu', 'AUR62030820' => 'cqu', 'BcaB03g14648' => 'bca', 'BcaB04g20492' => 'bca', 'BcaB06g26399' => 'bca', 'BcaC01g03416' => 'bca', 'BcaC01g03419' => 'bca', 'BcaC01g03421' => 'bca', 'BcaC01g03424' => 'bca', 'BcaC05g28012' => 'bca', 'BcaC09g49212' => 'bca', 'BcaC09g50140' => 'bca', 'BcaNung00346' => 'bca', 'BolC1t02785H' => 'bol', 'BolC1t04095H' => 'bol', 'BolC3t17545H' => 'bol', 'BolC5t32769H' => 'bol', 'BraA01t02211Z' => 'bra', 'BraA01t03359Z' => 'bra', 'BraA03t13441Z' => 'bra', 'BraA05t21476Z' => 'bra', 'C01p28420' => 'bna', 'C01p41350' => 'bna', 'C03p52750' => 'bna', 'C03p52780' => 'bna', 'C05p40270' => 'bna', 'CAN.G1437.9' => 'can', 'CANSAT78G0035' => 'cansat', 'CANSAT78G1036' => 'cansat', 'CANSAT78G2272' => 'cansat', 'CANSAT78G2478' => 'cansat', 'CARHR098700' => 'chi', 'CARHR221120' => 'chi', 'CARHR221150' => 'chi', 'Carub.0003s2297' => 'cru', 'Carub.0007s2749' => 'cru', 'Carub.0007s2750' => 'cru', 'Carub.0007s2751' => 'cru', 'Ca_10849_v3' => 'car', 'Cc03_g04300' => 'ccan', 'CDE02G3648' => 'cde', 'CDE05G0060' => 'cde', 'CDE05G0692' => 'cde', 'CDE05G2285' => 'cde', 'CDE05G2884' => 'cde', 'CDE05G3072' => 'cde', 'Cfa008439' => 'cfa', 'Cfa008441' => 'cfa', 'Cfa008443' => 'cfa', 'Cfa008448' => 'cfa', 'Ciclev10005974m.g' => 'ccl', 'Ciclev10006006m.g' => 'ccl', 'Ciclev10006775m.g' => 'ccl', 'CiPaw.02G120400' => 'cil', 'CiPaw.02G120500' => 'cil', 'CiPaw.02G120600' => 'cil', 'ClCG05G004850' => 'cla', 'COL.COLO4_21566' => 'col', 'Cpa.g.sc44.124' => 'cpa', 'Cre07.g320400' => 'cre', 'Cre07.g320450' => 'cre', 'Cre08.g384650' => 'cre', 'Cre09.g393173' => 'cre', 'Cre09.g394325' => 'cre', 'Cre14.g626750' => 'cre', 'Cre16.g679250' => 'cre', 'CsaV3_3G012890' => 'csa', 'CSS0010865' => 'camsi', 'CSS0044338' => 'camsi', 'DCAR_002366' => 'dca', 'DCAR_030687' => 'dca', 'DCAR_030688' => 'dca', 'Dinv14047' => 'din', 'Dinv14048' => 'din', 'Duzib151G0105' => 'dzi', 'Duzib151G0114' => 'dzi', 'Duzib212G1029' => 'dzi', 'ECA232G3536' => 'eca', 'ECA240G0786' => 'eca', 'ECA240G1802' => 'eca', 'ECA240G3760' => 'eca', 'ECA240G3920' => 'eca', 'EL10Ac5g12536' => 'bvu', 'EL10Ac5g12537' => 'bvu', 'EL10Ac5g12538' => 'bvu', 'Eucgr.B01004' => 'egr', 'Eucgr.B01006' => 'egr', 'Eucgr.B01007' => 'egr', 'Eucgr.B01008' => 'egr', 'Eucgr.B01895' => 'egr', 'Eucgr.B01896' => 'egr', 'FAN04G1456' => 'fan', 'FAN08G1769' => 'fan', 'FAN08G2160' => 'fan', 'FAN13G2403' => 'fan', 'FAN13G3303' => 'fan', 'FAN15G2435' => 'fan', 'FAN17G0672' => 'fan', 'FAN17G2441' => 'fan', 'FAN18G1024' => 'fan', 'FAN22G1458' => 'fan', 'FAN24G0037' => 'fan', 'FAN24G0429' => 'fan', 'FAN24G2387' => 'fan', 'FAN27G2746' => 'fan', 'FvH4_2g20400' => 'fve', 'FvH4_2g20420' => 'fve', 'FvH4_2g20430' => 'fve', 'FvH4_4g01270' => 'fve', 'FvH4_4g01290' => 'fve', 'FvH4_4g01300' => 'fve', 'FvH4_4g01310' => 'fve', 'FvH4_4g01330' => 'fve', 'FvH4_5g09070' => 'fve', 'Glyma.10G243800' => 'gma', 'Glyma.20G150600' => 'gma', 'Gohir.A09G219200' => 'ghi', 'Gohir.A09G219300' => 'ghi', 'Gohir.D09G221400' => 'ghi', 'Gohir.D09G221500' => 'ghi', 'Gorai.006G242600' => 'gra', 'Gorai.006G242700' => 'gra', 'GSVIVG01018044001' => 'vvi', 'HanXRQChr03g0083821' => 'han', 'HanXRQChr03g0083841' => 'han', 'HanXRQChr03g0083881' => 'han', 'HanXRQChr03g0083901' => 'han', 'HanXRQChr03g0083921' => 'han', 'HanXRQChr03g0085331' => 'han', 'HanXRQChr03g0085361' => 'han', 'HanXRQChr03g0085411' => 'han', 'HanXRQChr03g0085421' => 'han', 'HanXRQChr03g0085431' => 'han', 'HanXRQChr08g0221991' => 'han', 'HanXRQChr11g0336061' => 'han', 'HanXRQChr11g0336411' => 'han', 'Haze_11234' => 'cav', 'Hma1.2p1_0549F.1_g177010' => 'hma', 'Hma1.2p1_0602F.1_g187630' => 'hma', 'Hund14876' => 'sun', 'Hund14879' => 'sun', 'Lalb_Chr06g0160741' => 'lal', 'Lalb_Chr21g0304781' => 'lal', 'Lj3A726G19' => 'lonja', 'Lj3A726T23' => 'lonja', 'Lj3A726T24' => 'lonja', 'Lj3A726T25' => 'lonja', 'Lj3A727T17' => 'lonja', 'Lj3C726T0' => 'lonja', 'Lj3C726T2' => 'lonja', 'Lj3P725T35' => 'lonja', 'Lj3P727T10' => 'lonja', 'Lj3P727T12' => 'lonja', 'Lj3P727T14' => 'lonja', 'Lj5g0023109' => 'lja', 'Lj6P646T44' => 'lonja', 'Lsat_1_v5_gn_6_75760' => 'lsa', 'Lsat_1_v5_gn_6_75800' => 'lsa', 'Lsat_1_v5_gn_6_75900' => 'lsa', 'Lsat_1_v5_gn_6_76240' => 'lsa', 'Lsat_1_v5_gn_6_76441' => 'lsa', 'Lsat_1_v5_gn_6_76700' => 'lsa', 'Lsat_1_v5_gn_6_76760' => 'lsa', 'Manes.15G033100' => 'mes', 'Mapoly0004s0074' => 'mpo', 'Mapoly0004s0075' => 'mpo', 'Mapoly0004s0163' => 'mpo', 'Mapoly0004s0164' => 'mpo', 'Mapoly0021s0018' => 'mpo', 'Mapoly0041s0136' => 'mpo', 'Mapoly0041s0137' => 'mpo', 'Mapoly0041s0138' => 'mpo', 'Mapoly0041s0139' => 'mpo', 'Mapoly0041s0141' => 'mpo', 'Mapoly0041s0142' => 'mpo', 'Mapoly0041s0143' => 'mpo', 'Mapoly0041s0144' => 'mpo', 'Mapoly0041s0145' => 'mpo', 'Mapoly0047s0106' => 'mpo', 'Mapoly0047s0108' => 'mpo', 'Mapoly0050s0051' => 'mpo', 'Mapoly0050s0052' => 'mpo', 'Mapoly0050s0053' => 'mpo', 'Mapoly0058s0013' => 'mpo', 'Mapoly0091s0078' => 'mpo', 'Mapoly0091s0079' => 'mpo', 'Mapoly0091s0080' => 'mpo', 'Mapoly0091s0081' => 'mpo', 'Mapoly0278s0004' => 'mpo', 'Mapoly0278s0005' => 'mpo', 'Mapoly0278s0006' => 'mpo', 'MBI11_g30648_MAGBIO' => 'mbi', 'MCO03G194' => 'mco', 'MCO03G590' => 'mco', 'MCO07G312' => 'mco', 'MCO10G318' => 'mco', 'MCO12G244' => 'mco', 'MCO13G148' => 'mco', 'MCO13G194' => 'mco', 'MCO16G238' => 'mco', 'MD06G1134100' => 'mdo', 'MD13G1200100' => 'mdo', 'MD13G1200300' => 'mdo', 'MD13G1200600' => 'mdo', 'MD14G1150400' => 'mdo', 'MD16G1200000' => 'mdo', 'Medtr1g102570' => 'mtr', 'Medtr1g102780' => 'mtr', 'Medtr1g102800' => 'mtr', 'Medtr1g102810' => 'mtr', 'Medtr1g102830' => 'mtr', 'MELO3C006499.2' => 'cme', 'Migut.G00385' => 'egut', 'MSTRG.4063' => 'ama', 'Nitab4.5_0000090g0260' => 'nta', 'Nitab4.5_0000977g0030' => 'nta', 'Nitab4.5_0002541g0040' => 'nta', 'Nitab4.5_0007068g0040' => 'nta', 'Nn005s41408' => 'nnu', 'Nn005s41410' => 'nnu', 'Oeu010310.1' => 'oeu', 'Oeu010311.1' => 'oeu', 'Oeu043472.1' => 'oeu', 'Os01g0246400' => 'osa', 'Os04g0267950' => 'osa', 'Os07g0178700' => 'osa', 'Os07g0178800' => 'osa', 'Peaxi162Scf00316g00046' => 'pax', 'Peaxi162Scf00316g00049' => 'pax', 'Peaxi162Scf00316g00059' => 'pax', 'Peaxi162Scf00316g00328' => 'pax', 'Peaxi162Scf00316g00329' => 'pax', 'Peaxi162Scf00316g00411' => 'pax', 'Peaxi162Scf00316g00521' => 'pax', 'Peaxi162Scf00492g00068' => 'pax', 'Peaxi162Scf35631g00002' => 'pax', 'PGR142G3720' => 'pgr', 'PGSC0003DMG400006442' => 'stu', 'Phvul.007G062000' => 'pvu', 'Potri.008G157750' => 'ptr', 'Potri.008G157900' => 'ptr', 'Potri.008G158000' => 'ptr', 'Potri.008G158200' => 'ptr', 'Pp3c11_7280' => 'ppa', 'Pp3c11_7980' => 'ppa', 'Pp3c12_19450' => 'ppa', 'Pp3c14_1480' => 'ppa', 'Pp3c14_1501' => 'ppa', 'Pp3c16_4900' => 'ppa', 'Pp3c16_5010' => 'ppa', 'Pp3c16_5060' => 'ppa', 'Pp3c19_18250' => 'ppa', 'Pp3c23_8530' => 'ppa', 'Pp3c23_8550' => 'ppa', 'Pp3c24_9670' => 'ppa', 'Pp3c2_21390' => 'ppa', 'Pp3c2_31380' => 'ppa', 'Pp3c3_16620' => 'ppa', 'Pp3c3_8090' => 'ppa', 'Pp3c3_8110' => 'ppa', 'Pp3c3_8130' => 'ppa', 'Pp3c3_8150' => 'ppa', 'Pp3c4_14320' => 'ppa', 'Pp3c6_2560' => 'ppa', 'Pp3c9_16700' => 'ppa', 'PRCOL_00000234' => 'pco', 'PRCOL_00000235' => 'pco', 'PRCOL_00000777' => 'pco', 'PRCOL_00002344' => 'pco', 'PRCOL_00002372' => 'pco', 'PRCOL_00006120' => 'pco', 'Prupe.1G021400' => 'ppe', 'Prupe.1G021500' => 'ppe', 'Prupe.1G021600' => 'ppe', 'Prupe.1G021700' => 'ppe', 'Prupe.1G021800' => 'ppe', 'Prupe.5G145100' => 'ppe', 'Psat6g204040' => 'psa', 'Psat6g204800' => 'psa', 'Psat6g204920' => 'psa', 'Psat6g204960' => 'psa', 'Psat6g205080' => 'psa', 'PSO017G0271' => 'pso', 'PSO017G1276' => 'pso', 'PSO017G1429' => 'pso', 'PSO017G1861' => 'pso', 'PSO017G2787' => 'pso', 'PSO017G4466' => 'pso', 'PSO017G5118' => 'pso', 'PSO017G5420' => 'pso', 'PSO063G3678' => 'pso', 'PSO210G0546' => 'pso', 'PSO317G0001' => 'pso', 'PSO357G0512' => 'pso', 'PSO478G2682' => 'pso', 'PSO647G0001' => 'pso', 'PSO675G0001' => 'pso', 'PSO675G2699' => 'pso', 'PSO675G2849' => 'pso', 'PSO675G4991' => 'pso', 'PSO689G0001' => 'pso', 'QL06p000916' => 'qlo', 'QL06p000921' => 'qlo', 'QL06p001398' => 'qlo', 'QL06p001407' => 'qlo', 'QL06p002031' => 'qlo', 'RcHm_v2.0_Chr4g0387791' => 'rch', 'RcHm_v2.0_Chr4g0387801' => 'rch', 'RcHm_v2.0_Chr6g0286501' => 'rch', 'RcHm_v2.0_Chr6g0286511' => 'rch', 'RcHm_v2.0_Chr6g0286521' => 'rch', 'RcHm_v2.0_Chr6g0286531' => 'rch', 'RcHm_v2.0_Chr7g0189141' => 'rch', 'Rhsim02G0028700' => 'rsi', 'Rhsim02G0028800' => 'rsi', 'Rhsim02G0028900' => 'rsi', 'Rhsim02G0029000' => 'rsi', 'Rhsim02G0029100' => 'rsi', 'Rhsim02G0029200' => 'rsi', 'Rhsim02G0029300' => 'rsi', 'Rhsim02G0029400' => 'rsi', 'Rhsim02G0029500' => 'rsi', 'Rhsim02G0029600' => 'rsi', 'RhsimUnG0024000' => 'rsi', 'RhsimUnG0024100' => 'rsi', 'RhsimUnG0024200' => 'rsi', 'RhsimUnG0024300' => 'rsi', 'RhsimUnG0024400' => 'rsi', 'RhsimUnG0024500' => 'rsi', 'RhsimUnG0024700' => 'rsi', 'RhsimUnG0024800' => 'rsi', 'RhsimUnG0024900' => 'rsi', 'RhsimUnG0025100' => 'rsi', 'Sabra08G0120200' => 'sbr', 'Sabra08G0120300' => 'sbr', 'Sabra08G0120500' => 'sbr', 'Sabra08G0120600' => 'sbr', 'Sabra10G0158900' => 'sbr', 'SalBow2G3492' => 'sbo', 'Sc13g0004760' => 'sci', 'Sc13g0004770' => 'sci', 'Sed0003417' => 'sed', 'Sed0019750' => 'sed', 'SEGI_03419' => 'sgi', 'SEGI_05907' => 'sgi', 'SEGI_10682' => 'sgi', 'SEGI_13528' => 'sgi', 'SEGI_16081' => 'sgi', 'SEGI_19370' => 'sgi', 'SEGI_21015' => 'sgi', 'SEGI_21944' => 'sgi', 'SEGI_32906' => 'sgi', 'SEGI_33093' => 'sgi', 'SEGI_36110' => 'sgi', 'SEGI_40397' => 'sgi', 'SGA_v2.0_scaffold191G40426' => 'sas', 'SGA_v2.0_scaffold353G49717' => 'sas', 'SGA_v2.0_scaffold50G18550' => 'sas', 'SMO119G0173' => 'smo', 'SMO172G0002' => 'smo', 'Solyc09g082690.3' => 'sly', 'Solyc09g082700.2' => 'sly', 'Sopen09g031550' => 'spe', 'Sopen09g031560' => 'spe', 'Sp3g20540' => 'spa', 'Sp7g07580' => 'spa', 'TAR134G0002' => 'tar', 'TAR236G0001' => 'tar', 'TAR365G0892' => 'tar', 'TAR636G0166' => 'tar', 'TAR636G0646' => 'tar', 'TAR636G0869' => 'tar', 'TAR636G1317' => 'tar', 'TAR636G1744' => 'tar', 'TAR636G3358' => 'tar', 'TAR636G3436' => 'tar', 'THA.LOC104803047' => 'tha', 'Thecc.04G238900' => 'tca', 'Thhalv10021557m.g' => 'esa', 'Thhalv10026318m.g' => 'esa', 'Thhalv10026335m.g' => 'esa', 'TPR.G17433' => 'tpr', 'TPR.G18915' => 'tpr', 'TPR.G26125' => 'tpr', 'TWI09G0677' => 'twi', 'TWI73G0287' => 'twi', 'unitig_748.g8326' => 'ugi', 'vmacro15370' => 'vma', 'vmacro15371' => 'vma', 'vmacro15372' => 'vma', 'vmacro15373' => 'vma', 'vmacro15374' => 'vma', 'VMungo0720G2826' => 'vmu', 'Zm00001eb116960' => 'zma', 'Zm00001eb301260' => 'zma', 'Zm00001eb301270' => 'zma' ) $gf_id = 'HOM05D001460' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001460' ) $data_identifier = 'HOM05D001460' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 4, 'aag' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 2, 'aox' => (int) 2, 'arhy' => (int) 4, 'ath' => (int) 2, 'atr' => (int) 1, 'acertr' => (int) 10, 'cqu' => (int) 4, 'bca' => (int) 11, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 1, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 1, 'ccan' => (int) 1, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 1, 'col' => (int) 1, 'cpa' => (int) 1, 'cre' => (int) 7, 'csa' => (int) 1, 'camsi' => (int) 2, 'dca' => (int) 3, 'din' => (int) 2, 'dzi' => (int) 3, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 14, 'fve' => (int) 9, 'gma' => (int) 2, 'ghi' => (int) 4, 'gra' => (int) 2, 'vvi' => (int) 1, 'han' => (int) 13, 'cav' => (int) 1, 'hma' => (int) 2, 'sun' => (int) 2, 'lal' => (int) 2, 'lonja' => (int) 12, 'lja' => (int) 1, 'lsa' => (int) 7, 'mes' => (int) 1, 'mpo' => (int) 27, 'mbi' => (int) 1, 'mco' => (int) 8, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 1, 'egut' => (int) 1, 'ama' => (int) 1, 'nta' => (int) 4, 'nnu' => (int) 2, 'oeu' => (int) 3, 'osa' => (int) 4, 'pax' => (int) 9, 'pgr' => (int) 1, 'stu' => (int) 1, 'pvu' => (int) 1, 'ptr' => (int) 4, 'ppa' => (int) 22, 'pco' => (int) 6, 'ppe' => (int) 6, 'psa' => (int) 5, 'pso' => (int) 19, 'qlo' => (int) 5, 'rch' => (int) 7, 'rsi' => (int) 20, 'sbr' => (int) 5, 'sbo' => (int) 1, 'sci' => (int) 2, 'sed' => (int) 2, 'sgi' => (int) 12, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 2, 'tar' => (int) 10, 'tha' => (int) 1, 'tca' => (int) 1, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 2, 'ugi' => (int) 1, 'vma' => (int) 5, 'vmu' => (int) 1, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb301270' $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' => 'HOM05D001460', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '433', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p22980' => 'bna', 'A01p32340' => 'bna', 'A03p42970' => 'bna', 'A05p25880' => 'bna', 'Aa31LG8G9320' => 'aar', 'Aa31LG8G9330' => 'aar', 'Aa31LG8G9340' => 'aar', 'Aa31sc221G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1034' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1528' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.829' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2222' => 'aag', 'Ah.12g058830' => 'amhyb', 'Ah.12g058840' => 'amhyb', 'AL3G37160' => 'aly', 'AL7G41310' => 'aly', 'Aqoxy5G00395' => 'aox', 'Aqoxy5G00396' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0C8NZA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5185HY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JZ1PRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MD3LS0' => 'arhy', 'AT3G22840' => 'ath', 'AT4G14690' => 'ath', 'ATR0665G054' => 'atr', 'Atru.chr4.2344' => 'acertr', 'Atru.chr4.2346' => 'acertr', 'Atru.chr4.2347' => 'acertr', 'Atru.chr4.2348' => 'acertr', 'Atru.chr4.2355' => 'acertr', 'Atru.chr4.2356' => 'acertr', 'Atru.chr4.2358' => 'acertr', 'Atru.chr4.2359' => 'acertr', 'Atru.chr4.2360' => 'acertr', 'Atru.chr4.2361' => 'acertr', 'AUR62030476' => 'cqu', 'AUR62030478' => 'cqu', 'AUR62030819' => 'cqu', 'AUR62030820' => 'cqu', 'BcaB03g14648' => 'bca', 'BcaB04g20492' => 'bca', 'BcaB06g26399' => 'bca', 'BcaC01g03416' => 'bca', 'BcaC01g03419' => 'bca', 'BcaC01g03421' => 'bca', 'BcaC01g03424' => 'bca', 'BcaC05g28012' => 'bca', 'BcaC09g49212' => 'bca', 'BcaC09g50140' => 'bca', 'BcaNung00346' => 'bca', 'BolC1t02785H' => 'bol', 'BolC1t04095H' => 'bol', 'BolC3t17545H' => 'bol', 'BolC5t32769H' => 'bol', 'BraA01t02211Z' => 'bra', 'BraA01t03359Z' => 'bra', 'BraA03t13441Z' => 'bra', 'BraA05t21476Z' => 'bra', 'C01p28420' => 'bna', 'C01p41350' => 'bna', 'C03p52750' => 'bna', 'C03p52780' => 'bna', 'C05p40270' => 'bna', 'CAN.G1437.9' => 'can', 'CANSAT78G0035' => 'cansat', 'CANSAT78G1036' => 'cansat', 'CANSAT78G2272' => 'cansat', 'CANSAT78G2478' => 'cansat', 'CARHR098700' => 'chi', 'CARHR221120' => 'chi', 'CARHR221150' => 'chi', 'Carub.0003s2297' => 'cru', 'Carub.0007s2749' => 'cru', 'Carub.0007s2750' => 'cru', 'Carub.0007s2751' => 'cru', 'Ca_10849_v3' => 'car', 'Cc03_g04300' => 'ccan', 'CDE02G3648' => 'cde', 'CDE05G0060' => 'cde', 'CDE05G0692' => 'cde', 'CDE05G2285' => 'cde', 'CDE05G2884' => 'cde', 'CDE05G3072' => 'cde', 'Cfa008439' => 'cfa', 'Cfa008441' => 'cfa', 'Cfa008443' => 'cfa', 'Cfa008448' => 'cfa', 'Ciclev10005974m.g' => 'ccl', 'Ciclev10006006m.g' => 'ccl', 'Ciclev10006775m.g' => 'ccl', 'CiPaw.02G120400' => 'cil', 'CiPaw.02G120500' => 'cil', 'CiPaw.02G120600' => 'cil', 'ClCG05G004850' => 'cla', 'COL.COLO4_21566' => 'col', 'Cpa.g.sc44.124' => 'cpa', 'Cre07.g320400' => 'cre', 'Cre07.g320450' => 'cre', 'Cre08.g384650' => 'cre', 'Cre09.g393173' => 'cre', 'Cre09.g394325' => 'cre', 'Cre14.g626750' => 'cre', 'Cre16.g679250' => 'cre', 'CsaV3_3G012890' => 'csa', 'CSS0010865' => 'camsi', 'CSS0044338' => 'camsi', 'DCAR_002366' => 'dca', 'DCAR_030687' => 'dca', 'DCAR_030688' => 'dca', 'Dinv14047' => 'din', 'Dinv14048' => 'din', 'Duzib151G0105' => 'dzi', 'Duzib151G0114' => 'dzi', 'Duzib212G1029' => 'dzi', 'ECA232G3536' => 'eca', 'ECA240G0786' => 'eca', 'ECA240G1802' => 'eca', 'ECA240G3760' => 'eca', 'ECA240G3920' => 'eca', 'EL10Ac5g12536' => 'bvu', 'EL10Ac5g12537' => 'bvu', 'EL10Ac5g12538' => 'bvu', 'Eucgr.B01004' => 'egr', 'Eucgr.B01006' => 'egr', 'Eucgr.B01007' => 'egr', 'Eucgr.B01008' => 'egr', 'Eucgr.B01895' => 'egr', 'Eucgr.B01896' => 'egr', 'FAN04G1456' => 'fan', 'FAN08G1769' => 'fan', 'FAN08G2160' => 'fan', 'FAN13G2403' => 'fan', 'FAN13G3303' => 'fan', 'FAN15G2435' => 'fan', 'FAN17G0672' => 'fan', 'FAN17G2441' => 'fan', 'FAN18G1024' => 'fan', 'FAN22G1458' => 'fan', 'FAN24G0037' => 'fan', 'FAN24G0429' => 'fan', 'FAN24G2387' => 'fan', 'FAN27G2746' => 'fan', 'FvH4_2g20400' => 'fve', 'FvH4_2g20420' => 'fve', 'FvH4_2g20430' => 'fve', 'FvH4_4g01270' => 'fve', 'FvH4_4g01290' => 'fve', 'FvH4_4g01300' => 'fve', 'FvH4_4g01310' => 'fve', 'FvH4_4g01330' => 'fve', 'FvH4_5g09070' => 'fve', 'Glyma.10G243800' => 'gma', 'Glyma.20G150600' => 'gma', 'Gohir.A09G219200' => 'ghi', 'Gohir.A09G219300' => 'ghi', 'Gohir.D09G221400' => 'ghi', 'Gohir.D09G221500' => 'ghi', 'Gorai.006G242600' => 'gra', 'Gorai.006G242700' => 'gra', 'GSVIVG01018044001' => 'vvi', 'HanXRQChr03g0083821' => 'han', 'HanXRQChr03g0083841' => 'han', 'HanXRQChr03g0083881' => 'han', 'HanXRQChr03g0083901' => 'han', 'HanXRQChr03g0083921' => 'han', 'HanXRQChr03g0085331' => 'han', 'HanXRQChr03g0085361' => 'han', 'HanXRQChr03g0085411' => 'han', 'HanXRQChr03g0085421' => 'han', 'HanXRQChr03g0085431' => 'han', 'HanXRQChr08g0221991' => 'han', 'HanXRQChr11g0336061' => 'han', 'HanXRQChr11g0336411' => 'han', 'Haze_11234' => 'cav', 'Hma1.2p1_0549F.1_g177010' => 'hma', 'Hma1.2p1_0602F.1_g187630' => 'hma', 'Hund14876' => 'sun', 'Hund14879' => 'sun', 'Lalb_Chr06g0160741' => 'lal', 'Lalb_Chr21g0304781' => 'lal', 'Lj3A726G19' => 'lonja', 'Lj3A726T23' => 'lonja', 'Lj3A726T24' => 'lonja', 'Lj3A726T25' => 'lonja', 'Lj3A727T17' => 'lonja', 'Lj3C726T0' => 'lonja', 'Lj3C726T2' => 'lonja', 'Lj3P725T35' => 'lonja', 'Lj3P727T10' => 'lonja', 'Lj3P727T12' => 'lonja', 'Lj3P727T14' => 'lonja', 'Lj5g0023109' => 'lja', 'Lj6P646T44' => 'lonja', 'Lsat_1_v5_gn_6_75760' => 'lsa', 'Lsat_1_v5_gn_6_75800' => 'lsa', 'Lsat_1_v5_gn_6_75900' => 'lsa', 'Lsat_1_v5_gn_6_76240' => 'lsa', 'Lsat_1_v5_gn_6_76441' => 'lsa', 'Lsat_1_v5_gn_6_76700' => 'lsa', 'Lsat_1_v5_gn_6_76760' => 'lsa', 'Manes.15G033100' => 'mes', 'Mapoly0004s0074' => 'mpo', 'Mapoly0004s0075' => 'mpo', 'Mapoly0004s0163' => 'mpo', 'Mapoly0004s0164' => 'mpo', 'Mapoly0021s0018' => 'mpo', 'Mapoly0041s0136' => 'mpo', 'Mapoly0041s0137' => 'mpo', 'Mapoly0041s0138' => 'mpo', 'Mapoly0041s0139' => 'mpo', 'Mapoly0041s0141' => 'mpo', 'Mapoly0041s0142' => 'mpo', 'Mapoly0041s0143' => 'mpo', 'Mapoly0041s0144' => 'mpo', 'Mapoly0041s0145' => 'mpo', 'Mapoly0047s0106' => 'mpo', 'Mapoly0047s0108' => 'mpo', 'Mapoly0050s0051' => 'mpo', 'Mapoly0050s0052' => 'mpo', 'Mapoly0050s0053' => 'mpo', 'Mapoly0058s0013' => 'mpo', 'Mapoly0091s0078' => 'mpo', 'Mapoly0091s0079' => 'mpo', 'Mapoly0091s0080' => 'mpo', 'Mapoly0091s0081' => 'mpo', 'Mapoly0278s0004' => 'mpo', 'Mapoly0278s0005' => 'mpo', 'Mapoly0278s0006' => 'mpo', 'MBI11_g30648_MAGBIO' => 'mbi', 'MCO03G194' => 'mco', 'MCO03G590' => 'mco', 'MCO07G312' => 'mco', 'MCO10G318' => 'mco', 'MCO12G244' => 'mco', 'MCO13G148' => 'mco', 'MCO13G194' => 'mco', 'MCO16G238' => 'mco', 'MD06G1134100' => 'mdo', 'MD13G1200100' => 'mdo', 'MD13G1200300' => 'mdo', 'MD13G1200600' => 'mdo', 'MD14G1150400' => 'mdo', 'MD16G1200000' => 'mdo', 'Medtr1g102570' => 'mtr', 'Medtr1g102780' => 'mtr', 'Medtr1g102800' => 'mtr', 'Medtr1g102810' => 'mtr', 'Medtr1g102830' => 'mtr', 'MELO3C006499.2' => 'cme', 'Migut.G00385' => 'egut', 'MSTRG.4063' => 'ama', 'Nitab4.5_0000090g0260' => 'nta', 'Nitab4.5_0000977g0030' => 'nta', 'Nitab4.5_0002541g0040' => 'nta', 'Nitab4.5_0007068g0040' => 'nta', 'Nn005s41408' => 'nnu', 'Nn005s41410' => 'nnu', 'Oeu010310.1' => 'oeu', 'Oeu010311.1' => 'oeu', 'Oeu043472.1' => 'oeu', 'Os01g0246400' => 'osa', 'Os04g0267950' => 'osa', 'Os07g0178700' => 'osa', 'Os07g0178800' => 'osa', 'Peaxi162Scf00316g00046' => 'pax', 'Peaxi162Scf00316g00049' => 'pax', 'Peaxi162Scf00316g00059' => 'pax', 'Peaxi162Scf00316g00328' => 'pax', 'Peaxi162Scf00316g00329' => 'pax', 'Peaxi162Scf00316g00411' => 'pax', 'Peaxi162Scf00316g00521' => 'pax', 'Peaxi162Scf00492g00068' => 'pax', 'Peaxi162Scf35631g00002' => 'pax', 'PGR142G3720' => 'pgr', 'PGSC0003DMG400006442' => 'stu', 'Phvul.007G062000' => 'pvu', 'Potri.008G157750' => 'ptr', 'Potri.008G157900' => 'ptr', 'Potri.008G158000' => 'ptr', 'Potri.008G158200' => 'ptr', 'Pp3c11_7280' => 'ppa', 'Pp3c11_7980' => 'ppa', 'Pp3c12_19450' => 'ppa', 'Pp3c14_1480' => 'ppa', 'Pp3c14_1501' => 'ppa', 'Pp3c16_4900' => 'ppa', 'Pp3c16_5010' => 'ppa', 'Pp3c16_5060' => 'ppa', 'Pp3c19_18250' => 'ppa', 'Pp3c23_8530' => 'ppa', 'Pp3c23_8550' => 'ppa', 'Pp3c24_9670' => 'ppa', 'Pp3c2_21390' => 'ppa', 'Pp3c2_31380' => 'ppa', 'Pp3c3_16620' => 'ppa', 'Pp3c3_8090' => 'ppa', 'Pp3c3_8110' => 'ppa', 'Pp3c3_8130' => 'ppa', 'Pp3c3_8150' => 'ppa', 'Pp3c4_14320' => 'ppa', 'Pp3c6_2560' => 'ppa', 'Pp3c9_16700' => 'ppa', 'PRCOL_00000234' => 'pco', 'PRCOL_00000235' => 'pco', 'PRCOL_00000777' => 'pco', 'PRCOL_00002344' => 'pco', 'PRCOL_00002372' => 'pco', 'PRCOL_00006120' => 'pco', 'Prupe.1G021400' => 'ppe', 'Prupe.1G021500' => 'ppe', 'Prupe.1G021600' => 'ppe', 'Prupe.1G021700' => 'ppe', 'Prupe.1G021800' => 'ppe', 'Prupe.5G145100' => 'ppe', 'Psat6g204040' => 'psa', 'Psat6g204800' => 'psa', 'Psat6g204920' => 'psa', 'Psat6g204960' => 'psa', 'Psat6g205080' => 'psa', 'PSO017G0271' => 'pso', 'PSO017G1276' => 'pso', 'PSO017G1429' => 'pso', 'PSO017G1861' => 'pso', 'PSO017G2787' => 'pso', 'PSO017G4466' => 'pso', 'PSO017G5118' => 'pso', 'PSO017G5420' => 'pso', 'PSO063G3678' => 'pso', 'PSO210G0546' => 'pso', 'PSO317G0001' => 'pso', 'PSO357G0512' => 'pso', 'PSO478G2682' => 'pso', 'PSO647G0001' => 'pso', 'PSO675G0001' => 'pso', 'PSO675G2699' => 'pso', 'PSO675G2849' => 'pso', 'PSO675G4991' => 'pso', 'PSO689G0001' => 'pso', 'QL06p000916' => 'qlo', 'QL06p000921' => 'qlo', 'QL06p001398' => 'qlo', 'QL06p001407' => 'qlo', 'QL06p002031' => 'qlo', 'RcHm_v2.0_Chr4g0387791' => 'rch', 'RcHm_v2.0_Chr4g0387801' => 'rch', 'RcHm_v2.0_Chr6g0286501' => 'rch', 'RcHm_v2.0_Chr6g0286511' => 'rch', 'RcHm_v2.0_Chr6g0286521' => 'rch', 'RcHm_v2.0_Chr6g0286531' => 'rch', 'RcHm_v2.0_Chr7g0189141' => 'rch', 'Rhsim02G0028700' => 'rsi', 'Rhsim02G0028800' => 'rsi', 'Rhsim02G0028900' => 'rsi', 'Rhsim02G0029000' => 'rsi', 'Rhsim02G0029100' => 'rsi', 'Rhsim02G0029200' => 'rsi', 'Rhsim02G0029300' => 'rsi', 'Rhsim02G0029400' => 'rsi', 'Rhsim02G0029500' => 'rsi', 'Rhsim02G0029600' => 'rsi', 'RhsimUnG0024000' => 'rsi', 'RhsimUnG0024100' => 'rsi', 'RhsimUnG0024200' => 'rsi', 'RhsimUnG0024300' => 'rsi', 'RhsimUnG0024400' => 'rsi', 'RhsimUnG0024500' => 'rsi', 'RhsimUnG0024700' => 'rsi', 'RhsimUnG0024800' => 'rsi', 'RhsimUnG0024900' => 'rsi', 'RhsimUnG0025100' => 'rsi', 'Sabra08G0120200' => 'sbr', 'Sabra08G0120300' => 'sbr', 'Sabra08G0120500' => 'sbr', 'Sabra08G0120600' => 'sbr', 'Sabra10G0158900' => 'sbr', 'SalBow2G3492' => 'sbo', 'Sc13g0004760' => 'sci', 'Sc13g0004770' => 'sci', 'Sed0003417' => 'sed', 'Sed0019750' => 'sed', 'SEGI_03419' => 'sgi', 'SEGI_05907' => 'sgi', 'SEGI_10682' => 'sgi', 'SEGI_13528' => 'sgi', 'SEGI_16081' => 'sgi', 'SEGI_19370' => 'sgi', 'SEGI_21015' => 'sgi', 'SEGI_21944' => 'sgi', 'SEGI_32906' => 'sgi', 'SEGI_33093' => 'sgi', 'SEGI_36110' => 'sgi', 'SEGI_40397' => 'sgi', 'SGA_v2.0_scaffold191G40426' => 'sas', 'SGA_v2.0_scaffold353G49717' => 'sas', 'SGA_v2.0_scaffold50G18550' => 'sas', 'SMO119G0173' => 'smo', 'SMO172G0002' => 'smo', 'Solyc09g082690.3' => 'sly', 'Solyc09g082700.2' => 'sly', 'Sopen09g031550' => 'spe', 'Sopen09g031560' => 'spe', 'Sp3g20540' => 'spa', 'Sp7g07580' => 'spa', 'TAR134G0002' => 'tar', 'TAR236G0001' => 'tar', 'TAR365G0892' => 'tar', 'TAR636G0166' => 'tar', 'TAR636G0646' => 'tar', 'TAR636G0869' => 'tar', 'TAR636G1317' => 'tar', 'TAR636G1744' => 'tar', 'TAR636G3358' => 'tar', 'TAR636G3436' => 'tar', 'THA.LOC104803047' => 'tha', 'Thecc.04G238900' => 'tca', 'Thhalv10021557m.g' => 'esa', 'Thhalv10026318m.g' => 'esa', 'Thhalv10026335m.g' => 'esa', 'TPR.G17433' => 'tpr', 'TPR.G18915' => 'tpr', 'TPR.G26125' => 'tpr', 'TWI09G0677' => 'twi', 'TWI73G0287' => 'twi', 'unitig_748.g8326' => 'ugi', 'vmacro15370' => 'vma', 'vmacro15371' => 'vma', 'vmacro15372' => 'vma', 'vmacro15373' => 'vma', 'vmacro15374' => 'vma', 'VMungo0720G2826' => 'vmu', 'Zm00001eb116960' => 'zma', 'Zm00001eb301260' => 'zma', 'Zm00001eb301270' => 'zma' ), 'gf_id' => 'HOM05D001460', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001460' ), 'data_identifier' => 'HOM05D001460', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001460', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '433', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p22980' => 'bna', 'A01p32340' => 'bna', 'A03p42970' => 'bna', 'A05p25880' => 'bna', 'Aa31LG8G9320' => 'aar', 'Aa31LG8G9330' => 'aar', 'Aa31LG8G9340' => 'aar', 'Aa31sc221G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1034' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1528' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.829' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2222' => 'aag', 'Ah.12g058830' => 'amhyb', 'Ah.12g058840' => 'amhyb', 'AL3G37160' => 'aly', 'AL7G41310' => 'aly', 'Aqoxy5G00395' => 'aox', 'Aqoxy5G00396' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0C8NZA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5185HY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JZ1PRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MD3LS0' => 'arhy', 'AT3G22840' => 'ath', 'AT4G14690' => 'ath', 'ATR0665G054' => 'atr', 'Atru.chr4.2344' => 'acertr', 'Atru.chr4.2346' => 'acertr', 'Atru.chr4.2347' => 'acertr', 'Atru.chr4.2348' => 'acertr', 'Atru.chr4.2355' => 'acertr', 'Atru.chr4.2356' => 'acertr', 'Atru.chr4.2358' => 'acertr', 'Atru.chr4.2359' => 'acertr', 'Atru.chr4.2360' => 'acertr', 'Atru.chr4.2361' => 'acertr', 'AUR62030476' => 'cqu', 'AUR62030478' => 'cqu', 'AUR62030819' => 'cqu', 'AUR62030820' => 'cqu', 'BcaB03g14648' => 'bca', 'BcaB04g20492' => 'bca', 'BcaB06g26399' => 'bca', 'BcaC01g03416' => 'bca', 'BcaC01g03419' => 'bca', 'BcaC01g03421' => 'bca', 'BcaC01g03424' => 'bca', 'BcaC05g28012' => 'bca', 'BcaC09g49212' => 'bca', 'BcaC09g50140' => 'bca', 'BcaNung00346' => 'bca', 'BolC1t02785H' => 'bol', 'BolC1t04095H' => 'bol', 'BolC3t17545H' => 'bol', 'BolC5t32769H' => 'bol', 'BraA01t02211Z' => 'bra', 'BraA01t03359Z' => 'bra', 'BraA03t13441Z' => 'bra', 'BraA05t21476Z' => 'bra', 'C01p28420' => 'bna', 'C01p41350' => 'bna', 'C03p52750' => 'bna', 'C03p52780' => 'bna', 'C05p40270' => 'bna', 'CAN.G1437.9' => 'can', 'CANSAT78G0035' => 'cansat', 'CANSAT78G1036' => 'cansat', 'CANSAT78G2272' => 'cansat', 'CANSAT78G2478' => 'cansat', 'CARHR098700' => 'chi', 'CARHR221120' => 'chi', 'CARHR221150' => 'chi', 'Carub.0003s2297' => 'cru', 'Carub.0007s2749' => 'cru', 'Carub.0007s2750' => 'cru', 'Carub.0007s2751' => 'cru', 'Ca_10849_v3' => 'car', 'Cc03_g04300' => 'ccan', 'CDE02G3648' => 'cde', 'CDE05G0060' => 'cde', 'CDE05G0692' => 'cde', 'CDE05G2285' => 'cde', 'CDE05G2884' => 'cde', 'CDE05G3072' => 'cde', 'Cfa008439' => 'cfa', 'Cfa008441' => 'cfa', 'Cfa008443' => 'cfa', 'Cfa008448' => 'cfa', 'Ciclev10005974m.g' => 'ccl', 'Ciclev10006006m.g' => 'ccl', 'Ciclev10006775m.g' => 'ccl', 'CiPaw.02G120400' => 'cil', 'CiPaw.02G120500' => 'cil', 'CiPaw.02G120600' => 'cil', 'ClCG05G004850' => 'cla', 'COL.COLO4_21566' => 'col', 'Cpa.g.sc44.124' => 'cpa', 'Cre07.g320400' => 'cre', 'Cre07.g320450' => 'cre', 'Cre08.g384650' => 'cre', 'Cre09.g393173' => 'cre', 'Cre09.g394325' => 'cre', 'Cre14.g626750' => 'cre', 'Cre16.g679250' => 'cre', 'CsaV3_3G012890' => 'csa', 'CSS0010865' => 'camsi', 'CSS0044338' => 'camsi', 'DCAR_002366' => 'dca', 'DCAR_030687' => 'dca', 'DCAR_030688' => 'dca', 'Dinv14047' => 'din', 'Dinv14048' => 'din', 'Duzib151G0105' => 'dzi', 'Duzib151G0114' => 'dzi', 'Duzib212G1029' => 'dzi', 'ECA232G3536' => 'eca', 'ECA240G0786' => 'eca', 'ECA240G1802' => 'eca', 'ECA240G3760' => 'eca', 'ECA240G3920' => 'eca', 'EL10Ac5g12536' => 'bvu', 'EL10Ac5g12537' => 'bvu', 'EL10Ac5g12538' => 'bvu', 'Eucgr.B01004' => 'egr', 'Eucgr.B01006' => 'egr', 'Eucgr.B01007' => 'egr', 'Eucgr.B01008' => 'egr', 'Eucgr.B01895' => 'egr', 'Eucgr.B01896' => 'egr', 'FAN04G1456' => 'fan', 'FAN08G1769' => 'fan', 'FAN08G2160' => 'fan', 'FAN13G2403' => 'fan', 'FAN13G3303' => 'fan', 'FAN15G2435' => 'fan', 'FAN17G0672' => 'fan', 'FAN17G2441' => 'fan', 'FAN18G1024' => 'fan', 'FAN22G1458' => 'fan', 'FAN24G0037' => 'fan', 'FAN24G0429' => 'fan', 'FAN24G2387' => 'fan', 'FAN27G2746' => 'fan', 'FvH4_2g20400' => 'fve', 'FvH4_2g20420' => 'fve', 'FvH4_2g20430' => 'fve', 'FvH4_4g01270' => 'fve', 'FvH4_4g01290' => 'fve', 'FvH4_4g01300' => 'fve', 'FvH4_4g01310' => 'fve', 'FvH4_4g01330' => 'fve', 'FvH4_5g09070' => 'fve', 'Glyma.10G243800' => 'gma', 'Glyma.20G150600' => 'gma', 'Gohir.A09G219200' => 'ghi', 'Gohir.A09G219300' => 'ghi', 'Gohir.D09G221400' => 'ghi', 'Gohir.D09G221500' => 'ghi', 'Gorai.006G242600' => 'gra', 'Gorai.006G242700' => 'gra', 'GSVIVG01018044001' => 'vvi', 'HanXRQChr03g0083821' => 'han', 'HanXRQChr03g0083841' => 'han', 'HanXRQChr03g0083881' => 'han', 'HanXRQChr03g0083901' => 'han', 'HanXRQChr03g0083921' => 'han', 'HanXRQChr03g0085331' => 'han', 'HanXRQChr03g0085361' => 'han', 'HanXRQChr03g0085411' => 'han', 'HanXRQChr03g0085421' => 'han', 'HanXRQChr03g0085431' => 'han', 'HanXRQChr08g0221991' => 'han', 'HanXRQChr11g0336061' => 'han', 'HanXRQChr11g0336411' => 'han', 'Haze_11234' => 'cav', 'Hma1.2p1_0549F.1_g177010' => 'hma', 'Hma1.2p1_0602F.1_g187630' => 'hma', 'Hund14876' => 'sun', 'Hund14879' => 'sun', 'Lalb_Chr06g0160741' => 'lal', 'Lalb_Chr21g0304781' => 'lal', 'Lj3A726G19' => 'lonja', 'Lj3A726T23' => 'lonja', 'Lj3A726T24' => 'lonja', 'Lj3A726T25' => 'lonja', 'Lj3A727T17' => 'lonja', 'Lj3C726T0' => 'lonja', 'Lj3C726T2' => 'lonja', 'Lj3P725T35' => 'lonja', 'Lj3P727T10' => 'lonja', 'Lj3P727T12' => 'lonja', 'Lj3P727T14' => 'lonja', 'Lj5g0023109' => 'lja', 'Lj6P646T44' => 'lonja', 'Lsat_1_v5_gn_6_75760' => 'lsa', 'Lsat_1_v5_gn_6_75800' => 'lsa', 'Lsat_1_v5_gn_6_75900' => 'lsa', 'Lsat_1_v5_gn_6_76240' => 'lsa', 'Lsat_1_v5_gn_6_76441' => 'lsa', 'Lsat_1_v5_gn_6_76700' => 'lsa', 'Lsat_1_v5_gn_6_76760' => 'lsa', 'Manes.15G033100' => 'mes', 'Mapoly0004s0074' => 'mpo', 'Mapoly0004s0075' => 'mpo', 'Mapoly0004s0163' => 'mpo', 'Mapoly0004s0164' => 'mpo', 'Mapoly0021s0018' => 'mpo', 'Mapoly0041s0136' => 'mpo', 'Mapoly0041s0137' => 'mpo', 'Mapoly0041s0138' => 'mpo', 'Mapoly0041s0139' => 'mpo', 'Mapoly0041s0141' => 'mpo', 'Mapoly0041s0142' => 'mpo', 'Mapoly0041s0143' => 'mpo', 'Mapoly0041s0144' => 'mpo', 'Mapoly0041s0145' => 'mpo', 'Mapoly0047s0106' => 'mpo', 'Mapoly0047s0108' => 'mpo', 'Mapoly0050s0051' => 'mpo', 'Mapoly0050s0052' => 'mpo', 'Mapoly0050s0053' => 'mpo', 'Mapoly0058s0013' => 'mpo', 'Mapoly0091s0078' => 'mpo', 'Mapoly0091s0079' => 'mpo', 'Mapoly0091s0080' => 'mpo', 'Mapoly0091s0081' => 'mpo', 'Mapoly0278s0004' => 'mpo', 'Mapoly0278s0005' => 'mpo', 'Mapoly0278s0006' => 'mpo', 'MBI11_g30648_MAGBIO' => 'mbi', 'MCO03G194' => 'mco', 'MCO03G590' => 'mco', 'MCO07G312' => 'mco', 'MCO10G318' => 'mco', 'MCO12G244' => 'mco', 'MCO13G148' => 'mco', 'MCO13G194' => 'mco', 'MCO16G238' => 'mco', 'MD06G1134100' => 'mdo', 'MD13G1200100' => 'mdo', 'MD13G1200300' => 'mdo', 'MD13G1200600' => 'mdo', 'MD14G1150400' => 'mdo', 'MD16G1200000' => 'mdo', 'Medtr1g102570' => 'mtr', 'Medtr1g102780' => 'mtr', 'Medtr1g102800' => 'mtr', 'Medtr1g102810' => 'mtr', 'Medtr1g102830' => 'mtr', 'MELO3C006499.2' => 'cme', 'Migut.G00385' => 'egut', 'MSTRG.4063' => 'ama', 'Nitab4.5_0000090g0260' => 'nta', 'Nitab4.5_0000977g0030' => 'nta', 'Nitab4.5_0002541g0040' => 'nta', 'Nitab4.5_0007068g0040' => 'nta', 'Nn005s41408' => 'nnu', 'Nn005s41410' => 'nnu', 'Oeu010310.1' => 'oeu', 'Oeu010311.1' => 'oeu', 'Oeu043472.1' => 'oeu', 'Os01g0246400' => 'osa', 'Os04g0267950' => 'osa', 'Os07g0178700' => 'osa', 'Os07g0178800' => 'osa', 'Peaxi162Scf00316g00046' => 'pax', 'Peaxi162Scf00316g00049' => 'pax', 'Peaxi162Scf00316g00059' => 'pax', 'Peaxi162Scf00316g00328' => 'pax', 'Peaxi162Scf00316g00329' => 'pax', 'Peaxi162Scf00316g00411' => 'pax', 'Peaxi162Scf00316g00521' => 'pax', 'Peaxi162Scf00492g00068' => 'pax', 'Peaxi162Scf35631g00002' => 'pax', 'PGR142G3720' => 'pgr', 'PGSC0003DMG400006442' => 'stu', 'Phvul.007G062000' => 'pvu', 'Potri.008G157750' => 'ptr', 'Potri.008G157900' => 'ptr', 'Potri.008G158000' => 'ptr', 'Potri.008G158200' => 'ptr', 'Pp3c11_7280' => 'ppa', 'Pp3c11_7980' => 'ppa', 'Pp3c12_19450' => 'ppa', 'Pp3c14_1480' => 'ppa', 'Pp3c14_1501' => 'ppa', 'Pp3c16_4900' => 'ppa', 'Pp3c16_5010' => 'ppa', 'Pp3c16_5060' => 'ppa', 'Pp3c19_18250' => 'ppa', 'Pp3c23_8530' => 'ppa', 'Pp3c23_8550' => 'ppa', 'Pp3c24_9670' => 'ppa', 'Pp3c2_21390' => 'ppa', 'Pp3c2_31380' => 'ppa', 'Pp3c3_16620' => 'ppa', 'Pp3c3_8090' => 'ppa', 'Pp3c3_8110' => 'ppa', 'Pp3c3_8130' => 'ppa', 'Pp3c3_8150' => 'ppa', 'Pp3c4_14320' => 'ppa', 'Pp3c6_2560' => 'ppa', 'Pp3c9_16700' => 'ppa', 'PRCOL_00000234' => 'pco', 'PRCOL_00000235' => 'pco', 'PRCOL_00000777' => 'pco', 'PRCOL_00002344' => 'pco', 'PRCOL_00002372' => 'pco', 'PRCOL_00006120' => 'pco', 'Prupe.1G021400' => 'ppe', 'Prupe.1G021500' => 'ppe', 'Prupe.1G021600' => 'ppe', 'Prupe.1G021700' => 'ppe', 'Prupe.1G021800' => 'ppe', 'Prupe.5G145100' => 'ppe', 'Psat6g204040' => 'psa', 'Psat6g204800' => 'psa', 'Psat6g204920' => 'psa', 'Psat6g204960' => 'psa', 'Psat6g205080' => 'psa', 'PSO017G0271' => 'pso', 'PSO017G1276' => 'pso', 'PSO017G1429' => 'pso', 'PSO017G1861' => 'pso', 'PSO017G2787' => 'pso', 'PSO017G4466' => 'pso', 'PSO017G5118' => 'pso', 'PSO017G5420' => 'pso', 'PSO063G3678' => 'pso', 'PSO210G0546' => 'pso', 'PSO317G0001' => 'pso', 'PSO357G0512' => 'pso', 'PSO478G2682' => 'pso', 'PSO647G0001' => 'pso', 'PSO675G0001' => 'pso', 'PSO675G2699' => 'pso', 'PSO675G2849' => 'pso', 'PSO675G4991' => 'pso', 'PSO689G0001' => 'pso', 'QL06p000916' => 'qlo', 'QL06p000921' => 'qlo', 'QL06p001398' => 'qlo', 'QL06p001407' => 'qlo', 'QL06p002031' => 'qlo', 'RcHm_v2.0_Chr4g0387791' => 'rch', 'RcHm_v2.0_Chr4g0387801' => 'rch', 'RcHm_v2.0_Chr6g0286501' => 'rch', 'RcHm_v2.0_Chr6g0286511' => 'rch', 'RcHm_v2.0_Chr6g0286521' => 'rch', 'RcHm_v2.0_Chr6g0286531' => 'rch', 'RcHm_v2.0_Chr7g0189141' => 'rch', 'Rhsim02G0028700' => 'rsi', 'Rhsim02G0028800' => 'rsi', 'Rhsim02G0028900' => 'rsi', 'Rhsim02G0029000' => 'rsi', 'Rhsim02G0029100' => 'rsi', 'Rhsim02G0029200' => 'rsi', 'Rhsim02G0029300' => 'rsi', 'Rhsim02G0029400' => 'rsi', 'Rhsim02G0029500' => 'rsi', 'Rhsim02G0029600' => 'rsi', 'RhsimUnG0024000' => 'rsi', 'RhsimUnG0024100' => 'rsi', 'RhsimUnG0024200' => 'rsi', 'RhsimUnG0024300' => 'rsi', 'RhsimUnG0024400' => 'rsi', 'RhsimUnG0024500' => 'rsi', 'RhsimUnG0024700' => 'rsi', 'RhsimUnG0024800' => 'rsi', 'RhsimUnG0024900' => 'rsi', 'RhsimUnG0025100' => 'rsi', 'Sabra08G0120200' => 'sbr', 'Sabra08G0120300' => 'sbr', 'Sabra08G0120500' => 'sbr', 'Sabra08G0120600' => 'sbr', 'Sabra10G0158900' => 'sbr', 'SalBow2G3492' => 'sbo', 'Sc13g0004760' => 'sci', 'Sc13g0004770' => 'sci', 'Sed0003417' => 'sed', 'Sed0019750' => 'sed', 'SEGI_03419' => 'sgi', 'SEGI_05907' => 'sgi', 'SEGI_10682' => 'sgi', 'SEGI_13528' => 'sgi', 'SEGI_16081' => 'sgi', 'SEGI_19370' => 'sgi', 'SEGI_21015' => 'sgi', 'SEGI_21944' => 'sgi', 'SEGI_32906' => 'sgi', 'SEGI_33093' => 'sgi', 'SEGI_36110' => 'sgi', 'SEGI_40397' => 'sgi', 'SGA_v2.0_scaffold191G40426' => 'sas', 'SGA_v2.0_scaffold353G49717' => 'sas', 'SGA_v2.0_scaffold50G18550' => 'sas', 'SMO119G0173' => 'smo', 'SMO172G0002' => 'smo', 'Solyc09g082690.3' => 'sly', 'Solyc09g082700.2' => 'sly', 'Sopen09g031550' => 'spe', 'Sopen09g031560' => 'spe', 'Sp3g20540' => 'spa', 'Sp7g07580' => 'spa', 'TAR134G0002' => 'tar', 'TAR236G0001' => 'tar', 'TAR365G0892' => 'tar', 'TAR636G0166' => 'tar', 'TAR636G0646' => 'tar', 'TAR636G0869' => 'tar', 'TAR636G1317' => 'tar', 'TAR636G1744' => 'tar', 'TAR636G3358' => 'tar', 'TAR636G3436' => 'tar', 'THA.LOC104803047' => 'tha', 'Thecc.04G238900' => 'tca', 'Thhalv10021557m.g' => 'esa', 'Thhalv10026318m.g' => 'esa', 'Thhalv10026335m.g' => 'esa', 'TPR.G17433' => 'tpr', 'TPR.G18915' => 'tpr', 'TPR.G26125' => 'tpr', 'TWI09G0677' => 'twi', 'TWI73G0287' => 'twi', 'unitig_748.g8326' => 'ugi', 'vmacro15370' => 'vma', 'vmacro15371' => 'vma', 'vmacro15372' => 'vma', 'vmacro15373' => 'vma', 'vmacro15374' => 'vma', 'VMungo0720G2826' => 'vmu', 'Zm00001eb116960' => 'zma', 'Zm00001eb301260' => 'zma', 'Zm00001eb301270' => 'zma' ) $gf_id = 'HOM05D001460' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001460' ) $data_identifier = 'HOM05D001460' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 4, 'aag' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 2, 'aox' => (int) 2, 'arhy' => (int) 4, 'ath' => (int) 2, 'atr' => (int) 1, 'acertr' => (int) 10, 'cqu' => (int) 4, 'bca' => (int) 11, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 1, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 1, 'ccan' => (int) 1, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 1, 'col' => (int) 1, 'cpa' => (int) 1, 'cre' => (int) 7, 'csa' => (int) 1, 'camsi' => (int) 2, 'dca' => (int) 3, 'din' => (int) 2, 'dzi' => (int) 3, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 14, 'fve' => (int) 9, 'gma' => (int) 2, 'ghi' => (int) 4, 'gra' => (int) 2, 'vvi' => (int) 1, 'han' => (int) 13, 'cav' => (int) 1, 'hma' => (int) 2, 'sun' => (int) 2, 'lal' => (int) 2, 'lonja' => (int) 12, 'lja' => (int) 1, 'lsa' => (int) 7, 'mes' => (int) 1, 'mpo' => (int) 27, 'mbi' => (int) 1, 'mco' => (int) 8, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 1, 'egut' => (int) 1, 'ama' => (int) 1, 'nta' => (int) 4, 'nnu' => (int) 2, 'oeu' => (int) 3, 'osa' => (int) 4, 'pax' => (int) 9, 'pgr' => (int) 1, 'stu' => (int) 1, 'pvu' => (int) 1, 'ptr' => (int) 4, 'ppa' => (int) 22, 'pco' => (int) 6, 'ppe' => (int) 6, 'psa' => (int) 5, 'pso' => (int) 19, 'qlo' => (int) 5, 'rch' => (int) 7, 'rsi' => (int) 20, 'sbr' => (int) 5, 'sbo' => (int) 1, 'sci' => (int) 2, 'sed' => (int) 2, 'sgi' => (int) 12, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 2, 'tar' => (int) 10, 'tha' => (int) 1, 'tca' => (int) 1, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 2, 'ugi' => (int) 1, 'vma' => (int) 5, 'vmu' => (int) 1, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb301270' $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' => 'HOM05D001460', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '433', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p22980' => 'bna', 'A01p32340' => 'bna', 'A03p42970' => 'bna', 'A05p25880' => 'bna', 'Aa31LG8G9320' => 'aar', 'Aa31LG8G9330' => 'aar', 'Aa31LG8G9340' => 'aar', 'Aa31sc221G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1034' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1528' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.829' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2222' => 'aag', 'Ah.12g058830' => 'amhyb', 'Ah.12g058840' => 'amhyb', 'AL3G37160' => 'aly', 'AL7G41310' => 'aly', 'Aqoxy5G00395' => 'aox', 'Aqoxy5G00396' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0C8NZA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5185HY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JZ1PRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MD3LS0' => 'arhy', 'AT3G22840' => 'ath', 'AT4G14690' => 'ath', 'ATR0665G054' => 'atr', 'Atru.chr4.2344' => 'acertr', 'Atru.chr4.2346' => 'acertr', 'Atru.chr4.2347' => 'acertr', 'Atru.chr4.2348' => 'acertr', 'Atru.chr4.2355' => 'acertr', 'Atru.chr4.2356' => 'acertr', 'Atru.chr4.2358' => 'acertr', 'Atru.chr4.2359' => 'acertr', 'Atru.chr4.2360' => 'acertr', 'Atru.chr4.2361' => 'acertr', 'AUR62030476' => 'cqu', 'AUR62030478' => 'cqu', 'AUR62030819' => 'cqu', 'AUR62030820' => 'cqu', 'BcaB03g14648' => 'bca', 'BcaB04g20492' => 'bca', 'BcaB06g26399' => 'bca', 'BcaC01g03416' => 'bca', 'BcaC01g03419' => 'bca', 'BcaC01g03421' => 'bca', 'BcaC01g03424' => 'bca', 'BcaC05g28012' => 'bca', 'BcaC09g49212' => 'bca', 'BcaC09g50140' => 'bca', 'BcaNung00346' => 'bca', 'BolC1t02785H' => 'bol', 'BolC1t04095H' => 'bol', 'BolC3t17545H' => 'bol', 'BolC5t32769H' => 'bol', 'BraA01t02211Z' => 'bra', 'BraA01t03359Z' => 'bra', 'BraA03t13441Z' => 'bra', 'BraA05t21476Z' => 'bra', 'C01p28420' => 'bna', 'C01p41350' => 'bna', 'C03p52750' => 'bna', 'C03p52780' => 'bna', 'C05p40270' => 'bna', 'CAN.G1437.9' => 'can', 'CANSAT78G0035' => 'cansat', 'CANSAT78G1036' => 'cansat', 'CANSAT78G2272' => 'cansat', 'CANSAT78G2478' => 'cansat', 'CARHR098700' => 'chi', 'CARHR221120' => 'chi', 'CARHR221150' => 'chi', 'Carub.0003s2297' => 'cru', 'Carub.0007s2749' => 'cru', 'Carub.0007s2750' => 'cru', 'Carub.0007s2751' => 'cru', 'Ca_10849_v3' => 'car', 'Cc03_g04300' => 'ccan', 'CDE02G3648' => 'cde', 'CDE05G0060' => 'cde', 'CDE05G0692' => 'cde', 'CDE05G2285' => 'cde', 'CDE05G2884' => 'cde', 'CDE05G3072' => 'cde', 'Cfa008439' => 'cfa', 'Cfa008441' => 'cfa', 'Cfa008443' => 'cfa', 'Cfa008448' => 'cfa', 'Ciclev10005974m.g' => 'ccl', 'Ciclev10006006m.g' => 'ccl', 'Ciclev10006775m.g' => 'ccl', 'CiPaw.02G120400' => 'cil', 'CiPaw.02G120500' => 'cil', 'CiPaw.02G120600' => 'cil', 'ClCG05G004850' => 'cla', 'COL.COLO4_21566' => 'col', 'Cpa.g.sc44.124' => 'cpa', 'Cre07.g320400' => 'cre', 'Cre07.g320450' => 'cre', 'Cre08.g384650' => 'cre', 'Cre09.g393173' => 'cre', 'Cre09.g394325' => 'cre', 'Cre14.g626750' => 'cre', 'Cre16.g679250' => 'cre', 'CsaV3_3G012890' => 'csa', 'CSS0010865' => 'camsi', 'CSS0044338' => 'camsi', 'DCAR_002366' => 'dca', 'DCAR_030687' => 'dca', 'DCAR_030688' => 'dca', 'Dinv14047' => 'din', 'Dinv14048' => 'din', 'Duzib151G0105' => 'dzi', 'Duzib151G0114' => 'dzi', 'Duzib212G1029' => 'dzi', 'ECA232G3536' => 'eca', 'ECA240G0786' => 'eca', 'ECA240G1802' => 'eca', 'ECA240G3760' => 'eca', 'ECA240G3920' => 'eca', 'EL10Ac5g12536' => 'bvu', 'EL10Ac5g12537' => 'bvu', 'EL10Ac5g12538' => 'bvu', 'Eucgr.B01004' => 'egr', 'Eucgr.B01006' => 'egr', 'Eucgr.B01007' => 'egr', 'Eucgr.B01008' => 'egr', 'Eucgr.B01895' => 'egr', 'Eucgr.B01896' => 'egr', 'FAN04G1456' => 'fan', 'FAN08G1769' => 'fan', 'FAN08G2160' => 'fan', 'FAN13G2403' => 'fan', 'FAN13G3303' => 'fan', 'FAN15G2435' => 'fan', 'FAN17G0672' => 'fan', 'FAN17G2441' => 'fan', 'FAN18G1024' => 'fan', 'FAN22G1458' => 'fan', 'FAN24G0037' => 'fan', 'FAN24G0429' => 'fan', 'FAN24G2387' => 'fan', 'FAN27G2746' => 'fan', 'FvH4_2g20400' => 'fve', 'FvH4_2g20420' => 'fve', 'FvH4_2g20430' => 'fve', 'FvH4_4g01270' => 'fve', 'FvH4_4g01290' => 'fve', 'FvH4_4g01300' => 'fve', 'FvH4_4g01310' => 'fve', 'FvH4_4g01330' => 'fve', 'FvH4_5g09070' => 'fve', 'Glyma.10G243800' => 'gma', 'Glyma.20G150600' => 'gma', 'Gohir.A09G219200' => 'ghi', 'Gohir.A09G219300' => 'ghi', 'Gohir.D09G221400' => 'ghi', 'Gohir.D09G221500' => 'ghi', 'Gorai.006G242600' => 'gra', 'Gorai.006G242700' => 'gra', 'GSVIVG01018044001' => 'vvi', 'HanXRQChr03g0083821' => 'han', 'HanXRQChr03g0083841' => 'han', 'HanXRQChr03g0083881' => 'han', 'HanXRQChr03g0083901' => 'han', 'HanXRQChr03g0083921' => 'han', 'HanXRQChr03g0085331' => 'han', 'HanXRQChr03g0085361' => 'han', 'HanXRQChr03g0085411' => 'han', 'HanXRQChr03g0085421' => 'han', 'HanXRQChr03g0085431' => 'han', 'HanXRQChr08g0221991' => 'han', 'HanXRQChr11g0336061' => 'han', 'HanXRQChr11g0336411' => 'han', 'Haze_11234' => 'cav', 'Hma1.2p1_0549F.1_g177010' => 'hma', 'Hma1.2p1_0602F.1_g187630' => 'hma', 'Hund14876' => 'sun', 'Hund14879' => 'sun', 'Lalb_Chr06g0160741' => 'lal', 'Lalb_Chr21g0304781' => 'lal', 'Lj3A726G19' => 'lonja', 'Lj3A726T23' => 'lonja', 'Lj3A726T24' => 'lonja', 'Lj3A726T25' => 'lonja', 'Lj3A727T17' => 'lonja', 'Lj3C726T0' => 'lonja', 'Lj3C726T2' => 'lonja', 'Lj3P725T35' => 'lonja', 'Lj3P727T10' => 'lonja', 'Lj3P727T12' => 'lonja', 'Lj3P727T14' => 'lonja', 'Lj5g0023109' => 'lja', 'Lj6P646T44' => 'lonja', 'Lsat_1_v5_gn_6_75760' => 'lsa', 'Lsat_1_v5_gn_6_75800' => 'lsa', 'Lsat_1_v5_gn_6_75900' => 'lsa', 'Lsat_1_v5_gn_6_76240' => 'lsa', 'Lsat_1_v5_gn_6_76441' => 'lsa', 'Lsat_1_v5_gn_6_76700' => 'lsa', 'Lsat_1_v5_gn_6_76760' => 'lsa', 'Manes.15G033100' => 'mes', 'Mapoly0004s0074' => 'mpo', 'Mapoly0004s0075' => 'mpo', 'Mapoly0004s0163' => 'mpo', 'Mapoly0004s0164' => 'mpo', 'Mapoly0021s0018' => 'mpo', 'Mapoly0041s0136' => 'mpo', 'Mapoly0041s0137' => 'mpo', 'Mapoly0041s0138' => 'mpo', 'Mapoly0041s0139' => 'mpo', 'Mapoly0041s0141' => 'mpo', 'Mapoly0041s0142' => 'mpo', 'Mapoly0041s0143' => 'mpo', 'Mapoly0041s0144' => 'mpo', 'Mapoly0041s0145' => 'mpo', 'Mapoly0047s0106' => 'mpo', 'Mapoly0047s0108' => 'mpo', 'Mapoly0050s0051' => 'mpo', 'Mapoly0050s0052' => 'mpo', 'Mapoly0050s0053' => 'mpo', 'Mapoly0058s0013' => 'mpo', 'Mapoly0091s0078' => 'mpo', 'Mapoly0091s0079' => 'mpo', 'Mapoly0091s0080' => 'mpo', 'Mapoly0091s0081' => 'mpo', 'Mapoly0278s0004' => 'mpo', 'Mapoly0278s0005' => 'mpo', 'Mapoly0278s0006' => 'mpo', 'MBI11_g30648_MAGBIO' => 'mbi', 'MCO03G194' => 'mco', 'MCO03G590' => 'mco', 'MCO07G312' => 'mco', 'MCO10G318' => 'mco', 'MCO12G244' => 'mco', 'MCO13G148' => 'mco', 'MCO13G194' => 'mco', 'MCO16G238' => 'mco', 'MD06G1134100' => 'mdo', 'MD13G1200100' => 'mdo', 'MD13G1200300' => 'mdo', 'MD13G1200600' => 'mdo', 'MD14G1150400' => 'mdo', 'MD16G1200000' => 'mdo', 'Medtr1g102570' => 'mtr', 'Medtr1g102780' => 'mtr', 'Medtr1g102800' => 'mtr', 'Medtr1g102810' => 'mtr', 'Medtr1g102830' => 'mtr', 'MELO3C006499.2' => 'cme', 'Migut.G00385' => 'egut', 'MSTRG.4063' => 'ama', 'Nitab4.5_0000090g0260' => 'nta', 'Nitab4.5_0000977g0030' => 'nta', 'Nitab4.5_0002541g0040' => 'nta', 'Nitab4.5_0007068g0040' => 'nta', 'Nn005s41408' => 'nnu', 'Nn005s41410' => 'nnu', 'Oeu010310.1' => 'oeu', 'Oeu010311.1' => 'oeu', 'Oeu043472.1' => 'oeu', 'Os01g0246400' => 'osa', 'Os04g0267950' => 'osa', 'Os07g0178700' => 'osa', 'Os07g0178800' => 'osa', 'Peaxi162Scf00316g00046' => 'pax', 'Peaxi162Scf00316g00049' => 'pax', 'Peaxi162Scf00316g00059' => 'pax', 'Peaxi162Scf00316g00328' => 'pax', 'Peaxi162Scf00316g00329' => 'pax', 'Peaxi162Scf00316g00411' => 'pax', 'Peaxi162Scf00316g00521' => 'pax', 'Peaxi162Scf00492g00068' => 'pax', 'Peaxi162Scf35631g00002' => 'pax', 'PGR142G3720' => 'pgr', 'PGSC0003DMG400006442' => 'stu', 'Phvul.007G062000' => 'pvu', 'Potri.008G157750' => 'ptr', 'Potri.008G157900' => 'ptr', 'Potri.008G158000' => 'ptr', 'Potri.008G158200' => 'ptr', 'Pp3c11_7280' => 'ppa', 'Pp3c11_7980' => 'ppa', 'Pp3c12_19450' => 'ppa', 'Pp3c14_1480' => 'ppa', 'Pp3c14_1501' => 'ppa', 'Pp3c16_4900' => 'ppa', 'Pp3c16_5010' => 'ppa', 'Pp3c16_5060' => 'ppa', 'Pp3c19_18250' => 'ppa', 'Pp3c23_8530' => 'ppa', 'Pp3c23_8550' => 'ppa', 'Pp3c24_9670' => 'ppa', 'Pp3c2_21390' => 'ppa', 'Pp3c2_31380' => 'ppa', 'Pp3c3_16620' => 'ppa', 'Pp3c3_8090' => 'ppa', 'Pp3c3_8110' => 'ppa', 'Pp3c3_8130' => 'ppa', 'Pp3c3_8150' => 'ppa', 'Pp3c4_14320' => 'ppa', 'Pp3c6_2560' => 'ppa', 'Pp3c9_16700' => 'ppa', 'PRCOL_00000234' => 'pco', 'PRCOL_00000235' => 'pco', 'PRCOL_00000777' => 'pco', 'PRCOL_00002344' => 'pco', 'PRCOL_00002372' => 'pco', 'PRCOL_00006120' => 'pco', 'Prupe.1G021400' => 'ppe', 'Prupe.1G021500' => 'ppe', 'Prupe.1G021600' => 'ppe', 'Prupe.1G021700' => 'ppe', 'Prupe.1G021800' => 'ppe', 'Prupe.5G145100' => 'ppe', 'Psat6g204040' => 'psa', 'Psat6g204800' => 'psa', 'Psat6g204920' => 'psa', 'Psat6g204960' => 'psa', 'Psat6g205080' => 'psa', 'PSO017G0271' => 'pso', 'PSO017G1276' => 'pso', 'PSO017G1429' => 'pso', 'PSO017G1861' => 'pso', 'PSO017G2787' => 'pso', 'PSO017G4466' => 'pso', 'PSO017G5118' => 'pso', 'PSO017G5420' => 'pso', 'PSO063G3678' => 'pso', 'PSO210G0546' => 'pso', 'PSO317G0001' => 'pso', 'PSO357G0512' => 'pso', 'PSO478G2682' => 'pso', 'PSO647G0001' => 'pso', 'PSO675G0001' => 'pso', 'PSO675G2699' => 'pso', 'PSO675G2849' => 'pso', 'PSO675G4991' => 'pso', 'PSO689G0001' => 'pso', 'QL06p000916' => 'qlo', 'QL06p000921' => 'qlo', 'QL06p001398' => 'qlo', 'QL06p001407' => 'qlo', 'QL06p002031' => 'qlo', 'RcHm_v2.0_Chr4g0387791' => 'rch', 'RcHm_v2.0_Chr4g0387801' => 'rch', 'RcHm_v2.0_Chr6g0286501' => 'rch', 'RcHm_v2.0_Chr6g0286511' => 'rch', 'RcHm_v2.0_Chr6g0286521' => 'rch', 'RcHm_v2.0_Chr6g0286531' => 'rch', 'RcHm_v2.0_Chr7g0189141' => 'rch', 'Rhsim02G0028700' => 'rsi', 'Rhsim02G0028800' => 'rsi', 'Rhsim02G0028900' => 'rsi', 'Rhsim02G0029000' => 'rsi', 'Rhsim02G0029100' => 'rsi', 'Rhsim02G0029200' => 'rsi', 'Rhsim02G0029300' => 'rsi', 'Rhsim02G0029400' => 'rsi', 'Rhsim02G0029500' => 'rsi', 'Rhsim02G0029600' => 'rsi', 'RhsimUnG0024000' => 'rsi', 'RhsimUnG0024100' => 'rsi', 'RhsimUnG0024200' => 'rsi', 'RhsimUnG0024300' => 'rsi', 'RhsimUnG0024400' => 'rsi', 'RhsimUnG0024500' => 'rsi', 'RhsimUnG0024700' => 'rsi', 'RhsimUnG0024800' => 'rsi', 'RhsimUnG0024900' => 'rsi', 'RhsimUnG0025100' => 'rsi', 'Sabra08G0120200' => 'sbr', 'Sabra08G0120300' => 'sbr', 'Sabra08G0120500' => 'sbr', 'Sabra08G0120600' => 'sbr', 'Sabra10G0158900' => 'sbr', 'SalBow2G3492' => 'sbo', 'Sc13g0004760' => 'sci', 'Sc13g0004770' => 'sci', 'Sed0003417' => 'sed', 'Sed0019750' => 'sed', 'SEGI_03419' => 'sgi', 'SEGI_05907' => 'sgi', 'SEGI_10682' => 'sgi', 'SEGI_13528' => 'sgi', 'SEGI_16081' => 'sgi', 'SEGI_19370' => 'sgi', 'SEGI_21015' => 'sgi', 'SEGI_21944' => 'sgi', 'SEGI_32906' => 'sgi', 'SEGI_33093' => 'sgi', 'SEGI_36110' => 'sgi', 'SEGI_40397' => 'sgi', 'SGA_v2.0_scaffold191G40426' => 'sas', 'SGA_v2.0_scaffold353G49717' => 'sas', 'SGA_v2.0_scaffold50G18550' => 'sas', 'SMO119G0173' => 'smo', 'SMO172G0002' => 'smo', 'Solyc09g082690.3' => 'sly', 'Solyc09g082700.2' => 'sly', 'Sopen09g031550' => 'spe', 'Sopen09g031560' => 'spe', 'Sp3g20540' => 'spa', 'Sp7g07580' => 'spa', 'TAR134G0002' => 'tar', 'TAR236G0001' => 'tar', 'TAR365G0892' => 'tar', 'TAR636G0166' => 'tar', 'TAR636G0646' => 'tar', 'TAR636G0869' => 'tar', 'TAR636G1317' => 'tar', 'TAR636G1744' => 'tar', 'TAR636G3358' => 'tar', 'TAR636G3436' => 'tar', 'THA.LOC104803047' => 'tha', 'Thecc.04G238900' => 'tca', 'Thhalv10021557m.g' => 'esa', 'Thhalv10026318m.g' => 'esa', 'Thhalv10026335m.g' => 'esa', 'TPR.G17433' => 'tpr', 'TPR.G18915' => 'tpr', 'TPR.G26125' => 'tpr', 'TWI09G0677' => 'twi', 'TWI73G0287' => 'twi', 'unitig_748.g8326' => 'ugi', 'vmacro15370' => 'vma', 'vmacro15371' => 'vma', 'vmacro15372' => 'vma', 'vmacro15373' => 'vma', 'vmacro15374' => 'vma', 'VMungo0720G2826' => 'vmu', 'Zm00001eb116960' => 'zma', 'Zm00001eb301260' => 'zma', 'Zm00001eb301270' => 'zma' ), 'gf_id' => 'HOM05D001460', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001460' ), 'data_identifier' => 'HOM05D001460', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001460', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '433', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p22980' => 'bna', 'A01p32340' => 'bna', 'A03p42970' => 'bna', 'A05p25880' => 'bna', 'Aa31LG8G9320' => 'aar', 'Aa31LG8G9330' => 'aar', 'Aa31LG8G9340' => 'aar', 'Aa31sc221G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1034' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1528' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.829' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2222' => 'aag', 'Ah.12g058830' => 'amhyb', 'Ah.12g058840' => 'amhyb', 'AL3G37160' => 'aly', 'AL7G41310' => 'aly', 'Aqoxy5G00395' => 'aox', 'Aqoxy5G00396' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0C8NZA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5185HY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JZ1PRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MD3LS0' => 'arhy', 'AT3G22840' => 'ath', 'AT4G14690' => 'ath', 'ATR0665G054' => 'atr', 'Atru.chr4.2344' => 'acertr', 'Atru.chr4.2346' => 'acertr', 'Atru.chr4.2347' => 'acertr', 'Atru.chr4.2348' => 'acertr', 'Atru.chr4.2355' => 'acertr', 'Atru.chr4.2356' => 'acertr', 'Atru.chr4.2358' => 'acertr', 'Atru.chr4.2359' => 'acertr', 'Atru.chr4.2360' => 'acertr', 'Atru.chr4.2361' => 'acertr', 'AUR62030476' => 'cqu', 'AUR62030478' => 'cqu', 'AUR62030819' => 'cqu', 'AUR62030820' => 'cqu', 'BcaB03g14648' => 'bca', 'BcaB04g20492' => 'bca', 'BcaB06g26399' => 'bca', 'BcaC01g03416' => 'bca', 'BcaC01g03419' => 'bca', 'BcaC01g03421' => 'bca', 'BcaC01g03424' => 'bca', 'BcaC05g28012' => 'bca', 'BcaC09g49212' => 'bca', 'BcaC09g50140' => 'bca', 'BcaNung00346' => 'bca', 'BolC1t02785H' => 'bol', 'BolC1t04095H' => 'bol', 'BolC3t17545H' => 'bol', 'BolC5t32769H' => 'bol', 'BraA01t02211Z' => 'bra', 'BraA01t03359Z' => 'bra', 'BraA03t13441Z' => 'bra', 'BraA05t21476Z' => 'bra', 'C01p28420' => 'bna', 'C01p41350' => 'bna', 'C03p52750' => 'bna', 'C03p52780' => 'bna', 'C05p40270' => 'bna', 'CAN.G1437.9' => 'can', 'CANSAT78G0035' => 'cansat', 'CANSAT78G1036' => 'cansat', 'CANSAT78G2272' => 'cansat', 'CANSAT78G2478' => 'cansat', 'CARHR098700' => 'chi', 'CARHR221120' => 'chi', 'CARHR221150' => 'chi', 'Carub.0003s2297' => 'cru', 'Carub.0007s2749' => 'cru', 'Carub.0007s2750' => 'cru', 'Carub.0007s2751' => 'cru', 'Ca_10849_v3' => 'car', 'Cc03_g04300' => 'ccan', 'CDE02G3648' => 'cde', 'CDE05G0060' => 'cde', 'CDE05G0692' => 'cde', 'CDE05G2285' => 'cde', 'CDE05G2884' => 'cde', 'CDE05G3072' => 'cde', 'Cfa008439' => 'cfa', 'Cfa008441' => 'cfa', 'Cfa008443' => 'cfa', 'Cfa008448' => 'cfa', 'Ciclev10005974m.g' => 'ccl', 'Ciclev10006006m.g' => 'ccl', 'Ciclev10006775m.g' => 'ccl', 'CiPaw.02G120400' => 'cil', 'CiPaw.02G120500' => 'cil', 'CiPaw.02G120600' => 'cil', 'ClCG05G004850' => 'cla', 'COL.COLO4_21566' => 'col', 'Cpa.g.sc44.124' => 'cpa', 'Cre07.g320400' => 'cre', 'Cre07.g320450' => 'cre', 'Cre08.g384650' => 'cre', 'Cre09.g393173' => 'cre', 'Cre09.g394325' => 'cre', 'Cre14.g626750' => 'cre', 'Cre16.g679250' => 'cre', 'CsaV3_3G012890' => 'csa', 'CSS0010865' => 'camsi', 'CSS0044338' => 'camsi', 'DCAR_002366' => 'dca', 'DCAR_030687' => 'dca', 'DCAR_030688' => 'dca', 'Dinv14047' => 'din', 'Dinv14048' => 'din', 'Duzib151G0105' => 'dzi', 'Duzib151G0114' => 'dzi', 'Duzib212G1029' => 'dzi', 'ECA232G3536' => 'eca', 'ECA240G0786' => 'eca', 'ECA240G1802' => 'eca', 'ECA240G3760' => 'eca', 'ECA240G3920' => 'eca', 'EL10Ac5g12536' => 'bvu', 'EL10Ac5g12537' => 'bvu', 'EL10Ac5g12538' => 'bvu', 'Eucgr.B01004' => 'egr', 'Eucgr.B01006' => 'egr', 'Eucgr.B01007' => 'egr', 'Eucgr.B01008' => 'egr', 'Eucgr.B01895' => 'egr', 'Eucgr.B01896' => 'egr', 'FAN04G1456' => 'fan', 'FAN08G1769' => 'fan', 'FAN08G2160' => 'fan', 'FAN13G2403' => 'fan', 'FAN13G3303' => 'fan', 'FAN15G2435' => 'fan', 'FAN17G0672' => 'fan', 'FAN17G2441' => 'fan', 'FAN18G1024' => 'fan', 'FAN22G1458' => 'fan', 'FAN24G0037' => 'fan', 'FAN24G0429' => 'fan', 'FAN24G2387' => 'fan', 'FAN27G2746' => 'fan', 'FvH4_2g20400' => 'fve', 'FvH4_2g20420' => 'fve', 'FvH4_2g20430' => 'fve', 'FvH4_4g01270' => 'fve', 'FvH4_4g01290' => 'fve', 'FvH4_4g01300' => 'fve', 'FvH4_4g01310' => 'fve', 'FvH4_4g01330' => 'fve', 'FvH4_5g09070' => 'fve', 'Glyma.10G243800' => 'gma', 'Glyma.20G150600' => 'gma', 'Gohir.A09G219200' => 'ghi', 'Gohir.A09G219300' => 'ghi', 'Gohir.D09G221400' => 'ghi', 'Gohir.D09G221500' => 'ghi', 'Gorai.006G242600' => 'gra', 'Gorai.006G242700' => 'gra', 'GSVIVG01018044001' => 'vvi', 'HanXRQChr03g0083821' => 'han', 'HanXRQChr03g0083841' => 'han', 'HanXRQChr03g0083881' => 'han', 'HanXRQChr03g0083901' => 'han', 'HanXRQChr03g0083921' => 'han', 'HanXRQChr03g0085331' => 'han', 'HanXRQChr03g0085361' => 'han', 'HanXRQChr03g0085411' => 'han', 'HanXRQChr03g0085421' => 'han', 'HanXRQChr03g0085431' => 'han', 'HanXRQChr08g0221991' => 'han', 'HanXRQChr11g0336061' => 'han', 'HanXRQChr11g0336411' => 'han', 'Haze_11234' => 'cav', 'Hma1.2p1_0549F.1_g177010' => 'hma', 'Hma1.2p1_0602F.1_g187630' => 'hma', 'Hund14876' => 'sun', 'Hund14879' => 'sun', 'Lalb_Chr06g0160741' => 'lal', 'Lalb_Chr21g0304781' => 'lal', 'Lj3A726G19' => 'lonja', 'Lj3A726T23' => 'lonja', 'Lj3A726T24' => 'lonja', 'Lj3A726T25' => 'lonja', 'Lj3A727T17' => 'lonja', 'Lj3C726T0' => 'lonja', 'Lj3C726T2' => 'lonja', 'Lj3P725T35' => 'lonja', 'Lj3P727T10' => 'lonja', 'Lj3P727T12' => 'lonja', 'Lj3P727T14' => 'lonja', 'Lj5g0023109' => 'lja', 'Lj6P646T44' => 'lonja', 'Lsat_1_v5_gn_6_75760' => 'lsa', 'Lsat_1_v5_gn_6_75800' => 'lsa', 'Lsat_1_v5_gn_6_75900' => 'lsa', 'Lsat_1_v5_gn_6_76240' => 'lsa', 'Lsat_1_v5_gn_6_76441' => 'lsa', 'Lsat_1_v5_gn_6_76700' => 'lsa', 'Lsat_1_v5_gn_6_76760' => 'lsa', 'Manes.15G033100' => 'mes', 'Mapoly0004s0074' => 'mpo', 'Mapoly0004s0075' => 'mpo', 'Mapoly0004s0163' => 'mpo', 'Mapoly0004s0164' => 'mpo', 'Mapoly0021s0018' => 'mpo', 'Mapoly0041s0136' => 'mpo', 'Mapoly0041s0137' => 'mpo', 'Mapoly0041s0138' => 'mpo', 'Mapoly0041s0139' => 'mpo', 'Mapoly0041s0141' => 'mpo', 'Mapoly0041s0142' => 'mpo', 'Mapoly0041s0143' => 'mpo', 'Mapoly0041s0144' => 'mpo', 'Mapoly0041s0145' => 'mpo', 'Mapoly0047s0106' => 'mpo', 'Mapoly0047s0108' => 'mpo', 'Mapoly0050s0051' => 'mpo', 'Mapoly0050s0052' => 'mpo', 'Mapoly0050s0053' => 'mpo', 'Mapoly0058s0013' => 'mpo', 'Mapoly0091s0078' => 'mpo', 'Mapoly0091s0079' => 'mpo', 'Mapoly0091s0080' => 'mpo', 'Mapoly0091s0081' => 'mpo', 'Mapoly0278s0004' => 'mpo', 'Mapoly0278s0005' => 'mpo', 'Mapoly0278s0006' => 'mpo', 'MBI11_g30648_MAGBIO' => 'mbi', 'MCO03G194' => 'mco', 'MCO03G590' => 'mco', 'MCO07G312' => 'mco', 'MCO10G318' => 'mco', 'MCO12G244' => 'mco', 'MCO13G148' => 'mco', 'MCO13G194' => 'mco', 'MCO16G238' => 'mco', 'MD06G1134100' => 'mdo', 'MD13G1200100' => 'mdo', 'MD13G1200300' => 'mdo', 'MD13G1200600' => 'mdo', 'MD14G1150400' => 'mdo', 'MD16G1200000' => 'mdo', 'Medtr1g102570' => 'mtr', 'Medtr1g102780' => 'mtr', 'Medtr1g102800' => 'mtr', 'Medtr1g102810' => 'mtr', 'Medtr1g102830' => 'mtr', 'MELO3C006499.2' => 'cme', 'Migut.G00385' => 'egut', 'MSTRG.4063' => 'ama', 'Nitab4.5_0000090g0260' => 'nta', 'Nitab4.5_0000977g0030' => 'nta', 'Nitab4.5_0002541g0040' => 'nta', 'Nitab4.5_0007068g0040' => 'nta', 'Nn005s41408' => 'nnu', 'Nn005s41410' => 'nnu', 'Oeu010310.1' => 'oeu', 'Oeu010311.1' => 'oeu', 'Oeu043472.1' => 'oeu', 'Os01g0246400' => 'osa', 'Os04g0267950' => 'osa', 'Os07g0178700' => 'osa', 'Os07g0178800' => 'osa', 'Peaxi162Scf00316g00046' => 'pax', 'Peaxi162Scf00316g00049' => 'pax', 'Peaxi162Scf00316g00059' => 'pax', 'Peaxi162Scf00316g00328' => 'pax', 'Peaxi162Scf00316g00329' => 'pax', 'Peaxi162Scf00316g00411' => 'pax', 'Peaxi162Scf00316g00521' => 'pax', 'Peaxi162Scf00492g00068' => 'pax', 'Peaxi162Scf35631g00002' => 'pax', 'PGR142G3720' => 'pgr', 'PGSC0003DMG400006442' => 'stu', 'Phvul.007G062000' => 'pvu', 'Potri.008G157750' => 'ptr', 'Potri.008G157900' => 'ptr', 'Potri.008G158000' => 'ptr', 'Potri.008G158200' => 'ptr', 'Pp3c11_7280' => 'ppa', 'Pp3c11_7980' => 'ppa', 'Pp3c12_19450' => 'ppa', 'Pp3c14_1480' => 'ppa', 'Pp3c14_1501' => 'ppa', 'Pp3c16_4900' => 'ppa', 'Pp3c16_5010' => 'ppa', 'Pp3c16_5060' => 'ppa', 'Pp3c19_18250' => 'ppa', 'Pp3c23_8530' => 'ppa', 'Pp3c23_8550' => 'ppa', 'Pp3c24_9670' => 'ppa', 'Pp3c2_21390' => 'ppa', 'Pp3c2_31380' => 'ppa', 'Pp3c3_16620' => 'ppa', 'Pp3c3_8090' => 'ppa', 'Pp3c3_8110' => 'ppa', 'Pp3c3_8130' => 'ppa', 'Pp3c3_8150' => 'ppa', 'Pp3c4_14320' => 'ppa', 'Pp3c6_2560' => 'ppa', 'Pp3c9_16700' => 'ppa', 'PRCOL_00000234' => 'pco', 'PRCOL_00000235' => 'pco', 'PRCOL_00000777' => 'pco', 'PRCOL_00002344' => 'pco', 'PRCOL_00002372' => 'pco', 'PRCOL_00006120' => 'pco', 'Prupe.1G021400' => 'ppe', 'Prupe.1G021500' => 'ppe', 'Prupe.1G021600' => 'ppe', 'Prupe.1G021700' => 'ppe', 'Prupe.1G021800' => 'ppe', 'Prupe.5G145100' => 'ppe', 'Psat6g204040' => 'psa', 'Psat6g204800' => 'psa', 'Psat6g204920' => 'psa', 'Psat6g204960' => 'psa', 'Psat6g205080' => 'psa', 'PSO017G0271' => 'pso', 'PSO017G1276' => 'pso', 'PSO017G1429' => 'pso', 'PSO017G1861' => 'pso', 'PSO017G2787' => 'pso', 'PSO017G4466' => 'pso', 'PSO017G5118' => 'pso', 'PSO017G5420' => 'pso', 'PSO063G3678' => 'pso', 'PSO210G0546' => 'pso', 'PSO317G0001' => 'pso', 'PSO357G0512' => 'pso', 'PSO478G2682' => 'pso', 'PSO647G0001' => 'pso', 'PSO675G0001' => 'pso', 'PSO675G2699' => 'pso', 'PSO675G2849' => 'pso', 'PSO675G4991' => 'pso', 'PSO689G0001' => 'pso', 'QL06p000916' => 'qlo', 'QL06p000921' => 'qlo', 'QL06p001398' => 'qlo', 'QL06p001407' => 'qlo', 'QL06p002031' => 'qlo', 'RcHm_v2.0_Chr4g0387791' => 'rch', 'RcHm_v2.0_Chr4g0387801' => 'rch', 'RcHm_v2.0_Chr6g0286501' => 'rch', 'RcHm_v2.0_Chr6g0286511' => 'rch', 'RcHm_v2.0_Chr6g0286521' => 'rch', 'RcHm_v2.0_Chr6g0286531' => 'rch', 'RcHm_v2.0_Chr7g0189141' => 'rch', 'Rhsim02G0028700' => 'rsi', 'Rhsim02G0028800' => 'rsi', 'Rhsim02G0028900' => 'rsi', 'Rhsim02G0029000' => 'rsi', 'Rhsim02G0029100' => 'rsi', 'Rhsim02G0029200' => 'rsi', 'Rhsim02G0029300' => 'rsi', 'Rhsim02G0029400' => 'rsi', 'Rhsim02G0029500' => 'rsi', 'Rhsim02G0029600' => 'rsi', 'RhsimUnG0024000' => 'rsi', 'RhsimUnG0024100' => 'rsi', 'RhsimUnG0024200' => 'rsi', 'RhsimUnG0024300' => 'rsi', 'RhsimUnG0024400' => 'rsi', 'RhsimUnG0024500' => 'rsi', 'RhsimUnG0024700' => 'rsi', 'RhsimUnG0024800' => 'rsi', 'RhsimUnG0024900' => 'rsi', 'RhsimUnG0025100' => 'rsi', 'Sabra08G0120200' => 'sbr', 'Sabra08G0120300' => 'sbr', 'Sabra08G0120500' => 'sbr', 'Sabra08G0120600' => 'sbr', 'Sabra10G0158900' => 'sbr', 'SalBow2G3492' => 'sbo', 'Sc13g0004760' => 'sci', 'Sc13g0004770' => 'sci', 'Sed0003417' => 'sed', 'Sed0019750' => 'sed', 'SEGI_03419' => 'sgi', 'SEGI_05907' => 'sgi', 'SEGI_10682' => 'sgi', 'SEGI_13528' => 'sgi', 'SEGI_16081' => 'sgi', 'SEGI_19370' => 'sgi', 'SEGI_21015' => 'sgi', 'SEGI_21944' => 'sgi', 'SEGI_32906' => 'sgi', 'SEGI_33093' => 'sgi', 'SEGI_36110' => 'sgi', 'SEGI_40397' => 'sgi', 'SGA_v2.0_scaffold191G40426' => 'sas', 'SGA_v2.0_scaffold353G49717' => 'sas', 'SGA_v2.0_scaffold50G18550' => 'sas', 'SMO119G0173' => 'smo', 'SMO172G0002' => 'smo', 'Solyc09g082690.3' => 'sly', 'Solyc09g082700.2' => 'sly', 'Sopen09g031550' => 'spe', 'Sopen09g031560' => 'spe', 'Sp3g20540' => 'spa', 'Sp7g07580' => 'spa', 'TAR134G0002' => 'tar', 'TAR236G0001' => 'tar', 'TAR365G0892' => 'tar', 'TAR636G0166' => 'tar', 'TAR636G0646' => 'tar', 'TAR636G0869' => 'tar', 'TAR636G1317' => 'tar', 'TAR636G1744' => 'tar', 'TAR636G3358' => 'tar', 'TAR636G3436' => 'tar', 'THA.LOC104803047' => 'tha', 'Thecc.04G238900' => 'tca', 'Thhalv10021557m.g' => 'esa', 'Thhalv10026318m.g' => 'esa', 'Thhalv10026335m.g' => 'esa', 'TPR.G17433' => 'tpr', 'TPR.G18915' => 'tpr', 'TPR.G26125' => 'tpr', 'TWI09G0677' => 'twi', 'TWI73G0287' => 'twi', 'unitig_748.g8326' => 'ugi', 'vmacro15370' => 'vma', 'vmacro15371' => 'vma', 'vmacro15372' => 'vma', 'vmacro15373' => 'vma', 'vmacro15374' => 'vma', 'VMungo0720G2826' => 'vmu', 'Zm00001eb116960' => 'zma', 'Zm00001eb301260' => 'zma', 'Zm00001eb301270' => 'zma' ) $gf_id = 'HOM05D001460' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001460' ) $data_identifier = 'HOM05D001460' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 4, 'aag' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 2, 'aox' => (int) 2, 'arhy' => (int) 4, 'ath' => (int) 2, 'atr' => (int) 1, 'acertr' => (int) 10, 'cqu' => (int) 4, 'bca' => (int) 11, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 1, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 1, 'ccan' => (int) 1, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 1, 'col' => (int) 1, 'cpa' => (int) 1, 'cre' => (int) 7, 'csa' => (int) 1, 'camsi' => (int) 2, 'dca' => (int) 3, 'din' => (int) 2, 'dzi' => (int) 3, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 14, 'fve' => (int) 9, 'gma' => (int) 2, 'ghi' => (int) 4, 'gra' => (int) 2, 'vvi' => (int) 1, 'han' => (int) 13, 'cav' => (int) 1, 'hma' => (int) 2, 'sun' => (int) 2, 'lal' => (int) 2, 'lonja' => (int) 12, 'lja' => (int) 1, 'lsa' => (int) 7, 'mes' => (int) 1, 'mpo' => (int) 27, 'mbi' => (int) 1, 'mco' => (int) 8, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 1, 'egut' => (int) 1, 'ama' => (int) 1, 'nta' => (int) 4, 'nnu' => (int) 2, 'oeu' => (int) 3, 'osa' => (int) 4, 'pax' => (int) 9, 'pgr' => (int) 1, 'stu' => (int) 1, 'pvu' => (int) 1, 'ptr' => (int) 4, 'ppa' => (int) 22, 'pco' => (int) 6, 'ppe' => (int) 6, 'psa' => (int) 5, 'pso' => (int) 19, 'qlo' => (int) 5, 'rch' => (int) 7, 'rsi' => (int) 20, 'sbr' => (int) 5, 'sbo' => (int) 1, 'sci' => (int) 2, 'sed' => (int) 2, 'sgi' => (int) 12, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 2, 'tar' => (int) 10, 'tha' => (int) 1, 'tca' => (int) 1, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 2, 'ugi' => (int) 1, 'vma' => (int) 5, 'vmu' => (int) 1, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb301270' $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' => 'HOM05D001460', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '433', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p22980' => 'bna', 'A01p32340' => 'bna', 'A03p42970' => 'bna', 'A05p25880' => 'bna', 'Aa31LG8G9320' => 'aar', 'Aa31LG8G9330' => 'aar', 'Aa31LG8G9340' => 'aar', 'Aa31sc221G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1034' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1528' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.829' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2222' => 'aag', 'Ah.12g058830' => 'amhyb', 'Ah.12g058840' => 'amhyb', 'AL3G37160' => 'aly', 'AL7G41310' => 'aly', 'Aqoxy5G00395' => 'aox', 'Aqoxy5G00396' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0C8NZA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5185HY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JZ1PRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MD3LS0' => 'arhy', 'AT3G22840' => 'ath', 'AT4G14690' => 'ath', 'ATR0665G054' => 'atr', 'Atru.chr4.2344' => 'acertr', 'Atru.chr4.2346' => 'acertr', 'Atru.chr4.2347' => 'acertr', 'Atru.chr4.2348' => 'acertr', 'Atru.chr4.2355' => 'acertr', 'Atru.chr4.2356' => 'acertr', 'Atru.chr4.2358' => 'acertr', 'Atru.chr4.2359' => 'acertr', 'Atru.chr4.2360' => 'acertr', 'Atru.chr4.2361' => 'acertr', 'AUR62030476' => 'cqu', 'AUR62030478' => 'cqu', 'AUR62030819' => 'cqu', 'AUR62030820' => 'cqu', 'BcaB03g14648' => 'bca', 'BcaB04g20492' => 'bca', 'BcaB06g26399' => 'bca', 'BcaC01g03416' => 'bca', 'BcaC01g03419' => 'bca', 'BcaC01g03421' => 'bca', 'BcaC01g03424' => 'bca', 'BcaC05g28012' => 'bca', 'BcaC09g49212' => 'bca', 'BcaC09g50140' => 'bca', 'BcaNung00346' => 'bca', 'BolC1t02785H' => 'bol', 'BolC1t04095H' => 'bol', 'BolC3t17545H' => 'bol', 'BolC5t32769H' => 'bol', 'BraA01t02211Z' => 'bra', 'BraA01t03359Z' => 'bra', 'BraA03t13441Z' => 'bra', 'BraA05t21476Z' => 'bra', 'C01p28420' => 'bna', 'C01p41350' => 'bna', 'C03p52750' => 'bna', 'C03p52780' => 'bna', 'C05p40270' => 'bna', 'CAN.G1437.9' => 'can', 'CANSAT78G0035' => 'cansat', 'CANSAT78G1036' => 'cansat', 'CANSAT78G2272' => 'cansat', 'CANSAT78G2478' => 'cansat', 'CARHR098700' => 'chi', 'CARHR221120' => 'chi', 'CARHR221150' => 'chi', 'Carub.0003s2297' => 'cru', 'Carub.0007s2749' => 'cru', 'Carub.0007s2750' => 'cru', 'Carub.0007s2751' => 'cru', 'Ca_10849_v3' => 'car', 'Cc03_g04300' => 'ccan', 'CDE02G3648' => 'cde', 'CDE05G0060' => 'cde', 'CDE05G0692' => 'cde', 'CDE05G2285' => 'cde', 'CDE05G2884' => 'cde', 'CDE05G3072' => 'cde', 'Cfa008439' => 'cfa', 'Cfa008441' => 'cfa', 'Cfa008443' => 'cfa', 'Cfa008448' => 'cfa', 'Ciclev10005974m.g' => 'ccl', 'Ciclev10006006m.g' => 'ccl', 'Ciclev10006775m.g' => 'ccl', 'CiPaw.02G120400' => 'cil', 'CiPaw.02G120500' => 'cil', 'CiPaw.02G120600' => 'cil', 'ClCG05G004850' => 'cla', 'COL.COLO4_21566' => 'col', 'Cpa.g.sc44.124' => 'cpa', 'Cre07.g320400' => 'cre', 'Cre07.g320450' => 'cre', 'Cre08.g384650' => 'cre', 'Cre09.g393173' => 'cre', 'Cre09.g394325' => 'cre', 'Cre14.g626750' => 'cre', 'Cre16.g679250' => 'cre', 'CsaV3_3G012890' => 'csa', 'CSS0010865' => 'camsi', 'CSS0044338' => 'camsi', 'DCAR_002366' => 'dca', 'DCAR_030687' => 'dca', 'DCAR_030688' => 'dca', 'Dinv14047' => 'din', 'Dinv14048' => 'din', 'Duzib151G0105' => 'dzi', 'Duzib151G0114' => 'dzi', 'Duzib212G1029' => 'dzi', 'ECA232G3536' => 'eca', 'ECA240G0786' => 'eca', 'ECA240G1802' => 'eca', 'ECA240G3760' => 'eca', 'ECA240G3920' => 'eca', 'EL10Ac5g12536' => 'bvu', 'EL10Ac5g12537' => 'bvu', 'EL10Ac5g12538' => 'bvu', 'Eucgr.B01004' => 'egr', 'Eucgr.B01006' => 'egr', 'Eucgr.B01007' => 'egr', 'Eucgr.B01008' => 'egr', 'Eucgr.B01895' => 'egr', 'Eucgr.B01896' => 'egr', 'FAN04G1456' => 'fan', 'FAN08G1769' => 'fan', 'FAN08G2160' => 'fan', 'FAN13G2403' => 'fan', 'FAN13G3303' => 'fan', 'FAN15G2435' => 'fan', 'FAN17G0672' => 'fan', 'FAN17G2441' => 'fan', 'FAN18G1024' => 'fan', 'FAN22G1458' => 'fan', 'FAN24G0037' => 'fan', 'FAN24G0429' => 'fan', 'FAN24G2387' => 'fan', 'FAN27G2746' => 'fan', 'FvH4_2g20400' => 'fve', 'FvH4_2g20420' => 'fve', 'FvH4_2g20430' => 'fve', 'FvH4_4g01270' => 'fve', 'FvH4_4g01290' => 'fve', 'FvH4_4g01300' => 'fve', 'FvH4_4g01310' => 'fve', 'FvH4_4g01330' => 'fve', 'FvH4_5g09070' => 'fve', 'Glyma.10G243800' => 'gma', 'Glyma.20G150600' => 'gma', 'Gohir.A09G219200' => 'ghi', 'Gohir.A09G219300' => 'ghi', 'Gohir.D09G221400' => 'ghi', 'Gohir.D09G221500' => 'ghi', 'Gorai.006G242600' => 'gra', 'Gorai.006G242700' => 'gra', 'GSVIVG01018044001' => 'vvi', 'HanXRQChr03g0083821' => 'han', 'HanXRQChr03g0083841' => 'han', 'HanXRQChr03g0083881' => 'han', 'HanXRQChr03g0083901' => 'han', 'HanXRQChr03g0083921' => 'han', 'HanXRQChr03g0085331' => 'han', 'HanXRQChr03g0085361' => 'han', 'HanXRQChr03g0085411' => 'han', 'HanXRQChr03g0085421' => 'han', 'HanXRQChr03g0085431' => 'han', 'HanXRQChr08g0221991' => 'han', 'HanXRQChr11g0336061' => 'han', 'HanXRQChr11g0336411' => 'han', 'Haze_11234' => 'cav', 'Hma1.2p1_0549F.1_g177010' => 'hma', 'Hma1.2p1_0602F.1_g187630' => 'hma', 'Hund14876' => 'sun', 'Hund14879' => 'sun', 'Lalb_Chr06g0160741' => 'lal', 'Lalb_Chr21g0304781' => 'lal', 'Lj3A726G19' => 'lonja', 'Lj3A726T23' => 'lonja', 'Lj3A726T24' => 'lonja', 'Lj3A726T25' => 'lonja', 'Lj3A727T17' => 'lonja', 'Lj3C726T0' => 'lonja', 'Lj3C726T2' => 'lonja', 'Lj3P725T35' => 'lonja', 'Lj3P727T10' => 'lonja', 'Lj3P727T12' => 'lonja', 'Lj3P727T14' => 'lonja', 'Lj5g0023109' => 'lja', 'Lj6P646T44' => 'lonja', 'Lsat_1_v5_gn_6_75760' => 'lsa', 'Lsat_1_v5_gn_6_75800' => 'lsa', 'Lsat_1_v5_gn_6_75900' => 'lsa', 'Lsat_1_v5_gn_6_76240' => 'lsa', 'Lsat_1_v5_gn_6_76441' => 'lsa', 'Lsat_1_v5_gn_6_76700' => 'lsa', 'Lsat_1_v5_gn_6_76760' => 'lsa', 'Manes.15G033100' => 'mes', 'Mapoly0004s0074' => 'mpo', 'Mapoly0004s0075' => 'mpo', 'Mapoly0004s0163' => 'mpo', 'Mapoly0004s0164' => 'mpo', 'Mapoly0021s0018' => 'mpo', 'Mapoly0041s0136' => 'mpo', 'Mapoly0041s0137' => 'mpo', 'Mapoly0041s0138' => 'mpo', 'Mapoly0041s0139' => 'mpo', 'Mapoly0041s0141' => 'mpo', 'Mapoly0041s0142' => 'mpo', 'Mapoly0041s0143' => 'mpo', 'Mapoly0041s0144' => 'mpo', 'Mapoly0041s0145' => 'mpo', 'Mapoly0047s0106' => 'mpo', 'Mapoly0047s0108' => 'mpo', 'Mapoly0050s0051' => 'mpo', 'Mapoly0050s0052' => 'mpo', 'Mapoly0050s0053' => 'mpo', 'Mapoly0058s0013' => 'mpo', 'Mapoly0091s0078' => 'mpo', 'Mapoly0091s0079' => 'mpo', 'Mapoly0091s0080' => 'mpo', 'Mapoly0091s0081' => 'mpo', 'Mapoly0278s0004' => 'mpo', 'Mapoly0278s0005' => 'mpo', 'Mapoly0278s0006' => 'mpo', 'MBI11_g30648_MAGBIO' => 'mbi', 'MCO03G194' => 'mco', 'MCO03G590' => 'mco', 'MCO07G312' => 'mco', 'MCO10G318' => 'mco', 'MCO12G244' => 'mco', 'MCO13G148' => 'mco', 'MCO13G194' => 'mco', 'MCO16G238' => 'mco', 'MD06G1134100' => 'mdo', 'MD13G1200100' => 'mdo', 'MD13G1200300' => 'mdo', 'MD13G1200600' => 'mdo', 'MD14G1150400' => 'mdo', 'MD16G1200000' => 'mdo', 'Medtr1g102570' => 'mtr', 'Medtr1g102780' => 'mtr', 'Medtr1g102800' => 'mtr', 'Medtr1g102810' => 'mtr', 'Medtr1g102830' => 'mtr', 'MELO3C006499.2' => 'cme', 'Migut.G00385' => 'egut', 'MSTRG.4063' => 'ama', 'Nitab4.5_0000090g0260' => 'nta', 'Nitab4.5_0000977g0030' => 'nta', 'Nitab4.5_0002541g0040' => 'nta', 'Nitab4.5_0007068g0040' => 'nta', 'Nn005s41408' => 'nnu', 'Nn005s41410' => 'nnu', 'Oeu010310.1' => 'oeu', 'Oeu010311.1' => 'oeu', 'Oeu043472.1' => 'oeu', 'Os01g0246400' => 'osa', 'Os04g0267950' => 'osa', 'Os07g0178700' => 'osa', 'Os07g0178800' => 'osa', 'Peaxi162Scf00316g00046' => 'pax', 'Peaxi162Scf00316g00049' => 'pax', 'Peaxi162Scf00316g00059' => 'pax', 'Peaxi162Scf00316g00328' => 'pax', 'Peaxi162Scf00316g00329' => 'pax', 'Peaxi162Scf00316g00411' => 'pax', 'Peaxi162Scf00316g00521' => 'pax', 'Peaxi162Scf00492g00068' => 'pax', 'Peaxi162Scf35631g00002' => 'pax', 'PGR142G3720' => 'pgr', 'PGSC0003DMG400006442' => 'stu', 'Phvul.007G062000' => 'pvu', 'Potri.008G157750' => 'ptr', 'Potri.008G157900' => 'ptr', 'Potri.008G158000' => 'ptr', 'Potri.008G158200' => 'ptr', 'Pp3c11_7280' => 'ppa', 'Pp3c11_7980' => 'ppa', 'Pp3c12_19450' => 'ppa', 'Pp3c14_1480' => 'ppa', 'Pp3c14_1501' => 'ppa', 'Pp3c16_4900' => 'ppa', 'Pp3c16_5010' => 'ppa', 'Pp3c16_5060' => 'ppa', 'Pp3c19_18250' => 'ppa', 'Pp3c23_8530' => 'ppa', 'Pp3c23_8550' => 'ppa', 'Pp3c24_9670' => 'ppa', 'Pp3c2_21390' => 'ppa', 'Pp3c2_31380' => 'ppa', 'Pp3c3_16620' => 'ppa', 'Pp3c3_8090' => 'ppa', 'Pp3c3_8110' => 'ppa', 'Pp3c3_8130' => 'ppa', 'Pp3c3_8150' => 'ppa', 'Pp3c4_14320' => 'ppa', 'Pp3c6_2560' => 'ppa', 'Pp3c9_16700' => 'ppa', 'PRCOL_00000234' => 'pco', 'PRCOL_00000235' => 'pco', 'PRCOL_00000777' => 'pco', 'PRCOL_00002344' => 'pco', 'PRCOL_00002372' => 'pco', 'PRCOL_00006120' => 'pco', 'Prupe.1G021400' => 'ppe', 'Prupe.1G021500' => 'ppe', 'Prupe.1G021600' => 'ppe', 'Prupe.1G021700' => 'ppe', 'Prupe.1G021800' => 'ppe', 'Prupe.5G145100' => 'ppe', 'Psat6g204040' => 'psa', 'Psat6g204800' => 'psa', 'Psat6g204920' => 'psa', 'Psat6g204960' => 'psa', 'Psat6g205080' => 'psa', 'PSO017G0271' => 'pso', 'PSO017G1276' => 'pso', 'PSO017G1429' => 'pso', 'PSO017G1861' => 'pso', 'PSO017G2787' => 'pso', 'PSO017G4466' => 'pso', 'PSO017G5118' => 'pso', 'PSO017G5420' => 'pso', 'PSO063G3678' => 'pso', 'PSO210G0546' => 'pso', 'PSO317G0001' => 'pso', 'PSO357G0512' => 'pso', 'PSO478G2682' => 'pso', 'PSO647G0001' => 'pso', 'PSO675G0001' => 'pso', 'PSO675G2699' => 'pso', 'PSO675G2849' => 'pso', 'PSO675G4991' => 'pso', 'PSO689G0001' => 'pso', 'QL06p000916' => 'qlo', 'QL06p000921' => 'qlo', 'QL06p001398' => 'qlo', 'QL06p001407' => 'qlo', 'QL06p002031' => 'qlo', 'RcHm_v2.0_Chr4g0387791' => 'rch', 'RcHm_v2.0_Chr4g0387801' => 'rch', 'RcHm_v2.0_Chr6g0286501' => 'rch', 'RcHm_v2.0_Chr6g0286511' => 'rch', 'RcHm_v2.0_Chr6g0286521' => 'rch', 'RcHm_v2.0_Chr6g0286531' => 'rch', 'RcHm_v2.0_Chr7g0189141' => 'rch', 'Rhsim02G0028700' => 'rsi', 'Rhsim02G0028800' => 'rsi', 'Rhsim02G0028900' => 'rsi', 'Rhsim02G0029000' => 'rsi', 'Rhsim02G0029100' => 'rsi', 'Rhsim02G0029200' => 'rsi', 'Rhsim02G0029300' => 'rsi', 'Rhsim02G0029400' => 'rsi', 'Rhsim02G0029500' => 'rsi', 'Rhsim02G0029600' => 'rsi', 'RhsimUnG0024000' => 'rsi', 'RhsimUnG0024100' => 'rsi', 'RhsimUnG0024200' => 'rsi', 'RhsimUnG0024300' => 'rsi', 'RhsimUnG0024400' => 'rsi', 'RhsimUnG0024500' => 'rsi', 'RhsimUnG0024700' => 'rsi', 'RhsimUnG0024800' => 'rsi', 'RhsimUnG0024900' => 'rsi', 'RhsimUnG0025100' => 'rsi', 'Sabra08G0120200' => 'sbr', 'Sabra08G0120300' => 'sbr', 'Sabra08G0120500' => 'sbr', 'Sabra08G0120600' => 'sbr', 'Sabra10G0158900' => 'sbr', 'SalBow2G3492' => 'sbo', 'Sc13g0004760' => 'sci', 'Sc13g0004770' => 'sci', 'Sed0003417' => 'sed', 'Sed0019750' => 'sed', 'SEGI_03419' => 'sgi', 'SEGI_05907' => 'sgi', 'SEGI_10682' => 'sgi', 'SEGI_13528' => 'sgi', 'SEGI_16081' => 'sgi', 'SEGI_19370' => 'sgi', 'SEGI_21015' => 'sgi', 'SEGI_21944' => 'sgi', 'SEGI_32906' => 'sgi', 'SEGI_33093' => 'sgi', 'SEGI_36110' => 'sgi', 'SEGI_40397' => 'sgi', 'SGA_v2.0_scaffold191G40426' => 'sas', 'SGA_v2.0_scaffold353G49717' => 'sas', 'SGA_v2.0_scaffold50G18550' => 'sas', 'SMO119G0173' => 'smo', 'SMO172G0002' => 'smo', 'Solyc09g082690.3' => 'sly', 'Solyc09g082700.2' => 'sly', 'Sopen09g031550' => 'spe', 'Sopen09g031560' => 'spe', 'Sp3g20540' => 'spa', 'Sp7g07580' => 'spa', 'TAR134G0002' => 'tar', 'TAR236G0001' => 'tar', 'TAR365G0892' => 'tar', 'TAR636G0166' => 'tar', 'TAR636G0646' => 'tar', 'TAR636G0869' => 'tar', 'TAR636G1317' => 'tar', 'TAR636G1744' => 'tar', 'TAR636G3358' => 'tar', 'TAR636G3436' => 'tar', 'THA.LOC104803047' => 'tha', 'Thecc.04G238900' => 'tca', 'Thhalv10021557m.g' => 'esa', 'Thhalv10026318m.g' => 'esa', 'Thhalv10026335m.g' => 'esa', 'TPR.G17433' => 'tpr', 'TPR.G18915' => 'tpr', 'TPR.G26125' => 'tpr', 'TWI09G0677' => 'twi', 'TWI73G0287' => 'twi', 'unitig_748.g8326' => 'ugi', 'vmacro15370' => 'vma', 'vmacro15371' => 'vma', 'vmacro15372' => 'vma', 'vmacro15373' => 'vma', 'vmacro15374' => 'vma', 'VMungo0720G2826' => 'vmu', 'Zm00001eb116960' => 'zma', 'Zm00001eb301260' => 'zma', 'Zm00001eb301270' => 'zma' ), 'gf_id' => 'HOM05D001460', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001460' ), 'data_identifier' => 'HOM05D001460', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001460', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '433', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p22980' => 'bna', 'A01p32340' => 'bna', 'A03p42970' => 'bna', 'A05p25880' => 'bna', 'Aa31LG8G9320' => 'aar', 'Aa31LG8G9330' => 'aar', 'Aa31LG8G9340' => 'aar', 'Aa31sc221G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1034' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1528' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.829' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2222' => 'aag', 'Ah.12g058830' => 'amhyb', 'Ah.12g058840' => 'amhyb', 'AL3G37160' => 'aly', 'AL7G41310' => 'aly', 'Aqoxy5G00395' => 'aox', 'Aqoxy5G00396' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0C8NZA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5185HY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JZ1PRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MD3LS0' => 'arhy', 'AT3G22840' => 'ath', 'AT4G14690' => 'ath', 'ATR0665G054' => 'atr', 'Atru.chr4.2344' => 'acertr', 'Atru.chr4.2346' => 'acertr', 'Atru.chr4.2347' => 'acertr', 'Atru.chr4.2348' => 'acertr', 'Atru.chr4.2355' => 'acertr', 'Atru.chr4.2356' => 'acertr', 'Atru.chr4.2358' => 'acertr', 'Atru.chr4.2359' => 'acertr', 'Atru.chr4.2360' => 'acertr', 'Atru.chr4.2361' => 'acertr', 'AUR62030476' => 'cqu', 'AUR62030478' => 'cqu', 'AUR62030819' => 'cqu', 'AUR62030820' => 'cqu', 'BcaB03g14648' => 'bca', 'BcaB04g20492' => 'bca', 'BcaB06g26399' => 'bca', 'BcaC01g03416' => 'bca', 'BcaC01g03419' => 'bca', 'BcaC01g03421' => 'bca', 'BcaC01g03424' => 'bca', 'BcaC05g28012' => 'bca', 'BcaC09g49212' => 'bca', 'BcaC09g50140' => 'bca', 'BcaNung00346' => 'bca', 'BolC1t02785H' => 'bol', 'BolC1t04095H' => 'bol', 'BolC3t17545H' => 'bol', 'BolC5t32769H' => 'bol', 'BraA01t02211Z' => 'bra', 'BraA01t03359Z' => 'bra', 'BraA03t13441Z' => 'bra', 'BraA05t21476Z' => 'bra', 'C01p28420' => 'bna', 'C01p41350' => 'bna', 'C03p52750' => 'bna', 'C03p52780' => 'bna', 'C05p40270' => 'bna', 'CAN.G1437.9' => 'can', 'CANSAT78G0035' => 'cansat', 'CANSAT78G1036' => 'cansat', 'CANSAT78G2272' => 'cansat', 'CANSAT78G2478' => 'cansat', 'CARHR098700' => 'chi', 'CARHR221120' => 'chi', 'CARHR221150' => 'chi', 'Carub.0003s2297' => 'cru', 'Carub.0007s2749' => 'cru', 'Carub.0007s2750' => 'cru', 'Carub.0007s2751' => 'cru', 'Ca_10849_v3' => 'car', 'Cc03_g04300' => 'ccan', 'CDE02G3648' => 'cde', 'CDE05G0060' => 'cde', 'CDE05G0692' => 'cde', 'CDE05G2285' => 'cde', 'CDE05G2884' => 'cde', 'CDE05G3072' => 'cde', 'Cfa008439' => 'cfa', 'Cfa008441' => 'cfa', 'Cfa008443' => 'cfa', 'Cfa008448' => 'cfa', 'Ciclev10005974m.g' => 'ccl', 'Ciclev10006006m.g' => 'ccl', 'Ciclev10006775m.g' => 'ccl', 'CiPaw.02G120400' => 'cil', 'CiPaw.02G120500' => 'cil', 'CiPaw.02G120600' => 'cil', 'ClCG05G004850' => 'cla', 'COL.COLO4_21566' => 'col', 'Cpa.g.sc44.124' => 'cpa', 'Cre07.g320400' => 'cre', 'Cre07.g320450' => 'cre', 'Cre08.g384650' => 'cre', 'Cre09.g393173' => 'cre', 'Cre09.g394325' => 'cre', 'Cre14.g626750' => 'cre', 'Cre16.g679250' => 'cre', 'CsaV3_3G012890' => 'csa', 'CSS0010865' => 'camsi', 'CSS0044338' => 'camsi', 'DCAR_002366' => 'dca', 'DCAR_030687' => 'dca', 'DCAR_030688' => 'dca', 'Dinv14047' => 'din', 'Dinv14048' => 'din', 'Duzib151G0105' => 'dzi', 'Duzib151G0114' => 'dzi', 'Duzib212G1029' => 'dzi', 'ECA232G3536' => 'eca', 'ECA240G0786' => 'eca', 'ECA240G1802' => 'eca', 'ECA240G3760' => 'eca', 'ECA240G3920' => 'eca', 'EL10Ac5g12536' => 'bvu', 'EL10Ac5g12537' => 'bvu', 'EL10Ac5g12538' => 'bvu', 'Eucgr.B01004' => 'egr', 'Eucgr.B01006' => 'egr', 'Eucgr.B01007' => 'egr', 'Eucgr.B01008' => 'egr', 'Eucgr.B01895' => 'egr', 'Eucgr.B01896' => 'egr', 'FAN04G1456' => 'fan', 'FAN08G1769' => 'fan', 'FAN08G2160' => 'fan', 'FAN13G2403' => 'fan', 'FAN13G3303' => 'fan', 'FAN15G2435' => 'fan', 'FAN17G0672' => 'fan', 'FAN17G2441' => 'fan', 'FAN18G1024' => 'fan', 'FAN22G1458' => 'fan', 'FAN24G0037' => 'fan', 'FAN24G0429' => 'fan', 'FAN24G2387' => 'fan', 'FAN27G2746' => 'fan', 'FvH4_2g20400' => 'fve', 'FvH4_2g20420' => 'fve', 'FvH4_2g20430' => 'fve', 'FvH4_4g01270' => 'fve', 'FvH4_4g01290' => 'fve', 'FvH4_4g01300' => 'fve', 'FvH4_4g01310' => 'fve', 'FvH4_4g01330' => 'fve', 'FvH4_5g09070' => 'fve', 'Glyma.10G243800' => 'gma', 'Glyma.20G150600' => 'gma', 'Gohir.A09G219200' => 'ghi', 'Gohir.A09G219300' => 'ghi', 'Gohir.D09G221400' => 'ghi', 'Gohir.D09G221500' => 'ghi', 'Gorai.006G242600' => 'gra', 'Gorai.006G242700' => 'gra', 'GSVIVG01018044001' => 'vvi', 'HanXRQChr03g0083821' => 'han', 'HanXRQChr03g0083841' => 'han', 'HanXRQChr03g0083881' => 'han', 'HanXRQChr03g0083901' => 'han', 'HanXRQChr03g0083921' => 'han', 'HanXRQChr03g0085331' => 'han', 'HanXRQChr03g0085361' => 'han', 'HanXRQChr03g0085411' => 'han', 'HanXRQChr03g0085421' => 'han', 'HanXRQChr03g0085431' => 'han', 'HanXRQChr08g0221991' => 'han', 'HanXRQChr11g0336061' => 'han', 'HanXRQChr11g0336411' => 'han', 'Haze_11234' => 'cav', 'Hma1.2p1_0549F.1_g177010' => 'hma', 'Hma1.2p1_0602F.1_g187630' => 'hma', 'Hund14876' => 'sun', 'Hund14879' => 'sun', 'Lalb_Chr06g0160741' => 'lal', 'Lalb_Chr21g0304781' => 'lal', 'Lj3A726G19' => 'lonja', 'Lj3A726T23' => 'lonja', 'Lj3A726T24' => 'lonja', 'Lj3A726T25' => 'lonja', 'Lj3A727T17' => 'lonja', 'Lj3C726T0' => 'lonja', 'Lj3C726T2' => 'lonja', 'Lj3P725T35' => 'lonja', 'Lj3P727T10' => 'lonja', 'Lj3P727T12' => 'lonja', 'Lj3P727T14' => 'lonja', 'Lj5g0023109' => 'lja', 'Lj6P646T44' => 'lonja', 'Lsat_1_v5_gn_6_75760' => 'lsa', 'Lsat_1_v5_gn_6_75800' => 'lsa', 'Lsat_1_v5_gn_6_75900' => 'lsa', 'Lsat_1_v5_gn_6_76240' => 'lsa', 'Lsat_1_v5_gn_6_76441' => 'lsa', 'Lsat_1_v5_gn_6_76700' => 'lsa', 'Lsat_1_v5_gn_6_76760' => 'lsa', 'Manes.15G033100' => 'mes', 'Mapoly0004s0074' => 'mpo', 'Mapoly0004s0075' => 'mpo', 'Mapoly0004s0163' => 'mpo', 'Mapoly0004s0164' => 'mpo', 'Mapoly0021s0018' => 'mpo', 'Mapoly0041s0136' => 'mpo', 'Mapoly0041s0137' => 'mpo', 'Mapoly0041s0138' => 'mpo', 'Mapoly0041s0139' => 'mpo', 'Mapoly0041s0141' => 'mpo', 'Mapoly0041s0142' => 'mpo', 'Mapoly0041s0143' => 'mpo', 'Mapoly0041s0144' => 'mpo', 'Mapoly0041s0145' => 'mpo', 'Mapoly0047s0106' => 'mpo', 'Mapoly0047s0108' => 'mpo', 'Mapoly0050s0051' => 'mpo', 'Mapoly0050s0052' => 'mpo', 'Mapoly0050s0053' => 'mpo', 'Mapoly0058s0013' => 'mpo', 'Mapoly0091s0078' => 'mpo', 'Mapoly0091s0079' => 'mpo', 'Mapoly0091s0080' => 'mpo', 'Mapoly0091s0081' => 'mpo', 'Mapoly0278s0004' => 'mpo', 'Mapoly0278s0005' => 'mpo', 'Mapoly0278s0006' => 'mpo', 'MBI11_g30648_MAGBIO' => 'mbi', 'MCO03G194' => 'mco', 'MCO03G590' => 'mco', 'MCO07G312' => 'mco', 'MCO10G318' => 'mco', 'MCO12G244' => 'mco', 'MCO13G148' => 'mco', 'MCO13G194' => 'mco', 'MCO16G238' => 'mco', 'MD06G1134100' => 'mdo', 'MD13G1200100' => 'mdo', 'MD13G1200300' => 'mdo', 'MD13G1200600' => 'mdo', 'MD14G1150400' => 'mdo', 'MD16G1200000' => 'mdo', 'Medtr1g102570' => 'mtr', 'Medtr1g102780' => 'mtr', 'Medtr1g102800' => 'mtr', 'Medtr1g102810' => 'mtr', 'Medtr1g102830' => 'mtr', 'MELO3C006499.2' => 'cme', 'Migut.G00385' => 'egut', 'MSTRG.4063' => 'ama', 'Nitab4.5_0000090g0260' => 'nta', 'Nitab4.5_0000977g0030' => 'nta', 'Nitab4.5_0002541g0040' => 'nta', 'Nitab4.5_0007068g0040' => 'nta', 'Nn005s41408' => 'nnu', 'Nn005s41410' => 'nnu', 'Oeu010310.1' => 'oeu', 'Oeu010311.1' => 'oeu', 'Oeu043472.1' => 'oeu', 'Os01g0246400' => 'osa', 'Os04g0267950' => 'osa', 'Os07g0178700' => 'osa', 'Os07g0178800' => 'osa', 'Peaxi162Scf00316g00046' => 'pax', 'Peaxi162Scf00316g00049' => 'pax', 'Peaxi162Scf00316g00059' => 'pax', 'Peaxi162Scf00316g00328' => 'pax', 'Peaxi162Scf00316g00329' => 'pax', 'Peaxi162Scf00316g00411' => 'pax', 'Peaxi162Scf00316g00521' => 'pax', 'Peaxi162Scf00492g00068' => 'pax', 'Peaxi162Scf35631g00002' => 'pax', 'PGR142G3720' => 'pgr', 'PGSC0003DMG400006442' => 'stu', 'Phvul.007G062000' => 'pvu', 'Potri.008G157750' => 'ptr', 'Potri.008G157900' => 'ptr', 'Potri.008G158000' => 'ptr', 'Potri.008G158200' => 'ptr', 'Pp3c11_7280' => 'ppa', 'Pp3c11_7980' => 'ppa', 'Pp3c12_19450' => 'ppa', 'Pp3c14_1480' => 'ppa', 'Pp3c14_1501' => 'ppa', 'Pp3c16_4900' => 'ppa', 'Pp3c16_5010' => 'ppa', 'Pp3c16_5060' => 'ppa', 'Pp3c19_18250' => 'ppa', 'Pp3c23_8530' => 'ppa', 'Pp3c23_8550' => 'ppa', 'Pp3c24_9670' => 'ppa', 'Pp3c2_21390' => 'ppa', 'Pp3c2_31380' => 'ppa', 'Pp3c3_16620' => 'ppa', 'Pp3c3_8090' => 'ppa', 'Pp3c3_8110' => 'ppa', 'Pp3c3_8130' => 'ppa', 'Pp3c3_8150' => 'ppa', 'Pp3c4_14320' => 'ppa', 'Pp3c6_2560' => 'ppa', 'Pp3c9_16700' => 'ppa', 'PRCOL_00000234' => 'pco', 'PRCOL_00000235' => 'pco', 'PRCOL_00000777' => 'pco', 'PRCOL_00002344' => 'pco', 'PRCOL_00002372' => 'pco', 'PRCOL_00006120' => 'pco', 'Prupe.1G021400' => 'ppe', 'Prupe.1G021500' => 'ppe', 'Prupe.1G021600' => 'ppe', 'Prupe.1G021700' => 'ppe', 'Prupe.1G021800' => 'ppe', 'Prupe.5G145100' => 'ppe', 'Psat6g204040' => 'psa', 'Psat6g204800' => 'psa', 'Psat6g204920' => 'psa', 'Psat6g204960' => 'psa', 'Psat6g205080' => 'psa', 'PSO017G0271' => 'pso', 'PSO017G1276' => 'pso', 'PSO017G1429' => 'pso', 'PSO017G1861' => 'pso', 'PSO017G2787' => 'pso', 'PSO017G4466' => 'pso', 'PSO017G5118' => 'pso', 'PSO017G5420' => 'pso', 'PSO063G3678' => 'pso', 'PSO210G0546' => 'pso', 'PSO317G0001' => 'pso', 'PSO357G0512' => 'pso', 'PSO478G2682' => 'pso', 'PSO647G0001' => 'pso', 'PSO675G0001' => 'pso', 'PSO675G2699' => 'pso', 'PSO675G2849' => 'pso', 'PSO675G4991' => 'pso', 'PSO689G0001' => 'pso', 'QL06p000916' => 'qlo', 'QL06p000921' => 'qlo', 'QL06p001398' => 'qlo', 'QL06p001407' => 'qlo', 'QL06p002031' => 'qlo', 'RcHm_v2.0_Chr4g0387791' => 'rch', 'RcHm_v2.0_Chr4g0387801' => 'rch', 'RcHm_v2.0_Chr6g0286501' => 'rch', 'RcHm_v2.0_Chr6g0286511' => 'rch', 'RcHm_v2.0_Chr6g0286521' => 'rch', 'RcHm_v2.0_Chr6g0286531' => 'rch', 'RcHm_v2.0_Chr7g0189141' => 'rch', 'Rhsim02G0028700' => 'rsi', 'Rhsim02G0028800' => 'rsi', 'Rhsim02G0028900' => 'rsi', 'Rhsim02G0029000' => 'rsi', 'Rhsim02G0029100' => 'rsi', 'Rhsim02G0029200' => 'rsi', 'Rhsim02G0029300' => 'rsi', 'Rhsim02G0029400' => 'rsi', 'Rhsim02G0029500' => 'rsi', 'Rhsim02G0029600' => 'rsi', 'RhsimUnG0024000' => 'rsi', 'RhsimUnG0024100' => 'rsi', 'RhsimUnG0024200' => 'rsi', 'RhsimUnG0024300' => 'rsi', 'RhsimUnG0024400' => 'rsi', 'RhsimUnG0024500' => 'rsi', 'RhsimUnG0024700' => 'rsi', 'RhsimUnG0024800' => 'rsi', 'RhsimUnG0024900' => 'rsi', 'RhsimUnG0025100' => 'rsi', 'Sabra08G0120200' => 'sbr', 'Sabra08G0120300' => 'sbr', 'Sabra08G0120500' => 'sbr', 'Sabra08G0120600' => 'sbr', 'Sabra10G0158900' => 'sbr', 'SalBow2G3492' => 'sbo', 'Sc13g0004760' => 'sci', 'Sc13g0004770' => 'sci', 'Sed0003417' => 'sed', 'Sed0019750' => 'sed', 'SEGI_03419' => 'sgi', 'SEGI_05907' => 'sgi', 'SEGI_10682' => 'sgi', 'SEGI_13528' => 'sgi', 'SEGI_16081' => 'sgi', 'SEGI_19370' => 'sgi', 'SEGI_21015' => 'sgi', 'SEGI_21944' => 'sgi', 'SEGI_32906' => 'sgi', 'SEGI_33093' => 'sgi', 'SEGI_36110' => 'sgi', 'SEGI_40397' => 'sgi', 'SGA_v2.0_scaffold191G40426' => 'sas', 'SGA_v2.0_scaffold353G49717' => 'sas', 'SGA_v2.0_scaffold50G18550' => 'sas', 'SMO119G0173' => 'smo', 'SMO172G0002' => 'smo', 'Solyc09g082690.3' => 'sly', 'Solyc09g082700.2' => 'sly', 'Sopen09g031550' => 'spe', 'Sopen09g031560' => 'spe', 'Sp3g20540' => 'spa', 'Sp7g07580' => 'spa', 'TAR134G0002' => 'tar', 'TAR236G0001' => 'tar', 'TAR365G0892' => 'tar', 'TAR636G0166' => 'tar', 'TAR636G0646' => 'tar', 'TAR636G0869' => 'tar', 'TAR636G1317' => 'tar', 'TAR636G1744' => 'tar', 'TAR636G3358' => 'tar', 'TAR636G3436' => 'tar', 'THA.LOC104803047' => 'tha', 'Thecc.04G238900' => 'tca', 'Thhalv10021557m.g' => 'esa', 'Thhalv10026318m.g' => 'esa', 'Thhalv10026335m.g' => 'esa', 'TPR.G17433' => 'tpr', 'TPR.G18915' => 'tpr', 'TPR.G26125' => 'tpr', 'TWI09G0677' => 'twi', 'TWI73G0287' => 'twi', 'unitig_748.g8326' => 'ugi', 'vmacro15370' => 'vma', 'vmacro15371' => 'vma', 'vmacro15372' => 'vma', 'vmacro15373' => 'vma', 'vmacro15374' => 'vma', 'VMungo0720G2826' => 'vmu', 'Zm00001eb116960' => 'zma', 'Zm00001eb301260' => 'zma', 'Zm00001eb301270' => 'zma' ) $gf_id = 'HOM05D001460' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001460' ) $data_identifier = 'HOM05D001460' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 4, 'aag' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 2, 'aox' => (int) 2, 'arhy' => (int) 4, 'ath' => (int) 2, 'atr' => (int) 1, 'acertr' => (int) 10, 'cqu' => (int) 4, 'bca' => (int) 11, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 1, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 1, 'ccan' => (int) 1, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 1, 'col' => (int) 1, 'cpa' => (int) 1, 'cre' => (int) 7, 'csa' => (int) 1, 'camsi' => (int) 2, 'dca' => (int) 3, 'din' => (int) 2, 'dzi' => (int) 3, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 14, 'fve' => (int) 9, 'gma' => (int) 2, 'ghi' => (int) 4, 'gra' => (int) 2, 'vvi' => (int) 1, 'han' => (int) 13, 'cav' => (int) 1, 'hma' => (int) 2, 'sun' => (int) 2, 'lal' => (int) 2, 'lonja' => (int) 12, 'lja' => (int) 1, 'lsa' => (int) 7, 'mes' => (int) 1, 'mpo' => (int) 27, 'mbi' => (int) 1, 'mco' => (int) 8, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 1, 'egut' => (int) 1, 'ama' => (int) 1, 'nta' => (int) 4, 'nnu' => (int) 2, 'oeu' => (int) 3, 'osa' => (int) 4, 'pax' => (int) 9, 'pgr' => (int) 1, 'stu' => (int) 1, 'pvu' => (int) 1, 'ptr' => (int) 4, 'ppa' => (int) 22, 'pco' => (int) 6, 'ppe' => (int) 6, 'psa' => (int) 5, 'pso' => (int) 19, 'qlo' => (int) 5, 'rch' => (int) 7, 'rsi' => (int) 20, 'sbr' => (int) 5, 'sbo' => (int) 1, 'sci' => (int) 2, 'sed' => (int) 2, 'sgi' => (int) 12, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 2, 'tar' => (int) 10, 'tha' => (int) 1, 'tca' => (int) 1, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 2, 'ugi' => (int) 1, 'vma' => (int) 5, 'vmu' => (int) 1, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb301270' $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' => 'HOM05D001460', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '433', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p22980' => 'bna', 'A01p32340' => 'bna', 'A03p42970' => 'bna', 'A05p25880' => 'bna', 'Aa31LG8G9320' => 'aar', 'Aa31LG8G9330' => 'aar', 'Aa31LG8G9340' => 'aar', 'Aa31sc221G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1034' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1528' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.829' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2222' => 'aag', 'Ah.12g058830' => 'amhyb', 'Ah.12g058840' => 'amhyb', 'AL3G37160' => 'aly', 'AL7G41310' => 'aly', 'Aqoxy5G00395' => 'aox', 'Aqoxy5G00396' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0C8NZA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5185HY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JZ1PRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MD3LS0' => 'arhy', 'AT3G22840' => 'ath', 'AT4G14690' => 'ath', 'ATR0665G054' => 'atr', 'Atru.chr4.2344' => 'acertr', 'Atru.chr4.2346' => 'acertr', 'Atru.chr4.2347' => 'acertr', 'Atru.chr4.2348' => 'acertr', 'Atru.chr4.2355' => 'acertr', 'Atru.chr4.2356' => 'acertr', 'Atru.chr4.2358' => 'acertr', 'Atru.chr4.2359' => 'acertr', 'Atru.chr4.2360' => 'acertr', 'Atru.chr4.2361' => 'acertr', 'AUR62030476' => 'cqu', 'AUR62030478' => 'cqu', 'AUR62030819' => 'cqu', 'AUR62030820' => 'cqu', 'BcaB03g14648' => 'bca', 'BcaB04g20492' => 'bca', 'BcaB06g26399' => 'bca', 'BcaC01g03416' => 'bca', 'BcaC01g03419' => 'bca', 'BcaC01g03421' => 'bca', 'BcaC01g03424' => 'bca', 'BcaC05g28012' => 'bca', 'BcaC09g49212' => 'bca', 'BcaC09g50140' => 'bca', 'BcaNung00346' => 'bca', 'BolC1t02785H' => 'bol', 'BolC1t04095H' => 'bol', 'BolC3t17545H' => 'bol', 'BolC5t32769H' => 'bol', 'BraA01t02211Z' => 'bra', 'BraA01t03359Z' => 'bra', 'BraA03t13441Z' => 'bra', 'BraA05t21476Z' => 'bra', 'C01p28420' => 'bna', 'C01p41350' => 'bna', 'C03p52750' => 'bna', 'C03p52780' => 'bna', 'C05p40270' => 'bna', 'CAN.G1437.9' => 'can', 'CANSAT78G0035' => 'cansat', 'CANSAT78G1036' => 'cansat', 'CANSAT78G2272' => 'cansat', 'CANSAT78G2478' => 'cansat', 'CARHR098700' => 'chi', 'CARHR221120' => 'chi', 'CARHR221150' => 'chi', 'Carub.0003s2297' => 'cru', 'Carub.0007s2749' => 'cru', 'Carub.0007s2750' => 'cru', 'Carub.0007s2751' => 'cru', 'Ca_10849_v3' => 'car', 'Cc03_g04300' => 'ccan', 'CDE02G3648' => 'cde', 'CDE05G0060' => 'cde', 'CDE05G0692' => 'cde', 'CDE05G2285' => 'cde', 'CDE05G2884' => 'cde', 'CDE05G3072' => 'cde', 'Cfa008439' => 'cfa', 'Cfa008441' => 'cfa', 'Cfa008443' => 'cfa', 'Cfa008448' => 'cfa', 'Ciclev10005974m.g' => 'ccl', 'Ciclev10006006m.g' => 'ccl', 'Ciclev10006775m.g' => 'ccl', 'CiPaw.02G120400' => 'cil', 'CiPaw.02G120500' => 'cil', 'CiPaw.02G120600' => 'cil', 'ClCG05G004850' => 'cla', 'COL.COLO4_21566' => 'col', 'Cpa.g.sc44.124' => 'cpa', 'Cre07.g320400' => 'cre', 'Cre07.g320450' => 'cre', 'Cre08.g384650' => 'cre', 'Cre09.g393173' => 'cre', 'Cre09.g394325' => 'cre', 'Cre14.g626750' => 'cre', 'Cre16.g679250' => 'cre', 'CsaV3_3G012890' => 'csa', 'CSS0010865' => 'camsi', 'CSS0044338' => 'camsi', 'DCAR_002366' => 'dca', 'DCAR_030687' => 'dca', 'DCAR_030688' => 'dca', 'Dinv14047' => 'din', 'Dinv14048' => 'din', 'Duzib151G0105' => 'dzi', 'Duzib151G0114' => 'dzi', 'Duzib212G1029' => 'dzi', 'ECA232G3536' => 'eca', 'ECA240G0786' => 'eca', 'ECA240G1802' => 'eca', 'ECA240G3760' => 'eca', 'ECA240G3920' => 'eca', 'EL10Ac5g12536' => 'bvu', 'EL10Ac5g12537' => 'bvu', 'EL10Ac5g12538' => 'bvu', 'Eucgr.B01004' => 'egr', 'Eucgr.B01006' => 'egr', 'Eucgr.B01007' => 'egr', 'Eucgr.B01008' => 'egr', 'Eucgr.B01895' => 'egr', 'Eucgr.B01896' => 'egr', 'FAN04G1456' => 'fan', 'FAN08G1769' => 'fan', 'FAN08G2160' => 'fan', 'FAN13G2403' => 'fan', 'FAN13G3303' => 'fan', 'FAN15G2435' => 'fan', 'FAN17G0672' => 'fan', 'FAN17G2441' => 'fan', 'FAN18G1024' => 'fan', 'FAN22G1458' => 'fan', 'FAN24G0037' => 'fan', 'FAN24G0429' => 'fan', 'FAN24G2387' => 'fan', 'FAN27G2746' => 'fan', 'FvH4_2g20400' => 'fve', 'FvH4_2g20420' => 'fve', 'FvH4_2g20430' => 'fve', 'FvH4_4g01270' => 'fve', 'FvH4_4g01290' => 'fve', 'FvH4_4g01300' => 'fve', 'FvH4_4g01310' => 'fve', 'FvH4_4g01330' => 'fve', 'FvH4_5g09070' => 'fve', 'Glyma.10G243800' => 'gma', 'Glyma.20G150600' => 'gma', 'Gohir.A09G219200' => 'ghi', 'Gohir.A09G219300' => 'ghi', 'Gohir.D09G221400' => 'ghi', 'Gohir.D09G221500' => 'ghi', 'Gorai.006G242600' => 'gra', 'Gorai.006G242700' => 'gra', 'GSVIVG01018044001' => 'vvi', 'HanXRQChr03g0083821' => 'han', 'HanXRQChr03g0083841' => 'han', 'HanXRQChr03g0083881' => 'han', 'HanXRQChr03g0083901' => 'han', 'HanXRQChr03g0083921' => 'han', 'HanXRQChr03g0085331' => 'han', 'HanXRQChr03g0085361' => 'han', 'HanXRQChr03g0085411' => 'han', 'HanXRQChr03g0085421' => 'han', 'HanXRQChr03g0085431' => 'han', 'HanXRQChr08g0221991' => 'han', 'HanXRQChr11g0336061' => 'han', 'HanXRQChr11g0336411' => 'han', 'Haze_11234' => 'cav', 'Hma1.2p1_0549F.1_g177010' => 'hma', 'Hma1.2p1_0602F.1_g187630' => 'hma', 'Hund14876' => 'sun', 'Hund14879' => 'sun', 'Lalb_Chr06g0160741' => 'lal', 'Lalb_Chr21g0304781' => 'lal', 'Lj3A726G19' => 'lonja', 'Lj3A726T23' => 'lonja', 'Lj3A726T24' => 'lonja', 'Lj3A726T25' => 'lonja', 'Lj3A727T17' => 'lonja', 'Lj3C726T0' => 'lonja', 'Lj3C726T2' => 'lonja', 'Lj3P725T35' => 'lonja', 'Lj3P727T10' => 'lonja', 'Lj3P727T12' => 'lonja', 'Lj3P727T14' => 'lonja', 'Lj5g0023109' => 'lja', 'Lj6P646T44' => 'lonja', 'Lsat_1_v5_gn_6_75760' => 'lsa', 'Lsat_1_v5_gn_6_75800' => 'lsa', 'Lsat_1_v5_gn_6_75900' => 'lsa', 'Lsat_1_v5_gn_6_76240' => 'lsa', 'Lsat_1_v5_gn_6_76441' => 'lsa', 'Lsat_1_v5_gn_6_76700' => 'lsa', 'Lsat_1_v5_gn_6_76760' => 'lsa', 'Manes.15G033100' => 'mes', 'Mapoly0004s0074' => 'mpo', 'Mapoly0004s0075' => 'mpo', 'Mapoly0004s0163' => 'mpo', 'Mapoly0004s0164' => 'mpo', 'Mapoly0021s0018' => 'mpo', 'Mapoly0041s0136' => 'mpo', 'Mapoly0041s0137' => 'mpo', 'Mapoly0041s0138' => 'mpo', 'Mapoly0041s0139' => 'mpo', 'Mapoly0041s0141' => 'mpo', 'Mapoly0041s0142' => 'mpo', 'Mapoly0041s0143' => 'mpo', 'Mapoly0041s0144' => 'mpo', 'Mapoly0041s0145' => 'mpo', 'Mapoly0047s0106' => 'mpo', 'Mapoly0047s0108' => 'mpo', 'Mapoly0050s0051' => 'mpo', 'Mapoly0050s0052' => 'mpo', 'Mapoly0050s0053' => 'mpo', 'Mapoly0058s0013' => 'mpo', 'Mapoly0091s0078' => 'mpo', 'Mapoly0091s0079' => 'mpo', 'Mapoly0091s0080' => 'mpo', 'Mapoly0091s0081' => 'mpo', 'Mapoly0278s0004' => 'mpo', 'Mapoly0278s0005' => 'mpo', 'Mapoly0278s0006' => 'mpo', 'MBI11_g30648_MAGBIO' => 'mbi', 'MCO03G194' => 'mco', 'MCO03G590' => 'mco', 'MCO07G312' => 'mco', 'MCO10G318' => 'mco', 'MCO12G244' => 'mco', 'MCO13G148' => 'mco', 'MCO13G194' => 'mco', 'MCO16G238' => 'mco', 'MD06G1134100' => 'mdo', 'MD13G1200100' => 'mdo', 'MD13G1200300' => 'mdo', 'MD13G1200600' => 'mdo', 'MD14G1150400' => 'mdo', 'MD16G1200000' => 'mdo', 'Medtr1g102570' => 'mtr', 'Medtr1g102780' => 'mtr', 'Medtr1g102800' => 'mtr', 'Medtr1g102810' => 'mtr', 'Medtr1g102830' => 'mtr', 'MELO3C006499.2' => 'cme', 'Migut.G00385' => 'egut', 'MSTRG.4063' => 'ama', 'Nitab4.5_0000090g0260' => 'nta', 'Nitab4.5_0000977g0030' => 'nta', 'Nitab4.5_0002541g0040' => 'nta', 'Nitab4.5_0007068g0040' => 'nta', 'Nn005s41408' => 'nnu', 'Nn005s41410' => 'nnu', 'Oeu010310.1' => 'oeu', 'Oeu010311.1' => 'oeu', 'Oeu043472.1' => 'oeu', 'Os01g0246400' => 'osa', 'Os04g0267950' => 'osa', 'Os07g0178700' => 'osa', 'Os07g0178800' => 'osa', 'Peaxi162Scf00316g00046' => 'pax', 'Peaxi162Scf00316g00049' => 'pax', 'Peaxi162Scf00316g00059' => 'pax', 'Peaxi162Scf00316g00328' => 'pax', 'Peaxi162Scf00316g00329' => 'pax', 'Peaxi162Scf00316g00411' => 'pax', 'Peaxi162Scf00316g00521' => 'pax', 'Peaxi162Scf00492g00068' => 'pax', 'Peaxi162Scf35631g00002' => 'pax', 'PGR142G3720' => 'pgr', 'PGSC0003DMG400006442' => 'stu', 'Phvul.007G062000' => 'pvu', 'Potri.008G157750' => 'ptr', 'Potri.008G157900' => 'ptr', 'Potri.008G158000' => 'ptr', 'Potri.008G158200' => 'ptr', 'Pp3c11_7280' => 'ppa', 'Pp3c11_7980' => 'ppa', 'Pp3c12_19450' => 'ppa', 'Pp3c14_1480' => 'ppa', 'Pp3c14_1501' => 'ppa', 'Pp3c16_4900' => 'ppa', 'Pp3c16_5010' => 'ppa', 'Pp3c16_5060' => 'ppa', 'Pp3c19_18250' => 'ppa', 'Pp3c23_8530' => 'ppa', 'Pp3c23_8550' => 'ppa', 'Pp3c24_9670' => 'ppa', 'Pp3c2_21390' => 'ppa', 'Pp3c2_31380' => 'ppa', 'Pp3c3_16620' => 'ppa', 'Pp3c3_8090' => 'ppa', 'Pp3c3_8110' => 'ppa', 'Pp3c3_8130' => 'ppa', 'Pp3c3_8150' => 'ppa', 'Pp3c4_14320' => 'ppa', 'Pp3c6_2560' => 'ppa', 'Pp3c9_16700' => 'ppa', 'PRCOL_00000234' => 'pco', 'PRCOL_00000235' => 'pco', 'PRCOL_00000777' => 'pco', 'PRCOL_00002344' => 'pco', 'PRCOL_00002372' => 'pco', 'PRCOL_00006120' => 'pco', 'Prupe.1G021400' => 'ppe', 'Prupe.1G021500' => 'ppe', 'Prupe.1G021600' => 'ppe', 'Prupe.1G021700' => 'ppe', 'Prupe.1G021800' => 'ppe', 'Prupe.5G145100' => 'ppe', 'Psat6g204040' => 'psa', 'Psat6g204800' => 'psa', 'Psat6g204920' => 'psa', 'Psat6g204960' => 'psa', 'Psat6g205080' => 'psa', 'PSO017G0271' => 'pso', 'PSO017G1276' => 'pso', 'PSO017G1429' => 'pso', 'PSO017G1861' => 'pso', 'PSO017G2787' => 'pso', 'PSO017G4466' => 'pso', 'PSO017G5118' => 'pso', 'PSO017G5420' => 'pso', 'PSO063G3678' => 'pso', 'PSO210G0546' => 'pso', 'PSO317G0001' => 'pso', 'PSO357G0512' => 'pso', 'PSO478G2682' => 'pso', 'PSO647G0001' => 'pso', 'PSO675G0001' => 'pso', 'PSO675G2699' => 'pso', 'PSO675G2849' => 'pso', 'PSO675G4991' => 'pso', 'PSO689G0001' => 'pso', 'QL06p000916' => 'qlo', 'QL06p000921' => 'qlo', 'QL06p001398' => 'qlo', 'QL06p001407' => 'qlo', 'QL06p002031' => 'qlo', 'RcHm_v2.0_Chr4g0387791' => 'rch', 'RcHm_v2.0_Chr4g0387801' => 'rch', 'RcHm_v2.0_Chr6g0286501' => 'rch', 'RcHm_v2.0_Chr6g0286511' => 'rch', 'RcHm_v2.0_Chr6g0286521' => 'rch', 'RcHm_v2.0_Chr6g0286531' => 'rch', 'RcHm_v2.0_Chr7g0189141' => 'rch', 'Rhsim02G0028700' => 'rsi', 'Rhsim02G0028800' => 'rsi', 'Rhsim02G0028900' => 'rsi', 'Rhsim02G0029000' => 'rsi', 'Rhsim02G0029100' => 'rsi', 'Rhsim02G0029200' => 'rsi', 'Rhsim02G0029300' => 'rsi', 'Rhsim02G0029400' => 'rsi', 'Rhsim02G0029500' => 'rsi', 'Rhsim02G0029600' => 'rsi', 'RhsimUnG0024000' => 'rsi', 'RhsimUnG0024100' => 'rsi', 'RhsimUnG0024200' => 'rsi', 'RhsimUnG0024300' => 'rsi', 'RhsimUnG0024400' => 'rsi', 'RhsimUnG0024500' => 'rsi', 'RhsimUnG0024700' => 'rsi', 'RhsimUnG0024800' => 'rsi', 'RhsimUnG0024900' => 'rsi', 'RhsimUnG0025100' => 'rsi', 'Sabra08G0120200' => 'sbr', 'Sabra08G0120300' => 'sbr', 'Sabra08G0120500' => 'sbr', 'Sabra08G0120600' => 'sbr', 'Sabra10G0158900' => 'sbr', 'SalBow2G3492' => 'sbo', 'Sc13g0004760' => 'sci', 'Sc13g0004770' => 'sci', 'Sed0003417' => 'sed', 'Sed0019750' => 'sed', 'SEGI_03419' => 'sgi', 'SEGI_05907' => 'sgi', 'SEGI_10682' => 'sgi', 'SEGI_13528' => 'sgi', 'SEGI_16081' => 'sgi', 'SEGI_19370' => 'sgi', 'SEGI_21015' => 'sgi', 'SEGI_21944' => 'sgi', 'SEGI_32906' => 'sgi', 'SEGI_33093' => 'sgi', 'SEGI_36110' => 'sgi', 'SEGI_40397' => 'sgi', 'SGA_v2.0_scaffold191G40426' => 'sas', 'SGA_v2.0_scaffold353G49717' => 'sas', 'SGA_v2.0_scaffold50G18550' => 'sas', 'SMO119G0173' => 'smo', 'SMO172G0002' => 'smo', 'Solyc09g082690.3' => 'sly', 'Solyc09g082700.2' => 'sly', 'Sopen09g031550' => 'spe', 'Sopen09g031560' => 'spe', 'Sp3g20540' => 'spa', 'Sp7g07580' => 'spa', 'TAR134G0002' => 'tar', 'TAR236G0001' => 'tar', 'TAR365G0892' => 'tar', 'TAR636G0166' => 'tar', 'TAR636G0646' => 'tar', 'TAR636G0869' => 'tar', 'TAR636G1317' => 'tar', 'TAR636G1744' => 'tar', 'TAR636G3358' => 'tar', 'TAR636G3436' => 'tar', 'THA.LOC104803047' => 'tha', 'Thecc.04G238900' => 'tca', 'Thhalv10021557m.g' => 'esa', 'Thhalv10026318m.g' => 'esa', 'Thhalv10026335m.g' => 'esa', 'TPR.G17433' => 'tpr', 'TPR.G18915' => 'tpr', 'TPR.G26125' => 'tpr', 'TWI09G0677' => 'twi', 'TWI73G0287' => 'twi', 'unitig_748.g8326' => 'ugi', 'vmacro15370' => 'vma', 'vmacro15371' => 'vma', 'vmacro15372' => 'vma', 'vmacro15373' => 'vma', 'vmacro15374' => 'vma', 'VMungo0720G2826' => 'vmu', 'Zm00001eb116960' => 'zma', 'Zm00001eb301260' => 'zma', 'Zm00001eb301270' => 'zma' ), 'gf_id' => 'HOM05D001460', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001460' ), 'data_identifier' => 'HOM05D001460', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001460', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '433', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p22980' => 'bna', 'A01p32340' => 'bna', 'A03p42970' => 'bna', 'A05p25880' => 'bna', 'Aa31LG8G9320' => 'aar', 'Aa31LG8G9330' => 'aar', 'Aa31LG8G9340' => 'aar', 'Aa31sc221G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1034' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1528' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.829' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2222' => 'aag', 'Ah.12g058830' => 'amhyb', 'Ah.12g058840' => 'amhyb', 'AL3G37160' => 'aly', 'AL7G41310' => 'aly', 'Aqoxy5G00395' => 'aox', 'Aqoxy5G00396' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0C8NZA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5185HY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JZ1PRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MD3LS0' => 'arhy', 'AT3G22840' => 'ath', 'AT4G14690' => 'ath', 'ATR0665G054' => 'atr', 'Atru.chr4.2344' => 'acertr', 'Atru.chr4.2346' => 'acertr', 'Atru.chr4.2347' => 'acertr', 'Atru.chr4.2348' => 'acertr', 'Atru.chr4.2355' => 'acertr', 'Atru.chr4.2356' => 'acertr', 'Atru.chr4.2358' => 'acertr', 'Atru.chr4.2359' => 'acertr', 'Atru.chr4.2360' => 'acertr', 'Atru.chr4.2361' => 'acertr', 'AUR62030476' => 'cqu', 'AUR62030478' => 'cqu', 'AUR62030819' => 'cqu', 'AUR62030820' => 'cqu', 'BcaB03g14648' => 'bca', 'BcaB04g20492' => 'bca', 'BcaB06g26399' => 'bca', 'BcaC01g03416' => 'bca', 'BcaC01g03419' => 'bca', 'BcaC01g03421' => 'bca', 'BcaC01g03424' => 'bca', 'BcaC05g28012' => 'bca', 'BcaC09g49212' => 'bca', 'BcaC09g50140' => 'bca', 'BcaNung00346' => 'bca', 'BolC1t02785H' => 'bol', 'BolC1t04095H' => 'bol', 'BolC3t17545H' => 'bol', 'BolC5t32769H' => 'bol', 'BraA01t02211Z' => 'bra', 'BraA01t03359Z' => 'bra', 'BraA03t13441Z' => 'bra', 'BraA05t21476Z' => 'bra', 'C01p28420' => 'bna', 'C01p41350' => 'bna', 'C03p52750' => 'bna', 'C03p52780' => 'bna', 'C05p40270' => 'bna', 'CAN.G1437.9' => 'can', 'CANSAT78G0035' => 'cansat', 'CANSAT78G1036' => 'cansat', 'CANSAT78G2272' => 'cansat', 'CANSAT78G2478' => 'cansat', 'CARHR098700' => 'chi', 'CARHR221120' => 'chi', 'CARHR221150' => 'chi', 'Carub.0003s2297' => 'cru', 'Carub.0007s2749' => 'cru', 'Carub.0007s2750' => 'cru', 'Carub.0007s2751' => 'cru', 'Ca_10849_v3' => 'car', 'Cc03_g04300' => 'ccan', 'CDE02G3648' => 'cde', 'CDE05G0060' => 'cde', 'CDE05G0692' => 'cde', 'CDE05G2285' => 'cde', 'CDE05G2884' => 'cde', 'CDE05G3072' => 'cde', 'Cfa008439' => 'cfa', 'Cfa008441' => 'cfa', 'Cfa008443' => 'cfa', 'Cfa008448' => 'cfa', 'Ciclev10005974m.g' => 'ccl', 'Ciclev10006006m.g' => 'ccl', 'Ciclev10006775m.g' => 'ccl', 'CiPaw.02G120400' => 'cil', 'CiPaw.02G120500' => 'cil', 'CiPaw.02G120600' => 'cil', 'ClCG05G004850' => 'cla', 'COL.COLO4_21566' => 'col', 'Cpa.g.sc44.124' => 'cpa', 'Cre07.g320400' => 'cre', 'Cre07.g320450' => 'cre', 'Cre08.g384650' => 'cre', 'Cre09.g393173' => 'cre', 'Cre09.g394325' => 'cre', 'Cre14.g626750' => 'cre', 'Cre16.g679250' => 'cre', 'CsaV3_3G012890' => 'csa', 'CSS0010865' => 'camsi', 'CSS0044338' => 'camsi', 'DCAR_002366' => 'dca', 'DCAR_030687' => 'dca', 'DCAR_030688' => 'dca', 'Dinv14047' => 'din', 'Dinv14048' => 'din', 'Duzib151G0105' => 'dzi', 'Duzib151G0114' => 'dzi', 'Duzib212G1029' => 'dzi', 'ECA232G3536' => 'eca', 'ECA240G0786' => 'eca', 'ECA240G1802' => 'eca', 'ECA240G3760' => 'eca', 'ECA240G3920' => 'eca', 'EL10Ac5g12536' => 'bvu', 'EL10Ac5g12537' => 'bvu', 'EL10Ac5g12538' => 'bvu', 'Eucgr.B01004' => 'egr', 'Eucgr.B01006' => 'egr', 'Eucgr.B01007' => 'egr', 'Eucgr.B01008' => 'egr', 'Eucgr.B01895' => 'egr', 'Eucgr.B01896' => 'egr', 'FAN04G1456' => 'fan', 'FAN08G1769' => 'fan', 'FAN08G2160' => 'fan', 'FAN13G2403' => 'fan', 'FAN13G3303' => 'fan', 'FAN15G2435' => 'fan', 'FAN17G0672' => 'fan', 'FAN17G2441' => 'fan', 'FAN18G1024' => 'fan', 'FAN22G1458' => 'fan', 'FAN24G0037' => 'fan', 'FAN24G0429' => 'fan', 'FAN24G2387' => 'fan', 'FAN27G2746' => 'fan', 'FvH4_2g20400' => 'fve', 'FvH4_2g20420' => 'fve', 'FvH4_2g20430' => 'fve', 'FvH4_4g01270' => 'fve', 'FvH4_4g01290' => 'fve', 'FvH4_4g01300' => 'fve', 'FvH4_4g01310' => 'fve', 'FvH4_4g01330' => 'fve', 'FvH4_5g09070' => 'fve', 'Glyma.10G243800' => 'gma', 'Glyma.20G150600' => 'gma', 'Gohir.A09G219200' => 'ghi', 'Gohir.A09G219300' => 'ghi', 'Gohir.D09G221400' => 'ghi', 'Gohir.D09G221500' => 'ghi', 'Gorai.006G242600' => 'gra', 'Gorai.006G242700' => 'gra', 'GSVIVG01018044001' => 'vvi', 'HanXRQChr03g0083821' => 'han', 'HanXRQChr03g0083841' => 'han', 'HanXRQChr03g0083881' => 'han', 'HanXRQChr03g0083901' => 'han', 'HanXRQChr03g0083921' => 'han', 'HanXRQChr03g0085331' => 'han', 'HanXRQChr03g0085361' => 'han', 'HanXRQChr03g0085411' => 'han', 'HanXRQChr03g0085421' => 'han', 'HanXRQChr03g0085431' => 'han', 'HanXRQChr08g0221991' => 'han', 'HanXRQChr11g0336061' => 'han', 'HanXRQChr11g0336411' => 'han', 'Haze_11234' => 'cav', 'Hma1.2p1_0549F.1_g177010' => 'hma', 'Hma1.2p1_0602F.1_g187630' => 'hma', 'Hund14876' => 'sun', 'Hund14879' => 'sun', 'Lalb_Chr06g0160741' => 'lal', 'Lalb_Chr21g0304781' => 'lal', 'Lj3A726G19' => 'lonja', 'Lj3A726T23' => 'lonja', 'Lj3A726T24' => 'lonja', 'Lj3A726T25' => 'lonja', 'Lj3A727T17' => 'lonja', 'Lj3C726T0' => 'lonja', 'Lj3C726T2' => 'lonja', 'Lj3P725T35' => 'lonja', 'Lj3P727T10' => 'lonja', 'Lj3P727T12' => 'lonja', 'Lj3P727T14' => 'lonja', 'Lj5g0023109' => 'lja', 'Lj6P646T44' => 'lonja', 'Lsat_1_v5_gn_6_75760' => 'lsa', 'Lsat_1_v5_gn_6_75800' => 'lsa', 'Lsat_1_v5_gn_6_75900' => 'lsa', 'Lsat_1_v5_gn_6_76240' => 'lsa', 'Lsat_1_v5_gn_6_76441' => 'lsa', 'Lsat_1_v5_gn_6_76700' => 'lsa', 'Lsat_1_v5_gn_6_76760' => 'lsa', 'Manes.15G033100' => 'mes', 'Mapoly0004s0074' => 'mpo', 'Mapoly0004s0075' => 'mpo', 'Mapoly0004s0163' => 'mpo', 'Mapoly0004s0164' => 'mpo', 'Mapoly0021s0018' => 'mpo', 'Mapoly0041s0136' => 'mpo', 'Mapoly0041s0137' => 'mpo', 'Mapoly0041s0138' => 'mpo', 'Mapoly0041s0139' => 'mpo', 'Mapoly0041s0141' => 'mpo', 'Mapoly0041s0142' => 'mpo', 'Mapoly0041s0143' => 'mpo', 'Mapoly0041s0144' => 'mpo', 'Mapoly0041s0145' => 'mpo', 'Mapoly0047s0106' => 'mpo', 'Mapoly0047s0108' => 'mpo', 'Mapoly0050s0051' => 'mpo', 'Mapoly0050s0052' => 'mpo', 'Mapoly0050s0053' => 'mpo', 'Mapoly0058s0013' => 'mpo', 'Mapoly0091s0078' => 'mpo', 'Mapoly0091s0079' => 'mpo', 'Mapoly0091s0080' => 'mpo', 'Mapoly0091s0081' => 'mpo', 'Mapoly0278s0004' => 'mpo', 'Mapoly0278s0005' => 'mpo', 'Mapoly0278s0006' => 'mpo', 'MBI11_g30648_MAGBIO' => 'mbi', 'MCO03G194' => 'mco', 'MCO03G590' => 'mco', 'MCO07G312' => 'mco', 'MCO10G318' => 'mco', 'MCO12G244' => 'mco', 'MCO13G148' => 'mco', 'MCO13G194' => 'mco', 'MCO16G238' => 'mco', 'MD06G1134100' => 'mdo', 'MD13G1200100' => 'mdo', 'MD13G1200300' => 'mdo', 'MD13G1200600' => 'mdo', 'MD14G1150400' => 'mdo', 'MD16G1200000' => 'mdo', 'Medtr1g102570' => 'mtr', 'Medtr1g102780' => 'mtr', 'Medtr1g102800' => 'mtr', 'Medtr1g102810' => 'mtr', 'Medtr1g102830' => 'mtr', 'MELO3C006499.2' => 'cme', 'Migut.G00385' => 'egut', 'MSTRG.4063' => 'ama', 'Nitab4.5_0000090g0260' => 'nta', 'Nitab4.5_0000977g0030' => 'nta', 'Nitab4.5_0002541g0040' => 'nta', 'Nitab4.5_0007068g0040' => 'nta', 'Nn005s41408' => 'nnu', 'Nn005s41410' => 'nnu', 'Oeu010310.1' => 'oeu', 'Oeu010311.1' => 'oeu', 'Oeu043472.1' => 'oeu', 'Os01g0246400' => 'osa', 'Os04g0267950' => 'osa', 'Os07g0178700' => 'osa', 'Os07g0178800' => 'osa', 'Peaxi162Scf00316g00046' => 'pax', 'Peaxi162Scf00316g00049' => 'pax', 'Peaxi162Scf00316g00059' => 'pax', 'Peaxi162Scf00316g00328' => 'pax', 'Peaxi162Scf00316g00329' => 'pax', 'Peaxi162Scf00316g00411' => 'pax', 'Peaxi162Scf00316g00521' => 'pax', 'Peaxi162Scf00492g00068' => 'pax', 'Peaxi162Scf35631g00002' => 'pax', 'PGR142G3720' => 'pgr', 'PGSC0003DMG400006442' => 'stu', 'Phvul.007G062000' => 'pvu', 'Potri.008G157750' => 'ptr', 'Potri.008G157900' => 'ptr', 'Potri.008G158000' => 'ptr', 'Potri.008G158200' => 'ptr', 'Pp3c11_7280' => 'ppa', 'Pp3c11_7980' => 'ppa', 'Pp3c12_19450' => 'ppa', 'Pp3c14_1480' => 'ppa', 'Pp3c14_1501' => 'ppa', 'Pp3c16_4900' => 'ppa', 'Pp3c16_5010' => 'ppa', 'Pp3c16_5060' => 'ppa', 'Pp3c19_18250' => 'ppa', 'Pp3c23_8530' => 'ppa', 'Pp3c23_8550' => 'ppa', 'Pp3c24_9670' => 'ppa', 'Pp3c2_21390' => 'ppa', 'Pp3c2_31380' => 'ppa', 'Pp3c3_16620' => 'ppa', 'Pp3c3_8090' => 'ppa', 'Pp3c3_8110' => 'ppa', 'Pp3c3_8130' => 'ppa', 'Pp3c3_8150' => 'ppa', 'Pp3c4_14320' => 'ppa', 'Pp3c6_2560' => 'ppa', 'Pp3c9_16700' => 'ppa', 'PRCOL_00000234' => 'pco', 'PRCOL_00000235' => 'pco', 'PRCOL_00000777' => 'pco', 'PRCOL_00002344' => 'pco', 'PRCOL_00002372' => 'pco', 'PRCOL_00006120' => 'pco', 'Prupe.1G021400' => 'ppe', 'Prupe.1G021500' => 'ppe', 'Prupe.1G021600' => 'ppe', 'Prupe.1G021700' => 'ppe', 'Prupe.1G021800' => 'ppe', 'Prupe.5G145100' => 'ppe', 'Psat6g204040' => 'psa', 'Psat6g204800' => 'psa', 'Psat6g204920' => 'psa', 'Psat6g204960' => 'psa', 'Psat6g205080' => 'psa', 'PSO017G0271' => 'pso', 'PSO017G1276' => 'pso', 'PSO017G1429' => 'pso', 'PSO017G1861' => 'pso', 'PSO017G2787' => 'pso', 'PSO017G4466' => 'pso', 'PSO017G5118' => 'pso', 'PSO017G5420' => 'pso', 'PSO063G3678' => 'pso', 'PSO210G0546' => 'pso', 'PSO317G0001' => 'pso', 'PSO357G0512' => 'pso', 'PSO478G2682' => 'pso', 'PSO647G0001' => 'pso', 'PSO675G0001' => 'pso', 'PSO675G2699' => 'pso', 'PSO675G2849' => 'pso', 'PSO675G4991' => 'pso', 'PSO689G0001' => 'pso', 'QL06p000916' => 'qlo', 'QL06p000921' => 'qlo', 'QL06p001398' => 'qlo', 'QL06p001407' => 'qlo', 'QL06p002031' => 'qlo', 'RcHm_v2.0_Chr4g0387791' => 'rch', 'RcHm_v2.0_Chr4g0387801' => 'rch', 'RcHm_v2.0_Chr6g0286501' => 'rch', 'RcHm_v2.0_Chr6g0286511' => 'rch', 'RcHm_v2.0_Chr6g0286521' => 'rch', 'RcHm_v2.0_Chr6g0286531' => 'rch', 'RcHm_v2.0_Chr7g0189141' => 'rch', 'Rhsim02G0028700' => 'rsi', 'Rhsim02G0028800' => 'rsi', 'Rhsim02G0028900' => 'rsi', 'Rhsim02G0029000' => 'rsi', 'Rhsim02G0029100' => 'rsi', 'Rhsim02G0029200' => 'rsi', 'Rhsim02G0029300' => 'rsi', 'Rhsim02G0029400' => 'rsi', 'Rhsim02G0029500' => 'rsi', 'Rhsim02G0029600' => 'rsi', 'RhsimUnG0024000' => 'rsi', 'RhsimUnG0024100' => 'rsi', 'RhsimUnG0024200' => 'rsi', 'RhsimUnG0024300' => 'rsi', 'RhsimUnG0024400' => 'rsi', 'RhsimUnG0024500' => 'rsi', 'RhsimUnG0024700' => 'rsi', 'RhsimUnG0024800' => 'rsi', 'RhsimUnG0024900' => 'rsi', 'RhsimUnG0025100' => 'rsi', 'Sabra08G0120200' => 'sbr', 'Sabra08G0120300' => 'sbr', 'Sabra08G0120500' => 'sbr', 'Sabra08G0120600' => 'sbr', 'Sabra10G0158900' => 'sbr', 'SalBow2G3492' => 'sbo', 'Sc13g0004760' => 'sci', 'Sc13g0004770' => 'sci', 'Sed0003417' => 'sed', 'Sed0019750' => 'sed', 'SEGI_03419' => 'sgi', 'SEGI_05907' => 'sgi', 'SEGI_10682' => 'sgi', 'SEGI_13528' => 'sgi', 'SEGI_16081' => 'sgi', 'SEGI_19370' => 'sgi', 'SEGI_21015' => 'sgi', 'SEGI_21944' => 'sgi', 'SEGI_32906' => 'sgi', 'SEGI_33093' => 'sgi', 'SEGI_36110' => 'sgi', 'SEGI_40397' => 'sgi', 'SGA_v2.0_scaffold191G40426' => 'sas', 'SGA_v2.0_scaffold353G49717' => 'sas', 'SGA_v2.0_scaffold50G18550' => 'sas', 'SMO119G0173' => 'smo', 'SMO172G0002' => 'smo', 'Solyc09g082690.3' => 'sly', 'Solyc09g082700.2' => 'sly', 'Sopen09g031550' => 'spe', 'Sopen09g031560' => 'spe', 'Sp3g20540' => 'spa', 'Sp7g07580' => 'spa', 'TAR134G0002' => 'tar', 'TAR236G0001' => 'tar', 'TAR365G0892' => 'tar', 'TAR636G0166' => 'tar', 'TAR636G0646' => 'tar', 'TAR636G0869' => 'tar', 'TAR636G1317' => 'tar', 'TAR636G1744' => 'tar', 'TAR636G3358' => 'tar', 'TAR636G3436' => 'tar', 'THA.LOC104803047' => 'tha', 'Thecc.04G238900' => 'tca', 'Thhalv10021557m.g' => 'esa', 'Thhalv10026318m.g' => 'esa', 'Thhalv10026335m.g' => 'esa', 'TPR.G17433' => 'tpr', 'TPR.G18915' => 'tpr', 'TPR.G26125' => 'tpr', 'TWI09G0677' => 'twi', 'TWI73G0287' => 'twi', 'unitig_748.g8326' => 'ugi', 'vmacro15370' => 'vma', 'vmacro15371' => 'vma', 'vmacro15372' => 'vma', 'vmacro15373' => 'vma', 'vmacro15374' => 'vma', 'VMungo0720G2826' => 'vmu', 'Zm00001eb116960' => 'zma', 'Zm00001eb301260' => 'zma', 'Zm00001eb301270' => 'zma' ) $gf_id = 'HOM05D001460' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001460' ) $data_identifier = 'HOM05D001460' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 4, 'aag' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 2, 'aox' => (int) 2, 'arhy' => (int) 4, 'ath' => (int) 2, 'atr' => (int) 1, 'acertr' => (int) 10, 'cqu' => (int) 4, 'bca' => (int) 11, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 1, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 1, 'ccan' => (int) 1, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 1, 'col' => (int) 1, 'cpa' => (int) 1, 'cre' => (int) 7, 'csa' => (int) 1, 'camsi' => (int) 2, 'dca' => (int) 3, 'din' => (int) 2, 'dzi' => (int) 3, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 14, 'fve' => (int) 9, 'gma' => (int) 2, 'ghi' => (int) 4, 'gra' => (int) 2, 'vvi' => (int) 1, 'han' => (int) 13, 'cav' => (int) 1, 'hma' => (int) 2, 'sun' => (int) 2, 'lal' => (int) 2, 'lonja' => (int) 12, 'lja' => (int) 1, 'lsa' => (int) 7, 'mes' => (int) 1, 'mpo' => (int) 27, 'mbi' => (int) 1, 'mco' => (int) 8, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 1, 'egut' => (int) 1, 'ama' => (int) 1, 'nta' => (int) 4, 'nnu' => (int) 2, 'oeu' => (int) 3, 'osa' => (int) 4, 'pax' => (int) 9, 'pgr' => (int) 1, 'stu' => (int) 1, 'pvu' => (int) 1, 'ptr' => (int) 4, 'ppa' => (int) 22, 'pco' => (int) 6, 'ppe' => (int) 6, 'psa' => (int) 5, 'pso' => (int) 19, 'qlo' => (int) 5, 'rch' => (int) 7, 'rsi' => (int) 20, 'sbr' => (int) 5, 'sbo' => (int) 1, 'sci' => (int) 2, 'sed' => (int) 2, 'sgi' => (int) 12, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 2, 'tar' => (int) 10, 'tha' => (int) 1, 'tca' => (int) 1, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 2, 'ugi' => (int) 1, 'vma' => (int) 5, 'vmu' => (int) 1, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb301270' $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' => 'HOM05D001460', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '433', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p22980' => 'bna', 'A01p32340' => 'bna', 'A03p42970' => 'bna', 'A05p25880' => 'bna', 'Aa31LG8G9320' => 'aar', 'Aa31LG8G9330' => 'aar', 'Aa31LG8G9340' => 'aar', 'Aa31sc221G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1034' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1528' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.829' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2222' => 'aag', 'Ah.12g058830' => 'amhyb', 'Ah.12g058840' => 'amhyb', 'AL3G37160' => 'aly', 'AL7G41310' => 'aly', 'Aqoxy5G00395' => 'aox', 'Aqoxy5G00396' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0C8NZA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5185HY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JZ1PRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MD3LS0' => 'arhy', 'AT3G22840' => 'ath', 'AT4G14690' => 'ath', 'ATR0665G054' => 'atr', 'Atru.chr4.2344' => 'acertr', 'Atru.chr4.2346' => 'acertr', 'Atru.chr4.2347' => 'acertr', 'Atru.chr4.2348' => 'acertr', 'Atru.chr4.2355' => 'acertr', 'Atru.chr4.2356' => 'acertr', 'Atru.chr4.2358' => 'acertr', 'Atru.chr4.2359' => 'acertr', 'Atru.chr4.2360' => 'acertr', 'Atru.chr4.2361' => 'acertr', 'AUR62030476' => 'cqu', 'AUR62030478' => 'cqu', 'AUR62030819' => 'cqu', 'AUR62030820' => 'cqu', 'BcaB03g14648' => 'bca', 'BcaB04g20492' => 'bca', 'BcaB06g26399' => 'bca', 'BcaC01g03416' => 'bca', 'BcaC01g03419' => 'bca', 'BcaC01g03421' => 'bca', 'BcaC01g03424' => 'bca', 'BcaC05g28012' => 'bca', 'BcaC09g49212' => 'bca', 'BcaC09g50140' => 'bca', 'BcaNung00346' => 'bca', 'BolC1t02785H' => 'bol', 'BolC1t04095H' => 'bol', 'BolC3t17545H' => 'bol', 'BolC5t32769H' => 'bol', 'BraA01t02211Z' => 'bra', 'BraA01t03359Z' => 'bra', 'BraA03t13441Z' => 'bra', 'BraA05t21476Z' => 'bra', 'C01p28420' => 'bna', 'C01p41350' => 'bna', 'C03p52750' => 'bna', 'C03p52780' => 'bna', 'C05p40270' => 'bna', 'CAN.G1437.9' => 'can', 'CANSAT78G0035' => 'cansat', 'CANSAT78G1036' => 'cansat', 'CANSAT78G2272' => 'cansat', 'CANSAT78G2478' => 'cansat', 'CARHR098700' => 'chi', 'CARHR221120' => 'chi', 'CARHR221150' => 'chi', 'Carub.0003s2297' => 'cru', 'Carub.0007s2749' => 'cru', 'Carub.0007s2750' => 'cru', 'Carub.0007s2751' => 'cru', 'Ca_10849_v3' => 'car', 'Cc03_g04300' => 'ccan', 'CDE02G3648' => 'cde', 'CDE05G0060' => 'cde', 'CDE05G0692' => 'cde', 'CDE05G2285' => 'cde', 'CDE05G2884' => 'cde', 'CDE05G3072' => 'cde', 'Cfa008439' => 'cfa', 'Cfa008441' => 'cfa', 'Cfa008443' => 'cfa', 'Cfa008448' => 'cfa', 'Ciclev10005974m.g' => 'ccl', 'Ciclev10006006m.g' => 'ccl', 'Ciclev10006775m.g' => 'ccl', 'CiPaw.02G120400' => 'cil', 'CiPaw.02G120500' => 'cil', 'CiPaw.02G120600' => 'cil', 'ClCG05G004850' => 'cla', 'COL.COLO4_21566' => 'col', 'Cpa.g.sc44.124' => 'cpa', 'Cre07.g320400' => 'cre', 'Cre07.g320450' => 'cre', 'Cre08.g384650' => 'cre', 'Cre09.g393173' => 'cre', 'Cre09.g394325' => 'cre', 'Cre14.g626750' => 'cre', 'Cre16.g679250' => 'cre', 'CsaV3_3G012890' => 'csa', 'CSS0010865' => 'camsi', 'CSS0044338' => 'camsi', 'DCAR_002366' => 'dca', 'DCAR_030687' => 'dca', 'DCAR_030688' => 'dca', 'Dinv14047' => 'din', 'Dinv14048' => 'din', 'Duzib151G0105' => 'dzi', 'Duzib151G0114' => 'dzi', 'Duzib212G1029' => 'dzi', 'ECA232G3536' => 'eca', 'ECA240G0786' => 'eca', 'ECA240G1802' => 'eca', 'ECA240G3760' => 'eca', 'ECA240G3920' => 'eca', 'EL10Ac5g12536' => 'bvu', 'EL10Ac5g12537' => 'bvu', 'EL10Ac5g12538' => 'bvu', 'Eucgr.B01004' => 'egr', 'Eucgr.B01006' => 'egr', 'Eucgr.B01007' => 'egr', 'Eucgr.B01008' => 'egr', 'Eucgr.B01895' => 'egr', 'Eucgr.B01896' => 'egr', 'FAN04G1456' => 'fan', 'FAN08G1769' => 'fan', 'FAN08G2160' => 'fan', 'FAN13G2403' => 'fan', 'FAN13G3303' => 'fan', 'FAN15G2435' => 'fan', 'FAN17G0672' => 'fan', 'FAN17G2441' => 'fan', 'FAN18G1024' => 'fan', 'FAN22G1458' => 'fan', 'FAN24G0037' => 'fan', 'FAN24G0429' => 'fan', 'FAN24G2387' => 'fan', 'FAN27G2746' => 'fan', 'FvH4_2g20400' => 'fve', 'FvH4_2g20420' => 'fve', 'FvH4_2g20430' => 'fve', 'FvH4_4g01270' => 'fve', 'FvH4_4g01290' => 'fve', 'FvH4_4g01300' => 'fve', 'FvH4_4g01310' => 'fve', 'FvH4_4g01330' => 'fve', 'FvH4_5g09070' => 'fve', 'Glyma.10G243800' => 'gma', 'Glyma.20G150600' => 'gma', 'Gohir.A09G219200' => 'ghi', 'Gohir.A09G219300' => 'ghi', 'Gohir.D09G221400' => 'ghi', 'Gohir.D09G221500' => 'ghi', 'Gorai.006G242600' => 'gra', 'Gorai.006G242700' => 'gra', 'GSVIVG01018044001' => 'vvi', 'HanXRQChr03g0083821' => 'han', 'HanXRQChr03g0083841' => 'han', 'HanXRQChr03g0083881' => 'han', 'HanXRQChr03g0083901' => 'han', 'HanXRQChr03g0083921' => 'han', 'HanXRQChr03g0085331' => 'han', 'HanXRQChr03g0085361' => 'han', 'HanXRQChr03g0085411' => 'han', 'HanXRQChr03g0085421' => 'han', 'HanXRQChr03g0085431' => 'han', 'HanXRQChr08g0221991' => 'han', 'HanXRQChr11g0336061' => 'han', 'HanXRQChr11g0336411' => 'han', 'Haze_11234' => 'cav', 'Hma1.2p1_0549F.1_g177010' => 'hma', 'Hma1.2p1_0602F.1_g187630' => 'hma', 'Hund14876' => 'sun', 'Hund14879' => 'sun', 'Lalb_Chr06g0160741' => 'lal', 'Lalb_Chr21g0304781' => 'lal', 'Lj3A726G19' => 'lonja', 'Lj3A726T23' => 'lonja', 'Lj3A726T24' => 'lonja', 'Lj3A726T25' => 'lonja', 'Lj3A727T17' => 'lonja', 'Lj3C726T0' => 'lonja', 'Lj3C726T2' => 'lonja', 'Lj3P725T35' => 'lonja', 'Lj3P727T10' => 'lonja', 'Lj3P727T12' => 'lonja', 'Lj3P727T14' => 'lonja', 'Lj5g0023109' => 'lja', 'Lj6P646T44' => 'lonja', 'Lsat_1_v5_gn_6_75760' => 'lsa', 'Lsat_1_v5_gn_6_75800' => 'lsa', 'Lsat_1_v5_gn_6_75900' => 'lsa', 'Lsat_1_v5_gn_6_76240' => 'lsa', 'Lsat_1_v5_gn_6_76441' => 'lsa', 'Lsat_1_v5_gn_6_76700' => 'lsa', 'Lsat_1_v5_gn_6_76760' => 'lsa', 'Manes.15G033100' => 'mes', 'Mapoly0004s0074' => 'mpo', 'Mapoly0004s0075' => 'mpo', 'Mapoly0004s0163' => 'mpo', 'Mapoly0004s0164' => 'mpo', 'Mapoly0021s0018' => 'mpo', 'Mapoly0041s0136' => 'mpo', 'Mapoly0041s0137' => 'mpo', 'Mapoly0041s0138' => 'mpo', 'Mapoly0041s0139' => 'mpo', 'Mapoly0041s0141' => 'mpo', 'Mapoly0041s0142' => 'mpo', 'Mapoly0041s0143' => 'mpo', 'Mapoly0041s0144' => 'mpo', 'Mapoly0041s0145' => 'mpo', 'Mapoly0047s0106' => 'mpo', 'Mapoly0047s0108' => 'mpo', 'Mapoly0050s0051' => 'mpo', 'Mapoly0050s0052' => 'mpo', 'Mapoly0050s0053' => 'mpo', 'Mapoly0058s0013' => 'mpo', 'Mapoly0091s0078' => 'mpo', 'Mapoly0091s0079' => 'mpo', 'Mapoly0091s0080' => 'mpo', 'Mapoly0091s0081' => 'mpo', 'Mapoly0278s0004' => 'mpo', 'Mapoly0278s0005' => 'mpo', 'Mapoly0278s0006' => 'mpo', 'MBI11_g30648_MAGBIO' => 'mbi', 'MCO03G194' => 'mco', 'MCO03G590' => 'mco', 'MCO07G312' => 'mco', 'MCO10G318' => 'mco', 'MCO12G244' => 'mco', 'MCO13G148' => 'mco', 'MCO13G194' => 'mco', 'MCO16G238' => 'mco', 'MD06G1134100' => 'mdo', 'MD13G1200100' => 'mdo', 'MD13G1200300' => 'mdo', 'MD13G1200600' => 'mdo', 'MD14G1150400' => 'mdo', 'MD16G1200000' => 'mdo', 'Medtr1g102570' => 'mtr', 'Medtr1g102780' => 'mtr', 'Medtr1g102800' => 'mtr', 'Medtr1g102810' => 'mtr', 'Medtr1g102830' => 'mtr', 'MELO3C006499.2' => 'cme', 'Migut.G00385' => 'egut', 'MSTRG.4063' => 'ama', 'Nitab4.5_0000090g0260' => 'nta', 'Nitab4.5_0000977g0030' => 'nta', 'Nitab4.5_0002541g0040' => 'nta', 'Nitab4.5_0007068g0040' => 'nta', 'Nn005s41408' => 'nnu', 'Nn005s41410' => 'nnu', 'Oeu010310.1' => 'oeu', 'Oeu010311.1' => 'oeu', 'Oeu043472.1' => 'oeu', 'Os01g0246400' => 'osa', 'Os04g0267950' => 'osa', 'Os07g0178700' => 'osa', 'Os07g0178800' => 'osa', 'Peaxi162Scf00316g00046' => 'pax', 'Peaxi162Scf00316g00049' => 'pax', 'Peaxi162Scf00316g00059' => 'pax', 'Peaxi162Scf00316g00328' => 'pax', 'Peaxi162Scf00316g00329' => 'pax', 'Peaxi162Scf00316g00411' => 'pax', 'Peaxi162Scf00316g00521' => 'pax', 'Peaxi162Scf00492g00068' => 'pax', 'Peaxi162Scf35631g00002' => 'pax', 'PGR142G3720' => 'pgr', 'PGSC0003DMG400006442' => 'stu', 'Phvul.007G062000' => 'pvu', 'Potri.008G157750' => 'ptr', 'Potri.008G157900' => 'ptr', 'Potri.008G158000' => 'ptr', 'Potri.008G158200' => 'ptr', 'Pp3c11_7280' => 'ppa', 'Pp3c11_7980' => 'ppa', 'Pp3c12_19450' => 'ppa', 'Pp3c14_1480' => 'ppa', 'Pp3c14_1501' => 'ppa', 'Pp3c16_4900' => 'ppa', 'Pp3c16_5010' => 'ppa', 'Pp3c16_5060' => 'ppa', 'Pp3c19_18250' => 'ppa', 'Pp3c23_8530' => 'ppa', 'Pp3c23_8550' => 'ppa', 'Pp3c24_9670' => 'ppa', 'Pp3c2_21390' => 'ppa', 'Pp3c2_31380' => 'ppa', 'Pp3c3_16620' => 'ppa', 'Pp3c3_8090' => 'ppa', 'Pp3c3_8110' => 'ppa', 'Pp3c3_8130' => 'ppa', 'Pp3c3_8150' => 'ppa', 'Pp3c4_14320' => 'ppa', 'Pp3c6_2560' => 'ppa', 'Pp3c9_16700' => 'ppa', 'PRCOL_00000234' => 'pco', 'PRCOL_00000235' => 'pco', 'PRCOL_00000777' => 'pco', 'PRCOL_00002344' => 'pco', 'PRCOL_00002372' => 'pco', 'PRCOL_00006120' => 'pco', 'Prupe.1G021400' => 'ppe', 'Prupe.1G021500' => 'ppe', 'Prupe.1G021600' => 'ppe', 'Prupe.1G021700' => 'ppe', 'Prupe.1G021800' => 'ppe', 'Prupe.5G145100' => 'ppe', 'Psat6g204040' => 'psa', 'Psat6g204800' => 'psa', 'Psat6g204920' => 'psa', 'Psat6g204960' => 'psa', 'Psat6g205080' => 'psa', 'PSO017G0271' => 'pso', 'PSO017G1276' => 'pso', 'PSO017G1429' => 'pso', 'PSO017G1861' => 'pso', 'PSO017G2787' => 'pso', 'PSO017G4466' => 'pso', 'PSO017G5118' => 'pso', 'PSO017G5420' => 'pso', 'PSO063G3678' => 'pso', 'PSO210G0546' => 'pso', 'PSO317G0001' => 'pso', 'PSO357G0512' => 'pso', 'PSO478G2682' => 'pso', 'PSO647G0001' => 'pso', 'PSO675G0001' => 'pso', 'PSO675G2699' => 'pso', 'PSO675G2849' => 'pso', 'PSO675G4991' => 'pso', 'PSO689G0001' => 'pso', 'QL06p000916' => 'qlo', 'QL06p000921' => 'qlo', 'QL06p001398' => 'qlo', 'QL06p001407' => 'qlo', 'QL06p002031' => 'qlo', 'RcHm_v2.0_Chr4g0387791' => 'rch', 'RcHm_v2.0_Chr4g0387801' => 'rch', 'RcHm_v2.0_Chr6g0286501' => 'rch', 'RcHm_v2.0_Chr6g0286511' => 'rch', 'RcHm_v2.0_Chr6g0286521' => 'rch', 'RcHm_v2.0_Chr6g0286531' => 'rch', 'RcHm_v2.0_Chr7g0189141' => 'rch', 'Rhsim02G0028700' => 'rsi', 'Rhsim02G0028800' => 'rsi', 'Rhsim02G0028900' => 'rsi', 'Rhsim02G0029000' => 'rsi', 'Rhsim02G0029100' => 'rsi', 'Rhsim02G0029200' => 'rsi', 'Rhsim02G0029300' => 'rsi', 'Rhsim02G0029400' => 'rsi', 'Rhsim02G0029500' => 'rsi', 'Rhsim02G0029600' => 'rsi', 'RhsimUnG0024000' => 'rsi', 'RhsimUnG0024100' => 'rsi', 'RhsimUnG0024200' => 'rsi', 'RhsimUnG0024300' => 'rsi', 'RhsimUnG0024400' => 'rsi', 'RhsimUnG0024500' => 'rsi', 'RhsimUnG0024700' => 'rsi', 'RhsimUnG0024800' => 'rsi', 'RhsimUnG0024900' => 'rsi', 'RhsimUnG0025100' => 'rsi', 'Sabra08G0120200' => 'sbr', 'Sabra08G0120300' => 'sbr', 'Sabra08G0120500' => 'sbr', 'Sabra08G0120600' => 'sbr', 'Sabra10G0158900' => 'sbr', 'SalBow2G3492' => 'sbo', 'Sc13g0004760' => 'sci', 'Sc13g0004770' => 'sci', 'Sed0003417' => 'sed', 'Sed0019750' => 'sed', 'SEGI_03419' => 'sgi', 'SEGI_05907' => 'sgi', 'SEGI_10682' => 'sgi', 'SEGI_13528' => 'sgi', 'SEGI_16081' => 'sgi', 'SEGI_19370' => 'sgi', 'SEGI_21015' => 'sgi', 'SEGI_21944' => 'sgi', 'SEGI_32906' => 'sgi', 'SEGI_33093' => 'sgi', 'SEGI_36110' => 'sgi', 'SEGI_40397' => 'sgi', 'SGA_v2.0_scaffold191G40426' => 'sas', 'SGA_v2.0_scaffold353G49717' => 'sas', 'SGA_v2.0_scaffold50G18550' => 'sas', 'SMO119G0173' => 'smo', 'SMO172G0002' => 'smo', 'Solyc09g082690.3' => 'sly', 'Solyc09g082700.2' => 'sly', 'Sopen09g031550' => 'spe', 'Sopen09g031560' => 'spe', 'Sp3g20540' => 'spa', 'Sp7g07580' => 'spa', 'TAR134G0002' => 'tar', 'TAR236G0001' => 'tar', 'TAR365G0892' => 'tar', 'TAR636G0166' => 'tar', 'TAR636G0646' => 'tar', 'TAR636G0869' => 'tar', 'TAR636G1317' => 'tar', 'TAR636G1744' => 'tar', 'TAR636G3358' => 'tar', 'TAR636G3436' => 'tar', 'THA.LOC104803047' => 'tha', 'Thecc.04G238900' => 'tca', 'Thhalv10021557m.g' => 'esa', 'Thhalv10026318m.g' => 'esa', 'Thhalv10026335m.g' => 'esa', 'TPR.G17433' => 'tpr', 'TPR.G18915' => 'tpr', 'TPR.G26125' => 'tpr', 'TWI09G0677' => 'twi', 'TWI73G0287' => 'twi', 'unitig_748.g8326' => 'ugi', 'vmacro15370' => 'vma', 'vmacro15371' => 'vma', 'vmacro15372' => 'vma', 'vmacro15373' => 'vma', 'vmacro15374' => 'vma', 'VMungo0720G2826' => 'vmu', 'Zm00001eb116960' => 'zma', 'Zm00001eb301260' => 'zma', 'Zm00001eb301270' => 'zma' ), 'gf_id' => 'HOM05D001460', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001460' ), 'data_identifier' => 'HOM05D001460', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001460', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '433', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p22980' => 'bna', 'A01p32340' => 'bna', 'A03p42970' => 'bna', 'A05p25880' => 'bna', 'Aa31LG8G9320' => 'aar', 'Aa31LG8G9330' => 'aar', 'Aa31LG8G9340' => 'aar', 'Aa31sc221G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1034' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1528' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.829' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2222' => 'aag', 'Ah.12g058830' => 'amhyb', 'Ah.12g058840' => 'amhyb', 'AL3G37160' => 'aly', 'AL7G41310' => 'aly', 'Aqoxy5G00395' => 'aox', 'Aqoxy5G00396' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0C8NZA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5185HY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JZ1PRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MD3LS0' => 'arhy', 'AT3G22840' => 'ath', 'AT4G14690' => 'ath', 'ATR0665G054' => 'atr', 'Atru.chr4.2344' => 'acertr', 'Atru.chr4.2346' => 'acertr', 'Atru.chr4.2347' => 'acertr', 'Atru.chr4.2348' => 'acertr', 'Atru.chr4.2355' => 'acertr', 'Atru.chr4.2356' => 'acertr', 'Atru.chr4.2358' => 'acertr', 'Atru.chr4.2359' => 'acertr', 'Atru.chr4.2360' => 'acertr', 'Atru.chr4.2361' => 'acertr', 'AUR62030476' => 'cqu', 'AUR62030478' => 'cqu', 'AUR62030819' => 'cqu', 'AUR62030820' => 'cqu', 'BcaB03g14648' => 'bca', 'BcaB04g20492' => 'bca', 'BcaB06g26399' => 'bca', 'BcaC01g03416' => 'bca', 'BcaC01g03419' => 'bca', 'BcaC01g03421' => 'bca', 'BcaC01g03424' => 'bca', 'BcaC05g28012' => 'bca', 'BcaC09g49212' => 'bca', 'BcaC09g50140' => 'bca', 'BcaNung00346' => 'bca', 'BolC1t02785H' => 'bol', 'BolC1t04095H' => 'bol', 'BolC3t17545H' => 'bol', 'BolC5t32769H' => 'bol', 'BraA01t02211Z' => 'bra', 'BraA01t03359Z' => 'bra', 'BraA03t13441Z' => 'bra', 'BraA05t21476Z' => 'bra', 'C01p28420' => 'bna', 'C01p41350' => 'bna', 'C03p52750' => 'bna', 'C03p52780' => 'bna', 'C05p40270' => 'bna', 'CAN.G1437.9' => 'can', 'CANSAT78G0035' => 'cansat', 'CANSAT78G1036' => 'cansat', 'CANSAT78G2272' => 'cansat', 'CANSAT78G2478' => 'cansat', 'CARHR098700' => 'chi', 'CARHR221120' => 'chi', 'CARHR221150' => 'chi', 'Carub.0003s2297' => 'cru', 'Carub.0007s2749' => 'cru', 'Carub.0007s2750' => 'cru', 'Carub.0007s2751' => 'cru', 'Ca_10849_v3' => 'car', 'Cc03_g04300' => 'ccan', 'CDE02G3648' => 'cde', 'CDE05G0060' => 'cde', 'CDE05G0692' => 'cde', 'CDE05G2285' => 'cde', 'CDE05G2884' => 'cde', 'CDE05G3072' => 'cde', 'Cfa008439' => 'cfa', 'Cfa008441' => 'cfa', 'Cfa008443' => 'cfa', 'Cfa008448' => 'cfa', 'Ciclev10005974m.g' => 'ccl', 'Ciclev10006006m.g' => 'ccl', 'Ciclev10006775m.g' => 'ccl', 'CiPaw.02G120400' => 'cil', 'CiPaw.02G120500' => 'cil', 'CiPaw.02G120600' => 'cil', 'ClCG05G004850' => 'cla', 'COL.COLO4_21566' => 'col', 'Cpa.g.sc44.124' => 'cpa', 'Cre07.g320400' => 'cre', 'Cre07.g320450' => 'cre', 'Cre08.g384650' => 'cre', 'Cre09.g393173' => 'cre', 'Cre09.g394325' => 'cre', 'Cre14.g626750' => 'cre', 'Cre16.g679250' => 'cre', 'CsaV3_3G012890' => 'csa', 'CSS0010865' => 'camsi', 'CSS0044338' => 'camsi', 'DCAR_002366' => 'dca', 'DCAR_030687' => 'dca', 'DCAR_030688' => 'dca', 'Dinv14047' => 'din', 'Dinv14048' => 'din', 'Duzib151G0105' => 'dzi', 'Duzib151G0114' => 'dzi', 'Duzib212G1029' => 'dzi', 'ECA232G3536' => 'eca', 'ECA240G0786' => 'eca', 'ECA240G1802' => 'eca', 'ECA240G3760' => 'eca', 'ECA240G3920' => 'eca', 'EL10Ac5g12536' => 'bvu', 'EL10Ac5g12537' => 'bvu', 'EL10Ac5g12538' => 'bvu', 'Eucgr.B01004' => 'egr', 'Eucgr.B01006' => 'egr', 'Eucgr.B01007' => 'egr', 'Eucgr.B01008' => 'egr', 'Eucgr.B01895' => 'egr', 'Eucgr.B01896' => 'egr', 'FAN04G1456' => 'fan', 'FAN08G1769' => 'fan', 'FAN08G2160' => 'fan', 'FAN13G2403' => 'fan', 'FAN13G3303' => 'fan', 'FAN15G2435' => 'fan', 'FAN17G0672' => 'fan', 'FAN17G2441' => 'fan', 'FAN18G1024' => 'fan', 'FAN22G1458' => 'fan', 'FAN24G0037' => 'fan', 'FAN24G0429' => 'fan', 'FAN24G2387' => 'fan', 'FAN27G2746' => 'fan', 'FvH4_2g20400' => 'fve', 'FvH4_2g20420' => 'fve', 'FvH4_2g20430' => 'fve', 'FvH4_4g01270' => 'fve', 'FvH4_4g01290' => 'fve', 'FvH4_4g01300' => 'fve', 'FvH4_4g01310' => 'fve', 'FvH4_4g01330' => 'fve', 'FvH4_5g09070' => 'fve', 'Glyma.10G243800' => 'gma', 'Glyma.20G150600' => 'gma', 'Gohir.A09G219200' => 'ghi', 'Gohir.A09G219300' => 'ghi', 'Gohir.D09G221400' => 'ghi', 'Gohir.D09G221500' => 'ghi', 'Gorai.006G242600' => 'gra', 'Gorai.006G242700' => 'gra', 'GSVIVG01018044001' => 'vvi', 'HanXRQChr03g0083821' => 'han', 'HanXRQChr03g0083841' => 'han', 'HanXRQChr03g0083881' => 'han', 'HanXRQChr03g0083901' => 'han', 'HanXRQChr03g0083921' => 'han', 'HanXRQChr03g0085331' => 'han', 'HanXRQChr03g0085361' => 'han', 'HanXRQChr03g0085411' => 'han', 'HanXRQChr03g0085421' => 'han', 'HanXRQChr03g0085431' => 'han', 'HanXRQChr08g0221991' => 'han', 'HanXRQChr11g0336061' => 'han', 'HanXRQChr11g0336411' => 'han', 'Haze_11234' => 'cav', 'Hma1.2p1_0549F.1_g177010' => 'hma', 'Hma1.2p1_0602F.1_g187630' => 'hma', 'Hund14876' => 'sun', 'Hund14879' => 'sun', 'Lalb_Chr06g0160741' => 'lal', 'Lalb_Chr21g0304781' => 'lal', 'Lj3A726G19' => 'lonja', 'Lj3A726T23' => 'lonja', 'Lj3A726T24' => 'lonja', 'Lj3A726T25' => 'lonja', 'Lj3A727T17' => 'lonja', 'Lj3C726T0' => 'lonja', 'Lj3C726T2' => 'lonja', 'Lj3P725T35' => 'lonja', 'Lj3P727T10' => 'lonja', 'Lj3P727T12' => 'lonja', 'Lj3P727T14' => 'lonja', 'Lj5g0023109' => 'lja', 'Lj6P646T44' => 'lonja', 'Lsat_1_v5_gn_6_75760' => 'lsa', 'Lsat_1_v5_gn_6_75800' => 'lsa', 'Lsat_1_v5_gn_6_75900' => 'lsa', 'Lsat_1_v5_gn_6_76240' => 'lsa', 'Lsat_1_v5_gn_6_76441' => 'lsa', 'Lsat_1_v5_gn_6_76700' => 'lsa', 'Lsat_1_v5_gn_6_76760' => 'lsa', 'Manes.15G033100' => 'mes', 'Mapoly0004s0074' => 'mpo', 'Mapoly0004s0075' => 'mpo', 'Mapoly0004s0163' => 'mpo', 'Mapoly0004s0164' => 'mpo', 'Mapoly0021s0018' => 'mpo', 'Mapoly0041s0136' => 'mpo', 'Mapoly0041s0137' => 'mpo', 'Mapoly0041s0138' => 'mpo', 'Mapoly0041s0139' => 'mpo', 'Mapoly0041s0141' => 'mpo', 'Mapoly0041s0142' => 'mpo', 'Mapoly0041s0143' => 'mpo', 'Mapoly0041s0144' => 'mpo', 'Mapoly0041s0145' => 'mpo', 'Mapoly0047s0106' => 'mpo', 'Mapoly0047s0108' => 'mpo', 'Mapoly0050s0051' => 'mpo', 'Mapoly0050s0052' => 'mpo', 'Mapoly0050s0053' => 'mpo', 'Mapoly0058s0013' => 'mpo', 'Mapoly0091s0078' => 'mpo', 'Mapoly0091s0079' => 'mpo', 'Mapoly0091s0080' => 'mpo', 'Mapoly0091s0081' => 'mpo', 'Mapoly0278s0004' => 'mpo', 'Mapoly0278s0005' => 'mpo', 'Mapoly0278s0006' => 'mpo', 'MBI11_g30648_MAGBIO' => 'mbi', 'MCO03G194' => 'mco', 'MCO03G590' => 'mco', 'MCO07G312' => 'mco', 'MCO10G318' => 'mco', 'MCO12G244' => 'mco', 'MCO13G148' => 'mco', 'MCO13G194' => 'mco', 'MCO16G238' => 'mco', 'MD06G1134100' => 'mdo', 'MD13G1200100' => 'mdo', 'MD13G1200300' => 'mdo', 'MD13G1200600' => 'mdo', 'MD14G1150400' => 'mdo', 'MD16G1200000' => 'mdo', 'Medtr1g102570' => 'mtr', 'Medtr1g102780' => 'mtr', 'Medtr1g102800' => 'mtr', 'Medtr1g102810' => 'mtr', 'Medtr1g102830' => 'mtr', 'MELO3C006499.2' => 'cme', 'Migut.G00385' => 'egut', 'MSTRG.4063' => 'ama', 'Nitab4.5_0000090g0260' => 'nta', 'Nitab4.5_0000977g0030' => 'nta', 'Nitab4.5_0002541g0040' => 'nta', 'Nitab4.5_0007068g0040' => 'nta', 'Nn005s41408' => 'nnu', 'Nn005s41410' => 'nnu', 'Oeu010310.1' => 'oeu', 'Oeu010311.1' => 'oeu', 'Oeu043472.1' => 'oeu', 'Os01g0246400' => 'osa', 'Os04g0267950' => 'osa', 'Os07g0178700' => 'osa', 'Os07g0178800' => 'osa', 'Peaxi162Scf00316g00046' => 'pax', 'Peaxi162Scf00316g00049' => 'pax', 'Peaxi162Scf00316g00059' => 'pax', 'Peaxi162Scf00316g00328' => 'pax', 'Peaxi162Scf00316g00329' => 'pax', 'Peaxi162Scf00316g00411' => 'pax', 'Peaxi162Scf00316g00521' => 'pax', 'Peaxi162Scf00492g00068' => 'pax', 'Peaxi162Scf35631g00002' => 'pax', 'PGR142G3720' => 'pgr', 'PGSC0003DMG400006442' => 'stu', 'Phvul.007G062000' => 'pvu', 'Potri.008G157750' => 'ptr', 'Potri.008G157900' => 'ptr', 'Potri.008G158000' => 'ptr', 'Potri.008G158200' => 'ptr', 'Pp3c11_7280' => 'ppa', 'Pp3c11_7980' => 'ppa', 'Pp3c12_19450' => 'ppa', 'Pp3c14_1480' => 'ppa', 'Pp3c14_1501' => 'ppa', 'Pp3c16_4900' => 'ppa', 'Pp3c16_5010' => 'ppa', 'Pp3c16_5060' => 'ppa', 'Pp3c19_18250' => 'ppa', 'Pp3c23_8530' => 'ppa', 'Pp3c23_8550' => 'ppa', 'Pp3c24_9670' => 'ppa', 'Pp3c2_21390' => 'ppa', 'Pp3c2_31380' => 'ppa', 'Pp3c3_16620' => 'ppa', 'Pp3c3_8090' => 'ppa', 'Pp3c3_8110' => 'ppa', 'Pp3c3_8130' => 'ppa', 'Pp3c3_8150' => 'ppa', 'Pp3c4_14320' => 'ppa', 'Pp3c6_2560' => 'ppa', 'Pp3c9_16700' => 'ppa', 'PRCOL_00000234' => 'pco', 'PRCOL_00000235' => 'pco', 'PRCOL_00000777' => 'pco', 'PRCOL_00002344' => 'pco', 'PRCOL_00002372' => 'pco', 'PRCOL_00006120' => 'pco', 'Prupe.1G021400' => 'ppe', 'Prupe.1G021500' => 'ppe', 'Prupe.1G021600' => 'ppe', 'Prupe.1G021700' => 'ppe', 'Prupe.1G021800' => 'ppe', 'Prupe.5G145100' => 'ppe', 'Psat6g204040' => 'psa', 'Psat6g204800' => 'psa', 'Psat6g204920' => 'psa', 'Psat6g204960' => 'psa', 'Psat6g205080' => 'psa', 'PSO017G0271' => 'pso', 'PSO017G1276' => 'pso', 'PSO017G1429' => 'pso', 'PSO017G1861' => 'pso', 'PSO017G2787' => 'pso', 'PSO017G4466' => 'pso', 'PSO017G5118' => 'pso', 'PSO017G5420' => 'pso', 'PSO063G3678' => 'pso', 'PSO210G0546' => 'pso', 'PSO317G0001' => 'pso', 'PSO357G0512' => 'pso', 'PSO478G2682' => 'pso', 'PSO647G0001' => 'pso', 'PSO675G0001' => 'pso', 'PSO675G2699' => 'pso', 'PSO675G2849' => 'pso', 'PSO675G4991' => 'pso', 'PSO689G0001' => 'pso', 'QL06p000916' => 'qlo', 'QL06p000921' => 'qlo', 'QL06p001398' => 'qlo', 'QL06p001407' => 'qlo', 'QL06p002031' => 'qlo', 'RcHm_v2.0_Chr4g0387791' => 'rch', 'RcHm_v2.0_Chr4g0387801' => 'rch', 'RcHm_v2.0_Chr6g0286501' => 'rch', 'RcHm_v2.0_Chr6g0286511' => 'rch', 'RcHm_v2.0_Chr6g0286521' => 'rch', 'RcHm_v2.0_Chr6g0286531' => 'rch', 'RcHm_v2.0_Chr7g0189141' => 'rch', 'Rhsim02G0028700' => 'rsi', 'Rhsim02G0028800' => 'rsi', 'Rhsim02G0028900' => 'rsi', 'Rhsim02G0029000' => 'rsi', 'Rhsim02G0029100' => 'rsi', 'Rhsim02G0029200' => 'rsi', 'Rhsim02G0029300' => 'rsi', 'Rhsim02G0029400' => 'rsi', 'Rhsim02G0029500' => 'rsi', 'Rhsim02G0029600' => 'rsi', 'RhsimUnG0024000' => 'rsi', 'RhsimUnG0024100' => 'rsi', 'RhsimUnG0024200' => 'rsi', 'RhsimUnG0024300' => 'rsi', 'RhsimUnG0024400' => 'rsi', 'RhsimUnG0024500' => 'rsi', 'RhsimUnG0024700' => 'rsi', 'RhsimUnG0024800' => 'rsi', 'RhsimUnG0024900' => 'rsi', 'RhsimUnG0025100' => 'rsi', 'Sabra08G0120200' => 'sbr', 'Sabra08G0120300' => 'sbr', 'Sabra08G0120500' => 'sbr', 'Sabra08G0120600' => 'sbr', 'Sabra10G0158900' => 'sbr', 'SalBow2G3492' => 'sbo', 'Sc13g0004760' => 'sci', 'Sc13g0004770' => 'sci', 'Sed0003417' => 'sed', 'Sed0019750' => 'sed', 'SEGI_03419' => 'sgi', 'SEGI_05907' => 'sgi', 'SEGI_10682' => 'sgi', 'SEGI_13528' => 'sgi', 'SEGI_16081' => 'sgi', 'SEGI_19370' => 'sgi', 'SEGI_21015' => 'sgi', 'SEGI_21944' => 'sgi', 'SEGI_32906' => 'sgi', 'SEGI_33093' => 'sgi', 'SEGI_36110' => 'sgi', 'SEGI_40397' => 'sgi', 'SGA_v2.0_scaffold191G40426' => 'sas', 'SGA_v2.0_scaffold353G49717' => 'sas', 'SGA_v2.0_scaffold50G18550' => 'sas', 'SMO119G0173' => 'smo', 'SMO172G0002' => 'smo', 'Solyc09g082690.3' => 'sly', 'Solyc09g082700.2' => 'sly', 'Sopen09g031550' => 'spe', 'Sopen09g031560' => 'spe', 'Sp3g20540' => 'spa', 'Sp7g07580' => 'spa', 'TAR134G0002' => 'tar', 'TAR236G0001' => 'tar', 'TAR365G0892' => 'tar', 'TAR636G0166' => 'tar', 'TAR636G0646' => 'tar', 'TAR636G0869' => 'tar', 'TAR636G1317' => 'tar', 'TAR636G1744' => 'tar', 'TAR636G3358' => 'tar', 'TAR636G3436' => 'tar', 'THA.LOC104803047' => 'tha', 'Thecc.04G238900' => 'tca', 'Thhalv10021557m.g' => 'esa', 'Thhalv10026318m.g' => 'esa', 'Thhalv10026335m.g' => 'esa', 'TPR.G17433' => 'tpr', 'TPR.G18915' => 'tpr', 'TPR.G26125' => 'tpr', 'TWI09G0677' => 'twi', 'TWI73G0287' => 'twi', 'unitig_748.g8326' => 'ugi', 'vmacro15370' => 'vma', 'vmacro15371' => 'vma', 'vmacro15372' => 'vma', 'vmacro15373' => 'vma', 'vmacro15374' => 'vma', 'VMungo0720G2826' => 'vmu', 'Zm00001eb116960' => 'zma', 'Zm00001eb301260' => 'zma', 'Zm00001eb301270' => 'zma' ) $gf_id = 'HOM05D001460' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001460' ) $data_identifier = 'HOM05D001460' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 4, 'aag' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 2, 'aox' => (int) 2, 'arhy' => (int) 4, 'ath' => (int) 2, 'atr' => (int) 1, 'acertr' => (int) 10, 'cqu' => (int) 4, 'bca' => (int) 11, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 1, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 1, 'ccan' => (int) 1, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 1, 'col' => (int) 1, 'cpa' => (int) 1, 'cre' => (int) 7, 'csa' => (int) 1, 'camsi' => (int) 2, 'dca' => (int) 3, 'din' => (int) 2, 'dzi' => (int) 3, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 14, 'fve' => (int) 9, 'gma' => (int) 2, 'ghi' => (int) 4, 'gra' => (int) 2, 'vvi' => (int) 1, 'han' => (int) 13, 'cav' => (int) 1, 'hma' => (int) 2, 'sun' => (int) 2, 'lal' => (int) 2, 'lonja' => (int) 12, 'lja' => (int) 1, 'lsa' => (int) 7, 'mes' => (int) 1, 'mpo' => (int) 27, 'mbi' => (int) 1, 'mco' => (int) 8, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 1, 'egut' => (int) 1, 'ama' => (int) 1, 'nta' => (int) 4, 'nnu' => (int) 2, 'oeu' => (int) 3, 'osa' => (int) 4, 'pax' => (int) 9, 'pgr' => (int) 1, 'stu' => (int) 1, 'pvu' => (int) 1, 'ptr' => (int) 4, 'ppa' => (int) 22, 'pco' => (int) 6, 'ppe' => (int) 6, 'psa' => (int) 5, 'pso' => (int) 19, 'qlo' => (int) 5, 'rch' => (int) 7, 'rsi' => (int) 20, 'sbr' => (int) 5, 'sbo' => (int) 1, 'sci' => (int) 2, 'sed' => (int) 2, 'sgi' => (int) 12, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 2, 'tar' => (int) 10, 'tha' => (int) 1, 'tca' => (int) 1, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 2, 'ugi' => (int) 1, 'vma' => (int) 5, 'vmu' => (int) 1, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb301270' $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' => 'HOM05D001460', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '433', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p22980' => 'bna', 'A01p32340' => 'bna', 'A03p42970' => 'bna', 'A05p25880' => 'bna', 'Aa31LG8G9320' => 'aar', 'Aa31LG8G9330' => 'aar', 'Aa31LG8G9340' => 'aar', 'Aa31sc221G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1034' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1528' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.829' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2222' => 'aag', 'Ah.12g058830' => 'amhyb', 'Ah.12g058840' => 'amhyb', 'AL3G37160' => 'aly', 'AL7G41310' => 'aly', 'Aqoxy5G00395' => 'aox', 'Aqoxy5G00396' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0C8NZA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5185HY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JZ1PRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MD3LS0' => 'arhy', 'AT3G22840' => 'ath', 'AT4G14690' => 'ath', 'ATR0665G054' => 'atr', 'Atru.chr4.2344' => 'acertr', 'Atru.chr4.2346' => 'acertr', 'Atru.chr4.2347' => 'acertr', 'Atru.chr4.2348' => 'acertr', 'Atru.chr4.2355' => 'acertr', 'Atru.chr4.2356' => 'acertr', 'Atru.chr4.2358' => 'acertr', 'Atru.chr4.2359' => 'acertr', 'Atru.chr4.2360' => 'acertr', 'Atru.chr4.2361' => 'acertr', 'AUR62030476' => 'cqu', 'AUR62030478' => 'cqu', 'AUR62030819' => 'cqu', 'AUR62030820' => 'cqu', 'BcaB03g14648' => 'bca', 'BcaB04g20492' => 'bca', 'BcaB06g26399' => 'bca', 'BcaC01g03416' => 'bca', 'BcaC01g03419' => 'bca', 'BcaC01g03421' => 'bca', 'BcaC01g03424' => 'bca', 'BcaC05g28012' => 'bca', 'BcaC09g49212' => 'bca', 'BcaC09g50140' => 'bca', 'BcaNung00346' => 'bca', 'BolC1t02785H' => 'bol', 'BolC1t04095H' => 'bol', 'BolC3t17545H' => 'bol', 'BolC5t32769H' => 'bol', 'BraA01t02211Z' => 'bra', 'BraA01t03359Z' => 'bra', 'BraA03t13441Z' => 'bra', 'BraA05t21476Z' => 'bra', 'C01p28420' => 'bna', 'C01p41350' => 'bna', 'C03p52750' => 'bna', 'C03p52780' => 'bna', 'C05p40270' => 'bna', 'CAN.G1437.9' => 'can', 'CANSAT78G0035' => 'cansat', 'CANSAT78G1036' => 'cansat', 'CANSAT78G2272' => 'cansat', 'CANSAT78G2478' => 'cansat', 'CARHR098700' => 'chi', 'CARHR221120' => 'chi', 'CARHR221150' => 'chi', 'Carub.0003s2297' => 'cru', 'Carub.0007s2749' => 'cru', 'Carub.0007s2750' => 'cru', 'Carub.0007s2751' => 'cru', 'Ca_10849_v3' => 'car', 'Cc03_g04300' => 'ccan', 'CDE02G3648' => 'cde', 'CDE05G0060' => 'cde', 'CDE05G0692' => 'cde', 'CDE05G2285' => 'cde', 'CDE05G2884' => 'cde', 'CDE05G3072' => 'cde', 'Cfa008439' => 'cfa', 'Cfa008441' => 'cfa', 'Cfa008443' => 'cfa', 'Cfa008448' => 'cfa', 'Ciclev10005974m.g' => 'ccl', 'Ciclev10006006m.g' => 'ccl', 'Ciclev10006775m.g' => 'ccl', 'CiPaw.02G120400' => 'cil', 'CiPaw.02G120500' => 'cil', 'CiPaw.02G120600' => 'cil', 'ClCG05G004850' => 'cla', 'COL.COLO4_21566' => 'col', 'Cpa.g.sc44.124' => 'cpa', 'Cre07.g320400' => 'cre', 'Cre07.g320450' => 'cre', 'Cre08.g384650' => 'cre', 'Cre09.g393173' => 'cre', 'Cre09.g394325' => 'cre', 'Cre14.g626750' => 'cre', 'Cre16.g679250' => 'cre', 'CsaV3_3G012890' => 'csa', 'CSS0010865' => 'camsi', 'CSS0044338' => 'camsi', 'DCAR_002366' => 'dca', 'DCAR_030687' => 'dca', 'DCAR_030688' => 'dca', 'Dinv14047' => 'din', 'Dinv14048' => 'din', 'Duzib151G0105' => 'dzi', 'Duzib151G0114' => 'dzi', 'Duzib212G1029' => 'dzi', 'ECA232G3536' => 'eca', 'ECA240G0786' => 'eca', 'ECA240G1802' => 'eca', 'ECA240G3760' => 'eca', 'ECA240G3920' => 'eca', 'EL10Ac5g12536' => 'bvu', 'EL10Ac5g12537' => 'bvu', 'EL10Ac5g12538' => 'bvu', 'Eucgr.B01004' => 'egr', 'Eucgr.B01006' => 'egr', 'Eucgr.B01007' => 'egr', 'Eucgr.B01008' => 'egr', 'Eucgr.B01895' => 'egr', 'Eucgr.B01896' => 'egr', 'FAN04G1456' => 'fan', 'FAN08G1769' => 'fan', 'FAN08G2160' => 'fan', 'FAN13G2403' => 'fan', 'FAN13G3303' => 'fan', 'FAN15G2435' => 'fan', 'FAN17G0672' => 'fan', 'FAN17G2441' => 'fan', 'FAN18G1024' => 'fan', 'FAN22G1458' => 'fan', 'FAN24G0037' => 'fan', 'FAN24G0429' => 'fan', 'FAN24G2387' => 'fan', 'FAN27G2746' => 'fan', 'FvH4_2g20400' => 'fve', 'FvH4_2g20420' => 'fve', 'FvH4_2g20430' => 'fve', 'FvH4_4g01270' => 'fve', 'FvH4_4g01290' => 'fve', 'FvH4_4g01300' => 'fve', 'FvH4_4g01310' => 'fve', 'FvH4_4g01330' => 'fve', 'FvH4_5g09070' => 'fve', 'Glyma.10G243800' => 'gma', 'Glyma.20G150600' => 'gma', 'Gohir.A09G219200' => 'ghi', 'Gohir.A09G219300' => 'ghi', 'Gohir.D09G221400' => 'ghi', 'Gohir.D09G221500' => 'ghi', 'Gorai.006G242600' => 'gra', 'Gorai.006G242700' => 'gra', 'GSVIVG01018044001' => 'vvi', 'HanXRQChr03g0083821' => 'han', 'HanXRQChr03g0083841' => 'han', 'HanXRQChr03g0083881' => 'han', 'HanXRQChr03g0083901' => 'han', 'HanXRQChr03g0083921' => 'han', 'HanXRQChr03g0085331' => 'han', 'HanXRQChr03g0085361' => 'han', 'HanXRQChr03g0085411' => 'han', 'HanXRQChr03g0085421' => 'han', 'HanXRQChr03g0085431' => 'han', 'HanXRQChr08g0221991' => 'han', 'HanXRQChr11g0336061' => 'han', 'HanXRQChr11g0336411' => 'han', 'Haze_11234' => 'cav', 'Hma1.2p1_0549F.1_g177010' => 'hma', 'Hma1.2p1_0602F.1_g187630' => 'hma', 'Hund14876' => 'sun', 'Hund14879' => 'sun', 'Lalb_Chr06g0160741' => 'lal', 'Lalb_Chr21g0304781' => 'lal', 'Lj3A726G19' => 'lonja', 'Lj3A726T23' => 'lonja', 'Lj3A726T24' => 'lonja', 'Lj3A726T25' => 'lonja', 'Lj3A727T17' => 'lonja', 'Lj3C726T0' => 'lonja', 'Lj3C726T2' => 'lonja', 'Lj3P725T35' => 'lonja', 'Lj3P727T10' => 'lonja', 'Lj3P727T12' => 'lonja', 'Lj3P727T14' => 'lonja', 'Lj5g0023109' => 'lja', 'Lj6P646T44' => 'lonja', 'Lsat_1_v5_gn_6_75760' => 'lsa', 'Lsat_1_v5_gn_6_75800' => 'lsa', 'Lsat_1_v5_gn_6_75900' => 'lsa', 'Lsat_1_v5_gn_6_76240' => 'lsa', 'Lsat_1_v5_gn_6_76441' => 'lsa', 'Lsat_1_v5_gn_6_76700' => 'lsa', 'Lsat_1_v5_gn_6_76760' => 'lsa', 'Manes.15G033100' => 'mes', 'Mapoly0004s0074' => 'mpo', 'Mapoly0004s0075' => 'mpo', 'Mapoly0004s0163' => 'mpo', 'Mapoly0004s0164' => 'mpo', 'Mapoly0021s0018' => 'mpo', 'Mapoly0041s0136' => 'mpo', 'Mapoly0041s0137' => 'mpo', 'Mapoly0041s0138' => 'mpo', 'Mapoly0041s0139' => 'mpo', 'Mapoly0041s0141' => 'mpo', 'Mapoly0041s0142' => 'mpo', 'Mapoly0041s0143' => 'mpo', 'Mapoly0041s0144' => 'mpo', 'Mapoly0041s0145' => 'mpo', 'Mapoly0047s0106' => 'mpo', 'Mapoly0047s0108' => 'mpo', 'Mapoly0050s0051' => 'mpo', 'Mapoly0050s0052' => 'mpo', 'Mapoly0050s0053' => 'mpo', 'Mapoly0058s0013' => 'mpo', 'Mapoly0091s0078' => 'mpo', 'Mapoly0091s0079' => 'mpo', 'Mapoly0091s0080' => 'mpo', 'Mapoly0091s0081' => 'mpo', 'Mapoly0278s0004' => 'mpo', 'Mapoly0278s0005' => 'mpo', 'Mapoly0278s0006' => 'mpo', 'MBI11_g30648_MAGBIO' => 'mbi', 'MCO03G194' => 'mco', 'MCO03G590' => 'mco', 'MCO07G312' => 'mco', 'MCO10G318' => 'mco', 'MCO12G244' => 'mco', 'MCO13G148' => 'mco', 'MCO13G194' => 'mco', 'MCO16G238' => 'mco', 'MD06G1134100' => 'mdo', 'MD13G1200100' => 'mdo', 'MD13G1200300' => 'mdo', 'MD13G1200600' => 'mdo', 'MD14G1150400' => 'mdo', 'MD16G1200000' => 'mdo', 'Medtr1g102570' => 'mtr', 'Medtr1g102780' => 'mtr', 'Medtr1g102800' => 'mtr', 'Medtr1g102810' => 'mtr', 'Medtr1g102830' => 'mtr', 'MELO3C006499.2' => 'cme', 'Migut.G00385' => 'egut', 'MSTRG.4063' => 'ama', 'Nitab4.5_0000090g0260' => 'nta', 'Nitab4.5_0000977g0030' => 'nta', 'Nitab4.5_0002541g0040' => 'nta', 'Nitab4.5_0007068g0040' => 'nta', 'Nn005s41408' => 'nnu', 'Nn005s41410' => 'nnu', 'Oeu010310.1' => 'oeu', 'Oeu010311.1' => 'oeu', 'Oeu043472.1' => 'oeu', 'Os01g0246400' => 'osa', 'Os04g0267950' => 'osa', 'Os07g0178700' => 'osa', 'Os07g0178800' => 'osa', 'Peaxi162Scf00316g00046' => 'pax', 'Peaxi162Scf00316g00049' => 'pax', 'Peaxi162Scf00316g00059' => 'pax', 'Peaxi162Scf00316g00328' => 'pax', 'Peaxi162Scf00316g00329' => 'pax', 'Peaxi162Scf00316g00411' => 'pax', 'Peaxi162Scf00316g00521' => 'pax', 'Peaxi162Scf00492g00068' => 'pax', 'Peaxi162Scf35631g00002' => 'pax', 'PGR142G3720' => 'pgr', 'PGSC0003DMG400006442' => 'stu', 'Phvul.007G062000' => 'pvu', 'Potri.008G157750' => 'ptr', 'Potri.008G157900' => 'ptr', 'Potri.008G158000' => 'ptr', 'Potri.008G158200' => 'ptr', 'Pp3c11_7280' => 'ppa', 'Pp3c11_7980' => 'ppa', 'Pp3c12_19450' => 'ppa', 'Pp3c14_1480' => 'ppa', 'Pp3c14_1501' => 'ppa', 'Pp3c16_4900' => 'ppa', 'Pp3c16_5010' => 'ppa', 'Pp3c16_5060' => 'ppa', 'Pp3c19_18250' => 'ppa', 'Pp3c23_8530' => 'ppa', 'Pp3c23_8550' => 'ppa', 'Pp3c24_9670' => 'ppa', 'Pp3c2_21390' => 'ppa', 'Pp3c2_31380' => 'ppa', 'Pp3c3_16620' => 'ppa', 'Pp3c3_8090' => 'ppa', 'Pp3c3_8110' => 'ppa', 'Pp3c3_8130' => 'ppa', 'Pp3c3_8150' => 'ppa', 'Pp3c4_14320' => 'ppa', 'Pp3c6_2560' => 'ppa', 'Pp3c9_16700' => 'ppa', 'PRCOL_00000234' => 'pco', 'PRCOL_00000235' => 'pco', 'PRCOL_00000777' => 'pco', 'PRCOL_00002344' => 'pco', 'PRCOL_00002372' => 'pco', 'PRCOL_00006120' => 'pco', 'Prupe.1G021400' => 'ppe', 'Prupe.1G021500' => 'ppe', 'Prupe.1G021600' => 'ppe', 'Prupe.1G021700' => 'ppe', 'Prupe.1G021800' => 'ppe', 'Prupe.5G145100' => 'ppe', 'Psat6g204040' => 'psa', 'Psat6g204800' => 'psa', 'Psat6g204920' => 'psa', 'Psat6g204960' => 'psa', 'Psat6g205080' => 'psa', 'PSO017G0271' => 'pso', 'PSO017G1276' => 'pso', 'PSO017G1429' => 'pso', 'PSO017G1861' => 'pso', 'PSO017G2787' => 'pso', 'PSO017G4466' => 'pso', 'PSO017G5118' => 'pso', 'PSO017G5420' => 'pso', 'PSO063G3678' => 'pso', 'PSO210G0546' => 'pso', 'PSO317G0001' => 'pso', 'PSO357G0512' => 'pso', 'PSO478G2682' => 'pso', 'PSO647G0001' => 'pso', 'PSO675G0001' => 'pso', 'PSO675G2699' => 'pso', 'PSO675G2849' => 'pso', 'PSO675G4991' => 'pso', 'PSO689G0001' => 'pso', 'QL06p000916' => 'qlo', 'QL06p000921' => 'qlo', 'QL06p001398' => 'qlo', 'QL06p001407' => 'qlo', 'QL06p002031' => 'qlo', 'RcHm_v2.0_Chr4g0387791' => 'rch', 'RcHm_v2.0_Chr4g0387801' => 'rch', 'RcHm_v2.0_Chr6g0286501' => 'rch', 'RcHm_v2.0_Chr6g0286511' => 'rch', 'RcHm_v2.0_Chr6g0286521' => 'rch', 'RcHm_v2.0_Chr6g0286531' => 'rch', 'RcHm_v2.0_Chr7g0189141' => 'rch', 'Rhsim02G0028700' => 'rsi', 'Rhsim02G0028800' => 'rsi', 'Rhsim02G0028900' => 'rsi', 'Rhsim02G0029000' => 'rsi', 'Rhsim02G0029100' => 'rsi', 'Rhsim02G0029200' => 'rsi', 'Rhsim02G0029300' => 'rsi', 'Rhsim02G0029400' => 'rsi', 'Rhsim02G0029500' => 'rsi', 'Rhsim02G0029600' => 'rsi', 'RhsimUnG0024000' => 'rsi', 'RhsimUnG0024100' => 'rsi', 'RhsimUnG0024200' => 'rsi', 'RhsimUnG0024300' => 'rsi', 'RhsimUnG0024400' => 'rsi', 'RhsimUnG0024500' => 'rsi', 'RhsimUnG0024700' => 'rsi', 'RhsimUnG0024800' => 'rsi', 'RhsimUnG0024900' => 'rsi', 'RhsimUnG0025100' => 'rsi', 'Sabra08G0120200' => 'sbr', 'Sabra08G0120300' => 'sbr', 'Sabra08G0120500' => 'sbr', 'Sabra08G0120600' => 'sbr', 'Sabra10G0158900' => 'sbr', 'SalBow2G3492' => 'sbo', 'Sc13g0004760' => 'sci', 'Sc13g0004770' => 'sci', 'Sed0003417' => 'sed', 'Sed0019750' => 'sed', 'SEGI_03419' => 'sgi', 'SEGI_05907' => 'sgi', 'SEGI_10682' => 'sgi', 'SEGI_13528' => 'sgi', 'SEGI_16081' => 'sgi', 'SEGI_19370' => 'sgi', 'SEGI_21015' => 'sgi', 'SEGI_21944' => 'sgi', 'SEGI_32906' => 'sgi', 'SEGI_33093' => 'sgi', 'SEGI_36110' => 'sgi', 'SEGI_40397' => 'sgi', 'SGA_v2.0_scaffold191G40426' => 'sas', 'SGA_v2.0_scaffold353G49717' => 'sas', 'SGA_v2.0_scaffold50G18550' => 'sas', 'SMO119G0173' => 'smo', 'SMO172G0002' => 'smo', 'Solyc09g082690.3' => 'sly', 'Solyc09g082700.2' => 'sly', 'Sopen09g031550' => 'spe', 'Sopen09g031560' => 'spe', 'Sp3g20540' => 'spa', 'Sp7g07580' => 'spa', 'TAR134G0002' => 'tar', 'TAR236G0001' => 'tar', 'TAR365G0892' => 'tar', 'TAR636G0166' => 'tar', 'TAR636G0646' => 'tar', 'TAR636G0869' => 'tar', 'TAR636G1317' => 'tar', 'TAR636G1744' => 'tar', 'TAR636G3358' => 'tar', 'TAR636G3436' => 'tar', 'THA.LOC104803047' => 'tha', 'Thecc.04G238900' => 'tca', 'Thhalv10021557m.g' => 'esa', 'Thhalv10026318m.g' => 'esa', 'Thhalv10026335m.g' => 'esa', 'TPR.G17433' => 'tpr', 'TPR.G18915' => 'tpr', 'TPR.G26125' => 'tpr', 'TWI09G0677' => 'twi', 'TWI73G0287' => 'twi', 'unitig_748.g8326' => 'ugi', 'vmacro15370' => 'vma', 'vmacro15371' => 'vma', 'vmacro15372' => 'vma', 'vmacro15373' => 'vma', 'vmacro15374' => 'vma', 'VMungo0720G2826' => 'vmu', 'Zm00001eb116960' => 'zma', 'Zm00001eb301260' => 'zma', 'Zm00001eb301270' => 'zma' ), 'gf_id' => 'HOM05D001460', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001460' ), 'data_identifier' => 'HOM05D001460', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001460', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '433', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p22980' => 'bna', 'A01p32340' => 'bna', 'A03p42970' => 'bna', 'A05p25880' => 'bna', 'Aa31LG8G9320' => 'aar', 'Aa31LG8G9330' => 'aar', 'Aa31LG8G9340' => 'aar', 'Aa31sc221G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1034' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1528' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.829' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2222' => 'aag', 'Ah.12g058830' => 'amhyb', 'Ah.12g058840' => 'amhyb', 'AL3G37160' => 'aly', 'AL7G41310' => 'aly', 'Aqoxy5G00395' => 'aox', 'Aqoxy5G00396' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0C8NZA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5185HY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JZ1PRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MD3LS0' => 'arhy', 'AT3G22840' => 'ath', 'AT4G14690' => 'ath', 'ATR0665G054' => 'atr', 'Atru.chr4.2344' => 'acertr', 'Atru.chr4.2346' => 'acertr', 'Atru.chr4.2347' => 'acertr', 'Atru.chr4.2348' => 'acertr', 'Atru.chr4.2355' => 'acertr', 'Atru.chr4.2356' => 'acertr', 'Atru.chr4.2358' => 'acertr', 'Atru.chr4.2359' => 'acertr', 'Atru.chr4.2360' => 'acertr', 'Atru.chr4.2361' => 'acertr', 'AUR62030476' => 'cqu', 'AUR62030478' => 'cqu', 'AUR62030819' => 'cqu', 'AUR62030820' => 'cqu', 'BcaB03g14648' => 'bca', 'BcaB04g20492' => 'bca', 'BcaB06g26399' => 'bca', 'BcaC01g03416' => 'bca', 'BcaC01g03419' => 'bca', 'BcaC01g03421' => 'bca', 'BcaC01g03424' => 'bca', 'BcaC05g28012' => 'bca', 'BcaC09g49212' => 'bca', 'BcaC09g50140' => 'bca', 'BcaNung00346' => 'bca', 'BolC1t02785H' => 'bol', 'BolC1t04095H' => 'bol', 'BolC3t17545H' => 'bol', 'BolC5t32769H' => 'bol', 'BraA01t02211Z' => 'bra', 'BraA01t03359Z' => 'bra', 'BraA03t13441Z' => 'bra', 'BraA05t21476Z' => 'bra', 'C01p28420' => 'bna', 'C01p41350' => 'bna', 'C03p52750' => 'bna', 'C03p52780' => 'bna', 'C05p40270' => 'bna', 'CAN.G1437.9' => 'can', 'CANSAT78G0035' => 'cansat', 'CANSAT78G1036' => 'cansat', 'CANSAT78G2272' => 'cansat', 'CANSAT78G2478' => 'cansat', 'CARHR098700' => 'chi', 'CARHR221120' => 'chi', 'CARHR221150' => 'chi', 'Carub.0003s2297' => 'cru', 'Carub.0007s2749' => 'cru', 'Carub.0007s2750' => 'cru', 'Carub.0007s2751' => 'cru', 'Ca_10849_v3' => 'car', 'Cc03_g04300' => 'ccan', 'CDE02G3648' => 'cde', 'CDE05G0060' => 'cde', 'CDE05G0692' => 'cde', 'CDE05G2285' => 'cde', 'CDE05G2884' => 'cde', 'CDE05G3072' => 'cde', 'Cfa008439' => 'cfa', 'Cfa008441' => 'cfa', 'Cfa008443' => 'cfa', 'Cfa008448' => 'cfa', 'Ciclev10005974m.g' => 'ccl', 'Ciclev10006006m.g' => 'ccl', 'Ciclev10006775m.g' => 'ccl', 'CiPaw.02G120400' => 'cil', 'CiPaw.02G120500' => 'cil', 'CiPaw.02G120600' => 'cil', 'ClCG05G004850' => 'cla', 'COL.COLO4_21566' => 'col', 'Cpa.g.sc44.124' => 'cpa', 'Cre07.g320400' => 'cre', 'Cre07.g320450' => 'cre', 'Cre08.g384650' => 'cre', 'Cre09.g393173' => 'cre', 'Cre09.g394325' => 'cre', 'Cre14.g626750' => 'cre', 'Cre16.g679250' => 'cre', 'CsaV3_3G012890' => 'csa', 'CSS0010865' => 'camsi', 'CSS0044338' => 'camsi', 'DCAR_002366' => 'dca', 'DCAR_030687' => 'dca', 'DCAR_030688' => 'dca', 'Dinv14047' => 'din', 'Dinv14048' => 'din', 'Duzib151G0105' => 'dzi', 'Duzib151G0114' => 'dzi', 'Duzib212G1029' => 'dzi', 'ECA232G3536' => 'eca', 'ECA240G0786' => 'eca', 'ECA240G1802' => 'eca', 'ECA240G3760' => 'eca', 'ECA240G3920' => 'eca', 'EL10Ac5g12536' => 'bvu', 'EL10Ac5g12537' => 'bvu', 'EL10Ac5g12538' => 'bvu', 'Eucgr.B01004' => 'egr', 'Eucgr.B01006' => 'egr', 'Eucgr.B01007' => 'egr', 'Eucgr.B01008' => 'egr', 'Eucgr.B01895' => 'egr', 'Eucgr.B01896' => 'egr', 'FAN04G1456' => 'fan', 'FAN08G1769' => 'fan', 'FAN08G2160' => 'fan', 'FAN13G2403' => 'fan', 'FAN13G3303' => 'fan', 'FAN15G2435' => 'fan', 'FAN17G0672' => 'fan', 'FAN17G2441' => 'fan', 'FAN18G1024' => 'fan', 'FAN22G1458' => 'fan', 'FAN24G0037' => 'fan', 'FAN24G0429' => 'fan', 'FAN24G2387' => 'fan', 'FAN27G2746' => 'fan', 'FvH4_2g20400' => 'fve', 'FvH4_2g20420' => 'fve', 'FvH4_2g20430' => 'fve', 'FvH4_4g01270' => 'fve', 'FvH4_4g01290' => 'fve', 'FvH4_4g01300' => 'fve', 'FvH4_4g01310' => 'fve', 'FvH4_4g01330' => 'fve', 'FvH4_5g09070' => 'fve', 'Glyma.10G243800' => 'gma', 'Glyma.20G150600' => 'gma', 'Gohir.A09G219200' => 'ghi', 'Gohir.A09G219300' => 'ghi', 'Gohir.D09G221400' => 'ghi', 'Gohir.D09G221500' => 'ghi', 'Gorai.006G242600' => 'gra', 'Gorai.006G242700' => 'gra', 'GSVIVG01018044001' => 'vvi', 'HanXRQChr03g0083821' => 'han', 'HanXRQChr03g0083841' => 'han', 'HanXRQChr03g0083881' => 'han', 'HanXRQChr03g0083901' => 'han', 'HanXRQChr03g0083921' => 'han', 'HanXRQChr03g0085331' => 'han', 'HanXRQChr03g0085361' => 'han', 'HanXRQChr03g0085411' => 'han', 'HanXRQChr03g0085421' => 'han', 'HanXRQChr03g0085431' => 'han', 'HanXRQChr08g0221991' => 'han', 'HanXRQChr11g0336061' => 'han', 'HanXRQChr11g0336411' => 'han', 'Haze_11234' => 'cav', 'Hma1.2p1_0549F.1_g177010' => 'hma', 'Hma1.2p1_0602F.1_g187630' => 'hma', 'Hund14876' => 'sun', 'Hund14879' => 'sun', 'Lalb_Chr06g0160741' => 'lal', 'Lalb_Chr21g0304781' => 'lal', 'Lj3A726G19' => 'lonja', 'Lj3A726T23' => 'lonja', 'Lj3A726T24' => 'lonja', 'Lj3A726T25' => 'lonja', 'Lj3A727T17' => 'lonja', 'Lj3C726T0' => 'lonja', 'Lj3C726T2' => 'lonja', 'Lj3P725T35' => 'lonja', 'Lj3P727T10' => 'lonja', 'Lj3P727T12' => 'lonja', 'Lj3P727T14' => 'lonja', 'Lj5g0023109' => 'lja', 'Lj6P646T44' => 'lonja', 'Lsat_1_v5_gn_6_75760' => 'lsa', 'Lsat_1_v5_gn_6_75800' => 'lsa', 'Lsat_1_v5_gn_6_75900' => 'lsa', 'Lsat_1_v5_gn_6_76240' => 'lsa', 'Lsat_1_v5_gn_6_76441' => 'lsa', 'Lsat_1_v5_gn_6_76700' => 'lsa', 'Lsat_1_v5_gn_6_76760' => 'lsa', 'Manes.15G033100' => 'mes', 'Mapoly0004s0074' => 'mpo', 'Mapoly0004s0075' => 'mpo', 'Mapoly0004s0163' => 'mpo', 'Mapoly0004s0164' => 'mpo', 'Mapoly0021s0018' => 'mpo', 'Mapoly0041s0136' => 'mpo', 'Mapoly0041s0137' => 'mpo', 'Mapoly0041s0138' => 'mpo', 'Mapoly0041s0139' => 'mpo', 'Mapoly0041s0141' => 'mpo', 'Mapoly0041s0142' => 'mpo', 'Mapoly0041s0143' => 'mpo', 'Mapoly0041s0144' => 'mpo', 'Mapoly0041s0145' => 'mpo', 'Mapoly0047s0106' => 'mpo', 'Mapoly0047s0108' => 'mpo', 'Mapoly0050s0051' => 'mpo', 'Mapoly0050s0052' => 'mpo', 'Mapoly0050s0053' => 'mpo', 'Mapoly0058s0013' => 'mpo', 'Mapoly0091s0078' => 'mpo', 'Mapoly0091s0079' => 'mpo', 'Mapoly0091s0080' => 'mpo', 'Mapoly0091s0081' => 'mpo', 'Mapoly0278s0004' => 'mpo', 'Mapoly0278s0005' => 'mpo', 'Mapoly0278s0006' => 'mpo', 'MBI11_g30648_MAGBIO' => 'mbi', 'MCO03G194' => 'mco', 'MCO03G590' => 'mco', 'MCO07G312' => 'mco', 'MCO10G318' => 'mco', 'MCO12G244' => 'mco', 'MCO13G148' => 'mco', 'MCO13G194' => 'mco', 'MCO16G238' => 'mco', 'MD06G1134100' => 'mdo', 'MD13G1200100' => 'mdo', 'MD13G1200300' => 'mdo', 'MD13G1200600' => 'mdo', 'MD14G1150400' => 'mdo', 'MD16G1200000' => 'mdo', 'Medtr1g102570' => 'mtr', 'Medtr1g102780' => 'mtr', 'Medtr1g102800' => 'mtr', 'Medtr1g102810' => 'mtr', 'Medtr1g102830' => 'mtr', 'MELO3C006499.2' => 'cme', 'Migut.G00385' => 'egut', 'MSTRG.4063' => 'ama', 'Nitab4.5_0000090g0260' => 'nta', 'Nitab4.5_0000977g0030' => 'nta', 'Nitab4.5_0002541g0040' => 'nta', 'Nitab4.5_0007068g0040' => 'nta', 'Nn005s41408' => 'nnu', 'Nn005s41410' => 'nnu', 'Oeu010310.1' => 'oeu', 'Oeu010311.1' => 'oeu', 'Oeu043472.1' => 'oeu', 'Os01g0246400' => 'osa', 'Os04g0267950' => 'osa', 'Os07g0178700' => 'osa', 'Os07g0178800' => 'osa', 'Peaxi162Scf00316g00046' => 'pax', 'Peaxi162Scf00316g00049' => 'pax', 'Peaxi162Scf00316g00059' => 'pax', 'Peaxi162Scf00316g00328' => 'pax', 'Peaxi162Scf00316g00329' => 'pax', 'Peaxi162Scf00316g00411' => 'pax', 'Peaxi162Scf00316g00521' => 'pax', 'Peaxi162Scf00492g00068' => 'pax', 'Peaxi162Scf35631g00002' => 'pax', 'PGR142G3720' => 'pgr', 'PGSC0003DMG400006442' => 'stu', 'Phvul.007G062000' => 'pvu', 'Potri.008G157750' => 'ptr', 'Potri.008G157900' => 'ptr', 'Potri.008G158000' => 'ptr', 'Potri.008G158200' => 'ptr', 'Pp3c11_7280' => 'ppa', 'Pp3c11_7980' => 'ppa', 'Pp3c12_19450' => 'ppa', 'Pp3c14_1480' => 'ppa', 'Pp3c14_1501' => 'ppa', 'Pp3c16_4900' => 'ppa', 'Pp3c16_5010' => 'ppa', 'Pp3c16_5060' => 'ppa', 'Pp3c19_18250' => 'ppa', 'Pp3c23_8530' => 'ppa', 'Pp3c23_8550' => 'ppa', 'Pp3c24_9670' => 'ppa', 'Pp3c2_21390' => 'ppa', 'Pp3c2_31380' => 'ppa', 'Pp3c3_16620' => 'ppa', 'Pp3c3_8090' => 'ppa', 'Pp3c3_8110' => 'ppa', 'Pp3c3_8130' => 'ppa', 'Pp3c3_8150' => 'ppa', 'Pp3c4_14320' => 'ppa', 'Pp3c6_2560' => 'ppa', 'Pp3c9_16700' => 'ppa', 'PRCOL_00000234' => 'pco', 'PRCOL_00000235' => 'pco', 'PRCOL_00000777' => 'pco', 'PRCOL_00002344' => 'pco', 'PRCOL_00002372' => 'pco', 'PRCOL_00006120' => 'pco', 'Prupe.1G021400' => 'ppe', 'Prupe.1G021500' => 'ppe', 'Prupe.1G021600' => 'ppe', 'Prupe.1G021700' => 'ppe', 'Prupe.1G021800' => 'ppe', 'Prupe.5G145100' => 'ppe', 'Psat6g204040' => 'psa', 'Psat6g204800' => 'psa', 'Psat6g204920' => 'psa', 'Psat6g204960' => 'psa', 'Psat6g205080' => 'psa', 'PSO017G0271' => 'pso', 'PSO017G1276' => 'pso', 'PSO017G1429' => 'pso', 'PSO017G1861' => 'pso', 'PSO017G2787' => 'pso', 'PSO017G4466' => 'pso', 'PSO017G5118' => 'pso', 'PSO017G5420' => 'pso', 'PSO063G3678' => 'pso', 'PSO210G0546' => 'pso', 'PSO317G0001' => 'pso', 'PSO357G0512' => 'pso', 'PSO478G2682' => 'pso', 'PSO647G0001' => 'pso', 'PSO675G0001' => 'pso', 'PSO675G2699' => 'pso', 'PSO675G2849' => 'pso', 'PSO675G4991' => 'pso', 'PSO689G0001' => 'pso', 'QL06p000916' => 'qlo', 'QL06p000921' => 'qlo', 'QL06p001398' => 'qlo', 'QL06p001407' => 'qlo', 'QL06p002031' => 'qlo', 'RcHm_v2.0_Chr4g0387791' => 'rch', 'RcHm_v2.0_Chr4g0387801' => 'rch', 'RcHm_v2.0_Chr6g0286501' => 'rch', 'RcHm_v2.0_Chr6g0286511' => 'rch', 'RcHm_v2.0_Chr6g0286521' => 'rch', 'RcHm_v2.0_Chr6g0286531' => 'rch', 'RcHm_v2.0_Chr7g0189141' => 'rch', 'Rhsim02G0028700' => 'rsi', 'Rhsim02G0028800' => 'rsi', 'Rhsim02G0028900' => 'rsi', 'Rhsim02G0029000' => 'rsi', 'Rhsim02G0029100' => 'rsi', 'Rhsim02G0029200' => 'rsi', 'Rhsim02G0029300' => 'rsi', 'Rhsim02G0029400' => 'rsi', 'Rhsim02G0029500' => 'rsi', 'Rhsim02G0029600' => 'rsi', 'RhsimUnG0024000' => 'rsi', 'RhsimUnG0024100' => 'rsi', 'RhsimUnG0024200' => 'rsi', 'RhsimUnG0024300' => 'rsi', 'RhsimUnG0024400' => 'rsi', 'RhsimUnG0024500' => 'rsi', 'RhsimUnG0024700' => 'rsi', 'RhsimUnG0024800' => 'rsi', 'RhsimUnG0024900' => 'rsi', 'RhsimUnG0025100' => 'rsi', 'Sabra08G0120200' => 'sbr', 'Sabra08G0120300' => 'sbr', 'Sabra08G0120500' => 'sbr', 'Sabra08G0120600' => 'sbr', 'Sabra10G0158900' => 'sbr', 'SalBow2G3492' => 'sbo', 'Sc13g0004760' => 'sci', 'Sc13g0004770' => 'sci', 'Sed0003417' => 'sed', 'Sed0019750' => 'sed', 'SEGI_03419' => 'sgi', 'SEGI_05907' => 'sgi', 'SEGI_10682' => 'sgi', 'SEGI_13528' => 'sgi', 'SEGI_16081' => 'sgi', 'SEGI_19370' => 'sgi', 'SEGI_21015' => 'sgi', 'SEGI_21944' => 'sgi', 'SEGI_32906' => 'sgi', 'SEGI_33093' => 'sgi', 'SEGI_36110' => 'sgi', 'SEGI_40397' => 'sgi', 'SGA_v2.0_scaffold191G40426' => 'sas', 'SGA_v2.0_scaffold353G49717' => 'sas', 'SGA_v2.0_scaffold50G18550' => 'sas', 'SMO119G0173' => 'smo', 'SMO172G0002' => 'smo', 'Solyc09g082690.3' => 'sly', 'Solyc09g082700.2' => 'sly', 'Sopen09g031550' => 'spe', 'Sopen09g031560' => 'spe', 'Sp3g20540' => 'spa', 'Sp7g07580' => 'spa', 'TAR134G0002' => 'tar', 'TAR236G0001' => 'tar', 'TAR365G0892' => 'tar', 'TAR636G0166' => 'tar', 'TAR636G0646' => 'tar', 'TAR636G0869' => 'tar', 'TAR636G1317' => 'tar', 'TAR636G1744' => 'tar', 'TAR636G3358' => 'tar', 'TAR636G3436' => 'tar', 'THA.LOC104803047' => 'tha', 'Thecc.04G238900' => 'tca', 'Thhalv10021557m.g' => 'esa', 'Thhalv10026318m.g' => 'esa', 'Thhalv10026335m.g' => 'esa', 'TPR.G17433' => 'tpr', 'TPR.G18915' => 'tpr', 'TPR.G26125' => 'tpr', 'TWI09G0677' => 'twi', 'TWI73G0287' => 'twi', 'unitig_748.g8326' => 'ugi', 'vmacro15370' => 'vma', 'vmacro15371' => 'vma', 'vmacro15372' => 'vma', 'vmacro15373' => 'vma', 'vmacro15374' => 'vma', 'VMungo0720G2826' => 'vmu', 'Zm00001eb116960' => 'zma', 'Zm00001eb301260' => 'zma', 'Zm00001eb301270' => 'zma' ) $gf_id = 'HOM05D001460' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001460' ) $data_identifier = 'HOM05D001460' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 4, 'aag' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 2, 'aox' => (int) 2, 'arhy' => (int) 4, 'ath' => (int) 2, 'atr' => (int) 1, 'acertr' => (int) 10, 'cqu' => (int) 4, 'bca' => (int) 11, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 1, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 1, 'ccan' => (int) 1, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 1, 'col' => (int) 1, 'cpa' => (int) 1, 'cre' => (int) 7, 'csa' => (int) 1, 'camsi' => (int) 2, 'dca' => (int) 3, 'din' => (int) 2, 'dzi' => (int) 3, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 14, 'fve' => (int) 9, 'gma' => (int) 2, 'ghi' => (int) 4, 'gra' => (int) 2, 'vvi' => (int) 1, 'han' => (int) 13, 'cav' => (int) 1, 'hma' => (int) 2, 'sun' => (int) 2, 'lal' => (int) 2, 'lonja' => (int) 12, 'lja' => (int) 1, 'lsa' => (int) 7, 'mes' => (int) 1, 'mpo' => (int) 27, 'mbi' => (int) 1, 'mco' => (int) 8, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 1, 'egut' => (int) 1, 'ama' => (int) 1, 'nta' => (int) 4, 'nnu' => (int) 2, 'oeu' => (int) 3, 'osa' => (int) 4, 'pax' => (int) 9, 'pgr' => (int) 1, 'stu' => (int) 1, 'pvu' => (int) 1, 'ptr' => (int) 4, 'ppa' => (int) 22, 'pco' => (int) 6, 'ppe' => (int) 6, 'psa' => (int) 5, 'pso' => (int) 19, 'qlo' => (int) 5, 'rch' => (int) 7, 'rsi' => (int) 20, 'sbr' => (int) 5, 'sbo' => (int) 1, 'sci' => (int) 2, 'sed' => (int) 2, 'sgi' => (int) 12, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 2, 'tar' => (int) 10, 'tha' => (int) 1, 'tca' => (int) 1, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 2, 'ugi' => (int) 1, 'vma' => (int) 5, 'vmu' => (int) 1, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb301270' $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' => 'HOM05D001460', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '433', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p22980' => 'bna', 'A01p32340' => 'bna', 'A03p42970' => 'bna', 'A05p25880' => 'bna', 'Aa31LG8G9320' => 'aar', 'Aa31LG8G9330' => 'aar', 'Aa31LG8G9340' => 'aar', 'Aa31sc221G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1034' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1528' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.829' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2222' => 'aag', 'Ah.12g058830' => 'amhyb', 'Ah.12g058840' => 'amhyb', 'AL3G37160' => 'aly', 'AL7G41310' => 'aly', 'Aqoxy5G00395' => 'aox', 'Aqoxy5G00396' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0C8NZA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5185HY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JZ1PRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MD3LS0' => 'arhy', 'AT3G22840' => 'ath', 'AT4G14690' => 'ath', 'ATR0665G054' => 'atr', 'Atru.chr4.2344' => 'acertr', 'Atru.chr4.2346' => 'acertr', 'Atru.chr4.2347' => 'acertr', 'Atru.chr4.2348' => 'acertr', 'Atru.chr4.2355' => 'acertr', 'Atru.chr4.2356' => 'acertr', 'Atru.chr4.2358' => 'acertr', 'Atru.chr4.2359' => 'acertr', 'Atru.chr4.2360' => 'acertr', 'Atru.chr4.2361' => 'acertr', 'AUR62030476' => 'cqu', 'AUR62030478' => 'cqu', 'AUR62030819' => 'cqu', 'AUR62030820' => 'cqu', 'BcaB03g14648' => 'bca', 'BcaB04g20492' => 'bca', 'BcaB06g26399' => 'bca', 'BcaC01g03416' => 'bca', 'BcaC01g03419' => 'bca', 'BcaC01g03421' => 'bca', 'BcaC01g03424' => 'bca', 'BcaC05g28012' => 'bca', 'BcaC09g49212' => 'bca', 'BcaC09g50140' => 'bca', 'BcaNung00346' => 'bca', 'BolC1t02785H' => 'bol', 'BolC1t04095H' => 'bol', 'BolC3t17545H' => 'bol', 'BolC5t32769H' => 'bol', 'BraA01t02211Z' => 'bra', 'BraA01t03359Z' => 'bra', 'BraA03t13441Z' => 'bra', 'BraA05t21476Z' => 'bra', 'C01p28420' => 'bna', 'C01p41350' => 'bna', 'C03p52750' => 'bna', 'C03p52780' => 'bna', 'C05p40270' => 'bna', 'CAN.G1437.9' => 'can', 'CANSAT78G0035' => 'cansat', 'CANSAT78G1036' => 'cansat', 'CANSAT78G2272' => 'cansat', 'CANSAT78G2478' => 'cansat', 'CARHR098700' => 'chi', 'CARHR221120' => 'chi', 'CARHR221150' => 'chi', 'Carub.0003s2297' => 'cru', 'Carub.0007s2749' => 'cru', 'Carub.0007s2750' => 'cru', 'Carub.0007s2751' => 'cru', 'Ca_10849_v3' => 'car', 'Cc03_g04300' => 'ccan', 'CDE02G3648' => 'cde', 'CDE05G0060' => 'cde', 'CDE05G0692' => 'cde', 'CDE05G2285' => 'cde', 'CDE05G2884' => 'cde', 'CDE05G3072' => 'cde', 'Cfa008439' => 'cfa', 'Cfa008441' => 'cfa', 'Cfa008443' => 'cfa', 'Cfa008448' => 'cfa', 'Ciclev10005974m.g' => 'ccl', 'Ciclev10006006m.g' => 'ccl', 'Ciclev10006775m.g' => 'ccl', 'CiPaw.02G120400' => 'cil', 'CiPaw.02G120500' => 'cil', 'CiPaw.02G120600' => 'cil', 'ClCG05G004850' => 'cla', 'COL.COLO4_21566' => 'col', 'Cpa.g.sc44.124' => 'cpa', 'Cre07.g320400' => 'cre', 'Cre07.g320450' => 'cre', 'Cre08.g384650' => 'cre', 'Cre09.g393173' => 'cre', 'Cre09.g394325' => 'cre', 'Cre14.g626750' => 'cre', 'Cre16.g679250' => 'cre', 'CsaV3_3G012890' => 'csa', 'CSS0010865' => 'camsi', 'CSS0044338' => 'camsi', 'DCAR_002366' => 'dca', 'DCAR_030687' => 'dca', 'DCAR_030688' => 'dca', 'Dinv14047' => 'din', 'Dinv14048' => 'din', 'Duzib151G0105' => 'dzi', 'Duzib151G0114' => 'dzi', 'Duzib212G1029' => 'dzi', 'ECA232G3536' => 'eca', 'ECA240G0786' => 'eca', 'ECA240G1802' => 'eca', 'ECA240G3760' => 'eca', 'ECA240G3920' => 'eca', 'EL10Ac5g12536' => 'bvu', 'EL10Ac5g12537' => 'bvu', 'EL10Ac5g12538' => 'bvu', 'Eucgr.B01004' => 'egr', 'Eucgr.B01006' => 'egr', 'Eucgr.B01007' => 'egr', 'Eucgr.B01008' => 'egr', 'Eucgr.B01895' => 'egr', 'Eucgr.B01896' => 'egr', 'FAN04G1456' => 'fan', 'FAN08G1769' => 'fan', 'FAN08G2160' => 'fan', 'FAN13G2403' => 'fan', 'FAN13G3303' => 'fan', 'FAN15G2435' => 'fan', 'FAN17G0672' => 'fan', 'FAN17G2441' => 'fan', 'FAN18G1024' => 'fan', 'FAN22G1458' => 'fan', 'FAN24G0037' => 'fan', 'FAN24G0429' => 'fan', 'FAN24G2387' => 'fan', 'FAN27G2746' => 'fan', 'FvH4_2g20400' => 'fve', 'FvH4_2g20420' => 'fve', 'FvH4_2g20430' => 'fve', 'FvH4_4g01270' => 'fve', 'FvH4_4g01290' => 'fve', 'FvH4_4g01300' => 'fve', 'FvH4_4g01310' => 'fve', 'FvH4_4g01330' => 'fve', 'FvH4_5g09070' => 'fve', 'Glyma.10G243800' => 'gma', 'Glyma.20G150600' => 'gma', 'Gohir.A09G219200' => 'ghi', 'Gohir.A09G219300' => 'ghi', 'Gohir.D09G221400' => 'ghi', 'Gohir.D09G221500' => 'ghi', 'Gorai.006G242600' => 'gra', 'Gorai.006G242700' => 'gra', 'GSVIVG01018044001' => 'vvi', 'HanXRQChr03g0083821' => 'han', 'HanXRQChr03g0083841' => 'han', 'HanXRQChr03g0083881' => 'han', 'HanXRQChr03g0083901' => 'han', 'HanXRQChr03g0083921' => 'han', 'HanXRQChr03g0085331' => 'han', 'HanXRQChr03g0085361' => 'han', 'HanXRQChr03g0085411' => 'han', 'HanXRQChr03g0085421' => 'han', 'HanXRQChr03g0085431' => 'han', 'HanXRQChr08g0221991' => 'han', 'HanXRQChr11g0336061' => 'han', 'HanXRQChr11g0336411' => 'han', 'Haze_11234' => 'cav', 'Hma1.2p1_0549F.1_g177010' => 'hma', 'Hma1.2p1_0602F.1_g187630' => 'hma', 'Hund14876' => 'sun', 'Hund14879' => 'sun', 'Lalb_Chr06g0160741' => 'lal', 'Lalb_Chr21g0304781' => 'lal', 'Lj3A726G19' => 'lonja', 'Lj3A726T23' => 'lonja', 'Lj3A726T24' => 'lonja', 'Lj3A726T25' => 'lonja', 'Lj3A727T17' => 'lonja', 'Lj3C726T0' => 'lonja', 'Lj3C726T2' => 'lonja', 'Lj3P725T35' => 'lonja', 'Lj3P727T10' => 'lonja', 'Lj3P727T12' => 'lonja', 'Lj3P727T14' => 'lonja', 'Lj5g0023109' => 'lja', 'Lj6P646T44' => 'lonja', 'Lsat_1_v5_gn_6_75760' => 'lsa', 'Lsat_1_v5_gn_6_75800' => 'lsa', 'Lsat_1_v5_gn_6_75900' => 'lsa', 'Lsat_1_v5_gn_6_76240' => 'lsa', 'Lsat_1_v5_gn_6_76441' => 'lsa', 'Lsat_1_v5_gn_6_76700' => 'lsa', 'Lsat_1_v5_gn_6_76760' => 'lsa', 'Manes.15G033100' => 'mes', 'Mapoly0004s0074' => 'mpo', 'Mapoly0004s0075' => 'mpo', 'Mapoly0004s0163' => 'mpo', 'Mapoly0004s0164' => 'mpo', 'Mapoly0021s0018' => 'mpo', 'Mapoly0041s0136' => 'mpo', 'Mapoly0041s0137' => 'mpo', 'Mapoly0041s0138' => 'mpo', 'Mapoly0041s0139' => 'mpo', 'Mapoly0041s0141' => 'mpo', 'Mapoly0041s0142' => 'mpo', 'Mapoly0041s0143' => 'mpo', 'Mapoly0041s0144' => 'mpo', 'Mapoly0041s0145' => 'mpo', 'Mapoly0047s0106' => 'mpo', 'Mapoly0047s0108' => 'mpo', 'Mapoly0050s0051' => 'mpo', 'Mapoly0050s0052' => 'mpo', 'Mapoly0050s0053' => 'mpo', 'Mapoly0058s0013' => 'mpo', 'Mapoly0091s0078' => 'mpo', 'Mapoly0091s0079' => 'mpo', 'Mapoly0091s0080' => 'mpo', 'Mapoly0091s0081' => 'mpo', 'Mapoly0278s0004' => 'mpo', 'Mapoly0278s0005' => 'mpo', 'Mapoly0278s0006' => 'mpo', 'MBI11_g30648_MAGBIO' => 'mbi', 'MCO03G194' => 'mco', 'MCO03G590' => 'mco', 'MCO07G312' => 'mco', 'MCO10G318' => 'mco', 'MCO12G244' => 'mco', 'MCO13G148' => 'mco', 'MCO13G194' => 'mco', 'MCO16G238' => 'mco', 'MD06G1134100' => 'mdo', 'MD13G1200100' => 'mdo', 'MD13G1200300' => 'mdo', 'MD13G1200600' => 'mdo', 'MD14G1150400' => 'mdo', 'MD16G1200000' => 'mdo', 'Medtr1g102570' => 'mtr', 'Medtr1g102780' => 'mtr', 'Medtr1g102800' => 'mtr', 'Medtr1g102810' => 'mtr', 'Medtr1g102830' => 'mtr', 'MELO3C006499.2' => 'cme', 'Migut.G00385' => 'egut', 'MSTRG.4063' => 'ama', 'Nitab4.5_0000090g0260' => 'nta', 'Nitab4.5_0000977g0030' => 'nta', 'Nitab4.5_0002541g0040' => 'nta', 'Nitab4.5_0007068g0040' => 'nta', 'Nn005s41408' => 'nnu', 'Nn005s41410' => 'nnu', 'Oeu010310.1' => 'oeu', 'Oeu010311.1' => 'oeu', 'Oeu043472.1' => 'oeu', 'Os01g0246400' => 'osa', 'Os04g0267950' => 'osa', 'Os07g0178700' => 'osa', 'Os07g0178800' => 'osa', 'Peaxi162Scf00316g00046' => 'pax', 'Peaxi162Scf00316g00049' => 'pax', 'Peaxi162Scf00316g00059' => 'pax', 'Peaxi162Scf00316g00328' => 'pax', 'Peaxi162Scf00316g00329' => 'pax', 'Peaxi162Scf00316g00411' => 'pax', 'Peaxi162Scf00316g00521' => 'pax', 'Peaxi162Scf00492g00068' => 'pax', 'Peaxi162Scf35631g00002' => 'pax', 'PGR142G3720' => 'pgr', 'PGSC0003DMG400006442' => 'stu', 'Phvul.007G062000' => 'pvu', 'Potri.008G157750' => 'ptr', 'Potri.008G157900' => 'ptr', 'Potri.008G158000' => 'ptr', 'Potri.008G158200' => 'ptr', 'Pp3c11_7280' => 'ppa', 'Pp3c11_7980' => 'ppa', 'Pp3c12_19450' => 'ppa', 'Pp3c14_1480' => 'ppa', 'Pp3c14_1501' => 'ppa', 'Pp3c16_4900' => 'ppa', 'Pp3c16_5010' => 'ppa', 'Pp3c16_5060' => 'ppa', 'Pp3c19_18250' => 'ppa', 'Pp3c23_8530' => 'ppa', 'Pp3c23_8550' => 'ppa', 'Pp3c24_9670' => 'ppa', 'Pp3c2_21390' => 'ppa', 'Pp3c2_31380' => 'ppa', 'Pp3c3_16620' => 'ppa', 'Pp3c3_8090' => 'ppa', 'Pp3c3_8110' => 'ppa', 'Pp3c3_8130' => 'ppa', 'Pp3c3_8150' => 'ppa', 'Pp3c4_14320' => 'ppa', 'Pp3c6_2560' => 'ppa', 'Pp3c9_16700' => 'ppa', 'PRCOL_00000234' => 'pco', 'PRCOL_00000235' => 'pco', 'PRCOL_00000777' => 'pco', 'PRCOL_00002344' => 'pco', 'PRCOL_00002372' => 'pco', 'PRCOL_00006120' => 'pco', 'Prupe.1G021400' => 'ppe', 'Prupe.1G021500' => 'ppe', 'Prupe.1G021600' => 'ppe', 'Prupe.1G021700' => 'ppe', 'Prupe.1G021800' => 'ppe', 'Prupe.5G145100' => 'ppe', 'Psat6g204040' => 'psa', 'Psat6g204800' => 'psa', 'Psat6g204920' => 'psa', 'Psat6g204960' => 'psa', 'Psat6g205080' => 'psa', 'PSO017G0271' => 'pso', 'PSO017G1276' => 'pso', 'PSO017G1429' => 'pso', 'PSO017G1861' => 'pso', 'PSO017G2787' => 'pso', 'PSO017G4466' => 'pso', 'PSO017G5118' => 'pso', 'PSO017G5420' => 'pso', 'PSO063G3678' => 'pso', 'PSO210G0546' => 'pso', 'PSO317G0001' => 'pso', 'PSO357G0512' => 'pso', 'PSO478G2682' => 'pso', 'PSO647G0001' => 'pso', 'PSO675G0001' => 'pso', 'PSO675G2699' => 'pso', 'PSO675G2849' => 'pso', 'PSO675G4991' => 'pso', 'PSO689G0001' => 'pso', 'QL06p000916' => 'qlo', 'QL06p000921' => 'qlo', 'QL06p001398' => 'qlo', 'QL06p001407' => 'qlo', 'QL06p002031' => 'qlo', 'RcHm_v2.0_Chr4g0387791' => 'rch', 'RcHm_v2.0_Chr4g0387801' => 'rch', 'RcHm_v2.0_Chr6g0286501' => 'rch', 'RcHm_v2.0_Chr6g0286511' => 'rch', 'RcHm_v2.0_Chr6g0286521' => 'rch', 'RcHm_v2.0_Chr6g0286531' => 'rch', 'RcHm_v2.0_Chr7g0189141' => 'rch', 'Rhsim02G0028700' => 'rsi', 'Rhsim02G0028800' => 'rsi', 'Rhsim02G0028900' => 'rsi', 'Rhsim02G0029000' => 'rsi', 'Rhsim02G0029100' => 'rsi', 'Rhsim02G0029200' => 'rsi', 'Rhsim02G0029300' => 'rsi', 'Rhsim02G0029400' => 'rsi', 'Rhsim02G0029500' => 'rsi', 'Rhsim02G0029600' => 'rsi', 'RhsimUnG0024000' => 'rsi', 'RhsimUnG0024100' => 'rsi', 'RhsimUnG0024200' => 'rsi', 'RhsimUnG0024300' => 'rsi', 'RhsimUnG0024400' => 'rsi', 'RhsimUnG0024500' => 'rsi', 'RhsimUnG0024700' => 'rsi', 'RhsimUnG0024800' => 'rsi', 'RhsimUnG0024900' => 'rsi', 'RhsimUnG0025100' => 'rsi', 'Sabra08G0120200' => 'sbr', 'Sabra08G0120300' => 'sbr', 'Sabra08G0120500' => 'sbr', 'Sabra08G0120600' => 'sbr', 'Sabra10G0158900' => 'sbr', 'SalBow2G3492' => 'sbo', 'Sc13g0004760' => 'sci', 'Sc13g0004770' => 'sci', 'Sed0003417' => 'sed', 'Sed0019750' => 'sed', 'SEGI_03419' => 'sgi', 'SEGI_05907' => 'sgi', 'SEGI_10682' => 'sgi', 'SEGI_13528' => 'sgi', 'SEGI_16081' => 'sgi', 'SEGI_19370' => 'sgi', 'SEGI_21015' => 'sgi', 'SEGI_21944' => 'sgi', 'SEGI_32906' => 'sgi', 'SEGI_33093' => 'sgi', 'SEGI_36110' => 'sgi', 'SEGI_40397' => 'sgi', 'SGA_v2.0_scaffold191G40426' => 'sas', 'SGA_v2.0_scaffold353G49717' => 'sas', 'SGA_v2.0_scaffold50G18550' => 'sas', 'SMO119G0173' => 'smo', 'SMO172G0002' => 'smo', 'Solyc09g082690.3' => 'sly', 'Solyc09g082700.2' => 'sly', 'Sopen09g031550' => 'spe', 'Sopen09g031560' => 'spe', 'Sp3g20540' => 'spa', 'Sp7g07580' => 'spa', 'TAR134G0002' => 'tar', 'TAR236G0001' => 'tar', 'TAR365G0892' => 'tar', 'TAR636G0166' => 'tar', 'TAR636G0646' => 'tar', 'TAR636G0869' => 'tar', 'TAR636G1317' => 'tar', 'TAR636G1744' => 'tar', 'TAR636G3358' => 'tar', 'TAR636G3436' => 'tar', 'THA.LOC104803047' => 'tha', 'Thecc.04G238900' => 'tca', 'Thhalv10021557m.g' => 'esa', 'Thhalv10026318m.g' => 'esa', 'Thhalv10026335m.g' => 'esa', 'TPR.G17433' => 'tpr', 'TPR.G18915' => 'tpr', 'TPR.G26125' => 'tpr', 'TWI09G0677' => 'twi', 'TWI73G0287' => 'twi', 'unitig_748.g8326' => 'ugi', 'vmacro15370' => 'vma', 'vmacro15371' => 'vma', 'vmacro15372' => 'vma', 'vmacro15373' => 'vma', 'vmacro15374' => 'vma', 'VMungo0720G2826' => 'vmu', 'Zm00001eb116960' => 'zma', 'Zm00001eb301260' => 'zma', 'Zm00001eb301270' => 'zma' ), 'gf_id' => 'HOM05D001460', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001460' ), 'data_identifier' => 'HOM05D001460', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001460', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '433', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p22980' => 'bna', 'A01p32340' => 'bna', 'A03p42970' => 'bna', 'A05p25880' => 'bna', 'Aa31LG8G9320' => 'aar', 'Aa31LG8G9330' => 'aar', 'Aa31LG8G9340' => 'aar', 'Aa31sc221G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1034' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1528' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.829' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2222' => 'aag', 'Ah.12g058830' => 'amhyb', 'Ah.12g058840' => 'amhyb', 'AL3G37160' => 'aly', 'AL7G41310' => 'aly', 'Aqoxy5G00395' => 'aox', 'Aqoxy5G00396' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0C8NZA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5185HY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JZ1PRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MD3LS0' => 'arhy', 'AT3G22840' => 'ath', 'AT4G14690' => 'ath', 'ATR0665G054' => 'atr', 'Atru.chr4.2344' => 'acertr', 'Atru.chr4.2346' => 'acertr', 'Atru.chr4.2347' => 'acertr', 'Atru.chr4.2348' => 'acertr', 'Atru.chr4.2355' => 'acertr', 'Atru.chr4.2356' => 'acertr', 'Atru.chr4.2358' => 'acertr', 'Atru.chr4.2359' => 'acertr', 'Atru.chr4.2360' => 'acertr', 'Atru.chr4.2361' => 'acertr', 'AUR62030476' => 'cqu', 'AUR62030478' => 'cqu', 'AUR62030819' => 'cqu', 'AUR62030820' => 'cqu', 'BcaB03g14648' => 'bca', 'BcaB04g20492' => 'bca', 'BcaB06g26399' => 'bca', 'BcaC01g03416' => 'bca', 'BcaC01g03419' => 'bca', 'BcaC01g03421' => 'bca', 'BcaC01g03424' => 'bca', 'BcaC05g28012' => 'bca', 'BcaC09g49212' => 'bca', 'BcaC09g50140' => 'bca', 'BcaNung00346' => 'bca', 'BolC1t02785H' => 'bol', 'BolC1t04095H' => 'bol', 'BolC3t17545H' => 'bol', 'BolC5t32769H' => 'bol', 'BraA01t02211Z' => 'bra', 'BraA01t03359Z' => 'bra', 'BraA03t13441Z' => 'bra', 'BraA05t21476Z' => 'bra', 'C01p28420' => 'bna', 'C01p41350' => 'bna', 'C03p52750' => 'bna', 'C03p52780' => 'bna', 'C05p40270' => 'bna', 'CAN.G1437.9' => 'can', 'CANSAT78G0035' => 'cansat', 'CANSAT78G1036' => 'cansat', 'CANSAT78G2272' => 'cansat', 'CANSAT78G2478' => 'cansat', 'CARHR098700' => 'chi', 'CARHR221120' => 'chi', 'CARHR221150' => 'chi', 'Carub.0003s2297' => 'cru', 'Carub.0007s2749' => 'cru', 'Carub.0007s2750' => 'cru', 'Carub.0007s2751' => 'cru', 'Ca_10849_v3' => 'car', 'Cc03_g04300' => 'ccan', 'CDE02G3648' => 'cde', 'CDE05G0060' => 'cde', 'CDE05G0692' => 'cde', 'CDE05G2285' => 'cde', 'CDE05G2884' => 'cde', 'CDE05G3072' => 'cde', 'Cfa008439' => 'cfa', 'Cfa008441' => 'cfa', 'Cfa008443' => 'cfa', 'Cfa008448' => 'cfa', 'Ciclev10005974m.g' => 'ccl', 'Ciclev10006006m.g' => 'ccl', 'Ciclev10006775m.g' => 'ccl', 'CiPaw.02G120400' => 'cil', 'CiPaw.02G120500' => 'cil', 'CiPaw.02G120600' => 'cil', 'ClCG05G004850' => 'cla', 'COL.COLO4_21566' => 'col', 'Cpa.g.sc44.124' => 'cpa', 'Cre07.g320400' => 'cre', 'Cre07.g320450' => 'cre', 'Cre08.g384650' => 'cre', 'Cre09.g393173' => 'cre', 'Cre09.g394325' => 'cre', 'Cre14.g626750' => 'cre', 'Cre16.g679250' => 'cre', 'CsaV3_3G012890' => 'csa', 'CSS0010865' => 'camsi', 'CSS0044338' => 'camsi', 'DCAR_002366' => 'dca', 'DCAR_030687' => 'dca', 'DCAR_030688' => 'dca', 'Dinv14047' => 'din', 'Dinv14048' => 'din', 'Duzib151G0105' => 'dzi', 'Duzib151G0114' => 'dzi', 'Duzib212G1029' => 'dzi', 'ECA232G3536' => 'eca', 'ECA240G0786' => 'eca', 'ECA240G1802' => 'eca', 'ECA240G3760' => 'eca', 'ECA240G3920' => 'eca', 'EL10Ac5g12536' => 'bvu', 'EL10Ac5g12537' => 'bvu', 'EL10Ac5g12538' => 'bvu', 'Eucgr.B01004' => 'egr', 'Eucgr.B01006' => 'egr', 'Eucgr.B01007' => 'egr', 'Eucgr.B01008' => 'egr', 'Eucgr.B01895' => 'egr', 'Eucgr.B01896' => 'egr', 'FAN04G1456' => 'fan', 'FAN08G1769' => 'fan', 'FAN08G2160' => 'fan', 'FAN13G2403' => 'fan', 'FAN13G3303' => 'fan', 'FAN15G2435' => 'fan', 'FAN17G0672' => 'fan', 'FAN17G2441' => 'fan', 'FAN18G1024' => 'fan', 'FAN22G1458' => 'fan', 'FAN24G0037' => 'fan', 'FAN24G0429' => 'fan', 'FAN24G2387' => 'fan', 'FAN27G2746' => 'fan', 'FvH4_2g20400' => 'fve', 'FvH4_2g20420' => 'fve', 'FvH4_2g20430' => 'fve', 'FvH4_4g01270' => 'fve', 'FvH4_4g01290' => 'fve', 'FvH4_4g01300' => 'fve', 'FvH4_4g01310' => 'fve', 'FvH4_4g01330' => 'fve', 'FvH4_5g09070' => 'fve', 'Glyma.10G243800' => 'gma', 'Glyma.20G150600' => 'gma', 'Gohir.A09G219200' => 'ghi', 'Gohir.A09G219300' => 'ghi', 'Gohir.D09G221400' => 'ghi', 'Gohir.D09G221500' => 'ghi', 'Gorai.006G242600' => 'gra', 'Gorai.006G242700' => 'gra', 'GSVIVG01018044001' => 'vvi', 'HanXRQChr03g0083821' => 'han', 'HanXRQChr03g0083841' => 'han', 'HanXRQChr03g0083881' => 'han', 'HanXRQChr03g0083901' => 'han', 'HanXRQChr03g0083921' => 'han', 'HanXRQChr03g0085331' => 'han', 'HanXRQChr03g0085361' => 'han', 'HanXRQChr03g0085411' => 'han', 'HanXRQChr03g0085421' => 'han', 'HanXRQChr03g0085431' => 'han', 'HanXRQChr08g0221991' => 'han', 'HanXRQChr11g0336061' => 'han', 'HanXRQChr11g0336411' => 'han', 'Haze_11234' => 'cav', 'Hma1.2p1_0549F.1_g177010' => 'hma', 'Hma1.2p1_0602F.1_g187630' => 'hma', 'Hund14876' => 'sun', 'Hund14879' => 'sun', 'Lalb_Chr06g0160741' => 'lal', 'Lalb_Chr21g0304781' => 'lal', 'Lj3A726G19' => 'lonja', 'Lj3A726T23' => 'lonja', 'Lj3A726T24' => 'lonja', 'Lj3A726T25' => 'lonja', 'Lj3A727T17' => 'lonja', 'Lj3C726T0' => 'lonja', 'Lj3C726T2' => 'lonja', 'Lj3P725T35' => 'lonja', 'Lj3P727T10' => 'lonja', 'Lj3P727T12' => 'lonja', 'Lj3P727T14' => 'lonja', 'Lj5g0023109' => 'lja', 'Lj6P646T44' => 'lonja', 'Lsat_1_v5_gn_6_75760' => 'lsa', 'Lsat_1_v5_gn_6_75800' => 'lsa', 'Lsat_1_v5_gn_6_75900' => 'lsa', 'Lsat_1_v5_gn_6_76240' => 'lsa', 'Lsat_1_v5_gn_6_76441' => 'lsa', 'Lsat_1_v5_gn_6_76700' => 'lsa', 'Lsat_1_v5_gn_6_76760' => 'lsa', 'Manes.15G033100' => 'mes', 'Mapoly0004s0074' => 'mpo', 'Mapoly0004s0075' => 'mpo', 'Mapoly0004s0163' => 'mpo', 'Mapoly0004s0164' => 'mpo', 'Mapoly0021s0018' => 'mpo', 'Mapoly0041s0136' => 'mpo', 'Mapoly0041s0137' => 'mpo', 'Mapoly0041s0138' => 'mpo', 'Mapoly0041s0139' => 'mpo', 'Mapoly0041s0141' => 'mpo', 'Mapoly0041s0142' => 'mpo', 'Mapoly0041s0143' => 'mpo', 'Mapoly0041s0144' => 'mpo', 'Mapoly0041s0145' => 'mpo', 'Mapoly0047s0106' => 'mpo', 'Mapoly0047s0108' => 'mpo', 'Mapoly0050s0051' => 'mpo', 'Mapoly0050s0052' => 'mpo', 'Mapoly0050s0053' => 'mpo', 'Mapoly0058s0013' => 'mpo', 'Mapoly0091s0078' => 'mpo', 'Mapoly0091s0079' => 'mpo', 'Mapoly0091s0080' => 'mpo', 'Mapoly0091s0081' => 'mpo', 'Mapoly0278s0004' => 'mpo', 'Mapoly0278s0005' => 'mpo', 'Mapoly0278s0006' => 'mpo', 'MBI11_g30648_MAGBIO' => 'mbi', 'MCO03G194' => 'mco', 'MCO03G590' => 'mco', 'MCO07G312' => 'mco', 'MCO10G318' => 'mco', 'MCO12G244' => 'mco', 'MCO13G148' => 'mco', 'MCO13G194' => 'mco', 'MCO16G238' => 'mco', 'MD06G1134100' => 'mdo', 'MD13G1200100' => 'mdo', 'MD13G1200300' => 'mdo', 'MD13G1200600' => 'mdo', 'MD14G1150400' => 'mdo', 'MD16G1200000' => 'mdo', 'Medtr1g102570' => 'mtr', 'Medtr1g102780' => 'mtr', 'Medtr1g102800' => 'mtr', 'Medtr1g102810' => 'mtr', 'Medtr1g102830' => 'mtr', 'MELO3C006499.2' => 'cme', 'Migut.G00385' => 'egut', 'MSTRG.4063' => 'ama', 'Nitab4.5_0000090g0260' => 'nta', 'Nitab4.5_0000977g0030' => 'nta', 'Nitab4.5_0002541g0040' => 'nta', 'Nitab4.5_0007068g0040' => 'nta', 'Nn005s41408' => 'nnu', 'Nn005s41410' => 'nnu', 'Oeu010310.1' => 'oeu', 'Oeu010311.1' => 'oeu', 'Oeu043472.1' => 'oeu', 'Os01g0246400' => 'osa', 'Os04g0267950' => 'osa', 'Os07g0178700' => 'osa', 'Os07g0178800' => 'osa', 'Peaxi162Scf00316g00046' => 'pax', 'Peaxi162Scf00316g00049' => 'pax', 'Peaxi162Scf00316g00059' => 'pax', 'Peaxi162Scf00316g00328' => 'pax', 'Peaxi162Scf00316g00329' => 'pax', 'Peaxi162Scf00316g00411' => 'pax', 'Peaxi162Scf00316g00521' => 'pax', 'Peaxi162Scf00492g00068' => 'pax', 'Peaxi162Scf35631g00002' => 'pax', 'PGR142G3720' => 'pgr', 'PGSC0003DMG400006442' => 'stu', 'Phvul.007G062000' => 'pvu', 'Potri.008G157750' => 'ptr', 'Potri.008G157900' => 'ptr', 'Potri.008G158000' => 'ptr', 'Potri.008G158200' => 'ptr', 'Pp3c11_7280' => 'ppa', 'Pp3c11_7980' => 'ppa', 'Pp3c12_19450' => 'ppa', 'Pp3c14_1480' => 'ppa', 'Pp3c14_1501' => 'ppa', 'Pp3c16_4900' => 'ppa', 'Pp3c16_5010' => 'ppa', 'Pp3c16_5060' => 'ppa', 'Pp3c19_18250' => 'ppa', 'Pp3c23_8530' => 'ppa', 'Pp3c23_8550' => 'ppa', 'Pp3c24_9670' => 'ppa', 'Pp3c2_21390' => 'ppa', 'Pp3c2_31380' => 'ppa', 'Pp3c3_16620' => 'ppa', 'Pp3c3_8090' => 'ppa', 'Pp3c3_8110' => 'ppa', 'Pp3c3_8130' => 'ppa', 'Pp3c3_8150' => 'ppa', 'Pp3c4_14320' => 'ppa', 'Pp3c6_2560' => 'ppa', 'Pp3c9_16700' => 'ppa', 'PRCOL_00000234' => 'pco', 'PRCOL_00000235' => 'pco', 'PRCOL_00000777' => 'pco', 'PRCOL_00002344' => 'pco', 'PRCOL_00002372' => 'pco', 'PRCOL_00006120' => 'pco', 'Prupe.1G021400' => 'ppe', 'Prupe.1G021500' => 'ppe', 'Prupe.1G021600' => 'ppe', 'Prupe.1G021700' => 'ppe', 'Prupe.1G021800' => 'ppe', 'Prupe.5G145100' => 'ppe', 'Psat6g204040' => 'psa', 'Psat6g204800' => 'psa', 'Psat6g204920' => 'psa', 'Psat6g204960' => 'psa', 'Psat6g205080' => 'psa', 'PSO017G0271' => 'pso', 'PSO017G1276' => 'pso', 'PSO017G1429' => 'pso', 'PSO017G1861' => 'pso', 'PSO017G2787' => 'pso', 'PSO017G4466' => 'pso', 'PSO017G5118' => 'pso', 'PSO017G5420' => 'pso', 'PSO063G3678' => 'pso', 'PSO210G0546' => 'pso', 'PSO317G0001' => 'pso', 'PSO357G0512' => 'pso', 'PSO478G2682' => 'pso', 'PSO647G0001' => 'pso', 'PSO675G0001' => 'pso', 'PSO675G2699' => 'pso', 'PSO675G2849' => 'pso', 'PSO675G4991' => 'pso', 'PSO689G0001' => 'pso', 'QL06p000916' => 'qlo', 'QL06p000921' => 'qlo', 'QL06p001398' => 'qlo', 'QL06p001407' => 'qlo', 'QL06p002031' => 'qlo', 'RcHm_v2.0_Chr4g0387791' => 'rch', 'RcHm_v2.0_Chr4g0387801' => 'rch', 'RcHm_v2.0_Chr6g0286501' => 'rch', 'RcHm_v2.0_Chr6g0286511' => 'rch', 'RcHm_v2.0_Chr6g0286521' => 'rch', 'RcHm_v2.0_Chr6g0286531' => 'rch', 'RcHm_v2.0_Chr7g0189141' => 'rch', 'Rhsim02G0028700' => 'rsi', 'Rhsim02G0028800' => 'rsi', 'Rhsim02G0028900' => 'rsi', 'Rhsim02G0029000' => 'rsi', 'Rhsim02G0029100' => 'rsi', 'Rhsim02G0029200' => 'rsi', 'Rhsim02G0029300' => 'rsi', 'Rhsim02G0029400' => 'rsi', 'Rhsim02G0029500' => 'rsi', 'Rhsim02G0029600' => 'rsi', 'RhsimUnG0024000' => 'rsi', 'RhsimUnG0024100' => 'rsi', 'RhsimUnG0024200' => 'rsi', 'RhsimUnG0024300' => 'rsi', 'RhsimUnG0024400' => 'rsi', 'RhsimUnG0024500' => 'rsi', 'RhsimUnG0024700' => 'rsi', 'RhsimUnG0024800' => 'rsi', 'RhsimUnG0024900' => 'rsi', 'RhsimUnG0025100' => 'rsi', 'Sabra08G0120200' => 'sbr', 'Sabra08G0120300' => 'sbr', 'Sabra08G0120500' => 'sbr', 'Sabra08G0120600' => 'sbr', 'Sabra10G0158900' => 'sbr', 'SalBow2G3492' => 'sbo', 'Sc13g0004760' => 'sci', 'Sc13g0004770' => 'sci', 'Sed0003417' => 'sed', 'Sed0019750' => 'sed', 'SEGI_03419' => 'sgi', 'SEGI_05907' => 'sgi', 'SEGI_10682' => 'sgi', 'SEGI_13528' => 'sgi', 'SEGI_16081' => 'sgi', 'SEGI_19370' => 'sgi', 'SEGI_21015' => 'sgi', 'SEGI_21944' => 'sgi', 'SEGI_32906' => 'sgi', 'SEGI_33093' => 'sgi', 'SEGI_36110' => 'sgi', 'SEGI_40397' => 'sgi', 'SGA_v2.0_scaffold191G40426' => 'sas', 'SGA_v2.0_scaffold353G49717' => 'sas', 'SGA_v2.0_scaffold50G18550' => 'sas', 'SMO119G0173' => 'smo', 'SMO172G0002' => 'smo', 'Solyc09g082690.3' => 'sly', 'Solyc09g082700.2' => 'sly', 'Sopen09g031550' => 'spe', 'Sopen09g031560' => 'spe', 'Sp3g20540' => 'spa', 'Sp7g07580' => 'spa', 'TAR134G0002' => 'tar', 'TAR236G0001' => 'tar', 'TAR365G0892' => 'tar', 'TAR636G0166' => 'tar', 'TAR636G0646' => 'tar', 'TAR636G0869' => 'tar', 'TAR636G1317' => 'tar', 'TAR636G1744' => 'tar', 'TAR636G3358' => 'tar', 'TAR636G3436' => 'tar', 'THA.LOC104803047' => 'tha', 'Thecc.04G238900' => 'tca', 'Thhalv10021557m.g' => 'esa', 'Thhalv10026318m.g' => 'esa', 'Thhalv10026335m.g' => 'esa', 'TPR.G17433' => 'tpr', 'TPR.G18915' => 'tpr', 'TPR.G26125' => 'tpr', 'TWI09G0677' => 'twi', 'TWI73G0287' => 'twi', 'unitig_748.g8326' => 'ugi', 'vmacro15370' => 'vma', 'vmacro15371' => 'vma', 'vmacro15372' => 'vma', 'vmacro15373' => 'vma', 'vmacro15374' => 'vma', 'VMungo0720G2826' => 'vmu', 'Zm00001eb116960' => 'zma', 'Zm00001eb301260' => 'zma', 'Zm00001eb301270' => 'zma' ) $gf_id = 'HOM05D001460' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001460' ) $data_identifier = 'HOM05D001460' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 4, 'aag' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 2, 'aox' => (int) 2, 'arhy' => (int) 4, 'ath' => (int) 2, 'atr' => (int) 1, 'acertr' => (int) 10, 'cqu' => (int) 4, 'bca' => (int) 11, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 1, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 1, 'ccan' => (int) 1, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 1, 'col' => (int) 1, 'cpa' => (int) 1, 'cre' => (int) 7, 'csa' => (int) 1, 'camsi' => (int) 2, 'dca' => (int) 3, 'din' => (int) 2, 'dzi' => (int) 3, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 14, 'fve' => (int) 9, 'gma' => (int) 2, 'ghi' => (int) 4, 'gra' => (int) 2, 'vvi' => (int) 1, 'han' => (int) 13, 'cav' => (int) 1, 'hma' => (int) 2, 'sun' => (int) 2, 'lal' => (int) 2, 'lonja' => (int) 12, 'lja' => (int) 1, 'lsa' => (int) 7, 'mes' => (int) 1, 'mpo' => (int) 27, 'mbi' => (int) 1, 'mco' => (int) 8, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 1, 'egut' => (int) 1, 'ama' => (int) 1, 'nta' => (int) 4, 'nnu' => (int) 2, 'oeu' => (int) 3, 'osa' => (int) 4, 'pax' => (int) 9, 'pgr' => (int) 1, 'stu' => (int) 1, 'pvu' => (int) 1, 'ptr' => (int) 4, 'ppa' => (int) 22, 'pco' => (int) 6, 'ppe' => (int) 6, 'psa' => (int) 5, 'pso' => (int) 19, 'qlo' => (int) 5, 'rch' => (int) 7, 'rsi' => (int) 20, 'sbr' => (int) 5, 'sbo' => (int) 1, 'sci' => (int) 2, 'sed' => (int) 2, 'sgi' => (int) 12, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 2, 'tar' => (int) 10, 'tha' => (int) 1, 'tca' => (int) 1, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 2, 'ugi' => (int) 1, 'vma' => (int) 5, 'vmu' => (int) 1, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb301270' $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' => 'HOM05D001460', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '433', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p22980' => 'bna', 'A01p32340' => 'bna', 'A03p42970' => 'bna', 'A05p25880' => 'bna', 'Aa31LG8G9320' => 'aar', 'Aa31LG8G9330' => 'aar', 'Aa31LG8G9340' => 'aar', 'Aa31sc221G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1034' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1528' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.829' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2222' => 'aag', 'Ah.12g058830' => 'amhyb', 'Ah.12g058840' => 'amhyb', 'AL3G37160' => 'aly', 'AL7G41310' => 'aly', 'Aqoxy5G00395' => 'aox', 'Aqoxy5G00396' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0C8NZA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5185HY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JZ1PRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MD3LS0' => 'arhy', 'AT3G22840' => 'ath', 'AT4G14690' => 'ath', 'ATR0665G054' => 'atr', 'Atru.chr4.2344' => 'acertr', 'Atru.chr4.2346' => 'acertr', 'Atru.chr4.2347' => 'acertr', 'Atru.chr4.2348' => 'acertr', 'Atru.chr4.2355' => 'acertr', 'Atru.chr4.2356' => 'acertr', 'Atru.chr4.2358' => 'acertr', 'Atru.chr4.2359' => 'acertr', 'Atru.chr4.2360' => 'acertr', 'Atru.chr4.2361' => 'acertr', 'AUR62030476' => 'cqu', 'AUR62030478' => 'cqu', 'AUR62030819' => 'cqu', 'AUR62030820' => 'cqu', 'BcaB03g14648' => 'bca', 'BcaB04g20492' => 'bca', 'BcaB06g26399' => 'bca', 'BcaC01g03416' => 'bca', 'BcaC01g03419' => 'bca', 'BcaC01g03421' => 'bca', 'BcaC01g03424' => 'bca', 'BcaC05g28012' => 'bca', 'BcaC09g49212' => 'bca', 'BcaC09g50140' => 'bca', 'BcaNung00346' => 'bca', 'BolC1t02785H' => 'bol', 'BolC1t04095H' => 'bol', 'BolC3t17545H' => 'bol', 'BolC5t32769H' => 'bol', 'BraA01t02211Z' => 'bra', 'BraA01t03359Z' => 'bra', 'BraA03t13441Z' => 'bra', 'BraA05t21476Z' => 'bra', 'C01p28420' => 'bna', 'C01p41350' => 'bna', 'C03p52750' => 'bna', 'C03p52780' => 'bna', 'C05p40270' => 'bna', 'CAN.G1437.9' => 'can', 'CANSAT78G0035' => 'cansat', 'CANSAT78G1036' => 'cansat', 'CANSAT78G2272' => 'cansat', 'CANSAT78G2478' => 'cansat', 'CARHR098700' => 'chi', 'CARHR221120' => 'chi', 'CARHR221150' => 'chi', 'Carub.0003s2297' => 'cru', 'Carub.0007s2749' => 'cru', 'Carub.0007s2750' => 'cru', 'Carub.0007s2751' => 'cru', 'Ca_10849_v3' => 'car', 'Cc03_g04300' => 'ccan', 'CDE02G3648' => 'cde', 'CDE05G0060' => 'cde', 'CDE05G0692' => 'cde', 'CDE05G2285' => 'cde', 'CDE05G2884' => 'cde', 'CDE05G3072' => 'cde', 'Cfa008439' => 'cfa', 'Cfa008441' => 'cfa', 'Cfa008443' => 'cfa', 'Cfa008448' => 'cfa', 'Ciclev10005974m.g' => 'ccl', 'Ciclev10006006m.g' => 'ccl', 'Ciclev10006775m.g' => 'ccl', 'CiPaw.02G120400' => 'cil', 'CiPaw.02G120500' => 'cil', 'CiPaw.02G120600' => 'cil', 'ClCG05G004850' => 'cla', 'COL.COLO4_21566' => 'col', 'Cpa.g.sc44.124' => 'cpa', 'Cre07.g320400' => 'cre', 'Cre07.g320450' => 'cre', 'Cre08.g384650' => 'cre', 'Cre09.g393173' => 'cre', 'Cre09.g394325' => 'cre', 'Cre14.g626750' => 'cre', 'Cre16.g679250' => 'cre', 'CsaV3_3G012890' => 'csa', 'CSS0010865' => 'camsi', 'CSS0044338' => 'camsi', 'DCAR_002366' => 'dca', 'DCAR_030687' => 'dca', 'DCAR_030688' => 'dca', 'Dinv14047' => 'din', 'Dinv14048' => 'din', 'Duzib151G0105' => 'dzi', 'Duzib151G0114' => 'dzi', 'Duzib212G1029' => 'dzi', 'ECA232G3536' => 'eca', 'ECA240G0786' => 'eca', 'ECA240G1802' => 'eca', 'ECA240G3760' => 'eca', 'ECA240G3920' => 'eca', 'EL10Ac5g12536' => 'bvu', 'EL10Ac5g12537' => 'bvu', 'EL10Ac5g12538' => 'bvu', 'Eucgr.B01004' => 'egr', 'Eucgr.B01006' => 'egr', 'Eucgr.B01007' => 'egr', 'Eucgr.B01008' => 'egr', 'Eucgr.B01895' => 'egr', 'Eucgr.B01896' => 'egr', 'FAN04G1456' => 'fan', 'FAN08G1769' => 'fan', 'FAN08G2160' => 'fan', 'FAN13G2403' => 'fan', 'FAN13G3303' => 'fan', 'FAN15G2435' => 'fan', 'FAN17G0672' => 'fan', 'FAN17G2441' => 'fan', 'FAN18G1024' => 'fan', 'FAN22G1458' => 'fan', 'FAN24G0037' => 'fan', 'FAN24G0429' => 'fan', 'FAN24G2387' => 'fan', 'FAN27G2746' => 'fan', 'FvH4_2g20400' => 'fve', 'FvH4_2g20420' => 'fve', 'FvH4_2g20430' => 'fve', 'FvH4_4g01270' => 'fve', 'FvH4_4g01290' => 'fve', 'FvH4_4g01300' => 'fve', 'FvH4_4g01310' => 'fve', 'FvH4_4g01330' => 'fve', 'FvH4_5g09070' => 'fve', 'Glyma.10G243800' => 'gma', 'Glyma.20G150600' => 'gma', 'Gohir.A09G219200' => 'ghi', 'Gohir.A09G219300' => 'ghi', 'Gohir.D09G221400' => 'ghi', 'Gohir.D09G221500' => 'ghi', 'Gorai.006G242600' => 'gra', 'Gorai.006G242700' => 'gra', 'GSVIVG01018044001' => 'vvi', 'HanXRQChr03g0083821' => 'han', 'HanXRQChr03g0083841' => 'han', 'HanXRQChr03g0083881' => 'han', 'HanXRQChr03g0083901' => 'han', 'HanXRQChr03g0083921' => 'han', 'HanXRQChr03g0085331' => 'han', 'HanXRQChr03g0085361' => 'han', 'HanXRQChr03g0085411' => 'han', 'HanXRQChr03g0085421' => 'han', 'HanXRQChr03g0085431' => 'han', 'HanXRQChr08g0221991' => 'han', 'HanXRQChr11g0336061' => 'han', 'HanXRQChr11g0336411' => 'han', 'Haze_11234' => 'cav', 'Hma1.2p1_0549F.1_g177010' => 'hma', 'Hma1.2p1_0602F.1_g187630' => 'hma', 'Hund14876' => 'sun', 'Hund14879' => 'sun', 'Lalb_Chr06g0160741' => 'lal', 'Lalb_Chr21g0304781' => 'lal', 'Lj3A726G19' => 'lonja', 'Lj3A726T23' => 'lonja', 'Lj3A726T24' => 'lonja', 'Lj3A726T25' => 'lonja', 'Lj3A727T17' => 'lonja', 'Lj3C726T0' => 'lonja', 'Lj3C726T2' => 'lonja', 'Lj3P725T35' => 'lonja', 'Lj3P727T10' => 'lonja', 'Lj3P727T12' => 'lonja', 'Lj3P727T14' => 'lonja', 'Lj5g0023109' => 'lja', 'Lj6P646T44' => 'lonja', 'Lsat_1_v5_gn_6_75760' => 'lsa', 'Lsat_1_v5_gn_6_75800' => 'lsa', 'Lsat_1_v5_gn_6_75900' => 'lsa', 'Lsat_1_v5_gn_6_76240' => 'lsa', 'Lsat_1_v5_gn_6_76441' => 'lsa', 'Lsat_1_v5_gn_6_76700' => 'lsa', 'Lsat_1_v5_gn_6_76760' => 'lsa', 'Manes.15G033100' => 'mes', 'Mapoly0004s0074' => 'mpo', 'Mapoly0004s0075' => 'mpo', 'Mapoly0004s0163' => 'mpo', 'Mapoly0004s0164' => 'mpo', 'Mapoly0021s0018' => 'mpo', 'Mapoly0041s0136' => 'mpo', 'Mapoly0041s0137' => 'mpo', 'Mapoly0041s0138' => 'mpo', 'Mapoly0041s0139' => 'mpo', 'Mapoly0041s0141' => 'mpo', 'Mapoly0041s0142' => 'mpo', 'Mapoly0041s0143' => 'mpo', 'Mapoly0041s0144' => 'mpo', 'Mapoly0041s0145' => 'mpo', 'Mapoly0047s0106' => 'mpo', 'Mapoly0047s0108' => 'mpo', 'Mapoly0050s0051' => 'mpo', 'Mapoly0050s0052' => 'mpo', 'Mapoly0050s0053' => 'mpo', 'Mapoly0058s0013' => 'mpo', 'Mapoly0091s0078' => 'mpo', 'Mapoly0091s0079' => 'mpo', 'Mapoly0091s0080' => 'mpo', 'Mapoly0091s0081' => 'mpo', 'Mapoly0278s0004' => 'mpo', 'Mapoly0278s0005' => 'mpo', 'Mapoly0278s0006' => 'mpo', 'MBI11_g30648_MAGBIO' => 'mbi', 'MCO03G194' => 'mco', 'MCO03G590' => 'mco', 'MCO07G312' => 'mco', 'MCO10G318' => 'mco', 'MCO12G244' => 'mco', 'MCO13G148' => 'mco', 'MCO13G194' => 'mco', 'MCO16G238' => 'mco', 'MD06G1134100' => 'mdo', 'MD13G1200100' => 'mdo', 'MD13G1200300' => 'mdo', 'MD13G1200600' => 'mdo', 'MD14G1150400' => 'mdo', 'MD16G1200000' => 'mdo', 'Medtr1g102570' => 'mtr', 'Medtr1g102780' => 'mtr', 'Medtr1g102800' => 'mtr', 'Medtr1g102810' => 'mtr', 'Medtr1g102830' => 'mtr', 'MELO3C006499.2' => 'cme', 'Migut.G00385' => 'egut', 'MSTRG.4063' => 'ama', 'Nitab4.5_0000090g0260' => 'nta', 'Nitab4.5_0000977g0030' => 'nta', 'Nitab4.5_0002541g0040' => 'nta', 'Nitab4.5_0007068g0040' => 'nta', 'Nn005s41408' => 'nnu', 'Nn005s41410' => 'nnu', 'Oeu010310.1' => 'oeu', 'Oeu010311.1' => 'oeu', 'Oeu043472.1' => 'oeu', 'Os01g0246400' => 'osa', 'Os04g0267950' => 'osa', 'Os07g0178700' => 'osa', 'Os07g0178800' => 'osa', 'Peaxi162Scf00316g00046' => 'pax', 'Peaxi162Scf00316g00049' => 'pax', 'Peaxi162Scf00316g00059' => 'pax', 'Peaxi162Scf00316g00328' => 'pax', 'Peaxi162Scf00316g00329' => 'pax', 'Peaxi162Scf00316g00411' => 'pax', 'Peaxi162Scf00316g00521' => 'pax', 'Peaxi162Scf00492g00068' => 'pax', 'Peaxi162Scf35631g00002' => 'pax', 'PGR142G3720' => 'pgr', 'PGSC0003DMG400006442' => 'stu', 'Phvul.007G062000' => 'pvu', 'Potri.008G157750' => 'ptr', 'Potri.008G157900' => 'ptr', 'Potri.008G158000' => 'ptr', 'Potri.008G158200' => 'ptr', 'Pp3c11_7280' => 'ppa', 'Pp3c11_7980' => 'ppa', 'Pp3c12_19450' => 'ppa', 'Pp3c14_1480' => 'ppa', 'Pp3c14_1501' => 'ppa', 'Pp3c16_4900' => 'ppa', 'Pp3c16_5010' => 'ppa', 'Pp3c16_5060' => 'ppa', 'Pp3c19_18250' => 'ppa', 'Pp3c23_8530' => 'ppa', 'Pp3c23_8550' => 'ppa', 'Pp3c24_9670' => 'ppa', 'Pp3c2_21390' => 'ppa', 'Pp3c2_31380' => 'ppa', 'Pp3c3_16620' => 'ppa', 'Pp3c3_8090' => 'ppa', 'Pp3c3_8110' => 'ppa', 'Pp3c3_8130' => 'ppa', 'Pp3c3_8150' => 'ppa', 'Pp3c4_14320' => 'ppa', 'Pp3c6_2560' => 'ppa', 'Pp3c9_16700' => 'ppa', 'PRCOL_00000234' => 'pco', 'PRCOL_00000235' => 'pco', 'PRCOL_00000777' => 'pco', 'PRCOL_00002344' => 'pco', 'PRCOL_00002372' => 'pco', 'PRCOL_00006120' => 'pco', 'Prupe.1G021400' => 'ppe', 'Prupe.1G021500' => 'ppe', 'Prupe.1G021600' => 'ppe', 'Prupe.1G021700' => 'ppe', 'Prupe.1G021800' => 'ppe', 'Prupe.5G145100' => 'ppe', 'Psat6g204040' => 'psa', 'Psat6g204800' => 'psa', 'Psat6g204920' => 'psa', 'Psat6g204960' => 'psa', 'Psat6g205080' => 'psa', 'PSO017G0271' => 'pso', 'PSO017G1276' => 'pso', 'PSO017G1429' => 'pso', 'PSO017G1861' => 'pso', 'PSO017G2787' => 'pso', 'PSO017G4466' => 'pso', 'PSO017G5118' => 'pso', 'PSO017G5420' => 'pso', 'PSO063G3678' => 'pso', 'PSO210G0546' => 'pso', 'PSO317G0001' => 'pso', 'PSO357G0512' => 'pso', 'PSO478G2682' => 'pso', 'PSO647G0001' => 'pso', 'PSO675G0001' => 'pso', 'PSO675G2699' => 'pso', 'PSO675G2849' => 'pso', 'PSO675G4991' => 'pso', 'PSO689G0001' => 'pso', 'QL06p000916' => 'qlo', 'QL06p000921' => 'qlo', 'QL06p001398' => 'qlo', 'QL06p001407' => 'qlo', 'QL06p002031' => 'qlo', 'RcHm_v2.0_Chr4g0387791' => 'rch', 'RcHm_v2.0_Chr4g0387801' => 'rch', 'RcHm_v2.0_Chr6g0286501' => 'rch', 'RcHm_v2.0_Chr6g0286511' => 'rch', 'RcHm_v2.0_Chr6g0286521' => 'rch', 'RcHm_v2.0_Chr6g0286531' => 'rch', 'RcHm_v2.0_Chr7g0189141' => 'rch', 'Rhsim02G0028700' => 'rsi', 'Rhsim02G0028800' => 'rsi', 'Rhsim02G0028900' => 'rsi', 'Rhsim02G0029000' => 'rsi', 'Rhsim02G0029100' => 'rsi', 'Rhsim02G0029200' => 'rsi', 'Rhsim02G0029300' => 'rsi', 'Rhsim02G0029400' => 'rsi', 'Rhsim02G0029500' => 'rsi', 'Rhsim02G0029600' => 'rsi', 'RhsimUnG0024000' => 'rsi', 'RhsimUnG0024100' => 'rsi', 'RhsimUnG0024200' => 'rsi', 'RhsimUnG0024300' => 'rsi', 'RhsimUnG0024400' => 'rsi', 'RhsimUnG0024500' => 'rsi', 'RhsimUnG0024700' => 'rsi', 'RhsimUnG0024800' => 'rsi', 'RhsimUnG0024900' => 'rsi', 'RhsimUnG0025100' => 'rsi', 'Sabra08G0120200' => 'sbr', 'Sabra08G0120300' => 'sbr', 'Sabra08G0120500' => 'sbr', 'Sabra08G0120600' => 'sbr', 'Sabra10G0158900' => 'sbr', 'SalBow2G3492' => 'sbo', 'Sc13g0004760' => 'sci', 'Sc13g0004770' => 'sci', 'Sed0003417' => 'sed', 'Sed0019750' => 'sed', 'SEGI_03419' => 'sgi', 'SEGI_05907' => 'sgi', 'SEGI_10682' => 'sgi', 'SEGI_13528' => 'sgi', 'SEGI_16081' => 'sgi', 'SEGI_19370' => 'sgi', 'SEGI_21015' => 'sgi', 'SEGI_21944' => 'sgi', 'SEGI_32906' => 'sgi', 'SEGI_33093' => 'sgi', 'SEGI_36110' => 'sgi', 'SEGI_40397' => 'sgi', 'SGA_v2.0_scaffold191G40426' => 'sas', 'SGA_v2.0_scaffold353G49717' => 'sas', 'SGA_v2.0_scaffold50G18550' => 'sas', 'SMO119G0173' => 'smo', 'SMO172G0002' => 'smo', 'Solyc09g082690.3' => 'sly', 'Solyc09g082700.2' => 'sly', 'Sopen09g031550' => 'spe', 'Sopen09g031560' => 'spe', 'Sp3g20540' => 'spa', 'Sp7g07580' => 'spa', 'TAR134G0002' => 'tar', 'TAR236G0001' => 'tar', 'TAR365G0892' => 'tar', 'TAR636G0166' => 'tar', 'TAR636G0646' => 'tar', 'TAR636G0869' => 'tar', 'TAR636G1317' => 'tar', 'TAR636G1744' => 'tar', 'TAR636G3358' => 'tar', 'TAR636G3436' => 'tar', 'THA.LOC104803047' => 'tha', 'Thecc.04G238900' => 'tca', 'Thhalv10021557m.g' => 'esa', 'Thhalv10026318m.g' => 'esa', 'Thhalv10026335m.g' => 'esa', 'TPR.G17433' => 'tpr', 'TPR.G18915' => 'tpr', 'TPR.G26125' => 'tpr', 'TWI09G0677' => 'twi', 'TWI73G0287' => 'twi', 'unitig_748.g8326' => 'ugi', 'vmacro15370' => 'vma', 'vmacro15371' => 'vma', 'vmacro15372' => 'vma', 'vmacro15373' => 'vma', 'vmacro15374' => 'vma', 'VMungo0720G2826' => 'vmu', 'Zm00001eb116960' => 'zma', 'Zm00001eb301260' => 'zma', 'Zm00001eb301270' => 'zma' ), 'gf_id' => 'HOM05D001460', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001460' ), 'data_identifier' => 'HOM05D001460', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001460', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '433', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p22980' => 'bna', 'A01p32340' => 'bna', 'A03p42970' => 'bna', 'A05p25880' => 'bna', 'Aa31LG8G9320' => 'aar', 'Aa31LG8G9330' => 'aar', 'Aa31LG8G9340' => 'aar', 'Aa31sc221G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1034' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1528' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.829' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2222' => 'aag', 'Ah.12g058830' => 'amhyb', 'Ah.12g058840' => 'amhyb', 'AL3G37160' => 'aly', 'AL7G41310' => 'aly', 'Aqoxy5G00395' => 'aox', 'Aqoxy5G00396' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0C8NZA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5185HY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JZ1PRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MD3LS0' => 'arhy', 'AT3G22840' => 'ath', 'AT4G14690' => 'ath', 'ATR0665G054' => 'atr', 'Atru.chr4.2344' => 'acertr', 'Atru.chr4.2346' => 'acertr', 'Atru.chr4.2347' => 'acertr', 'Atru.chr4.2348' => 'acertr', 'Atru.chr4.2355' => 'acertr', 'Atru.chr4.2356' => 'acertr', 'Atru.chr4.2358' => 'acertr', 'Atru.chr4.2359' => 'acertr', 'Atru.chr4.2360' => 'acertr', 'Atru.chr4.2361' => 'acertr', 'AUR62030476' => 'cqu', 'AUR62030478' => 'cqu', 'AUR62030819' => 'cqu', 'AUR62030820' => 'cqu', 'BcaB03g14648' => 'bca', 'BcaB04g20492' => 'bca', 'BcaB06g26399' => 'bca', 'BcaC01g03416' => 'bca', 'BcaC01g03419' => 'bca', 'BcaC01g03421' => 'bca', 'BcaC01g03424' => 'bca', 'BcaC05g28012' => 'bca', 'BcaC09g49212' => 'bca', 'BcaC09g50140' => 'bca', 'BcaNung00346' => 'bca', 'BolC1t02785H' => 'bol', 'BolC1t04095H' => 'bol', 'BolC3t17545H' => 'bol', 'BolC5t32769H' => 'bol', 'BraA01t02211Z' => 'bra', 'BraA01t03359Z' => 'bra', 'BraA03t13441Z' => 'bra', 'BraA05t21476Z' => 'bra', 'C01p28420' => 'bna', 'C01p41350' => 'bna', 'C03p52750' => 'bna', 'C03p52780' => 'bna', 'C05p40270' => 'bna', 'CAN.G1437.9' => 'can', 'CANSAT78G0035' => 'cansat', 'CANSAT78G1036' => 'cansat', 'CANSAT78G2272' => 'cansat', 'CANSAT78G2478' => 'cansat', 'CARHR098700' => 'chi', 'CARHR221120' => 'chi', 'CARHR221150' => 'chi', 'Carub.0003s2297' => 'cru', 'Carub.0007s2749' => 'cru', 'Carub.0007s2750' => 'cru', 'Carub.0007s2751' => 'cru', 'Ca_10849_v3' => 'car', 'Cc03_g04300' => 'ccan', 'CDE02G3648' => 'cde', 'CDE05G0060' => 'cde', 'CDE05G0692' => 'cde', 'CDE05G2285' => 'cde', 'CDE05G2884' => 'cde', 'CDE05G3072' => 'cde', 'Cfa008439' => 'cfa', 'Cfa008441' => 'cfa', 'Cfa008443' => 'cfa', 'Cfa008448' => 'cfa', 'Ciclev10005974m.g' => 'ccl', 'Ciclev10006006m.g' => 'ccl', 'Ciclev10006775m.g' => 'ccl', 'CiPaw.02G120400' => 'cil', 'CiPaw.02G120500' => 'cil', 'CiPaw.02G120600' => 'cil', 'ClCG05G004850' => 'cla', 'COL.COLO4_21566' => 'col', 'Cpa.g.sc44.124' => 'cpa', 'Cre07.g320400' => 'cre', 'Cre07.g320450' => 'cre', 'Cre08.g384650' => 'cre', 'Cre09.g393173' => 'cre', 'Cre09.g394325' => 'cre', 'Cre14.g626750' => 'cre', 'Cre16.g679250' => 'cre', 'CsaV3_3G012890' => 'csa', 'CSS0010865' => 'camsi', 'CSS0044338' => 'camsi', 'DCAR_002366' => 'dca', 'DCAR_030687' => 'dca', 'DCAR_030688' => 'dca', 'Dinv14047' => 'din', 'Dinv14048' => 'din', 'Duzib151G0105' => 'dzi', 'Duzib151G0114' => 'dzi', 'Duzib212G1029' => 'dzi', 'ECA232G3536' => 'eca', 'ECA240G0786' => 'eca', 'ECA240G1802' => 'eca', 'ECA240G3760' => 'eca', 'ECA240G3920' => 'eca', 'EL10Ac5g12536' => 'bvu', 'EL10Ac5g12537' => 'bvu', 'EL10Ac5g12538' => 'bvu', 'Eucgr.B01004' => 'egr', 'Eucgr.B01006' => 'egr', 'Eucgr.B01007' => 'egr', 'Eucgr.B01008' => 'egr', 'Eucgr.B01895' => 'egr', 'Eucgr.B01896' => 'egr', 'FAN04G1456' => 'fan', 'FAN08G1769' => 'fan', 'FAN08G2160' => 'fan', 'FAN13G2403' => 'fan', 'FAN13G3303' => 'fan', 'FAN15G2435' => 'fan', 'FAN17G0672' => 'fan', 'FAN17G2441' => 'fan', 'FAN18G1024' => 'fan', 'FAN22G1458' => 'fan', 'FAN24G0037' => 'fan', 'FAN24G0429' => 'fan', 'FAN24G2387' => 'fan', 'FAN27G2746' => 'fan', 'FvH4_2g20400' => 'fve', 'FvH4_2g20420' => 'fve', 'FvH4_2g20430' => 'fve', 'FvH4_4g01270' => 'fve', 'FvH4_4g01290' => 'fve', 'FvH4_4g01300' => 'fve', 'FvH4_4g01310' => 'fve', 'FvH4_4g01330' => 'fve', 'FvH4_5g09070' => 'fve', 'Glyma.10G243800' => 'gma', 'Glyma.20G150600' => 'gma', 'Gohir.A09G219200' => 'ghi', 'Gohir.A09G219300' => 'ghi', 'Gohir.D09G221400' => 'ghi', 'Gohir.D09G221500' => 'ghi', 'Gorai.006G242600' => 'gra', 'Gorai.006G242700' => 'gra', 'GSVIVG01018044001' => 'vvi', 'HanXRQChr03g0083821' => 'han', 'HanXRQChr03g0083841' => 'han', 'HanXRQChr03g0083881' => 'han', 'HanXRQChr03g0083901' => 'han', 'HanXRQChr03g0083921' => 'han', 'HanXRQChr03g0085331' => 'han', 'HanXRQChr03g0085361' => 'han', 'HanXRQChr03g0085411' => 'han', 'HanXRQChr03g0085421' => 'han', 'HanXRQChr03g0085431' => 'han', 'HanXRQChr08g0221991' => 'han', 'HanXRQChr11g0336061' => 'han', 'HanXRQChr11g0336411' => 'han', 'Haze_11234' => 'cav', 'Hma1.2p1_0549F.1_g177010' => 'hma', 'Hma1.2p1_0602F.1_g187630' => 'hma', 'Hund14876' => 'sun', 'Hund14879' => 'sun', 'Lalb_Chr06g0160741' => 'lal', 'Lalb_Chr21g0304781' => 'lal', 'Lj3A726G19' => 'lonja', 'Lj3A726T23' => 'lonja', 'Lj3A726T24' => 'lonja', 'Lj3A726T25' => 'lonja', 'Lj3A727T17' => 'lonja', 'Lj3C726T0' => 'lonja', 'Lj3C726T2' => 'lonja', 'Lj3P725T35' => 'lonja', 'Lj3P727T10' => 'lonja', 'Lj3P727T12' => 'lonja', 'Lj3P727T14' => 'lonja', 'Lj5g0023109' => 'lja', 'Lj6P646T44' => 'lonja', 'Lsat_1_v5_gn_6_75760' => 'lsa', 'Lsat_1_v5_gn_6_75800' => 'lsa', 'Lsat_1_v5_gn_6_75900' => 'lsa', 'Lsat_1_v5_gn_6_76240' => 'lsa', 'Lsat_1_v5_gn_6_76441' => 'lsa', 'Lsat_1_v5_gn_6_76700' => 'lsa', 'Lsat_1_v5_gn_6_76760' => 'lsa', 'Manes.15G033100' => 'mes', 'Mapoly0004s0074' => 'mpo', 'Mapoly0004s0075' => 'mpo', 'Mapoly0004s0163' => 'mpo', 'Mapoly0004s0164' => 'mpo', 'Mapoly0021s0018' => 'mpo', 'Mapoly0041s0136' => 'mpo', 'Mapoly0041s0137' => 'mpo', 'Mapoly0041s0138' => 'mpo', 'Mapoly0041s0139' => 'mpo', 'Mapoly0041s0141' => 'mpo', 'Mapoly0041s0142' => 'mpo', 'Mapoly0041s0143' => 'mpo', 'Mapoly0041s0144' => 'mpo', 'Mapoly0041s0145' => 'mpo', 'Mapoly0047s0106' => 'mpo', 'Mapoly0047s0108' => 'mpo', 'Mapoly0050s0051' => 'mpo', 'Mapoly0050s0052' => 'mpo', 'Mapoly0050s0053' => 'mpo', 'Mapoly0058s0013' => 'mpo', 'Mapoly0091s0078' => 'mpo', 'Mapoly0091s0079' => 'mpo', 'Mapoly0091s0080' => 'mpo', 'Mapoly0091s0081' => 'mpo', 'Mapoly0278s0004' => 'mpo', 'Mapoly0278s0005' => 'mpo', 'Mapoly0278s0006' => 'mpo', 'MBI11_g30648_MAGBIO' => 'mbi', 'MCO03G194' => 'mco', 'MCO03G590' => 'mco', 'MCO07G312' => 'mco', 'MCO10G318' => 'mco', 'MCO12G244' => 'mco', 'MCO13G148' => 'mco', 'MCO13G194' => 'mco', 'MCO16G238' => 'mco', 'MD06G1134100' => 'mdo', 'MD13G1200100' => 'mdo', 'MD13G1200300' => 'mdo', 'MD13G1200600' => 'mdo', 'MD14G1150400' => 'mdo', 'MD16G1200000' => 'mdo', 'Medtr1g102570' => 'mtr', 'Medtr1g102780' => 'mtr', 'Medtr1g102800' => 'mtr', 'Medtr1g102810' => 'mtr', 'Medtr1g102830' => 'mtr', 'MELO3C006499.2' => 'cme', 'Migut.G00385' => 'egut', 'MSTRG.4063' => 'ama', 'Nitab4.5_0000090g0260' => 'nta', 'Nitab4.5_0000977g0030' => 'nta', 'Nitab4.5_0002541g0040' => 'nta', 'Nitab4.5_0007068g0040' => 'nta', 'Nn005s41408' => 'nnu', 'Nn005s41410' => 'nnu', 'Oeu010310.1' => 'oeu', 'Oeu010311.1' => 'oeu', 'Oeu043472.1' => 'oeu', 'Os01g0246400' => 'osa', 'Os04g0267950' => 'osa', 'Os07g0178700' => 'osa', 'Os07g0178800' => 'osa', 'Peaxi162Scf00316g00046' => 'pax', 'Peaxi162Scf00316g00049' => 'pax', 'Peaxi162Scf00316g00059' => 'pax', 'Peaxi162Scf00316g00328' => 'pax', 'Peaxi162Scf00316g00329' => 'pax', 'Peaxi162Scf00316g00411' => 'pax', 'Peaxi162Scf00316g00521' => 'pax', 'Peaxi162Scf00492g00068' => 'pax', 'Peaxi162Scf35631g00002' => 'pax', 'PGR142G3720' => 'pgr', 'PGSC0003DMG400006442' => 'stu', 'Phvul.007G062000' => 'pvu', 'Potri.008G157750' => 'ptr', 'Potri.008G157900' => 'ptr', 'Potri.008G158000' => 'ptr', 'Potri.008G158200' => 'ptr', 'Pp3c11_7280' => 'ppa', 'Pp3c11_7980' => 'ppa', 'Pp3c12_19450' => 'ppa', 'Pp3c14_1480' => 'ppa', 'Pp3c14_1501' => 'ppa', 'Pp3c16_4900' => 'ppa', 'Pp3c16_5010' => 'ppa', 'Pp3c16_5060' => 'ppa', 'Pp3c19_18250' => 'ppa', 'Pp3c23_8530' => 'ppa', 'Pp3c23_8550' => 'ppa', 'Pp3c24_9670' => 'ppa', 'Pp3c2_21390' => 'ppa', 'Pp3c2_31380' => 'ppa', 'Pp3c3_16620' => 'ppa', 'Pp3c3_8090' => 'ppa', 'Pp3c3_8110' => 'ppa', 'Pp3c3_8130' => 'ppa', 'Pp3c3_8150' => 'ppa', 'Pp3c4_14320' => 'ppa', 'Pp3c6_2560' => 'ppa', 'Pp3c9_16700' => 'ppa', 'PRCOL_00000234' => 'pco', 'PRCOL_00000235' => 'pco', 'PRCOL_00000777' => 'pco', 'PRCOL_00002344' => 'pco', 'PRCOL_00002372' => 'pco', 'PRCOL_00006120' => 'pco', 'Prupe.1G021400' => 'ppe', 'Prupe.1G021500' => 'ppe', 'Prupe.1G021600' => 'ppe', 'Prupe.1G021700' => 'ppe', 'Prupe.1G021800' => 'ppe', 'Prupe.5G145100' => 'ppe', 'Psat6g204040' => 'psa', 'Psat6g204800' => 'psa', 'Psat6g204920' => 'psa', 'Psat6g204960' => 'psa', 'Psat6g205080' => 'psa', 'PSO017G0271' => 'pso', 'PSO017G1276' => 'pso', 'PSO017G1429' => 'pso', 'PSO017G1861' => 'pso', 'PSO017G2787' => 'pso', 'PSO017G4466' => 'pso', 'PSO017G5118' => 'pso', 'PSO017G5420' => 'pso', 'PSO063G3678' => 'pso', 'PSO210G0546' => 'pso', 'PSO317G0001' => 'pso', 'PSO357G0512' => 'pso', 'PSO478G2682' => 'pso', 'PSO647G0001' => 'pso', 'PSO675G0001' => 'pso', 'PSO675G2699' => 'pso', 'PSO675G2849' => 'pso', 'PSO675G4991' => 'pso', 'PSO689G0001' => 'pso', 'QL06p000916' => 'qlo', 'QL06p000921' => 'qlo', 'QL06p001398' => 'qlo', 'QL06p001407' => 'qlo', 'QL06p002031' => 'qlo', 'RcHm_v2.0_Chr4g0387791' => 'rch', 'RcHm_v2.0_Chr4g0387801' => 'rch', 'RcHm_v2.0_Chr6g0286501' => 'rch', 'RcHm_v2.0_Chr6g0286511' => 'rch', 'RcHm_v2.0_Chr6g0286521' => 'rch', 'RcHm_v2.0_Chr6g0286531' => 'rch', 'RcHm_v2.0_Chr7g0189141' => 'rch', 'Rhsim02G0028700' => 'rsi', 'Rhsim02G0028800' => 'rsi', 'Rhsim02G0028900' => 'rsi', 'Rhsim02G0029000' => 'rsi', 'Rhsim02G0029100' => 'rsi', 'Rhsim02G0029200' => 'rsi', 'Rhsim02G0029300' => 'rsi', 'Rhsim02G0029400' => 'rsi', 'Rhsim02G0029500' => 'rsi', 'Rhsim02G0029600' => 'rsi', 'RhsimUnG0024000' => 'rsi', 'RhsimUnG0024100' => 'rsi', 'RhsimUnG0024200' => 'rsi', 'RhsimUnG0024300' => 'rsi', 'RhsimUnG0024400' => 'rsi', 'RhsimUnG0024500' => 'rsi', 'RhsimUnG0024700' => 'rsi', 'RhsimUnG0024800' => 'rsi', 'RhsimUnG0024900' => 'rsi', 'RhsimUnG0025100' => 'rsi', 'Sabra08G0120200' => 'sbr', 'Sabra08G0120300' => 'sbr', 'Sabra08G0120500' => 'sbr', 'Sabra08G0120600' => 'sbr', 'Sabra10G0158900' => 'sbr', 'SalBow2G3492' => 'sbo', 'Sc13g0004760' => 'sci', 'Sc13g0004770' => 'sci', 'Sed0003417' => 'sed', 'Sed0019750' => 'sed', 'SEGI_03419' => 'sgi', 'SEGI_05907' => 'sgi', 'SEGI_10682' => 'sgi', 'SEGI_13528' => 'sgi', 'SEGI_16081' => 'sgi', 'SEGI_19370' => 'sgi', 'SEGI_21015' => 'sgi', 'SEGI_21944' => 'sgi', 'SEGI_32906' => 'sgi', 'SEGI_33093' => 'sgi', 'SEGI_36110' => 'sgi', 'SEGI_40397' => 'sgi', 'SGA_v2.0_scaffold191G40426' => 'sas', 'SGA_v2.0_scaffold353G49717' => 'sas', 'SGA_v2.0_scaffold50G18550' => 'sas', 'SMO119G0173' => 'smo', 'SMO172G0002' => 'smo', 'Solyc09g082690.3' => 'sly', 'Solyc09g082700.2' => 'sly', 'Sopen09g031550' => 'spe', 'Sopen09g031560' => 'spe', 'Sp3g20540' => 'spa', 'Sp7g07580' => 'spa', 'TAR134G0002' => 'tar', 'TAR236G0001' => 'tar', 'TAR365G0892' => 'tar', 'TAR636G0166' => 'tar', 'TAR636G0646' => 'tar', 'TAR636G0869' => 'tar', 'TAR636G1317' => 'tar', 'TAR636G1744' => 'tar', 'TAR636G3358' => 'tar', 'TAR636G3436' => 'tar', 'THA.LOC104803047' => 'tha', 'Thecc.04G238900' => 'tca', 'Thhalv10021557m.g' => 'esa', 'Thhalv10026318m.g' => 'esa', 'Thhalv10026335m.g' => 'esa', 'TPR.G17433' => 'tpr', 'TPR.G18915' => 'tpr', 'TPR.G26125' => 'tpr', 'TWI09G0677' => 'twi', 'TWI73G0287' => 'twi', 'unitig_748.g8326' => 'ugi', 'vmacro15370' => 'vma', 'vmacro15371' => 'vma', 'vmacro15372' => 'vma', 'vmacro15373' => 'vma', 'vmacro15374' => 'vma', 'VMungo0720G2826' => 'vmu', 'Zm00001eb116960' => 'zma', 'Zm00001eb301260' => 'zma', 'Zm00001eb301270' => 'zma' ) $gf_id = 'HOM05D001460' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001460' ) $data_identifier = 'HOM05D001460' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 4, 'aag' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 2, 'aox' => (int) 2, 'arhy' => (int) 4, 'ath' => (int) 2, 'atr' => (int) 1, 'acertr' => (int) 10, 'cqu' => (int) 4, 'bca' => (int) 11, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 1, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 1, 'ccan' => (int) 1, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 1, 'col' => (int) 1, 'cpa' => (int) 1, 'cre' => (int) 7, 'csa' => (int) 1, 'camsi' => (int) 2, 'dca' => (int) 3, 'din' => (int) 2, 'dzi' => (int) 3, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 14, 'fve' => (int) 9, 'gma' => (int) 2, 'ghi' => (int) 4, 'gra' => (int) 2, 'vvi' => (int) 1, 'han' => (int) 13, 'cav' => (int) 1, 'hma' => (int) 2, 'sun' => (int) 2, 'lal' => (int) 2, 'lonja' => (int) 12, 'lja' => (int) 1, 'lsa' => (int) 7, 'mes' => (int) 1, 'mpo' => (int) 27, 'mbi' => (int) 1, 'mco' => (int) 8, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 1, 'egut' => (int) 1, 'ama' => (int) 1, 'nta' => (int) 4, 'nnu' => (int) 2, 'oeu' => (int) 3, 'osa' => (int) 4, 'pax' => (int) 9, 'pgr' => (int) 1, 'stu' => (int) 1, 'pvu' => (int) 1, 'ptr' => (int) 4, 'ppa' => (int) 22, 'pco' => (int) 6, 'ppe' => (int) 6, 'psa' => (int) 5, 'pso' => (int) 19, 'qlo' => (int) 5, 'rch' => (int) 7, 'rsi' => (int) 20, 'sbr' => (int) 5, 'sbo' => (int) 1, 'sci' => (int) 2, 'sed' => (int) 2, 'sgi' => (int) 12, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 2, 'tar' => (int) 10, 'tha' => (int) 1, 'tca' => (int) 1, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 2, 'ugi' => (int) 1, 'vma' => (int) 5, 'vmu' => (int) 1, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb301270' $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' => 'HOM05D001460', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '433', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p22980' => 'bna', 'A01p32340' => 'bna', 'A03p42970' => 'bna', 'A05p25880' => 'bna', 'Aa31LG8G9320' => 'aar', 'Aa31LG8G9330' => 'aar', 'Aa31LG8G9340' => 'aar', 'Aa31sc221G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1034' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1528' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.829' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2222' => 'aag', 'Ah.12g058830' => 'amhyb', 'Ah.12g058840' => 'amhyb', 'AL3G37160' => 'aly', 'AL7G41310' => 'aly', 'Aqoxy5G00395' => 'aox', 'Aqoxy5G00396' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0C8NZA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5185HY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JZ1PRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MD3LS0' => 'arhy', 'AT3G22840' => 'ath', 'AT4G14690' => 'ath', 'ATR0665G054' => 'atr', 'Atru.chr4.2344' => 'acertr', 'Atru.chr4.2346' => 'acertr', 'Atru.chr4.2347' => 'acertr', 'Atru.chr4.2348' => 'acertr', 'Atru.chr4.2355' => 'acertr', 'Atru.chr4.2356' => 'acertr', 'Atru.chr4.2358' => 'acertr', 'Atru.chr4.2359' => 'acertr', 'Atru.chr4.2360' => 'acertr', 'Atru.chr4.2361' => 'acertr', 'AUR62030476' => 'cqu', 'AUR62030478' => 'cqu', 'AUR62030819' => 'cqu', 'AUR62030820' => 'cqu', 'BcaB03g14648' => 'bca', 'BcaB04g20492' => 'bca', 'BcaB06g26399' => 'bca', 'BcaC01g03416' => 'bca', 'BcaC01g03419' => 'bca', 'BcaC01g03421' => 'bca', 'BcaC01g03424' => 'bca', 'BcaC05g28012' => 'bca', 'BcaC09g49212' => 'bca', 'BcaC09g50140' => 'bca', 'BcaNung00346' => 'bca', 'BolC1t02785H' => 'bol', 'BolC1t04095H' => 'bol', 'BolC3t17545H' => 'bol', 'BolC5t32769H' => 'bol', 'BraA01t02211Z' => 'bra', 'BraA01t03359Z' => 'bra', 'BraA03t13441Z' => 'bra', 'BraA05t21476Z' => 'bra', 'C01p28420' => 'bna', 'C01p41350' => 'bna', 'C03p52750' => 'bna', 'C03p52780' => 'bna', 'C05p40270' => 'bna', 'CAN.G1437.9' => 'can', 'CANSAT78G0035' => 'cansat', 'CANSAT78G1036' => 'cansat', 'CANSAT78G2272' => 'cansat', 'CANSAT78G2478' => 'cansat', 'CARHR098700' => 'chi', 'CARHR221120' => 'chi', 'CARHR221150' => 'chi', 'Carub.0003s2297' => 'cru', 'Carub.0007s2749' => 'cru', 'Carub.0007s2750' => 'cru', 'Carub.0007s2751' => 'cru', 'Ca_10849_v3' => 'car', 'Cc03_g04300' => 'ccan', 'CDE02G3648' => 'cde', 'CDE05G0060' => 'cde', 'CDE05G0692' => 'cde', 'CDE05G2285' => 'cde', 'CDE05G2884' => 'cde', 'CDE05G3072' => 'cde', 'Cfa008439' => 'cfa', 'Cfa008441' => 'cfa', 'Cfa008443' => 'cfa', 'Cfa008448' => 'cfa', 'Ciclev10005974m.g' => 'ccl', 'Ciclev10006006m.g' => 'ccl', 'Ciclev10006775m.g' => 'ccl', 'CiPaw.02G120400' => 'cil', 'CiPaw.02G120500' => 'cil', 'CiPaw.02G120600' => 'cil', 'ClCG05G004850' => 'cla', 'COL.COLO4_21566' => 'col', 'Cpa.g.sc44.124' => 'cpa', 'Cre07.g320400' => 'cre', 'Cre07.g320450' => 'cre', 'Cre08.g384650' => 'cre', 'Cre09.g393173' => 'cre', 'Cre09.g394325' => 'cre', 'Cre14.g626750' => 'cre', 'Cre16.g679250' => 'cre', 'CsaV3_3G012890' => 'csa', 'CSS0010865' => 'camsi', 'CSS0044338' => 'camsi', 'DCAR_002366' => 'dca', 'DCAR_030687' => 'dca', 'DCAR_030688' => 'dca', 'Dinv14047' => 'din', 'Dinv14048' => 'din', 'Duzib151G0105' => 'dzi', 'Duzib151G0114' => 'dzi', 'Duzib212G1029' => 'dzi', 'ECA232G3536' => 'eca', 'ECA240G0786' => 'eca', 'ECA240G1802' => 'eca', 'ECA240G3760' => 'eca', 'ECA240G3920' => 'eca', 'EL10Ac5g12536' => 'bvu', 'EL10Ac5g12537' => 'bvu', 'EL10Ac5g12538' => 'bvu', 'Eucgr.B01004' => 'egr', 'Eucgr.B01006' => 'egr', 'Eucgr.B01007' => 'egr', 'Eucgr.B01008' => 'egr', 'Eucgr.B01895' => 'egr', 'Eucgr.B01896' => 'egr', 'FAN04G1456' => 'fan', 'FAN08G1769' => 'fan', 'FAN08G2160' => 'fan', 'FAN13G2403' => 'fan', 'FAN13G3303' => 'fan', 'FAN15G2435' => 'fan', 'FAN17G0672' => 'fan', 'FAN17G2441' => 'fan', 'FAN18G1024' => 'fan', 'FAN22G1458' => 'fan', 'FAN24G0037' => 'fan', 'FAN24G0429' => 'fan', 'FAN24G2387' => 'fan', 'FAN27G2746' => 'fan', 'FvH4_2g20400' => 'fve', 'FvH4_2g20420' => 'fve', 'FvH4_2g20430' => 'fve', 'FvH4_4g01270' => 'fve', 'FvH4_4g01290' => 'fve', 'FvH4_4g01300' => 'fve', 'FvH4_4g01310' => 'fve', 'FvH4_4g01330' => 'fve', 'FvH4_5g09070' => 'fve', 'Glyma.10G243800' => 'gma', 'Glyma.20G150600' => 'gma', 'Gohir.A09G219200' => 'ghi', 'Gohir.A09G219300' => 'ghi', 'Gohir.D09G221400' => 'ghi', 'Gohir.D09G221500' => 'ghi', 'Gorai.006G242600' => 'gra', 'Gorai.006G242700' => 'gra', 'GSVIVG01018044001' => 'vvi', 'HanXRQChr03g0083821' => 'han', 'HanXRQChr03g0083841' => 'han', 'HanXRQChr03g0083881' => 'han', 'HanXRQChr03g0083901' => 'han', 'HanXRQChr03g0083921' => 'han', 'HanXRQChr03g0085331' => 'han', 'HanXRQChr03g0085361' => 'han', 'HanXRQChr03g0085411' => 'han', 'HanXRQChr03g0085421' => 'han', 'HanXRQChr03g0085431' => 'han', 'HanXRQChr08g0221991' => 'han', 'HanXRQChr11g0336061' => 'han', 'HanXRQChr11g0336411' => 'han', 'Haze_11234' => 'cav', 'Hma1.2p1_0549F.1_g177010' => 'hma', 'Hma1.2p1_0602F.1_g187630' => 'hma', 'Hund14876' => 'sun', 'Hund14879' => 'sun', 'Lalb_Chr06g0160741' => 'lal', 'Lalb_Chr21g0304781' => 'lal', 'Lj3A726G19' => 'lonja', 'Lj3A726T23' => 'lonja', 'Lj3A726T24' => 'lonja', 'Lj3A726T25' => 'lonja', 'Lj3A727T17' => 'lonja', 'Lj3C726T0' => 'lonja', 'Lj3C726T2' => 'lonja', 'Lj3P725T35' => 'lonja', 'Lj3P727T10' => 'lonja', 'Lj3P727T12' => 'lonja', 'Lj3P727T14' => 'lonja', 'Lj5g0023109' => 'lja', 'Lj6P646T44' => 'lonja', 'Lsat_1_v5_gn_6_75760' => 'lsa', 'Lsat_1_v5_gn_6_75800' => 'lsa', 'Lsat_1_v5_gn_6_75900' => 'lsa', 'Lsat_1_v5_gn_6_76240' => 'lsa', 'Lsat_1_v5_gn_6_76441' => 'lsa', 'Lsat_1_v5_gn_6_76700' => 'lsa', 'Lsat_1_v5_gn_6_76760' => 'lsa', 'Manes.15G033100' => 'mes', 'Mapoly0004s0074' => 'mpo', 'Mapoly0004s0075' => 'mpo', 'Mapoly0004s0163' => 'mpo', 'Mapoly0004s0164' => 'mpo', 'Mapoly0021s0018' => 'mpo', 'Mapoly0041s0136' => 'mpo', 'Mapoly0041s0137' => 'mpo', 'Mapoly0041s0138' => 'mpo', 'Mapoly0041s0139' => 'mpo', 'Mapoly0041s0141' => 'mpo', 'Mapoly0041s0142' => 'mpo', 'Mapoly0041s0143' => 'mpo', 'Mapoly0041s0144' => 'mpo', 'Mapoly0041s0145' => 'mpo', 'Mapoly0047s0106' => 'mpo', 'Mapoly0047s0108' => 'mpo', 'Mapoly0050s0051' => 'mpo', 'Mapoly0050s0052' => 'mpo', 'Mapoly0050s0053' => 'mpo', 'Mapoly0058s0013' => 'mpo', 'Mapoly0091s0078' => 'mpo', 'Mapoly0091s0079' => 'mpo', 'Mapoly0091s0080' => 'mpo', 'Mapoly0091s0081' => 'mpo', 'Mapoly0278s0004' => 'mpo', 'Mapoly0278s0005' => 'mpo', 'Mapoly0278s0006' => 'mpo', 'MBI11_g30648_MAGBIO' => 'mbi', 'MCO03G194' => 'mco', 'MCO03G590' => 'mco', 'MCO07G312' => 'mco', 'MCO10G318' => 'mco', 'MCO12G244' => 'mco', 'MCO13G148' => 'mco', 'MCO13G194' => 'mco', 'MCO16G238' => 'mco', 'MD06G1134100' => 'mdo', 'MD13G1200100' => 'mdo', 'MD13G1200300' => 'mdo', 'MD13G1200600' => 'mdo', 'MD14G1150400' => 'mdo', 'MD16G1200000' => 'mdo', 'Medtr1g102570' => 'mtr', 'Medtr1g102780' => 'mtr', 'Medtr1g102800' => 'mtr', 'Medtr1g102810' => 'mtr', 'Medtr1g102830' => 'mtr', 'MELO3C006499.2' => 'cme', 'Migut.G00385' => 'egut', 'MSTRG.4063' => 'ama', 'Nitab4.5_0000090g0260' => 'nta', 'Nitab4.5_0000977g0030' => 'nta', 'Nitab4.5_0002541g0040' => 'nta', 'Nitab4.5_0007068g0040' => 'nta', 'Nn005s41408' => 'nnu', 'Nn005s41410' => 'nnu', 'Oeu010310.1' => 'oeu', 'Oeu010311.1' => 'oeu', 'Oeu043472.1' => 'oeu', 'Os01g0246400' => 'osa', 'Os04g0267950' => 'osa', 'Os07g0178700' => 'osa', 'Os07g0178800' => 'osa', 'Peaxi162Scf00316g00046' => 'pax', 'Peaxi162Scf00316g00049' => 'pax', 'Peaxi162Scf00316g00059' => 'pax', 'Peaxi162Scf00316g00328' => 'pax', 'Peaxi162Scf00316g00329' => 'pax', 'Peaxi162Scf00316g00411' => 'pax', 'Peaxi162Scf00316g00521' => 'pax', 'Peaxi162Scf00492g00068' => 'pax', 'Peaxi162Scf35631g00002' => 'pax', 'PGR142G3720' => 'pgr', 'PGSC0003DMG400006442' => 'stu', 'Phvul.007G062000' => 'pvu', 'Potri.008G157750' => 'ptr', 'Potri.008G157900' => 'ptr', 'Potri.008G158000' => 'ptr', 'Potri.008G158200' => 'ptr', 'Pp3c11_7280' => 'ppa', 'Pp3c11_7980' => 'ppa', 'Pp3c12_19450' => 'ppa', 'Pp3c14_1480' => 'ppa', 'Pp3c14_1501' => 'ppa', 'Pp3c16_4900' => 'ppa', 'Pp3c16_5010' => 'ppa', 'Pp3c16_5060' => 'ppa', 'Pp3c19_18250' => 'ppa', 'Pp3c23_8530' => 'ppa', 'Pp3c23_8550' => 'ppa', 'Pp3c24_9670' => 'ppa', 'Pp3c2_21390' => 'ppa', 'Pp3c2_31380' => 'ppa', 'Pp3c3_16620' => 'ppa', 'Pp3c3_8090' => 'ppa', 'Pp3c3_8110' => 'ppa', 'Pp3c3_8130' => 'ppa', 'Pp3c3_8150' => 'ppa', 'Pp3c4_14320' => 'ppa', 'Pp3c6_2560' => 'ppa', 'Pp3c9_16700' => 'ppa', 'PRCOL_00000234' => 'pco', 'PRCOL_00000235' => 'pco', 'PRCOL_00000777' => 'pco', 'PRCOL_00002344' => 'pco', 'PRCOL_00002372' => 'pco', 'PRCOL_00006120' => 'pco', 'Prupe.1G021400' => 'ppe', 'Prupe.1G021500' => 'ppe', 'Prupe.1G021600' => 'ppe', 'Prupe.1G021700' => 'ppe', 'Prupe.1G021800' => 'ppe', 'Prupe.5G145100' => 'ppe', 'Psat6g204040' => 'psa', 'Psat6g204800' => 'psa', 'Psat6g204920' => 'psa', 'Psat6g204960' => 'psa', 'Psat6g205080' => 'psa', 'PSO017G0271' => 'pso', 'PSO017G1276' => 'pso', 'PSO017G1429' => 'pso', 'PSO017G1861' => 'pso', 'PSO017G2787' => 'pso', 'PSO017G4466' => 'pso', 'PSO017G5118' => 'pso', 'PSO017G5420' => 'pso', 'PSO063G3678' => 'pso', 'PSO210G0546' => 'pso', 'PSO317G0001' => 'pso', 'PSO357G0512' => 'pso', 'PSO478G2682' => 'pso', 'PSO647G0001' => 'pso', 'PSO675G0001' => 'pso', 'PSO675G2699' => 'pso', 'PSO675G2849' => 'pso', 'PSO675G4991' => 'pso', 'PSO689G0001' => 'pso', 'QL06p000916' => 'qlo', 'QL06p000921' => 'qlo', 'QL06p001398' => 'qlo', 'QL06p001407' => 'qlo', 'QL06p002031' => 'qlo', 'RcHm_v2.0_Chr4g0387791' => 'rch', 'RcHm_v2.0_Chr4g0387801' => 'rch', 'RcHm_v2.0_Chr6g0286501' => 'rch', 'RcHm_v2.0_Chr6g0286511' => 'rch', 'RcHm_v2.0_Chr6g0286521' => 'rch', 'RcHm_v2.0_Chr6g0286531' => 'rch', 'RcHm_v2.0_Chr7g0189141' => 'rch', 'Rhsim02G0028700' => 'rsi', 'Rhsim02G0028800' => 'rsi', 'Rhsim02G0028900' => 'rsi', 'Rhsim02G0029000' => 'rsi', 'Rhsim02G0029100' => 'rsi', 'Rhsim02G0029200' => 'rsi', 'Rhsim02G0029300' => 'rsi', 'Rhsim02G0029400' => 'rsi', 'Rhsim02G0029500' => 'rsi', 'Rhsim02G0029600' => 'rsi', 'RhsimUnG0024000' => 'rsi', 'RhsimUnG0024100' => 'rsi', 'RhsimUnG0024200' => 'rsi', 'RhsimUnG0024300' => 'rsi', 'RhsimUnG0024400' => 'rsi', 'RhsimUnG0024500' => 'rsi', 'RhsimUnG0024700' => 'rsi', 'RhsimUnG0024800' => 'rsi', 'RhsimUnG0024900' => 'rsi', 'RhsimUnG0025100' => 'rsi', 'Sabra08G0120200' => 'sbr', 'Sabra08G0120300' => 'sbr', 'Sabra08G0120500' => 'sbr', 'Sabra08G0120600' => 'sbr', 'Sabra10G0158900' => 'sbr', 'SalBow2G3492' => 'sbo', 'Sc13g0004760' => 'sci', 'Sc13g0004770' => 'sci', 'Sed0003417' => 'sed', 'Sed0019750' => 'sed', 'SEGI_03419' => 'sgi', 'SEGI_05907' => 'sgi', 'SEGI_10682' => 'sgi', 'SEGI_13528' => 'sgi', 'SEGI_16081' => 'sgi', 'SEGI_19370' => 'sgi', 'SEGI_21015' => 'sgi', 'SEGI_21944' => 'sgi', 'SEGI_32906' => 'sgi', 'SEGI_33093' => 'sgi', 'SEGI_36110' => 'sgi', 'SEGI_40397' => 'sgi', 'SGA_v2.0_scaffold191G40426' => 'sas', 'SGA_v2.0_scaffold353G49717' => 'sas', 'SGA_v2.0_scaffold50G18550' => 'sas', 'SMO119G0173' => 'smo', 'SMO172G0002' => 'smo', 'Solyc09g082690.3' => 'sly', 'Solyc09g082700.2' => 'sly', 'Sopen09g031550' => 'spe', 'Sopen09g031560' => 'spe', 'Sp3g20540' => 'spa', 'Sp7g07580' => 'spa', 'TAR134G0002' => 'tar', 'TAR236G0001' => 'tar', 'TAR365G0892' => 'tar', 'TAR636G0166' => 'tar', 'TAR636G0646' => 'tar', 'TAR636G0869' => 'tar', 'TAR636G1317' => 'tar', 'TAR636G1744' => 'tar', 'TAR636G3358' => 'tar', 'TAR636G3436' => 'tar', 'THA.LOC104803047' => 'tha', 'Thecc.04G238900' => 'tca', 'Thhalv10021557m.g' => 'esa', 'Thhalv10026318m.g' => 'esa', 'Thhalv10026335m.g' => 'esa', 'TPR.G17433' => 'tpr', 'TPR.G18915' => 'tpr', 'TPR.G26125' => 'tpr', 'TWI09G0677' => 'twi', 'TWI73G0287' => 'twi', 'unitig_748.g8326' => 'ugi', 'vmacro15370' => 'vma', 'vmacro15371' => 'vma', 'vmacro15372' => 'vma', 'vmacro15373' => 'vma', 'vmacro15374' => 'vma', 'VMungo0720G2826' => 'vmu', 'Zm00001eb116960' => 'zma', 'Zm00001eb301260' => 'zma', 'Zm00001eb301270' => 'zma' ), 'gf_id' => 'HOM05D001460', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001460' ), 'data_identifier' => 'HOM05D001460', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001460', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '433', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p22980' => 'bna', 'A01p32340' => 'bna', 'A03p42970' => 'bna', 'A05p25880' => 'bna', 'Aa31LG8G9320' => 'aar', 'Aa31LG8G9330' => 'aar', 'Aa31LG8G9340' => 'aar', 'Aa31sc221G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1034' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1528' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.829' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2222' => 'aag', 'Ah.12g058830' => 'amhyb', 'Ah.12g058840' => 'amhyb', 'AL3G37160' => 'aly', 'AL7G41310' => 'aly', 'Aqoxy5G00395' => 'aox', 'Aqoxy5G00396' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0C8NZA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5185HY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JZ1PRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MD3LS0' => 'arhy', 'AT3G22840' => 'ath', 'AT4G14690' => 'ath', 'ATR0665G054' => 'atr', 'Atru.chr4.2344' => 'acertr', 'Atru.chr4.2346' => 'acertr', 'Atru.chr4.2347' => 'acertr', 'Atru.chr4.2348' => 'acertr', 'Atru.chr4.2355' => 'acertr', 'Atru.chr4.2356' => 'acertr', 'Atru.chr4.2358' => 'acertr', 'Atru.chr4.2359' => 'acertr', 'Atru.chr4.2360' => 'acertr', 'Atru.chr4.2361' => 'acertr', 'AUR62030476' => 'cqu', 'AUR62030478' => 'cqu', 'AUR62030819' => 'cqu', 'AUR62030820' => 'cqu', 'BcaB03g14648' => 'bca', 'BcaB04g20492' => 'bca', 'BcaB06g26399' => 'bca', 'BcaC01g03416' => 'bca', 'BcaC01g03419' => 'bca', 'BcaC01g03421' => 'bca', 'BcaC01g03424' => 'bca', 'BcaC05g28012' => 'bca', 'BcaC09g49212' => 'bca', 'BcaC09g50140' => 'bca', 'BcaNung00346' => 'bca', 'BolC1t02785H' => 'bol', 'BolC1t04095H' => 'bol', 'BolC3t17545H' => 'bol', 'BolC5t32769H' => 'bol', 'BraA01t02211Z' => 'bra', 'BraA01t03359Z' => 'bra', 'BraA03t13441Z' => 'bra', 'BraA05t21476Z' => 'bra', 'C01p28420' => 'bna', 'C01p41350' => 'bna', 'C03p52750' => 'bna', 'C03p52780' => 'bna', 'C05p40270' => 'bna', 'CAN.G1437.9' => 'can', 'CANSAT78G0035' => 'cansat', 'CANSAT78G1036' => 'cansat', 'CANSAT78G2272' => 'cansat', 'CANSAT78G2478' => 'cansat', 'CARHR098700' => 'chi', 'CARHR221120' => 'chi', 'CARHR221150' => 'chi', 'Carub.0003s2297' => 'cru', 'Carub.0007s2749' => 'cru', 'Carub.0007s2750' => 'cru', 'Carub.0007s2751' => 'cru', 'Ca_10849_v3' => 'car', 'Cc03_g04300' => 'ccan', 'CDE02G3648' => 'cde', 'CDE05G0060' => 'cde', 'CDE05G0692' => 'cde', 'CDE05G2285' => 'cde', 'CDE05G2884' => 'cde', 'CDE05G3072' => 'cde', 'Cfa008439' => 'cfa', 'Cfa008441' => 'cfa', 'Cfa008443' => 'cfa', 'Cfa008448' => 'cfa', 'Ciclev10005974m.g' => 'ccl', 'Ciclev10006006m.g' => 'ccl', 'Ciclev10006775m.g' => 'ccl', 'CiPaw.02G120400' => 'cil', 'CiPaw.02G120500' => 'cil', 'CiPaw.02G120600' => 'cil', 'ClCG05G004850' => 'cla', 'COL.COLO4_21566' => 'col', 'Cpa.g.sc44.124' => 'cpa', 'Cre07.g320400' => 'cre', 'Cre07.g320450' => 'cre', 'Cre08.g384650' => 'cre', 'Cre09.g393173' => 'cre', 'Cre09.g394325' => 'cre', 'Cre14.g626750' => 'cre', 'Cre16.g679250' => 'cre', 'CsaV3_3G012890' => 'csa', 'CSS0010865' => 'camsi', 'CSS0044338' => 'camsi', 'DCAR_002366' => 'dca', 'DCAR_030687' => 'dca', 'DCAR_030688' => 'dca', 'Dinv14047' => 'din', 'Dinv14048' => 'din', 'Duzib151G0105' => 'dzi', 'Duzib151G0114' => 'dzi', 'Duzib212G1029' => 'dzi', 'ECA232G3536' => 'eca', 'ECA240G0786' => 'eca', 'ECA240G1802' => 'eca', 'ECA240G3760' => 'eca', 'ECA240G3920' => 'eca', 'EL10Ac5g12536' => 'bvu', 'EL10Ac5g12537' => 'bvu', 'EL10Ac5g12538' => 'bvu', 'Eucgr.B01004' => 'egr', 'Eucgr.B01006' => 'egr', 'Eucgr.B01007' => 'egr', 'Eucgr.B01008' => 'egr', 'Eucgr.B01895' => 'egr', 'Eucgr.B01896' => 'egr', 'FAN04G1456' => 'fan', 'FAN08G1769' => 'fan', 'FAN08G2160' => 'fan', 'FAN13G2403' => 'fan', 'FAN13G3303' => 'fan', 'FAN15G2435' => 'fan', 'FAN17G0672' => 'fan', 'FAN17G2441' => 'fan', 'FAN18G1024' => 'fan', 'FAN22G1458' => 'fan', 'FAN24G0037' => 'fan', 'FAN24G0429' => 'fan', 'FAN24G2387' => 'fan', 'FAN27G2746' => 'fan', 'FvH4_2g20400' => 'fve', 'FvH4_2g20420' => 'fve', 'FvH4_2g20430' => 'fve', 'FvH4_4g01270' => 'fve', 'FvH4_4g01290' => 'fve', 'FvH4_4g01300' => 'fve', 'FvH4_4g01310' => 'fve', 'FvH4_4g01330' => 'fve', 'FvH4_5g09070' => 'fve', 'Glyma.10G243800' => 'gma', 'Glyma.20G150600' => 'gma', 'Gohir.A09G219200' => 'ghi', 'Gohir.A09G219300' => 'ghi', 'Gohir.D09G221400' => 'ghi', 'Gohir.D09G221500' => 'ghi', 'Gorai.006G242600' => 'gra', 'Gorai.006G242700' => 'gra', 'GSVIVG01018044001' => 'vvi', 'HanXRQChr03g0083821' => 'han', 'HanXRQChr03g0083841' => 'han', 'HanXRQChr03g0083881' => 'han', 'HanXRQChr03g0083901' => 'han', 'HanXRQChr03g0083921' => 'han', 'HanXRQChr03g0085331' => 'han', 'HanXRQChr03g0085361' => 'han', 'HanXRQChr03g0085411' => 'han', 'HanXRQChr03g0085421' => 'han', 'HanXRQChr03g0085431' => 'han', 'HanXRQChr08g0221991' => 'han', 'HanXRQChr11g0336061' => 'han', 'HanXRQChr11g0336411' => 'han', 'Haze_11234' => 'cav', 'Hma1.2p1_0549F.1_g177010' => 'hma', 'Hma1.2p1_0602F.1_g187630' => 'hma', 'Hund14876' => 'sun', 'Hund14879' => 'sun', 'Lalb_Chr06g0160741' => 'lal', 'Lalb_Chr21g0304781' => 'lal', 'Lj3A726G19' => 'lonja', 'Lj3A726T23' => 'lonja', 'Lj3A726T24' => 'lonja', 'Lj3A726T25' => 'lonja', 'Lj3A727T17' => 'lonja', 'Lj3C726T0' => 'lonja', 'Lj3C726T2' => 'lonja', 'Lj3P725T35' => 'lonja', 'Lj3P727T10' => 'lonja', 'Lj3P727T12' => 'lonja', 'Lj3P727T14' => 'lonja', 'Lj5g0023109' => 'lja', 'Lj6P646T44' => 'lonja', 'Lsat_1_v5_gn_6_75760' => 'lsa', 'Lsat_1_v5_gn_6_75800' => 'lsa', 'Lsat_1_v5_gn_6_75900' => 'lsa', 'Lsat_1_v5_gn_6_76240' => 'lsa', 'Lsat_1_v5_gn_6_76441' => 'lsa', 'Lsat_1_v5_gn_6_76700' => 'lsa', 'Lsat_1_v5_gn_6_76760' => 'lsa', 'Manes.15G033100' => 'mes', 'Mapoly0004s0074' => 'mpo', 'Mapoly0004s0075' => 'mpo', 'Mapoly0004s0163' => 'mpo', 'Mapoly0004s0164' => 'mpo', 'Mapoly0021s0018' => 'mpo', 'Mapoly0041s0136' => 'mpo', 'Mapoly0041s0137' => 'mpo', 'Mapoly0041s0138' => 'mpo', 'Mapoly0041s0139' => 'mpo', 'Mapoly0041s0141' => 'mpo', 'Mapoly0041s0142' => 'mpo', 'Mapoly0041s0143' => 'mpo', 'Mapoly0041s0144' => 'mpo', 'Mapoly0041s0145' => 'mpo', 'Mapoly0047s0106' => 'mpo', 'Mapoly0047s0108' => 'mpo', 'Mapoly0050s0051' => 'mpo', 'Mapoly0050s0052' => 'mpo', 'Mapoly0050s0053' => 'mpo', 'Mapoly0058s0013' => 'mpo', 'Mapoly0091s0078' => 'mpo', 'Mapoly0091s0079' => 'mpo', 'Mapoly0091s0080' => 'mpo', 'Mapoly0091s0081' => 'mpo', 'Mapoly0278s0004' => 'mpo', 'Mapoly0278s0005' => 'mpo', 'Mapoly0278s0006' => 'mpo', 'MBI11_g30648_MAGBIO' => 'mbi', 'MCO03G194' => 'mco', 'MCO03G590' => 'mco', 'MCO07G312' => 'mco', 'MCO10G318' => 'mco', 'MCO12G244' => 'mco', 'MCO13G148' => 'mco', 'MCO13G194' => 'mco', 'MCO16G238' => 'mco', 'MD06G1134100' => 'mdo', 'MD13G1200100' => 'mdo', 'MD13G1200300' => 'mdo', 'MD13G1200600' => 'mdo', 'MD14G1150400' => 'mdo', 'MD16G1200000' => 'mdo', 'Medtr1g102570' => 'mtr', 'Medtr1g102780' => 'mtr', 'Medtr1g102800' => 'mtr', 'Medtr1g102810' => 'mtr', 'Medtr1g102830' => 'mtr', 'MELO3C006499.2' => 'cme', 'Migut.G00385' => 'egut', 'MSTRG.4063' => 'ama', 'Nitab4.5_0000090g0260' => 'nta', 'Nitab4.5_0000977g0030' => 'nta', 'Nitab4.5_0002541g0040' => 'nta', 'Nitab4.5_0007068g0040' => 'nta', 'Nn005s41408' => 'nnu', 'Nn005s41410' => 'nnu', 'Oeu010310.1' => 'oeu', 'Oeu010311.1' => 'oeu', 'Oeu043472.1' => 'oeu', 'Os01g0246400' => 'osa', 'Os04g0267950' => 'osa', 'Os07g0178700' => 'osa', 'Os07g0178800' => 'osa', 'Peaxi162Scf00316g00046' => 'pax', 'Peaxi162Scf00316g00049' => 'pax', 'Peaxi162Scf00316g00059' => 'pax', 'Peaxi162Scf00316g00328' => 'pax', 'Peaxi162Scf00316g00329' => 'pax', 'Peaxi162Scf00316g00411' => 'pax', 'Peaxi162Scf00316g00521' => 'pax', 'Peaxi162Scf00492g00068' => 'pax', 'Peaxi162Scf35631g00002' => 'pax', 'PGR142G3720' => 'pgr', 'PGSC0003DMG400006442' => 'stu', 'Phvul.007G062000' => 'pvu', 'Potri.008G157750' => 'ptr', 'Potri.008G157900' => 'ptr', 'Potri.008G158000' => 'ptr', 'Potri.008G158200' => 'ptr', 'Pp3c11_7280' => 'ppa', 'Pp3c11_7980' => 'ppa', 'Pp3c12_19450' => 'ppa', 'Pp3c14_1480' => 'ppa', 'Pp3c14_1501' => 'ppa', 'Pp3c16_4900' => 'ppa', 'Pp3c16_5010' => 'ppa', 'Pp3c16_5060' => 'ppa', 'Pp3c19_18250' => 'ppa', 'Pp3c23_8530' => 'ppa', 'Pp3c23_8550' => 'ppa', 'Pp3c24_9670' => 'ppa', 'Pp3c2_21390' => 'ppa', 'Pp3c2_31380' => 'ppa', 'Pp3c3_16620' => 'ppa', 'Pp3c3_8090' => 'ppa', 'Pp3c3_8110' => 'ppa', 'Pp3c3_8130' => 'ppa', 'Pp3c3_8150' => 'ppa', 'Pp3c4_14320' => 'ppa', 'Pp3c6_2560' => 'ppa', 'Pp3c9_16700' => 'ppa', 'PRCOL_00000234' => 'pco', 'PRCOL_00000235' => 'pco', 'PRCOL_00000777' => 'pco', 'PRCOL_00002344' => 'pco', 'PRCOL_00002372' => 'pco', 'PRCOL_00006120' => 'pco', 'Prupe.1G021400' => 'ppe', 'Prupe.1G021500' => 'ppe', 'Prupe.1G021600' => 'ppe', 'Prupe.1G021700' => 'ppe', 'Prupe.1G021800' => 'ppe', 'Prupe.5G145100' => 'ppe', 'Psat6g204040' => 'psa', 'Psat6g204800' => 'psa', 'Psat6g204920' => 'psa', 'Psat6g204960' => 'psa', 'Psat6g205080' => 'psa', 'PSO017G0271' => 'pso', 'PSO017G1276' => 'pso', 'PSO017G1429' => 'pso', 'PSO017G1861' => 'pso', 'PSO017G2787' => 'pso', 'PSO017G4466' => 'pso', 'PSO017G5118' => 'pso', 'PSO017G5420' => 'pso', 'PSO063G3678' => 'pso', 'PSO210G0546' => 'pso', 'PSO317G0001' => 'pso', 'PSO357G0512' => 'pso', 'PSO478G2682' => 'pso', 'PSO647G0001' => 'pso', 'PSO675G0001' => 'pso', 'PSO675G2699' => 'pso', 'PSO675G2849' => 'pso', 'PSO675G4991' => 'pso', 'PSO689G0001' => 'pso', 'QL06p000916' => 'qlo', 'QL06p000921' => 'qlo', 'QL06p001398' => 'qlo', 'QL06p001407' => 'qlo', 'QL06p002031' => 'qlo', 'RcHm_v2.0_Chr4g0387791' => 'rch', 'RcHm_v2.0_Chr4g0387801' => 'rch', 'RcHm_v2.0_Chr6g0286501' => 'rch', 'RcHm_v2.0_Chr6g0286511' => 'rch', 'RcHm_v2.0_Chr6g0286521' => 'rch', 'RcHm_v2.0_Chr6g0286531' => 'rch', 'RcHm_v2.0_Chr7g0189141' => 'rch', 'Rhsim02G0028700' => 'rsi', 'Rhsim02G0028800' => 'rsi', 'Rhsim02G0028900' => 'rsi', 'Rhsim02G0029000' => 'rsi', 'Rhsim02G0029100' => 'rsi', 'Rhsim02G0029200' => 'rsi', 'Rhsim02G0029300' => 'rsi', 'Rhsim02G0029400' => 'rsi', 'Rhsim02G0029500' => 'rsi', 'Rhsim02G0029600' => 'rsi', 'RhsimUnG0024000' => 'rsi', 'RhsimUnG0024100' => 'rsi', 'RhsimUnG0024200' => 'rsi', 'RhsimUnG0024300' => 'rsi', 'RhsimUnG0024400' => 'rsi', 'RhsimUnG0024500' => 'rsi', 'RhsimUnG0024700' => 'rsi', 'RhsimUnG0024800' => 'rsi', 'RhsimUnG0024900' => 'rsi', 'RhsimUnG0025100' => 'rsi', 'Sabra08G0120200' => 'sbr', 'Sabra08G0120300' => 'sbr', 'Sabra08G0120500' => 'sbr', 'Sabra08G0120600' => 'sbr', 'Sabra10G0158900' => 'sbr', 'SalBow2G3492' => 'sbo', 'Sc13g0004760' => 'sci', 'Sc13g0004770' => 'sci', 'Sed0003417' => 'sed', 'Sed0019750' => 'sed', 'SEGI_03419' => 'sgi', 'SEGI_05907' => 'sgi', 'SEGI_10682' => 'sgi', 'SEGI_13528' => 'sgi', 'SEGI_16081' => 'sgi', 'SEGI_19370' => 'sgi', 'SEGI_21015' => 'sgi', 'SEGI_21944' => 'sgi', 'SEGI_32906' => 'sgi', 'SEGI_33093' => 'sgi', 'SEGI_36110' => 'sgi', 'SEGI_40397' => 'sgi', 'SGA_v2.0_scaffold191G40426' => 'sas', 'SGA_v2.0_scaffold353G49717' => 'sas', 'SGA_v2.0_scaffold50G18550' => 'sas', 'SMO119G0173' => 'smo', 'SMO172G0002' => 'smo', 'Solyc09g082690.3' => 'sly', 'Solyc09g082700.2' => 'sly', 'Sopen09g031550' => 'spe', 'Sopen09g031560' => 'spe', 'Sp3g20540' => 'spa', 'Sp7g07580' => 'spa', 'TAR134G0002' => 'tar', 'TAR236G0001' => 'tar', 'TAR365G0892' => 'tar', 'TAR636G0166' => 'tar', 'TAR636G0646' => 'tar', 'TAR636G0869' => 'tar', 'TAR636G1317' => 'tar', 'TAR636G1744' => 'tar', 'TAR636G3358' => 'tar', 'TAR636G3436' => 'tar', 'THA.LOC104803047' => 'tha', 'Thecc.04G238900' => 'tca', 'Thhalv10021557m.g' => 'esa', 'Thhalv10026318m.g' => 'esa', 'Thhalv10026335m.g' => 'esa', 'TPR.G17433' => 'tpr', 'TPR.G18915' => 'tpr', 'TPR.G26125' => 'tpr', 'TWI09G0677' => 'twi', 'TWI73G0287' => 'twi', 'unitig_748.g8326' => 'ugi', 'vmacro15370' => 'vma', 'vmacro15371' => 'vma', 'vmacro15372' => 'vma', 'vmacro15373' => 'vma', 'vmacro15374' => 'vma', 'VMungo0720G2826' => 'vmu', 'Zm00001eb116960' => 'zma', 'Zm00001eb301260' => 'zma', 'Zm00001eb301270' => 'zma' ) $gf_id = 'HOM05D001460' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001460' ) $data_identifier = 'HOM05D001460' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 4, 'aag' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 2, 'aox' => (int) 2, 'arhy' => (int) 4, 'ath' => (int) 2, 'atr' => (int) 1, 'acertr' => (int) 10, 'cqu' => (int) 4, 'bca' => (int) 11, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 1, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 1, 'ccan' => (int) 1, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 1, 'col' => (int) 1, 'cpa' => (int) 1, 'cre' => (int) 7, 'csa' => (int) 1, 'camsi' => (int) 2, 'dca' => (int) 3, 'din' => (int) 2, 'dzi' => (int) 3, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 14, 'fve' => (int) 9, 'gma' => (int) 2, 'ghi' => (int) 4, 'gra' => (int) 2, 'vvi' => (int) 1, 'han' => (int) 13, 'cav' => (int) 1, 'hma' => (int) 2, 'sun' => (int) 2, 'lal' => (int) 2, 'lonja' => (int) 12, 'lja' => (int) 1, 'lsa' => (int) 7, 'mes' => (int) 1, 'mpo' => (int) 27, 'mbi' => (int) 1, 'mco' => (int) 8, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 1, 'egut' => (int) 1, 'ama' => (int) 1, 'nta' => (int) 4, 'nnu' => (int) 2, 'oeu' => (int) 3, 'osa' => (int) 4, 'pax' => (int) 9, 'pgr' => (int) 1, 'stu' => (int) 1, 'pvu' => (int) 1, 'ptr' => (int) 4, 'ppa' => (int) 22, 'pco' => (int) 6, 'ppe' => (int) 6, 'psa' => (int) 5, 'pso' => (int) 19, 'qlo' => (int) 5, 'rch' => (int) 7, 'rsi' => (int) 20, 'sbr' => (int) 5, 'sbo' => (int) 1, 'sci' => (int) 2, 'sed' => (int) 2, 'sgi' => (int) 12, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 2, 'tar' => (int) 10, 'tha' => (int) 1, 'tca' => (int) 1, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 2, 'ugi' => (int) 1, 'vma' => (int) 5, 'vmu' => (int) 1, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb301270' $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' => 'HOM05D001460', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '433', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p22980' => 'bna', 'A01p32340' => 'bna', 'A03p42970' => 'bna', 'A05p25880' => 'bna', 'Aa31LG8G9320' => 'aar', 'Aa31LG8G9330' => 'aar', 'Aa31LG8G9340' => 'aar', 'Aa31sc221G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1034' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1528' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.829' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2222' => 'aag', 'Ah.12g058830' => 'amhyb', 'Ah.12g058840' => 'amhyb', 'AL3G37160' => 'aly', 'AL7G41310' => 'aly', 'Aqoxy5G00395' => 'aox', 'Aqoxy5G00396' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0C8NZA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5185HY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JZ1PRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MD3LS0' => 'arhy', 'AT3G22840' => 'ath', 'AT4G14690' => 'ath', 'ATR0665G054' => 'atr', 'Atru.chr4.2344' => 'acertr', 'Atru.chr4.2346' => 'acertr', 'Atru.chr4.2347' => 'acertr', 'Atru.chr4.2348' => 'acertr', 'Atru.chr4.2355' => 'acertr', 'Atru.chr4.2356' => 'acertr', 'Atru.chr4.2358' => 'acertr', 'Atru.chr4.2359' => 'acertr', 'Atru.chr4.2360' => 'acertr', 'Atru.chr4.2361' => 'acertr', 'AUR62030476' => 'cqu', 'AUR62030478' => 'cqu', 'AUR62030819' => 'cqu', 'AUR62030820' => 'cqu', 'BcaB03g14648' => 'bca', 'BcaB04g20492' => 'bca', 'BcaB06g26399' => 'bca', 'BcaC01g03416' => 'bca', 'BcaC01g03419' => 'bca', 'BcaC01g03421' => 'bca', 'BcaC01g03424' => 'bca', 'BcaC05g28012' => 'bca', 'BcaC09g49212' => 'bca', 'BcaC09g50140' => 'bca', 'BcaNung00346' => 'bca', 'BolC1t02785H' => 'bol', 'BolC1t04095H' => 'bol', 'BolC3t17545H' => 'bol', 'BolC5t32769H' => 'bol', 'BraA01t02211Z' => 'bra', 'BraA01t03359Z' => 'bra', 'BraA03t13441Z' => 'bra', 'BraA05t21476Z' => 'bra', 'C01p28420' => 'bna', 'C01p41350' => 'bna', 'C03p52750' => 'bna', 'C03p52780' => 'bna', 'C05p40270' => 'bna', 'CAN.G1437.9' => 'can', 'CANSAT78G0035' => 'cansat', 'CANSAT78G1036' => 'cansat', 'CANSAT78G2272' => 'cansat', 'CANSAT78G2478' => 'cansat', 'CARHR098700' => 'chi', 'CARHR221120' => 'chi', 'CARHR221150' => 'chi', 'Carub.0003s2297' => 'cru', 'Carub.0007s2749' => 'cru', 'Carub.0007s2750' => 'cru', 'Carub.0007s2751' => 'cru', 'Ca_10849_v3' => 'car', 'Cc03_g04300' => 'ccan', 'CDE02G3648' => 'cde', 'CDE05G0060' => 'cde', 'CDE05G0692' => 'cde', 'CDE05G2285' => 'cde', 'CDE05G2884' => 'cde', 'CDE05G3072' => 'cde', 'Cfa008439' => 'cfa', 'Cfa008441' => 'cfa', 'Cfa008443' => 'cfa', 'Cfa008448' => 'cfa', 'Ciclev10005974m.g' => 'ccl', 'Ciclev10006006m.g' => 'ccl', 'Ciclev10006775m.g' => 'ccl', 'CiPaw.02G120400' => 'cil', 'CiPaw.02G120500' => 'cil', 'CiPaw.02G120600' => 'cil', 'ClCG05G004850' => 'cla', 'COL.COLO4_21566' => 'col', 'Cpa.g.sc44.124' => 'cpa', 'Cre07.g320400' => 'cre', 'Cre07.g320450' => 'cre', 'Cre08.g384650' => 'cre', 'Cre09.g393173' => 'cre', 'Cre09.g394325' => 'cre', 'Cre14.g626750' => 'cre', 'Cre16.g679250' => 'cre', 'CsaV3_3G012890' => 'csa', 'CSS0010865' => 'camsi', 'CSS0044338' => 'camsi', 'DCAR_002366' => 'dca', 'DCAR_030687' => 'dca', 'DCAR_030688' => 'dca', 'Dinv14047' => 'din', 'Dinv14048' => 'din', 'Duzib151G0105' => 'dzi', 'Duzib151G0114' => 'dzi', 'Duzib212G1029' => 'dzi', 'ECA232G3536' => 'eca', 'ECA240G0786' => 'eca', 'ECA240G1802' => 'eca', 'ECA240G3760' => 'eca', 'ECA240G3920' => 'eca', 'EL10Ac5g12536' => 'bvu', 'EL10Ac5g12537' => 'bvu', 'EL10Ac5g12538' => 'bvu', 'Eucgr.B01004' => 'egr', 'Eucgr.B01006' => 'egr', 'Eucgr.B01007' => 'egr', 'Eucgr.B01008' => 'egr', 'Eucgr.B01895' => 'egr', 'Eucgr.B01896' => 'egr', 'FAN04G1456' => 'fan', 'FAN08G1769' => 'fan', 'FAN08G2160' => 'fan', 'FAN13G2403' => 'fan', 'FAN13G3303' => 'fan', 'FAN15G2435' => 'fan', 'FAN17G0672' => 'fan', 'FAN17G2441' => 'fan', 'FAN18G1024' => 'fan', 'FAN22G1458' => 'fan', 'FAN24G0037' => 'fan', 'FAN24G0429' => 'fan', 'FAN24G2387' => 'fan', 'FAN27G2746' => 'fan', 'FvH4_2g20400' => 'fve', 'FvH4_2g20420' => 'fve', 'FvH4_2g20430' => 'fve', 'FvH4_4g01270' => 'fve', 'FvH4_4g01290' => 'fve', 'FvH4_4g01300' => 'fve', 'FvH4_4g01310' => 'fve', 'FvH4_4g01330' => 'fve', 'FvH4_5g09070' => 'fve', 'Glyma.10G243800' => 'gma', 'Glyma.20G150600' => 'gma', 'Gohir.A09G219200' => 'ghi', 'Gohir.A09G219300' => 'ghi', 'Gohir.D09G221400' => 'ghi', 'Gohir.D09G221500' => 'ghi', 'Gorai.006G242600' => 'gra', 'Gorai.006G242700' => 'gra', 'GSVIVG01018044001' => 'vvi', 'HanXRQChr03g0083821' => 'han', 'HanXRQChr03g0083841' => 'han', 'HanXRQChr03g0083881' => 'han', 'HanXRQChr03g0083901' => 'han', 'HanXRQChr03g0083921' => 'han', 'HanXRQChr03g0085331' => 'han', 'HanXRQChr03g0085361' => 'han', 'HanXRQChr03g0085411' => 'han', 'HanXRQChr03g0085421' => 'han', 'HanXRQChr03g0085431' => 'han', 'HanXRQChr08g0221991' => 'han', 'HanXRQChr11g0336061' => 'han', 'HanXRQChr11g0336411' => 'han', 'Haze_11234' => 'cav', 'Hma1.2p1_0549F.1_g177010' => 'hma', 'Hma1.2p1_0602F.1_g187630' => 'hma', 'Hund14876' => 'sun', 'Hund14879' => 'sun', 'Lalb_Chr06g0160741' => 'lal', 'Lalb_Chr21g0304781' => 'lal', 'Lj3A726G19' => 'lonja', 'Lj3A726T23' => 'lonja', 'Lj3A726T24' => 'lonja', 'Lj3A726T25' => 'lonja', 'Lj3A727T17' => 'lonja', 'Lj3C726T0' => 'lonja', 'Lj3C726T2' => 'lonja', 'Lj3P725T35' => 'lonja', 'Lj3P727T10' => 'lonja', 'Lj3P727T12' => 'lonja', 'Lj3P727T14' => 'lonja', 'Lj5g0023109' => 'lja', 'Lj6P646T44' => 'lonja', 'Lsat_1_v5_gn_6_75760' => 'lsa', 'Lsat_1_v5_gn_6_75800' => 'lsa', 'Lsat_1_v5_gn_6_75900' => 'lsa', 'Lsat_1_v5_gn_6_76240' => 'lsa', 'Lsat_1_v5_gn_6_76441' => 'lsa', 'Lsat_1_v5_gn_6_76700' => 'lsa', 'Lsat_1_v5_gn_6_76760' => 'lsa', 'Manes.15G033100' => 'mes', 'Mapoly0004s0074' => 'mpo', 'Mapoly0004s0075' => 'mpo', 'Mapoly0004s0163' => 'mpo', 'Mapoly0004s0164' => 'mpo', 'Mapoly0021s0018' => 'mpo', 'Mapoly0041s0136' => 'mpo', 'Mapoly0041s0137' => 'mpo', 'Mapoly0041s0138' => 'mpo', 'Mapoly0041s0139' => 'mpo', 'Mapoly0041s0141' => 'mpo', 'Mapoly0041s0142' => 'mpo', 'Mapoly0041s0143' => 'mpo', 'Mapoly0041s0144' => 'mpo', 'Mapoly0041s0145' => 'mpo', 'Mapoly0047s0106' => 'mpo', 'Mapoly0047s0108' => 'mpo', 'Mapoly0050s0051' => 'mpo', 'Mapoly0050s0052' => 'mpo', 'Mapoly0050s0053' => 'mpo', 'Mapoly0058s0013' => 'mpo', 'Mapoly0091s0078' => 'mpo', 'Mapoly0091s0079' => 'mpo', 'Mapoly0091s0080' => 'mpo', 'Mapoly0091s0081' => 'mpo', 'Mapoly0278s0004' => 'mpo', 'Mapoly0278s0005' => 'mpo', 'Mapoly0278s0006' => 'mpo', 'MBI11_g30648_MAGBIO' => 'mbi', 'MCO03G194' => 'mco', 'MCO03G590' => 'mco', 'MCO07G312' => 'mco', 'MCO10G318' => 'mco', 'MCO12G244' => 'mco', 'MCO13G148' => 'mco', 'MCO13G194' => 'mco', 'MCO16G238' => 'mco', 'MD06G1134100' => 'mdo', 'MD13G1200100' => 'mdo', 'MD13G1200300' => 'mdo', 'MD13G1200600' => 'mdo', 'MD14G1150400' => 'mdo', 'MD16G1200000' => 'mdo', 'Medtr1g102570' => 'mtr', 'Medtr1g102780' => 'mtr', 'Medtr1g102800' => 'mtr', 'Medtr1g102810' => 'mtr', 'Medtr1g102830' => 'mtr', 'MELO3C006499.2' => 'cme', 'Migut.G00385' => 'egut', 'MSTRG.4063' => 'ama', 'Nitab4.5_0000090g0260' => 'nta', 'Nitab4.5_0000977g0030' => 'nta', 'Nitab4.5_0002541g0040' => 'nta', 'Nitab4.5_0007068g0040' => 'nta', 'Nn005s41408' => 'nnu', 'Nn005s41410' => 'nnu', 'Oeu010310.1' => 'oeu', 'Oeu010311.1' => 'oeu', 'Oeu043472.1' => 'oeu', 'Os01g0246400' => 'osa', 'Os04g0267950' => 'osa', 'Os07g0178700' => 'osa', 'Os07g0178800' => 'osa', 'Peaxi162Scf00316g00046' => 'pax', 'Peaxi162Scf00316g00049' => 'pax', 'Peaxi162Scf00316g00059' => 'pax', 'Peaxi162Scf00316g00328' => 'pax', 'Peaxi162Scf00316g00329' => 'pax', 'Peaxi162Scf00316g00411' => 'pax', 'Peaxi162Scf00316g00521' => 'pax', 'Peaxi162Scf00492g00068' => 'pax', 'Peaxi162Scf35631g00002' => 'pax', 'PGR142G3720' => 'pgr', 'PGSC0003DMG400006442' => 'stu', 'Phvul.007G062000' => 'pvu', 'Potri.008G157750' => 'ptr', 'Potri.008G157900' => 'ptr', 'Potri.008G158000' => 'ptr', 'Potri.008G158200' => 'ptr', 'Pp3c11_7280' => 'ppa', 'Pp3c11_7980' => 'ppa', 'Pp3c12_19450' => 'ppa', 'Pp3c14_1480' => 'ppa', 'Pp3c14_1501' => 'ppa', 'Pp3c16_4900' => 'ppa', 'Pp3c16_5010' => 'ppa', 'Pp3c16_5060' => 'ppa', 'Pp3c19_18250' => 'ppa', 'Pp3c23_8530' => 'ppa', 'Pp3c23_8550' => 'ppa', 'Pp3c24_9670' => 'ppa', 'Pp3c2_21390' => 'ppa', 'Pp3c2_31380' => 'ppa', 'Pp3c3_16620' => 'ppa', 'Pp3c3_8090' => 'ppa', 'Pp3c3_8110' => 'ppa', 'Pp3c3_8130' => 'ppa', 'Pp3c3_8150' => 'ppa', 'Pp3c4_14320' => 'ppa', 'Pp3c6_2560' => 'ppa', 'Pp3c9_16700' => 'ppa', 'PRCOL_00000234' => 'pco', 'PRCOL_00000235' => 'pco', 'PRCOL_00000777' => 'pco', 'PRCOL_00002344' => 'pco', 'PRCOL_00002372' => 'pco', 'PRCOL_00006120' => 'pco', 'Prupe.1G021400' => 'ppe', 'Prupe.1G021500' => 'ppe', 'Prupe.1G021600' => 'ppe', 'Prupe.1G021700' => 'ppe', 'Prupe.1G021800' => 'ppe', 'Prupe.5G145100' => 'ppe', 'Psat6g204040' => 'psa', 'Psat6g204800' => 'psa', 'Psat6g204920' => 'psa', 'Psat6g204960' => 'psa', 'Psat6g205080' => 'psa', 'PSO017G0271' => 'pso', 'PSO017G1276' => 'pso', 'PSO017G1429' => 'pso', 'PSO017G1861' => 'pso', 'PSO017G2787' => 'pso', 'PSO017G4466' => 'pso', 'PSO017G5118' => 'pso', 'PSO017G5420' => 'pso', 'PSO063G3678' => 'pso', 'PSO210G0546' => 'pso', 'PSO317G0001' => 'pso', 'PSO357G0512' => 'pso', 'PSO478G2682' => 'pso', 'PSO647G0001' => 'pso', 'PSO675G0001' => 'pso', 'PSO675G2699' => 'pso', 'PSO675G2849' => 'pso', 'PSO675G4991' => 'pso', 'PSO689G0001' => 'pso', 'QL06p000916' => 'qlo', 'QL06p000921' => 'qlo', 'QL06p001398' => 'qlo', 'QL06p001407' => 'qlo', 'QL06p002031' => 'qlo', 'RcHm_v2.0_Chr4g0387791' => 'rch', 'RcHm_v2.0_Chr4g0387801' => 'rch', 'RcHm_v2.0_Chr6g0286501' => 'rch', 'RcHm_v2.0_Chr6g0286511' => 'rch', 'RcHm_v2.0_Chr6g0286521' => 'rch', 'RcHm_v2.0_Chr6g0286531' => 'rch', 'RcHm_v2.0_Chr7g0189141' => 'rch', 'Rhsim02G0028700' => 'rsi', 'Rhsim02G0028800' => 'rsi', 'Rhsim02G0028900' => 'rsi', 'Rhsim02G0029000' => 'rsi', 'Rhsim02G0029100' => 'rsi', 'Rhsim02G0029200' => 'rsi', 'Rhsim02G0029300' => 'rsi', 'Rhsim02G0029400' => 'rsi', 'Rhsim02G0029500' => 'rsi', 'Rhsim02G0029600' => 'rsi', 'RhsimUnG0024000' => 'rsi', 'RhsimUnG0024100' => 'rsi', 'RhsimUnG0024200' => 'rsi', 'RhsimUnG0024300' => 'rsi', 'RhsimUnG0024400' => 'rsi', 'RhsimUnG0024500' => 'rsi', 'RhsimUnG0024700' => 'rsi', 'RhsimUnG0024800' => 'rsi', 'RhsimUnG0024900' => 'rsi', 'RhsimUnG0025100' => 'rsi', 'Sabra08G0120200' => 'sbr', 'Sabra08G0120300' => 'sbr', 'Sabra08G0120500' => 'sbr', 'Sabra08G0120600' => 'sbr', 'Sabra10G0158900' => 'sbr', 'SalBow2G3492' => 'sbo', 'Sc13g0004760' => 'sci', 'Sc13g0004770' => 'sci', 'Sed0003417' => 'sed', 'Sed0019750' => 'sed', 'SEGI_03419' => 'sgi', 'SEGI_05907' => 'sgi', 'SEGI_10682' => 'sgi', 'SEGI_13528' => 'sgi', 'SEGI_16081' => 'sgi', 'SEGI_19370' => 'sgi', 'SEGI_21015' => 'sgi', 'SEGI_21944' => 'sgi', 'SEGI_32906' => 'sgi', 'SEGI_33093' => 'sgi', 'SEGI_36110' => 'sgi', 'SEGI_40397' => 'sgi', 'SGA_v2.0_scaffold191G40426' => 'sas', 'SGA_v2.0_scaffold353G49717' => 'sas', 'SGA_v2.0_scaffold50G18550' => 'sas', 'SMO119G0173' => 'smo', 'SMO172G0002' => 'smo', 'Solyc09g082690.3' => 'sly', 'Solyc09g082700.2' => 'sly', 'Sopen09g031550' => 'spe', 'Sopen09g031560' => 'spe', 'Sp3g20540' => 'spa', 'Sp7g07580' => 'spa', 'TAR134G0002' => 'tar', 'TAR236G0001' => 'tar', 'TAR365G0892' => 'tar', 'TAR636G0166' => 'tar', 'TAR636G0646' => 'tar', 'TAR636G0869' => 'tar', 'TAR636G1317' => 'tar', 'TAR636G1744' => 'tar', 'TAR636G3358' => 'tar', 'TAR636G3436' => 'tar', 'THA.LOC104803047' => 'tha', 'Thecc.04G238900' => 'tca', 'Thhalv10021557m.g' => 'esa', 'Thhalv10026318m.g' => 'esa', 'Thhalv10026335m.g' => 'esa', 'TPR.G17433' => 'tpr', 'TPR.G18915' => 'tpr', 'TPR.G26125' => 'tpr', 'TWI09G0677' => 'twi', 'TWI73G0287' => 'twi', 'unitig_748.g8326' => 'ugi', 'vmacro15370' => 'vma', 'vmacro15371' => 'vma', 'vmacro15372' => 'vma', 'vmacro15373' => 'vma', 'vmacro15374' => 'vma', 'VMungo0720G2826' => 'vmu', 'Zm00001eb116960' => 'zma', 'Zm00001eb301260' => 'zma', 'Zm00001eb301270' => 'zma' ), 'gf_id' => 'HOM05D001460', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001460' ), 'data_identifier' => 'HOM05D001460', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001460', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '433', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p22980' => 'bna', 'A01p32340' => 'bna', 'A03p42970' => 'bna', 'A05p25880' => 'bna', 'Aa31LG8G9320' => 'aar', 'Aa31LG8G9330' => 'aar', 'Aa31LG8G9340' => 'aar', 'Aa31sc221G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1034' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1528' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.829' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2222' => 'aag', 'Ah.12g058830' => 'amhyb', 'Ah.12g058840' => 'amhyb', 'AL3G37160' => 'aly', 'AL7G41310' => 'aly', 'Aqoxy5G00395' => 'aox', 'Aqoxy5G00396' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0C8NZA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5185HY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JZ1PRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MD3LS0' => 'arhy', 'AT3G22840' => 'ath', 'AT4G14690' => 'ath', 'ATR0665G054' => 'atr', 'Atru.chr4.2344' => 'acertr', 'Atru.chr4.2346' => 'acertr', 'Atru.chr4.2347' => 'acertr', 'Atru.chr4.2348' => 'acertr', 'Atru.chr4.2355' => 'acertr', 'Atru.chr4.2356' => 'acertr', 'Atru.chr4.2358' => 'acertr', 'Atru.chr4.2359' => 'acertr', 'Atru.chr4.2360' => 'acertr', 'Atru.chr4.2361' => 'acertr', 'AUR62030476' => 'cqu', 'AUR62030478' => 'cqu', 'AUR62030819' => 'cqu', 'AUR62030820' => 'cqu', 'BcaB03g14648' => 'bca', 'BcaB04g20492' => 'bca', 'BcaB06g26399' => 'bca', 'BcaC01g03416' => 'bca', 'BcaC01g03419' => 'bca', 'BcaC01g03421' => 'bca', 'BcaC01g03424' => 'bca', 'BcaC05g28012' => 'bca', 'BcaC09g49212' => 'bca', 'BcaC09g50140' => 'bca', 'BcaNung00346' => 'bca', 'BolC1t02785H' => 'bol', 'BolC1t04095H' => 'bol', 'BolC3t17545H' => 'bol', 'BolC5t32769H' => 'bol', 'BraA01t02211Z' => 'bra', 'BraA01t03359Z' => 'bra', 'BraA03t13441Z' => 'bra', 'BraA05t21476Z' => 'bra', 'C01p28420' => 'bna', 'C01p41350' => 'bna', 'C03p52750' => 'bna', 'C03p52780' => 'bna', 'C05p40270' => 'bna', 'CAN.G1437.9' => 'can', 'CANSAT78G0035' => 'cansat', 'CANSAT78G1036' => 'cansat', 'CANSAT78G2272' => 'cansat', 'CANSAT78G2478' => 'cansat', 'CARHR098700' => 'chi', 'CARHR221120' => 'chi', 'CARHR221150' => 'chi', 'Carub.0003s2297' => 'cru', 'Carub.0007s2749' => 'cru', 'Carub.0007s2750' => 'cru', 'Carub.0007s2751' => 'cru', 'Ca_10849_v3' => 'car', 'Cc03_g04300' => 'ccan', 'CDE02G3648' => 'cde', 'CDE05G0060' => 'cde', 'CDE05G0692' => 'cde', 'CDE05G2285' => 'cde', 'CDE05G2884' => 'cde', 'CDE05G3072' => 'cde', 'Cfa008439' => 'cfa', 'Cfa008441' => 'cfa', 'Cfa008443' => 'cfa', 'Cfa008448' => 'cfa', 'Ciclev10005974m.g' => 'ccl', 'Ciclev10006006m.g' => 'ccl', 'Ciclev10006775m.g' => 'ccl', 'CiPaw.02G120400' => 'cil', 'CiPaw.02G120500' => 'cil', 'CiPaw.02G120600' => 'cil', 'ClCG05G004850' => 'cla', 'COL.COLO4_21566' => 'col', 'Cpa.g.sc44.124' => 'cpa', 'Cre07.g320400' => 'cre', 'Cre07.g320450' => 'cre', 'Cre08.g384650' => 'cre', 'Cre09.g393173' => 'cre', 'Cre09.g394325' => 'cre', 'Cre14.g626750' => 'cre', 'Cre16.g679250' => 'cre', 'CsaV3_3G012890' => 'csa', 'CSS0010865' => 'camsi', 'CSS0044338' => 'camsi', 'DCAR_002366' => 'dca', 'DCAR_030687' => 'dca', 'DCAR_030688' => 'dca', 'Dinv14047' => 'din', 'Dinv14048' => 'din', 'Duzib151G0105' => 'dzi', 'Duzib151G0114' => 'dzi', 'Duzib212G1029' => 'dzi', 'ECA232G3536' => 'eca', 'ECA240G0786' => 'eca', 'ECA240G1802' => 'eca', 'ECA240G3760' => 'eca', 'ECA240G3920' => 'eca', 'EL10Ac5g12536' => 'bvu', 'EL10Ac5g12537' => 'bvu', 'EL10Ac5g12538' => 'bvu', 'Eucgr.B01004' => 'egr', 'Eucgr.B01006' => 'egr', 'Eucgr.B01007' => 'egr', 'Eucgr.B01008' => 'egr', 'Eucgr.B01895' => 'egr', 'Eucgr.B01896' => 'egr', 'FAN04G1456' => 'fan', 'FAN08G1769' => 'fan', 'FAN08G2160' => 'fan', 'FAN13G2403' => 'fan', 'FAN13G3303' => 'fan', 'FAN15G2435' => 'fan', 'FAN17G0672' => 'fan', 'FAN17G2441' => 'fan', 'FAN18G1024' => 'fan', 'FAN22G1458' => 'fan', 'FAN24G0037' => 'fan', 'FAN24G0429' => 'fan', 'FAN24G2387' => 'fan', 'FAN27G2746' => 'fan', 'FvH4_2g20400' => 'fve', 'FvH4_2g20420' => 'fve', 'FvH4_2g20430' => 'fve', 'FvH4_4g01270' => 'fve', 'FvH4_4g01290' => 'fve', 'FvH4_4g01300' => 'fve', 'FvH4_4g01310' => 'fve', 'FvH4_4g01330' => 'fve', 'FvH4_5g09070' => 'fve', 'Glyma.10G243800' => 'gma', 'Glyma.20G150600' => 'gma', 'Gohir.A09G219200' => 'ghi', 'Gohir.A09G219300' => 'ghi', 'Gohir.D09G221400' => 'ghi', 'Gohir.D09G221500' => 'ghi', 'Gorai.006G242600' => 'gra', 'Gorai.006G242700' => 'gra', 'GSVIVG01018044001' => 'vvi', 'HanXRQChr03g0083821' => 'han', 'HanXRQChr03g0083841' => 'han', 'HanXRQChr03g0083881' => 'han', 'HanXRQChr03g0083901' => 'han', 'HanXRQChr03g0083921' => 'han', 'HanXRQChr03g0085331' => 'han', 'HanXRQChr03g0085361' => 'han', 'HanXRQChr03g0085411' => 'han', 'HanXRQChr03g0085421' => 'han', 'HanXRQChr03g0085431' => 'han', 'HanXRQChr08g0221991' => 'han', 'HanXRQChr11g0336061' => 'han', 'HanXRQChr11g0336411' => 'han', 'Haze_11234' => 'cav', 'Hma1.2p1_0549F.1_g177010' => 'hma', 'Hma1.2p1_0602F.1_g187630' => 'hma', 'Hund14876' => 'sun', 'Hund14879' => 'sun', 'Lalb_Chr06g0160741' => 'lal', 'Lalb_Chr21g0304781' => 'lal', 'Lj3A726G19' => 'lonja', 'Lj3A726T23' => 'lonja', 'Lj3A726T24' => 'lonja', 'Lj3A726T25' => 'lonja', 'Lj3A727T17' => 'lonja', 'Lj3C726T0' => 'lonja', 'Lj3C726T2' => 'lonja', 'Lj3P725T35' => 'lonja', 'Lj3P727T10' => 'lonja', 'Lj3P727T12' => 'lonja', 'Lj3P727T14' => 'lonja', 'Lj5g0023109' => 'lja', 'Lj6P646T44' => 'lonja', 'Lsat_1_v5_gn_6_75760' => 'lsa', 'Lsat_1_v5_gn_6_75800' => 'lsa', 'Lsat_1_v5_gn_6_75900' => 'lsa', 'Lsat_1_v5_gn_6_76240' => 'lsa', 'Lsat_1_v5_gn_6_76441' => 'lsa', 'Lsat_1_v5_gn_6_76700' => 'lsa', 'Lsat_1_v5_gn_6_76760' => 'lsa', 'Manes.15G033100' => 'mes', 'Mapoly0004s0074' => 'mpo', 'Mapoly0004s0075' => 'mpo', 'Mapoly0004s0163' => 'mpo', 'Mapoly0004s0164' => 'mpo', 'Mapoly0021s0018' => 'mpo', 'Mapoly0041s0136' => 'mpo', 'Mapoly0041s0137' => 'mpo', 'Mapoly0041s0138' => 'mpo', 'Mapoly0041s0139' => 'mpo', 'Mapoly0041s0141' => 'mpo', 'Mapoly0041s0142' => 'mpo', 'Mapoly0041s0143' => 'mpo', 'Mapoly0041s0144' => 'mpo', 'Mapoly0041s0145' => 'mpo', 'Mapoly0047s0106' => 'mpo', 'Mapoly0047s0108' => 'mpo', 'Mapoly0050s0051' => 'mpo', 'Mapoly0050s0052' => 'mpo', 'Mapoly0050s0053' => 'mpo', 'Mapoly0058s0013' => 'mpo', 'Mapoly0091s0078' => 'mpo', 'Mapoly0091s0079' => 'mpo', 'Mapoly0091s0080' => 'mpo', 'Mapoly0091s0081' => 'mpo', 'Mapoly0278s0004' => 'mpo', 'Mapoly0278s0005' => 'mpo', 'Mapoly0278s0006' => 'mpo', 'MBI11_g30648_MAGBIO' => 'mbi', 'MCO03G194' => 'mco', 'MCO03G590' => 'mco', 'MCO07G312' => 'mco', 'MCO10G318' => 'mco', 'MCO12G244' => 'mco', 'MCO13G148' => 'mco', 'MCO13G194' => 'mco', 'MCO16G238' => 'mco', 'MD06G1134100' => 'mdo', 'MD13G1200100' => 'mdo', 'MD13G1200300' => 'mdo', 'MD13G1200600' => 'mdo', 'MD14G1150400' => 'mdo', 'MD16G1200000' => 'mdo', 'Medtr1g102570' => 'mtr', 'Medtr1g102780' => 'mtr', 'Medtr1g102800' => 'mtr', 'Medtr1g102810' => 'mtr', 'Medtr1g102830' => 'mtr', 'MELO3C006499.2' => 'cme', 'Migut.G00385' => 'egut', 'MSTRG.4063' => 'ama', 'Nitab4.5_0000090g0260' => 'nta', 'Nitab4.5_0000977g0030' => 'nta', 'Nitab4.5_0002541g0040' => 'nta', 'Nitab4.5_0007068g0040' => 'nta', 'Nn005s41408' => 'nnu', 'Nn005s41410' => 'nnu', 'Oeu010310.1' => 'oeu', 'Oeu010311.1' => 'oeu', 'Oeu043472.1' => 'oeu', 'Os01g0246400' => 'osa', 'Os04g0267950' => 'osa', 'Os07g0178700' => 'osa', 'Os07g0178800' => 'osa', 'Peaxi162Scf00316g00046' => 'pax', 'Peaxi162Scf00316g00049' => 'pax', 'Peaxi162Scf00316g00059' => 'pax', 'Peaxi162Scf00316g00328' => 'pax', 'Peaxi162Scf00316g00329' => 'pax', 'Peaxi162Scf00316g00411' => 'pax', 'Peaxi162Scf00316g00521' => 'pax', 'Peaxi162Scf00492g00068' => 'pax', 'Peaxi162Scf35631g00002' => 'pax', 'PGR142G3720' => 'pgr', 'PGSC0003DMG400006442' => 'stu', 'Phvul.007G062000' => 'pvu', 'Potri.008G157750' => 'ptr', 'Potri.008G157900' => 'ptr', 'Potri.008G158000' => 'ptr', 'Potri.008G158200' => 'ptr', 'Pp3c11_7280' => 'ppa', 'Pp3c11_7980' => 'ppa', 'Pp3c12_19450' => 'ppa', 'Pp3c14_1480' => 'ppa', 'Pp3c14_1501' => 'ppa', 'Pp3c16_4900' => 'ppa', 'Pp3c16_5010' => 'ppa', 'Pp3c16_5060' => 'ppa', 'Pp3c19_18250' => 'ppa', 'Pp3c23_8530' => 'ppa', 'Pp3c23_8550' => 'ppa', 'Pp3c24_9670' => 'ppa', 'Pp3c2_21390' => 'ppa', 'Pp3c2_31380' => 'ppa', 'Pp3c3_16620' => 'ppa', 'Pp3c3_8090' => 'ppa', 'Pp3c3_8110' => 'ppa', 'Pp3c3_8130' => 'ppa', 'Pp3c3_8150' => 'ppa', 'Pp3c4_14320' => 'ppa', 'Pp3c6_2560' => 'ppa', 'Pp3c9_16700' => 'ppa', 'PRCOL_00000234' => 'pco', 'PRCOL_00000235' => 'pco', 'PRCOL_00000777' => 'pco', 'PRCOL_00002344' => 'pco', 'PRCOL_00002372' => 'pco', 'PRCOL_00006120' => 'pco', 'Prupe.1G021400' => 'ppe', 'Prupe.1G021500' => 'ppe', 'Prupe.1G021600' => 'ppe', 'Prupe.1G021700' => 'ppe', 'Prupe.1G021800' => 'ppe', 'Prupe.5G145100' => 'ppe', 'Psat6g204040' => 'psa', 'Psat6g204800' => 'psa', 'Psat6g204920' => 'psa', 'Psat6g204960' => 'psa', 'Psat6g205080' => 'psa', 'PSO017G0271' => 'pso', 'PSO017G1276' => 'pso', 'PSO017G1429' => 'pso', 'PSO017G1861' => 'pso', 'PSO017G2787' => 'pso', 'PSO017G4466' => 'pso', 'PSO017G5118' => 'pso', 'PSO017G5420' => 'pso', 'PSO063G3678' => 'pso', 'PSO210G0546' => 'pso', 'PSO317G0001' => 'pso', 'PSO357G0512' => 'pso', 'PSO478G2682' => 'pso', 'PSO647G0001' => 'pso', 'PSO675G0001' => 'pso', 'PSO675G2699' => 'pso', 'PSO675G2849' => 'pso', 'PSO675G4991' => 'pso', 'PSO689G0001' => 'pso', 'QL06p000916' => 'qlo', 'QL06p000921' => 'qlo', 'QL06p001398' => 'qlo', 'QL06p001407' => 'qlo', 'QL06p002031' => 'qlo', 'RcHm_v2.0_Chr4g0387791' => 'rch', 'RcHm_v2.0_Chr4g0387801' => 'rch', 'RcHm_v2.0_Chr6g0286501' => 'rch', 'RcHm_v2.0_Chr6g0286511' => 'rch', 'RcHm_v2.0_Chr6g0286521' => 'rch', 'RcHm_v2.0_Chr6g0286531' => 'rch', 'RcHm_v2.0_Chr7g0189141' => 'rch', 'Rhsim02G0028700' => 'rsi', 'Rhsim02G0028800' => 'rsi', 'Rhsim02G0028900' => 'rsi', 'Rhsim02G0029000' => 'rsi', 'Rhsim02G0029100' => 'rsi', 'Rhsim02G0029200' => 'rsi', 'Rhsim02G0029300' => 'rsi', 'Rhsim02G0029400' => 'rsi', 'Rhsim02G0029500' => 'rsi', 'Rhsim02G0029600' => 'rsi', 'RhsimUnG0024000' => 'rsi', 'RhsimUnG0024100' => 'rsi', 'RhsimUnG0024200' => 'rsi', 'RhsimUnG0024300' => 'rsi', 'RhsimUnG0024400' => 'rsi', 'RhsimUnG0024500' => 'rsi', 'RhsimUnG0024700' => 'rsi', 'RhsimUnG0024800' => 'rsi', 'RhsimUnG0024900' => 'rsi', 'RhsimUnG0025100' => 'rsi', 'Sabra08G0120200' => 'sbr', 'Sabra08G0120300' => 'sbr', 'Sabra08G0120500' => 'sbr', 'Sabra08G0120600' => 'sbr', 'Sabra10G0158900' => 'sbr', 'SalBow2G3492' => 'sbo', 'Sc13g0004760' => 'sci', 'Sc13g0004770' => 'sci', 'Sed0003417' => 'sed', 'Sed0019750' => 'sed', 'SEGI_03419' => 'sgi', 'SEGI_05907' => 'sgi', 'SEGI_10682' => 'sgi', 'SEGI_13528' => 'sgi', 'SEGI_16081' => 'sgi', 'SEGI_19370' => 'sgi', 'SEGI_21015' => 'sgi', 'SEGI_21944' => 'sgi', 'SEGI_32906' => 'sgi', 'SEGI_33093' => 'sgi', 'SEGI_36110' => 'sgi', 'SEGI_40397' => 'sgi', 'SGA_v2.0_scaffold191G40426' => 'sas', 'SGA_v2.0_scaffold353G49717' => 'sas', 'SGA_v2.0_scaffold50G18550' => 'sas', 'SMO119G0173' => 'smo', 'SMO172G0002' => 'smo', 'Solyc09g082690.3' => 'sly', 'Solyc09g082700.2' => 'sly', 'Sopen09g031550' => 'spe', 'Sopen09g031560' => 'spe', 'Sp3g20540' => 'spa', 'Sp7g07580' => 'spa', 'TAR134G0002' => 'tar', 'TAR236G0001' => 'tar', 'TAR365G0892' => 'tar', 'TAR636G0166' => 'tar', 'TAR636G0646' => 'tar', 'TAR636G0869' => 'tar', 'TAR636G1317' => 'tar', 'TAR636G1744' => 'tar', 'TAR636G3358' => 'tar', 'TAR636G3436' => 'tar', 'THA.LOC104803047' => 'tha', 'Thecc.04G238900' => 'tca', 'Thhalv10021557m.g' => 'esa', 'Thhalv10026318m.g' => 'esa', 'Thhalv10026335m.g' => 'esa', 'TPR.G17433' => 'tpr', 'TPR.G18915' => 'tpr', 'TPR.G26125' => 'tpr', 'TWI09G0677' => 'twi', 'TWI73G0287' => 'twi', 'unitig_748.g8326' => 'ugi', 'vmacro15370' => 'vma', 'vmacro15371' => 'vma', 'vmacro15372' => 'vma', 'vmacro15373' => 'vma', 'vmacro15374' => 'vma', 'VMungo0720G2826' => 'vmu', 'Zm00001eb116960' => 'zma', 'Zm00001eb301260' => 'zma', 'Zm00001eb301270' => 'zma' ) $gf_id = 'HOM05D001460' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001460' ) $data_identifier = 'HOM05D001460' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 4, 'aag' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 2, 'aox' => (int) 2, 'arhy' => (int) 4, 'ath' => (int) 2, 'atr' => (int) 1, 'acertr' => (int) 10, 'cqu' => (int) 4, 'bca' => (int) 11, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 1, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 1, 'ccan' => (int) 1, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 1, 'col' => (int) 1, 'cpa' => (int) 1, 'cre' => (int) 7, 'csa' => (int) 1, 'camsi' => (int) 2, 'dca' => (int) 3, 'din' => (int) 2, 'dzi' => (int) 3, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 14, 'fve' => (int) 9, 'gma' => (int) 2, 'ghi' => (int) 4, 'gra' => (int) 2, 'vvi' => (int) 1, 'han' => (int) 13, 'cav' => (int) 1, 'hma' => (int) 2, 'sun' => (int) 2, 'lal' => (int) 2, 'lonja' => (int) 12, 'lja' => (int) 1, 'lsa' => (int) 7, 'mes' => (int) 1, 'mpo' => (int) 27, 'mbi' => (int) 1, 'mco' => (int) 8, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 1, 'egut' => (int) 1, 'ama' => (int) 1, 'nta' => (int) 4, 'nnu' => (int) 2, 'oeu' => (int) 3, 'osa' => (int) 4, 'pax' => (int) 9, 'pgr' => (int) 1, 'stu' => (int) 1, 'pvu' => (int) 1, 'ptr' => (int) 4, 'ppa' => (int) 22, 'pco' => (int) 6, 'ppe' => (int) 6, 'psa' => (int) 5, 'pso' => (int) 19, 'qlo' => (int) 5, 'rch' => (int) 7, 'rsi' => (int) 20, 'sbr' => (int) 5, 'sbo' => (int) 1, 'sci' => (int) 2, 'sed' => (int) 2, 'sgi' => (int) 12, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 2, 'tar' => (int) 10, 'tha' => (int) 1, 'tca' => (int) 1, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 2, 'ugi' => (int) 1, 'vma' => (int) 5, 'vmu' => (int) 1, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb301270' $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' => 'HOM05D001460', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '433', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p22980' => 'bna', 'A01p32340' => 'bna', 'A03p42970' => 'bna', 'A05p25880' => 'bna', 'Aa31LG8G9320' => 'aar', 'Aa31LG8G9330' => 'aar', 'Aa31LG8G9340' => 'aar', 'Aa31sc221G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1034' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1528' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.829' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2222' => 'aag', 'Ah.12g058830' => 'amhyb', 'Ah.12g058840' => 'amhyb', 'AL3G37160' => 'aly', 'AL7G41310' => 'aly', 'Aqoxy5G00395' => 'aox', 'Aqoxy5G00396' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0C8NZA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5185HY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JZ1PRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MD3LS0' => 'arhy', 'AT3G22840' => 'ath', 'AT4G14690' => 'ath', 'ATR0665G054' => 'atr', 'Atru.chr4.2344' => 'acertr', 'Atru.chr4.2346' => 'acertr', 'Atru.chr4.2347' => 'acertr', 'Atru.chr4.2348' => 'acertr', 'Atru.chr4.2355' => 'acertr', 'Atru.chr4.2356' => 'acertr', 'Atru.chr4.2358' => 'acertr', 'Atru.chr4.2359' => 'acertr', 'Atru.chr4.2360' => 'acertr', 'Atru.chr4.2361' => 'acertr', 'AUR62030476' => 'cqu', 'AUR62030478' => 'cqu', 'AUR62030819' => 'cqu', 'AUR62030820' => 'cqu', 'BcaB03g14648' => 'bca', 'BcaB04g20492' => 'bca', 'BcaB06g26399' => 'bca', 'BcaC01g03416' => 'bca', 'BcaC01g03419' => 'bca', 'BcaC01g03421' => 'bca', 'BcaC01g03424' => 'bca', 'BcaC05g28012' => 'bca', 'BcaC09g49212' => 'bca', 'BcaC09g50140' => 'bca', 'BcaNung00346' => 'bca', 'BolC1t02785H' => 'bol', 'BolC1t04095H' => 'bol', 'BolC3t17545H' => 'bol', 'BolC5t32769H' => 'bol', 'BraA01t02211Z' => 'bra', 'BraA01t03359Z' => 'bra', 'BraA03t13441Z' => 'bra', 'BraA05t21476Z' => 'bra', 'C01p28420' => 'bna', 'C01p41350' => 'bna', 'C03p52750' => 'bna', 'C03p52780' => 'bna', 'C05p40270' => 'bna', 'CAN.G1437.9' => 'can', 'CANSAT78G0035' => 'cansat', 'CANSAT78G1036' => 'cansat', 'CANSAT78G2272' => 'cansat', 'CANSAT78G2478' => 'cansat', 'CARHR098700' => 'chi', 'CARHR221120' => 'chi', 'CARHR221150' => 'chi', 'Carub.0003s2297' => 'cru', 'Carub.0007s2749' => 'cru', 'Carub.0007s2750' => 'cru', 'Carub.0007s2751' => 'cru', 'Ca_10849_v3' => 'car', 'Cc03_g04300' => 'ccan', 'CDE02G3648' => 'cde', 'CDE05G0060' => 'cde', 'CDE05G0692' => 'cde', 'CDE05G2285' => 'cde', 'CDE05G2884' => 'cde', 'CDE05G3072' => 'cde', 'Cfa008439' => 'cfa', 'Cfa008441' => 'cfa', 'Cfa008443' => 'cfa', 'Cfa008448' => 'cfa', 'Ciclev10005974m.g' => 'ccl', 'Ciclev10006006m.g' => 'ccl', 'Ciclev10006775m.g' => 'ccl', 'CiPaw.02G120400' => 'cil', 'CiPaw.02G120500' => 'cil', 'CiPaw.02G120600' => 'cil', 'ClCG05G004850' => 'cla', 'COL.COLO4_21566' => 'col', 'Cpa.g.sc44.124' => 'cpa', 'Cre07.g320400' => 'cre', 'Cre07.g320450' => 'cre', 'Cre08.g384650' => 'cre', 'Cre09.g393173' => 'cre', 'Cre09.g394325' => 'cre', 'Cre14.g626750' => 'cre', 'Cre16.g679250' => 'cre', 'CsaV3_3G012890' => 'csa', 'CSS0010865' => 'camsi', 'CSS0044338' => 'camsi', 'DCAR_002366' => 'dca', 'DCAR_030687' => 'dca', 'DCAR_030688' => 'dca', 'Dinv14047' => 'din', 'Dinv14048' => 'din', 'Duzib151G0105' => 'dzi', 'Duzib151G0114' => 'dzi', 'Duzib212G1029' => 'dzi', 'ECA232G3536' => 'eca', 'ECA240G0786' => 'eca', 'ECA240G1802' => 'eca', 'ECA240G3760' => 'eca', 'ECA240G3920' => 'eca', 'EL10Ac5g12536' => 'bvu', 'EL10Ac5g12537' => 'bvu', 'EL10Ac5g12538' => 'bvu', 'Eucgr.B01004' => 'egr', 'Eucgr.B01006' => 'egr', 'Eucgr.B01007' => 'egr', 'Eucgr.B01008' => 'egr', 'Eucgr.B01895' => 'egr', 'Eucgr.B01896' => 'egr', 'FAN04G1456' => 'fan', 'FAN08G1769' => 'fan', 'FAN08G2160' => 'fan', 'FAN13G2403' => 'fan', 'FAN13G3303' => 'fan', 'FAN15G2435' => 'fan', 'FAN17G0672' => 'fan', 'FAN17G2441' => 'fan', 'FAN18G1024' => 'fan', 'FAN22G1458' => 'fan', 'FAN24G0037' => 'fan', 'FAN24G0429' => 'fan', 'FAN24G2387' => 'fan', 'FAN27G2746' => 'fan', 'FvH4_2g20400' => 'fve', 'FvH4_2g20420' => 'fve', 'FvH4_2g20430' => 'fve', 'FvH4_4g01270' => 'fve', 'FvH4_4g01290' => 'fve', 'FvH4_4g01300' => 'fve', 'FvH4_4g01310' => 'fve', 'FvH4_4g01330' => 'fve', 'FvH4_5g09070' => 'fve', 'Glyma.10G243800' => 'gma', 'Glyma.20G150600' => 'gma', 'Gohir.A09G219200' => 'ghi', 'Gohir.A09G219300' => 'ghi', 'Gohir.D09G221400' => 'ghi', 'Gohir.D09G221500' => 'ghi', 'Gorai.006G242600' => 'gra', 'Gorai.006G242700' => 'gra', 'GSVIVG01018044001' => 'vvi', 'HanXRQChr03g0083821' => 'han', 'HanXRQChr03g0083841' => 'han', 'HanXRQChr03g0083881' => 'han', 'HanXRQChr03g0083901' => 'han', 'HanXRQChr03g0083921' => 'han', 'HanXRQChr03g0085331' => 'han', 'HanXRQChr03g0085361' => 'han', 'HanXRQChr03g0085411' => 'han', 'HanXRQChr03g0085421' => 'han', 'HanXRQChr03g0085431' => 'han', 'HanXRQChr08g0221991' => 'han', 'HanXRQChr11g0336061' => 'han', 'HanXRQChr11g0336411' => 'han', 'Haze_11234' => 'cav', 'Hma1.2p1_0549F.1_g177010' => 'hma', 'Hma1.2p1_0602F.1_g187630' => 'hma', 'Hund14876' => 'sun', 'Hund14879' => 'sun', 'Lalb_Chr06g0160741' => 'lal', 'Lalb_Chr21g0304781' => 'lal', 'Lj3A726G19' => 'lonja', 'Lj3A726T23' => 'lonja', 'Lj3A726T24' => 'lonja', 'Lj3A726T25' => 'lonja', 'Lj3A727T17' => 'lonja', 'Lj3C726T0' => 'lonja', 'Lj3C726T2' => 'lonja', 'Lj3P725T35' => 'lonja', 'Lj3P727T10' => 'lonja', 'Lj3P727T12' => 'lonja', 'Lj3P727T14' => 'lonja', 'Lj5g0023109' => 'lja', 'Lj6P646T44' => 'lonja', 'Lsat_1_v5_gn_6_75760' => 'lsa', 'Lsat_1_v5_gn_6_75800' => 'lsa', 'Lsat_1_v5_gn_6_75900' => 'lsa', 'Lsat_1_v5_gn_6_76240' => 'lsa', 'Lsat_1_v5_gn_6_76441' => 'lsa', 'Lsat_1_v5_gn_6_76700' => 'lsa', 'Lsat_1_v5_gn_6_76760' => 'lsa', 'Manes.15G033100' => 'mes', 'Mapoly0004s0074' => 'mpo', 'Mapoly0004s0075' => 'mpo', 'Mapoly0004s0163' => 'mpo', 'Mapoly0004s0164' => 'mpo', 'Mapoly0021s0018' => 'mpo', 'Mapoly0041s0136' => 'mpo', 'Mapoly0041s0137' => 'mpo', 'Mapoly0041s0138' => 'mpo', 'Mapoly0041s0139' => 'mpo', 'Mapoly0041s0141' => 'mpo', 'Mapoly0041s0142' => 'mpo', 'Mapoly0041s0143' => 'mpo', 'Mapoly0041s0144' => 'mpo', 'Mapoly0041s0145' => 'mpo', 'Mapoly0047s0106' => 'mpo', 'Mapoly0047s0108' => 'mpo', 'Mapoly0050s0051' => 'mpo', 'Mapoly0050s0052' => 'mpo', 'Mapoly0050s0053' => 'mpo', 'Mapoly0058s0013' => 'mpo', 'Mapoly0091s0078' => 'mpo', 'Mapoly0091s0079' => 'mpo', 'Mapoly0091s0080' => 'mpo', 'Mapoly0091s0081' => 'mpo', 'Mapoly0278s0004' => 'mpo', 'Mapoly0278s0005' => 'mpo', 'Mapoly0278s0006' => 'mpo', 'MBI11_g30648_MAGBIO' => 'mbi', 'MCO03G194' => 'mco', 'MCO03G590' => 'mco', 'MCO07G312' => 'mco', 'MCO10G318' => 'mco', 'MCO12G244' => 'mco', 'MCO13G148' => 'mco', 'MCO13G194' => 'mco', 'MCO16G238' => 'mco', 'MD06G1134100' => 'mdo', 'MD13G1200100' => 'mdo', 'MD13G1200300' => 'mdo', 'MD13G1200600' => 'mdo', 'MD14G1150400' => 'mdo', 'MD16G1200000' => 'mdo', 'Medtr1g102570' => 'mtr', 'Medtr1g102780' => 'mtr', 'Medtr1g102800' => 'mtr', 'Medtr1g102810' => 'mtr', 'Medtr1g102830' => 'mtr', 'MELO3C006499.2' => 'cme', 'Migut.G00385' => 'egut', 'MSTRG.4063' => 'ama', 'Nitab4.5_0000090g0260' => 'nta', 'Nitab4.5_0000977g0030' => 'nta', 'Nitab4.5_0002541g0040' => 'nta', 'Nitab4.5_0007068g0040' => 'nta', 'Nn005s41408' => 'nnu', 'Nn005s41410' => 'nnu', 'Oeu010310.1' => 'oeu', 'Oeu010311.1' => 'oeu', 'Oeu043472.1' => 'oeu', 'Os01g0246400' => 'osa', 'Os04g0267950' => 'osa', 'Os07g0178700' => 'osa', 'Os07g0178800' => 'osa', 'Peaxi162Scf00316g00046' => 'pax', 'Peaxi162Scf00316g00049' => 'pax', 'Peaxi162Scf00316g00059' => 'pax', 'Peaxi162Scf00316g00328' => 'pax', 'Peaxi162Scf00316g00329' => 'pax', 'Peaxi162Scf00316g00411' => 'pax', 'Peaxi162Scf00316g00521' => 'pax', 'Peaxi162Scf00492g00068' => 'pax', 'Peaxi162Scf35631g00002' => 'pax', 'PGR142G3720' => 'pgr', 'PGSC0003DMG400006442' => 'stu', 'Phvul.007G062000' => 'pvu', 'Potri.008G157750' => 'ptr', 'Potri.008G157900' => 'ptr', 'Potri.008G158000' => 'ptr', 'Potri.008G158200' => 'ptr', 'Pp3c11_7280' => 'ppa', 'Pp3c11_7980' => 'ppa', 'Pp3c12_19450' => 'ppa', 'Pp3c14_1480' => 'ppa', 'Pp3c14_1501' => 'ppa', 'Pp3c16_4900' => 'ppa', 'Pp3c16_5010' => 'ppa', 'Pp3c16_5060' => 'ppa', 'Pp3c19_18250' => 'ppa', 'Pp3c23_8530' => 'ppa', 'Pp3c23_8550' => 'ppa', 'Pp3c24_9670' => 'ppa', 'Pp3c2_21390' => 'ppa', 'Pp3c2_31380' => 'ppa', 'Pp3c3_16620' => 'ppa', 'Pp3c3_8090' => 'ppa', 'Pp3c3_8110' => 'ppa', 'Pp3c3_8130' => 'ppa', 'Pp3c3_8150' => 'ppa', 'Pp3c4_14320' => 'ppa', 'Pp3c6_2560' => 'ppa', 'Pp3c9_16700' => 'ppa', 'PRCOL_00000234' => 'pco', 'PRCOL_00000235' => 'pco', 'PRCOL_00000777' => 'pco', 'PRCOL_00002344' => 'pco', 'PRCOL_00002372' => 'pco', 'PRCOL_00006120' => 'pco', 'Prupe.1G021400' => 'ppe', 'Prupe.1G021500' => 'ppe', 'Prupe.1G021600' => 'ppe', 'Prupe.1G021700' => 'ppe', 'Prupe.1G021800' => 'ppe', 'Prupe.5G145100' => 'ppe', 'Psat6g204040' => 'psa', 'Psat6g204800' => 'psa', 'Psat6g204920' => 'psa', 'Psat6g204960' => 'psa', 'Psat6g205080' => 'psa', 'PSO017G0271' => 'pso', 'PSO017G1276' => 'pso', 'PSO017G1429' => 'pso', 'PSO017G1861' => 'pso', 'PSO017G2787' => 'pso', 'PSO017G4466' => 'pso', 'PSO017G5118' => 'pso', 'PSO017G5420' => 'pso', 'PSO063G3678' => 'pso', 'PSO210G0546' => 'pso', 'PSO317G0001' => 'pso', 'PSO357G0512' => 'pso', 'PSO478G2682' => 'pso', 'PSO647G0001' => 'pso', 'PSO675G0001' => 'pso', 'PSO675G2699' => 'pso', 'PSO675G2849' => 'pso', 'PSO675G4991' => 'pso', 'PSO689G0001' => 'pso', 'QL06p000916' => 'qlo', 'QL06p000921' => 'qlo', 'QL06p001398' => 'qlo', 'QL06p001407' => 'qlo', 'QL06p002031' => 'qlo', 'RcHm_v2.0_Chr4g0387791' => 'rch', 'RcHm_v2.0_Chr4g0387801' => 'rch', 'RcHm_v2.0_Chr6g0286501' => 'rch', 'RcHm_v2.0_Chr6g0286511' => 'rch', 'RcHm_v2.0_Chr6g0286521' => 'rch', 'RcHm_v2.0_Chr6g0286531' => 'rch', 'RcHm_v2.0_Chr7g0189141' => 'rch', 'Rhsim02G0028700' => 'rsi', 'Rhsim02G0028800' => 'rsi', 'Rhsim02G0028900' => 'rsi', 'Rhsim02G0029000' => 'rsi', 'Rhsim02G0029100' => 'rsi', 'Rhsim02G0029200' => 'rsi', 'Rhsim02G0029300' => 'rsi', 'Rhsim02G0029400' => 'rsi', 'Rhsim02G0029500' => 'rsi', 'Rhsim02G0029600' => 'rsi', 'RhsimUnG0024000' => 'rsi', 'RhsimUnG0024100' => 'rsi', 'RhsimUnG0024200' => 'rsi', 'RhsimUnG0024300' => 'rsi', 'RhsimUnG0024400' => 'rsi', 'RhsimUnG0024500' => 'rsi', 'RhsimUnG0024700' => 'rsi', 'RhsimUnG0024800' => 'rsi', 'RhsimUnG0024900' => 'rsi', 'RhsimUnG0025100' => 'rsi', 'Sabra08G0120200' => 'sbr', 'Sabra08G0120300' => 'sbr', 'Sabra08G0120500' => 'sbr', 'Sabra08G0120600' => 'sbr', 'Sabra10G0158900' => 'sbr', 'SalBow2G3492' => 'sbo', 'Sc13g0004760' => 'sci', 'Sc13g0004770' => 'sci', 'Sed0003417' => 'sed', 'Sed0019750' => 'sed', 'SEGI_03419' => 'sgi', 'SEGI_05907' => 'sgi', 'SEGI_10682' => 'sgi', 'SEGI_13528' => 'sgi', 'SEGI_16081' => 'sgi', 'SEGI_19370' => 'sgi', 'SEGI_21015' => 'sgi', 'SEGI_21944' => 'sgi', 'SEGI_32906' => 'sgi', 'SEGI_33093' => 'sgi', 'SEGI_36110' => 'sgi', 'SEGI_40397' => 'sgi', 'SGA_v2.0_scaffold191G40426' => 'sas', 'SGA_v2.0_scaffold353G49717' => 'sas', 'SGA_v2.0_scaffold50G18550' => 'sas', 'SMO119G0173' => 'smo', 'SMO172G0002' => 'smo', 'Solyc09g082690.3' => 'sly', 'Solyc09g082700.2' => 'sly', 'Sopen09g031550' => 'spe', 'Sopen09g031560' => 'spe', 'Sp3g20540' => 'spa', 'Sp7g07580' => 'spa', 'TAR134G0002' => 'tar', 'TAR236G0001' => 'tar', 'TAR365G0892' => 'tar', 'TAR636G0166' => 'tar', 'TAR636G0646' => 'tar', 'TAR636G0869' => 'tar', 'TAR636G1317' => 'tar', 'TAR636G1744' => 'tar', 'TAR636G3358' => 'tar', 'TAR636G3436' => 'tar', 'THA.LOC104803047' => 'tha', 'Thecc.04G238900' => 'tca', 'Thhalv10021557m.g' => 'esa', 'Thhalv10026318m.g' => 'esa', 'Thhalv10026335m.g' => 'esa', 'TPR.G17433' => 'tpr', 'TPR.G18915' => 'tpr', 'TPR.G26125' => 'tpr', 'TWI09G0677' => 'twi', 'TWI73G0287' => 'twi', 'unitig_748.g8326' => 'ugi', 'vmacro15370' => 'vma', 'vmacro15371' => 'vma', 'vmacro15372' => 'vma', 'vmacro15373' => 'vma', 'vmacro15374' => 'vma', 'VMungo0720G2826' => 'vmu', 'Zm00001eb116960' => 'zma', 'Zm00001eb301260' => 'zma', 'Zm00001eb301270' => 'zma' ), 'gf_id' => 'HOM05D001460', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001460' ), 'data_identifier' => 'HOM05D001460', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001460', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '433', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p22980' => 'bna', 'A01p32340' => 'bna', 'A03p42970' => 'bna', 'A05p25880' => 'bna', 'Aa31LG8G9320' => 'aar', 'Aa31LG8G9330' => 'aar', 'Aa31LG8G9340' => 'aar', 'Aa31sc221G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1034' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1528' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.829' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2222' => 'aag', 'Ah.12g058830' => 'amhyb', 'Ah.12g058840' => 'amhyb', 'AL3G37160' => 'aly', 'AL7G41310' => 'aly', 'Aqoxy5G00395' => 'aox', 'Aqoxy5G00396' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0C8NZA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5185HY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JZ1PRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MD3LS0' => 'arhy', 'AT3G22840' => 'ath', 'AT4G14690' => 'ath', 'ATR0665G054' => 'atr', 'Atru.chr4.2344' => 'acertr', 'Atru.chr4.2346' => 'acertr', 'Atru.chr4.2347' => 'acertr', 'Atru.chr4.2348' => 'acertr', 'Atru.chr4.2355' => 'acertr', 'Atru.chr4.2356' => 'acertr', 'Atru.chr4.2358' => 'acertr', 'Atru.chr4.2359' => 'acertr', 'Atru.chr4.2360' => 'acertr', 'Atru.chr4.2361' => 'acertr', 'AUR62030476' => 'cqu', 'AUR62030478' => 'cqu', 'AUR62030819' => 'cqu', 'AUR62030820' => 'cqu', 'BcaB03g14648' => 'bca', 'BcaB04g20492' => 'bca', 'BcaB06g26399' => 'bca', 'BcaC01g03416' => 'bca', 'BcaC01g03419' => 'bca', 'BcaC01g03421' => 'bca', 'BcaC01g03424' => 'bca', 'BcaC05g28012' => 'bca', 'BcaC09g49212' => 'bca', 'BcaC09g50140' => 'bca', 'BcaNung00346' => 'bca', 'BolC1t02785H' => 'bol', 'BolC1t04095H' => 'bol', 'BolC3t17545H' => 'bol', 'BolC5t32769H' => 'bol', 'BraA01t02211Z' => 'bra', 'BraA01t03359Z' => 'bra', 'BraA03t13441Z' => 'bra', 'BraA05t21476Z' => 'bra', 'C01p28420' => 'bna', 'C01p41350' => 'bna', 'C03p52750' => 'bna', 'C03p52780' => 'bna', 'C05p40270' => 'bna', 'CAN.G1437.9' => 'can', 'CANSAT78G0035' => 'cansat', 'CANSAT78G1036' => 'cansat', 'CANSAT78G2272' => 'cansat', 'CANSAT78G2478' => 'cansat', 'CARHR098700' => 'chi', 'CARHR221120' => 'chi', 'CARHR221150' => 'chi', 'Carub.0003s2297' => 'cru', 'Carub.0007s2749' => 'cru', 'Carub.0007s2750' => 'cru', 'Carub.0007s2751' => 'cru', 'Ca_10849_v3' => 'car', 'Cc03_g04300' => 'ccan', 'CDE02G3648' => 'cde', 'CDE05G0060' => 'cde', 'CDE05G0692' => 'cde', 'CDE05G2285' => 'cde', 'CDE05G2884' => 'cde', 'CDE05G3072' => 'cde', 'Cfa008439' => 'cfa', 'Cfa008441' => 'cfa', 'Cfa008443' => 'cfa', 'Cfa008448' => 'cfa', 'Ciclev10005974m.g' => 'ccl', 'Ciclev10006006m.g' => 'ccl', 'Ciclev10006775m.g' => 'ccl', 'CiPaw.02G120400' => 'cil', 'CiPaw.02G120500' => 'cil', 'CiPaw.02G120600' => 'cil', 'ClCG05G004850' => 'cla', 'COL.COLO4_21566' => 'col', 'Cpa.g.sc44.124' => 'cpa', 'Cre07.g320400' => 'cre', 'Cre07.g320450' => 'cre', 'Cre08.g384650' => 'cre', 'Cre09.g393173' => 'cre', 'Cre09.g394325' => 'cre', 'Cre14.g626750' => 'cre', 'Cre16.g679250' => 'cre', 'CsaV3_3G012890' => 'csa', 'CSS0010865' => 'camsi', 'CSS0044338' => 'camsi', 'DCAR_002366' => 'dca', 'DCAR_030687' => 'dca', 'DCAR_030688' => 'dca', 'Dinv14047' => 'din', 'Dinv14048' => 'din', 'Duzib151G0105' => 'dzi', 'Duzib151G0114' => 'dzi', 'Duzib212G1029' => 'dzi', 'ECA232G3536' => 'eca', 'ECA240G0786' => 'eca', 'ECA240G1802' => 'eca', 'ECA240G3760' => 'eca', 'ECA240G3920' => 'eca', 'EL10Ac5g12536' => 'bvu', 'EL10Ac5g12537' => 'bvu', 'EL10Ac5g12538' => 'bvu', 'Eucgr.B01004' => 'egr', 'Eucgr.B01006' => 'egr', 'Eucgr.B01007' => 'egr', 'Eucgr.B01008' => 'egr', 'Eucgr.B01895' => 'egr', 'Eucgr.B01896' => 'egr', 'FAN04G1456' => 'fan', 'FAN08G1769' => 'fan', 'FAN08G2160' => 'fan', 'FAN13G2403' => 'fan', 'FAN13G3303' => 'fan', 'FAN15G2435' => 'fan', 'FAN17G0672' => 'fan', 'FAN17G2441' => 'fan', 'FAN18G1024' => 'fan', 'FAN22G1458' => 'fan', 'FAN24G0037' => 'fan', 'FAN24G0429' => 'fan', 'FAN24G2387' => 'fan', 'FAN27G2746' => 'fan', 'FvH4_2g20400' => 'fve', 'FvH4_2g20420' => 'fve', 'FvH4_2g20430' => 'fve', 'FvH4_4g01270' => 'fve', 'FvH4_4g01290' => 'fve', 'FvH4_4g01300' => 'fve', 'FvH4_4g01310' => 'fve', 'FvH4_4g01330' => 'fve', 'FvH4_5g09070' => 'fve', 'Glyma.10G243800' => 'gma', 'Glyma.20G150600' => 'gma', 'Gohir.A09G219200' => 'ghi', 'Gohir.A09G219300' => 'ghi', 'Gohir.D09G221400' => 'ghi', 'Gohir.D09G221500' => 'ghi', 'Gorai.006G242600' => 'gra', 'Gorai.006G242700' => 'gra', 'GSVIVG01018044001' => 'vvi', 'HanXRQChr03g0083821' => 'han', 'HanXRQChr03g0083841' => 'han', 'HanXRQChr03g0083881' => 'han', 'HanXRQChr03g0083901' => 'han', 'HanXRQChr03g0083921' => 'han', 'HanXRQChr03g0085331' => 'han', 'HanXRQChr03g0085361' => 'han', 'HanXRQChr03g0085411' => 'han', 'HanXRQChr03g0085421' => 'han', 'HanXRQChr03g0085431' => 'han', 'HanXRQChr08g0221991' => 'han', 'HanXRQChr11g0336061' => 'han', 'HanXRQChr11g0336411' => 'han', 'Haze_11234' => 'cav', 'Hma1.2p1_0549F.1_g177010' => 'hma', 'Hma1.2p1_0602F.1_g187630' => 'hma', 'Hund14876' => 'sun', 'Hund14879' => 'sun', 'Lalb_Chr06g0160741' => 'lal', 'Lalb_Chr21g0304781' => 'lal', 'Lj3A726G19' => 'lonja', 'Lj3A726T23' => 'lonja', 'Lj3A726T24' => 'lonja', 'Lj3A726T25' => 'lonja', 'Lj3A727T17' => 'lonja', 'Lj3C726T0' => 'lonja', 'Lj3C726T2' => 'lonja', 'Lj3P725T35' => 'lonja', 'Lj3P727T10' => 'lonja', 'Lj3P727T12' => 'lonja', 'Lj3P727T14' => 'lonja', 'Lj5g0023109' => 'lja', 'Lj6P646T44' => 'lonja', 'Lsat_1_v5_gn_6_75760' => 'lsa', 'Lsat_1_v5_gn_6_75800' => 'lsa', 'Lsat_1_v5_gn_6_75900' => 'lsa', 'Lsat_1_v5_gn_6_76240' => 'lsa', 'Lsat_1_v5_gn_6_76441' => 'lsa', 'Lsat_1_v5_gn_6_76700' => 'lsa', 'Lsat_1_v5_gn_6_76760' => 'lsa', 'Manes.15G033100' => 'mes', 'Mapoly0004s0074' => 'mpo', 'Mapoly0004s0075' => 'mpo', 'Mapoly0004s0163' => 'mpo', 'Mapoly0004s0164' => 'mpo', 'Mapoly0021s0018' => 'mpo', 'Mapoly0041s0136' => 'mpo', 'Mapoly0041s0137' => 'mpo', 'Mapoly0041s0138' => 'mpo', 'Mapoly0041s0139' => 'mpo', 'Mapoly0041s0141' => 'mpo', 'Mapoly0041s0142' => 'mpo', 'Mapoly0041s0143' => 'mpo', 'Mapoly0041s0144' => 'mpo', 'Mapoly0041s0145' => 'mpo', 'Mapoly0047s0106' => 'mpo', 'Mapoly0047s0108' => 'mpo', 'Mapoly0050s0051' => 'mpo', 'Mapoly0050s0052' => 'mpo', 'Mapoly0050s0053' => 'mpo', 'Mapoly0058s0013' => 'mpo', 'Mapoly0091s0078' => 'mpo', 'Mapoly0091s0079' => 'mpo', 'Mapoly0091s0080' => 'mpo', 'Mapoly0091s0081' => 'mpo', 'Mapoly0278s0004' => 'mpo', 'Mapoly0278s0005' => 'mpo', 'Mapoly0278s0006' => 'mpo', 'MBI11_g30648_MAGBIO' => 'mbi', 'MCO03G194' => 'mco', 'MCO03G590' => 'mco', 'MCO07G312' => 'mco', 'MCO10G318' => 'mco', 'MCO12G244' => 'mco', 'MCO13G148' => 'mco', 'MCO13G194' => 'mco', 'MCO16G238' => 'mco', 'MD06G1134100' => 'mdo', 'MD13G1200100' => 'mdo', 'MD13G1200300' => 'mdo', 'MD13G1200600' => 'mdo', 'MD14G1150400' => 'mdo', 'MD16G1200000' => 'mdo', 'Medtr1g102570' => 'mtr', 'Medtr1g102780' => 'mtr', 'Medtr1g102800' => 'mtr', 'Medtr1g102810' => 'mtr', 'Medtr1g102830' => 'mtr', 'MELO3C006499.2' => 'cme', 'Migut.G00385' => 'egut', 'MSTRG.4063' => 'ama', 'Nitab4.5_0000090g0260' => 'nta', 'Nitab4.5_0000977g0030' => 'nta', 'Nitab4.5_0002541g0040' => 'nta', 'Nitab4.5_0007068g0040' => 'nta', 'Nn005s41408' => 'nnu', 'Nn005s41410' => 'nnu', 'Oeu010310.1' => 'oeu', 'Oeu010311.1' => 'oeu', 'Oeu043472.1' => 'oeu', 'Os01g0246400' => 'osa', 'Os04g0267950' => 'osa', 'Os07g0178700' => 'osa', 'Os07g0178800' => 'osa', 'Peaxi162Scf00316g00046' => 'pax', 'Peaxi162Scf00316g00049' => 'pax', 'Peaxi162Scf00316g00059' => 'pax', 'Peaxi162Scf00316g00328' => 'pax', 'Peaxi162Scf00316g00329' => 'pax', 'Peaxi162Scf00316g00411' => 'pax', 'Peaxi162Scf00316g00521' => 'pax', 'Peaxi162Scf00492g00068' => 'pax', 'Peaxi162Scf35631g00002' => 'pax', 'PGR142G3720' => 'pgr', 'PGSC0003DMG400006442' => 'stu', 'Phvul.007G062000' => 'pvu', 'Potri.008G157750' => 'ptr', 'Potri.008G157900' => 'ptr', 'Potri.008G158000' => 'ptr', 'Potri.008G158200' => 'ptr', 'Pp3c11_7280' => 'ppa', 'Pp3c11_7980' => 'ppa', 'Pp3c12_19450' => 'ppa', 'Pp3c14_1480' => 'ppa', 'Pp3c14_1501' => 'ppa', 'Pp3c16_4900' => 'ppa', 'Pp3c16_5010' => 'ppa', 'Pp3c16_5060' => 'ppa', 'Pp3c19_18250' => 'ppa', 'Pp3c23_8530' => 'ppa', 'Pp3c23_8550' => 'ppa', 'Pp3c24_9670' => 'ppa', 'Pp3c2_21390' => 'ppa', 'Pp3c2_31380' => 'ppa', 'Pp3c3_16620' => 'ppa', 'Pp3c3_8090' => 'ppa', 'Pp3c3_8110' => 'ppa', 'Pp3c3_8130' => 'ppa', 'Pp3c3_8150' => 'ppa', 'Pp3c4_14320' => 'ppa', 'Pp3c6_2560' => 'ppa', 'Pp3c9_16700' => 'ppa', 'PRCOL_00000234' => 'pco', 'PRCOL_00000235' => 'pco', 'PRCOL_00000777' => 'pco', 'PRCOL_00002344' => 'pco', 'PRCOL_00002372' => 'pco', 'PRCOL_00006120' => 'pco', 'Prupe.1G021400' => 'ppe', 'Prupe.1G021500' => 'ppe', 'Prupe.1G021600' => 'ppe', 'Prupe.1G021700' => 'ppe', 'Prupe.1G021800' => 'ppe', 'Prupe.5G145100' => 'ppe', 'Psat6g204040' => 'psa', 'Psat6g204800' => 'psa', 'Psat6g204920' => 'psa', 'Psat6g204960' => 'psa', 'Psat6g205080' => 'psa', 'PSO017G0271' => 'pso', 'PSO017G1276' => 'pso', 'PSO017G1429' => 'pso', 'PSO017G1861' => 'pso', 'PSO017G2787' => 'pso', 'PSO017G4466' => 'pso', 'PSO017G5118' => 'pso', 'PSO017G5420' => 'pso', 'PSO063G3678' => 'pso', 'PSO210G0546' => 'pso', 'PSO317G0001' => 'pso', 'PSO357G0512' => 'pso', 'PSO478G2682' => 'pso', 'PSO647G0001' => 'pso', 'PSO675G0001' => 'pso', 'PSO675G2699' => 'pso', 'PSO675G2849' => 'pso', 'PSO675G4991' => 'pso', 'PSO689G0001' => 'pso', 'QL06p000916' => 'qlo', 'QL06p000921' => 'qlo', 'QL06p001398' => 'qlo', 'QL06p001407' => 'qlo', 'QL06p002031' => 'qlo', 'RcHm_v2.0_Chr4g0387791' => 'rch', 'RcHm_v2.0_Chr4g0387801' => 'rch', 'RcHm_v2.0_Chr6g0286501' => 'rch', 'RcHm_v2.0_Chr6g0286511' => 'rch', 'RcHm_v2.0_Chr6g0286521' => 'rch', 'RcHm_v2.0_Chr6g0286531' => 'rch', 'RcHm_v2.0_Chr7g0189141' => 'rch', 'Rhsim02G0028700' => 'rsi', 'Rhsim02G0028800' => 'rsi', 'Rhsim02G0028900' => 'rsi', 'Rhsim02G0029000' => 'rsi', 'Rhsim02G0029100' => 'rsi', 'Rhsim02G0029200' => 'rsi', 'Rhsim02G0029300' => 'rsi', 'Rhsim02G0029400' => 'rsi', 'Rhsim02G0029500' => 'rsi', 'Rhsim02G0029600' => 'rsi', 'RhsimUnG0024000' => 'rsi', 'RhsimUnG0024100' => 'rsi', 'RhsimUnG0024200' => 'rsi', 'RhsimUnG0024300' => 'rsi', 'RhsimUnG0024400' => 'rsi', 'RhsimUnG0024500' => 'rsi', 'RhsimUnG0024700' => 'rsi', 'RhsimUnG0024800' => 'rsi', 'RhsimUnG0024900' => 'rsi', 'RhsimUnG0025100' => 'rsi', 'Sabra08G0120200' => 'sbr', 'Sabra08G0120300' => 'sbr', 'Sabra08G0120500' => 'sbr', 'Sabra08G0120600' => 'sbr', 'Sabra10G0158900' => 'sbr', 'SalBow2G3492' => 'sbo', 'Sc13g0004760' => 'sci', 'Sc13g0004770' => 'sci', 'Sed0003417' => 'sed', 'Sed0019750' => 'sed', 'SEGI_03419' => 'sgi', 'SEGI_05907' => 'sgi', 'SEGI_10682' => 'sgi', 'SEGI_13528' => 'sgi', 'SEGI_16081' => 'sgi', 'SEGI_19370' => 'sgi', 'SEGI_21015' => 'sgi', 'SEGI_21944' => 'sgi', 'SEGI_32906' => 'sgi', 'SEGI_33093' => 'sgi', 'SEGI_36110' => 'sgi', 'SEGI_40397' => 'sgi', 'SGA_v2.0_scaffold191G40426' => 'sas', 'SGA_v2.0_scaffold353G49717' => 'sas', 'SGA_v2.0_scaffold50G18550' => 'sas', 'SMO119G0173' => 'smo', 'SMO172G0002' => 'smo', 'Solyc09g082690.3' => 'sly', 'Solyc09g082700.2' => 'sly', 'Sopen09g031550' => 'spe', 'Sopen09g031560' => 'spe', 'Sp3g20540' => 'spa', 'Sp7g07580' => 'spa', 'TAR134G0002' => 'tar', 'TAR236G0001' => 'tar', 'TAR365G0892' => 'tar', 'TAR636G0166' => 'tar', 'TAR636G0646' => 'tar', 'TAR636G0869' => 'tar', 'TAR636G1317' => 'tar', 'TAR636G1744' => 'tar', 'TAR636G3358' => 'tar', 'TAR636G3436' => 'tar', 'THA.LOC104803047' => 'tha', 'Thecc.04G238900' => 'tca', 'Thhalv10021557m.g' => 'esa', 'Thhalv10026318m.g' => 'esa', 'Thhalv10026335m.g' => 'esa', 'TPR.G17433' => 'tpr', 'TPR.G18915' => 'tpr', 'TPR.G26125' => 'tpr', 'TWI09G0677' => 'twi', 'TWI73G0287' => 'twi', 'unitig_748.g8326' => 'ugi', 'vmacro15370' => 'vma', 'vmacro15371' => 'vma', 'vmacro15372' => 'vma', 'vmacro15373' => 'vma', 'vmacro15374' => 'vma', 'VMungo0720G2826' => 'vmu', 'Zm00001eb116960' => 'zma', 'Zm00001eb301260' => 'zma', 'Zm00001eb301270' => 'zma' ) $gf_id = 'HOM05D001460' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001460' ) $data_identifier = 'HOM05D001460' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 4, 'aag' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 2, 'aox' => (int) 2, 'arhy' => (int) 4, 'ath' => (int) 2, 'atr' => (int) 1, 'acertr' => (int) 10, 'cqu' => (int) 4, 'bca' => (int) 11, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 1, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 1, 'ccan' => (int) 1, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 1, 'col' => (int) 1, 'cpa' => (int) 1, 'cre' => (int) 7, 'csa' => (int) 1, 'camsi' => (int) 2, 'dca' => (int) 3, 'din' => (int) 2, 'dzi' => (int) 3, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 14, 'fve' => (int) 9, 'gma' => (int) 2, 'ghi' => (int) 4, 'gra' => (int) 2, 'vvi' => (int) 1, 'han' => (int) 13, 'cav' => (int) 1, 'hma' => (int) 2, 'sun' => (int) 2, 'lal' => (int) 2, 'lonja' => (int) 12, 'lja' => (int) 1, 'lsa' => (int) 7, 'mes' => (int) 1, 'mpo' => (int) 27, 'mbi' => (int) 1, 'mco' => (int) 8, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 1, 'egut' => (int) 1, 'ama' => (int) 1, 'nta' => (int) 4, 'nnu' => (int) 2, 'oeu' => (int) 3, 'osa' => (int) 4, 'pax' => (int) 9, 'pgr' => (int) 1, 'stu' => (int) 1, 'pvu' => (int) 1, 'ptr' => (int) 4, 'ppa' => (int) 22, 'pco' => (int) 6, 'ppe' => (int) 6, 'psa' => (int) 5, 'pso' => (int) 19, 'qlo' => (int) 5, 'rch' => (int) 7, 'rsi' => (int) 20, 'sbr' => (int) 5, 'sbo' => (int) 1, 'sci' => (int) 2, 'sed' => (int) 2, 'sgi' => (int) 12, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 2, 'tar' => (int) 10, 'tha' => (int) 1, 'tca' => (int) 1, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 2, 'ugi' => (int) 1, 'vma' => (int) 5, 'vmu' => (int) 1, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb301270' $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' => 'HOM05D001460', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '433', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p22980' => 'bna', 'A01p32340' => 'bna', 'A03p42970' => 'bna', 'A05p25880' => 'bna', 'Aa31LG8G9320' => 'aar', 'Aa31LG8G9330' => 'aar', 'Aa31LG8G9340' => 'aar', 'Aa31sc221G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1034' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1528' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.829' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2222' => 'aag', 'Ah.12g058830' => 'amhyb', 'Ah.12g058840' => 'amhyb', 'AL3G37160' => 'aly', 'AL7G41310' => 'aly', 'Aqoxy5G00395' => 'aox', 'Aqoxy5G00396' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0C8NZA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5185HY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JZ1PRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MD3LS0' => 'arhy', 'AT3G22840' => 'ath', 'AT4G14690' => 'ath', 'ATR0665G054' => 'atr', 'Atru.chr4.2344' => 'acertr', 'Atru.chr4.2346' => 'acertr', 'Atru.chr4.2347' => 'acertr', 'Atru.chr4.2348' => 'acertr', 'Atru.chr4.2355' => 'acertr', 'Atru.chr4.2356' => 'acertr', 'Atru.chr4.2358' => 'acertr', 'Atru.chr4.2359' => 'acertr', 'Atru.chr4.2360' => 'acertr', 'Atru.chr4.2361' => 'acertr', 'AUR62030476' => 'cqu', 'AUR62030478' => 'cqu', 'AUR62030819' => 'cqu', 'AUR62030820' => 'cqu', 'BcaB03g14648' => 'bca', 'BcaB04g20492' => 'bca', 'BcaB06g26399' => 'bca', 'BcaC01g03416' => 'bca', 'BcaC01g03419' => 'bca', 'BcaC01g03421' => 'bca', 'BcaC01g03424' => 'bca', 'BcaC05g28012' => 'bca', 'BcaC09g49212' => 'bca', 'BcaC09g50140' => 'bca', 'BcaNung00346' => 'bca', 'BolC1t02785H' => 'bol', 'BolC1t04095H' => 'bol', 'BolC3t17545H' => 'bol', 'BolC5t32769H' => 'bol', 'BraA01t02211Z' => 'bra', 'BraA01t03359Z' => 'bra', 'BraA03t13441Z' => 'bra', 'BraA05t21476Z' => 'bra', 'C01p28420' => 'bna', 'C01p41350' => 'bna', 'C03p52750' => 'bna', 'C03p52780' => 'bna', 'C05p40270' => 'bna', 'CAN.G1437.9' => 'can', 'CANSAT78G0035' => 'cansat', 'CANSAT78G1036' => 'cansat', 'CANSAT78G2272' => 'cansat', 'CANSAT78G2478' => 'cansat', 'CARHR098700' => 'chi', 'CARHR221120' => 'chi', 'CARHR221150' => 'chi', 'Carub.0003s2297' => 'cru', 'Carub.0007s2749' => 'cru', 'Carub.0007s2750' => 'cru', 'Carub.0007s2751' => 'cru', 'Ca_10849_v3' => 'car', 'Cc03_g04300' => 'ccan', 'CDE02G3648' => 'cde', 'CDE05G0060' => 'cde', 'CDE05G0692' => 'cde', 'CDE05G2285' => 'cde', 'CDE05G2884' => 'cde', 'CDE05G3072' => 'cde', 'Cfa008439' => 'cfa', 'Cfa008441' => 'cfa', 'Cfa008443' => 'cfa', 'Cfa008448' => 'cfa', 'Ciclev10005974m.g' => 'ccl', 'Ciclev10006006m.g' => 'ccl', 'Ciclev10006775m.g' => 'ccl', 'CiPaw.02G120400' => 'cil', 'CiPaw.02G120500' => 'cil', 'CiPaw.02G120600' => 'cil', 'ClCG05G004850' => 'cla', 'COL.COLO4_21566' => 'col', 'Cpa.g.sc44.124' => 'cpa', 'Cre07.g320400' => 'cre', 'Cre07.g320450' => 'cre', 'Cre08.g384650' => 'cre', 'Cre09.g393173' => 'cre', 'Cre09.g394325' => 'cre', 'Cre14.g626750' => 'cre', 'Cre16.g679250' => 'cre', 'CsaV3_3G012890' => 'csa', 'CSS0010865' => 'camsi', 'CSS0044338' => 'camsi', 'DCAR_002366' => 'dca', 'DCAR_030687' => 'dca', 'DCAR_030688' => 'dca', 'Dinv14047' => 'din', 'Dinv14048' => 'din', 'Duzib151G0105' => 'dzi', 'Duzib151G0114' => 'dzi', 'Duzib212G1029' => 'dzi', 'ECA232G3536' => 'eca', 'ECA240G0786' => 'eca', 'ECA240G1802' => 'eca', 'ECA240G3760' => 'eca', 'ECA240G3920' => 'eca', 'EL10Ac5g12536' => 'bvu', 'EL10Ac5g12537' => 'bvu', 'EL10Ac5g12538' => 'bvu', 'Eucgr.B01004' => 'egr', 'Eucgr.B01006' => 'egr', 'Eucgr.B01007' => 'egr', 'Eucgr.B01008' => 'egr', 'Eucgr.B01895' => 'egr', 'Eucgr.B01896' => 'egr', 'FAN04G1456' => 'fan', 'FAN08G1769' => 'fan', 'FAN08G2160' => 'fan', 'FAN13G2403' => 'fan', 'FAN13G3303' => 'fan', 'FAN15G2435' => 'fan', 'FAN17G0672' => 'fan', 'FAN17G2441' => 'fan', 'FAN18G1024' => 'fan', 'FAN22G1458' => 'fan', 'FAN24G0037' => 'fan', 'FAN24G0429' => 'fan', 'FAN24G2387' => 'fan', 'FAN27G2746' => 'fan', 'FvH4_2g20400' => 'fve', 'FvH4_2g20420' => 'fve', 'FvH4_2g20430' => 'fve', 'FvH4_4g01270' => 'fve', 'FvH4_4g01290' => 'fve', 'FvH4_4g01300' => 'fve', 'FvH4_4g01310' => 'fve', 'FvH4_4g01330' => 'fve', 'FvH4_5g09070' => 'fve', 'Glyma.10G243800' => 'gma', 'Glyma.20G150600' => 'gma', 'Gohir.A09G219200' => 'ghi', 'Gohir.A09G219300' => 'ghi', 'Gohir.D09G221400' => 'ghi', 'Gohir.D09G221500' => 'ghi', 'Gorai.006G242600' => 'gra', 'Gorai.006G242700' => 'gra', 'GSVIVG01018044001' => 'vvi', 'HanXRQChr03g0083821' => 'han', 'HanXRQChr03g0083841' => 'han', 'HanXRQChr03g0083881' => 'han', 'HanXRQChr03g0083901' => 'han', 'HanXRQChr03g0083921' => 'han', 'HanXRQChr03g0085331' => 'han', 'HanXRQChr03g0085361' => 'han', 'HanXRQChr03g0085411' => 'han', 'HanXRQChr03g0085421' => 'han', 'HanXRQChr03g0085431' => 'han', 'HanXRQChr08g0221991' => 'han', 'HanXRQChr11g0336061' => 'han', 'HanXRQChr11g0336411' => 'han', 'Haze_11234' => 'cav', 'Hma1.2p1_0549F.1_g177010' => 'hma', 'Hma1.2p1_0602F.1_g187630' => 'hma', 'Hund14876' => 'sun', 'Hund14879' => 'sun', 'Lalb_Chr06g0160741' => 'lal', 'Lalb_Chr21g0304781' => 'lal', 'Lj3A726G19' => 'lonja', 'Lj3A726T23' => 'lonja', 'Lj3A726T24' => 'lonja', 'Lj3A726T25' => 'lonja', 'Lj3A727T17' => 'lonja', 'Lj3C726T0' => 'lonja', 'Lj3C726T2' => 'lonja', 'Lj3P725T35' => 'lonja', 'Lj3P727T10' => 'lonja', 'Lj3P727T12' => 'lonja', 'Lj3P727T14' => 'lonja', 'Lj5g0023109' => 'lja', 'Lj6P646T44' => 'lonja', 'Lsat_1_v5_gn_6_75760' => 'lsa', 'Lsat_1_v5_gn_6_75800' => 'lsa', 'Lsat_1_v5_gn_6_75900' => 'lsa', 'Lsat_1_v5_gn_6_76240' => 'lsa', 'Lsat_1_v5_gn_6_76441' => 'lsa', 'Lsat_1_v5_gn_6_76700' => 'lsa', 'Lsat_1_v5_gn_6_76760' => 'lsa', 'Manes.15G033100' => 'mes', 'Mapoly0004s0074' => 'mpo', 'Mapoly0004s0075' => 'mpo', 'Mapoly0004s0163' => 'mpo', 'Mapoly0004s0164' => 'mpo', 'Mapoly0021s0018' => 'mpo', 'Mapoly0041s0136' => 'mpo', 'Mapoly0041s0137' => 'mpo', 'Mapoly0041s0138' => 'mpo', 'Mapoly0041s0139' => 'mpo', 'Mapoly0041s0141' => 'mpo', 'Mapoly0041s0142' => 'mpo', 'Mapoly0041s0143' => 'mpo', 'Mapoly0041s0144' => 'mpo', 'Mapoly0041s0145' => 'mpo', 'Mapoly0047s0106' => 'mpo', 'Mapoly0047s0108' => 'mpo', 'Mapoly0050s0051' => 'mpo', 'Mapoly0050s0052' => 'mpo', 'Mapoly0050s0053' => 'mpo', 'Mapoly0058s0013' => 'mpo', 'Mapoly0091s0078' => 'mpo', 'Mapoly0091s0079' => 'mpo', 'Mapoly0091s0080' => 'mpo', 'Mapoly0091s0081' => 'mpo', 'Mapoly0278s0004' => 'mpo', 'Mapoly0278s0005' => 'mpo', 'Mapoly0278s0006' => 'mpo', 'MBI11_g30648_MAGBIO' => 'mbi', 'MCO03G194' => 'mco', 'MCO03G590' => 'mco', 'MCO07G312' => 'mco', 'MCO10G318' => 'mco', 'MCO12G244' => 'mco', 'MCO13G148' => 'mco', 'MCO13G194' => 'mco', 'MCO16G238' => 'mco', 'MD06G1134100' => 'mdo', 'MD13G1200100' => 'mdo', 'MD13G1200300' => 'mdo', 'MD13G1200600' => 'mdo', 'MD14G1150400' => 'mdo', 'MD16G1200000' => 'mdo', 'Medtr1g102570' => 'mtr', 'Medtr1g102780' => 'mtr', 'Medtr1g102800' => 'mtr', 'Medtr1g102810' => 'mtr', 'Medtr1g102830' => 'mtr', 'MELO3C006499.2' => 'cme', 'Migut.G00385' => 'egut', 'MSTRG.4063' => 'ama', 'Nitab4.5_0000090g0260' => 'nta', 'Nitab4.5_0000977g0030' => 'nta', 'Nitab4.5_0002541g0040' => 'nta', 'Nitab4.5_0007068g0040' => 'nta', 'Nn005s41408' => 'nnu', 'Nn005s41410' => 'nnu', 'Oeu010310.1' => 'oeu', 'Oeu010311.1' => 'oeu', 'Oeu043472.1' => 'oeu', 'Os01g0246400' => 'osa', 'Os04g0267950' => 'osa', 'Os07g0178700' => 'osa', 'Os07g0178800' => 'osa', 'Peaxi162Scf00316g00046' => 'pax', 'Peaxi162Scf00316g00049' => 'pax', 'Peaxi162Scf00316g00059' => 'pax', 'Peaxi162Scf00316g00328' => 'pax', 'Peaxi162Scf00316g00329' => 'pax', 'Peaxi162Scf00316g00411' => 'pax', 'Peaxi162Scf00316g00521' => 'pax', 'Peaxi162Scf00492g00068' => 'pax', 'Peaxi162Scf35631g00002' => 'pax', 'PGR142G3720' => 'pgr', 'PGSC0003DMG400006442' => 'stu', 'Phvul.007G062000' => 'pvu', 'Potri.008G157750' => 'ptr', 'Potri.008G157900' => 'ptr', 'Potri.008G158000' => 'ptr', 'Potri.008G158200' => 'ptr', 'Pp3c11_7280' => 'ppa', 'Pp3c11_7980' => 'ppa', 'Pp3c12_19450' => 'ppa', 'Pp3c14_1480' => 'ppa', 'Pp3c14_1501' => 'ppa', 'Pp3c16_4900' => 'ppa', 'Pp3c16_5010' => 'ppa', 'Pp3c16_5060' => 'ppa', 'Pp3c19_18250' => 'ppa', 'Pp3c23_8530' => 'ppa', 'Pp3c23_8550' => 'ppa', 'Pp3c24_9670' => 'ppa', 'Pp3c2_21390' => 'ppa', 'Pp3c2_31380' => 'ppa', 'Pp3c3_16620' => 'ppa', 'Pp3c3_8090' => 'ppa', 'Pp3c3_8110' => 'ppa', 'Pp3c3_8130' => 'ppa', 'Pp3c3_8150' => 'ppa', 'Pp3c4_14320' => 'ppa', 'Pp3c6_2560' => 'ppa', 'Pp3c9_16700' => 'ppa', 'PRCOL_00000234' => 'pco', 'PRCOL_00000235' => 'pco', 'PRCOL_00000777' => 'pco', 'PRCOL_00002344' => 'pco', 'PRCOL_00002372' => 'pco', 'PRCOL_00006120' => 'pco', 'Prupe.1G021400' => 'ppe', 'Prupe.1G021500' => 'ppe', 'Prupe.1G021600' => 'ppe', 'Prupe.1G021700' => 'ppe', 'Prupe.1G021800' => 'ppe', 'Prupe.5G145100' => 'ppe', 'Psat6g204040' => 'psa', 'Psat6g204800' => 'psa', 'Psat6g204920' => 'psa', 'Psat6g204960' => 'psa', 'Psat6g205080' => 'psa', 'PSO017G0271' => 'pso', 'PSO017G1276' => 'pso', 'PSO017G1429' => 'pso', 'PSO017G1861' => 'pso', 'PSO017G2787' => 'pso', 'PSO017G4466' => 'pso', 'PSO017G5118' => 'pso', 'PSO017G5420' => 'pso', 'PSO063G3678' => 'pso', 'PSO210G0546' => 'pso', 'PSO317G0001' => 'pso', 'PSO357G0512' => 'pso', 'PSO478G2682' => 'pso', 'PSO647G0001' => 'pso', 'PSO675G0001' => 'pso', 'PSO675G2699' => 'pso', 'PSO675G2849' => 'pso', 'PSO675G4991' => 'pso', 'PSO689G0001' => 'pso', 'QL06p000916' => 'qlo', 'QL06p000921' => 'qlo', 'QL06p001398' => 'qlo', 'QL06p001407' => 'qlo', 'QL06p002031' => 'qlo', 'RcHm_v2.0_Chr4g0387791' => 'rch', 'RcHm_v2.0_Chr4g0387801' => 'rch', 'RcHm_v2.0_Chr6g0286501' => 'rch', 'RcHm_v2.0_Chr6g0286511' => 'rch', 'RcHm_v2.0_Chr6g0286521' => 'rch', 'RcHm_v2.0_Chr6g0286531' => 'rch', 'RcHm_v2.0_Chr7g0189141' => 'rch', 'Rhsim02G0028700' => 'rsi', 'Rhsim02G0028800' => 'rsi', 'Rhsim02G0028900' => 'rsi', 'Rhsim02G0029000' => 'rsi', 'Rhsim02G0029100' => 'rsi', 'Rhsim02G0029200' => 'rsi', 'Rhsim02G0029300' => 'rsi', 'Rhsim02G0029400' => 'rsi', 'Rhsim02G0029500' => 'rsi', 'Rhsim02G0029600' => 'rsi', 'RhsimUnG0024000' => 'rsi', 'RhsimUnG0024100' => 'rsi', 'RhsimUnG0024200' => 'rsi', 'RhsimUnG0024300' => 'rsi', 'RhsimUnG0024400' => 'rsi', 'RhsimUnG0024500' => 'rsi', 'RhsimUnG0024700' => 'rsi', 'RhsimUnG0024800' => 'rsi', 'RhsimUnG0024900' => 'rsi', 'RhsimUnG0025100' => 'rsi', 'Sabra08G0120200' => 'sbr', 'Sabra08G0120300' => 'sbr', 'Sabra08G0120500' => 'sbr', 'Sabra08G0120600' => 'sbr', 'Sabra10G0158900' => 'sbr', 'SalBow2G3492' => 'sbo', 'Sc13g0004760' => 'sci', 'Sc13g0004770' => 'sci', 'Sed0003417' => 'sed', 'Sed0019750' => 'sed', 'SEGI_03419' => 'sgi', 'SEGI_05907' => 'sgi', 'SEGI_10682' => 'sgi', 'SEGI_13528' => 'sgi', 'SEGI_16081' => 'sgi', 'SEGI_19370' => 'sgi', 'SEGI_21015' => 'sgi', 'SEGI_21944' => 'sgi', 'SEGI_32906' => 'sgi', 'SEGI_33093' => 'sgi', 'SEGI_36110' => 'sgi', 'SEGI_40397' => 'sgi', 'SGA_v2.0_scaffold191G40426' => 'sas', 'SGA_v2.0_scaffold353G49717' => 'sas', 'SGA_v2.0_scaffold50G18550' => 'sas', 'SMO119G0173' => 'smo', 'SMO172G0002' => 'smo', 'Solyc09g082690.3' => 'sly', 'Solyc09g082700.2' => 'sly', 'Sopen09g031550' => 'spe', 'Sopen09g031560' => 'spe', 'Sp3g20540' => 'spa', 'Sp7g07580' => 'spa', 'TAR134G0002' => 'tar', 'TAR236G0001' => 'tar', 'TAR365G0892' => 'tar', 'TAR636G0166' => 'tar', 'TAR636G0646' => 'tar', 'TAR636G0869' => 'tar', 'TAR636G1317' => 'tar', 'TAR636G1744' => 'tar', 'TAR636G3358' => 'tar', 'TAR636G3436' => 'tar', 'THA.LOC104803047' => 'tha', 'Thecc.04G238900' => 'tca', 'Thhalv10021557m.g' => 'esa', 'Thhalv10026318m.g' => 'esa', 'Thhalv10026335m.g' => 'esa', 'TPR.G17433' => 'tpr', 'TPR.G18915' => 'tpr', 'TPR.G26125' => 'tpr', 'TWI09G0677' => 'twi', 'TWI73G0287' => 'twi', 'unitig_748.g8326' => 'ugi', 'vmacro15370' => 'vma', 'vmacro15371' => 'vma', 'vmacro15372' => 'vma', 'vmacro15373' => 'vma', 'vmacro15374' => 'vma', 'VMungo0720G2826' => 'vmu', 'Zm00001eb116960' => 'zma', 'Zm00001eb301260' => 'zma', 'Zm00001eb301270' => 'zma' ), 'gf_id' => 'HOM05D001460', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001460' ), 'data_identifier' => 'HOM05D001460', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001460', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '433', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p22980' => 'bna', 'A01p32340' => 'bna', 'A03p42970' => 'bna', 'A05p25880' => 'bna', 'Aa31LG8G9320' => 'aar', 'Aa31LG8G9330' => 'aar', 'Aa31LG8G9340' => 'aar', 'Aa31sc221G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1034' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1528' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.829' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2222' => 'aag', 'Ah.12g058830' => 'amhyb', 'Ah.12g058840' => 'amhyb', 'AL3G37160' => 'aly', 'AL7G41310' => 'aly', 'Aqoxy5G00395' => 'aox', 'Aqoxy5G00396' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0C8NZA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5185HY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JZ1PRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MD3LS0' => 'arhy', 'AT3G22840' => 'ath', 'AT4G14690' => 'ath', 'ATR0665G054' => 'atr', 'Atru.chr4.2344' => 'acertr', 'Atru.chr4.2346' => 'acertr', 'Atru.chr4.2347' => 'acertr', 'Atru.chr4.2348' => 'acertr', 'Atru.chr4.2355' => 'acertr', 'Atru.chr4.2356' => 'acertr', 'Atru.chr4.2358' => 'acertr', 'Atru.chr4.2359' => 'acertr', 'Atru.chr4.2360' => 'acertr', 'Atru.chr4.2361' => 'acertr', 'AUR62030476' => 'cqu', 'AUR62030478' => 'cqu', 'AUR62030819' => 'cqu', 'AUR62030820' => 'cqu', 'BcaB03g14648' => 'bca', 'BcaB04g20492' => 'bca', 'BcaB06g26399' => 'bca', 'BcaC01g03416' => 'bca', 'BcaC01g03419' => 'bca', 'BcaC01g03421' => 'bca', 'BcaC01g03424' => 'bca', 'BcaC05g28012' => 'bca', 'BcaC09g49212' => 'bca', 'BcaC09g50140' => 'bca', 'BcaNung00346' => 'bca', 'BolC1t02785H' => 'bol', 'BolC1t04095H' => 'bol', 'BolC3t17545H' => 'bol', 'BolC5t32769H' => 'bol', 'BraA01t02211Z' => 'bra', 'BraA01t03359Z' => 'bra', 'BraA03t13441Z' => 'bra', 'BraA05t21476Z' => 'bra', 'C01p28420' => 'bna', 'C01p41350' => 'bna', 'C03p52750' => 'bna', 'C03p52780' => 'bna', 'C05p40270' => 'bna', 'CAN.G1437.9' => 'can', 'CANSAT78G0035' => 'cansat', 'CANSAT78G1036' => 'cansat', 'CANSAT78G2272' => 'cansat', 'CANSAT78G2478' => 'cansat', 'CARHR098700' => 'chi', 'CARHR221120' => 'chi', 'CARHR221150' => 'chi', 'Carub.0003s2297' => 'cru', 'Carub.0007s2749' => 'cru', 'Carub.0007s2750' => 'cru', 'Carub.0007s2751' => 'cru', 'Ca_10849_v3' => 'car', 'Cc03_g04300' => 'ccan', 'CDE02G3648' => 'cde', 'CDE05G0060' => 'cde', 'CDE05G0692' => 'cde', 'CDE05G2285' => 'cde', 'CDE05G2884' => 'cde', 'CDE05G3072' => 'cde', 'Cfa008439' => 'cfa', 'Cfa008441' => 'cfa', 'Cfa008443' => 'cfa', 'Cfa008448' => 'cfa', 'Ciclev10005974m.g' => 'ccl', 'Ciclev10006006m.g' => 'ccl', 'Ciclev10006775m.g' => 'ccl', 'CiPaw.02G120400' => 'cil', 'CiPaw.02G120500' => 'cil', 'CiPaw.02G120600' => 'cil', 'ClCG05G004850' => 'cla', 'COL.COLO4_21566' => 'col', 'Cpa.g.sc44.124' => 'cpa', 'Cre07.g320400' => 'cre', 'Cre07.g320450' => 'cre', 'Cre08.g384650' => 'cre', 'Cre09.g393173' => 'cre', 'Cre09.g394325' => 'cre', 'Cre14.g626750' => 'cre', 'Cre16.g679250' => 'cre', 'CsaV3_3G012890' => 'csa', 'CSS0010865' => 'camsi', 'CSS0044338' => 'camsi', 'DCAR_002366' => 'dca', 'DCAR_030687' => 'dca', 'DCAR_030688' => 'dca', 'Dinv14047' => 'din', 'Dinv14048' => 'din', 'Duzib151G0105' => 'dzi', 'Duzib151G0114' => 'dzi', 'Duzib212G1029' => 'dzi', 'ECA232G3536' => 'eca', 'ECA240G0786' => 'eca', 'ECA240G1802' => 'eca', 'ECA240G3760' => 'eca', 'ECA240G3920' => 'eca', 'EL10Ac5g12536' => 'bvu', 'EL10Ac5g12537' => 'bvu', 'EL10Ac5g12538' => 'bvu', 'Eucgr.B01004' => 'egr', 'Eucgr.B01006' => 'egr', 'Eucgr.B01007' => 'egr', 'Eucgr.B01008' => 'egr', 'Eucgr.B01895' => 'egr', 'Eucgr.B01896' => 'egr', 'FAN04G1456' => 'fan', 'FAN08G1769' => 'fan', 'FAN08G2160' => 'fan', 'FAN13G2403' => 'fan', 'FAN13G3303' => 'fan', 'FAN15G2435' => 'fan', 'FAN17G0672' => 'fan', 'FAN17G2441' => 'fan', 'FAN18G1024' => 'fan', 'FAN22G1458' => 'fan', 'FAN24G0037' => 'fan', 'FAN24G0429' => 'fan', 'FAN24G2387' => 'fan', 'FAN27G2746' => 'fan', 'FvH4_2g20400' => 'fve', 'FvH4_2g20420' => 'fve', 'FvH4_2g20430' => 'fve', 'FvH4_4g01270' => 'fve', 'FvH4_4g01290' => 'fve', 'FvH4_4g01300' => 'fve', 'FvH4_4g01310' => 'fve', 'FvH4_4g01330' => 'fve', 'FvH4_5g09070' => 'fve', 'Glyma.10G243800' => 'gma', 'Glyma.20G150600' => 'gma', 'Gohir.A09G219200' => 'ghi', 'Gohir.A09G219300' => 'ghi', 'Gohir.D09G221400' => 'ghi', 'Gohir.D09G221500' => 'ghi', 'Gorai.006G242600' => 'gra', 'Gorai.006G242700' => 'gra', 'GSVIVG01018044001' => 'vvi', 'HanXRQChr03g0083821' => 'han', 'HanXRQChr03g0083841' => 'han', 'HanXRQChr03g0083881' => 'han', 'HanXRQChr03g0083901' => 'han', 'HanXRQChr03g0083921' => 'han', 'HanXRQChr03g0085331' => 'han', 'HanXRQChr03g0085361' => 'han', 'HanXRQChr03g0085411' => 'han', 'HanXRQChr03g0085421' => 'han', 'HanXRQChr03g0085431' => 'han', 'HanXRQChr08g0221991' => 'han', 'HanXRQChr11g0336061' => 'han', 'HanXRQChr11g0336411' => 'han', 'Haze_11234' => 'cav', 'Hma1.2p1_0549F.1_g177010' => 'hma', 'Hma1.2p1_0602F.1_g187630' => 'hma', 'Hund14876' => 'sun', 'Hund14879' => 'sun', 'Lalb_Chr06g0160741' => 'lal', 'Lalb_Chr21g0304781' => 'lal', 'Lj3A726G19' => 'lonja', 'Lj3A726T23' => 'lonja', 'Lj3A726T24' => 'lonja', 'Lj3A726T25' => 'lonja', 'Lj3A727T17' => 'lonja', 'Lj3C726T0' => 'lonja', 'Lj3C726T2' => 'lonja', 'Lj3P725T35' => 'lonja', 'Lj3P727T10' => 'lonja', 'Lj3P727T12' => 'lonja', 'Lj3P727T14' => 'lonja', 'Lj5g0023109' => 'lja', 'Lj6P646T44' => 'lonja', 'Lsat_1_v5_gn_6_75760' => 'lsa', 'Lsat_1_v5_gn_6_75800' => 'lsa', 'Lsat_1_v5_gn_6_75900' => 'lsa', 'Lsat_1_v5_gn_6_76240' => 'lsa', 'Lsat_1_v5_gn_6_76441' => 'lsa', 'Lsat_1_v5_gn_6_76700' => 'lsa', 'Lsat_1_v5_gn_6_76760' => 'lsa', 'Manes.15G033100' => 'mes', 'Mapoly0004s0074' => 'mpo', 'Mapoly0004s0075' => 'mpo', 'Mapoly0004s0163' => 'mpo', 'Mapoly0004s0164' => 'mpo', 'Mapoly0021s0018' => 'mpo', 'Mapoly0041s0136' => 'mpo', 'Mapoly0041s0137' => 'mpo', 'Mapoly0041s0138' => 'mpo', 'Mapoly0041s0139' => 'mpo', 'Mapoly0041s0141' => 'mpo', 'Mapoly0041s0142' => 'mpo', 'Mapoly0041s0143' => 'mpo', 'Mapoly0041s0144' => 'mpo', 'Mapoly0041s0145' => 'mpo', 'Mapoly0047s0106' => 'mpo', 'Mapoly0047s0108' => 'mpo', 'Mapoly0050s0051' => 'mpo', 'Mapoly0050s0052' => 'mpo', 'Mapoly0050s0053' => 'mpo', 'Mapoly0058s0013' => 'mpo', 'Mapoly0091s0078' => 'mpo', 'Mapoly0091s0079' => 'mpo', 'Mapoly0091s0080' => 'mpo', 'Mapoly0091s0081' => 'mpo', 'Mapoly0278s0004' => 'mpo', 'Mapoly0278s0005' => 'mpo', 'Mapoly0278s0006' => 'mpo', 'MBI11_g30648_MAGBIO' => 'mbi', 'MCO03G194' => 'mco', 'MCO03G590' => 'mco', 'MCO07G312' => 'mco', 'MCO10G318' => 'mco', 'MCO12G244' => 'mco', 'MCO13G148' => 'mco', 'MCO13G194' => 'mco', 'MCO16G238' => 'mco', 'MD06G1134100' => 'mdo', 'MD13G1200100' => 'mdo', 'MD13G1200300' => 'mdo', 'MD13G1200600' => 'mdo', 'MD14G1150400' => 'mdo', 'MD16G1200000' => 'mdo', 'Medtr1g102570' => 'mtr', 'Medtr1g102780' => 'mtr', 'Medtr1g102800' => 'mtr', 'Medtr1g102810' => 'mtr', 'Medtr1g102830' => 'mtr', 'MELO3C006499.2' => 'cme', 'Migut.G00385' => 'egut', 'MSTRG.4063' => 'ama', 'Nitab4.5_0000090g0260' => 'nta', 'Nitab4.5_0000977g0030' => 'nta', 'Nitab4.5_0002541g0040' => 'nta', 'Nitab4.5_0007068g0040' => 'nta', 'Nn005s41408' => 'nnu', 'Nn005s41410' => 'nnu', 'Oeu010310.1' => 'oeu', 'Oeu010311.1' => 'oeu', 'Oeu043472.1' => 'oeu', 'Os01g0246400' => 'osa', 'Os04g0267950' => 'osa', 'Os07g0178700' => 'osa', 'Os07g0178800' => 'osa', 'Peaxi162Scf00316g00046' => 'pax', 'Peaxi162Scf00316g00049' => 'pax', 'Peaxi162Scf00316g00059' => 'pax', 'Peaxi162Scf00316g00328' => 'pax', 'Peaxi162Scf00316g00329' => 'pax', 'Peaxi162Scf00316g00411' => 'pax', 'Peaxi162Scf00316g00521' => 'pax', 'Peaxi162Scf00492g00068' => 'pax', 'Peaxi162Scf35631g00002' => 'pax', 'PGR142G3720' => 'pgr', 'PGSC0003DMG400006442' => 'stu', 'Phvul.007G062000' => 'pvu', 'Potri.008G157750' => 'ptr', 'Potri.008G157900' => 'ptr', 'Potri.008G158000' => 'ptr', 'Potri.008G158200' => 'ptr', 'Pp3c11_7280' => 'ppa', 'Pp3c11_7980' => 'ppa', 'Pp3c12_19450' => 'ppa', 'Pp3c14_1480' => 'ppa', 'Pp3c14_1501' => 'ppa', 'Pp3c16_4900' => 'ppa', 'Pp3c16_5010' => 'ppa', 'Pp3c16_5060' => 'ppa', 'Pp3c19_18250' => 'ppa', 'Pp3c23_8530' => 'ppa', 'Pp3c23_8550' => 'ppa', 'Pp3c24_9670' => 'ppa', 'Pp3c2_21390' => 'ppa', 'Pp3c2_31380' => 'ppa', 'Pp3c3_16620' => 'ppa', 'Pp3c3_8090' => 'ppa', 'Pp3c3_8110' => 'ppa', 'Pp3c3_8130' => 'ppa', 'Pp3c3_8150' => 'ppa', 'Pp3c4_14320' => 'ppa', 'Pp3c6_2560' => 'ppa', 'Pp3c9_16700' => 'ppa', 'PRCOL_00000234' => 'pco', 'PRCOL_00000235' => 'pco', 'PRCOL_00000777' => 'pco', 'PRCOL_00002344' => 'pco', 'PRCOL_00002372' => 'pco', 'PRCOL_00006120' => 'pco', 'Prupe.1G021400' => 'ppe', 'Prupe.1G021500' => 'ppe', 'Prupe.1G021600' => 'ppe', 'Prupe.1G021700' => 'ppe', 'Prupe.1G021800' => 'ppe', 'Prupe.5G145100' => 'ppe', 'Psat6g204040' => 'psa', 'Psat6g204800' => 'psa', 'Psat6g204920' => 'psa', 'Psat6g204960' => 'psa', 'Psat6g205080' => 'psa', 'PSO017G0271' => 'pso', 'PSO017G1276' => 'pso', 'PSO017G1429' => 'pso', 'PSO017G1861' => 'pso', 'PSO017G2787' => 'pso', 'PSO017G4466' => 'pso', 'PSO017G5118' => 'pso', 'PSO017G5420' => 'pso', 'PSO063G3678' => 'pso', 'PSO210G0546' => 'pso', 'PSO317G0001' => 'pso', 'PSO357G0512' => 'pso', 'PSO478G2682' => 'pso', 'PSO647G0001' => 'pso', 'PSO675G0001' => 'pso', 'PSO675G2699' => 'pso', 'PSO675G2849' => 'pso', 'PSO675G4991' => 'pso', 'PSO689G0001' => 'pso', 'QL06p000916' => 'qlo', 'QL06p000921' => 'qlo', 'QL06p001398' => 'qlo', 'QL06p001407' => 'qlo', 'QL06p002031' => 'qlo', 'RcHm_v2.0_Chr4g0387791' => 'rch', 'RcHm_v2.0_Chr4g0387801' => 'rch', 'RcHm_v2.0_Chr6g0286501' => 'rch', 'RcHm_v2.0_Chr6g0286511' => 'rch', 'RcHm_v2.0_Chr6g0286521' => 'rch', 'RcHm_v2.0_Chr6g0286531' => 'rch', 'RcHm_v2.0_Chr7g0189141' => 'rch', 'Rhsim02G0028700' => 'rsi', 'Rhsim02G0028800' => 'rsi', 'Rhsim02G0028900' => 'rsi', 'Rhsim02G0029000' => 'rsi', 'Rhsim02G0029100' => 'rsi', 'Rhsim02G0029200' => 'rsi', 'Rhsim02G0029300' => 'rsi', 'Rhsim02G0029400' => 'rsi', 'Rhsim02G0029500' => 'rsi', 'Rhsim02G0029600' => 'rsi', 'RhsimUnG0024000' => 'rsi', 'RhsimUnG0024100' => 'rsi', 'RhsimUnG0024200' => 'rsi', 'RhsimUnG0024300' => 'rsi', 'RhsimUnG0024400' => 'rsi', 'RhsimUnG0024500' => 'rsi', 'RhsimUnG0024700' => 'rsi', 'RhsimUnG0024800' => 'rsi', 'RhsimUnG0024900' => 'rsi', 'RhsimUnG0025100' => 'rsi', 'Sabra08G0120200' => 'sbr', 'Sabra08G0120300' => 'sbr', 'Sabra08G0120500' => 'sbr', 'Sabra08G0120600' => 'sbr', 'Sabra10G0158900' => 'sbr', 'SalBow2G3492' => 'sbo', 'Sc13g0004760' => 'sci', 'Sc13g0004770' => 'sci', 'Sed0003417' => 'sed', 'Sed0019750' => 'sed', 'SEGI_03419' => 'sgi', 'SEGI_05907' => 'sgi', 'SEGI_10682' => 'sgi', 'SEGI_13528' => 'sgi', 'SEGI_16081' => 'sgi', 'SEGI_19370' => 'sgi', 'SEGI_21015' => 'sgi', 'SEGI_21944' => 'sgi', 'SEGI_32906' => 'sgi', 'SEGI_33093' => 'sgi', 'SEGI_36110' => 'sgi', 'SEGI_40397' => 'sgi', 'SGA_v2.0_scaffold191G40426' => 'sas', 'SGA_v2.0_scaffold353G49717' => 'sas', 'SGA_v2.0_scaffold50G18550' => 'sas', 'SMO119G0173' => 'smo', 'SMO172G0002' => 'smo', 'Solyc09g082690.3' => 'sly', 'Solyc09g082700.2' => 'sly', 'Sopen09g031550' => 'spe', 'Sopen09g031560' => 'spe', 'Sp3g20540' => 'spa', 'Sp7g07580' => 'spa', 'TAR134G0002' => 'tar', 'TAR236G0001' => 'tar', 'TAR365G0892' => 'tar', 'TAR636G0166' => 'tar', 'TAR636G0646' => 'tar', 'TAR636G0869' => 'tar', 'TAR636G1317' => 'tar', 'TAR636G1744' => 'tar', 'TAR636G3358' => 'tar', 'TAR636G3436' => 'tar', 'THA.LOC104803047' => 'tha', 'Thecc.04G238900' => 'tca', 'Thhalv10021557m.g' => 'esa', 'Thhalv10026318m.g' => 'esa', 'Thhalv10026335m.g' => 'esa', 'TPR.G17433' => 'tpr', 'TPR.G18915' => 'tpr', 'TPR.G26125' => 'tpr', 'TWI09G0677' => 'twi', 'TWI73G0287' => 'twi', 'unitig_748.g8326' => 'ugi', 'vmacro15370' => 'vma', 'vmacro15371' => 'vma', 'vmacro15372' => 'vma', 'vmacro15373' => 'vma', 'vmacro15374' => 'vma', 'VMungo0720G2826' => 'vmu', 'Zm00001eb116960' => 'zma', 'Zm00001eb301260' => 'zma', 'Zm00001eb301270' => 'zma' ) $gf_id = 'HOM05D001460' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001460' ) $data_identifier = 'HOM05D001460' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 4, 'aag' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 2, 'aox' => (int) 2, 'arhy' => (int) 4, 'ath' => (int) 2, 'atr' => (int) 1, 'acertr' => (int) 10, 'cqu' => (int) 4, 'bca' => (int) 11, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 1, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 1, 'ccan' => (int) 1, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 1, 'col' => (int) 1, 'cpa' => (int) 1, 'cre' => (int) 7, 'csa' => (int) 1, 'camsi' => (int) 2, 'dca' => (int) 3, 'din' => (int) 2, 'dzi' => (int) 3, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 14, 'fve' => (int) 9, 'gma' => (int) 2, 'ghi' => (int) 4, 'gra' => (int) 2, 'vvi' => (int) 1, 'han' => (int) 13, 'cav' => (int) 1, 'hma' => (int) 2, 'sun' => (int) 2, 'lal' => (int) 2, 'lonja' => (int) 12, 'lja' => (int) 1, 'lsa' => (int) 7, 'mes' => (int) 1, 'mpo' => (int) 27, 'mbi' => (int) 1, 'mco' => (int) 8, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 1, 'egut' => (int) 1, 'ama' => (int) 1, 'nta' => (int) 4, 'nnu' => (int) 2, 'oeu' => (int) 3, 'osa' => (int) 4, 'pax' => (int) 9, 'pgr' => (int) 1, 'stu' => (int) 1, 'pvu' => (int) 1, 'ptr' => (int) 4, 'ppa' => (int) 22, 'pco' => (int) 6, 'ppe' => (int) 6, 'psa' => (int) 5, 'pso' => (int) 19, 'qlo' => (int) 5, 'rch' => (int) 7, 'rsi' => (int) 20, 'sbr' => (int) 5, 'sbo' => (int) 1, 'sci' => (int) 2, 'sed' => (int) 2, 'sgi' => (int) 12, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 2, 'tar' => (int) 10, 'tha' => (int) 1, 'tca' => (int) 1, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 2, 'ugi' => (int) 1, 'vma' => (int) 5, 'vmu' => (int) 1, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb301270' $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' => 'HOM05D001460', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '433', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p22980' => 'bna', 'A01p32340' => 'bna', 'A03p42970' => 'bna', 'A05p25880' => 'bna', 'Aa31LG8G9320' => 'aar', 'Aa31LG8G9330' => 'aar', 'Aa31LG8G9340' => 'aar', 'Aa31sc221G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1034' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1528' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.829' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2222' => 'aag', 'Ah.12g058830' => 'amhyb', 'Ah.12g058840' => 'amhyb', 'AL3G37160' => 'aly', 'AL7G41310' => 'aly', 'Aqoxy5G00395' => 'aox', 'Aqoxy5G00396' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0C8NZA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5185HY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JZ1PRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MD3LS0' => 'arhy', 'AT3G22840' => 'ath', 'AT4G14690' => 'ath', 'ATR0665G054' => 'atr', 'Atru.chr4.2344' => 'acertr', 'Atru.chr4.2346' => 'acertr', 'Atru.chr4.2347' => 'acertr', 'Atru.chr4.2348' => 'acertr', 'Atru.chr4.2355' => 'acertr', 'Atru.chr4.2356' => 'acertr', 'Atru.chr4.2358' => 'acertr', 'Atru.chr4.2359' => 'acertr', 'Atru.chr4.2360' => 'acertr', 'Atru.chr4.2361' => 'acertr', 'AUR62030476' => 'cqu', 'AUR62030478' => 'cqu', 'AUR62030819' => 'cqu', 'AUR62030820' => 'cqu', 'BcaB03g14648' => 'bca', 'BcaB04g20492' => 'bca', 'BcaB06g26399' => 'bca', 'BcaC01g03416' => 'bca', 'BcaC01g03419' => 'bca', 'BcaC01g03421' => 'bca', 'BcaC01g03424' => 'bca', 'BcaC05g28012' => 'bca', 'BcaC09g49212' => 'bca', 'BcaC09g50140' => 'bca', 'BcaNung00346' => 'bca', 'BolC1t02785H' => 'bol', 'BolC1t04095H' => 'bol', 'BolC3t17545H' => 'bol', 'BolC5t32769H' => 'bol', 'BraA01t02211Z' => 'bra', 'BraA01t03359Z' => 'bra', 'BraA03t13441Z' => 'bra', 'BraA05t21476Z' => 'bra', 'C01p28420' => 'bna', 'C01p41350' => 'bna', 'C03p52750' => 'bna', 'C03p52780' => 'bna', 'C05p40270' => 'bna', 'CAN.G1437.9' => 'can', 'CANSAT78G0035' => 'cansat', 'CANSAT78G1036' => 'cansat', 'CANSAT78G2272' => 'cansat', 'CANSAT78G2478' => 'cansat', 'CARHR098700' => 'chi', 'CARHR221120' => 'chi', 'CARHR221150' => 'chi', 'Carub.0003s2297' => 'cru', 'Carub.0007s2749' => 'cru', 'Carub.0007s2750' => 'cru', 'Carub.0007s2751' => 'cru', 'Ca_10849_v3' => 'car', 'Cc03_g04300' => 'ccan', 'CDE02G3648' => 'cde', 'CDE05G0060' => 'cde', 'CDE05G0692' => 'cde', 'CDE05G2285' => 'cde', 'CDE05G2884' => 'cde', 'CDE05G3072' => 'cde', 'Cfa008439' => 'cfa', 'Cfa008441' => 'cfa', 'Cfa008443' => 'cfa', 'Cfa008448' => 'cfa', 'Ciclev10005974m.g' => 'ccl', 'Ciclev10006006m.g' => 'ccl', 'Ciclev10006775m.g' => 'ccl', 'CiPaw.02G120400' => 'cil', 'CiPaw.02G120500' => 'cil', 'CiPaw.02G120600' => 'cil', 'ClCG05G004850' => 'cla', 'COL.COLO4_21566' => 'col', 'Cpa.g.sc44.124' => 'cpa', 'Cre07.g320400' => 'cre', 'Cre07.g320450' => 'cre', 'Cre08.g384650' => 'cre', 'Cre09.g393173' => 'cre', 'Cre09.g394325' => 'cre', 'Cre14.g626750' => 'cre', 'Cre16.g679250' => 'cre', 'CsaV3_3G012890' => 'csa', 'CSS0010865' => 'camsi', 'CSS0044338' => 'camsi', 'DCAR_002366' => 'dca', 'DCAR_030687' => 'dca', 'DCAR_030688' => 'dca', 'Dinv14047' => 'din', 'Dinv14048' => 'din', 'Duzib151G0105' => 'dzi', 'Duzib151G0114' => 'dzi', 'Duzib212G1029' => 'dzi', 'ECA232G3536' => 'eca', 'ECA240G0786' => 'eca', 'ECA240G1802' => 'eca', 'ECA240G3760' => 'eca', 'ECA240G3920' => 'eca', 'EL10Ac5g12536' => 'bvu', 'EL10Ac5g12537' => 'bvu', 'EL10Ac5g12538' => 'bvu', 'Eucgr.B01004' => 'egr', 'Eucgr.B01006' => 'egr', 'Eucgr.B01007' => 'egr', 'Eucgr.B01008' => 'egr', 'Eucgr.B01895' => 'egr', 'Eucgr.B01896' => 'egr', 'FAN04G1456' => 'fan', 'FAN08G1769' => 'fan', 'FAN08G2160' => 'fan', 'FAN13G2403' => 'fan', 'FAN13G3303' => 'fan', 'FAN15G2435' => 'fan', 'FAN17G0672' => 'fan', 'FAN17G2441' => 'fan', 'FAN18G1024' => 'fan', 'FAN22G1458' => 'fan', 'FAN24G0037' => 'fan', 'FAN24G0429' => 'fan', 'FAN24G2387' => 'fan', 'FAN27G2746' => 'fan', 'FvH4_2g20400' => 'fve', 'FvH4_2g20420' => 'fve', 'FvH4_2g20430' => 'fve', 'FvH4_4g01270' => 'fve', 'FvH4_4g01290' => 'fve', 'FvH4_4g01300' => 'fve', 'FvH4_4g01310' => 'fve', 'FvH4_4g01330' => 'fve', 'FvH4_5g09070' => 'fve', 'Glyma.10G243800' => 'gma', 'Glyma.20G150600' => 'gma', 'Gohir.A09G219200' => 'ghi', 'Gohir.A09G219300' => 'ghi', 'Gohir.D09G221400' => 'ghi', 'Gohir.D09G221500' => 'ghi', 'Gorai.006G242600' => 'gra', 'Gorai.006G242700' => 'gra', 'GSVIVG01018044001' => 'vvi', 'HanXRQChr03g0083821' => 'han', 'HanXRQChr03g0083841' => 'han', 'HanXRQChr03g0083881' => 'han', 'HanXRQChr03g0083901' => 'han', 'HanXRQChr03g0083921' => 'han', 'HanXRQChr03g0085331' => 'han', 'HanXRQChr03g0085361' => 'han', 'HanXRQChr03g0085411' => 'han', 'HanXRQChr03g0085421' => 'han', 'HanXRQChr03g0085431' => 'han', 'HanXRQChr08g0221991' => 'han', 'HanXRQChr11g0336061' => 'han', 'HanXRQChr11g0336411' => 'han', 'Haze_11234' => 'cav', 'Hma1.2p1_0549F.1_g177010' => 'hma', 'Hma1.2p1_0602F.1_g187630' => 'hma', 'Hund14876' => 'sun', 'Hund14879' => 'sun', 'Lalb_Chr06g0160741' => 'lal', 'Lalb_Chr21g0304781' => 'lal', 'Lj3A726G19' => 'lonja', 'Lj3A726T23' => 'lonja', 'Lj3A726T24' => 'lonja', 'Lj3A726T25' => 'lonja', 'Lj3A727T17' => 'lonja', 'Lj3C726T0' => 'lonja', 'Lj3C726T2' => 'lonja', 'Lj3P725T35' => 'lonja', 'Lj3P727T10' => 'lonja', 'Lj3P727T12' => 'lonja', 'Lj3P727T14' => 'lonja', 'Lj5g0023109' => 'lja', 'Lj6P646T44' => 'lonja', 'Lsat_1_v5_gn_6_75760' => 'lsa', 'Lsat_1_v5_gn_6_75800' => 'lsa', 'Lsat_1_v5_gn_6_75900' => 'lsa', 'Lsat_1_v5_gn_6_76240' => 'lsa', 'Lsat_1_v5_gn_6_76441' => 'lsa', 'Lsat_1_v5_gn_6_76700' => 'lsa', 'Lsat_1_v5_gn_6_76760' => 'lsa', 'Manes.15G033100' => 'mes', 'Mapoly0004s0074' => 'mpo', 'Mapoly0004s0075' => 'mpo', 'Mapoly0004s0163' => 'mpo', 'Mapoly0004s0164' => 'mpo', 'Mapoly0021s0018' => 'mpo', 'Mapoly0041s0136' => 'mpo', 'Mapoly0041s0137' => 'mpo', 'Mapoly0041s0138' => 'mpo', 'Mapoly0041s0139' => 'mpo', 'Mapoly0041s0141' => 'mpo', 'Mapoly0041s0142' => 'mpo', 'Mapoly0041s0143' => 'mpo', 'Mapoly0041s0144' => 'mpo', 'Mapoly0041s0145' => 'mpo', 'Mapoly0047s0106' => 'mpo', 'Mapoly0047s0108' => 'mpo', 'Mapoly0050s0051' => 'mpo', 'Mapoly0050s0052' => 'mpo', 'Mapoly0050s0053' => 'mpo', 'Mapoly0058s0013' => 'mpo', 'Mapoly0091s0078' => 'mpo', 'Mapoly0091s0079' => 'mpo', 'Mapoly0091s0080' => 'mpo', 'Mapoly0091s0081' => 'mpo', 'Mapoly0278s0004' => 'mpo', 'Mapoly0278s0005' => 'mpo', 'Mapoly0278s0006' => 'mpo', 'MBI11_g30648_MAGBIO' => 'mbi', 'MCO03G194' => 'mco', 'MCO03G590' => 'mco', 'MCO07G312' => 'mco', 'MCO10G318' => 'mco', 'MCO12G244' => 'mco', 'MCO13G148' => 'mco', 'MCO13G194' => 'mco', 'MCO16G238' => 'mco', 'MD06G1134100' => 'mdo', 'MD13G1200100' => 'mdo', 'MD13G1200300' => 'mdo', 'MD13G1200600' => 'mdo', 'MD14G1150400' => 'mdo', 'MD16G1200000' => 'mdo', 'Medtr1g102570' => 'mtr', 'Medtr1g102780' => 'mtr', 'Medtr1g102800' => 'mtr', 'Medtr1g102810' => 'mtr', 'Medtr1g102830' => 'mtr', 'MELO3C006499.2' => 'cme', 'Migut.G00385' => 'egut', 'MSTRG.4063' => 'ama', 'Nitab4.5_0000090g0260' => 'nta', 'Nitab4.5_0000977g0030' => 'nta', 'Nitab4.5_0002541g0040' => 'nta', 'Nitab4.5_0007068g0040' => 'nta', 'Nn005s41408' => 'nnu', 'Nn005s41410' => 'nnu', 'Oeu010310.1' => 'oeu', 'Oeu010311.1' => 'oeu', 'Oeu043472.1' => 'oeu', 'Os01g0246400' => 'osa', 'Os04g0267950' => 'osa', 'Os07g0178700' => 'osa', 'Os07g0178800' => 'osa', 'Peaxi162Scf00316g00046' => 'pax', 'Peaxi162Scf00316g00049' => 'pax', 'Peaxi162Scf00316g00059' => 'pax', 'Peaxi162Scf00316g00328' => 'pax', 'Peaxi162Scf00316g00329' => 'pax', 'Peaxi162Scf00316g00411' => 'pax', 'Peaxi162Scf00316g00521' => 'pax', 'Peaxi162Scf00492g00068' => 'pax', 'Peaxi162Scf35631g00002' => 'pax', 'PGR142G3720' => 'pgr', 'PGSC0003DMG400006442' => 'stu', 'Phvul.007G062000' => 'pvu', 'Potri.008G157750' => 'ptr', 'Potri.008G157900' => 'ptr', 'Potri.008G158000' => 'ptr', 'Potri.008G158200' => 'ptr', 'Pp3c11_7280' => 'ppa', 'Pp3c11_7980' => 'ppa', 'Pp3c12_19450' => 'ppa', 'Pp3c14_1480' => 'ppa', 'Pp3c14_1501' => 'ppa', 'Pp3c16_4900' => 'ppa', 'Pp3c16_5010' => 'ppa', 'Pp3c16_5060' => 'ppa', 'Pp3c19_18250' => 'ppa', 'Pp3c23_8530' => 'ppa', 'Pp3c23_8550' => 'ppa', 'Pp3c24_9670' => 'ppa', 'Pp3c2_21390' => 'ppa', 'Pp3c2_31380' => 'ppa', 'Pp3c3_16620' => 'ppa', 'Pp3c3_8090' => 'ppa', 'Pp3c3_8110' => 'ppa', 'Pp3c3_8130' => 'ppa', 'Pp3c3_8150' => 'ppa', 'Pp3c4_14320' => 'ppa', 'Pp3c6_2560' => 'ppa', 'Pp3c9_16700' => 'ppa', 'PRCOL_00000234' => 'pco', 'PRCOL_00000235' => 'pco', 'PRCOL_00000777' => 'pco', 'PRCOL_00002344' => 'pco', 'PRCOL_00002372' => 'pco', 'PRCOL_00006120' => 'pco', 'Prupe.1G021400' => 'ppe', 'Prupe.1G021500' => 'ppe', 'Prupe.1G021600' => 'ppe', 'Prupe.1G021700' => 'ppe', 'Prupe.1G021800' => 'ppe', 'Prupe.5G145100' => 'ppe', 'Psat6g204040' => 'psa', 'Psat6g204800' => 'psa', 'Psat6g204920' => 'psa', 'Psat6g204960' => 'psa', 'Psat6g205080' => 'psa', 'PSO017G0271' => 'pso', 'PSO017G1276' => 'pso', 'PSO017G1429' => 'pso', 'PSO017G1861' => 'pso', 'PSO017G2787' => 'pso', 'PSO017G4466' => 'pso', 'PSO017G5118' => 'pso', 'PSO017G5420' => 'pso', 'PSO063G3678' => 'pso', 'PSO210G0546' => 'pso', 'PSO317G0001' => 'pso', 'PSO357G0512' => 'pso', 'PSO478G2682' => 'pso', 'PSO647G0001' => 'pso', 'PSO675G0001' => 'pso', 'PSO675G2699' => 'pso', 'PSO675G2849' => 'pso', 'PSO675G4991' => 'pso', 'PSO689G0001' => 'pso', 'QL06p000916' => 'qlo', 'QL06p000921' => 'qlo', 'QL06p001398' => 'qlo', 'QL06p001407' => 'qlo', 'QL06p002031' => 'qlo', 'RcHm_v2.0_Chr4g0387791' => 'rch', 'RcHm_v2.0_Chr4g0387801' => 'rch', 'RcHm_v2.0_Chr6g0286501' => 'rch', 'RcHm_v2.0_Chr6g0286511' => 'rch', 'RcHm_v2.0_Chr6g0286521' => 'rch', 'RcHm_v2.0_Chr6g0286531' => 'rch', 'RcHm_v2.0_Chr7g0189141' => 'rch', 'Rhsim02G0028700' => 'rsi', 'Rhsim02G0028800' => 'rsi', 'Rhsim02G0028900' => 'rsi', 'Rhsim02G0029000' => 'rsi', 'Rhsim02G0029100' => 'rsi', 'Rhsim02G0029200' => 'rsi', 'Rhsim02G0029300' => 'rsi', 'Rhsim02G0029400' => 'rsi', 'Rhsim02G0029500' => 'rsi', 'Rhsim02G0029600' => 'rsi', 'RhsimUnG0024000' => 'rsi', 'RhsimUnG0024100' => 'rsi', 'RhsimUnG0024200' => 'rsi', 'RhsimUnG0024300' => 'rsi', 'RhsimUnG0024400' => 'rsi', 'RhsimUnG0024500' => 'rsi', 'RhsimUnG0024700' => 'rsi', 'RhsimUnG0024800' => 'rsi', 'RhsimUnG0024900' => 'rsi', 'RhsimUnG0025100' => 'rsi', 'Sabra08G0120200' => 'sbr', 'Sabra08G0120300' => 'sbr', 'Sabra08G0120500' => 'sbr', 'Sabra08G0120600' => 'sbr', 'Sabra10G0158900' => 'sbr', 'SalBow2G3492' => 'sbo', 'Sc13g0004760' => 'sci', 'Sc13g0004770' => 'sci', 'Sed0003417' => 'sed', 'Sed0019750' => 'sed', 'SEGI_03419' => 'sgi', 'SEGI_05907' => 'sgi', 'SEGI_10682' => 'sgi', 'SEGI_13528' => 'sgi', 'SEGI_16081' => 'sgi', 'SEGI_19370' => 'sgi', 'SEGI_21015' => 'sgi', 'SEGI_21944' => 'sgi', 'SEGI_32906' => 'sgi', 'SEGI_33093' => 'sgi', 'SEGI_36110' => 'sgi', 'SEGI_40397' => 'sgi', 'SGA_v2.0_scaffold191G40426' => 'sas', 'SGA_v2.0_scaffold353G49717' => 'sas', 'SGA_v2.0_scaffold50G18550' => 'sas', 'SMO119G0173' => 'smo', 'SMO172G0002' => 'smo', 'Solyc09g082690.3' => 'sly', 'Solyc09g082700.2' => 'sly', 'Sopen09g031550' => 'spe', 'Sopen09g031560' => 'spe', 'Sp3g20540' => 'spa', 'Sp7g07580' => 'spa', 'TAR134G0002' => 'tar', 'TAR236G0001' => 'tar', 'TAR365G0892' => 'tar', 'TAR636G0166' => 'tar', 'TAR636G0646' => 'tar', 'TAR636G0869' => 'tar', 'TAR636G1317' => 'tar', 'TAR636G1744' => 'tar', 'TAR636G3358' => 'tar', 'TAR636G3436' => 'tar', 'THA.LOC104803047' => 'tha', 'Thecc.04G238900' => 'tca', 'Thhalv10021557m.g' => 'esa', 'Thhalv10026318m.g' => 'esa', 'Thhalv10026335m.g' => 'esa', 'TPR.G17433' => 'tpr', 'TPR.G18915' => 'tpr', 'TPR.G26125' => 'tpr', 'TWI09G0677' => 'twi', 'TWI73G0287' => 'twi', 'unitig_748.g8326' => 'ugi', 'vmacro15370' => 'vma', 'vmacro15371' => 'vma', 'vmacro15372' => 'vma', 'vmacro15373' => 'vma', 'vmacro15374' => 'vma', 'VMungo0720G2826' => 'vmu', 'Zm00001eb116960' => 'zma', 'Zm00001eb301260' => 'zma', 'Zm00001eb301270' => 'zma' ), 'gf_id' => 'HOM05D001460', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001460' ), 'data_identifier' => 'HOM05D001460', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001460', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '433', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p22980' => 'bna', 'A01p32340' => 'bna', 'A03p42970' => 'bna', 'A05p25880' => 'bna', 'Aa31LG8G9320' => 'aar', 'Aa31LG8G9330' => 'aar', 'Aa31LG8G9340' => 'aar', 'Aa31sc221G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1034' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1528' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.829' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2222' => 'aag', 'Ah.12g058830' => 'amhyb', 'Ah.12g058840' => 'amhyb', 'AL3G37160' => 'aly', 'AL7G41310' => 'aly', 'Aqoxy5G00395' => 'aox', 'Aqoxy5G00396' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0C8NZA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5185HY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JZ1PRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MD3LS0' => 'arhy', 'AT3G22840' => 'ath', 'AT4G14690' => 'ath', 'ATR0665G054' => 'atr', 'Atru.chr4.2344' => 'acertr', 'Atru.chr4.2346' => 'acertr', 'Atru.chr4.2347' => 'acertr', 'Atru.chr4.2348' => 'acertr', 'Atru.chr4.2355' => 'acertr', 'Atru.chr4.2356' => 'acertr', 'Atru.chr4.2358' => 'acertr', 'Atru.chr4.2359' => 'acertr', 'Atru.chr4.2360' => 'acertr', 'Atru.chr4.2361' => 'acertr', 'AUR62030476' => 'cqu', 'AUR62030478' => 'cqu', 'AUR62030819' => 'cqu', 'AUR62030820' => 'cqu', 'BcaB03g14648' => 'bca', 'BcaB04g20492' => 'bca', 'BcaB06g26399' => 'bca', 'BcaC01g03416' => 'bca', 'BcaC01g03419' => 'bca', 'BcaC01g03421' => 'bca', 'BcaC01g03424' => 'bca', 'BcaC05g28012' => 'bca', 'BcaC09g49212' => 'bca', 'BcaC09g50140' => 'bca', 'BcaNung00346' => 'bca', 'BolC1t02785H' => 'bol', 'BolC1t04095H' => 'bol', 'BolC3t17545H' => 'bol', 'BolC5t32769H' => 'bol', 'BraA01t02211Z' => 'bra', 'BraA01t03359Z' => 'bra', 'BraA03t13441Z' => 'bra', 'BraA05t21476Z' => 'bra', 'C01p28420' => 'bna', 'C01p41350' => 'bna', 'C03p52750' => 'bna', 'C03p52780' => 'bna', 'C05p40270' => 'bna', 'CAN.G1437.9' => 'can', 'CANSAT78G0035' => 'cansat', 'CANSAT78G1036' => 'cansat', 'CANSAT78G2272' => 'cansat', 'CANSAT78G2478' => 'cansat', 'CARHR098700' => 'chi', 'CARHR221120' => 'chi', 'CARHR221150' => 'chi', 'Carub.0003s2297' => 'cru', 'Carub.0007s2749' => 'cru', 'Carub.0007s2750' => 'cru', 'Carub.0007s2751' => 'cru', 'Ca_10849_v3' => 'car', 'Cc03_g04300' => 'ccan', 'CDE02G3648' => 'cde', 'CDE05G0060' => 'cde', 'CDE05G0692' => 'cde', 'CDE05G2285' => 'cde', 'CDE05G2884' => 'cde', 'CDE05G3072' => 'cde', 'Cfa008439' => 'cfa', 'Cfa008441' => 'cfa', 'Cfa008443' => 'cfa', 'Cfa008448' => 'cfa', 'Ciclev10005974m.g' => 'ccl', 'Ciclev10006006m.g' => 'ccl', 'Ciclev10006775m.g' => 'ccl', 'CiPaw.02G120400' => 'cil', 'CiPaw.02G120500' => 'cil', 'CiPaw.02G120600' => 'cil', 'ClCG05G004850' => 'cla', 'COL.COLO4_21566' => 'col', 'Cpa.g.sc44.124' => 'cpa', 'Cre07.g320400' => 'cre', 'Cre07.g320450' => 'cre', 'Cre08.g384650' => 'cre', 'Cre09.g393173' => 'cre', 'Cre09.g394325' => 'cre', 'Cre14.g626750' => 'cre', 'Cre16.g679250' => 'cre', 'CsaV3_3G012890' => 'csa', 'CSS0010865' => 'camsi', 'CSS0044338' => 'camsi', 'DCAR_002366' => 'dca', 'DCAR_030687' => 'dca', 'DCAR_030688' => 'dca', 'Dinv14047' => 'din', 'Dinv14048' => 'din', 'Duzib151G0105' => 'dzi', 'Duzib151G0114' => 'dzi', 'Duzib212G1029' => 'dzi', 'ECA232G3536' => 'eca', 'ECA240G0786' => 'eca', 'ECA240G1802' => 'eca', 'ECA240G3760' => 'eca', 'ECA240G3920' => 'eca', 'EL10Ac5g12536' => 'bvu', 'EL10Ac5g12537' => 'bvu', 'EL10Ac5g12538' => 'bvu', 'Eucgr.B01004' => 'egr', 'Eucgr.B01006' => 'egr', 'Eucgr.B01007' => 'egr', 'Eucgr.B01008' => 'egr', 'Eucgr.B01895' => 'egr', 'Eucgr.B01896' => 'egr', 'FAN04G1456' => 'fan', 'FAN08G1769' => 'fan', 'FAN08G2160' => 'fan', 'FAN13G2403' => 'fan', 'FAN13G3303' => 'fan', 'FAN15G2435' => 'fan', 'FAN17G0672' => 'fan', 'FAN17G2441' => 'fan', 'FAN18G1024' => 'fan', 'FAN22G1458' => 'fan', 'FAN24G0037' => 'fan', 'FAN24G0429' => 'fan', 'FAN24G2387' => 'fan', 'FAN27G2746' => 'fan', 'FvH4_2g20400' => 'fve', 'FvH4_2g20420' => 'fve', 'FvH4_2g20430' => 'fve', 'FvH4_4g01270' => 'fve', 'FvH4_4g01290' => 'fve', 'FvH4_4g01300' => 'fve', 'FvH4_4g01310' => 'fve', 'FvH4_4g01330' => 'fve', 'FvH4_5g09070' => 'fve', 'Glyma.10G243800' => 'gma', 'Glyma.20G150600' => 'gma', 'Gohir.A09G219200' => 'ghi', 'Gohir.A09G219300' => 'ghi', 'Gohir.D09G221400' => 'ghi', 'Gohir.D09G221500' => 'ghi', 'Gorai.006G242600' => 'gra', 'Gorai.006G242700' => 'gra', 'GSVIVG01018044001' => 'vvi', 'HanXRQChr03g0083821' => 'han', 'HanXRQChr03g0083841' => 'han', 'HanXRQChr03g0083881' => 'han', 'HanXRQChr03g0083901' => 'han', 'HanXRQChr03g0083921' => 'han', 'HanXRQChr03g0085331' => 'han', 'HanXRQChr03g0085361' => 'han', 'HanXRQChr03g0085411' => 'han', 'HanXRQChr03g0085421' => 'han', 'HanXRQChr03g0085431' => 'han', 'HanXRQChr08g0221991' => 'han', 'HanXRQChr11g0336061' => 'han', 'HanXRQChr11g0336411' => 'han', 'Haze_11234' => 'cav', 'Hma1.2p1_0549F.1_g177010' => 'hma', 'Hma1.2p1_0602F.1_g187630' => 'hma', 'Hund14876' => 'sun', 'Hund14879' => 'sun', 'Lalb_Chr06g0160741' => 'lal', 'Lalb_Chr21g0304781' => 'lal', 'Lj3A726G19' => 'lonja', 'Lj3A726T23' => 'lonja', 'Lj3A726T24' => 'lonja', 'Lj3A726T25' => 'lonja', 'Lj3A727T17' => 'lonja', 'Lj3C726T0' => 'lonja', 'Lj3C726T2' => 'lonja', 'Lj3P725T35' => 'lonja', 'Lj3P727T10' => 'lonja', 'Lj3P727T12' => 'lonja', 'Lj3P727T14' => 'lonja', 'Lj5g0023109' => 'lja', 'Lj6P646T44' => 'lonja', 'Lsat_1_v5_gn_6_75760' => 'lsa', 'Lsat_1_v5_gn_6_75800' => 'lsa', 'Lsat_1_v5_gn_6_75900' => 'lsa', 'Lsat_1_v5_gn_6_76240' => 'lsa', 'Lsat_1_v5_gn_6_76441' => 'lsa', 'Lsat_1_v5_gn_6_76700' => 'lsa', 'Lsat_1_v5_gn_6_76760' => 'lsa', 'Manes.15G033100' => 'mes', 'Mapoly0004s0074' => 'mpo', 'Mapoly0004s0075' => 'mpo', 'Mapoly0004s0163' => 'mpo', 'Mapoly0004s0164' => 'mpo', 'Mapoly0021s0018' => 'mpo', 'Mapoly0041s0136' => 'mpo', 'Mapoly0041s0137' => 'mpo', 'Mapoly0041s0138' => 'mpo', 'Mapoly0041s0139' => 'mpo', 'Mapoly0041s0141' => 'mpo', 'Mapoly0041s0142' => 'mpo', 'Mapoly0041s0143' => 'mpo', 'Mapoly0041s0144' => 'mpo', 'Mapoly0041s0145' => 'mpo', 'Mapoly0047s0106' => 'mpo', 'Mapoly0047s0108' => 'mpo', 'Mapoly0050s0051' => 'mpo', 'Mapoly0050s0052' => 'mpo', 'Mapoly0050s0053' => 'mpo', 'Mapoly0058s0013' => 'mpo', 'Mapoly0091s0078' => 'mpo', 'Mapoly0091s0079' => 'mpo', 'Mapoly0091s0080' => 'mpo', 'Mapoly0091s0081' => 'mpo', 'Mapoly0278s0004' => 'mpo', 'Mapoly0278s0005' => 'mpo', 'Mapoly0278s0006' => 'mpo', 'MBI11_g30648_MAGBIO' => 'mbi', 'MCO03G194' => 'mco', 'MCO03G590' => 'mco', 'MCO07G312' => 'mco', 'MCO10G318' => 'mco', 'MCO12G244' => 'mco', 'MCO13G148' => 'mco', 'MCO13G194' => 'mco', 'MCO16G238' => 'mco', 'MD06G1134100' => 'mdo', 'MD13G1200100' => 'mdo', 'MD13G1200300' => 'mdo', 'MD13G1200600' => 'mdo', 'MD14G1150400' => 'mdo', 'MD16G1200000' => 'mdo', 'Medtr1g102570' => 'mtr', 'Medtr1g102780' => 'mtr', 'Medtr1g102800' => 'mtr', 'Medtr1g102810' => 'mtr', 'Medtr1g102830' => 'mtr', 'MELO3C006499.2' => 'cme', 'Migut.G00385' => 'egut', 'MSTRG.4063' => 'ama', 'Nitab4.5_0000090g0260' => 'nta', 'Nitab4.5_0000977g0030' => 'nta', 'Nitab4.5_0002541g0040' => 'nta', 'Nitab4.5_0007068g0040' => 'nta', 'Nn005s41408' => 'nnu', 'Nn005s41410' => 'nnu', 'Oeu010310.1' => 'oeu', 'Oeu010311.1' => 'oeu', 'Oeu043472.1' => 'oeu', 'Os01g0246400' => 'osa', 'Os04g0267950' => 'osa', 'Os07g0178700' => 'osa', 'Os07g0178800' => 'osa', 'Peaxi162Scf00316g00046' => 'pax', 'Peaxi162Scf00316g00049' => 'pax', 'Peaxi162Scf00316g00059' => 'pax', 'Peaxi162Scf00316g00328' => 'pax', 'Peaxi162Scf00316g00329' => 'pax', 'Peaxi162Scf00316g00411' => 'pax', 'Peaxi162Scf00316g00521' => 'pax', 'Peaxi162Scf00492g00068' => 'pax', 'Peaxi162Scf35631g00002' => 'pax', 'PGR142G3720' => 'pgr', 'PGSC0003DMG400006442' => 'stu', 'Phvul.007G062000' => 'pvu', 'Potri.008G157750' => 'ptr', 'Potri.008G157900' => 'ptr', 'Potri.008G158000' => 'ptr', 'Potri.008G158200' => 'ptr', 'Pp3c11_7280' => 'ppa', 'Pp3c11_7980' => 'ppa', 'Pp3c12_19450' => 'ppa', 'Pp3c14_1480' => 'ppa', 'Pp3c14_1501' => 'ppa', 'Pp3c16_4900' => 'ppa', 'Pp3c16_5010' => 'ppa', 'Pp3c16_5060' => 'ppa', 'Pp3c19_18250' => 'ppa', 'Pp3c23_8530' => 'ppa', 'Pp3c23_8550' => 'ppa', 'Pp3c24_9670' => 'ppa', 'Pp3c2_21390' => 'ppa', 'Pp3c2_31380' => 'ppa', 'Pp3c3_16620' => 'ppa', 'Pp3c3_8090' => 'ppa', 'Pp3c3_8110' => 'ppa', 'Pp3c3_8130' => 'ppa', 'Pp3c3_8150' => 'ppa', 'Pp3c4_14320' => 'ppa', 'Pp3c6_2560' => 'ppa', 'Pp3c9_16700' => 'ppa', 'PRCOL_00000234' => 'pco', 'PRCOL_00000235' => 'pco', 'PRCOL_00000777' => 'pco', 'PRCOL_00002344' => 'pco', 'PRCOL_00002372' => 'pco', 'PRCOL_00006120' => 'pco', 'Prupe.1G021400' => 'ppe', 'Prupe.1G021500' => 'ppe', 'Prupe.1G021600' => 'ppe', 'Prupe.1G021700' => 'ppe', 'Prupe.1G021800' => 'ppe', 'Prupe.5G145100' => 'ppe', 'Psat6g204040' => 'psa', 'Psat6g204800' => 'psa', 'Psat6g204920' => 'psa', 'Psat6g204960' => 'psa', 'Psat6g205080' => 'psa', 'PSO017G0271' => 'pso', 'PSO017G1276' => 'pso', 'PSO017G1429' => 'pso', 'PSO017G1861' => 'pso', 'PSO017G2787' => 'pso', 'PSO017G4466' => 'pso', 'PSO017G5118' => 'pso', 'PSO017G5420' => 'pso', 'PSO063G3678' => 'pso', 'PSO210G0546' => 'pso', 'PSO317G0001' => 'pso', 'PSO357G0512' => 'pso', 'PSO478G2682' => 'pso', 'PSO647G0001' => 'pso', 'PSO675G0001' => 'pso', 'PSO675G2699' => 'pso', 'PSO675G2849' => 'pso', 'PSO675G4991' => 'pso', 'PSO689G0001' => 'pso', 'QL06p000916' => 'qlo', 'QL06p000921' => 'qlo', 'QL06p001398' => 'qlo', 'QL06p001407' => 'qlo', 'QL06p002031' => 'qlo', 'RcHm_v2.0_Chr4g0387791' => 'rch', 'RcHm_v2.0_Chr4g0387801' => 'rch', 'RcHm_v2.0_Chr6g0286501' => 'rch', 'RcHm_v2.0_Chr6g0286511' => 'rch', 'RcHm_v2.0_Chr6g0286521' => 'rch', 'RcHm_v2.0_Chr6g0286531' => 'rch', 'RcHm_v2.0_Chr7g0189141' => 'rch', 'Rhsim02G0028700' => 'rsi', 'Rhsim02G0028800' => 'rsi', 'Rhsim02G0028900' => 'rsi', 'Rhsim02G0029000' => 'rsi', 'Rhsim02G0029100' => 'rsi', 'Rhsim02G0029200' => 'rsi', 'Rhsim02G0029300' => 'rsi', 'Rhsim02G0029400' => 'rsi', 'Rhsim02G0029500' => 'rsi', 'Rhsim02G0029600' => 'rsi', 'RhsimUnG0024000' => 'rsi', 'RhsimUnG0024100' => 'rsi', 'RhsimUnG0024200' => 'rsi', 'RhsimUnG0024300' => 'rsi', 'RhsimUnG0024400' => 'rsi', 'RhsimUnG0024500' => 'rsi', 'RhsimUnG0024700' => 'rsi', 'RhsimUnG0024800' => 'rsi', 'RhsimUnG0024900' => 'rsi', 'RhsimUnG0025100' => 'rsi', 'Sabra08G0120200' => 'sbr', 'Sabra08G0120300' => 'sbr', 'Sabra08G0120500' => 'sbr', 'Sabra08G0120600' => 'sbr', 'Sabra10G0158900' => 'sbr', 'SalBow2G3492' => 'sbo', 'Sc13g0004760' => 'sci', 'Sc13g0004770' => 'sci', 'Sed0003417' => 'sed', 'Sed0019750' => 'sed', 'SEGI_03419' => 'sgi', 'SEGI_05907' => 'sgi', 'SEGI_10682' => 'sgi', 'SEGI_13528' => 'sgi', 'SEGI_16081' => 'sgi', 'SEGI_19370' => 'sgi', 'SEGI_21015' => 'sgi', 'SEGI_21944' => 'sgi', 'SEGI_32906' => 'sgi', 'SEGI_33093' => 'sgi', 'SEGI_36110' => 'sgi', 'SEGI_40397' => 'sgi', 'SGA_v2.0_scaffold191G40426' => 'sas', 'SGA_v2.0_scaffold353G49717' => 'sas', 'SGA_v2.0_scaffold50G18550' => 'sas', 'SMO119G0173' => 'smo', 'SMO172G0002' => 'smo', 'Solyc09g082690.3' => 'sly', 'Solyc09g082700.2' => 'sly', 'Sopen09g031550' => 'spe', 'Sopen09g031560' => 'spe', 'Sp3g20540' => 'spa', 'Sp7g07580' => 'spa', 'TAR134G0002' => 'tar', 'TAR236G0001' => 'tar', 'TAR365G0892' => 'tar', 'TAR636G0166' => 'tar', 'TAR636G0646' => 'tar', 'TAR636G0869' => 'tar', 'TAR636G1317' => 'tar', 'TAR636G1744' => 'tar', 'TAR636G3358' => 'tar', 'TAR636G3436' => 'tar', 'THA.LOC104803047' => 'tha', 'Thecc.04G238900' => 'tca', 'Thhalv10021557m.g' => 'esa', 'Thhalv10026318m.g' => 'esa', 'Thhalv10026335m.g' => 'esa', 'TPR.G17433' => 'tpr', 'TPR.G18915' => 'tpr', 'TPR.G26125' => 'tpr', 'TWI09G0677' => 'twi', 'TWI73G0287' => 'twi', 'unitig_748.g8326' => 'ugi', 'vmacro15370' => 'vma', 'vmacro15371' => 'vma', 'vmacro15372' => 'vma', 'vmacro15373' => 'vma', 'vmacro15374' => 'vma', 'VMungo0720G2826' => 'vmu', 'Zm00001eb116960' => 'zma', 'Zm00001eb301260' => 'zma', 'Zm00001eb301270' => 'zma' ) $gf_id = 'HOM05D001460' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001460' ) $data_identifier = 'HOM05D001460' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 4, 'aag' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 2, 'aox' => (int) 2, 'arhy' => (int) 4, 'ath' => (int) 2, 'atr' => (int) 1, 'acertr' => (int) 10, 'cqu' => (int) 4, 'bca' => (int) 11, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 1, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 1, 'ccan' => (int) 1, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 1, 'col' => (int) 1, 'cpa' => (int) 1, 'cre' => (int) 7, 'csa' => (int) 1, 'camsi' => (int) 2, 'dca' => (int) 3, 'din' => (int) 2, 'dzi' => (int) 3, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 14, 'fve' => (int) 9, 'gma' => (int) 2, 'ghi' => (int) 4, 'gra' => (int) 2, 'vvi' => (int) 1, 'han' => (int) 13, 'cav' => (int) 1, 'hma' => (int) 2, 'sun' => (int) 2, 'lal' => (int) 2, 'lonja' => (int) 12, 'lja' => (int) 1, 'lsa' => (int) 7, 'mes' => (int) 1, 'mpo' => (int) 27, 'mbi' => (int) 1, 'mco' => (int) 8, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 1, 'egut' => (int) 1, 'ama' => (int) 1, 'nta' => (int) 4, 'nnu' => (int) 2, 'oeu' => (int) 3, 'osa' => (int) 4, 'pax' => (int) 9, 'pgr' => (int) 1, 'stu' => (int) 1, 'pvu' => (int) 1, 'ptr' => (int) 4, 'ppa' => (int) 22, 'pco' => (int) 6, 'ppe' => (int) 6, 'psa' => (int) 5, 'pso' => (int) 19, 'qlo' => (int) 5, 'rch' => (int) 7, 'rsi' => (int) 20, 'sbr' => (int) 5, 'sbo' => (int) 1, 'sci' => (int) 2, 'sed' => (int) 2, 'sgi' => (int) 12, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 2, 'tar' => (int) 10, 'tha' => (int) 1, 'tca' => (int) 1, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 2, 'ugi' => (int) 1, 'vma' => (int) 5, 'vmu' => (int) 1, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb301270' $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' => 'HOM05D001460', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '433', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p22980' => 'bna', 'A01p32340' => 'bna', 'A03p42970' => 'bna', 'A05p25880' => 'bna', 'Aa31LG8G9320' => 'aar', 'Aa31LG8G9330' => 'aar', 'Aa31LG8G9340' => 'aar', 'Aa31sc221G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1034' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1528' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.829' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2222' => 'aag', 'Ah.12g058830' => 'amhyb', 'Ah.12g058840' => 'amhyb', 'AL3G37160' => 'aly', 'AL7G41310' => 'aly', 'Aqoxy5G00395' => 'aox', 'Aqoxy5G00396' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0C8NZA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5185HY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JZ1PRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MD3LS0' => 'arhy', 'AT3G22840' => 'ath', 'AT4G14690' => 'ath', 'ATR0665G054' => 'atr', 'Atru.chr4.2344' => 'acertr', 'Atru.chr4.2346' => 'acertr', 'Atru.chr4.2347' => 'acertr', 'Atru.chr4.2348' => 'acertr', 'Atru.chr4.2355' => 'acertr', 'Atru.chr4.2356' => 'acertr', 'Atru.chr4.2358' => 'acertr', 'Atru.chr4.2359' => 'acertr', 'Atru.chr4.2360' => 'acertr', 'Atru.chr4.2361' => 'acertr', 'AUR62030476' => 'cqu', 'AUR62030478' => 'cqu', 'AUR62030819' => 'cqu', 'AUR62030820' => 'cqu', 'BcaB03g14648' => 'bca', 'BcaB04g20492' => 'bca', 'BcaB06g26399' => 'bca', 'BcaC01g03416' => 'bca', 'BcaC01g03419' => 'bca', 'BcaC01g03421' => 'bca', 'BcaC01g03424' => 'bca', 'BcaC05g28012' => 'bca', 'BcaC09g49212' => 'bca', 'BcaC09g50140' => 'bca', 'BcaNung00346' => 'bca', 'BolC1t02785H' => 'bol', 'BolC1t04095H' => 'bol', 'BolC3t17545H' => 'bol', 'BolC5t32769H' => 'bol', 'BraA01t02211Z' => 'bra', 'BraA01t03359Z' => 'bra', 'BraA03t13441Z' => 'bra', 'BraA05t21476Z' => 'bra', 'C01p28420' => 'bna', 'C01p41350' => 'bna', 'C03p52750' => 'bna', 'C03p52780' => 'bna', 'C05p40270' => 'bna', 'CAN.G1437.9' => 'can', 'CANSAT78G0035' => 'cansat', 'CANSAT78G1036' => 'cansat', 'CANSAT78G2272' => 'cansat', 'CANSAT78G2478' => 'cansat', 'CARHR098700' => 'chi', 'CARHR221120' => 'chi', 'CARHR221150' => 'chi', 'Carub.0003s2297' => 'cru', 'Carub.0007s2749' => 'cru', 'Carub.0007s2750' => 'cru', 'Carub.0007s2751' => 'cru', 'Ca_10849_v3' => 'car', 'Cc03_g04300' => 'ccan', 'CDE02G3648' => 'cde', 'CDE05G0060' => 'cde', 'CDE05G0692' => 'cde', 'CDE05G2285' => 'cde', 'CDE05G2884' => 'cde', 'CDE05G3072' => 'cde', 'Cfa008439' => 'cfa', 'Cfa008441' => 'cfa', 'Cfa008443' => 'cfa', 'Cfa008448' => 'cfa', 'Ciclev10005974m.g' => 'ccl', 'Ciclev10006006m.g' => 'ccl', 'Ciclev10006775m.g' => 'ccl', 'CiPaw.02G120400' => 'cil', 'CiPaw.02G120500' => 'cil', 'CiPaw.02G120600' => 'cil', 'ClCG05G004850' => 'cla', 'COL.COLO4_21566' => 'col', 'Cpa.g.sc44.124' => 'cpa', 'Cre07.g320400' => 'cre', 'Cre07.g320450' => 'cre', 'Cre08.g384650' => 'cre', 'Cre09.g393173' => 'cre', 'Cre09.g394325' => 'cre', 'Cre14.g626750' => 'cre', 'Cre16.g679250' => 'cre', 'CsaV3_3G012890' => 'csa', 'CSS0010865' => 'camsi', 'CSS0044338' => 'camsi', 'DCAR_002366' => 'dca', 'DCAR_030687' => 'dca', 'DCAR_030688' => 'dca', 'Dinv14047' => 'din', 'Dinv14048' => 'din', 'Duzib151G0105' => 'dzi', 'Duzib151G0114' => 'dzi', 'Duzib212G1029' => 'dzi', 'ECA232G3536' => 'eca', 'ECA240G0786' => 'eca', 'ECA240G1802' => 'eca', 'ECA240G3760' => 'eca', 'ECA240G3920' => 'eca', 'EL10Ac5g12536' => 'bvu', 'EL10Ac5g12537' => 'bvu', 'EL10Ac5g12538' => 'bvu', 'Eucgr.B01004' => 'egr', 'Eucgr.B01006' => 'egr', 'Eucgr.B01007' => 'egr', 'Eucgr.B01008' => 'egr', 'Eucgr.B01895' => 'egr', 'Eucgr.B01896' => 'egr', 'FAN04G1456' => 'fan', 'FAN08G1769' => 'fan', 'FAN08G2160' => 'fan', 'FAN13G2403' => 'fan', 'FAN13G3303' => 'fan', 'FAN15G2435' => 'fan', 'FAN17G0672' => 'fan', 'FAN17G2441' => 'fan', 'FAN18G1024' => 'fan', 'FAN22G1458' => 'fan', 'FAN24G0037' => 'fan', 'FAN24G0429' => 'fan', 'FAN24G2387' => 'fan', 'FAN27G2746' => 'fan', 'FvH4_2g20400' => 'fve', 'FvH4_2g20420' => 'fve', 'FvH4_2g20430' => 'fve', 'FvH4_4g01270' => 'fve', 'FvH4_4g01290' => 'fve', 'FvH4_4g01300' => 'fve', 'FvH4_4g01310' => 'fve', 'FvH4_4g01330' => 'fve', 'FvH4_5g09070' => 'fve', 'Glyma.10G243800' => 'gma', 'Glyma.20G150600' => 'gma', 'Gohir.A09G219200' => 'ghi', 'Gohir.A09G219300' => 'ghi', 'Gohir.D09G221400' => 'ghi', 'Gohir.D09G221500' => 'ghi', 'Gorai.006G242600' => 'gra', 'Gorai.006G242700' => 'gra', 'GSVIVG01018044001' => 'vvi', 'HanXRQChr03g0083821' => 'han', 'HanXRQChr03g0083841' => 'han', 'HanXRQChr03g0083881' => 'han', 'HanXRQChr03g0083901' => 'han', 'HanXRQChr03g0083921' => 'han', 'HanXRQChr03g0085331' => 'han', 'HanXRQChr03g0085361' => 'han', 'HanXRQChr03g0085411' => 'han', 'HanXRQChr03g0085421' => 'han', 'HanXRQChr03g0085431' => 'han', 'HanXRQChr08g0221991' => 'han', 'HanXRQChr11g0336061' => 'han', 'HanXRQChr11g0336411' => 'han', 'Haze_11234' => 'cav', 'Hma1.2p1_0549F.1_g177010' => 'hma', 'Hma1.2p1_0602F.1_g187630' => 'hma', 'Hund14876' => 'sun', 'Hund14879' => 'sun', 'Lalb_Chr06g0160741' => 'lal', 'Lalb_Chr21g0304781' => 'lal', 'Lj3A726G19' => 'lonja', 'Lj3A726T23' => 'lonja', 'Lj3A726T24' => 'lonja', 'Lj3A726T25' => 'lonja', 'Lj3A727T17' => 'lonja', 'Lj3C726T0' => 'lonja', 'Lj3C726T2' => 'lonja', 'Lj3P725T35' => 'lonja', 'Lj3P727T10' => 'lonja', 'Lj3P727T12' => 'lonja', 'Lj3P727T14' => 'lonja', 'Lj5g0023109' => 'lja', 'Lj6P646T44' => 'lonja', 'Lsat_1_v5_gn_6_75760' => 'lsa', 'Lsat_1_v5_gn_6_75800' => 'lsa', 'Lsat_1_v5_gn_6_75900' => 'lsa', 'Lsat_1_v5_gn_6_76240' => 'lsa', 'Lsat_1_v5_gn_6_76441' => 'lsa', 'Lsat_1_v5_gn_6_76700' => 'lsa', 'Lsat_1_v5_gn_6_76760' => 'lsa', 'Manes.15G033100' => 'mes', 'Mapoly0004s0074' => 'mpo', 'Mapoly0004s0075' => 'mpo', 'Mapoly0004s0163' => 'mpo', 'Mapoly0004s0164' => 'mpo', 'Mapoly0021s0018' => 'mpo', 'Mapoly0041s0136' => 'mpo', 'Mapoly0041s0137' => 'mpo', 'Mapoly0041s0138' => 'mpo', 'Mapoly0041s0139' => 'mpo', 'Mapoly0041s0141' => 'mpo', 'Mapoly0041s0142' => 'mpo', 'Mapoly0041s0143' => 'mpo', 'Mapoly0041s0144' => 'mpo', 'Mapoly0041s0145' => 'mpo', 'Mapoly0047s0106' => 'mpo', 'Mapoly0047s0108' => 'mpo', 'Mapoly0050s0051' => 'mpo', 'Mapoly0050s0052' => 'mpo', 'Mapoly0050s0053' => 'mpo', 'Mapoly0058s0013' => 'mpo', 'Mapoly0091s0078' => 'mpo', 'Mapoly0091s0079' => 'mpo', 'Mapoly0091s0080' => 'mpo', 'Mapoly0091s0081' => 'mpo', 'Mapoly0278s0004' => 'mpo', 'Mapoly0278s0005' => 'mpo', 'Mapoly0278s0006' => 'mpo', 'MBI11_g30648_MAGBIO' => 'mbi', 'MCO03G194' => 'mco', 'MCO03G590' => 'mco', 'MCO07G312' => 'mco', 'MCO10G318' => 'mco', 'MCO12G244' => 'mco', 'MCO13G148' => 'mco', 'MCO13G194' => 'mco', 'MCO16G238' => 'mco', 'MD06G1134100' => 'mdo', 'MD13G1200100' => 'mdo', 'MD13G1200300' => 'mdo', 'MD13G1200600' => 'mdo', 'MD14G1150400' => 'mdo', 'MD16G1200000' => 'mdo', 'Medtr1g102570' => 'mtr', 'Medtr1g102780' => 'mtr', 'Medtr1g102800' => 'mtr', 'Medtr1g102810' => 'mtr', 'Medtr1g102830' => 'mtr', 'MELO3C006499.2' => 'cme', 'Migut.G00385' => 'egut', 'MSTRG.4063' => 'ama', 'Nitab4.5_0000090g0260' => 'nta', 'Nitab4.5_0000977g0030' => 'nta', 'Nitab4.5_0002541g0040' => 'nta', 'Nitab4.5_0007068g0040' => 'nta', 'Nn005s41408' => 'nnu', 'Nn005s41410' => 'nnu', 'Oeu010310.1' => 'oeu', 'Oeu010311.1' => 'oeu', 'Oeu043472.1' => 'oeu', 'Os01g0246400' => 'osa', 'Os04g0267950' => 'osa', 'Os07g0178700' => 'osa', 'Os07g0178800' => 'osa', 'Peaxi162Scf00316g00046' => 'pax', 'Peaxi162Scf00316g00049' => 'pax', 'Peaxi162Scf00316g00059' => 'pax', 'Peaxi162Scf00316g00328' => 'pax', 'Peaxi162Scf00316g00329' => 'pax', 'Peaxi162Scf00316g00411' => 'pax', 'Peaxi162Scf00316g00521' => 'pax', 'Peaxi162Scf00492g00068' => 'pax', 'Peaxi162Scf35631g00002' => 'pax', 'PGR142G3720' => 'pgr', 'PGSC0003DMG400006442' => 'stu', 'Phvul.007G062000' => 'pvu', 'Potri.008G157750' => 'ptr', 'Potri.008G157900' => 'ptr', 'Potri.008G158000' => 'ptr', 'Potri.008G158200' => 'ptr', 'Pp3c11_7280' => 'ppa', 'Pp3c11_7980' => 'ppa', 'Pp3c12_19450' => 'ppa', 'Pp3c14_1480' => 'ppa', 'Pp3c14_1501' => 'ppa', 'Pp3c16_4900' => 'ppa', 'Pp3c16_5010' => 'ppa', 'Pp3c16_5060' => 'ppa', 'Pp3c19_18250' => 'ppa', 'Pp3c23_8530' => 'ppa', 'Pp3c23_8550' => 'ppa', 'Pp3c24_9670' => 'ppa', 'Pp3c2_21390' => 'ppa', 'Pp3c2_31380' => 'ppa', 'Pp3c3_16620' => 'ppa', 'Pp3c3_8090' => 'ppa', 'Pp3c3_8110' => 'ppa', 'Pp3c3_8130' => 'ppa', 'Pp3c3_8150' => 'ppa', 'Pp3c4_14320' => 'ppa', 'Pp3c6_2560' => 'ppa', 'Pp3c9_16700' => 'ppa', 'PRCOL_00000234' => 'pco', 'PRCOL_00000235' => 'pco', 'PRCOL_00000777' => 'pco', 'PRCOL_00002344' => 'pco', 'PRCOL_00002372' => 'pco', 'PRCOL_00006120' => 'pco', 'Prupe.1G021400' => 'ppe', 'Prupe.1G021500' => 'ppe', 'Prupe.1G021600' => 'ppe', 'Prupe.1G021700' => 'ppe', 'Prupe.1G021800' => 'ppe', 'Prupe.5G145100' => 'ppe', 'Psat6g204040' => 'psa', 'Psat6g204800' => 'psa', 'Psat6g204920' => 'psa', 'Psat6g204960' => 'psa', 'Psat6g205080' => 'psa', 'PSO017G0271' => 'pso', 'PSO017G1276' => 'pso', 'PSO017G1429' => 'pso', 'PSO017G1861' => 'pso', 'PSO017G2787' => 'pso', 'PSO017G4466' => 'pso', 'PSO017G5118' => 'pso', 'PSO017G5420' => 'pso', 'PSO063G3678' => 'pso', 'PSO210G0546' => 'pso', 'PSO317G0001' => 'pso', 'PSO357G0512' => 'pso', 'PSO478G2682' => 'pso', 'PSO647G0001' => 'pso', 'PSO675G0001' => 'pso', 'PSO675G2699' => 'pso', 'PSO675G2849' => 'pso', 'PSO675G4991' => 'pso', 'PSO689G0001' => 'pso', 'QL06p000916' => 'qlo', 'QL06p000921' => 'qlo', 'QL06p001398' => 'qlo', 'QL06p001407' => 'qlo', 'QL06p002031' => 'qlo', 'RcHm_v2.0_Chr4g0387791' => 'rch', 'RcHm_v2.0_Chr4g0387801' => 'rch', 'RcHm_v2.0_Chr6g0286501' => 'rch', 'RcHm_v2.0_Chr6g0286511' => 'rch', 'RcHm_v2.0_Chr6g0286521' => 'rch', 'RcHm_v2.0_Chr6g0286531' => 'rch', 'RcHm_v2.0_Chr7g0189141' => 'rch', 'Rhsim02G0028700' => 'rsi', 'Rhsim02G0028800' => 'rsi', 'Rhsim02G0028900' => 'rsi', 'Rhsim02G0029000' => 'rsi', 'Rhsim02G0029100' => 'rsi', 'Rhsim02G0029200' => 'rsi', 'Rhsim02G0029300' => 'rsi', 'Rhsim02G0029400' => 'rsi', 'Rhsim02G0029500' => 'rsi', 'Rhsim02G0029600' => 'rsi', 'RhsimUnG0024000' => 'rsi', 'RhsimUnG0024100' => 'rsi', 'RhsimUnG0024200' => 'rsi', 'RhsimUnG0024300' => 'rsi', 'RhsimUnG0024400' => 'rsi', 'RhsimUnG0024500' => 'rsi', 'RhsimUnG0024700' => 'rsi', 'RhsimUnG0024800' => 'rsi', 'RhsimUnG0024900' => 'rsi', 'RhsimUnG0025100' => 'rsi', 'Sabra08G0120200' => 'sbr', 'Sabra08G0120300' => 'sbr', 'Sabra08G0120500' => 'sbr', 'Sabra08G0120600' => 'sbr', 'Sabra10G0158900' => 'sbr', 'SalBow2G3492' => 'sbo', 'Sc13g0004760' => 'sci', 'Sc13g0004770' => 'sci', 'Sed0003417' => 'sed', 'Sed0019750' => 'sed', 'SEGI_03419' => 'sgi', 'SEGI_05907' => 'sgi', 'SEGI_10682' => 'sgi', 'SEGI_13528' => 'sgi', 'SEGI_16081' => 'sgi', 'SEGI_19370' => 'sgi', 'SEGI_21015' => 'sgi', 'SEGI_21944' => 'sgi', 'SEGI_32906' => 'sgi', 'SEGI_33093' => 'sgi', 'SEGI_36110' => 'sgi', 'SEGI_40397' => 'sgi', 'SGA_v2.0_scaffold191G40426' => 'sas', 'SGA_v2.0_scaffold353G49717' => 'sas', 'SGA_v2.0_scaffold50G18550' => 'sas', 'SMO119G0173' => 'smo', 'SMO172G0002' => 'smo', 'Solyc09g082690.3' => 'sly', 'Solyc09g082700.2' => 'sly', 'Sopen09g031550' => 'spe', 'Sopen09g031560' => 'spe', 'Sp3g20540' => 'spa', 'Sp7g07580' => 'spa', 'TAR134G0002' => 'tar', 'TAR236G0001' => 'tar', 'TAR365G0892' => 'tar', 'TAR636G0166' => 'tar', 'TAR636G0646' => 'tar', 'TAR636G0869' => 'tar', 'TAR636G1317' => 'tar', 'TAR636G1744' => 'tar', 'TAR636G3358' => 'tar', 'TAR636G3436' => 'tar', 'THA.LOC104803047' => 'tha', 'Thecc.04G238900' => 'tca', 'Thhalv10021557m.g' => 'esa', 'Thhalv10026318m.g' => 'esa', 'Thhalv10026335m.g' => 'esa', 'TPR.G17433' => 'tpr', 'TPR.G18915' => 'tpr', 'TPR.G26125' => 'tpr', 'TWI09G0677' => 'twi', 'TWI73G0287' => 'twi', 'unitig_748.g8326' => 'ugi', 'vmacro15370' => 'vma', 'vmacro15371' => 'vma', 'vmacro15372' => 'vma', 'vmacro15373' => 'vma', 'vmacro15374' => 'vma', 'VMungo0720G2826' => 'vmu', 'Zm00001eb116960' => 'zma', 'Zm00001eb301260' => 'zma', 'Zm00001eb301270' => 'zma' ), 'gf_id' => 'HOM05D001460', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001460' ), 'data_identifier' => 'HOM05D001460', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001460', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '433', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p22980' => 'bna', 'A01p32340' => 'bna', 'A03p42970' => 'bna', 'A05p25880' => 'bna', 'Aa31LG8G9320' => 'aar', 'Aa31LG8G9330' => 'aar', 'Aa31LG8G9340' => 'aar', 'Aa31sc221G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1034' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1528' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.829' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2222' => 'aag', 'Ah.12g058830' => 'amhyb', 'Ah.12g058840' => 'amhyb', 'AL3G37160' => 'aly', 'AL7G41310' => 'aly', 'Aqoxy5G00395' => 'aox', 'Aqoxy5G00396' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0C8NZA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5185HY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JZ1PRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MD3LS0' => 'arhy', 'AT3G22840' => 'ath', 'AT4G14690' => 'ath', 'ATR0665G054' => 'atr', 'Atru.chr4.2344' => 'acertr', 'Atru.chr4.2346' => 'acertr', 'Atru.chr4.2347' => 'acertr', 'Atru.chr4.2348' => 'acertr', 'Atru.chr4.2355' => 'acertr', 'Atru.chr4.2356' => 'acertr', 'Atru.chr4.2358' => 'acertr', 'Atru.chr4.2359' => 'acertr', 'Atru.chr4.2360' => 'acertr', 'Atru.chr4.2361' => 'acertr', 'AUR62030476' => 'cqu', 'AUR62030478' => 'cqu', 'AUR62030819' => 'cqu', 'AUR62030820' => 'cqu', 'BcaB03g14648' => 'bca', 'BcaB04g20492' => 'bca', 'BcaB06g26399' => 'bca', 'BcaC01g03416' => 'bca', 'BcaC01g03419' => 'bca', 'BcaC01g03421' => 'bca', 'BcaC01g03424' => 'bca', 'BcaC05g28012' => 'bca', 'BcaC09g49212' => 'bca', 'BcaC09g50140' => 'bca', 'BcaNung00346' => 'bca', 'BolC1t02785H' => 'bol', 'BolC1t04095H' => 'bol', 'BolC3t17545H' => 'bol', 'BolC5t32769H' => 'bol', 'BraA01t02211Z' => 'bra', 'BraA01t03359Z' => 'bra', 'BraA03t13441Z' => 'bra', 'BraA05t21476Z' => 'bra', 'C01p28420' => 'bna', 'C01p41350' => 'bna', 'C03p52750' => 'bna', 'C03p52780' => 'bna', 'C05p40270' => 'bna', 'CAN.G1437.9' => 'can', 'CANSAT78G0035' => 'cansat', 'CANSAT78G1036' => 'cansat', 'CANSAT78G2272' => 'cansat', 'CANSAT78G2478' => 'cansat', 'CARHR098700' => 'chi', 'CARHR221120' => 'chi', 'CARHR221150' => 'chi', 'Carub.0003s2297' => 'cru', 'Carub.0007s2749' => 'cru', 'Carub.0007s2750' => 'cru', 'Carub.0007s2751' => 'cru', 'Ca_10849_v3' => 'car', 'Cc03_g04300' => 'ccan', 'CDE02G3648' => 'cde', 'CDE05G0060' => 'cde', 'CDE05G0692' => 'cde', 'CDE05G2285' => 'cde', 'CDE05G2884' => 'cde', 'CDE05G3072' => 'cde', 'Cfa008439' => 'cfa', 'Cfa008441' => 'cfa', 'Cfa008443' => 'cfa', 'Cfa008448' => 'cfa', 'Ciclev10005974m.g' => 'ccl', 'Ciclev10006006m.g' => 'ccl', 'Ciclev10006775m.g' => 'ccl', 'CiPaw.02G120400' => 'cil', 'CiPaw.02G120500' => 'cil', 'CiPaw.02G120600' => 'cil', 'ClCG05G004850' => 'cla', 'COL.COLO4_21566' => 'col', 'Cpa.g.sc44.124' => 'cpa', 'Cre07.g320400' => 'cre', 'Cre07.g320450' => 'cre', 'Cre08.g384650' => 'cre', 'Cre09.g393173' => 'cre', 'Cre09.g394325' => 'cre', 'Cre14.g626750' => 'cre', 'Cre16.g679250' => 'cre', 'CsaV3_3G012890' => 'csa', 'CSS0010865' => 'camsi', 'CSS0044338' => 'camsi', 'DCAR_002366' => 'dca', 'DCAR_030687' => 'dca', 'DCAR_030688' => 'dca', 'Dinv14047' => 'din', 'Dinv14048' => 'din', 'Duzib151G0105' => 'dzi', 'Duzib151G0114' => 'dzi', 'Duzib212G1029' => 'dzi', 'ECA232G3536' => 'eca', 'ECA240G0786' => 'eca', 'ECA240G1802' => 'eca', 'ECA240G3760' => 'eca', 'ECA240G3920' => 'eca', 'EL10Ac5g12536' => 'bvu', 'EL10Ac5g12537' => 'bvu', 'EL10Ac5g12538' => 'bvu', 'Eucgr.B01004' => 'egr', 'Eucgr.B01006' => 'egr', 'Eucgr.B01007' => 'egr', 'Eucgr.B01008' => 'egr', 'Eucgr.B01895' => 'egr', 'Eucgr.B01896' => 'egr', 'FAN04G1456' => 'fan', 'FAN08G1769' => 'fan', 'FAN08G2160' => 'fan', 'FAN13G2403' => 'fan', 'FAN13G3303' => 'fan', 'FAN15G2435' => 'fan', 'FAN17G0672' => 'fan', 'FAN17G2441' => 'fan', 'FAN18G1024' => 'fan', 'FAN22G1458' => 'fan', 'FAN24G0037' => 'fan', 'FAN24G0429' => 'fan', 'FAN24G2387' => 'fan', 'FAN27G2746' => 'fan', 'FvH4_2g20400' => 'fve', 'FvH4_2g20420' => 'fve', 'FvH4_2g20430' => 'fve', 'FvH4_4g01270' => 'fve', 'FvH4_4g01290' => 'fve', 'FvH4_4g01300' => 'fve', 'FvH4_4g01310' => 'fve', 'FvH4_4g01330' => 'fve', 'FvH4_5g09070' => 'fve', 'Glyma.10G243800' => 'gma', 'Glyma.20G150600' => 'gma', 'Gohir.A09G219200' => 'ghi', 'Gohir.A09G219300' => 'ghi', 'Gohir.D09G221400' => 'ghi', 'Gohir.D09G221500' => 'ghi', 'Gorai.006G242600' => 'gra', 'Gorai.006G242700' => 'gra', 'GSVIVG01018044001' => 'vvi', 'HanXRQChr03g0083821' => 'han', 'HanXRQChr03g0083841' => 'han', 'HanXRQChr03g0083881' => 'han', 'HanXRQChr03g0083901' => 'han', 'HanXRQChr03g0083921' => 'han', 'HanXRQChr03g0085331' => 'han', 'HanXRQChr03g0085361' => 'han', 'HanXRQChr03g0085411' => 'han', 'HanXRQChr03g0085421' => 'han', 'HanXRQChr03g0085431' => 'han', 'HanXRQChr08g0221991' => 'han', 'HanXRQChr11g0336061' => 'han', 'HanXRQChr11g0336411' => 'han', 'Haze_11234' => 'cav', 'Hma1.2p1_0549F.1_g177010' => 'hma', 'Hma1.2p1_0602F.1_g187630' => 'hma', 'Hund14876' => 'sun', 'Hund14879' => 'sun', 'Lalb_Chr06g0160741' => 'lal', 'Lalb_Chr21g0304781' => 'lal', 'Lj3A726G19' => 'lonja', 'Lj3A726T23' => 'lonja', 'Lj3A726T24' => 'lonja', 'Lj3A726T25' => 'lonja', 'Lj3A727T17' => 'lonja', 'Lj3C726T0' => 'lonja', 'Lj3C726T2' => 'lonja', 'Lj3P725T35' => 'lonja', 'Lj3P727T10' => 'lonja', 'Lj3P727T12' => 'lonja', 'Lj3P727T14' => 'lonja', 'Lj5g0023109' => 'lja', 'Lj6P646T44' => 'lonja', 'Lsat_1_v5_gn_6_75760' => 'lsa', 'Lsat_1_v5_gn_6_75800' => 'lsa', 'Lsat_1_v5_gn_6_75900' => 'lsa', 'Lsat_1_v5_gn_6_76240' => 'lsa', 'Lsat_1_v5_gn_6_76441' => 'lsa', 'Lsat_1_v5_gn_6_76700' => 'lsa', 'Lsat_1_v5_gn_6_76760' => 'lsa', 'Manes.15G033100' => 'mes', 'Mapoly0004s0074' => 'mpo', 'Mapoly0004s0075' => 'mpo', 'Mapoly0004s0163' => 'mpo', 'Mapoly0004s0164' => 'mpo', 'Mapoly0021s0018' => 'mpo', 'Mapoly0041s0136' => 'mpo', 'Mapoly0041s0137' => 'mpo', 'Mapoly0041s0138' => 'mpo', 'Mapoly0041s0139' => 'mpo', 'Mapoly0041s0141' => 'mpo', 'Mapoly0041s0142' => 'mpo', 'Mapoly0041s0143' => 'mpo', 'Mapoly0041s0144' => 'mpo', 'Mapoly0041s0145' => 'mpo', 'Mapoly0047s0106' => 'mpo', 'Mapoly0047s0108' => 'mpo', 'Mapoly0050s0051' => 'mpo', 'Mapoly0050s0052' => 'mpo', 'Mapoly0050s0053' => 'mpo', 'Mapoly0058s0013' => 'mpo', 'Mapoly0091s0078' => 'mpo', 'Mapoly0091s0079' => 'mpo', 'Mapoly0091s0080' => 'mpo', 'Mapoly0091s0081' => 'mpo', 'Mapoly0278s0004' => 'mpo', 'Mapoly0278s0005' => 'mpo', 'Mapoly0278s0006' => 'mpo', 'MBI11_g30648_MAGBIO' => 'mbi', 'MCO03G194' => 'mco', 'MCO03G590' => 'mco', 'MCO07G312' => 'mco', 'MCO10G318' => 'mco', 'MCO12G244' => 'mco', 'MCO13G148' => 'mco', 'MCO13G194' => 'mco', 'MCO16G238' => 'mco', 'MD06G1134100' => 'mdo', 'MD13G1200100' => 'mdo', 'MD13G1200300' => 'mdo', 'MD13G1200600' => 'mdo', 'MD14G1150400' => 'mdo', 'MD16G1200000' => 'mdo', 'Medtr1g102570' => 'mtr', 'Medtr1g102780' => 'mtr', 'Medtr1g102800' => 'mtr', 'Medtr1g102810' => 'mtr', 'Medtr1g102830' => 'mtr', 'MELO3C006499.2' => 'cme', 'Migut.G00385' => 'egut', 'MSTRG.4063' => 'ama', 'Nitab4.5_0000090g0260' => 'nta', 'Nitab4.5_0000977g0030' => 'nta', 'Nitab4.5_0002541g0040' => 'nta', 'Nitab4.5_0007068g0040' => 'nta', 'Nn005s41408' => 'nnu', 'Nn005s41410' => 'nnu', 'Oeu010310.1' => 'oeu', 'Oeu010311.1' => 'oeu', 'Oeu043472.1' => 'oeu', 'Os01g0246400' => 'osa', 'Os04g0267950' => 'osa', 'Os07g0178700' => 'osa', 'Os07g0178800' => 'osa', 'Peaxi162Scf00316g00046' => 'pax', 'Peaxi162Scf00316g00049' => 'pax', 'Peaxi162Scf00316g00059' => 'pax', 'Peaxi162Scf00316g00328' => 'pax', 'Peaxi162Scf00316g00329' => 'pax', 'Peaxi162Scf00316g00411' => 'pax', 'Peaxi162Scf00316g00521' => 'pax', 'Peaxi162Scf00492g00068' => 'pax', 'Peaxi162Scf35631g00002' => 'pax', 'PGR142G3720' => 'pgr', 'PGSC0003DMG400006442' => 'stu', 'Phvul.007G062000' => 'pvu', 'Potri.008G157750' => 'ptr', 'Potri.008G157900' => 'ptr', 'Potri.008G158000' => 'ptr', 'Potri.008G158200' => 'ptr', 'Pp3c11_7280' => 'ppa', 'Pp3c11_7980' => 'ppa', 'Pp3c12_19450' => 'ppa', 'Pp3c14_1480' => 'ppa', 'Pp3c14_1501' => 'ppa', 'Pp3c16_4900' => 'ppa', 'Pp3c16_5010' => 'ppa', 'Pp3c16_5060' => 'ppa', 'Pp3c19_18250' => 'ppa', 'Pp3c23_8530' => 'ppa', 'Pp3c23_8550' => 'ppa', 'Pp3c24_9670' => 'ppa', 'Pp3c2_21390' => 'ppa', 'Pp3c2_31380' => 'ppa', 'Pp3c3_16620' => 'ppa', 'Pp3c3_8090' => 'ppa', 'Pp3c3_8110' => 'ppa', 'Pp3c3_8130' => 'ppa', 'Pp3c3_8150' => 'ppa', 'Pp3c4_14320' => 'ppa', 'Pp3c6_2560' => 'ppa', 'Pp3c9_16700' => 'ppa', 'PRCOL_00000234' => 'pco', 'PRCOL_00000235' => 'pco', 'PRCOL_00000777' => 'pco', 'PRCOL_00002344' => 'pco', 'PRCOL_00002372' => 'pco', 'PRCOL_00006120' => 'pco', 'Prupe.1G021400' => 'ppe', 'Prupe.1G021500' => 'ppe', 'Prupe.1G021600' => 'ppe', 'Prupe.1G021700' => 'ppe', 'Prupe.1G021800' => 'ppe', 'Prupe.5G145100' => 'ppe', 'Psat6g204040' => 'psa', 'Psat6g204800' => 'psa', 'Psat6g204920' => 'psa', 'Psat6g204960' => 'psa', 'Psat6g205080' => 'psa', 'PSO017G0271' => 'pso', 'PSO017G1276' => 'pso', 'PSO017G1429' => 'pso', 'PSO017G1861' => 'pso', 'PSO017G2787' => 'pso', 'PSO017G4466' => 'pso', 'PSO017G5118' => 'pso', 'PSO017G5420' => 'pso', 'PSO063G3678' => 'pso', 'PSO210G0546' => 'pso', 'PSO317G0001' => 'pso', 'PSO357G0512' => 'pso', 'PSO478G2682' => 'pso', 'PSO647G0001' => 'pso', 'PSO675G0001' => 'pso', 'PSO675G2699' => 'pso', 'PSO675G2849' => 'pso', 'PSO675G4991' => 'pso', 'PSO689G0001' => 'pso', 'QL06p000916' => 'qlo', 'QL06p000921' => 'qlo', 'QL06p001398' => 'qlo', 'QL06p001407' => 'qlo', 'QL06p002031' => 'qlo', 'RcHm_v2.0_Chr4g0387791' => 'rch', 'RcHm_v2.0_Chr4g0387801' => 'rch', 'RcHm_v2.0_Chr6g0286501' => 'rch', 'RcHm_v2.0_Chr6g0286511' => 'rch', 'RcHm_v2.0_Chr6g0286521' => 'rch', 'RcHm_v2.0_Chr6g0286531' => 'rch', 'RcHm_v2.0_Chr7g0189141' => 'rch', 'Rhsim02G0028700' => 'rsi', 'Rhsim02G0028800' => 'rsi', 'Rhsim02G0028900' => 'rsi', 'Rhsim02G0029000' => 'rsi', 'Rhsim02G0029100' => 'rsi', 'Rhsim02G0029200' => 'rsi', 'Rhsim02G0029300' => 'rsi', 'Rhsim02G0029400' => 'rsi', 'Rhsim02G0029500' => 'rsi', 'Rhsim02G0029600' => 'rsi', 'RhsimUnG0024000' => 'rsi', 'RhsimUnG0024100' => 'rsi', 'RhsimUnG0024200' => 'rsi', 'RhsimUnG0024300' => 'rsi', 'RhsimUnG0024400' => 'rsi', 'RhsimUnG0024500' => 'rsi', 'RhsimUnG0024700' => 'rsi', 'RhsimUnG0024800' => 'rsi', 'RhsimUnG0024900' => 'rsi', 'RhsimUnG0025100' => 'rsi', 'Sabra08G0120200' => 'sbr', 'Sabra08G0120300' => 'sbr', 'Sabra08G0120500' => 'sbr', 'Sabra08G0120600' => 'sbr', 'Sabra10G0158900' => 'sbr', 'SalBow2G3492' => 'sbo', 'Sc13g0004760' => 'sci', 'Sc13g0004770' => 'sci', 'Sed0003417' => 'sed', 'Sed0019750' => 'sed', 'SEGI_03419' => 'sgi', 'SEGI_05907' => 'sgi', 'SEGI_10682' => 'sgi', 'SEGI_13528' => 'sgi', 'SEGI_16081' => 'sgi', 'SEGI_19370' => 'sgi', 'SEGI_21015' => 'sgi', 'SEGI_21944' => 'sgi', 'SEGI_32906' => 'sgi', 'SEGI_33093' => 'sgi', 'SEGI_36110' => 'sgi', 'SEGI_40397' => 'sgi', 'SGA_v2.0_scaffold191G40426' => 'sas', 'SGA_v2.0_scaffold353G49717' => 'sas', 'SGA_v2.0_scaffold50G18550' => 'sas', 'SMO119G0173' => 'smo', 'SMO172G0002' => 'smo', 'Solyc09g082690.3' => 'sly', 'Solyc09g082700.2' => 'sly', 'Sopen09g031550' => 'spe', 'Sopen09g031560' => 'spe', 'Sp3g20540' => 'spa', 'Sp7g07580' => 'spa', 'TAR134G0002' => 'tar', 'TAR236G0001' => 'tar', 'TAR365G0892' => 'tar', 'TAR636G0166' => 'tar', 'TAR636G0646' => 'tar', 'TAR636G0869' => 'tar', 'TAR636G1317' => 'tar', 'TAR636G1744' => 'tar', 'TAR636G3358' => 'tar', 'TAR636G3436' => 'tar', 'THA.LOC104803047' => 'tha', 'Thecc.04G238900' => 'tca', 'Thhalv10021557m.g' => 'esa', 'Thhalv10026318m.g' => 'esa', 'Thhalv10026335m.g' => 'esa', 'TPR.G17433' => 'tpr', 'TPR.G18915' => 'tpr', 'TPR.G26125' => 'tpr', 'TWI09G0677' => 'twi', 'TWI73G0287' => 'twi', 'unitig_748.g8326' => 'ugi', 'vmacro15370' => 'vma', 'vmacro15371' => 'vma', 'vmacro15372' => 'vma', 'vmacro15373' => 'vma', 'vmacro15374' => 'vma', 'VMungo0720G2826' => 'vmu', 'Zm00001eb116960' => 'zma', 'Zm00001eb301260' => 'zma', 'Zm00001eb301270' => 'zma' ) $gf_id = 'HOM05D001460' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001460' ) $data_identifier = 'HOM05D001460' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 4, 'aag' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 2, 'aox' => (int) 2, 'arhy' => (int) 4, 'ath' => (int) 2, 'atr' => (int) 1, 'acertr' => (int) 10, 'cqu' => (int) 4, 'bca' => (int) 11, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 1, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 1, 'ccan' => (int) 1, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 1, 'col' => (int) 1, 'cpa' => (int) 1, 'cre' => (int) 7, 'csa' => (int) 1, 'camsi' => (int) 2, 'dca' => (int) 3, 'din' => (int) 2, 'dzi' => (int) 3, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 14, 'fve' => (int) 9, 'gma' => (int) 2, 'ghi' => (int) 4, 'gra' => (int) 2, 'vvi' => (int) 1, 'han' => (int) 13, 'cav' => (int) 1, 'hma' => (int) 2, 'sun' => (int) 2, 'lal' => (int) 2, 'lonja' => (int) 12, 'lja' => (int) 1, 'lsa' => (int) 7, 'mes' => (int) 1, 'mpo' => (int) 27, 'mbi' => (int) 1, 'mco' => (int) 8, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 1, 'egut' => (int) 1, 'ama' => (int) 1, 'nta' => (int) 4, 'nnu' => (int) 2, 'oeu' => (int) 3, 'osa' => (int) 4, 'pax' => (int) 9, 'pgr' => (int) 1, 'stu' => (int) 1, 'pvu' => (int) 1, 'ptr' => (int) 4, 'ppa' => (int) 22, 'pco' => (int) 6, 'ppe' => (int) 6, 'psa' => (int) 5, 'pso' => (int) 19, 'qlo' => (int) 5, 'rch' => (int) 7, 'rsi' => (int) 20, 'sbr' => (int) 5, 'sbo' => (int) 1, 'sci' => (int) 2, 'sed' => (int) 2, 'sgi' => (int) 12, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 2, 'tar' => (int) 10, 'tha' => (int) 1, 'tca' => (int) 1, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 2, 'ugi' => (int) 1, 'vma' => (int) 5, 'vmu' => (int) 1, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb301270' $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' => 'HOM05D001460', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '433', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p22980' => 'bna', 'A01p32340' => 'bna', 'A03p42970' => 'bna', 'A05p25880' => 'bna', 'Aa31LG8G9320' => 'aar', 'Aa31LG8G9330' => 'aar', 'Aa31LG8G9340' => 'aar', 'Aa31sc221G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1034' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1528' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.829' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2222' => 'aag', 'Ah.12g058830' => 'amhyb', 'Ah.12g058840' => 'amhyb', 'AL3G37160' => 'aly', 'AL7G41310' => 'aly', 'Aqoxy5G00395' => 'aox', 'Aqoxy5G00396' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0C8NZA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5185HY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JZ1PRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MD3LS0' => 'arhy', 'AT3G22840' => 'ath', 'AT4G14690' => 'ath', 'ATR0665G054' => 'atr', 'Atru.chr4.2344' => 'acertr', 'Atru.chr4.2346' => 'acertr', 'Atru.chr4.2347' => 'acertr', 'Atru.chr4.2348' => 'acertr', 'Atru.chr4.2355' => 'acertr', 'Atru.chr4.2356' => 'acertr', 'Atru.chr4.2358' => 'acertr', 'Atru.chr4.2359' => 'acertr', 'Atru.chr4.2360' => 'acertr', 'Atru.chr4.2361' => 'acertr', 'AUR62030476' => 'cqu', 'AUR62030478' => 'cqu', 'AUR62030819' => 'cqu', 'AUR62030820' => 'cqu', 'BcaB03g14648' => 'bca', 'BcaB04g20492' => 'bca', 'BcaB06g26399' => 'bca', 'BcaC01g03416' => 'bca', 'BcaC01g03419' => 'bca', 'BcaC01g03421' => 'bca', 'BcaC01g03424' => 'bca', 'BcaC05g28012' => 'bca', 'BcaC09g49212' => 'bca', 'BcaC09g50140' => 'bca', 'BcaNung00346' => 'bca', 'BolC1t02785H' => 'bol', 'BolC1t04095H' => 'bol', 'BolC3t17545H' => 'bol', 'BolC5t32769H' => 'bol', 'BraA01t02211Z' => 'bra', 'BraA01t03359Z' => 'bra', 'BraA03t13441Z' => 'bra', 'BraA05t21476Z' => 'bra', 'C01p28420' => 'bna', 'C01p41350' => 'bna', 'C03p52750' => 'bna', 'C03p52780' => 'bna', 'C05p40270' => 'bna', 'CAN.G1437.9' => 'can', 'CANSAT78G0035' => 'cansat', 'CANSAT78G1036' => 'cansat', 'CANSAT78G2272' => 'cansat', 'CANSAT78G2478' => 'cansat', 'CARHR098700' => 'chi', 'CARHR221120' => 'chi', 'CARHR221150' => 'chi', 'Carub.0003s2297' => 'cru', 'Carub.0007s2749' => 'cru', 'Carub.0007s2750' => 'cru', 'Carub.0007s2751' => 'cru', 'Ca_10849_v3' => 'car', 'Cc03_g04300' => 'ccan', 'CDE02G3648' => 'cde', 'CDE05G0060' => 'cde', 'CDE05G0692' => 'cde', 'CDE05G2285' => 'cde', 'CDE05G2884' => 'cde', 'CDE05G3072' => 'cde', 'Cfa008439' => 'cfa', 'Cfa008441' => 'cfa', 'Cfa008443' => 'cfa', 'Cfa008448' => 'cfa', 'Ciclev10005974m.g' => 'ccl', 'Ciclev10006006m.g' => 'ccl', 'Ciclev10006775m.g' => 'ccl', 'CiPaw.02G120400' => 'cil', 'CiPaw.02G120500' => 'cil', 'CiPaw.02G120600' => 'cil', 'ClCG05G004850' => 'cla', 'COL.COLO4_21566' => 'col', 'Cpa.g.sc44.124' => 'cpa', 'Cre07.g320400' => 'cre', 'Cre07.g320450' => 'cre', 'Cre08.g384650' => 'cre', 'Cre09.g393173' => 'cre', 'Cre09.g394325' => 'cre', 'Cre14.g626750' => 'cre', 'Cre16.g679250' => 'cre', 'CsaV3_3G012890' => 'csa', 'CSS0010865' => 'camsi', 'CSS0044338' => 'camsi', 'DCAR_002366' => 'dca', 'DCAR_030687' => 'dca', 'DCAR_030688' => 'dca', 'Dinv14047' => 'din', 'Dinv14048' => 'din', 'Duzib151G0105' => 'dzi', 'Duzib151G0114' => 'dzi', 'Duzib212G1029' => 'dzi', 'ECA232G3536' => 'eca', 'ECA240G0786' => 'eca', 'ECA240G1802' => 'eca', 'ECA240G3760' => 'eca', 'ECA240G3920' => 'eca', 'EL10Ac5g12536' => 'bvu', 'EL10Ac5g12537' => 'bvu', 'EL10Ac5g12538' => 'bvu', 'Eucgr.B01004' => 'egr', 'Eucgr.B01006' => 'egr', 'Eucgr.B01007' => 'egr', 'Eucgr.B01008' => 'egr', 'Eucgr.B01895' => 'egr', 'Eucgr.B01896' => 'egr', 'FAN04G1456' => 'fan', 'FAN08G1769' => 'fan', 'FAN08G2160' => 'fan', 'FAN13G2403' => 'fan', 'FAN13G3303' => 'fan', 'FAN15G2435' => 'fan', 'FAN17G0672' => 'fan', 'FAN17G2441' => 'fan', 'FAN18G1024' => 'fan', 'FAN22G1458' => 'fan', 'FAN24G0037' => 'fan', 'FAN24G0429' => 'fan', 'FAN24G2387' => 'fan', 'FAN27G2746' => 'fan', 'FvH4_2g20400' => 'fve', 'FvH4_2g20420' => 'fve', 'FvH4_2g20430' => 'fve', 'FvH4_4g01270' => 'fve', 'FvH4_4g01290' => 'fve', 'FvH4_4g01300' => 'fve', 'FvH4_4g01310' => 'fve', 'FvH4_4g01330' => 'fve', 'FvH4_5g09070' => 'fve', 'Glyma.10G243800' => 'gma', 'Glyma.20G150600' => 'gma', 'Gohir.A09G219200' => 'ghi', 'Gohir.A09G219300' => 'ghi', 'Gohir.D09G221400' => 'ghi', 'Gohir.D09G221500' => 'ghi', 'Gorai.006G242600' => 'gra', 'Gorai.006G242700' => 'gra', 'GSVIVG01018044001' => 'vvi', 'HanXRQChr03g0083821' => 'han', 'HanXRQChr03g0083841' => 'han', 'HanXRQChr03g0083881' => 'han', 'HanXRQChr03g0083901' => 'han', 'HanXRQChr03g0083921' => 'han', 'HanXRQChr03g0085331' => 'han', 'HanXRQChr03g0085361' => 'han', 'HanXRQChr03g0085411' => 'han', 'HanXRQChr03g0085421' => 'han', 'HanXRQChr03g0085431' => 'han', 'HanXRQChr08g0221991' => 'han', 'HanXRQChr11g0336061' => 'han', 'HanXRQChr11g0336411' => 'han', 'Haze_11234' => 'cav', 'Hma1.2p1_0549F.1_g177010' => 'hma', 'Hma1.2p1_0602F.1_g187630' => 'hma', 'Hund14876' => 'sun', 'Hund14879' => 'sun', 'Lalb_Chr06g0160741' => 'lal', 'Lalb_Chr21g0304781' => 'lal', 'Lj3A726G19' => 'lonja', 'Lj3A726T23' => 'lonja', 'Lj3A726T24' => 'lonja', 'Lj3A726T25' => 'lonja', 'Lj3A727T17' => 'lonja', 'Lj3C726T0' => 'lonja', 'Lj3C726T2' => 'lonja', 'Lj3P725T35' => 'lonja', 'Lj3P727T10' => 'lonja', 'Lj3P727T12' => 'lonja', 'Lj3P727T14' => 'lonja', 'Lj5g0023109' => 'lja', 'Lj6P646T44' => 'lonja', 'Lsat_1_v5_gn_6_75760' => 'lsa', 'Lsat_1_v5_gn_6_75800' => 'lsa', 'Lsat_1_v5_gn_6_75900' => 'lsa', 'Lsat_1_v5_gn_6_76240' => 'lsa', 'Lsat_1_v5_gn_6_76441' => 'lsa', 'Lsat_1_v5_gn_6_76700' => 'lsa', 'Lsat_1_v5_gn_6_76760' => 'lsa', 'Manes.15G033100' => 'mes', 'Mapoly0004s0074' => 'mpo', 'Mapoly0004s0075' => 'mpo', 'Mapoly0004s0163' => 'mpo', 'Mapoly0004s0164' => 'mpo', 'Mapoly0021s0018' => 'mpo', 'Mapoly0041s0136' => 'mpo', 'Mapoly0041s0137' => 'mpo', 'Mapoly0041s0138' => 'mpo', 'Mapoly0041s0139' => 'mpo', 'Mapoly0041s0141' => 'mpo', 'Mapoly0041s0142' => 'mpo', 'Mapoly0041s0143' => 'mpo', 'Mapoly0041s0144' => 'mpo', 'Mapoly0041s0145' => 'mpo', 'Mapoly0047s0106' => 'mpo', 'Mapoly0047s0108' => 'mpo', 'Mapoly0050s0051' => 'mpo', 'Mapoly0050s0052' => 'mpo', 'Mapoly0050s0053' => 'mpo', 'Mapoly0058s0013' => 'mpo', 'Mapoly0091s0078' => 'mpo', 'Mapoly0091s0079' => 'mpo', 'Mapoly0091s0080' => 'mpo', 'Mapoly0091s0081' => 'mpo', 'Mapoly0278s0004' => 'mpo', 'Mapoly0278s0005' => 'mpo', 'Mapoly0278s0006' => 'mpo', 'MBI11_g30648_MAGBIO' => 'mbi', 'MCO03G194' => 'mco', 'MCO03G590' => 'mco', 'MCO07G312' => 'mco', 'MCO10G318' => 'mco', 'MCO12G244' => 'mco', 'MCO13G148' => 'mco', 'MCO13G194' => 'mco', 'MCO16G238' => 'mco', 'MD06G1134100' => 'mdo', 'MD13G1200100' => 'mdo', 'MD13G1200300' => 'mdo', 'MD13G1200600' => 'mdo', 'MD14G1150400' => 'mdo', 'MD16G1200000' => 'mdo', 'Medtr1g102570' => 'mtr', 'Medtr1g102780' => 'mtr', 'Medtr1g102800' => 'mtr', 'Medtr1g102810' => 'mtr', 'Medtr1g102830' => 'mtr', 'MELO3C006499.2' => 'cme', 'Migut.G00385' => 'egut', 'MSTRG.4063' => 'ama', 'Nitab4.5_0000090g0260' => 'nta', 'Nitab4.5_0000977g0030' => 'nta', 'Nitab4.5_0002541g0040' => 'nta', 'Nitab4.5_0007068g0040' => 'nta', 'Nn005s41408' => 'nnu', 'Nn005s41410' => 'nnu', 'Oeu010310.1' => 'oeu', 'Oeu010311.1' => 'oeu', 'Oeu043472.1' => 'oeu', 'Os01g0246400' => 'osa', 'Os04g0267950' => 'osa', 'Os07g0178700' => 'osa', 'Os07g0178800' => 'osa', 'Peaxi162Scf00316g00046' => 'pax', 'Peaxi162Scf00316g00049' => 'pax', 'Peaxi162Scf00316g00059' => 'pax', 'Peaxi162Scf00316g00328' => 'pax', 'Peaxi162Scf00316g00329' => 'pax', 'Peaxi162Scf00316g00411' => 'pax', 'Peaxi162Scf00316g00521' => 'pax', 'Peaxi162Scf00492g00068' => 'pax', 'Peaxi162Scf35631g00002' => 'pax', 'PGR142G3720' => 'pgr', 'PGSC0003DMG400006442' => 'stu', 'Phvul.007G062000' => 'pvu', 'Potri.008G157750' => 'ptr', 'Potri.008G157900' => 'ptr', 'Potri.008G158000' => 'ptr', 'Potri.008G158200' => 'ptr', 'Pp3c11_7280' => 'ppa', 'Pp3c11_7980' => 'ppa', 'Pp3c12_19450' => 'ppa', 'Pp3c14_1480' => 'ppa', 'Pp3c14_1501' => 'ppa', 'Pp3c16_4900' => 'ppa', 'Pp3c16_5010' => 'ppa', 'Pp3c16_5060' => 'ppa', 'Pp3c19_18250' => 'ppa', 'Pp3c23_8530' => 'ppa', 'Pp3c23_8550' => 'ppa', 'Pp3c24_9670' => 'ppa', 'Pp3c2_21390' => 'ppa', 'Pp3c2_31380' => 'ppa', 'Pp3c3_16620' => 'ppa', 'Pp3c3_8090' => 'ppa', 'Pp3c3_8110' => 'ppa', 'Pp3c3_8130' => 'ppa', 'Pp3c3_8150' => 'ppa', 'Pp3c4_14320' => 'ppa', 'Pp3c6_2560' => 'ppa', 'Pp3c9_16700' => 'ppa', 'PRCOL_00000234' => 'pco', 'PRCOL_00000235' => 'pco', 'PRCOL_00000777' => 'pco', 'PRCOL_00002344' => 'pco', 'PRCOL_00002372' => 'pco', 'PRCOL_00006120' => 'pco', 'Prupe.1G021400' => 'ppe', 'Prupe.1G021500' => 'ppe', 'Prupe.1G021600' => 'ppe', 'Prupe.1G021700' => 'ppe', 'Prupe.1G021800' => 'ppe', 'Prupe.5G145100' => 'ppe', 'Psat6g204040' => 'psa', 'Psat6g204800' => 'psa', 'Psat6g204920' => 'psa', 'Psat6g204960' => 'psa', 'Psat6g205080' => 'psa', 'PSO017G0271' => 'pso', 'PSO017G1276' => 'pso', 'PSO017G1429' => 'pso', 'PSO017G1861' => 'pso', 'PSO017G2787' => 'pso', 'PSO017G4466' => 'pso', 'PSO017G5118' => 'pso', 'PSO017G5420' => 'pso', 'PSO063G3678' => 'pso', 'PSO210G0546' => 'pso', 'PSO317G0001' => 'pso', 'PSO357G0512' => 'pso', 'PSO478G2682' => 'pso', 'PSO647G0001' => 'pso', 'PSO675G0001' => 'pso', 'PSO675G2699' => 'pso', 'PSO675G2849' => 'pso', 'PSO675G4991' => 'pso', 'PSO689G0001' => 'pso', 'QL06p000916' => 'qlo', 'QL06p000921' => 'qlo', 'QL06p001398' => 'qlo', 'QL06p001407' => 'qlo', 'QL06p002031' => 'qlo', 'RcHm_v2.0_Chr4g0387791' => 'rch', 'RcHm_v2.0_Chr4g0387801' => 'rch', 'RcHm_v2.0_Chr6g0286501' => 'rch', 'RcHm_v2.0_Chr6g0286511' => 'rch', 'RcHm_v2.0_Chr6g0286521' => 'rch', 'RcHm_v2.0_Chr6g0286531' => 'rch', 'RcHm_v2.0_Chr7g0189141' => 'rch', 'Rhsim02G0028700' => 'rsi', 'Rhsim02G0028800' => 'rsi', 'Rhsim02G0028900' => 'rsi', 'Rhsim02G0029000' => 'rsi', 'Rhsim02G0029100' => 'rsi', 'Rhsim02G0029200' => 'rsi', 'Rhsim02G0029300' => 'rsi', 'Rhsim02G0029400' => 'rsi', 'Rhsim02G0029500' => 'rsi', 'Rhsim02G0029600' => 'rsi', 'RhsimUnG0024000' => 'rsi', 'RhsimUnG0024100' => 'rsi', 'RhsimUnG0024200' => 'rsi', 'RhsimUnG0024300' => 'rsi', 'RhsimUnG0024400' => 'rsi', 'RhsimUnG0024500' => 'rsi', 'RhsimUnG0024700' => 'rsi', 'RhsimUnG0024800' => 'rsi', 'RhsimUnG0024900' => 'rsi', 'RhsimUnG0025100' => 'rsi', 'Sabra08G0120200' => 'sbr', 'Sabra08G0120300' => 'sbr', 'Sabra08G0120500' => 'sbr', 'Sabra08G0120600' => 'sbr', 'Sabra10G0158900' => 'sbr', 'SalBow2G3492' => 'sbo', 'Sc13g0004760' => 'sci', 'Sc13g0004770' => 'sci', 'Sed0003417' => 'sed', 'Sed0019750' => 'sed', 'SEGI_03419' => 'sgi', 'SEGI_05907' => 'sgi', 'SEGI_10682' => 'sgi', 'SEGI_13528' => 'sgi', 'SEGI_16081' => 'sgi', 'SEGI_19370' => 'sgi', 'SEGI_21015' => 'sgi', 'SEGI_21944' => 'sgi', 'SEGI_32906' => 'sgi', 'SEGI_33093' => 'sgi', 'SEGI_36110' => 'sgi', 'SEGI_40397' => 'sgi', 'SGA_v2.0_scaffold191G40426' => 'sas', 'SGA_v2.0_scaffold353G49717' => 'sas', 'SGA_v2.0_scaffold50G18550' => 'sas', 'SMO119G0173' => 'smo', 'SMO172G0002' => 'smo', 'Solyc09g082690.3' => 'sly', 'Solyc09g082700.2' => 'sly', 'Sopen09g031550' => 'spe', 'Sopen09g031560' => 'spe', 'Sp3g20540' => 'spa', 'Sp7g07580' => 'spa', 'TAR134G0002' => 'tar', 'TAR236G0001' => 'tar', 'TAR365G0892' => 'tar', 'TAR636G0166' => 'tar', 'TAR636G0646' => 'tar', 'TAR636G0869' => 'tar', 'TAR636G1317' => 'tar', 'TAR636G1744' => 'tar', 'TAR636G3358' => 'tar', 'TAR636G3436' => 'tar', 'THA.LOC104803047' => 'tha', 'Thecc.04G238900' => 'tca', 'Thhalv10021557m.g' => 'esa', 'Thhalv10026318m.g' => 'esa', 'Thhalv10026335m.g' => 'esa', 'TPR.G17433' => 'tpr', 'TPR.G18915' => 'tpr', 'TPR.G26125' => 'tpr', 'TWI09G0677' => 'twi', 'TWI73G0287' => 'twi', 'unitig_748.g8326' => 'ugi', 'vmacro15370' => 'vma', 'vmacro15371' => 'vma', 'vmacro15372' => 'vma', 'vmacro15373' => 'vma', 'vmacro15374' => 'vma', 'VMungo0720G2826' => 'vmu', 'Zm00001eb116960' => 'zma', 'Zm00001eb301260' => 'zma', 'Zm00001eb301270' => 'zma' ), 'gf_id' => 'HOM05D001460', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001460' ), 'data_identifier' => 'HOM05D001460', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001460', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '433', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p22980' => 'bna', 'A01p32340' => 'bna', 'A03p42970' => 'bna', 'A05p25880' => 'bna', 'Aa31LG8G9320' => 'aar', 'Aa31LG8G9330' => 'aar', 'Aa31LG8G9340' => 'aar', 'Aa31sc221G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1034' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1528' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.829' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2222' => 'aag', 'Ah.12g058830' => 'amhyb', 'Ah.12g058840' => 'amhyb', 'AL3G37160' => 'aly', 'AL7G41310' => 'aly', 'Aqoxy5G00395' => 'aox', 'Aqoxy5G00396' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0C8NZA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5185HY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JZ1PRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MD3LS0' => 'arhy', 'AT3G22840' => 'ath', 'AT4G14690' => 'ath', 'ATR0665G054' => 'atr', 'Atru.chr4.2344' => 'acertr', 'Atru.chr4.2346' => 'acertr', 'Atru.chr4.2347' => 'acertr', 'Atru.chr4.2348' => 'acertr', 'Atru.chr4.2355' => 'acertr', 'Atru.chr4.2356' => 'acertr', 'Atru.chr4.2358' => 'acertr', 'Atru.chr4.2359' => 'acertr', 'Atru.chr4.2360' => 'acertr', 'Atru.chr4.2361' => 'acertr', 'AUR62030476' => 'cqu', 'AUR62030478' => 'cqu', 'AUR62030819' => 'cqu', 'AUR62030820' => 'cqu', 'BcaB03g14648' => 'bca', 'BcaB04g20492' => 'bca', 'BcaB06g26399' => 'bca', 'BcaC01g03416' => 'bca', 'BcaC01g03419' => 'bca', 'BcaC01g03421' => 'bca', 'BcaC01g03424' => 'bca', 'BcaC05g28012' => 'bca', 'BcaC09g49212' => 'bca', 'BcaC09g50140' => 'bca', 'BcaNung00346' => 'bca', 'BolC1t02785H' => 'bol', 'BolC1t04095H' => 'bol', 'BolC3t17545H' => 'bol', 'BolC5t32769H' => 'bol', 'BraA01t02211Z' => 'bra', 'BraA01t03359Z' => 'bra', 'BraA03t13441Z' => 'bra', 'BraA05t21476Z' => 'bra', 'C01p28420' => 'bna', 'C01p41350' => 'bna', 'C03p52750' => 'bna', 'C03p52780' => 'bna', 'C05p40270' => 'bna', 'CAN.G1437.9' => 'can', 'CANSAT78G0035' => 'cansat', 'CANSAT78G1036' => 'cansat', 'CANSAT78G2272' => 'cansat', 'CANSAT78G2478' => 'cansat', 'CARHR098700' => 'chi', 'CARHR221120' => 'chi', 'CARHR221150' => 'chi', 'Carub.0003s2297' => 'cru', 'Carub.0007s2749' => 'cru', 'Carub.0007s2750' => 'cru', 'Carub.0007s2751' => 'cru', 'Ca_10849_v3' => 'car', 'Cc03_g04300' => 'ccan', 'CDE02G3648' => 'cde', 'CDE05G0060' => 'cde', 'CDE05G0692' => 'cde', 'CDE05G2285' => 'cde', 'CDE05G2884' => 'cde', 'CDE05G3072' => 'cde', 'Cfa008439' => 'cfa', 'Cfa008441' => 'cfa', 'Cfa008443' => 'cfa', 'Cfa008448' => 'cfa', 'Ciclev10005974m.g' => 'ccl', 'Ciclev10006006m.g' => 'ccl', 'Ciclev10006775m.g' => 'ccl', 'CiPaw.02G120400' => 'cil', 'CiPaw.02G120500' => 'cil', 'CiPaw.02G120600' => 'cil', 'ClCG05G004850' => 'cla', 'COL.COLO4_21566' => 'col', 'Cpa.g.sc44.124' => 'cpa', 'Cre07.g320400' => 'cre', 'Cre07.g320450' => 'cre', 'Cre08.g384650' => 'cre', 'Cre09.g393173' => 'cre', 'Cre09.g394325' => 'cre', 'Cre14.g626750' => 'cre', 'Cre16.g679250' => 'cre', 'CsaV3_3G012890' => 'csa', 'CSS0010865' => 'camsi', 'CSS0044338' => 'camsi', 'DCAR_002366' => 'dca', 'DCAR_030687' => 'dca', 'DCAR_030688' => 'dca', 'Dinv14047' => 'din', 'Dinv14048' => 'din', 'Duzib151G0105' => 'dzi', 'Duzib151G0114' => 'dzi', 'Duzib212G1029' => 'dzi', 'ECA232G3536' => 'eca', 'ECA240G0786' => 'eca', 'ECA240G1802' => 'eca', 'ECA240G3760' => 'eca', 'ECA240G3920' => 'eca', 'EL10Ac5g12536' => 'bvu', 'EL10Ac5g12537' => 'bvu', 'EL10Ac5g12538' => 'bvu', 'Eucgr.B01004' => 'egr', 'Eucgr.B01006' => 'egr', 'Eucgr.B01007' => 'egr', 'Eucgr.B01008' => 'egr', 'Eucgr.B01895' => 'egr', 'Eucgr.B01896' => 'egr', 'FAN04G1456' => 'fan', 'FAN08G1769' => 'fan', 'FAN08G2160' => 'fan', 'FAN13G2403' => 'fan', 'FAN13G3303' => 'fan', 'FAN15G2435' => 'fan', 'FAN17G0672' => 'fan', 'FAN17G2441' => 'fan', 'FAN18G1024' => 'fan', 'FAN22G1458' => 'fan', 'FAN24G0037' => 'fan', 'FAN24G0429' => 'fan', 'FAN24G2387' => 'fan', 'FAN27G2746' => 'fan', 'FvH4_2g20400' => 'fve', 'FvH4_2g20420' => 'fve', 'FvH4_2g20430' => 'fve', 'FvH4_4g01270' => 'fve', 'FvH4_4g01290' => 'fve', 'FvH4_4g01300' => 'fve', 'FvH4_4g01310' => 'fve', 'FvH4_4g01330' => 'fve', 'FvH4_5g09070' => 'fve', 'Glyma.10G243800' => 'gma', 'Glyma.20G150600' => 'gma', 'Gohir.A09G219200' => 'ghi', 'Gohir.A09G219300' => 'ghi', 'Gohir.D09G221400' => 'ghi', 'Gohir.D09G221500' => 'ghi', 'Gorai.006G242600' => 'gra', 'Gorai.006G242700' => 'gra', 'GSVIVG01018044001' => 'vvi', 'HanXRQChr03g0083821' => 'han', 'HanXRQChr03g0083841' => 'han', 'HanXRQChr03g0083881' => 'han', 'HanXRQChr03g0083901' => 'han', 'HanXRQChr03g0083921' => 'han', 'HanXRQChr03g0085331' => 'han', 'HanXRQChr03g0085361' => 'han', 'HanXRQChr03g0085411' => 'han', 'HanXRQChr03g0085421' => 'han', 'HanXRQChr03g0085431' => 'han', 'HanXRQChr08g0221991' => 'han', 'HanXRQChr11g0336061' => 'han', 'HanXRQChr11g0336411' => 'han', 'Haze_11234' => 'cav', 'Hma1.2p1_0549F.1_g177010' => 'hma', 'Hma1.2p1_0602F.1_g187630' => 'hma', 'Hund14876' => 'sun', 'Hund14879' => 'sun', 'Lalb_Chr06g0160741' => 'lal', 'Lalb_Chr21g0304781' => 'lal', 'Lj3A726G19' => 'lonja', 'Lj3A726T23' => 'lonja', 'Lj3A726T24' => 'lonja', 'Lj3A726T25' => 'lonja', 'Lj3A727T17' => 'lonja', 'Lj3C726T0' => 'lonja', 'Lj3C726T2' => 'lonja', 'Lj3P725T35' => 'lonja', 'Lj3P727T10' => 'lonja', 'Lj3P727T12' => 'lonja', 'Lj3P727T14' => 'lonja', 'Lj5g0023109' => 'lja', 'Lj6P646T44' => 'lonja', 'Lsat_1_v5_gn_6_75760' => 'lsa', 'Lsat_1_v5_gn_6_75800' => 'lsa', 'Lsat_1_v5_gn_6_75900' => 'lsa', 'Lsat_1_v5_gn_6_76240' => 'lsa', 'Lsat_1_v5_gn_6_76441' => 'lsa', 'Lsat_1_v5_gn_6_76700' => 'lsa', 'Lsat_1_v5_gn_6_76760' => 'lsa', 'Manes.15G033100' => 'mes', 'Mapoly0004s0074' => 'mpo', 'Mapoly0004s0075' => 'mpo', 'Mapoly0004s0163' => 'mpo', 'Mapoly0004s0164' => 'mpo', 'Mapoly0021s0018' => 'mpo', 'Mapoly0041s0136' => 'mpo', 'Mapoly0041s0137' => 'mpo', 'Mapoly0041s0138' => 'mpo', 'Mapoly0041s0139' => 'mpo', 'Mapoly0041s0141' => 'mpo', 'Mapoly0041s0142' => 'mpo', 'Mapoly0041s0143' => 'mpo', 'Mapoly0041s0144' => 'mpo', 'Mapoly0041s0145' => 'mpo', 'Mapoly0047s0106' => 'mpo', 'Mapoly0047s0108' => 'mpo', 'Mapoly0050s0051' => 'mpo', 'Mapoly0050s0052' => 'mpo', 'Mapoly0050s0053' => 'mpo', 'Mapoly0058s0013' => 'mpo', 'Mapoly0091s0078' => 'mpo', 'Mapoly0091s0079' => 'mpo', 'Mapoly0091s0080' => 'mpo', 'Mapoly0091s0081' => 'mpo', 'Mapoly0278s0004' => 'mpo', 'Mapoly0278s0005' => 'mpo', 'Mapoly0278s0006' => 'mpo', 'MBI11_g30648_MAGBIO' => 'mbi', 'MCO03G194' => 'mco', 'MCO03G590' => 'mco', 'MCO07G312' => 'mco', 'MCO10G318' => 'mco', 'MCO12G244' => 'mco', 'MCO13G148' => 'mco', 'MCO13G194' => 'mco', 'MCO16G238' => 'mco', 'MD06G1134100' => 'mdo', 'MD13G1200100' => 'mdo', 'MD13G1200300' => 'mdo', 'MD13G1200600' => 'mdo', 'MD14G1150400' => 'mdo', 'MD16G1200000' => 'mdo', 'Medtr1g102570' => 'mtr', 'Medtr1g102780' => 'mtr', 'Medtr1g102800' => 'mtr', 'Medtr1g102810' => 'mtr', 'Medtr1g102830' => 'mtr', 'MELO3C006499.2' => 'cme', 'Migut.G00385' => 'egut', 'MSTRG.4063' => 'ama', 'Nitab4.5_0000090g0260' => 'nta', 'Nitab4.5_0000977g0030' => 'nta', 'Nitab4.5_0002541g0040' => 'nta', 'Nitab4.5_0007068g0040' => 'nta', 'Nn005s41408' => 'nnu', 'Nn005s41410' => 'nnu', 'Oeu010310.1' => 'oeu', 'Oeu010311.1' => 'oeu', 'Oeu043472.1' => 'oeu', 'Os01g0246400' => 'osa', 'Os04g0267950' => 'osa', 'Os07g0178700' => 'osa', 'Os07g0178800' => 'osa', 'Peaxi162Scf00316g00046' => 'pax', 'Peaxi162Scf00316g00049' => 'pax', 'Peaxi162Scf00316g00059' => 'pax', 'Peaxi162Scf00316g00328' => 'pax', 'Peaxi162Scf00316g00329' => 'pax', 'Peaxi162Scf00316g00411' => 'pax', 'Peaxi162Scf00316g00521' => 'pax', 'Peaxi162Scf00492g00068' => 'pax', 'Peaxi162Scf35631g00002' => 'pax', 'PGR142G3720' => 'pgr', 'PGSC0003DMG400006442' => 'stu', 'Phvul.007G062000' => 'pvu', 'Potri.008G157750' => 'ptr', 'Potri.008G157900' => 'ptr', 'Potri.008G158000' => 'ptr', 'Potri.008G158200' => 'ptr', 'Pp3c11_7280' => 'ppa', 'Pp3c11_7980' => 'ppa', 'Pp3c12_19450' => 'ppa', 'Pp3c14_1480' => 'ppa', 'Pp3c14_1501' => 'ppa', 'Pp3c16_4900' => 'ppa', 'Pp3c16_5010' => 'ppa', 'Pp3c16_5060' => 'ppa', 'Pp3c19_18250' => 'ppa', 'Pp3c23_8530' => 'ppa', 'Pp3c23_8550' => 'ppa', 'Pp3c24_9670' => 'ppa', 'Pp3c2_21390' => 'ppa', 'Pp3c2_31380' => 'ppa', 'Pp3c3_16620' => 'ppa', 'Pp3c3_8090' => 'ppa', 'Pp3c3_8110' => 'ppa', 'Pp3c3_8130' => 'ppa', 'Pp3c3_8150' => 'ppa', 'Pp3c4_14320' => 'ppa', 'Pp3c6_2560' => 'ppa', 'Pp3c9_16700' => 'ppa', 'PRCOL_00000234' => 'pco', 'PRCOL_00000235' => 'pco', 'PRCOL_00000777' => 'pco', 'PRCOL_00002344' => 'pco', 'PRCOL_00002372' => 'pco', 'PRCOL_00006120' => 'pco', 'Prupe.1G021400' => 'ppe', 'Prupe.1G021500' => 'ppe', 'Prupe.1G021600' => 'ppe', 'Prupe.1G021700' => 'ppe', 'Prupe.1G021800' => 'ppe', 'Prupe.5G145100' => 'ppe', 'Psat6g204040' => 'psa', 'Psat6g204800' => 'psa', 'Psat6g204920' => 'psa', 'Psat6g204960' => 'psa', 'Psat6g205080' => 'psa', 'PSO017G0271' => 'pso', 'PSO017G1276' => 'pso', 'PSO017G1429' => 'pso', 'PSO017G1861' => 'pso', 'PSO017G2787' => 'pso', 'PSO017G4466' => 'pso', 'PSO017G5118' => 'pso', 'PSO017G5420' => 'pso', 'PSO063G3678' => 'pso', 'PSO210G0546' => 'pso', 'PSO317G0001' => 'pso', 'PSO357G0512' => 'pso', 'PSO478G2682' => 'pso', 'PSO647G0001' => 'pso', 'PSO675G0001' => 'pso', 'PSO675G2699' => 'pso', 'PSO675G2849' => 'pso', 'PSO675G4991' => 'pso', 'PSO689G0001' => 'pso', 'QL06p000916' => 'qlo', 'QL06p000921' => 'qlo', 'QL06p001398' => 'qlo', 'QL06p001407' => 'qlo', 'QL06p002031' => 'qlo', 'RcHm_v2.0_Chr4g0387791' => 'rch', 'RcHm_v2.0_Chr4g0387801' => 'rch', 'RcHm_v2.0_Chr6g0286501' => 'rch', 'RcHm_v2.0_Chr6g0286511' => 'rch', 'RcHm_v2.0_Chr6g0286521' => 'rch', 'RcHm_v2.0_Chr6g0286531' => 'rch', 'RcHm_v2.0_Chr7g0189141' => 'rch', 'Rhsim02G0028700' => 'rsi', 'Rhsim02G0028800' => 'rsi', 'Rhsim02G0028900' => 'rsi', 'Rhsim02G0029000' => 'rsi', 'Rhsim02G0029100' => 'rsi', 'Rhsim02G0029200' => 'rsi', 'Rhsim02G0029300' => 'rsi', 'Rhsim02G0029400' => 'rsi', 'Rhsim02G0029500' => 'rsi', 'Rhsim02G0029600' => 'rsi', 'RhsimUnG0024000' => 'rsi', 'RhsimUnG0024100' => 'rsi', 'RhsimUnG0024200' => 'rsi', 'RhsimUnG0024300' => 'rsi', 'RhsimUnG0024400' => 'rsi', 'RhsimUnG0024500' => 'rsi', 'RhsimUnG0024700' => 'rsi', 'RhsimUnG0024800' => 'rsi', 'RhsimUnG0024900' => 'rsi', 'RhsimUnG0025100' => 'rsi', 'Sabra08G0120200' => 'sbr', 'Sabra08G0120300' => 'sbr', 'Sabra08G0120500' => 'sbr', 'Sabra08G0120600' => 'sbr', 'Sabra10G0158900' => 'sbr', 'SalBow2G3492' => 'sbo', 'Sc13g0004760' => 'sci', 'Sc13g0004770' => 'sci', 'Sed0003417' => 'sed', 'Sed0019750' => 'sed', 'SEGI_03419' => 'sgi', 'SEGI_05907' => 'sgi', 'SEGI_10682' => 'sgi', 'SEGI_13528' => 'sgi', 'SEGI_16081' => 'sgi', 'SEGI_19370' => 'sgi', 'SEGI_21015' => 'sgi', 'SEGI_21944' => 'sgi', 'SEGI_32906' => 'sgi', 'SEGI_33093' => 'sgi', 'SEGI_36110' => 'sgi', 'SEGI_40397' => 'sgi', 'SGA_v2.0_scaffold191G40426' => 'sas', 'SGA_v2.0_scaffold353G49717' => 'sas', 'SGA_v2.0_scaffold50G18550' => 'sas', 'SMO119G0173' => 'smo', 'SMO172G0002' => 'smo', 'Solyc09g082690.3' => 'sly', 'Solyc09g082700.2' => 'sly', 'Sopen09g031550' => 'spe', 'Sopen09g031560' => 'spe', 'Sp3g20540' => 'spa', 'Sp7g07580' => 'spa', 'TAR134G0002' => 'tar', 'TAR236G0001' => 'tar', 'TAR365G0892' => 'tar', 'TAR636G0166' => 'tar', 'TAR636G0646' => 'tar', 'TAR636G0869' => 'tar', 'TAR636G1317' => 'tar', 'TAR636G1744' => 'tar', 'TAR636G3358' => 'tar', 'TAR636G3436' => 'tar', 'THA.LOC104803047' => 'tha', 'Thecc.04G238900' => 'tca', 'Thhalv10021557m.g' => 'esa', 'Thhalv10026318m.g' => 'esa', 'Thhalv10026335m.g' => 'esa', 'TPR.G17433' => 'tpr', 'TPR.G18915' => 'tpr', 'TPR.G26125' => 'tpr', 'TWI09G0677' => 'twi', 'TWI73G0287' => 'twi', 'unitig_748.g8326' => 'ugi', 'vmacro15370' => 'vma', 'vmacro15371' => 'vma', 'vmacro15372' => 'vma', 'vmacro15373' => 'vma', 'vmacro15374' => 'vma', 'VMungo0720G2826' => 'vmu', 'Zm00001eb116960' => 'zma', 'Zm00001eb301260' => 'zma', 'Zm00001eb301270' => 'zma' ) $gf_id = 'HOM05D001460' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001460' ) $data_identifier = 'HOM05D001460' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 4, 'aag' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 2, 'aox' => (int) 2, 'arhy' => (int) 4, 'ath' => (int) 2, 'atr' => (int) 1, 'acertr' => (int) 10, 'cqu' => (int) 4, 'bca' => (int) 11, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 1, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 1, 'ccan' => (int) 1, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 1, 'col' => (int) 1, 'cpa' => (int) 1, 'cre' => (int) 7, 'csa' => (int) 1, 'camsi' => (int) 2, 'dca' => (int) 3, 'din' => (int) 2, 'dzi' => (int) 3, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 14, 'fve' => (int) 9, 'gma' => (int) 2, 'ghi' => (int) 4, 'gra' => (int) 2, 'vvi' => (int) 1, 'han' => (int) 13, 'cav' => (int) 1, 'hma' => (int) 2, 'sun' => (int) 2, 'lal' => (int) 2, 'lonja' => (int) 12, 'lja' => (int) 1, 'lsa' => (int) 7, 'mes' => (int) 1, 'mpo' => (int) 27, 'mbi' => (int) 1, 'mco' => (int) 8, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 1, 'egut' => (int) 1, 'ama' => (int) 1, 'nta' => (int) 4, 'nnu' => (int) 2, 'oeu' => (int) 3, 'osa' => (int) 4, 'pax' => (int) 9, 'pgr' => (int) 1, 'stu' => (int) 1, 'pvu' => (int) 1, 'ptr' => (int) 4, 'ppa' => (int) 22, 'pco' => (int) 6, 'ppe' => (int) 6, 'psa' => (int) 5, 'pso' => (int) 19, 'qlo' => (int) 5, 'rch' => (int) 7, 'rsi' => (int) 20, 'sbr' => (int) 5, 'sbo' => (int) 1, 'sci' => (int) 2, 'sed' => (int) 2, 'sgi' => (int) 12, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 2, 'tar' => (int) 10, 'tha' => (int) 1, 'tca' => (int) 1, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 2, 'ugi' => (int) 1, 'vma' => (int) 5, 'vmu' => (int) 1, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb301270' $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' => 'HOM05D001460', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '433', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p22980' => 'bna', 'A01p32340' => 'bna', 'A03p42970' => 'bna', 'A05p25880' => 'bna', 'Aa31LG8G9320' => 'aar', 'Aa31LG8G9330' => 'aar', 'Aa31LG8G9340' => 'aar', 'Aa31sc221G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1034' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1528' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.829' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2222' => 'aag', 'Ah.12g058830' => 'amhyb', 'Ah.12g058840' => 'amhyb', 'AL3G37160' => 'aly', 'AL7G41310' => 'aly', 'Aqoxy5G00395' => 'aox', 'Aqoxy5G00396' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0C8NZA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5185HY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JZ1PRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MD3LS0' => 'arhy', 'AT3G22840' => 'ath', 'AT4G14690' => 'ath', 'ATR0665G054' => 'atr', 'Atru.chr4.2344' => 'acertr', 'Atru.chr4.2346' => 'acertr', 'Atru.chr4.2347' => 'acertr', 'Atru.chr4.2348' => 'acertr', 'Atru.chr4.2355' => 'acertr', 'Atru.chr4.2356' => 'acertr', 'Atru.chr4.2358' => 'acertr', 'Atru.chr4.2359' => 'acertr', 'Atru.chr4.2360' => 'acertr', 'Atru.chr4.2361' => 'acertr', 'AUR62030476' => 'cqu', 'AUR62030478' => 'cqu', 'AUR62030819' => 'cqu', 'AUR62030820' => 'cqu', 'BcaB03g14648' => 'bca', 'BcaB04g20492' => 'bca', 'BcaB06g26399' => 'bca', 'BcaC01g03416' => 'bca', 'BcaC01g03419' => 'bca', 'BcaC01g03421' => 'bca', 'BcaC01g03424' => 'bca', 'BcaC05g28012' => 'bca', 'BcaC09g49212' => 'bca', 'BcaC09g50140' => 'bca', 'BcaNung00346' => 'bca', 'BolC1t02785H' => 'bol', 'BolC1t04095H' => 'bol', 'BolC3t17545H' => 'bol', 'BolC5t32769H' => 'bol', 'BraA01t02211Z' => 'bra', 'BraA01t03359Z' => 'bra', 'BraA03t13441Z' => 'bra', 'BraA05t21476Z' => 'bra', 'C01p28420' => 'bna', 'C01p41350' => 'bna', 'C03p52750' => 'bna', 'C03p52780' => 'bna', 'C05p40270' => 'bna', 'CAN.G1437.9' => 'can', 'CANSAT78G0035' => 'cansat', 'CANSAT78G1036' => 'cansat', 'CANSAT78G2272' => 'cansat', 'CANSAT78G2478' => 'cansat', 'CARHR098700' => 'chi', 'CARHR221120' => 'chi', 'CARHR221150' => 'chi', 'Carub.0003s2297' => 'cru', 'Carub.0007s2749' => 'cru', 'Carub.0007s2750' => 'cru', 'Carub.0007s2751' => 'cru', 'Ca_10849_v3' => 'car', 'Cc03_g04300' => 'ccan', 'CDE02G3648' => 'cde', 'CDE05G0060' => 'cde', 'CDE05G0692' => 'cde', 'CDE05G2285' => 'cde', 'CDE05G2884' => 'cde', 'CDE05G3072' => 'cde', 'Cfa008439' => 'cfa', 'Cfa008441' => 'cfa', 'Cfa008443' => 'cfa', 'Cfa008448' => 'cfa', 'Ciclev10005974m.g' => 'ccl', 'Ciclev10006006m.g' => 'ccl', 'Ciclev10006775m.g' => 'ccl', 'CiPaw.02G120400' => 'cil', 'CiPaw.02G120500' => 'cil', 'CiPaw.02G120600' => 'cil', 'ClCG05G004850' => 'cla', 'COL.COLO4_21566' => 'col', 'Cpa.g.sc44.124' => 'cpa', 'Cre07.g320400' => 'cre', 'Cre07.g320450' => 'cre', 'Cre08.g384650' => 'cre', 'Cre09.g393173' => 'cre', 'Cre09.g394325' => 'cre', 'Cre14.g626750' => 'cre', 'Cre16.g679250' => 'cre', 'CsaV3_3G012890' => 'csa', 'CSS0010865' => 'camsi', 'CSS0044338' => 'camsi', 'DCAR_002366' => 'dca', 'DCAR_030687' => 'dca', 'DCAR_030688' => 'dca', 'Dinv14047' => 'din', 'Dinv14048' => 'din', 'Duzib151G0105' => 'dzi', 'Duzib151G0114' => 'dzi', 'Duzib212G1029' => 'dzi', 'ECA232G3536' => 'eca', 'ECA240G0786' => 'eca', 'ECA240G1802' => 'eca', 'ECA240G3760' => 'eca', 'ECA240G3920' => 'eca', 'EL10Ac5g12536' => 'bvu', 'EL10Ac5g12537' => 'bvu', 'EL10Ac5g12538' => 'bvu', 'Eucgr.B01004' => 'egr', 'Eucgr.B01006' => 'egr', 'Eucgr.B01007' => 'egr', 'Eucgr.B01008' => 'egr', 'Eucgr.B01895' => 'egr', 'Eucgr.B01896' => 'egr', 'FAN04G1456' => 'fan', 'FAN08G1769' => 'fan', 'FAN08G2160' => 'fan', 'FAN13G2403' => 'fan', 'FAN13G3303' => 'fan', 'FAN15G2435' => 'fan', 'FAN17G0672' => 'fan', 'FAN17G2441' => 'fan', 'FAN18G1024' => 'fan', 'FAN22G1458' => 'fan', 'FAN24G0037' => 'fan', 'FAN24G0429' => 'fan', 'FAN24G2387' => 'fan', 'FAN27G2746' => 'fan', 'FvH4_2g20400' => 'fve', 'FvH4_2g20420' => 'fve', 'FvH4_2g20430' => 'fve', 'FvH4_4g01270' => 'fve', 'FvH4_4g01290' => 'fve', 'FvH4_4g01300' => 'fve', 'FvH4_4g01310' => 'fve', 'FvH4_4g01330' => 'fve', 'FvH4_5g09070' => 'fve', 'Glyma.10G243800' => 'gma', 'Glyma.20G150600' => 'gma', 'Gohir.A09G219200' => 'ghi', 'Gohir.A09G219300' => 'ghi', 'Gohir.D09G221400' => 'ghi', 'Gohir.D09G221500' => 'ghi', 'Gorai.006G242600' => 'gra', 'Gorai.006G242700' => 'gra', 'GSVIVG01018044001' => 'vvi', 'HanXRQChr03g0083821' => 'han', 'HanXRQChr03g0083841' => 'han', 'HanXRQChr03g0083881' => 'han', 'HanXRQChr03g0083901' => 'han', 'HanXRQChr03g0083921' => 'han', 'HanXRQChr03g0085331' => 'han', 'HanXRQChr03g0085361' => 'han', 'HanXRQChr03g0085411' => 'han', 'HanXRQChr03g0085421' => 'han', 'HanXRQChr03g0085431' => 'han', 'HanXRQChr08g0221991' => 'han', 'HanXRQChr11g0336061' => 'han', 'HanXRQChr11g0336411' => 'han', 'Haze_11234' => 'cav', 'Hma1.2p1_0549F.1_g177010' => 'hma', 'Hma1.2p1_0602F.1_g187630' => 'hma', 'Hund14876' => 'sun', 'Hund14879' => 'sun', 'Lalb_Chr06g0160741' => 'lal', 'Lalb_Chr21g0304781' => 'lal', 'Lj3A726G19' => 'lonja', 'Lj3A726T23' => 'lonja', 'Lj3A726T24' => 'lonja', 'Lj3A726T25' => 'lonja', 'Lj3A727T17' => 'lonja', 'Lj3C726T0' => 'lonja', 'Lj3C726T2' => 'lonja', 'Lj3P725T35' => 'lonja', 'Lj3P727T10' => 'lonja', 'Lj3P727T12' => 'lonja', 'Lj3P727T14' => 'lonja', 'Lj5g0023109' => 'lja', 'Lj6P646T44' => 'lonja', 'Lsat_1_v5_gn_6_75760' => 'lsa', 'Lsat_1_v5_gn_6_75800' => 'lsa', 'Lsat_1_v5_gn_6_75900' => 'lsa', 'Lsat_1_v5_gn_6_76240' => 'lsa', 'Lsat_1_v5_gn_6_76441' => 'lsa', 'Lsat_1_v5_gn_6_76700' => 'lsa', 'Lsat_1_v5_gn_6_76760' => 'lsa', 'Manes.15G033100' => 'mes', 'Mapoly0004s0074' => 'mpo', 'Mapoly0004s0075' => 'mpo', 'Mapoly0004s0163' => 'mpo', 'Mapoly0004s0164' => 'mpo', 'Mapoly0021s0018' => 'mpo', 'Mapoly0041s0136' => 'mpo', 'Mapoly0041s0137' => 'mpo', 'Mapoly0041s0138' => 'mpo', 'Mapoly0041s0139' => 'mpo', 'Mapoly0041s0141' => 'mpo', 'Mapoly0041s0142' => 'mpo', 'Mapoly0041s0143' => 'mpo', 'Mapoly0041s0144' => 'mpo', 'Mapoly0041s0145' => 'mpo', 'Mapoly0047s0106' => 'mpo', 'Mapoly0047s0108' => 'mpo', 'Mapoly0050s0051' => 'mpo', 'Mapoly0050s0052' => 'mpo', 'Mapoly0050s0053' => 'mpo', 'Mapoly0058s0013' => 'mpo', 'Mapoly0091s0078' => 'mpo', 'Mapoly0091s0079' => 'mpo', 'Mapoly0091s0080' => 'mpo', 'Mapoly0091s0081' => 'mpo', 'Mapoly0278s0004' => 'mpo', 'Mapoly0278s0005' => 'mpo', 'Mapoly0278s0006' => 'mpo', 'MBI11_g30648_MAGBIO' => 'mbi', 'MCO03G194' => 'mco', 'MCO03G590' => 'mco', 'MCO07G312' => 'mco', 'MCO10G318' => 'mco', 'MCO12G244' => 'mco', 'MCO13G148' => 'mco', 'MCO13G194' => 'mco', 'MCO16G238' => 'mco', 'MD06G1134100' => 'mdo', 'MD13G1200100' => 'mdo', 'MD13G1200300' => 'mdo', 'MD13G1200600' => 'mdo', 'MD14G1150400' => 'mdo', 'MD16G1200000' => 'mdo', 'Medtr1g102570' => 'mtr', 'Medtr1g102780' => 'mtr', 'Medtr1g102800' => 'mtr', 'Medtr1g102810' => 'mtr', 'Medtr1g102830' => 'mtr', 'MELO3C006499.2' => 'cme', 'Migut.G00385' => 'egut', 'MSTRG.4063' => 'ama', 'Nitab4.5_0000090g0260' => 'nta', 'Nitab4.5_0000977g0030' => 'nta', 'Nitab4.5_0002541g0040' => 'nta', 'Nitab4.5_0007068g0040' => 'nta', 'Nn005s41408' => 'nnu', 'Nn005s41410' => 'nnu', 'Oeu010310.1' => 'oeu', 'Oeu010311.1' => 'oeu', 'Oeu043472.1' => 'oeu', 'Os01g0246400' => 'osa', 'Os04g0267950' => 'osa', 'Os07g0178700' => 'osa', 'Os07g0178800' => 'osa', 'Peaxi162Scf00316g00046' => 'pax', 'Peaxi162Scf00316g00049' => 'pax', 'Peaxi162Scf00316g00059' => 'pax', 'Peaxi162Scf00316g00328' => 'pax', 'Peaxi162Scf00316g00329' => 'pax', 'Peaxi162Scf00316g00411' => 'pax', 'Peaxi162Scf00316g00521' => 'pax', 'Peaxi162Scf00492g00068' => 'pax', 'Peaxi162Scf35631g00002' => 'pax', 'PGR142G3720' => 'pgr', 'PGSC0003DMG400006442' => 'stu', 'Phvul.007G062000' => 'pvu', 'Potri.008G157750' => 'ptr', 'Potri.008G157900' => 'ptr', 'Potri.008G158000' => 'ptr', 'Potri.008G158200' => 'ptr', 'Pp3c11_7280' => 'ppa', 'Pp3c11_7980' => 'ppa', 'Pp3c12_19450' => 'ppa', 'Pp3c14_1480' => 'ppa', 'Pp3c14_1501' => 'ppa', 'Pp3c16_4900' => 'ppa', 'Pp3c16_5010' => 'ppa', 'Pp3c16_5060' => 'ppa', 'Pp3c19_18250' => 'ppa', 'Pp3c23_8530' => 'ppa', 'Pp3c23_8550' => 'ppa', 'Pp3c24_9670' => 'ppa', 'Pp3c2_21390' => 'ppa', 'Pp3c2_31380' => 'ppa', 'Pp3c3_16620' => 'ppa', 'Pp3c3_8090' => 'ppa', 'Pp3c3_8110' => 'ppa', 'Pp3c3_8130' => 'ppa', 'Pp3c3_8150' => 'ppa', 'Pp3c4_14320' => 'ppa', 'Pp3c6_2560' => 'ppa', 'Pp3c9_16700' => 'ppa', 'PRCOL_00000234' => 'pco', 'PRCOL_00000235' => 'pco', 'PRCOL_00000777' => 'pco', 'PRCOL_00002344' => 'pco', 'PRCOL_00002372' => 'pco', 'PRCOL_00006120' => 'pco', 'Prupe.1G021400' => 'ppe', 'Prupe.1G021500' => 'ppe', 'Prupe.1G021600' => 'ppe', 'Prupe.1G021700' => 'ppe', 'Prupe.1G021800' => 'ppe', 'Prupe.5G145100' => 'ppe', 'Psat6g204040' => 'psa', 'Psat6g204800' => 'psa', 'Psat6g204920' => 'psa', 'Psat6g204960' => 'psa', 'Psat6g205080' => 'psa', 'PSO017G0271' => 'pso', 'PSO017G1276' => 'pso', 'PSO017G1429' => 'pso', 'PSO017G1861' => 'pso', 'PSO017G2787' => 'pso', 'PSO017G4466' => 'pso', 'PSO017G5118' => 'pso', 'PSO017G5420' => 'pso', 'PSO063G3678' => 'pso', 'PSO210G0546' => 'pso', 'PSO317G0001' => 'pso', 'PSO357G0512' => 'pso', 'PSO478G2682' => 'pso', 'PSO647G0001' => 'pso', 'PSO675G0001' => 'pso', 'PSO675G2699' => 'pso', 'PSO675G2849' => 'pso', 'PSO675G4991' => 'pso', 'PSO689G0001' => 'pso', 'QL06p000916' => 'qlo', 'QL06p000921' => 'qlo', 'QL06p001398' => 'qlo', 'QL06p001407' => 'qlo', 'QL06p002031' => 'qlo', 'RcHm_v2.0_Chr4g0387791' => 'rch', 'RcHm_v2.0_Chr4g0387801' => 'rch', 'RcHm_v2.0_Chr6g0286501' => 'rch', 'RcHm_v2.0_Chr6g0286511' => 'rch', 'RcHm_v2.0_Chr6g0286521' => 'rch', 'RcHm_v2.0_Chr6g0286531' => 'rch', 'RcHm_v2.0_Chr7g0189141' => 'rch', 'Rhsim02G0028700' => 'rsi', 'Rhsim02G0028800' => 'rsi', 'Rhsim02G0028900' => 'rsi', 'Rhsim02G0029000' => 'rsi', 'Rhsim02G0029100' => 'rsi', 'Rhsim02G0029200' => 'rsi', 'Rhsim02G0029300' => 'rsi', 'Rhsim02G0029400' => 'rsi', 'Rhsim02G0029500' => 'rsi', 'Rhsim02G0029600' => 'rsi', 'RhsimUnG0024000' => 'rsi', 'RhsimUnG0024100' => 'rsi', 'RhsimUnG0024200' => 'rsi', 'RhsimUnG0024300' => 'rsi', 'RhsimUnG0024400' => 'rsi', 'RhsimUnG0024500' => 'rsi', 'RhsimUnG0024700' => 'rsi', 'RhsimUnG0024800' => 'rsi', 'RhsimUnG0024900' => 'rsi', 'RhsimUnG0025100' => 'rsi', 'Sabra08G0120200' => 'sbr', 'Sabra08G0120300' => 'sbr', 'Sabra08G0120500' => 'sbr', 'Sabra08G0120600' => 'sbr', 'Sabra10G0158900' => 'sbr', 'SalBow2G3492' => 'sbo', 'Sc13g0004760' => 'sci', 'Sc13g0004770' => 'sci', 'Sed0003417' => 'sed', 'Sed0019750' => 'sed', 'SEGI_03419' => 'sgi', 'SEGI_05907' => 'sgi', 'SEGI_10682' => 'sgi', 'SEGI_13528' => 'sgi', 'SEGI_16081' => 'sgi', 'SEGI_19370' => 'sgi', 'SEGI_21015' => 'sgi', 'SEGI_21944' => 'sgi', 'SEGI_32906' => 'sgi', 'SEGI_33093' => 'sgi', 'SEGI_36110' => 'sgi', 'SEGI_40397' => 'sgi', 'SGA_v2.0_scaffold191G40426' => 'sas', 'SGA_v2.0_scaffold353G49717' => 'sas', 'SGA_v2.0_scaffold50G18550' => 'sas', 'SMO119G0173' => 'smo', 'SMO172G0002' => 'smo', 'Solyc09g082690.3' => 'sly', 'Solyc09g082700.2' => 'sly', 'Sopen09g031550' => 'spe', 'Sopen09g031560' => 'spe', 'Sp3g20540' => 'spa', 'Sp7g07580' => 'spa', 'TAR134G0002' => 'tar', 'TAR236G0001' => 'tar', 'TAR365G0892' => 'tar', 'TAR636G0166' => 'tar', 'TAR636G0646' => 'tar', 'TAR636G0869' => 'tar', 'TAR636G1317' => 'tar', 'TAR636G1744' => 'tar', 'TAR636G3358' => 'tar', 'TAR636G3436' => 'tar', 'THA.LOC104803047' => 'tha', 'Thecc.04G238900' => 'tca', 'Thhalv10021557m.g' => 'esa', 'Thhalv10026318m.g' => 'esa', 'Thhalv10026335m.g' => 'esa', 'TPR.G17433' => 'tpr', 'TPR.G18915' => 'tpr', 'TPR.G26125' => 'tpr', 'TWI09G0677' => 'twi', 'TWI73G0287' => 'twi', 'unitig_748.g8326' => 'ugi', 'vmacro15370' => 'vma', 'vmacro15371' => 'vma', 'vmacro15372' => 'vma', 'vmacro15373' => 'vma', 'vmacro15374' => 'vma', 'VMungo0720G2826' => 'vmu', 'Zm00001eb116960' => 'zma', 'Zm00001eb301260' => 'zma', 'Zm00001eb301270' => 'zma' ), 'gf_id' => 'HOM05D001460', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001460' ), 'data_identifier' => 'HOM05D001460', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001460', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '433', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p22980' => 'bna', 'A01p32340' => 'bna', 'A03p42970' => 'bna', 'A05p25880' => 'bna', 'Aa31LG8G9320' => 'aar', 'Aa31LG8G9330' => 'aar', 'Aa31LG8G9340' => 'aar', 'Aa31sc221G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1034' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1528' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.829' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2222' => 'aag', 'Ah.12g058830' => 'amhyb', 'Ah.12g058840' => 'amhyb', 'AL3G37160' => 'aly', 'AL7G41310' => 'aly', 'Aqoxy5G00395' => 'aox', 'Aqoxy5G00396' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0C8NZA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5185HY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JZ1PRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MD3LS0' => 'arhy', 'AT3G22840' => 'ath', 'AT4G14690' => 'ath', 'ATR0665G054' => 'atr', 'Atru.chr4.2344' => 'acertr', 'Atru.chr4.2346' => 'acertr', 'Atru.chr4.2347' => 'acertr', 'Atru.chr4.2348' => 'acertr', 'Atru.chr4.2355' => 'acertr', 'Atru.chr4.2356' => 'acertr', 'Atru.chr4.2358' => 'acertr', 'Atru.chr4.2359' => 'acertr', 'Atru.chr4.2360' => 'acertr', 'Atru.chr4.2361' => 'acertr', 'AUR62030476' => 'cqu', 'AUR62030478' => 'cqu', 'AUR62030819' => 'cqu', 'AUR62030820' => 'cqu', 'BcaB03g14648' => 'bca', 'BcaB04g20492' => 'bca', 'BcaB06g26399' => 'bca', 'BcaC01g03416' => 'bca', 'BcaC01g03419' => 'bca', 'BcaC01g03421' => 'bca', 'BcaC01g03424' => 'bca', 'BcaC05g28012' => 'bca', 'BcaC09g49212' => 'bca', 'BcaC09g50140' => 'bca', 'BcaNung00346' => 'bca', 'BolC1t02785H' => 'bol', 'BolC1t04095H' => 'bol', 'BolC3t17545H' => 'bol', 'BolC5t32769H' => 'bol', 'BraA01t02211Z' => 'bra', 'BraA01t03359Z' => 'bra', 'BraA03t13441Z' => 'bra', 'BraA05t21476Z' => 'bra', 'C01p28420' => 'bna', 'C01p41350' => 'bna', 'C03p52750' => 'bna', 'C03p52780' => 'bna', 'C05p40270' => 'bna', 'CAN.G1437.9' => 'can', 'CANSAT78G0035' => 'cansat', 'CANSAT78G1036' => 'cansat', 'CANSAT78G2272' => 'cansat', 'CANSAT78G2478' => 'cansat', 'CARHR098700' => 'chi', 'CARHR221120' => 'chi', 'CARHR221150' => 'chi', 'Carub.0003s2297' => 'cru', 'Carub.0007s2749' => 'cru', 'Carub.0007s2750' => 'cru', 'Carub.0007s2751' => 'cru', 'Ca_10849_v3' => 'car', 'Cc03_g04300' => 'ccan', 'CDE02G3648' => 'cde', 'CDE05G0060' => 'cde', 'CDE05G0692' => 'cde', 'CDE05G2285' => 'cde', 'CDE05G2884' => 'cde', 'CDE05G3072' => 'cde', 'Cfa008439' => 'cfa', 'Cfa008441' => 'cfa', 'Cfa008443' => 'cfa', 'Cfa008448' => 'cfa', 'Ciclev10005974m.g' => 'ccl', 'Ciclev10006006m.g' => 'ccl', 'Ciclev10006775m.g' => 'ccl', 'CiPaw.02G120400' => 'cil', 'CiPaw.02G120500' => 'cil', 'CiPaw.02G120600' => 'cil', 'ClCG05G004850' => 'cla', 'COL.COLO4_21566' => 'col', 'Cpa.g.sc44.124' => 'cpa', 'Cre07.g320400' => 'cre', 'Cre07.g320450' => 'cre', 'Cre08.g384650' => 'cre', 'Cre09.g393173' => 'cre', 'Cre09.g394325' => 'cre', 'Cre14.g626750' => 'cre', 'Cre16.g679250' => 'cre', 'CsaV3_3G012890' => 'csa', 'CSS0010865' => 'camsi', 'CSS0044338' => 'camsi', 'DCAR_002366' => 'dca', 'DCAR_030687' => 'dca', 'DCAR_030688' => 'dca', 'Dinv14047' => 'din', 'Dinv14048' => 'din', 'Duzib151G0105' => 'dzi', 'Duzib151G0114' => 'dzi', 'Duzib212G1029' => 'dzi', 'ECA232G3536' => 'eca', 'ECA240G0786' => 'eca', 'ECA240G1802' => 'eca', 'ECA240G3760' => 'eca', 'ECA240G3920' => 'eca', 'EL10Ac5g12536' => 'bvu', 'EL10Ac5g12537' => 'bvu', 'EL10Ac5g12538' => 'bvu', 'Eucgr.B01004' => 'egr', 'Eucgr.B01006' => 'egr', 'Eucgr.B01007' => 'egr', 'Eucgr.B01008' => 'egr', 'Eucgr.B01895' => 'egr', 'Eucgr.B01896' => 'egr', 'FAN04G1456' => 'fan', 'FAN08G1769' => 'fan', 'FAN08G2160' => 'fan', 'FAN13G2403' => 'fan', 'FAN13G3303' => 'fan', 'FAN15G2435' => 'fan', 'FAN17G0672' => 'fan', 'FAN17G2441' => 'fan', 'FAN18G1024' => 'fan', 'FAN22G1458' => 'fan', 'FAN24G0037' => 'fan', 'FAN24G0429' => 'fan', 'FAN24G2387' => 'fan', 'FAN27G2746' => 'fan', 'FvH4_2g20400' => 'fve', 'FvH4_2g20420' => 'fve', 'FvH4_2g20430' => 'fve', 'FvH4_4g01270' => 'fve', 'FvH4_4g01290' => 'fve', 'FvH4_4g01300' => 'fve', 'FvH4_4g01310' => 'fve', 'FvH4_4g01330' => 'fve', 'FvH4_5g09070' => 'fve', 'Glyma.10G243800' => 'gma', 'Glyma.20G150600' => 'gma', 'Gohir.A09G219200' => 'ghi', 'Gohir.A09G219300' => 'ghi', 'Gohir.D09G221400' => 'ghi', 'Gohir.D09G221500' => 'ghi', 'Gorai.006G242600' => 'gra', 'Gorai.006G242700' => 'gra', 'GSVIVG01018044001' => 'vvi', 'HanXRQChr03g0083821' => 'han', 'HanXRQChr03g0083841' => 'han', 'HanXRQChr03g0083881' => 'han', 'HanXRQChr03g0083901' => 'han', 'HanXRQChr03g0083921' => 'han', 'HanXRQChr03g0085331' => 'han', 'HanXRQChr03g0085361' => 'han', 'HanXRQChr03g0085411' => 'han', 'HanXRQChr03g0085421' => 'han', 'HanXRQChr03g0085431' => 'han', 'HanXRQChr08g0221991' => 'han', 'HanXRQChr11g0336061' => 'han', 'HanXRQChr11g0336411' => 'han', 'Haze_11234' => 'cav', 'Hma1.2p1_0549F.1_g177010' => 'hma', 'Hma1.2p1_0602F.1_g187630' => 'hma', 'Hund14876' => 'sun', 'Hund14879' => 'sun', 'Lalb_Chr06g0160741' => 'lal', 'Lalb_Chr21g0304781' => 'lal', 'Lj3A726G19' => 'lonja', 'Lj3A726T23' => 'lonja', 'Lj3A726T24' => 'lonja', 'Lj3A726T25' => 'lonja', 'Lj3A727T17' => 'lonja', 'Lj3C726T0' => 'lonja', 'Lj3C726T2' => 'lonja', 'Lj3P725T35' => 'lonja', 'Lj3P727T10' => 'lonja', 'Lj3P727T12' => 'lonja', 'Lj3P727T14' => 'lonja', 'Lj5g0023109' => 'lja', 'Lj6P646T44' => 'lonja', 'Lsat_1_v5_gn_6_75760' => 'lsa', 'Lsat_1_v5_gn_6_75800' => 'lsa', 'Lsat_1_v5_gn_6_75900' => 'lsa', 'Lsat_1_v5_gn_6_76240' => 'lsa', 'Lsat_1_v5_gn_6_76441' => 'lsa', 'Lsat_1_v5_gn_6_76700' => 'lsa', 'Lsat_1_v5_gn_6_76760' => 'lsa', 'Manes.15G033100' => 'mes', 'Mapoly0004s0074' => 'mpo', 'Mapoly0004s0075' => 'mpo', 'Mapoly0004s0163' => 'mpo', 'Mapoly0004s0164' => 'mpo', 'Mapoly0021s0018' => 'mpo', 'Mapoly0041s0136' => 'mpo', 'Mapoly0041s0137' => 'mpo', 'Mapoly0041s0138' => 'mpo', 'Mapoly0041s0139' => 'mpo', 'Mapoly0041s0141' => 'mpo', 'Mapoly0041s0142' => 'mpo', 'Mapoly0041s0143' => 'mpo', 'Mapoly0041s0144' => 'mpo', 'Mapoly0041s0145' => 'mpo', 'Mapoly0047s0106' => 'mpo', 'Mapoly0047s0108' => 'mpo', 'Mapoly0050s0051' => 'mpo', 'Mapoly0050s0052' => 'mpo', 'Mapoly0050s0053' => 'mpo', 'Mapoly0058s0013' => 'mpo', 'Mapoly0091s0078' => 'mpo', 'Mapoly0091s0079' => 'mpo', 'Mapoly0091s0080' => 'mpo', 'Mapoly0091s0081' => 'mpo', 'Mapoly0278s0004' => 'mpo', 'Mapoly0278s0005' => 'mpo', 'Mapoly0278s0006' => 'mpo', 'MBI11_g30648_MAGBIO' => 'mbi', 'MCO03G194' => 'mco', 'MCO03G590' => 'mco', 'MCO07G312' => 'mco', 'MCO10G318' => 'mco', 'MCO12G244' => 'mco', 'MCO13G148' => 'mco', 'MCO13G194' => 'mco', 'MCO16G238' => 'mco', 'MD06G1134100' => 'mdo', 'MD13G1200100' => 'mdo', 'MD13G1200300' => 'mdo', 'MD13G1200600' => 'mdo', 'MD14G1150400' => 'mdo', 'MD16G1200000' => 'mdo', 'Medtr1g102570' => 'mtr', 'Medtr1g102780' => 'mtr', 'Medtr1g102800' => 'mtr', 'Medtr1g102810' => 'mtr', 'Medtr1g102830' => 'mtr', 'MELO3C006499.2' => 'cme', 'Migut.G00385' => 'egut', 'MSTRG.4063' => 'ama', 'Nitab4.5_0000090g0260' => 'nta', 'Nitab4.5_0000977g0030' => 'nta', 'Nitab4.5_0002541g0040' => 'nta', 'Nitab4.5_0007068g0040' => 'nta', 'Nn005s41408' => 'nnu', 'Nn005s41410' => 'nnu', 'Oeu010310.1' => 'oeu', 'Oeu010311.1' => 'oeu', 'Oeu043472.1' => 'oeu', 'Os01g0246400' => 'osa', 'Os04g0267950' => 'osa', 'Os07g0178700' => 'osa', 'Os07g0178800' => 'osa', 'Peaxi162Scf00316g00046' => 'pax', 'Peaxi162Scf00316g00049' => 'pax', 'Peaxi162Scf00316g00059' => 'pax', 'Peaxi162Scf00316g00328' => 'pax', 'Peaxi162Scf00316g00329' => 'pax', 'Peaxi162Scf00316g00411' => 'pax', 'Peaxi162Scf00316g00521' => 'pax', 'Peaxi162Scf00492g00068' => 'pax', 'Peaxi162Scf35631g00002' => 'pax', 'PGR142G3720' => 'pgr', 'PGSC0003DMG400006442' => 'stu', 'Phvul.007G062000' => 'pvu', 'Potri.008G157750' => 'ptr', 'Potri.008G157900' => 'ptr', 'Potri.008G158000' => 'ptr', 'Potri.008G158200' => 'ptr', 'Pp3c11_7280' => 'ppa', 'Pp3c11_7980' => 'ppa', 'Pp3c12_19450' => 'ppa', 'Pp3c14_1480' => 'ppa', 'Pp3c14_1501' => 'ppa', 'Pp3c16_4900' => 'ppa', 'Pp3c16_5010' => 'ppa', 'Pp3c16_5060' => 'ppa', 'Pp3c19_18250' => 'ppa', 'Pp3c23_8530' => 'ppa', 'Pp3c23_8550' => 'ppa', 'Pp3c24_9670' => 'ppa', 'Pp3c2_21390' => 'ppa', 'Pp3c2_31380' => 'ppa', 'Pp3c3_16620' => 'ppa', 'Pp3c3_8090' => 'ppa', 'Pp3c3_8110' => 'ppa', 'Pp3c3_8130' => 'ppa', 'Pp3c3_8150' => 'ppa', 'Pp3c4_14320' => 'ppa', 'Pp3c6_2560' => 'ppa', 'Pp3c9_16700' => 'ppa', 'PRCOL_00000234' => 'pco', 'PRCOL_00000235' => 'pco', 'PRCOL_00000777' => 'pco', 'PRCOL_00002344' => 'pco', 'PRCOL_00002372' => 'pco', 'PRCOL_00006120' => 'pco', 'Prupe.1G021400' => 'ppe', 'Prupe.1G021500' => 'ppe', 'Prupe.1G021600' => 'ppe', 'Prupe.1G021700' => 'ppe', 'Prupe.1G021800' => 'ppe', 'Prupe.5G145100' => 'ppe', 'Psat6g204040' => 'psa', 'Psat6g204800' => 'psa', 'Psat6g204920' => 'psa', 'Psat6g204960' => 'psa', 'Psat6g205080' => 'psa', 'PSO017G0271' => 'pso', 'PSO017G1276' => 'pso', 'PSO017G1429' => 'pso', 'PSO017G1861' => 'pso', 'PSO017G2787' => 'pso', 'PSO017G4466' => 'pso', 'PSO017G5118' => 'pso', 'PSO017G5420' => 'pso', 'PSO063G3678' => 'pso', 'PSO210G0546' => 'pso', 'PSO317G0001' => 'pso', 'PSO357G0512' => 'pso', 'PSO478G2682' => 'pso', 'PSO647G0001' => 'pso', 'PSO675G0001' => 'pso', 'PSO675G2699' => 'pso', 'PSO675G2849' => 'pso', 'PSO675G4991' => 'pso', 'PSO689G0001' => 'pso', 'QL06p000916' => 'qlo', 'QL06p000921' => 'qlo', 'QL06p001398' => 'qlo', 'QL06p001407' => 'qlo', 'QL06p002031' => 'qlo', 'RcHm_v2.0_Chr4g0387791' => 'rch', 'RcHm_v2.0_Chr4g0387801' => 'rch', 'RcHm_v2.0_Chr6g0286501' => 'rch', 'RcHm_v2.0_Chr6g0286511' => 'rch', 'RcHm_v2.0_Chr6g0286521' => 'rch', 'RcHm_v2.0_Chr6g0286531' => 'rch', 'RcHm_v2.0_Chr7g0189141' => 'rch', 'Rhsim02G0028700' => 'rsi', 'Rhsim02G0028800' => 'rsi', 'Rhsim02G0028900' => 'rsi', 'Rhsim02G0029000' => 'rsi', 'Rhsim02G0029100' => 'rsi', 'Rhsim02G0029200' => 'rsi', 'Rhsim02G0029300' => 'rsi', 'Rhsim02G0029400' => 'rsi', 'Rhsim02G0029500' => 'rsi', 'Rhsim02G0029600' => 'rsi', 'RhsimUnG0024000' => 'rsi', 'RhsimUnG0024100' => 'rsi', 'RhsimUnG0024200' => 'rsi', 'RhsimUnG0024300' => 'rsi', 'RhsimUnG0024400' => 'rsi', 'RhsimUnG0024500' => 'rsi', 'RhsimUnG0024700' => 'rsi', 'RhsimUnG0024800' => 'rsi', 'RhsimUnG0024900' => 'rsi', 'RhsimUnG0025100' => 'rsi', 'Sabra08G0120200' => 'sbr', 'Sabra08G0120300' => 'sbr', 'Sabra08G0120500' => 'sbr', 'Sabra08G0120600' => 'sbr', 'Sabra10G0158900' => 'sbr', 'SalBow2G3492' => 'sbo', 'Sc13g0004760' => 'sci', 'Sc13g0004770' => 'sci', 'Sed0003417' => 'sed', 'Sed0019750' => 'sed', 'SEGI_03419' => 'sgi', 'SEGI_05907' => 'sgi', 'SEGI_10682' => 'sgi', 'SEGI_13528' => 'sgi', 'SEGI_16081' => 'sgi', 'SEGI_19370' => 'sgi', 'SEGI_21015' => 'sgi', 'SEGI_21944' => 'sgi', 'SEGI_32906' => 'sgi', 'SEGI_33093' => 'sgi', 'SEGI_36110' => 'sgi', 'SEGI_40397' => 'sgi', 'SGA_v2.0_scaffold191G40426' => 'sas', 'SGA_v2.0_scaffold353G49717' => 'sas', 'SGA_v2.0_scaffold50G18550' => 'sas', 'SMO119G0173' => 'smo', 'SMO172G0002' => 'smo', 'Solyc09g082690.3' => 'sly', 'Solyc09g082700.2' => 'sly', 'Sopen09g031550' => 'spe', 'Sopen09g031560' => 'spe', 'Sp3g20540' => 'spa', 'Sp7g07580' => 'spa', 'TAR134G0002' => 'tar', 'TAR236G0001' => 'tar', 'TAR365G0892' => 'tar', 'TAR636G0166' => 'tar', 'TAR636G0646' => 'tar', 'TAR636G0869' => 'tar', 'TAR636G1317' => 'tar', 'TAR636G1744' => 'tar', 'TAR636G3358' => 'tar', 'TAR636G3436' => 'tar', 'THA.LOC104803047' => 'tha', 'Thecc.04G238900' => 'tca', 'Thhalv10021557m.g' => 'esa', 'Thhalv10026318m.g' => 'esa', 'Thhalv10026335m.g' => 'esa', 'TPR.G17433' => 'tpr', 'TPR.G18915' => 'tpr', 'TPR.G26125' => 'tpr', 'TWI09G0677' => 'twi', 'TWI73G0287' => 'twi', 'unitig_748.g8326' => 'ugi', 'vmacro15370' => 'vma', 'vmacro15371' => 'vma', 'vmacro15372' => 'vma', 'vmacro15373' => 'vma', 'vmacro15374' => 'vma', 'VMungo0720G2826' => 'vmu', 'Zm00001eb116960' => 'zma', 'Zm00001eb301260' => 'zma', 'Zm00001eb301270' => 'zma' ) $gf_id = 'HOM05D001460' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001460' ) $data_identifier = 'HOM05D001460' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 4, 'aag' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 2, 'aox' => (int) 2, 'arhy' => (int) 4, 'ath' => (int) 2, 'atr' => (int) 1, 'acertr' => (int) 10, 'cqu' => (int) 4, 'bca' => (int) 11, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 1, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 1, 'ccan' => (int) 1, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 1, 'col' => (int) 1, 'cpa' => (int) 1, 'cre' => (int) 7, 'csa' => (int) 1, 'camsi' => (int) 2, 'dca' => (int) 3, 'din' => (int) 2, 'dzi' => (int) 3, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 14, 'fve' => (int) 9, 'gma' => (int) 2, 'ghi' => (int) 4, 'gra' => (int) 2, 'vvi' => (int) 1, 'han' => (int) 13, 'cav' => (int) 1, 'hma' => (int) 2, 'sun' => (int) 2, 'lal' => (int) 2, 'lonja' => (int) 12, 'lja' => (int) 1, 'lsa' => (int) 7, 'mes' => (int) 1, 'mpo' => (int) 27, 'mbi' => (int) 1, 'mco' => (int) 8, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 1, 'egut' => (int) 1, 'ama' => (int) 1, 'nta' => (int) 4, 'nnu' => (int) 2, 'oeu' => (int) 3, 'osa' => (int) 4, 'pax' => (int) 9, 'pgr' => (int) 1, 'stu' => (int) 1, 'pvu' => (int) 1, 'ptr' => (int) 4, 'ppa' => (int) 22, 'pco' => (int) 6, 'ppe' => (int) 6, 'psa' => (int) 5, 'pso' => (int) 19, 'qlo' => (int) 5, 'rch' => (int) 7, 'rsi' => (int) 20, 'sbr' => (int) 5, 'sbo' => (int) 1, 'sci' => (int) 2, 'sed' => (int) 2, 'sgi' => (int) 12, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 2, 'tar' => (int) 10, 'tha' => (int) 1, 'tca' => (int) 1, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 2, 'ugi' => (int) 1, 'vma' => (int) 5, 'vmu' => (int) 1, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb301270' $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' => 'HOM05D001460', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '433', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p22980' => 'bna', 'A01p32340' => 'bna', 'A03p42970' => 'bna', 'A05p25880' => 'bna', 'Aa31LG8G9320' => 'aar', 'Aa31LG8G9330' => 'aar', 'Aa31LG8G9340' => 'aar', 'Aa31sc221G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1034' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1528' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.829' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2222' => 'aag', 'Ah.12g058830' => 'amhyb', 'Ah.12g058840' => 'amhyb', 'AL3G37160' => 'aly', 'AL7G41310' => 'aly', 'Aqoxy5G00395' => 'aox', 'Aqoxy5G00396' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0C8NZA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5185HY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JZ1PRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MD3LS0' => 'arhy', 'AT3G22840' => 'ath', 'AT4G14690' => 'ath', 'ATR0665G054' => 'atr', 'Atru.chr4.2344' => 'acertr', 'Atru.chr4.2346' => 'acertr', 'Atru.chr4.2347' => 'acertr', 'Atru.chr4.2348' => 'acertr', 'Atru.chr4.2355' => 'acertr', 'Atru.chr4.2356' => 'acertr', 'Atru.chr4.2358' => 'acertr', 'Atru.chr4.2359' => 'acertr', 'Atru.chr4.2360' => 'acertr', 'Atru.chr4.2361' => 'acertr', 'AUR62030476' => 'cqu', 'AUR62030478' => 'cqu', 'AUR62030819' => 'cqu', 'AUR62030820' => 'cqu', 'BcaB03g14648' => 'bca', 'BcaB04g20492' => 'bca', 'BcaB06g26399' => 'bca', 'BcaC01g03416' => 'bca', 'BcaC01g03419' => 'bca', 'BcaC01g03421' => 'bca', 'BcaC01g03424' => 'bca', 'BcaC05g28012' => 'bca', 'BcaC09g49212' => 'bca', 'BcaC09g50140' => 'bca', 'BcaNung00346' => 'bca', 'BolC1t02785H' => 'bol', 'BolC1t04095H' => 'bol', 'BolC3t17545H' => 'bol', 'BolC5t32769H' => 'bol', 'BraA01t02211Z' => 'bra', 'BraA01t03359Z' => 'bra', 'BraA03t13441Z' => 'bra', 'BraA05t21476Z' => 'bra', 'C01p28420' => 'bna', 'C01p41350' => 'bna', 'C03p52750' => 'bna', 'C03p52780' => 'bna', 'C05p40270' => 'bna', 'CAN.G1437.9' => 'can', 'CANSAT78G0035' => 'cansat', 'CANSAT78G1036' => 'cansat', 'CANSAT78G2272' => 'cansat', 'CANSAT78G2478' => 'cansat', 'CARHR098700' => 'chi', 'CARHR221120' => 'chi', 'CARHR221150' => 'chi', 'Carub.0003s2297' => 'cru', 'Carub.0007s2749' => 'cru', 'Carub.0007s2750' => 'cru', 'Carub.0007s2751' => 'cru', 'Ca_10849_v3' => 'car', 'Cc03_g04300' => 'ccan', 'CDE02G3648' => 'cde', 'CDE05G0060' => 'cde', 'CDE05G0692' => 'cde', 'CDE05G2285' => 'cde', 'CDE05G2884' => 'cde', 'CDE05G3072' => 'cde', 'Cfa008439' => 'cfa', 'Cfa008441' => 'cfa', 'Cfa008443' => 'cfa', 'Cfa008448' => 'cfa', 'Ciclev10005974m.g' => 'ccl', 'Ciclev10006006m.g' => 'ccl', 'Ciclev10006775m.g' => 'ccl', 'CiPaw.02G120400' => 'cil', 'CiPaw.02G120500' => 'cil', 'CiPaw.02G120600' => 'cil', 'ClCG05G004850' => 'cla', 'COL.COLO4_21566' => 'col', 'Cpa.g.sc44.124' => 'cpa', 'Cre07.g320400' => 'cre', 'Cre07.g320450' => 'cre', 'Cre08.g384650' => 'cre', 'Cre09.g393173' => 'cre', 'Cre09.g394325' => 'cre', 'Cre14.g626750' => 'cre', 'Cre16.g679250' => 'cre', 'CsaV3_3G012890' => 'csa', 'CSS0010865' => 'camsi', 'CSS0044338' => 'camsi', 'DCAR_002366' => 'dca', 'DCAR_030687' => 'dca', 'DCAR_030688' => 'dca', 'Dinv14047' => 'din', 'Dinv14048' => 'din', 'Duzib151G0105' => 'dzi', 'Duzib151G0114' => 'dzi', 'Duzib212G1029' => 'dzi', 'ECA232G3536' => 'eca', 'ECA240G0786' => 'eca', 'ECA240G1802' => 'eca', 'ECA240G3760' => 'eca', 'ECA240G3920' => 'eca', 'EL10Ac5g12536' => 'bvu', 'EL10Ac5g12537' => 'bvu', 'EL10Ac5g12538' => 'bvu', 'Eucgr.B01004' => 'egr', 'Eucgr.B01006' => 'egr', 'Eucgr.B01007' => 'egr', 'Eucgr.B01008' => 'egr', 'Eucgr.B01895' => 'egr', 'Eucgr.B01896' => 'egr', 'FAN04G1456' => 'fan', 'FAN08G1769' => 'fan', 'FAN08G2160' => 'fan', 'FAN13G2403' => 'fan', 'FAN13G3303' => 'fan', 'FAN15G2435' => 'fan', 'FAN17G0672' => 'fan', 'FAN17G2441' => 'fan', 'FAN18G1024' => 'fan', 'FAN22G1458' => 'fan', 'FAN24G0037' => 'fan', 'FAN24G0429' => 'fan', 'FAN24G2387' => 'fan', 'FAN27G2746' => 'fan', 'FvH4_2g20400' => 'fve', 'FvH4_2g20420' => 'fve', 'FvH4_2g20430' => 'fve', 'FvH4_4g01270' => 'fve', 'FvH4_4g01290' => 'fve', 'FvH4_4g01300' => 'fve', 'FvH4_4g01310' => 'fve', 'FvH4_4g01330' => 'fve', 'FvH4_5g09070' => 'fve', 'Glyma.10G243800' => 'gma', 'Glyma.20G150600' => 'gma', 'Gohir.A09G219200' => 'ghi', 'Gohir.A09G219300' => 'ghi', 'Gohir.D09G221400' => 'ghi', 'Gohir.D09G221500' => 'ghi', 'Gorai.006G242600' => 'gra', 'Gorai.006G242700' => 'gra', 'GSVIVG01018044001' => 'vvi', 'HanXRQChr03g0083821' => 'han', 'HanXRQChr03g0083841' => 'han', 'HanXRQChr03g0083881' => 'han', 'HanXRQChr03g0083901' => 'han', 'HanXRQChr03g0083921' => 'han', 'HanXRQChr03g0085331' => 'han', 'HanXRQChr03g0085361' => 'han', 'HanXRQChr03g0085411' => 'han', 'HanXRQChr03g0085421' => 'han', 'HanXRQChr03g0085431' => 'han', 'HanXRQChr08g0221991' => 'han', 'HanXRQChr11g0336061' => 'han', 'HanXRQChr11g0336411' => 'han', 'Haze_11234' => 'cav', 'Hma1.2p1_0549F.1_g177010' => 'hma', 'Hma1.2p1_0602F.1_g187630' => 'hma', 'Hund14876' => 'sun', 'Hund14879' => 'sun', 'Lalb_Chr06g0160741' => 'lal', 'Lalb_Chr21g0304781' => 'lal', 'Lj3A726G19' => 'lonja', 'Lj3A726T23' => 'lonja', 'Lj3A726T24' => 'lonja', 'Lj3A726T25' => 'lonja', 'Lj3A727T17' => 'lonja', 'Lj3C726T0' => 'lonja', 'Lj3C726T2' => 'lonja', 'Lj3P725T35' => 'lonja', 'Lj3P727T10' => 'lonja', 'Lj3P727T12' => 'lonja', 'Lj3P727T14' => 'lonja', 'Lj5g0023109' => 'lja', 'Lj6P646T44' => 'lonja', 'Lsat_1_v5_gn_6_75760' => 'lsa', 'Lsat_1_v5_gn_6_75800' => 'lsa', 'Lsat_1_v5_gn_6_75900' => 'lsa', 'Lsat_1_v5_gn_6_76240' => 'lsa', 'Lsat_1_v5_gn_6_76441' => 'lsa', 'Lsat_1_v5_gn_6_76700' => 'lsa', 'Lsat_1_v5_gn_6_76760' => 'lsa', 'Manes.15G033100' => 'mes', 'Mapoly0004s0074' => 'mpo', 'Mapoly0004s0075' => 'mpo', 'Mapoly0004s0163' => 'mpo', 'Mapoly0004s0164' => 'mpo', 'Mapoly0021s0018' => 'mpo', 'Mapoly0041s0136' => 'mpo', 'Mapoly0041s0137' => 'mpo', 'Mapoly0041s0138' => 'mpo', 'Mapoly0041s0139' => 'mpo', 'Mapoly0041s0141' => 'mpo', 'Mapoly0041s0142' => 'mpo', 'Mapoly0041s0143' => 'mpo', 'Mapoly0041s0144' => 'mpo', 'Mapoly0041s0145' => 'mpo', 'Mapoly0047s0106' => 'mpo', 'Mapoly0047s0108' => 'mpo', 'Mapoly0050s0051' => 'mpo', 'Mapoly0050s0052' => 'mpo', 'Mapoly0050s0053' => 'mpo', 'Mapoly0058s0013' => 'mpo', 'Mapoly0091s0078' => 'mpo', 'Mapoly0091s0079' => 'mpo', 'Mapoly0091s0080' => 'mpo', 'Mapoly0091s0081' => 'mpo', 'Mapoly0278s0004' => 'mpo', 'Mapoly0278s0005' => 'mpo', 'Mapoly0278s0006' => 'mpo', 'MBI11_g30648_MAGBIO' => 'mbi', 'MCO03G194' => 'mco', 'MCO03G590' => 'mco', 'MCO07G312' => 'mco', 'MCO10G318' => 'mco', 'MCO12G244' => 'mco', 'MCO13G148' => 'mco', 'MCO13G194' => 'mco', 'MCO16G238' => 'mco', 'MD06G1134100' => 'mdo', 'MD13G1200100' => 'mdo', 'MD13G1200300' => 'mdo', 'MD13G1200600' => 'mdo', 'MD14G1150400' => 'mdo', 'MD16G1200000' => 'mdo', 'Medtr1g102570' => 'mtr', 'Medtr1g102780' => 'mtr', 'Medtr1g102800' => 'mtr', 'Medtr1g102810' => 'mtr', 'Medtr1g102830' => 'mtr', 'MELO3C006499.2' => 'cme', 'Migut.G00385' => 'egut', 'MSTRG.4063' => 'ama', 'Nitab4.5_0000090g0260' => 'nta', 'Nitab4.5_0000977g0030' => 'nta', 'Nitab4.5_0002541g0040' => 'nta', 'Nitab4.5_0007068g0040' => 'nta', 'Nn005s41408' => 'nnu', 'Nn005s41410' => 'nnu', 'Oeu010310.1' => 'oeu', 'Oeu010311.1' => 'oeu', 'Oeu043472.1' => 'oeu', 'Os01g0246400' => 'osa', 'Os04g0267950' => 'osa', 'Os07g0178700' => 'osa', 'Os07g0178800' => 'osa', 'Peaxi162Scf00316g00046' => 'pax', 'Peaxi162Scf00316g00049' => 'pax', 'Peaxi162Scf00316g00059' => 'pax', 'Peaxi162Scf00316g00328' => 'pax', 'Peaxi162Scf00316g00329' => 'pax', 'Peaxi162Scf00316g00411' => 'pax', 'Peaxi162Scf00316g00521' => 'pax', 'Peaxi162Scf00492g00068' => 'pax', 'Peaxi162Scf35631g00002' => 'pax', 'PGR142G3720' => 'pgr', 'PGSC0003DMG400006442' => 'stu', 'Phvul.007G062000' => 'pvu', 'Potri.008G157750' => 'ptr', 'Potri.008G157900' => 'ptr', 'Potri.008G158000' => 'ptr', 'Potri.008G158200' => 'ptr', 'Pp3c11_7280' => 'ppa', 'Pp3c11_7980' => 'ppa', 'Pp3c12_19450' => 'ppa', 'Pp3c14_1480' => 'ppa', 'Pp3c14_1501' => 'ppa', 'Pp3c16_4900' => 'ppa', 'Pp3c16_5010' => 'ppa', 'Pp3c16_5060' => 'ppa', 'Pp3c19_18250' => 'ppa', 'Pp3c23_8530' => 'ppa', 'Pp3c23_8550' => 'ppa', 'Pp3c24_9670' => 'ppa', 'Pp3c2_21390' => 'ppa', 'Pp3c2_31380' => 'ppa', 'Pp3c3_16620' => 'ppa', 'Pp3c3_8090' => 'ppa', 'Pp3c3_8110' => 'ppa', 'Pp3c3_8130' => 'ppa', 'Pp3c3_8150' => 'ppa', 'Pp3c4_14320' => 'ppa', 'Pp3c6_2560' => 'ppa', 'Pp3c9_16700' => 'ppa', 'PRCOL_00000234' => 'pco', 'PRCOL_00000235' => 'pco', 'PRCOL_00000777' => 'pco', 'PRCOL_00002344' => 'pco', 'PRCOL_00002372' => 'pco', 'PRCOL_00006120' => 'pco', 'Prupe.1G021400' => 'ppe', 'Prupe.1G021500' => 'ppe', 'Prupe.1G021600' => 'ppe', 'Prupe.1G021700' => 'ppe', 'Prupe.1G021800' => 'ppe', 'Prupe.5G145100' => 'ppe', 'Psat6g204040' => 'psa', 'Psat6g204800' => 'psa', 'Psat6g204920' => 'psa', 'Psat6g204960' => 'psa', 'Psat6g205080' => 'psa', 'PSO017G0271' => 'pso', 'PSO017G1276' => 'pso', 'PSO017G1429' => 'pso', 'PSO017G1861' => 'pso', 'PSO017G2787' => 'pso', 'PSO017G4466' => 'pso', 'PSO017G5118' => 'pso', 'PSO017G5420' => 'pso', 'PSO063G3678' => 'pso', 'PSO210G0546' => 'pso', 'PSO317G0001' => 'pso', 'PSO357G0512' => 'pso', 'PSO478G2682' => 'pso', 'PSO647G0001' => 'pso', 'PSO675G0001' => 'pso', 'PSO675G2699' => 'pso', 'PSO675G2849' => 'pso', 'PSO675G4991' => 'pso', 'PSO689G0001' => 'pso', 'QL06p000916' => 'qlo', 'QL06p000921' => 'qlo', 'QL06p001398' => 'qlo', 'QL06p001407' => 'qlo', 'QL06p002031' => 'qlo', 'RcHm_v2.0_Chr4g0387791' => 'rch', 'RcHm_v2.0_Chr4g0387801' => 'rch', 'RcHm_v2.0_Chr6g0286501' => 'rch', 'RcHm_v2.0_Chr6g0286511' => 'rch', 'RcHm_v2.0_Chr6g0286521' => 'rch', 'RcHm_v2.0_Chr6g0286531' => 'rch', 'RcHm_v2.0_Chr7g0189141' => 'rch', 'Rhsim02G0028700' => 'rsi', 'Rhsim02G0028800' => 'rsi', 'Rhsim02G0028900' => 'rsi', 'Rhsim02G0029000' => 'rsi', 'Rhsim02G0029100' => 'rsi', 'Rhsim02G0029200' => 'rsi', 'Rhsim02G0029300' => 'rsi', 'Rhsim02G0029400' => 'rsi', 'Rhsim02G0029500' => 'rsi', 'Rhsim02G0029600' => 'rsi', 'RhsimUnG0024000' => 'rsi', 'RhsimUnG0024100' => 'rsi', 'RhsimUnG0024200' => 'rsi', 'RhsimUnG0024300' => 'rsi', 'RhsimUnG0024400' => 'rsi', 'RhsimUnG0024500' => 'rsi', 'RhsimUnG0024700' => 'rsi', 'RhsimUnG0024800' => 'rsi', 'RhsimUnG0024900' => 'rsi', 'RhsimUnG0025100' => 'rsi', 'Sabra08G0120200' => 'sbr', 'Sabra08G0120300' => 'sbr', 'Sabra08G0120500' => 'sbr', 'Sabra08G0120600' => 'sbr', 'Sabra10G0158900' => 'sbr', 'SalBow2G3492' => 'sbo', 'Sc13g0004760' => 'sci', 'Sc13g0004770' => 'sci', 'Sed0003417' => 'sed', 'Sed0019750' => 'sed', 'SEGI_03419' => 'sgi', 'SEGI_05907' => 'sgi', 'SEGI_10682' => 'sgi', 'SEGI_13528' => 'sgi', 'SEGI_16081' => 'sgi', 'SEGI_19370' => 'sgi', 'SEGI_21015' => 'sgi', 'SEGI_21944' => 'sgi', 'SEGI_32906' => 'sgi', 'SEGI_33093' => 'sgi', 'SEGI_36110' => 'sgi', 'SEGI_40397' => 'sgi', 'SGA_v2.0_scaffold191G40426' => 'sas', 'SGA_v2.0_scaffold353G49717' => 'sas', 'SGA_v2.0_scaffold50G18550' => 'sas', 'SMO119G0173' => 'smo', 'SMO172G0002' => 'smo', 'Solyc09g082690.3' => 'sly', 'Solyc09g082700.2' => 'sly', 'Sopen09g031550' => 'spe', 'Sopen09g031560' => 'spe', 'Sp3g20540' => 'spa', 'Sp7g07580' => 'spa', 'TAR134G0002' => 'tar', 'TAR236G0001' => 'tar', 'TAR365G0892' => 'tar', 'TAR636G0166' => 'tar', 'TAR636G0646' => 'tar', 'TAR636G0869' => 'tar', 'TAR636G1317' => 'tar', 'TAR636G1744' => 'tar', 'TAR636G3358' => 'tar', 'TAR636G3436' => 'tar', 'THA.LOC104803047' => 'tha', 'Thecc.04G238900' => 'tca', 'Thhalv10021557m.g' => 'esa', 'Thhalv10026318m.g' => 'esa', 'Thhalv10026335m.g' => 'esa', 'TPR.G17433' => 'tpr', 'TPR.G18915' => 'tpr', 'TPR.G26125' => 'tpr', 'TWI09G0677' => 'twi', 'TWI73G0287' => 'twi', 'unitig_748.g8326' => 'ugi', 'vmacro15370' => 'vma', 'vmacro15371' => 'vma', 'vmacro15372' => 'vma', 'vmacro15373' => 'vma', 'vmacro15374' => 'vma', 'VMungo0720G2826' => 'vmu', 'Zm00001eb116960' => 'zma', 'Zm00001eb301260' => 'zma', 'Zm00001eb301270' => 'zma' ), 'gf_id' => 'HOM05D001460', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001460' ), 'data_identifier' => 'HOM05D001460', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001460', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '433', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p22980' => 'bna', 'A01p32340' => 'bna', 'A03p42970' => 'bna', 'A05p25880' => 'bna', 'Aa31LG8G9320' => 'aar', 'Aa31LG8G9330' => 'aar', 'Aa31LG8G9340' => 'aar', 'Aa31sc221G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1034' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1528' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.829' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2222' => 'aag', 'Ah.12g058830' => 'amhyb', 'Ah.12g058840' => 'amhyb', 'AL3G37160' => 'aly', 'AL7G41310' => 'aly', 'Aqoxy5G00395' => 'aox', 'Aqoxy5G00396' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0C8NZA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5185HY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JZ1PRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MD3LS0' => 'arhy', 'AT3G22840' => 'ath', 'AT4G14690' => 'ath', 'ATR0665G054' => 'atr', 'Atru.chr4.2344' => 'acertr', 'Atru.chr4.2346' => 'acertr', 'Atru.chr4.2347' => 'acertr', 'Atru.chr4.2348' => 'acertr', 'Atru.chr4.2355' => 'acertr', 'Atru.chr4.2356' => 'acertr', 'Atru.chr4.2358' => 'acertr', 'Atru.chr4.2359' => 'acertr', 'Atru.chr4.2360' => 'acertr', 'Atru.chr4.2361' => 'acertr', 'AUR62030476' => 'cqu', 'AUR62030478' => 'cqu', 'AUR62030819' => 'cqu', 'AUR62030820' => 'cqu', 'BcaB03g14648' => 'bca', 'BcaB04g20492' => 'bca', 'BcaB06g26399' => 'bca', 'BcaC01g03416' => 'bca', 'BcaC01g03419' => 'bca', 'BcaC01g03421' => 'bca', 'BcaC01g03424' => 'bca', 'BcaC05g28012' => 'bca', 'BcaC09g49212' => 'bca', 'BcaC09g50140' => 'bca', 'BcaNung00346' => 'bca', 'BolC1t02785H' => 'bol', 'BolC1t04095H' => 'bol', 'BolC3t17545H' => 'bol', 'BolC5t32769H' => 'bol', 'BraA01t02211Z' => 'bra', 'BraA01t03359Z' => 'bra', 'BraA03t13441Z' => 'bra', 'BraA05t21476Z' => 'bra', 'C01p28420' => 'bna', 'C01p41350' => 'bna', 'C03p52750' => 'bna', 'C03p52780' => 'bna', 'C05p40270' => 'bna', 'CAN.G1437.9' => 'can', 'CANSAT78G0035' => 'cansat', 'CANSAT78G1036' => 'cansat', 'CANSAT78G2272' => 'cansat', 'CANSAT78G2478' => 'cansat', 'CARHR098700' => 'chi', 'CARHR221120' => 'chi', 'CARHR221150' => 'chi', 'Carub.0003s2297' => 'cru', 'Carub.0007s2749' => 'cru', 'Carub.0007s2750' => 'cru', 'Carub.0007s2751' => 'cru', 'Ca_10849_v3' => 'car', 'Cc03_g04300' => 'ccan', 'CDE02G3648' => 'cde', 'CDE05G0060' => 'cde', 'CDE05G0692' => 'cde', 'CDE05G2285' => 'cde', 'CDE05G2884' => 'cde', 'CDE05G3072' => 'cde', 'Cfa008439' => 'cfa', 'Cfa008441' => 'cfa', 'Cfa008443' => 'cfa', 'Cfa008448' => 'cfa', 'Ciclev10005974m.g' => 'ccl', 'Ciclev10006006m.g' => 'ccl', 'Ciclev10006775m.g' => 'ccl', 'CiPaw.02G120400' => 'cil', 'CiPaw.02G120500' => 'cil', 'CiPaw.02G120600' => 'cil', 'ClCG05G004850' => 'cla', 'COL.COLO4_21566' => 'col', 'Cpa.g.sc44.124' => 'cpa', 'Cre07.g320400' => 'cre', 'Cre07.g320450' => 'cre', 'Cre08.g384650' => 'cre', 'Cre09.g393173' => 'cre', 'Cre09.g394325' => 'cre', 'Cre14.g626750' => 'cre', 'Cre16.g679250' => 'cre', 'CsaV3_3G012890' => 'csa', 'CSS0010865' => 'camsi', 'CSS0044338' => 'camsi', 'DCAR_002366' => 'dca', 'DCAR_030687' => 'dca', 'DCAR_030688' => 'dca', 'Dinv14047' => 'din', 'Dinv14048' => 'din', 'Duzib151G0105' => 'dzi', 'Duzib151G0114' => 'dzi', 'Duzib212G1029' => 'dzi', 'ECA232G3536' => 'eca', 'ECA240G0786' => 'eca', 'ECA240G1802' => 'eca', 'ECA240G3760' => 'eca', 'ECA240G3920' => 'eca', 'EL10Ac5g12536' => 'bvu', 'EL10Ac5g12537' => 'bvu', 'EL10Ac5g12538' => 'bvu', 'Eucgr.B01004' => 'egr', 'Eucgr.B01006' => 'egr', 'Eucgr.B01007' => 'egr', 'Eucgr.B01008' => 'egr', 'Eucgr.B01895' => 'egr', 'Eucgr.B01896' => 'egr', 'FAN04G1456' => 'fan', 'FAN08G1769' => 'fan', 'FAN08G2160' => 'fan', 'FAN13G2403' => 'fan', 'FAN13G3303' => 'fan', 'FAN15G2435' => 'fan', 'FAN17G0672' => 'fan', 'FAN17G2441' => 'fan', 'FAN18G1024' => 'fan', 'FAN22G1458' => 'fan', 'FAN24G0037' => 'fan', 'FAN24G0429' => 'fan', 'FAN24G2387' => 'fan', 'FAN27G2746' => 'fan', 'FvH4_2g20400' => 'fve', 'FvH4_2g20420' => 'fve', 'FvH4_2g20430' => 'fve', 'FvH4_4g01270' => 'fve', 'FvH4_4g01290' => 'fve', 'FvH4_4g01300' => 'fve', 'FvH4_4g01310' => 'fve', 'FvH4_4g01330' => 'fve', 'FvH4_5g09070' => 'fve', 'Glyma.10G243800' => 'gma', 'Glyma.20G150600' => 'gma', 'Gohir.A09G219200' => 'ghi', 'Gohir.A09G219300' => 'ghi', 'Gohir.D09G221400' => 'ghi', 'Gohir.D09G221500' => 'ghi', 'Gorai.006G242600' => 'gra', 'Gorai.006G242700' => 'gra', 'GSVIVG01018044001' => 'vvi', 'HanXRQChr03g0083821' => 'han', 'HanXRQChr03g0083841' => 'han', 'HanXRQChr03g0083881' => 'han', 'HanXRQChr03g0083901' => 'han', 'HanXRQChr03g0083921' => 'han', 'HanXRQChr03g0085331' => 'han', 'HanXRQChr03g0085361' => 'han', 'HanXRQChr03g0085411' => 'han', 'HanXRQChr03g0085421' => 'han', 'HanXRQChr03g0085431' => 'han', 'HanXRQChr08g0221991' => 'han', 'HanXRQChr11g0336061' => 'han', 'HanXRQChr11g0336411' => 'han', 'Haze_11234' => 'cav', 'Hma1.2p1_0549F.1_g177010' => 'hma', 'Hma1.2p1_0602F.1_g187630' => 'hma', 'Hund14876' => 'sun', 'Hund14879' => 'sun', 'Lalb_Chr06g0160741' => 'lal', 'Lalb_Chr21g0304781' => 'lal', 'Lj3A726G19' => 'lonja', 'Lj3A726T23' => 'lonja', 'Lj3A726T24' => 'lonja', 'Lj3A726T25' => 'lonja', 'Lj3A727T17' => 'lonja', 'Lj3C726T0' => 'lonja', 'Lj3C726T2' => 'lonja', 'Lj3P725T35' => 'lonja', 'Lj3P727T10' => 'lonja', 'Lj3P727T12' => 'lonja', 'Lj3P727T14' => 'lonja', 'Lj5g0023109' => 'lja', 'Lj6P646T44' => 'lonja', 'Lsat_1_v5_gn_6_75760' => 'lsa', 'Lsat_1_v5_gn_6_75800' => 'lsa', 'Lsat_1_v5_gn_6_75900' => 'lsa', 'Lsat_1_v5_gn_6_76240' => 'lsa', 'Lsat_1_v5_gn_6_76441' => 'lsa', 'Lsat_1_v5_gn_6_76700' => 'lsa', 'Lsat_1_v5_gn_6_76760' => 'lsa', 'Manes.15G033100' => 'mes', 'Mapoly0004s0074' => 'mpo', 'Mapoly0004s0075' => 'mpo', 'Mapoly0004s0163' => 'mpo', 'Mapoly0004s0164' => 'mpo', 'Mapoly0021s0018' => 'mpo', 'Mapoly0041s0136' => 'mpo', 'Mapoly0041s0137' => 'mpo', 'Mapoly0041s0138' => 'mpo', 'Mapoly0041s0139' => 'mpo', 'Mapoly0041s0141' => 'mpo', 'Mapoly0041s0142' => 'mpo', 'Mapoly0041s0143' => 'mpo', 'Mapoly0041s0144' => 'mpo', 'Mapoly0041s0145' => 'mpo', 'Mapoly0047s0106' => 'mpo', 'Mapoly0047s0108' => 'mpo', 'Mapoly0050s0051' => 'mpo', 'Mapoly0050s0052' => 'mpo', 'Mapoly0050s0053' => 'mpo', 'Mapoly0058s0013' => 'mpo', 'Mapoly0091s0078' => 'mpo', 'Mapoly0091s0079' => 'mpo', 'Mapoly0091s0080' => 'mpo', 'Mapoly0091s0081' => 'mpo', 'Mapoly0278s0004' => 'mpo', 'Mapoly0278s0005' => 'mpo', 'Mapoly0278s0006' => 'mpo', 'MBI11_g30648_MAGBIO' => 'mbi', 'MCO03G194' => 'mco', 'MCO03G590' => 'mco', 'MCO07G312' => 'mco', 'MCO10G318' => 'mco', 'MCO12G244' => 'mco', 'MCO13G148' => 'mco', 'MCO13G194' => 'mco', 'MCO16G238' => 'mco', 'MD06G1134100' => 'mdo', 'MD13G1200100' => 'mdo', 'MD13G1200300' => 'mdo', 'MD13G1200600' => 'mdo', 'MD14G1150400' => 'mdo', 'MD16G1200000' => 'mdo', 'Medtr1g102570' => 'mtr', 'Medtr1g102780' => 'mtr', 'Medtr1g102800' => 'mtr', 'Medtr1g102810' => 'mtr', 'Medtr1g102830' => 'mtr', 'MELO3C006499.2' => 'cme', 'Migut.G00385' => 'egut', 'MSTRG.4063' => 'ama', 'Nitab4.5_0000090g0260' => 'nta', 'Nitab4.5_0000977g0030' => 'nta', 'Nitab4.5_0002541g0040' => 'nta', 'Nitab4.5_0007068g0040' => 'nta', 'Nn005s41408' => 'nnu', 'Nn005s41410' => 'nnu', 'Oeu010310.1' => 'oeu', 'Oeu010311.1' => 'oeu', 'Oeu043472.1' => 'oeu', 'Os01g0246400' => 'osa', 'Os04g0267950' => 'osa', 'Os07g0178700' => 'osa', 'Os07g0178800' => 'osa', 'Peaxi162Scf00316g00046' => 'pax', 'Peaxi162Scf00316g00049' => 'pax', 'Peaxi162Scf00316g00059' => 'pax', 'Peaxi162Scf00316g00328' => 'pax', 'Peaxi162Scf00316g00329' => 'pax', 'Peaxi162Scf00316g00411' => 'pax', 'Peaxi162Scf00316g00521' => 'pax', 'Peaxi162Scf00492g00068' => 'pax', 'Peaxi162Scf35631g00002' => 'pax', 'PGR142G3720' => 'pgr', 'PGSC0003DMG400006442' => 'stu', 'Phvul.007G062000' => 'pvu', 'Potri.008G157750' => 'ptr', 'Potri.008G157900' => 'ptr', 'Potri.008G158000' => 'ptr', 'Potri.008G158200' => 'ptr', 'Pp3c11_7280' => 'ppa', 'Pp3c11_7980' => 'ppa', 'Pp3c12_19450' => 'ppa', 'Pp3c14_1480' => 'ppa', 'Pp3c14_1501' => 'ppa', 'Pp3c16_4900' => 'ppa', 'Pp3c16_5010' => 'ppa', 'Pp3c16_5060' => 'ppa', 'Pp3c19_18250' => 'ppa', 'Pp3c23_8530' => 'ppa', 'Pp3c23_8550' => 'ppa', 'Pp3c24_9670' => 'ppa', 'Pp3c2_21390' => 'ppa', 'Pp3c2_31380' => 'ppa', 'Pp3c3_16620' => 'ppa', 'Pp3c3_8090' => 'ppa', 'Pp3c3_8110' => 'ppa', 'Pp3c3_8130' => 'ppa', 'Pp3c3_8150' => 'ppa', 'Pp3c4_14320' => 'ppa', 'Pp3c6_2560' => 'ppa', 'Pp3c9_16700' => 'ppa', 'PRCOL_00000234' => 'pco', 'PRCOL_00000235' => 'pco', 'PRCOL_00000777' => 'pco', 'PRCOL_00002344' => 'pco', 'PRCOL_00002372' => 'pco', 'PRCOL_00006120' => 'pco', 'Prupe.1G021400' => 'ppe', 'Prupe.1G021500' => 'ppe', 'Prupe.1G021600' => 'ppe', 'Prupe.1G021700' => 'ppe', 'Prupe.1G021800' => 'ppe', 'Prupe.5G145100' => 'ppe', 'Psat6g204040' => 'psa', 'Psat6g204800' => 'psa', 'Psat6g204920' => 'psa', 'Psat6g204960' => 'psa', 'Psat6g205080' => 'psa', 'PSO017G0271' => 'pso', 'PSO017G1276' => 'pso', 'PSO017G1429' => 'pso', 'PSO017G1861' => 'pso', 'PSO017G2787' => 'pso', 'PSO017G4466' => 'pso', 'PSO017G5118' => 'pso', 'PSO017G5420' => 'pso', 'PSO063G3678' => 'pso', 'PSO210G0546' => 'pso', 'PSO317G0001' => 'pso', 'PSO357G0512' => 'pso', 'PSO478G2682' => 'pso', 'PSO647G0001' => 'pso', 'PSO675G0001' => 'pso', 'PSO675G2699' => 'pso', 'PSO675G2849' => 'pso', 'PSO675G4991' => 'pso', 'PSO689G0001' => 'pso', 'QL06p000916' => 'qlo', 'QL06p000921' => 'qlo', 'QL06p001398' => 'qlo', 'QL06p001407' => 'qlo', 'QL06p002031' => 'qlo', 'RcHm_v2.0_Chr4g0387791' => 'rch', 'RcHm_v2.0_Chr4g0387801' => 'rch', 'RcHm_v2.0_Chr6g0286501' => 'rch', 'RcHm_v2.0_Chr6g0286511' => 'rch', 'RcHm_v2.0_Chr6g0286521' => 'rch', 'RcHm_v2.0_Chr6g0286531' => 'rch', 'RcHm_v2.0_Chr7g0189141' => 'rch', 'Rhsim02G0028700' => 'rsi', 'Rhsim02G0028800' => 'rsi', 'Rhsim02G0028900' => 'rsi', 'Rhsim02G0029000' => 'rsi', 'Rhsim02G0029100' => 'rsi', 'Rhsim02G0029200' => 'rsi', 'Rhsim02G0029300' => 'rsi', 'Rhsim02G0029400' => 'rsi', 'Rhsim02G0029500' => 'rsi', 'Rhsim02G0029600' => 'rsi', 'RhsimUnG0024000' => 'rsi', 'RhsimUnG0024100' => 'rsi', 'RhsimUnG0024200' => 'rsi', 'RhsimUnG0024300' => 'rsi', 'RhsimUnG0024400' => 'rsi', 'RhsimUnG0024500' => 'rsi', 'RhsimUnG0024700' => 'rsi', 'RhsimUnG0024800' => 'rsi', 'RhsimUnG0024900' => 'rsi', 'RhsimUnG0025100' => 'rsi', 'Sabra08G0120200' => 'sbr', 'Sabra08G0120300' => 'sbr', 'Sabra08G0120500' => 'sbr', 'Sabra08G0120600' => 'sbr', 'Sabra10G0158900' => 'sbr', 'SalBow2G3492' => 'sbo', 'Sc13g0004760' => 'sci', 'Sc13g0004770' => 'sci', 'Sed0003417' => 'sed', 'Sed0019750' => 'sed', 'SEGI_03419' => 'sgi', 'SEGI_05907' => 'sgi', 'SEGI_10682' => 'sgi', 'SEGI_13528' => 'sgi', 'SEGI_16081' => 'sgi', 'SEGI_19370' => 'sgi', 'SEGI_21015' => 'sgi', 'SEGI_21944' => 'sgi', 'SEGI_32906' => 'sgi', 'SEGI_33093' => 'sgi', 'SEGI_36110' => 'sgi', 'SEGI_40397' => 'sgi', 'SGA_v2.0_scaffold191G40426' => 'sas', 'SGA_v2.0_scaffold353G49717' => 'sas', 'SGA_v2.0_scaffold50G18550' => 'sas', 'SMO119G0173' => 'smo', 'SMO172G0002' => 'smo', 'Solyc09g082690.3' => 'sly', 'Solyc09g082700.2' => 'sly', 'Sopen09g031550' => 'spe', 'Sopen09g031560' => 'spe', 'Sp3g20540' => 'spa', 'Sp7g07580' => 'spa', 'TAR134G0002' => 'tar', 'TAR236G0001' => 'tar', 'TAR365G0892' => 'tar', 'TAR636G0166' => 'tar', 'TAR636G0646' => 'tar', 'TAR636G0869' => 'tar', 'TAR636G1317' => 'tar', 'TAR636G1744' => 'tar', 'TAR636G3358' => 'tar', 'TAR636G3436' => 'tar', 'THA.LOC104803047' => 'tha', 'Thecc.04G238900' => 'tca', 'Thhalv10021557m.g' => 'esa', 'Thhalv10026318m.g' => 'esa', 'Thhalv10026335m.g' => 'esa', 'TPR.G17433' => 'tpr', 'TPR.G18915' => 'tpr', 'TPR.G26125' => 'tpr', 'TWI09G0677' => 'twi', 'TWI73G0287' => 'twi', 'unitig_748.g8326' => 'ugi', 'vmacro15370' => 'vma', 'vmacro15371' => 'vma', 'vmacro15372' => 'vma', 'vmacro15373' => 'vma', 'vmacro15374' => 'vma', 'VMungo0720G2826' => 'vmu', 'Zm00001eb116960' => 'zma', 'Zm00001eb301260' => 'zma', 'Zm00001eb301270' => 'zma' ) $gf_id = 'HOM05D001460' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001460' ) $data_identifier = 'HOM05D001460' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 4, 'aag' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 2, 'aox' => (int) 2, 'arhy' => (int) 4, 'ath' => (int) 2, 'atr' => (int) 1, 'acertr' => (int) 10, 'cqu' => (int) 4, 'bca' => (int) 11, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 1, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 1, 'ccan' => (int) 1, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 1, 'col' => (int) 1, 'cpa' => (int) 1, 'cre' => (int) 7, 'csa' => (int) 1, 'camsi' => (int) 2, 'dca' => (int) 3, 'din' => (int) 2, 'dzi' => (int) 3, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 14, 'fve' => (int) 9, 'gma' => (int) 2, 'ghi' => (int) 4, 'gra' => (int) 2, 'vvi' => (int) 1, 'han' => (int) 13, 'cav' => (int) 1, 'hma' => (int) 2, 'sun' => (int) 2, 'lal' => (int) 2, 'lonja' => (int) 12, 'lja' => (int) 1, 'lsa' => (int) 7, 'mes' => (int) 1, 'mpo' => (int) 27, 'mbi' => (int) 1, 'mco' => (int) 8, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 1, 'egut' => (int) 1, 'ama' => (int) 1, 'nta' => (int) 4, 'nnu' => (int) 2, 'oeu' => (int) 3, 'osa' => (int) 4, 'pax' => (int) 9, 'pgr' => (int) 1, 'stu' => (int) 1, 'pvu' => (int) 1, 'ptr' => (int) 4, 'ppa' => (int) 22, 'pco' => (int) 6, 'ppe' => (int) 6, 'psa' => (int) 5, 'pso' => (int) 19, 'qlo' => (int) 5, 'rch' => (int) 7, 'rsi' => (int) 20, 'sbr' => (int) 5, 'sbo' => (int) 1, 'sci' => (int) 2, 'sed' => (int) 2, 'sgi' => (int) 12, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 2, 'tar' => (int) 10, 'tha' => (int) 1, 'tca' => (int) 1, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 2, 'ugi' => (int) 1, 'vma' => (int) 5, 'vmu' => (int) 1, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb301270' $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' => 'HOM05D001460', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '433', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p22980' => 'bna', 'A01p32340' => 'bna', 'A03p42970' => 'bna', 'A05p25880' => 'bna', 'Aa31LG8G9320' => 'aar', 'Aa31LG8G9330' => 'aar', 'Aa31LG8G9340' => 'aar', 'Aa31sc221G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1034' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1528' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.829' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2222' => 'aag', 'Ah.12g058830' => 'amhyb', 'Ah.12g058840' => 'amhyb', 'AL3G37160' => 'aly', 'AL7G41310' => 'aly', 'Aqoxy5G00395' => 'aox', 'Aqoxy5G00396' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0C8NZA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5185HY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JZ1PRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MD3LS0' => 'arhy', 'AT3G22840' => 'ath', 'AT4G14690' => 'ath', 'ATR0665G054' => 'atr', 'Atru.chr4.2344' => 'acertr', 'Atru.chr4.2346' => 'acertr', 'Atru.chr4.2347' => 'acertr', 'Atru.chr4.2348' => 'acertr', 'Atru.chr4.2355' => 'acertr', 'Atru.chr4.2356' => 'acertr', 'Atru.chr4.2358' => 'acertr', 'Atru.chr4.2359' => 'acertr', 'Atru.chr4.2360' => 'acertr', 'Atru.chr4.2361' => 'acertr', 'AUR62030476' => 'cqu', 'AUR62030478' => 'cqu', 'AUR62030819' => 'cqu', 'AUR62030820' => 'cqu', 'BcaB03g14648' => 'bca', 'BcaB04g20492' => 'bca', 'BcaB06g26399' => 'bca', 'BcaC01g03416' => 'bca', 'BcaC01g03419' => 'bca', 'BcaC01g03421' => 'bca', 'BcaC01g03424' => 'bca', 'BcaC05g28012' => 'bca', 'BcaC09g49212' => 'bca', 'BcaC09g50140' => 'bca', 'BcaNung00346' => 'bca', 'BolC1t02785H' => 'bol', 'BolC1t04095H' => 'bol', 'BolC3t17545H' => 'bol', 'BolC5t32769H' => 'bol', 'BraA01t02211Z' => 'bra', 'BraA01t03359Z' => 'bra', 'BraA03t13441Z' => 'bra', 'BraA05t21476Z' => 'bra', 'C01p28420' => 'bna', 'C01p41350' => 'bna', 'C03p52750' => 'bna', 'C03p52780' => 'bna', 'C05p40270' => 'bna', 'CAN.G1437.9' => 'can', 'CANSAT78G0035' => 'cansat', 'CANSAT78G1036' => 'cansat', 'CANSAT78G2272' => 'cansat', 'CANSAT78G2478' => 'cansat', 'CARHR098700' => 'chi', 'CARHR221120' => 'chi', 'CARHR221150' => 'chi', 'Carub.0003s2297' => 'cru', 'Carub.0007s2749' => 'cru', 'Carub.0007s2750' => 'cru', 'Carub.0007s2751' => 'cru', 'Ca_10849_v3' => 'car', 'Cc03_g04300' => 'ccan', 'CDE02G3648' => 'cde', 'CDE05G0060' => 'cde', 'CDE05G0692' => 'cde', 'CDE05G2285' => 'cde', 'CDE05G2884' => 'cde', 'CDE05G3072' => 'cde', 'Cfa008439' => 'cfa', 'Cfa008441' => 'cfa', 'Cfa008443' => 'cfa', 'Cfa008448' => 'cfa', 'Ciclev10005974m.g' => 'ccl', 'Ciclev10006006m.g' => 'ccl', 'Ciclev10006775m.g' => 'ccl', 'CiPaw.02G120400' => 'cil', 'CiPaw.02G120500' => 'cil', 'CiPaw.02G120600' => 'cil', 'ClCG05G004850' => 'cla', 'COL.COLO4_21566' => 'col', 'Cpa.g.sc44.124' => 'cpa', 'Cre07.g320400' => 'cre', 'Cre07.g320450' => 'cre', 'Cre08.g384650' => 'cre', 'Cre09.g393173' => 'cre', 'Cre09.g394325' => 'cre', 'Cre14.g626750' => 'cre', 'Cre16.g679250' => 'cre', 'CsaV3_3G012890' => 'csa', 'CSS0010865' => 'camsi', 'CSS0044338' => 'camsi', 'DCAR_002366' => 'dca', 'DCAR_030687' => 'dca', 'DCAR_030688' => 'dca', 'Dinv14047' => 'din', 'Dinv14048' => 'din', 'Duzib151G0105' => 'dzi', 'Duzib151G0114' => 'dzi', 'Duzib212G1029' => 'dzi', 'ECA232G3536' => 'eca', 'ECA240G0786' => 'eca', 'ECA240G1802' => 'eca', 'ECA240G3760' => 'eca', 'ECA240G3920' => 'eca', 'EL10Ac5g12536' => 'bvu', 'EL10Ac5g12537' => 'bvu', 'EL10Ac5g12538' => 'bvu', 'Eucgr.B01004' => 'egr', 'Eucgr.B01006' => 'egr', 'Eucgr.B01007' => 'egr', 'Eucgr.B01008' => 'egr', 'Eucgr.B01895' => 'egr', 'Eucgr.B01896' => 'egr', 'FAN04G1456' => 'fan', 'FAN08G1769' => 'fan', 'FAN08G2160' => 'fan', 'FAN13G2403' => 'fan', 'FAN13G3303' => 'fan', 'FAN15G2435' => 'fan', 'FAN17G0672' => 'fan', 'FAN17G2441' => 'fan', 'FAN18G1024' => 'fan', 'FAN22G1458' => 'fan', 'FAN24G0037' => 'fan', 'FAN24G0429' => 'fan', 'FAN24G2387' => 'fan', 'FAN27G2746' => 'fan', 'FvH4_2g20400' => 'fve', 'FvH4_2g20420' => 'fve', 'FvH4_2g20430' => 'fve', 'FvH4_4g01270' => 'fve', 'FvH4_4g01290' => 'fve', 'FvH4_4g01300' => 'fve', 'FvH4_4g01310' => 'fve', 'FvH4_4g01330' => 'fve', 'FvH4_5g09070' => 'fve', 'Glyma.10G243800' => 'gma', 'Glyma.20G150600' => 'gma', 'Gohir.A09G219200' => 'ghi', 'Gohir.A09G219300' => 'ghi', 'Gohir.D09G221400' => 'ghi', 'Gohir.D09G221500' => 'ghi', 'Gorai.006G242600' => 'gra', 'Gorai.006G242700' => 'gra', 'GSVIVG01018044001' => 'vvi', 'HanXRQChr03g0083821' => 'han', 'HanXRQChr03g0083841' => 'han', 'HanXRQChr03g0083881' => 'han', 'HanXRQChr03g0083901' => 'han', 'HanXRQChr03g0083921' => 'han', 'HanXRQChr03g0085331' => 'han', 'HanXRQChr03g0085361' => 'han', 'HanXRQChr03g0085411' => 'han', 'HanXRQChr03g0085421' => 'han', 'HanXRQChr03g0085431' => 'han', 'HanXRQChr08g0221991' => 'han', 'HanXRQChr11g0336061' => 'han', 'HanXRQChr11g0336411' => 'han', 'Haze_11234' => 'cav', 'Hma1.2p1_0549F.1_g177010' => 'hma', 'Hma1.2p1_0602F.1_g187630' => 'hma', 'Hund14876' => 'sun', 'Hund14879' => 'sun', 'Lalb_Chr06g0160741' => 'lal', 'Lalb_Chr21g0304781' => 'lal', 'Lj3A726G19' => 'lonja', 'Lj3A726T23' => 'lonja', 'Lj3A726T24' => 'lonja', 'Lj3A726T25' => 'lonja', 'Lj3A727T17' => 'lonja', 'Lj3C726T0' => 'lonja', 'Lj3C726T2' => 'lonja', 'Lj3P725T35' => 'lonja', 'Lj3P727T10' => 'lonja', 'Lj3P727T12' => 'lonja', 'Lj3P727T14' => 'lonja', 'Lj5g0023109' => 'lja', 'Lj6P646T44' => 'lonja', 'Lsat_1_v5_gn_6_75760' => 'lsa', 'Lsat_1_v5_gn_6_75800' => 'lsa', 'Lsat_1_v5_gn_6_75900' => 'lsa', 'Lsat_1_v5_gn_6_76240' => 'lsa', 'Lsat_1_v5_gn_6_76441' => 'lsa', 'Lsat_1_v5_gn_6_76700' => 'lsa', 'Lsat_1_v5_gn_6_76760' => 'lsa', 'Manes.15G033100' => 'mes', 'Mapoly0004s0074' => 'mpo', 'Mapoly0004s0075' => 'mpo', 'Mapoly0004s0163' => 'mpo', 'Mapoly0004s0164' => 'mpo', 'Mapoly0021s0018' => 'mpo', 'Mapoly0041s0136' => 'mpo', 'Mapoly0041s0137' => 'mpo', 'Mapoly0041s0138' => 'mpo', 'Mapoly0041s0139' => 'mpo', 'Mapoly0041s0141' => 'mpo', 'Mapoly0041s0142' => 'mpo', 'Mapoly0041s0143' => 'mpo', 'Mapoly0041s0144' => 'mpo', 'Mapoly0041s0145' => 'mpo', 'Mapoly0047s0106' => 'mpo', 'Mapoly0047s0108' => 'mpo', 'Mapoly0050s0051' => 'mpo', 'Mapoly0050s0052' => 'mpo', 'Mapoly0050s0053' => 'mpo', 'Mapoly0058s0013' => 'mpo', 'Mapoly0091s0078' => 'mpo', 'Mapoly0091s0079' => 'mpo', 'Mapoly0091s0080' => 'mpo', 'Mapoly0091s0081' => 'mpo', 'Mapoly0278s0004' => 'mpo', 'Mapoly0278s0005' => 'mpo', 'Mapoly0278s0006' => 'mpo', 'MBI11_g30648_MAGBIO' => 'mbi', 'MCO03G194' => 'mco', 'MCO03G590' => 'mco', 'MCO07G312' => 'mco', 'MCO10G318' => 'mco', 'MCO12G244' => 'mco', 'MCO13G148' => 'mco', 'MCO13G194' => 'mco', 'MCO16G238' => 'mco', 'MD06G1134100' => 'mdo', 'MD13G1200100' => 'mdo', 'MD13G1200300' => 'mdo', 'MD13G1200600' => 'mdo', 'MD14G1150400' => 'mdo', 'MD16G1200000' => 'mdo', 'Medtr1g102570' => 'mtr', 'Medtr1g102780' => 'mtr', 'Medtr1g102800' => 'mtr', 'Medtr1g102810' => 'mtr', 'Medtr1g102830' => 'mtr', 'MELO3C006499.2' => 'cme', 'Migut.G00385' => 'egut', 'MSTRG.4063' => 'ama', 'Nitab4.5_0000090g0260' => 'nta', 'Nitab4.5_0000977g0030' => 'nta', 'Nitab4.5_0002541g0040' => 'nta', 'Nitab4.5_0007068g0040' => 'nta', 'Nn005s41408' => 'nnu', 'Nn005s41410' => 'nnu', 'Oeu010310.1' => 'oeu', 'Oeu010311.1' => 'oeu', 'Oeu043472.1' => 'oeu', 'Os01g0246400' => 'osa', 'Os04g0267950' => 'osa', 'Os07g0178700' => 'osa', 'Os07g0178800' => 'osa', 'Peaxi162Scf00316g00046' => 'pax', 'Peaxi162Scf00316g00049' => 'pax', 'Peaxi162Scf00316g00059' => 'pax', 'Peaxi162Scf00316g00328' => 'pax', 'Peaxi162Scf00316g00329' => 'pax', 'Peaxi162Scf00316g00411' => 'pax', 'Peaxi162Scf00316g00521' => 'pax', 'Peaxi162Scf00492g00068' => 'pax', 'Peaxi162Scf35631g00002' => 'pax', 'PGR142G3720' => 'pgr', 'PGSC0003DMG400006442' => 'stu', 'Phvul.007G062000' => 'pvu', 'Potri.008G157750' => 'ptr', 'Potri.008G157900' => 'ptr', 'Potri.008G158000' => 'ptr', 'Potri.008G158200' => 'ptr', 'Pp3c11_7280' => 'ppa', 'Pp3c11_7980' => 'ppa', 'Pp3c12_19450' => 'ppa', 'Pp3c14_1480' => 'ppa', 'Pp3c14_1501' => 'ppa', 'Pp3c16_4900' => 'ppa', 'Pp3c16_5010' => 'ppa', 'Pp3c16_5060' => 'ppa', 'Pp3c19_18250' => 'ppa', 'Pp3c23_8530' => 'ppa', 'Pp3c23_8550' => 'ppa', 'Pp3c24_9670' => 'ppa', 'Pp3c2_21390' => 'ppa', 'Pp3c2_31380' => 'ppa', 'Pp3c3_16620' => 'ppa', 'Pp3c3_8090' => 'ppa', 'Pp3c3_8110' => 'ppa', 'Pp3c3_8130' => 'ppa', 'Pp3c3_8150' => 'ppa', 'Pp3c4_14320' => 'ppa', 'Pp3c6_2560' => 'ppa', 'Pp3c9_16700' => 'ppa', 'PRCOL_00000234' => 'pco', 'PRCOL_00000235' => 'pco', 'PRCOL_00000777' => 'pco', 'PRCOL_00002344' => 'pco', 'PRCOL_00002372' => 'pco', 'PRCOL_00006120' => 'pco', 'Prupe.1G021400' => 'ppe', 'Prupe.1G021500' => 'ppe', 'Prupe.1G021600' => 'ppe', 'Prupe.1G021700' => 'ppe', 'Prupe.1G021800' => 'ppe', 'Prupe.5G145100' => 'ppe', 'Psat6g204040' => 'psa', 'Psat6g204800' => 'psa', 'Psat6g204920' => 'psa', 'Psat6g204960' => 'psa', 'Psat6g205080' => 'psa', 'PSO017G0271' => 'pso', 'PSO017G1276' => 'pso', 'PSO017G1429' => 'pso', 'PSO017G1861' => 'pso', 'PSO017G2787' => 'pso', 'PSO017G4466' => 'pso', 'PSO017G5118' => 'pso', 'PSO017G5420' => 'pso', 'PSO063G3678' => 'pso', 'PSO210G0546' => 'pso', 'PSO317G0001' => 'pso', 'PSO357G0512' => 'pso', 'PSO478G2682' => 'pso', 'PSO647G0001' => 'pso', 'PSO675G0001' => 'pso', 'PSO675G2699' => 'pso', 'PSO675G2849' => 'pso', 'PSO675G4991' => 'pso', 'PSO689G0001' => 'pso', 'QL06p000916' => 'qlo', 'QL06p000921' => 'qlo', 'QL06p001398' => 'qlo', 'QL06p001407' => 'qlo', 'QL06p002031' => 'qlo', 'RcHm_v2.0_Chr4g0387791' => 'rch', 'RcHm_v2.0_Chr4g0387801' => 'rch', 'RcHm_v2.0_Chr6g0286501' => 'rch', 'RcHm_v2.0_Chr6g0286511' => 'rch', 'RcHm_v2.0_Chr6g0286521' => 'rch', 'RcHm_v2.0_Chr6g0286531' => 'rch', 'RcHm_v2.0_Chr7g0189141' => 'rch', 'Rhsim02G0028700' => 'rsi', 'Rhsim02G0028800' => 'rsi', 'Rhsim02G0028900' => 'rsi', 'Rhsim02G0029000' => 'rsi', 'Rhsim02G0029100' => 'rsi', 'Rhsim02G0029200' => 'rsi', 'Rhsim02G0029300' => 'rsi', 'Rhsim02G0029400' => 'rsi', 'Rhsim02G0029500' => 'rsi', 'Rhsim02G0029600' => 'rsi', 'RhsimUnG0024000' => 'rsi', 'RhsimUnG0024100' => 'rsi', 'RhsimUnG0024200' => 'rsi', 'RhsimUnG0024300' => 'rsi', 'RhsimUnG0024400' => 'rsi', 'RhsimUnG0024500' => 'rsi', 'RhsimUnG0024700' => 'rsi', 'RhsimUnG0024800' => 'rsi', 'RhsimUnG0024900' => 'rsi', 'RhsimUnG0025100' => 'rsi', 'Sabra08G0120200' => 'sbr', 'Sabra08G0120300' => 'sbr', 'Sabra08G0120500' => 'sbr', 'Sabra08G0120600' => 'sbr', 'Sabra10G0158900' => 'sbr', 'SalBow2G3492' => 'sbo', 'Sc13g0004760' => 'sci', 'Sc13g0004770' => 'sci', 'Sed0003417' => 'sed', 'Sed0019750' => 'sed', 'SEGI_03419' => 'sgi', 'SEGI_05907' => 'sgi', 'SEGI_10682' => 'sgi', 'SEGI_13528' => 'sgi', 'SEGI_16081' => 'sgi', 'SEGI_19370' => 'sgi', 'SEGI_21015' => 'sgi', 'SEGI_21944' => 'sgi', 'SEGI_32906' => 'sgi', 'SEGI_33093' => 'sgi', 'SEGI_36110' => 'sgi', 'SEGI_40397' => 'sgi', 'SGA_v2.0_scaffold191G40426' => 'sas', 'SGA_v2.0_scaffold353G49717' => 'sas', 'SGA_v2.0_scaffold50G18550' => 'sas', 'SMO119G0173' => 'smo', 'SMO172G0002' => 'smo', 'Solyc09g082690.3' => 'sly', 'Solyc09g082700.2' => 'sly', 'Sopen09g031550' => 'spe', 'Sopen09g031560' => 'spe', 'Sp3g20540' => 'spa', 'Sp7g07580' => 'spa', 'TAR134G0002' => 'tar', 'TAR236G0001' => 'tar', 'TAR365G0892' => 'tar', 'TAR636G0166' => 'tar', 'TAR636G0646' => 'tar', 'TAR636G0869' => 'tar', 'TAR636G1317' => 'tar', 'TAR636G1744' => 'tar', 'TAR636G3358' => 'tar', 'TAR636G3436' => 'tar', 'THA.LOC104803047' => 'tha', 'Thecc.04G238900' => 'tca', 'Thhalv10021557m.g' => 'esa', 'Thhalv10026318m.g' => 'esa', 'Thhalv10026335m.g' => 'esa', 'TPR.G17433' => 'tpr', 'TPR.G18915' => 'tpr', 'TPR.G26125' => 'tpr', 'TWI09G0677' => 'twi', 'TWI73G0287' => 'twi', 'unitig_748.g8326' => 'ugi', 'vmacro15370' => 'vma', 'vmacro15371' => 'vma', 'vmacro15372' => 'vma', 'vmacro15373' => 'vma', 'vmacro15374' => 'vma', 'VMungo0720G2826' => 'vmu', 'Zm00001eb116960' => 'zma', 'Zm00001eb301260' => 'zma', 'Zm00001eb301270' => 'zma' ), 'gf_id' => 'HOM05D001460', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001460' ), 'data_identifier' => 'HOM05D001460', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001460', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '433', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p22980' => 'bna', 'A01p32340' => 'bna', 'A03p42970' => 'bna', 'A05p25880' => 'bna', 'Aa31LG8G9320' => 'aar', 'Aa31LG8G9330' => 'aar', 'Aa31LG8G9340' => 'aar', 'Aa31sc221G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1034' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1528' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.829' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2222' => 'aag', 'Ah.12g058830' => 'amhyb', 'Ah.12g058840' => 'amhyb', 'AL3G37160' => 'aly', 'AL7G41310' => 'aly', 'Aqoxy5G00395' => 'aox', 'Aqoxy5G00396' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0C8NZA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5185HY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JZ1PRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MD3LS0' => 'arhy', 'AT3G22840' => 'ath', 'AT4G14690' => 'ath', 'ATR0665G054' => 'atr', 'Atru.chr4.2344' => 'acertr', 'Atru.chr4.2346' => 'acertr', 'Atru.chr4.2347' => 'acertr', 'Atru.chr4.2348' => 'acertr', 'Atru.chr4.2355' => 'acertr', 'Atru.chr4.2356' => 'acertr', 'Atru.chr4.2358' => 'acertr', 'Atru.chr4.2359' => 'acertr', 'Atru.chr4.2360' => 'acertr', 'Atru.chr4.2361' => 'acertr', 'AUR62030476' => 'cqu', 'AUR62030478' => 'cqu', 'AUR62030819' => 'cqu', 'AUR62030820' => 'cqu', 'BcaB03g14648' => 'bca', 'BcaB04g20492' => 'bca', 'BcaB06g26399' => 'bca', 'BcaC01g03416' => 'bca', 'BcaC01g03419' => 'bca', 'BcaC01g03421' => 'bca', 'BcaC01g03424' => 'bca', 'BcaC05g28012' => 'bca', 'BcaC09g49212' => 'bca', 'BcaC09g50140' => 'bca', 'BcaNung00346' => 'bca', 'BolC1t02785H' => 'bol', 'BolC1t04095H' => 'bol', 'BolC3t17545H' => 'bol', 'BolC5t32769H' => 'bol', 'BraA01t02211Z' => 'bra', 'BraA01t03359Z' => 'bra', 'BraA03t13441Z' => 'bra', 'BraA05t21476Z' => 'bra', 'C01p28420' => 'bna', 'C01p41350' => 'bna', 'C03p52750' => 'bna', 'C03p52780' => 'bna', 'C05p40270' => 'bna', 'CAN.G1437.9' => 'can', 'CANSAT78G0035' => 'cansat', 'CANSAT78G1036' => 'cansat', 'CANSAT78G2272' => 'cansat', 'CANSAT78G2478' => 'cansat', 'CARHR098700' => 'chi', 'CARHR221120' => 'chi', 'CARHR221150' => 'chi', 'Carub.0003s2297' => 'cru', 'Carub.0007s2749' => 'cru', 'Carub.0007s2750' => 'cru', 'Carub.0007s2751' => 'cru', 'Ca_10849_v3' => 'car', 'Cc03_g04300' => 'ccan', 'CDE02G3648' => 'cde', 'CDE05G0060' => 'cde', 'CDE05G0692' => 'cde', 'CDE05G2285' => 'cde', 'CDE05G2884' => 'cde', 'CDE05G3072' => 'cde', 'Cfa008439' => 'cfa', 'Cfa008441' => 'cfa', 'Cfa008443' => 'cfa', 'Cfa008448' => 'cfa', 'Ciclev10005974m.g' => 'ccl', 'Ciclev10006006m.g' => 'ccl', 'Ciclev10006775m.g' => 'ccl', 'CiPaw.02G120400' => 'cil', 'CiPaw.02G120500' => 'cil', 'CiPaw.02G120600' => 'cil', 'ClCG05G004850' => 'cla', 'COL.COLO4_21566' => 'col', 'Cpa.g.sc44.124' => 'cpa', 'Cre07.g320400' => 'cre', 'Cre07.g320450' => 'cre', 'Cre08.g384650' => 'cre', 'Cre09.g393173' => 'cre', 'Cre09.g394325' => 'cre', 'Cre14.g626750' => 'cre', 'Cre16.g679250' => 'cre', 'CsaV3_3G012890' => 'csa', 'CSS0010865' => 'camsi', 'CSS0044338' => 'camsi', 'DCAR_002366' => 'dca', 'DCAR_030687' => 'dca', 'DCAR_030688' => 'dca', 'Dinv14047' => 'din', 'Dinv14048' => 'din', 'Duzib151G0105' => 'dzi', 'Duzib151G0114' => 'dzi', 'Duzib212G1029' => 'dzi', 'ECA232G3536' => 'eca', 'ECA240G0786' => 'eca', 'ECA240G1802' => 'eca', 'ECA240G3760' => 'eca', 'ECA240G3920' => 'eca', 'EL10Ac5g12536' => 'bvu', 'EL10Ac5g12537' => 'bvu', 'EL10Ac5g12538' => 'bvu', 'Eucgr.B01004' => 'egr', 'Eucgr.B01006' => 'egr', 'Eucgr.B01007' => 'egr', 'Eucgr.B01008' => 'egr', 'Eucgr.B01895' => 'egr', 'Eucgr.B01896' => 'egr', 'FAN04G1456' => 'fan', 'FAN08G1769' => 'fan', 'FAN08G2160' => 'fan', 'FAN13G2403' => 'fan', 'FAN13G3303' => 'fan', 'FAN15G2435' => 'fan', 'FAN17G0672' => 'fan', 'FAN17G2441' => 'fan', 'FAN18G1024' => 'fan', 'FAN22G1458' => 'fan', 'FAN24G0037' => 'fan', 'FAN24G0429' => 'fan', 'FAN24G2387' => 'fan', 'FAN27G2746' => 'fan', 'FvH4_2g20400' => 'fve', 'FvH4_2g20420' => 'fve', 'FvH4_2g20430' => 'fve', 'FvH4_4g01270' => 'fve', 'FvH4_4g01290' => 'fve', 'FvH4_4g01300' => 'fve', 'FvH4_4g01310' => 'fve', 'FvH4_4g01330' => 'fve', 'FvH4_5g09070' => 'fve', 'Glyma.10G243800' => 'gma', 'Glyma.20G150600' => 'gma', 'Gohir.A09G219200' => 'ghi', 'Gohir.A09G219300' => 'ghi', 'Gohir.D09G221400' => 'ghi', 'Gohir.D09G221500' => 'ghi', 'Gorai.006G242600' => 'gra', 'Gorai.006G242700' => 'gra', 'GSVIVG01018044001' => 'vvi', 'HanXRQChr03g0083821' => 'han', 'HanXRQChr03g0083841' => 'han', 'HanXRQChr03g0083881' => 'han', 'HanXRQChr03g0083901' => 'han', 'HanXRQChr03g0083921' => 'han', 'HanXRQChr03g0085331' => 'han', 'HanXRQChr03g0085361' => 'han', 'HanXRQChr03g0085411' => 'han', 'HanXRQChr03g0085421' => 'han', 'HanXRQChr03g0085431' => 'han', 'HanXRQChr08g0221991' => 'han', 'HanXRQChr11g0336061' => 'han', 'HanXRQChr11g0336411' => 'han', 'Haze_11234' => 'cav', 'Hma1.2p1_0549F.1_g177010' => 'hma', 'Hma1.2p1_0602F.1_g187630' => 'hma', 'Hund14876' => 'sun', 'Hund14879' => 'sun', 'Lalb_Chr06g0160741' => 'lal', 'Lalb_Chr21g0304781' => 'lal', 'Lj3A726G19' => 'lonja', 'Lj3A726T23' => 'lonja', 'Lj3A726T24' => 'lonja', 'Lj3A726T25' => 'lonja', 'Lj3A727T17' => 'lonja', 'Lj3C726T0' => 'lonja', 'Lj3C726T2' => 'lonja', 'Lj3P725T35' => 'lonja', 'Lj3P727T10' => 'lonja', 'Lj3P727T12' => 'lonja', 'Lj3P727T14' => 'lonja', 'Lj5g0023109' => 'lja', 'Lj6P646T44' => 'lonja', 'Lsat_1_v5_gn_6_75760' => 'lsa', 'Lsat_1_v5_gn_6_75800' => 'lsa', 'Lsat_1_v5_gn_6_75900' => 'lsa', 'Lsat_1_v5_gn_6_76240' => 'lsa', 'Lsat_1_v5_gn_6_76441' => 'lsa', 'Lsat_1_v5_gn_6_76700' => 'lsa', 'Lsat_1_v5_gn_6_76760' => 'lsa', 'Manes.15G033100' => 'mes', 'Mapoly0004s0074' => 'mpo', 'Mapoly0004s0075' => 'mpo', 'Mapoly0004s0163' => 'mpo', 'Mapoly0004s0164' => 'mpo', 'Mapoly0021s0018' => 'mpo', 'Mapoly0041s0136' => 'mpo', 'Mapoly0041s0137' => 'mpo', 'Mapoly0041s0138' => 'mpo', 'Mapoly0041s0139' => 'mpo', 'Mapoly0041s0141' => 'mpo', 'Mapoly0041s0142' => 'mpo', 'Mapoly0041s0143' => 'mpo', 'Mapoly0041s0144' => 'mpo', 'Mapoly0041s0145' => 'mpo', 'Mapoly0047s0106' => 'mpo', 'Mapoly0047s0108' => 'mpo', 'Mapoly0050s0051' => 'mpo', 'Mapoly0050s0052' => 'mpo', 'Mapoly0050s0053' => 'mpo', 'Mapoly0058s0013' => 'mpo', 'Mapoly0091s0078' => 'mpo', 'Mapoly0091s0079' => 'mpo', 'Mapoly0091s0080' => 'mpo', 'Mapoly0091s0081' => 'mpo', 'Mapoly0278s0004' => 'mpo', 'Mapoly0278s0005' => 'mpo', 'Mapoly0278s0006' => 'mpo', 'MBI11_g30648_MAGBIO' => 'mbi', 'MCO03G194' => 'mco', 'MCO03G590' => 'mco', 'MCO07G312' => 'mco', 'MCO10G318' => 'mco', 'MCO12G244' => 'mco', 'MCO13G148' => 'mco', 'MCO13G194' => 'mco', 'MCO16G238' => 'mco', 'MD06G1134100' => 'mdo', 'MD13G1200100' => 'mdo', 'MD13G1200300' => 'mdo', 'MD13G1200600' => 'mdo', 'MD14G1150400' => 'mdo', 'MD16G1200000' => 'mdo', 'Medtr1g102570' => 'mtr', 'Medtr1g102780' => 'mtr', 'Medtr1g102800' => 'mtr', 'Medtr1g102810' => 'mtr', 'Medtr1g102830' => 'mtr', 'MELO3C006499.2' => 'cme', 'Migut.G00385' => 'egut', 'MSTRG.4063' => 'ama', 'Nitab4.5_0000090g0260' => 'nta', 'Nitab4.5_0000977g0030' => 'nta', 'Nitab4.5_0002541g0040' => 'nta', 'Nitab4.5_0007068g0040' => 'nta', 'Nn005s41408' => 'nnu', 'Nn005s41410' => 'nnu', 'Oeu010310.1' => 'oeu', 'Oeu010311.1' => 'oeu', 'Oeu043472.1' => 'oeu', 'Os01g0246400' => 'osa', 'Os04g0267950' => 'osa', 'Os07g0178700' => 'osa', 'Os07g0178800' => 'osa', 'Peaxi162Scf00316g00046' => 'pax', 'Peaxi162Scf00316g00049' => 'pax', 'Peaxi162Scf00316g00059' => 'pax', 'Peaxi162Scf00316g00328' => 'pax', 'Peaxi162Scf00316g00329' => 'pax', 'Peaxi162Scf00316g00411' => 'pax', 'Peaxi162Scf00316g00521' => 'pax', 'Peaxi162Scf00492g00068' => 'pax', 'Peaxi162Scf35631g00002' => 'pax', 'PGR142G3720' => 'pgr', 'PGSC0003DMG400006442' => 'stu', 'Phvul.007G062000' => 'pvu', 'Potri.008G157750' => 'ptr', 'Potri.008G157900' => 'ptr', 'Potri.008G158000' => 'ptr', 'Potri.008G158200' => 'ptr', 'Pp3c11_7280' => 'ppa', 'Pp3c11_7980' => 'ppa', 'Pp3c12_19450' => 'ppa', 'Pp3c14_1480' => 'ppa', 'Pp3c14_1501' => 'ppa', 'Pp3c16_4900' => 'ppa', 'Pp3c16_5010' => 'ppa', 'Pp3c16_5060' => 'ppa', 'Pp3c19_18250' => 'ppa', 'Pp3c23_8530' => 'ppa', 'Pp3c23_8550' => 'ppa', 'Pp3c24_9670' => 'ppa', 'Pp3c2_21390' => 'ppa', 'Pp3c2_31380' => 'ppa', 'Pp3c3_16620' => 'ppa', 'Pp3c3_8090' => 'ppa', 'Pp3c3_8110' => 'ppa', 'Pp3c3_8130' => 'ppa', 'Pp3c3_8150' => 'ppa', 'Pp3c4_14320' => 'ppa', 'Pp3c6_2560' => 'ppa', 'Pp3c9_16700' => 'ppa', 'PRCOL_00000234' => 'pco', 'PRCOL_00000235' => 'pco', 'PRCOL_00000777' => 'pco', 'PRCOL_00002344' => 'pco', 'PRCOL_00002372' => 'pco', 'PRCOL_00006120' => 'pco', 'Prupe.1G021400' => 'ppe', 'Prupe.1G021500' => 'ppe', 'Prupe.1G021600' => 'ppe', 'Prupe.1G021700' => 'ppe', 'Prupe.1G021800' => 'ppe', 'Prupe.5G145100' => 'ppe', 'Psat6g204040' => 'psa', 'Psat6g204800' => 'psa', 'Psat6g204920' => 'psa', 'Psat6g204960' => 'psa', 'Psat6g205080' => 'psa', 'PSO017G0271' => 'pso', 'PSO017G1276' => 'pso', 'PSO017G1429' => 'pso', 'PSO017G1861' => 'pso', 'PSO017G2787' => 'pso', 'PSO017G4466' => 'pso', 'PSO017G5118' => 'pso', 'PSO017G5420' => 'pso', 'PSO063G3678' => 'pso', 'PSO210G0546' => 'pso', 'PSO317G0001' => 'pso', 'PSO357G0512' => 'pso', 'PSO478G2682' => 'pso', 'PSO647G0001' => 'pso', 'PSO675G0001' => 'pso', 'PSO675G2699' => 'pso', 'PSO675G2849' => 'pso', 'PSO675G4991' => 'pso', 'PSO689G0001' => 'pso', 'QL06p000916' => 'qlo', 'QL06p000921' => 'qlo', 'QL06p001398' => 'qlo', 'QL06p001407' => 'qlo', 'QL06p002031' => 'qlo', 'RcHm_v2.0_Chr4g0387791' => 'rch', 'RcHm_v2.0_Chr4g0387801' => 'rch', 'RcHm_v2.0_Chr6g0286501' => 'rch', 'RcHm_v2.0_Chr6g0286511' => 'rch', 'RcHm_v2.0_Chr6g0286521' => 'rch', 'RcHm_v2.0_Chr6g0286531' => 'rch', 'RcHm_v2.0_Chr7g0189141' => 'rch', 'Rhsim02G0028700' => 'rsi', 'Rhsim02G0028800' => 'rsi', 'Rhsim02G0028900' => 'rsi', 'Rhsim02G0029000' => 'rsi', 'Rhsim02G0029100' => 'rsi', 'Rhsim02G0029200' => 'rsi', 'Rhsim02G0029300' => 'rsi', 'Rhsim02G0029400' => 'rsi', 'Rhsim02G0029500' => 'rsi', 'Rhsim02G0029600' => 'rsi', 'RhsimUnG0024000' => 'rsi', 'RhsimUnG0024100' => 'rsi', 'RhsimUnG0024200' => 'rsi', 'RhsimUnG0024300' => 'rsi', 'RhsimUnG0024400' => 'rsi', 'RhsimUnG0024500' => 'rsi', 'RhsimUnG0024700' => 'rsi', 'RhsimUnG0024800' => 'rsi', 'RhsimUnG0024900' => 'rsi', 'RhsimUnG0025100' => 'rsi', 'Sabra08G0120200' => 'sbr', 'Sabra08G0120300' => 'sbr', 'Sabra08G0120500' => 'sbr', 'Sabra08G0120600' => 'sbr', 'Sabra10G0158900' => 'sbr', 'SalBow2G3492' => 'sbo', 'Sc13g0004760' => 'sci', 'Sc13g0004770' => 'sci', 'Sed0003417' => 'sed', 'Sed0019750' => 'sed', 'SEGI_03419' => 'sgi', 'SEGI_05907' => 'sgi', 'SEGI_10682' => 'sgi', 'SEGI_13528' => 'sgi', 'SEGI_16081' => 'sgi', 'SEGI_19370' => 'sgi', 'SEGI_21015' => 'sgi', 'SEGI_21944' => 'sgi', 'SEGI_32906' => 'sgi', 'SEGI_33093' => 'sgi', 'SEGI_36110' => 'sgi', 'SEGI_40397' => 'sgi', 'SGA_v2.0_scaffold191G40426' => 'sas', 'SGA_v2.0_scaffold353G49717' => 'sas', 'SGA_v2.0_scaffold50G18550' => 'sas', 'SMO119G0173' => 'smo', 'SMO172G0002' => 'smo', 'Solyc09g082690.3' => 'sly', 'Solyc09g082700.2' => 'sly', 'Sopen09g031550' => 'spe', 'Sopen09g031560' => 'spe', 'Sp3g20540' => 'spa', 'Sp7g07580' => 'spa', 'TAR134G0002' => 'tar', 'TAR236G0001' => 'tar', 'TAR365G0892' => 'tar', 'TAR636G0166' => 'tar', 'TAR636G0646' => 'tar', 'TAR636G0869' => 'tar', 'TAR636G1317' => 'tar', 'TAR636G1744' => 'tar', 'TAR636G3358' => 'tar', 'TAR636G3436' => 'tar', 'THA.LOC104803047' => 'tha', 'Thecc.04G238900' => 'tca', 'Thhalv10021557m.g' => 'esa', 'Thhalv10026318m.g' => 'esa', 'Thhalv10026335m.g' => 'esa', 'TPR.G17433' => 'tpr', 'TPR.G18915' => 'tpr', 'TPR.G26125' => 'tpr', 'TWI09G0677' => 'twi', 'TWI73G0287' => 'twi', 'unitig_748.g8326' => 'ugi', 'vmacro15370' => 'vma', 'vmacro15371' => 'vma', 'vmacro15372' => 'vma', 'vmacro15373' => 'vma', 'vmacro15374' => 'vma', 'VMungo0720G2826' => 'vmu', 'Zm00001eb116960' => 'zma', 'Zm00001eb301260' => 'zma', 'Zm00001eb301270' => 'zma' ) $gf_id = 'HOM05D001460' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001460' ) $data_identifier = 'HOM05D001460' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 4, 'aag' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 2, 'aox' => (int) 2, 'arhy' => (int) 4, 'ath' => (int) 2, 'atr' => (int) 1, 'acertr' => (int) 10, 'cqu' => (int) 4, 'bca' => (int) 11, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 1, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 1, 'ccan' => (int) 1, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 1, 'col' => (int) 1, 'cpa' => (int) 1, 'cre' => (int) 7, 'csa' => (int) 1, 'camsi' => (int) 2, 'dca' => (int) 3, 'din' => (int) 2, 'dzi' => (int) 3, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 14, 'fve' => (int) 9, 'gma' => (int) 2, 'ghi' => (int) 4, 'gra' => (int) 2, 'vvi' => (int) 1, 'han' => (int) 13, 'cav' => (int) 1, 'hma' => (int) 2, 'sun' => (int) 2, 'lal' => (int) 2, 'lonja' => (int) 12, 'lja' => (int) 1, 'lsa' => (int) 7, 'mes' => (int) 1, 'mpo' => (int) 27, 'mbi' => (int) 1, 'mco' => (int) 8, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 1, 'egut' => (int) 1, 'ama' => (int) 1, 'nta' => (int) 4, 'nnu' => (int) 2, 'oeu' => (int) 3, 'osa' => (int) 4, 'pax' => (int) 9, 'pgr' => (int) 1, 'stu' => (int) 1, 'pvu' => (int) 1, 'ptr' => (int) 4, 'ppa' => (int) 22, 'pco' => (int) 6, 'ppe' => (int) 6, 'psa' => (int) 5, 'pso' => (int) 19, 'qlo' => (int) 5, 'rch' => (int) 7, 'rsi' => (int) 20, 'sbr' => (int) 5, 'sbo' => (int) 1, 'sci' => (int) 2, 'sed' => (int) 2, 'sgi' => (int) 12, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 2, 'tar' => (int) 10, 'tha' => (int) 1, 'tca' => (int) 1, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 2, 'ugi' => (int) 1, 'vma' => (int) 5, 'vmu' => (int) 1, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb301270' $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' => 'HOM05D001460', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '433', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p22980' => 'bna', 'A01p32340' => 'bna', 'A03p42970' => 'bna', 'A05p25880' => 'bna', 'Aa31LG8G9320' => 'aar', 'Aa31LG8G9330' => 'aar', 'Aa31LG8G9340' => 'aar', 'Aa31sc221G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1034' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1528' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.829' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2222' => 'aag', 'Ah.12g058830' => 'amhyb', 'Ah.12g058840' => 'amhyb', 'AL3G37160' => 'aly', 'AL7G41310' => 'aly', 'Aqoxy5G00395' => 'aox', 'Aqoxy5G00396' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0C8NZA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5185HY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JZ1PRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MD3LS0' => 'arhy', 'AT3G22840' => 'ath', 'AT4G14690' => 'ath', 'ATR0665G054' => 'atr', 'Atru.chr4.2344' => 'acertr', 'Atru.chr4.2346' => 'acertr', 'Atru.chr4.2347' => 'acertr', 'Atru.chr4.2348' => 'acertr', 'Atru.chr4.2355' => 'acertr', 'Atru.chr4.2356' => 'acertr', 'Atru.chr4.2358' => 'acertr', 'Atru.chr4.2359' => 'acertr', 'Atru.chr4.2360' => 'acertr', 'Atru.chr4.2361' => 'acertr', 'AUR62030476' => 'cqu', 'AUR62030478' => 'cqu', 'AUR62030819' => 'cqu', 'AUR62030820' => 'cqu', 'BcaB03g14648' => 'bca', 'BcaB04g20492' => 'bca', 'BcaB06g26399' => 'bca', 'BcaC01g03416' => 'bca', 'BcaC01g03419' => 'bca', 'BcaC01g03421' => 'bca', 'BcaC01g03424' => 'bca', 'BcaC05g28012' => 'bca', 'BcaC09g49212' => 'bca', 'BcaC09g50140' => 'bca', 'BcaNung00346' => 'bca', 'BolC1t02785H' => 'bol', 'BolC1t04095H' => 'bol', 'BolC3t17545H' => 'bol', 'BolC5t32769H' => 'bol', 'BraA01t02211Z' => 'bra', 'BraA01t03359Z' => 'bra', 'BraA03t13441Z' => 'bra', 'BraA05t21476Z' => 'bra', 'C01p28420' => 'bna', 'C01p41350' => 'bna', 'C03p52750' => 'bna', 'C03p52780' => 'bna', 'C05p40270' => 'bna', 'CAN.G1437.9' => 'can', 'CANSAT78G0035' => 'cansat', 'CANSAT78G1036' => 'cansat', 'CANSAT78G2272' => 'cansat', 'CANSAT78G2478' => 'cansat', 'CARHR098700' => 'chi', 'CARHR221120' => 'chi', 'CARHR221150' => 'chi', 'Carub.0003s2297' => 'cru', 'Carub.0007s2749' => 'cru', 'Carub.0007s2750' => 'cru', 'Carub.0007s2751' => 'cru', 'Ca_10849_v3' => 'car', 'Cc03_g04300' => 'ccan', 'CDE02G3648' => 'cde', 'CDE05G0060' => 'cde', 'CDE05G0692' => 'cde', 'CDE05G2285' => 'cde', 'CDE05G2884' => 'cde', 'CDE05G3072' => 'cde', 'Cfa008439' => 'cfa', 'Cfa008441' => 'cfa', 'Cfa008443' => 'cfa', 'Cfa008448' => 'cfa', 'Ciclev10005974m.g' => 'ccl', 'Ciclev10006006m.g' => 'ccl', 'Ciclev10006775m.g' => 'ccl', 'CiPaw.02G120400' => 'cil', 'CiPaw.02G120500' => 'cil', 'CiPaw.02G120600' => 'cil', 'ClCG05G004850' => 'cla', 'COL.COLO4_21566' => 'col', 'Cpa.g.sc44.124' => 'cpa', 'Cre07.g320400' => 'cre', 'Cre07.g320450' => 'cre', 'Cre08.g384650' => 'cre', 'Cre09.g393173' => 'cre', 'Cre09.g394325' => 'cre', 'Cre14.g626750' => 'cre', 'Cre16.g679250' => 'cre', 'CsaV3_3G012890' => 'csa', 'CSS0010865' => 'camsi', 'CSS0044338' => 'camsi', 'DCAR_002366' => 'dca', 'DCAR_030687' => 'dca', 'DCAR_030688' => 'dca', 'Dinv14047' => 'din', 'Dinv14048' => 'din', 'Duzib151G0105' => 'dzi', 'Duzib151G0114' => 'dzi', 'Duzib212G1029' => 'dzi', 'ECA232G3536' => 'eca', 'ECA240G0786' => 'eca', 'ECA240G1802' => 'eca', 'ECA240G3760' => 'eca', 'ECA240G3920' => 'eca', 'EL10Ac5g12536' => 'bvu', 'EL10Ac5g12537' => 'bvu', 'EL10Ac5g12538' => 'bvu', 'Eucgr.B01004' => 'egr', 'Eucgr.B01006' => 'egr', 'Eucgr.B01007' => 'egr', 'Eucgr.B01008' => 'egr', 'Eucgr.B01895' => 'egr', 'Eucgr.B01896' => 'egr', 'FAN04G1456' => 'fan', 'FAN08G1769' => 'fan', 'FAN08G2160' => 'fan', 'FAN13G2403' => 'fan', 'FAN13G3303' => 'fan', 'FAN15G2435' => 'fan', 'FAN17G0672' => 'fan', 'FAN17G2441' => 'fan', 'FAN18G1024' => 'fan', 'FAN22G1458' => 'fan', 'FAN24G0037' => 'fan', 'FAN24G0429' => 'fan', 'FAN24G2387' => 'fan', 'FAN27G2746' => 'fan', 'FvH4_2g20400' => 'fve', 'FvH4_2g20420' => 'fve', 'FvH4_2g20430' => 'fve', 'FvH4_4g01270' => 'fve', 'FvH4_4g01290' => 'fve', 'FvH4_4g01300' => 'fve', 'FvH4_4g01310' => 'fve', 'FvH4_4g01330' => 'fve', 'FvH4_5g09070' => 'fve', 'Glyma.10G243800' => 'gma', 'Glyma.20G150600' => 'gma', 'Gohir.A09G219200' => 'ghi', 'Gohir.A09G219300' => 'ghi', 'Gohir.D09G221400' => 'ghi', 'Gohir.D09G221500' => 'ghi', 'Gorai.006G242600' => 'gra', 'Gorai.006G242700' => 'gra', 'GSVIVG01018044001' => 'vvi', 'HanXRQChr03g0083821' => 'han', 'HanXRQChr03g0083841' => 'han', 'HanXRQChr03g0083881' => 'han', 'HanXRQChr03g0083901' => 'han', 'HanXRQChr03g0083921' => 'han', 'HanXRQChr03g0085331' => 'han', 'HanXRQChr03g0085361' => 'han', 'HanXRQChr03g0085411' => 'han', 'HanXRQChr03g0085421' => 'han', 'HanXRQChr03g0085431' => 'han', 'HanXRQChr08g0221991' => 'han', 'HanXRQChr11g0336061' => 'han', 'HanXRQChr11g0336411' => 'han', 'Haze_11234' => 'cav', 'Hma1.2p1_0549F.1_g177010' => 'hma', 'Hma1.2p1_0602F.1_g187630' => 'hma', 'Hund14876' => 'sun', 'Hund14879' => 'sun', 'Lalb_Chr06g0160741' => 'lal', 'Lalb_Chr21g0304781' => 'lal', 'Lj3A726G19' => 'lonja', 'Lj3A726T23' => 'lonja', 'Lj3A726T24' => 'lonja', 'Lj3A726T25' => 'lonja', 'Lj3A727T17' => 'lonja', 'Lj3C726T0' => 'lonja', 'Lj3C726T2' => 'lonja', 'Lj3P725T35' => 'lonja', 'Lj3P727T10' => 'lonja', 'Lj3P727T12' => 'lonja', 'Lj3P727T14' => 'lonja', 'Lj5g0023109' => 'lja', 'Lj6P646T44' => 'lonja', 'Lsat_1_v5_gn_6_75760' => 'lsa', 'Lsat_1_v5_gn_6_75800' => 'lsa', 'Lsat_1_v5_gn_6_75900' => 'lsa', 'Lsat_1_v5_gn_6_76240' => 'lsa', 'Lsat_1_v5_gn_6_76441' => 'lsa', 'Lsat_1_v5_gn_6_76700' => 'lsa', 'Lsat_1_v5_gn_6_76760' => 'lsa', 'Manes.15G033100' => 'mes', 'Mapoly0004s0074' => 'mpo', 'Mapoly0004s0075' => 'mpo', 'Mapoly0004s0163' => 'mpo', 'Mapoly0004s0164' => 'mpo', 'Mapoly0021s0018' => 'mpo', 'Mapoly0041s0136' => 'mpo', 'Mapoly0041s0137' => 'mpo', 'Mapoly0041s0138' => 'mpo', 'Mapoly0041s0139' => 'mpo', 'Mapoly0041s0141' => 'mpo', 'Mapoly0041s0142' => 'mpo', 'Mapoly0041s0143' => 'mpo', 'Mapoly0041s0144' => 'mpo', 'Mapoly0041s0145' => 'mpo', 'Mapoly0047s0106' => 'mpo', 'Mapoly0047s0108' => 'mpo', 'Mapoly0050s0051' => 'mpo', 'Mapoly0050s0052' => 'mpo', 'Mapoly0050s0053' => 'mpo', 'Mapoly0058s0013' => 'mpo', 'Mapoly0091s0078' => 'mpo', 'Mapoly0091s0079' => 'mpo', 'Mapoly0091s0080' => 'mpo', 'Mapoly0091s0081' => 'mpo', 'Mapoly0278s0004' => 'mpo', 'Mapoly0278s0005' => 'mpo', 'Mapoly0278s0006' => 'mpo', 'MBI11_g30648_MAGBIO' => 'mbi', 'MCO03G194' => 'mco', 'MCO03G590' => 'mco', 'MCO07G312' => 'mco', 'MCO10G318' => 'mco', 'MCO12G244' => 'mco', 'MCO13G148' => 'mco', 'MCO13G194' => 'mco', 'MCO16G238' => 'mco', 'MD06G1134100' => 'mdo', 'MD13G1200100' => 'mdo', 'MD13G1200300' => 'mdo', 'MD13G1200600' => 'mdo', 'MD14G1150400' => 'mdo', 'MD16G1200000' => 'mdo', 'Medtr1g102570' => 'mtr', 'Medtr1g102780' => 'mtr', 'Medtr1g102800' => 'mtr', 'Medtr1g102810' => 'mtr', 'Medtr1g102830' => 'mtr', 'MELO3C006499.2' => 'cme', 'Migut.G00385' => 'egut', 'MSTRG.4063' => 'ama', 'Nitab4.5_0000090g0260' => 'nta', 'Nitab4.5_0000977g0030' => 'nta', 'Nitab4.5_0002541g0040' => 'nta', 'Nitab4.5_0007068g0040' => 'nta', 'Nn005s41408' => 'nnu', 'Nn005s41410' => 'nnu', 'Oeu010310.1' => 'oeu', 'Oeu010311.1' => 'oeu', 'Oeu043472.1' => 'oeu', 'Os01g0246400' => 'osa', 'Os04g0267950' => 'osa', 'Os07g0178700' => 'osa', 'Os07g0178800' => 'osa', 'Peaxi162Scf00316g00046' => 'pax', 'Peaxi162Scf00316g00049' => 'pax', 'Peaxi162Scf00316g00059' => 'pax', 'Peaxi162Scf00316g00328' => 'pax', 'Peaxi162Scf00316g00329' => 'pax', 'Peaxi162Scf00316g00411' => 'pax', 'Peaxi162Scf00316g00521' => 'pax', 'Peaxi162Scf00492g00068' => 'pax', 'Peaxi162Scf35631g00002' => 'pax', 'PGR142G3720' => 'pgr', 'PGSC0003DMG400006442' => 'stu', 'Phvul.007G062000' => 'pvu', 'Potri.008G157750' => 'ptr', 'Potri.008G157900' => 'ptr', 'Potri.008G158000' => 'ptr', 'Potri.008G158200' => 'ptr', 'Pp3c11_7280' => 'ppa', 'Pp3c11_7980' => 'ppa', 'Pp3c12_19450' => 'ppa', 'Pp3c14_1480' => 'ppa', 'Pp3c14_1501' => 'ppa', 'Pp3c16_4900' => 'ppa', 'Pp3c16_5010' => 'ppa', 'Pp3c16_5060' => 'ppa', 'Pp3c19_18250' => 'ppa', 'Pp3c23_8530' => 'ppa', 'Pp3c23_8550' => 'ppa', 'Pp3c24_9670' => 'ppa', 'Pp3c2_21390' => 'ppa', 'Pp3c2_31380' => 'ppa', 'Pp3c3_16620' => 'ppa', 'Pp3c3_8090' => 'ppa', 'Pp3c3_8110' => 'ppa', 'Pp3c3_8130' => 'ppa', 'Pp3c3_8150' => 'ppa', 'Pp3c4_14320' => 'ppa', 'Pp3c6_2560' => 'ppa', 'Pp3c9_16700' => 'ppa', 'PRCOL_00000234' => 'pco', 'PRCOL_00000235' => 'pco', 'PRCOL_00000777' => 'pco', 'PRCOL_00002344' => 'pco', 'PRCOL_00002372' => 'pco', 'PRCOL_00006120' => 'pco', 'Prupe.1G021400' => 'ppe', 'Prupe.1G021500' => 'ppe', 'Prupe.1G021600' => 'ppe', 'Prupe.1G021700' => 'ppe', 'Prupe.1G021800' => 'ppe', 'Prupe.5G145100' => 'ppe', 'Psat6g204040' => 'psa', 'Psat6g204800' => 'psa', 'Psat6g204920' => 'psa', 'Psat6g204960' => 'psa', 'Psat6g205080' => 'psa', 'PSO017G0271' => 'pso', 'PSO017G1276' => 'pso', 'PSO017G1429' => 'pso', 'PSO017G1861' => 'pso', 'PSO017G2787' => 'pso', 'PSO017G4466' => 'pso', 'PSO017G5118' => 'pso', 'PSO017G5420' => 'pso', 'PSO063G3678' => 'pso', 'PSO210G0546' => 'pso', 'PSO317G0001' => 'pso', 'PSO357G0512' => 'pso', 'PSO478G2682' => 'pso', 'PSO647G0001' => 'pso', 'PSO675G0001' => 'pso', 'PSO675G2699' => 'pso', 'PSO675G2849' => 'pso', 'PSO675G4991' => 'pso', 'PSO689G0001' => 'pso', 'QL06p000916' => 'qlo', 'QL06p000921' => 'qlo', 'QL06p001398' => 'qlo', 'QL06p001407' => 'qlo', 'QL06p002031' => 'qlo', 'RcHm_v2.0_Chr4g0387791' => 'rch', 'RcHm_v2.0_Chr4g0387801' => 'rch', 'RcHm_v2.0_Chr6g0286501' => 'rch', 'RcHm_v2.0_Chr6g0286511' => 'rch', 'RcHm_v2.0_Chr6g0286521' => 'rch', 'RcHm_v2.0_Chr6g0286531' => 'rch', 'RcHm_v2.0_Chr7g0189141' => 'rch', 'Rhsim02G0028700' => 'rsi', 'Rhsim02G0028800' => 'rsi', 'Rhsim02G0028900' => 'rsi', 'Rhsim02G0029000' => 'rsi', 'Rhsim02G0029100' => 'rsi', 'Rhsim02G0029200' => 'rsi', 'Rhsim02G0029300' => 'rsi', 'Rhsim02G0029400' => 'rsi', 'Rhsim02G0029500' => 'rsi', 'Rhsim02G0029600' => 'rsi', 'RhsimUnG0024000' => 'rsi', 'RhsimUnG0024100' => 'rsi', 'RhsimUnG0024200' => 'rsi', 'RhsimUnG0024300' => 'rsi', 'RhsimUnG0024400' => 'rsi', 'RhsimUnG0024500' => 'rsi', 'RhsimUnG0024700' => 'rsi', 'RhsimUnG0024800' => 'rsi', 'RhsimUnG0024900' => 'rsi', 'RhsimUnG0025100' => 'rsi', 'Sabra08G0120200' => 'sbr', 'Sabra08G0120300' => 'sbr', 'Sabra08G0120500' => 'sbr', 'Sabra08G0120600' => 'sbr', 'Sabra10G0158900' => 'sbr', 'SalBow2G3492' => 'sbo', 'Sc13g0004760' => 'sci', 'Sc13g0004770' => 'sci', 'Sed0003417' => 'sed', 'Sed0019750' => 'sed', 'SEGI_03419' => 'sgi', 'SEGI_05907' => 'sgi', 'SEGI_10682' => 'sgi', 'SEGI_13528' => 'sgi', 'SEGI_16081' => 'sgi', 'SEGI_19370' => 'sgi', 'SEGI_21015' => 'sgi', 'SEGI_21944' => 'sgi', 'SEGI_32906' => 'sgi', 'SEGI_33093' => 'sgi', 'SEGI_36110' => 'sgi', 'SEGI_40397' => 'sgi', 'SGA_v2.0_scaffold191G40426' => 'sas', 'SGA_v2.0_scaffold353G49717' => 'sas', 'SGA_v2.0_scaffold50G18550' => 'sas', 'SMO119G0173' => 'smo', 'SMO172G0002' => 'smo', 'Solyc09g082690.3' => 'sly', 'Solyc09g082700.2' => 'sly', 'Sopen09g031550' => 'spe', 'Sopen09g031560' => 'spe', 'Sp3g20540' => 'spa', 'Sp7g07580' => 'spa', 'TAR134G0002' => 'tar', 'TAR236G0001' => 'tar', 'TAR365G0892' => 'tar', 'TAR636G0166' => 'tar', 'TAR636G0646' => 'tar', 'TAR636G0869' => 'tar', 'TAR636G1317' => 'tar', 'TAR636G1744' => 'tar', 'TAR636G3358' => 'tar', 'TAR636G3436' => 'tar', 'THA.LOC104803047' => 'tha', 'Thecc.04G238900' => 'tca', 'Thhalv10021557m.g' => 'esa', 'Thhalv10026318m.g' => 'esa', 'Thhalv10026335m.g' => 'esa', 'TPR.G17433' => 'tpr', 'TPR.G18915' => 'tpr', 'TPR.G26125' => 'tpr', 'TWI09G0677' => 'twi', 'TWI73G0287' => 'twi', 'unitig_748.g8326' => 'ugi', 'vmacro15370' => 'vma', 'vmacro15371' => 'vma', 'vmacro15372' => 'vma', 'vmacro15373' => 'vma', 'vmacro15374' => 'vma', 'VMungo0720G2826' => 'vmu', 'Zm00001eb116960' => 'zma', 'Zm00001eb301260' => 'zma', 'Zm00001eb301270' => 'zma' ), 'gf_id' => 'HOM05D001460', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001460' ), 'data_identifier' => 'HOM05D001460', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001460', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '433', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p22980' => 'bna', 'A01p32340' => 'bna', 'A03p42970' => 'bna', 'A05p25880' => 'bna', 'Aa31LG8G9320' => 'aar', 'Aa31LG8G9330' => 'aar', 'Aa31LG8G9340' => 'aar', 'Aa31sc221G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1034' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1528' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.829' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2222' => 'aag', 'Ah.12g058830' => 'amhyb', 'Ah.12g058840' => 'amhyb', 'AL3G37160' => 'aly', 'AL7G41310' => 'aly', 'Aqoxy5G00395' => 'aox', 'Aqoxy5G00396' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0C8NZA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5185HY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JZ1PRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MD3LS0' => 'arhy', 'AT3G22840' => 'ath', 'AT4G14690' => 'ath', 'ATR0665G054' => 'atr', 'Atru.chr4.2344' => 'acertr', 'Atru.chr4.2346' => 'acertr', 'Atru.chr4.2347' => 'acertr', 'Atru.chr4.2348' => 'acertr', 'Atru.chr4.2355' => 'acertr', 'Atru.chr4.2356' => 'acertr', 'Atru.chr4.2358' => 'acertr', 'Atru.chr4.2359' => 'acertr', 'Atru.chr4.2360' => 'acertr', 'Atru.chr4.2361' => 'acertr', 'AUR62030476' => 'cqu', 'AUR62030478' => 'cqu', 'AUR62030819' => 'cqu', 'AUR62030820' => 'cqu', 'BcaB03g14648' => 'bca', 'BcaB04g20492' => 'bca', 'BcaB06g26399' => 'bca', 'BcaC01g03416' => 'bca', 'BcaC01g03419' => 'bca', 'BcaC01g03421' => 'bca', 'BcaC01g03424' => 'bca', 'BcaC05g28012' => 'bca', 'BcaC09g49212' => 'bca', 'BcaC09g50140' => 'bca', 'BcaNung00346' => 'bca', 'BolC1t02785H' => 'bol', 'BolC1t04095H' => 'bol', 'BolC3t17545H' => 'bol', 'BolC5t32769H' => 'bol', 'BraA01t02211Z' => 'bra', 'BraA01t03359Z' => 'bra', 'BraA03t13441Z' => 'bra', 'BraA05t21476Z' => 'bra', 'C01p28420' => 'bna', 'C01p41350' => 'bna', 'C03p52750' => 'bna', 'C03p52780' => 'bna', 'C05p40270' => 'bna', 'CAN.G1437.9' => 'can', 'CANSAT78G0035' => 'cansat', 'CANSAT78G1036' => 'cansat', 'CANSAT78G2272' => 'cansat', 'CANSAT78G2478' => 'cansat', 'CARHR098700' => 'chi', 'CARHR221120' => 'chi', 'CARHR221150' => 'chi', 'Carub.0003s2297' => 'cru', 'Carub.0007s2749' => 'cru', 'Carub.0007s2750' => 'cru', 'Carub.0007s2751' => 'cru', 'Ca_10849_v3' => 'car', 'Cc03_g04300' => 'ccan', 'CDE02G3648' => 'cde', 'CDE05G0060' => 'cde', 'CDE05G0692' => 'cde', 'CDE05G2285' => 'cde', 'CDE05G2884' => 'cde', 'CDE05G3072' => 'cde', 'Cfa008439' => 'cfa', 'Cfa008441' => 'cfa', 'Cfa008443' => 'cfa', 'Cfa008448' => 'cfa', 'Ciclev10005974m.g' => 'ccl', 'Ciclev10006006m.g' => 'ccl', 'Ciclev10006775m.g' => 'ccl', 'CiPaw.02G120400' => 'cil', 'CiPaw.02G120500' => 'cil', 'CiPaw.02G120600' => 'cil', 'ClCG05G004850' => 'cla', 'COL.COLO4_21566' => 'col', 'Cpa.g.sc44.124' => 'cpa', 'Cre07.g320400' => 'cre', 'Cre07.g320450' => 'cre', 'Cre08.g384650' => 'cre', 'Cre09.g393173' => 'cre', 'Cre09.g394325' => 'cre', 'Cre14.g626750' => 'cre', 'Cre16.g679250' => 'cre', 'CsaV3_3G012890' => 'csa', 'CSS0010865' => 'camsi', 'CSS0044338' => 'camsi', 'DCAR_002366' => 'dca', 'DCAR_030687' => 'dca', 'DCAR_030688' => 'dca', 'Dinv14047' => 'din', 'Dinv14048' => 'din', 'Duzib151G0105' => 'dzi', 'Duzib151G0114' => 'dzi', 'Duzib212G1029' => 'dzi', 'ECA232G3536' => 'eca', 'ECA240G0786' => 'eca', 'ECA240G1802' => 'eca', 'ECA240G3760' => 'eca', 'ECA240G3920' => 'eca', 'EL10Ac5g12536' => 'bvu', 'EL10Ac5g12537' => 'bvu', 'EL10Ac5g12538' => 'bvu', 'Eucgr.B01004' => 'egr', 'Eucgr.B01006' => 'egr', 'Eucgr.B01007' => 'egr', 'Eucgr.B01008' => 'egr', 'Eucgr.B01895' => 'egr', 'Eucgr.B01896' => 'egr', 'FAN04G1456' => 'fan', 'FAN08G1769' => 'fan', 'FAN08G2160' => 'fan', 'FAN13G2403' => 'fan', 'FAN13G3303' => 'fan', 'FAN15G2435' => 'fan', 'FAN17G0672' => 'fan', 'FAN17G2441' => 'fan', 'FAN18G1024' => 'fan', 'FAN22G1458' => 'fan', 'FAN24G0037' => 'fan', 'FAN24G0429' => 'fan', 'FAN24G2387' => 'fan', 'FAN27G2746' => 'fan', 'FvH4_2g20400' => 'fve', 'FvH4_2g20420' => 'fve', 'FvH4_2g20430' => 'fve', 'FvH4_4g01270' => 'fve', 'FvH4_4g01290' => 'fve', 'FvH4_4g01300' => 'fve', 'FvH4_4g01310' => 'fve', 'FvH4_4g01330' => 'fve', 'FvH4_5g09070' => 'fve', 'Glyma.10G243800' => 'gma', 'Glyma.20G150600' => 'gma', 'Gohir.A09G219200' => 'ghi', 'Gohir.A09G219300' => 'ghi', 'Gohir.D09G221400' => 'ghi', 'Gohir.D09G221500' => 'ghi', 'Gorai.006G242600' => 'gra', 'Gorai.006G242700' => 'gra', 'GSVIVG01018044001' => 'vvi', 'HanXRQChr03g0083821' => 'han', 'HanXRQChr03g0083841' => 'han', 'HanXRQChr03g0083881' => 'han', 'HanXRQChr03g0083901' => 'han', 'HanXRQChr03g0083921' => 'han', 'HanXRQChr03g0085331' => 'han', 'HanXRQChr03g0085361' => 'han', 'HanXRQChr03g0085411' => 'han', 'HanXRQChr03g0085421' => 'han', 'HanXRQChr03g0085431' => 'han', 'HanXRQChr08g0221991' => 'han', 'HanXRQChr11g0336061' => 'han', 'HanXRQChr11g0336411' => 'han', 'Haze_11234' => 'cav', 'Hma1.2p1_0549F.1_g177010' => 'hma', 'Hma1.2p1_0602F.1_g187630' => 'hma', 'Hund14876' => 'sun', 'Hund14879' => 'sun', 'Lalb_Chr06g0160741' => 'lal', 'Lalb_Chr21g0304781' => 'lal', 'Lj3A726G19' => 'lonja', 'Lj3A726T23' => 'lonja', 'Lj3A726T24' => 'lonja', 'Lj3A726T25' => 'lonja', 'Lj3A727T17' => 'lonja', 'Lj3C726T0' => 'lonja', 'Lj3C726T2' => 'lonja', 'Lj3P725T35' => 'lonja', 'Lj3P727T10' => 'lonja', 'Lj3P727T12' => 'lonja', 'Lj3P727T14' => 'lonja', 'Lj5g0023109' => 'lja', 'Lj6P646T44' => 'lonja', 'Lsat_1_v5_gn_6_75760' => 'lsa', 'Lsat_1_v5_gn_6_75800' => 'lsa', 'Lsat_1_v5_gn_6_75900' => 'lsa', 'Lsat_1_v5_gn_6_76240' => 'lsa', 'Lsat_1_v5_gn_6_76441' => 'lsa', 'Lsat_1_v5_gn_6_76700' => 'lsa', 'Lsat_1_v5_gn_6_76760' => 'lsa', 'Manes.15G033100' => 'mes', 'Mapoly0004s0074' => 'mpo', 'Mapoly0004s0075' => 'mpo', 'Mapoly0004s0163' => 'mpo', 'Mapoly0004s0164' => 'mpo', 'Mapoly0021s0018' => 'mpo', 'Mapoly0041s0136' => 'mpo', 'Mapoly0041s0137' => 'mpo', 'Mapoly0041s0138' => 'mpo', 'Mapoly0041s0139' => 'mpo', 'Mapoly0041s0141' => 'mpo', 'Mapoly0041s0142' => 'mpo', 'Mapoly0041s0143' => 'mpo', 'Mapoly0041s0144' => 'mpo', 'Mapoly0041s0145' => 'mpo', 'Mapoly0047s0106' => 'mpo', 'Mapoly0047s0108' => 'mpo', 'Mapoly0050s0051' => 'mpo', 'Mapoly0050s0052' => 'mpo', 'Mapoly0050s0053' => 'mpo', 'Mapoly0058s0013' => 'mpo', 'Mapoly0091s0078' => 'mpo', 'Mapoly0091s0079' => 'mpo', 'Mapoly0091s0080' => 'mpo', 'Mapoly0091s0081' => 'mpo', 'Mapoly0278s0004' => 'mpo', 'Mapoly0278s0005' => 'mpo', 'Mapoly0278s0006' => 'mpo', 'MBI11_g30648_MAGBIO' => 'mbi', 'MCO03G194' => 'mco', 'MCO03G590' => 'mco', 'MCO07G312' => 'mco', 'MCO10G318' => 'mco', 'MCO12G244' => 'mco', 'MCO13G148' => 'mco', 'MCO13G194' => 'mco', 'MCO16G238' => 'mco', 'MD06G1134100' => 'mdo', 'MD13G1200100' => 'mdo', 'MD13G1200300' => 'mdo', 'MD13G1200600' => 'mdo', 'MD14G1150400' => 'mdo', 'MD16G1200000' => 'mdo', 'Medtr1g102570' => 'mtr', 'Medtr1g102780' => 'mtr', 'Medtr1g102800' => 'mtr', 'Medtr1g102810' => 'mtr', 'Medtr1g102830' => 'mtr', 'MELO3C006499.2' => 'cme', 'Migut.G00385' => 'egut', 'MSTRG.4063' => 'ama', 'Nitab4.5_0000090g0260' => 'nta', 'Nitab4.5_0000977g0030' => 'nta', 'Nitab4.5_0002541g0040' => 'nta', 'Nitab4.5_0007068g0040' => 'nta', 'Nn005s41408' => 'nnu', 'Nn005s41410' => 'nnu', 'Oeu010310.1' => 'oeu', 'Oeu010311.1' => 'oeu', 'Oeu043472.1' => 'oeu', 'Os01g0246400' => 'osa', 'Os04g0267950' => 'osa', 'Os07g0178700' => 'osa', 'Os07g0178800' => 'osa', 'Peaxi162Scf00316g00046' => 'pax', 'Peaxi162Scf00316g00049' => 'pax', 'Peaxi162Scf00316g00059' => 'pax', 'Peaxi162Scf00316g00328' => 'pax', 'Peaxi162Scf00316g00329' => 'pax', 'Peaxi162Scf00316g00411' => 'pax', 'Peaxi162Scf00316g00521' => 'pax', 'Peaxi162Scf00492g00068' => 'pax', 'Peaxi162Scf35631g00002' => 'pax', 'PGR142G3720' => 'pgr', 'PGSC0003DMG400006442' => 'stu', 'Phvul.007G062000' => 'pvu', 'Potri.008G157750' => 'ptr', 'Potri.008G157900' => 'ptr', 'Potri.008G158000' => 'ptr', 'Potri.008G158200' => 'ptr', 'Pp3c11_7280' => 'ppa', 'Pp3c11_7980' => 'ppa', 'Pp3c12_19450' => 'ppa', 'Pp3c14_1480' => 'ppa', 'Pp3c14_1501' => 'ppa', 'Pp3c16_4900' => 'ppa', 'Pp3c16_5010' => 'ppa', 'Pp3c16_5060' => 'ppa', 'Pp3c19_18250' => 'ppa', 'Pp3c23_8530' => 'ppa', 'Pp3c23_8550' => 'ppa', 'Pp3c24_9670' => 'ppa', 'Pp3c2_21390' => 'ppa', 'Pp3c2_31380' => 'ppa', 'Pp3c3_16620' => 'ppa', 'Pp3c3_8090' => 'ppa', 'Pp3c3_8110' => 'ppa', 'Pp3c3_8130' => 'ppa', 'Pp3c3_8150' => 'ppa', 'Pp3c4_14320' => 'ppa', 'Pp3c6_2560' => 'ppa', 'Pp3c9_16700' => 'ppa', 'PRCOL_00000234' => 'pco', 'PRCOL_00000235' => 'pco', 'PRCOL_00000777' => 'pco', 'PRCOL_00002344' => 'pco', 'PRCOL_00002372' => 'pco', 'PRCOL_00006120' => 'pco', 'Prupe.1G021400' => 'ppe', 'Prupe.1G021500' => 'ppe', 'Prupe.1G021600' => 'ppe', 'Prupe.1G021700' => 'ppe', 'Prupe.1G021800' => 'ppe', 'Prupe.5G145100' => 'ppe', 'Psat6g204040' => 'psa', 'Psat6g204800' => 'psa', 'Psat6g204920' => 'psa', 'Psat6g204960' => 'psa', 'Psat6g205080' => 'psa', 'PSO017G0271' => 'pso', 'PSO017G1276' => 'pso', 'PSO017G1429' => 'pso', 'PSO017G1861' => 'pso', 'PSO017G2787' => 'pso', 'PSO017G4466' => 'pso', 'PSO017G5118' => 'pso', 'PSO017G5420' => 'pso', 'PSO063G3678' => 'pso', 'PSO210G0546' => 'pso', 'PSO317G0001' => 'pso', 'PSO357G0512' => 'pso', 'PSO478G2682' => 'pso', 'PSO647G0001' => 'pso', 'PSO675G0001' => 'pso', 'PSO675G2699' => 'pso', 'PSO675G2849' => 'pso', 'PSO675G4991' => 'pso', 'PSO689G0001' => 'pso', 'QL06p000916' => 'qlo', 'QL06p000921' => 'qlo', 'QL06p001398' => 'qlo', 'QL06p001407' => 'qlo', 'QL06p002031' => 'qlo', 'RcHm_v2.0_Chr4g0387791' => 'rch', 'RcHm_v2.0_Chr4g0387801' => 'rch', 'RcHm_v2.0_Chr6g0286501' => 'rch', 'RcHm_v2.0_Chr6g0286511' => 'rch', 'RcHm_v2.0_Chr6g0286521' => 'rch', 'RcHm_v2.0_Chr6g0286531' => 'rch', 'RcHm_v2.0_Chr7g0189141' => 'rch', 'Rhsim02G0028700' => 'rsi', 'Rhsim02G0028800' => 'rsi', 'Rhsim02G0028900' => 'rsi', 'Rhsim02G0029000' => 'rsi', 'Rhsim02G0029100' => 'rsi', 'Rhsim02G0029200' => 'rsi', 'Rhsim02G0029300' => 'rsi', 'Rhsim02G0029400' => 'rsi', 'Rhsim02G0029500' => 'rsi', 'Rhsim02G0029600' => 'rsi', 'RhsimUnG0024000' => 'rsi', 'RhsimUnG0024100' => 'rsi', 'RhsimUnG0024200' => 'rsi', 'RhsimUnG0024300' => 'rsi', 'RhsimUnG0024400' => 'rsi', 'RhsimUnG0024500' => 'rsi', 'RhsimUnG0024700' => 'rsi', 'RhsimUnG0024800' => 'rsi', 'RhsimUnG0024900' => 'rsi', 'RhsimUnG0025100' => 'rsi', 'Sabra08G0120200' => 'sbr', 'Sabra08G0120300' => 'sbr', 'Sabra08G0120500' => 'sbr', 'Sabra08G0120600' => 'sbr', 'Sabra10G0158900' => 'sbr', 'SalBow2G3492' => 'sbo', 'Sc13g0004760' => 'sci', 'Sc13g0004770' => 'sci', 'Sed0003417' => 'sed', 'Sed0019750' => 'sed', 'SEGI_03419' => 'sgi', 'SEGI_05907' => 'sgi', 'SEGI_10682' => 'sgi', 'SEGI_13528' => 'sgi', 'SEGI_16081' => 'sgi', 'SEGI_19370' => 'sgi', 'SEGI_21015' => 'sgi', 'SEGI_21944' => 'sgi', 'SEGI_32906' => 'sgi', 'SEGI_33093' => 'sgi', 'SEGI_36110' => 'sgi', 'SEGI_40397' => 'sgi', 'SGA_v2.0_scaffold191G40426' => 'sas', 'SGA_v2.0_scaffold353G49717' => 'sas', 'SGA_v2.0_scaffold50G18550' => 'sas', 'SMO119G0173' => 'smo', 'SMO172G0002' => 'smo', 'Solyc09g082690.3' => 'sly', 'Solyc09g082700.2' => 'sly', 'Sopen09g031550' => 'spe', 'Sopen09g031560' => 'spe', 'Sp3g20540' => 'spa', 'Sp7g07580' => 'spa', 'TAR134G0002' => 'tar', 'TAR236G0001' => 'tar', 'TAR365G0892' => 'tar', 'TAR636G0166' => 'tar', 'TAR636G0646' => 'tar', 'TAR636G0869' => 'tar', 'TAR636G1317' => 'tar', 'TAR636G1744' => 'tar', 'TAR636G3358' => 'tar', 'TAR636G3436' => 'tar', 'THA.LOC104803047' => 'tha', 'Thecc.04G238900' => 'tca', 'Thhalv10021557m.g' => 'esa', 'Thhalv10026318m.g' => 'esa', 'Thhalv10026335m.g' => 'esa', 'TPR.G17433' => 'tpr', 'TPR.G18915' => 'tpr', 'TPR.G26125' => 'tpr', 'TWI09G0677' => 'twi', 'TWI73G0287' => 'twi', 'unitig_748.g8326' => 'ugi', 'vmacro15370' => 'vma', 'vmacro15371' => 'vma', 'vmacro15372' => 'vma', 'vmacro15373' => 'vma', 'vmacro15374' => 'vma', 'VMungo0720G2826' => 'vmu', 'Zm00001eb116960' => 'zma', 'Zm00001eb301260' => 'zma', 'Zm00001eb301270' => 'zma' ) $gf_id = 'HOM05D001460' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001460' ) $data_identifier = 'HOM05D001460' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 4, 'aag' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 2, 'aox' => (int) 2, 'arhy' => (int) 4, 'ath' => (int) 2, 'atr' => (int) 1, 'acertr' => (int) 10, 'cqu' => (int) 4, 'bca' => (int) 11, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 1, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 1, 'ccan' => (int) 1, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 1, 'col' => (int) 1, 'cpa' => (int) 1, 'cre' => (int) 7, 'csa' => (int) 1, 'camsi' => (int) 2, 'dca' => (int) 3, 'din' => (int) 2, 'dzi' => (int) 3, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 14, 'fve' => (int) 9, 'gma' => (int) 2, 'ghi' => (int) 4, 'gra' => (int) 2, 'vvi' => (int) 1, 'han' => (int) 13, 'cav' => (int) 1, 'hma' => (int) 2, 'sun' => (int) 2, 'lal' => (int) 2, 'lonja' => (int) 12, 'lja' => (int) 1, 'lsa' => (int) 7, 'mes' => (int) 1, 'mpo' => (int) 27, 'mbi' => (int) 1, 'mco' => (int) 8, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 1, 'egut' => (int) 1, 'ama' => (int) 1, 'nta' => (int) 4, 'nnu' => (int) 2, 'oeu' => (int) 3, 'osa' => (int) 4, 'pax' => (int) 9, 'pgr' => (int) 1, 'stu' => (int) 1, 'pvu' => (int) 1, 'ptr' => (int) 4, 'ppa' => (int) 22, 'pco' => (int) 6, 'ppe' => (int) 6, 'psa' => (int) 5, 'pso' => (int) 19, 'qlo' => (int) 5, 'rch' => (int) 7, 'rsi' => (int) 20, 'sbr' => (int) 5, 'sbo' => (int) 1, 'sci' => (int) 2, 'sed' => (int) 2, 'sgi' => (int) 12, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 2, 'tar' => (int) 10, 'tha' => (int) 1, 'tca' => (int) 1, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 2, 'ugi' => (int) 1, 'vma' => (int) 5, 'vmu' => (int) 1, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb301270' $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' => 'HOM05D001460', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '433', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p22980' => 'bna', 'A01p32340' => 'bna', 'A03p42970' => 'bna', 'A05p25880' => 'bna', 'Aa31LG8G9320' => 'aar', 'Aa31LG8G9330' => 'aar', 'Aa31LG8G9340' => 'aar', 'Aa31sc221G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1034' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1528' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.829' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2222' => 'aag', 'Ah.12g058830' => 'amhyb', 'Ah.12g058840' => 'amhyb', 'AL3G37160' => 'aly', 'AL7G41310' => 'aly', 'Aqoxy5G00395' => 'aox', 'Aqoxy5G00396' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0C8NZA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5185HY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JZ1PRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MD3LS0' => 'arhy', 'AT3G22840' => 'ath', 'AT4G14690' => 'ath', 'ATR0665G054' => 'atr', 'Atru.chr4.2344' => 'acertr', 'Atru.chr4.2346' => 'acertr', 'Atru.chr4.2347' => 'acertr', 'Atru.chr4.2348' => 'acertr', 'Atru.chr4.2355' => 'acertr', 'Atru.chr4.2356' => 'acertr', 'Atru.chr4.2358' => 'acertr', 'Atru.chr4.2359' => 'acertr', 'Atru.chr4.2360' => 'acertr', 'Atru.chr4.2361' => 'acertr', 'AUR62030476' => 'cqu', 'AUR62030478' => 'cqu', 'AUR62030819' => 'cqu', 'AUR62030820' => 'cqu', 'BcaB03g14648' => 'bca', 'BcaB04g20492' => 'bca', 'BcaB06g26399' => 'bca', 'BcaC01g03416' => 'bca', 'BcaC01g03419' => 'bca', 'BcaC01g03421' => 'bca', 'BcaC01g03424' => 'bca', 'BcaC05g28012' => 'bca', 'BcaC09g49212' => 'bca', 'BcaC09g50140' => 'bca', 'BcaNung00346' => 'bca', 'BolC1t02785H' => 'bol', 'BolC1t04095H' => 'bol', 'BolC3t17545H' => 'bol', 'BolC5t32769H' => 'bol', 'BraA01t02211Z' => 'bra', 'BraA01t03359Z' => 'bra', 'BraA03t13441Z' => 'bra', 'BraA05t21476Z' => 'bra', 'C01p28420' => 'bna', 'C01p41350' => 'bna', 'C03p52750' => 'bna', 'C03p52780' => 'bna', 'C05p40270' => 'bna', 'CAN.G1437.9' => 'can', 'CANSAT78G0035' => 'cansat', 'CANSAT78G1036' => 'cansat', 'CANSAT78G2272' => 'cansat', 'CANSAT78G2478' => 'cansat', 'CARHR098700' => 'chi', 'CARHR221120' => 'chi', 'CARHR221150' => 'chi', 'Carub.0003s2297' => 'cru', 'Carub.0007s2749' => 'cru', 'Carub.0007s2750' => 'cru', 'Carub.0007s2751' => 'cru', 'Ca_10849_v3' => 'car', 'Cc03_g04300' => 'ccan', 'CDE02G3648' => 'cde', 'CDE05G0060' => 'cde', 'CDE05G0692' => 'cde', 'CDE05G2285' => 'cde', 'CDE05G2884' => 'cde', 'CDE05G3072' => 'cde', 'Cfa008439' => 'cfa', 'Cfa008441' => 'cfa', 'Cfa008443' => 'cfa', 'Cfa008448' => 'cfa', 'Ciclev10005974m.g' => 'ccl', 'Ciclev10006006m.g' => 'ccl', 'Ciclev10006775m.g' => 'ccl', 'CiPaw.02G120400' => 'cil', 'CiPaw.02G120500' => 'cil', 'CiPaw.02G120600' => 'cil', 'ClCG05G004850' => 'cla', 'COL.COLO4_21566' => 'col', 'Cpa.g.sc44.124' => 'cpa', 'Cre07.g320400' => 'cre', 'Cre07.g320450' => 'cre', 'Cre08.g384650' => 'cre', 'Cre09.g393173' => 'cre', 'Cre09.g394325' => 'cre', 'Cre14.g626750' => 'cre', 'Cre16.g679250' => 'cre', 'CsaV3_3G012890' => 'csa', 'CSS0010865' => 'camsi', 'CSS0044338' => 'camsi', 'DCAR_002366' => 'dca', 'DCAR_030687' => 'dca', 'DCAR_030688' => 'dca', 'Dinv14047' => 'din', 'Dinv14048' => 'din', 'Duzib151G0105' => 'dzi', 'Duzib151G0114' => 'dzi', 'Duzib212G1029' => 'dzi', 'ECA232G3536' => 'eca', 'ECA240G0786' => 'eca', 'ECA240G1802' => 'eca', 'ECA240G3760' => 'eca', 'ECA240G3920' => 'eca', 'EL10Ac5g12536' => 'bvu', 'EL10Ac5g12537' => 'bvu', 'EL10Ac5g12538' => 'bvu', 'Eucgr.B01004' => 'egr', 'Eucgr.B01006' => 'egr', 'Eucgr.B01007' => 'egr', 'Eucgr.B01008' => 'egr', 'Eucgr.B01895' => 'egr', 'Eucgr.B01896' => 'egr', 'FAN04G1456' => 'fan', 'FAN08G1769' => 'fan', 'FAN08G2160' => 'fan', 'FAN13G2403' => 'fan', 'FAN13G3303' => 'fan', 'FAN15G2435' => 'fan', 'FAN17G0672' => 'fan', 'FAN17G2441' => 'fan', 'FAN18G1024' => 'fan', 'FAN22G1458' => 'fan', 'FAN24G0037' => 'fan', 'FAN24G0429' => 'fan', 'FAN24G2387' => 'fan', 'FAN27G2746' => 'fan', 'FvH4_2g20400' => 'fve', 'FvH4_2g20420' => 'fve', 'FvH4_2g20430' => 'fve', 'FvH4_4g01270' => 'fve', 'FvH4_4g01290' => 'fve', 'FvH4_4g01300' => 'fve', 'FvH4_4g01310' => 'fve', 'FvH4_4g01330' => 'fve', 'FvH4_5g09070' => 'fve', 'Glyma.10G243800' => 'gma', 'Glyma.20G150600' => 'gma', 'Gohir.A09G219200' => 'ghi', 'Gohir.A09G219300' => 'ghi', 'Gohir.D09G221400' => 'ghi', 'Gohir.D09G221500' => 'ghi', 'Gorai.006G242600' => 'gra', 'Gorai.006G242700' => 'gra', 'GSVIVG01018044001' => 'vvi', 'HanXRQChr03g0083821' => 'han', 'HanXRQChr03g0083841' => 'han', 'HanXRQChr03g0083881' => 'han', 'HanXRQChr03g0083901' => 'han', 'HanXRQChr03g0083921' => 'han', 'HanXRQChr03g0085331' => 'han', 'HanXRQChr03g0085361' => 'han', 'HanXRQChr03g0085411' => 'han', 'HanXRQChr03g0085421' => 'han', 'HanXRQChr03g0085431' => 'han', 'HanXRQChr08g0221991' => 'han', 'HanXRQChr11g0336061' => 'han', 'HanXRQChr11g0336411' => 'han', 'Haze_11234' => 'cav', 'Hma1.2p1_0549F.1_g177010' => 'hma', 'Hma1.2p1_0602F.1_g187630' => 'hma', 'Hund14876' => 'sun', 'Hund14879' => 'sun', 'Lalb_Chr06g0160741' => 'lal', 'Lalb_Chr21g0304781' => 'lal', 'Lj3A726G19' => 'lonja', 'Lj3A726T23' => 'lonja', 'Lj3A726T24' => 'lonja', 'Lj3A726T25' => 'lonja', 'Lj3A727T17' => 'lonja', 'Lj3C726T0' => 'lonja', 'Lj3C726T2' => 'lonja', 'Lj3P725T35' => 'lonja', 'Lj3P727T10' => 'lonja', 'Lj3P727T12' => 'lonja', 'Lj3P727T14' => 'lonja', 'Lj5g0023109' => 'lja', 'Lj6P646T44' => 'lonja', 'Lsat_1_v5_gn_6_75760' => 'lsa', 'Lsat_1_v5_gn_6_75800' => 'lsa', 'Lsat_1_v5_gn_6_75900' => 'lsa', 'Lsat_1_v5_gn_6_76240' => 'lsa', 'Lsat_1_v5_gn_6_76441' => 'lsa', 'Lsat_1_v5_gn_6_76700' => 'lsa', 'Lsat_1_v5_gn_6_76760' => 'lsa', 'Manes.15G033100' => 'mes', 'Mapoly0004s0074' => 'mpo', 'Mapoly0004s0075' => 'mpo', 'Mapoly0004s0163' => 'mpo', 'Mapoly0004s0164' => 'mpo', 'Mapoly0021s0018' => 'mpo', 'Mapoly0041s0136' => 'mpo', 'Mapoly0041s0137' => 'mpo', 'Mapoly0041s0138' => 'mpo', 'Mapoly0041s0139' => 'mpo', 'Mapoly0041s0141' => 'mpo', 'Mapoly0041s0142' => 'mpo', 'Mapoly0041s0143' => 'mpo', 'Mapoly0041s0144' => 'mpo', 'Mapoly0041s0145' => 'mpo', 'Mapoly0047s0106' => 'mpo', 'Mapoly0047s0108' => 'mpo', 'Mapoly0050s0051' => 'mpo', 'Mapoly0050s0052' => 'mpo', 'Mapoly0050s0053' => 'mpo', 'Mapoly0058s0013' => 'mpo', 'Mapoly0091s0078' => 'mpo', 'Mapoly0091s0079' => 'mpo', 'Mapoly0091s0080' => 'mpo', 'Mapoly0091s0081' => 'mpo', 'Mapoly0278s0004' => 'mpo', 'Mapoly0278s0005' => 'mpo', 'Mapoly0278s0006' => 'mpo', 'MBI11_g30648_MAGBIO' => 'mbi', 'MCO03G194' => 'mco', 'MCO03G590' => 'mco', 'MCO07G312' => 'mco', 'MCO10G318' => 'mco', 'MCO12G244' => 'mco', 'MCO13G148' => 'mco', 'MCO13G194' => 'mco', 'MCO16G238' => 'mco', 'MD06G1134100' => 'mdo', 'MD13G1200100' => 'mdo', 'MD13G1200300' => 'mdo', 'MD13G1200600' => 'mdo', 'MD14G1150400' => 'mdo', 'MD16G1200000' => 'mdo', 'Medtr1g102570' => 'mtr', 'Medtr1g102780' => 'mtr', 'Medtr1g102800' => 'mtr', 'Medtr1g102810' => 'mtr', 'Medtr1g102830' => 'mtr', 'MELO3C006499.2' => 'cme', 'Migut.G00385' => 'egut', 'MSTRG.4063' => 'ama', 'Nitab4.5_0000090g0260' => 'nta', 'Nitab4.5_0000977g0030' => 'nta', 'Nitab4.5_0002541g0040' => 'nta', 'Nitab4.5_0007068g0040' => 'nta', 'Nn005s41408' => 'nnu', 'Nn005s41410' => 'nnu', 'Oeu010310.1' => 'oeu', 'Oeu010311.1' => 'oeu', 'Oeu043472.1' => 'oeu', 'Os01g0246400' => 'osa', 'Os04g0267950' => 'osa', 'Os07g0178700' => 'osa', 'Os07g0178800' => 'osa', 'Peaxi162Scf00316g00046' => 'pax', 'Peaxi162Scf00316g00049' => 'pax', 'Peaxi162Scf00316g00059' => 'pax', 'Peaxi162Scf00316g00328' => 'pax', 'Peaxi162Scf00316g00329' => 'pax', 'Peaxi162Scf00316g00411' => 'pax', 'Peaxi162Scf00316g00521' => 'pax', 'Peaxi162Scf00492g00068' => 'pax', 'Peaxi162Scf35631g00002' => 'pax', 'PGR142G3720' => 'pgr', 'PGSC0003DMG400006442' => 'stu', 'Phvul.007G062000' => 'pvu', 'Potri.008G157750' => 'ptr', 'Potri.008G157900' => 'ptr', 'Potri.008G158000' => 'ptr', 'Potri.008G158200' => 'ptr', 'Pp3c11_7280' => 'ppa', 'Pp3c11_7980' => 'ppa', 'Pp3c12_19450' => 'ppa', 'Pp3c14_1480' => 'ppa', 'Pp3c14_1501' => 'ppa', 'Pp3c16_4900' => 'ppa', 'Pp3c16_5010' => 'ppa', 'Pp3c16_5060' => 'ppa', 'Pp3c19_18250' => 'ppa', 'Pp3c23_8530' => 'ppa', 'Pp3c23_8550' => 'ppa', 'Pp3c24_9670' => 'ppa', 'Pp3c2_21390' => 'ppa', 'Pp3c2_31380' => 'ppa', 'Pp3c3_16620' => 'ppa', 'Pp3c3_8090' => 'ppa', 'Pp3c3_8110' => 'ppa', 'Pp3c3_8130' => 'ppa', 'Pp3c3_8150' => 'ppa', 'Pp3c4_14320' => 'ppa', 'Pp3c6_2560' => 'ppa', 'Pp3c9_16700' => 'ppa', 'PRCOL_00000234' => 'pco', 'PRCOL_00000235' => 'pco', 'PRCOL_00000777' => 'pco', 'PRCOL_00002344' => 'pco', 'PRCOL_00002372' => 'pco', 'PRCOL_00006120' => 'pco', 'Prupe.1G021400' => 'ppe', 'Prupe.1G021500' => 'ppe', 'Prupe.1G021600' => 'ppe', 'Prupe.1G021700' => 'ppe', 'Prupe.1G021800' => 'ppe', 'Prupe.5G145100' => 'ppe', 'Psat6g204040' => 'psa', 'Psat6g204800' => 'psa', 'Psat6g204920' => 'psa', 'Psat6g204960' => 'psa', 'Psat6g205080' => 'psa', 'PSO017G0271' => 'pso', 'PSO017G1276' => 'pso', 'PSO017G1429' => 'pso', 'PSO017G1861' => 'pso', 'PSO017G2787' => 'pso', 'PSO017G4466' => 'pso', 'PSO017G5118' => 'pso', 'PSO017G5420' => 'pso', 'PSO063G3678' => 'pso', 'PSO210G0546' => 'pso', 'PSO317G0001' => 'pso', 'PSO357G0512' => 'pso', 'PSO478G2682' => 'pso', 'PSO647G0001' => 'pso', 'PSO675G0001' => 'pso', 'PSO675G2699' => 'pso', 'PSO675G2849' => 'pso', 'PSO675G4991' => 'pso', 'PSO689G0001' => 'pso', 'QL06p000916' => 'qlo', 'QL06p000921' => 'qlo', 'QL06p001398' => 'qlo', 'QL06p001407' => 'qlo', 'QL06p002031' => 'qlo', 'RcHm_v2.0_Chr4g0387791' => 'rch', 'RcHm_v2.0_Chr4g0387801' => 'rch', 'RcHm_v2.0_Chr6g0286501' => 'rch', 'RcHm_v2.0_Chr6g0286511' => 'rch', 'RcHm_v2.0_Chr6g0286521' => 'rch', 'RcHm_v2.0_Chr6g0286531' => 'rch', 'RcHm_v2.0_Chr7g0189141' => 'rch', 'Rhsim02G0028700' => 'rsi', 'Rhsim02G0028800' => 'rsi', 'Rhsim02G0028900' => 'rsi', 'Rhsim02G0029000' => 'rsi', 'Rhsim02G0029100' => 'rsi', 'Rhsim02G0029200' => 'rsi', 'Rhsim02G0029300' => 'rsi', 'Rhsim02G0029400' => 'rsi', 'Rhsim02G0029500' => 'rsi', 'Rhsim02G0029600' => 'rsi', 'RhsimUnG0024000' => 'rsi', 'RhsimUnG0024100' => 'rsi', 'RhsimUnG0024200' => 'rsi', 'RhsimUnG0024300' => 'rsi', 'RhsimUnG0024400' => 'rsi', 'RhsimUnG0024500' => 'rsi', 'RhsimUnG0024700' => 'rsi', 'RhsimUnG0024800' => 'rsi', 'RhsimUnG0024900' => 'rsi', 'RhsimUnG0025100' => 'rsi', 'Sabra08G0120200' => 'sbr', 'Sabra08G0120300' => 'sbr', 'Sabra08G0120500' => 'sbr', 'Sabra08G0120600' => 'sbr', 'Sabra10G0158900' => 'sbr', 'SalBow2G3492' => 'sbo', 'Sc13g0004760' => 'sci', 'Sc13g0004770' => 'sci', 'Sed0003417' => 'sed', 'Sed0019750' => 'sed', 'SEGI_03419' => 'sgi', 'SEGI_05907' => 'sgi', 'SEGI_10682' => 'sgi', 'SEGI_13528' => 'sgi', 'SEGI_16081' => 'sgi', 'SEGI_19370' => 'sgi', 'SEGI_21015' => 'sgi', 'SEGI_21944' => 'sgi', 'SEGI_32906' => 'sgi', 'SEGI_33093' => 'sgi', 'SEGI_36110' => 'sgi', 'SEGI_40397' => 'sgi', 'SGA_v2.0_scaffold191G40426' => 'sas', 'SGA_v2.0_scaffold353G49717' => 'sas', 'SGA_v2.0_scaffold50G18550' => 'sas', 'SMO119G0173' => 'smo', 'SMO172G0002' => 'smo', 'Solyc09g082690.3' => 'sly', 'Solyc09g082700.2' => 'sly', 'Sopen09g031550' => 'spe', 'Sopen09g031560' => 'spe', 'Sp3g20540' => 'spa', 'Sp7g07580' => 'spa', 'TAR134G0002' => 'tar', 'TAR236G0001' => 'tar', 'TAR365G0892' => 'tar', 'TAR636G0166' => 'tar', 'TAR636G0646' => 'tar', 'TAR636G0869' => 'tar', 'TAR636G1317' => 'tar', 'TAR636G1744' => 'tar', 'TAR636G3358' => 'tar', 'TAR636G3436' => 'tar', 'THA.LOC104803047' => 'tha', 'Thecc.04G238900' => 'tca', 'Thhalv10021557m.g' => 'esa', 'Thhalv10026318m.g' => 'esa', 'Thhalv10026335m.g' => 'esa', 'TPR.G17433' => 'tpr', 'TPR.G18915' => 'tpr', 'TPR.G26125' => 'tpr', 'TWI09G0677' => 'twi', 'TWI73G0287' => 'twi', 'unitig_748.g8326' => 'ugi', 'vmacro15370' => 'vma', 'vmacro15371' => 'vma', 'vmacro15372' => 'vma', 'vmacro15373' => 'vma', 'vmacro15374' => 'vma', 'VMungo0720G2826' => 'vmu', 'Zm00001eb116960' => 'zma', 'Zm00001eb301260' => 'zma', 'Zm00001eb301270' => 'zma' ), 'gf_id' => 'HOM05D001460', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001460' ), 'data_identifier' => 'HOM05D001460', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001460', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '433', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p22980' => 'bna', 'A01p32340' => 'bna', 'A03p42970' => 'bna', 'A05p25880' => 'bna', 'Aa31LG8G9320' => 'aar', 'Aa31LG8G9330' => 'aar', 'Aa31LG8G9340' => 'aar', 'Aa31sc221G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1034' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1528' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.829' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2222' => 'aag', 'Ah.12g058830' => 'amhyb', 'Ah.12g058840' => 'amhyb', 'AL3G37160' => 'aly', 'AL7G41310' => 'aly', 'Aqoxy5G00395' => 'aox', 'Aqoxy5G00396' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0C8NZA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5185HY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JZ1PRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MD3LS0' => 'arhy', 'AT3G22840' => 'ath', 'AT4G14690' => 'ath', 'ATR0665G054' => 'atr', 'Atru.chr4.2344' => 'acertr', 'Atru.chr4.2346' => 'acertr', 'Atru.chr4.2347' => 'acertr', 'Atru.chr4.2348' => 'acertr', 'Atru.chr4.2355' => 'acertr', 'Atru.chr4.2356' => 'acertr', 'Atru.chr4.2358' => 'acertr', 'Atru.chr4.2359' => 'acertr', 'Atru.chr4.2360' => 'acertr', 'Atru.chr4.2361' => 'acertr', 'AUR62030476' => 'cqu', 'AUR62030478' => 'cqu', 'AUR62030819' => 'cqu', 'AUR62030820' => 'cqu', 'BcaB03g14648' => 'bca', 'BcaB04g20492' => 'bca', 'BcaB06g26399' => 'bca', 'BcaC01g03416' => 'bca', 'BcaC01g03419' => 'bca', 'BcaC01g03421' => 'bca', 'BcaC01g03424' => 'bca', 'BcaC05g28012' => 'bca', 'BcaC09g49212' => 'bca', 'BcaC09g50140' => 'bca', 'BcaNung00346' => 'bca', 'BolC1t02785H' => 'bol', 'BolC1t04095H' => 'bol', 'BolC3t17545H' => 'bol', 'BolC5t32769H' => 'bol', 'BraA01t02211Z' => 'bra', 'BraA01t03359Z' => 'bra', 'BraA03t13441Z' => 'bra', 'BraA05t21476Z' => 'bra', 'C01p28420' => 'bna', 'C01p41350' => 'bna', 'C03p52750' => 'bna', 'C03p52780' => 'bna', 'C05p40270' => 'bna', 'CAN.G1437.9' => 'can', 'CANSAT78G0035' => 'cansat', 'CANSAT78G1036' => 'cansat', 'CANSAT78G2272' => 'cansat', 'CANSAT78G2478' => 'cansat', 'CARHR098700' => 'chi', 'CARHR221120' => 'chi', 'CARHR221150' => 'chi', 'Carub.0003s2297' => 'cru', 'Carub.0007s2749' => 'cru', 'Carub.0007s2750' => 'cru', 'Carub.0007s2751' => 'cru', 'Ca_10849_v3' => 'car', 'Cc03_g04300' => 'ccan', 'CDE02G3648' => 'cde', 'CDE05G0060' => 'cde', 'CDE05G0692' => 'cde', 'CDE05G2285' => 'cde', 'CDE05G2884' => 'cde', 'CDE05G3072' => 'cde', 'Cfa008439' => 'cfa', 'Cfa008441' => 'cfa', 'Cfa008443' => 'cfa', 'Cfa008448' => 'cfa', 'Ciclev10005974m.g' => 'ccl', 'Ciclev10006006m.g' => 'ccl', 'Ciclev10006775m.g' => 'ccl', 'CiPaw.02G120400' => 'cil', 'CiPaw.02G120500' => 'cil', 'CiPaw.02G120600' => 'cil', 'ClCG05G004850' => 'cla', 'COL.COLO4_21566' => 'col', 'Cpa.g.sc44.124' => 'cpa', 'Cre07.g320400' => 'cre', 'Cre07.g320450' => 'cre', 'Cre08.g384650' => 'cre', 'Cre09.g393173' => 'cre', 'Cre09.g394325' => 'cre', 'Cre14.g626750' => 'cre', 'Cre16.g679250' => 'cre', 'CsaV3_3G012890' => 'csa', 'CSS0010865' => 'camsi', 'CSS0044338' => 'camsi', 'DCAR_002366' => 'dca', 'DCAR_030687' => 'dca', 'DCAR_030688' => 'dca', 'Dinv14047' => 'din', 'Dinv14048' => 'din', 'Duzib151G0105' => 'dzi', 'Duzib151G0114' => 'dzi', 'Duzib212G1029' => 'dzi', 'ECA232G3536' => 'eca', 'ECA240G0786' => 'eca', 'ECA240G1802' => 'eca', 'ECA240G3760' => 'eca', 'ECA240G3920' => 'eca', 'EL10Ac5g12536' => 'bvu', 'EL10Ac5g12537' => 'bvu', 'EL10Ac5g12538' => 'bvu', 'Eucgr.B01004' => 'egr', 'Eucgr.B01006' => 'egr', 'Eucgr.B01007' => 'egr', 'Eucgr.B01008' => 'egr', 'Eucgr.B01895' => 'egr', 'Eucgr.B01896' => 'egr', 'FAN04G1456' => 'fan', 'FAN08G1769' => 'fan', 'FAN08G2160' => 'fan', 'FAN13G2403' => 'fan', 'FAN13G3303' => 'fan', 'FAN15G2435' => 'fan', 'FAN17G0672' => 'fan', 'FAN17G2441' => 'fan', 'FAN18G1024' => 'fan', 'FAN22G1458' => 'fan', 'FAN24G0037' => 'fan', 'FAN24G0429' => 'fan', 'FAN24G2387' => 'fan', 'FAN27G2746' => 'fan', 'FvH4_2g20400' => 'fve', 'FvH4_2g20420' => 'fve', 'FvH4_2g20430' => 'fve', 'FvH4_4g01270' => 'fve', 'FvH4_4g01290' => 'fve', 'FvH4_4g01300' => 'fve', 'FvH4_4g01310' => 'fve', 'FvH4_4g01330' => 'fve', 'FvH4_5g09070' => 'fve', 'Glyma.10G243800' => 'gma', 'Glyma.20G150600' => 'gma', 'Gohir.A09G219200' => 'ghi', 'Gohir.A09G219300' => 'ghi', 'Gohir.D09G221400' => 'ghi', 'Gohir.D09G221500' => 'ghi', 'Gorai.006G242600' => 'gra', 'Gorai.006G242700' => 'gra', 'GSVIVG01018044001' => 'vvi', 'HanXRQChr03g0083821' => 'han', 'HanXRQChr03g0083841' => 'han', 'HanXRQChr03g0083881' => 'han', 'HanXRQChr03g0083901' => 'han', 'HanXRQChr03g0083921' => 'han', 'HanXRQChr03g0085331' => 'han', 'HanXRQChr03g0085361' => 'han', 'HanXRQChr03g0085411' => 'han', 'HanXRQChr03g0085421' => 'han', 'HanXRQChr03g0085431' => 'han', 'HanXRQChr08g0221991' => 'han', 'HanXRQChr11g0336061' => 'han', 'HanXRQChr11g0336411' => 'han', 'Haze_11234' => 'cav', 'Hma1.2p1_0549F.1_g177010' => 'hma', 'Hma1.2p1_0602F.1_g187630' => 'hma', 'Hund14876' => 'sun', 'Hund14879' => 'sun', 'Lalb_Chr06g0160741' => 'lal', 'Lalb_Chr21g0304781' => 'lal', 'Lj3A726G19' => 'lonja', 'Lj3A726T23' => 'lonja', 'Lj3A726T24' => 'lonja', 'Lj3A726T25' => 'lonja', 'Lj3A727T17' => 'lonja', 'Lj3C726T0' => 'lonja', 'Lj3C726T2' => 'lonja', 'Lj3P725T35' => 'lonja', 'Lj3P727T10' => 'lonja', 'Lj3P727T12' => 'lonja', 'Lj3P727T14' => 'lonja', 'Lj5g0023109' => 'lja', 'Lj6P646T44' => 'lonja', 'Lsat_1_v5_gn_6_75760' => 'lsa', 'Lsat_1_v5_gn_6_75800' => 'lsa', 'Lsat_1_v5_gn_6_75900' => 'lsa', 'Lsat_1_v5_gn_6_76240' => 'lsa', 'Lsat_1_v5_gn_6_76441' => 'lsa', 'Lsat_1_v5_gn_6_76700' => 'lsa', 'Lsat_1_v5_gn_6_76760' => 'lsa', 'Manes.15G033100' => 'mes', 'Mapoly0004s0074' => 'mpo', 'Mapoly0004s0075' => 'mpo', 'Mapoly0004s0163' => 'mpo', 'Mapoly0004s0164' => 'mpo', 'Mapoly0021s0018' => 'mpo', 'Mapoly0041s0136' => 'mpo', 'Mapoly0041s0137' => 'mpo', 'Mapoly0041s0138' => 'mpo', 'Mapoly0041s0139' => 'mpo', 'Mapoly0041s0141' => 'mpo', 'Mapoly0041s0142' => 'mpo', 'Mapoly0041s0143' => 'mpo', 'Mapoly0041s0144' => 'mpo', 'Mapoly0041s0145' => 'mpo', 'Mapoly0047s0106' => 'mpo', 'Mapoly0047s0108' => 'mpo', 'Mapoly0050s0051' => 'mpo', 'Mapoly0050s0052' => 'mpo', 'Mapoly0050s0053' => 'mpo', 'Mapoly0058s0013' => 'mpo', 'Mapoly0091s0078' => 'mpo', 'Mapoly0091s0079' => 'mpo', 'Mapoly0091s0080' => 'mpo', 'Mapoly0091s0081' => 'mpo', 'Mapoly0278s0004' => 'mpo', 'Mapoly0278s0005' => 'mpo', 'Mapoly0278s0006' => 'mpo', 'MBI11_g30648_MAGBIO' => 'mbi', 'MCO03G194' => 'mco', 'MCO03G590' => 'mco', 'MCO07G312' => 'mco', 'MCO10G318' => 'mco', 'MCO12G244' => 'mco', 'MCO13G148' => 'mco', 'MCO13G194' => 'mco', 'MCO16G238' => 'mco', 'MD06G1134100' => 'mdo', 'MD13G1200100' => 'mdo', 'MD13G1200300' => 'mdo', 'MD13G1200600' => 'mdo', 'MD14G1150400' => 'mdo', 'MD16G1200000' => 'mdo', 'Medtr1g102570' => 'mtr', 'Medtr1g102780' => 'mtr', 'Medtr1g102800' => 'mtr', 'Medtr1g102810' => 'mtr', 'Medtr1g102830' => 'mtr', 'MELO3C006499.2' => 'cme', 'Migut.G00385' => 'egut', 'MSTRG.4063' => 'ama', 'Nitab4.5_0000090g0260' => 'nta', 'Nitab4.5_0000977g0030' => 'nta', 'Nitab4.5_0002541g0040' => 'nta', 'Nitab4.5_0007068g0040' => 'nta', 'Nn005s41408' => 'nnu', 'Nn005s41410' => 'nnu', 'Oeu010310.1' => 'oeu', 'Oeu010311.1' => 'oeu', 'Oeu043472.1' => 'oeu', 'Os01g0246400' => 'osa', 'Os04g0267950' => 'osa', 'Os07g0178700' => 'osa', 'Os07g0178800' => 'osa', 'Peaxi162Scf00316g00046' => 'pax', 'Peaxi162Scf00316g00049' => 'pax', 'Peaxi162Scf00316g00059' => 'pax', 'Peaxi162Scf00316g00328' => 'pax', 'Peaxi162Scf00316g00329' => 'pax', 'Peaxi162Scf00316g00411' => 'pax', 'Peaxi162Scf00316g00521' => 'pax', 'Peaxi162Scf00492g00068' => 'pax', 'Peaxi162Scf35631g00002' => 'pax', 'PGR142G3720' => 'pgr', 'PGSC0003DMG400006442' => 'stu', 'Phvul.007G062000' => 'pvu', 'Potri.008G157750' => 'ptr', 'Potri.008G157900' => 'ptr', 'Potri.008G158000' => 'ptr', 'Potri.008G158200' => 'ptr', 'Pp3c11_7280' => 'ppa', 'Pp3c11_7980' => 'ppa', 'Pp3c12_19450' => 'ppa', 'Pp3c14_1480' => 'ppa', 'Pp3c14_1501' => 'ppa', 'Pp3c16_4900' => 'ppa', 'Pp3c16_5010' => 'ppa', 'Pp3c16_5060' => 'ppa', 'Pp3c19_18250' => 'ppa', 'Pp3c23_8530' => 'ppa', 'Pp3c23_8550' => 'ppa', 'Pp3c24_9670' => 'ppa', 'Pp3c2_21390' => 'ppa', 'Pp3c2_31380' => 'ppa', 'Pp3c3_16620' => 'ppa', 'Pp3c3_8090' => 'ppa', 'Pp3c3_8110' => 'ppa', 'Pp3c3_8130' => 'ppa', 'Pp3c3_8150' => 'ppa', 'Pp3c4_14320' => 'ppa', 'Pp3c6_2560' => 'ppa', 'Pp3c9_16700' => 'ppa', 'PRCOL_00000234' => 'pco', 'PRCOL_00000235' => 'pco', 'PRCOL_00000777' => 'pco', 'PRCOL_00002344' => 'pco', 'PRCOL_00002372' => 'pco', 'PRCOL_00006120' => 'pco', 'Prupe.1G021400' => 'ppe', 'Prupe.1G021500' => 'ppe', 'Prupe.1G021600' => 'ppe', 'Prupe.1G021700' => 'ppe', 'Prupe.1G021800' => 'ppe', 'Prupe.5G145100' => 'ppe', 'Psat6g204040' => 'psa', 'Psat6g204800' => 'psa', 'Psat6g204920' => 'psa', 'Psat6g204960' => 'psa', 'Psat6g205080' => 'psa', 'PSO017G0271' => 'pso', 'PSO017G1276' => 'pso', 'PSO017G1429' => 'pso', 'PSO017G1861' => 'pso', 'PSO017G2787' => 'pso', 'PSO017G4466' => 'pso', 'PSO017G5118' => 'pso', 'PSO017G5420' => 'pso', 'PSO063G3678' => 'pso', 'PSO210G0546' => 'pso', 'PSO317G0001' => 'pso', 'PSO357G0512' => 'pso', 'PSO478G2682' => 'pso', 'PSO647G0001' => 'pso', 'PSO675G0001' => 'pso', 'PSO675G2699' => 'pso', 'PSO675G2849' => 'pso', 'PSO675G4991' => 'pso', 'PSO689G0001' => 'pso', 'QL06p000916' => 'qlo', 'QL06p000921' => 'qlo', 'QL06p001398' => 'qlo', 'QL06p001407' => 'qlo', 'QL06p002031' => 'qlo', 'RcHm_v2.0_Chr4g0387791' => 'rch', 'RcHm_v2.0_Chr4g0387801' => 'rch', 'RcHm_v2.0_Chr6g0286501' => 'rch', 'RcHm_v2.0_Chr6g0286511' => 'rch', 'RcHm_v2.0_Chr6g0286521' => 'rch', 'RcHm_v2.0_Chr6g0286531' => 'rch', 'RcHm_v2.0_Chr7g0189141' => 'rch', 'Rhsim02G0028700' => 'rsi', 'Rhsim02G0028800' => 'rsi', 'Rhsim02G0028900' => 'rsi', 'Rhsim02G0029000' => 'rsi', 'Rhsim02G0029100' => 'rsi', 'Rhsim02G0029200' => 'rsi', 'Rhsim02G0029300' => 'rsi', 'Rhsim02G0029400' => 'rsi', 'Rhsim02G0029500' => 'rsi', 'Rhsim02G0029600' => 'rsi', 'RhsimUnG0024000' => 'rsi', 'RhsimUnG0024100' => 'rsi', 'RhsimUnG0024200' => 'rsi', 'RhsimUnG0024300' => 'rsi', 'RhsimUnG0024400' => 'rsi', 'RhsimUnG0024500' => 'rsi', 'RhsimUnG0024700' => 'rsi', 'RhsimUnG0024800' => 'rsi', 'RhsimUnG0024900' => 'rsi', 'RhsimUnG0025100' => 'rsi', 'Sabra08G0120200' => 'sbr', 'Sabra08G0120300' => 'sbr', 'Sabra08G0120500' => 'sbr', 'Sabra08G0120600' => 'sbr', 'Sabra10G0158900' => 'sbr', 'SalBow2G3492' => 'sbo', 'Sc13g0004760' => 'sci', 'Sc13g0004770' => 'sci', 'Sed0003417' => 'sed', 'Sed0019750' => 'sed', 'SEGI_03419' => 'sgi', 'SEGI_05907' => 'sgi', 'SEGI_10682' => 'sgi', 'SEGI_13528' => 'sgi', 'SEGI_16081' => 'sgi', 'SEGI_19370' => 'sgi', 'SEGI_21015' => 'sgi', 'SEGI_21944' => 'sgi', 'SEGI_32906' => 'sgi', 'SEGI_33093' => 'sgi', 'SEGI_36110' => 'sgi', 'SEGI_40397' => 'sgi', 'SGA_v2.0_scaffold191G40426' => 'sas', 'SGA_v2.0_scaffold353G49717' => 'sas', 'SGA_v2.0_scaffold50G18550' => 'sas', 'SMO119G0173' => 'smo', 'SMO172G0002' => 'smo', 'Solyc09g082690.3' => 'sly', 'Solyc09g082700.2' => 'sly', 'Sopen09g031550' => 'spe', 'Sopen09g031560' => 'spe', 'Sp3g20540' => 'spa', 'Sp7g07580' => 'spa', 'TAR134G0002' => 'tar', 'TAR236G0001' => 'tar', 'TAR365G0892' => 'tar', 'TAR636G0166' => 'tar', 'TAR636G0646' => 'tar', 'TAR636G0869' => 'tar', 'TAR636G1317' => 'tar', 'TAR636G1744' => 'tar', 'TAR636G3358' => 'tar', 'TAR636G3436' => 'tar', 'THA.LOC104803047' => 'tha', 'Thecc.04G238900' => 'tca', 'Thhalv10021557m.g' => 'esa', 'Thhalv10026318m.g' => 'esa', 'Thhalv10026335m.g' => 'esa', 'TPR.G17433' => 'tpr', 'TPR.G18915' => 'tpr', 'TPR.G26125' => 'tpr', 'TWI09G0677' => 'twi', 'TWI73G0287' => 'twi', 'unitig_748.g8326' => 'ugi', 'vmacro15370' => 'vma', 'vmacro15371' => 'vma', 'vmacro15372' => 'vma', 'vmacro15373' => 'vma', 'vmacro15374' => 'vma', 'VMungo0720G2826' => 'vmu', 'Zm00001eb116960' => 'zma', 'Zm00001eb301260' => 'zma', 'Zm00001eb301270' => 'zma' ) $gf_id = 'HOM05D001460' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001460' ) $data_identifier = 'HOM05D001460' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 4, 'aag' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 2, 'aox' => (int) 2, 'arhy' => (int) 4, 'ath' => (int) 2, 'atr' => (int) 1, 'acertr' => (int) 10, 'cqu' => (int) 4, 'bca' => (int) 11, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 1, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 1, 'ccan' => (int) 1, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 1, 'col' => (int) 1, 'cpa' => (int) 1, 'cre' => (int) 7, 'csa' => (int) 1, 'camsi' => (int) 2, 'dca' => (int) 3, 'din' => (int) 2, 'dzi' => (int) 3, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 14, 'fve' => (int) 9, 'gma' => (int) 2, 'ghi' => (int) 4, 'gra' => (int) 2, 'vvi' => (int) 1, 'han' => (int) 13, 'cav' => (int) 1, 'hma' => (int) 2, 'sun' => (int) 2, 'lal' => (int) 2, 'lonja' => (int) 12, 'lja' => (int) 1, 'lsa' => (int) 7, 'mes' => (int) 1, 'mpo' => (int) 27, 'mbi' => (int) 1, 'mco' => (int) 8, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 1, 'egut' => (int) 1, 'ama' => (int) 1, 'nta' => (int) 4, 'nnu' => (int) 2, 'oeu' => (int) 3, 'osa' => (int) 4, 'pax' => (int) 9, 'pgr' => (int) 1, 'stu' => (int) 1, 'pvu' => (int) 1, 'ptr' => (int) 4, 'ppa' => (int) 22, 'pco' => (int) 6, 'ppe' => (int) 6, 'psa' => (int) 5, 'pso' => (int) 19, 'qlo' => (int) 5, 'rch' => (int) 7, 'rsi' => (int) 20, 'sbr' => (int) 5, 'sbo' => (int) 1, 'sci' => (int) 2, 'sed' => (int) 2, 'sgi' => (int) 12, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 2, 'tar' => (int) 10, 'tha' => (int) 1, 'tca' => (int) 1, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 2, 'ugi' => (int) 1, 'vma' => (int) 5, 'vmu' => (int) 1, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb301270' $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' => 'HOM05D001460', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '433', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p22980' => 'bna', 'A01p32340' => 'bna', 'A03p42970' => 'bna', 'A05p25880' => 'bna', 'Aa31LG8G9320' => 'aar', 'Aa31LG8G9330' => 'aar', 'Aa31LG8G9340' => 'aar', 'Aa31sc221G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1034' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1528' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.829' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2222' => 'aag', 'Ah.12g058830' => 'amhyb', 'Ah.12g058840' => 'amhyb', 'AL3G37160' => 'aly', 'AL7G41310' => 'aly', 'Aqoxy5G00395' => 'aox', 'Aqoxy5G00396' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0C8NZA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5185HY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JZ1PRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MD3LS0' => 'arhy', 'AT3G22840' => 'ath', 'AT4G14690' => 'ath', 'ATR0665G054' => 'atr', 'Atru.chr4.2344' => 'acertr', 'Atru.chr4.2346' => 'acertr', 'Atru.chr4.2347' => 'acertr', 'Atru.chr4.2348' => 'acertr', 'Atru.chr4.2355' => 'acertr', 'Atru.chr4.2356' => 'acertr', 'Atru.chr4.2358' => 'acertr', 'Atru.chr4.2359' => 'acertr', 'Atru.chr4.2360' => 'acertr', 'Atru.chr4.2361' => 'acertr', 'AUR62030476' => 'cqu', 'AUR62030478' => 'cqu', 'AUR62030819' => 'cqu', 'AUR62030820' => 'cqu', 'BcaB03g14648' => 'bca', 'BcaB04g20492' => 'bca', 'BcaB06g26399' => 'bca', 'BcaC01g03416' => 'bca', 'BcaC01g03419' => 'bca', 'BcaC01g03421' => 'bca', 'BcaC01g03424' => 'bca', 'BcaC05g28012' => 'bca', 'BcaC09g49212' => 'bca', 'BcaC09g50140' => 'bca', 'BcaNung00346' => 'bca', 'BolC1t02785H' => 'bol', 'BolC1t04095H' => 'bol', 'BolC3t17545H' => 'bol', 'BolC5t32769H' => 'bol', 'BraA01t02211Z' => 'bra', 'BraA01t03359Z' => 'bra', 'BraA03t13441Z' => 'bra', 'BraA05t21476Z' => 'bra', 'C01p28420' => 'bna', 'C01p41350' => 'bna', 'C03p52750' => 'bna', 'C03p52780' => 'bna', 'C05p40270' => 'bna', 'CAN.G1437.9' => 'can', 'CANSAT78G0035' => 'cansat', 'CANSAT78G1036' => 'cansat', 'CANSAT78G2272' => 'cansat', 'CANSAT78G2478' => 'cansat', 'CARHR098700' => 'chi', 'CARHR221120' => 'chi', 'CARHR221150' => 'chi', 'Carub.0003s2297' => 'cru', 'Carub.0007s2749' => 'cru', 'Carub.0007s2750' => 'cru', 'Carub.0007s2751' => 'cru', 'Ca_10849_v3' => 'car', 'Cc03_g04300' => 'ccan', 'CDE02G3648' => 'cde', 'CDE05G0060' => 'cde', 'CDE05G0692' => 'cde', 'CDE05G2285' => 'cde', 'CDE05G2884' => 'cde', 'CDE05G3072' => 'cde', 'Cfa008439' => 'cfa', 'Cfa008441' => 'cfa', 'Cfa008443' => 'cfa', 'Cfa008448' => 'cfa', 'Ciclev10005974m.g' => 'ccl', 'Ciclev10006006m.g' => 'ccl', 'Ciclev10006775m.g' => 'ccl', 'CiPaw.02G120400' => 'cil', 'CiPaw.02G120500' => 'cil', 'CiPaw.02G120600' => 'cil', 'ClCG05G004850' => 'cla', 'COL.COLO4_21566' => 'col', 'Cpa.g.sc44.124' => 'cpa', 'Cre07.g320400' => 'cre', 'Cre07.g320450' => 'cre', 'Cre08.g384650' => 'cre', 'Cre09.g393173' => 'cre', 'Cre09.g394325' => 'cre', 'Cre14.g626750' => 'cre', 'Cre16.g679250' => 'cre', 'CsaV3_3G012890' => 'csa', 'CSS0010865' => 'camsi', 'CSS0044338' => 'camsi', 'DCAR_002366' => 'dca', 'DCAR_030687' => 'dca', 'DCAR_030688' => 'dca', 'Dinv14047' => 'din', 'Dinv14048' => 'din', 'Duzib151G0105' => 'dzi', 'Duzib151G0114' => 'dzi', 'Duzib212G1029' => 'dzi', 'ECA232G3536' => 'eca', 'ECA240G0786' => 'eca', 'ECA240G1802' => 'eca', 'ECA240G3760' => 'eca', 'ECA240G3920' => 'eca', 'EL10Ac5g12536' => 'bvu', 'EL10Ac5g12537' => 'bvu', 'EL10Ac5g12538' => 'bvu', 'Eucgr.B01004' => 'egr', 'Eucgr.B01006' => 'egr', 'Eucgr.B01007' => 'egr', 'Eucgr.B01008' => 'egr', 'Eucgr.B01895' => 'egr', 'Eucgr.B01896' => 'egr', 'FAN04G1456' => 'fan', 'FAN08G1769' => 'fan', 'FAN08G2160' => 'fan', 'FAN13G2403' => 'fan', 'FAN13G3303' => 'fan', 'FAN15G2435' => 'fan', 'FAN17G0672' => 'fan', 'FAN17G2441' => 'fan', 'FAN18G1024' => 'fan', 'FAN22G1458' => 'fan', 'FAN24G0037' => 'fan', 'FAN24G0429' => 'fan', 'FAN24G2387' => 'fan', 'FAN27G2746' => 'fan', 'FvH4_2g20400' => 'fve', 'FvH4_2g20420' => 'fve', 'FvH4_2g20430' => 'fve', 'FvH4_4g01270' => 'fve', 'FvH4_4g01290' => 'fve', 'FvH4_4g01300' => 'fve', 'FvH4_4g01310' => 'fve', 'FvH4_4g01330' => 'fve', 'FvH4_5g09070' => 'fve', 'Glyma.10G243800' => 'gma', 'Glyma.20G150600' => 'gma', 'Gohir.A09G219200' => 'ghi', 'Gohir.A09G219300' => 'ghi', 'Gohir.D09G221400' => 'ghi', 'Gohir.D09G221500' => 'ghi', 'Gorai.006G242600' => 'gra', 'Gorai.006G242700' => 'gra', 'GSVIVG01018044001' => 'vvi', 'HanXRQChr03g0083821' => 'han', 'HanXRQChr03g0083841' => 'han', 'HanXRQChr03g0083881' => 'han', 'HanXRQChr03g0083901' => 'han', 'HanXRQChr03g0083921' => 'han', 'HanXRQChr03g0085331' => 'han', 'HanXRQChr03g0085361' => 'han', 'HanXRQChr03g0085411' => 'han', 'HanXRQChr03g0085421' => 'han', 'HanXRQChr03g0085431' => 'han', 'HanXRQChr08g0221991' => 'han', 'HanXRQChr11g0336061' => 'han', 'HanXRQChr11g0336411' => 'han', 'Haze_11234' => 'cav', 'Hma1.2p1_0549F.1_g177010' => 'hma', 'Hma1.2p1_0602F.1_g187630' => 'hma', 'Hund14876' => 'sun', 'Hund14879' => 'sun', 'Lalb_Chr06g0160741' => 'lal', 'Lalb_Chr21g0304781' => 'lal', 'Lj3A726G19' => 'lonja', 'Lj3A726T23' => 'lonja', 'Lj3A726T24' => 'lonja', 'Lj3A726T25' => 'lonja', 'Lj3A727T17' => 'lonja', 'Lj3C726T0' => 'lonja', 'Lj3C726T2' => 'lonja', 'Lj3P725T35' => 'lonja', 'Lj3P727T10' => 'lonja', 'Lj3P727T12' => 'lonja', 'Lj3P727T14' => 'lonja', 'Lj5g0023109' => 'lja', 'Lj6P646T44' => 'lonja', 'Lsat_1_v5_gn_6_75760' => 'lsa', 'Lsat_1_v5_gn_6_75800' => 'lsa', 'Lsat_1_v5_gn_6_75900' => 'lsa', 'Lsat_1_v5_gn_6_76240' => 'lsa', 'Lsat_1_v5_gn_6_76441' => 'lsa', 'Lsat_1_v5_gn_6_76700' => 'lsa', 'Lsat_1_v5_gn_6_76760' => 'lsa', 'Manes.15G033100' => 'mes', 'Mapoly0004s0074' => 'mpo', 'Mapoly0004s0075' => 'mpo', 'Mapoly0004s0163' => 'mpo', 'Mapoly0004s0164' => 'mpo', 'Mapoly0021s0018' => 'mpo', 'Mapoly0041s0136' => 'mpo', 'Mapoly0041s0137' => 'mpo', 'Mapoly0041s0138' => 'mpo', 'Mapoly0041s0139' => 'mpo', 'Mapoly0041s0141' => 'mpo', 'Mapoly0041s0142' => 'mpo', 'Mapoly0041s0143' => 'mpo', 'Mapoly0041s0144' => 'mpo', 'Mapoly0041s0145' => 'mpo', 'Mapoly0047s0106' => 'mpo', 'Mapoly0047s0108' => 'mpo', 'Mapoly0050s0051' => 'mpo', 'Mapoly0050s0052' => 'mpo', 'Mapoly0050s0053' => 'mpo', 'Mapoly0058s0013' => 'mpo', 'Mapoly0091s0078' => 'mpo', 'Mapoly0091s0079' => 'mpo', 'Mapoly0091s0080' => 'mpo', 'Mapoly0091s0081' => 'mpo', 'Mapoly0278s0004' => 'mpo', 'Mapoly0278s0005' => 'mpo', 'Mapoly0278s0006' => 'mpo', 'MBI11_g30648_MAGBIO' => 'mbi', 'MCO03G194' => 'mco', 'MCO03G590' => 'mco', 'MCO07G312' => 'mco', 'MCO10G318' => 'mco', 'MCO12G244' => 'mco', 'MCO13G148' => 'mco', 'MCO13G194' => 'mco', 'MCO16G238' => 'mco', 'MD06G1134100' => 'mdo', 'MD13G1200100' => 'mdo', 'MD13G1200300' => 'mdo', 'MD13G1200600' => 'mdo', 'MD14G1150400' => 'mdo', 'MD16G1200000' => 'mdo', 'Medtr1g102570' => 'mtr', 'Medtr1g102780' => 'mtr', 'Medtr1g102800' => 'mtr', 'Medtr1g102810' => 'mtr', 'Medtr1g102830' => 'mtr', 'MELO3C006499.2' => 'cme', 'Migut.G00385' => 'egut', 'MSTRG.4063' => 'ama', 'Nitab4.5_0000090g0260' => 'nta', 'Nitab4.5_0000977g0030' => 'nta', 'Nitab4.5_0002541g0040' => 'nta', 'Nitab4.5_0007068g0040' => 'nta', 'Nn005s41408' => 'nnu', 'Nn005s41410' => 'nnu', 'Oeu010310.1' => 'oeu', 'Oeu010311.1' => 'oeu', 'Oeu043472.1' => 'oeu', 'Os01g0246400' => 'osa', 'Os04g0267950' => 'osa', 'Os07g0178700' => 'osa', 'Os07g0178800' => 'osa', 'Peaxi162Scf00316g00046' => 'pax', 'Peaxi162Scf00316g00049' => 'pax', 'Peaxi162Scf00316g00059' => 'pax', 'Peaxi162Scf00316g00328' => 'pax', 'Peaxi162Scf00316g00329' => 'pax', 'Peaxi162Scf00316g00411' => 'pax', 'Peaxi162Scf00316g00521' => 'pax', 'Peaxi162Scf00492g00068' => 'pax', 'Peaxi162Scf35631g00002' => 'pax', 'PGR142G3720' => 'pgr', 'PGSC0003DMG400006442' => 'stu', 'Phvul.007G062000' => 'pvu', 'Potri.008G157750' => 'ptr', 'Potri.008G157900' => 'ptr', 'Potri.008G158000' => 'ptr', 'Potri.008G158200' => 'ptr', 'Pp3c11_7280' => 'ppa', 'Pp3c11_7980' => 'ppa', 'Pp3c12_19450' => 'ppa', 'Pp3c14_1480' => 'ppa', 'Pp3c14_1501' => 'ppa', 'Pp3c16_4900' => 'ppa', 'Pp3c16_5010' => 'ppa', 'Pp3c16_5060' => 'ppa', 'Pp3c19_18250' => 'ppa', 'Pp3c23_8530' => 'ppa', 'Pp3c23_8550' => 'ppa', 'Pp3c24_9670' => 'ppa', 'Pp3c2_21390' => 'ppa', 'Pp3c2_31380' => 'ppa', 'Pp3c3_16620' => 'ppa', 'Pp3c3_8090' => 'ppa', 'Pp3c3_8110' => 'ppa', 'Pp3c3_8130' => 'ppa', 'Pp3c3_8150' => 'ppa', 'Pp3c4_14320' => 'ppa', 'Pp3c6_2560' => 'ppa', 'Pp3c9_16700' => 'ppa', 'PRCOL_00000234' => 'pco', 'PRCOL_00000235' => 'pco', 'PRCOL_00000777' => 'pco', 'PRCOL_00002344' => 'pco', 'PRCOL_00002372' => 'pco', 'PRCOL_00006120' => 'pco', 'Prupe.1G021400' => 'ppe', 'Prupe.1G021500' => 'ppe', 'Prupe.1G021600' => 'ppe', 'Prupe.1G021700' => 'ppe', 'Prupe.1G021800' => 'ppe', 'Prupe.5G145100' => 'ppe', 'Psat6g204040' => 'psa', 'Psat6g204800' => 'psa', 'Psat6g204920' => 'psa', 'Psat6g204960' => 'psa', 'Psat6g205080' => 'psa', 'PSO017G0271' => 'pso', 'PSO017G1276' => 'pso', 'PSO017G1429' => 'pso', 'PSO017G1861' => 'pso', 'PSO017G2787' => 'pso', 'PSO017G4466' => 'pso', 'PSO017G5118' => 'pso', 'PSO017G5420' => 'pso', 'PSO063G3678' => 'pso', 'PSO210G0546' => 'pso', 'PSO317G0001' => 'pso', 'PSO357G0512' => 'pso', 'PSO478G2682' => 'pso', 'PSO647G0001' => 'pso', 'PSO675G0001' => 'pso', 'PSO675G2699' => 'pso', 'PSO675G2849' => 'pso', 'PSO675G4991' => 'pso', 'PSO689G0001' => 'pso', 'QL06p000916' => 'qlo', 'QL06p000921' => 'qlo', 'QL06p001398' => 'qlo', 'QL06p001407' => 'qlo', 'QL06p002031' => 'qlo', 'RcHm_v2.0_Chr4g0387791' => 'rch', 'RcHm_v2.0_Chr4g0387801' => 'rch', 'RcHm_v2.0_Chr6g0286501' => 'rch', 'RcHm_v2.0_Chr6g0286511' => 'rch', 'RcHm_v2.0_Chr6g0286521' => 'rch', 'RcHm_v2.0_Chr6g0286531' => 'rch', 'RcHm_v2.0_Chr7g0189141' => 'rch', 'Rhsim02G0028700' => 'rsi', 'Rhsim02G0028800' => 'rsi', 'Rhsim02G0028900' => 'rsi', 'Rhsim02G0029000' => 'rsi', 'Rhsim02G0029100' => 'rsi', 'Rhsim02G0029200' => 'rsi', 'Rhsim02G0029300' => 'rsi', 'Rhsim02G0029400' => 'rsi', 'Rhsim02G0029500' => 'rsi', 'Rhsim02G0029600' => 'rsi', 'RhsimUnG0024000' => 'rsi', 'RhsimUnG0024100' => 'rsi', 'RhsimUnG0024200' => 'rsi', 'RhsimUnG0024300' => 'rsi', 'RhsimUnG0024400' => 'rsi', 'RhsimUnG0024500' => 'rsi', 'RhsimUnG0024700' => 'rsi', 'RhsimUnG0024800' => 'rsi', 'RhsimUnG0024900' => 'rsi', 'RhsimUnG0025100' => 'rsi', 'Sabra08G0120200' => 'sbr', 'Sabra08G0120300' => 'sbr', 'Sabra08G0120500' => 'sbr', 'Sabra08G0120600' => 'sbr', 'Sabra10G0158900' => 'sbr', 'SalBow2G3492' => 'sbo', 'Sc13g0004760' => 'sci', 'Sc13g0004770' => 'sci', 'Sed0003417' => 'sed', 'Sed0019750' => 'sed', 'SEGI_03419' => 'sgi', 'SEGI_05907' => 'sgi', 'SEGI_10682' => 'sgi', 'SEGI_13528' => 'sgi', 'SEGI_16081' => 'sgi', 'SEGI_19370' => 'sgi', 'SEGI_21015' => 'sgi', 'SEGI_21944' => 'sgi', 'SEGI_32906' => 'sgi', 'SEGI_33093' => 'sgi', 'SEGI_36110' => 'sgi', 'SEGI_40397' => 'sgi', 'SGA_v2.0_scaffold191G40426' => 'sas', 'SGA_v2.0_scaffold353G49717' => 'sas', 'SGA_v2.0_scaffold50G18550' => 'sas', 'SMO119G0173' => 'smo', 'SMO172G0002' => 'smo', 'Solyc09g082690.3' => 'sly', 'Solyc09g082700.2' => 'sly', 'Sopen09g031550' => 'spe', 'Sopen09g031560' => 'spe', 'Sp3g20540' => 'spa', 'Sp7g07580' => 'spa', 'TAR134G0002' => 'tar', 'TAR236G0001' => 'tar', 'TAR365G0892' => 'tar', 'TAR636G0166' => 'tar', 'TAR636G0646' => 'tar', 'TAR636G0869' => 'tar', 'TAR636G1317' => 'tar', 'TAR636G1744' => 'tar', 'TAR636G3358' => 'tar', 'TAR636G3436' => 'tar', 'THA.LOC104803047' => 'tha', 'Thecc.04G238900' => 'tca', 'Thhalv10021557m.g' => 'esa', 'Thhalv10026318m.g' => 'esa', 'Thhalv10026335m.g' => 'esa', 'TPR.G17433' => 'tpr', 'TPR.G18915' => 'tpr', 'TPR.G26125' => 'tpr', 'TWI09G0677' => 'twi', 'TWI73G0287' => 'twi', 'unitig_748.g8326' => 'ugi', 'vmacro15370' => 'vma', 'vmacro15371' => 'vma', 'vmacro15372' => 'vma', 'vmacro15373' => 'vma', 'vmacro15374' => 'vma', 'VMungo0720G2826' => 'vmu', 'Zm00001eb116960' => 'zma', 'Zm00001eb301260' => 'zma', 'Zm00001eb301270' => 'zma' ), 'gf_id' => 'HOM05D001460', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001460' ), 'data_identifier' => 'HOM05D001460', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001460', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '433', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p22980' => 'bna', 'A01p32340' => 'bna', 'A03p42970' => 'bna', 'A05p25880' => 'bna', 'Aa31LG8G9320' => 'aar', 'Aa31LG8G9330' => 'aar', 'Aa31LG8G9340' => 'aar', 'Aa31sc221G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1034' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1528' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.829' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2222' => 'aag', 'Ah.12g058830' => 'amhyb', 'Ah.12g058840' => 'amhyb', 'AL3G37160' => 'aly', 'AL7G41310' => 'aly', 'Aqoxy5G00395' => 'aox', 'Aqoxy5G00396' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0C8NZA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5185HY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JZ1PRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MD3LS0' => 'arhy', 'AT3G22840' => 'ath', 'AT4G14690' => 'ath', 'ATR0665G054' => 'atr', 'Atru.chr4.2344' => 'acertr', 'Atru.chr4.2346' => 'acertr', 'Atru.chr4.2347' => 'acertr', 'Atru.chr4.2348' => 'acertr', 'Atru.chr4.2355' => 'acertr', 'Atru.chr4.2356' => 'acertr', 'Atru.chr4.2358' => 'acertr', 'Atru.chr4.2359' => 'acertr', 'Atru.chr4.2360' => 'acertr', 'Atru.chr4.2361' => 'acertr', 'AUR62030476' => 'cqu', 'AUR62030478' => 'cqu', 'AUR62030819' => 'cqu', 'AUR62030820' => 'cqu', 'BcaB03g14648' => 'bca', 'BcaB04g20492' => 'bca', 'BcaB06g26399' => 'bca', 'BcaC01g03416' => 'bca', 'BcaC01g03419' => 'bca', 'BcaC01g03421' => 'bca', 'BcaC01g03424' => 'bca', 'BcaC05g28012' => 'bca', 'BcaC09g49212' => 'bca', 'BcaC09g50140' => 'bca', 'BcaNung00346' => 'bca', 'BolC1t02785H' => 'bol', 'BolC1t04095H' => 'bol', 'BolC3t17545H' => 'bol', 'BolC5t32769H' => 'bol', 'BraA01t02211Z' => 'bra', 'BraA01t03359Z' => 'bra', 'BraA03t13441Z' => 'bra', 'BraA05t21476Z' => 'bra', 'C01p28420' => 'bna', 'C01p41350' => 'bna', 'C03p52750' => 'bna', 'C03p52780' => 'bna', 'C05p40270' => 'bna', 'CAN.G1437.9' => 'can', 'CANSAT78G0035' => 'cansat', 'CANSAT78G1036' => 'cansat', 'CANSAT78G2272' => 'cansat', 'CANSAT78G2478' => 'cansat', 'CARHR098700' => 'chi', 'CARHR221120' => 'chi', 'CARHR221150' => 'chi', 'Carub.0003s2297' => 'cru', 'Carub.0007s2749' => 'cru', 'Carub.0007s2750' => 'cru', 'Carub.0007s2751' => 'cru', 'Ca_10849_v3' => 'car', 'Cc03_g04300' => 'ccan', 'CDE02G3648' => 'cde', 'CDE05G0060' => 'cde', 'CDE05G0692' => 'cde', 'CDE05G2285' => 'cde', 'CDE05G2884' => 'cde', 'CDE05G3072' => 'cde', 'Cfa008439' => 'cfa', 'Cfa008441' => 'cfa', 'Cfa008443' => 'cfa', 'Cfa008448' => 'cfa', 'Ciclev10005974m.g' => 'ccl', 'Ciclev10006006m.g' => 'ccl', 'Ciclev10006775m.g' => 'ccl', 'CiPaw.02G120400' => 'cil', 'CiPaw.02G120500' => 'cil', 'CiPaw.02G120600' => 'cil', 'ClCG05G004850' => 'cla', 'COL.COLO4_21566' => 'col', 'Cpa.g.sc44.124' => 'cpa', 'Cre07.g320400' => 'cre', 'Cre07.g320450' => 'cre', 'Cre08.g384650' => 'cre', 'Cre09.g393173' => 'cre', 'Cre09.g394325' => 'cre', 'Cre14.g626750' => 'cre', 'Cre16.g679250' => 'cre', 'CsaV3_3G012890' => 'csa', 'CSS0010865' => 'camsi', 'CSS0044338' => 'camsi', 'DCAR_002366' => 'dca', 'DCAR_030687' => 'dca', 'DCAR_030688' => 'dca', 'Dinv14047' => 'din', 'Dinv14048' => 'din', 'Duzib151G0105' => 'dzi', 'Duzib151G0114' => 'dzi', 'Duzib212G1029' => 'dzi', 'ECA232G3536' => 'eca', 'ECA240G0786' => 'eca', 'ECA240G1802' => 'eca', 'ECA240G3760' => 'eca', 'ECA240G3920' => 'eca', 'EL10Ac5g12536' => 'bvu', 'EL10Ac5g12537' => 'bvu', 'EL10Ac5g12538' => 'bvu', 'Eucgr.B01004' => 'egr', 'Eucgr.B01006' => 'egr', 'Eucgr.B01007' => 'egr', 'Eucgr.B01008' => 'egr', 'Eucgr.B01895' => 'egr', 'Eucgr.B01896' => 'egr', 'FAN04G1456' => 'fan', 'FAN08G1769' => 'fan', 'FAN08G2160' => 'fan', 'FAN13G2403' => 'fan', 'FAN13G3303' => 'fan', 'FAN15G2435' => 'fan', 'FAN17G0672' => 'fan', 'FAN17G2441' => 'fan', 'FAN18G1024' => 'fan', 'FAN22G1458' => 'fan', 'FAN24G0037' => 'fan', 'FAN24G0429' => 'fan', 'FAN24G2387' => 'fan', 'FAN27G2746' => 'fan', 'FvH4_2g20400' => 'fve', 'FvH4_2g20420' => 'fve', 'FvH4_2g20430' => 'fve', 'FvH4_4g01270' => 'fve', 'FvH4_4g01290' => 'fve', 'FvH4_4g01300' => 'fve', 'FvH4_4g01310' => 'fve', 'FvH4_4g01330' => 'fve', 'FvH4_5g09070' => 'fve', 'Glyma.10G243800' => 'gma', 'Glyma.20G150600' => 'gma', 'Gohir.A09G219200' => 'ghi', 'Gohir.A09G219300' => 'ghi', 'Gohir.D09G221400' => 'ghi', 'Gohir.D09G221500' => 'ghi', 'Gorai.006G242600' => 'gra', 'Gorai.006G242700' => 'gra', 'GSVIVG01018044001' => 'vvi', 'HanXRQChr03g0083821' => 'han', 'HanXRQChr03g0083841' => 'han', 'HanXRQChr03g0083881' => 'han', 'HanXRQChr03g0083901' => 'han', 'HanXRQChr03g0083921' => 'han', 'HanXRQChr03g0085331' => 'han', 'HanXRQChr03g0085361' => 'han', 'HanXRQChr03g0085411' => 'han', 'HanXRQChr03g0085421' => 'han', 'HanXRQChr03g0085431' => 'han', 'HanXRQChr08g0221991' => 'han', 'HanXRQChr11g0336061' => 'han', 'HanXRQChr11g0336411' => 'han', 'Haze_11234' => 'cav', 'Hma1.2p1_0549F.1_g177010' => 'hma', 'Hma1.2p1_0602F.1_g187630' => 'hma', 'Hund14876' => 'sun', 'Hund14879' => 'sun', 'Lalb_Chr06g0160741' => 'lal', 'Lalb_Chr21g0304781' => 'lal', 'Lj3A726G19' => 'lonja', 'Lj3A726T23' => 'lonja', 'Lj3A726T24' => 'lonja', 'Lj3A726T25' => 'lonja', 'Lj3A727T17' => 'lonja', 'Lj3C726T0' => 'lonja', 'Lj3C726T2' => 'lonja', 'Lj3P725T35' => 'lonja', 'Lj3P727T10' => 'lonja', 'Lj3P727T12' => 'lonja', 'Lj3P727T14' => 'lonja', 'Lj5g0023109' => 'lja', 'Lj6P646T44' => 'lonja', 'Lsat_1_v5_gn_6_75760' => 'lsa', 'Lsat_1_v5_gn_6_75800' => 'lsa', 'Lsat_1_v5_gn_6_75900' => 'lsa', 'Lsat_1_v5_gn_6_76240' => 'lsa', 'Lsat_1_v5_gn_6_76441' => 'lsa', 'Lsat_1_v5_gn_6_76700' => 'lsa', 'Lsat_1_v5_gn_6_76760' => 'lsa', 'Manes.15G033100' => 'mes', 'Mapoly0004s0074' => 'mpo', 'Mapoly0004s0075' => 'mpo', 'Mapoly0004s0163' => 'mpo', 'Mapoly0004s0164' => 'mpo', 'Mapoly0021s0018' => 'mpo', 'Mapoly0041s0136' => 'mpo', 'Mapoly0041s0137' => 'mpo', 'Mapoly0041s0138' => 'mpo', 'Mapoly0041s0139' => 'mpo', 'Mapoly0041s0141' => 'mpo', 'Mapoly0041s0142' => 'mpo', 'Mapoly0041s0143' => 'mpo', 'Mapoly0041s0144' => 'mpo', 'Mapoly0041s0145' => 'mpo', 'Mapoly0047s0106' => 'mpo', 'Mapoly0047s0108' => 'mpo', 'Mapoly0050s0051' => 'mpo', 'Mapoly0050s0052' => 'mpo', 'Mapoly0050s0053' => 'mpo', 'Mapoly0058s0013' => 'mpo', 'Mapoly0091s0078' => 'mpo', 'Mapoly0091s0079' => 'mpo', 'Mapoly0091s0080' => 'mpo', 'Mapoly0091s0081' => 'mpo', 'Mapoly0278s0004' => 'mpo', 'Mapoly0278s0005' => 'mpo', 'Mapoly0278s0006' => 'mpo', 'MBI11_g30648_MAGBIO' => 'mbi', 'MCO03G194' => 'mco', 'MCO03G590' => 'mco', 'MCO07G312' => 'mco', 'MCO10G318' => 'mco', 'MCO12G244' => 'mco', 'MCO13G148' => 'mco', 'MCO13G194' => 'mco', 'MCO16G238' => 'mco', 'MD06G1134100' => 'mdo', 'MD13G1200100' => 'mdo', 'MD13G1200300' => 'mdo', 'MD13G1200600' => 'mdo', 'MD14G1150400' => 'mdo', 'MD16G1200000' => 'mdo', 'Medtr1g102570' => 'mtr', 'Medtr1g102780' => 'mtr', 'Medtr1g102800' => 'mtr', 'Medtr1g102810' => 'mtr', 'Medtr1g102830' => 'mtr', 'MELO3C006499.2' => 'cme', 'Migut.G00385' => 'egut', 'MSTRG.4063' => 'ama', 'Nitab4.5_0000090g0260' => 'nta', 'Nitab4.5_0000977g0030' => 'nta', 'Nitab4.5_0002541g0040' => 'nta', 'Nitab4.5_0007068g0040' => 'nta', 'Nn005s41408' => 'nnu', 'Nn005s41410' => 'nnu', 'Oeu010310.1' => 'oeu', 'Oeu010311.1' => 'oeu', 'Oeu043472.1' => 'oeu', 'Os01g0246400' => 'osa', 'Os04g0267950' => 'osa', 'Os07g0178700' => 'osa', 'Os07g0178800' => 'osa', 'Peaxi162Scf00316g00046' => 'pax', 'Peaxi162Scf00316g00049' => 'pax', 'Peaxi162Scf00316g00059' => 'pax', 'Peaxi162Scf00316g00328' => 'pax', 'Peaxi162Scf00316g00329' => 'pax', 'Peaxi162Scf00316g00411' => 'pax', 'Peaxi162Scf00316g00521' => 'pax', 'Peaxi162Scf00492g00068' => 'pax', 'Peaxi162Scf35631g00002' => 'pax', 'PGR142G3720' => 'pgr', 'PGSC0003DMG400006442' => 'stu', 'Phvul.007G062000' => 'pvu', 'Potri.008G157750' => 'ptr', 'Potri.008G157900' => 'ptr', 'Potri.008G158000' => 'ptr', 'Potri.008G158200' => 'ptr', 'Pp3c11_7280' => 'ppa', 'Pp3c11_7980' => 'ppa', 'Pp3c12_19450' => 'ppa', 'Pp3c14_1480' => 'ppa', 'Pp3c14_1501' => 'ppa', 'Pp3c16_4900' => 'ppa', 'Pp3c16_5010' => 'ppa', 'Pp3c16_5060' => 'ppa', 'Pp3c19_18250' => 'ppa', 'Pp3c23_8530' => 'ppa', 'Pp3c23_8550' => 'ppa', 'Pp3c24_9670' => 'ppa', 'Pp3c2_21390' => 'ppa', 'Pp3c2_31380' => 'ppa', 'Pp3c3_16620' => 'ppa', 'Pp3c3_8090' => 'ppa', 'Pp3c3_8110' => 'ppa', 'Pp3c3_8130' => 'ppa', 'Pp3c3_8150' => 'ppa', 'Pp3c4_14320' => 'ppa', 'Pp3c6_2560' => 'ppa', 'Pp3c9_16700' => 'ppa', 'PRCOL_00000234' => 'pco', 'PRCOL_00000235' => 'pco', 'PRCOL_00000777' => 'pco', 'PRCOL_00002344' => 'pco', 'PRCOL_00002372' => 'pco', 'PRCOL_00006120' => 'pco', 'Prupe.1G021400' => 'ppe', 'Prupe.1G021500' => 'ppe', 'Prupe.1G021600' => 'ppe', 'Prupe.1G021700' => 'ppe', 'Prupe.1G021800' => 'ppe', 'Prupe.5G145100' => 'ppe', 'Psat6g204040' => 'psa', 'Psat6g204800' => 'psa', 'Psat6g204920' => 'psa', 'Psat6g204960' => 'psa', 'Psat6g205080' => 'psa', 'PSO017G0271' => 'pso', 'PSO017G1276' => 'pso', 'PSO017G1429' => 'pso', 'PSO017G1861' => 'pso', 'PSO017G2787' => 'pso', 'PSO017G4466' => 'pso', 'PSO017G5118' => 'pso', 'PSO017G5420' => 'pso', 'PSO063G3678' => 'pso', 'PSO210G0546' => 'pso', 'PSO317G0001' => 'pso', 'PSO357G0512' => 'pso', 'PSO478G2682' => 'pso', 'PSO647G0001' => 'pso', 'PSO675G0001' => 'pso', 'PSO675G2699' => 'pso', 'PSO675G2849' => 'pso', 'PSO675G4991' => 'pso', 'PSO689G0001' => 'pso', 'QL06p000916' => 'qlo', 'QL06p000921' => 'qlo', 'QL06p001398' => 'qlo', 'QL06p001407' => 'qlo', 'QL06p002031' => 'qlo', 'RcHm_v2.0_Chr4g0387791' => 'rch', 'RcHm_v2.0_Chr4g0387801' => 'rch', 'RcHm_v2.0_Chr6g0286501' => 'rch', 'RcHm_v2.0_Chr6g0286511' => 'rch', 'RcHm_v2.0_Chr6g0286521' => 'rch', 'RcHm_v2.0_Chr6g0286531' => 'rch', 'RcHm_v2.0_Chr7g0189141' => 'rch', 'Rhsim02G0028700' => 'rsi', 'Rhsim02G0028800' => 'rsi', 'Rhsim02G0028900' => 'rsi', 'Rhsim02G0029000' => 'rsi', 'Rhsim02G0029100' => 'rsi', 'Rhsim02G0029200' => 'rsi', 'Rhsim02G0029300' => 'rsi', 'Rhsim02G0029400' => 'rsi', 'Rhsim02G0029500' => 'rsi', 'Rhsim02G0029600' => 'rsi', 'RhsimUnG0024000' => 'rsi', 'RhsimUnG0024100' => 'rsi', 'RhsimUnG0024200' => 'rsi', 'RhsimUnG0024300' => 'rsi', 'RhsimUnG0024400' => 'rsi', 'RhsimUnG0024500' => 'rsi', 'RhsimUnG0024700' => 'rsi', 'RhsimUnG0024800' => 'rsi', 'RhsimUnG0024900' => 'rsi', 'RhsimUnG0025100' => 'rsi', 'Sabra08G0120200' => 'sbr', 'Sabra08G0120300' => 'sbr', 'Sabra08G0120500' => 'sbr', 'Sabra08G0120600' => 'sbr', 'Sabra10G0158900' => 'sbr', 'SalBow2G3492' => 'sbo', 'Sc13g0004760' => 'sci', 'Sc13g0004770' => 'sci', 'Sed0003417' => 'sed', 'Sed0019750' => 'sed', 'SEGI_03419' => 'sgi', 'SEGI_05907' => 'sgi', 'SEGI_10682' => 'sgi', 'SEGI_13528' => 'sgi', 'SEGI_16081' => 'sgi', 'SEGI_19370' => 'sgi', 'SEGI_21015' => 'sgi', 'SEGI_21944' => 'sgi', 'SEGI_32906' => 'sgi', 'SEGI_33093' => 'sgi', 'SEGI_36110' => 'sgi', 'SEGI_40397' => 'sgi', 'SGA_v2.0_scaffold191G40426' => 'sas', 'SGA_v2.0_scaffold353G49717' => 'sas', 'SGA_v2.0_scaffold50G18550' => 'sas', 'SMO119G0173' => 'smo', 'SMO172G0002' => 'smo', 'Solyc09g082690.3' => 'sly', 'Solyc09g082700.2' => 'sly', 'Sopen09g031550' => 'spe', 'Sopen09g031560' => 'spe', 'Sp3g20540' => 'spa', 'Sp7g07580' => 'spa', 'TAR134G0002' => 'tar', 'TAR236G0001' => 'tar', 'TAR365G0892' => 'tar', 'TAR636G0166' => 'tar', 'TAR636G0646' => 'tar', 'TAR636G0869' => 'tar', 'TAR636G1317' => 'tar', 'TAR636G1744' => 'tar', 'TAR636G3358' => 'tar', 'TAR636G3436' => 'tar', 'THA.LOC104803047' => 'tha', 'Thecc.04G238900' => 'tca', 'Thhalv10021557m.g' => 'esa', 'Thhalv10026318m.g' => 'esa', 'Thhalv10026335m.g' => 'esa', 'TPR.G17433' => 'tpr', 'TPR.G18915' => 'tpr', 'TPR.G26125' => 'tpr', 'TWI09G0677' => 'twi', 'TWI73G0287' => 'twi', 'unitig_748.g8326' => 'ugi', 'vmacro15370' => 'vma', 'vmacro15371' => 'vma', 'vmacro15372' => 'vma', 'vmacro15373' => 'vma', 'vmacro15374' => 'vma', 'VMungo0720G2826' => 'vmu', 'Zm00001eb116960' => 'zma', 'Zm00001eb301260' => 'zma', 'Zm00001eb301270' => 'zma' ) $gf_id = 'HOM05D001460' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001460' ) $data_identifier = 'HOM05D001460' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 4, 'aag' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 2, 'aox' => (int) 2, 'arhy' => (int) 4, 'ath' => (int) 2, 'atr' => (int) 1, 'acertr' => (int) 10, 'cqu' => (int) 4, 'bca' => (int) 11, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 1, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 1, 'ccan' => (int) 1, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 1, 'col' => (int) 1, 'cpa' => (int) 1, 'cre' => (int) 7, 'csa' => (int) 1, 'camsi' => (int) 2, 'dca' => (int) 3, 'din' => (int) 2, 'dzi' => (int) 3, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 14, 'fve' => (int) 9, 'gma' => (int) 2, 'ghi' => (int) 4, 'gra' => (int) 2, 'vvi' => (int) 1, 'han' => (int) 13, 'cav' => (int) 1, 'hma' => (int) 2, 'sun' => (int) 2, 'lal' => (int) 2, 'lonja' => (int) 12, 'lja' => (int) 1, 'lsa' => (int) 7, 'mes' => (int) 1, 'mpo' => (int) 27, 'mbi' => (int) 1, 'mco' => (int) 8, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 1, 'egut' => (int) 1, 'ama' => (int) 1, 'nta' => (int) 4, 'nnu' => (int) 2, 'oeu' => (int) 3, 'osa' => (int) 4, 'pax' => (int) 9, 'pgr' => (int) 1, 'stu' => (int) 1, 'pvu' => (int) 1, 'ptr' => (int) 4, 'ppa' => (int) 22, 'pco' => (int) 6, 'ppe' => (int) 6, 'psa' => (int) 5, 'pso' => (int) 19, 'qlo' => (int) 5, 'rch' => (int) 7, 'rsi' => (int) 20, 'sbr' => (int) 5, 'sbo' => (int) 1, 'sci' => (int) 2, 'sed' => (int) 2, 'sgi' => (int) 12, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 2, 'tar' => (int) 10, 'tha' => (int) 1, 'tca' => (int) 1, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 2, 'ugi' => (int) 1, 'vma' => (int) 5, 'vmu' => (int) 1, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb301270' $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' => 'HOM05D001460', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '433', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p22980' => 'bna', 'A01p32340' => 'bna', 'A03p42970' => 'bna', 'A05p25880' => 'bna', 'Aa31LG8G9320' => 'aar', 'Aa31LG8G9330' => 'aar', 'Aa31LG8G9340' => 'aar', 'Aa31sc221G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1034' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1528' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.829' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2222' => 'aag', 'Ah.12g058830' => 'amhyb', 'Ah.12g058840' => 'amhyb', 'AL3G37160' => 'aly', 'AL7G41310' => 'aly', 'Aqoxy5G00395' => 'aox', 'Aqoxy5G00396' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0C8NZA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5185HY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JZ1PRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MD3LS0' => 'arhy', 'AT3G22840' => 'ath', 'AT4G14690' => 'ath', 'ATR0665G054' => 'atr', 'Atru.chr4.2344' => 'acertr', 'Atru.chr4.2346' => 'acertr', 'Atru.chr4.2347' => 'acertr', 'Atru.chr4.2348' => 'acertr', 'Atru.chr4.2355' => 'acertr', 'Atru.chr4.2356' => 'acertr', 'Atru.chr4.2358' => 'acertr', 'Atru.chr4.2359' => 'acertr', 'Atru.chr4.2360' => 'acertr', 'Atru.chr4.2361' => 'acertr', 'AUR62030476' => 'cqu', 'AUR62030478' => 'cqu', 'AUR62030819' => 'cqu', 'AUR62030820' => 'cqu', 'BcaB03g14648' => 'bca', 'BcaB04g20492' => 'bca', 'BcaB06g26399' => 'bca', 'BcaC01g03416' => 'bca', 'BcaC01g03419' => 'bca', 'BcaC01g03421' => 'bca', 'BcaC01g03424' => 'bca', 'BcaC05g28012' => 'bca', 'BcaC09g49212' => 'bca', 'BcaC09g50140' => 'bca', 'BcaNung00346' => 'bca', 'BolC1t02785H' => 'bol', 'BolC1t04095H' => 'bol', 'BolC3t17545H' => 'bol', 'BolC5t32769H' => 'bol', 'BraA01t02211Z' => 'bra', 'BraA01t03359Z' => 'bra', 'BraA03t13441Z' => 'bra', 'BraA05t21476Z' => 'bra', 'C01p28420' => 'bna', 'C01p41350' => 'bna', 'C03p52750' => 'bna', 'C03p52780' => 'bna', 'C05p40270' => 'bna', 'CAN.G1437.9' => 'can', 'CANSAT78G0035' => 'cansat', 'CANSAT78G1036' => 'cansat', 'CANSAT78G2272' => 'cansat', 'CANSAT78G2478' => 'cansat', 'CARHR098700' => 'chi', 'CARHR221120' => 'chi', 'CARHR221150' => 'chi', 'Carub.0003s2297' => 'cru', 'Carub.0007s2749' => 'cru', 'Carub.0007s2750' => 'cru', 'Carub.0007s2751' => 'cru', 'Ca_10849_v3' => 'car', 'Cc03_g04300' => 'ccan', 'CDE02G3648' => 'cde', 'CDE05G0060' => 'cde', 'CDE05G0692' => 'cde', 'CDE05G2285' => 'cde', 'CDE05G2884' => 'cde', 'CDE05G3072' => 'cde', 'Cfa008439' => 'cfa', 'Cfa008441' => 'cfa', 'Cfa008443' => 'cfa', 'Cfa008448' => 'cfa', 'Ciclev10005974m.g' => 'ccl', 'Ciclev10006006m.g' => 'ccl', 'Ciclev10006775m.g' => 'ccl', 'CiPaw.02G120400' => 'cil', 'CiPaw.02G120500' => 'cil', 'CiPaw.02G120600' => 'cil', 'ClCG05G004850' => 'cla', 'COL.COLO4_21566' => 'col', 'Cpa.g.sc44.124' => 'cpa', 'Cre07.g320400' => 'cre', 'Cre07.g320450' => 'cre', 'Cre08.g384650' => 'cre', 'Cre09.g393173' => 'cre', 'Cre09.g394325' => 'cre', 'Cre14.g626750' => 'cre', 'Cre16.g679250' => 'cre', 'CsaV3_3G012890' => 'csa', 'CSS0010865' => 'camsi', 'CSS0044338' => 'camsi', 'DCAR_002366' => 'dca', 'DCAR_030687' => 'dca', 'DCAR_030688' => 'dca', 'Dinv14047' => 'din', 'Dinv14048' => 'din', 'Duzib151G0105' => 'dzi', 'Duzib151G0114' => 'dzi', 'Duzib212G1029' => 'dzi', 'ECA232G3536' => 'eca', 'ECA240G0786' => 'eca', 'ECA240G1802' => 'eca', 'ECA240G3760' => 'eca', 'ECA240G3920' => 'eca', 'EL10Ac5g12536' => 'bvu', 'EL10Ac5g12537' => 'bvu', 'EL10Ac5g12538' => 'bvu', 'Eucgr.B01004' => 'egr', 'Eucgr.B01006' => 'egr', 'Eucgr.B01007' => 'egr', 'Eucgr.B01008' => 'egr', 'Eucgr.B01895' => 'egr', 'Eucgr.B01896' => 'egr', 'FAN04G1456' => 'fan', 'FAN08G1769' => 'fan', 'FAN08G2160' => 'fan', 'FAN13G2403' => 'fan', 'FAN13G3303' => 'fan', 'FAN15G2435' => 'fan', 'FAN17G0672' => 'fan', 'FAN17G2441' => 'fan', 'FAN18G1024' => 'fan', 'FAN22G1458' => 'fan', 'FAN24G0037' => 'fan', 'FAN24G0429' => 'fan', 'FAN24G2387' => 'fan', 'FAN27G2746' => 'fan', 'FvH4_2g20400' => 'fve', 'FvH4_2g20420' => 'fve', 'FvH4_2g20430' => 'fve', 'FvH4_4g01270' => 'fve', 'FvH4_4g01290' => 'fve', 'FvH4_4g01300' => 'fve', 'FvH4_4g01310' => 'fve', 'FvH4_4g01330' => 'fve', 'FvH4_5g09070' => 'fve', 'Glyma.10G243800' => 'gma', 'Glyma.20G150600' => 'gma', 'Gohir.A09G219200' => 'ghi', 'Gohir.A09G219300' => 'ghi', 'Gohir.D09G221400' => 'ghi', 'Gohir.D09G221500' => 'ghi', 'Gorai.006G242600' => 'gra', 'Gorai.006G242700' => 'gra', 'GSVIVG01018044001' => 'vvi', 'HanXRQChr03g0083821' => 'han', 'HanXRQChr03g0083841' => 'han', 'HanXRQChr03g0083881' => 'han', 'HanXRQChr03g0083901' => 'han', 'HanXRQChr03g0083921' => 'han', 'HanXRQChr03g0085331' => 'han', 'HanXRQChr03g0085361' => 'han', 'HanXRQChr03g0085411' => 'han', 'HanXRQChr03g0085421' => 'han', 'HanXRQChr03g0085431' => 'han', 'HanXRQChr08g0221991' => 'han', 'HanXRQChr11g0336061' => 'han', 'HanXRQChr11g0336411' => 'han', 'Haze_11234' => 'cav', 'Hma1.2p1_0549F.1_g177010' => 'hma', 'Hma1.2p1_0602F.1_g187630' => 'hma', 'Hund14876' => 'sun', 'Hund14879' => 'sun', 'Lalb_Chr06g0160741' => 'lal', 'Lalb_Chr21g0304781' => 'lal', 'Lj3A726G19' => 'lonja', 'Lj3A726T23' => 'lonja', 'Lj3A726T24' => 'lonja', 'Lj3A726T25' => 'lonja', 'Lj3A727T17' => 'lonja', 'Lj3C726T0' => 'lonja', 'Lj3C726T2' => 'lonja', 'Lj3P725T35' => 'lonja', 'Lj3P727T10' => 'lonja', 'Lj3P727T12' => 'lonja', 'Lj3P727T14' => 'lonja', 'Lj5g0023109' => 'lja', 'Lj6P646T44' => 'lonja', 'Lsat_1_v5_gn_6_75760' => 'lsa', 'Lsat_1_v5_gn_6_75800' => 'lsa', 'Lsat_1_v5_gn_6_75900' => 'lsa', 'Lsat_1_v5_gn_6_76240' => 'lsa', 'Lsat_1_v5_gn_6_76441' => 'lsa', 'Lsat_1_v5_gn_6_76700' => 'lsa', 'Lsat_1_v5_gn_6_76760' => 'lsa', 'Manes.15G033100' => 'mes', 'Mapoly0004s0074' => 'mpo', 'Mapoly0004s0075' => 'mpo', 'Mapoly0004s0163' => 'mpo', 'Mapoly0004s0164' => 'mpo', 'Mapoly0021s0018' => 'mpo', 'Mapoly0041s0136' => 'mpo', 'Mapoly0041s0137' => 'mpo', 'Mapoly0041s0138' => 'mpo', 'Mapoly0041s0139' => 'mpo', 'Mapoly0041s0141' => 'mpo', 'Mapoly0041s0142' => 'mpo', 'Mapoly0041s0143' => 'mpo', 'Mapoly0041s0144' => 'mpo', 'Mapoly0041s0145' => 'mpo', 'Mapoly0047s0106' => 'mpo', 'Mapoly0047s0108' => 'mpo', 'Mapoly0050s0051' => 'mpo', 'Mapoly0050s0052' => 'mpo', 'Mapoly0050s0053' => 'mpo', 'Mapoly0058s0013' => 'mpo', 'Mapoly0091s0078' => 'mpo', 'Mapoly0091s0079' => 'mpo', 'Mapoly0091s0080' => 'mpo', 'Mapoly0091s0081' => 'mpo', 'Mapoly0278s0004' => 'mpo', 'Mapoly0278s0005' => 'mpo', 'Mapoly0278s0006' => 'mpo', 'MBI11_g30648_MAGBIO' => 'mbi', 'MCO03G194' => 'mco', 'MCO03G590' => 'mco', 'MCO07G312' => 'mco', 'MCO10G318' => 'mco', 'MCO12G244' => 'mco', 'MCO13G148' => 'mco', 'MCO13G194' => 'mco', 'MCO16G238' => 'mco', 'MD06G1134100' => 'mdo', 'MD13G1200100' => 'mdo', 'MD13G1200300' => 'mdo', 'MD13G1200600' => 'mdo', 'MD14G1150400' => 'mdo', 'MD16G1200000' => 'mdo', 'Medtr1g102570' => 'mtr', 'Medtr1g102780' => 'mtr', 'Medtr1g102800' => 'mtr', 'Medtr1g102810' => 'mtr', 'Medtr1g102830' => 'mtr', 'MELO3C006499.2' => 'cme', 'Migut.G00385' => 'egut', 'MSTRG.4063' => 'ama', 'Nitab4.5_0000090g0260' => 'nta', 'Nitab4.5_0000977g0030' => 'nta', 'Nitab4.5_0002541g0040' => 'nta', 'Nitab4.5_0007068g0040' => 'nta', 'Nn005s41408' => 'nnu', 'Nn005s41410' => 'nnu', 'Oeu010310.1' => 'oeu', 'Oeu010311.1' => 'oeu', 'Oeu043472.1' => 'oeu', 'Os01g0246400' => 'osa', 'Os04g0267950' => 'osa', 'Os07g0178700' => 'osa', 'Os07g0178800' => 'osa', 'Peaxi162Scf00316g00046' => 'pax', 'Peaxi162Scf00316g00049' => 'pax', 'Peaxi162Scf00316g00059' => 'pax', 'Peaxi162Scf00316g00328' => 'pax', 'Peaxi162Scf00316g00329' => 'pax', 'Peaxi162Scf00316g00411' => 'pax', 'Peaxi162Scf00316g00521' => 'pax', 'Peaxi162Scf00492g00068' => 'pax', 'Peaxi162Scf35631g00002' => 'pax', 'PGR142G3720' => 'pgr', 'PGSC0003DMG400006442' => 'stu', 'Phvul.007G062000' => 'pvu', 'Potri.008G157750' => 'ptr', 'Potri.008G157900' => 'ptr', 'Potri.008G158000' => 'ptr', 'Potri.008G158200' => 'ptr', 'Pp3c11_7280' => 'ppa', 'Pp3c11_7980' => 'ppa', 'Pp3c12_19450' => 'ppa', 'Pp3c14_1480' => 'ppa', 'Pp3c14_1501' => 'ppa', 'Pp3c16_4900' => 'ppa', 'Pp3c16_5010' => 'ppa', 'Pp3c16_5060' => 'ppa', 'Pp3c19_18250' => 'ppa', 'Pp3c23_8530' => 'ppa', 'Pp3c23_8550' => 'ppa', 'Pp3c24_9670' => 'ppa', 'Pp3c2_21390' => 'ppa', 'Pp3c2_31380' => 'ppa', 'Pp3c3_16620' => 'ppa', 'Pp3c3_8090' => 'ppa', 'Pp3c3_8110' => 'ppa', 'Pp3c3_8130' => 'ppa', 'Pp3c3_8150' => 'ppa', 'Pp3c4_14320' => 'ppa', 'Pp3c6_2560' => 'ppa', 'Pp3c9_16700' => 'ppa', 'PRCOL_00000234' => 'pco', 'PRCOL_00000235' => 'pco', 'PRCOL_00000777' => 'pco', 'PRCOL_00002344' => 'pco', 'PRCOL_00002372' => 'pco', 'PRCOL_00006120' => 'pco', 'Prupe.1G021400' => 'ppe', 'Prupe.1G021500' => 'ppe', 'Prupe.1G021600' => 'ppe', 'Prupe.1G021700' => 'ppe', 'Prupe.1G021800' => 'ppe', 'Prupe.5G145100' => 'ppe', 'Psat6g204040' => 'psa', 'Psat6g204800' => 'psa', 'Psat6g204920' => 'psa', 'Psat6g204960' => 'psa', 'Psat6g205080' => 'psa', 'PSO017G0271' => 'pso', 'PSO017G1276' => 'pso', 'PSO017G1429' => 'pso', 'PSO017G1861' => 'pso', 'PSO017G2787' => 'pso', 'PSO017G4466' => 'pso', 'PSO017G5118' => 'pso', 'PSO017G5420' => 'pso', 'PSO063G3678' => 'pso', 'PSO210G0546' => 'pso', 'PSO317G0001' => 'pso', 'PSO357G0512' => 'pso', 'PSO478G2682' => 'pso', 'PSO647G0001' => 'pso', 'PSO675G0001' => 'pso', 'PSO675G2699' => 'pso', 'PSO675G2849' => 'pso', 'PSO675G4991' => 'pso', 'PSO689G0001' => 'pso', 'QL06p000916' => 'qlo', 'QL06p000921' => 'qlo', 'QL06p001398' => 'qlo', 'QL06p001407' => 'qlo', 'QL06p002031' => 'qlo', 'RcHm_v2.0_Chr4g0387791' => 'rch', 'RcHm_v2.0_Chr4g0387801' => 'rch', 'RcHm_v2.0_Chr6g0286501' => 'rch', 'RcHm_v2.0_Chr6g0286511' => 'rch', 'RcHm_v2.0_Chr6g0286521' => 'rch', 'RcHm_v2.0_Chr6g0286531' => 'rch', 'RcHm_v2.0_Chr7g0189141' => 'rch', 'Rhsim02G0028700' => 'rsi', 'Rhsim02G0028800' => 'rsi', 'Rhsim02G0028900' => 'rsi', 'Rhsim02G0029000' => 'rsi', 'Rhsim02G0029100' => 'rsi', 'Rhsim02G0029200' => 'rsi', 'Rhsim02G0029300' => 'rsi', 'Rhsim02G0029400' => 'rsi', 'Rhsim02G0029500' => 'rsi', 'Rhsim02G0029600' => 'rsi', 'RhsimUnG0024000' => 'rsi', 'RhsimUnG0024100' => 'rsi', 'RhsimUnG0024200' => 'rsi', 'RhsimUnG0024300' => 'rsi', 'RhsimUnG0024400' => 'rsi', 'RhsimUnG0024500' => 'rsi', 'RhsimUnG0024700' => 'rsi', 'RhsimUnG0024800' => 'rsi', 'RhsimUnG0024900' => 'rsi', 'RhsimUnG0025100' => 'rsi', 'Sabra08G0120200' => 'sbr', 'Sabra08G0120300' => 'sbr', 'Sabra08G0120500' => 'sbr', 'Sabra08G0120600' => 'sbr', 'Sabra10G0158900' => 'sbr', 'SalBow2G3492' => 'sbo', 'Sc13g0004760' => 'sci', 'Sc13g0004770' => 'sci', 'Sed0003417' => 'sed', 'Sed0019750' => 'sed', 'SEGI_03419' => 'sgi', 'SEGI_05907' => 'sgi', 'SEGI_10682' => 'sgi', 'SEGI_13528' => 'sgi', 'SEGI_16081' => 'sgi', 'SEGI_19370' => 'sgi', 'SEGI_21015' => 'sgi', 'SEGI_21944' => 'sgi', 'SEGI_32906' => 'sgi', 'SEGI_33093' => 'sgi', 'SEGI_36110' => 'sgi', 'SEGI_40397' => 'sgi', 'SGA_v2.0_scaffold191G40426' => 'sas', 'SGA_v2.0_scaffold353G49717' => 'sas', 'SGA_v2.0_scaffold50G18550' => 'sas', 'SMO119G0173' => 'smo', 'SMO172G0002' => 'smo', 'Solyc09g082690.3' => 'sly', 'Solyc09g082700.2' => 'sly', 'Sopen09g031550' => 'spe', 'Sopen09g031560' => 'spe', 'Sp3g20540' => 'spa', 'Sp7g07580' => 'spa', 'TAR134G0002' => 'tar', 'TAR236G0001' => 'tar', 'TAR365G0892' => 'tar', 'TAR636G0166' => 'tar', 'TAR636G0646' => 'tar', 'TAR636G0869' => 'tar', 'TAR636G1317' => 'tar', 'TAR636G1744' => 'tar', 'TAR636G3358' => 'tar', 'TAR636G3436' => 'tar', 'THA.LOC104803047' => 'tha', 'Thecc.04G238900' => 'tca', 'Thhalv10021557m.g' => 'esa', 'Thhalv10026318m.g' => 'esa', 'Thhalv10026335m.g' => 'esa', 'TPR.G17433' => 'tpr', 'TPR.G18915' => 'tpr', 'TPR.G26125' => 'tpr', 'TWI09G0677' => 'twi', 'TWI73G0287' => 'twi', 'unitig_748.g8326' => 'ugi', 'vmacro15370' => 'vma', 'vmacro15371' => 'vma', 'vmacro15372' => 'vma', 'vmacro15373' => 'vma', 'vmacro15374' => 'vma', 'VMungo0720G2826' => 'vmu', 'Zm00001eb116960' => 'zma', 'Zm00001eb301260' => 'zma', 'Zm00001eb301270' => 'zma' ), 'gf_id' => 'HOM05D001460', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001460' ), 'data_identifier' => 'HOM05D001460', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001460', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '433', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p22980' => 'bna', 'A01p32340' => 'bna', 'A03p42970' => 'bna', 'A05p25880' => 'bna', 'Aa31LG8G9320' => 'aar', 'Aa31LG8G9330' => 'aar', 'Aa31LG8G9340' => 'aar', 'Aa31sc221G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1034' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1528' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.829' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2222' => 'aag', 'Ah.12g058830' => 'amhyb', 'Ah.12g058840' => 'amhyb', 'AL3G37160' => 'aly', 'AL7G41310' => 'aly', 'Aqoxy5G00395' => 'aox', 'Aqoxy5G00396' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0C8NZA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5185HY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JZ1PRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MD3LS0' => 'arhy', 'AT3G22840' => 'ath', 'AT4G14690' => 'ath', 'ATR0665G054' => 'atr', 'Atru.chr4.2344' => 'acertr', 'Atru.chr4.2346' => 'acertr', 'Atru.chr4.2347' => 'acertr', 'Atru.chr4.2348' => 'acertr', 'Atru.chr4.2355' => 'acertr', 'Atru.chr4.2356' => 'acertr', 'Atru.chr4.2358' => 'acertr', 'Atru.chr4.2359' => 'acertr', 'Atru.chr4.2360' => 'acertr', 'Atru.chr4.2361' => 'acertr', 'AUR62030476' => 'cqu', 'AUR62030478' => 'cqu', 'AUR62030819' => 'cqu', 'AUR62030820' => 'cqu', 'BcaB03g14648' => 'bca', 'BcaB04g20492' => 'bca', 'BcaB06g26399' => 'bca', 'BcaC01g03416' => 'bca', 'BcaC01g03419' => 'bca', 'BcaC01g03421' => 'bca', 'BcaC01g03424' => 'bca', 'BcaC05g28012' => 'bca', 'BcaC09g49212' => 'bca', 'BcaC09g50140' => 'bca', 'BcaNung00346' => 'bca', 'BolC1t02785H' => 'bol', 'BolC1t04095H' => 'bol', 'BolC3t17545H' => 'bol', 'BolC5t32769H' => 'bol', 'BraA01t02211Z' => 'bra', 'BraA01t03359Z' => 'bra', 'BraA03t13441Z' => 'bra', 'BraA05t21476Z' => 'bra', 'C01p28420' => 'bna', 'C01p41350' => 'bna', 'C03p52750' => 'bna', 'C03p52780' => 'bna', 'C05p40270' => 'bna', 'CAN.G1437.9' => 'can', 'CANSAT78G0035' => 'cansat', 'CANSAT78G1036' => 'cansat', 'CANSAT78G2272' => 'cansat', 'CANSAT78G2478' => 'cansat', 'CARHR098700' => 'chi', 'CARHR221120' => 'chi', 'CARHR221150' => 'chi', 'Carub.0003s2297' => 'cru', 'Carub.0007s2749' => 'cru', 'Carub.0007s2750' => 'cru', 'Carub.0007s2751' => 'cru', 'Ca_10849_v3' => 'car', 'Cc03_g04300' => 'ccan', 'CDE02G3648' => 'cde', 'CDE05G0060' => 'cde', 'CDE05G0692' => 'cde', 'CDE05G2285' => 'cde', 'CDE05G2884' => 'cde', 'CDE05G3072' => 'cde', 'Cfa008439' => 'cfa', 'Cfa008441' => 'cfa', 'Cfa008443' => 'cfa', 'Cfa008448' => 'cfa', 'Ciclev10005974m.g' => 'ccl', 'Ciclev10006006m.g' => 'ccl', 'Ciclev10006775m.g' => 'ccl', 'CiPaw.02G120400' => 'cil', 'CiPaw.02G120500' => 'cil', 'CiPaw.02G120600' => 'cil', 'ClCG05G004850' => 'cla', 'COL.COLO4_21566' => 'col', 'Cpa.g.sc44.124' => 'cpa', 'Cre07.g320400' => 'cre', 'Cre07.g320450' => 'cre', 'Cre08.g384650' => 'cre', 'Cre09.g393173' => 'cre', 'Cre09.g394325' => 'cre', 'Cre14.g626750' => 'cre', 'Cre16.g679250' => 'cre', 'CsaV3_3G012890' => 'csa', 'CSS0010865' => 'camsi', 'CSS0044338' => 'camsi', 'DCAR_002366' => 'dca', 'DCAR_030687' => 'dca', 'DCAR_030688' => 'dca', 'Dinv14047' => 'din', 'Dinv14048' => 'din', 'Duzib151G0105' => 'dzi', 'Duzib151G0114' => 'dzi', 'Duzib212G1029' => 'dzi', 'ECA232G3536' => 'eca', 'ECA240G0786' => 'eca', 'ECA240G1802' => 'eca', 'ECA240G3760' => 'eca', 'ECA240G3920' => 'eca', 'EL10Ac5g12536' => 'bvu', 'EL10Ac5g12537' => 'bvu', 'EL10Ac5g12538' => 'bvu', 'Eucgr.B01004' => 'egr', 'Eucgr.B01006' => 'egr', 'Eucgr.B01007' => 'egr', 'Eucgr.B01008' => 'egr', 'Eucgr.B01895' => 'egr', 'Eucgr.B01896' => 'egr', 'FAN04G1456' => 'fan', 'FAN08G1769' => 'fan', 'FAN08G2160' => 'fan', 'FAN13G2403' => 'fan', 'FAN13G3303' => 'fan', 'FAN15G2435' => 'fan', 'FAN17G0672' => 'fan', 'FAN17G2441' => 'fan', 'FAN18G1024' => 'fan', 'FAN22G1458' => 'fan', 'FAN24G0037' => 'fan', 'FAN24G0429' => 'fan', 'FAN24G2387' => 'fan', 'FAN27G2746' => 'fan', 'FvH4_2g20400' => 'fve', 'FvH4_2g20420' => 'fve', 'FvH4_2g20430' => 'fve', 'FvH4_4g01270' => 'fve', 'FvH4_4g01290' => 'fve', 'FvH4_4g01300' => 'fve', 'FvH4_4g01310' => 'fve', 'FvH4_4g01330' => 'fve', 'FvH4_5g09070' => 'fve', 'Glyma.10G243800' => 'gma', 'Glyma.20G150600' => 'gma', 'Gohir.A09G219200' => 'ghi', 'Gohir.A09G219300' => 'ghi', 'Gohir.D09G221400' => 'ghi', 'Gohir.D09G221500' => 'ghi', 'Gorai.006G242600' => 'gra', 'Gorai.006G242700' => 'gra', 'GSVIVG01018044001' => 'vvi', 'HanXRQChr03g0083821' => 'han', 'HanXRQChr03g0083841' => 'han', 'HanXRQChr03g0083881' => 'han', 'HanXRQChr03g0083901' => 'han', 'HanXRQChr03g0083921' => 'han', 'HanXRQChr03g0085331' => 'han', 'HanXRQChr03g0085361' => 'han', 'HanXRQChr03g0085411' => 'han', 'HanXRQChr03g0085421' => 'han', 'HanXRQChr03g0085431' => 'han', 'HanXRQChr08g0221991' => 'han', 'HanXRQChr11g0336061' => 'han', 'HanXRQChr11g0336411' => 'han', 'Haze_11234' => 'cav', 'Hma1.2p1_0549F.1_g177010' => 'hma', 'Hma1.2p1_0602F.1_g187630' => 'hma', 'Hund14876' => 'sun', 'Hund14879' => 'sun', 'Lalb_Chr06g0160741' => 'lal', 'Lalb_Chr21g0304781' => 'lal', 'Lj3A726G19' => 'lonja', 'Lj3A726T23' => 'lonja', 'Lj3A726T24' => 'lonja', 'Lj3A726T25' => 'lonja', 'Lj3A727T17' => 'lonja', 'Lj3C726T0' => 'lonja', 'Lj3C726T2' => 'lonja', 'Lj3P725T35' => 'lonja', 'Lj3P727T10' => 'lonja', 'Lj3P727T12' => 'lonja', 'Lj3P727T14' => 'lonja', 'Lj5g0023109' => 'lja', 'Lj6P646T44' => 'lonja', 'Lsat_1_v5_gn_6_75760' => 'lsa', 'Lsat_1_v5_gn_6_75800' => 'lsa', 'Lsat_1_v5_gn_6_75900' => 'lsa', 'Lsat_1_v5_gn_6_76240' => 'lsa', 'Lsat_1_v5_gn_6_76441' => 'lsa', 'Lsat_1_v5_gn_6_76700' => 'lsa', 'Lsat_1_v5_gn_6_76760' => 'lsa', 'Manes.15G033100' => 'mes', 'Mapoly0004s0074' => 'mpo', 'Mapoly0004s0075' => 'mpo', 'Mapoly0004s0163' => 'mpo', 'Mapoly0004s0164' => 'mpo', 'Mapoly0021s0018' => 'mpo', 'Mapoly0041s0136' => 'mpo', 'Mapoly0041s0137' => 'mpo', 'Mapoly0041s0138' => 'mpo', 'Mapoly0041s0139' => 'mpo', 'Mapoly0041s0141' => 'mpo', 'Mapoly0041s0142' => 'mpo', 'Mapoly0041s0143' => 'mpo', 'Mapoly0041s0144' => 'mpo', 'Mapoly0041s0145' => 'mpo', 'Mapoly0047s0106' => 'mpo', 'Mapoly0047s0108' => 'mpo', 'Mapoly0050s0051' => 'mpo', 'Mapoly0050s0052' => 'mpo', 'Mapoly0050s0053' => 'mpo', 'Mapoly0058s0013' => 'mpo', 'Mapoly0091s0078' => 'mpo', 'Mapoly0091s0079' => 'mpo', 'Mapoly0091s0080' => 'mpo', 'Mapoly0091s0081' => 'mpo', 'Mapoly0278s0004' => 'mpo', 'Mapoly0278s0005' => 'mpo', 'Mapoly0278s0006' => 'mpo', 'MBI11_g30648_MAGBIO' => 'mbi', 'MCO03G194' => 'mco', 'MCO03G590' => 'mco', 'MCO07G312' => 'mco', 'MCO10G318' => 'mco', 'MCO12G244' => 'mco', 'MCO13G148' => 'mco', 'MCO13G194' => 'mco', 'MCO16G238' => 'mco', 'MD06G1134100' => 'mdo', 'MD13G1200100' => 'mdo', 'MD13G1200300' => 'mdo', 'MD13G1200600' => 'mdo', 'MD14G1150400' => 'mdo', 'MD16G1200000' => 'mdo', 'Medtr1g102570' => 'mtr', 'Medtr1g102780' => 'mtr', 'Medtr1g102800' => 'mtr', 'Medtr1g102810' => 'mtr', 'Medtr1g102830' => 'mtr', 'MELO3C006499.2' => 'cme', 'Migut.G00385' => 'egut', 'MSTRG.4063' => 'ama', 'Nitab4.5_0000090g0260' => 'nta', 'Nitab4.5_0000977g0030' => 'nta', 'Nitab4.5_0002541g0040' => 'nta', 'Nitab4.5_0007068g0040' => 'nta', 'Nn005s41408' => 'nnu', 'Nn005s41410' => 'nnu', 'Oeu010310.1' => 'oeu', 'Oeu010311.1' => 'oeu', 'Oeu043472.1' => 'oeu', 'Os01g0246400' => 'osa', 'Os04g0267950' => 'osa', 'Os07g0178700' => 'osa', 'Os07g0178800' => 'osa', 'Peaxi162Scf00316g00046' => 'pax', 'Peaxi162Scf00316g00049' => 'pax', 'Peaxi162Scf00316g00059' => 'pax', 'Peaxi162Scf00316g00328' => 'pax', 'Peaxi162Scf00316g00329' => 'pax', 'Peaxi162Scf00316g00411' => 'pax', 'Peaxi162Scf00316g00521' => 'pax', 'Peaxi162Scf00492g00068' => 'pax', 'Peaxi162Scf35631g00002' => 'pax', 'PGR142G3720' => 'pgr', 'PGSC0003DMG400006442' => 'stu', 'Phvul.007G062000' => 'pvu', 'Potri.008G157750' => 'ptr', 'Potri.008G157900' => 'ptr', 'Potri.008G158000' => 'ptr', 'Potri.008G158200' => 'ptr', 'Pp3c11_7280' => 'ppa', 'Pp3c11_7980' => 'ppa', 'Pp3c12_19450' => 'ppa', 'Pp3c14_1480' => 'ppa', 'Pp3c14_1501' => 'ppa', 'Pp3c16_4900' => 'ppa', 'Pp3c16_5010' => 'ppa', 'Pp3c16_5060' => 'ppa', 'Pp3c19_18250' => 'ppa', 'Pp3c23_8530' => 'ppa', 'Pp3c23_8550' => 'ppa', 'Pp3c24_9670' => 'ppa', 'Pp3c2_21390' => 'ppa', 'Pp3c2_31380' => 'ppa', 'Pp3c3_16620' => 'ppa', 'Pp3c3_8090' => 'ppa', 'Pp3c3_8110' => 'ppa', 'Pp3c3_8130' => 'ppa', 'Pp3c3_8150' => 'ppa', 'Pp3c4_14320' => 'ppa', 'Pp3c6_2560' => 'ppa', 'Pp3c9_16700' => 'ppa', 'PRCOL_00000234' => 'pco', 'PRCOL_00000235' => 'pco', 'PRCOL_00000777' => 'pco', 'PRCOL_00002344' => 'pco', 'PRCOL_00002372' => 'pco', 'PRCOL_00006120' => 'pco', 'Prupe.1G021400' => 'ppe', 'Prupe.1G021500' => 'ppe', 'Prupe.1G021600' => 'ppe', 'Prupe.1G021700' => 'ppe', 'Prupe.1G021800' => 'ppe', 'Prupe.5G145100' => 'ppe', 'Psat6g204040' => 'psa', 'Psat6g204800' => 'psa', 'Psat6g204920' => 'psa', 'Psat6g204960' => 'psa', 'Psat6g205080' => 'psa', 'PSO017G0271' => 'pso', 'PSO017G1276' => 'pso', 'PSO017G1429' => 'pso', 'PSO017G1861' => 'pso', 'PSO017G2787' => 'pso', 'PSO017G4466' => 'pso', 'PSO017G5118' => 'pso', 'PSO017G5420' => 'pso', 'PSO063G3678' => 'pso', 'PSO210G0546' => 'pso', 'PSO317G0001' => 'pso', 'PSO357G0512' => 'pso', 'PSO478G2682' => 'pso', 'PSO647G0001' => 'pso', 'PSO675G0001' => 'pso', 'PSO675G2699' => 'pso', 'PSO675G2849' => 'pso', 'PSO675G4991' => 'pso', 'PSO689G0001' => 'pso', 'QL06p000916' => 'qlo', 'QL06p000921' => 'qlo', 'QL06p001398' => 'qlo', 'QL06p001407' => 'qlo', 'QL06p002031' => 'qlo', 'RcHm_v2.0_Chr4g0387791' => 'rch', 'RcHm_v2.0_Chr4g0387801' => 'rch', 'RcHm_v2.0_Chr6g0286501' => 'rch', 'RcHm_v2.0_Chr6g0286511' => 'rch', 'RcHm_v2.0_Chr6g0286521' => 'rch', 'RcHm_v2.0_Chr6g0286531' => 'rch', 'RcHm_v2.0_Chr7g0189141' => 'rch', 'Rhsim02G0028700' => 'rsi', 'Rhsim02G0028800' => 'rsi', 'Rhsim02G0028900' => 'rsi', 'Rhsim02G0029000' => 'rsi', 'Rhsim02G0029100' => 'rsi', 'Rhsim02G0029200' => 'rsi', 'Rhsim02G0029300' => 'rsi', 'Rhsim02G0029400' => 'rsi', 'Rhsim02G0029500' => 'rsi', 'Rhsim02G0029600' => 'rsi', 'RhsimUnG0024000' => 'rsi', 'RhsimUnG0024100' => 'rsi', 'RhsimUnG0024200' => 'rsi', 'RhsimUnG0024300' => 'rsi', 'RhsimUnG0024400' => 'rsi', 'RhsimUnG0024500' => 'rsi', 'RhsimUnG0024700' => 'rsi', 'RhsimUnG0024800' => 'rsi', 'RhsimUnG0024900' => 'rsi', 'RhsimUnG0025100' => 'rsi', 'Sabra08G0120200' => 'sbr', 'Sabra08G0120300' => 'sbr', 'Sabra08G0120500' => 'sbr', 'Sabra08G0120600' => 'sbr', 'Sabra10G0158900' => 'sbr', 'SalBow2G3492' => 'sbo', 'Sc13g0004760' => 'sci', 'Sc13g0004770' => 'sci', 'Sed0003417' => 'sed', 'Sed0019750' => 'sed', 'SEGI_03419' => 'sgi', 'SEGI_05907' => 'sgi', 'SEGI_10682' => 'sgi', 'SEGI_13528' => 'sgi', 'SEGI_16081' => 'sgi', 'SEGI_19370' => 'sgi', 'SEGI_21015' => 'sgi', 'SEGI_21944' => 'sgi', 'SEGI_32906' => 'sgi', 'SEGI_33093' => 'sgi', 'SEGI_36110' => 'sgi', 'SEGI_40397' => 'sgi', 'SGA_v2.0_scaffold191G40426' => 'sas', 'SGA_v2.0_scaffold353G49717' => 'sas', 'SGA_v2.0_scaffold50G18550' => 'sas', 'SMO119G0173' => 'smo', 'SMO172G0002' => 'smo', 'Solyc09g082690.3' => 'sly', 'Solyc09g082700.2' => 'sly', 'Sopen09g031550' => 'spe', 'Sopen09g031560' => 'spe', 'Sp3g20540' => 'spa', 'Sp7g07580' => 'spa', 'TAR134G0002' => 'tar', 'TAR236G0001' => 'tar', 'TAR365G0892' => 'tar', 'TAR636G0166' => 'tar', 'TAR636G0646' => 'tar', 'TAR636G0869' => 'tar', 'TAR636G1317' => 'tar', 'TAR636G1744' => 'tar', 'TAR636G3358' => 'tar', 'TAR636G3436' => 'tar', 'THA.LOC104803047' => 'tha', 'Thecc.04G238900' => 'tca', 'Thhalv10021557m.g' => 'esa', 'Thhalv10026318m.g' => 'esa', 'Thhalv10026335m.g' => 'esa', 'TPR.G17433' => 'tpr', 'TPR.G18915' => 'tpr', 'TPR.G26125' => 'tpr', 'TWI09G0677' => 'twi', 'TWI73G0287' => 'twi', 'unitig_748.g8326' => 'ugi', 'vmacro15370' => 'vma', 'vmacro15371' => 'vma', 'vmacro15372' => 'vma', 'vmacro15373' => 'vma', 'vmacro15374' => 'vma', 'VMungo0720G2826' => 'vmu', 'Zm00001eb116960' => 'zma', 'Zm00001eb301260' => 'zma', 'Zm00001eb301270' => 'zma' ) $gf_id = 'HOM05D001460' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001460' ) $data_identifier = 'HOM05D001460' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 4, 'aag' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 2, 'aox' => (int) 2, 'arhy' => (int) 4, 'ath' => (int) 2, 'atr' => (int) 1, 'acertr' => (int) 10, 'cqu' => (int) 4, 'bca' => (int) 11, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 1, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 1, 'ccan' => (int) 1, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 1, 'col' => (int) 1, 'cpa' => (int) 1, 'cre' => (int) 7, 'csa' => (int) 1, 'camsi' => (int) 2, 'dca' => (int) 3, 'din' => (int) 2, 'dzi' => (int) 3, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 14, 'fve' => (int) 9, 'gma' => (int) 2, 'ghi' => (int) 4, 'gra' => (int) 2, 'vvi' => (int) 1, 'han' => (int) 13, 'cav' => (int) 1, 'hma' => (int) 2, 'sun' => (int) 2, 'lal' => (int) 2, 'lonja' => (int) 12, 'lja' => (int) 1, 'lsa' => (int) 7, 'mes' => (int) 1, 'mpo' => (int) 27, 'mbi' => (int) 1, 'mco' => (int) 8, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 1, 'egut' => (int) 1, 'ama' => (int) 1, 'nta' => (int) 4, 'nnu' => (int) 2, 'oeu' => (int) 3, 'osa' => (int) 4, 'pax' => (int) 9, 'pgr' => (int) 1, 'stu' => (int) 1, 'pvu' => (int) 1, 'ptr' => (int) 4, 'ppa' => (int) 22, 'pco' => (int) 6, 'ppe' => (int) 6, 'psa' => (int) 5, 'pso' => (int) 19, 'qlo' => (int) 5, 'rch' => (int) 7, 'rsi' => (int) 20, 'sbr' => (int) 5, 'sbo' => (int) 1, 'sci' => (int) 2, 'sed' => (int) 2, 'sgi' => (int) 12, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 2, 'tar' => (int) 10, 'tha' => (int) 1, 'tca' => (int) 1, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 2, 'ugi' => (int) 1, 'vma' => (int) 5, 'vmu' => (int) 1, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb301270' $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' => 'HOM05D001460', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '433', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p22980' => 'bna', 'A01p32340' => 'bna', 'A03p42970' => 'bna', 'A05p25880' => 'bna', 'Aa31LG8G9320' => 'aar', 'Aa31LG8G9330' => 'aar', 'Aa31LG8G9340' => 'aar', 'Aa31sc221G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1034' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1528' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.829' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2222' => 'aag', 'Ah.12g058830' => 'amhyb', 'Ah.12g058840' => 'amhyb', 'AL3G37160' => 'aly', 'AL7G41310' => 'aly', 'Aqoxy5G00395' => 'aox', 'Aqoxy5G00396' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0C8NZA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5185HY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JZ1PRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MD3LS0' => 'arhy', 'AT3G22840' => 'ath', 'AT4G14690' => 'ath', 'ATR0665G054' => 'atr', 'Atru.chr4.2344' => 'acertr', 'Atru.chr4.2346' => 'acertr', 'Atru.chr4.2347' => 'acertr', 'Atru.chr4.2348' => 'acertr', 'Atru.chr4.2355' => 'acertr', 'Atru.chr4.2356' => 'acertr', 'Atru.chr4.2358' => 'acertr', 'Atru.chr4.2359' => 'acertr', 'Atru.chr4.2360' => 'acertr', 'Atru.chr4.2361' => 'acertr', 'AUR62030476' => 'cqu', 'AUR62030478' => 'cqu', 'AUR62030819' => 'cqu', 'AUR62030820' => 'cqu', 'BcaB03g14648' => 'bca', 'BcaB04g20492' => 'bca', 'BcaB06g26399' => 'bca', 'BcaC01g03416' => 'bca', 'BcaC01g03419' => 'bca', 'BcaC01g03421' => 'bca', 'BcaC01g03424' => 'bca', 'BcaC05g28012' => 'bca', 'BcaC09g49212' => 'bca', 'BcaC09g50140' => 'bca', 'BcaNung00346' => 'bca', 'BolC1t02785H' => 'bol', 'BolC1t04095H' => 'bol', 'BolC3t17545H' => 'bol', 'BolC5t32769H' => 'bol', 'BraA01t02211Z' => 'bra', 'BraA01t03359Z' => 'bra', 'BraA03t13441Z' => 'bra', 'BraA05t21476Z' => 'bra', 'C01p28420' => 'bna', 'C01p41350' => 'bna', 'C03p52750' => 'bna', 'C03p52780' => 'bna', 'C05p40270' => 'bna', 'CAN.G1437.9' => 'can', 'CANSAT78G0035' => 'cansat', 'CANSAT78G1036' => 'cansat', 'CANSAT78G2272' => 'cansat', 'CANSAT78G2478' => 'cansat', 'CARHR098700' => 'chi', 'CARHR221120' => 'chi', 'CARHR221150' => 'chi', 'Carub.0003s2297' => 'cru', 'Carub.0007s2749' => 'cru', 'Carub.0007s2750' => 'cru', 'Carub.0007s2751' => 'cru', 'Ca_10849_v3' => 'car', 'Cc03_g04300' => 'ccan', 'CDE02G3648' => 'cde', 'CDE05G0060' => 'cde', 'CDE05G0692' => 'cde', 'CDE05G2285' => 'cde', 'CDE05G2884' => 'cde', 'CDE05G3072' => 'cde', 'Cfa008439' => 'cfa', 'Cfa008441' => 'cfa', 'Cfa008443' => 'cfa', 'Cfa008448' => 'cfa', 'Ciclev10005974m.g' => 'ccl', 'Ciclev10006006m.g' => 'ccl', 'Ciclev10006775m.g' => 'ccl', 'CiPaw.02G120400' => 'cil', 'CiPaw.02G120500' => 'cil', 'CiPaw.02G120600' => 'cil', 'ClCG05G004850' => 'cla', 'COL.COLO4_21566' => 'col', 'Cpa.g.sc44.124' => 'cpa', 'Cre07.g320400' => 'cre', 'Cre07.g320450' => 'cre', 'Cre08.g384650' => 'cre', 'Cre09.g393173' => 'cre', 'Cre09.g394325' => 'cre', 'Cre14.g626750' => 'cre', 'Cre16.g679250' => 'cre', 'CsaV3_3G012890' => 'csa', 'CSS0010865' => 'camsi', 'CSS0044338' => 'camsi', 'DCAR_002366' => 'dca', 'DCAR_030687' => 'dca', 'DCAR_030688' => 'dca', 'Dinv14047' => 'din', 'Dinv14048' => 'din', 'Duzib151G0105' => 'dzi', 'Duzib151G0114' => 'dzi', 'Duzib212G1029' => 'dzi', 'ECA232G3536' => 'eca', 'ECA240G0786' => 'eca', 'ECA240G1802' => 'eca', 'ECA240G3760' => 'eca', 'ECA240G3920' => 'eca', 'EL10Ac5g12536' => 'bvu', 'EL10Ac5g12537' => 'bvu', 'EL10Ac5g12538' => 'bvu', 'Eucgr.B01004' => 'egr', 'Eucgr.B01006' => 'egr', 'Eucgr.B01007' => 'egr', 'Eucgr.B01008' => 'egr', 'Eucgr.B01895' => 'egr', 'Eucgr.B01896' => 'egr', 'FAN04G1456' => 'fan', 'FAN08G1769' => 'fan', 'FAN08G2160' => 'fan', 'FAN13G2403' => 'fan', 'FAN13G3303' => 'fan', 'FAN15G2435' => 'fan', 'FAN17G0672' => 'fan', 'FAN17G2441' => 'fan', 'FAN18G1024' => 'fan', 'FAN22G1458' => 'fan', 'FAN24G0037' => 'fan', 'FAN24G0429' => 'fan', 'FAN24G2387' => 'fan', 'FAN27G2746' => 'fan', 'FvH4_2g20400' => 'fve', 'FvH4_2g20420' => 'fve', 'FvH4_2g20430' => 'fve', 'FvH4_4g01270' => 'fve', 'FvH4_4g01290' => 'fve', 'FvH4_4g01300' => 'fve', 'FvH4_4g01310' => 'fve', 'FvH4_4g01330' => 'fve', 'FvH4_5g09070' => 'fve', 'Glyma.10G243800' => 'gma', 'Glyma.20G150600' => 'gma', 'Gohir.A09G219200' => 'ghi', 'Gohir.A09G219300' => 'ghi', 'Gohir.D09G221400' => 'ghi', 'Gohir.D09G221500' => 'ghi', 'Gorai.006G242600' => 'gra', 'Gorai.006G242700' => 'gra', 'GSVIVG01018044001' => 'vvi', 'HanXRQChr03g0083821' => 'han', 'HanXRQChr03g0083841' => 'han', 'HanXRQChr03g0083881' => 'han', 'HanXRQChr03g0083901' => 'han', 'HanXRQChr03g0083921' => 'han', 'HanXRQChr03g0085331' => 'han', 'HanXRQChr03g0085361' => 'han', 'HanXRQChr03g0085411' => 'han', 'HanXRQChr03g0085421' => 'han', 'HanXRQChr03g0085431' => 'han', 'HanXRQChr08g0221991' => 'han', 'HanXRQChr11g0336061' => 'han', 'HanXRQChr11g0336411' => 'han', 'Haze_11234' => 'cav', 'Hma1.2p1_0549F.1_g177010' => 'hma', 'Hma1.2p1_0602F.1_g187630' => 'hma', 'Hund14876' => 'sun', 'Hund14879' => 'sun', 'Lalb_Chr06g0160741' => 'lal', 'Lalb_Chr21g0304781' => 'lal', 'Lj3A726G19' => 'lonja', 'Lj3A726T23' => 'lonja', 'Lj3A726T24' => 'lonja', 'Lj3A726T25' => 'lonja', 'Lj3A727T17' => 'lonja', 'Lj3C726T0' => 'lonja', 'Lj3C726T2' => 'lonja', 'Lj3P725T35' => 'lonja', 'Lj3P727T10' => 'lonja', 'Lj3P727T12' => 'lonja', 'Lj3P727T14' => 'lonja', 'Lj5g0023109' => 'lja', 'Lj6P646T44' => 'lonja', 'Lsat_1_v5_gn_6_75760' => 'lsa', 'Lsat_1_v5_gn_6_75800' => 'lsa', 'Lsat_1_v5_gn_6_75900' => 'lsa', 'Lsat_1_v5_gn_6_76240' => 'lsa', 'Lsat_1_v5_gn_6_76441' => 'lsa', 'Lsat_1_v5_gn_6_76700' => 'lsa', 'Lsat_1_v5_gn_6_76760' => 'lsa', 'Manes.15G033100' => 'mes', 'Mapoly0004s0074' => 'mpo', 'Mapoly0004s0075' => 'mpo', 'Mapoly0004s0163' => 'mpo', 'Mapoly0004s0164' => 'mpo', 'Mapoly0021s0018' => 'mpo', 'Mapoly0041s0136' => 'mpo', 'Mapoly0041s0137' => 'mpo', 'Mapoly0041s0138' => 'mpo', 'Mapoly0041s0139' => 'mpo', 'Mapoly0041s0141' => 'mpo', 'Mapoly0041s0142' => 'mpo', 'Mapoly0041s0143' => 'mpo', 'Mapoly0041s0144' => 'mpo', 'Mapoly0041s0145' => 'mpo', 'Mapoly0047s0106' => 'mpo', 'Mapoly0047s0108' => 'mpo', 'Mapoly0050s0051' => 'mpo', 'Mapoly0050s0052' => 'mpo', 'Mapoly0050s0053' => 'mpo', 'Mapoly0058s0013' => 'mpo', 'Mapoly0091s0078' => 'mpo', 'Mapoly0091s0079' => 'mpo', 'Mapoly0091s0080' => 'mpo', 'Mapoly0091s0081' => 'mpo', 'Mapoly0278s0004' => 'mpo', 'Mapoly0278s0005' => 'mpo', 'Mapoly0278s0006' => 'mpo', 'MBI11_g30648_MAGBIO' => 'mbi', 'MCO03G194' => 'mco', 'MCO03G590' => 'mco', 'MCO07G312' => 'mco', 'MCO10G318' => 'mco', 'MCO12G244' => 'mco', 'MCO13G148' => 'mco', 'MCO13G194' => 'mco', 'MCO16G238' => 'mco', 'MD06G1134100' => 'mdo', 'MD13G1200100' => 'mdo', 'MD13G1200300' => 'mdo', 'MD13G1200600' => 'mdo', 'MD14G1150400' => 'mdo', 'MD16G1200000' => 'mdo', 'Medtr1g102570' => 'mtr', 'Medtr1g102780' => 'mtr', 'Medtr1g102800' => 'mtr', 'Medtr1g102810' => 'mtr', 'Medtr1g102830' => 'mtr', 'MELO3C006499.2' => 'cme', 'Migut.G00385' => 'egut', 'MSTRG.4063' => 'ama', 'Nitab4.5_0000090g0260' => 'nta', 'Nitab4.5_0000977g0030' => 'nta', 'Nitab4.5_0002541g0040' => 'nta', 'Nitab4.5_0007068g0040' => 'nta', 'Nn005s41408' => 'nnu', 'Nn005s41410' => 'nnu', 'Oeu010310.1' => 'oeu', 'Oeu010311.1' => 'oeu', 'Oeu043472.1' => 'oeu', 'Os01g0246400' => 'osa', 'Os04g0267950' => 'osa', 'Os07g0178700' => 'osa', 'Os07g0178800' => 'osa', 'Peaxi162Scf00316g00046' => 'pax', 'Peaxi162Scf00316g00049' => 'pax', 'Peaxi162Scf00316g00059' => 'pax', 'Peaxi162Scf00316g00328' => 'pax', 'Peaxi162Scf00316g00329' => 'pax', 'Peaxi162Scf00316g00411' => 'pax', 'Peaxi162Scf00316g00521' => 'pax', 'Peaxi162Scf00492g00068' => 'pax', 'Peaxi162Scf35631g00002' => 'pax', 'PGR142G3720' => 'pgr', 'PGSC0003DMG400006442' => 'stu', 'Phvul.007G062000' => 'pvu', 'Potri.008G157750' => 'ptr', 'Potri.008G157900' => 'ptr', 'Potri.008G158000' => 'ptr', 'Potri.008G158200' => 'ptr', 'Pp3c11_7280' => 'ppa', 'Pp3c11_7980' => 'ppa', 'Pp3c12_19450' => 'ppa', 'Pp3c14_1480' => 'ppa', 'Pp3c14_1501' => 'ppa', 'Pp3c16_4900' => 'ppa', 'Pp3c16_5010' => 'ppa', 'Pp3c16_5060' => 'ppa', 'Pp3c19_18250' => 'ppa', 'Pp3c23_8530' => 'ppa', 'Pp3c23_8550' => 'ppa', 'Pp3c24_9670' => 'ppa', 'Pp3c2_21390' => 'ppa', 'Pp3c2_31380' => 'ppa', 'Pp3c3_16620' => 'ppa', 'Pp3c3_8090' => 'ppa', 'Pp3c3_8110' => 'ppa', 'Pp3c3_8130' => 'ppa', 'Pp3c3_8150' => 'ppa', 'Pp3c4_14320' => 'ppa', 'Pp3c6_2560' => 'ppa', 'Pp3c9_16700' => 'ppa', 'PRCOL_00000234' => 'pco', 'PRCOL_00000235' => 'pco', 'PRCOL_00000777' => 'pco', 'PRCOL_00002344' => 'pco', 'PRCOL_00002372' => 'pco', 'PRCOL_00006120' => 'pco', 'Prupe.1G021400' => 'ppe', 'Prupe.1G021500' => 'ppe', 'Prupe.1G021600' => 'ppe', 'Prupe.1G021700' => 'ppe', 'Prupe.1G021800' => 'ppe', 'Prupe.5G145100' => 'ppe', 'Psat6g204040' => 'psa', 'Psat6g204800' => 'psa', 'Psat6g204920' => 'psa', 'Psat6g204960' => 'psa', 'Psat6g205080' => 'psa', 'PSO017G0271' => 'pso', 'PSO017G1276' => 'pso', 'PSO017G1429' => 'pso', 'PSO017G1861' => 'pso', 'PSO017G2787' => 'pso', 'PSO017G4466' => 'pso', 'PSO017G5118' => 'pso', 'PSO017G5420' => 'pso', 'PSO063G3678' => 'pso', 'PSO210G0546' => 'pso', 'PSO317G0001' => 'pso', 'PSO357G0512' => 'pso', 'PSO478G2682' => 'pso', 'PSO647G0001' => 'pso', 'PSO675G0001' => 'pso', 'PSO675G2699' => 'pso', 'PSO675G2849' => 'pso', 'PSO675G4991' => 'pso', 'PSO689G0001' => 'pso', 'QL06p000916' => 'qlo', 'QL06p000921' => 'qlo', 'QL06p001398' => 'qlo', 'QL06p001407' => 'qlo', 'QL06p002031' => 'qlo', 'RcHm_v2.0_Chr4g0387791' => 'rch', 'RcHm_v2.0_Chr4g0387801' => 'rch', 'RcHm_v2.0_Chr6g0286501' => 'rch', 'RcHm_v2.0_Chr6g0286511' => 'rch', 'RcHm_v2.0_Chr6g0286521' => 'rch', 'RcHm_v2.0_Chr6g0286531' => 'rch', 'RcHm_v2.0_Chr7g0189141' => 'rch', 'Rhsim02G0028700' => 'rsi', 'Rhsim02G0028800' => 'rsi', 'Rhsim02G0028900' => 'rsi', 'Rhsim02G0029000' => 'rsi', 'Rhsim02G0029100' => 'rsi', 'Rhsim02G0029200' => 'rsi', 'Rhsim02G0029300' => 'rsi', 'Rhsim02G0029400' => 'rsi', 'Rhsim02G0029500' => 'rsi', 'Rhsim02G0029600' => 'rsi', 'RhsimUnG0024000' => 'rsi', 'RhsimUnG0024100' => 'rsi', 'RhsimUnG0024200' => 'rsi', 'RhsimUnG0024300' => 'rsi', 'RhsimUnG0024400' => 'rsi', 'RhsimUnG0024500' => 'rsi', 'RhsimUnG0024700' => 'rsi', 'RhsimUnG0024800' => 'rsi', 'RhsimUnG0024900' => 'rsi', 'RhsimUnG0025100' => 'rsi', 'Sabra08G0120200' => 'sbr', 'Sabra08G0120300' => 'sbr', 'Sabra08G0120500' => 'sbr', 'Sabra08G0120600' => 'sbr', 'Sabra10G0158900' => 'sbr', 'SalBow2G3492' => 'sbo', 'Sc13g0004760' => 'sci', 'Sc13g0004770' => 'sci', 'Sed0003417' => 'sed', 'Sed0019750' => 'sed', 'SEGI_03419' => 'sgi', 'SEGI_05907' => 'sgi', 'SEGI_10682' => 'sgi', 'SEGI_13528' => 'sgi', 'SEGI_16081' => 'sgi', 'SEGI_19370' => 'sgi', 'SEGI_21015' => 'sgi', 'SEGI_21944' => 'sgi', 'SEGI_32906' => 'sgi', 'SEGI_33093' => 'sgi', 'SEGI_36110' => 'sgi', 'SEGI_40397' => 'sgi', 'SGA_v2.0_scaffold191G40426' => 'sas', 'SGA_v2.0_scaffold353G49717' => 'sas', 'SGA_v2.0_scaffold50G18550' => 'sas', 'SMO119G0173' => 'smo', 'SMO172G0002' => 'smo', 'Solyc09g082690.3' => 'sly', 'Solyc09g082700.2' => 'sly', 'Sopen09g031550' => 'spe', 'Sopen09g031560' => 'spe', 'Sp3g20540' => 'spa', 'Sp7g07580' => 'spa', 'TAR134G0002' => 'tar', 'TAR236G0001' => 'tar', 'TAR365G0892' => 'tar', 'TAR636G0166' => 'tar', 'TAR636G0646' => 'tar', 'TAR636G0869' => 'tar', 'TAR636G1317' => 'tar', 'TAR636G1744' => 'tar', 'TAR636G3358' => 'tar', 'TAR636G3436' => 'tar', 'THA.LOC104803047' => 'tha', 'Thecc.04G238900' => 'tca', 'Thhalv10021557m.g' => 'esa', 'Thhalv10026318m.g' => 'esa', 'Thhalv10026335m.g' => 'esa', 'TPR.G17433' => 'tpr', 'TPR.G18915' => 'tpr', 'TPR.G26125' => 'tpr', 'TWI09G0677' => 'twi', 'TWI73G0287' => 'twi', 'unitig_748.g8326' => 'ugi', 'vmacro15370' => 'vma', 'vmacro15371' => 'vma', 'vmacro15372' => 'vma', 'vmacro15373' => 'vma', 'vmacro15374' => 'vma', 'VMungo0720G2826' => 'vmu', 'Zm00001eb116960' => 'zma', 'Zm00001eb301260' => 'zma', 'Zm00001eb301270' => 'zma' ), 'gf_id' => 'HOM05D001460', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001460' ), 'data_identifier' => 'HOM05D001460', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001460', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '433', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p22980' => 'bna', 'A01p32340' => 'bna', 'A03p42970' => 'bna', 'A05p25880' => 'bna', 'Aa31LG8G9320' => 'aar', 'Aa31LG8G9330' => 'aar', 'Aa31LG8G9340' => 'aar', 'Aa31sc221G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1034' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1528' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.829' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2222' => 'aag', 'Ah.12g058830' => 'amhyb', 'Ah.12g058840' => 'amhyb', 'AL3G37160' => 'aly', 'AL7G41310' => 'aly', 'Aqoxy5G00395' => 'aox', 'Aqoxy5G00396' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0C8NZA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5185HY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JZ1PRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MD3LS0' => 'arhy', 'AT3G22840' => 'ath', 'AT4G14690' => 'ath', 'ATR0665G054' => 'atr', 'Atru.chr4.2344' => 'acertr', 'Atru.chr4.2346' => 'acertr', 'Atru.chr4.2347' => 'acertr', 'Atru.chr4.2348' => 'acertr', 'Atru.chr4.2355' => 'acertr', 'Atru.chr4.2356' => 'acertr', 'Atru.chr4.2358' => 'acertr', 'Atru.chr4.2359' => 'acertr', 'Atru.chr4.2360' => 'acertr', 'Atru.chr4.2361' => 'acertr', 'AUR62030476' => 'cqu', 'AUR62030478' => 'cqu', 'AUR62030819' => 'cqu', 'AUR62030820' => 'cqu', 'BcaB03g14648' => 'bca', 'BcaB04g20492' => 'bca', 'BcaB06g26399' => 'bca', 'BcaC01g03416' => 'bca', 'BcaC01g03419' => 'bca', 'BcaC01g03421' => 'bca', 'BcaC01g03424' => 'bca', 'BcaC05g28012' => 'bca', 'BcaC09g49212' => 'bca', 'BcaC09g50140' => 'bca', 'BcaNung00346' => 'bca', 'BolC1t02785H' => 'bol', 'BolC1t04095H' => 'bol', 'BolC3t17545H' => 'bol', 'BolC5t32769H' => 'bol', 'BraA01t02211Z' => 'bra', 'BraA01t03359Z' => 'bra', 'BraA03t13441Z' => 'bra', 'BraA05t21476Z' => 'bra', 'C01p28420' => 'bna', 'C01p41350' => 'bna', 'C03p52750' => 'bna', 'C03p52780' => 'bna', 'C05p40270' => 'bna', 'CAN.G1437.9' => 'can', 'CANSAT78G0035' => 'cansat', 'CANSAT78G1036' => 'cansat', 'CANSAT78G2272' => 'cansat', 'CANSAT78G2478' => 'cansat', 'CARHR098700' => 'chi', 'CARHR221120' => 'chi', 'CARHR221150' => 'chi', 'Carub.0003s2297' => 'cru', 'Carub.0007s2749' => 'cru', 'Carub.0007s2750' => 'cru', 'Carub.0007s2751' => 'cru', 'Ca_10849_v3' => 'car', 'Cc03_g04300' => 'ccan', 'CDE02G3648' => 'cde', 'CDE05G0060' => 'cde', 'CDE05G0692' => 'cde', 'CDE05G2285' => 'cde', 'CDE05G2884' => 'cde', 'CDE05G3072' => 'cde', 'Cfa008439' => 'cfa', 'Cfa008441' => 'cfa', 'Cfa008443' => 'cfa', 'Cfa008448' => 'cfa', 'Ciclev10005974m.g' => 'ccl', 'Ciclev10006006m.g' => 'ccl', 'Ciclev10006775m.g' => 'ccl', 'CiPaw.02G120400' => 'cil', 'CiPaw.02G120500' => 'cil', 'CiPaw.02G120600' => 'cil', 'ClCG05G004850' => 'cla', 'COL.COLO4_21566' => 'col', 'Cpa.g.sc44.124' => 'cpa', 'Cre07.g320400' => 'cre', 'Cre07.g320450' => 'cre', 'Cre08.g384650' => 'cre', 'Cre09.g393173' => 'cre', 'Cre09.g394325' => 'cre', 'Cre14.g626750' => 'cre', 'Cre16.g679250' => 'cre', 'CsaV3_3G012890' => 'csa', 'CSS0010865' => 'camsi', 'CSS0044338' => 'camsi', 'DCAR_002366' => 'dca', 'DCAR_030687' => 'dca', 'DCAR_030688' => 'dca', 'Dinv14047' => 'din', 'Dinv14048' => 'din', 'Duzib151G0105' => 'dzi', 'Duzib151G0114' => 'dzi', 'Duzib212G1029' => 'dzi', 'ECA232G3536' => 'eca', 'ECA240G0786' => 'eca', 'ECA240G1802' => 'eca', 'ECA240G3760' => 'eca', 'ECA240G3920' => 'eca', 'EL10Ac5g12536' => 'bvu', 'EL10Ac5g12537' => 'bvu', 'EL10Ac5g12538' => 'bvu', 'Eucgr.B01004' => 'egr', 'Eucgr.B01006' => 'egr', 'Eucgr.B01007' => 'egr', 'Eucgr.B01008' => 'egr', 'Eucgr.B01895' => 'egr', 'Eucgr.B01896' => 'egr', 'FAN04G1456' => 'fan', 'FAN08G1769' => 'fan', 'FAN08G2160' => 'fan', 'FAN13G2403' => 'fan', 'FAN13G3303' => 'fan', 'FAN15G2435' => 'fan', 'FAN17G0672' => 'fan', 'FAN17G2441' => 'fan', 'FAN18G1024' => 'fan', 'FAN22G1458' => 'fan', 'FAN24G0037' => 'fan', 'FAN24G0429' => 'fan', 'FAN24G2387' => 'fan', 'FAN27G2746' => 'fan', 'FvH4_2g20400' => 'fve', 'FvH4_2g20420' => 'fve', 'FvH4_2g20430' => 'fve', 'FvH4_4g01270' => 'fve', 'FvH4_4g01290' => 'fve', 'FvH4_4g01300' => 'fve', 'FvH4_4g01310' => 'fve', 'FvH4_4g01330' => 'fve', 'FvH4_5g09070' => 'fve', 'Glyma.10G243800' => 'gma', 'Glyma.20G150600' => 'gma', 'Gohir.A09G219200' => 'ghi', 'Gohir.A09G219300' => 'ghi', 'Gohir.D09G221400' => 'ghi', 'Gohir.D09G221500' => 'ghi', 'Gorai.006G242600' => 'gra', 'Gorai.006G242700' => 'gra', 'GSVIVG01018044001' => 'vvi', 'HanXRQChr03g0083821' => 'han', 'HanXRQChr03g0083841' => 'han', 'HanXRQChr03g0083881' => 'han', 'HanXRQChr03g0083901' => 'han', 'HanXRQChr03g0083921' => 'han', 'HanXRQChr03g0085331' => 'han', 'HanXRQChr03g0085361' => 'han', 'HanXRQChr03g0085411' => 'han', 'HanXRQChr03g0085421' => 'han', 'HanXRQChr03g0085431' => 'han', 'HanXRQChr08g0221991' => 'han', 'HanXRQChr11g0336061' => 'han', 'HanXRQChr11g0336411' => 'han', 'Haze_11234' => 'cav', 'Hma1.2p1_0549F.1_g177010' => 'hma', 'Hma1.2p1_0602F.1_g187630' => 'hma', 'Hund14876' => 'sun', 'Hund14879' => 'sun', 'Lalb_Chr06g0160741' => 'lal', 'Lalb_Chr21g0304781' => 'lal', 'Lj3A726G19' => 'lonja', 'Lj3A726T23' => 'lonja', 'Lj3A726T24' => 'lonja', 'Lj3A726T25' => 'lonja', 'Lj3A727T17' => 'lonja', 'Lj3C726T0' => 'lonja', 'Lj3C726T2' => 'lonja', 'Lj3P725T35' => 'lonja', 'Lj3P727T10' => 'lonja', 'Lj3P727T12' => 'lonja', 'Lj3P727T14' => 'lonja', 'Lj5g0023109' => 'lja', 'Lj6P646T44' => 'lonja', 'Lsat_1_v5_gn_6_75760' => 'lsa', 'Lsat_1_v5_gn_6_75800' => 'lsa', 'Lsat_1_v5_gn_6_75900' => 'lsa', 'Lsat_1_v5_gn_6_76240' => 'lsa', 'Lsat_1_v5_gn_6_76441' => 'lsa', 'Lsat_1_v5_gn_6_76700' => 'lsa', 'Lsat_1_v5_gn_6_76760' => 'lsa', 'Manes.15G033100' => 'mes', 'Mapoly0004s0074' => 'mpo', 'Mapoly0004s0075' => 'mpo', 'Mapoly0004s0163' => 'mpo', 'Mapoly0004s0164' => 'mpo', 'Mapoly0021s0018' => 'mpo', 'Mapoly0041s0136' => 'mpo', 'Mapoly0041s0137' => 'mpo', 'Mapoly0041s0138' => 'mpo', 'Mapoly0041s0139' => 'mpo', 'Mapoly0041s0141' => 'mpo', 'Mapoly0041s0142' => 'mpo', 'Mapoly0041s0143' => 'mpo', 'Mapoly0041s0144' => 'mpo', 'Mapoly0041s0145' => 'mpo', 'Mapoly0047s0106' => 'mpo', 'Mapoly0047s0108' => 'mpo', 'Mapoly0050s0051' => 'mpo', 'Mapoly0050s0052' => 'mpo', 'Mapoly0050s0053' => 'mpo', 'Mapoly0058s0013' => 'mpo', 'Mapoly0091s0078' => 'mpo', 'Mapoly0091s0079' => 'mpo', 'Mapoly0091s0080' => 'mpo', 'Mapoly0091s0081' => 'mpo', 'Mapoly0278s0004' => 'mpo', 'Mapoly0278s0005' => 'mpo', 'Mapoly0278s0006' => 'mpo', 'MBI11_g30648_MAGBIO' => 'mbi', 'MCO03G194' => 'mco', 'MCO03G590' => 'mco', 'MCO07G312' => 'mco', 'MCO10G318' => 'mco', 'MCO12G244' => 'mco', 'MCO13G148' => 'mco', 'MCO13G194' => 'mco', 'MCO16G238' => 'mco', 'MD06G1134100' => 'mdo', 'MD13G1200100' => 'mdo', 'MD13G1200300' => 'mdo', 'MD13G1200600' => 'mdo', 'MD14G1150400' => 'mdo', 'MD16G1200000' => 'mdo', 'Medtr1g102570' => 'mtr', 'Medtr1g102780' => 'mtr', 'Medtr1g102800' => 'mtr', 'Medtr1g102810' => 'mtr', 'Medtr1g102830' => 'mtr', 'MELO3C006499.2' => 'cme', 'Migut.G00385' => 'egut', 'MSTRG.4063' => 'ama', 'Nitab4.5_0000090g0260' => 'nta', 'Nitab4.5_0000977g0030' => 'nta', 'Nitab4.5_0002541g0040' => 'nta', 'Nitab4.5_0007068g0040' => 'nta', 'Nn005s41408' => 'nnu', 'Nn005s41410' => 'nnu', 'Oeu010310.1' => 'oeu', 'Oeu010311.1' => 'oeu', 'Oeu043472.1' => 'oeu', 'Os01g0246400' => 'osa', 'Os04g0267950' => 'osa', 'Os07g0178700' => 'osa', 'Os07g0178800' => 'osa', 'Peaxi162Scf00316g00046' => 'pax', 'Peaxi162Scf00316g00049' => 'pax', 'Peaxi162Scf00316g00059' => 'pax', 'Peaxi162Scf00316g00328' => 'pax', 'Peaxi162Scf00316g00329' => 'pax', 'Peaxi162Scf00316g00411' => 'pax', 'Peaxi162Scf00316g00521' => 'pax', 'Peaxi162Scf00492g00068' => 'pax', 'Peaxi162Scf35631g00002' => 'pax', 'PGR142G3720' => 'pgr', 'PGSC0003DMG400006442' => 'stu', 'Phvul.007G062000' => 'pvu', 'Potri.008G157750' => 'ptr', 'Potri.008G157900' => 'ptr', 'Potri.008G158000' => 'ptr', 'Potri.008G158200' => 'ptr', 'Pp3c11_7280' => 'ppa', 'Pp3c11_7980' => 'ppa', 'Pp3c12_19450' => 'ppa', 'Pp3c14_1480' => 'ppa', 'Pp3c14_1501' => 'ppa', 'Pp3c16_4900' => 'ppa', 'Pp3c16_5010' => 'ppa', 'Pp3c16_5060' => 'ppa', 'Pp3c19_18250' => 'ppa', 'Pp3c23_8530' => 'ppa', 'Pp3c23_8550' => 'ppa', 'Pp3c24_9670' => 'ppa', 'Pp3c2_21390' => 'ppa', 'Pp3c2_31380' => 'ppa', 'Pp3c3_16620' => 'ppa', 'Pp3c3_8090' => 'ppa', 'Pp3c3_8110' => 'ppa', 'Pp3c3_8130' => 'ppa', 'Pp3c3_8150' => 'ppa', 'Pp3c4_14320' => 'ppa', 'Pp3c6_2560' => 'ppa', 'Pp3c9_16700' => 'ppa', 'PRCOL_00000234' => 'pco', 'PRCOL_00000235' => 'pco', 'PRCOL_00000777' => 'pco', 'PRCOL_00002344' => 'pco', 'PRCOL_00002372' => 'pco', 'PRCOL_00006120' => 'pco', 'Prupe.1G021400' => 'ppe', 'Prupe.1G021500' => 'ppe', 'Prupe.1G021600' => 'ppe', 'Prupe.1G021700' => 'ppe', 'Prupe.1G021800' => 'ppe', 'Prupe.5G145100' => 'ppe', 'Psat6g204040' => 'psa', 'Psat6g204800' => 'psa', 'Psat6g204920' => 'psa', 'Psat6g204960' => 'psa', 'Psat6g205080' => 'psa', 'PSO017G0271' => 'pso', 'PSO017G1276' => 'pso', 'PSO017G1429' => 'pso', 'PSO017G1861' => 'pso', 'PSO017G2787' => 'pso', 'PSO017G4466' => 'pso', 'PSO017G5118' => 'pso', 'PSO017G5420' => 'pso', 'PSO063G3678' => 'pso', 'PSO210G0546' => 'pso', 'PSO317G0001' => 'pso', 'PSO357G0512' => 'pso', 'PSO478G2682' => 'pso', 'PSO647G0001' => 'pso', 'PSO675G0001' => 'pso', 'PSO675G2699' => 'pso', 'PSO675G2849' => 'pso', 'PSO675G4991' => 'pso', 'PSO689G0001' => 'pso', 'QL06p000916' => 'qlo', 'QL06p000921' => 'qlo', 'QL06p001398' => 'qlo', 'QL06p001407' => 'qlo', 'QL06p002031' => 'qlo', 'RcHm_v2.0_Chr4g0387791' => 'rch', 'RcHm_v2.0_Chr4g0387801' => 'rch', 'RcHm_v2.0_Chr6g0286501' => 'rch', 'RcHm_v2.0_Chr6g0286511' => 'rch', 'RcHm_v2.0_Chr6g0286521' => 'rch', 'RcHm_v2.0_Chr6g0286531' => 'rch', 'RcHm_v2.0_Chr7g0189141' => 'rch', 'Rhsim02G0028700' => 'rsi', 'Rhsim02G0028800' => 'rsi', 'Rhsim02G0028900' => 'rsi', 'Rhsim02G0029000' => 'rsi', 'Rhsim02G0029100' => 'rsi', 'Rhsim02G0029200' => 'rsi', 'Rhsim02G0029300' => 'rsi', 'Rhsim02G0029400' => 'rsi', 'Rhsim02G0029500' => 'rsi', 'Rhsim02G0029600' => 'rsi', 'RhsimUnG0024000' => 'rsi', 'RhsimUnG0024100' => 'rsi', 'RhsimUnG0024200' => 'rsi', 'RhsimUnG0024300' => 'rsi', 'RhsimUnG0024400' => 'rsi', 'RhsimUnG0024500' => 'rsi', 'RhsimUnG0024700' => 'rsi', 'RhsimUnG0024800' => 'rsi', 'RhsimUnG0024900' => 'rsi', 'RhsimUnG0025100' => 'rsi', 'Sabra08G0120200' => 'sbr', 'Sabra08G0120300' => 'sbr', 'Sabra08G0120500' => 'sbr', 'Sabra08G0120600' => 'sbr', 'Sabra10G0158900' => 'sbr', 'SalBow2G3492' => 'sbo', 'Sc13g0004760' => 'sci', 'Sc13g0004770' => 'sci', 'Sed0003417' => 'sed', 'Sed0019750' => 'sed', 'SEGI_03419' => 'sgi', 'SEGI_05907' => 'sgi', 'SEGI_10682' => 'sgi', 'SEGI_13528' => 'sgi', 'SEGI_16081' => 'sgi', 'SEGI_19370' => 'sgi', 'SEGI_21015' => 'sgi', 'SEGI_21944' => 'sgi', 'SEGI_32906' => 'sgi', 'SEGI_33093' => 'sgi', 'SEGI_36110' => 'sgi', 'SEGI_40397' => 'sgi', 'SGA_v2.0_scaffold191G40426' => 'sas', 'SGA_v2.0_scaffold353G49717' => 'sas', 'SGA_v2.0_scaffold50G18550' => 'sas', 'SMO119G0173' => 'smo', 'SMO172G0002' => 'smo', 'Solyc09g082690.3' => 'sly', 'Solyc09g082700.2' => 'sly', 'Sopen09g031550' => 'spe', 'Sopen09g031560' => 'spe', 'Sp3g20540' => 'spa', 'Sp7g07580' => 'spa', 'TAR134G0002' => 'tar', 'TAR236G0001' => 'tar', 'TAR365G0892' => 'tar', 'TAR636G0166' => 'tar', 'TAR636G0646' => 'tar', 'TAR636G0869' => 'tar', 'TAR636G1317' => 'tar', 'TAR636G1744' => 'tar', 'TAR636G3358' => 'tar', 'TAR636G3436' => 'tar', 'THA.LOC104803047' => 'tha', 'Thecc.04G238900' => 'tca', 'Thhalv10021557m.g' => 'esa', 'Thhalv10026318m.g' => 'esa', 'Thhalv10026335m.g' => 'esa', 'TPR.G17433' => 'tpr', 'TPR.G18915' => 'tpr', 'TPR.G26125' => 'tpr', 'TWI09G0677' => 'twi', 'TWI73G0287' => 'twi', 'unitig_748.g8326' => 'ugi', 'vmacro15370' => 'vma', 'vmacro15371' => 'vma', 'vmacro15372' => 'vma', 'vmacro15373' => 'vma', 'vmacro15374' => 'vma', 'VMungo0720G2826' => 'vmu', 'Zm00001eb116960' => 'zma', 'Zm00001eb301260' => 'zma', 'Zm00001eb301270' => 'zma' ) $gf_id = 'HOM05D001460' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001460' ) $data_identifier = 'HOM05D001460' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 4, 'aag' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 2, 'aox' => (int) 2, 'arhy' => (int) 4, 'ath' => (int) 2, 'atr' => (int) 1, 'acertr' => (int) 10, 'cqu' => (int) 4, 'bca' => (int) 11, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 1, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 1, 'ccan' => (int) 1, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 1, 'col' => (int) 1, 'cpa' => (int) 1, 'cre' => (int) 7, 'csa' => (int) 1, 'camsi' => (int) 2, 'dca' => (int) 3, 'din' => (int) 2, 'dzi' => (int) 3, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 14, 'fve' => (int) 9, 'gma' => (int) 2, 'ghi' => (int) 4, 'gra' => (int) 2, 'vvi' => (int) 1, 'han' => (int) 13, 'cav' => (int) 1, 'hma' => (int) 2, 'sun' => (int) 2, 'lal' => (int) 2, 'lonja' => (int) 12, 'lja' => (int) 1, 'lsa' => (int) 7, 'mes' => (int) 1, 'mpo' => (int) 27, 'mbi' => (int) 1, 'mco' => (int) 8, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 1, 'egut' => (int) 1, 'ama' => (int) 1, 'nta' => (int) 4, 'nnu' => (int) 2, 'oeu' => (int) 3, 'osa' => (int) 4, 'pax' => (int) 9, 'pgr' => (int) 1, 'stu' => (int) 1, 'pvu' => (int) 1, 'ptr' => (int) 4, 'ppa' => (int) 22, 'pco' => (int) 6, 'ppe' => (int) 6, 'psa' => (int) 5, 'pso' => (int) 19, 'qlo' => (int) 5, 'rch' => (int) 7, 'rsi' => (int) 20, 'sbr' => (int) 5, 'sbo' => (int) 1, 'sci' => (int) 2, 'sed' => (int) 2, 'sgi' => (int) 12, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 2, 'tar' => (int) 10, 'tha' => (int) 1, 'tca' => (int) 1, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 2, 'ugi' => (int) 1, 'vma' => (int) 5, 'vmu' => (int) 1, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb301270' $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' => 'HOM05D001460', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '433', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p22980' => 'bna', 'A01p32340' => 'bna', 'A03p42970' => 'bna', 'A05p25880' => 'bna', 'Aa31LG8G9320' => 'aar', 'Aa31LG8G9330' => 'aar', 'Aa31LG8G9340' => 'aar', 'Aa31sc221G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1034' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1528' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.829' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2222' => 'aag', 'Ah.12g058830' => 'amhyb', 'Ah.12g058840' => 'amhyb', 'AL3G37160' => 'aly', 'AL7G41310' => 'aly', 'Aqoxy5G00395' => 'aox', 'Aqoxy5G00396' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0C8NZA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5185HY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JZ1PRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MD3LS0' => 'arhy', 'AT3G22840' => 'ath', 'AT4G14690' => 'ath', 'ATR0665G054' => 'atr', 'Atru.chr4.2344' => 'acertr', 'Atru.chr4.2346' => 'acertr', 'Atru.chr4.2347' => 'acertr', 'Atru.chr4.2348' => 'acertr', 'Atru.chr4.2355' => 'acertr', 'Atru.chr4.2356' => 'acertr', 'Atru.chr4.2358' => 'acertr', 'Atru.chr4.2359' => 'acertr', 'Atru.chr4.2360' => 'acertr', 'Atru.chr4.2361' => 'acertr', 'AUR62030476' => 'cqu', 'AUR62030478' => 'cqu', 'AUR62030819' => 'cqu', 'AUR62030820' => 'cqu', 'BcaB03g14648' => 'bca', 'BcaB04g20492' => 'bca', 'BcaB06g26399' => 'bca', 'BcaC01g03416' => 'bca', 'BcaC01g03419' => 'bca', 'BcaC01g03421' => 'bca', 'BcaC01g03424' => 'bca', 'BcaC05g28012' => 'bca', 'BcaC09g49212' => 'bca', 'BcaC09g50140' => 'bca', 'BcaNung00346' => 'bca', 'BolC1t02785H' => 'bol', 'BolC1t04095H' => 'bol', 'BolC3t17545H' => 'bol', 'BolC5t32769H' => 'bol', 'BraA01t02211Z' => 'bra', 'BraA01t03359Z' => 'bra', 'BraA03t13441Z' => 'bra', 'BraA05t21476Z' => 'bra', 'C01p28420' => 'bna', 'C01p41350' => 'bna', 'C03p52750' => 'bna', 'C03p52780' => 'bna', 'C05p40270' => 'bna', 'CAN.G1437.9' => 'can', 'CANSAT78G0035' => 'cansat', 'CANSAT78G1036' => 'cansat', 'CANSAT78G2272' => 'cansat', 'CANSAT78G2478' => 'cansat', 'CARHR098700' => 'chi', 'CARHR221120' => 'chi', 'CARHR221150' => 'chi', 'Carub.0003s2297' => 'cru', 'Carub.0007s2749' => 'cru', 'Carub.0007s2750' => 'cru', 'Carub.0007s2751' => 'cru', 'Ca_10849_v3' => 'car', 'Cc03_g04300' => 'ccan', 'CDE02G3648' => 'cde', 'CDE05G0060' => 'cde', 'CDE05G0692' => 'cde', 'CDE05G2285' => 'cde', 'CDE05G2884' => 'cde', 'CDE05G3072' => 'cde', 'Cfa008439' => 'cfa', 'Cfa008441' => 'cfa', 'Cfa008443' => 'cfa', 'Cfa008448' => 'cfa', 'Ciclev10005974m.g' => 'ccl', 'Ciclev10006006m.g' => 'ccl', 'Ciclev10006775m.g' => 'ccl', 'CiPaw.02G120400' => 'cil', 'CiPaw.02G120500' => 'cil', 'CiPaw.02G120600' => 'cil', 'ClCG05G004850' => 'cla', 'COL.COLO4_21566' => 'col', 'Cpa.g.sc44.124' => 'cpa', 'Cre07.g320400' => 'cre', 'Cre07.g320450' => 'cre', 'Cre08.g384650' => 'cre', 'Cre09.g393173' => 'cre', 'Cre09.g394325' => 'cre', 'Cre14.g626750' => 'cre', 'Cre16.g679250' => 'cre', 'CsaV3_3G012890' => 'csa', 'CSS0010865' => 'camsi', 'CSS0044338' => 'camsi', 'DCAR_002366' => 'dca', 'DCAR_030687' => 'dca', 'DCAR_030688' => 'dca', 'Dinv14047' => 'din', 'Dinv14048' => 'din', 'Duzib151G0105' => 'dzi', 'Duzib151G0114' => 'dzi', 'Duzib212G1029' => 'dzi', 'ECA232G3536' => 'eca', 'ECA240G0786' => 'eca', 'ECA240G1802' => 'eca', 'ECA240G3760' => 'eca', 'ECA240G3920' => 'eca', 'EL10Ac5g12536' => 'bvu', 'EL10Ac5g12537' => 'bvu', 'EL10Ac5g12538' => 'bvu', 'Eucgr.B01004' => 'egr', 'Eucgr.B01006' => 'egr', 'Eucgr.B01007' => 'egr', 'Eucgr.B01008' => 'egr', 'Eucgr.B01895' => 'egr', 'Eucgr.B01896' => 'egr', 'FAN04G1456' => 'fan', 'FAN08G1769' => 'fan', 'FAN08G2160' => 'fan', 'FAN13G2403' => 'fan', 'FAN13G3303' => 'fan', 'FAN15G2435' => 'fan', 'FAN17G0672' => 'fan', 'FAN17G2441' => 'fan', 'FAN18G1024' => 'fan', 'FAN22G1458' => 'fan', 'FAN24G0037' => 'fan', 'FAN24G0429' => 'fan', 'FAN24G2387' => 'fan', 'FAN27G2746' => 'fan', 'FvH4_2g20400' => 'fve', 'FvH4_2g20420' => 'fve', 'FvH4_2g20430' => 'fve', 'FvH4_4g01270' => 'fve', 'FvH4_4g01290' => 'fve', 'FvH4_4g01300' => 'fve', 'FvH4_4g01310' => 'fve', 'FvH4_4g01330' => 'fve', 'FvH4_5g09070' => 'fve', 'Glyma.10G243800' => 'gma', 'Glyma.20G150600' => 'gma', 'Gohir.A09G219200' => 'ghi', 'Gohir.A09G219300' => 'ghi', 'Gohir.D09G221400' => 'ghi', 'Gohir.D09G221500' => 'ghi', 'Gorai.006G242600' => 'gra', 'Gorai.006G242700' => 'gra', 'GSVIVG01018044001' => 'vvi', 'HanXRQChr03g0083821' => 'han', 'HanXRQChr03g0083841' => 'han', 'HanXRQChr03g0083881' => 'han', 'HanXRQChr03g0083901' => 'han', 'HanXRQChr03g0083921' => 'han', 'HanXRQChr03g0085331' => 'han', 'HanXRQChr03g0085361' => 'han', 'HanXRQChr03g0085411' => 'han', 'HanXRQChr03g0085421' => 'han', 'HanXRQChr03g0085431' => 'han', 'HanXRQChr08g0221991' => 'han', 'HanXRQChr11g0336061' => 'han', 'HanXRQChr11g0336411' => 'han', 'Haze_11234' => 'cav', 'Hma1.2p1_0549F.1_g177010' => 'hma', 'Hma1.2p1_0602F.1_g187630' => 'hma', 'Hund14876' => 'sun', 'Hund14879' => 'sun', 'Lalb_Chr06g0160741' => 'lal', 'Lalb_Chr21g0304781' => 'lal', 'Lj3A726G19' => 'lonja', 'Lj3A726T23' => 'lonja', 'Lj3A726T24' => 'lonja', 'Lj3A726T25' => 'lonja', 'Lj3A727T17' => 'lonja', 'Lj3C726T0' => 'lonja', 'Lj3C726T2' => 'lonja', 'Lj3P725T35' => 'lonja', 'Lj3P727T10' => 'lonja', 'Lj3P727T12' => 'lonja', 'Lj3P727T14' => 'lonja', 'Lj5g0023109' => 'lja', 'Lj6P646T44' => 'lonja', 'Lsat_1_v5_gn_6_75760' => 'lsa', 'Lsat_1_v5_gn_6_75800' => 'lsa', 'Lsat_1_v5_gn_6_75900' => 'lsa', 'Lsat_1_v5_gn_6_76240' => 'lsa', 'Lsat_1_v5_gn_6_76441' => 'lsa', 'Lsat_1_v5_gn_6_76700' => 'lsa', 'Lsat_1_v5_gn_6_76760' => 'lsa', 'Manes.15G033100' => 'mes', 'Mapoly0004s0074' => 'mpo', 'Mapoly0004s0075' => 'mpo', 'Mapoly0004s0163' => 'mpo', 'Mapoly0004s0164' => 'mpo', 'Mapoly0021s0018' => 'mpo', 'Mapoly0041s0136' => 'mpo', 'Mapoly0041s0137' => 'mpo', 'Mapoly0041s0138' => 'mpo', 'Mapoly0041s0139' => 'mpo', 'Mapoly0041s0141' => 'mpo', 'Mapoly0041s0142' => 'mpo', 'Mapoly0041s0143' => 'mpo', 'Mapoly0041s0144' => 'mpo', 'Mapoly0041s0145' => 'mpo', 'Mapoly0047s0106' => 'mpo', 'Mapoly0047s0108' => 'mpo', 'Mapoly0050s0051' => 'mpo', 'Mapoly0050s0052' => 'mpo', 'Mapoly0050s0053' => 'mpo', 'Mapoly0058s0013' => 'mpo', 'Mapoly0091s0078' => 'mpo', 'Mapoly0091s0079' => 'mpo', 'Mapoly0091s0080' => 'mpo', 'Mapoly0091s0081' => 'mpo', 'Mapoly0278s0004' => 'mpo', 'Mapoly0278s0005' => 'mpo', 'Mapoly0278s0006' => 'mpo', 'MBI11_g30648_MAGBIO' => 'mbi', 'MCO03G194' => 'mco', 'MCO03G590' => 'mco', 'MCO07G312' => 'mco', 'MCO10G318' => 'mco', 'MCO12G244' => 'mco', 'MCO13G148' => 'mco', 'MCO13G194' => 'mco', 'MCO16G238' => 'mco', 'MD06G1134100' => 'mdo', 'MD13G1200100' => 'mdo', 'MD13G1200300' => 'mdo', 'MD13G1200600' => 'mdo', 'MD14G1150400' => 'mdo', 'MD16G1200000' => 'mdo', 'Medtr1g102570' => 'mtr', 'Medtr1g102780' => 'mtr', 'Medtr1g102800' => 'mtr', 'Medtr1g102810' => 'mtr', 'Medtr1g102830' => 'mtr', 'MELO3C006499.2' => 'cme', 'Migut.G00385' => 'egut', 'MSTRG.4063' => 'ama', 'Nitab4.5_0000090g0260' => 'nta', 'Nitab4.5_0000977g0030' => 'nta', 'Nitab4.5_0002541g0040' => 'nta', 'Nitab4.5_0007068g0040' => 'nta', 'Nn005s41408' => 'nnu', 'Nn005s41410' => 'nnu', 'Oeu010310.1' => 'oeu', 'Oeu010311.1' => 'oeu', 'Oeu043472.1' => 'oeu', 'Os01g0246400' => 'osa', 'Os04g0267950' => 'osa', 'Os07g0178700' => 'osa', 'Os07g0178800' => 'osa', 'Peaxi162Scf00316g00046' => 'pax', 'Peaxi162Scf00316g00049' => 'pax', 'Peaxi162Scf00316g00059' => 'pax', 'Peaxi162Scf00316g00328' => 'pax', 'Peaxi162Scf00316g00329' => 'pax', 'Peaxi162Scf00316g00411' => 'pax', 'Peaxi162Scf00316g00521' => 'pax', 'Peaxi162Scf00492g00068' => 'pax', 'Peaxi162Scf35631g00002' => 'pax', 'PGR142G3720' => 'pgr', 'PGSC0003DMG400006442' => 'stu', 'Phvul.007G062000' => 'pvu', 'Potri.008G157750' => 'ptr', 'Potri.008G157900' => 'ptr', 'Potri.008G158000' => 'ptr', 'Potri.008G158200' => 'ptr', 'Pp3c11_7280' => 'ppa', 'Pp3c11_7980' => 'ppa', 'Pp3c12_19450' => 'ppa', 'Pp3c14_1480' => 'ppa', 'Pp3c14_1501' => 'ppa', 'Pp3c16_4900' => 'ppa', 'Pp3c16_5010' => 'ppa', 'Pp3c16_5060' => 'ppa', 'Pp3c19_18250' => 'ppa', 'Pp3c23_8530' => 'ppa', 'Pp3c23_8550' => 'ppa', 'Pp3c24_9670' => 'ppa', 'Pp3c2_21390' => 'ppa', 'Pp3c2_31380' => 'ppa', 'Pp3c3_16620' => 'ppa', 'Pp3c3_8090' => 'ppa', 'Pp3c3_8110' => 'ppa', 'Pp3c3_8130' => 'ppa', 'Pp3c3_8150' => 'ppa', 'Pp3c4_14320' => 'ppa', 'Pp3c6_2560' => 'ppa', 'Pp3c9_16700' => 'ppa', 'PRCOL_00000234' => 'pco', 'PRCOL_00000235' => 'pco', 'PRCOL_00000777' => 'pco', 'PRCOL_00002344' => 'pco', 'PRCOL_00002372' => 'pco', 'PRCOL_00006120' => 'pco', 'Prupe.1G021400' => 'ppe', 'Prupe.1G021500' => 'ppe', 'Prupe.1G021600' => 'ppe', 'Prupe.1G021700' => 'ppe', 'Prupe.1G021800' => 'ppe', 'Prupe.5G145100' => 'ppe', 'Psat6g204040' => 'psa', 'Psat6g204800' => 'psa', 'Psat6g204920' => 'psa', 'Psat6g204960' => 'psa', 'Psat6g205080' => 'psa', 'PSO017G0271' => 'pso', 'PSO017G1276' => 'pso', 'PSO017G1429' => 'pso', 'PSO017G1861' => 'pso', 'PSO017G2787' => 'pso', 'PSO017G4466' => 'pso', 'PSO017G5118' => 'pso', 'PSO017G5420' => 'pso', 'PSO063G3678' => 'pso', 'PSO210G0546' => 'pso', 'PSO317G0001' => 'pso', 'PSO357G0512' => 'pso', 'PSO478G2682' => 'pso', 'PSO647G0001' => 'pso', 'PSO675G0001' => 'pso', 'PSO675G2699' => 'pso', 'PSO675G2849' => 'pso', 'PSO675G4991' => 'pso', 'PSO689G0001' => 'pso', 'QL06p000916' => 'qlo', 'QL06p000921' => 'qlo', 'QL06p001398' => 'qlo', 'QL06p001407' => 'qlo', 'QL06p002031' => 'qlo', 'RcHm_v2.0_Chr4g0387791' => 'rch', 'RcHm_v2.0_Chr4g0387801' => 'rch', 'RcHm_v2.0_Chr6g0286501' => 'rch', 'RcHm_v2.0_Chr6g0286511' => 'rch', 'RcHm_v2.0_Chr6g0286521' => 'rch', 'RcHm_v2.0_Chr6g0286531' => 'rch', 'RcHm_v2.0_Chr7g0189141' => 'rch', 'Rhsim02G0028700' => 'rsi', 'Rhsim02G0028800' => 'rsi', 'Rhsim02G0028900' => 'rsi', 'Rhsim02G0029000' => 'rsi', 'Rhsim02G0029100' => 'rsi', 'Rhsim02G0029200' => 'rsi', 'Rhsim02G0029300' => 'rsi', 'Rhsim02G0029400' => 'rsi', 'Rhsim02G0029500' => 'rsi', 'Rhsim02G0029600' => 'rsi', 'RhsimUnG0024000' => 'rsi', 'RhsimUnG0024100' => 'rsi', 'RhsimUnG0024200' => 'rsi', 'RhsimUnG0024300' => 'rsi', 'RhsimUnG0024400' => 'rsi', 'RhsimUnG0024500' => 'rsi', 'RhsimUnG0024700' => 'rsi', 'RhsimUnG0024800' => 'rsi', 'RhsimUnG0024900' => 'rsi', 'RhsimUnG0025100' => 'rsi', 'Sabra08G0120200' => 'sbr', 'Sabra08G0120300' => 'sbr', 'Sabra08G0120500' => 'sbr', 'Sabra08G0120600' => 'sbr', 'Sabra10G0158900' => 'sbr', 'SalBow2G3492' => 'sbo', 'Sc13g0004760' => 'sci', 'Sc13g0004770' => 'sci', 'Sed0003417' => 'sed', 'Sed0019750' => 'sed', 'SEGI_03419' => 'sgi', 'SEGI_05907' => 'sgi', 'SEGI_10682' => 'sgi', 'SEGI_13528' => 'sgi', 'SEGI_16081' => 'sgi', 'SEGI_19370' => 'sgi', 'SEGI_21015' => 'sgi', 'SEGI_21944' => 'sgi', 'SEGI_32906' => 'sgi', 'SEGI_33093' => 'sgi', 'SEGI_36110' => 'sgi', 'SEGI_40397' => 'sgi', 'SGA_v2.0_scaffold191G40426' => 'sas', 'SGA_v2.0_scaffold353G49717' => 'sas', 'SGA_v2.0_scaffold50G18550' => 'sas', 'SMO119G0173' => 'smo', 'SMO172G0002' => 'smo', 'Solyc09g082690.3' => 'sly', 'Solyc09g082700.2' => 'sly', 'Sopen09g031550' => 'spe', 'Sopen09g031560' => 'spe', 'Sp3g20540' => 'spa', 'Sp7g07580' => 'spa', 'TAR134G0002' => 'tar', 'TAR236G0001' => 'tar', 'TAR365G0892' => 'tar', 'TAR636G0166' => 'tar', 'TAR636G0646' => 'tar', 'TAR636G0869' => 'tar', 'TAR636G1317' => 'tar', 'TAR636G1744' => 'tar', 'TAR636G3358' => 'tar', 'TAR636G3436' => 'tar', 'THA.LOC104803047' => 'tha', 'Thecc.04G238900' => 'tca', 'Thhalv10021557m.g' => 'esa', 'Thhalv10026318m.g' => 'esa', 'Thhalv10026335m.g' => 'esa', 'TPR.G17433' => 'tpr', 'TPR.G18915' => 'tpr', 'TPR.G26125' => 'tpr', 'TWI09G0677' => 'twi', 'TWI73G0287' => 'twi', 'unitig_748.g8326' => 'ugi', 'vmacro15370' => 'vma', 'vmacro15371' => 'vma', 'vmacro15372' => 'vma', 'vmacro15373' => 'vma', 'vmacro15374' => 'vma', 'VMungo0720G2826' => 'vmu', 'Zm00001eb116960' => 'zma', 'Zm00001eb301260' => 'zma', 'Zm00001eb301270' => 'zma' ), 'gf_id' => 'HOM05D001460', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001460' ), 'data_identifier' => 'HOM05D001460', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001460', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '433', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p22980' => 'bna', 'A01p32340' => 'bna', 'A03p42970' => 'bna', 'A05p25880' => 'bna', 'Aa31LG8G9320' => 'aar', 'Aa31LG8G9330' => 'aar', 'Aa31LG8G9340' => 'aar', 'Aa31sc221G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1034' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1528' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.829' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2222' => 'aag', 'Ah.12g058830' => 'amhyb', 'Ah.12g058840' => 'amhyb', 'AL3G37160' => 'aly', 'AL7G41310' => 'aly', 'Aqoxy5G00395' => 'aox', 'Aqoxy5G00396' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0C8NZA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5185HY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JZ1PRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MD3LS0' => 'arhy', 'AT3G22840' => 'ath', 'AT4G14690' => 'ath', 'ATR0665G054' => 'atr', 'Atru.chr4.2344' => 'acertr', 'Atru.chr4.2346' => 'acertr', 'Atru.chr4.2347' => 'acertr', 'Atru.chr4.2348' => 'acertr', 'Atru.chr4.2355' => 'acertr', 'Atru.chr4.2356' => 'acertr', 'Atru.chr4.2358' => 'acertr', 'Atru.chr4.2359' => 'acertr', 'Atru.chr4.2360' => 'acertr', 'Atru.chr4.2361' => 'acertr', 'AUR62030476' => 'cqu', 'AUR62030478' => 'cqu', 'AUR62030819' => 'cqu', 'AUR62030820' => 'cqu', 'BcaB03g14648' => 'bca', 'BcaB04g20492' => 'bca', 'BcaB06g26399' => 'bca', 'BcaC01g03416' => 'bca', 'BcaC01g03419' => 'bca', 'BcaC01g03421' => 'bca', 'BcaC01g03424' => 'bca', 'BcaC05g28012' => 'bca', 'BcaC09g49212' => 'bca', 'BcaC09g50140' => 'bca', 'BcaNung00346' => 'bca', 'BolC1t02785H' => 'bol', 'BolC1t04095H' => 'bol', 'BolC3t17545H' => 'bol', 'BolC5t32769H' => 'bol', 'BraA01t02211Z' => 'bra', 'BraA01t03359Z' => 'bra', 'BraA03t13441Z' => 'bra', 'BraA05t21476Z' => 'bra', 'C01p28420' => 'bna', 'C01p41350' => 'bna', 'C03p52750' => 'bna', 'C03p52780' => 'bna', 'C05p40270' => 'bna', 'CAN.G1437.9' => 'can', 'CANSAT78G0035' => 'cansat', 'CANSAT78G1036' => 'cansat', 'CANSAT78G2272' => 'cansat', 'CANSAT78G2478' => 'cansat', 'CARHR098700' => 'chi', 'CARHR221120' => 'chi', 'CARHR221150' => 'chi', 'Carub.0003s2297' => 'cru', 'Carub.0007s2749' => 'cru', 'Carub.0007s2750' => 'cru', 'Carub.0007s2751' => 'cru', 'Ca_10849_v3' => 'car', 'Cc03_g04300' => 'ccan', 'CDE02G3648' => 'cde', 'CDE05G0060' => 'cde', 'CDE05G0692' => 'cde', 'CDE05G2285' => 'cde', 'CDE05G2884' => 'cde', 'CDE05G3072' => 'cde', 'Cfa008439' => 'cfa', 'Cfa008441' => 'cfa', 'Cfa008443' => 'cfa', 'Cfa008448' => 'cfa', 'Ciclev10005974m.g' => 'ccl', 'Ciclev10006006m.g' => 'ccl', 'Ciclev10006775m.g' => 'ccl', 'CiPaw.02G120400' => 'cil', 'CiPaw.02G120500' => 'cil', 'CiPaw.02G120600' => 'cil', 'ClCG05G004850' => 'cla', 'COL.COLO4_21566' => 'col', 'Cpa.g.sc44.124' => 'cpa', 'Cre07.g320400' => 'cre', 'Cre07.g320450' => 'cre', 'Cre08.g384650' => 'cre', 'Cre09.g393173' => 'cre', 'Cre09.g394325' => 'cre', 'Cre14.g626750' => 'cre', 'Cre16.g679250' => 'cre', 'CsaV3_3G012890' => 'csa', 'CSS0010865' => 'camsi', 'CSS0044338' => 'camsi', 'DCAR_002366' => 'dca', 'DCAR_030687' => 'dca', 'DCAR_030688' => 'dca', 'Dinv14047' => 'din', 'Dinv14048' => 'din', 'Duzib151G0105' => 'dzi', 'Duzib151G0114' => 'dzi', 'Duzib212G1029' => 'dzi', 'ECA232G3536' => 'eca', 'ECA240G0786' => 'eca', 'ECA240G1802' => 'eca', 'ECA240G3760' => 'eca', 'ECA240G3920' => 'eca', 'EL10Ac5g12536' => 'bvu', 'EL10Ac5g12537' => 'bvu', 'EL10Ac5g12538' => 'bvu', 'Eucgr.B01004' => 'egr', 'Eucgr.B01006' => 'egr', 'Eucgr.B01007' => 'egr', 'Eucgr.B01008' => 'egr', 'Eucgr.B01895' => 'egr', 'Eucgr.B01896' => 'egr', 'FAN04G1456' => 'fan', 'FAN08G1769' => 'fan', 'FAN08G2160' => 'fan', 'FAN13G2403' => 'fan', 'FAN13G3303' => 'fan', 'FAN15G2435' => 'fan', 'FAN17G0672' => 'fan', 'FAN17G2441' => 'fan', 'FAN18G1024' => 'fan', 'FAN22G1458' => 'fan', 'FAN24G0037' => 'fan', 'FAN24G0429' => 'fan', 'FAN24G2387' => 'fan', 'FAN27G2746' => 'fan', 'FvH4_2g20400' => 'fve', 'FvH4_2g20420' => 'fve', 'FvH4_2g20430' => 'fve', 'FvH4_4g01270' => 'fve', 'FvH4_4g01290' => 'fve', 'FvH4_4g01300' => 'fve', 'FvH4_4g01310' => 'fve', 'FvH4_4g01330' => 'fve', 'FvH4_5g09070' => 'fve', 'Glyma.10G243800' => 'gma', 'Glyma.20G150600' => 'gma', 'Gohir.A09G219200' => 'ghi', 'Gohir.A09G219300' => 'ghi', 'Gohir.D09G221400' => 'ghi', 'Gohir.D09G221500' => 'ghi', 'Gorai.006G242600' => 'gra', 'Gorai.006G242700' => 'gra', 'GSVIVG01018044001' => 'vvi', 'HanXRQChr03g0083821' => 'han', 'HanXRQChr03g0083841' => 'han', 'HanXRQChr03g0083881' => 'han', 'HanXRQChr03g0083901' => 'han', 'HanXRQChr03g0083921' => 'han', 'HanXRQChr03g0085331' => 'han', 'HanXRQChr03g0085361' => 'han', 'HanXRQChr03g0085411' => 'han', 'HanXRQChr03g0085421' => 'han', 'HanXRQChr03g0085431' => 'han', 'HanXRQChr08g0221991' => 'han', 'HanXRQChr11g0336061' => 'han', 'HanXRQChr11g0336411' => 'han', 'Haze_11234' => 'cav', 'Hma1.2p1_0549F.1_g177010' => 'hma', 'Hma1.2p1_0602F.1_g187630' => 'hma', 'Hund14876' => 'sun', 'Hund14879' => 'sun', 'Lalb_Chr06g0160741' => 'lal', 'Lalb_Chr21g0304781' => 'lal', 'Lj3A726G19' => 'lonja', 'Lj3A726T23' => 'lonja', 'Lj3A726T24' => 'lonja', 'Lj3A726T25' => 'lonja', 'Lj3A727T17' => 'lonja', 'Lj3C726T0' => 'lonja', 'Lj3C726T2' => 'lonja', 'Lj3P725T35' => 'lonja', 'Lj3P727T10' => 'lonja', 'Lj3P727T12' => 'lonja', 'Lj3P727T14' => 'lonja', 'Lj5g0023109' => 'lja', 'Lj6P646T44' => 'lonja', 'Lsat_1_v5_gn_6_75760' => 'lsa', 'Lsat_1_v5_gn_6_75800' => 'lsa', 'Lsat_1_v5_gn_6_75900' => 'lsa', 'Lsat_1_v5_gn_6_76240' => 'lsa', 'Lsat_1_v5_gn_6_76441' => 'lsa', 'Lsat_1_v5_gn_6_76700' => 'lsa', 'Lsat_1_v5_gn_6_76760' => 'lsa', 'Manes.15G033100' => 'mes', 'Mapoly0004s0074' => 'mpo', 'Mapoly0004s0075' => 'mpo', 'Mapoly0004s0163' => 'mpo', 'Mapoly0004s0164' => 'mpo', 'Mapoly0021s0018' => 'mpo', 'Mapoly0041s0136' => 'mpo', 'Mapoly0041s0137' => 'mpo', 'Mapoly0041s0138' => 'mpo', 'Mapoly0041s0139' => 'mpo', 'Mapoly0041s0141' => 'mpo', 'Mapoly0041s0142' => 'mpo', 'Mapoly0041s0143' => 'mpo', 'Mapoly0041s0144' => 'mpo', 'Mapoly0041s0145' => 'mpo', 'Mapoly0047s0106' => 'mpo', 'Mapoly0047s0108' => 'mpo', 'Mapoly0050s0051' => 'mpo', 'Mapoly0050s0052' => 'mpo', 'Mapoly0050s0053' => 'mpo', 'Mapoly0058s0013' => 'mpo', 'Mapoly0091s0078' => 'mpo', 'Mapoly0091s0079' => 'mpo', 'Mapoly0091s0080' => 'mpo', 'Mapoly0091s0081' => 'mpo', 'Mapoly0278s0004' => 'mpo', 'Mapoly0278s0005' => 'mpo', 'Mapoly0278s0006' => 'mpo', 'MBI11_g30648_MAGBIO' => 'mbi', 'MCO03G194' => 'mco', 'MCO03G590' => 'mco', 'MCO07G312' => 'mco', 'MCO10G318' => 'mco', 'MCO12G244' => 'mco', 'MCO13G148' => 'mco', 'MCO13G194' => 'mco', 'MCO16G238' => 'mco', 'MD06G1134100' => 'mdo', 'MD13G1200100' => 'mdo', 'MD13G1200300' => 'mdo', 'MD13G1200600' => 'mdo', 'MD14G1150400' => 'mdo', 'MD16G1200000' => 'mdo', 'Medtr1g102570' => 'mtr', 'Medtr1g102780' => 'mtr', 'Medtr1g102800' => 'mtr', 'Medtr1g102810' => 'mtr', 'Medtr1g102830' => 'mtr', 'MELO3C006499.2' => 'cme', 'Migut.G00385' => 'egut', 'MSTRG.4063' => 'ama', 'Nitab4.5_0000090g0260' => 'nta', 'Nitab4.5_0000977g0030' => 'nta', 'Nitab4.5_0002541g0040' => 'nta', 'Nitab4.5_0007068g0040' => 'nta', 'Nn005s41408' => 'nnu', 'Nn005s41410' => 'nnu', 'Oeu010310.1' => 'oeu', 'Oeu010311.1' => 'oeu', 'Oeu043472.1' => 'oeu', 'Os01g0246400' => 'osa', 'Os04g0267950' => 'osa', 'Os07g0178700' => 'osa', 'Os07g0178800' => 'osa', 'Peaxi162Scf00316g00046' => 'pax', 'Peaxi162Scf00316g00049' => 'pax', 'Peaxi162Scf00316g00059' => 'pax', 'Peaxi162Scf00316g00328' => 'pax', 'Peaxi162Scf00316g00329' => 'pax', 'Peaxi162Scf00316g00411' => 'pax', 'Peaxi162Scf00316g00521' => 'pax', 'Peaxi162Scf00492g00068' => 'pax', 'Peaxi162Scf35631g00002' => 'pax', 'PGR142G3720' => 'pgr', 'PGSC0003DMG400006442' => 'stu', 'Phvul.007G062000' => 'pvu', 'Potri.008G157750' => 'ptr', 'Potri.008G157900' => 'ptr', 'Potri.008G158000' => 'ptr', 'Potri.008G158200' => 'ptr', 'Pp3c11_7280' => 'ppa', 'Pp3c11_7980' => 'ppa', 'Pp3c12_19450' => 'ppa', 'Pp3c14_1480' => 'ppa', 'Pp3c14_1501' => 'ppa', 'Pp3c16_4900' => 'ppa', 'Pp3c16_5010' => 'ppa', 'Pp3c16_5060' => 'ppa', 'Pp3c19_18250' => 'ppa', 'Pp3c23_8530' => 'ppa', 'Pp3c23_8550' => 'ppa', 'Pp3c24_9670' => 'ppa', 'Pp3c2_21390' => 'ppa', 'Pp3c2_31380' => 'ppa', 'Pp3c3_16620' => 'ppa', 'Pp3c3_8090' => 'ppa', 'Pp3c3_8110' => 'ppa', 'Pp3c3_8130' => 'ppa', 'Pp3c3_8150' => 'ppa', 'Pp3c4_14320' => 'ppa', 'Pp3c6_2560' => 'ppa', 'Pp3c9_16700' => 'ppa', 'PRCOL_00000234' => 'pco', 'PRCOL_00000235' => 'pco', 'PRCOL_00000777' => 'pco', 'PRCOL_00002344' => 'pco', 'PRCOL_00002372' => 'pco', 'PRCOL_00006120' => 'pco', 'Prupe.1G021400' => 'ppe', 'Prupe.1G021500' => 'ppe', 'Prupe.1G021600' => 'ppe', 'Prupe.1G021700' => 'ppe', 'Prupe.1G021800' => 'ppe', 'Prupe.5G145100' => 'ppe', 'Psat6g204040' => 'psa', 'Psat6g204800' => 'psa', 'Psat6g204920' => 'psa', 'Psat6g204960' => 'psa', 'Psat6g205080' => 'psa', 'PSO017G0271' => 'pso', 'PSO017G1276' => 'pso', 'PSO017G1429' => 'pso', 'PSO017G1861' => 'pso', 'PSO017G2787' => 'pso', 'PSO017G4466' => 'pso', 'PSO017G5118' => 'pso', 'PSO017G5420' => 'pso', 'PSO063G3678' => 'pso', 'PSO210G0546' => 'pso', 'PSO317G0001' => 'pso', 'PSO357G0512' => 'pso', 'PSO478G2682' => 'pso', 'PSO647G0001' => 'pso', 'PSO675G0001' => 'pso', 'PSO675G2699' => 'pso', 'PSO675G2849' => 'pso', 'PSO675G4991' => 'pso', 'PSO689G0001' => 'pso', 'QL06p000916' => 'qlo', 'QL06p000921' => 'qlo', 'QL06p001398' => 'qlo', 'QL06p001407' => 'qlo', 'QL06p002031' => 'qlo', 'RcHm_v2.0_Chr4g0387791' => 'rch', 'RcHm_v2.0_Chr4g0387801' => 'rch', 'RcHm_v2.0_Chr6g0286501' => 'rch', 'RcHm_v2.0_Chr6g0286511' => 'rch', 'RcHm_v2.0_Chr6g0286521' => 'rch', 'RcHm_v2.0_Chr6g0286531' => 'rch', 'RcHm_v2.0_Chr7g0189141' => 'rch', 'Rhsim02G0028700' => 'rsi', 'Rhsim02G0028800' => 'rsi', 'Rhsim02G0028900' => 'rsi', 'Rhsim02G0029000' => 'rsi', 'Rhsim02G0029100' => 'rsi', 'Rhsim02G0029200' => 'rsi', 'Rhsim02G0029300' => 'rsi', 'Rhsim02G0029400' => 'rsi', 'Rhsim02G0029500' => 'rsi', 'Rhsim02G0029600' => 'rsi', 'RhsimUnG0024000' => 'rsi', 'RhsimUnG0024100' => 'rsi', 'RhsimUnG0024200' => 'rsi', 'RhsimUnG0024300' => 'rsi', 'RhsimUnG0024400' => 'rsi', 'RhsimUnG0024500' => 'rsi', 'RhsimUnG0024700' => 'rsi', 'RhsimUnG0024800' => 'rsi', 'RhsimUnG0024900' => 'rsi', 'RhsimUnG0025100' => 'rsi', 'Sabra08G0120200' => 'sbr', 'Sabra08G0120300' => 'sbr', 'Sabra08G0120500' => 'sbr', 'Sabra08G0120600' => 'sbr', 'Sabra10G0158900' => 'sbr', 'SalBow2G3492' => 'sbo', 'Sc13g0004760' => 'sci', 'Sc13g0004770' => 'sci', 'Sed0003417' => 'sed', 'Sed0019750' => 'sed', 'SEGI_03419' => 'sgi', 'SEGI_05907' => 'sgi', 'SEGI_10682' => 'sgi', 'SEGI_13528' => 'sgi', 'SEGI_16081' => 'sgi', 'SEGI_19370' => 'sgi', 'SEGI_21015' => 'sgi', 'SEGI_21944' => 'sgi', 'SEGI_32906' => 'sgi', 'SEGI_33093' => 'sgi', 'SEGI_36110' => 'sgi', 'SEGI_40397' => 'sgi', 'SGA_v2.0_scaffold191G40426' => 'sas', 'SGA_v2.0_scaffold353G49717' => 'sas', 'SGA_v2.0_scaffold50G18550' => 'sas', 'SMO119G0173' => 'smo', 'SMO172G0002' => 'smo', 'Solyc09g082690.3' => 'sly', 'Solyc09g082700.2' => 'sly', 'Sopen09g031550' => 'spe', 'Sopen09g031560' => 'spe', 'Sp3g20540' => 'spa', 'Sp7g07580' => 'spa', 'TAR134G0002' => 'tar', 'TAR236G0001' => 'tar', 'TAR365G0892' => 'tar', 'TAR636G0166' => 'tar', 'TAR636G0646' => 'tar', 'TAR636G0869' => 'tar', 'TAR636G1317' => 'tar', 'TAR636G1744' => 'tar', 'TAR636G3358' => 'tar', 'TAR636G3436' => 'tar', 'THA.LOC104803047' => 'tha', 'Thecc.04G238900' => 'tca', 'Thhalv10021557m.g' => 'esa', 'Thhalv10026318m.g' => 'esa', 'Thhalv10026335m.g' => 'esa', 'TPR.G17433' => 'tpr', 'TPR.G18915' => 'tpr', 'TPR.G26125' => 'tpr', 'TWI09G0677' => 'twi', 'TWI73G0287' => 'twi', 'unitig_748.g8326' => 'ugi', 'vmacro15370' => 'vma', 'vmacro15371' => 'vma', 'vmacro15372' => 'vma', 'vmacro15373' => 'vma', 'vmacro15374' => 'vma', 'VMungo0720G2826' => 'vmu', 'Zm00001eb116960' => 'zma', 'Zm00001eb301260' => 'zma', 'Zm00001eb301270' => 'zma' ) $gf_id = 'HOM05D001460' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001460' ) $data_identifier = 'HOM05D001460' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 4, 'aag' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 2, 'aox' => (int) 2, 'arhy' => (int) 4, 'ath' => (int) 2, 'atr' => (int) 1, 'acertr' => (int) 10, 'cqu' => (int) 4, 'bca' => (int) 11, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 1, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 1, 'ccan' => (int) 1, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 1, 'col' => (int) 1, 'cpa' => (int) 1, 'cre' => (int) 7, 'csa' => (int) 1, 'camsi' => (int) 2, 'dca' => (int) 3, 'din' => (int) 2, 'dzi' => (int) 3, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 14, 'fve' => (int) 9, 'gma' => (int) 2, 'ghi' => (int) 4, 'gra' => (int) 2, 'vvi' => (int) 1, 'han' => (int) 13, 'cav' => (int) 1, 'hma' => (int) 2, 'sun' => (int) 2, 'lal' => (int) 2, 'lonja' => (int) 12, 'lja' => (int) 1, 'lsa' => (int) 7, 'mes' => (int) 1, 'mpo' => (int) 27, 'mbi' => (int) 1, 'mco' => (int) 8, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 1, 'egut' => (int) 1, 'ama' => (int) 1, 'nta' => (int) 4, 'nnu' => (int) 2, 'oeu' => (int) 3, 'osa' => (int) 4, 'pax' => (int) 9, 'pgr' => (int) 1, 'stu' => (int) 1, 'pvu' => (int) 1, 'ptr' => (int) 4, 'ppa' => (int) 22, 'pco' => (int) 6, 'ppe' => (int) 6, 'psa' => (int) 5, 'pso' => (int) 19, 'qlo' => (int) 5, 'rch' => (int) 7, 'rsi' => (int) 20, 'sbr' => (int) 5, 'sbo' => (int) 1, 'sci' => (int) 2, 'sed' => (int) 2, 'sgi' => (int) 12, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 2, 'tar' => (int) 10, 'tha' => (int) 1, 'tca' => (int) 1, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 2, 'ugi' => (int) 1, 'vma' => (int) 5, 'vmu' => (int) 1, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb301270' $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' => 'HOM05D001460', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '433', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p22980' => 'bna', 'A01p32340' => 'bna', 'A03p42970' => 'bna', 'A05p25880' => 'bna', 'Aa31LG8G9320' => 'aar', 'Aa31LG8G9330' => 'aar', 'Aa31LG8G9340' => 'aar', 'Aa31sc221G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1034' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1528' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.829' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2222' => 'aag', 'Ah.12g058830' => 'amhyb', 'Ah.12g058840' => 'amhyb', 'AL3G37160' => 'aly', 'AL7G41310' => 'aly', 'Aqoxy5G00395' => 'aox', 'Aqoxy5G00396' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0C8NZA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5185HY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JZ1PRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MD3LS0' => 'arhy', 'AT3G22840' => 'ath', 'AT4G14690' => 'ath', 'ATR0665G054' => 'atr', 'Atru.chr4.2344' => 'acertr', 'Atru.chr4.2346' => 'acertr', 'Atru.chr4.2347' => 'acertr', 'Atru.chr4.2348' => 'acertr', 'Atru.chr4.2355' => 'acertr', 'Atru.chr4.2356' => 'acertr', 'Atru.chr4.2358' => 'acertr', 'Atru.chr4.2359' => 'acertr', 'Atru.chr4.2360' => 'acertr', 'Atru.chr4.2361' => 'acertr', 'AUR62030476' => 'cqu', 'AUR62030478' => 'cqu', 'AUR62030819' => 'cqu', 'AUR62030820' => 'cqu', 'BcaB03g14648' => 'bca', 'BcaB04g20492' => 'bca', 'BcaB06g26399' => 'bca', 'BcaC01g03416' => 'bca', 'BcaC01g03419' => 'bca', 'BcaC01g03421' => 'bca', 'BcaC01g03424' => 'bca', 'BcaC05g28012' => 'bca', 'BcaC09g49212' => 'bca', 'BcaC09g50140' => 'bca', 'BcaNung00346' => 'bca', 'BolC1t02785H' => 'bol', 'BolC1t04095H' => 'bol', 'BolC3t17545H' => 'bol', 'BolC5t32769H' => 'bol', 'BraA01t02211Z' => 'bra', 'BraA01t03359Z' => 'bra', 'BraA03t13441Z' => 'bra', 'BraA05t21476Z' => 'bra', 'C01p28420' => 'bna', 'C01p41350' => 'bna', 'C03p52750' => 'bna', 'C03p52780' => 'bna', 'C05p40270' => 'bna', 'CAN.G1437.9' => 'can', 'CANSAT78G0035' => 'cansat', 'CANSAT78G1036' => 'cansat', 'CANSAT78G2272' => 'cansat', 'CANSAT78G2478' => 'cansat', 'CARHR098700' => 'chi', 'CARHR221120' => 'chi', 'CARHR221150' => 'chi', 'Carub.0003s2297' => 'cru', 'Carub.0007s2749' => 'cru', 'Carub.0007s2750' => 'cru', 'Carub.0007s2751' => 'cru', 'Ca_10849_v3' => 'car', 'Cc03_g04300' => 'ccan', 'CDE02G3648' => 'cde', 'CDE05G0060' => 'cde', 'CDE05G0692' => 'cde', 'CDE05G2285' => 'cde', 'CDE05G2884' => 'cde', 'CDE05G3072' => 'cde', 'Cfa008439' => 'cfa', 'Cfa008441' => 'cfa', 'Cfa008443' => 'cfa', 'Cfa008448' => 'cfa', 'Ciclev10005974m.g' => 'ccl', 'Ciclev10006006m.g' => 'ccl', 'Ciclev10006775m.g' => 'ccl', 'CiPaw.02G120400' => 'cil', 'CiPaw.02G120500' => 'cil', 'CiPaw.02G120600' => 'cil', 'ClCG05G004850' => 'cla', 'COL.COLO4_21566' => 'col', 'Cpa.g.sc44.124' => 'cpa', 'Cre07.g320400' => 'cre', 'Cre07.g320450' => 'cre', 'Cre08.g384650' => 'cre', 'Cre09.g393173' => 'cre', 'Cre09.g394325' => 'cre', 'Cre14.g626750' => 'cre', 'Cre16.g679250' => 'cre', 'CsaV3_3G012890' => 'csa', 'CSS0010865' => 'camsi', 'CSS0044338' => 'camsi', 'DCAR_002366' => 'dca', 'DCAR_030687' => 'dca', 'DCAR_030688' => 'dca', 'Dinv14047' => 'din', 'Dinv14048' => 'din', 'Duzib151G0105' => 'dzi', 'Duzib151G0114' => 'dzi', 'Duzib212G1029' => 'dzi', 'ECA232G3536' => 'eca', 'ECA240G0786' => 'eca', 'ECA240G1802' => 'eca', 'ECA240G3760' => 'eca', 'ECA240G3920' => 'eca', 'EL10Ac5g12536' => 'bvu', 'EL10Ac5g12537' => 'bvu', 'EL10Ac5g12538' => 'bvu', 'Eucgr.B01004' => 'egr', 'Eucgr.B01006' => 'egr', 'Eucgr.B01007' => 'egr', 'Eucgr.B01008' => 'egr', 'Eucgr.B01895' => 'egr', 'Eucgr.B01896' => 'egr', 'FAN04G1456' => 'fan', 'FAN08G1769' => 'fan', 'FAN08G2160' => 'fan', 'FAN13G2403' => 'fan', 'FAN13G3303' => 'fan', 'FAN15G2435' => 'fan', 'FAN17G0672' => 'fan', 'FAN17G2441' => 'fan', 'FAN18G1024' => 'fan', 'FAN22G1458' => 'fan', 'FAN24G0037' => 'fan', 'FAN24G0429' => 'fan', 'FAN24G2387' => 'fan', 'FAN27G2746' => 'fan', 'FvH4_2g20400' => 'fve', 'FvH4_2g20420' => 'fve', 'FvH4_2g20430' => 'fve', 'FvH4_4g01270' => 'fve', 'FvH4_4g01290' => 'fve', 'FvH4_4g01300' => 'fve', 'FvH4_4g01310' => 'fve', 'FvH4_4g01330' => 'fve', 'FvH4_5g09070' => 'fve', 'Glyma.10G243800' => 'gma', 'Glyma.20G150600' => 'gma', 'Gohir.A09G219200' => 'ghi', 'Gohir.A09G219300' => 'ghi', 'Gohir.D09G221400' => 'ghi', 'Gohir.D09G221500' => 'ghi', 'Gorai.006G242600' => 'gra', 'Gorai.006G242700' => 'gra', 'GSVIVG01018044001' => 'vvi', 'HanXRQChr03g0083821' => 'han', 'HanXRQChr03g0083841' => 'han', 'HanXRQChr03g0083881' => 'han', 'HanXRQChr03g0083901' => 'han', 'HanXRQChr03g0083921' => 'han', 'HanXRQChr03g0085331' => 'han', 'HanXRQChr03g0085361' => 'han', 'HanXRQChr03g0085411' => 'han', 'HanXRQChr03g0085421' => 'han', 'HanXRQChr03g0085431' => 'han', 'HanXRQChr08g0221991' => 'han', 'HanXRQChr11g0336061' => 'han', 'HanXRQChr11g0336411' => 'han', 'Haze_11234' => 'cav', 'Hma1.2p1_0549F.1_g177010' => 'hma', 'Hma1.2p1_0602F.1_g187630' => 'hma', 'Hund14876' => 'sun', 'Hund14879' => 'sun', 'Lalb_Chr06g0160741' => 'lal', 'Lalb_Chr21g0304781' => 'lal', 'Lj3A726G19' => 'lonja', 'Lj3A726T23' => 'lonja', 'Lj3A726T24' => 'lonja', 'Lj3A726T25' => 'lonja', 'Lj3A727T17' => 'lonja', 'Lj3C726T0' => 'lonja', 'Lj3C726T2' => 'lonja', 'Lj3P725T35' => 'lonja', 'Lj3P727T10' => 'lonja', 'Lj3P727T12' => 'lonja', 'Lj3P727T14' => 'lonja', 'Lj5g0023109' => 'lja', 'Lj6P646T44' => 'lonja', 'Lsat_1_v5_gn_6_75760' => 'lsa', 'Lsat_1_v5_gn_6_75800' => 'lsa', 'Lsat_1_v5_gn_6_75900' => 'lsa', 'Lsat_1_v5_gn_6_76240' => 'lsa', 'Lsat_1_v5_gn_6_76441' => 'lsa', 'Lsat_1_v5_gn_6_76700' => 'lsa', 'Lsat_1_v5_gn_6_76760' => 'lsa', 'Manes.15G033100' => 'mes', 'Mapoly0004s0074' => 'mpo', 'Mapoly0004s0075' => 'mpo', 'Mapoly0004s0163' => 'mpo', 'Mapoly0004s0164' => 'mpo', 'Mapoly0021s0018' => 'mpo', 'Mapoly0041s0136' => 'mpo', 'Mapoly0041s0137' => 'mpo', 'Mapoly0041s0138' => 'mpo', 'Mapoly0041s0139' => 'mpo', 'Mapoly0041s0141' => 'mpo', 'Mapoly0041s0142' => 'mpo', 'Mapoly0041s0143' => 'mpo', 'Mapoly0041s0144' => 'mpo', 'Mapoly0041s0145' => 'mpo', 'Mapoly0047s0106' => 'mpo', 'Mapoly0047s0108' => 'mpo', 'Mapoly0050s0051' => 'mpo', 'Mapoly0050s0052' => 'mpo', 'Mapoly0050s0053' => 'mpo', 'Mapoly0058s0013' => 'mpo', 'Mapoly0091s0078' => 'mpo', 'Mapoly0091s0079' => 'mpo', 'Mapoly0091s0080' => 'mpo', 'Mapoly0091s0081' => 'mpo', 'Mapoly0278s0004' => 'mpo', 'Mapoly0278s0005' => 'mpo', 'Mapoly0278s0006' => 'mpo', 'MBI11_g30648_MAGBIO' => 'mbi', 'MCO03G194' => 'mco', 'MCO03G590' => 'mco', 'MCO07G312' => 'mco', 'MCO10G318' => 'mco', 'MCO12G244' => 'mco', 'MCO13G148' => 'mco', 'MCO13G194' => 'mco', 'MCO16G238' => 'mco', 'MD06G1134100' => 'mdo', 'MD13G1200100' => 'mdo', 'MD13G1200300' => 'mdo', 'MD13G1200600' => 'mdo', 'MD14G1150400' => 'mdo', 'MD16G1200000' => 'mdo', 'Medtr1g102570' => 'mtr', 'Medtr1g102780' => 'mtr', 'Medtr1g102800' => 'mtr', 'Medtr1g102810' => 'mtr', 'Medtr1g102830' => 'mtr', 'MELO3C006499.2' => 'cme', 'Migut.G00385' => 'egut', 'MSTRG.4063' => 'ama', 'Nitab4.5_0000090g0260' => 'nta', 'Nitab4.5_0000977g0030' => 'nta', 'Nitab4.5_0002541g0040' => 'nta', 'Nitab4.5_0007068g0040' => 'nta', 'Nn005s41408' => 'nnu', 'Nn005s41410' => 'nnu', 'Oeu010310.1' => 'oeu', 'Oeu010311.1' => 'oeu', 'Oeu043472.1' => 'oeu', 'Os01g0246400' => 'osa', 'Os04g0267950' => 'osa', 'Os07g0178700' => 'osa', 'Os07g0178800' => 'osa', 'Peaxi162Scf00316g00046' => 'pax', 'Peaxi162Scf00316g00049' => 'pax', 'Peaxi162Scf00316g00059' => 'pax', 'Peaxi162Scf00316g00328' => 'pax', 'Peaxi162Scf00316g00329' => 'pax', 'Peaxi162Scf00316g00411' => 'pax', 'Peaxi162Scf00316g00521' => 'pax', 'Peaxi162Scf00492g00068' => 'pax', 'Peaxi162Scf35631g00002' => 'pax', 'PGR142G3720' => 'pgr', 'PGSC0003DMG400006442' => 'stu', 'Phvul.007G062000' => 'pvu', 'Potri.008G157750' => 'ptr', 'Potri.008G157900' => 'ptr', 'Potri.008G158000' => 'ptr', 'Potri.008G158200' => 'ptr', 'Pp3c11_7280' => 'ppa', 'Pp3c11_7980' => 'ppa', 'Pp3c12_19450' => 'ppa', 'Pp3c14_1480' => 'ppa', 'Pp3c14_1501' => 'ppa', 'Pp3c16_4900' => 'ppa', 'Pp3c16_5010' => 'ppa', 'Pp3c16_5060' => 'ppa', 'Pp3c19_18250' => 'ppa', 'Pp3c23_8530' => 'ppa', 'Pp3c23_8550' => 'ppa', 'Pp3c24_9670' => 'ppa', 'Pp3c2_21390' => 'ppa', 'Pp3c2_31380' => 'ppa', 'Pp3c3_16620' => 'ppa', 'Pp3c3_8090' => 'ppa', 'Pp3c3_8110' => 'ppa', 'Pp3c3_8130' => 'ppa', 'Pp3c3_8150' => 'ppa', 'Pp3c4_14320' => 'ppa', 'Pp3c6_2560' => 'ppa', 'Pp3c9_16700' => 'ppa', 'PRCOL_00000234' => 'pco', 'PRCOL_00000235' => 'pco', 'PRCOL_00000777' => 'pco', 'PRCOL_00002344' => 'pco', 'PRCOL_00002372' => 'pco', 'PRCOL_00006120' => 'pco', 'Prupe.1G021400' => 'ppe', 'Prupe.1G021500' => 'ppe', 'Prupe.1G021600' => 'ppe', 'Prupe.1G021700' => 'ppe', 'Prupe.1G021800' => 'ppe', 'Prupe.5G145100' => 'ppe', 'Psat6g204040' => 'psa', 'Psat6g204800' => 'psa', 'Psat6g204920' => 'psa', 'Psat6g204960' => 'psa', 'Psat6g205080' => 'psa', 'PSO017G0271' => 'pso', 'PSO017G1276' => 'pso', 'PSO017G1429' => 'pso', 'PSO017G1861' => 'pso', 'PSO017G2787' => 'pso', 'PSO017G4466' => 'pso', 'PSO017G5118' => 'pso', 'PSO017G5420' => 'pso', 'PSO063G3678' => 'pso', 'PSO210G0546' => 'pso', 'PSO317G0001' => 'pso', 'PSO357G0512' => 'pso', 'PSO478G2682' => 'pso', 'PSO647G0001' => 'pso', 'PSO675G0001' => 'pso', 'PSO675G2699' => 'pso', 'PSO675G2849' => 'pso', 'PSO675G4991' => 'pso', 'PSO689G0001' => 'pso', 'QL06p000916' => 'qlo', 'QL06p000921' => 'qlo', 'QL06p001398' => 'qlo', 'QL06p001407' => 'qlo', 'QL06p002031' => 'qlo', 'RcHm_v2.0_Chr4g0387791' => 'rch', 'RcHm_v2.0_Chr4g0387801' => 'rch', 'RcHm_v2.0_Chr6g0286501' => 'rch', 'RcHm_v2.0_Chr6g0286511' => 'rch', 'RcHm_v2.0_Chr6g0286521' => 'rch', 'RcHm_v2.0_Chr6g0286531' => 'rch', 'RcHm_v2.0_Chr7g0189141' => 'rch', 'Rhsim02G0028700' => 'rsi', 'Rhsim02G0028800' => 'rsi', 'Rhsim02G0028900' => 'rsi', 'Rhsim02G0029000' => 'rsi', 'Rhsim02G0029100' => 'rsi', 'Rhsim02G0029200' => 'rsi', 'Rhsim02G0029300' => 'rsi', 'Rhsim02G0029400' => 'rsi', 'Rhsim02G0029500' => 'rsi', 'Rhsim02G0029600' => 'rsi', 'RhsimUnG0024000' => 'rsi', 'RhsimUnG0024100' => 'rsi', 'RhsimUnG0024200' => 'rsi', 'RhsimUnG0024300' => 'rsi', 'RhsimUnG0024400' => 'rsi', 'RhsimUnG0024500' => 'rsi', 'RhsimUnG0024700' => 'rsi', 'RhsimUnG0024800' => 'rsi', 'RhsimUnG0024900' => 'rsi', 'RhsimUnG0025100' => 'rsi', 'Sabra08G0120200' => 'sbr', 'Sabra08G0120300' => 'sbr', 'Sabra08G0120500' => 'sbr', 'Sabra08G0120600' => 'sbr', 'Sabra10G0158900' => 'sbr', 'SalBow2G3492' => 'sbo', 'Sc13g0004760' => 'sci', 'Sc13g0004770' => 'sci', 'Sed0003417' => 'sed', 'Sed0019750' => 'sed', 'SEGI_03419' => 'sgi', 'SEGI_05907' => 'sgi', 'SEGI_10682' => 'sgi', 'SEGI_13528' => 'sgi', 'SEGI_16081' => 'sgi', 'SEGI_19370' => 'sgi', 'SEGI_21015' => 'sgi', 'SEGI_21944' => 'sgi', 'SEGI_32906' => 'sgi', 'SEGI_33093' => 'sgi', 'SEGI_36110' => 'sgi', 'SEGI_40397' => 'sgi', 'SGA_v2.0_scaffold191G40426' => 'sas', 'SGA_v2.0_scaffold353G49717' => 'sas', 'SGA_v2.0_scaffold50G18550' => 'sas', 'SMO119G0173' => 'smo', 'SMO172G0002' => 'smo', 'Solyc09g082690.3' => 'sly', 'Solyc09g082700.2' => 'sly', 'Sopen09g031550' => 'spe', 'Sopen09g031560' => 'spe', 'Sp3g20540' => 'spa', 'Sp7g07580' => 'spa', 'TAR134G0002' => 'tar', 'TAR236G0001' => 'tar', 'TAR365G0892' => 'tar', 'TAR636G0166' => 'tar', 'TAR636G0646' => 'tar', 'TAR636G0869' => 'tar', 'TAR636G1317' => 'tar', 'TAR636G1744' => 'tar', 'TAR636G3358' => 'tar', 'TAR636G3436' => 'tar', 'THA.LOC104803047' => 'tha', 'Thecc.04G238900' => 'tca', 'Thhalv10021557m.g' => 'esa', 'Thhalv10026318m.g' => 'esa', 'Thhalv10026335m.g' => 'esa', 'TPR.G17433' => 'tpr', 'TPR.G18915' => 'tpr', 'TPR.G26125' => 'tpr', 'TWI09G0677' => 'twi', 'TWI73G0287' => 'twi', 'unitig_748.g8326' => 'ugi', 'vmacro15370' => 'vma', 'vmacro15371' => 'vma', 'vmacro15372' => 'vma', 'vmacro15373' => 'vma', 'vmacro15374' => 'vma', 'VMungo0720G2826' => 'vmu', 'Zm00001eb116960' => 'zma', 'Zm00001eb301260' => 'zma', 'Zm00001eb301270' => 'zma' ), 'gf_id' => 'HOM05D001460', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001460' ), 'data_identifier' => 'HOM05D001460', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001460', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '433', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p22980' => 'bna', 'A01p32340' => 'bna', 'A03p42970' => 'bna', 'A05p25880' => 'bna', 'Aa31LG8G9320' => 'aar', 'Aa31LG8G9330' => 'aar', 'Aa31LG8G9340' => 'aar', 'Aa31sc221G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1034' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1528' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.829' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2222' => 'aag', 'Ah.12g058830' => 'amhyb', 'Ah.12g058840' => 'amhyb', 'AL3G37160' => 'aly', 'AL7G41310' => 'aly', 'Aqoxy5G00395' => 'aox', 'Aqoxy5G00396' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0C8NZA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5185HY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JZ1PRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MD3LS0' => 'arhy', 'AT3G22840' => 'ath', 'AT4G14690' => 'ath', 'ATR0665G054' => 'atr', 'Atru.chr4.2344' => 'acertr', 'Atru.chr4.2346' => 'acertr', 'Atru.chr4.2347' => 'acertr', 'Atru.chr4.2348' => 'acertr', 'Atru.chr4.2355' => 'acertr', 'Atru.chr4.2356' => 'acertr', 'Atru.chr4.2358' => 'acertr', 'Atru.chr4.2359' => 'acertr', 'Atru.chr4.2360' => 'acertr', 'Atru.chr4.2361' => 'acertr', 'AUR62030476' => 'cqu', 'AUR62030478' => 'cqu', 'AUR62030819' => 'cqu', 'AUR62030820' => 'cqu', 'BcaB03g14648' => 'bca', 'BcaB04g20492' => 'bca', 'BcaB06g26399' => 'bca', 'BcaC01g03416' => 'bca', 'BcaC01g03419' => 'bca', 'BcaC01g03421' => 'bca', 'BcaC01g03424' => 'bca', 'BcaC05g28012' => 'bca', 'BcaC09g49212' => 'bca', 'BcaC09g50140' => 'bca', 'BcaNung00346' => 'bca', 'BolC1t02785H' => 'bol', 'BolC1t04095H' => 'bol', 'BolC3t17545H' => 'bol', 'BolC5t32769H' => 'bol', 'BraA01t02211Z' => 'bra', 'BraA01t03359Z' => 'bra', 'BraA03t13441Z' => 'bra', 'BraA05t21476Z' => 'bra', 'C01p28420' => 'bna', 'C01p41350' => 'bna', 'C03p52750' => 'bna', 'C03p52780' => 'bna', 'C05p40270' => 'bna', 'CAN.G1437.9' => 'can', 'CANSAT78G0035' => 'cansat', 'CANSAT78G1036' => 'cansat', 'CANSAT78G2272' => 'cansat', 'CANSAT78G2478' => 'cansat', 'CARHR098700' => 'chi', 'CARHR221120' => 'chi', 'CARHR221150' => 'chi', 'Carub.0003s2297' => 'cru', 'Carub.0007s2749' => 'cru', 'Carub.0007s2750' => 'cru', 'Carub.0007s2751' => 'cru', 'Ca_10849_v3' => 'car', 'Cc03_g04300' => 'ccan', 'CDE02G3648' => 'cde', 'CDE05G0060' => 'cde', 'CDE05G0692' => 'cde', 'CDE05G2285' => 'cde', 'CDE05G2884' => 'cde', 'CDE05G3072' => 'cde', 'Cfa008439' => 'cfa', 'Cfa008441' => 'cfa', 'Cfa008443' => 'cfa', 'Cfa008448' => 'cfa', 'Ciclev10005974m.g' => 'ccl', 'Ciclev10006006m.g' => 'ccl', 'Ciclev10006775m.g' => 'ccl', 'CiPaw.02G120400' => 'cil', 'CiPaw.02G120500' => 'cil', 'CiPaw.02G120600' => 'cil', 'ClCG05G004850' => 'cla', 'COL.COLO4_21566' => 'col', 'Cpa.g.sc44.124' => 'cpa', 'Cre07.g320400' => 'cre', 'Cre07.g320450' => 'cre', 'Cre08.g384650' => 'cre', 'Cre09.g393173' => 'cre', 'Cre09.g394325' => 'cre', 'Cre14.g626750' => 'cre', 'Cre16.g679250' => 'cre', 'CsaV3_3G012890' => 'csa', 'CSS0010865' => 'camsi', 'CSS0044338' => 'camsi', 'DCAR_002366' => 'dca', 'DCAR_030687' => 'dca', 'DCAR_030688' => 'dca', 'Dinv14047' => 'din', 'Dinv14048' => 'din', 'Duzib151G0105' => 'dzi', 'Duzib151G0114' => 'dzi', 'Duzib212G1029' => 'dzi', 'ECA232G3536' => 'eca', 'ECA240G0786' => 'eca', 'ECA240G1802' => 'eca', 'ECA240G3760' => 'eca', 'ECA240G3920' => 'eca', 'EL10Ac5g12536' => 'bvu', 'EL10Ac5g12537' => 'bvu', 'EL10Ac5g12538' => 'bvu', 'Eucgr.B01004' => 'egr', 'Eucgr.B01006' => 'egr', 'Eucgr.B01007' => 'egr', 'Eucgr.B01008' => 'egr', 'Eucgr.B01895' => 'egr', 'Eucgr.B01896' => 'egr', 'FAN04G1456' => 'fan', 'FAN08G1769' => 'fan', 'FAN08G2160' => 'fan', 'FAN13G2403' => 'fan', 'FAN13G3303' => 'fan', 'FAN15G2435' => 'fan', 'FAN17G0672' => 'fan', 'FAN17G2441' => 'fan', 'FAN18G1024' => 'fan', 'FAN22G1458' => 'fan', 'FAN24G0037' => 'fan', 'FAN24G0429' => 'fan', 'FAN24G2387' => 'fan', 'FAN27G2746' => 'fan', 'FvH4_2g20400' => 'fve', 'FvH4_2g20420' => 'fve', 'FvH4_2g20430' => 'fve', 'FvH4_4g01270' => 'fve', 'FvH4_4g01290' => 'fve', 'FvH4_4g01300' => 'fve', 'FvH4_4g01310' => 'fve', 'FvH4_4g01330' => 'fve', 'FvH4_5g09070' => 'fve', 'Glyma.10G243800' => 'gma', 'Glyma.20G150600' => 'gma', 'Gohir.A09G219200' => 'ghi', 'Gohir.A09G219300' => 'ghi', 'Gohir.D09G221400' => 'ghi', 'Gohir.D09G221500' => 'ghi', 'Gorai.006G242600' => 'gra', 'Gorai.006G242700' => 'gra', 'GSVIVG01018044001' => 'vvi', 'HanXRQChr03g0083821' => 'han', 'HanXRQChr03g0083841' => 'han', 'HanXRQChr03g0083881' => 'han', 'HanXRQChr03g0083901' => 'han', 'HanXRQChr03g0083921' => 'han', 'HanXRQChr03g0085331' => 'han', 'HanXRQChr03g0085361' => 'han', 'HanXRQChr03g0085411' => 'han', 'HanXRQChr03g0085421' => 'han', 'HanXRQChr03g0085431' => 'han', 'HanXRQChr08g0221991' => 'han', 'HanXRQChr11g0336061' => 'han', 'HanXRQChr11g0336411' => 'han', 'Haze_11234' => 'cav', 'Hma1.2p1_0549F.1_g177010' => 'hma', 'Hma1.2p1_0602F.1_g187630' => 'hma', 'Hund14876' => 'sun', 'Hund14879' => 'sun', 'Lalb_Chr06g0160741' => 'lal', 'Lalb_Chr21g0304781' => 'lal', 'Lj3A726G19' => 'lonja', 'Lj3A726T23' => 'lonja', 'Lj3A726T24' => 'lonja', 'Lj3A726T25' => 'lonja', 'Lj3A727T17' => 'lonja', 'Lj3C726T0' => 'lonja', 'Lj3C726T2' => 'lonja', 'Lj3P725T35' => 'lonja', 'Lj3P727T10' => 'lonja', 'Lj3P727T12' => 'lonja', 'Lj3P727T14' => 'lonja', 'Lj5g0023109' => 'lja', 'Lj6P646T44' => 'lonja', 'Lsat_1_v5_gn_6_75760' => 'lsa', 'Lsat_1_v5_gn_6_75800' => 'lsa', 'Lsat_1_v5_gn_6_75900' => 'lsa', 'Lsat_1_v5_gn_6_76240' => 'lsa', 'Lsat_1_v5_gn_6_76441' => 'lsa', 'Lsat_1_v5_gn_6_76700' => 'lsa', 'Lsat_1_v5_gn_6_76760' => 'lsa', 'Manes.15G033100' => 'mes', 'Mapoly0004s0074' => 'mpo', 'Mapoly0004s0075' => 'mpo', 'Mapoly0004s0163' => 'mpo', 'Mapoly0004s0164' => 'mpo', 'Mapoly0021s0018' => 'mpo', 'Mapoly0041s0136' => 'mpo', 'Mapoly0041s0137' => 'mpo', 'Mapoly0041s0138' => 'mpo', 'Mapoly0041s0139' => 'mpo', 'Mapoly0041s0141' => 'mpo', 'Mapoly0041s0142' => 'mpo', 'Mapoly0041s0143' => 'mpo', 'Mapoly0041s0144' => 'mpo', 'Mapoly0041s0145' => 'mpo', 'Mapoly0047s0106' => 'mpo', 'Mapoly0047s0108' => 'mpo', 'Mapoly0050s0051' => 'mpo', 'Mapoly0050s0052' => 'mpo', 'Mapoly0050s0053' => 'mpo', 'Mapoly0058s0013' => 'mpo', 'Mapoly0091s0078' => 'mpo', 'Mapoly0091s0079' => 'mpo', 'Mapoly0091s0080' => 'mpo', 'Mapoly0091s0081' => 'mpo', 'Mapoly0278s0004' => 'mpo', 'Mapoly0278s0005' => 'mpo', 'Mapoly0278s0006' => 'mpo', 'MBI11_g30648_MAGBIO' => 'mbi', 'MCO03G194' => 'mco', 'MCO03G590' => 'mco', 'MCO07G312' => 'mco', 'MCO10G318' => 'mco', 'MCO12G244' => 'mco', 'MCO13G148' => 'mco', 'MCO13G194' => 'mco', 'MCO16G238' => 'mco', 'MD06G1134100' => 'mdo', 'MD13G1200100' => 'mdo', 'MD13G1200300' => 'mdo', 'MD13G1200600' => 'mdo', 'MD14G1150400' => 'mdo', 'MD16G1200000' => 'mdo', 'Medtr1g102570' => 'mtr', 'Medtr1g102780' => 'mtr', 'Medtr1g102800' => 'mtr', 'Medtr1g102810' => 'mtr', 'Medtr1g102830' => 'mtr', 'MELO3C006499.2' => 'cme', 'Migut.G00385' => 'egut', 'MSTRG.4063' => 'ama', 'Nitab4.5_0000090g0260' => 'nta', 'Nitab4.5_0000977g0030' => 'nta', 'Nitab4.5_0002541g0040' => 'nta', 'Nitab4.5_0007068g0040' => 'nta', 'Nn005s41408' => 'nnu', 'Nn005s41410' => 'nnu', 'Oeu010310.1' => 'oeu', 'Oeu010311.1' => 'oeu', 'Oeu043472.1' => 'oeu', 'Os01g0246400' => 'osa', 'Os04g0267950' => 'osa', 'Os07g0178700' => 'osa', 'Os07g0178800' => 'osa', 'Peaxi162Scf00316g00046' => 'pax', 'Peaxi162Scf00316g00049' => 'pax', 'Peaxi162Scf00316g00059' => 'pax', 'Peaxi162Scf00316g00328' => 'pax', 'Peaxi162Scf00316g00329' => 'pax', 'Peaxi162Scf00316g00411' => 'pax', 'Peaxi162Scf00316g00521' => 'pax', 'Peaxi162Scf00492g00068' => 'pax', 'Peaxi162Scf35631g00002' => 'pax', 'PGR142G3720' => 'pgr', 'PGSC0003DMG400006442' => 'stu', 'Phvul.007G062000' => 'pvu', 'Potri.008G157750' => 'ptr', 'Potri.008G157900' => 'ptr', 'Potri.008G158000' => 'ptr', 'Potri.008G158200' => 'ptr', 'Pp3c11_7280' => 'ppa', 'Pp3c11_7980' => 'ppa', 'Pp3c12_19450' => 'ppa', 'Pp3c14_1480' => 'ppa', 'Pp3c14_1501' => 'ppa', 'Pp3c16_4900' => 'ppa', 'Pp3c16_5010' => 'ppa', 'Pp3c16_5060' => 'ppa', 'Pp3c19_18250' => 'ppa', 'Pp3c23_8530' => 'ppa', 'Pp3c23_8550' => 'ppa', 'Pp3c24_9670' => 'ppa', 'Pp3c2_21390' => 'ppa', 'Pp3c2_31380' => 'ppa', 'Pp3c3_16620' => 'ppa', 'Pp3c3_8090' => 'ppa', 'Pp3c3_8110' => 'ppa', 'Pp3c3_8130' => 'ppa', 'Pp3c3_8150' => 'ppa', 'Pp3c4_14320' => 'ppa', 'Pp3c6_2560' => 'ppa', 'Pp3c9_16700' => 'ppa', 'PRCOL_00000234' => 'pco', 'PRCOL_00000235' => 'pco', 'PRCOL_00000777' => 'pco', 'PRCOL_00002344' => 'pco', 'PRCOL_00002372' => 'pco', 'PRCOL_00006120' => 'pco', 'Prupe.1G021400' => 'ppe', 'Prupe.1G021500' => 'ppe', 'Prupe.1G021600' => 'ppe', 'Prupe.1G021700' => 'ppe', 'Prupe.1G021800' => 'ppe', 'Prupe.5G145100' => 'ppe', 'Psat6g204040' => 'psa', 'Psat6g204800' => 'psa', 'Psat6g204920' => 'psa', 'Psat6g204960' => 'psa', 'Psat6g205080' => 'psa', 'PSO017G0271' => 'pso', 'PSO017G1276' => 'pso', 'PSO017G1429' => 'pso', 'PSO017G1861' => 'pso', 'PSO017G2787' => 'pso', 'PSO017G4466' => 'pso', 'PSO017G5118' => 'pso', 'PSO017G5420' => 'pso', 'PSO063G3678' => 'pso', 'PSO210G0546' => 'pso', 'PSO317G0001' => 'pso', 'PSO357G0512' => 'pso', 'PSO478G2682' => 'pso', 'PSO647G0001' => 'pso', 'PSO675G0001' => 'pso', 'PSO675G2699' => 'pso', 'PSO675G2849' => 'pso', 'PSO675G4991' => 'pso', 'PSO689G0001' => 'pso', 'QL06p000916' => 'qlo', 'QL06p000921' => 'qlo', 'QL06p001398' => 'qlo', 'QL06p001407' => 'qlo', 'QL06p002031' => 'qlo', 'RcHm_v2.0_Chr4g0387791' => 'rch', 'RcHm_v2.0_Chr4g0387801' => 'rch', 'RcHm_v2.0_Chr6g0286501' => 'rch', 'RcHm_v2.0_Chr6g0286511' => 'rch', 'RcHm_v2.0_Chr6g0286521' => 'rch', 'RcHm_v2.0_Chr6g0286531' => 'rch', 'RcHm_v2.0_Chr7g0189141' => 'rch', 'Rhsim02G0028700' => 'rsi', 'Rhsim02G0028800' => 'rsi', 'Rhsim02G0028900' => 'rsi', 'Rhsim02G0029000' => 'rsi', 'Rhsim02G0029100' => 'rsi', 'Rhsim02G0029200' => 'rsi', 'Rhsim02G0029300' => 'rsi', 'Rhsim02G0029400' => 'rsi', 'Rhsim02G0029500' => 'rsi', 'Rhsim02G0029600' => 'rsi', 'RhsimUnG0024000' => 'rsi', 'RhsimUnG0024100' => 'rsi', 'RhsimUnG0024200' => 'rsi', 'RhsimUnG0024300' => 'rsi', 'RhsimUnG0024400' => 'rsi', 'RhsimUnG0024500' => 'rsi', 'RhsimUnG0024700' => 'rsi', 'RhsimUnG0024800' => 'rsi', 'RhsimUnG0024900' => 'rsi', 'RhsimUnG0025100' => 'rsi', 'Sabra08G0120200' => 'sbr', 'Sabra08G0120300' => 'sbr', 'Sabra08G0120500' => 'sbr', 'Sabra08G0120600' => 'sbr', 'Sabra10G0158900' => 'sbr', 'SalBow2G3492' => 'sbo', 'Sc13g0004760' => 'sci', 'Sc13g0004770' => 'sci', 'Sed0003417' => 'sed', 'Sed0019750' => 'sed', 'SEGI_03419' => 'sgi', 'SEGI_05907' => 'sgi', 'SEGI_10682' => 'sgi', 'SEGI_13528' => 'sgi', 'SEGI_16081' => 'sgi', 'SEGI_19370' => 'sgi', 'SEGI_21015' => 'sgi', 'SEGI_21944' => 'sgi', 'SEGI_32906' => 'sgi', 'SEGI_33093' => 'sgi', 'SEGI_36110' => 'sgi', 'SEGI_40397' => 'sgi', 'SGA_v2.0_scaffold191G40426' => 'sas', 'SGA_v2.0_scaffold353G49717' => 'sas', 'SGA_v2.0_scaffold50G18550' => 'sas', 'SMO119G0173' => 'smo', 'SMO172G0002' => 'smo', 'Solyc09g082690.3' => 'sly', 'Solyc09g082700.2' => 'sly', 'Sopen09g031550' => 'spe', 'Sopen09g031560' => 'spe', 'Sp3g20540' => 'spa', 'Sp7g07580' => 'spa', 'TAR134G0002' => 'tar', 'TAR236G0001' => 'tar', 'TAR365G0892' => 'tar', 'TAR636G0166' => 'tar', 'TAR636G0646' => 'tar', 'TAR636G0869' => 'tar', 'TAR636G1317' => 'tar', 'TAR636G1744' => 'tar', 'TAR636G3358' => 'tar', 'TAR636G3436' => 'tar', 'THA.LOC104803047' => 'tha', 'Thecc.04G238900' => 'tca', 'Thhalv10021557m.g' => 'esa', 'Thhalv10026318m.g' => 'esa', 'Thhalv10026335m.g' => 'esa', 'TPR.G17433' => 'tpr', 'TPR.G18915' => 'tpr', 'TPR.G26125' => 'tpr', 'TWI09G0677' => 'twi', 'TWI73G0287' => 'twi', 'unitig_748.g8326' => 'ugi', 'vmacro15370' => 'vma', 'vmacro15371' => 'vma', 'vmacro15372' => 'vma', 'vmacro15373' => 'vma', 'vmacro15374' => 'vma', 'VMungo0720G2826' => 'vmu', 'Zm00001eb116960' => 'zma', 'Zm00001eb301260' => 'zma', 'Zm00001eb301270' => 'zma' ) $gf_id = 'HOM05D001460' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001460' ) $data_identifier = 'HOM05D001460' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 4, 'aag' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 2, 'aox' => (int) 2, 'arhy' => (int) 4, 'ath' => (int) 2, 'atr' => (int) 1, 'acertr' => (int) 10, 'cqu' => (int) 4, 'bca' => (int) 11, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 1, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 1, 'ccan' => (int) 1, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 1, 'col' => (int) 1, 'cpa' => (int) 1, 'cre' => (int) 7, 'csa' => (int) 1, 'camsi' => (int) 2, 'dca' => (int) 3, 'din' => (int) 2, 'dzi' => (int) 3, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 14, 'fve' => (int) 9, 'gma' => (int) 2, 'ghi' => (int) 4, 'gra' => (int) 2, 'vvi' => (int) 1, 'han' => (int) 13, 'cav' => (int) 1, 'hma' => (int) 2, 'sun' => (int) 2, 'lal' => (int) 2, 'lonja' => (int) 12, 'lja' => (int) 1, 'lsa' => (int) 7, 'mes' => (int) 1, 'mpo' => (int) 27, 'mbi' => (int) 1, 'mco' => (int) 8, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 1, 'egut' => (int) 1, 'ama' => (int) 1, 'nta' => (int) 4, 'nnu' => (int) 2, 'oeu' => (int) 3, 'osa' => (int) 4, 'pax' => (int) 9, 'pgr' => (int) 1, 'stu' => (int) 1, 'pvu' => (int) 1, 'ptr' => (int) 4, 'ppa' => (int) 22, 'pco' => (int) 6, 'ppe' => (int) 6, 'psa' => (int) 5, 'pso' => (int) 19, 'qlo' => (int) 5, 'rch' => (int) 7, 'rsi' => (int) 20, 'sbr' => (int) 5, 'sbo' => (int) 1, 'sci' => (int) 2, 'sed' => (int) 2, 'sgi' => (int) 12, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 2, 'tar' => (int) 10, 'tha' => (int) 1, 'tca' => (int) 1, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 2, 'ugi' => (int) 1, 'vma' => (int) 5, 'vmu' => (int) 1, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb301270' $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' => 'HOM05D001460', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '433', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p22980' => 'bna', 'A01p32340' => 'bna', 'A03p42970' => 'bna', 'A05p25880' => 'bna', 'Aa31LG8G9320' => 'aar', 'Aa31LG8G9330' => 'aar', 'Aa31LG8G9340' => 'aar', 'Aa31sc221G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1034' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1528' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.829' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2222' => 'aag', 'Ah.12g058830' => 'amhyb', 'Ah.12g058840' => 'amhyb', 'AL3G37160' => 'aly', 'AL7G41310' => 'aly', 'Aqoxy5G00395' => 'aox', 'Aqoxy5G00396' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0C8NZA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5185HY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JZ1PRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MD3LS0' => 'arhy', 'AT3G22840' => 'ath', 'AT4G14690' => 'ath', 'ATR0665G054' => 'atr', 'Atru.chr4.2344' => 'acertr', 'Atru.chr4.2346' => 'acertr', 'Atru.chr4.2347' => 'acertr', 'Atru.chr4.2348' => 'acertr', 'Atru.chr4.2355' => 'acertr', 'Atru.chr4.2356' => 'acertr', 'Atru.chr4.2358' => 'acertr', 'Atru.chr4.2359' => 'acertr', 'Atru.chr4.2360' => 'acertr', 'Atru.chr4.2361' => 'acertr', 'AUR62030476' => 'cqu', 'AUR62030478' => 'cqu', 'AUR62030819' => 'cqu', 'AUR62030820' => 'cqu', 'BcaB03g14648' => 'bca', 'BcaB04g20492' => 'bca', 'BcaB06g26399' => 'bca', 'BcaC01g03416' => 'bca', 'BcaC01g03419' => 'bca', 'BcaC01g03421' => 'bca', 'BcaC01g03424' => 'bca', 'BcaC05g28012' => 'bca', 'BcaC09g49212' => 'bca', 'BcaC09g50140' => 'bca', 'BcaNung00346' => 'bca', 'BolC1t02785H' => 'bol', 'BolC1t04095H' => 'bol', 'BolC3t17545H' => 'bol', 'BolC5t32769H' => 'bol', 'BraA01t02211Z' => 'bra', 'BraA01t03359Z' => 'bra', 'BraA03t13441Z' => 'bra', 'BraA05t21476Z' => 'bra', 'C01p28420' => 'bna', 'C01p41350' => 'bna', 'C03p52750' => 'bna', 'C03p52780' => 'bna', 'C05p40270' => 'bna', 'CAN.G1437.9' => 'can', 'CANSAT78G0035' => 'cansat', 'CANSAT78G1036' => 'cansat', 'CANSAT78G2272' => 'cansat', 'CANSAT78G2478' => 'cansat', 'CARHR098700' => 'chi', 'CARHR221120' => 'chi', 'CARHR221150' => 'chi', 'Carub.0003s2297' => 'cru', 'Carub.0007s2749' => 'cru', 'Carub.0007s2750' => 'cru', 'Carub.0007s2751' => 'cru', 'Ca_10849_v3' => 'car', 'Cc03_g04300' => 'ccan', 'CDE02G3648' => 'cde', 'CDE05G0060' => 'cde', 'CDE05G0692' => 'cde', 'CDE05G2285' => 'cde', 'CDE05G2884' => 'cde', 'CDE05G3072' => 'cde', 'Cfa008439' => 'cfa', 'Cfa008441' => 'cfa', 'Cfa008443' => 'cfa', 'Cfa008448' => 'cfa', 'Ciclev10005974m.g' => 'ccl', 'Ciclev10006006m.g' => 'ccl', 'Ciclev10006775m.g' => 'ccl', 'CiPaw.02G120400' => 'cil', 'CiPaw.02G120500' => 'cil', 'CiPaw.02G120600' => 'cil', 'ClCG05G004850' => 'cla', 'COL.COLO4_21566' => 'col', 'Cpa.g.sc44.124' => 'cpa', 'Cre07.g320400' => 'cre', 'Cre07.g320450' => 'cre', 'Cre08.g384650' => 'cre', 'Cre09.g393173' => 'cre', 'Cre09.g394325' => 'cre', 'Cre14.g626750' => 'cre', 'Cre16.g679250' => 'cre', 'CsaV3_3G012890' => 'csa', 'CSS0010865' => 'camsi', 'CSS0044338' => 'camsi', 'DCAR_002366' => 'dca', 'DCAR_030687' => 'dca', 'DCAR_030688' => 'dca', 'Dinv14047' => 'din', 'Dinv14048' => 'din', 'Duzib151G0105' => 'dzi', 'Duzib151G0114' => 'dzi', 'Duzib212G1029' => 'dzi', 'ECA232G3536' => 'eca', 'ECA240G0786' => 'eca', 'ECA240G1802' => 'eca', 'ECA240G3760' => 'eca', 'ECA240G3920' => 'eca', 'EL10Ac5g12536' => 'bvu', 'EL10Ac5g12537' => 'bvu', 'EL10Ac5g12538' => 'bvu', 'Eucgr.B01004' => 'egr', 'Eucgr.B01006' => 'egr', 'Eucgr.B01007' => 'egr', 'Eucgr.B01008' => 'egr', 'Eucgr.B01895' => 'egr', 'Eucgr.B01896' => 'egr', 'FAN04G1456' => 'fan', 'FAN08G1769' => 'fan', 'FAN08G2160' => 'fan', 'FAN13G2403' => 'fan', 'FAN13G3303' => 'fan', 'FAN15G2435' => 'fan', 'FAN17G0672' => 'fan', 'FAN17G2441' => 'fan', 'FAN18G1024' => 'fan', 'FAN22G1458' => 'fan', 'FAN24G0037' => 'fan', 'FAN24G0429' => 'fan', 'FAN24G2387' => 'fan', 'FAN27G2746' => 'fan', 'FvH4_2g20400' => 'fve', 'FvH4_2g20420' => 'fve', 'FvH4_2g20430' => 'fve', 'FvH4_4g01270' => 'fve', 'FvH4_4g01290' => 'fve', 'FvH4_4g01300' => 'fve', 'FvH4_4g01310' => 'fve', 'FvH4_4g01330' => 'fve', 'FvH4_5g09070' => 'fve', 'Glyma.10G243800' => 'gma', 'Glyma.20G150600' => 'gma', 'Gohir.A09G219200' => 'ghi', 'Gohir.A09G219300' => 'ghi', 'Gohir.D09G221400' => 'ghi', 'Gohir.D09G221500' => 'ghi', 'Gorai.006G242600' => 'gra', 'Gorai.006G242700' => 'gra', 'GSVIVG01018044001' => 'vvi', 'HanXRQChr03g0083821' => 'han', 'HanXRQChr03g0083841' => 'han', 'HanXRQChr03g0083881' => 'han', 'HanXRQChr03g0083901' => 'han', 'HanXRQChr03g0083921' => 'han', 'HanXRQChr03g0085331' => 'han', 'HanXRQChr03g0085361' => 'han', 'HanXRQChr03g0085411' => 'han', 'HanXRQChr03g0085421' => 'han', 'HanXRQChr03g0085431' => 'han', 'HanXRQChr08g0221991' => 'han', 'HanXRQChr11g0336061' => 'han', 'HanXRQChr11g0336411' => 'han', 'Haze_11234' => 'cav', 'Hma1.2p1_0549F.1_g177010' => 'hma', 'Hma1.2p1_0602F.1_g187630' => 'hma', 'Hund14876' => 'sun', 'Hund14879' => 'sun', 'Lalb_Chr06g0160741' => 'lal', 'Lalb_Chr21g0304781' => 'lal', 'Lj3A726G19' => 'lonja', 'Lj3A726T23' => 'lonja', 'Lj3A726T24' => 'lonja', 'Lj3A726T25' => 'lonja', 'Lj3A727T17' => 'lonja', 'Lj3C726T0' => 'lonja', 'Lj3C726T2' => 'lonja', 'Lj3P725T35' => 'lonja', 'Lj3P727T10' => 'lonja', 'Lj3P727T12' => 'lonja', 'Lj3P727T14' => 'lonja', 'Lj5g0023109' => 'lja', 'Lj6P646T44' => 'lonja', 'Lsat_1_v5_gn_6_75760' => 'lsa', 'Lsat_1_v5_gn_6_75800' => 'lsa', 'Lsat_1_v5_gn_6_75900' => 'lsa', 'Lsat_1_v5_gn_6_76240' => 'lsa', 'Lsat_1_v5_gn_6_76441' => 'lsa', 'Lsat_1_v5_gn_6_76700' => 'lsa', 'Lsat_1_v5_gn_6_76760' => 'lsa', 'Manes.15G033100' => 'mes', 'Mapoly0004s0074' => 'mpo', 'Mapoly0004s0075' => 'mpo', 'Mapoly0004s0163' => 'mpo', 'Mapoly0004s0164' => 'mpo', 'Mapoly0021s0018' => 'mpo', 'Mapoly0041s0136' => 'mpo', 'Mapoly0041s0137' => 'mpo', 'Mapoly0041s0138' => 'mpo', 'Mapoly0041s0139' => 'mpo', 'Mapoly0041s0141' => 'mpo', 'Mapoly0041s0142' => 'mpo', 'Mapoly0041s0143' => 'mpo', 'Mapoly0041s0144' => 'mpo', 'Mapoly0041s0145' => 'mpo', 'Mapoly0047s0106' => 'mpo', 'Mapoly0047s0108' => 'mpo', 'Mapoly0050s0051' => 'mpo', 'Mapoly0050s0052' => 'mpo', 'Mapoly0050s0053' => 'mpo', 'Mapoly0058s0013' => 'mpo', 'Mapoly0091s0078' => 'mpo', 'Mapoly0091s0079' => 'mpo', 'Mapoly0091s0080' => 'mpo', 'Mapoly0091s0081' => 'mpo', 'Mapoly0278s0004' => 'mpo', 'Mapoly0278s0005' => 'mpo', 'Mapoly0278s0006' => 'mpo', 'MBI11_g30648_MAGBIO' => 'mbi', 'MCO03G194' => 'mco', 'MCO03G590' => 'mco', 'MCO07G312' => 'mco', 'MCO10G318' => 'mco', 'MCO12G244' => 'mco', 'MCO13G148' => 'mco', 'MCO13G194' => 'mco', 'MCO16G238' => 'mco', 'MD06G1134100' => 'mdo', 'MD13G1200100' => 'mdo', 'MD13G1200300' => 'mdo', 'MD13G1200600' => 'mdo', 'MD14G1150400' => 'mdo', 'MD16G1200000' => 'mdo', 'Medtr1g102570' => 'mtr', 'Medtr1g102780' => 'mtr', 'Medtr1g102800' => 'mtr', 'Medtr1g102810' => 'mtr', 'Medtr1g102830' => 'mtr', 'MELO3C006499.2' => 'cme', 'Migut.G00385' => 'egut', 'MSTRG.4063' => 'ama', 'Nitab4.5_0000090g0260' => 'nta', 'Nitab4.5_0000977g0030' => 'nta', 'Nitab4.5_0002541g0040' => 'nta', 'Nitab4.5_0007068g0040' => 'nta', 'Nn005s41408' => 'nnu', 'Nn005s41410' => 'nnu', 'Oeu010310.1' => 'oeu', 'Oeu010311.1' => 'oeu', 'Oeu043472.1' => 'oeu', 'Os01g0246400' => 'osa', 'Os04g0267950' => 'osa', 'Os07g0178700' => 'osa', 'Os07g0178800' => 'osa', 'Peaxi162Scf00316g00046' => 'pax', 'Peaxi162Scf00316g00049' => 'pax', 'Peaxi162Scf00316g00059' => 'pax', 'Peaxi162Scf00316g00328' => 'pax', 'Peaxi162Scf00316g00329' => 'pax', 'Peaxi162Scf00316g00411' => 'pax', 'Peaxi162Scf00316g00521' => 'pax', 'Peaxi162Scf00492g00068' => 'pax', 'Peaxi162Scf35631g00002' => 'pax', 'PGR142G3720' => 'pgr', 'PGSC0003DMG400006442' => 'stu', 'Phvul.007G062000' => 'pvu', 'Potri.008G157750' => 'ptr', 'Potri.008G157900' => 'ptr', 'Potri.008G158000' => 'ptr', 'Potri.008G158200' => 'ptr', 'Pp3c11_7280' => 'ppa', 'Pp3c11_7980' => 'ppa', 'Pp3c12_19450' => 'ppa', 'Pp3c14_1480' => 'ppa', 'Pp3c14_1501' => 'ppa', 'Pp3c16_4900' => 'ppa', 'Pp3c16_5010' => 'ppa', 'Pp3c16_5060' => 'ppa', 'Pp3c19_18250' => 'ppa', 'Pp3c23_8530' => 'ppa', 'Pp3c23_8550' => 'ppa', 'Pp3c24_9670' => 'ppa', 'Pp3c2_21390' => 'ppa', 'Pp3c2_31380' => 'ppa', 'Pp3c3_16620' => 'ppa', 'Pp3c3_8090' => 'ppa', 'Pp3c3_8110' => 'ppa', 'Pp3c3_8130' => 'ppa', 'Pp3c3_8150' => 'ppa', 'Pp3c4_14320' => 'ppa', 'Pp3c6_2560' => 'ppa', 'Pp3c9_16700' => 'ppa', 'PRCOL_00000234' => 'pco', 'PRCOL_00000235' => 'pco', 'PRCOL_00000777' => 'pco', 'PRCOL_00002344' => 'pco', 'PRCOL_00002372' => 'pco', 'PRCOL_00006120' => 'pco', 'Prupe.1G021400' => 'ppe', 'Prupe.1G021500' => 'ppe', 'Prupe.1G021600' => 'ppe', 'Prupe.1G021700' => 'ppe', 'Prupe.1G021800' => 'ppe', 'Prupe.5G145100' => 'ppe', 'Psat6g204040' => 'psa', 'Psat6g204800' => 'psa', 'Psat6g204920' => 'psa', 'Psat6g204960' => 'psa', 'Psat6g205080' => 'psa', 'PSO017G0271' => 'pso', 'PSO017G1276' => 'pso', 'PSO017G1429' => 'pso', 'PSO017G1861' => 'pso', 'PSO017G2787' => 'pso', 'PSO017G4466' => 'pso', 'PSO017G5118' => 'pso', 'PSO017G5420' => 'pso', 'PSO063G3678' => 'pso', 'PSO210G0546' => 'pso', 'PSO317G0001' => 'pso', 'PSO357G0512' => 'pso', 'PSO478G2682' => 'pso', 'PSO647G0001' => 'pso', 'PSO675G0001' => 'pso', 'PSO675G2699' => 'pso', 'PSO675G2849' => 'pso', 'PSO675G4991' => 'pso', 'PSO689G0001' => 'pso', 'QL06p000916' => 'qlo', 'QL06p000921' => 'qlo', 'QL06p001398' => 'qlo', 'QL06p001407' => 'qlo', 'QL06p002031' => 'qlo', 'RcHm_v2.0_Chr4g0387791' => 'rch', 'RcHm_v2.0_Chr4g0387801' => 'rch', 'RcHm_v2.0_Chr6g0286501' => 'rch', 'RcHm_v2.0_Chr6g0286511' => 'rch', 'RcHm_v2.0_Chr6g0286521' => 'rch', 'RcHm_v2.0_Chr6g0286531' => 'rch', 'RcHm_v2.0_Chr7g0189141' => 'rch', 'Rhsim02G0028700' => 'rsi', 'Rhsim02G0028800' => 'rsi', 'Rhsim02G0028900' => 'rsi', 'Rhsim02G0029000' => 'rsi', 'Rhsim02G0029100' => 'rsi', 'Rhsim02G0029200' => 'rsi', 'Rhsim02G0029300' => 'rsi', 'Rhsim02G0029400' => 'rsi', 'Rhsim02G0029500' => 'rsi', 'Rhsim02G0029600' => 'rsi', 'RhsimUnG0024000' => 'rsi', 'RhsimUnG0024100' => 'rsi', 'RhsimUnG0024200' => 'rsi', 'RhsimUnG0024300' => 'rsi', 'RhsimUnG0024400' => 'rsi', 'RhsimUnG0024500' => 'rsi', 'RhsimUnG0024700' => 'rsi', 'RhsimUnG0024800' => 'rsi', 'RhsimUnG0024900' => 'rsi', 'RhsimUnG0025100' => 'rsi', 'Sabra08G0120200' => 'sbr', 'Sabra08G0120300' => 'sbr', 'Sabra08G0120500' => 'sbr', 'Sabra08G0120600' => 'sbr', 'Sabra10G0158900' => 'sbr', 'SalBow2G3492' => 'sbo', 'Sc13g0004760' => 'sci', 'Sc13g0004770' => 'sci', 'Sed0003417' => 'sed', 'Sed0019750' => 'sed', 'SEGI_03419' => 'sgi', 'SEGI_05907' => 'sgi', 'SEGI_10682' => 'sgi', 'SEGI_13528' => 'sgi', 'SEGI_16081' => 'sgi', 'SEGI_19370' => 'sgi', 'SEGI_21015' => 'sgi', 'SEGI_21944' => 'sgi', 'SEGI_32906' => 'sgi', 'SEGI_33093' => 'sgi', 'SEGI_36110' => 'sgi', 'SEGI_40397' => 'sgi', 'SGA_v2.0_scaffold191G40426' => 'sas', 'SGA_v2.0_scaffold353G49717' => 'sas', 'SGA_v2.0_scaffold50G18550' => 'sas', 'SMO119G0173' => 'smo', 'SMO172G0002' => 'smo', 'Solyc09g082690.3' => 'sly', 'Solyc09g082700.2' => 'sly', 'Sopen09g031550' => 'spe', 'Sopen09g031560' => 'spe', 'Sp3g20540' => 'spa', 'Sp7g07580' => 'spa', 'TAR134G0002' => 'tar', 'TAR236G0001' => 'tar', 'TAR365G0892' => 'tar', 'TAR636G0166' => 'tar', 'TAR636G0646' => 'tar', 'TAR636G0869' => 'tar', 'TAR636G1317' => 'tar', 'TAR636G1744' => 'tar', 'TAR636G3358' => 'tar', 'TAR636G3436' => 'tar', 'THA.LOC104803047' => 'tha', 'Thecc.04G238900' => 'tca', 'Thhalv10021557m.g' => 'esa', 'Thhalv10026318m.g' => 'esa', 'Thhalv10026335m.g' => 'esa', 'TPR.G17433' => 'tpr', 'TPR.G18915' => 'tpr', 'TPR.G26125' => 'tpr', 'TWI09G0677' => 'twi', 'TWI73G0287' => 'twi', 'unitig_748.g8326' => 'ugi', 'vmacro15370' => 'vma', 'vmacro15371' => 'vma', 'vmacro15372' => 'vma', 'vmacro15373' => 'vma', 'vmacro15374' => 'vma', 'VMungo0720G2826' => 'vmu', 'Zm00001eb116960' => 'zma', 'Zm00001eb301260' => 'zma', 'Zm00001eb301270' => 'zma' ), 'gf_id' => 'HOM05D001460', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001460' ), 'data_identifier' => 'HOM05D001460', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001460', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '433', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p22980' => 'bna', 'A01p32340' => 'bna', 'A03p42970' => 'bna', 'A05p25880' => 'bna', 'Aa31LG8G9320' => 'aar', 'Aa31LG8G9330' => 'aar', 'Aa31LG8G9340' => 'aar', 'Aa31sc221G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1034' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1528' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.829' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2222' => 'aag', 'Ah.12g058830' => 'amhyb', 'Ah.12g058840' => 'amhyb', 'AL3G37160' => 'aly', 'AL7G41310' => 'aly', 'Aqoxy5G00395' => 'aox', 'Aqoxy5G00396' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0C8NZA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5185HY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JZ1PRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MD3LS0' => 'arhy', 'AT3G22840' => 'ath', 'AT4G14690' => 'ath', 'ATR0665G054' => 'atr', 'Atru.chr4.2344' => 'acertr', 'Atru.chr4.2346' => 'acertr', 'Atru.chr4.2347' => 'acertr', 'Atru.chr4.2348' => 'acertr', 'Atru.chr4.2355' => 'acertr', 'Atru.chr4.2356' => 'acertr', 'Atru.chr4.2358' => 'acertr', 'Atru.chr4.2359' => 'acertr', 'Atru.chr4.2360' => 'acertr', 'Atru.chr4.2361' => 'acertr', 'AUR62030476' => 'cqu', 'AUR62030478' => 'cqu', 'AUR62030819' => 'cqu', 'AUR62030820' => 'cqu', 'BcaB03g14648' => 'bca', 'BcaB04g20492' => 'bca', 'BcaB06g26399' => 'bca', 'BcaC01g03416' => 'bca', 'BcaC01g03419' => 'bca', 'BcaC01g03421' => 'bca', 'BcaC01g03424' => 'bca', 'BcaC05g28012' => 'bca', 'BcaC09g49212' => 'bca', 'BcaC09g50140' => 'bca', 'BcaNung00346' => 'bca', 'BolC1t02785H' => 'bol', 'BolC1t04095H' => 'bol', 'BolC3t17545H' => 'bol', 'BolC5t32769H' => 'bol', 'BraA01t02211Z' => 'bra', 'BraA01t03359Z' => 'bra', 'BraA03t13441Z' => 'bra', 'BraA05t21476Z' => 'bra', 'C01p28420' => 'bna', 'C01p41350' => 'bna', 'C03p52750' => 'bna', 'C03p52780' => 'bna', 'C05p40270' => 'bna', 'CAN.G1437.9' => 'can', 'CANSAT78G0035' => 'cansat', 'CANSAT78G1036' => 'cansat', 'CANSAT78G2272' => 'cansat', 'CANSAT78G2478' => 'cansat', 'CARHR098700' => 'chi', 'CARHR221120' => 'chi', 'CARHR221150' => 'chi', 'Carub.0003s2297' => 'cru', 'Carub.0007s2749' => 'cru', 'Carub.0007s2750' => 'cru', 'Carub.0007s2751' => 'cru', 'Ca_10849_v3' => 'car', 'Cc03_g04300' => 'ccan', 'CDE02G3648' => 'cde', 'CDE05G0060' => 'cde', 'CDE05G0692' => 'cde', 'CDE05G2285' => 'cde', 'CDE05G2884' => 'cde', 'CDE05G3072' => 'cde', 'Cfa008439' => 'cfa', 'Cfa008441' => 'cfa', 'Cfa008443' => 'cfa', 'Cfa008448' => 'cfa', 'Ciclev10005974m.g' => 'ccl', 'Ciclev10006006m.g' => 'ccl', 'Ciclev10006775m.g' => 'ccl', 'CiPaw.02G120400' => 'cil', 'CiPaw.02G120500' => 'cil', 'CiPaw.02G120600' => 'cil', 'ClCG05G004850' => 'cla', 'COL.COLO4_21566' => 'col', 'Cpa.g.sc44.124' => 'cpa', 'Cre07.g320400' => 'cre', 'Cre07.g320450' => 'cre', 'Cre08.g384650' => 'cre', 'Cre09.g393173' => 'cre', 'Cre09.g394325' => 'cre', 'Cre14.g626750' => 'cre', 'Cre16.g679250' => 'cre', 'CsaV3_3G012890' => 'csa', 'CSS0010865' => 'camsi', 'CSS0044338' => 'camsi', 'DCAR_002366' => 'dca', 'DCAR_030687' => 'dca', 'DCAR_030688' => 'dca', 'Dinv14047' => 'din', 'Dinv14048' => 'din', 'Duzib151G0105' => 'dzi', 'Duzib151G0114' => 'dzi', 'Duzib212G1029' => 'dzi', 'ECA232G3536' => 'eca', 'ECA240G0786' => 'eca', 'ECA240G1802' => 'eca', 'ECA240G3760' => 'eca', 'ECA240G3920' => 'eca', 'EL10Ac5g12536' => 'bvu', 'EL10Ac5g12537' => 'bvu', 'EL10Ac5g12538' => 'bvu', 'Eucgr.B01004' => 'egr', 'Eucgr.B01006' => 'egr', 'Eucgr.B01007' => 'egr', 'Eucgr.B01008' => 'egr', 'Eucgr.B01895' => 'egr', 'Eucgr.B01896' => 'egr', 'FAN04G1456' => 'fan', 'FAN08G1769' => 'fan', 'FAN08G2160' => 'fan', 'FAN13G2403' => 'fan', 'FAN13G3303' => 'fan', 'FAN15G2435' => 'fan', 'FAN17G0672' => 'fan', 'FAN17G2441' => 'fan', 'FAN18G1024' => 'fan', 'FAN22G1458' => 'fan', 'FAN24G0037' => 'fan', 'FAN24G0429' => 'fan', 'FAN24G2387' => 'fan', 'FAN27G2746' => 'fan', 'FvH4_2g20400' => 'fve', 'FvH4_2g20420' => 'fve', 'FvH4_2g20430' => 'fve', 'FvH4_4g01270' => 'fve', 'FvH4_4g01290' => 'fve', 'FvH4_4g01300' => 'fve', 'FvH4_4g01310' => 'fve', 'FvH4_4g01330' => 'fve', 'FvH4_5g09070' => 'fve', 'Glyma.10G243800' => 'gma', 'Glyma.20G150600' => 'gma', 'Gohir.A09G219200' => 'ghi', 'Gohir.A09G219300' => 'ghi', 'Gohir.D09G221400' => 'ghi', 'Gohir.D09G221500' => 'ghi', 'Gorai.006G242600' => 'gra', 'Gorai.006G242700' => 'gra', 'GSVIVG01018044001' => 'vvi', 'HanXRQChr03g0083821' => 'han', 'HanXRQChr03g0083841' => 'han', 'HanXRQChr03g0083881' => 'han', 'HanXRQChr03g0083901' => 'han', 'HanXRQChr03g0083921' => 'han', 'HanXRQChr03g0085331' => 'han', 'HanXRQChr03g0085361' => 'han', 'HanXRQChr03g0085411' => 'han', 'HanXRQChr03g0085421' => 'han', 'HanXRQChr03g0085431' => 'han', 'HanXRQChr08g0221991' => 'han', 'HanXRQChr11g0336061' => 'han', 'HanXRQChr11g0336411' => 'han', 'Haze_11234' => 'cav', 'Hma1.2p1_0549F.1_g177010' => 'hma', 'Hma1.2p1_0602F.1_g187630' => 'hma', 'Hund14876' => 'sun', 'Hund14879' => 'sun', 'Lalb_Chr06g0160741' => 'lal', 'Lalb_Chr21g0304781' => 'lal', 'Lj3A726G19' => 'lonja', 'Lj3A726T23' => 'lonja', 'Lj3A726T24' => 'lonja', 'Lj3A726T25' => 'lonja', 'Lj3A727T17' => 'lonja', 'Lj3C726T0' => 'lonja', 'Lj3C726T2' => 'lonja', 'Lj3P725T35' => 'lonja', 'Lj3P727T10' => 'lonja', 'Lj3P727T12' => 'lonja', 'Lj3P727T14' => 'lonja', 'Lj5g0023109' => 'lja', 'Lj6P646T44' => 'lonja', 'Lsat_1_v5_gn_6_75760' => 'lsa', 'Lsat_1_v5_gn_6_75800' => 'lsa', 'Lsat_1_v5_gn_6_75900' => 'lsa', 'Lsat_1_v5_gn_6_76240' => 'lsa', 'Lsat_1_v5_gn_6_76441' => 'lsa', 'Lsat_1_v5_gn_6_76700' => 'lsa', 'Lsat_1_v5_gn_6_76760' => 'lsa', 'Manes.15G033100' => 'mes', 'Mapoly0004s0074' => 'mpo', 'Mapoly0004s0075' => 'mpo', 'Mapoly0004s0163' => 'mpo', 'Mapoly0004s0164' => 'mpo', 'Mapoly0021s0018' => 'mpo', 'Mapoly0041s0136' => 'mpo', 'Mapoly0041s0137' => 'mpo', 'Mapoly0041s0138' => 'mpo', 'Mapoly0041s0139' => 'mpo', 'Mapoly0041s0141' => 'mpo', 'Mapoly0041s0142' => 'mpo', 'Mapoly0041s0143' => 'mpo', 'Mapoly0041s0144' => 'mpo', 'Mapoly0041s0145' => 'mpo', 'Mapoly0047s0106' => 'mpo', 'Mapoly0047s0108' => 'mpo', 'Mapoly0050s0051' => 'mpo', 'Mapoly0050s0052' => 'mpo', 'Mapoly0050s0053' => 'mpo', 'Mapoly0058s0013' => 'mpo', 'Mapoly0091s0078' => 'mpo', 'Mapoly0091s0079' => 'mpo', 'Mapoly0091s0080' => 'mpo', 'Mapoly0091s0081' => 'mpo', 'Mapoly0278s0004' => 'mpo', 'Mapoly0278s0005' => 'mpo', 'Mapoly0278s0006' => 'mpo', 'MBI11_g30648_MAGBIO' => 'mbi', 'MCO03G194' => 'mco', 'MCO03G590' => 'mco', 'MCO07G312' => 'mco', 'MCO10G318' => 'mco', 'MCO12G244' => 'mco', 'MCO13G148' => 'mco', 'MCO13G194' => 'mco', 'MCO16G238' => 'mco', 'MD06G1134100' => 'mdo', 'MD13G1200100' => 'mdo', 'MD13G1200300' => 'mdo', 'MD13G1200600' => 'mdo', 'MD14G1150400' => 'mdo', 'MD16G1200000' => 'mdo', 'Medtr1g102570' => 'mtr', 'Medtr1g102780' => 'mtr', 'Medtr1g102800' => 'mtr', 'Medtr1g102810' => 'mtr', 'Medtr1g102830' => 'mtr', 'MELO3C006499.2' => 'cme', 'Migut.G00385' => 'egut', 'MSTRG.4063' => 'ama', 'Nitab4.5_0000090g0260' => 'nta', 'Nitab4.5_0000977g0030' => 'nta', 'Nitab4.5_0002541g0040' => 'nta', 'Nitab4.5_0007068g0040' => 'nta', 'Nn005s41408' => 'nnu', 'Nn005s41410' => 'nnu', 'Oeu010310.1' => 'oeu', 'Oeu010311.1' => 'oeu', 'Oeu043472.1' => 'oeu', 'Os01g0246400' => 'osa', 'Os04g0267950' => 'osa', 'Os07g0178700' => 'osa', 'Os07g0178800' => 'osa', 'Peaxi162Scf00316g00046' => 'pax', 'Peaxi162Scf00316g00049' => 'pax', 'Peaxi162Scf00316g00059' => 'pax', 'Peaxi162Scf00316g00328' => 'pax', 'Peaxi162Scf00316g00329' => 'pax', 'Peaxi162Scf00316g00411' => 'pax', 'Peaxi162Scf00316g00521' => 'pax', 'Peaxi162Scf00492g00068' => 'pax', 'Peaxi162Scf35631g00002' => 'pax', 'PGR142G3720' => 'pgr', 'PGSC0003DMG400006442' => 'stu', 'Phvul.007G062000' => 'pvu', 'Potri.008G157750' => 'ptr', 'Potri.008G157900' => 'ptr', 'Potri.008G158000' => 'ptr', 'Potri.008G158200' => 'ptr', 'Pp3c11_7280' => 'ppa', 'Pp3c11_7980' => 'ppa', 'Pp3c12_19450' => 'ppa', 'Pp3c14_1480' => 'ppa', 'Pp3c14_1501' => 'ppa', 'Pp3c16_4900' => 'ppa', 'Pp3c16_5010' => 'ppa', 'Pp3c16_5060' => 'ppa', 'Pp3c19_18250' => 'ppa', 'Pp3c23_8530' => 'ppa', 'Pp3c23_8550' => 'ppa', 'Pp3c24_9670' => 'ppa', 'Pp3c2_21390' => 'ppa', 'Pp3c2_31380' => 'ppa', 'Pp3c3_16620' => 'ppa', 'Pp3c3_8090' => 'ppa', 'Pp3c3_8110' => 'ppa', 'Pp3c3_8130' => 'ppa', 'Pp3c3_8150' => 'ppa', 'Pp3c4_14320' => 'ppa', 'Pp3c6_2560' => 'ppa', 'Pp3c9_16700' => 'ppa', 'PRCOL_00000234' => 'pco', 'PRCOL_00000235' => 'pco', 'PRCOL_00000777' => 'pco', 'PRCOL_00002344' => 'pco', 'PRCOL_00002372' => 'pco', 'PRCOL_00006120' => 'pco', 'Prupe.1G021400' => 'ppe', 'Prupe.1G021500' => 'ppe', 'Prupe.1G021600' => 'ppe', 'Prupe.1G021700' => 'ppe', 'Prupe.1G021800' => 'ppe', 'Prupe.5G145100' => 'ppe', 'Psat6g204040' => 'psa', 'Psat6g204800' => 'psa', 'Psat6g204920' => 'psa', 'Psat6g204960' => 'psa', 'Psat6g205080' => 'psa', 'PSO017G0271' => 'pso', 'PSO017G1276' => 'pso', 'PSO017G1429' => 'pso', 'PSO017G1861' => 'pso', 'PSO017G2787' => 'pso', 'PSO017G4466' => 'pso', 'PSO017G5118' => 'pso', 'PSO017G5420' => 'pso', 'PSO063G3678' => 'pso', 'PSO210G0546' => 'pso', 'PSO317G0001' => 'pso', 'PSO357G0512' => 'pso', 'PSO478G2682' => 'pso', 'PSO647G0001' => 'pso', 'PSO675G0001' => 'pso', 'PSO675G2699' => 'pso', 'PSO675G2849' => 'pso', 'PSO675G4991' => 'pso', 'PSO689G0001' => 'pso', 'QL06p000916' => 'qlo', 'QL06p000921' => 'qlo', 'QL06p001398' => 'qlo', 'QL06p001407' => 'qlo', 'QL06p002031' => 'qlo', 'RcHm_v2.0_Chr4g0387791' => 'rch', 'RcHm_v2.0_Chr4g0387801' => 'rch', 'RcHm_v2.0_Chr6g0286501' => 'rch', 'RcHm_v2.0_Chr6g0286511' => 'rch', 'RcHm_v2.0_Chr6g0286521' => 'rch', 'RcHm_v2.0_Chr6g0286531' => 'rch', 'RcHm_v2.0_Chr7g0189141' => 'rch', 'Rhsim02G0028700' => 'rsi', 'Rhsim02G0028800' => 'rsi', 'Rhsim02G0028900' => 'rsi', 'Rhsim02G0029000' => 'rsi', 'Rhsim02G0029100' => 'rsi', 'Rhsim02G0029200' => 'rsi', 'Rhsim02G0029300' => 'rsi', 'Rhsim02G0029400' => 'rsi', 'Rhsim02G0029500' => 'rsi', 'Rhsim02G0029600' => 'rsi', 'RhsimUnG0024000' => 'rsi', 'RhsimUnG0024100' => 'rsi', 'RhsimUnG0024200' => 'rsi', 'RhsimUnG0024300' => 'rsi', 'RhsimUnG0024400' => 'rsi', 'RhsimUnG0024500' => 'rsi', 'RhsimUnG0024700' => 'rsi', 'RhsimUnG0024800' => 'rsi', 'RhsimUnG0024900' => 'rsi', 'RhsimUnG0025100' => 'rsi', 'Sabra08G0120200' => 'sbr', 'Sabra08G0120300' => 'sbr', 'Sabra08G0120500' => 'sbr', 'Sabra08G0120600' => 'sbr', 'Sabra10G0158900' => 'sbr', 'SalBow2G3492' => 'sbo', 'Sc13g0004760' => 'sci', 'Sc13g0004770' => 'sci', 'Sed0003417' => 'sed', 'Sed0019750' => 'sed', 'SEGI_03419' => 'sgi', 'SEGI_05907' => 'sgi', 'SEGI_10682' => 'sgi', 'SEGI_13528' => 'sgi', 'SEGI_16081' => 'sgi', 'SEGI_19370' => 'sgi', 'SEGI_21015' => 'sgi', 'SEGI_21944' => 'sgi', 'SEGI_32906' => 'sgi', 'SEGI_33093' => 'sgi', 'SEGI_36110' => 'sgi', 'SEGI_40397' => 'sgi', 'SGA_v2.0_scaffold191G40426' => 'sas', 'SGA_v2.0_scaffold353G49717' => 'sas', 'SGA_v2.0_scaffold50G18550' => 'sas', 'SMO119G0173' => 'smo', 'SMO172G0002' => 'smo', 'Solyc09g082690.3' => 'sly', 'Solyc09g082700.2' => 'sly', 'Sopen09g031550' => 'spe', 'Sopen09g031560' => 'spe', 'Sp3g20540' => 'spa', 'Sp7g07580' => 'spa', 'TAR134G0002' => 'tar', 'TAR236G0001' => 'tar', 'TAR365G0892' => 'tar', 'TAR636G0166' => 'tar', 'TAR636G0646' => 'tar', 'TAR636G0869' => 'tar', 'TAR636G1317' => 'tar', 'TAR636G1744' => 'tar', 'TAR636G3358' => 'tar', 'TAR636G3436' => 'tar', 'THA.LOC104803047' => 'tha', 'Thecc.04G238900' => 'tca', 'Thhalv10021557m.g' => 'esa', 'Thhalv10026318m.g' => 'esa', 'Thhalv10026335m.g' => 'esa', 'TPR.G17433' => 'tpr', 'TPR.G18915' => 'tpr', 'TPR.G26125' => 'tpr', 'TWI09G0677' => 'twi', 'TWI73G0287' => 'twi', 'unitig_748.g8326' => 'ugi', 'vmacro15370' => 'vma', 'vmacro15371' => 'vma', 'vmacro15372' => 'vma', 'vmacro15373' => 'vma', 'vmacro15374' => 'vma', 'VMungo0720G2826' => 'vmu', 'Zm00001eb116960' => 'zma', 'Zm00001eb301260' => 'zma', 'Zm00001eb301270' => 'zma' ) $gf_id = 'HOM05D001460' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001460' ) $data_identifier = 'HOM05D001460' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 4, 'aag' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 2, 'aox' => (int) 2, 'arhy' => (int) 4, 'ath' => (int) 2, 'atr' => (int) 1, 'acertr' => (int) 10, 'cqu' => (int) 4, 'bca' => (int) 11, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 1, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 1, 'ccan' => (int) 1, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 1, 'col' => (int) 1, 'cpa' => (int) 1, 'cre' => (int) 7, 'csa' => (int) 1, 'camsi' => (int) 2, 'dca' => (int) 3, 'din' => (int) 2, 'dzi' => (int) 3, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 14, 'fve' => (int) 9, 'gma' => (int) 2, 'ghi' => (int) 4, 'gra' => (int) 2, 'vvi' => (int) 1, 'han' => (int) 13, 'cav' => (int) 1, 'hma' => (int) 2, 'sun' => (int) 2, 'lal' => (int) 2, 'lonja' => (int) 12, 'lja' => (int) 1, 'lsa' => (int) 7, 'mes' => (int) 1, 'mpo' => (int) 27, 'mbi' => (int) 1, 'mco' => (int) 8, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 1, 'egut' => (int) 1, 'ama' => (int) 1, 'nta' => (int) 4, 'nnu' => (int) 2, 'oeu' => (int) 3, 'osa' => (int) 4, 'pax' => (int) 9, 'pgr' => (int) 1, 'stu' => (int) 1, 'pvu' => (int) 1, 'ptr' => (int) 4, 'ppa' => (int) 22, 'pco' => (int) 6, 'ppe' => (int) 6, 'psa' => (int) 5, 'pso' => (int) 19, 'qlo' => (int) 5, 'rch' => (int) 7, 'rsi' => (int) 20, 'sbr' => (int) 5, 'sbo' => (int) 1, 'sci' => (int) 2, 'sed' => (int) 2, 'sgi' => (int) 12, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 2, 'tar' => (int) 10, 'tha' => (int) 1, 'tca' => (int) 1, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 2, 'ugi' => (int) 1, 'vma' => (int) 5, 'vmu' => (int) 1, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb301270' $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' => 'HOM05D001460', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '433', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p22980' => 'bna', 'A01p32340' => 'bna', 'A03p42970' => 'bna', 'A05p25880' => 'bna', 'Aa31LG8G9320' => 'aar', 'Aa31LG8G9330' => 'aar', 'Aa31LG8G9340' => 'aar', 'Aa31sc221G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1034' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1528' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.829' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2222' => 'aag', 'Ah.12g058830' => 'amhyb', 'Ah.12g058840' => 'amhyb', 'AL3G37160' => 'aly', 'AL7G41310' => 'aly', 'Aqoxy5G00395' => 'aox', 'Aqoxy5G00396' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0C8NZA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5185HY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JZ1PRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MD3LS0' => 'arhy', 'AT3G22840' => 'ath', 'AT4G14690' => 'ath', 'ATR0665G054' => 'atr', 'Atru.chr4.2344' => 'acertr', 'Atru.chr4.2346' => 'acertr', 'Atru.chr4.2347' => 'acertr', 'Atru.chr4.2348' => 'acertr', 'Atru.chr4.2355' => 'acertr', 'Atru.chr4.2356' => 'acertr', 'Atru.chr4.2358' => 'acertr', 'Atru.chr4.2359' => 'acertr', 'Atru.chr4.2360' => 'acertr', 'Atru.chr4.2361' => 'acertr', 'AUR62030476' => 'cqu', 'AUR62030478' => 'cqu', 'AUR62030819' => 'cqu', 'AUR62030820' => 'cqu', 'BcaB03g14648' => 'bca', 'BcaB04g20492' => 'bca', 'BcaB06g26399' => 'bca', 'BcaC01g03416' => 'bca', 'BcaC01g03419' => 'bca', 'BcaC01g03421' => 'bca', 'BcaC01g03424' => 'bca', 'BcaC05g28012' => 'bca', 'BcaC09g49212' => 'bca', 'BcaC09g50140' => 'bca', 'BcaNung00346' => 'bca', 'BolC1t02785H' => 'bol', 'BolC1t04095H' => 'bol', 'BolC3t17545H' => 'bol', 'BolC5t32769H' => 'bol', 'BraA01t02211Z' => 'bra', 'BraA01t03359Z' => 'bra', 'BraA03t13441Z' => 'bra', 'BraA05t21476Z' => 'bra', 'C01p28420' => 'bna', 'C01p41350' => 'bna', 'C03p52750' => 'bna', 'C03p52780' => 'bna', 'C05p40270' => 'bna', 'CAN.G1437.9' => 'can', 'CANSAT78G0035' => 'cansat', 'CANSAT78G1036' => 'cansat', 'CANSAT78G2272' => 'cansat', 'CANSAT78G2478' => 'cansat', 'CARHR098700' => 'chi', 'CARHR221120' => 'chi', 'CARHR221150' => 'chi', 'Carub.0003s2297' => 'cru', 'Carub.0007s2749' => 'cru', 'Carub.0007s2750' => 'cru', 'Carub.0007s2751' => 'cru', 'Ca_10849_v3' => 'car', 'Cc03_g04300' => 'ccan', 'CDE02G3648' => 'cde', 'CDE05G0060' => 'cde', 'CDE05G0692' => 'cde', 'CDE05G2285' => 'cde', 'CDE05G2884' => 'cde', 'CDE05G3072' => 'cde', 'Cfa008439' => 'cfa', 'Cfa008441' => 'cfa', 'Cfa008443' => 'cfa', 'Cfa008448' => 'cfa', 'Ciclev10005974m.g' => 'ccl', 'Ciclev10006006m.g' => 'ccl', 'Ciclev10006775m.g' => 'ccl', 'CiPaw.02G120400' => 'cil', 'CiPaw.02G120500' => 'cil', 'CiPaw.02G120600' => 'cil', 'ClCG05G004850' => 'cla', 'COL.COLO4_21566' => 'col', 'Cpa.g.sc44.124' => 'cpa', 'Cre07.g320400' => 'cre', 'Cre07.g320450' => 'cre', 'Cre08.g384650' => 'cre', 'Cre09.g393173' => 'cre', 'Cre09.g394325' => 'cre', 'Cre14.g626750' => 'cre', 'Cre16.g679250' => 'cre', 'CsaV3_3G012890' => 'csa', 'CSS0010865' => 'camsi', 'CSS0044338' => 'camsi', 'DCAR_002366' => 'dca', 'DCAR_030687' => 'dca', 'DCAR_030688' => 'dca', 'Dinv14047' => 'din', 'Dinv14048' => 'din', 'Duzib151G0105' => 'dzi', 'Duzib151G0114' => 'dzi', 'Duzib212G1029' => 'dzi', 'ECA232G3536' => 'eca', 'ECA240G0786' => 'eca', 'ECA240G1802' => 'eca', 'ECA240G3760' => 'eca', 'ECA240G3920' => 'eca', 'EL10Ac5g12536' => 'bvu', 'EL10Ac5g12537' => 'bvu', 'EL10Ac5g12538' => 'bvu', 'Eucgr.B01004' => 'egr', 'Eucgr.B01006' => 'egr', 'Eucgr.B01007' => 'egr', 'Eucgr.B01008' => 'egr', 'Eucgr.B01895' => 'egr', 'Eucgr.B01896' => 'egr', 'FAN04G1456' => 'fan', 'FAN08G1769' => 'fan', 'FAN08G2160' => 'fan', 'FAN13G2403' => 'fan', 'FAN13G3303' => 'fan', 'FAN15G2435' => 'fan', 'FAN17G0672' => 'fan', 'FAN17G2441' => 'fan', 'FAN18G1024' => 'fan', 'FAN22G1458' => 'fan', 'FAN24G0037' => 'fan', 'FAN24G0429' => 'fan', 'FAN24G2387' => 'fan', 'FAN27G2746' => 'fan', 'FvH4_2g20400' => 'fve', 'FvH4_2g20420' => 'fve', 'FvH4_2g20430' => 'fve', 'FvH4_4g01270' => 'fve', 'FvH4_4g01290' => 'fve', 'FvH4_4g01300' => 'fve', 'FvH4_4g01310' => 'fve', 'FvH4_4g01330' => 'fve', 'FvH4_5g09070' => 'fve', 'Glyma.10G243800' => 'gma', 'Glyma.20G150600' => 'gma', 'Gohir.A09G219200' => 'ghi', 'Gohir.A09G219300' => 'ghi', 'Gohir.D09G221400' => 'ghi', 'Gohir.D09G221500' => 'ghi', 'Gorai.006G242600' => 'gra', 'Gorai.006G242700' => 'gra', 'GSVIVG01018044001' => 'vvi', 'HanXRQChr03g0083821' => 'han', 'HanXRQChr03g0083841' => 'han', 'HanXRQChr03g0083881' => 'han', 'HanXRQChr03g0083901' => 'han', 'HanXRQChr03g0083921' => 'han', 'HanXRQChr03g0085331' => 'han', 'HanXRQChr03g0085361' => 'han', 'HanXRQChr03g0085411' => 'han', 'HanXRQChr03g0085421' => 'han', 'HanXRQChr03g0085431' => 'han', 'HanXRQChr08g0221991' => 'han', 'HanXRQChr11g0336061' => 'han', 'HanXRQChr11g0336411' => 'han', 'Haze_11234' => 'cav', 'Hma1.2p1_0549F.1_g177010' => 'hma', 'Hma1.2p1_0602F.1_g187630' => 'hma', 'Hund14876' => 'sun', 'Hund14879' => 'sun', 'Lalb_Chr06g0160741' => 'lal', 'Lalb_Chr21g0304781' => 'lal', 'Lj3A726G19' => 'lonja', 'Lj3A726T23' => 'lonja', 'Lj3A726T24' => 'lonja', 'Lj3A726T25' => 'lonja', 'Lj3A727T17' => 'lonja', 'Lj3C726T0' => 'lonja', 'Lj3C726T2' => 'lonja', 'Lj3P725T35' => 'lonja', 'Lj3P727T10' => 'lonja', 'Lj3P727T12' => 'lonja', 'Lj3P727T14' => 'lonja', 'Lj5g0023109' => 'lja', 'Lj6P646T44' => 'lonja', 'Lsat_1_v5_gn_6_75760' => 'lsa', 'Lsat_1_v5_gn_6_75800' => 'lsa', 'Lsat_1_v5_gn_6_75900' => 'lsa', 'Lsat_1_v5_gn_6_76240' => 'lsa', 'Lsat_1_v5_gn_6_76441' => 'lsa', 'Lsat_1_v5_gn_6_76700' => 'lsa', 'Lsat_1_v5_gn_6_76760' => 'lsa', 'Manes.15G033100' => 'mes', 'Mapoly0004s0074' => 'mpo', 'Mapoly0004s0075' => 'mpo', 'Mapoly0004s0163' => 'mpo', 'Mapoly0004s0164' => 'mpo', 'Mapoly0021s0018' => 'mpo', 'Mapoly0041s0136' => 'mpo', 'Mapoly0041s0137' => 'mpo', 'Mapoly0041s0138' => 'mpo', 'Mapoly0041s0139' => 'mpo', 'Mapoly0041s0141' => 'mpo', 'Mapoly0041s0142' => 'mpo', 'Mapoly0041s0143' => 'mpo', 'Mapoly0041s0144' => 'mpo', 'Mapoly0041s0145' => 'mpo', 'Mapoly0047s0106' => 'mpo', 'Mapoly0047s0108' => 'mpo', 'Mapoly0050s0051' => 'mpo', 'Mapoly0050s0052' => 'mpo', 'Mapoly0050s0053' => 'mpo', 'Mapoly0058s0013' => 'mpo', 'Mapoly0091s0078' => 'mpo', 'Mapoly0091s0079' => 'mpo', 'Mapoly0091s0080' => 'mpo', 'Mapoly0091s0081' => 'mpo', 'Mapoly0278s0004' => 'mpo', 'Mapoly0278s0005' => 'mpo', 'Mapoly0278s0006' => 'mpo', 'MBI11_g30648_MAGBIO' => 'mbi', 'MCO03G194' => 'mco', 'MCO03G590' => 'mco', 'MCO07G312' => 'mco', 'MCO10G318' => 'mco', 'MCO12G244' => 'mco', 'MCO13G148' => 'mco', 'MCO13G194' => 'mco', 'MCO16G238' => 'mco', 'MD06G1134100' => 'mdo', 'MD13G1200100' => 'mdo', 'MD13G1200300' => 'mdo', 'MD13G1200600' => 'mdo', 'MD14G1150400' => 'mdo', 'MD16G1200000' => 'mdo', 'Medtr1g102570' => 'mtr', 'Medtr1g102780' => 'mtr', 'Medtr1g102800' => 'mtr', 'Medtr1g102810' => 'mtr', 'Medtr1g102830' => 'mtr', 'MELO3C006499.2' => 'cme', 'Migut.G00385' => 'egut', 'MSTRG.4063' => 'ama', 'Nitab4.5_0000090g0260' => 'nta', 'Nitab4.5_0000977g0030' => 'nta', 'Nitab4.5_0002541g0040' => 'nta', 'Nitab4.5_0007068g0040' => 'nta', 'Nn005s41408' => 'nnu', 'Nn005s41410' => 'nnu', 'Oeu010310.1' => 'oeu', 'Oeu010311.1' => 'oeu', 'Oeu043472.1' => 'oeu', 'Os01g0246400' => 'osa', 'Os04g0267950' => 'osa', 'Os07g0178700' => 'osa', 'Os07g0178800' => 'osa', 'Peaxi162Scf00316g00046' => 'pax', 'Peaxi162Scf00316g00049' => 'pax', 'Peaxi162Scf00316g00059' => 'pax', 'Peaxi162Scf00316g00328' => 'pax', 'Peaxi162Scf00316g00329' => 'pax', 'Peaxi162Scf00316g00411' => 'pax', 'Peaxi162Scf00316g00521' => 'pax', 'Peaxi162Scf00492g00068' => 'pax', 'Peaxi162Scf35631g00002' => 'pax', 'PGR142G3720' => 'pgr', 'PGSC0003DMG400006442' => 'stu', 'Phvul.007G062000' => 'pvu', 'Potri.008G157750' => 'ptr', 'Potri.008G157900' => 'ptr', 'Potri.008G158000' => 'ptr', 'Potri.008G158200' => 'ptr', 'Pp3c11_7280' => 'ppa', 'Pp3c11_7980' => 'ppa', 'Pp3c12_19450' => 'ppa', 'Pp3c14_1480' => 'ppa', 'Pp3c14_1501' => 'ppa', 'Pp3c16_4900' => 'ppa', 'Pp3c16_5010' => 'ppa', 'Pp3c16_5060' => 'ppa', 'Pp3c19_18250' => 'ppa', 'Pp3c23_8530' => 'ppa', 'Pp3c23_8550' => 'ppa', 'Pp3c24_9670' => 'ppa', 'Pp3c2_21390' => 'ppa', 'Pp3c2_31380' => 'ppa', 'Pp3c3_16620' => 'ppa', 'Pp3c3_8090' => 'ppa', 'Pp3c3_8110' => 'ppa', 'Pp3c3_8130' => 'ppa', 'Pp3c3_8150' => 'ppa', 'Pp3c4_14320' => 'ppa', 'Pp3c6_2560' => 'ppa', 'Pp3c9_16700' => 'ppa', 'PRCOL_00000234' => 'pco', 'PRCOL_00000235' => 'pco', 'PRCOL_00000777' => 'pco', 'PRCOL_00002344' => 'pco', 'PRCOL_00002372' => 'pco', 'PRCOL_00006120' => 'pco', 'Prupe.1G021400' => 'ppe', 'Prupe.1G021500' => 'ppe', 'Prupe.1G021600' => 'ppe', 'Prupe.1G021700' => 'ppe', 'Prupe.1G021800' => 'ppe', 'Prupe.5G145100' => 'ppe', 'Psat6g204040' => 'psa', 'Psat6g204800' => 'psa', 'Psat6g204920' => 'psa', 'Psat6g204960' => 'psa', 'Psat6g205080' => 'psa', 'PSO017G0271' => 'pso', 'PSO017G1276' => 'pso', 'PSO017G1429' => 'pso', 'PSO017G1861' => 'pso', 'PSO017G2787' => 'pso', 'PSO017G4466' => 'pso', 'PSO017G5118' => 'pso', 'PSO017G5420' => 'pso', 'PSO063G3678' => 'pso', 'PSO210G0546' => 'pso', 'PSO317G0001' => 'pso', 'PSO357G0512' => 'pso', 'PSO478G2682' => 'pso', 'PSO647G0001' => 'pso', 'PSO675G0001' => 'pso', 'PSO675G2699' => 'pso', 'PSO675G2849' => 'pso', 'PSO675G4991' => 'pso', 'PSO689G0001' => 'pso', 'QL06p000916' => 'qlo', 'QL06p000921' => 'qlo', 'QL06p001398' => 'qlo', 'QL06p001407' => 'qlo', 'QL06p002031' => 'qlo', 'RcHm_v2.0_Chr4g0387791' => 'rch', 'RcHm_v2.0_Chr4g0387801' => 'rch', 'RcHm_v2.0_Chr6g0286501' => 'rch', 'RcHm_v2.0_Chr6g0286511' => 'rch', 'RcHm_v2.0_Chr6g0286521' => 'rch', 'RcHm_v2.0_Chr6g0286531' => 'rch', 'RcHm_v2.0_Chr7g0189141' => 'rch', 'Rhsim02G0028700' => 'rsi', 'Rhsim02G0028800' => 'rsi', 'Rhsim02G0028900' => 'rsi', 'Rhsim02G0029000' => 'rsi', 'Rhsim02G0029100' => 'rsi', 'Rhsim02G0029200' => 'rsi', 'Rhsim02G0029300' => 'rsi', 'Rhsim02G0029400' => 'rsi', 'Rhsim02G0029500' => 'rsi', 'Rhsim02G0029600' => 'rsi', 'RhsimUnG0024000' => 'rsi', 'RhsimUnG0024100' => 'rsi', 'RhsimUnG0024200' => 'rsi', 'RhsimUnG0024300' => 'rsi', 'RhsimUnG0024400' => 'rsi', 'RhsimUnG0024500' => 'rsi', 'RhsimUnG0024700' => 'rsi', 'RhsimUnG0024800' => 'rsi', 'RhsimUnG0024900' => 'rsi', 'RhsimUnG0025100' => 'rsi', 'Sabra08G0120200' => 'sbr', 'Sabra08G0120300' => 'sbr', 'Sabra08G0120500' => 'sbr', 'Sabra08G0120600' => 'sbr', 'Sabra10G0158900' => 'sbr', 'SalBow2G3492' => 'sbo', 'Sc13g0004760' => 'sci', 'Sc13g0004770' => 'sci', 'Sed0003417' => 'sed', 'Sed0019750' => 'sed', 'SEGI_03419' => 'sgi', 'SEGI_05907' => 'sgi', 'SEGI_10682' => 'sgi', 'SEGI_13528' => 'sgi', 'SEGI_16081' => 'sgi', 'SEGI_19370' => 'sgi', 'SEGI_21015' => 'sgi', 'SEGI_21944' => 'sgi', 'SEGI_32906' => 'sgi', 'SEGI_33093' => 'sgi', 'SEGI_36110' => 'sgi', 'SEGI_40397' => 'sgi', 'SGA_v2.0_scaffold191G40426' => 'sas', 'SGA_v2.0_scaffold353G49717' => 'sas', 'SGA_v2.0_scaffold50G18550' => 'sas', 'SMO119G0173' => 'smo', 'SMO172G0002' => 'smo', 'Solyc09g082690.3' => 'sly', 'Solyc09g082700.2' => 'sly', 'Sopen09g031550' => 'spe', 'Sopen09g031560' => 'spe', 'Sp3g20540' => 'spa', 'Sp7g07580' => 'spa', 'TAR134G0002' => 'tar', 'TAR236G0001' => 'tar', 'TAR365G0892' => 'tar', 'TAR636G0166' => 'tar', 'TAR636G0646' => 'tar', 'TAR636G0869' => 'tar', 'TAR636G1317' => 'tar', 'TAR636G1744' => 'tar', 'TAR636G3358' => 'tar', 'TAR636G3436' => 'tar', 'THA.LOC104803047' => 'tha', 'Thecc.04G238900' => 'tca', 'Thhalv10021557m.g' => 'esa', 'Thhalv10026318m.g' => 'esa', 'Thhalv10026335m.g' => 'esa', 'TPR.G17433' => 'tpr', 'TPR.G18915' => 'tpr', 'TPR.G26125' => 'tpr', 'TWI09G0677' => 'twi', 'TWI73G0287' => 'twi', 'unitig_748.g8326' => 'ugi', 'vmacro15370' => 'vma', 'vmacro15371' => 'vma', 'vmacro15372' => 'vma', 'vmacro15373' => 'vma', 'vmacro15374' => 'vma', 'VMungo0720G2826' => 'vmu', 'Zm00001eb116960' => 'zma', 'Zm00001eb301260' => 'zma', 'Zm00001eb301270' => 'zma' ), 'gf_id' => 'HOM05D001460', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001460' ), 'data_identifier' => 'HOM05D001460', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001460', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '433', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p22980' => 'bna', 'A01p32340' => 'bna', 'A03p42970' => 'bna', 'A05p25880' => 'bna', 'Aa31LG8G9320' => 'aar', 'Aa31LG8G9330' => 'aar', 'Aa31LG8G9340' => 'aar', 'Aa31sc221G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1034' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1528' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.829' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2222' => 'aag', 'Ah.12g058830' => 'amhyb', 'Ah.12g058840' => 'amhyb', 'AL3G37160' => 'aly', 'AL7G41310' => 'aly', 'Aqoxy5G00395' => 'aox', 'Aqoxy5G00396' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0C8NZA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5185HY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JZ1PRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MD3LS0' => 'arhy', 'AT3G22840' => 'ath', 'AT4G14690' => 'ath', 'ATR0665G054' => 'atr', 'Atru.chr4.2344' => 'acertr', 'Atru.chr4.2346' => 'acertr', 'Atru.chr4.2347' => 'acertr', 'Atru.chr4.2348' => 'acertr', 'Atru.chr4.2355' => 'acertr', 'Atru.chr4.2356' => 'acertr', 'Atru.chr4.2358' => 'acertr', 'Atru.chr4.2359' => 'acertr', 'Atru.chr4.2360' => 'acertr', 'Atru.chr4.2361' => 'acertr', 'AUR62030476' => 'cqu', 'AUR62030478' => 'cqu', 'AUR62030819' => 'cqu', 'AUR62030820' => 'cqu', 'BcaB03g14648' => 'bca', 'BcaB04g20492' => 'bca', 'BcaB06g26399' => 'bca', 'BcaC01g03416' => 'bca', 'BcaC01g03419' => 'bca', 'BcaC01g03421' => 'bca', 'BcaC01g03424' => 'bca', 'BcaC05g28012' => 'bca', 'BcaC09g49212' => 'bca', 'BcaC09g50140' => 'bca', 'BcaNung00346' => 'bca', 'BolC1t02785H' => 'bol', 'BolC1t04095H' => 'bol', 'BolC3t17545H' => 'bol', 'BolC5t32769H' => 'bol', 'BraA01t02211Z' => 'bra', 'BraA01t03359Z' => 'bra', 'BraA03t13441Z' => 'bra', 'BraA05t21476Z' => 'bra', 'C01p28420' => 'bna', 'C01p41350' => 'bna', 'C03p52750' => 'bna', 'C03p52780' => 'bna', 'C05p40270' => 'bna', 'CAN.G1437.9' => 'can', 'CANSAT78G0035' => 'cansat', 'CANSAT78G1036' => 'cansat', 'CANSAT78G2272' => 'cansat', 'CANSAT78G2478' => 'cansat', 'CARHR098700' => 'chi', 'CARHR221120' => 'chi', 'CARHR221150' => 'chi', 'Carub.0003s2297' => 'cru', 'Carub.0007s2749' => 'cru', 'Carub.0007s2750' => 'cru', 'Carub.0007s2751' => 'cru', 'Ca_10849_v3' => 'car', 'Cc03_g04300' => 'ccan', 'CDE02G3648' => 'cde', 'CDE05G0060' => 'cde', 'CDE05G0692' => 'cde', 'CDE05G2285' => 'cde', 'CDE05G2884' => 'cde', 'CDE05G3072' => 'cde', 'Cfa008439' => 'cfa', 'Cfa008441' => 'cfa', 'Cfa008443' => 'cfa', 'Cfa008448' => 'cfa', 'Ciclev10005974m.g' => 'ccl', 'Ciclev10006006m.g' => 'ccl', 'Ciclev10006775m.g' => 'ccl', 'CiPaw.02G120400' => 'cil', 'CiPaw.02G120500' => 'cil', 'CiPaw.02G120600' => 'cil', 'ClCG05G004850' => 'cla', 'COL.COLO4_21566' => 'col', 'Cpa.g.sc44.124' => 'cpa', 'Cre07.g320400' => 'cre', 'Cre07.g320450' => 'cre', 'Cre08.g384650' => 'cre', 'Cre09.g393173' => 'cre', 'Cre09.g394325' => 'cre', 'Cre14.g626750' => 'cre', 'Cre16.g679250' => 'cre', 'CsaV3_3G012890' => 'csa', 'CSS0010865' => 'camsi', 'CSS0044338' => 'camsi', 'DCAR_002366' => 'dca', 'DCAR_030687' => 'dca', 'DCAR_030688' => 'dca', 'Dinv14047' => 'din', 'Dinv14048' => 'din', 'Duzib151G0105' => 'dzi', 'Duzib151G0114' => 'dzi', 'Duzib212G1029' => 'dzi', 'ECA232G3536' => 'eca', 'ECA240G0786' => 'eca', 'ECA240G1802' => 'eca', 'ECA240G3760' => 'eca', 'ECA240G3920' => 'eca', 'EL10Ac5g12536' => 'bvu', 'EL10Ac5g12537' => 'bvu', 'EL10Ac5g12538' => 'bvu', 'Eucgr.B01004' => 'egr', 'Eucgr.B01006' => 'egr', 'Eucgr.B01007' => 'egr', 'Eucgr.B01008' => 'egr', 'Eucgr.B01895' => 'egr', 'Eucgr.B01896' => 'egr', 'FAN04G1456' => 'fan', 'FAN08G1769' => 'fan', 'FAN08G2160' => 'fan', 'FAN13G2403' => 'fan', 'FAN13G3303' => 'fan', 'FAN15G2435' => 'fan', 'FAN17G0672' => 'fan', 'FAN17G2441' => 'fan', 'FAN18G1024' => 'fan', 'FAN22G1458' => 'fan', 'FAN24G0037' => 'fan', 'FAN24G0429' => 'fan', 'FAN24G2387' => 'fan', 'FAN27G2746' => 'fan', 'FvH4_2g20400' => 'fve', 'FvH4_2g20420' => 'fve', 'FvH4_2g20430' => 'fve', 'FvH4_4g01270' => 'fve', 'FvH4_4g01290' => 'fve', 'FvH4_4g01300' => 'fve', 'FvH4_4g01310' => 'fve', 'FvH4_4g01330' => 'fve', 'FvH4_5g09070' => 'fve', 'Glyma.10G243800' => 'gma', 'Glyma.20G150600' => 'gma', 'Gohir.A09G219200' => 'ghi', 'Gohir.A09G219300' => 'ghi', 'Gohir.D09G221400' => 'ghi', 'Gohir.D09G221500' => 'ghi', 'Gorai.006G242600' => 'gra', 'Gorai.006G242700' => 'gra', 'GSVIVG01018044001' => 'vvi', 'HanXRQChr03g0083821' => 'han', 'HanXRQChr03g0083841' => 'han', 'HanXRQChr03g0083881' => 'han', 'HanXRQChr03g0083901' => 'han', 'HanXRQChr03g0083921' => 'han', 'HanXRQChr03g0085331' => 'han', 'HanXRQChr03g0085361' => 'han', 'HanXRQChr03g0085411' => 'han', 'HanXRQChr03g0085421' => 'han', 'HanXRQChr03g0085431' => 'han', 'HanXRQChr08g0221991' => 'han', 'HanXRQChr11g0336061' => 'han', 'HanXRQChr11g0336411' => 'han', 'Haze_11234' => 'cav', 'Hma1.2p1_0549F.1_g177010' => 'hma', 'Hma1.2p1_0602F.1_g187630' => 'hma', 'Hund14876' => 'sun', 'Hund14879' => 'sun', 'Lalb_Chr06g0160741' => 'lal', 'Lalb_Chr21g0304781' => 'lal', 'Lj3A726G19' => 'lonja', 'Lj3A726T23' => 'lonja', 'Lj3A726T24' => 'lonja', 'Lj3A726T25' => 'lonja', 'Lj3A727T17' => 'lonja', 'Lj3C726T0' => 'lonja', 'Lj3C726T2' => 'lonja', 'Lj3P725T35' => 'lonja', 'Lj3P727T10' => 'lonja', 'Lj3P727T12' => 'lonja', 'Lj3P727T14' => 'lonja', 'Lj5g0023109' => 'lja', 'Lj6P646T44' => 'lonja', 'Lsat_1_v5_gn_6_75760' => 'lsa', 'Lsat_1_v5_gn_6_75800' => 'lsa', 'Lsat_1_v5_gn_6_75900' => 'lsa', 'Lsat_1_v5_gn_6_76240' => 'lsa', 'Lsat_1_v5_gn_6_76441' => 'lsa', 'Lsat_1_v5_gn_6_76700' => 'lsa', 'Lsat_1_v5_gn_6_76760' => 'lsa', 'Manes.15G033100' => 'mes', 'Mapoly0004s0074' => 'mpo', 'Mapoly0004s0075' => 'mpo', 'Mapoly0004s0163' => 'mpo', 'Mapoly0004s0164' => 'mpo', 'Mapoly0021s0018' => 'mpo', 'Mapoly0041s0136' => 'mpo', 'Mapoly0041s0137' => 'mpo', 'Mapoly0041s0138' => 'mpo', 'Mapoly0041s0139' => 'mpo', 'Mapoly0041s0141' => 'mpo', 'Mapoly0041s0142' => 'mpo', 'Mapoly0041s0143' => 'mpo', 'Mapoly0041s0144' => 'mpo', 'Mapoly0041s0145' => 'mpo', 'Mapoly0047s0106' => 'mpo', 'Mapoly0047s0108' => 'mpo', 'Mapoly0050s0051' => 'mpo', 'Mapoly0050s0052' => 'mpo', 'Mapoly0050s0053' => 'mpo', 'Mapoly0058s0013' => 'mpo', 'Mapoly0091s0078' => 'mpo', 'Mapoly0091s0079' => 'mpo', 'Mapoly0091s0080' => 'mpo', 'Mapoly0091s0081' => 'mpo', 'Mapoly0278s0004' => 'mpo', 'Mapoly0278s0005' => 'mpo', 'Mapoly0278s0006' => 'mpo', 'MBI11_g30648_MAGBIO' => 'mbi', 'MCO03G194' => 'mco', 'MCO03G590' => 'mco', 'MCO07G312' => 'mco', 'MCO10G318' => 'mco', 'MCO12G244' => 'mco', 'MCO13G148' => 'mco', 'MCO13G194' => 'mco', 'MCO16G238' => 'mco', 'MD06G1134100' => 'mdo', 'MD13G1200100' => 'mdo', 'MD13G1200300' => 'mdo', 'MD13G1200600' => 'mdo', 'MD14G1150400' => 'mdo', 'MD16G1200000' => 'mdo', 'Medtr1g102570' => 'mtr', 'Medtr1g102780' => 'mtr', 'Medtr1g102800' => 'mtr', 'Medtr1g102810' => 'mtr', 'Medtr1g102830' => 'mtr', 'MELO3C006499.2' => 'cme', 'Migut.G00385' => 'egut', 'MSTRG.4063' => 'ama', 'Nitab4.5_0000090g0260' => 'nta', 'Nitab4.5_0000977g0030' => 'nta', 'Nitab4.5_0002541g0040' => 'nta', 'Nitab4.5_0007068g0040' => 'nta', 'Nn005s41408' => 'nnu', 'Nn005s41410' => 'nnu', 'Oeu010310.1' => 'oeu', 'Oeu010311.1' => 'oeu', 'Oeu043472.1' => 'oeu', 'Os01g0246400' => 'osa', 'Os04g0267950' => 'osa', 'Os07g0178700' => 'osa', 'Os07g0178800' => 'osa', 'Peaxi162Scf00316g00046' => 'pax', 'Peaxi162Scf00316g00049' => 'pax', 'Peaxi162Scf00316g00059' => 'pax', 'Peaxi162Scf00316g00328' => 'pax', 'Peaxi162Scf00316g00329' => 'pax', 'Peaxi162Scf00316g00411' => 'pax', 'Peaxi162Scf00316g00521' => 'pax', 'Peaxi162Scf00492g00068' => 'pax', 'Peaxi162Scf35631g00002' => 'pax', 'PGR142G3720' => 'pgr', 'PGSC0003DMG400006442' => 'stu', 'Phvul.007G062000' => 'pvu', 'Potri.008G157750' => 'ptr', 'Potri.008G157900' => 'ptr', 'Potri.008G158000' => 'ptr', 'Potri.008G158200' => 'ptr', 'Pp3c11_7280' => 'ppa', 'Pp3c11_7980' => 'ppa', 'Pp3c12_19450' => 'ppa', 'Pp3c14_1480' => 'ppa', 'Pp3c14_1501' => 'ppa', 'Pp3c16_4900' => 'ppa', 'Pp3c16_5010' => 'ppa', 'Pp3c16_5060' => 'ppa', 'Pp3c19_18250' => 'ppa', 'Pp3c23_8530' => 'ppa', 'Pp3c23_8550' => 'ppa', 'Pp3c24_9670' => 'ppa', 'Pp3c2_21390' => 'ppa', 'Pp3c2_31380' => 'ppa', 'Pp3c3_16620' => 'ppa', 'Pp3c3_8090' => 'ppa', 'Pp3c3_8110' => 'ppa', 'Pp3c3_8130' => 'ppa', 'Pp3c3_8150' => 'ppa', 'Pp3c4_14320' => 'ppa', 'Pp3c6_2560' => 'ppa', 'Pp3c9_16700' => 'ppa', 'PRCOL_00000234' => 'pco', 'PRCOL_00000235' => 'pco', 'PRCOL_00000777' => 'pco', 'PRCOL_00002344' => 'pco', 'PRCOL_00002372' => 'pco', 'PRCOL_00006120' => 'pco', 'Prupe.1G021400' => 'ppe', 'Prupe.1G021500' => 'ppe', 'Prupe.1G021600' => 'ppe', 'Prupe.1G021700' => 'ppe', 'Prupe.1G021800' => 'ppe', 'Prupe.5G145100' => 'ppe', 'Psat6g204040' => 'psa', 'Psat6g204800' => 'psa', 'Psat6g204920' => 'psa', 'Psat6g204960' => 'psa', 'Psat6g205080' => 'psa', 'PSO017G0271' => 'pso', 'PSO017G1276' => 'pso', 'PSO017G1429' => 'pso', 'PSO017G1861' => 'pso', 'PSO017G2787' => 'pso', 'PSO017G4466' => 'pso', 'PSO017G5118' => 'pso', 'PSO017G5420' => 'pso', 'PSO063G3678' => 'pso', 'PSO210G0546' => 'pso', 'PSO317G0001' => 'pso', 'PSO357G0512' => 'pso', 'PSO478G2682' => 'pso', 'PSO647G0001' => 'pso', 'PSO675G0001' => 'pso', 'PSO675G2699' => 'pso', 'PSO675G2849' => 'pso', 'PSO675G4991' => 'pso', 'PSO689G0001' => 'pso', 'QL06p000916' => 'qlo', 'QL06p000921' => 'qlo', 'QL06p001398' => 'qlo', 'QL06p001407' => 'qlo', 'QL06p002031' => 'qlo', 'RcHm_v2.0_Chr4g0387791' => 'rch', 'RcHm_v2.0_Chr4g0387801' => 'rch', 'RcHm_v2.0_Chr6g0286501' => 'rch', 'RcHm_v2.0_Chr6g0286511' => 'rch', 'RcHm_v2.0_Chr6g0286521' => 'rch', 'RcHm_v2.0_Chr6g0286531' => 'rch', 'RcHm_v2.0_Chr7g0189141' => 'rch', 'Rhsim02G0028700' => 'rsi', 'Rhsim02G0028800' => 'rsi', 'Rhsim02G0028900' => 'rsi', 'Rhsim02G0029000' => 'rsi', 'Rhsim02G0029100' => 'rsi', 'Rhsim02G0029200' => 'rsi', 'Rhsim02G0029300' => 'rsi', 'Rhsim02G0029400' => 'rsi', 'Rhsim02G0029500' => 'rsi', 'Rhsim02G0029600' => 'rsi', 'RhsimUnG0024000' => 'rsi', 'RhsimUnG0024100' => 'rsi', 'RhsimUnG0024200' => 'rsi', 'RhsimUnG0024300' => 'rsi', 'RhsimUnG0024400' => 'rsi', 'RhsimUnG0024500' => 'rsi', 'RhsimUnG0024700' => 'rsi', 'RhsimUnG0024800' => 'rsi', 'RhsimUnG0024900' => 'rsi', 'RhsimUnG0025100' => 'rsi', 'Sabra08G0120200' => 'sbr', 'Sabra08G0120300' => 'sbr', 'Sabra08G0120500' => 'sbr', 'Sabra08G0120600' => 'sbr', 'Sabra10G0158900' => 'sbr', 'SalBow2G3492' => 'sbo', 'Sc13g0004760' => 'sci', 'Sc13g0004770' => 'sci', 'Sed0003417' => 'sed', 'Sed0019750' => 'sed', 'SEGI_03419' => 'sgi', 'SEGI_05907' => 'sgi', 'SEGI_10682' => 'sgi', 'SEGI_13528' => 'sgi', 'SEGI_16081' => 'sgi', 'SEGI_19370' => 'sgi', 'SEGI_21015' => 'sgi', 'SEGI_21944' => 'sgi', 'SEGI_32906' => 'sgi', 'SEGI_33093' => 'sgi', 'SEGI_36110' => 'sgi', 'SEGI_40397' => 'sgi', 'SGA_v2.0_scaffold191G40426' => 'sas', 'SGA_v2.0_scaffold353G49717' => 'sas', 'SGA_v2.0_scaffold50G18550' => 'sas', 'SMO119G0173' => 'smo', 'SMO172G0002' => 'smo', 'Solyc09g082690.3' => 'sly', 'Solyc09g082700.2' => 'sly', 'Sopen09g031550' => 'spe', 'Sopen09g031560' => 'spe', 'Sp3g20540' => 'spa', 'Sp7g07580' => 'spa', 'TAR134G0002' => 'tar', 'TAR236G0001' => 'tar', 'TAR365G0892' => 'tar', 'TAR636G0166' => 'tar', 'TAR636G0646' => 'tar', 'TAR636G0869' => 'tar', 'TAR636G1317' => 'tar', 'TAR636G1744' => 'tar', 'TAR636G3358' => 'tar', 'TAR636G3436' => 'tar', 'THA.LOC104803047' => 'tha', 'Thecc.04G238900' => 'tca', 'Thhalv10021557m.g' => 'esa', 'Thhalv10026318m.g' => 'esa', 'Thhalv10026335m.g' => 'esa', 'TPR.G17433' => 'tpr', 'TPR.G18915' => 'tpr', 'TPR.G26125' => 'tpr', 'TWI09G0677' => 'twi', 'TWI73G0287' => 'twi', 'unitig_748.g8326' => 'ugi', 'vmacro15370' => 'vma', 'vmacro15371' => 'vma', 'vmacro15372' => 'vma', 'vmacro15373' => 'vma', 'vmacro15374' => 'vma', 'VMungo0720G2826' => 'vmu', 'Zm00001eb116960' => 'zma', 'Zm00001eb301260' => 'zma', 'Zm00001eb301270' => 'zma' ) $gf_id = 'HOM05D001460' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001460' ) $data_identifier = 'HOM05D001460' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 4, 'aag' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 2, 'aox' => (int) 2, 'arhy' => (int) 4, 'ath' => (int) 2, 'atr' => (int) 1, 'acertr' => (int) 10, 'cqu' => (int) 4, 'bca' => (int) 11, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 1, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 1, 'ccan' => (int) 1, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 1, 'col' => (int) 1, 'cpa' => (int) 1, 'cre' => (int) 7, 'csa' => (int) 1, 'camsi' => (int) 2, 'dca' => (int) 3, 'din' => (int) 2, 'dzi' => (int) 3, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 14, 'fve' => (int) 9, 'gma' => (int) 2, 'ghi' => (int) 4, 'gra' => (int) 2, 'vvi' => (int) 1, 'han' => (int) 13, 'cav' => (int) 1, 'hma' => (int) 2, 'sun' => (int) 2, 'lal' => (int) 2, 'lonja' => (int) 12, 'lja' => (int) 1, 'lsa' => (int) 7, 'mes' => (int) 1, 'mpo' => (int) 27, 'mbi' => (int) 1, 'mco' => (int) 8, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 1, 'egut' => (int) 1, 'ama' => (int) 1, 'nta' => (int) 4, 'nnu' => (int) 2, 'oeu' => (int) 3, 'osa' => (int) 4, 'pax' => (int) 9, 'pgr' => (int) 1, 'stu' => (int) 1, 'pvu' => (int) 1, 'ptr' => (int) 4, 'ppa' => (int) 22, 'pco' => (int) 6, 'ppe' => (int) 6, 'psa' => (int) 5, 'pso' => (int) 19, 'qlo' => (int) 5, 'rch' => (int) 7, 'rsi' => (int) 20, 'sbr' => (int) 5, 'sbo' => (int) 1, 'sci' => (int) 2, 'sed' => (int) 2, 'sgi' => (int) 12, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 2, 'tar' => (int) 10, 'tha' => (int) 1, 'tca' => (int) 1, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 2, 'ugi' => (int) 1, 'vma' => (int) 5, 'vmu' => (int) 1, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb301270' $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' => 'HOM05D001460', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '433', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p22980' => 'bna', 'A01p32340' => 'bna', 'A03p42970' => 'bna', 'A05p25880' => 'bna', 'Aa31LG8G9320' => 'aar', 'Aa31LG8G9330' => 'aar', 'Aa31LG8G9340' => 'aar', 'Aa31sc221G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1034' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1528' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.829' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2222' => 'aag', 'Ah.12g058830' => 'amhyb', 'Ah.12g058840' => 'amhyb', 'AL3G37160' => 'aly', 'AL7G41310' => 'aly', 'Aqoxy5G00395' => 'aox', 'Aqoxy5G00396' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0C8NZA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5185HY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JZ1PRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MD3LS0' => 'arhy', 'AT3G22840' => 'ath', 'AT4G14690' => 'ath', 'ATR0665G054' => 'atr', 'Atru.chr4.2344' => 'acertr', 'Atru.chr4.2346' => 'acertr', 'Atru.chr4.2347' => 'acertr', 'Atru.chr4.2348' => 'acertr', 'Atru.chr4.2355' => 'acertr', 'Atru.chr4.2356' => 'acertr', 'Atru.chr4.2358' => 'acertr', 'Atru.chr4.2359' => 'acertr', 'Atru.chr4.2360' => 'acertr', 'Atru.chr4.2361' => 'acertr', 'AUR62030476' => 'cqu', 'AUR62030478' => 'cqu', 'AUR62030819' => 'cqu', 'AUR62030820' => 'cqu', 'BcaB03g14648' => 'bca', 'BcaB04g20492' => 'bca', 'BcaB06g26399' => 'bca', 'BcaC01g03416' => 'bca', 'BcaC01g03419' => 'bca', 'BcaC01g03421' => 'bca', 'BcaC01g03424' => 'bca', 'BcaC05g28012' => 'bca', 'BcaC09g49212' => 'bca', 'BcaC09g50140' => 'bca', 'BcaNung00346' => 'bca', 'BolC1t02785H' => 'bol', 'BolC1t04095H' => 'bol', 'BolC3t17545H' => 'bol', 'BolC5t32769H' => 'bol', 'BraA01t02211Z' => 'bra', 'BraA01t03359Z' => 'bra', 'BraA03t13441Z' => 'bra', 'BraA05t21476Z' => 'bra', 'C01p28420' => 'bna', 'C01p41350' => 'bna', 'C03p52750' => 'bna', 'C03p52780' => 'bna', 'C05p40270' => 'bna', 'CAN.G1437.9' => 'can', 'CANSAT78G0035' => 'cansat', 'CANSAT78G1036' => 'cansat', 'CANSAT78G2272' => 'cansat', 'CANSAT78G2478' => 'cansat', 'CARHR098700' => 'chi', 'CARHR221120' => 'chi', 'CARHR221150' => 'chi', 'Carub.0003s2297' => 'cru', 'Carub.0007s2749' => 'cru', 'Carub.0007s2750' => 'cru', 'Carub.0007s2751' => 'cru', 'Ca_10849_v3' => 'car', 'Cc03_g04300' => 'ccan', 'CDE02G3648' => 'cde', 'CDE05G0060' => 'cde', 'CDE05G0692' => 'cde', 'CDE05G2285' => 'cde', 'CDE05G2884' => 'cde', 'CDE05G3072' => 'cde', 'Cfa008439' => 'cfa', 'Cfa008441' => 'cfa', 'Cfa008443' => 'cfa', 'Cfa008448' => 'cfa', 'Ciclev10005974m.g' => 'ccl', 'Ciclev10006006m.g' => 'ccl', 'Ciclev10006775m.g' => 'ccl', 'CiPaw.02G120400' => 'cil', 'CiPaw.02G120500' => 'cil', 'CiPaw.02G120600' => 'cil', 'ClCG05G004850' => 'cla', 'COL.COLO4_21566' => 'col', 'Cpa.g.sc44.124' => 'cpa', 'Cre07.g320400' => 'cre', 'Cre07.g320450' => 'cre', 'Cre08.g384650' => 'cre', 'Cre09.g393173' => 'cre', 'Cre09.g394325' => 'cre', 'Cre14.g626750' => 'cre', 'Cre16.g679250' => 'cre', 'CsaV3_3G012890' => 'csa', 'CSS0010865' => 'camsi', 'CSS0044338' => 'camsi', 'DCAR_002366' => 'dca', 'DCAR_030687' => 'dca', 'DCAR_030688' => 'dca', 'Dinv14047' => 'din', 'Dinv14048' => 'din', 'Duzib151G0105' => 'dzi', 'Duzib151G0114' => 'dzi', 'Duzib212G1029' => 'dzi', 'ECA232G3536' => 'eca', 'ECA240G0786' => 'eca', 'ECA240G1802' => 'eca', 'ECA240G3760' => 'eca', 'ECA240G3920' => 'eca', 'EL10Ac5g12536' => 'bvu', 'EL10Ac5g12537' => 'bvu', 'EL10Ac5g12538' => 'bvu', 'Eucgr.B01004' => 'egr', 'Eucgr.B01006' => 'egr', 'Eucgr.B01007' => 'egr', 'Eucgr.B01008' => 'egr', 'Eucgr.B01895' => 'egr', 'Eucgr.B01896' => 'egr', 'FAN04G1456' => 'fan', 'FAN08G1769' => 'fan', 'FAN08G2160' => 'fan', 'FAN13G2403' => 'fan', 'FAN13G3303' => 'fan', 'FAN15G2435' => 'fan', 'FAN17G0672' => 'fan', 'FAN17G2441' => 'fan', 'FAN18G1024' => 'fan', 'FAN22G1458' => 'fan', 'FAN24G0037' => 'fan', 'FAN24G0429' => 'fan', 'FAN24G2387' => 'fan', 'FAN27G2746' => 'fan', 'FvH4_2g20400' => 'fve', 'FvH4_2g20420' => 'fve', 'FvH4_2g20430' => 'fve', 'FvH4_4g01270' => 'fve', 'FvH4_4g01290' => 'fve', 'FvH4_4g01300' => 'fve', 'FvH4_4g01310' => 'fve', 'FvH4_4g01330' => 'fve', 'FvH4_5g09070' => 'fve', 'Glyma.10G243800' => 'gma', 'Glyma.20G150600' => 'gma', 'Gohir.A09G219200' => 'ghi', 'Gohir.A09G219300' => 'ghi', 'Gohir.D09G221400' => 'ghi', 'Gohir.D09G221500' => 'ghi', 'Gorai.006G242600' => 'gra', 'Gorai.006G242700' => 'gra', 'GSVIVG01018044001' => 'vvi', 'HanXRQChr03g0083821' => 'han', 'HanXRQChr03g0083841' => 'han', 'HanXRQChr03g0083881' => 'han', 'HanXRQChr03g0083901' => 'han', 'HanXRQChr03g0083921' => 'han', 'HanXRQChr03g0085331' => 'han', 'HanXRQChr03g0085361' => 'han', 'HanXRQChr03g0085411' => 'han', 'HanXRQChr03g0085421' => 'han', 'HanXRQChr03g0085431' => 'han', 'HanXRQChr08g0221991' => 'han', 'HanXRQChr11g0336061' => 'han', 'HanXRQChr11g0336411' => 'han', 'Haze_11234' => 'cav', 'Hma1.2p1_0549F.1_g177010' => 'hma', 'Hma1.2p1_0602F.1_g187630' => 'hma', 'Hund14876' => 'sun', 'Hund14879' => 'sun', 'Lalb_Chr06g0160741' => 'lal', 'Lalb_Chr21g0304781' => 'lal', 'Lj3A726G19' => 'lonja', 'Lj3A726T23' => 'lonja', 'Lj3A726T24' => 'lonja', 'Lj3A726T25' => 'lonja', 'Lj3A727T17' => 'lonja', 'Lj3C726T0' => 'lonja', 'Lj3C726T2' => 'lonja', 'Lj3P725T35' => 'lonja', 'Lj3P727T10' => 'lonja', 'Lj3P727T12' => 'lonja', 'Lj3P727T14' => 'lonja', 'Lj5g0023109' => 'lja', 'Lj6P646T44' => 'lonja', 'Lsat_1_v5_gn_6_75760' => 'lsa', 'Lsat_1_v5_gn_6_75800' => 'lsa', 'Lsat_1_v5_gn_6_75900' => 'lsa', 'Lsat_1_v5_gn_6_76240' => 'lsa', 'Lsat_1_v5_gn_6_76441' => 'lsa', 'Lsat_1_v5_gn_6_76700' => 'lsa', 'Lsat_1_v5_gn_6_76760' => 'lsa', 'Manes.15G033100' => 'mes', 'Mapoly0004s0074' => 'mpo', 'Mapoly0004s0075' => 'mpo', 'Mapoly0004s0163' => 'mpo', 'Mapoly0004s0164' => 'mpo', 'Mapoly0021s0018' => 'mpo', 'Mapoly0041s0136' => 'mpo', 'Mapoly0041s0137' => 'mpo', 'Mapoly0041s0138' => 'mpo', 'Mapoly0041s0139' => 'mpo', 'Mapoly0041s0141' => 'mpo', 'Mapoly0041s0142' => 'mpo', 'Mapoly0041s0143' => 'mpo', 'Mapoly0041s0144' => 'mpo', 'Mapoly0041s0145' => 'mpo', 'Mapoly0047s0106' => 'mpo', 'Mapoly0047s0108' => 'mpo', 'Mapoly0050s0051' => 'mpo', 'Mapoly0050s0052' => 'mpo', 'Mapoly0050s0053' => 'mpo', 'Mapoly0058s0013' => 'mpo', 'Mapoly0091s0078' => 'mpo', 'Mapoly0091s0079' => 'mpo', 'Mapoly0091s0080' => 'mpo', 'Mapoly0091s0081' => 'mpo', 'Mapoly0278s0004' => 'mpo', 'Mapoly0278s0005' => 'mpo', 'Mapoly0278s0006' => 'mpo', 'MBI11_g30648_MAGBIO' => 'mbi', 'MCO03G194' => 'mco', 'MCO03G590' => 'mco', 'MCO07G312' => 'mco', 'MCO10G318' => 'mco', 'MCO12G244' => 'mco', 'MCO13G148' => 'mco', 'MCO13G194' => 'mco', 'MCO16G238' => 'mco', 'MD06G1134100' => 'mdo', 'MD13G1200100' => 'mdo', 'MD13G1200300' => 'mdo', 'MD13G1200600' => 'mdo', 'MD14G1150400' => 'mdo', 'MD16G1200000' => 'mdo', 'Medtr1g102570' => 'mtr', 'Medtr1g102780' => 'mtr', 'Medtr1g102800' => 'mtr', 'Medtr1g102810' => 'mtr', 'Medtr1g102830' => 'mtr', 'MELO3C006499.2' => 'cme', 'Migut.G00385' => 'egut', 'MSTRG.4063' => 'ama', 'Nitab4.5_0000090g0260' => 'nta', 'Nitab4.5_0000977g0030' => 'nta', 'Nitab4.5_0002541g0040' => 'nta', 'Nitab4.5_0007068g0040' => 'nta', 'Nn005s41408' => 'nnu', 'Nn005s41410' => 'nnu', 'Oeu010310.1' => 'oeu', 'Oeu010311.1' => 'oeu', 'Oeu043472.1' => 'oeu', 'Os01g0246400' => 'osa', 'Os04g0267950' => 'osa', 'Os07g0178700' => 'osa', 'Os07g0178800' => 'osa', 'Peaxi162Scf00316g00046' => 'pax', 'Peaxi162Scf00316g00049' => 'pax', 'Peaxi162Scf00316g00059' => 'pax', 'Peaxi162Scf00316g00328' => 'pax', 'Peaxi162Scf00316g00329' => 'pax', 'Peaxi162Scf00316g00411' => 'pax', 'Peaxi162Scf00316g00521' => 'pax', 'Peaxi162Scf00492g00068' => 'pax', 'Peaxi162Scf35631g00002' => 'pax', 'PGR142G3720' => 'pgr', 'PGSC0003DMG400006442' => 'stu', 'Phvul.007G062000' => 'pvu', 'Potri.008G157750' => 'ptr', 'Potri.008G157900' => 'ptr', 'Potri.008G158000' => 'ptr', 'Potri.008G158200' => 'ptr', 'Pp3c11_7280' => 'ppa', 'Pp3c11_7980' => 'ppa', 'Pp3c12_19450' => 'ppa', 'Pp3c14_1480' => 'ppa', 'Pp3c14_1501' => 'ppa', 'Pp3c16_4900' => 'ppa', 'Pp3c16_5010' => 'ppa', 'Pp3c16_5060' => 'ppa', 'Pp3c19_18250' => 'ppa', 'Pp3c23_8530' => 'ppa', 'Pp3c23_8550' => 'ppa', 'Pp3c24_9670' => 'ppa', 'Pp3c2_21390' => 'ppa', 'Pp3c2_31380' => 'ppa', 'Pp3c3_16620' => 'ppa', 'Pp3c3_8090' => 'ppa', 'Pp3c3_8110' => 'ppa', 'Pp3c3_8130' => 'ppa', 'Pp3c3_8150' => 'ppa', 'Pp3c4_14320' => 'ppa', 'Pp3c6_2560' => 'ppa', 'Pp3c9_16700' => 'ppa', 'PRCOL_00000234' => 'pco', 'PRCOL_00000235' => 'pco', 'PRCOL_00000777' => 'pco', 'PRCOL_00002344' => 'pco', 'PRCOL_00002372' => 'pco', 'PRCOL_00006120' => 'pco', 'Prupe.1G021400' => 'ppe', 'Prupe.1G021500' => 'ppe', 'Prupe.1G021600' => 'ppe', 'Prupe.1G021700' => 'ppe', 'Prupe.1G021800' => 'ppe', 'Prupe.5G145100' => 'ppe', 'Psat6g204040' => 'psa', 'Psat6g204800' => 'psa', 'Psat6g204920' => 'psa', 'Psat6g204960' => 'psa', 'Psat6g205080' => 'psa', 'PSO017G0271' => 'pso', 'PSO017G1276' => 'pso', 'PSO017G1429' => 'pso', 'PSO017G1861' => 'pso', 'PSO017G2787' => 'pso', 'PSO017G4466' => 'pso', 'PSO017G5118' => 'pso', 'PSO017G5420' => 'pso', 'PSO063G3678' => 'pso', 'PSO210G0546' => 'pso', 'PSO317G0001' => 'pso', 'PSO357G0512' => 'pso', 'PSO478G2682' => 'pso', 'PSO647G0001' => 'pso', 'PSO675G0001' => 'pso', 'PSO675G2699' => 'pso', 'PSO675G2849' => 'pso', 'PSO675G4991' => 'pso', 'PSO689G0001' => 'pso', 'QL06p000916' => 'qlo', 'QL06p000921' => 'qlo', 'QL06p001398' => 'qlo', 'QL06p001407' => 'qlo', 'QL06p002031' => 'qlo', 'RcHm_v2.0_Chr4g0387791' => 'rch', 'RcHm_v2.0_Chr4g0387801' => 'rch', 'RcHm_v2.0_Chr6g0286501' => 'rch', 'RcHm_v2.0_Chr6g0286511' => 'rch', 'RcHm_v2.0_Chr6g0286521' => 'rch', 'RcHm_v2.0_Chr6g0286531' => 'rch', 'RcHm_v2.0_Chr7g0189141' => 'rch', 'Rhsim02G0028700' => 'rsi', 'Rhsim02G0028800' => 'rsi', 'Rhsim02G0028900' => 'rsi', 'Rhsim02G0029000' => 'rsi', 'Rhsim02G0029100' => 'rsi', 'Rhsim02G0029200' => 'rsi', 'Rhsim02G0029300' => 'rsi', 'Rhsim02G0029400' => 'rsi', 'Rhsim02G0029500' => 'rsi', 'Rhsim02G0029600' => 'rsi', 'RhsimUnG0024000' => 'rsi', 'RhsimUnG0024100' => 'rsi', 'RhsimUnG0024200' => 'rsi', 'RhsimUnG0024300' => 'rsi', 'RhsimUnG0024400' => 'rsi', 'RhsimUnG0024500' => 'rsi', 'RhsimUnG0024700' => 'rsi', 'RhsimUnG0024800' => 'rsi', 'RhsimUnG0024900' => 'rsi', 'RhsimUnG0025100' => 'rsi', 'Sabra08G0120200' => 'sbr', 'Sabra08G0120300' => 'sbr', 'Sabra08G0120500' => 'sbr', 'Sabra08G0120600' => 'sbr', 'Sabra10G0158900' => 'sbr', 'SalBow2G3492' => 'sbo', 'Sc13g0004760' => 'sci', 'Sc13g0004770' => 'sci', 'Sed0003417' => 'sed', 'Sed0019750' => 'sed', 'SEGI_03419' => 'sgi', 'SEGI_05907' => 'sgi', 'SEGI_10682' => 'sgi', 'SEGI_13528' => 'sgi', 'SEGI_16081' => 'sgi', 'SEGI_19370' => 'sgi', 'SEGI_21015' => 'sgi', 'SEGI_21944' => 'sgi', 'SEGI_32906' => 'sgi', 'SEGI_33093' => 'sgi', 'SEGI_36110' => 'sgi', 'SEGI_40397' => 'sgi', 'SGA_v2.0_scaffold191G40426' => 'sas', 'SGA_v2.0_scaffold353G49717' => 'sas', 'SGA_v2.0_scaffold50G18550' => 'sas', 'SMO119G0173' => 'smo', 'SMO172G0002' => 'smo', 'Solyc09g082690.3' => 'sly', 'Solyc09g082700.2' => 'sly', 'Sopen09g031550' => 'spe', 'Sopen09g031560' => 'spe', 'Sp3g20540' => 'spa', 'Sp7g07580' => 'spa', 'TAR134G0002' => 'tar', 'TAR236G0001' => 'tar', 'TAR365G0892' => 'tar', 'TAR636G0166' => 'tar', 'TAR636G0646' => 'tar', 'TAR636G0869' => 'tar', 'TAR636G1317' => 'tar', 'TAR636G1744' => 'tar', 'TAR636G3358' => 'tar', 'TAR636G3436' => 'tar', 'THA.LOC104803047' => 'tha', 'Thecc.04G238900' => 'tca', 'Thhalv10021557m.g' => 'esa', 'Thhalv10026318m.g' => 'esa', 'Thhalv10026335m.g' => 'esa', 'TPR.G17433' => 'tpr', 'TPR.G18915' => 'tpr', 'TPR.G26125' => 'tpr', 'TWI09G0677' => 'twi', 'TWI73G0287' => 'twi', 'unitig_748.g8326' => 'ugi', 'vmacro15370' => 'vma', 'vmacro15371' => 'vma', 'vmacro15372' => 'vma', 'vmacro15373' => 'vma', 'vmacro15374' => 'vma', 'VMungo0720G2826' => 'vmu', 'Zm00001eb116960' => 'zma', 'Zm00001eb301260' => 'zma', 'Zm00001eb301270' => 'zma' ), 'gf_id' => 'HOM05D001460', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001460' ), 'data_identifier' => 'HOM05D001460', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001460', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '433', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p22980' => 'bna', 'A01p32340' => 'bna', 'A03p42970' => 'bna', 'A05p25880' => 'bna', 'Aa31LG8G9320' => 'aar', 'Aa31LG8G9330' => 'aar', 'Aa31LG8G9340' => 'aar', 'Aa31sc221G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1034' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1528' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.829' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2222' => 'aag', 'Ah.12g058830' => 'amhyb', 'Ah.12g058840' => 'amhyb', 'AL3G37160' => 'aly', 'AL7G41310' => 'aly', 'Aqoxy5G00395' => 'aox', 'Aqoxy5G00396' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0C8NZA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5185HY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JZ1PRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MD3LS0' => 'arhy', 'AT3G22840' => 'ath', 'AT4G14690' => 'ath', 'ATR0665G054' => 'atr', 'Atru.chr4.2344' => 'acertr', 'Atru.chr4.2346' => 'acertr', 'Atru.chr4.2347' => 'acertr', 'Atru.chr4.2348' => 'acertr', 'Atru.chr4.2355' => 'acertr', 'Atru.chr4.2356' => 'acertr', 'Atru.chr4.2358' => 'acertr', 'Atru.chr4.2359' => 'acertr', 'Atru.chr4.2360' => 'acertr', 'Atru.chr4.2361' => 'acertr', 'AUR62030476' => 'cqu', 'AUR62030478' => 'cqu', 'AUR62030819' => 'cqu', 'AUR62030820' => 'cqu', 'BcaB03g14648' => 'bca', 'BcaB04g20492' => 'bca', 'BcaB06g26399' => 'bca', 'BcaC01g03416' => 'bca', 'BcaC01g03419' => 'bca', 'BcaC01g03421' => 'bca', 'BcaC01g03424' => 'bca', 'BcaC05g28012' => 'bca', 'BcaC09g49212' => 'bca', 'BcaC09g50140' => 'bca', 'BcaNung00346' => 'bca', 'BolC1t02785H' => 'bol', 'BolC1t04095H' => 'bol', 'BolC3t17545H' => 'bol', 'BolC5t32769H' => 'bol', 'BraA01t02211Z' => 'bra', 'BraA01t03359Z' => 'bra', 'BraA03t13441Z' => 'bra', 'BraA05t21476Z' => 'bra', 'C01p28420' => 'bna', 'C01p41350' => 'bna', 'C03p52750' => 'bna', 'C03p52780' => 'bna', 'C05p40270' => 'bna', 'CAN.G1437.9' => 'can', 'CANSAT78G0035' => 'cansat', 'CANSAT78G1036' => 'cansat', 'CANSAT78G2272' => 'cansat', 'CANSAT78G2478' => 'cansat', 'CARHR098700' => 'chi', 'CARHR221120' => 'chi', 'CARHR221150' => 'chi', 'Carub.0003s2297' => 'cru', 'Carub.0007s2749' => 'cru', 'Carub.0007s2750' => 'cru', 'Carub.0007s2751' => 'cru', 'Ca_10849_v3' => 'car', 'Cc03_g04300' => 'ccan', 'CDE02G3648' => 'cde', 'CDE05G0060' => 'cde', 'CDE05G0692' => 'cde', 'CDE05G2285' => 'cde', 'CDE05G2884' => 'cde', 'CDE05G3072' => 'cde', 'Cfa008439' => 'cfa', 'Cfa008441' => 'cfa', 'Cfa008443' => 'cfa', 'Cfa008448' => 'cfa', 'Ciclev10005974m.g' => 'ccl', 'Ciclev10006006m.g' => 'ccl', 'Ciclev10006775m.g' => 'ccl', 'CiPaw.02G120400' => 'cil', 'CiPaw.02G120500' => 'cil', 'CiPaw.02G120600' => 'cil', 'ClCG05G004850' => 'cla', 'COL.COLO4_21566' => 'col', 'Cpa.g.sc44.124' => 'cpa', 'Cre07.g320400' => 'cre', 'Cre07.g320450' => 'cre', 'Cre08.g384650' => 'cre', 'Cre09.g393173' => 'cre', 'Cre09.g394325' => 'cre', 'Cre14.g626750' => 'cre', 'Cre16.g679250' => 'cre', 'CsaV3_3G012890' => 'csa', 'CSS0010865' => 'camsi', 'CSS0044338' => 'camsi', 'DCAR_002366' => 'dca', 'DCAR_030687' => 'dca', 'DCAR_030688' => 'dca', 'Dinv14047' => 'din', 'Dinv14048' => 'din', 'Duzib151G0105' => 'dzi', 'Duzib151G0114' => 'dzi', 'Duzib212G1029' => 'dzi', 'ECA232G3536' => 'eca', 'ECA240G0786' => 'eca', 'ECA240G1802' => 'eca', 'ECA240G3760' => 'eca', 'ECA240G3920' => 'eca', 'EL10Ac5g12536' => 'bvu', 'EL10Ac5g12537' => 'bvu', 'EL10Ac5g12538' => 'bvu', 'Eucgr.B01004' => 'egr', 'Eucgr.B01006' => 'egr', 'Eucgr.B01007' => 'egr', 'Eucgr.B01008' => 'egr', 'Eucgr.B01895' => 'egr', 'Eucgr.B01896' => 'egr', 'FAN04G1456' => 'fan', 'FAN08G1769' => 'fan', 'FAN08G2160' => 'fan', 'FAN13G2403' => 'fan', 'FAN13G3303' => 'fan', 'FAN15G2435' => 'fan', 'FAN17G0672' => 'fan', 'FAN17G2441' => 'fan', 'FAN18G1024' => 'fan', 'FAN22G1458' => 'fan', 'FAN24G0037' => 'fan', 'FAN24G0429' => 'fan', 'FAN24G2387' => 'fan', 'FAN27G2746' => 'fan', 'FvH4_2g20400' => 'fve', 'FvH4_2g20420' => 'fve', 'FvH4_2g20430' => 'fve', 'FvH4_4g01270' => 'fve', 'FvH4_4g01290' => 'fve', 'FvH4_4g01300' => 'fve', 'FvH4_4g01310' => 'fve', 'FvH4_4g01330' => 'fve', 'FvH4_5g09070' => 'fve', 'Glyma.10G243800' => 'gma', 'Glyma.20G150600' => 'gma', 'Gohir.A09G219200' => 'ghi', 'Gohir.A09G219300' => 'ghi', 'Gohir.D09G221400' => 'ghi', 'Gohir.D09G221500' => 'ghi', 'Gorai.006G242600' => 'gra', 'Gorai.006G242700' => 'gra', 'GSVIVG01018044001' => 'vvi', 'HanXRQChr03g0083821' => 'han', 'HanXRQChr03g0083841' => 'han', 'HanXRQChr03g0083881' => 'han', 'HanXRQChr03g0083901' => 'han', 'HanXRQChr03g0083921' => 'han', 'HanXRQChr03g0085331' => 'han', 'HanXRQChr03g0085361' => 'han', 'HanXRQChr03g0085411' => 'han', 'HanXRQChr03g0085421' => 'han', 'HanXRQChr03g0085431' => 'han', 'HanXRQChr08g0221991' => 'han', 'HanXRQChr11g0336061' => 'han', 'HanXRQChr11g0336411' => 'han', 'Haze_11234' => 'cav', 'Hma1.2p1_0549F.1_g177010' => 'hma', 'Hma1.2p1_0602F.1_g187630' => 'hma', 'Hund14876' => 'sun', 'Hund14879' => 'sun', 'Lalb_Chr06g0160741' => 'lal', 'Lalb_Chr21g0304781' => 'lal', 'Lj3A726G19' => 'lonja', 'Lj3A726T23' => 'lonja', 'Lj3A726T24' => 'lonja', 'Lj3A726T25' => 'lonja', 'Lj3A727T17' => 'lonja', 'Lj3C726T0' => 'lonja', 'Lj3C726T2' => 'lonja', 'Lj3P725T35' => 'lonja', 'Lj3P727T10' => 'lonja', 'Lj3P727T12' => 'lonja', 'Lj3P727T14' => 'lonja', 'Lj5g0023109' => 'lja', 'Lj6P646T44' => 'lonja', 'Lsat_1_v5_gn_6_75760' => 'lsa', 'Lsat_1_v5_gn_6_75800' => 'lsa', 'Lsat_1_v5_gn_6_75900' => 'lsa', 'Lsat_1_v5_gn_6_76240' => 'lsa', 'Lsat_1_v5_gn_6_76441' => 'lsa', 'Lsat_1_v5_gn_6_76700' => 'lsa', 'Lsat_1_v5_gn_6_76760' => 'lsa', 'Manes.15G033100' => 'mes', 'Mapoly0004s0074' => 'mpo', 'Mapoly0004s0075' => 'mpo', 'Mapoly0004s0163' => 'mpo', 'Mapoly0004s0164' => 'mpo', 'Mapoly0021s0018' => 'mpo', 'Mapoly0041s0136' => 'mpo', 'Mapoly0041s0137' => 'mpo', 'Mapoly0041s0138' => 'mpo', 'Mapoly0041s0139' => 'mpo', 'Mapoly0041s0141' => 'mpo', 'Mapoly0041s0142' => 'mpo', 'Mapoly0041s0143' => 'mpo', 'Mapoly0041s0144' => 'mpo', 'Mapoly0041s0145' => 'mpo', 'Mapoly0047s0106' => 'mpo', 'Mapoly0047s0108' => 'mpo', 'Mapoly0050s0051' => 'mpo', 'Mapoly0050s0052' => 'mpo', 'Mapoly0050s0053' => 'mpo', 'Mapoly0058s0013' => 'mpo', 'Mapoly0091s0078' => 'mpo', 'Mapoly0091s0079' => 'mpo', 'Mapoly0091s0080' => 'mpo', 'Mapoly0091s0081' => 'mpo', 'Mapoly0278s0004' => 'mpo', 'Mapoly0278s0005' => 'mpo', 'Mapoly0278s0006' => 'mpo', 'MBI11_g30648_MAGBIO' => 'mbi', 'MCO03G194' => 'mco', 'MCO03G590' => 'mco', 'MCO07G312' => 'mco', 'MCO10G318' => 'mco', 'MCO12G244' => 'mco', 'MCO13G148' => 'mco', 'MCO13G194' => 'mco', 'MCO16G238' => 'mco', 'MD06G1134100' => 'mdo', 'MD13G1200100' => 'mdo', 'MD13G1200300' => 'mdo', 'MD13G1200600' => 'mdo', 'MD14G1150400' => 'mdo', 'MD16G1200000' => 'mdo', 'Medtr1g102570' => 'mtr', 'Medtr1g102780' => 'mtr', 'Medtr1g102800' => 'mtr', 'Medtr1g102810' => 'mtr', 'Medtr1g102830' => 'mtr', 'MELO3C006499.2' => 'cme', 'Migut.G00385' => 'egut', 'MSTRG.4063' => 'ama', 'Nitab4.5_0000090g0260' => 'nta', 'Nitab4.5_0000977g0030' => 'nta', 'Nitab4.5_0002541g0040' => 'nta', 'Nitab4.5_0007068g0040' => 'nta', 'Nn005s41408' => 'nnu', 'Nn005s41410' => 'nnu', 'Oeu010310.1' => 'oeu', 'Oeu010311.1' => 'oeu', 'Oeu043472.1' => 'oeu', 'Os01g0246400' => 'osa', 'Os04g0267950' => 'osa', 'Os07g0178700' => 'osa', 'Os07g0178800' => 'osa', 'Peaxi162Scf00316g00046' => 'pax', 'Peaxi162Scf00316g00049' => 'pax', 'Peaxi162Scf00316g00059' => 'pax', 'Peaxi162Scf00316g00328' => 'pax', 'Peaxi162Scf00316g00329' => 'pax', 'Peaxi162Scf00316g00411' => 'pax', 'Peaxi162Scf00316g00521' => 'pax', 'Peaxi162Scf00492g00068' => 'pax', 'Peaxi162Scf35631g00002' => 'pax', 'PGR142G3720' => 'pgr', 'PGSC0003DMG400006442' => 'stu', 'Phvul.007G062000' => 'pvu', 'Potri.008G157750' => 'ptr', 'Potri.008G157900' => 'ptr', 'Potri.008G158000' => 'ptr', 'Potri.008G158200' => 'ptr', 'Pp3c11_7280' => 'ppa', 'Pp3c11_7980' => 'ppa', 'Pp3c12_19450' => 'ppa', 'Pp3c14_1480' => 'ppa', 'Pp3c14_1501' => 'ppa', 'Pp3c16_4900' => 'ppa', 'Pp3c16_5010' => 'ppa', 'Pp3c16_5060' => 'ppa', 'Pp3c19_18250' => 'ppa', 'Pp3c23_8530' => 'ppa', 'Pp3c23_8550' => 'ppa', 'Pp3c24_9670' => 'ppa', 'Pp3c2_21390' => 'ppa', 'Pp3c2_31380' => 'ppa', 'Pp3c3_16620' => 'ppa', 'Pp3c3_8090' => 'ppa', 'Pp3c3_8110' => 'ppa', 'Pp3c3_8130' => 'ppa', 'Pp3c3_8150' => 'ppa', 'Pp3c4_14320' => 'ppa', 'Pp3c6_2560' => 'ppa', 'Pp3c9_16700' => 'ppa', 'PRCOL_00000234' => 'pco', 'PRCOL_00000235' => 'pco', 'PRCOL_00000777' => 'pco', 'PRCOL_00002344' => 'pco', 'PRCOL_00002372' => 'pco', 'PRCOL_00006120' => 'pco', 'Prupe.1G021400' => 'ppe', 'Prupe.1G021500' => 'ppe', 'Prupe.1G021600' => 'ppe', 'Prupe.1G021700' => 'ppe', 'Prupe.1G021800' => 'ppe', 'Prupe.5G145100' => 'ppe', 'Psat6g204040' => 'psa', 'Psat6g204800' => 'psa', 'Psat6g204920' => 'psa', 'Psat6g204960' => 'psa', 'Psat6g205080' => 'psa', 'PSO017G0271' => 'pso', 'PSO017G1276' => 'pso', 'PSO017G1429' => 'pso', 'PSO017G1861' => 'pso', 'PSO017G2787' => 'pso', 'PSO017G4466' => 'pso', 'PSO017G5118' => 'pso', 'PSO017G5420' => 'pso', 'PSO063G3678' => 'pso', 'PSO210G0546' => 'pso', 'PSO317G0001' => 'pso', 'PSO357G0512' => 'pso', 'PSO478G2682' => 'pso', 'PSO647G0001' => 'pso', 'PSO675G0001' => 'pso', 'PSO675G2699' => 'pso', 'PSO675G2849' => 'pso', 'PSO675G4991' => 'pso', 'PSO689G0001' => 'pso', 'QL06p000916' => 'qlo', 'QL06p000921' => 'qlo', 'QL06p001398' => 'qlo', 'QL06p001407' => 'qlo', 'QL06p002031' => 'qlo', 'RcHm_v2.0_Chr4g0387791' => 'rch', 'RcHm_v2.0_Chr4g0387801' => 'rch', 'RcHm_v2.0_Chr6g0286501' => 'rch', 'RcHm_v2.0_Chr6g0286511' => 'rch', 'RcHm_v2.0_Chr6g0286521' => 'rch', 'RcHm_v2.0_Chr6g0286531' => 'rch', 'RcHm_v2.0_Chr7g0189141' => 'rch', 'Rhsim02G0028700' => 'rsi', 'Rhsim02G0028800' => 'rsi', 'Rhsim02G0028900' => 'rsi', 'Rhsim02G0029000' => 'rsi', 'Rhsim02G0029100' => 'rsi', 'Rhsim02G0029200' => 'rsi', 'Rhsim02G0029300' => 'rsi', 'Rhsim02G0029400' => 'rsi', 'Rhsim02G0029500' => 'rsi', 'Rhsim02G0029600' => 'rsi', 'RhsimUnG0024000' => 'rsi', 'RhsimUnG0024100' => 'rsi', 'RhsimUnG0024200' => 'rsi', 'RhsimUnG0024300' => 'rsi', 'RhsimUnG0024400' => 'rsi', 'RhsimUnG0024500' => 'rsi', 'RhsimUnG0024700' => 'rsi', 'RhsimUnG0024800' => 'rsi', 'RhsimUnG0024900' => 'rsi', 'RhsimUnG0025100' => 'rsi', 'Sabra08G0120200' => 'sbr', 'Sabra08G0120300' => 'sbr', 'Sabra08G0120500' => 'sbr', 'Sabra08G0120600' => 'sbr', 'Sabra10G0158900' => 'sbr', 'SalBow2G3492' => 'sbo', 'Sc13g0004760' => 'sci', 'Sc13g0004770' => 'sci', 'Sed0003417' => 'sed', 'Sed0019750' => 'sed', 'SEGI_03419' => 'sgi', 'SEGI_05907' => 'sgi', 'SEGI_10682' => 'sgi', 'SEGI_13528' => 'sgi', 'SEGI_16081' => 'sgi', 'SEGI_19370' => 'sgi', 'SEGI_21015' => 'sgi', 'SEGI_21944' => 'sgi', 'SEGI_32906' => 'sgi', 'SEGI_33093' => 'sgi', 'SEGI_36110' => 'sgi', 'SEGI_40397' => 'sgi', 'SGA_v2.0_scaffold191G40426' => 'sas', 'SGA_v2.0_scaffold353G49717' => 'sas', 'SGA_v2.0_scaffold50G18550' => 'sas', 'SMO119G0173' => 'smo', 'SMO172G0002' => 'smo', 'Solyc09g082690.3' => 'sly', 'Solyc09g082700.2' => 'sly', 'Sopen09g031550' => 'spe', 'Sopen09g031560' => 'spe', 'Sp3g20540' => 'spa', 'Sp7g07580' => 'spa', 'TAR134G0002' => 'tar', 'TAR236G0001' => 'tar', 'TAR365G0892' => 'tar', 'TAR636G0166' => 'tar', 'TAR636G0646' => 'tar', 'TAR636G0869' => 'tar', 'TAR636G1317' => 'tar', 'TAR636G1744' => 'tar', 'TAR636G3358' => 'tar', 'TAR636G3436' => 'tar', 'THA.LOC104803047' => 'tha', 'Thecc.04G238900' => 'tca', 'Thhalv10021557m.g' => 'esa', 'Thhalv10026318m.g' => 'esa', 'Thhalv10026335m.g' => 'esa', 'TPR.G17433' => 'tpr', 'TPR.G18915' => 'tpr', 'TPR.G26125' => 'tpr', 'TWI09G0677' => 'twi', 'TWI73G0287' => 'twi', 'unitig_748.g8326' => 'ugi', 'vmacro15370' => 'vma', 'vmacro15371' => 'vma', 'vmacro15372' => 'vma', 'vmacro15373' => 'vma', 'vmacro15374' => 'vma', 'VMungo0720G2826' => 'vmu', 'Zm00001eb116960' => 'zma', 'Zm00001eb301260' => 'zma', 'Zm00001eb301270' => 'zma' ) $gf_id = 'HOM05D001460' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001460' ) $data_identifier = 'HOM05D001460' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 4, 'aag' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 2, 'aox' => (int) 2, 'arhy' => (int) 4, 'ath' => (int) 2, 'atr' => (int) 1, 'acertr' => (int) 10, 'cqu' => (int) 4, 'bca' => (int) 11, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 1, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 1, 'ccan' => (int) 1, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 1, 'col' => (int) 1, 'cpa' => (int) 1, 'cre' => (int) 7, 'csa' => (int) 1, 'camsi' => (int) 2, 'dca' => (int) 3, 'din' => (int) 2, 'dzi' => (int) 3, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 14, 'fve' => (int) 9, 'gma' => (int) 2, 'ghi' => (int) 4, 'gra' => (int) 2, 'vvi' => (int) 1, 'han' => (int) 13, 'cav' => (int) 1, 'hma' => (int) 2, 'sun' => (int) 2, 'lal' => (int) 2, 'lonja' => (int) 12, 'lja' => (int) 1, 'lsa' => (int) 7, 'mes' => (int) 1, 'mpo' => (int) 27, 'mbi' => (int) 1, 'mco' => (int) 8, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 1, 'egut' => (int) 1, 'ama' => (int) 1, 'nta' => (int) 4, 'nnu' => (int) 2, 'oeu' => (int) 3, 'osa' => (int) 4, 'pax' => (int) 9, 'pgr' => (int) 1, 'stu' => (int) 1, 'pvu' => (int) 1, 'ptr' => (int) 4, 'ppa' => (int) 22, 'pco' => (int) 6, 'ppe' => (int) 6, 'psa' => (int) 5, 'pso' => (int) 19, 'qlo' => (int) 5, 'rch' => (int) 7, 'rsi' => (int) 20, 'sbr' => (int) 5, 'sbo' => (int) 1, 'sci' => (int) 2, 'sed' => (int) 2, 'sgi' => (int) 12, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 2, 'tar' => (int) 10, 'tha' => (int) 1, 'tca' => (int) 1, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 2, 'ugi' => (int) 1, 'vma' => (int) 5, 'vmu' => (int) 1, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb301270' $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' => 'HOM05D001460', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '433', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p22980' => 'bna', 'A01p32340' => 'bna', 'A03p42970' => 'bna', 'A05p25880' => 'bna', 'Aa31LG8G9320' => 'aar', 'Aa31LG8G9330' => 'aar', 'Aa31LG8G9340' => 'aar', 'Aa31sc221G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1034' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1528' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.829' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2222' => 'aag', 'Ah.12g058830' => 'amhyb', 'Ah.12g058840' => 'amhyb', 'AL3G37160' => 'aly', 'AL7G41310' => 'aly', 'Aqoxy5G00395' => 'aox', 'Aqoxy5G00396' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0C8NZA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5185HY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JZ1PRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MD3LS0' => 'arhy', 'AT3G22840' => 'ath', 'AT4G14690' => 'ath', 'ATR0665G054' => 'atr', 'Atru.chr4.2344' => 'acertr', 'Atru.chr4.2346' => 'acertr', 'Atru.chr4.2347' => 'acertr', 'Atru.chr4.2348' => 'acertr', 'Atru.chr4.2355' => 'acertr', 'Atru.chr4.2356' => 'acertr', 'Atru.chr4.2358' => 'acertr', 'Atru.chr4.2359' => 'acertr', 'Atru.chr4.2360' => 'acertr', 'Atru.chr4.2361' => 'acertr', 'AUR62030476' => 'cqu', 'AUR62030478' => 'cqu', 'AUR62030819' => 'cqu', 'AUR62030820' => 'cqu', 'BcaB03g14648' => 'bca', 'BcaB04g20492' => 'bca', 'BcaB06g26399' => 'bca', 'BcaC01g03416' => 'bca', 'BcaC01g03419' => 'bca', 'BcaC01g03421' => 'bca', 'BcaC01g03424' => 'bca', 'BcaC05g28012' => 'bca', 'BcaC09g49212' => 'bca', 'BcaC09g50140' => 'bca', 'BcaNung00346' => 'bca', 'BolC1t02785H' => 'bol', 'BolC1t04095H' => 'bol', 'BolC3t17545H' => 'bol', 'BolC5t32769H' => 'bol', 'BraA01t02211Z' => 'bra', 'BraA01t03359Z' => 'bra', 'BraA03t13441Z' => 'bra', 'BraA05t21476Z' => 'bra', 'C01p28420' => 'bna', 'C01p41350' => 'bna', 'C03p52750' => 'bna', 'C03p52780' => 'bna', 'C05p40270' => 'bna', 'CAN.G1437.9' => 'can', 'CANSAT78G0035' => 'cansat', 'CANSAT78G1036' => 'cansat', 'CANSAT78G2272' => 'cansat', 'CANSAT78G2478' => 'cansat', 'CARHR098700' => 'chi', 'CARHR221120' => 'chi', 'CARHR221150' => 'chi', 'Carub.0003s2297' => 'cru', 'Carub.0007s2749' => 'cru', 'Carub.0007s2750' => 'cru', 'Carub.0007s2751' => 'cru', 'Ca_10849_v3' => 'car', 'Cc03_g04300' => 'ccan', 'CDE02G3648' => 'cde', 'CDE05G0060' => 'cde', 'CDE05G0692' => 'cde', 'CDE05G2285' => 'cde', 'CDE05G2884' => 'cde', 'CDE05G3072' => 'cde', 'Cfa008439' => 'cfa', 'Cfa008441' => 'cfa', 'Cfa008443' => 'cfa', 'Cfa008448' => 'cfa', 'Ciclev10005974m.g' => 'ccl', 'Ciclev10006006m.g' => 'ccl', 'Ciclev10006775m.g' => 'ccl', 'CiPaw.02G120400' => 'cil', 'CiPaw.02G120500' => 'cil', 'CiPaw.02G120600' => 'cil', 'ClCG05G004850' => 'cla', 'COL.COLO4_21566' => 'col', 'Cpa.g.sc44.124' => 'cpa', 'Cre07.g320400' => 'cre', 'Cre07.g320450' => 'cre', 'Cre08.g384650' => 'cre', 'Cre09.g393173' => 'cre', 'Cre09.g394325' => 'cre', 'Cre14.g626750' => 'cre', 'Cre16.g679250' => 'cre', 'CsaV3_3G012890' => 'csa', 'CSS0010865' => 'camsi', 'CSS0044338' => 'camsi', 'DCAR_002366' => 'dca', 'DCAR_030687' => 'dca', 'DCAR_030688' => 'dca', 'Dinv14047' => 'din', 'Dinv14048' => 'din', 'Duzib151G0105' => 'dzi', 'Duzib151G0114' => 'dzi', 'Duzib212G1029' => 'dzi', 'ECA232G3536' => 'eca', 'ECA240G0786' => 'eca', 'ECA240G1802' => 'eca', 'ECA240G3760' => 'eca', 'ECA240G3920' => 'eca', 'EL10Ac5g12536' => 'bvu', 'EL10Ac5g12537' => 'bvu', 'EL10Ac5g12538' => 'bvu', 'Eucgr.B01004' => 'egr', 'Eucgr.B01006' => 'egr', 'Eucgr.B01007' => 'egr', 'Eucgr.B01008' => 'egr', 'Eucgr.B01895' => 'egr', 'Eucgr.B01896' => 'egr', 'FAN04G1456' => 'fan', 'FAN08G1769' => 'fan', 'FAN08G2160' => 'fan', 'FAN13G2403' => 'fan', 'FAN13G3303' => 'fan', 'FAN15G2435' => 'fan', 'FAN17G0672' => 'fan', 'FAN17G2441' => 'fan', 'FAN18G1024' => 'fan', 'FAN22G1458' => 'fan', 'FAN24G0037' => 'fan', 'FAN24G0429' => 'fan', 'FAN24G2387' => 'fan', 'FAN27G2746' => 'fan', 'FvH4_2g20400' => 'fve', 'FvH4_2g20420' => 'fve', 'FvH4_2g20430' => 'fve', 'FvH4_4g01270' => 'fve', 'FvH4_4g01290' => 'fve', 'FvH4_4g01300' => 'fve', 'FvH4_4g01310' => 'fve', 'FvH4_4g01330' => 'fve', 'FvH4_5g09070' => 'fve', 'Glyma.10G243800' => 'gma', 'Glyma.20G150600' => 'gma', 'Gohir.A09G219200' => 'ghi', 'Gohir.A09G219300' => 'ghi', 'Gohir.D09G221400' => 'ghi', 'Gohir.D09G221500' => 'ghi', 'Gorai.006G242600' => 'gra', 'Gorai.006G242700' => 'gra', 'GSVIVG01018044001' => 'vvi', 'HanXRQChr03g0083821' => 'han', 'HanXRQChr03g0083841' => 'han', 'HanXRQChr03g0083881' => 'han', 'HanXRQChr03g0083901' => 'han', 'HanXRQChr03g0083921' => 'han', 'HanXRQChr03g0085331' => 'han', 'HanXRQChr03g0085361' => 'han', 'HanXRQChr03g0085411' => 'han', 'HanXRQChr03g0085421' => 'han', 'HanXRQChr03g0085431' => 'han', 'HanXRQChr08g0221991' => 'han', 'HanXRQChr11g0336061' => 'han', 'HanXRQChr11g0336411' => 'han', 'Haze_11234' => 'cav', 'Hma1.2p1_0549F.1_g177010' => 'hma', 'Hma1.2p1_0602F.1_g187630' => 'hma', 'Hund14876' => 'sun', 'Hund14879' => 'sun', 'Lalb_Chr06g0160741' => 'lal', 'Lalb_Chr21g0304781' => 'lal', 'Lj3A726G19' => 'lonja', 'Lj3A726T23' => 'lonja', 'Lj3A726T24' => 'lonja', 'Lj3A726T25' => 'lonja', 'Lj3A727T17' => 'lonja', 'Lj3C726T0' => 'lonja', 'Lj3C726T2' => 'lonja', 'Lj3P725T35' => 'lonja', 'Lj3P727T10' => 'lonja', 'Lj3P727T12' => 'lonja', 'Lj3P727T14' => 'lonja', 'Lj5g0023109' => 'lja', 'Lj6P646T44' => 'lonja', 'Lsat_1_v5_gn_6_75760' => 'lsa', 'Lsat_1_v5_gn_6_75800' => 'lsa', 'Lsat_1_v5_gn_6_75900' => 'lsa', 'Lsat_1_v5_gn_6_76240' => 'lsa', 'Lsat_1_v5_gn_6_76441' => 'lsa', 'Lsat_1_v5_gn_6_76700' => 'lsa', 'Lsat_1_v5_gn_6_76760' => 'lsa', 'Manes.15G033100' => 'mes', 'Mapoly0004s0074' => 'mpo', 'Mapoly0004s0075' => 'mpo', 'Mapoly0004s0163' => 'mpo', 'Mapoly0004s0164' => 'mpo', 'Mapoly0021s0018' => 'mpo', 'Mapoly0041s0136' => 'mpo', 'Mapoly0041s0137' => 'mpo', 'Mapoly0041s0138' => 'mpo', 'Mapoly0041s0139' => 'mpo', 'Mapoly0041s0141' => 'mpo', 'Mapoly0041s0142' => 'mpo', 'Mapoly0041s0143' => 'mpo', 'Mapoly0041s0144' => 'mpo', 'Mapoly0041s0145' => 'mpo', 'Mapoly0047s0106' => 'mpo', 'Mapoly0047s0108' => 'mpo', 'Mapoly0050s0051' => 'mpo', 'Mapoly0050s0052' => 'mpo', 'Mapoly0050s0053' => 'mpo', 'Mapoly0058s0013' => 'mpo', 'Mapoly0091s0078' => 'mpo', 'Mapoly0091s0079' => 'mpo', 'Mapoly0091s0080' => 'mpo', 'Mapoly0091s0081' => 'mpo', 'Mapoly0278s0004' => 'mpo', 'Mapoly0278s0005' => 'mpo', 'Mapoly0278s0006' => 'mpo', 'MBI11_g30648_MAGBIO' => 'mbi', 'MCO03G194' => 'mco', 'MCO03G590' => 'mco', 'MCO07G312' => 'mco', 'MCO10G318' => 'mco', 'MCO12G244' => 'mco', 'MCO13G148' => 'mco', 'MCO13G194' => 'mco', 'MCO16G238' => 'mco', 'MD06G1134100' => 'mdo', 'MD13G1200100' => 'mdo', 'MD13G1200300' => 'mdo', 'MD13G1200600' => 'mdo', 'MD14G1150400' => 'mdo', 'MD16G1200000' => 'mdo', 'Medtr1g102570' => 'mtr', 'Medtr1g102780' => 'mtr', 'Medtr1g102800' => 'mtr', 'Medtr1g102810' => 'mtr', 'Medtr1g102830' => 'mtr', 'MELO3C006499.2' => 'cme', 'Migut.G00385' => 'egut', 'MSTRG.4063' => 'ama', 'Nitab4.5_0000090g0260' => 'nta', 'Nitab4.5_0000977g0030' => 'nta', 'Nitab4.5_0002541g0040' => 'nta', 'Nitab4.5_0007068g0040' => 'nta', 'Nn005s41408' => 'nnu', 'Nn005s41410' => 'nnu', 'Oeu010310.1' => 'oeu', 'Oeu010311.1' => 'oeu', 'Oeu043472.1' => 'oeu', 'Os01g0246400' => 'osa', 'Os04g0267950' => 'osa', 'Os07g0178700' => 'osa', 'Os07g0178800' => 'osa', 'Peaxi162Scf00316g00046' => 'pax', 'Peaxi162Scf00316g00049' => 'pax', 'Peaxi162Scf00316g00059' => 'pax', 'Peaxi162Scf00316g00328' => 'pax', 'Peaxi162Scf00316g00329' => 'pax', 'Peaxi162Scf00316g00411' => 'pax', 'Peaxi162Scf00316g00521' => 'pax', 'Peaxi162Scf00492g00068' => 'pax', 'Peaxi162Scf35631g00002' => 'pax', 'PGR142G3720' => 'pgr', 'PGSC0003DMG400006442' => 'stu', 'Phvul.007G062000' => 'pvu', 'Potri.008G157750' => 'ptr', 'Potri.008G157900' => 'ptr', 'Potri.008G158000' => 'ptr', 'Potri.008G158200' => 'ptr', 'Pp3c11_7280' => 'ppa', 'Pp3c11_7980' => 'ppa', 'Pp3c12_19450' => 'ppa', 'Pp3c14_1480' => 'ppa', 'Pp3c14_1501' => 'ppa', 'Pp3c16_4900' => 'ppa', 'Pp3c16_5010' => 'ppa', 'Pp3c16_5060' => 'ppa', 'Pp3c19_18250' => 'ppa', 'Pp3c23_8530' => 'ppa', 'Pp3c23_8550' => 'ppa', 'Pp3c24_9670' => 'ppa', 'Pp3c2_21390' => 'ppa', 'Pp3c2_31380' => 'ppa', 'Pp3c3_16620' => 'ppa', 'Pp3c3_8090' => 'ppa', 'Pp3c3_8110' => 'ppa', 'Pp3c3_8130' => 'ppa', 'Pp3c3_8150' => 'ppa', 'Pp3c4_14320' => 'ppa', 'Pp3c6_2560' => 'ppa', 'Pp3c9_16700' => 'ppa', 'PRCOL_00000234' => 'pco', 'PRCOL_00000235' => 'pco', 'PRCOL_00000777' => 'pco', 'PRCOL_00002344' => 'pco', 'PRCOL_00002372' => 'pco', 'PRCOL_00006120' => 'pco', 'Prupe.1G021400' => 'ppe', 'Prupe.1G021500' => 'ppe', 'Prupe.1G021600' => 'ppe', 'Prupe.1G021700' => 'ppe', 'Prupe.1G021800' => 'ppe', 'Prupe.5G145100' => 'ppe', 'Psat6g204040' => 'psa', 'Psat6g204800' => 'psa', 'Psat6g204920' => 'psa', 'Psat6g204960' => 'psa', 'Psat6g205080' => 'psa', 'PSO017G0271' => 'pso', 'PSO017G1276' => 'pso', 'PSO017G1429' => 'pso', 'PSO017G1861' => 'pso', 'PSO017G2787' => 'pso', 'PSO017G4466' => 'pso', 'PSO017G5118' => 'pso', 'PSO017G5420' => 'pso', 'PSO063G3678' => 'pso', 'PSO210G0546' => 'pso', 'PSO317G0001' => 'pso', 'PSO357G0512' => 'pso', 'PSO478G2682' => 'pso', 'PSO647G0001' => 'pso', 'PSO675G0001' => 'pso', 'PSO675G2699' => 'pso', 'PSO675G2849' => 'pso', 'PSO675G4991' => 'pso', 'PSO689G0001' => 'pso', 'QL06p000916' => 'qlo', 'QL06p000921' => 'qlo', 'QL06p001398' => 'qlo', 'QL06p001407' => 'qlo', 'QL06p002031' => 'qlo', 'RcHm_v2.0_Chr4g0387791' => 'rch', 'RcHm_v2.0_Chr4g0387801' => 'rch', 'RcHm_v2.0_Chr6g0286501' => 'rch', 'RcHm_v2.0_Chr6g0286511' => 'rch', 'RcHm_v2.0_Chr6g0286521' => 'rch', 'RcHm_v2.0_Chr6g0286531' => 'rch', 'RcHm_v2.0_Chr7g0189141' => 'rch', 'Rhsim02G0028700' => 'rsi', 'Rhsim02G0028800' => 'rsi', 'Rhsim02G0028900' => 'rsi', 'Rhsim02G0029000' => 'rsi', 'Rhsim02G0029100' => 'rsi', 'Rhsim02G0029200' => 'rsi', 'Rhsim02G0029300' => 'rsi', 'Rhsim02G0029400' => 'rsi', 'Rhsim02G0029500' => 'rsi', 'Rhsim02G0029600' => 'rsi', 'RhsimUnG0024000' => 'rsi', 'RhsimUnG0024100' => 'rsi', 'RhsimUnG0024200' => 'rsi', 'RhsimUnG0024300' => 'rsi', 'RhsimUnG0024400' => 'rsi', 'RhsimUnG0024500' => 'rsi', 'RhsimUnG0024700' => 'rsi', 'RhsimUnG0024800' => 'rsi', 'RhsimUnG0024900' => 'rsi', 'RhsimUnG0025100' => 'rsi', 'Sabra08G0120200' => 'sbr', 'Sabra08G0120300' => 'sbr', 'Sabra08G0120500' => 'sbr', 'Sabra08G0120600' => 'sbr', 'Sabra10G0158900' => 'sbr', 'SalBow2G3492' => 'sbo', 'Sc13g0004760' => 'sci', 'Sc13g0004770' => 'sci', 'Sed0003417' => 'sed', 'Sed0019750' => 'sed', 'SEGI_03419' => 'sgi', 'SEGI_05907' => 'sgi', 'SEGI_10682' => 'sgi', 'SEGI_13528' => 'sgi', 'SEGI_16081' => 'sgi', 'SEGI_19370' => 'sgi', 'SEGI_21015' => 'sgi', 'SEGI_21944' => 'sgi', 'SEGI_32906' => 'sgi', 'SEGI_33093' => 'sgi', 'SEGI_36110' => 'sgi', 'SEGI_40397' => 'sgi', 'SGA_v2.0_scaffold191G40426' => 'sas', 'SGA_v2.0_scaffold353G49717' => 'sas', 'SGA_v2.0_scaffold50G18550' => 'sas', 'SMO119G0173' => 'smo', 'SMO172G0002' => 'smo', 'Solyc09g082690.3' => 'sly', 'Solyc09g082700.2' => 'sly', 'Sopen09g031550' => 'spe', 'Sopen09g031560' => 'spe', 'Sp3g20540' => 'spa', 'Sp7g07580' => 'spa', 'TAR134G0002' => 'tar', 'TAR236G0001' => 'tar', 'TAR365G0892' => 'tar', 'TAR636G0166' => 'tar', 'TAR636G0646' => 'tar', 'TAR636G0869' => 'tar', 'TAR636G1317' => 'tar', 'TAR636G1744' => 'tar', 'TAR636G3358' => 'tar', 'TAR636G3436' => 'tar', 'THA.LOC104803047' => 'tha', 'Thecc.04G238900' => 'tca', 'Thhalv10021557m.g' => 'esa', 'Thhalv10026318m.g' => 'esa', 'Thhalv10026335m.g' => 'esa', 'TPR.G17433' => 'tpr', 'TPR.G18915' => 'tpr', 'TPR.G26125' => 'tpr', 'TWI09G0677' => 'twi', 'TWI73G0287' => 'twi', 'unitig_748.g8326' => 'ugi', 'vmacro15370' => 'vma', 'vmacro15371' => 'vma', 'vmacro15372' => 'vma', 'vmacro15373' => 'vma', 'vmacro15374' => 'vma', 'VMungo0720G2826' => 'vmu', 'Zm00001eb116960' => 'zma', 'Zm00001eb301260' => 'zma', 'Zm00001eb301270' => 'zma' ), 'gf_id' => 'HOM05D001460', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001460' ), 'data_identifier' => 'HOM05D001460', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001460', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '433', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p22980' => 'bna', 'A01p32340' => 'bna', 'A03p42970' => 'bna', 'A05p25880' => 'bna', 'Aa31LG8G9320' => 'aar', 'Aa31LG8G9330' => 'aar', 'Aa31LG8G9340' => 'aar', 'Aa31sc221G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1034' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1528' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.829' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2222' => 'aag', 'Ah.12g058830' => 'amhyb', 'Ah.12g058840' => 'amhyb', 'AL3G37160' => 'aly', 'AL7G41310' => 'aly', 'Aqoxy5G00395' => 'aox', 'Aqoxy5G00396' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0C8NZA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5185HY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JZ1PRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MD3LS0' => 'arhy', 'AT3G22840' => 'ath', 'AT4G14690' => 'ath', 'ATR0665G054' => 'atr', 'Atru.chr4.2344' => 'acertr', 'Atru.chr4.2346' => 'acertr', 'Atru.chr4.2347' => 'acertr', 'Atru.chr4.2348' => 'acertr', 'Atru.chr4.2355' => 'acertr', 'Atru.chr4.2356' => 'acertr', 'Atru.chr4.2358' => 'acertr', 'Atru.chr4.2359' => 'acertr', 'Atru.chr4.2360' => 'acertr', 'Atru.chr4.2361' => 'acertr', 'AUR62030476' => 'cqu', 'AUR62030478' => 'cqu', 'AUR62030819' => 'cqu', 'AUR62030820' => 'cqu', 'BcaB03g14648' => 'bca', 'BcaB04g20492' => 'bca', 'BcaB06g26399' => 'bca', 'BcaC01g03416' => 'bca', 'BcaC01g03419' => 'bca', 'BcaC01g03421' => 'bca', 'BcaC01g03424' => 'bca', 'BcaC05g28012' => 'bca', 'BcaC09g49212' => 'bca', 'BcaC09g50140' => 'bca', 'BcaNung00346' => 'bca', 'BolC1t02785H' => 'bol', 'BolC1t04095H' => 'bol', 'BolC3t17545H' => 'bol', 'BolC5t32769H' => 'bol', 'BraA01t02211Z' => 'bra', 'BraA01t03359Z' => 'bra', 'BraA03t13441Z' => 'bra', 'BraA05t21476Z' => 'bra', 'C01p28420' => 'bna', 'C01p41350' => 'bna', 'C03p52750' => 'bna', 'C03p52780' => 'bna', 'C05p40270' => 'bna', 'CAN.G1437.9' => 'can', 'CANSAT78G0035' => 'cansat', 'CANSAT78G1036' => 'cansat', 'CANSAT78G2272' => 'cansat', 'CANSAT78G2478' => 'cansat', 'CARHR098700' => 'chi', 'CARHR221120' => 'chi', 'CARHR221150' => 'chi', 'Carub.0003s2297' => 'cru', 'Carub.0007s2749' => 'cru', 'Carub.0007s2750' => 'cru', 'Carub.0007s2751' => 'cru', 'Ca_10849_v3' => 'car', 'Cc03_g04300' => 'ccan', 'CDE02G3648' => 'cde', 'CDE05G0060' => 'cde', 'CDE05G0692' => 'cde', 'CDE05G2285' => 'cde', 'CDE05G2884' => 'cde', 'CDE05G3072' => 'cde', 'Cfa008439' => 'cfa', 'Cfa008441' => 'cfa', 'Cfa008443' => 'cfa', 'Cfa008448' => 'cfa', 'Ciclev10005974m.g' => 'ccl', 'Ciclev10006006m.g' => 'ccl', 'Ciclev10006775m.g' => 'ccl', 'CiPaw.02G120400' => 'cil', 'CiPaw.02G120500' => 'cil', 'CiPaw.02G120600' => 'cil', 'ClCG05G004850' => 'cla', 'COL.COLO4_21566' => 'col', 'Cpa.g.sc44.124' => 'cpa', 'Cre07.g320400' => 'cre', 'Cre07.g320450' => 'cre', 'Cre08.g384650' => 'cre', 'Cre09.g393173' => 'cre', 'Cre09.g394325' => 'cre', 'Cre14.g626750' => 'cre', 'Cre16.g679250' => 'cre', 'CsaV3_3G012890' => 'csa', 'CSS0010865' => 'camsi', 'CSS0044338' => 'camsi', 'DCAR_002366' => 'dca', 'DCAR_030687' => 'dca', 'DCAR_030688' => 'dca', 'Dinv14047' => 'din', 'Dinv14048' => 'din', 'Duzib151G0105' => 'dzi', 'Duzib151G0114' => 'dzi', 'Duzib212G1029' => 'dzi', 'ECA232G3536' => 'eca', 'ECA240G0786' => 'eca', 'ECA240G1802' => 'eca', 'ECA240G3760' => 'eca', 'ECA240G3920' => 'eca', 'EL10Ac5g12536' => 'bvu', 'EL10Ac5g12537' => 'bvu', 'EL10Ac5g12538' => 'bvu', 'Eucgr.B01004' => 'egr', 'Eucgr.B01006' => 'egr', 'Eucgr.B01007' => 'egr', 'Eucgr.B01008' => 'egr', 'Eucgr.B01895' => 'egr', 'Eucgr.B01896' => 'egr', 'FAN04G1456' => 'fan', 'FAN08G1769' => 'fan', 'FAN08G2160' => 'fan', 'FAN13G2403' => 'fan', 'FAN13G3303' => 'fan', 'FAN15G2435' => 'fan', 'FAN17G0672' => 'fan', 'FAN17G2441' => 'fan', 'FAN18G1024' => 'fan', 'FAN22G1458' => 'fan', 'FAN24G0037' => 'fan', 'FAN24G0429' => 'fan', 'FAN24G2387' => 'fan', 'FAN27G2746' => 'fan', 'FvH4_2g20400' => 'fve', 'FvH4_2g20420' => 'fve', 'FvH4_2g20430' => 'fve', 'FvH4_4g01270' => 'fve', 'FvH4_4g01290' => 'fve', 'FvH4_4g01300' => 'fve', 'FvH4_4g01310' => 'fve', 'FvH4_4g01330' => 'fve', 'FvH4_5g09070' => 'fve', 'Glyma.10G243800' => 'gma', 'Glyma.20G150600' => 'gma', 'Gohir.A09G219200' => 'ghi', 'Gohir.A09G219300' => 'ghi', 'Gohir.D09G221400' => 'ghi', 'Gohir.D09G221500' => 'ghi', 'Gorai.006G242600' => 'gra', 'Gorai.006G242700' => 'gra', 'GSVIVG01018044001' => 'vvi', 'HanXRQChr03g0083821' => 'han', 'HanXRQChr03g0083841' => 'han', 'HanXRQChr03g0083881' => 'han', 'HanXRQChr03g0083901' => 'han', 'HanXRQChr03g0083921' => 'han', 'HanXRQChr03g0085331' => 'han', 'HanXRQChr03g0085361' => 'han', 'HanXRQChr03g0085411' => 'han', 'HanXRQChr03g0085421' => 'han', 'HanXRQChr03g0085431' => 'han', 'HanXRQChr08g0221991' => 'han', 'HanXRQChr11g0336061' => 'han', 'HanXRQChr11g0336411' => 'han', 'Haze_11234' => 'cav', 'Hma1.2p1_0549F.1_g177010' => 'hma', 'Hma1.2p1_0602F.1_g187630' => 'hma', 'Hund14876' => 'sun', 'Hund14879' => 'sun', 'Lalb_Chr06g0160741' => 'lal', 'Lalb_Chr21g0304781' => 'lal', 'Lj3A726G19' => 'lonja', 'Lj3A726T23' => 'lonja', 'Lj3A726T24' => 'lonja', 'Lj3A726T25' => 'lonja', 'Lj3A727T17' => 'lonja', 'Lj3C726T0' => 'lonja', 'Lj3C726T2' => 'lonja', 'Lj3P725T35' => 'lonja', 'Lj3P727T10' => 'lonja', 'Lj3P727T12' => 'lonja', 'Lj3P727T14' => 'lonja', 'Lj5g0023109' => 'lja', 'Lj6P646T44' => 'lonja', 'Lsat_1_v5_gn_6_75760' => 'lsa', 'Lsat_1_v5_gn_6_75800' => 'lsa', 'Lsat_1_v5_gn_6_75900' => 'lsa', 'Lsat_1_v5_gn_6_76240' => 'lsa', 'Lsat_1_v5_gn_6_76441' => 'lsa', 'Lsat_1_v5_gn_6_76700' => 'lsa', 'Lsat_1_v5_gn_6_76760' => 'lsa', 'Manes.15G033100' => 'mes', 'Mapoly0004s0074' => 'mpo', 'Mapoly0004s0075' => 'mpo', 'Mapoly0004s0163' => 'mpo', 'Mapoly0004s0164' => 'mpo', 'Mapoly0021s0018' => 'mpo', 'Mapoly0041s0136' => 'mpo', 'Mapoly0041s0137' => 'mpo', 'Mapoly0041s0138' => 'mpo', 'Mapoly0041s0139' => 'mpo', 'Mapoly0041s0141' => 'mpo', 'Mapoly0041s0142' => 'mpo', 'Mapoly0041s0143' => 'mpo', 'Mapoly0041s0144' => 'mpo', 'Mapoly0041s0145' => 'mpo', 'Mapoly0047s0106' => 'mpo', 'Mapoly0047s0108' => 'mpo', 'Mapoly0050s0051' => 'mpo', 'Mapoly0050s0052' => 'mpo', 'Mapoly0050s0053' => 'mpo', 'Mapoly0058s0013' => 'mpo', 'Mapoly0091s0078' => 'mpo', 'Mapoly0091s0079' => 'mpo', 'Mapoly0091s0080' => 'mpo', 'Mapoly0091s0081' => 'mpo', 'Mapoly0278s0004' => 'mpo', 'Mapoly0278s0005' => 'mpo', 'Mapoly0278s0006' => 'mpo', 'MBI11_g30648_MAGBIO' => 'mbi', 'MCO03G194' => 'mco', 'MCO03G590' => 'mco', 'MCO07G312' => 'mco', 'MCO10G318' => 'mco', 'MCO12G244' => 'mco', 'MCO13G148' => 'mco', 'MCO13G194' => 'mco', 'MCO16G238' => 'mco', 'MD06G1134100' => 'mdo', 'MD13G1200100' => 'mdo', 'MD13G1200300' => 'mdo', 'MD13G1200600' => 'mdo', 'MD14G1150400' => 'mdo', 'MD16G1200000' => 'mdo', 'Medtr1g102570' => 'mtr', 'Medtr1g102780' => 'mtr', 'Medtr1g102800' => 'mtr', 'Medtr1g102810' => 'mtr', 'Medtr1g102830' => 'mtr', 'MELO3C006499.2' => 'cme', 'Migut.G00385' => 'egut', 'MSTRG.4063' => 'ama', 'Nitab4.5_0000090g0260' => 'nta', 'Nitab4.5_0000977g0030' => 'nta', 'Nitab4.5_0002541g0040' => 'nta', 'Nitab4.5_0007068g0040' => 'nta', 'Nn005s41408' => 'nnu', 'Nn005s41410' => 'nnu', 'Oeu010310.1' => 'oeu', 'Oeu010311.1' => 'oeu', 'Oeu043472.1' => 'oeu', 'Os01g0246400' => 'osa', 'Os04g0267950' => 'osa', 'Os07g0178700' => 'osa', 'Os07g0178800' => 'osa', 'Peaxi162Scf00316g00046' => 'pax', 'Peaxi162Scf00316g00049' => 'pax', 'Peaxi162Scf00316g00059' => 'pax', 'Peaxi162Scf00316g00328' => 'pax', 'Peaxi162Scf00316g00329' => 'pax', 'Peaxi162Scf00316g00411' => 'pax', 'Peaxi162Scf00316g00521' => 'pax', 'Peaxi162Scf00492g00068' => 'pax', 'Peaxi162Scf35631g00002' => 'pax', 'PGR142G3720' => 'pgr', 'PGSC0003DMG400006442' => 'stu', 'Phvul.007G062000' => 'pvu', 'Potri.008G157750' => 'ptr', 'Potri.008G157900' => 'ptr', 'Potri.008G158000' => 'ptr', 'Potri.008G158200' => 'ptr', 'Pp3c11_7280' => 'ppa', 'Pp3c11_7980' => 'ppa', 'Pp3c12_19450' => 'ppa', 'Pp3c14_1480' => 'ppa', 'Pp3c14_1501' => 'ppa', 'Pp3c16_4900' => 'ppa', 'Pp3c16_5010' => 'ppa', 'Pp3c16_5060' => 'ppa', 'Pp3c19_18250' => 'ppa', 'Pp3c23_8530' => 'ppa', 'Pp3c23_8550' => 'ppa', 'Pp3c24_9670' => 'ppa', 'Pp3c2_21390' => 'ppa', 'Pp3c2_31380' => 'ppa', 'Pp3c3_16620' => 'ppa', 'Pp3c3_8090' => 'ppa', 'Pp3c3_8110' => 'ppa', 'Pp3c3_8130' => 'ppa', 'Pp3c3_8150' => 'ppa', 'Pp3c4_14320' => 'ppa', 'Pp3c6_2560' => 'ppa', 'Pp3c9_16700' => 'ppa', 'PRCOL_00000234' => 'pco', 'PRCOL_00000235' => 'pco', 'PRCOL_00000777' => 'pco', 'PRCOL_00002344' => 'pco', 'PRCOL_00002372' => 'pco', 'PRCOL_00006120' => 'pco', 'Prupe.1G021400' => 'ppe', 'Prupe.1G021500' => 'ppe', 'Prupe.1G021600' => 'ppe', 'Prupe.1G021700' => 'ppe', 'Prupe.1G021800' => 'ppe', 'Prupe.5G145100' => 'ppe', 'Psat6g204040' => 'psa', 'Psat6g204800' => 'psa', 'Psat6g204920' => 'psa', 'Psat6g204960' => 'psa', 'Psat6g205080' => 'psa', 'PSO017G0271' => 'pso', 'PSO017G1276' => 'pso', 'PSO017G1429' => 'pso', 'PSO017G1861' => 'pso', 'PSO017G2787' => 'pso', 'PSO017G4466' => 'pso', 'PSO017G5118' => 'pso', 'PSO017G5420' => 'pso', 'PSO063G3678' => 'pso', 'PSO210G0546' => 'pso', 'PSO317G0001' => 'pso', 'PSO357G0512' => 'pso', 'PSO478G2682' => 'pso', 'PSO647G0001' => 'pso', 'PSO675G0001' => 'pso', 'PSO675G2699' => 'pso', 'PSO675G2849' => 'pso', 'PSO675G4991' => 'pso', 'PSO689G0001' => 'pso', 'QL06p000916' => 'qlo', 'QL06p000921' => 'qlo', 'QL06p001398' => 'qlo', 'QL06p001407' => 'qlo', 'QL06p002031' => 'qlo', 'RcHm_v2.0_Chr4g0387791' => 'rch', 'RcHm_v2.0_Chr4g0387801' => 'rch', 'RcHm_v2.0_Chr6g0286501' => 'rch', 'RcHm_v2.0_Chr6g0286511' => 'rch', 'RcHm_v2.0_Chr6g0286521' => 'rch', 'RcHm_v2.0_Chr6g0286531' => 'rch', 'RcHm_v2.0_Chr7g0189141' => 'rch', 'Rhsim02G0028700' => 'rsi', 'Rhsim02G0028800' => 'rsi', 'Rhsim02G0028900' => 'rsi', 'Rhsim02G0029000' => 'rsi', 'Rhsim02G0029100' => 'rsi', 'Rhsim02G0029200' => 'rsi', 'Rhsim02G0029300' => 'rsi', 'Rhsim02G0029400' => 'rsi', 'Rhsim02G0029500' => 'rsi', 'Rhsim02G0029600' => 'rsi', 'RhsimUnG0024000' => 'rsi', 'RhsimUnG0024100' => 'rsi', 'RhsimUnG0024200' => 'rsi', 'RhsimUnG0024300' => 'rsi', 'RhsimUnG0024400' => 'rsi', 'RhsimUnG0024500' => 'rsi', 'RhsimUnG0024700' => 'rsi', 'RhsimUnG0024800' => 'rsi', 'RhsimUnG0024900' => 'rsi', 'RhsimUnG0025100' => 'rsi', 'Sabra08G0120200' => 'sbr', 'Sabra08G0120300' => 'sbr', 'Sabra08G0120500' => 'sbr', 'Sabra08G0120600' => 'sbr', 'Sabra10G0158900' => 'sbr', 'SalBow2G3492' => 'sbo', 'Sc13g0004760' => 'sci', 'Sc13g0004770' => 'sci', 'Sed0003417' => 'sed', 'Sed0019750' => 'sed', 'SEGI_03419' => 'sgi', 'SEGI_05907' => 'sgi', 'SEGI_10682' => 'sgi', 'SEGI_13528' => 'sgi', 'SEGI_16081' => 'sgi', 'SEGI_19370' => 'sgi', 'SEGI_21015' => 'sgi', 'SEGI_21944' => 'sgi', 'SEGI_32906' => 'sgi', 'SEGI_33093' => 'sgi', 'SEGI_36110' => 'sgi', 'SEGI_40397' => 'sgi', 'SGA_v2.0_scaffold191G40426' => 'sas', 'SGA_v2.0_scaffold353G49717' => 'sas', 'SGA_v2.0_scaffold50G18550' => 'sas', 'SMO119G0173' => 'smo', 'SMO172G0002' => 'smo', 'Solyc09g082690.3' => 'sly', 'Solyc09g082700.2' => 'sly', 'Sopen09g031550' => 'spe', 'Sopen09g031560' => 'spe', 'Sp3g20540' => 'spa', 'Sp7g07580' => 'spa', 'TAR134G0002' => 'tar', 'TAR236G0001' => 'tar', 'TAR365G0892' => 'tar', 'TAR636G0166' => 'tar', 'TAR636G0646' => 'tar', 'TAR636G0869' => 'tar', 'TAR636G1317' => 'tar', 'TAR636G1744' => 'tar', 'TAR636G3358' => 'tar', 'TAR636G3436' => 'tar', 'THA.LOC104803047' => 'tha', 'Thecc.04G238900' => 'tca', 'Thhalv10021557m.g' => 'esa', 'Thhalv10026318m.g' => 'esa', 'Thhalv10026335m.g' => 'esa', 'TPR.G17433' => 'tpr', 'TPR.G18915' => 'tpr', 'TPR.G26125' => 'tpr', 'TWI09G0677' => 'twi', 'TWI73G0287' => 'twi', 'unitig_748.g8326' => 'ugi', 'vmacro15370' => 'vma', 'vmacro15371' => 'vma', 'vmacro15372' => 'vma', 'vmacro15373' => 'vma', 'vmacro15374' => 'vma', 'VMungo0720G2826' => 'vmu', 'Zm00001eb116960' => 'zma', 'Zm00001eb301260' => 'zma', 'Zm00001eb301270' => 'zma' ) $gf_id = 'HOM05D001460' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001460' ) $data_identifier = 'HOM05D001460' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 4, 'aag' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 2, 'aox' => (int) 2, 'arhy' => (int) 4, 'ath' => (int) 2, 'atr' => (int) 1, 'acertr' => (int) 10, 'cqu' => (int) 4, 'bca' => (int) 11, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 1, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 1, 'ccan' => (int) 1, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 1, 'col' => (int) 1, 'cpa' => (int) 1, 'cre' => (int) 7, 'csa' => (int) 1, 'camsi' => (int) 2, 'dca' => (int) 3, 'din' => (int) 2, 'dzi' => (int) 3, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 14, 'fve' => (int) 9, 'gma' => (int) 2, 'ghi' => (int) 4, 'gra' => (int) 2, 'vvi' => (int) 1, 'han' => (int) 13, 'cav' => (int) 1, 'hma' => (int) 2, 'sun' => (int) 2, 'lal' => (int) 2, 'lonja' => (int) 12, 'lja' => (int) 1, 'lsa' => (int) 7, 'mes' => (int) 1, 'mpo' => (int) 27, 'mbi' => (int) 1, 'mco' => (int) 8, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 1, 'egut' => (int) 1, 'ama' => (int) 1, 'nta' => (int) 4, 'nnu' => (int) 2, 'oeu' => (int) 3, 'osa' => (int) 4, 'pax' => (int) 9, 'pgr' => (int) 1, 'stu' => (int) 1, 'pvu' => (int) 1, 'ptr' => (int) 4, 'ppa' => (int) 22, 'pco' => (int) 6, 'ppe' => (int) 6, 'psa' => (int) 5, 'pso' => (int) 19, 'qlo' => (int) 5, 'rch' => (int) 7, 'rsi' => (int) 20, 'sbr' => (int) 5, 'sbo' => (int) 1, 'sci' => (int) 2, 'sed' => (int) 2, 'sgi' => (int) 12, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 2, 'tar' => (int) 10, 'tha' => (int) 1, 'tca' => (int) 1, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 2, 'ugi' => (int) 1, 'vma' => (int) 5, 'vmu' => (int) 1, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb301270' $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' => 'HOM05D001460', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '433', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p22980' => 'bna', 'A01p32340' => 'bna', 'A03p42970' => 'bna', 'A05p25880' => 'bna', 'Aa31LG8G9320' => 'aar', 'Aa31LG8G9330' => 'aar', 'Aa31LG8G9340' => 'aar', 'Aa31sc221G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1034' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1528' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.829' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2222' => 'aag', 'Ah.12g058830' => 'amhyb', 'Ah.12g058840' => 'amhyb', 'AL3G37160' => 'aly', 'AL7G41310' => 'aly', 'Aqoxy5G00395' => 'aox', 'Aqoxy5G00396' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0C8NZA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5185HY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JZ1PRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MD3LS0' => 'arhy', 'AT3G22840' => 'ath', 'AT4G14690' => 'ath', 'ATR0665G054' => 'atr', 'Atru.chr4.2344' => 'acertr', 'Atru.chr4.2346' => 'acertr', 'Atru.chr4.2347' => 'acertr', 'Atru.chr4.2348' => 'acertr', 'Atru.chr4.2355' => 'acertr', 'Atru.chr4.2356' => 'acertr', 'Atru.chr4.2358' => 'acertr', 'Atru.chr4.2359' => 'acertr', 'Atru.chr4.2360' => 'acertr', 'Atru.chr4.2361' => 'acertr', 'AUR62030476' => 'cqu', 'AUR62030478' => 'cqu', 'AUR62030819' => 'cqu', 'AUR62030820' => 'cqu', 'BcaB03g14648' => 'bca', 'BcaB04g20492' => 'bca', 'BcaB06g26399' => 'bca', 'BcaC01g03416' => 'bca', 'BcaC01g03419' => 'bca', 'BcaC01g03421' => 'bca', 'BcaC01g03424' => 'bca', 'BcaC05g28012' => 'bca', 'BcaC09g49212' => 'bca', 'BcaC09g50140' => 'bca', 'BcaNung00346' => 'bca', 'BolC1t02785H' => 'bol', 'BolC1t04095H' => 'bol', 'BolC3t17545H' => 'bol', 'BolC5t32769H' => 'bol', 'BraA01t02211Z' => 'bra', 'BraA01t03359Z' => 'bra', 'BraA03t13441Z' => 'bra', 'BraA05t21476Z' => 'bra', 'C01p28420' => 'bna', 'C01p41350' => 'bna', 'C03p52750' => 'bna', 'C03p52780' => 'bna', 'C05p40270' => 'bna', 'CAN.G1437.9' => 'can', 'CANSAT78G0035' => 'cansat', 'CANSAT78G1036' => 'cansat', 'CANSAT78G2272' => 'cansat', 'CANSAT78G2478' => 'cansat', 'CARHR098700' => 'chi', 'CARHR221120' => 'chi', 'CARHR221150' => 'chi', 'Carub.0003s2297' => 'cru', 'Carub.0007s2749' => 'cru', 'Carub.0007s2750' => 'cru', 'Carub.0007s2751' => 'cru', 'Ca_10849_v3' => 'car', 'Cc03_g04300' => 'ccan', 'CDE02G3648' => 'cde', 'CDE05G0060' => 'cde', 'CDE05G0692' => 'cde', 'CDE05G2285' => 'cde', 'CDE05G2884' => 'cde', 'CDE05G3072' => 'cde', 'Cfa008439' => 'cfa', 'Cfa008441' => 'cfa', 'Cfa008443' => 'cfa', 'Cfa008448' => 'cfa', 'Ciclev10005974m.g' => 'ccl', 'Ciclev10006006m.g' => 'ccl', 'Ciclev10006775m.g' => 'ccl', 'CiPaw.02G120400' => 'cil', 'CiPaw.02G120500' => 'cil', 'CiPaw.02G120600' => 'cil', 'ClCG05G004850' => 'cla', 'COL.COLO4_21566' => 'col', 'Cpa.g.sc44.124' => 'cpa', 'Cre07.g320400' => 'cre', 'Cre07.g320450' => 'cre', 'Cre08.g384650' => 'cre', 'Cre09.g393173' => 'cre', 'Cre09.g394325' => 'cre', 'Cre14.g626750' => 'cre', 'Cre16.g679250' => 'cre', 'CsaV3_3G012890' => 'csa', 'CSS0010865' => 'camsi', 'CSS0044338' => 'camsi', 'DCAR_002366' => 'dca', 'DCAR_030687' => 'dca', 'DCAR_030688' => 'dca', 'Dinv14047' => 'din', 'Dinv14048' => 'din', 'Duzib151G0105' => 'dzi', 'Duzib151G0114' => 'dzi', 'Duzib212G1029' => 'dzi', 'ECA232G3536' => 'eca', 'ECA240G0786' => 'eca', 'ECA240G1802' => 'eca', 'ECA240G3760' => 'eca', 'ECA240G3920' => 'eca', 'EL10Ac5g12536' => 'bvu', 'EL10Ac5g12537' => 'bvu', 'EL10Ac5g12538' => 'bvu', 'Eucgr.B01004' => 'egr', 'Eucgr.B01006' => 'egr', 'Eucgr.B01007' => 'egr', 'Eucgr.B01008' => 'egr', 'Eucgr.B01895' => 'egr', 'Eucgr.B01896' => 'egr', 'FAN04G1456' => 'fan', 'FAN08G1769' => 'fan', 'FAN08G2160' => 'fan', 'FAN13G2403' => 'fan', 'FAN13G3303' => 'fan', 'FAN15G2435' => 'fan', 'FAN17G0672' => 'fan', 'FAN17G2441' => 'fan', 'FAN18G1024' => 'fan', 'FAN22G1458' => 'fan', 'FAN24G0037' => 'fan', 'FAN24G0429' => 'fan', 'FAN24G2387' => 'fan', 'FAN27G2746' => 'fan', 'FvH4_2g20400' => 'fve', 'FvH4_2g20420' => 'fve', 'FvH4_2g20430' => 'fve', 'FvH4_4g01270' => 'fve', 'FvH4_4g01290' => 'fve', 'FvH4_4g01300' => 'fve', 'FvH4_4g01310' => 'fve', 'FvH4_4g01330' => 'fve', 'FvH4_5g09070' => 'fve', 'Glyma.10G243800' => 'gma', 'Glyma.20G150600' => 'gma', 'Gohir.A09G219200' => 'ghi', 'Gohir.A09G219300' => 'ghi', 'Gohir.D09G221400' => 'ghi', 'Gohir.D09G221500' => 'ghi', 'Gorai.006G242600' => 'gra', 'Gorai.006G242700' => 'gra', 'GSVIVG01018044001' => 'vvi', 'HanXRQChr03g0083821' => 'han', 'HanXRQChr03g0083841' => 'han', 'HanXRQChr03g0083881' => 'han', 'HanXRQChr03g0083901' => 'han', 'HanXRQChr03g0083921' => 'han', 'HanXRQChr03g0085331' => 'han', 'HanXRQChr03g0085361' => 'han', 'HanXRQChr03g0085411' => 'han', 'HanXRQChr03g0085421' => 'han', 'HanXRQChr03g0085431' => 'han', 'HanXRQChr08g0221991' => 'han', 'HanXRQChr11g0336061' => 'han', 'HanXRQChr11g0336411' => 'han', 'Haze_11234' => 'cav', 'Hma1.2p1_0549F.1_g177010' => 'hma', 'Hma1.2p1_0602F.1_g187630' => 'hma', 'Hund14876' => 'sun', 'Hund14879' => 'sun', 'Lalb_Chr06g0160741' => 'lal', 'Lalb_Chr21g0304781' => 'lal', 'Lj3A726G19' => 'lonja', 'Lj3A726T23' => 'lonja', 'Lj3A726T24' => 'lonja', 'Lj3A726T25' => 'lonja', 'Lj3A727T17' => 'lonja', 'Lj3C726T0' => 'lonja', 'Lj3C726T2' => 'lonja', 'Lj3P725T35' => 'lonja', 'Lj3P727T10' => 'lonja', 'Lj3P727T12' => 'lonja', 'Lj3P727T14' => 'lonja', 'Lj5g0023109' => 'lja', 'Lj6P646T44' => 'lonja', 'Lsat_1_v5_gn_6_75760' => 'lsa', 'Lsat_1_v5_gn_6_75800' => 'lsa', 'Lsat_1_v5_gn_6_75900' => 'lsa', 'Lsat_1_v5_gn_6_76240' => 'lsa', 'Lsat_1_v5_gn_6_76441' => 'lsa', 'Lsat_1_v5_gn_6_76700' => 'lsa', 'Lsat_1_v5_gn_6_76760' => 'lsa', 'Manes.15G033100' => 'mes', 'Mapoly0004s0074' => 'mpo', 'Mapoly0004s0075' => 'mpo', 'Mapoly0004s0163' => 'mpo', 'Mapoly0004s0164' => 'mpo', 'Mapoly0021s0018' => 'mpo', 'Mapoly0041s0136' => 'mpo', 'Mapoly0041s0137' => 'mpo', 'Mapoly0041s0138' => 'mpo', 'Mapoly0041s0139' => 'mpo', 'Mapoly0041s0141' => 'mpo', 'Mapoly0041s0142' => 'mpo', 'Mapoly0041s0143' => 'mpo', 'Mapoly0041s0144' => 'mpo', 'Mapoly0041s0145' => 'mpo', 'Mapoly0047s0106' => 'mpo', 'Mapoly0047s0108' => 'mpo', 'Mapoly0050s0051' => 'mpo', 'Mapoly0050s0052' => 'mpo', 'Mapoly0050s0053' => 'mpo', 'Mapoly0058s0013' => 'mpo', 'Mapoly0091s0078' => 'mpo', 'Mapoly0091s0079' => 'mpo', 'Mapoly0091s0080' => 'mpo', 'Mapoly0091s0081' => 'mpo', 'Mapoly0278s0004' => 'mpo', 'Mapoly0278s0005' => 'mpo', 'Mapoly0278s0006' => 'mpo', 'MBI11_g30648_MAGBIO' => 'mbi', 'MCO03G194' => 'mco', 'MCO03G590' => 'mco', 'MCO07G312' => 'mco', 'MCO10G318' => 'mco', 'MCO12G244' => 'mco', 'MCO13G148' => 'mco', 'MCO13G194' => 'mco', 'MCO16G238' => 'mco', 'MD06G1134100' => 'mdo', 'MD13G1200100' => 'mdo', 'MD13G1200300' => 'mdo', 'MD13G1200600' => 'mdo', 'MD14G1150400' => 'mdo', 'MD16G1200000' => 'mdo', 'Medtr1g102570' => 'mtr', 'Medtr1g102780' => 'mtr', 'Medtr1g102800' => 'mtr', 'Medtr1g102810' => 'mtr', 'Medtr1g102830' => 'mtr', 'MELO3C006499.2' => 'cme', 'Migut.G00385' => 'egut', 'MSTRG.4063' => 'ama', 'Nitab4.5_0000090g0260' => 'nta', 'Nitab4.5_0000977g0030' => 'nta', 'Nitab4.5_0002541g0040' => 'nta', 'Nitab4.5_0007068g0040' => 'nta', 'Nn005s41408' => 'nnu', 'Nn005s41410' => 'nnu', 'Oeu010310.1' => 'oeu', 'Oeu010311.1' => 'oeu', 'Oeu043472.1' => 'oeu', 'Os01g0246400' => 'osa', 'Os04g0267950' => 'osa', 'Os07g0178700' => 'osa', 'Os07g0178800' => 'osa', 'Peaxi162Scf00316g00046' => 'pax', 'Peaxi162Scf00316g00049' => 'pax', 'Peaxi162Scf00316g00059' => 'pax', 'Peaxi162Scf00316g00328' => 'pax', 'Peaxi162Scf00316g00329' => 'pax', 'Peaxi162Scf00316g00411' => 'pax', 'Peaxi162Scf00316g00521' => 'pax', 'Peaxi162Scf00492g00068' => 'pax', 'Peaxi162Scf35631g00002' => 'pax', 'PGR142G3720' => 'pgr', 'PGSC0003DMG400006442' => 'stu', 'Phvul.007G062000' => 'pvu', 'Potri.008G157750' => 'ptr', 'Potri.008G157900' => 'ptr', 'Potri.008G158000' => 'ptr', 'Potri.008G158200' => 'ptr', 'Pp3c11_7280' => 'ppa', 'Pp3c11_7980' => 'ppa', 'Pp3c12_19450' => 'ppa', 'Pp3c14_1480' => 'ppa', 'Pp3c14_1501' => 'ppa', 'Pp3c16_4900' => 'ppa', 'Pp3c16_5010' => 'ppa', 'Pp3c16_5060' => 'ppa', 'Pp3c19_18250' => 'ppa', 'Pp3c23_8530' => 'ppa', 'Pp3c23_8550' => 'ppa', 'Pp3c24_9670' => 'ppa', 'Pp3c2_21390' => 'ppa', 'Pp3c2_31380' => 'ppa', 'Pp3c3_16620' => 'ppa', 'Pp3c3_8090' => 'ppa', 'Pp3c3_8110' => 'ppa', 'Pp3c3_8130' => 'ppa', 'Pp3c3_8150' => 'ppa', 'Pp3c4_14320' => 'ppa', 'Pp3c6_2560' => 'ppa', 'Pp3c9_16700' => 'ppa', 'PRCOL_00000234' => 'pco', 'PRCOL_00000235' => 'pco', 'PRCOL_00000777' => 'pco', 'PRCOL_00002344' => 'pco', 'PRCOL_00002372' => 'pco', 'PRCOL_00006120' => 'pco', 'Prupe.1G021400' => 'ppe', 'Prupe.1G021500' => 'ppe', 'Prupe.1G021600' => 'ppe', 'Prupe.1G021700' => 'ppe', 'Prupe.1G021800' => 'ppe', 'Prupe.5G145100' => 'ppe', 'Psat6g204040' => 'psa', 'Psat6g204800' => 'psa', 'Psat6g204920' => 'psa', 'Psat6g204960' => 'psa', 'Psat6g205080' => 'psa', 'PSO017G0271' => 'pso', 'PSO017G1276' => 'pso', 'PSO017G1429' => 'pso', 'PSO017G1861' => 'pso', 'PSO017G2787' => 'pso', 'PSO017G4466' => 'pso', 'PSO017G5118' => 'pso', 'PSO017G5420' => 'pso', 'PSO063G3678' => 'pso', 'PSO210G0546' => 'pso', 'PSO317G0001' => 'pso', 'PSO357G0512' => 'pso', 'PSO478G2682' => 'pso', 'PSO647G0001' => 'pso', 'PSO675G0001' => 'pso', 'PSO675G2699' => 'pso', 'PSO675G2849' => 'pso', 'PSO675G4991' => 'pso', 'PSO689G0001' => 'pso', 'QL06p000916' => 'qlo', 'QL06p000921' => 'qlo', 'QL06p001398' => 'qlo', 'QL06p001407' => 'qlo', 'QL06p002031' => 'qlo', 'RcHm_v2.0_Chr4g0387791' => 'rch', 'RcHm_v2.0_Chr4g0387801' => 'rch', 'RcHm_v2.0_Chr6g0286501' => 'rch', 'RcHm_v2.0_Chr6g0286511' => 'rch', 'RcHm_v2.0_Chr6g0286521' => 'rch', 'RcHm_v2.0_Chr6g0286531' => 'rch', 'RcHm_v2.0_Chr7g0189141' => 'rch', 'Rhsim02G0028700' => 'rsi', 'Rhsim02G0028800' => 'rsi', 'Rhsim02G0028900' => 'rsi', 'Rhsim02G0029000' => 'rsi', 'Rhsim02G0029100' => 'rsi', 'Rhsim02G0029200' => 'rsi', 'Rhsim02G0029300' => 'rsi', 'Rhsim02G0029400' => 'rsi', 'Rhsim02G0029500' => 'rsi', 'Rhsim02G0029600' => 'rsi', 'RhsimUnG0024000' => 'rsi', 'RhsimUnG0024100' => 'rsi', 'RhsimUnG0024200' => 'rsi', 'RhsimUnG0024300' => 'rsi', 'RhsimUnG0024400' => 'rsi', 'RhsimUnG0024500' => 'rsi', 'RhsimUnG0024700' => 'rsi', 'RhsimUnG0024800' => 'rsi', 'RhsimUnG0024900' => 'rsi', 'RhsimUnG0025100' => 'rsi', 'Sabra08G0120200' => 'sbr', 'Sabra08G0120300' => 'sbr', 'Sabra08G0120500' => 'sbr', 'Sabra08G0120600' => 'sbr', 'Sabra10G0158900' => 'sbr', 'SalBow2G3492' => 'sbo', 'Sc13g0004760' => 'sci', 'Sc13g0004770' => 'sci', 'Sed0003417' => 'sed', 'Sed0019750' => 'sed', 'SEGI_03419' => 'sgi', 'SEGI_05907' => 'sgi', 'SEGI_10682' => 'sgi', 'SEGI_13528' => 'sgi', 'SEGI_16081' => 'sgi', 'SEGI_19370' => 'sgi', 'SEGI_21015' => 'sgi', 'SEGI_21944' => 'sgi', 'SEGI_32906' => 'sgi', 'SEGI_33093' => 'sgi', 'SEGI_36110' => 'sgi', 'SEGI_40397' => 'sgi', 'SGA_v2.0_scaffold191G40426' => 'sas', 'SGA_v2.0_scaffold353G49717' => 'sas', 'SGA_v2.0_scaffold50G18550' => 'sas', 'SMO119G0173' => 'smo', 'SMO172G0002' => 'smo', 'Solyc09g082690.3' => 'sly', 'Solyc09g082700.2' => 'sly', 'Sopen09g031550' => 'spe', 'Sopen09g031560' => 'spe', 'Sp3g20540' => 'spa', 'Sp7g07580' => 'spa', 'TAR134G0002' => 'tar', 'TAR236G0001' => 'tar', 'TAR365G0892' => 'tar', 'TAR636G0166' => 'tar', 'TAR636G0646' => 'tar', 'TAR636G0869' => 'tar', 'TAR636G1317' => 'tar', 'TAR636G1744' => 'tar', 'TAR636G3358' => 'tar', 'TAR636G3436' => 'tar', 'THA.LOC104803047' => 'tha', 'Thecc.04G238900' => 'tca', 'Thhalv10021557m.g' => 'esa', 'Thhalv10026318m.g' => 'esa', 'Thhalv10026335m.g' => 'esa', 'TPR.G17433' => 'tpr', 'TPR.G18915' => 'tpr', 'TPR.G26125' => 'tpr', 'TWI09G0677' => 'twi', 'TWI73G0287' => 'twi', 'unitig_748.g8326' => 'ugi', 'vmacro15370' => 'vma', 'vmacro15371' => 'vma', 'vmacro15372' => 'vma', 'vmacro15373' => 'vma', 'vmacro15374' => 'vma', 'VMungo0720G2826' => 'vmu', 'Zm00001eb116960' => 'zma', 'Zm00001eb301260' => 'zma', 'Zm00001eb301270' => 'zma' ), 'gf_id' => 'HOM05D001460', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001460' ), 'data_identifier' => 'HOM05D001460', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001460', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '433', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p22980' => 'bna', 'A01p32340' => 'bna', 'A03p42970' => 'bna', 'A05p25880' => 'bna', 'Aa31LG8G9320' => 'aar', 'Aa31LG8G9330' => 'aar', 'Aa31LG8G9340' => 'aar', 'Aa31sc221G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1034' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1528' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.829' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2222' => 'aag', 'Ah.12g058830' => 'amhyb', 'Ah.12g058840' => 'amhyb', 'AL3G37160' => 'aly', 'AL7G41310' => 'aly', 'Aqoxy5G00395' => 'aox', 'Aqoxy5G00396' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0C8NZA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5185HY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JZ1PRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MD3LS0' => 'arhy', 'AT3G22840' => 'ath', 'AT4G14690' => 'ath', 'ATR0665G054' => 'atr', 'Atru.chr4.2344' => 'acertr', 'Atru.chr4.2346' => 'acertr', 'Atru.chr4.2347' => 'acertr', 'Atru.chr4.2348' => 'acertr', 'Atru.chr4.2355' => 'acertr', 'Atru.chr4.2356' => 'acertr', 'Atru.chr4.2358' => 'acertr', 'Atru.chr4.2359' => 'acertr', 'Atru.chr4.2360' => 'acertr', 'Atru.chr4.2361' => 'acertr', 'AUR62030476' => 'cqu', 'AUR62030478' => 'cqu', 'AUR62030819' => 'cqu', 'AUR62030820' => 'cqu', 'BcaB03g14648' => 'bca', 'BcaB04g20492' => 'bca', 'BcaB06g26399' => 'bca', 'BcaC01g03416' => 'bca', 'BcaC01g03419' => 'bca', 'BcaC01g03421' => 'bca', 'BcaC01g03424' => 'bca', 'BcaC05g28012' => 'bca', 'BcaC09g49212' => 'bca', 'BcaC09g50140' => 'bca', 'BcaNung00346' => 'bca', 'BolC1t02785H' => 'bol', 'BolC1t04095H' => 'bol', 'BolC3t17545H' => 'bol', 'BolC5t32769H' => 'bol', 'BraA01t02211Z' => 'bra', 'BraA01t03359Z' => 'bra', 'BraA03t13441Z' => 'bra', 'BraA05t21476Z' => 'bra', 'C01p28420' => 'bna', 'C01p41350' => 'bna', 'C03p52750' => 'bna', 'C03p52780' => 'bna', 'C05p40270' => 'bna', 'CAN.G1437.9' => 'can', 'CANSAT78G0035' => 'cansat', 'CANSAT78G1036' => 'cansat', 'CANSAT78G2272' => 'cansat', 'CANSAT78G2478' => 'cansat', 'CARHR098700' => 'chi', 'CARHR221120' => 'chi', 'CARHR221150' => 'chi', 'Carub.0003s2297' => 'cru', 'Carub.0007s2749' => 'cru', 'Carub.0007s2750' => 'cru', 'Carub.0007s2751' => 'cru', 'Ca_10849_v3' => 'car', 'Cc03_g04300' => 'ccan', 'CDE02G3648' => 'cde', 'CDE05G0060' => 'cde', 'CDE05G0692' => 'cde', 'CDE05G2285' => 'cde', 'CDE05G2884' => 'cde', 'CDE05G3072' => 'cde', 'Cfa008439' => 'cfa', 'Cfa008441' => 'cfa', 'Cfa008443' => 'cfa', 'Cfa008448' => 'cfa', 'Ciclev10005974m.g' => 'ccl', 'Ciclev10006006m.g' => 'ccl', 'Ciclev10006775m.g' => 'ccl', 'CiPaw.02G120400' => 'cil', 'CiPaw.02G120500' => 'cil', 'CiPaw.02G120600' => 'cil', 'ClCG05G004850' => 'cla', 'COL.COLO4_21566' => 'col', 'Cpa.g.sc44.124' => 'cpa', 'Cre07.g320400' => 'cre', 'Cre07.g320450' => 'cre', 'Cre08.g384650' => 'cre', 'Cre09.g393173' => 'cre', 'Cre09.g394325' => 'cre', 'Cre14.g626750' => 'cre', 'Cre16.g679250' => 'cre', 'CsaV3_3G012890' => 'csa', 'CSS0010865' => 'camsi', 'CSS0044338' => 'camsi', 'DCAR_002366' => 'dca', 'DCAR_030687' => 'dca', 'DCAR_030688' => 'dca', 'Dinv14047' => 'din', 'Dinv14048' => 'din', 'Duzib151G0105' => 'dzi', 'Duzib151G0114' => 'dzi', 'Duzib212G1029' => 'dzi', 'ECA232G3536' => 'eca', 'ECA240G0786' => 'eca', 'ECA240G1802' => 'eca', 'ECA240G3760' => 'eca', 'ECA240G3920' => 'eca', 'EL10Ac5g12536' => 'bvu', 'EL10Ac5g12537' => 'bvu', 'EL10Ac5g12538' => 'bvu', 'Eucgr.B01004' => 'egr', 'Eucgr.B01006' => 'egr', 'Eucgr.B01007' => 'egr', 'Eucgr.B01008' => 'egr', 'Eucgr.B01895' => 'egr', 'Eucgr.B01896' => 'egr', 'FAN04G1456' => 'fan', 'FAN08G1769' => 'fan', 'FAN08G2160' => 'fan', 'FAN13G2403' => 'fan', 'FAN13G3303' => 'fan', 'FAN15G2435' => 'fan', 'FAN17G0672' => 'fan', 'FAN17G2441' => 'fan', 'FAN18G1024' => 'fan', 'FAN22G1458' => 'fan', 'FAN24G0037' => 'fan', 'FAN24G0429' => 'fan', 'FAN24G2387' => 'fan', 'FAN27G2746' => 'fan', 'FvH4_2g20400' => 'fve', 'FvH4_2g20420' => 'fve', 'FvH4_2g20430' => 'fve', 'FvH4_4g01270' => 'fve', 'FvH4_4g01290' => 'fve', 'FvH4_4g01300' => 'fve', 'FvH4_4g01310' => 'fve', 'FvH4_4g01330' => 'fve', 'FvH4_5g09070' => 'fve', 'Glyma.10G243800' => 'gma', 'Glyma.20G150600' => 'gma', 'Gohir.A09G219200' => 'ghi', 'Gohir.A09G219300' => 'ghi', 'Gohir.D09G221400' => 'ghi', 'Gohir.D09G221500' => 'ghi', 'Gorai.006G242600' => 'gra', 'Gorai.006G242700' => 'gra', 'GSVIVG01018044001' => 'vvi', 'HanXRQChr03g0083821' => 'han', 'HanXRQChr03g0083841' => 'han', 'HanXRQChr03g0083881' => 'han', 'HanXRQChr03g0083901' => 'han', 'HanXRQChr03g0083921' => 'han', 'HanXRQChr03g0085331' => 'han', 'HanXRQChr03g0085361' => 'han', 'HanXRQChr03g0085411' => 'han', 'HanXRQChr03g0085421' => 'han', 'HanXRQChr03g0085431' => 'han', 'HanXRQChr08g0221991' => 'han', 'HanXRQChr11g0336061' => 'han', 'HanXRQChr11g0336411' => 'han', 'Haze_11234' => 'cav', 'Hma1.2p1_0549F.1_g177010' => 'hma', 'Hma1.2p1_0602F.1_g187630' => 'hma', 'Hund14876' => 'sun', 'Hund14879' => 'sun', 'Lalb_Chr06g0160741' => 'lal', 'Lalb_Chr21g0304781' => 'lal', 'Lj3A726G19' => 'lonja', 'Lj3A726T23' => 'lonja', 'Lj3A726T24' => 'lonja', 'Lj3A726T25' => 'lonja', 'Lj3A727T17' => 'lonja', 'Lj3C726T0' => 'lonja', 'Lj3C726T2' => 'lonja', 'Lj3P725T35' => 'lonja', 'Lj3P727T10' => 'lonja', 'Lj3P727T12' => 'lonja', 'Lj3P727T14' => 'lonja', 'Lj5g0023109' => 'lja', 'Lj6P646T44' => 'lonja', 'Lsat_1_v5_gn_6_75760' => 'lsa', 'Lsat_1_v5_gn_6_75800' => 'lsa', 'Lsat_1_v5_gn_6_75900' => 'lsa', 'Lsat_1_v5_gn_6_76240' => 'lsa', 'Lsat_1_v5_gn_6_76441' => 'lsa', 'Lsat_1_v5_gn_6_76700' => 'lsa', 'Lsat_1_v5_gn_6_76760' => 'lsa', 'Manes.15G033100' => 'mes', 'Mapoly0004s0074' => 'mpo', 'Mapoly0004s0075' => 'mpo', 'Mapoly0004s0163' => 'mpo', 'Mapoly0004s0164' => 'mpo', 'Mapoly0021s0018' => 'mpo', 'Mapoly0041s0136' => 'mpo', 'Mapoly0041s0137' => 'mpo', 'Mapoly0041s0138' => 'mpo', 'Mapoly0041s0139' => 'mpo', 'Mapoly0041s0141' => 'mpo', 'Mapoly0041s0142' => 'mpo', 'Mapoly0041s0143' => 'mpo', 'Mapoly0041s0144' => 'mpo', 'Mapoly0041s0145' => 'mpo', 'Mapoly0047s0106' => 'mpo', 'Mapoly0047s0108' => 'mpo', 'Mapoly0050s0051' => 'mpo', 'Mapoly0050s0052' => 'mpo', 'Mapoly0050s0053' => 'mpo', 'Mapoly0058s0013' => 'mpo', 'Mapoly0091s0078' => 'mpo', 'Mapoly0091s0079' => 'mpo', 'Mapoly0091s0080' => 'mpo', 'Mapoly0091s0081' => 'mpo', 'Mapoly0278s0004' => 'mpo', 'Mapoly0278s0005' => 'mpo', 'Mapoly0278s0006' => 'mpo', 'MBI11_g30648_MAGBIO' => 'mbi', 'MCO03G194' => 'mco', 'MCO03G590' => 'mco', 'MCO07G312' => 'mco', 'MCO10G318' => 'mco', 'MCO12G244' => 'mco', 'MCO13G148' => 'mco', 'MCO13G194' => 'mco', 'MCO16G238' => 'mco', 'MD06G1134100' => 'mdo', 'MD13G1200100' => 'mdo', 'MD13G1200300' => 'mdo', 'MD13G1200600' => 'mdo', 'MD14G1150400' => 'mdo', 'MD16G1200000' => 'mdo', 'Medtr1g102570' => 'mtr', 'Medtr1g102780' => 'mtr', 'Medtr1g102800' => 'mtr', 'Medtr1g102810' => 'mtr', 'Medtr1g102830' => 'mtr', 'MELO3C006499.2' => 'cme', 'Migut.G00385' => 'egut', 'MSTRG.4063' => 'ama', 'Nitab4.5_0000090g0260' => 'nta', 'Nitab4.5_0000977g0030' => 'nta', 'Nitab4.5_0002541g0040' => 'nta', 'Nitab4.5_0007068g0040' => 'nta', 'Nn005s41408' => 'nnu', 'Nn005s41410' => 'nnu', 'Oeu010310.1' => 'oeu', 'Oeu010311.1' => 'oeu', 'Oeu043472.1' => 'oeu', 'Os01g0246400' => 'osa', 'Os04g0267950' => 'osa', 'Os07g0178700' => 'osa', 'Os07g0178800' => 'osa', 'Peaxi162Scf00316g00046' => 'pax', 'Peaxi162Scf00316g00049' => 'pax', 'Peaxi162Scf00316g00059' => 'pax', 'Peaxi162Scf00316g00328' => 'pax', 'Peaxi162Scf00316g00329' => 'pax', 'Peaxi162Scf00316g00411' => 'pax', 'Peaxi162Scf00316g00521' => 'pax', 'Peaxi162Scf00492g00068' => 'pax', 'Peaxi162Scf35631g00002' => 'pax', 'PGR142G3720' => 'pgr', 'PGSC0003DMG400006442' => 'stu', 'Phvul.007G062000' => 'pvu', 'Potri.008G157750' => 'ptr', 'Potri.008G157900' => 'ptr', 'Potri.008G158000' => 'ptr', 'Potri.008G158200' => 'ptr', 'Pp3c11_7280' => 'ppa', 'Pp3c11_7980' => 'ppa', 'Pp3c12_19450' => 'ppa', 'Pp3c14_1480' => 'ppa', 'Pp3c14_1501' => 'ppa', 'Pp3c16_4900' => 'ppa', 'Pp3c16_5010' => 'ppa', 'Pp3c16_5060' => 'ppa', 'Pp3c19_18250' => 'ppa', 'Pp3c23_8530' => 'ppa', 'Pp3c23_8550' => 'ppa', 'Pp3c24_9670' => 'ppa', 'Pp3c2_21390' => 'ppa', 'Pp3c2_31380' => 'ppa', 'Pp3c3_16620' => 'ppa', 'Pp3c3_8090' => 'ppa', 'Pp3c3_8110' => 'ppa', 'Pp3c3_8130' => 'ppa', 'Pp3c3_8150' => 'ppa', 'Pp3c4_14320' => 'ppa', 'Pp3c6_2560' => 'ppa', 'Pp3c9_16700' => 'ppa', 'PRCOL_00000234' => 'pco', 'PRCOL_00000235' => 'pco', 'PRCOL_00000777' => 'pco', 'PRCOL_00002344' => 'pco', 'PRCOL_00002372' => 'pco', 'PRCOL_00006120' => 'pco', 'Prupe.1G021400' => 'ppe', 'Prupe.1G021500' => 'ppe', 'Prupe.1G021600' => 'ppe', 'Prupe.1G021700' => 'ppe', 'Prupe.1G021800' => 'ppe', 'Prupe.5G145100' => 'ppe', 'Psat6g204040' => 'psa', 'Psat6g204800' => 'psa', 'Psat6g204920' => 'psa', 'Psat6g204960' => 'psa', 'Psat6g205080' => 'psa', 'PSO017G0271' => 'pso', 'PSO017G1276' => 'pso', 'PSO017G1429' => 'pso', 'PSO017G1861' => 'pso', 'PSO017G2787' => 'pso', 'PSO017G4466' => 'pso', 'PSO017G5118' => 'pso', 'PSO017G5420' => 'pso', 'PSO063G3678' => 'pso', 'PSO210G0546' => 'pso', 'PSO317G0001' => 'pso', 'PSO357G0512' => 'pso', 'PSO478G2682' => 'pso', 'PSO647G0001' => 'pso', 'PSO675G0001' => 'pso', 'PSO675G2699' => 'pso', 'PSO675G2849' => 'pso', 'PSO675G4991' => 'pso', 'PSO689G0001' => 'pso', 'QL06p000916' => 'qlo', 'QL06p000921' => 'qlo', 'QL06p001398' => 'qlo', 'QL06p001407' => 'qlo', 'QL06p002031' => 'qlo', 'RcHm_v2.0_Chr4g0387791' => 'rch', 'RcHm_v2.0_Chr4g0387801' => 'rch', 'RcHm_v2.0_Chr6g0286501' => 'rch', 'RcHm_v2.0_Chr6g0286511' => 'rch', 'RcHm_v2.0_Chr6g0286521' => 'rch', 'RcHm_v2.0_Chr6g0286531' => 'rch', 'RcHm_v2.0_Chr7g0189141' => 'rch', 'Rhsim02G0028700' => 'rsi', 'Rhsim02G0028800' => 'rsi', 'Rhsim02G0028900' => 'rsi', 'Rhsim02G0029000' => 'rsi', 'Rhsim02G0029100' => 'rsi', 'Rhsim02G0029200' => 'rsi', 'Rhsim02G0029300' => 'rsi', 'Rhsim02G0029400' => 'rsi', 'Rhsim02G0029500' => 'rsi', 'Rhsim02G0029600' => 'rsi', 'RhsimUnG0024000' => 'rsi', 'RhsimUnG0024100' => 'rsi', 'RhsimUnG0024200' => 'rsi', 'RhsimUnG0024300' => 'rsi', 'RhsimUnG0024400' => 'rsi', 'RhsimUnG0024500' => 'rsi', 'RhsimUnG0024700' => 'rsi', 'RhsimUnG0024800' => 'rsi', 'RhsimUnG0024900' => 'rsi', 'RhsimUnG0025100' => 'rsi', 'Sabra08G0120200' => 'sbr', 'Sabra08G0120300' => 'sbr', 'Sabra08G0120500' => 'sbr', 'Sabra08G0120600' => 'sbr', 'Sabra10G0158900' => 'sbr', 'SalBow2G3492' => 'sbo', 'Sc13g0004760' => 'sci', 'Sc13g0004770' => 'sci', 'Sed0003417' => 'sed', 'Sed0019750' => 'sed', 'SEGI_03419' => 'sgi', 'SEGI_05907' => 'sgi', 'SEGI_10682' => 'sgi', 'SEGI_13528' => 'sgi', 'SEGI_16081' => 'sgi', 'SEGI_19370' => 'sgi', 'SEGI_21015' => 'sgi', 'SEGI_21944' => 'sgi', 'SEGI_32906' => 'sgi', 'SEGI_33093' => 'sgi', 'SEGI_36110' => 'sgi', 'SEGI_40397' => 'sgi', 'SGA_v2.0_scaffold191G40426' => 'sas', 'SGA_v2.0_scaffold353G49717' => 'sas', 'SGA_v2.0_scaffold50G18550' => 'sas', 'SMO119G0173' => 'smo', 'SMO172G0002' => 'smo', 'Solyc09g082690.3' => 'sly', 'Solyc09g082700.2' => 'sly', 'Sopen09g031550' => 'spe', 'Sopen09g031560' => 'spe', 'Sp3g20540' => 'spa', 'Sp7g07580' => 'spa', 'TAR134G0002' => 'tar', 'TAR236G0001' => 'tar', 'TAR365G0892' => 'tar', 'TAR636G0166' => 'tar', 'TAR636G0646' => 'tar', 'TAR636G0869' => 'tar', 'TAR636G1317' => 'tar', 'TAR636G1744' => 'tar', 'TAR636G3358' => 'tar', 'TAR636G3436' => 'tar', 'THA.LOC104803047' => 'tha', 'Thecc.04G238900' => 'tca', 'Thhalv10021557m.g' => 'esa', 'Thhalv10026318m.g' => 'esa', 'Thhalv10026335m.g' => 'esa', 'TPR.G17433' => 'tpr', 'TPR.G18915' => 'tpr', 'TPR.G26125' => 'tpr', 'TWI09G0677' => 'twi', 'TWI73G0287' => 'twi', 'unitig_748.g8326' => 'ugi', 'vmacro15370' => 'vma', 'vmacro15371' => 'vma', 'vmacro15372' => 'vma', 'vmacro15373' => 'vma', 'vmacro15374' => 'vma', 'VMungo0720G2826' => 'vmu', 'Zm00001eb116960' => 'zma', 'Zm00001eb301260' => 'zma', 'Zm00001eb301270' => 'zma' ) $gf_id = 'HOM05D001460' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001460' ) $data_identifier = 'HOM05D001460' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 4, 'aag' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 2, 'aox' => (int) 2, 'arhy' => (int) 4, 'ath' => (int) 2, 'atr' => (int) 1, 'acertr' => (int) 10, 'cqu' => (int) 4, 'bca' => (int) 11, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 1, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 1, 'ccan' => (int) 1, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 1, 'col' => (int) 1, 'cpa' => (int) 1, 'cre' => (int) 7, 'csa' => (int) 1, 'camsi' => (int) 2, 'dca' => (int) 3, 'din' => (int) 2, 'dzi' => (int) 3, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 14, 'fve' => (int) 9, 'gma' => (int) 2, 'ghi' => (int) 4, 'gra' => (int) 2, 'vvi' => (int) 1, 'han' => (int) 13, 'cav' => (int) 1, 'hma' => (int) 2, 'sun' => (int) 2, 'lal' => (int) 2, 'lonja' => (int) 12, 'lja' => (int) 1, 'lsa' => (int) 7, 'mes' => (int) 1, 'mpo' => (int) 27, 'mbi' => (int) 1, 'mco' => (int) 8, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 1, 'egut' => (int) 1, 'ama' => (int) 1, 'nta' => (int) 4, 'nnu' => (int) 2, 'oeu' => (int) 3, 'osa' => (int) 4, 'pax' => (int) 9, 'pgr' => (int) 1, 'stu' => (int) 1, 'pvu' => (int) 1, 'ptr' => (int) 4, 'ppa' => (int) 22, 'pco' => (int) 6, 'ppe' => (int) 6, 'psa' => (int) 5, 'pso' => (int) 19, 'qlo' => (int) 5, 'rch' => (int) 7, 'rsi' => (int) 20, 'sbr' => (int) 5, 'sbo' => (int) 1, 'sci' => (int) 2, 'sed' => (int) 2, 'sgi' => (int) 12, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 2, 'tar' => (int) 10, 'tha' => (int) 1, 'tca' => (int) 1, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 2, 'ugi' => (int) 1, 'vma' => (int) 5, 'vmu' => (int) 1, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb301270' $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' => 'HOM05D001460', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '433', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p22980' => 'bna', 'A01p32340' => 'bna', 'A03p42970' => 'bna', 'A05p25880' => 'bna', 'Aa31LG8G9320' => 'aar', 'Aa31LG8G9330' => 'aar', 'Aa31LG8G9340' => 'aar', 'Aa31sc221G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1034' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1528' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.829' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2222' => 'aag', 'Ah.12g058830' => 'amhyb', 'Ah.12g058840' => 'amhyb', 'AL3G37160' => 'aly', 'AL7G41310' => 'aly', 'Aqoxy5G00395' => 'aox', 'Aqoxy5G00396' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0C8NZA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5185HY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JZ1PRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MD3LS0' => 'arhy', 'AT3G22840' => 'ath', 'AT4G14690' => 'ath', 'ATR0665G054' => 'atr', 'Atru.chr4.2344' => 'acertr', 'Atru.chr4.2346' => 'acertr', 'Atru.chr4.2347' => 'acertr', 'Atru.chr4.2348' => 'acertr', 'Atru.chr4.2355' => 'acertr', 'Atru.chr4.2356' => 'acertr', 'Atru.chr4.2358' => 'acertr', 'Atru.chr4.2359' => 'acertr', 'Atru.chr4.2360' => 'acertr', 'Atru.chr4.2361' => 'acertr', 'AUR62030476' => 'cqu', 'AUR62030478' => 'cqu', 'AUR62030819' => 'cqu', 'AUR62030820' => 'cqu', 'BcaB03g14648' => 'bca', 'BcaB04g20492' => 'bca', 'BcaB06g26399' => 'bca', 'BcaC01g03416' => 'bca', 'BcaC01g03419' => 'bca', 'BcaC01g03421' => 'bca', 'BcaC01g03424' => 'bca', 'BcaC05g28012' => 'bca', 'BcaC09g49212' => 'bca', 'BcaC09g50140' => 'bca', 'BcaNung00346' => 'bca', 'BolC1t02785H' => 'bol', 'BolC1t04095H' => 'bol', 'BolC3t17545H' => 'bol', 'BolC5t32769H' => 'bol', 'BraA01t02211Z' => 'bra', 'BraA01t03359Z' => 'bra', 'BraA03t13441Z' => 'bra', 'BraA05t21476Z' => 'bra', 'C01p28420' => 'bna', 'C01p41350' => 'bna', 'C03p52750' => 'bna', 'C03p52780' => 'bna', 'C05p40270' => 'bna', 'CAN.G1437.9' => 'can', 'CANSAT78G0035' => 'cansat', 'CANSAT78G1036' => 'cansat', 'CANSAT78G2272' => 'cansat', 'CANSAT78G2478' => 'cansat', 'CARHR098700' => 'chi', 'CARHR221120' => 'chi', 'CARHR221150' => 'chi', 'Carub.0003s2297' => 'cru', 'Carub.0007s2749' => 'cru', 'Carub.0007s2750' => 'cru', 'Carub.0007s2751' => 'cru', 'Ca_10849_v3' => 'car', 'Cc03_g04300' => 'ccan', 'CDE02G3648' => 'cde', 'CDE05G0060' => 'cde', 'CDE05G0692' => 'cde', 'CDE05G2285' => 'cde', 'CDE05G2884' => 'cde', 'CDE05G3072' => 'cde', 'Cfa008439' => 'cfa', 'Cfa008441' => 'cfa', 'Cfa008443' => 'cfa', 'Cfa008448' => 'cfa', 'Ciclev10005974m.g' => 'ccl', 'Ciclev10006006m.g' => 'ccl', 'Ciclev10006775m.g' => 'ccl', 'CiPaw.02G120400' => 'cil', 'CiPaw.02G120500' => 'cil', 'CiPaw.02G120600' => 'cil', 'ClCG05G004850' => 'cla', 'COL.COLO4_21566' => 'col', 'Cpa.g.sc44.124' => 'cpa', 'Cre07.g320400' => 'cre', 'Cre07.g320450' => 'cre', 'Cre08.g384650' => 'cre', 'Cre09.g393173' => 'cre', 'Cre09.g394325' => 'cre', 'Cre14.g626750' => 'cre', 'Cre16.g679250' => 'cre', 'CsaV3_3G012890' => 'csa', 'CSS0010865' => 'camsi', 'CSS0044338' => 'camsi', 'DCAR_002366' => 'dca', 'DCAR_030687' => 'dca', 'DCAR_030688' => 'dca', 'Dinv14047' => 'din', 'Dinv14048' => 'din', 'Duzib151G0105' => 'dzi', 'Duzib151G0114' => 'dzi', 'Duzib212G1029' => 'dzi', 'ECA232G3536' => 'eca', 'ECA240G0786' => 'eca', 'ECA240G1802' => 'eca', 'ECA240G3760' => 'eca', 'ECA240G3920' => 'eca', 'EL10Ac5g12536' => 'bvu', 'EL10Ac5g12537' => 'bvu', 'EL10Ac5g12538' => 'bvu', 'Eucgr.B01004' => 'egr', 'Eucgr.B01006' => 'egr', 'Eucgr.B01007' => 'egr', 'Eucgr.B01008' => 'egr', 'Eucgr.B01895' => 'egr', 'Eucgr.B01896' => 'egr', 'FAN04G1456' => 'fan', 'FAN08G1769' => 'fan', 'FAN08G2160' => 'fan', 'FAN13G2403' => 'fan', 'FAN13G3303' => 'fan', 'FAN15G2435' => 'fan', 'FAN17G0672' => 'fan', 'FAN17G2441' => 'fan', 'FAN18G1024' => 'fan', 'FAN22G1458' => 'fan', 'FAN24G0037' => 'fan', 'FAN24G0429' => 'fan', 'FAN24G2387' => 'fan', 'FAN27G2746' => 'fan', 'FvH4_2g20400' => 'fve', 'FvH4_2g20420' => 'fve', 'FvH4_2g20430' => 'fve', 'FvH4_4g01270' => 'fve', 'FvH4_4g01290' => 'fve', 'FvH4_4g01300' => 'fve', 'FvH4_4g01310' => 'fve', 'FvH4_4g01330' => 'fve', 'FvH4_5g09070' => 'fve', 'Glyma.10G243800' => 'gma', 'Glyma.20G150600' => 'gma', 'Gohir.A09G219200' => 'ghi', 'Gohir.A09G219300' => 'ghi', 'Gohir.D09G221400' => 'ghi', 'Gohir.D09G221500' => 'ghi', 'Gorai.006G242600' => 'gra', 'Gorai.006G242700' => 'gra', 'GSVIVG01018044001' => 'vvi', 'HanXRQChr03g0083821' => 'han', 'HanXRQChr03g0083841' => 'han', 'HanXRQChr03g0083881' => 'han', 'HanXRQChr03g0083901' => 'han', 'HanXRQChr03g0083921' => 'han', 'HanXRQChr03g0085331' => 'han', 'HanXRQChr03g0085361' => 'han', 'HanXRQChr03g0085411' => 'han', 'HanXRQChr03g0085421' => 'han', 'HanXRQChr03g0085431' => 'han', 'HanXRQChr08g0221991' => 'han', 'HanXRQChr11g0336061' => 'han', 'HanXRQChr11g0336411' => 'han', 'Haze_11234' => 'cav', 'Hma1.2p1_0549F.1_g177010' => 'hma', 'Hma1.2p1_0602F.1_g187630' => 'hma', 'Hund14876' => 'sun', 'Hund14879' => 'sun', 'Lalb_Chr06g0160741' => 'lal', 'Lalb_Chr21g0304781' => 'lal', 'Lj3A726G19' => 'lonja', 'Lj3A726T23' => 'lonja', 'Lj3A726T24' => 'lonja', 'Lj3A726T25' => 'lonja', 'Lj3A727T17' => 'lonja', 'Lj3C726T0' => 'lonja', 'Lj3C726T2' => 'lonja', 'Lj3P725T35' => 'lonja', 'Lj3P727T10' => 'lonja', 'Lj3P727T12' => 'lonja', 'Lj3P727T14' => 'lonja', 'Lj5g0023109' => 'lja', 'Lj6P646T44' => 'lonja', 'Lsat_1_v5_gn_6_75760' => 'lsa', 'Lsat_1_v5_gn_6_75800' => 'lsa', 'Lsat_1_v5_gn_6_75900' => 'lsa', 'Lsat_1_v5_gn_6_76240' => 'lsa', 'Lsat_1_v5_gn_6_76441' => 'lsa', 'Lsat_1_v5_gn_6_76700' => 'lsa', 'Lsat_1_v5_gn_6_76760' => 'lsa', 'Manes.15G033100' => 'mes', 'Mapoly0004s0074' => 'mpo', 'Mapoly0004s0075' => 'mpo', 'Mapoly0004s0163' => 'mpo', 'Mapoly0004s0164' => 'mpo', 'Mapoly0021s0018' => 'mpo', 'Mapoly0041s0136' => 'mpo', 'Mapoly0041s0137' => 'mpo', 'Mapoly0041s0138' => 'mpo', 'Mapoly0041s0139' => 'mpo', 'Mapoly0041s0141' => 'mpo', 'Mapoly0041s0142' => 'mpo', 'Mapoly0041s0143' => 'mpo', 'Mapoly0041s0144' => 'mpo', 'Mapoly0041s0145' => 'mpo', 'Mapoly0047s0106' => 'mpo', 'Mapoly0047s0108' => 'mpo', 'Mapoly0050s0051' => 'mpo', 'Mapoly0050s0052' => 'mpo', 'Mapoly0050s0053' => 'mpo', 'Mapoly0058s0013' => 'mpo', 'Mapoly0091s0078' => 'mpo', 'Mapoly0091s0079' => 'mpo', 'Mapoly0091s0080' => 'mpo', 'Mapoly0091s0081' => 'mpo', 'Mapoly0278s0004' => 'mpo', 'Mapoly0278s0005' => 'mpo', 'Mapoly0278s0006' => 'mpo', 'MBI11_g30648_MAGBIO' => 'mbi', 'MCO03G194' => 'mco', 'MCO03G590' => 'mco', 'MCO07G312' => 'mco', 'MCO10G318' => 'mco', 'MCO12G244' => 'mco', 'MCO13G148' => 'mco', 'MCO13G194' => 'mco', 'MCO16G238' => 'mco', 'MD06G1134100' => 'mdo', 'MD13G1200100' => 'mdo', 'MD13G1200300' => 'mdo', 'MD13G1200600' => 'mdo', 'MD14G1150400' => 'mdo', 'MD16G1200000' => 'mdo', 'Medtr1g102570' => 'mtr', 'Medtr1g102780' => 'mtr', 'Medtr1g102800' => 'mtr', 'Medtr1g102810' => 'mtr', 'Medtr1g102830' => 'mtr', 'MELO3C006499.2' => 'cme', 'Migut.G00385' => 'egut', 'MSTRG.4063' => 'ama', 'Nitab4.5_0000090g0260' => 'nta', 'Nitab4.5_0000977g0030' => 'nta', 'Nitab4.5_0002541g0040' => 'nta', 'Nitab4.5_0007068g0040' => 'nta', 'Nn005s41408' => 'nnu', 'Nn005s41410' => 'nnu', 'Oeu010310.1' => 'oeu', 'Oeu010311.1' => 'oeu', 'Oeu043472.1' => 'oeu', 'Os01g0246400' => 'osa', 'Os04g0267950' => 'osa', 'Os07g0178700' => 'osa', 'Os07g0178800' => 'osa', 'Peaxi162Scf00316g00046' => 'pax', 'Peaxi162Scf00316g00049' => 'pax', 'Peaxi162Scf00316g00059' => 'pax', 'Peaxi162Scf00316g00328' => 'pax', 'Peaxi162Scf00316g00329' => 'pax', 'Peaxi162Scf00316g00411' => 'pax', 'Peaxi162Scf00316g00521' => 'pax', 'Peaxi162Scf00492g00068' => 'pax', 'Peaxi162Scf35631g00002' => 'pax', 'PGR142G3720' => 'pgr', 'PGSC0003DMG400006442' => 'stu', 'Phvul.007G062000' => 'pvu', 'Potri.008G157750' => 'ptr', 'Potri.008G157900' => 'ptr', 'Potri.008G158000' => 'ptr', 'Potri.008G158200' => 'ptr', 'Pp3c11_7280' => 'ppa', 'Pp3c11_7980' => 'ppa', 'Pp3c12_19450' => 'ppa', 'Pp3c14_1480' => 'ppa', 'Pp3c14_1501' => 'ppa', 'Pp3c16_4900' => 'ppa', 'Pp3c16_5010' => 'ppa', 'Pp3c16_5060' => 'ppa', 'Pp3c19_18250' => 'ppa', 'Pp3c23_8530' => 'ppa', 'Pp3c23_8550' => 'ppa', 'Pp3c24_9670' => 'ppa', 'Pp3c2_21390' => 'ppa', 'Pp3c2_31380' => 'ppa', 'Pp3c3_16620' => 'ppa', 'Pp3c3_8090' => 'ppa', 'Pp3c3_8110' => 'ppa', 'Pp3c3_8130' => 'ppa', 'Pp3c3_8150' => 'ppa', 'Pp3c4_14320' => 'ppa', 'Pp3c6_2560' => 'ppa', 'Pp3c9_16700' => 'ppa', 'PRCOL_00000234' => 'pco', 'PRCOL_00000235' => 'pco', 'PRCOL_00000777' => 'pco', 'PRCOL_00002344' => 'pco', 'PRCOL_00002372' => 'pco', 'PRCOL_00006120' => 'pco', 'Prupe.1G021400' => 'ppe', 'Prupe.1G021500' => 'ppe', 'Prupe.1G021600' => 'ppe', 'Prupe.1G021700' => 'ppe', 'Prupe.1G021800' => 'ppe', 'Prupe.5G145100' => 'ppe', 'Psat6g204040' => 'psa', 'Psat6g204800' => 'psa', 'Psat6g204920' => 'psa', 'Psat6g204960' => 'psa', 'Psat6g205080' => 'psa', 'PSO017G0271' => 'pso', 'PSO017G1276' => 'pso', 'PSO017G1429' => 'pso', 'PSO017G1861' => 'pso', 'PSO017G2787' => 'pso', 'PSO017G4466' => 'pso', 'PSO017G5118' => 'pso', 'PSO017G5420' => 'pso', 'PSO063G3678' => 'pso', 'PSO210G0546' => 'pso', 'PSO317G0001' => 'pso', 'PSO357G0512' => 'pso', 'PSO478G2682' => 'pso', 'PSO647G0001' => 'pso', 'PSO675G0001' => 'pso', 'PSO675G2699' => 'pso', 'PSO675G2849' => 'pso', 'PSO675G4991' => 'pso', 'PSO689G0001' => 'pso', 'QL06p000916' => 'qlo', 'QL06p000921' => 'qlo', 'QL06p001398' => 'qlo', 'QL06p001407' => 'qlo', 'QL06p002031' => 'qlo', 'RcHm_v2.0_Chr4g0387791' => 'rch', 'RcHm_v2.0_Chr4g0387801' => 'rch', 'RcHm_v2.0_Chr6g0286501' => 'rch', 'RcHm_v2.0_Chr6g0286511' => 'rch', 'RcHm_v2.0_Chr6g0286521' => 'rch', 'RcHm_v2.0_Chr6g0286531' => 'rch', 'RcHm_v2.0_Chr7g0189141' => 'rch', 'Rhsim02G0028700' => 'rsi', 'Rhsim02G0028800' => 'rsi', 'Rhsim02G0028900' => 'rsi', 'Rhsim02G0029000' => 'rsi', 'Rhsim02G0029100' => 'rsi', 'Rhsim02G0029200' => 'rsi', 'Rhsim02G0029300' => 'rsi', 'Rhsim02G0029400' => 'rsi', 'Rhsim02G0029500' => 'rsi', 'Rhsim02G0029600' => 'rsi', 'RhsimUnG0024000' => 'rsi', 'RhsimUnG0024100' => 'rsi', 'RhsimUnG0024200' => 'rsi', 'RhsimUnG0024300' => 'rsi', 'RhsimUnG0024400' => 'rsi', 'RhsimUnG0024500' => 'rsi', 'RhsimUnG0024700' => 'rsi', 'RhsimUnG0024800' => 'rsi', 'RhsimUnG0024900' => 'rsi', 'RhsimUnG0025100' => 'rsi', 'Sabra08G0120200' => 'sbr', 'Sabra08G0120300' => 'sbr', 'Sabra08G0120500' => 'sbr', 'Sabra08G0120600' => 'sbr', 'Sabra10G0158900' => 'sbr', 'SalBow2G3492' => 'sbo', 'Sc13g0004760' => 'sci', 'Sc13g0004770' => 'sci', 'Sed0003417' => 'sed', 'Sed0019750' => 'sed', 'SEGI_03419' => 'sgi', 'SEGI_05907' => 'sgi', 'SEGI_10682' => 'sgi', 'SEGI_13528' => 'sgi', 'SEGI_16081' => 'sgi', 'SEGI_19370' => 'sgi', 'SEGI_21015' => 'sgi', 'SEGI_21944' => 'sgi', 'SEGI_32906' => 'sgi', 'SEGI_33093' => 'sgi', 'SEGI_36110' => 'sgi', 'SEGI_40397' => 'sgi', 'SGA_v2.0_scaffold191G40426' => 'sas', 'SGA_v2.0_scaffold353G49717' => 'sas', 'SGA_v2.0_scaffold50G18550' => 'sas', 'SMO119G0173' => 'smo', 'SMO172G0002' => 'smo', 'Solyc09g082690.3' => 'sly', 'Solyc09g082700.2' => 'sly', 'Sopen09g031550' => 'spe', 'Sopen09g031560' => 'spe', 'Sp3g20540' => 'spa', 'Sp7g07580' => 'spa', 'TAR134G0002' => 'tar', 'TAR236G0001' => 'tar', 'TAR365G0892' => 'tar', 'TAR636G0166' => 'tar', 'TAR636G0646' => 'tar', 'TAR636G0869' => 'tar', 'TAR636G1317' => 'tar', 'TAR636G1744' => 'tar', 'TAR636G3358' => 'tar', 'TAR636G3436' => 'tar', 'THA.LOC104803047' => 'tha', 'Thecc.04G238900' => 'tca', 'Thhalv10021557m.g' => 'esa', 'Thhalv10026318m.g' => 'esa', 'Thhalv10026335m.g' => 'esa', 'TPR.G17433' => 'tpr', 'TPR.G18915' => 'tpr', 'TPR.G26125' => 'tpr', 'TWI09G0677' => 'twi', 'TWI73G0287' => 'twi', 'unitig_748.g8326' => 'ugi', 'vmacro15370' => 'vma', 'vmacro15371' => 'vma', 'vmacro15372' => 'vma', 'vmacro15373' => 'vma', 'vmacro15374' => 'vma', 'VMungo0720G2826' => 'vmu', 'Zm00001eb116960' => 'zma', 'Zm00001eb301260' => 'zma', 'Zm00001eb301270' => 'zma' ), 'gf_id' => 'HOM05D001460', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001460' ), 'data_identifier' => 'HOM05D001460', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001460', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '433', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p22980' => 'bna', 'A01p32340' => 'bna', 'A03p42970' => 'bna', 'A05p25880' => 'bna', 'Aa31LG8G9320' => 'aar', 'Aa31LG8G9330' => 'aar', 'Aa31LG8G9340' => 'aar', 'Aa31sc221G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1034' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1528' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.829' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2222' => 'aag', 'Ah.12g058830' => 'amhyb', 'Ah.12g058840' => 'amhyb', 'AL3G37160' => 'aly', 'AL7G41310' => 'aly', 'Aqoxy5G00395' => 'aox', 'Aqoxy5G00396' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0C8NZA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5185HY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JZ1PRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MD3LS0' => 'arhy', 'AT3G22840' => 'ath', 'AT4G14690' => 'ath', 'ATR0665G054' => 'atr', 'Atru.chr4.2344' => 'acertr', 'Atru.chr4.2346' => 'acertr', 'Atru.chr4.2347' => 'acertr', 'Atru.chr4.2348' => 'acertr', 'Atru.chr4.2355' => 'acertr', 'Atru.chr4.2356' => 'acertr', 'Atru.chr4.2358' => 'acertr', 'Atru.chr4.2359' => 'acertr', 'Atru.chr4.2360' => 'acertr', 'Atru.chr4.2361' => 'acertr', 'AUR62030476' => 'cqu', 'AUR62030478' => 'cqu', 'AUR62030819' => 'cqu', 'AUR62030820' => 'cqu', 'BcaB03g14648' => 'bca', 'BcaB04g20492' => 'bca', 'BcaB06g26399' => 'bca', 'BcaC01g03416' => 'bca', 'BcaC01g03419' => 'bca', 'BcaC01g03421' => 'bca', 'BcaC01g03424' => 'bca', 'BcaC05g28012' => 'bca', 'BcaC09g49212' => 'bca', 'BcaC09g50140' => 'bca', 'BcaNung00346' => 'bca', 'BolC1t02785H' => 'bol', 'BolC1t04095H' => 'bol', 'BolC3t17545H' => 'bol', 'BolC5t32769H' => 'bol', 'BraA01t02211Z' => 'bra', 'BraA01t03359Z' => 'bra', 'BraA03t13441Z' => 'bra', 'BraA05t21476Z' => 'bra', 'C01p28420' => 'bna', 'C01p41350' => 'bna', 'C03p52750' => 'bna', 'C03p52780' => 'bna', 'C05p40270' => 'bna', 'CAN.G1437.9' => 'can', 'CANSAT78G0035' => 'cansat', 'CANSAT78G1036' => 'cansat', 'CANSAT78G2272' => 'cansat', 'CANSAT78G2478' => 'cansat', 'CARHR098700' => 'chi', 'CARHR221120' => 'chi', 'CARHR221150' => 'chi', 'Carub.0003s2297' => 'cru', 'Carub.0007s2749' => 'cru', 'Carub.0007s2750' => 'cru', 'Carub.0007s2751' => 'cru', 'Ca_10849_v3' => 'car', 'Cc03_g04300' => 'ccan', 'CDE02G3648' => 'cde', 'CDE05G0060' => 'cde', 'CDE05G0692' => 'cde', 'CDE05G2285' => 'cde', 'CDE05G2884' => 'cde', 'CDE05G3072' => 'cde', 'Cfa008439' => 'cfa', 'Cfa008441' => 'cfa', 'Cfa008443' => 'cfa', 'Cfa008448' => 'cfa', 'Ciclev10005974m.g' => 'ccl', 'Ciclev10006006m.g' => 'ccl', 'Ciclev10006775m.g' => 'ccl', 'CiPaw.02G120400' => 'cil', 'CiPaw.02G120500' => 'cil', 'CiPaw.02G120600' => 'cil', 'ClCG05G004850' => 'cla', 'COL.COLO4_21566' => 'col', 'Cpa.g.sc44.124' => 'cpa', 'Cre07.g320400' => 'cre', 'Cre07.g320450' => 'cre', 'Cre08.g384650' => 'cre', 'Cre09.g393173' => 'cre', 'Cre09.g394325' => 'cre', 'Cre14.g626750' => 'cre', 'Cre16.g679250' => 'cre', 'CsaV3_3G012890' => 'csa', 'CSS0010865' => 'camsi', 'CSS0044338' => 'camsi', 'DCAR_002366' => 'dca', 'DCAR_030687' => 'dca', 'DCAR_030688' => 'dca', 'Dinv14047' => 'din', 'Dinv14048' => 'din', 'Duzib151G0105' => 'dzi', 'Duzib151G0114' => 'dzi', 'Duzib212G1029' => 'dzi', 'ECA232G3536' => 'eca', 'ECA240G0786' => 'eca', 'ECA240G1802' => 'eca', 'ECA240G3760' => 'eca', 'ECA240G3920' => 'eca', 'EL10Ac5g12536' => 'bvu', 'EL10Ac5g12537' => 'bvu', 'EL10Ac5g12538' => 'bvu', 'Eucgr.B01004' => 'egr', 'Eucgr.B01006' => 'egr', 'Eucgr.B01007' => 'egr', 'Eucgr.B01008' => 'egr', 'Eucgr.B01895' => 'egr', 'Eucgr.B01896' => 'egr', 'FAN04G1456' => 'fan', 'FAN08G1769' => 'fan', 'FAN08G2160' => 'fan', 'FAN13G2403' => 'fan', 'FAN13G3303' => 'fan', 'FAN15G2435' => 'fan', 'FAN17G0672' => 'fan', 'FAN17G2441' => 'fan', 'FAN18G1024' => 'fan', 'FAN22G1458' => 'fan', 'FAN24G0037' => 'fan', 'FAN24G0429' => 'fan', 'FAN24G2387' => 'fan', 'FAN27G2746' => 'fan', 'FvH4_2g20400' => 'fve', 'FvH4_2g20420' => 'fve', 'FvH4_2g20430' => 'fve', 'FvH4_4g01270' => 'fve', 'FvH4_4g01290' => 'fve', 'FvH4_4g01300' => 'fve', 'FvH4_4g01310' => 'fve', 'FvH4_4g01330' => 'fve', 'FvH4_5g09070' => 'fve', 'Glyma.10G243800' => 'gma', 'Glyma.20G150600' => 'gma', 'Gohir.A09G219200' => 'ghi', 'Gohir.A09G219300' => 'ghi', 'Gohir.D09G221400' => 'ghi', 'Gohir.D09G221500' => 'ghi', 'Gorai.006G242600' => 'gra', 'Gorai.006G242700' => 'gra', 'GSVIVG01018044001' => 'vvi', 'HanXRQChr03g0083821' => 'han', 'HanXRQChr03g0083841' => 'han', 'HanXRQChr03g0083881' => 'han', 'HanXRQChr03g0083901' => 'han', 'HanXRQChr03g0083921' => 'han', 'HanXRQChr03g0085331' => 'han', 'HanXRQChr03g0085361' => 'han', 'HanXRQChr03g0085411' => 'han', 'HanXRQChr03g0085421' => 'han', 'HanXRQChr03g0085431' => 'han', 'HanXRQChr08g0221991' => 'han', 'HanXRQChr11g0336061' => 'han', 'HanXRQChr11g0336411' => 'han', 'Haze_11234' => 'cav', 'Hma1.2p1_0549F.1_g177010' => 'hma', 'Hma1.2p1_0602F.1_g187630' => 'hma', 'Hund14876' => 'sun', 'Hund14879' => 'sun', 'Lalb_Chr06g0160741' => 'lal', 'Lalb_Chr21g0304781' => 'lal', 'Lj3A726G19' => 'lonja', 'Lj3A726T23' => 'lonja', 'Lj3A726T24' => 'lonja', 'Lj3A726T25' => 'lonja', 'Lj3A727T17' => 'lonja', 'Lj3C726T0' => 'lonja', 'Lj3C726T2' => 'lonja', 'Lj3P725T35' => 'lonja', 'Lj3P727T10' => 'lonja', 'Lj3P727T12' => 'lonja', 'Lj3P727T14' => 'lonja', 'Lj5g0023109' => 'lja', 'Lj6P646T44' => 'lonja', 'Lsat_1_v5_gn_6_75760' => 'lsa', 'Lsat_1_v5_gn_6_75800' => 'lsa', 'Lsat_1_v5_gn_6_75900' => 'lsa', 'Lsat_1_v5_gn_6_76240' => 'lsa', 'Lsat_1_v5_gn_6_76441' => 'lsa', 'Lsat_1_v5_gn_6_76700' => 'lsa', 'Lsat_1_v5_gn_6_76760' => 'lsa', 'Manes.15G033100' => 'mes', 'Mapoly0004s0074' => 'mpo', 'Mapoly0004s0075' => 'mpo', 'Mapoly0004s0163' => 'mpo', 'Mapoly0004s0164' => 'mpo', 'Mapoly0021s0018' => 'mpo', 'Mapoly0041s0136' => 'mpo', 'Mapoly0041s0137' => 'mpo', 'Mapoly0041s0138' => 'mpo', 'Mapoly0041s0139' => 'mpo', 'Mapoly0041s0141' => 'mpo', 'Mapoly0041s0142' => 'mpo', 'Mapoly0041s0143' => 'mpo', 'Mapoly0041s0144' => 'mpo', 'Mapoly0041s0145' => 'mpo', 'Mapoly0047s0106' => 'mpo', 'Mapoly0047s0108' => 'mpo', 'Mapoly0050s0051' => 'mpo', 'Mapoly0050s0052' => 'mpo', 'Mapoly0050s0053' => 'mpo', 'Mapoly0058s0013' => 'mpo', 'Mapoly0091s0078' => 'mpo', 'Mapoly0091s0079' => 'mpo', 'Mapoly0091s0080' => 'mpo', 'Mapoly0091s0081' => 'mpo', 'Mapoly0278s0004' => 'mpo', 'Mapoly0278s0005' => 'mpo', 'Mapoly0278s0006' => 'mpo', 'MBI11_g30648_MAGBIO' => 'mbi', 'MCO03G194' => 'mco', 'MCO03G590' => 'mco', 'MCO07G312' => 'mco', 'MCO10G318' => 'mco', 'MCO12G244' => 'mco', 'MCO13G148' => 'mco', 'MCO13G194' => 'mco', 'MCO16G238' => 'mco', 'MD06G1134100' => 'mdo', 'MD13G1200100' => 'mdo', 'MD13G1200300' => 'mdo', 'MD13G1200600' => 'mdo', 'MD14G1150400' => 'mdo', 'MD16G1200000' => 'mdo', 'Medtr1g102570' => 'mtr', 'Medtr1g102780' => 'mtr', 'Medtr1g102800' => 'mtr', 'Medtr1g102810' => 'mtr', 'Medtr1g102830' => 'mtr', 'MELO3C006499.2' => 'cme', 'Migut.G00385' => 'egut', 'MSTRG.4063' => 'ama', 'Nitab4.5_0000090g0260' => 'nta', 'Nitab4.5_0000977g0030' => 'nta', 'Nitab4.5_0002541g0040' => 'nta', 'Nitab4.5_0007068g0040' => 'nta', 'Nn005s41408' => 'nnu', 'Nn005s41410' => 'nnu', 'Oeu010310.1' => 'oeu', 'Oeu010311.1' => 'oeu', 'Oeu043472.1' => 'oeu', 'Os01g0246400' => 'osa', 'Os04g0267950' => 'osa', 'Os07g0178700' => 'osa', 'Os07g0178800' => 'osa', 'Peaxi162Scf00316g00046' => 'pax', 'Peaxi162Scf00316g00049' => 'pax', 'Peaxi162Scf00316g00059' => 'pax', 'Peaxi162Scf00316g00328' => 'pax', 'Peaxi162Scf00316g00329' => 'pax', 'Peaxi162Scf00316g00411' => 'pax', 'Peaxi162Scf00316g00521' => 'pax', 'Peaxi162Scf00492g00068' => 'pax', 'Peaxi162Scf35631g00002' => 'pax', 'PGR142G3720' => 'pgr', 'PGSC0003DMG400006442' => 'stu', 'Phvul.007G062000' => 'pvu', 'Potri.008G157750' => 'ptr', 'Potri.008G157900' => 'ptr', 'Potri.008G158000' => 'ptr', 'Potri.008G158200' => 'ptr', 'Pp3c11_7280' => 'ppa', 'Pp3c11_7980' => 'ppa', 'Pp3c12_19450' => 'ppa', 'Pp3c14_1480' => 'ppa', 'Pp3c14_1501' => 'ppa', 'Pp3c16_4900' => 'ppa', 'Pp3c16_5010' => 'ppa', 'Pp3c16_5060' => 'ppa', 'Pp3c19_18250' => 'ppa', 'Pp3c23_8530' => 'ppa', 'Pp3c23_8550' => 'ppa', 'Pp3c24_9670' => 'ppa', 'Pp3c2_21390' => 'ppa', 'Pp3c2_31380' => 'ppa', 'Pp3c3_16620' => 'ppa', 'Pp3c3_8090' => 'ppa', 'Pp3c3_8110' => 'ppa', 'Pp3c3_8130' => 'ppa', 'Pp3c3_8150' => 'ppa', 'Pp3c4_14320' => 'ppa', 'Pp3c6_2560' => 'ppa', 'Pp3c9_16700' => 'ppa', 'PRCOL_00000234' => 'pco', 'PRCOL_00000235' => 'pco', 'PRCOL_00000777' => 'pco', 'PRCOL_00002344' => 'pco', 'PRCOL_00002372' => 'pco', 'PRCOL_00006120' => 'pco', 'Prupe.1G021400' => 'ppe', 'Prupe.1G021500' => 'ppe', 'Prupe.1G021600' => 'ppe', 'Prupe.1G021700' => 'ppe', 'Prupe.1G021800' => 'ppe', 'Prupe.5G145100' => 'ppe', 'Psat6g204040' => 'psa', 'Psat6g204800' => 'psa', 'Psat6g204920' => 'psa', 'Psat6g204960' => 'psa', 'Psat6g205080' => 'psa', 'PSO017G0271' => 'pso', 'PSO017G1276' => 'pso', 'PSO017G1429' => 'pso', 'PSO017G1861' => 'pso', 'PSO017G2787' => 'pso', 'PSO017G4466' => 'pso', 'PSO017G5118' => 'pso', 'PSO017G5420' => 'pso', 'PSO063G3678' => 'pso', 'PSO210G0546' => 'pso', 'PSO317G0001' => 'pso', 'PSO357G0512' => 'pso', 'PSO478G2682' => 'pso', 'PSO647G0001' => 'pso', 'PSO675G0001' => 'pso', 'PSO675G2699' => 'pso', 'PSO675G2849' => 'pso', 'PSO675G4991' => 'pso', 'PSO689G0001' => 'pso', 'QL06p000916' => 'qlo', 'QL06p000921' => 'qlo', 'QL06p001398' => 'qlo', 'QL06p001407' => 'qlo', 'QL06p002031' => 'qlo', 'RcHm_v2.0_Chr4g0387791' => 'rch', 'RcHm_v2.0_Chr4g0387801' => 'rch', 'RcHm_v2.0_Chr6g0286501' => 'rch', 'RcHm_v2.0_Chr6g0286511' => 'rch', 'RcHm_v2.0_Chr6g0286521' => 'rch', 'RcHm_v2.0_Chr6g0286531' => 'rch', 'RcHm_v2.0_Chr7g0189141' => 'rch', 'Rhsim02G0028700' => 'rsi', 'Rhsim02G0028800' => 'rsi', 'Rhsim02G0028900' => 'rsi', 'Rhsim02G0029000' => 'rsi', 'Rhsim02G0029100' => 'rsi', 'Rhsim02G0029200' => 'rsi', 'Rhsim02G0029300' => 'rsi', 'Rhsim02G0029400' => 'rsi', 'Rhsim02G0029500' => 'rsi', 'Rhsim02G0029600' => 'rsi', 'RhsimUnG0024000' => 'rsi', 'RhsimUnG0024100' => 'rsi', 'RhsimUnG0024200' => 'rsi', 'RhsimUnG0024300' => 'rsi', 'RhsimUnG0024400' => 'rsi', 'RhsimUnG0024500' => 'rsi', 'RhsimUnG0024700' => 'rsi', 'RhsimUnG0024800' => 'rsi', 'RhsimUnG0024900' => 'rsi', 'RhsimUnG0025100' => 'rsi', 'Sabra08G0120200' => 'sbr', 'Sabra08G0120300' => 'sbr', 'Sabra08G0120500' => 'sbr', 'Sabra08G0120600' => 'sbr', 'Sabra10G0158900' => 'sbr', 'SalBow2G3492' => 'sbo', 'Sc13g0004760' => 'sci', 'Sc13g0004770' => 'sci', 'Sed0003417' => 'sed', 'Sed0019750' => 'sed', 'SEGI_03419' => 'sgi', 'SEGI_05907' => 'sgi', 'SEGI_10682' => 'sgi', 'SEGI_13528' => 'sgi', 'SEGI_16081' => 'sgi', 'SEGI_19370' => 'sgi', 'SEGI_21015' => 'sgi', 'SEGI_21944' => 'sgi', 'SEGI_32906' => 'sgi', 'SEGI_33093' => 'sgi', 'SEGI_36110' => 'sgi', 'SEGI_40397' => 'sgi', 'SGA_v2.0_scaffold191G40426' => 'sas', 'SGA_v2.0_scaffold353G49717' => 'sas', 'SGA_v2.0_scaffold50G18550' => 'sas', 'SMO119G0173' => 'smo', 'SMO172G0002' => 'smo', 'Solyc09g082690.3' => 'sly', 'Solyc09g082700.2' => 'sly', 'Sopen09g031550' => 'spe', 'Sopen09g031560' => 'spe', 'Sp3g20540' => 'spa', 'Sp7g07580' => 'spa', 'TAR134G0002' => 'tar', 'TAR236G0001' => 'tar', 'TAR365G0892' => 'tar', 'TAR636G0166' => 'tar', 'TAR636G0646' => 'tar', 'TAR636G0869' => 'tar', 'TAR636G1317' => 'tar', 'TAR636G1744' => 'tar', 'TAR636G3358' => 'tar', 'TAR636G3436' => 'tar', 'THA.LOC104803047' => 'tha', 'Thecc.04G238900' => 'tca', 'Thhalv10021557m.g' => 'esa', 'Thhalv10026318m.g' => 'esa', 'Thhalv10026335m.g' => 'esa', 'TPR.G17433' => 'tpr', 'TPR.G18915' => 'tpr', 'TPR.G26125' => 'tpr', 'TWI09G0677' => 'twi', 'TWI73G0287' => 'twi', 'unitig_748.g8326' => 'ugi', 'vmacro15370' => 'vma', 'vmacro15371' => 'vma', 'vmacro15372' => 'vma', 'vmacro15373' => 'vma', 'vmacro15374' => 'vma', 'VMungo0720G2826' => 'vmu', 'Zm00001eb116960' => 'zma', 'Zm00001eb301260' => 'zma', 'Zm00001eb301270' => 'zma' ) $gf_id = 'HOM05D001460' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001460' ) $data_identifier = 'HOM05D001460' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 4, 'aag' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 2, 'aox' => (int) 2, 'arhy' => (int) 4, 'ath' => (int) 2, 'atr' => (int) 1, 'acertr' => (int) 10, 'cqu' => (int) 4, 'bca' => (int) 11, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 1, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 1, 'ccan' => (int) 1, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 1, 'col' => (int) 1, 'cpa' => (int) 1, 'cre' => (int) 7, 'csa' => (int) 1, 'camsi' => (int) 2, 'dca' => (int) 3, 'din' => (int) 2, 'dzi' => (int) 3, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 14, 'fve' => (int) 9, 'gma' => (int) 2, 'ghi' => (int) 4, 'gra' => (int) 2, 'vvi' => (int) 1, 'han' => (int) 13, 'cav' => (int) 1, 'hma' => (int) 2, 'sun' => (int) 2, 'lal' => (int) 2, 'lonja' => (int) 12, 'lja' => (int) 1, 'lsa' => (int) 7, 'mes' => (int) 1, 'mpo' => (int) 27, 'mbi' => (int) 1, 'mco' => (int) 8, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 1, 'egut' => (int) 1, 'ama' => (int) 1, 'nta' => (int) 4, 'nnu' => (int) 2, 'oeu' => (int) 3, 'osa' => (int) 4, 'pax' => (int) 9, 'pgr' => (int) 1, 'stu' => (int) 1, 'pvu' => (int) 1, 'ptr' => (int) 4, 'ppa' => (int) 22, 'pco' => (int) 6, 'ppe' => (int) 6, 'psa' => (int) 5, 'pso' => (int) 19, 'qlo' => (int) 5, 'rch' => (int) 7, 'rsi' => (int) 20, 'sbr' => (int) 5, 'sbo' => (int) 1, 'sci' => (int) 2, 'sed' => (int) 2, 'sgi' => (int) 12, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 2, 'tar' => (int) 10, 'tha' => (int) 1, 'tca' => (int) 1, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 2, 'ugi' => (int) 1, 'vma' => (int) 5, 'vmu' => (int) 1, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb301270' $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' => 'HOM05D001460', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '433', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p22980' => 'bna', 'A01p32340' => 'bna', 'A03p42970' => 'bna', 'A05p25880' => 'bna', 'Aa31LG8G9320' => 'aar', 'Aa31LG8G9330' => 'aar', 'Aa31LG8G9340' => 'aar', 'Aa31sc221G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1034' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1528' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.829' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2222' => 'aag', 'Ah.12g058830' => 'amhyb', 'Ah.12g058840' => 'amhyb', 'AL3G37160' => 'aly', 'AL7G41310' => 'aly', 'Aqoxy5G00395' => 'aox', 'Aqoxy5G00396' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0C8NZA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5185HY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JZ1PRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MD3LS0' => 'arhy', 'AT3G22840' => 'ath', 'AT4G14690' => 'ath', 'ATR0665G054' => 'atr', 'Atru.chr4.2344' => 'acertr', 'Atru.chr4.2346' => 'acertr', 'Atru.chr4.2347' => 'acertr', 'Atru.chr4.2348' => 'acertr', 'Atru.chr4.2355' => 'acertr', 'Atru.chr4.2356' => 'acertr', 'Atru.chr4.2358' => 'acertr', 'Atru.chr4.2359' => 'acertr', 'Atru.chr4.2360' => 'acertr', 'Atru.chr4.2361' => 'acertr', 'AUR62030476' => 'cqu', 'AUR62030478' => 'cqu', 'AUR62030819' => 'cqu', 'AUR62030820' => 'cqu', 'BcaB03g14648' => 'bca', 'BcaB04g20492' => 'bca', 'BcaB06g26399' => 'bca', 'BcaC01g03416' => 'bca', 'BcaC01g03419' => 'bca', 'BcaC01g03421' => 'bca', 'BcaC01g03424' => 'bca', 'BcaC05g28012' => 'bca', 'BcaC09g49212' => 'bca', 'BcaC09g50140' => 'bca', 'BcaNung00346' => 'bca', 'BolC1t02785H' => 'bol', 'BolC1t04095H' => 'bol', 'BolC3t17545H' => 'bol', 'BolC5t32769H' => 'bol', 'BraA01t02211Z' => 'bra', 'BraA01t03359Z' => 'bra', 'BraA03t13441Z' => 'bra', 'BraA05t21476Z' => 'bra', 'C01p28420' => 'bna', 'C01p41350' => 'bna', 'C03p52750' => 'bna', 'C03p52780' => 'bna', 'C05p40270' => 'bna', 'CAN.G1437.9' => 'can', 'CANSAT78G0035' => 'cansat', 'CANSAT78G1036' => 'cansat', 'CANSAT78G2272' => 'cansat', 'CANSAT78G2478' => 'cansat', 'CARHR098700' => 'chi', 'CARHR221120' => 'chi', 'CARHR221150' => 'chi', 'Carub.0003s2297' => 'cru', 'Carub.0007s2749' => 'cru', 'Carub.0007s2750' => 'cru', 'Carub.0007s2751' => 'cru', 'Ca_10849_v3' => 'car', 'Cc03_g04300' => 'ccan', 'CDE02G3648' => 'cde', 'CDE05G0060' => 'cde', 'CDE05G0692' => 'cde', 'CDE05G2285' => 'cde', 'CDE05G2884' => 'cde', 'CDE05G3072' => 'cde', 'Cfa008439' => 'cfa', 'Cfa008441' => 'cfa', 'Cfa008443' => 'cfa', 'Cfa008448' => 'cfa', 'Ciclev10005974m.g' => 'ccl', 'Ciclev10006006m.g' => 'ccl', 'Ciclev10006775m.g' => 'ccl', 'CiPaw.02G120400' => 'cil', 'CiPaw.02G120500' => 'cil', 'CiPaw.02G120600' => 'cil', 'ClCG05G004850' => 'cla', 'COL.COLO4_21566' => 'col', 'Cpa.g.sc44.124' => 'cpa', 'Cre07.g320400' => 'cre', 'Cre07.g320450' => 'cre', 'Cre08.g384650' => 'cre', 'Cre09.g393173' => 'cre', 'Cre09.g394325' => 'cre', 'Cre14.g626750' => 'cre', 'Cre16.g679250' => 'cre', 'CsaV3_3G012890' => 'csa', 'CSS0010865' => 'camsi', 'CSS0044338' => 'camsi', 'DCAR_002366' => 'dca', 'DCAR_030687' => 'dca', 'DCAR_030688' => 'dca', 'Dinv14047' => 'din', 'Dinv14048' => 'din', 'Duzib151G0105' => 'dzi', 'Duzib151G0114' => 'dzi', 'Duzib212G1029' => 'dzi', 'ECA232G3536' => 'eca', 'ECA240G0786' => 'eca', 'ECA240G1802' => 'eca', 'ECA240G3760' => 'eca', 'ECA240G3920' => 'eca', 'EL10Ac5g12536' => 'bvu', 'EL10Ac5g12537' => 'bvu', 'EL10Ac5g12538' => 'bvu', 'Eucgr.B01004' => 'egr', 'Eucgr.B01006' => 'egr', 'Eucgr.B01007' => 'egr', 'Eucgr.B01008' => 'egr', 'Eucgr.B01895' => 'egr', 'Eucgr.B01896' => 'egr', 'FAN04G1456' => 'fan', 'FAN08G1769' => 'fan', 'FAN08G2160' => 'fan', 'FAN13G2403' => 'fan', 'FAN13G3303' => 'fan', 'FAN15G2435' => 'fan', 'FAN17G0672' => 'fan', 'FAN17G2441' => 'fan', 'FAN18G1024' => 'fan', 'FAN22G1458' => 'fan', 'FAN24G0037' => 'fan', 'FAN24G0429' => 'fan', 'FAN24G2387' => 'fan', 'FAN27G2746' => 'fan', 'FvH4_2g20400' => 'fve', 'FvH4_2g20420' => 'fve', 'FvH4_2g20430' => 'fve', 'FvH4_4g01270' => 'fve', 'FvH4_4g01290' => 'fve', 'FvH4_4g01300' => 'fve', 'FvH4_4g01310' => 'fve', 'FvH4_4g01330' => 'fve', 'FvH4_5g09070' => 'fve', 'Glyma.10G243800' => 'gma', 'Glyma.20G150600' => 'gma', 'Gohir.A09G219200' => 'ghi', 'Gohir.A09G219300' => 'ghi', 'Gohir.D09G221400' => 'ghi', 'Gohir.D09G221500' => 'ghi', 'Gorai.006G242600' => 'gra', 'Gorai.006G242700' => 'gra', 'GSVIVG01018044001' => 'vvi', 'HanXRQChr03g0083821' => 'han', 'HanXRQChr03g0083841' => 'han', 'HanXRQChr03g0083881' => 'han', 'HanXRQChr03g0083901' => 'han', 'HanXRQChr03g0083921' => 'han', 'HanXRQChr03g0085331' => 'han', 'HanXRQChr03g0085361' => 'han', 'HanXRQChr03g0085411' => 'han', 'HanXRQChr03g0085421' => 'han', 'HanXRQChr03g0085431' => 'han', 'HanXRQChr08g0221991' => 'han', 'HanXRQChr11g0336061' => 'han', 'HanXRQChr11g0336411' => 'han', 'Haze_11234' => 'cav', 'Hma1.2p1_0549F.1_g177010' => 'hma', 'Hma1.2p1_0602F.1_g187630' => 'hma', 'Hund14876' => 'sun', 'Hund14879' => 'sun', 'Lalb_Chr06g0160741' => 'lal', 'Lalb_Chr21g0304781' => 'lal', 'Lj3A726G19' => 'lonja', 'Lj3A726T23' => 'lonja', 'Lj3A726T24' => 'lonja', 'Lj3A726T25' => 'lonja', 'Lj3A727T17' => 'lonja', 'Lj3C726T0' => 'lonja', 'Lj3C726T2' => 'lonja', 'Lj3P725T35' => 'lonja', 'Lj3P727T10' => 'lonja', 'Lj3P727T12' => 'lonja', 'Lj3P727T14' => 'lonja', 'Lj5g0023109' => 'lja', 'Lj6P646T44' => 'lonja', 'Lsat_1_v5_gn_6_75760' => 'lsa', 'Lsat_1_v5_gn_6_75800' => 'lsa', 'Lsat_1_v5_gn_6_75900' => 'lsa', 'Lsat_1_v5_gn_6_76240' => 'lsa', 'Lsat_1_v5_gn_6_76441' => 'lsa', 'Lsat_1_v5_gn_6_76700' => 'lsa', 'Lsat_1_v5_gn_6_76760' => 'lsa', 'Manes.15G033100' => 'mes', 'Mapoly0004s0074' => 'mpo', 'Mapoly0004s0075' => 'mpo', 'Mapoly0004s0163' => 'mpo', 'Mapoly0004s0164' => 'mpo', 'Mapoly0021s0018' => 'mpo', 'Mapoly0041s0136' => 'mpo', 'Mapoly0041s0137' => 'mpo', 'Mapoly0041s0138' => 'mpo', 'Mapoly0041s0139' => 'mpo', 'Mapoly0041s0141' => 'mpo', 'Mapoly0041s0142' => 'mpo', 'Mapoly0041s0143' => 'mpo', 'Mapoly0041s0144' => 'mpo', 'Mapoly0041s0145' => 'mpo', 'Mapoly0047s0106' => 'mpo', 'Mapoly0047s0108' => 'mpo', 'Mapoly0050s0051' => 'mpo', 'Mapoly0050s0052' => 'mpo', 'Mapoly0050s0053' => 'mpo', 'Mapoly0058s0013' => 'mpo', 'Mapoly0091s0078' => 'mpo', 'Mapoly0091s0079' => 'mpo', 'Mapoly0091s0080' => 'mpo', 'Mapoly0091s0081' => 'mpo', 'Mapoly0278s0004' => 'mpo', 'Mapoly0278s0005' => 'mpo', 'Mapoly0278s0006' => 'mpo', 'MBI11_g30648_MAGBIO' => 'mbi', 'MCO03G194' => 'mco', 'MCO03G590' => 'mco', 'MCO07G312' => 'mco', 'MCO10G318' => 'mco', 'MCO12G244' => 'mco', 'MCO13G148' => 'mco', 'MCO13G194' => 'mco', 'MCO16G238' => 'mco', 'MD06G1134100' => 'mdo', 'MD13G1200100' => 'mdo', 'MD13G1200300' => 'mdo', 'MD13G1200600' => 'mdo', 'MD14G1150400' => 'mdo', 'MD16G1200000' => 'mdo', 'Medtr1g102570' => 'mtr', 'Medtr1g102780' => 'mtr', 'Medtr1g102800' => 'mtr', 'Medtr1g102810' => 'mtr', 'Medtr1g102830' => 'mtr', 'MELO3C006499.2' => 'cme', 'Migut.G00385' => 'egut', 'MSTRG.4063' => 'ama', 'Nitab4.5_0000090g0260' => 'nta', 'Nitab4.5_0000977g0030' => 'nta', 'Nitab4.5_0002541g0040' => 'nta', 'Nitab4.5_0007068g0040' => 'nta', 'Nn005s41408' => 'nnu', 'Nn005s41410' => 'nnu', 'Oeu010310.1' => 'oeu', 'Oeu010311.1' => 'oeu', 'Oeu043472.1' => 'oeu', 'Os01g0246400' => 'osa', 'Os04g0267950' => 'osa', 'Os07g0178700' => 'osa', 'Os07g0178800' => 'osa', 'Peaxi162Scf00316g00046' => 'pax', 'Peaxi162Scf00316g00049' => 'pax', 'Peaxi162Scf00316g00059' => 'pax', 'Peaxi162Scf00316g00328' => 'pax', 'Peaxi162Scf00316g00329' => 'pax', 'Peaxi162Scf00316g00411' => 'pax', 'Peaxi162Scf00316g00521' => 'pax', 'Peaxi162Scf00492g00068' => 'pax', 'Peaxi162Scf35631g00002' => 'pax', 'PGR142G3720' => 'pgr', 'PGSC0003DMG400006442' => 'stu', 'Phvul.007G062000' => 'pvu', 'Potri.008G157750' => 'ptr', 'Potri.008G157900' => 'ptr', 'Potri.008G158000' => 'ptr', 'Potri.008G158200' => 'ptr', 'Pp3c11_7280' => 'ppa', 'Pp3c11_7980' => 'ppa', 'Pp3c12_19450' => 'ppa', 'Pp3c14_1480' => 'ppa', 'Pp3c14_1501' => 'ppa', 'Pp3c16_4900' => 'ppa', 'Pp3c16_5010' => 'ppa', 'Pp3c16_5060' => 'ppa', 'Pp3c19_18250' => 'ppa', 'Pp3c23_8530' => 'ppa', 'Pp3c23_8550' => 'ppa', 'Pp3c24_9670' => 'ppa', 'Pp3c2_21390' => 'ppa', 'Pp3c2_31380' => 'ppa', 'Pp3c3_16620' => 'ppa', 'Pp3c3_8090' => 'ppa', 'Pp3c3_8110' => 'ppa', 'Pp3c3_8130' => 'ppa', 'Pp3c3_8150' => 'ppa', 'Pp3c4_14320' => 'ppa', 'Pp3c6_2560' => 'ppa', 'Pp3c9_16700' => 'ppa', 'PRCOL_00000234' => 'pco', 'PRCOL_00000235' => 'pco', 'PRCOL_00000777' => 'pco', 'PRCOL_00002344' => 'pco', 'PRCOL_00002372' => 'pco', 'PRCOL_00006120' => 'pco', 'Prupe.1G021400' => 'ppe', 'Prupe.1G021500' => 'ppe', 'Prupe.1G021600' => 'ppe', 'Prupe.1G021700' => 'ppe', 'Prupe.1G021800' => 'ppe', 'Prupe.5G145100' => 'ppe', 'Psat6g204040' => 'psa', 'Psat6g204800' => 'psa', 'Psat6g204920' => 'psa', 'Psat6g204960' => 'psa', 'Psat6g205080' => 'psa', 'PSO017G0271' => 'pso', 'PSO017G1276' => 'pso', 'PSO017G1429' => 'pso', 'PSO017G1861' => 'pso', 'PSO017G2787' => 'pso', 'PSO017G4466' => 'pso', 'PSO017G5118' => 'pso', 'PSO017G5420' => 'pso', 'PSO063G3678' => 'pso', 'PSO210G0546' => 'pso', 'PSO317G0001' => 'pso', 'PSO357G0512' => 'pso', 'PSO478G2682' => 'pso', 'PSO647G0001' => 'pso', 'PSO675G0001' => 'pso', 'PSO675G2699' => 'pso', 'PSO675G2849' => 'pso', 'PSO675G4991' => 'pso', 'PSO689G0001' => 'pso', 'QL06p000916' => 'qlo', 'QL06p000921' => 'qlo', 'QL06p001398' => 'qlo', 'QL06p001407' => 'qlo', 'QL06p002031' => 'qlo', 'RcHm_v2.0_Chr4g0387791' => 'rch', 'RcHm_v2.0_Chr4g0387801' => 'rch', 'RcHm_v2.0_Chr6g0286501' => 'rch', 'RcHm_v2.0_Chr6g0286511' => 'rch', 'RcHm_v2.0_Chr6g0286521' => 'rch', 'RcHm_v2.0_Chr6g0286531' => 'rch', 'RcHm_v2.0_Chr7g0189141' => 'rch', 'Rhsim02G0028700' => 'rsi', 'Rhsim02G0028800' => 'rsi', 'Rhsim02G0028900' => 'rsi', 'Rhsim02G0029000' => 'rsi', 'Rhsim02G0029100' => 'rsi', 'Rhsim02G0029200' => 'rsi', 'Rhsim02G0029300' => 'rsi', 'Rhsim02G0029400' => 'rsi', 'Rhsim02G0029500' => 'rsi', 'Rhsim02G0029600' => 'rsi', 'RhsimUnG0024000' => 'rsi', 'RhsimUnG0024100' => 'rsi', 'RhsimUnG0024200' => 'rsi', 'RhsimUnG0024300' => 'rsi', 'RhsimUnG0024400' => 'rsi', 'RhsimUnG0024500' => 'rsi', 'RhsimUnG0024700' => 'rsi', 'RhsimUnG0024800' => 'rsi', 'RhsimUnG0024900' => 'rsi', 'RhsimUnG0025100' => 'rsi', 'Sabra08G0120200' => 'sbr', 'Sabra08G0120300' => 'sbr', 'Sabra08G0120500' => 'sbr', 'Sabra08G0120600' => 'sbr', 'Sabra10G0158900' => 'sbr', 'SalBow2G3492' => 'sbo', 'Sc13g0004760' => 'sci', 'Sc13g0004770' => 'sci', 'Sed0003417' => 'sed', 'Sed0019750' => 'sed', 'SEGI_03419' => 'sgi', 'SEGI_05907' => 'sgi', 'SEGI_10682' => 'sgi', 'SEGI_13528' => 'sgi', 'SEGI_16081' => 'sgi', 'SEGI_19370' => 'sgi', 'SEGI_21015' => 'sgi', 'SEGI_21944' => 'sgi', 'SEGI_32906' => 'sgi', 'SEGI_33093' => 'sgi', 'SEGI_36110' => 'sgi', 'SEGI_40397' => 'sgi', 'SGA_v2.0_scaffold191G40426' => 'sas', 'SGA_v2.0_scaffold353G49717' => 'sas', 'SGA_v2.0_scaffold50G18550' => 'sas', 'SMO119G0173' => 'smo', 'SMO172G0002' => 'smo', 'Solyc09g082690.3' => 'sly', 'Solyc09g082700.2' => 'sly', 'Sopen09g031550' => 'spe', 'Sopen09g031560' => 'spe', 'Sp3g20540' => 'spa', 'Sp7g07580' => 'spa', 'TAR134G0002' => 'tar', 'TAR236G0001' => 'tar', 'TAR365G0892' => 'tar', 'TAR636G0166' => 'tar', 'TAR636G0646' => 'tar', 'TAR636G0869' => 'tar', 'TAR636G1317' => 'tar', 'TAR636G1744' => 'tar', 'TAR636G3358' => 'tar', 'TAR636G3436' => 'tar', 'THA.LOC104803047' => 'tha', 'Thecc.04G238900' => 'tca', 'Thhalv10021557m.g' => 'esa', 'Thhalv10026318m.g' => 'esa', 'Thhalv10026335m.g' => 'esa', 'TPR.G17433' => 'tpr', 'TPR.G18915' => 'tpr', 'TPR.G26125' => 'tpr', 'TWI09G0677' => 'twi', 'TWI73G0287' => 'twi', 'unitig_748.g8326' => 'ugi', 'vmacro15370' => 'vma', 'vmacro15371' => 'vma', 'vmacro15372' => 'vma', 'vmacro15373' => 'vma', 'vmacro15374' => 'vma', 'VMungo0720G2826' => 'vmu', 'Zm00001eb116960' => 'zma', 'Zm00001eb301260' => 'zma', 'Zm00001eb301270' => 'zma' ), 'gf_id' => 'HOM05D001460', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001460' ), 'data_identifier' => 'HOM05D001460', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001460', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '433', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p22980' => 'bna', 'A01p32340' => 'bna', 'A03p42970' => 'bna', 'A05p25880' => 'bna', 'Aa31LG8G9320' => 'aar', 'Aa31LG8G9330' => 'aar', 'Aa31LG8G9340' => 'aar', 'Aa31sc221G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1034' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1528' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.829' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2222' => 'aag', 'Ah.12g058830' => 'amhyb', 'Ah.12g058840' => 'amhyb', 'AL3G37160' => 'aly', 'AL7G41310' => 'aly', 'Aqoxy5G00395' => 'aox', 'Aqoxy5G00396' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0C8NZA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5185HY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JZ1PRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MD3LS0' => 'arhy', 'AT3G22840' => 'ath', 'AT4G14690' => 'ath', 'ATR0665G054' => 'atr', 'Atru.chr4.2344' => 'acertr', 'Atru.chr4.2346' => 'acertr', 'Atru.chr4.2347' => 'acertr', 'Atru.chr4.2348' => 'acertr', 'Atru.chr4.2355' => 'acertr', 'Atru.chr4.2356' => 'acertr', 'Atru.chr4.2358' => 'acertr', 'Atru.chr4.2359' => 'acertr', 'Atru.chr4.2360' => 'acertr', 'Atru.chr4.2361' => 'acertr', 'AUR62030476' => 'cqu', 'AUR62030478' => 'cqu', 'AUR62030819' => 'cqu', 'AUR62030820' => 'cqu', 'BcaB03g14648' => 'bca', 'BcaB04g20492' => 'bca', 'BcaB06g26399' => 'bca', 'BcaC01g03416' => 'bca', 'BcaC01g03419' => 'bca', 'BcaC01g03421' => 'bca', 'BcaC01g03424' => 'bca', 'BcaC05g28012' => 'bca', 'BcaC09g49212' => 'bca', 'BcaC09g50140' => 'bca', 'BcaNung00346' => 'bca', 'BolC1t02785H' => 'bol', 'BolC1t04095H' => 'bol', 'BolC3t17545H' => 'bol', 'BolC5t32769H' => 'bol', 'BraA01t02211Z' => 'bra', 'BraA01t03359Z' => 'bra', 'BraA03t13441Z' => 'bra', 'BraA05t21476Z' => 'bra', 'C01p28420' => 'bna', 'C01p41350' => 'bna', 'C03p52750' => 'bna', 'C03p52780' => 'bna', 'C05p40270' => 'bna', 'CAN.G1437.9' => 'can', 'CANSAT78G0035' => 'cansat', 'CANSAT78G1036' => 'cansat', 'CANSAT78G2272' => 'cansat', 'CANSAT78G2478' => 'cansat', 'CARHR098700' => 'chi', 'CARHR221120' => 'chi', 'CARHR221150' => 'chi', 'Carub.0003s2297' => 'cru', 'Carub.0007s2749' => 'cru', 'Carub.0007s2750' => 'cru', 'Carub.0007s2751' => 'cru', 'Ca_10849_v3' => 'car', 'Cc03_g04300' => 'ccan', 'CDE02G3648' => 'cde', 'CDE05G0060' => 'cde', 'CDE05G0692' => 'cde', 'CDE05G2285' => 'cde', 'CDE05G2884' => 'cde', 'CDE05G3072' => 'cde', 'Cfa008439' => 'cfa', 'Cfa008441' => 'cfa', 'Cfa008443' => 'cfa', 'Cfa008448' => 'cfa', 'Ciclev10005974m.g' => 'ccl', 'Ciclev10006006m.g' => 'ccl', 'Ciclev10006775m.g' => 'ccl', 'CiPaw.02G120400' => 'cil', 'CiPaw.02G120500' => 'cil', 'CiPaw.02G120600' => 'cil', 'ClCG05G004850' => 'cla', 'COL.COLO4_21566' => 'col', 'Cpa.g.sc44.124' => 'cpa', 'Cre07.g320400' => 'cre', 'Cre07.g320450' => 'cre', 'Cre08.g384650' => 'cre', 'Cre09.g393173' => 'cre', 'Cre09.g394325' => 'cre', 'Cre14.g626750' => 'cre', 'Cre16.g679250' => 'cre', 'CsaV3_3G012890' => 'csa', 'CSS0010865' => 'camsi', 'CSS0044338' => 'camsi', 'DCAR_002366' => 'dca', 'DCAR_030687' => 'dca', 'DCAR_030688' => 'dca', 'Dinv14047' => 'din', 'Dinv14048' => 'din', 'Duzib151G0105' => 'dzi', 'Duzib151G0114' => 'dzi', 'Duzib212G1029' => 'dzi', 'ECA232G3536' => 'eca', 'ECA240G0786' => 'eca', 'ECA240G1802' => 'eca', 'ECA240G3760' => 'eca', 'ECA240G3920' => 'eca', 'EL10Ac5g12536' => 'bvu', 'EL10Ac5g12537' => 'bvu', 'EL10Ac5g12538' => 'bvu', 'Eucgr.B01004' => 'egr', 'Eucgr.B01006' => 'egr', 'Eucgr.B01007' => 'egr', 'Eucgr.B01008' => 'egr', 'Eucgr.B01895' => 'egr', 'Eucgr.B01896' => 'egr', 'FAN04G1456' => 'fan', 'FAN08G1769' => 'fan', 'FAN08G2160' => 'fan', 'FAN13G2403' => 'fan', 'FAN13G3303' => 'fan', 'FAN15G2435' => 'fan', 'FAN17G0672' => 'fan', 'FAN17G2441' => 'fan', 'FAN18G1024' => 'fan', 'FAN22G1458' => 'fan', 'FAN24G0037' => 'fan', 'FAN24G0429' => 'fan', 'FAN24G2387' => 'fan', 'FAN27G2746' => 'fan', 'FvH4_2g20400' => 'fve', 'FvH4_2g20420' => 'fve', 'FvH4_2g20430' => 'fve', 'FvH4_4g01270' => 'fve', 'FvH4_4g01290' => 'fve', 'FvH4_4g01300' => 'fve', 'FvH4_4g01310' => 'fve', 'FvH4_4g01330' => 'fve', 'FvH4_5g09070' => 'fve', 'Glyma.10G243800' => 'gma', 'Glyma.20G150600' => 'gma', 'Gohir.A09G219200' => 'ghi', 'Gohir.A09G219300' => 'ghi', 'Gohir.D09G221400' => 'ghi', 'Gohir.D09G221500' => 'ghi', 'Gorai.006G242600' => 'gra', 'Gorai.006G242700' => 'gra', 'GSVIVG01018044001' => 'vvi', 'HanXRQChr03g0083821' => 'han', 'HanXRQChr03g0083841' => 'han', 'HanXRQChr03g0083881' => 'han', 'HanXRQChr03g0083901' => 'han', 'HanXRQChr03g0083921' => 'han', 'HanXRQChr03g0085331' => 'han', 'HanXRQChr03g0085361' => 'han', 'HanXRQChr03g0085411' => 'han', 'HanXRQChr03g0085421' => 'han', 'HanXRQChr03g0085431' => 'han', 'HanXRQChr08g0221991' => 'han', 'HanXRQChr11g0336061' => 'han', 'HanXRQChr11g0336411' => 'han', 'Haze_11234' => 'cav', 'Hma1.2p1_0549F.1_g177010' => 'hma', 'Hma1.2p1_0602F.1_g187630' => 'hma', 'Hund14876' => 'sun', 'Hund14879' => 'sun', 'Lalb_Chr06g0160741' => 'lal', 'Lalb_Chr21g0304781' => 'lal', 'Lj3A726G19' => 'lonja', 'Lj3A726T23' => 'lonja', 'Lj3A726T24' => 'lonja', 'Lj3A726T25' => 'lonja', 'Lj3A727T17' => 'lonja', 'Lj3C726T0' => 'lonja', 'Lj3C726T2' => 'lonja', 'Lj3P725T35' => 'lonja', 'Lj3P727T10' => 'lonja', 'Lj3P727T12' => 'lonja', 'Lj3P727T14' => 'lonja', 'Lj5g0023109' => 'lja', 'Lj6P646T44' => 'lonja', 'Lsat_1_v5_gn_6_75760' => 'lsa', 'Lsat_1_v5_gn_6_75800' => 'lsa', 'Lsat_1_v5_gn_6_75900' => 'lsa', 'Lsat_1_v5_gn_6_76240' => 'lsa', 'Lsat_1_v5_gn_6_76441' => 'lsa', 'Lsat_1_v5_gn_6_76700' => 'lsa', 'Lsat_1_v5_gn_6_76760' => 'lsa', 'Manes.15G033100' => 'mes', 'Mapoly0004s0074' => 'mpo', 'Mapoly0004s0075' => 'mpo', 'Mapoly0004s0163' => 'mpo', 'Mapoly0004s0164' => 'mpo', 'Mapoly0021s0018' => 'mpo', 'Mapoly0041s0136' => 'mpo', 'Mapoly0041s0137' => 'mpo', 'Mapoly0041s0138' => 'mpo', 'Mapoly0041s0139' => 'mpo', 'Mapoly0041s0141' => 'mpo', 'Mapoly0041s0142' => 'mpo', 'Mapoly0041s0143' => 'mpo', 'Mapoly0041s0144' => 'mpo', 'Mapoly0041s0145' => 'mpo', 'Mapoly0047s0106' => 'mpo', 'Mapoly0047s0108' => 'mpo', 'Mapoly0050s0051' => 'mpo', 'Mapoly0050s0052' => 'mpo', 'Mapoly0050s0053' => 'mpo', 'Mapoly0058s0013' => 'mpo', 'Mapoly0091s0078' => 'mpo', 'Mapoly0091s0079' => 'mpo', 'Mapoly0091s0080' => 'mpo', 'Mapoly0091s0081' => 'mpo', 'Mapoly0278s0004' => 'mpo', 'Mapoly0278s0005' => 'mpo', 'Mapoly0278s0006' => 'mpo', 'MBI11_g30648_MAGBIO' => 'mbi', 'MCO03G194' => 'mco', 'MCO03G590' => 'mco', 'MCO07G312' => 'mco', 'MCO10G318' => 'mco', 'MCO12G244' => 'mco', 'MCO13G148' => 'mco', 'MCO13G194' => 'mco', 'MCO16G238' => 'mco', 'MD06G1134100' => 'mdo', 'MD13G1200100' => 'mdo', 'MD13G1200300' => 'mdo', 'MD13G1200600' => 'mdo', 'MD14G1150400' => 'mdo', 'MD16G1200000' => 'mdo', 'Medtr1g102570' => 'mtr', 'Medtr1g102780' => 'mtr', 'Medtr1g102800' => 'mtr', 'Medtr1g102810' => 'mtr', 'Medtr1g102830' => 'mtr', 'MELO3C006499.2' => 'cme', 'Migut.G00385' => 'egut', 'MSTRG.4063' => 'ama', 'Nitab4.5_0000090g0260' => 'nta', 'Nitab4.5_0000977g0030' => 'nta', 'Nitab4.5_0002541g0040' => 'nta', 'Nitab4.5_0007068g0040' => 'nta', 'Nn005s41408' => 'nnu', 'Nn005s41410' => 'nnu', 'Oeu010310.1' => 'oeu', 'Oeu010311.1' => 'oeu', 'Oeu043472.1' => 'oeu', 'Os01g0246400' => 'osa', 'Os04g0267950' => 'osa', 'Os07g0178700' => 'osa', 'Os07g0178800' => 'osa', 'Peaxi162Scf00316g00046' => 'pax', 'Peaxi162Scf00316g00049' => 'pax', 'Peaxi162Scf00316g00059' => 'pax', 'Peaxi162Scf00316g00328' => 'pax', 'Peaxi162Scf00316g00329' => 'pax', 'Peaxi162Scf00316g00411' => 'pax', 'Peaxi162Scf00316g00521' => 'pax', 'Peaxi162Scf00492g00068' => 'pax', 'Peaxi162Scf35631g00002' => 'pax', 'PGR142G3720' => 'pgr', 'PGSC0003DMG400006442' => 'stu', 'Phvul.007G062000' => 'pvu', 'Potri.008G157750' => 'ptr', 'Potri.008G157900' => 'ptr', 'Potri.008G158000' => 'ptr', 'Potri.008G158200' => 'ptr', 'Pp3c11_7280' => 'ppa', 'Pp3c11_7980' => 'ppa', 'Pp3c12_19450' => 'ppa', 'Pp3c14_1480' => 'ppa', 'Pp3c14_1501' => 'ppa', 'Pp3c16_4900' => 'ppa', 'Pp3c16_5010' => 'ppa', 'Pp3c16_5060' => 'ppa', 'Pp3c19_18250' => 'ppa', 'Pp3c23_8530' => 'ppa', 'Pp3c23_8550' => 'ppa', 'Pp3c24_9670' => 'ppa', 'Pp3c2_21390' => 'ppa', 'Pp3c2_31380' => 'ppa', 'Pp3c3_16620' => 'ppa', 'Pp3c3_8090' => 'ppa', 'Pp3c3_8110' => 'ppa', 'Pp3c3_8130' => 'ppa', 'Pp3c3_8150' => 'ppa', 'Pp3c4_14320' => 'ppa', 'Pp3c6_2560' => 'ppa', 'Pp3c9_16700' => 'ppa', 'PRCOL_00000234' => 'pco', 'PRCOL_00000235' => 'pco', 'PRCOL_00000777' => 'pco', 'PRCOL_00002344' => 'pco', 'PRCOL_00002372' => 'pco', 'PRCOL_00006120' => 'pco', 'Prupe.1G021400' => 'ppe', 'Prupe.1G021500' => 'ppe', 'Prupe.1G021600' => 'ppe', 'Prupe.1G021700' => 'ppe', 'Prupe.1G021800' => 'ppe', 'Prupe.5G145100' => 'ppe', 'Psat6g204040' => 'psa', 'Psat6g204800' => 'psa', 'Psat6g204920' => 'psa', 'Psat6g204960' => 'psa', 'Psat6g205080' => 'psa', 'PSO017G0271' => 'pso', 'PSO017G1276' => 'pso', 'PSO017G1429' => 'pso', 'PSO017G1861' => 'pso', 'PSO017G2787' => 'pso', 'PSO017G4466' => 'pso', 'PSO017G5118' => 'pso', 'PSO017G5420' => 'pso', 'PSO063G3678' => 'pso', 'PSO210G0546' => 'pso', 'PSO317G0001' => 'pso', 'PSO357G0512' => 'pso', 'PSO478G2682' => 'pso', 'PSO647G0001' => 'pso', 'PSO675G0001' => 'pso', 'PSO675G2699' => 'pso', 'PSO675G2849' => 'pso', 'PSO675G4991' => 'pso', 'PSO689G0001' => 'pso', 'QL06p000916' => 'qlo', 'QL06p000921' => 'qlo', 'QL06p001398' => 'qlo', 'QL06p001407' => 'qlo', 'QL06p002031' => 'qlo', 'RcHm_v2.0_Chr4g0387791' => 'rch', 'RcHm_v2.0_Chr4g0387801' => 'rch', 'RcHm_v2.0_Chr6g0286501' => 'rch', 'RcHm_v2.0_Chr6g0286511' => 'rch', 'RcHm_v2.0_Chr6g0286521' => 'rch', 'RcHm_v2.0_Chr6g0286531' => 'rch', 'RcHm_v2.0_Chr7g0189141' => 'rch', 'Rhsim02G0028700' => 'rsi', 'Rhsim02G0028800' => 'rsi', 'Rhsim02G0028900' => 'rsi', 'Rhsim02G0029000' => 'rsi', 'Rhsim02G0029100' => 'rsi', 'Rhsim02G0029200' => 'rsi', 'Rhsim02G0029300' => 'rsi', 'Rhsim02G0029400' => 'rsi', 'Rhsim02G0029500' => 'rsi', 'Rhsim02G0029600' => 'rsi', 'RhsimUnG0024000' => 'rsi', 'RhsimUnG0024100' => 'rsi', 'RhsimUnG0024200' => 'rsi', 'RhsimUnG0024300' => 'rsi', 'RhsimUnG0024400' => 'rsi', 'RhsimUnG0024500' => 'rsi', 'RhsimUnG0024700' => 'rsi', 'RhsimUnG0024800' => 'rsi', 'RhsimUnG0024900' => 'rsi', 'RhsimUnG0025100' => 'rsi', 'Sabra08G0120200' => 'sbr', 'Sabra08G0120300' => 'sbr', 'Sabra08G0120500' => 'sbr', 'Sabra08G0120600' => 'sbr', 'Sabra10G0158900' => 'sbr', 'SalBow2G3492' => 'sbo', 'Sc13g0004760' => 'sci', 'Sc13g0004770' => 'sci', 'Sed0003417' => 'sed', 'Sed0019750' => 'sed', 'SEGI_03419' => 'sgi', 'SEGI_05907' => 'sgi', 'SEGI_10682' => 'sgi', 'SEGI_13528' => 'sgi', 'SEGI_16081' => 'sgi', 'SEGI_19370' => 'sgi', 'SEGI_21015' => 'sgi', 'SEGI_21944' => 'sgi', 'SEGI_32906' => 'sgi', 'SEGI_33093' => 'sgi', 'SEGI_36110' => 'sgi', 'SEGI_40397' => 'sgi', 'SGA_v2.0_scaffold191G40426' => 'sas', 'SGA_v2.0_scaffold353G49717' => 'sas', 'SGA_v2.0_scaffold50G18550' => 'sas', 'SMO119G0173' => 'smo', 'SMO172G0002' => 'smo', 'Solyc09g082690.3' => 'sly', 'Solyc09g082700.2' => 'sly', 'Sopen09g031550' => 'spe', 'Sopen09g031560' => 'spe', 'Sp3g20540' => 'spa', 'Sp7g07580' => 'spa', 'TAR134G0002' => 'tar', 'TAR236G0001' => 'tar', 'TAR365G0892' => 'tar', 'TAR636G0166' => 'tar', 'TAR636G0646' => 'tar', 'TAR636G0869' => 'tar', 'TAR636G1317' => 'tar', 'TAR636G1744' => 'tar', 'TAR636G3358' => 'tar', 'TAR636G3436' => 'tar', 'THA.LOC104803047' => 'tha', 'Thecc.04G238900' => 'tca', 'Thhalv10021557m.g' => 'esa', 'Thhalv10026318m.g' => 'esa', 'Thhalv10026335m.g' => 'esa', 'TPR.G17433' => 'tpr', 'TPR.G18915' => 'tpr', 'TPR.G26125' => 'tpr', 'TWI09G0677' => 'twi', 'TWI73G0287' => 'twi', 'unitig_748.g8326' => 'ugi', 'vmacro15370' => 'vma', 'vmacro15371' => 'vma', 'vmacro15372' => 'vma', 'vmacro15373' => 'vma', 'vmacro15374' => 'vma', 'VMungo0720G2826' => 'vmu', 'Zm00001eb116960' => 'zma', 'Zm00001eb301260' => 'zma', 'Zm00001eb301270' => 'zma' ) $gf_id = 'HOM05D001460' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001460' ) $data_identifier = 'HOM05D001460' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 4, 'aag' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 2, 'aox' => (int) 2, 'arhy' => (int) 4, 'ath' => (int) 2, 'atr' => (int) 1, 'acertr' => (int) 10, 'cqu' => (int) 4, 'bca' => (int) 11, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 1, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 1, 'ccan' => (int) 1, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 1, 'col' => (int) 1, 'cpa' => (int) 1, 'cre' => (int) 7, 'csa' => (int) 1, 'camsi' => (int) 2, 'dca' => (int) 3, 'din' => (int) 2, 'dzi' => (int) 3, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 14, 'fve' => (int) 9, 'gma' => (int) 2, 'ghi' => (int) 4, 'gra' => (int) 2, 'vvi' => (int) 1, 'han' => (int) 13, 'cav' => (int) 1, 'hma' => (int) 2, 'sun' => (int) 2, 'lal' => (int) 2, 'lonja' => (int) 12, 'lja' => (int) 1, 'lsa' => (int) 7, 'mes' => (int) 1, 'mpo' => (int) 27, 'mbi' => (int) 1, 'mco' => (int) 8, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 1, 'egut' => (int) 1, 'ama' => (int) 1, 'nta' => (int) 4, 'nnu' => (int) 2, 'oeu' => (int) 3, 'osa' => (int) 4, 'pax' => (int) 9, 'pgr' => (int) 1, 'stu' => (int) 1, 'pvu' => (int) 1, 'ptr' => (int) 4, 'ppa' => (int) 22, 'pco' => (int) 6, 'ppe' => (int) 6, 'psa' => (int) 5, 'pso' => (int) 19, 'qlo' => (int) 5, 'rch' => (int) 7, 'rsi' => (int) 20, 'sbr' => (int) 5, 'sbo' => (int) 1, 'sci' => (int) 2, 'sed' => (int) 2, 'sgi' => (int) 12, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 2, 'tar' => (int) 10, 'tha' => (int) 1, 'tca' => (int) 1, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 2, 'ugi' => (int) 1, 'vma' => (int) 5, 'vmu' => (int) 1, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb301270' $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' => 'HOM05D001460', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '433', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p22980' => 'bna', 'A01p32340' => 'bna', 'A03p42970' => 'bna', 'A05p25880' => 'bna', 'Aa31LG8G9320' => 'aar', 'Aa31LG8G9330' => 'aar', 'Aa31LG8G9340' => 'aar', 'Aa31sc221G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1034' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1528' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.829' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2222' => 'aag', 'Ah.12g058830' => 'amhyb', 'Ah.12g058840' => 'amhyb', 'AL3G37160' => 'aly', 'AL7G41310' => 'aly', 'Aqoxy5G00395' => 'aox', 'Aqoxy5G00396' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0C8NZA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5185HY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JZ1PRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MD3LS0' => 'arhy', 'AT3G22840' => 'ath', 'AT4G14690' => 'ath', 'ATR0665G054' => 'atr', 'Atru.chr4.2344' => 'acertr', 'Atru.chr4.2346' => 'acertr', 'Atru.chr4.2347' => 'acertr', 'Atru.chr4.2348' => 'acertr', 'Atru.chr4.2355' => 'acertr', 'Atru.chr4.2356' => 'acertr', 'Atru.chr4.2358' => 'acertr', 'Atru.chr4.2359' => 'acertr', 'Atru.chr4.2360' => 'acertr', 'Atru.chr4.2361' => 'acertr', 'AUR62030476' => 'cqu', 'AUR62030478' => 'cqu', 'AUR62030819' => 'cqu', 'AUR62030820' => 'cqu', 'BcaB03g14648' => 'bca', 'BcaB04g20492' => 'bca', 'BcaB06g26399' => 'bca', 'BcaC01g03416' => 'bca', 'BcaC01g03419' => 'bca', 'BcaC01g03421' => 'bca', 'BcaC01g03424' => 'bca', 'BcaC05g28012' => 'bca', 'BcaC09g49212' => 'bca', 'BcaC09g50140' => 'bca', 'BcaNung00346' => 'bca', 'BolC1t02785H' => 'bol', 'BolC1t04095H' => 'bol', 'BolC3t17545H' => 'bol', 'BolC5t32769H' => 'bol', 'BraA01t02211Z' => 'bra', 'BraA01t03359Z' => 'bra', 'BraA03t13441Z' => 'bra', 'BraA05t21476Z' => 'bra', 'C01p28420' => 'bna', 'C01p41350' => 'bna', 'C03p52750' => 'bna', 'C03p52780' => 'bna', 'C05p40270' => 'bna', 'CAN.G1437.9' => 'can', 'CANSAT78G0035' => 'cansat', 'CANSAT78G1036' => 'cansat', 'CANSAT78G2272' => 'cansat', 'CANSAT78G2478' => 'cansat', 'CARHR098700' => 'chi', 'CARHR221120' => 'chi', 'CARHR221150' => 'chi', 'Carub.0003s2297' => 'cru', 'Carub.0007s2749' => 'cru', 'Carub.0007s2750' => 'cru', 'Carub.0007s2751' => 'cru', 'Ca_10849_v3' => 'car', 'Cc03_g04300' => 'ccan', 'CDE02G3648' => 'cde', 'CDE05G0060' => 'cde', 'CDE05G0692' => 'cde', 'CDE05G2285' => 'cde', 'CDE05G2884' => 'cde', 'CDE05G3072' => 'cde', 'Cfa008439' => 'cfa', 'Cfa008441' => 'cfa', 'Cfa008443' => 'cfa', 'Cfa008448' => 'cfa', 'Ciclev10005974m.g' => 'ccl', 'Ciclev10006006m.g' => 'ccl', 'Ciclev10006775m.g' => 'ccl', 'CiPaw.02G120400' => 'cil', 'CiPaw.02G120500' => 'cil', 'CiPaw.02G120600' => 'cil', 'ClCG05G004850' => 'cla', 'COL.COLO4_21566' => 'col', 'Cpa.g.sc44.124' => 'cpa', 'Cre07.g320400' => 'cre', 'Cre07.g320450' => 'cre', 'Cre08.g384650' => 'cre', 'Cre09.g393173' => 'cre', 'Cre09.g394325' => 'cre', 'Cre14.g626750' => 'cre', 'Cre16.g679250' => 'cre', 'CsaV3_3G012890' => 'csa', 'CSS0010865' => 'camsi', 'CSS0044338' => 'camsi', 'DCAR_002366' => 'dca', 'DCAR_030687' => 'dca', 'DCAR_030688' => 'dca', 'Dinv14047' => 'din', 'Dinv14048' => 'din', 'Duzib151G0105' => 'dzi', 'Duzib151G0114' => 'dzi', 'Duzib212G1029' => 'dzi', 'ECA232G3536' => 'eca', 'ECA240G0786' => 'eca', 'ECA240G1802' => 'eca', 'ECA240G3760' => 'eca', 'ECA240G3920' => 'eca', 'EL10Ac5g12536' => 'bvu', 'EL10Ac5g12537' => 'bvu', 'EL10Ac5g12538' => 'bvu', 'Eucgr.B01004' => 'egr', 'Eucgr.B01006' => 'egr', 'Eucgr.B01007' => 'egr', 'Eucgr.B01008' => 'egr', 'Eucgr.B01895' => 'egr', 'Eucgr.B01896' => 'egr', 'FAN04G1456' => 'fan', 'FAN08G1769' => 'fan', 'FAN08G2160' => 'fan', 'FAN13G2403' => 'fan', 'FAN13G3303' => 'fan', 'FAN15G2435' => 'fan', 'FAN17G0672' => 'fan', 'FAN17G2441' => 'fan', 'FAN18G1024' => 'fan', 'FAN22G1458' => 'fan', 'FAN24G0037' => 'fan', 'FAN24G0429' => 'fan', 'FAN24G2387' => 'fan', 'FAN27G2746' => 'fan', 'FvH4_2g20400' => 'fve', 'FvH4_2g20420' => 'fve', 'FvH4_2g20430' => 'fve', 'FvH4_4g01270' => 'fve', 'FvH4_4g01290' => 'fve', 'FvH4_4g01300' => 'fve', 'FvH4_4g01310' => 'fve', 'FvH4_4g01330' => 'fve', 'FvH4_5g09070' => 'fve', 'Glyma.10G243800' => 'gma', 'Glyma.20G150600' => 'gma', 'Gohir.A09G219200' => 'ghi', 'Gohir.A09G219300' => 'ghi', 'Gohir.D09G221400' => 'ghi', 'Gohir.D09G221500' => 'ghi', 'Gorai.006G242600' => 'gra', 'Gorai.006G242700' => 'gra', 'GSVIVG01018044001' => 'vvi', 'HanXRQChr03g0083821' => 'han', 'HanXRQChr03g0083841' => 'han', 'HanXRQChr03g0083881' => 'han', 'HanXRQChr03g0083901' => 'han', 'HanXRQChr03g0083921' => 'han', 'HanXRQChr03g0085331' => 'han', 'HanXRQChr03g0085361' => 'han', 'HanXRQChr03g0085411' => 'han', 'HanXRQChr03g0085421' => 'han', 'HanXRQChr03g0085431' => 'han', 'HanXRQChr08g0221991' => 'han', 'HanXRQChr11g0336061' => 'han', 'HanXRQChr11g0336411' => 'han', 'Haze_11234' => 'cav', 'Hma1.2p1_0549F.1_g177010' => 'hma', 'Hma1.2p1_0602F.1_g187630' => 'hma', 'Hund14876' => 'sun', 'Hund14879' => 'sun', 'Lalb_Chr06g0160741' => 'lal', 'Lalb_Chr21g0304781' => 'lal', 'Lj3A726G19' => 'lonja', 'Lj3A726T23' => 'lonja', 'Lj3A726T24' => 'lonja', 'Lj3A726T25' => 'lonja', 'Lj3A727T17' => 'lonja', 'Lj3C726T0' => 'lonja', 'Lj3C726T2' => 'lonja', 'Lj3P725T35' => 'lonja', 'Lj3P727T10' => 'lonja', 'Lj3P727T12' => 'lonja', 'Lj3P727T14' => 'lonja', 'Lj5g0023109' => 'lja', 'Lj6P646T44' => 'lonja', 'Lsat_1_v5_gn_6_75760' => 'lsa', 'Lsat_1_v5_gn_6_75800' => 'lsa', 'Lsat_1_v5_gn_6_75900' => 'lsa', 'Lsat_1_v5_gn_6_76240' => 'lsa', 'Lsat_1_v5_gn_6_76441' => 'lsa', 'Lsat_1_v5_gn_6_76700' => 'lsa', 'Lsat_1_v5_gn_6_76760' => 'lsa', 'Manes.15G033100' => 'mes', 'Mapoly0004s0074' => 'mpo', 'Mapoly0004s0075' => 'mpo', 'Mapoly0004s0163' => 'mpo', 'Mapoly0004s0164' => 'mpo', 'Mapoly0021s0018' => 'mpo', 'Mapoly0041s0136' => 'mpo', 'Mapoly0041s0137' => 'mpo', 'Mapoly0041s0138' => 'mpo', 'Mapoly0041s0139' => 'mpo', 'Mapoly0041s0141' => 'mpo', 'Mapoly0041s0142' => 'mpo', 'Mapoly0041s0143' => 'mpo', 'Mapoly0041s0144' => 'mpo', 'Mapoly0041s0145' => 'mpo', 'Mapoly0047s0106' => 'mpo', 'Mapoly0047s0108' => 'mpo', 'Mapoly0050s0051' => 'mpo', 'Mapoly0050s0052' => 'mpo', 'Mapoly0050s0053' => 'mpo', 'Mapoly0058s0013' => 'mpo', 'Mapoly0091s0078' => 'mpo', 'Mapoly0091s0079' => 'mpo', 'Mapoly0091s0080' => 'mpo', 'Mapoly0091s0081' => 'mpo', 'Mapoly0278s0004' => 'mpo', 'Mapoly0278s0005' => 'mpo', 'Mapoly0278s0006' => 'mpo', 'MBI11_g30648_MAGBIO' => 'mbi', 'MCO03G194' => 'mco', 'MCO03G590' => 'mco', 'MCO07G312' => 'mco', 'MCO10G318' => 'mco', 'MCO12G244' => 'mco', 'MCO13G148' => 'mco', 'MCO13G194' => 'mco', 'MCO16G238' => 'mco', 'MD06G1134100' => 'mdo', 'MD13G1200100' => 'mdo', 'MD13G1200300' => 'mdo', 'MD13G1200600' => 'mdo', 'MD14G1150400' => 'mdo', 'MD16G1200000' => 'mdo', 'Medtr1g102570' => 'mtr', 'Medtr1g102780' => 'mtr', 'Medtr1g102800' => 'mtr', 'Medtr1g102810' => 'mtr', 'Medtr1g102830' => 'mtr', 'MELO3C006499.2' => 'cme', 'Migut.G00385' => 'egut', 'MSTRG.4063' => 'ama', 'Nitab4.5_0000090g0260' => 'nta', 'Nitab4.5_0000977g0030' => 'nta', 'Nitab4.5_0002541g0040' => 'nta', 'Nitab4.5_0007068g0040' => 'nta', 'Nn005s41408' => 'nnu', 'Nn005s41410' => 'nnu', 'Oeu010310.1' => 'oeu', 'Oeu010311.1' => 'oeu', 'Oeu043472.1' => 'oeu', 'Os01g0246400' => 'osa', 'Os04g0267950' => 'osa', 'Os07g0178700' => 'osa', 'Os07g0178800' => 'osa', 'Peaxi162Scf00316g00046' => 'pax', 'Peaxi162Scf00316g00049' => 'pax', 'Peaxi162Scf00316g00059' => 'pax', 'Peaxi162Scf00316g00328' => 'pax', 'Peaxi162Scf00316g00329' => 'pax', 'Peaxi162Scf00316g00411' => 'pax', 'Peaxi162Scf00316g00521' => 'pax', 'Peaxi162Scf00492g00068' => 'pax', 'Peaxi162Scf35631g00002' => 'pax', 'PGR142G3720' => 'pgr', 'PGSC0003DMG400006442' => 'stu', 'Phvul.007G062000' => 'pvu', 'Potri.008G157750' => 'ptr', 'Potri.008G157900' => 'ptr', 'Potri.008G158000' => 'ptr', 'Potri.008G158200' => 'ptr', 'Pp3c11_7280' => 'ppa', 'Pp3c11_7980' => 'ppa', 'Pp3c12_19450' => 'ppa', 'Pp3c14_1480' => 'ppa', 'Pp3c14_1501' => 'ppa', 'Pp3c16_4900' => 'ppa', 'Pp3c16_5010' => 'ppa', 'Pp3c16_5060' => 'ppa', 'Pp3c19_18250' => 'ppa', 'Pp3c23_8530' => 'ppa', 'Pp3c23_8550' => 'ppa', 'Pp3c24_9670' => 'ppa', 'Pp3c2_21390' => 'ppa', 'Pp3c2_31380' => 'ppa', 'Pp3c3_16620' => 'ppa', 'Pp3c3_8090' => 'ppa', 'Pp3c3_8110' => 'ppa', 'Pp3c3_8130' => 'ppa', 'Pp3c3_8150' => 'ppa', 'Pp3c4_14320' => 'ppa', 'Pp3c6_2560' => 'ppa', 'Pp3c9_16700' => 'ppa', 'PRCOL_00000234' => 'pco', 'PRCOL_00000235' => 'pco', 'PRCOL_00000777' => 'pco', 'PRCOL_00002344' => 'pco', 'PRCOL_00002372' => 'pco', 'PRCOL_00006120' => 'pco', 'Prupe.1G021400' => 'ppe', 'Prupe.1G021500' => 'ppe', 'Prupe.1G021600' => 'ppe', 'Prupe.1G021700' => 'ppe', 'Prupe.1G021800' => 'ppe', 'Prupe.5G145100' => 'ppe', 'Psat6g204040' => 'psa', 'Psat6g204800' => 'psa', 'Psat6g204920' => 'psa', 'Psat6g204960' => 'psa', 'Psat6g205080' => 'psa', 'PSO017G0271' => 'pso', 'PSO017G1276' => 'pso', 'PSO017G1429' => 'pso', 'PSO017G1861' => 'pso', 'PSO017G2787' => 'pso', 'PSO017G4466' => 'pso', 'PSO017G5118' => 'pso', 'PSO017G5420' => 'pso', 'PSO063G3678' => 'pso', 'PSO210G0546' => 'pso', 'PSO317G0001' => 'pso', 'PSO357G0512' => 'pso', 'PSO478G2682' => 'pso', 'PSO647G0001' => 'pso', 'PSO675G0001' => 'pso', 'PSO675G2699' => 'pso', 'PSO675G2849' => 'pso', 'PSO675G4991' => 'pso', 'PSO689G0001' => 'pso', 'QL06p000916' => 'qlo', 'QL06p000921' => 'qlo', 'QL06p001398' => 'qlo', 'QL06p001407' => 'qlo', 'QL06p002031' => 'qlo', 'RcHm_v2.0_Chr4g0387791' => 'rch', 'RcHm_v2.0_Chr4g0387801' => 'rch', 'RcHm_v2.0_Chr6g0286501' => 'rch', 'RcHm_v2.0_Chr6g0286511' => 'rch', 'RcHm_v2.0_Chr6g0286521' => 'rch', 'RcHm_v2.0_Chr6g0286531' => 'rch', 'RcHm_v2.0_Chr7g0189141' => 'rch', 'Rhsim02G0028700' => 'rsi', 'Rhsim02G0028800' => 'rsi', 'Rhsim02G0028900' => 'rsi', 'Rhsim02G0029000' => 'rsi', 'Rhsim02G0029100' => 'rsi', 'Rhsim02G0029200' => 'rsi', 'Rhsim02G0029300' => 'rsi', 'Rhsim02G0029400' => 'rsi', 'Rhsim02G0029500' => 'rsi', 'Rhsim02G0029600' => 'rsi', 'RhsimUnG0024000' => 'rsi', 'RhsimUnG0024100' => 'rsi', 'RhsimUnG0024200' => 'rsi', 'RhsimUnG0024300' => 'rsi', 'RhsimUnG0024400' => 'rsi', 'RhsimUnG0024500' => 'rsi', 'RhsimUnG0024700' => 'rsi', 'RhsimUnG0024800' => 'rsi', 'RhsimUnG0024900' => 'rsi', 'RhsimUnG0025100' => 'rsi', 'Sabra08G0120200' => 'sbr', 'Sabra08G0120300' => 'sbr', 'Sabra08G0120500' => 'sbr', 'Sabra08G0120600' => 'sbr', 'Sabra10G0158900' => 'sbr', 'SalBow2G3492' => 'sbo', 'Sc13g0004760' => 'sci', 'Sc13g0004770' => 'sci', 'Sed0003417' => 'sed', 'Sed0019750' => 'sed', 'SEGI_03419' => 'sgi', 'SEGI_05907' => 'sgi', 'SEGI_10682' => 'sgi', 'SEGI_13528' => 'sgi', 'SEGI_16081' => 'sgi', 'SEGI_19370' => 'sgi', 'SEGI_21015' => 'sgi', 'SEGI_21944' => 'sgi', 'SEGI_32906' => 'sgi', 'SEGI_33093' => 'sgi', 'SEGI_36110' => 'sgi', 'SEGI_40397' => 'sgi', 'SGA_v2.0_scaffold191G40426' => 'sas', 'SGA_v2.0_scaffold353G49717' => 'sas', 'SGA_v2.0_scaffold50G18550' => 'sas', 'SMO119G0173' => 'smo', 'SMO172G0002' => 'smo', 'Solyc09g082690.3' => 'sly', 'Solyc09g082700.2' => 'sly', 'Sopen09g031550' => 'spe', 'Sopen09g031560' => 'spe', 'Sp3g20540' => 'spa', 'Sp7g07580' => 'spa', 'TAR134G0002' => 'tar', 'TAR236G0001' => 'tar', 'TAR365G0892' => 'tar', 'TAR636G0166' => 'tar', 'TAR636G0646' => 'tar', 'TAR636G0869' => 'tar', 'TAR636G1317' => 'tar', 'TAR636G1744' => 'tar', 'TAR636G3358' => 'tar', 'TAR636G3436' => 'tar', 'THA.LOC104803047' => 'tha', 'Thecc.04G238900' => 'tca', 'Thhalv10021557m.g' => 'esa', 'Thhalv10026318m.g' => 'esa', 'Thhalv10026335m.g' => 'esa', 'TPR.G17433' => 'tpr', 'TPR.G18915' => 'tpr', 'TPR.G26125' => 'tpr', 'TWI09G0677' => 'twi', 'TWI73G0287' => 'twi', 'unitig_748.g8326' => 'ugi', 'vmacro15370' => 'vma', 'vmacro15371' => 'vma', 'vmacro15372' => 'vma', 'vmacro15373' => 'vma', 'vmacro15374' => 'vma', 'VMungo0720G2826' => 'vmu', 'Zm00001eb116960' => 'zma', 'Zm00001eb301260' => 'zma', 'Zm00001eb301270' => 'zma' ), 'gf_id' => 'HOM05D001460', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001460' ), 'data_identifier' => 'HOM05D001460', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001460', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '433', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p22980' => 'bna', 'A01p32340' => 'bna', 'A03p42970' => 'bna', 'A05p25880' => 'bna', 'Aa31LG8G9320' => 'aar', 'Aa31LG8G9330' => 'aar', 'Aa31LG8G9340' => 'aar', 'Aa31sc221G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1034' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1528' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.829' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2222' => 'aag', 'Ah.12g058830' => 'amhyb', 'Ah.12g058840' => 'amhyb', 'AL3G37160' => 'aly', 'AL7G41310' => 'aly', 'Aqoxy5G00395' => 'aox', 'Aqoxy5G00396' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0C8NZA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5185HY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JZ1PRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MD3LS0' => 'arhy', 'AT3G22840' => 'ath', 'AT4G14690' => 'ath', 'ATR0665G054' => 'atr', 'Atru.chr4.2344' => 'acertr', 'Atru.chr4.2346' => 'acertr', 'Atru.chr4.2347' => 'acertr', 'Atru.chr4.2348' => 'acertr', 'Atru.chr4.2355' => 'acertr', 'Atru.chr4.2356' => 'acertr', 'Atru.chr4.2358' => 'acertr', 'Atru.chr4.2359' => 'acertr', 'Atru.chr4.2360' => 'acertr', 'Atru.chr4.2361' => 'acertr', 'AUR62030476' => 'cqu', 'AUR62030478' => 'cqu', 'AUR62030819' => 'cqu', 'AUR62030820' => 'cqu', 'BcaB03g14648' => 'bca', 'BcaB04g20492' => 'bca', 'BcaB06g26399' => 'bca', 'BcaC01g03416' => 'bca', 'BcaC01g03419' => 'bca', 'BcaC01g03421' => 'bca', 'BcaC01g03424' => 'bca', 'BcaC05g28012' => 'bca', 'BcaC09g49212' => 'bca', 'BcaC09g50140' => 'bca', 'BcaNung00346' => 'bca', 'BolC1t02785H' => 'bol', 'BolC1t04095H' => 'bol', 'BolC3t17545H' => 'bol', 'BolC5t32769H' => 'bol', 'BraA01t02211Z' => 'bra', 'BraA01t03359Z' => 'bra', 'BraA03t13441Z' => 'bra', 'BraA05t21476Z' => 'bra', 'C01p28420' => 'bna', 'C01p41350' => 'bna', 'C03p52750' => 'bna', 'C03p52780' => 'bna', 'C05p40270' => 'bna', 'CAN.G1437.9' => 'can', 'CANSAT78G0035' => 'cansat', 'CANSAT78G1036' => 'cansat', 'CANSAT78G2272' => 'cansat', 'CANSAT78G2478' => 'cansat', 'CARHR098700' => 'chi', 'CARHR221120' => 'chi', 'CARHR221150' => 'chi', 'Carub.0003s2297' => 'cru', 'Carub.0007s2749' => 'cru', 'Carub.0007s2750' => 'cru', 'Carub.0007s2751' => 'cru', 'Ca_10849_v3' => 'car', 'Cc03_g04300' => 'ccan', 'CDE02G3648' => 'cde', 'CDE05G0060' => 'cde', 'CDE05G0692' => 'cde', 'CDE05G2285' => 'cde', 'CDE05G2884' => 'cde', 'CDE05G3072' => 'cde', 'Cfa008439' => 'cfa', 'Cfa008441' => 'cfa', 'Cfa008443' => 'cfa', 'Cfa008448' => 'cfa', 'Ciclev10005974m.g' => 'ccl', 'Ciclev10006006m.g' => 'ccl', 'Ciclev10006775m.g' => 'ccl', 'CiPaw.02G120400' => 'cil', 'CiPaw.02G120500' => 'cil', 'CiPaw.02G120600' => 'cil', 'ClCG05G004850' => 'cla', 'COL.COLO4_21566' => 'col', 'Cpa.g.sc44.124' => 'cpa', 'Cre07.g320400' => 'cre', 'Cre07.g320450' => 'cre', 'Cre08.g384650' => 'cre', 'Cre09.g393173' => 'cre', 'Cre09.g394325' => 'cre', 'Cre14.g626750' => 'cre', 'Cre16.g679250' => 'cre', 'CsaV3_3G012890' => 'csa', 'CSS0010865' => 'camsi', 'CSS0044338' => 'camsi', 'DCAR_002366' => 'dca', 'DCAR_030687' => 'dca', 'DCAR_030688' => 'dca', 'Dinv14047' => 'din', 'Dinv14048' => 'din', 'Duzib151G0105' => 'dzi', 'Duzib151G0114' => 'dzi', 'Duzib212G1029' => 'dzi', 'ECA232G3536' => 'eca', 'ECA240G0786' => 'eca', 'ECA240G1802' => 'eca', 'ECA240G3760' => 'eca', 'ECA240G3920' => 'eca', 'EL10Ac5g12536' => 'bvu', 'EL10Ac5g12537' => 'bvu', 'EL10Ac5g12538' => 'bvu', 'Eucgr.B01004' => 'egr', 'Eucgr.B01006' => 'egr', 'Eucgr.B01007' => 'egr', 'Eucgr.B01008' => 'egr', 'Eucgr.B01895' => 'egr', 'Eucgr.B01896' => 'egr', 'FAN04G1456' => 'fan', 'FAN08G1769' => 'fan', 'FAN08G2160' => 'fan', 'FAN13G2403' => 'fan', 'FAN13G3303' => 'fan', 'FAN15G2435' => 'fan', 'FAN17G0672' => 'fan', 'FAN17G2441' => 'fan', 'FAN18G1024' => 'fan', 'FAN22G1458' => 'fan', 'FAN24G0037' => 'fan', 'FAN24G0429' => 'fan', 'FAN24G2387' => 'fan', 'FAN27G2746' => 'fan', 'FvH4_2g20400' => 'fve', 'FvH4_2g20420' => 'fve', 'FvH4_2g20430' => 'fve', 'FvH4_4g01270' => 'fve', 'FvH4_4g01290' => 'fve', 'FvH4_4g01300' => 'fve', 'FvH4_4g01310' => 'fve', 'FvH4_4g01330' => 'fve', 'FvH4_5g09070' => 'fve', 'Glyma.10G243800' => 'gma', 'Glyma.20G150600' => 'gma', 'Gohir.A09G219200' => 'ghi', 'Gohir.A09G219300' => 'ghi', 'Gohir.D09G221400' => 'ghi', 'Gohir.D09G221500' => 'ghi', 'Gorai.006G242600' => 'gra', 'Gorai.006G242700' => 'gra', 'GSVIVG01018044001' => 'vvi', 'HanXRQChr03g0083821' => 'han', 'HanXRQChr03g0083841' => 'han', 'HanXRQChr03g0083881' => 'han', 'HanXRQChr03g0083901' => 'han', 'HanXRQChr03g0083921' => 'han', 'HanXRQChr03g0085331' => 'han', 'HanXRQChr03g0085361' => 'han', 'HanXRQChr03g0085411' => 'han', 'HanXRQChr03g0085421' => 'han', 'HanXRQChr03g0085431' => 'han', 'HanXRQChr08g0221991' => 'han', 'HanXRQChr11g0336061' => 'han', 'HanXRQChr11g0336411' => 'han', 'Haze_11234' => 'cav', 'Hma1.2p1_0549F.1_g177010' => 'hma', 'Hma1.2p1_0602F.1_g187630' => 'hma', 'Hund14876' => 'sun', 'Hund14879' => 'sun', 'Lalb_Chr06g0160741' => 'lal', 'Lalb_Chr21g0304781' => 'lal', 'Lj3A726G19' => 'lonja', 'Lj3A726T23' => 'lonja', 'Lj3A726T24' => 'lonja', 'Lj3A726T25' => 'lonja', 'Lj3A727T17' => 'lonja', 'Lj3C726T0' => 'lonja', 'Lj3C726T2' => 'lonja', 'Lj3P725T35' => 'lonja', 'Lj3P727T10' => 'lonja', 'Lj3P727T12' => 'lonja', 'Lj3P727T14' => 'lonja', 'Lj5g0023109' => 'lja', 'Lj6P646T44' => 'lonja', 'Lsat_1_v5_gn_6_75760' => 'lsa', 'Lsat_1_v5_gn_6_75800' => 'lsa', 'Lsat_1_v5_gn_6_75900' => 'lsa', 'Lsat_1_v5_gn_6_76240' => 'lsa', 'Lsat_1_v5_gn_6_76441' => 'lsa', 'Lsat_1_v5_gn_6_76700' => 'lsa', 'Lsat_1_v5_gn_6_76760' => 'lsa', 'Manes.15G033100' => 'mes', 'Mapoly0004s0074' => 'mpo', 'Mapoly0004s0075' => 'mpo', 'Mapoly0004s0163' => 'mpo', 'Mapoly0004s0164' => 'mpo', 'Mapoly0021s0018' => 'mpo', 'Mapoly0041s0136' => 'mpo', 'Mapoly0041s0137' => 'mpo', 'Mapoly0041s0138' => 'mpo', 'Mapoly0041s0139' => 'mpo', 'Mapoly0041s0141' => 'mpo', 'Mapoly0041s0142' => 'mpo', 'Mapoly0041s0143' => 'mpo', 'Mapoly0041s0144' => 'mpo', 'Mapoly0041s0145' => 'mpo', 'Mapoly0047s0106' => 'mpo', 'Mapoly0047s0108' => 'mpo', 'Mapoly0050s0051' => 'mpo', 'Mapoly0050s0052' => 'mpo', 'Mapoly0050s0053' => 'mpo', 'Mapoly0058s0013' => 'mpo', 'Mapoly0091s0078' => 'mpo', 'Mapoly0091s0079' => 'mpo', 'Mapoly0091s0080' => 'mpo', 'Mapoly0091s0081' => 'mpo', 'Mapoly0278s0004' => 'mpo', 'Mapoly0278s0005' => 'mpo', 'Mapoly0278s0006' => 'mpo', 'MBI11_g30648_MAGBIO' => 'mbi', 'MCO03G194' => 'mco', 'MCO03G590' => 'mco', 'MCO07G312' => 'mco', 'MCO10G318' => 'mco', 'MCO12G244' => 'mco', 'MCO13G148' => 'mco', 'MCO13G194' => 'mco', 'MCO16G238' => 'mco', 'MD06G1134100' => 'mdo', 'MD13G1200100' => 'mdo', 'MD13G1200300' => 'mdo', 'MD13G1200600' => 'mdo', 'MD14G1150400' => 'mdo', 'MD16G1200000' => 'mdo', 'Medtr1g102570' => 'mtr', 'Medtr1g102780' => 'mtr', 'Medtr1g102800' => 'mtr', 'Medtr1g102810' => 'mtr', 'Medtr1g102830' => 'mtr', 'MELO3C006499.2' => 'cme', 'Migut.G00385' => 'egut', 'MSTRG.4063' => 'ama', 'Nitab4.5_0000090g0260' => 'nta', 'Nitab4.5_0000977g0030' => 'nta', 'Nitab4.5_0002541g0040' => 'nta', 'Nitab4.5_0007068g0040' => 'nta', 'Nn005s41408' => 'nnu', 'Nn005s41410' => 'nnu', 'Oeu010310.1' => 'oeu', 'Oeu010311.1' => 'oeu', 'Oeu043472.1' => 'oeu', 'Os01g0246400' => 'osa', 'Os04g0267950' => 'osa', 'Os07g0178700' => 'osa', 'Os07g0178800' => 'osa', 'Peaxi162Scf00316g00046' => 'pax', 'Peaxi162Scf00316g00049' => 'pax', 'Peaxi162Scf00316g00059' => 'pax', 'Peaxi162Scf00316g00328' => 'pax', 'Peaxi162Scf00316g00329' => 'pax', 'Peaxi162Scf00316g00411' => 'pax', 'Peaxi162Scf00316g00521' => 'pax', 'Peaxi162Scf00492g00068' => 'pax', 'Peaxi162Scf35631g00002' => 'pax', 'PGR142G3720' => 'pgr', 'PGSC0003DMG400006442' => 'stu', 'Phvul.007G062000' => 'pvu', 'Potri.008G157750' => 'ptr', 'Potri.008G157900' => 'ptr', 'Potri.008G158000' => 'ptr', 'Potri.008G158200' => 'ptr', 'Pp3c11_7280' => 'ppa', 'Pp3c11_7980' => 'ppa', 'Pp3c12_19450' => 'ppa', 'Pp3c14_1480' => 'ppa', 'Pp3c14_1501' => 'ppa', 'Pp3c16_4900' => 'ppa', 'Pp3c16_5010' => 'ppa', 'Pp3c16_5060' => 'ppa', 'Pp3c19_18250' => 'ppa', 'Pp3c23_8530' => 'ppa', 'Pp3c23_8550' => 'ppa', 'Pp3c24_9670' => 'ppa', 'Pp3c2_21390' => 'ppa', 'Pp3c2_31380' => 'ppa', 'Pp3c3_16620' => 'ppa', 'Pp3c3_8090' => 'ppa', 'Pp3c3_8110' => 'ppa', 'Pp3c3_8130' => 'ppa', 'Pp3c3_8150' => 'ppa', 'Pp3c4_14320' => 'ppa', 'Pp3c6_2560' => 'ppa', 'Pp3c9_16700' => 'ppa', 'PRCOL_00000234' => 'pco', 'PRCOL_00000235' => 'pco', 'PRCOL_00000777' => 'pco', 'PRCOL_00002344' => 'pco', 'PRCOL_00002372' => 'pco', 'PRCOL_00006120' => 'pco', 'Prupe.1G021400' => 'ppe', 'Prupe.1G021500' => 'ppe', 'Prupe.1G021600' => 'ppe', 'Prupe.1G021700' => 'ppe', 'Prupe.1G021800' => 'ppe', 'Prupe.5G145100' => 'ppe', 'Psat6g204040' => 'psa', 'Psat6g204800' => 'psa', 'Psat6g204920' => 'psa', 'Psat6g204960' => 'psa', 'Psat6g205080' => 'psa', 'PSO017G0271' => 'pso', 'PSO017G1276' => 'pso', 'PSO017G1429' => 'pso', 'PSO017G1861' => 'pso', 'PSO017G2787' => 'pso', 'PSO017G4466' => 'pso', 'PSO017G5118' => 'pso', 'PSO017G5420' => 'pso', 'PSO063G3678' => 'pso', 'PSO210G0546' => 'pso', 'PSO317G0001' => 'pso', 'PSO357G0512' => 'pso', 'PSO478G2682' => 'pso', 'PSO647G0001' => 'pso', 'PSO675G0001' => 'pso', 'PSO675G2699' => 'pso', 'PSO675G2849' => 'pso', 'PSO675G4991' => 'pso', 'PSO689G0001' => 'pso', 'QL06p000916' => 'qlo', 'QL06p000921' => 'qlo', 'QL06p001398' => 'qlo', 'QL06p001407' => 'qlo', 'QL06p002031' => 'qlo', 'RcHm_v2.0_Chr4g0387791' => 'rch', 'RcHm_v2.0_Chr4g0387801' => 'rch', 'RcHm_v2.0_Chr6g0286501' => 'rch', 'RcHm_v2.0_Chr6g0286511' => 'rch', 'RcHm_v2.0_Chr6g0286521' => 'rch', 'RcHm_v2.0_Chr6g0286531' => 'rch', 'RcHm_v2.0_Chr7g0189141' => 'rch', 'Rhsim02G0028700' => 'rsi', 'Rhsim02G0028800' => 'rsi', 'Rhsim02G0028900' => 'rsi', 'Rhsim02G0029000' => 'rsi', 'Rhsim02G0029100' => 'rsi', 'Rhsim02G0029200' => 'rsi', 'Rhsim02G0029300' => 'rsi', 'Rhsim02G0029400' => 'rsi', 'Rhsim02G0029500' => 'rsi', 'Rhsim02G0029600' => 'rsi', 'RhsimUnG0024000' => 'rsi', 'RhsimUnG0024100' => 'rsi', 'RhsimUnG0024200' => 'rsi', 'RhsimUnG0024300' => 'rsi', 'RhsimUnG0024400' => 'rsi', 'RhsimUnG0024500' => 'rsi', 'RhsimUnG0024700' => 'rsi', 'RhsimUnG0024800' => 'rsi', 'RhsimUnG0024900' => 'rsi', 'RhsimUnG0025100' => 'rsi', 'Sabra08G0120200' => 'sbr', 'Sabra08G0120300' => 'sbr', 'Sabra08G0120500' => 'sbr', 'Sabra08G0120600' => 'sbr', 'Sabra10G0158900' => 'sbr', 'SalBow2G3492' => 'sbo', 'Sc13g0004760' => 'sci', 'Sc13g0004770' => 'sci', 'Sed0003417' => 'sed', 'Sed0019750' => 'sed', 'SEGI_03419' => 'sgi', 'SEGI_05907' => 'sgi', 'SEGI_10682' => 'sgi', 'SEGI_13528' => 'sgi', 'SEGI_16081' => 'sgi', 'SEGI_19370' => 'sgi', 'SEGI_21015' => 'sgi', 'SEGI_21944' => 'sgi', 'SEGI_32906' => 'sgi', 'SEGI_33093' => 'sgi', 'SEGI_36110' => 'sgi', 'SEGI_40397' => 'sgi', 'SGA_v2.0_scaffold191G40426' => 'sas', 'SGA_v2.0_scaffold353G49717' => 'sas', 'SGA_v2.0_scaffold50G18550' => 'sas', 'SMO119G0173' => 'smo', 'SMO172G0002' => 'smo', 'Solyc09g082690.3' => 'sly', 'Solyc09g082700.2' => 'sly', 'Sopen09g031550' => 'spe', 'Sopen09g031560' => 'spe', 'Sp3g20540' => 'spa', 'Sp7g07580' => 'spa', 'TAR134G0002' => 'tar', 'TAR236G0001' => 'tar', 'TAR365G0892' => 'tar', 'TAR636G0166' => 'tar', 'TAR636G0646' => 'tar', 'TAR636G0869' => 'tar', 'TAR636G1317' => 'tar', 'TAR636G1744' => 'tar', 'TAR636G3358' => 'tar', 'TAR636G3436' => 'tar', 'THA.LOC104803047' => 'tha', 'Thecc.04G238900' => 'tca', 'Thhalv10021557m.g' => 'esa', 'Thhalv10026318m.g' => 'esa', 'Thhalv10026335m.g' => 'esa', 'TPR.G17433' => 'tpr', 'TPR.G18915' => 'tpr', 'TPR.G26125' => 'tpr', 'TWI09G0677' => 'twi', 'TWI73G0287' => 'twi', 'unitig_748.g8326' => 'ugi', 'vmacro15370' => 'vma', 'vmacro15371' => 'vma', 'vmacro15372' => 'vma', 'vmacro15373' => 'vma', 'vmacro15374' => 'vma', 'VMungo0720G2826' => 'vmu', 'Zm00001eb116960' => 'zma', 'Zm00001eb301260' => 'zma', 'Zm00001eb301270' => 'zma' ) $gf_id = 'HOM05D001460' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001460' ) $data_identifier = 'HOM05D001460' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 4, 'aag' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 2, 'aox' => (int) 2, 'arhy' => (int) 4, 'ath' => (int) 2, 'atr' => (int) 1, 'acertr' => (int) 10, 'cqu' => (int) 4, 'bca' => (int) 11, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 1, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 1, 'ccan' => (int) 1, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 1, 'col' => (int) 1, 'cpa' => (int) 1, 'cre' => (int) 7, 'csa' => (int) 1, 'camsi' => (int) 2, 'dca' => (int) 3, 'din' => (int) 2, 'dzi' => (int) 3, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 14, 'fve' => (int) 9, 'gma' => (int) 2, 'ghi' => (int) 4, 'gra' => (int) 2, 'vvi' => (int) 1, 'han' => (int) 13, 'cav' => (int) 1, 'hma' => (int) 2, 'sun' => (int) 2, 'lal' => (int) 2, 'lonja' => (int) 12, 'lja' => (int) 1, 'lsa' => (int) 7, 'mes' => (int) 1, 'mpo' => (int) 27, 'mbi' => (int) 1, 'mco' => (int) 8, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 1, 'egut' => (int) 1, 'ama' => (int) 1, 'nta' => (int) 4, 'nnu' => (int) 2, 'oeu' => (int) 3, 'osa' => (int) 4, 'pax' => (int) 9, 'pgr' => (int) 1, 'stu' => (int) 1, 'pvu' => (int) 1, 'ptr' => (int) 4, 'ppa' => (int) 22, 'pco' => (int) 6, 'ppe' => (int) 6, 'psa' => (int) 5, 'pso' => (int) 19, 'qlo' => (int) 5, 'rch' => (int) 7, 'rsi' => (int) 20, 'sbr' => (int) 5, 'sbo' => (int) 1, 'sci' => (int) 2, 'sed' => (int) 2, 'sgi' => (int) 12, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 2, 'tar' => (int) 10, 'tha' => (int) 1, 'tca' => (int) 1, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 2, 'ugi' => (int) 1, 'vma' => (int) 5, 'vmu' => (int) 1, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb301270' $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' => 'HOM05D001460', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '433', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p22980' => 'bna', 'A01p32340' => 'bna', 'A03p42970' => 'bna', 'A05p25880' => 'bna', 'Aa31LG8G9320' => 'aar', 'Aa31LG8G9330' => 'aar', 'Aa31LG8G9340' => 'aar', 'Aa31sc221G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1034' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1528' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.829' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2222' => 'aag', 'Ah.12g058830' => 'amhyb', 'Ah.12g058840' => 'amhyb', 'AL3G37160' => 'aly', 'AL7G41310' => 'aly', 'Aqoxy5G00395' => 'aox', 'Aqoxy5G00396' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0C8NZA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5185HY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JZ1PRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MD3LS0' => 'arhy', 'AT3G22840' => 'ath', 'AT4G14690' => 'ath', 'ATR0665G054' => 'atr', 'Atru.chr4.2344' => 'acertr', 'Atru.chr4.2346' => 'acertr', 'Atru.chr4.2347' => 'acertr', 'Atru.chr4.2348' => 'acertr', 'Atru.chr4.2355' => 'acertr', 'Atru.chr4.2356' => 'acertr', 'Atru.chr4.2358' => 'acertr', 'Atru.chr4.2359' => 'acertr', 'Atru.chr4.2360' => 'acertr', 'Atru.chr4.2361' => 'acertr', 'AUR62030476' => 'cqu', 'AUR62030478' => 'cqu', 'AUR62030819' => 'cqu', 'AUR62030820' => 'cqu', 'BcaB03g14648' => 'bca', 'BcaB04g20492' => 'bca', 'BcaB06g26399' => 'bca', 'BcaC01g03416' => 'bca', 'BcaC01g03419' => 'bca', 'BcaC01g03421' => 'bca', 'BcaC01g03424' => 'bca', 'BcaC05g28012' => 'bca', 'BcaC09g49212' => 'bca', 'BcaC09g50140' => 'bca', 'BcaNung00346' => 'bca', 'BolC1t02785H' => 'bol', 'BolC1t04095H' => 'bol', 'BolC3t17545H' => 'bol', 'BolC5t32769H' => 'bol', 'BraA01t02211Z' => 'bra', 'BraA01t03359Z' => 'bra', 'BraA03t13441Z' => 'bra', 'BraA05t21476Z' => 'bra', 'C01p28420' => 'bna', 'C01p41350' => 'bna', 'C03p52750' => 'bna', 'C03p52780' => 'bna', 'C05p40270' => 'bna', 'CAN.G1437.9' => 'can', 'CANSAT78G0035' => 'cansat', 'CANSAT78G1036' => 'cansat', 'CANSAT78G2272' => 'cansat', 'CANSAT78G2478' => 'cansat', 'CARHR098700' => 'chi', 'CARHR221120' => 'chi', 'CARHR221150' => 'chi', 'Carub.0003s2297' => 'cru', 'Carub.0007s2749' => 'cru', 'Carub.0007s2750' => 'cru', 'Carub.0007s2751' => 'cru', 'Ca_10849_v3' => 'car', 'Cc03_g04300' => 'ccan', 'CDE02G3648' => 'cde', 'CDE05G0060' => 'cde', 'CDE05G0692' => 'cde', 'CDE05G2285' => 'cde', 'CDE05G2884' => 'cde', 'CDE05G3072' => 'cde', 'Cfa008439' => 'cfa', 'Cfa008441' => 'cfa', 'Cfa008443' => 'cfa', 'Cfa008448' => 'cfa', 'Ciclev10005974m.g' => 'ccl', 'Ciclev10006006m.g' => 'ccl', 'Ciclev10006775m.g' => 'ccl', 'CiPaw.02G120400' => 'cil', 'CiPaw.02G120500' => 'cil', 'CiPaw.02G120600' => 'cil', 'ClCG05G004850' => 'cla', 'COL.COLO4_21566' => 'col', 'Cpa.g.sc44.124' => 'cpa', 'Cre07.g320400' => 'cre', 'Cre07.g320450' => 'cre', 'Cre08.g384650' => 'cre', 'Cre09.g393173' => 'cre', 'Cre09.g394325' => 'cre', 'Cre14.g626750' => 'cre', 'Cre16.g679250' => 'cre', 'CsaV3_3G012890' => 'csa', 'CSS0010865' => 'camsi', 'CSS0044338' => 'camsi', 'DCAR_002366' => 'dca', 'DCAR_030687' => 'dca', 'DCAR_030688' => 'dca', 'Dinv14047' => 'din', 'Dinv14048' => 'din', 'Duzib151G0105' => 'dzi', 'Duzib151G0114' => 'dzi', 'Duzib212G1029' => 'dzi', 'ECA232G3536' => 'eca', 'ECA240G0786' => 'eca', 'ECA240G1802' => 'eca', 'ECA240G3760' => 'eca', 'ECA240G3920' => 'eca', 'EL10Ac5g12536' => 'bvu', 'EL10Ac5g12537' => 'bvu', 'EL10Ac5g12538' => 'bvu', 'Eucgr.B01004' => 'egr', 'Eucgr.B01006' => 'egr', 'Eucgr.B01007' => 'egr', 'Eucgr.B01008' => 'egr', 'Eucgr.B01895' => 'egr', 'Eucgr.B01896' => 'egr', 'FAN04G1456' => 'fan', 'FAN08G1769' => 'fan', 'FAN08G2160' => 'fan', 'FAN13G2403' => 'fan', 'FAN13G3303' => 'fan', 'FAN15G2435' => 'fan', 'FAN17G0672' => 'fan', 'FAN17G2441' => 'fan', 'FAN18G1024' => 'fan', 'FAN22G1458' => 'fan', 'FAN24G0037' => 'fan', 'FAN24G0429' => 'fan', 'FAN24G2387' => 'fan', 'FAN27G2746' => 'fan', 'FvH4_2g20400' => 'fve', 'FvH4_2g20420' => 'fve', 'FvH4_2g20430' => 'fve', 'FvH4_4g01270' => 'fve', 'FvH4_4g01290' => 'fve', 'FvH4_4g01300' => 'fve', 'FvH4_4g01310' => 'fve', 'FvH4_4g01330' => 'fve', 'FvH4_5g09070' => 'fve', 'Glyma.10G243800' => 'gma', 'Glyma.20G150600' => 'gma', 'Gohir.A09G219200' => 'ghi', 'Gohir.A09G219300' => 'ghi', 'Gohir.D09G221400' => 'ghi', 'Gohir.D09G221500' => 'ghi', 'Gorai.006G242600' => 'gra', 'Gorai.006G242700' => 'gra', 'GSVIVG01018044001' => 'vvi', 'HanXRQChr03g0083821' => 'han', 'HanXRQChr03g0083841' => 'han', 'HanXRQChr03g0083881' => 'han', 'HanXRQChr03g0083901' => 'han', 'HanXRQChr03g0083921' => 'han', 'HanXRQChr03g0085331' => 'han', 'HanXRQChr03g0085361' => 'han', 'HanXRQChr03g0085411' => 'han', 'HanXRQChr03g0085421' => 'han', 'HanXRQChr03g0085431' => 'han', 'HanXRQChr08g0221991' => 'han', 'HanXRQChr11g0336061' => 'han', 'HanXRQChr11g0336411' => 'han', 'Haze_11234' => 'cav', 'Hma1.2p1_0549F.1_g177010' => 'hma', 'Hma1.2p1_0602F.1_g187630' => 'hma', 'Hund14876' => 'sun', 'Hund14879' => 'sun', 'Lalb_Chr06g0160741' => 'lal', 'Lalb_Chr21g0304781' => 'lal', 'Lj3A726G19' => 'lonja', 'Lj3A726T23' => 'lonja', 'Lj3A726T24' => 'lonja', 'Lj3A726T25' => 'lonja', 'Lj3A727T17' => 'lonja', 'Lj3C726T0' => 'lonja', 'Lj3C726T2' => 'lonja', 'Lj3P725T35' => 'lonja', 'Lj3P727T10' => 'lonja', 'Lj3P727T12' => 'lonja', 'Lj3P727T14' => 'lonja', 'Lj5g0023109' => 'lja', 'Lj6P646T44' => 'lonja', 'Lsat_1_v5_gn_6_75760' => 'lsa', 'Lsat_1_v5_gn_6_75800' => 'lsa', 'Lsat_1_v5_gn_6_75900' => 'lsa', 'Lsat_1_v5_gn_6_76240' => 'lsa', 'Lsat_1_v5_gn_6_76441' => 'lsa', 'Lsat_1_v5_gn_6_76700' => 'lsa', 'Lsat_1_v5_gn_6_76760' => 'lsa', 'Manes.15G033100' => 'mes', 'Mapoly0004s0074' => 'mpo', 'Mapoly0004s0075' => 'mpo', 'Mapoly0004s0163' => 'mpo', 'Mapoly0004s0164' => 'mpo', 'Mapoly0021s0018' => 'mpo', 'Mapoly0041s0136' => 'mpo', 'Mapoly0041s0137' => 'mpo', 'Mapoly0041s0138' => 'mpo', 'Mapoly0041s0139' => 'mpo', 'Mapoly0041s0141' => 'mpo', 'Mapoly0041s0142' => 'mpo', 'Mapoly0041s0143' => 'mpo', 'Mapoly0041s0144' => 'mpo', 'Mapoly0041s0145' => 'mpo', 'Mapoly0047s0106' => 'mpo', 'Mapoly0047s0108' => 'mpo', 'Mapoly0050s0051' => 'mpo', 'Mapoly0050s0052' => 'mpo', 'Mapoly0050s0053' => 'mpo', 'Mapoly0058s0013' => 'mpo', 'Mapoly0091s0078' => 'mpo', 'Mapoly0091s0079' => 'mpo', 'Mapoly0091s0080' => 'mpo', 'Mapoly0091s0081' => 'mpo', 'Mapoly0278s0004' => 'mpo', 'Mapoly0278s0005' => 'mpo', 'Mapoly0278s0006' => 'mpo', 'MBI11_g30648_MAGBIO' => 'mbi', 'MCO03G194' => 'mco', 'MCO03G590' => 'mco', 'MCO07G312' => 'mco', 'MCO10G318' => 'mco', 'MCO12G244' => 'mco', 'MCO13G148' => 'mco', 'MCO13G194' => 'mco', 'MCO16G238' => 'mco', 'MD06G1134100' => 'mdo', 'MD13G1200100' => 'mdo', 'MD13G1200300' => 'mdo', 'MD13G1200600' => 'mdo', 'MD14G1150400' => 'mdo', 'MD16G1200000' => 'mdo', 'Medtr1g102570' => 'mtr', 'Medtr1g102780' => 'mtr', 'Medtr1g102800' => 'mtr', 'Medtr1g102810' => 'mtr', 'Medtr1g102830' => 'mtr', 'MELO3C006499.2' => 'cme', 'Migut.G00385' => 'egut', 'MSTRG.4063' => 'ama', 'Nitab4.5_0000090g0260' => 'nta', 'Nitab4.5_0000977g0030' => 'nta', 'Nitab4.5_0002541g0040' => 'nta', 'Nitab4.5_0007068g0040' => 'nta', 'Nn005s41408' => 'nnu', 'Nn005s41410' => 'nnu', 'Oeu010310.1' => 'oeu', 'Oeu010311.1' => 'oeu', 'Oeu043472.1' => 'oeu', 'Os01g0246400' => 'osa', 'Os04g0267950' => 'osa', 'Os07g0178700' => 'osa', 'Os07g0178800' => 'osa', 'Peaxi162Scf00316g00046' => 'pax', 'Peaxi162Scf00316g00049' => 'pax', 'Peaxi162Scf00316g00059' => 'pax', 'Peaxi162Scf00316g00328' => 'pax', 'Peaxi162Scf00316g00329' => 'pax', 'Peaxi162Scf00316g00411' => 'pax', 'Peaxi162Scf00316g00521' => 'pax', 'Peaxi162Scf00492g00068' => 'pax', 'Peaxi162Scf35631g00002' => 'pax', 'PGR142G3720' => 'pgr', 'PGSC0003DMG400006442' => 'stu', 'Phvul.007G062000' => 'pvu', 'Potri.008G157750' => 'ptr', 'Potri.008G157900' => 'ptr', 'Potri.008G158000' => 'ptr', 'Potri.008G158200' => 'ptr', 'Pp3c11_7280' => 'ppa', 'Pp3c11_7980' => 'ppa', 'Pp3c12_19450' => 'ppa', 'Pp3c14_1480' => 'ppa', 'Pp3c14_1501' => 'ppa', 'Pp3c16_4900' => 'ppa', 'Pp3c16_5010' => 'ppa', 'Pp3c16_5060' => 'ppa', 'Pp3c19_18250' => 'ppa', 'Pp3c23_8530' => 'ppa', 'Pp3c23_8550' => 'ppa', 'Pp3c24_9670' => 'ppa', 'Pp3c2_21390' => 'ppa', 'Pp3c2_31380' => 'ppa', 'Pp3c3_16620' => 'ppa', 'Pp3c3_8090' => 'ppa', 'Pp3c3_8110' => 'ppa', 'Pp3c3_8130' => 'ppa', 'Pp3c3_8150' => 'ppa', 'Pp3c4_14320' => 'ppa', 'Pp3c6_2560' => 'ppa', 'Pp3c9_16700' => 'ppa', 'PRCOL_00000234' => 'pco', 'PRCOL_00000235' => 'pco', 'PRCOL_00000777' => 'pco', 'PRCOL_00002344' => 'pco', 'PRCOL_00002372' => 'pco', 'PRCOL_00006120' => 'pco', 'Prupe.1G021400' => 'ppe', 'Prupe.1G021500' => 'ppe', 'Prupe.1G021600' => 'ppe', 'Prupe.1G021700' => 'ppe', 'Prupe.1G021800' => 'ppe', 'Prupe.5G145100' => 'ppe', 'Psat6g204040' => 'psa', 'Psat6g204800' => 'psa', 'Psat6g204920' => 'psa', 'Psat6g204960' => 'psa', 'Psat6g205080' => 'psa', 'PSO017G0271' => 'pso', 'PSO017G1276' => 'pso', 'PSO017G1429' => 'pso', 'PSO017G1861' => 'pso', 'PSO017G2787' => 'pso', 'PSO017G4466' => 'pso', 'PSO017G5118' => 'pso', 'PSO017G5420' => 'pso', 'PSO063G3678' => 'pso', 'PSO210G0546' => 'pso', 'PSO317G0001' => 'pso', 'PSO357G0512' => 'pso', 'PSO478G2682' => 'pso', 'PSO647G0001' => 'pso', 'PSO675G0001' => 'pso', 'PSO675G2699' => 'pso', 'PSO675G2849' => 'pso', 'PSO675G4991' => 'pso', 'PSO689G0001' => 'pso', 'QL06p000916' => 'qlo', 'QL06p000921' => 'qlo', 'QL06p001398' => 'qlo', 'QL06p001407' => 'qlo', 'QL06p002031' => 'qlo', 'RcHm_v2.0_Chr4g0387791' => 'rch', 'RcHm_v2.0_Chr4g0387801' => 'rch', 'RcHm_v2.0_Chr6g0286501' => 'rch', 'RcHm_v2.0_Chr6g0286511' => 'rch', 'RcHm_v2.0_Chr6g0286521' => 'rch', 'RcHm_v2.0_Chr6g0286531' => 'rch', 'RcHm_v2.0_Chr7g0189141' => 'rch', 'Rhsim02G0028700' => 'rsi', 'Rhsim02G0028800' => 'rsi', 'Rhsim02G0028900' => 'rsi', 'Rhsim02G0029000' => 'rsi', 'Rhsim02G0029100' => 'rsi', 'Rhsim02G0029200' => 'rsi', 'Rhsim02G0029300' => 'rsi', 'Rhsim02G0029400' => 'rsi', 'Rhsim02G0029500' => 'rsi', 'Rhsim02G0029600' => 'rsi', 'RhsimUnG0024000' => 'rsi', 'RhsimUnG0024100' => 'rsi', 'RhsimUnG0024200' => 'rsi', 'RhsimUnG0024300' => 'rsi', 'RhsimUnG0024400' => 'rsi', 'RhsimUnG0024500' => 'rsi', 'RhsimUnG0024700' => 'rsi', 'RhsimUnG0024800' => 'rsi', 'RhsimUnG0024900' => 'rsi', 'RhsimUnG0025100' => 'rsi', 'Sabra08G0120200' => 'sbr', 'Sabra08G0120300' => 'sbr', 'Sabra08G0120500' => 'sbr', 'Sabra08G0120600' => 'sbr', 'Sabra10G0158900' => 'sbr', 'SalBow2G3492' => 'sbo', 'Sc13g0004760' => 'sci', 'Sc13g0004770' => 'sci', 'Sed0003417' => 'sed', 'Sed0019750' => 'sed', 'SEGI_03419' => 'sgi', 'SEGI_05907' => 'sgi', 'SEGI_10682' => 'sgi', 'SEGI_13528' => 'sgi', 'SEGI_16081' => 'sgi', 'SEGI_19370' => 'sgi', 'SEGI_21015' => 'sgi', 'SEGI_21944' => 'sgi', 'SEGI_32906' => 'sgi', 'SEGI_33093' => 'sgi', 'SEGI_36110' => 'sgi', 'SEGI_40397' => 'sgi', 'SGA_v2.0_scaffold191G40426' => 'sas', 'SGA_v2.0_scaffold353G49717' => 'sas', 'SGA_v2.0_scaffold50G18550' => 'sas', 'SMO119G0173' => 'smo', 'SMO172G0002' => 'smo', 'Solyc09g082690.3' => 'sly', 'Solyc09g082700.2' => 'sly', 'Sopen09g031550' => 'spe', 'Sopen09g031560' => 'spe', 'Sp3g20540' => 'spa', 'Sp7g07580' => 'spa', 'TAR134G0002' => 'tar', 'TAR236G0001' => 'tar', 'TAR365G0892' => 'tar', 'TAR636G0166' => 'tar', 'TAR636G0646' => 'tar', 'TAR636G0869' => 'tar', 'TAR636G1317' => 'tar', 'TAR636G1744' => 'tar', 'TAR636G3358' => 'tar', 'TAR636G3436' => 'tar', 'THA.LOC104803047' => 'tha', 'Thecc.04G238900' => 'tca', 'Thhalv10021557m.g' => 'esa', 'Thhalv10026318m.g' => 'esa', 'Thhalv10026335m.g' => 'esa', 'TPR.G17433' => 'tpr', 'TPR.G18915' => 'tpr', 'TPR.G26125' => 'tpr', 'TWI09G0677' => 'twi', 'TWI73G0287' => 'twi', 'unitig_748.g8326' => 'ugi', 'vmacro15370' => 'vma', 'vmacro15371' => 'vma', 'vmacro15372' => 'vma', 'vmacro15373' => 'vma', 'vmacro15374' => 'vma', 'VMungo0720G2826' => 'vmu', 'Zm00001eb116960' => 'zma', 'Zm00001eb301260' => 'zma', 'Zm00001eb301270' => 'zma' ), 'gf_id' => 'HOM05D001460', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001460' ), 'data_identifier' => 'HOM05D001460', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001460', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '433', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p22980' => 'bna', 'A01p32340' => 'bna', 'A03p42970' => 'bna', 'A05p25880' => 'bna', 'Aa31LG8G9320' => 'aar', 'Aa31LG8G9330' => 'aar', 'Aa31LG8G9340' => 'aar', 'Aa31sc221G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1034' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1528' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.829' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2222' => 'aag', 'Ah.12g058830' => 'amhyb', 'Ah.12g058840' => 'amhyb', 'AL3G37160' => 'aly', 'AL7G41310' => 'aly', 'Aqoxy5G00395' => 'aox', 'Aqoxy5G00396' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0C8NZA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5185HY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JZ1PRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MD3LS0' => 'arhy', 'AT3G22840' => 'ath', 'AT4G14690' => 'ath', 'ATR0665G054' => 'atr', 'Atru.chr4.2344' => 'acertr', 'Atru.chr4.2346' => 'acertr', 'Atru.chr4.2347' => 'acertr', 'Atru.chr4.2348' => 'acertr', 'Atru.chr4.2355' => 'acertr', 'Atru.chr4.2356' => 'acertr', 'Atru.chr4.2358' => 'acertr', 'Atru.chr4.2359' => 'acertr', 'Atru.chr4.2360' => 'acertr', 'Atru.chr4.2361' => 'acertr', 'AUR62030476' => 'cqu', 'AUR62030478' => 'cqu', 'AUR62030819' => 'cqu', 'AUR62030820' => 'cqu', 'BcaB03g14648' => 'bca', 'BcaB04g20492' => 'bca', 'BcaB06g26399' => 'bca', 'BcaC01g03416' => 'bca', 'BcaC01g03419' => 'bca', 'BcaC01g03421' => 'bca', 'BcaC01g03424' => 'bca', 'BcaC05g28012' => 'bca', 'BcaC09g49212' => 'bca', 'BcaC09g50140' => 'bca', 'BcaNung00346' => 'bca', 'BolC1t02785H' => 'bol', 'BolC1t04095H' => 'bol', 'BolC3t17545H' => 'bol', 'BolC5t32769H' => 'bol', 'BraA01t02211Z' => 'bra', 'BraA01t03359Z' => 'bra', 'BraA03t13441Z' => 'bra', 'BraA05t21476Z' => 'bra', 'C01p28420' => 'bna', 'C01p41350' => 'bna', 'C03p52750' => 'bna', 'C03p52780' => 'bna', 'C05p40270' => 'bna', 'CAN.G1437.9' => 'can', 'CANSAT78G0035' => 'cansat', 'CANSAT78G1036' => 'cansat', 'CANSAT78G2272' => 'cansat', 'CANSAT78G2478' => 'cansat', 'CARHR098700' => 'chi', 'CARHR221120' => 'chi', 'CARHR221150' => 'chi', 'Carub.0003s2297' => 'cru', 'Carub.0007s2749' => 'cru', 'Carub.0007s2750' => 'cru', 'Carub.0007s2751' => 'cru', 'Ca_10849_v3' => 'car', 'Cc03_g04300' => 'ccan', 'CDE02G3648' => 'cde', 'CDE05G0060' => 'cde', 'CDE05G0692' => 'cde', 'CDE05G2285' => 'cde', 'CDE05G2884' => 'cde', 'CDE05G3072' => 'cde', 'Cfa008439' => 'cfa', 'Cfa008441' => 'cfa', 'Cfa008443' => 'cfa', 'Cfa008448' => 'cfa', 'Ciclev10005974m.g' => 'ccl', 'Ciclev10006006m.g' => 'ccl', 'Ciclev10006775m.g' => 'ccl', 'CiPaw.02G120400' => 'cil', 'CiPaw.02G120500' => 'cil', 'CiPaw.02G120600' => 'cil', 'ClCG05G004850' => 'cla', 'COL.COLO4_21566' => 'col', 'Cpa.g.sc44.124' => 'cpa', 'Cre07.g320400' => 'cre', 'Cre07.g320450' => 'cre', 'Cre08.g384650' => 'cre', 'Cre09.g393173' => 'cre', 'Cre09.g394325' => 'cre', 'Cre14.g626750' => 'cre', 'Cre16.g679250' => 'cre', 'CsaV3_3G012890' => 'csa', 'CSS0010865' => 'camsi', 'CSS0044338' => 'camsi', 'DCAR_002366' => 'dca', 'DCAR_030687' => 'dca', 'DCAR_030688' => 'dca', 'Dinv14047' => 'din', 'Dinv14048' => 'din', 'Duzib151G0105' => 'dzi', 'Duzib151G0114' => 'dzi', 'Duzib212G1029' => 'dzi', 'ECA232G3536' => 'eca', 'ECA240G0786' => 'eca', 'ECA240G1802' => 'eca', 'ECA240G3760' => 'eca', 'ECA240G3920' => 'eca', 'EL10Ac5g12536' => 'bvu', 'EL10Ac5g12537' => 'bvu', 'EL10Ac5g12538' => 'bvu', 'Eucgr.B01004' => 'egr', 'Eucgr.B01006' => 'egr', 'Eucgr.B01007' => 'egr', 'Eucgr.B01008' => 'egr', 'Eucgr.B01895' => 'egr', 'Eucgr.B01896' => 'egr', 'FAN04G1456' => 'fan', 'FAN08G1769' => 'fan', 'FAN08G2160' => 'fan', 'FAN13G2403' => 'fan', 'FAN13G3303' => 'fan', 'FAN15G2435' => 'fan', 'FAN17G0672' => 'fan', 'FAN17G2441' => 'fan', 'FAN18G1024' => 'fan', 'FAN22G1458' => 'fan', 'FAN24G0037' => 'fan', 'FAN24G0429' => 'fan', 'FAN24G2387' => 'fan', 'FAN27G2746' => 'fan', 'FvH4_2g20400' => 'fve', 'FvH4_2g20420' => 'fve', 'FvH4_2g20430' => 'fve', 'FvH4_4g01270' => 'fve', 'FvH4_4g01290' => 'fve', 'FvH4_4g01300' => 'fve', 'FvH4_4g01310' => 'fve', 'FvH4_4g01330' => 'fve', 'FvH4_5g09070' => 'fve', 'Glyma.10G243800' => 'gma', 'Glyma.20G150600' => 'gma', 'Gohir.A09G219200' => 'ghi', 'Gohir.A09G219300' => 'ghi', 'Gohir.D09G221400' => 'ghi', 'Gohir.D09G221500' => 'ghi', 'Gorai.006G242600' => 'gra', 'Gorai.006G242700' => 'gra', 'GSVIVG01018044001' => 'vvi', 'HanXRQChr03g0083821' => 'han', 'HanXRQChr03g0083841' => 'han', 'HanXRQChr03g0083881' => 'han', 'HanXRQChr03g0083901' => 'han', 'HanXRQChr03g0083921' => 'han', 'HanXRQChr03g0085331' => 'han', 'HanXRQChr03g0085361' => 'han', 'HanXRQChr03g0085411' => 'han', 'HanXRQChr03g0085421' => 'han', 'HanXRQChr03g0085431' => 'han', 'HanXRQChr08g0221991' => 'han', 'HanXRQChr11g0336061' => 'han', 'HanXRQChr11g0336411' => 'han', 'Haze_11234' => 'cav', 'Hma1.2p1_0549F.1_g177010' => 'hma', 'Hma1.2p1_0602F.1_g187630' => 'hma', 'Hund14876' => 'sun', 'Hund14879' => 'sun', 'Lalb_Chr06g0160741' => 'lal', 'Lalb_Chr21g0304781' => 'lal', 'Lj3A726G19' => 'lonja', 'Lj3A726T23' => 'lonja', 'Lj3A726T24' => 'lonja', 'Lj3A726T25' => 'lonja', 'Lj3A727T17' => 'lonja', 'Lj3C726T0' => 'lonja', 'Lj3C726T2' => 'lonja', 'Lj3P725T35' => 'lonja', 'Lj3P727T10' => 'lonja', 'Lj3P727T12' => 'lonja', 'Lj3P727T14' => 'lonja', 'Lj5g0023109' => 'lja', 'Lj6P646T44' => 'lonja', 'Lsat_1_v5_gn_6_75760' => 'lsa', 'Lsat_1_v5_gn_6_75800' => 'lsa', 'Lsat_1_v5_gn_6_75900' => 'lsa', 'Lsat_1_v5_gn_6_76240' => 'lsa', 'Lsat_1_v5_gn_6_76441' => 'lsa', 'Lsat_1_v5_gn_6_76700' => 'lsa', 'Lsat_1_v5_gn_6_76760' => 'lsa', 'Manes.15G033100' => 'mes', 'Mapoly0004s0074' => 'mpo', 'Mapoly0004s0075' => 'mpo', 'Mapoly0004s0163' => 'mpo', 'Mapoly0004s0164' => 'mpo', 'Mapoly0021s0018' => 'mpo', 'Mapoly0041s0136' => 'mpo', 'Mapoly0041s0137' => 'mpo', 'Mapoly0041s0138' => 'mpo', 'Mapoly0041s0139' => 'mpo', 'Mapoly0041s0141' => 'mpo', 'Mapoly0041s0142' => 'mpo', 'Mapoly0041s0143' => 'mpo', 'Mapoly0041s0144' => 'mpo', 'Mapoly0041s0145' => 'mpo', 'Mapoly0047s0106' => 'mpo', 'Mapoly0047s0108' => 'mpo', 'Mapoly0050s0051' => 'mpo', 'Mapoly0050s0052' => 'mpo', 'Mapoly0050s0053' => 'mpo', 'Mapoly0058s0013' => 'mpo', 'Mapoly0091s0078' => 'mpo', 'Mapoly0091s0079' => 'mpo', 'Mapoly0091s0080' => 'mpo', 'Mapoly0091s0081' => 'mpo', 'Mapoly0278s0004' => 'mpo', 'Mapoly0278s0005' => 'mpo', 'Mapoly0278s0006' => 'mpo', 'MBI11_g30648_MAGBIO' => 'mbi', 'MCO03G194' => 'mco', 'MCO03G590' => 'mco', 'MCO07G312' => 'mco', 'MCO10G318' => 'mco', 'MCO12G244' => 'mco', 'MCO13G148' => 'mco', 'MCO13G194' => 'mco', 'MCO16G238' => 'mco', 'MD06G1134100' => 'mdo', 'MD13G1200100' => 'mdo', 'MD13G1200300' => 'mdo', 'MD13G1200600' => 'mdo', 'MD14G1150400' => 'mdo', 'MD16G1200000' => 'mdo', 'Medtr1g102570' => 'mtr', 'Medtr1g102780' => 'mtr', 'Medtr1g102800' => 'mtr', 'Medtr1g102810' => 'mtr', 'Medtr1g102830' => 'mtr', 'MELO3C006499.2' => 'cme', 'Migut.G00385' => 'egut', 'MSTRG.4063' => 'ama', 'Nitab4.5_0000090g0260' => 'nta', 'Nitab4.5_0000977g0030' => 'nta', 'Nitab4.5_0002541g0040' => 'nta', 'Nitab4.5_0007068g0040' => 'nta', 'Nn005s41408' => 'nnu', 'Nn005s41410' => 'nnu', 'Oeu010310.1' => 'oeu', 'Oeu010311.1' => 'oeu', 'Oeu043472.1' => 'oeu', 'Os01g0246400' => 'osa', 'Os04g0267950' => 'osa', 'Os07g0178700' => 'osa', 'Os07g0178800' => 'osa', 'Peaxi162Scf00316g00046' => 'pax', 'Peaxi162Scf00316g00049' => 'pax', 'Peaxi162Scf00316g00059' => 'pax', 'Peaxi162Scf00316g00328' => 'pax', 'Peaxi162Scf00316g00329' => 'pax', 'Peaxi162Scf00316g00411' => 'pax', 'Peaxi162Scf00316g00521' => 'pax', 'Peaxi162Scf00492g00068' => 'pax', 'Peaxi162Scf35631g00002' => 'pax', 'PGR142G3720' => 'pgr', 'PGSC0003DMG400006442' => 'stu', 'Phvul.007G062000' => 'pvu', 'Potri.008G157750' => 'ptr', 'Potri.008G157900' => 'ptr', 'Potri.008G158000' => 'ptr', 'Potri.008G158200' => 'ptr', 'Pp3c11_7280' => 'ppa', 'Pp3c11_7980' => 'ppa', 'Pp3c12_19450' => 'ppa', 'Pp3c14_1480' => 'ppa', 'Pp3c14_1501' => 'ppa', 'Pp3c16_4900' => 'ppa', 'Pp3c16_5010' => 'ppa', 'Pp3c16_5060' => 'ppa', 'Pp3c19_18250' => 'ppa', 'Pp3c23_8530' => 'ppa', 'Pp3c23_8550' => 'ppa', 'Pp3c24_9670' => 'ppa', 'Pp3c2_21390' => 'ppa', 'Pp3c2_31380' => 'ppa', 'Pp3c3_16620' => 'ppa', 'Pp3c3_8090' => 'ppa', 'Pp3c3_8110' => 'ppa', 'Pp3c3_8130' => 'ppa', 'Pp3c3_8150' => 'ppa', 'Pp3c4_14320' => 'ppa', 'Pp3c6_2560' => 'ppa', 'Pp3c9_16700' => 'ppa', 'PRCOL_00000234' => 'pco', 'PRCOL_00000235' => 'pco', 'PRCOL_00000777' => 'pco', 'PRCOL_00002344' => 'pco', 'PRCOL_00002372' => 'pco', 'PRCOL_00006120' => 'pco', 'Prupe.1G021400' => 'ppe', 'Prupe.1G021500' => 'ppe', 'Prupe.1G021600' => 'ppe', 'Prupe.1G021700' => 'ppe', 'Prupe.1G021800' => 'ppe', 'Prupe.5G145100' => 'ppe', 'Psat6g204040' => 'psa', 'Psat6g204800' => 'psa', 'Psat6g204920' => 'psa', 'Psat6g204960' => 'psa', 'Psat6g205080' => 'psa', 'PSO017G0271' => 'pso', 'PSO017G1276' => 'pso', 'PSO017G1429' => 'pso', 'PSO017G1861' => 'pso', 'PSO017G2787' => 'pso', 'PSO017G4466' => 'pso', 'PSO017G5118' => 'pso', 'PSO017G5420' => 'pso', 'PSO063G3678' => 'pso', 'PSO210G0546' => 'pso', 'PSO317G0001' => 'pso', 'PSO357G0512' => 'pso', 'PSO478G2682' => 'pso', 'PSO647G0001' => 'pso', 'PSO675G0001' => 'pso', 'PSO675G2699' => 'pso', 'PSO675G2849' => 'pso', 'PSO675G4991' => 'pso', 'PSO689G0001' => 'pso', 'QL06p000916' => 'qlo', 'QL06p000921' => 'qlo', 'QL06p001398' => 'qlo', 'QL06p001407' => 'qlo', 'QL06p002031' => 'qlo', 'RcHm_v2.0_Chr4g0387791' => 'rch', 'RcHm_v2.0_Chr4g0387801' => 'rch', 'RcHm_v2.0_Chr6g0286501' => 'rch', 'RcHm_v2.0_Chr6g0286511' => 'rch', 'RcHm_v2.0_Chr6g0286521' => 'rch', 'RcHm_v2.0_Chr6g0286531' => 'rch', 'RcHm_v2.0_Chr7g0189141' => 'rch', 'Rhsim02G0028700' => 'rsi', 'Rhsim02G0028800' => 'rsi', 'Rhsim02G0028900' => 'rsi', 'Rhsim02G0029000' => 'rsi', 'Rhsim02G0029100' => 'rsi', 'Rhsim02G0029200' => 'rsi', 'Rhsim02G0029300' => 'rsi', 'Rhsim02G0029400' => 'rsi', 'Rhsim02G0029500' => 'rsi', 'Rhsim02G0029600' => 'rsi', 'RhsimUnG0024000' => 'rsi', 'RhsimUnG0024100' => 'rsi', 'RhsimUnG0024200' => 'rsi', 'RhsimUnG0024300' => 'rsi', 'RhsimUnG0024400' => 'rsi', 'RhsimUnG0024500' => 'rsi', 'RhsimUnG0024700' => 'rsi', 'RhsimUnG0024800' => 'rsi', 'RhsimUnG0024900' => 'rsi', 'RhsimUnG0025100' => 'rsi', 'Sabra08G0120200' => 'sbr', 'Sabra08G0120300' => 'sbr', 'Sabra08G0120500' => 'sbr', 'Sabra08G0120600' => 'sbr', 'Sabra10G0158900' => 'sbr', 'SalBow2G3492' => 'sbo', 'Sc13g0004760' => 'sci', 'Sc13g0004770' => 'sci', 'Sed0003417' => 'sed', 'Sed0019750' => 'sed', 'SEGI_03419' => 'sgi', 'SEGI_05907' => 'sgi', 'SEGI_10682' => 'sgi', 'SEGI_13528' => 'sgi', 'SEGI_16081' => 'sgi', 'SEGI_19370' => 'sgi', 'SEGI_21015' => 'sgi', 'SEGI_21944' => 'sgi', 'SEGI_32906' => 'sgi', 'SEGI_33093' => 'sgi', 'SEGI_36110' => 'sgi', 'SEGI_40397' => 'sgi', 'SGA_v2.0_scaffold191G40426' => 'sas', 'SGA_v2.0_scaffold353G49717' => 'sas', 'SGA_v2.0_scaffold50G18550' => 'sas', 'SMO119G0173' => 'smo', 'SMO172G0002' => 'smo', 'Solyc09g082690.3' => 'sly', 'Solyc09g082700.2' => 'sly', 'Sopen09g031550' => 'spe', 'Sopen09g031560' => 'spe', 'Sp3g20540' => 'spa', 'Sp7g07580' => 'spa', 'TAR134G0002' => 'tar', 'TAR236G0001' => 'tar', 'TAR365G0892' => 'tar', 'TAR636G0166' => 'tar', 'TAR636G0646' => 'tar', 'TAR636G0869' => 'tar', 'TAR636G1317' => 'tar', 'TAR636G1744' => 'tar', 'TAR636G3358' => 'tar', 'TAR636G3436' => 'tar', 'THA.LOC104803047' => 'tha', 'Thecc.04G238900' => 'tca', 'Thhalv10021557m.g' => 'esa', 'Thhalv10026318m.g' => 'esa', 'Thhalv10026335m.g' => 'esa', 'TPR.G17433' => 'tpr', 'TPR.G18915' => 'tpr', 'TPR.G26125' => 'tpr', 'TWI09G0677' => 'twi', 'TWI73G0287' => 'twi', 'unitig_748.g8326' => 'ugi', 'vmacro15370' => 'vma', 'vmacro15371' => 'vma', 'vmacro15372' => 'vma', 'vmacro15373' => 'vma', 'vmacro15374' => 'vma', 'VMungo0720G2826' => 'vmu', 'Zm00001eb116960' => 'zma', 'Zm00001eb301260' => 'zma', 'Zm00001eb301270' => 'zma' ) $gf_id = 'HOM05D001460' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001460' ) $data_identifier = 'HOM05D001460' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 4, 'aag' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 2, 'aox' => (int) 2, 'arhy' => (int) 4, 'ath' => (int) 2, 'atr' => (int) 1, 'acertr' => (int) 10, 'cqu' => (int) 4, 'bca' => (int) 11, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 1, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 1, 'ccan' => (int) 1, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 1, 'col' => (int) 1, 'cpa' => (int) 1, 'cre' => (int) 7, 'csa' => (int) 1, 'camsi' => (int) 2, 'dca' => (int) 3, 'din' => (int) 2, 'dzi' => (int) 3, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 14, 'fve' => (int) 9, 'gma' => (int) 2, 'ghi' => (int) 4, 'gra' => (int) 2, 'vvi' => (int) 1, 'han' => (int) 13, 'cav' => (int) 1, 'hma' => (int) 2, 'sun' => (int) 2, 'lal' => (int) 2, 'lonja' => (int) 12, 'lja' => (int) 1, 'lsa' => (int) 7, 'mes' => (int) 1, 'mpo' => (int) 27, 'mbi' => (int) 1, 'mco' => (int) 8, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 1, 'egut' => (int) 1, 'ama' => (int) 1, 'nta' => (int) 4, 'nnu' => (int) 2, 'oeu' => (int) 3, 'osa' => (int) 4, 'pax' => (int) 9, 'pgr' => (int) 1, 'stu' => (int) 1, 'pvu' => (int) 1, 'ptr' => (int) 4, 'ppa' => (int) 22, 'pco' => (int) 6, 'ppe' => (int) 6, 'psa' => (int) 5, 'pso' => (int) 19, 'qlo' => (int) 5, 'rch' => (int) 7, 'rsi' => (int) 20, 'sbr' => (int) 5, 'sbo' => (int) 1, 'sci' => (int) 2, 'sed' => (int) 2, 'sgi' => (int) 12, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 2, 'tar' => (int) 10, 'tha' => (int) 1, 'tca' => (int) 1, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 2, 'ugi' => (int) 1, 'vma' => (int) 5, 'vmu' => (int) 1, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb301270' $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' => 'HOM05D001460', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '433', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p22980' => 'bna', 'A01p32340' => 'bna', 'A03p42970' => 'bna', 'A05p25880' => 'bna', 'Aa31LG8G9320' => 'aar', 'Aa31LG8G9330' => 'aar', 'Aa31LG8G9340' => 'aar', 'Aa31sc221G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1034' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1528' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.829' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2222' => 'aag', 'Ah.12g058830' => 'amhyb', 'Ah.12g058840' => 'amhyb', 'AL3G37160' => 'aly', 'AL7G41310' => 'aly', 'Aqoxy5G00395' => 'aox', 'Aqoxy5G00396' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0C8NZA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5185HY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JZ1PRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MD3LS0' => 'arhy', 'AT3G22840' => 'ath', 'AT4G14690' => 'ath', 'ATR0665G054' => 'atr', 'Atru.chr4.2344' => 'acertr', 'Atru.chr4.2346' => 'acertr', 'Atru.chr4.2347' => 'acertr', 'Atru.chr4.2348' => 'acertr', 'Atru.chr4.2355' => 'acertr', 'Atru.chr4.2356' => 'acertr', 'Atru.chr4.2358' => 'acertr', 'Atru.chr4.2359' => 'acertr', 'Atru.chr4.2360' => 'acertr', 'Atru.chr4.2361' => 'acertr', 'AUR62030476' => 'cqu', 'AUR62030478' => 'cqu', 'AUR62030819' => 'cqu', 'AUR62030820' => 'cqu', 'BcaB03g14648' => 'bca', 'BcaB04g20492' => 'bca', 'BcaB06g26399' => 'bca', 'BcaC01g03416' => 'bca', 'BcaC01g03419' => 'bca', 'BcaC01g03421' => 'bca', 'BcaC01g03424' => 'bca', 'BcaC05g28012' => 'bca', 'BcaC09g49212' => 'bca', 'BcaC09g50140' => 'bca', 'BcaNung00346' => 'bca', 'BolC1t02785H' => 'bol', 'BolC1t04095H' => 'bol', 'BolC3t17545H' => 'bol', 'BolC5t32769H' => 'bol', 'BraA01t02211Z' => 'bra', 'BraA01t03359Z' => 'bra', 'BraA03t13441Z' => 'bra', 'BraA05t21476Z' => 'bra', 'C01p28420' => 'bna', 'C01p41350' => 'bna', 'C03p52750' => 'bna', 'C03p52780' => 'bna', 'C05p40270' => 'bna', 'CAN.G1437.9' => 'can', 'CANSAT78G0035' => 'cansat', 'CANSAT78G1036' => 'cansat', 'CANSAT78G2272' => 'cansat', 'CANSAT78G2478' => 'cansat', 'CARHR098700' => 'chi', 'CARHR221120' => 'chi', 'CARHR221150' => 'chi', 'Carub.0003s2297' => 'cru', 'Carub.0007s2749' => 'cru', 'Carub.0007s2750' => 'cru', 'Carub.0007s2751' => 'cru', 'Ca_10849_v3' => 'car', 'Cc03_g04300' => 'ccan', 'CDE02G3648' => 'cde', 'CDE05G0060' => 'cde', 'CDE05G0692' => 'cde', 'CDE05G2285' => 'cde', 'CDE05G2884' => 'cde', 'CDE05G3072' => 'cde', 'Cfa008439' => 'cfa', 'Cfa008441' => 'cfa', 'Cfa008443' => 'cfa', 'Cfa008448' => 'cfa', 'Ciclev10005974m.g' => 'ccl', 'Ciclev10006006m.g' => 'ccl', 'Ciclev10006775m.g' => 'ccl', 'CiPaw.02G120400' => 'cil', 'CiPaw.02G120500' => 'cil', 'CiPaw.02G120600' => 'cil', 'ClCG05G004850' => 'cla', 'COL.COLO4_21566' => 'col', 'Cpa.g.sc44.124' => 'cpa', 'Cre07.g320400' => 'cre', 'Cre07.g320450' => 'cre', 'Cre08.g384650' => 'cre', 'Cre09.g393173' => 'cre', 'Cre09.g394325' => 'cre', 'Cre14.g626750' => 'cre', 'Cre16.g679250' => 'cre', 'CsaV3_3G012890' => 'csa', 'CSS0010865' => 'camsi', 'CSS0044338' => 'camsi', 'DCAR_002366' => 'dca', 'DCAR_030687' => 'dca', 'DCAR_030688' => 'dca', 'Dinv14047' => 'din', 'Dinv14048' => 'din', 'Duzib151G0105' => 'dzi', 'Duzib151G0114' => 'dzi', 'Duzib212G1029' => 'dzi', 'ECA232G3536' => 'eca', 'ECA240G0786' => 'eca', 'ECA240G1802' => 'eca', 'ECA240G3760' => 'eca', 'ECA240G3920' => 'eca', 'EL10Ac5g12536' => 'bvu', 'EL10Ac5g12537' => 'bvu', 'EL10Ac5g12538' => 'bvu', 'Eucgr.B01004' => 'egr', 'Eucgr.B01006' => 'egr', 'Eucgr.B01007' => 'egr', 'Eucgr.B01008' => 'egr', 'Eucgr.B01895' => 'egr', 'Eucgr.B01896' => 'egr', 'FAN04G1456' => 'fan', 'FAN08G1769' => 'fan', 'FAN08G2160' => 'fan', 'FAN13G2403' => 'fan', 'FAN13G3303' => 'fan', 'FAN15G2435' => 'fan', 'FAN17G0672' => 'fan', 'FAN17G2441' => 'fan', 'FAN18G1024' => 'fan', 'FAN22G1458' => 'fan', 'FAN24G0037' => 'fan', 'FAN24G0429' => 'fan', 'FAN24G2387' => 'fan', 'FAN27G2746' => 'fan', 'FvH4_2g20400' => 'fve', 'FvH4_2g20420' => 'fve', 'FvH4_2g20430' => 'fve', 'FvH4_4g01270' => 'fve', 'FvH4_4g01290' => 'fve', 'FvH4_4g01300' => 'fve', 'FvH4_4g01310' => 'fve', 'FvH4_4g01330' => 'fve', 'FvH4_5g09070' => 'fve', 'Glyma.10G243800' => 'gma', 'Glyma.20G150600' => 'gma', 'Gohir.A09G219200' => 'ghi', 'Gohir.A09G219300' => 'ghi', 'Gohir.D09G221400' => 'ghi', 'Gohir.D09G221500' => 'ghi', 'Gorai.006G242600' => 'gra', 'Gorai.006G242700' => 'gra', 'GSVIVG01018044001' => 'vvi', 'HanXRQChr03g0083821' => 'han', 'HanXRQChr03g0083841' => 'han', 'HanXRQChr03g0083881' => 'han', 'HanXRQChr03g0083901' => 'han', 'HanXRQChr03g0083921' => 'han', 'HanXRQChr03g0085331' => 'han', 'HanXRQChr03g0085361' => 'han', 'HanXRQChr03g0085411' => 'han', 'HanXRQChr03g0085421' => 'han', 'HanXRQChr03g0085431' => 'han', 'HanXRQChr08g0221991' => 'han', 'HanXRQChr11g0336061' => 'han', 'HanXRQChr11g0336411' => 'han', 'Haze_11234' => 'cav', 'Hma1.2p1_0549F.1_g177010' => 'hma', 'Hma1.2p1_0602F.1_g187630' => 'hma', 'Hund14876' => 'sun', 'Hund14879' => 'sun', 'Lalb_Chr06g0160741' => 'lal', 'Lalb_Chr21g0304781' => 'lal', 'Lj3A726G19' => 'lonja', 'Lj3A726T23' => 'lonja', 'Lj3A726T24' => 'lonja', 'Lj3A726T25' => 'lonja', 'Lj3A727T17' => 'lonja', 'Lj3C726T0' => 'lonja', 'Lj3C726T2' => 'lonja', 'Lj3P725T35' => 'lonja', 'Lj3P727T10' => 'lonja', 'Lj3P727T12' => 'lonja', 'Lj3P727T14' => 'lonja', 'Lj5g0023109' => 'lja', 'Lj6P646T44' => 'lonja', 'Lsat_1_v5_gn_6_75760' => 'lsa', 'Lsat_1_v5_gn_6_75800' => 'lsa', 'Lsat_1_v5_gn_6_75900' => 'lsa', 'Lsat_1_v5_gn_6_76240' => 'lsa', 'Lsat_1_v5_gn_6_76441' => 'lsa', 'Lsat_1_v5_gn_6_76700' => 'lsa', 'Lsat_1_v5_gn_6_76760' => 'lsa', 'Manes.15G033100' => 'mes', 'Mapoly0004s0074' => 'mpo', 'Mapoly0004s0075' => 'mpo', 'Mapoly0004s0163' => 'mpo', 'Mapoly0004s0164' => 'mpo', 'Mapoly0021s0018' => 'mpo', 'Mapoly0041s0136' => 'mpo', 'Mapoly0041s0137' => 'mpo', 'Mapoly0041s0138' => 'mpo', 'Mapoly0041s0139' => 'mpo', 'Mapoly0041s0141' => 'mpo', 'Mapoly0041s0142' => 'mpo', 'Mapoly0041s0143' => 'mpo', 'Mapoly0041s0144' => 'mpo', 'Mapoly0041s0145' => 'mpo', 'Mapoly0047s0106' => 'mpo', 'Mapoly0047s0108' => 'mpo', 'Mapoly0050s0051' => 'mpo', 'Mapoly0050s0052' => 'mpo', 'Mapoly0050s0053' => 'mpo', 'Mapoly0058s0013' => 'mpo', 'Mapoly0091s0078' => 'mpo', 'Mapoly0091s0079' => 'mpo', 'Mapoly0091s0080' => 'mpo', 'Mapoly0091s0081' => 'mpo', 'Mapoly0278s0004' => 'mpo', 'Mapoly0278s0005' => 'mpo', 'Mapoly0278s0006' => 'mpo', 'MBI11_g30648_MAGBIO' => 'mbi', 'MCO03G194' => 'mco', 'MCO03G590' => 'mco', 'MCO07G312' => 'mco', 'MCO10G318' => 'mco', 'MCO12G244' => 'mco', 'MCO13G148' => 'mco', 'MCO13G194' => 'mco', 'MCO16G238' => 'mco', 'MD06G1134100' => 'mdo', 'MD13G1200100' => 'mdo', 'MD13G1200300' => 'mdo', 'MD13G1200600' => 'mdo', 'MD14G1150400' => 'mdo', 'MD16G1200000' => 'mdo', 'Medtr1g102570' => 'mtr', 'Medtr1g102780' => 'mtr', 'Medtr1g102800' => 'mtr', 'Medtr1g102810' => 'mtr', 'Medtr1g102830' => 'mtr', 'MELO3C006499.2' => 'cme', 'Migut.G00385' => 'egut', 'MSTRG.4063' => 'ama', 'Nitab4.5_0000090g0260' => 'nta', 'Nitab4.5_0000977g0030' => 'nta', 'Nitab4.5_0002541g0040' => 'nta', 'Nitab4.5_0007068g0040' => 'nta', 'Nn005s41408' => 'nnu', 'Nn005s41410' => 'nnu', 'Oeu010310.1' => 'oeu', 'Oeu010311.1' => 'oeu', 'Oeu043472.1' => 'oeu', 'Os01g0246400' => 'osa', 'Os04g0267950' => 'osa', 'Os07g0178700' => 'osa', 'Os07g0178800' => 'osa', 'Peaxi162Scf00316g00046' => 'pax', 'Peaxi162Scf00316g00049' => 'pax', 'Peaxi162Scf00316g00059' => 'pax', 'Peaxi162Scf00316g00328' => 'pax', 'Peaxi162Scf00316g00329' => 'pax', 'Peaxi162Scf00316g00411' => 'pax', 'Peaxi162Scf00316g00521' => 'pax', 'Peaxi162Scf00492g00068' => 'pax', 'Peaxi162Scf35631g00002' => 'pax', 'PGR142G3720' => 'pgr', 'PGSC0003DMG400006442' => 'stu', 'Phvul.007G062000' => 'pvu', 'Potri.008G157750' => 'ptr', 'Potri.008G157900' => 'ptr', 'Potri.008G158000' => 'ptr', 'Potri.008G158200' => 'ptr', 'Pp3c11_7280' => 'ppa', 'Pp3c11_7980' => 'ppa', 'Pp3c12_19450' => 'ppa', 'Pp3c14_1480' => 'ppa', 'Pp3c14_1501' => 'ppa', 'Pp3c16_4900' => 'ppa', 'Pp3c16_5010' => 'ppa', 'Pp3c16_5060' => 'ppa', 'Pp3c19_18250' => 'ppa', 'Pp3c23_8530' => 'ppa', 'Pp3c23_8550' => 'ppa', 'Pp3c24_9670' => 'ppa', 'Pp3c2_21390' => 'ppa', 'Pp3c2_31380' => 'ppa', 'Pp3c3_16620' => 'ppa', 'Pp3c3_8090' => 'ppa', 'Pp3c3_8110' => 'ppa', 'Pp3c3_8130' => 'ppa', 'Pp3c3_8150' => 'ppa', 'Pp3c4_14320' => 'ppa', 'Pp3c6_2560' => 'ppa', 'Pp3c9_16700' => 'ppa', 'PRCOL_00000234' => 'pco', 'PRCOL_00000235' => 'pco', 'PRCOL_00000777' => 'pco', 'PRCOL_00002344' => 'pco', 'PRCOL_00002372' => 'pco', 'PRCOL_00006120' => 'pco', 'Prupe.1G021400' => 'ppe', 'Prupe.1G021500' => 'ppe', 'Prupe.1G021600' => 'ppe', 'Prupe.1G021700' => 'ppe', 'Prupe.1G021800' => 'ppe', 'Prupe.5G145100' => 'ppe', 'Psat6g204040' => 'psa', 'Psat6g204800' => 'psa', 'Psat6g204920' => 'psa', 'Psat6g204960' => 'psa', 'Psat6g205080' => 'psa', 'PSO017G0271' => 'pso', 'PSO017G1276' => 'pso', 'PSO017G1429' => 'pso', 'PSO017G1861' => 'pso', 'PSO017G2787' => 'pso', 'PSO017G4466' => 'pso', 'PSO017G5118' => 'pso', 'PSO017G5420' => 'pso', 'PSO063G3678' => 'pso', 'PSO210G0546' => 'pso', 'PSO317G0001' => 'pso', 'PSO357G0512' => 'pso', 'PSO478G2682' => 'pso', 'PSO647G0001' => 'pso', 'PSO675G0001' => 'pso', 'PSO675G2699' => 'pso', 'PSO675G2849' => 'pso', 'PSO675G4991' => 'pso', 'PSO689G0001' => 'pso', 'QL06p000916' => 'qlo', 'QL06p000921' => 'qlo', 'QL06p001398' => 'qlo', 'QL06p001407' => 'qlo', 'QL06p002031' => 'qlo', 'RcHm_v2.0_Chr4g0387791' => 'rch', 'RcHm_v2.0_Chr4g0387801' => 'rch', 'RcHm_v2.0_Chr6g0286501' => 'rch', 'RcHm_v2.0_Chr6g0286511' => 'rch', 'RcHm_v2.0_Chr6g0286521' => 'rch', 'RcHm_v2.0_Chr6g0286531' => 'rch', 'RcHm_v2.0_Chr7g0189141' => 'rch', 'Rhsim02G0028700' => 'rsi', 'Rhsim02G0028800' => 'rsi', 'Rhsim02G0028900' => 'rsi', 'Rhsim02G0029000' => 'rsi', 'Rhsim02G0029100' => 'rsi', 'Rhsim02G0029200' => 'rsi', 'Rhsim02G0029300' => 'rsi', 'Rhsim02G0029400' => 'rsi', 'Rhsim02G0029500' => 'rsi', 'Rhsim02G0029600' => 'rsi', 'RhsimUnG0024000' => 'rsi', 'RhsimUnG0024100' => 'rsi', 'RhsimUnG0024200' => 'rsi', 'RhsimUnG0024300' => 'rsi', 'RhsimUnG0024400' => 'rsi', 'RhsimUnG0024500' => 'rsi', 'RhsimUnG0024700' => 'rsi', 'RhsimUnG0024800' => 'rsi', 'RhsimUnG0024900' => 'rsi', 'RhsimUnG0025100' => 'rsi', 'Sabra08G0120200' => 'sbr', 'Sabra08G0120300' => 'sbr', 'Sabra08G0120500' => 'sbr', 'Sabra08G0120600' => 'sbr', 'Sabra10G0158900' => 'sbr', 'SalBow2G3492' => 'sbo', 'Sc13g0004760' => 'sci', 'Sc13g0004770' => 'sci', 'Sed0003417' => 'sed', 'Sed0019750' => 'sed', 'SEGI_03419' => 'sgi', 'SEGI_05907' => 'sgi', 'SEGI_10682' => 'sgi', 'SEGI_13528' => 'sgi', 'SEGI_16081' => 'sgi', 'SEGI_19370' => 'sgi', 'SEGI_21015' => 'sgi', 'SEGI_21944' => 'sgi', 'SEGI_32906' => 'sgi', 'SEGI_33093' => 'sgi', 'SEGI_36110' => 'sgi', 'SEGI_40397' => 'sgi', 'SGA_v2.0_scaffold191G40426' => 'sas', 'SGA_v2.0_scaffold353G49717' => 'sas', 'SGA_v2.0_scaffold50G18550' => 'sas', 'SMO119G0173' => 'smo', 'SMO172G0002' => 'smo', 'Solyc09g082690.3' => 'sly', 'Solyc09g082700.2' => 'sly', 'Sopen09g031550' => 'spe', 'Sopen09g031560' => 'spe', 'Sp3g20540' => 'spa', 'Sp7g07580' => 'spa', 'TAR134G0002' => 'tar', 'TAR236G0001' => 'tar', 'TAR365G0892' => 'tar', 'TAR636G0166' => 'tar', 'TAR636G0646' => 'tar', 'TAR636G0869' => 'tar', 'TAR636G1317' => 'tar', 'TAR636G1744' => 'tar', 'TAR636G3358' => 'tar', 'TAR636G3436' => 'tar', 'THA.LOC104803047' => 'tha', 'Thecc.04G238900' => 'tca', 'Thhalv10021557m.g' => 'esa', 'Thhalv10026318m.g' => 'esa', 'Thhalv10026335m.g' => 'esa', 'TPR.G17433' => 'tpr', 'TPR.G18915' => 'tpr', 'TPR.G26125' => 'tpr', 'TWI09G0677' => 'twi', 'TWI73G0287' => 'twi', 'unitig_748.g8326' => 'ugi', 'vmacro15370' => 'vma', 'vmacro15371' => 'vma', 'vmacro15372' => 'vma', 'vmacro15373' => 'vma', 'vmacro15374' => 'vma', 'VMungo0720G2826' => 'vmu', 'Zm00001eb116960' => 'zma', 'Zm00001eb301260' => 'zma', 'Zm00001eb301270' => 'zma' ), 'gf_id' => 'HOM05D001460', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001460' ), 'data_identifier' => 'HOM05D001460', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001460', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '433', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p22980' => 'bna', 'A01p32340' => 'bna', 'A03p42970' => 'bna', 'A05p25880' => 'bna', 'Aa31LG8G9320' => 'aar', 'Aa31LG8G9330' => 'aar', 'Aa31LG8G9340' => 'aar', 'Aa31sc221G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1034' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1528' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.829' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2222' => 'aag', 'Ah.12g058830' => 'amhyb', 'Ah.12g058840' => 'amhyb', 'AL3G37160' => 'aly', 'AL7G41310' => 'aly', 'Aqoxy5G00395' => 'aox', 'Aqoxy5G00396' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0C8NZA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5185HY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JZ1PRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MD3LS0' => 'arhy', 'AT3G22840' => 'ath', 'AT4G14690' => 'ath', 'ATR0665G054' => 'atr', 'Atru.chr4.2344' => 'acertr', 'Atru.chr4.2346' => 'acertr', 'Atru.chr4.2347' => 'acertr', 'Atru.chr4.2348' => 'acertr', 'Atru.chr4.2355' => 'acertr', 'Atru.chr4.2356' => 'acertr', 'Atru.chr4.2358' => 'acertr', 'Atru.chr4.2359' => 'acertr', 'Atru.chr4.2360' => 'acertr', 'Atru.chr4.2361' => 'acertr', 'AUR62030476' => 'cqu', 'AUR62030478' => 'cqu', 'AUR62030819' => 'cqu', 'AUR62030820' => 'cqu', 'BcaB03g14648' => 'bca', 'BcaB04g20492' => 'bca', 'BcaB06g26399' => 'bca', 'BcaC01g03416' => 'bca', 'BcaC01g03419' => 'bca', 'BcaC01g03421' => 'bca', 'BcaC01g03424' => 'bca', 'BcaC05g28012' => 'bca', 'BcaC09g49212' => 'bca', 'BcaC09g50140' => 'bca', 'BcaNung00346' => 'bca', 'BolC1t02785H' => 'bol', 'BolC1t04095H' => 'bol', 'BolC3t17545H' => 'bol', 'BolC5t32769H' => 'bol', 'BraA01t02211Z' => 'bra', 'BraA01t03359Z' => 'bra', 'BraA03t13441Z' => 'bra', 'BraA05t21476Z' => 'bra', 'C01p28420' => 'bna', 'C01p41350' => 'bna', 'C03p52750' => 'bna', 'C03p52780' => 'bna', 'C05p40270' => 'bna', 'CAN.G1437.9' => 'can', 'CANSAT78G0035' => 'cansat', 'CANSAT78G1036' => 'cansat', 'CANSAT78G2272' => 'cansat', 'CANSAT78G2478' => 'cansat', 'CARHR098700' => 'chi', 'CARHR221120' => 'chi', 'CARHR221150' => 'chi', 'Carub.0003s2297' => 'cru', 'Carub.0007s2749' => 'cru', 'Carub.0007s2750' => 'cru', 'Carub.0007s2751' => 'cru', 'Ca_10849_v3' => 'car', 'Cc03_g04300' => 'ccan', 'CDE02G3648' => 'cde', 'CDE05G0060' => 'cde', 'CDE05G0692' => 'cde', 'CDE05G2285' => 'cde', 'CDE05G2884' => 'cde', 'CDE05G3072' => 'cde', 'Cfa008439' => 'cfa', 'Cfa008441' => 'cfa', 'Cfa008443' => 'cfa', 'Cfa008448' => 'cfa', 'Ciclev10005974m.g' => 'ccl', 'Ciclev10006006m.g' => 'ccl', 'Ciclev10006775m.g' => 'ccl', 'CiPaw.02G120400' => 'cil', 'CiPaw.02G120500' => 'cil', 'CiPaw.02G120600' => 'cil', 'ClCG05G004850' => 'cla', 'COL.COLO4_21566' => 'col', 'Cpa.g.sc44.124' => 'cpa', 'Cre07.g320400' => 'cre', 'Cre07.g320450' => 'cre', 'Cre08.g384650' => 'cre', 'Cre09.g393173' => 'cre', 'Cre09.g394325' => 'cre', 'Cre14.g626750' => 'cre', 'Cre16.g679250' => 'cre', 'CsaV3_3G012890' => 'csa', 'CSS0010865' => 'camsi', 'CSS0044338' => 'camsi', 'DCAR_002366' => 'dca', 'DCAR_030687' => 'dca', 'DCAR_030688' => 'dca', 'Dinv14047' => 'din', 'Dinv14048' => 'din', 'Duzib151G0105' => 'dzi', 'Duzib151G0114' => 'dzi', 'Duzib212G1029' => 'dzi', 'ECA232G3536' => 'eca', 'ECA240G0786' => 'eca', 'ECA240G1802' => 'eca', 'ECA240G3760' => 'eca', 'ECA240G3920' => 'eca', 'EL10Ac5g12536' => 'bvu', 'EL10Ac5g12537' => 'bvu', 'EL10Ac5g12538' => 'bvu', 'Eucgr.B01004' => 'egr', 'Eucgr.B01006' => 'egr', 'Eucgr.B01007' => 'egr', 'Eucgr.B01008' => 'egr', 'Eucgr.B01895' => 'egr', 'Eucgr.B01896' => 'egr', 'FAN04G1456' => 'fan', 'FAN08G1769' => 'fan', 'FAN08G2160' => 'fan', 'FAN13G2403' => 'fan', 'FAN13G3303' => 'fan', 'FAN15G2435' => 'fan', 'FAN17G0672' => 'fan', 'FAN17G2441' => 'fan', 'FAN18G1024' => 'fan', 'FAN22G1458' => 'fan', 'FAN24G0037' => 'fan', 'FAN24G0429' => 'fan', 'FAN24G2387' => 'fan', 'FAN27G2746' => 'fan', 'FvH4_2g20400' => 'fve', 'FvH4_2g20420' => 'fve', 'FvH4_2g20430' => 'fve', 'FvH4_4g01270' => 'fve', 'FvH4_4g01290' => 'fve', 'FvH4_4g01300' => 'fve', 'FvH4_4g01310' => 'fve', 'FvH4_4g01330' => 'fve', 'FvH4_5g09070' => 'fve', 'Glyma.10G243800' => 'gma', 'Glyma.20G150600' => 'gma', 'Gohir.A09G219200' => 'ghi', 'Gohir.A09G219300' => 'ghi', 'Gohir.D09G221400' => 'ghi', 'Gohir.D09G221500' => 'ghi', 'Gorai.006G242600' => 'gra', 'Gorai.006G242700' => 'gra', 'GSVIVG01018044001' => 'vvi', 'HanXRQChr03g0083821' => 'han', 'HanXRQChr03g0083841' => 'han', 'HanXRQChr03g0083881' => 'han', 'HanXRQChr03g0083901' => 'han', 'HanXRQChr03g0083921' => 'han', 'HanXRQChr03g0085331' => 'han', 'HanXRQChr03g0085361' => 'han', 'HanXRQChr03g0085411' => 'han', 'HanXRQChr03g0085421' => 'han', 'HanXRQChr03g0085431' => 'han', 'HanXRQChr08g0221991' => 'han', 'HanXRQChr11g0336061' => 'han', 'HanXRQChr11g0336411' => 'han', 'Haze_11234' => 'cav', 'Hma1.2p1_0549F.1_g177010' => 'hma', 'Hma1.2p1_0602F.1_g187630' => 'hma', 'Hund14876' => 'sun', 'Hund14879' => 'sun', 'Lalb_Chr06g0160741' => 'lal', 'Lalb_Chr21g0304781' => 'lal', 'Lj3A726G19' => 'lonja', 'Lj3A726T23' => 'lonja', 'Lj3A726T24' => 'lonja', 'Lj3A726T25' => 'lonja', 'Lj3A727T17' => 'lonja', 'Lj3C726T0' => 'lonja', 'Lj3C726T2' => 'lonja', 'Lj3P725T35' => 'lonja', 'Lj3P727T10' => 'lonja', 'Lj3P727T12' => 'lonja', 'Lj3P727T14' => 'lonja', 'Lj5g0023109' => 'lja', 'Lj6P646T44' => 'lonja', 'Lsat_1_v5_gn_6_75760' => 'lsa', 'Lsat_1_v5_gn_6_75800' => 'lsa', 'Lsat_1_v5_gn_6_75900' => 'lsa', 'Lsat_1_v5_gn_6_76240' => 'lsa', 'Lsat_1_v5_gn_6_76441' => 'lsa', 'Lsat_1_v5_gn_6_76700' => 'lsa', 'Lsat_1_v5_gn_6_76760' => 'lsa', 'Manes.15G033100' => 'mes', 'Mapoly0004s0074' => 'mpo', 'Mapoly0004s0075' => 'mpo', 'Mapoly0004s0163' => 'mpo', 'Mapoly0004s0164' => 'mpo', 'Mapoly0021s0018' => 'mpo', 'Mapoly0041s0136' => 'mpo', 'Mapoly0041s0137' => 'mpo', 'Mapoly0041s0138' => 'mpo', 'Mapoly0041s0139' => 'mpo', 'Mapoly0041s0141' => 'mpo', 'Mapoly0041s0142' => 'mpo', 'Mapoly0041s0143' => 'mpo', 'Mapoly0041s0144' => 'mpo', 'Mapoly0041s0145' => 'mpo', 'Mapoly0047s0106' => 'mpo', 'Mapoly0047s0108' => 'mpo', 'Mapoly0050s0051' => 'mpo', 'Mapoly0050s0052' => 'mpo', 'Mapoly0050s0053' => 'mpo', 'Mapoly0058s0013' => 'mpo', 'Mapoly0091s0078' => 'mpo', 'Mapoly0091s0079' => 'mpo', 'Mapoly0091s0080' => 'mpo', 'Mapoly0091s0081' => 'mpo', 'Mapoly0278s0004' => 'mpo', 'Mapoly0278s0005' => 'mpo', 'Mapoly0278s0006' => 'mpo', 'MBI11_g30648_MAGBIO' => 'mbi', 'MCO03G194' => 'mco', 'MCO03G590' => 'mco', 'MCO07G312' => 'mco', 'MCO10G318' => 'mco', 'MCO12G244' => 'mco', 'MCO13G148' => 'mco', 'MCO13G194' => 'mco', 'MCO16G238' => 'mco', 'MD06G1134100' => 'mdo', 'MD13G1200100' => 'mdo', 'MD13G1200300' => 'mdo', 'MD13G1200600' => 'mdo', 'MD14G1150400' => 'mdo', 'MD16G1200000' => 'mdo', 'Medtr1g102570' => 'mtr', 'Medtr1g102780' => 'mtr', 'Medtr1g102800' => 'mtr', 'Medtr1g102810' => 'mtr', 'Medtr1g102830' => 'mtr', 'MELO3C006499.2' => 'cme', 'Migut.G00385' => 'egut', 'MSTRG.4063' => 'ama', 'Nitab4.5_0000090g0260' => 'nta', 'Nitab4.5_0000977g0030' => 'nta', 'Nitab4.5_0002541g0040' => 'nta', 'Nitab4.5_0007068g0040' => 'nta', 'Nn005s41408' => 'nnu', 'Nn005s41410' => 'nnu', 'Oeu010310.1' => 'oeu', 'Oeu010311.1' => 'oeu', 'Oeu043472.1' => 'oeu', 'Os01g0246400' => 'osa', 'Os04g0267950' => 'osa', 'Os07g0178700' => 'osa', 'Os07g0178800' => 'osa', 'Peaxi162Scf00316g00046' => 'pax', 'Peaxi162Scf00316g00049' => 'pax', 'Peaxi162Scf00316g00059' => 'pax', 'Peaxi162Scf00316g00328' => 'pax', 'Peaxi162Scf00316g00329' => 'pax', 'Peaxi162Scf00316g00411' => 'pax', 'Peaxi162Scf00316g00521' => 'pax', 'Peaxi162Scf00492g00068' => 'pax', 'Peaxi162Scf35631g00002' => 'pax', 'PGR142G3720' => 'pgr', 'PGSC0003DMG400006442' => 'stu', 'Phvul.007G062000' => 'pvu', 'Potri.008G157750' => 'ptr', 'Potri.008G157900' => 'ptr', 'Potri.008G158000' => 'ptr', 'Potri.008G158200' => 'ptr', 'Pp3c11_7280' => 'ppa', 'Pp3c11_7980' => 'ppa', 'Pp3c12_19450' => 'ppa', 'Pp3c14_1480' => 'ppa', 'Pp3c14_1501' => 'ppa', 'Pp3c16_4900' => 'ppa', 'Pp3c16_5010' => 'ppa', 'Pp3c16_5060' => 'ppa', 'Pp3c19_18250' => 'ppa', 'Pp3c23_8530' => 'ppa', 'Pp3c23_8550' => 'ppa', 'Pp3c24_9670' => 'ppa', 'Pp3c2_21390' => 'ppa', 'Pp3c2_31380' => 'ppa', 'Pp3c3_16620' => 'ppa', 'Pp3c3_8090' => 'ppa', 'Pp3c3_8110' => 'ppa', 'Pp3c3_8130' => 'ppa', 'Pp3c3_8150' => 'ppa', 'Pp3c4_14320' => 'ppa', 'Pp3c6_2560' => 'ppa', 'Pp3c9_16700' => 'ppa', 'PRCOL_00000234' => 'pco', 'PRCOL_00000235' => 'pco', 'PRCOL_00000777' => 'pco', 'PRCOL_00002344' => 'pco', 'PRCOL_00002372' => 'pco', 'PRCOL_00006120' => 'pco', 'Prupe.1G021400' => 'ppe', 'Prupe.1G021500' => 'ppe', 'Prupe.1G021600' => 'ppe', 'Prupe.1G021700' => 'ppe', 'Prupe.1G021800' => 'ppe', 'Prupe.5G145100' => 'ppe', 'Psat6g204040' => 'psa', 'Psat6g204800' => 'psa', 'Psat6g204920' => 'psa', 'Psat6g204960' => 'psa', 'Psat6g205080' => 'psa', 'PSO017G0271' => 'pso', 'PSO017G1276' => 'pso', 'PSO017G1429' => 'pso', 'PSO017G1861' => 'pso', 'PSO017G2787' => 'pso', 'PSO017G4466' => 'pso', 'PSO017G5118' => 'pso', 'PSO017G5420' => 'pso', 'PSO063G3678' => 'pso', 'PSO210G0546' => 'pso', 'PSO317G0001' => 'pso', 'PSO357G0512' => 'pso', 'PSO478G2682' => 'pso', 'PSO647G0001' => 'pso', 'PSO675G0001' => 'pso', 'PSO675G2699' => 'pso', 'PSO675G2849' => 'pso', 'PSO675G4991' => 'pso', 'PSO689G0001' => 'pso', 'QL06p000916' => 'qlo', 'QL06p000921' => 'qlo', 'QL06p001398' => 'qlo', 'QL06p001407' => 'qlo', 'QL06p002031' => 'qlo', 'RcHm_v2.0_Chr4g0387791' => 'rch', 'RcHm_v2.0_Chr4g0387801' => 'rch', 'RcHm_v2.0_Chr6g0286501' => 'rch', 'RcHm_v2.0_Chr6g0286511' => 'rch', 'RcHm_v2.0_Chr6g0286521' => 'rch', 'RcHm_v2.0_Chr6g0286531' => 'rch', 'RcHm_v2.0_Chr7g0189141' => 'rch', 'Rhsim02G0028700' => 'rsi', 'Rhsim02G0028800' => 'rsi', 'Rhsim02G0028900' => 'rsi', 'Rhsim02G0029000' => 'rsi', 'Rhsim02G0029100' => 'rsi', 'Rhsim02G0029200' => 'rsi', 'Rhsim02G0029300' => 'rsi', 'Rhsim02G0029400' => 'rsi', 'Rhsim02G0029500' => 'rsi', 'Rhsim02G0029600' => 'rsi', 'RhsimUnG0024000' => 'rsi', 'RhsimUnG0024100' => 'rsi', 'RhsimUnG0024200' => 'rsi', 'RhsimUnG0024300' => 'rsi', 'RhsimUnG0024400' => 'rsi', 'RhsimUnG0024500' => 'rsi', 'RhsimUnG0024700' => 'rsi', 'RhsimUnG0024800' => 'rsi', 'RhsimUnG0024900' => 'rsi', 'RhsimUnG0025100' => 'rsi', 'Sabra08G0120200' => 'sbr', 'Sabra08G0120300' => 'sbr', 'Sabra08G0120500' => 'sbr', 'Sabra08G0120600' => 'sbr', 'Sabra10G0158900' => 'sbr', 'SalBow2G3492' => 'sbo', 'Sc13g0004760' => 'sci', 'Sc13g0004770' => 'sci', 'Sed0003417' => 'sed', 'Sed0019750' => 'sed', 'SEGI_03419' => 'sgi', 'SEGI_05907' => 'sgi', 'SEGI_10682' => 'sgi', 'SEGI_13528' => 'sgi', 'SEGI_16081' => 'sgi', 'SEGI_19370' => 'sgi', 'SEGI_21015' => 'sgi', 'SEGI_21944' => 'sgi', 'SEGI_32906' => 'sgi', 'SEGI_33093' => 'sgi', 'SEGI_36110' => 'sgi', 'SEGI_40397' => 'sgi', 'SGA_v2.0_scaffold191G40426' => 'sas', 'SGA_v2.0_scaffold353G49717' => 'sas', 'SGA_v2.0_scaffold50G18550' => 'sas', 'SMO119G0173' => 'smo', 'SMO172G0002' => 'smo', 'Solyc09g082690.3' => 'sly', 'Solyc09g082700.2' => 'sly', 'Sopen09g031550' => 'spe', 'Sopen09g031560' => 'spe', 'Sp3g20540' => 'spa', 'Sp7g07580' => 'spa', 'TAR134G0002' => 'tar', 'TAR236G0001' => 'tar', 'TAR365G0892' => 'tar', 'TAR636G0166' => 'tar', 'TAR636G0646' => 'tar', 'TAR636G0869' => 'tar', 'TAR636G1317' => 'tar', 'TAR636G1744' => 'tar', 'TAR636G3358' => 'tar', 'TAR636G3436' => 'tar', 'THA.LOC104803047' => 'tha', 'Thecc.04G238900' => 'tca', 'Thhalv10021557m.g' => 'esa', 'Thhalv10026318m.g' => 'esa', 'Thhalv10026335m.g' => 'esa', 'TPR.G17433' => 'tpr', 'TPR.G18915' => 'tpr', 'TPR.G26125' => 'tpr', 'TWI09G0677' => 'twi', 'TWI73G0287' => 'twi', 'unitig_748.g8326' => 'ugi', 'vmacro15370' => 'vma', 'vmacro15371' => 'vma', 'vmacro15372' => 'vma', 'vmacro15373' => 'vma', 'vmacro15374' => 'vma', 'VMungo0720G2826' => 'vmu', 'Zm00001eb116960' => 'zma', 'Zm00001eb301260' => 'zma', 'Zm00001eb301270' => 'zma' ) $gf_id = 'HOM05D001460' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001460' ) $data_identifier = 'HOM05D001460' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 4, 'aag' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 2, 'aox' => (int) 2, 'arhy' => (int) 4, 'ath' => (int) 2, 'atr' => (int) 1, 'acertr' => (int) 10, 'cqu' => (int) 4, 'bca' => (int) 11, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 1, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 1, 'ccan' => (int) 1, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 1, 'col' => (int) 1, 'cpa' => (int) 1, 'cre' => (int) 7, 'csa' => (int) 1, 'camsi' => (int) 2, 'dca' => (int) 3, 'din' => (int) 2, 'dzi' => (int) 3, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 14, 'fve' => (int) 9, 'gma' => (int) 2, 'ghi' => (int) 4, 'gra' => (int) 2, 'vvi' => (int) 1, 'han' => (int) 13, 'cav' => (int) 1, 'hma' => (int) 2, 'sun' => (int) 2, 'lal' => (int) 2, 'lonja' => (int) 12, 'lja' => (int) 1, 'lsa' => (int) 7, 'mes' => (int) 1, 'mpo' => (int) 27, 'mbi' => (int) 1, 'mco' => (int) 8, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 1, 'egut' => (int) 1, 'ama' => (int) 1, 'nta' => (int) 4, 'nnu' => (int) 2, 'oeu' => (int) 3, 'osa' => (int) 4, 'pax' => (int) 9, 'pgr' => (int) 1, 'stu' => (int) 1, 'pvu' => (int) 1, 'ptr' => (int) 4, 'ppa' => (int) 22, 'pco' => (int) 6, 'ppe' => (int) 6, 'psa' => (int) 5, 'pso' => (int) 19, 'qlo' => (int) 5, 'rch' => (int) 7, 'rsi' => (int) 20, 'sbr' => (int) 5, 'sbo' => (int) 1, 'sci' => (int) 2, 'sed' => (int) 2, 'sgi' => (int) 12, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 2, 'tar' => (int) 10, 'tha' => (int) 1, 'tca' => (int) 1, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 2, 'ugi' => (int) 1, 'vma' => (int) 5, 'vmu' => (int) 1, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb301270' $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' => 'HOM05D001460', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '433', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p22980' => 'bna', 'A01p32340' => 'bna', 'A03p42970' => 'bna', 'A05p25880' => 'bna', 'Aa31LG8G9320' => 'aar', 'Aa31LG8G9330' => 'aar', 'Aa31LG8G9340' => 'aar', 'Aa31sc221G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1034' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1528' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.829' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2222' => 'aag', 'Ah.12g058830' => 'amhyb', 'Ah.12g058840' => 'amhyb', 'AL3G37160' => 'aly', 'AL7G41310' => 'aly', 'Aqoxy5G00395' => 'aox', 'Aqoxy5G00396' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0C8NZA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5185HY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JZ1PRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MD3LS0' => 'arhy', 'AT3G22840' => 'ath', 'AT4G14690' => 'ath', 'ATR0665G054' => 'atr', 'Atru.chr4.2344' => 'acertr', 'Atru.chr4.2346' => 'acertr', 'Atru.chr4.2347' => 'acertr', 'Atru.chr4.2348' => 'acertr', 'Atru.chr4.2355' => 'acertr', 'Atru.chr4.2356' => 'acertr', 'Atru.chr4.2358' => 'acertr', 'Atru.chr4.2359' => 'acertr', 'Atru.chr4.2360' => 'acertr', 'Atru.chr4.2361' => 'acertr', 'AUR62030476' => 'cqu', 'AUR62030478' => 'cqu', 'AUR62030819' => 'cqu', 'AUR62030820' => 'cqu', 'BcaB03g14648' => 'bca', 'BcaB04g20492' => 'bca', 'BcaB06g26399' => 'bca', 'BcaC01g03416' => 'bca', 'BcaC01g03419' => 'bca', 'BcaC01g03421' => 'bca', 'BcaC01g03424' => 'bca', 'BcaC05g28012' => 'bca', 'BcaC09g49212' => 'bca', 'BcaC09g50140' => 'bca', 'BcaNung00346' => 'bca', 'BolC1t02785H' => 'bol', 'BolC1t04095H' => 'bol', 'BolC3t17545H' => 'bol', 'BolC5t32769H' => 'bol', 'BraA01t02211Z' => 'bra', 'BraA01t03359Z' => 'bra', 'BraA03t13441Z' => 'bra', 'BraA05t21476Z' => 'bra', 'C01p28420' => 'bna', 'C01p41350' => 'bna', 'C03p52750' => 'bna', 'C03p52780' => 'bna', 'C05p40270' => 'bna', 'CAN.G1437.9' => 'can', 'CANSAT78G0035' => 'cansat', 'CANSAT78G1036' => 'cansat', 'CANSAT78G2272' => 'cansat', 'CANSAT78G2478' => 'cansat', 'CARHR098700' => 'chi', 'CARHR221120' => 'chi', 'CARHR221150' => 'chi', 'Carub.0003s2297' => 'cru', 'Carub.0007s2749' => 'cru', 'Carub.0007s2750' => 'cru', 'Carub.0007s2751' => 'cru', 'Ca_10849_v3' => 'car', 'Cc03_g04300' => 'ccan', 'CDE02G3648' => 'cde', 'CDE05G0060' => 'cde', 'CDE05G0692' => 'cde', 'CDE05G2285' => 'cde', 'CDE05G2884' => 'cde', 'CDE05G3072' => 'cde', 'Cfa008439' => 'cfa', 'Cfa008441' => 'cfa', 'Cfa008443' => 'cfa', 'Cfa008448' => 'cfa', 'Ciclev10005974m.g' => 'ccl', 'Ciclev10006006m.g' => 'ccl', 'Ciclev10006775m.g' => 'ccl', 'CiPaw.02G120400' => 'cil', 'CiPaw.02G120500' => 'cil', 'CiPaw.02G120600' => 'cil', 'ClCG05G004850' => 'cla', 'COL.COLO4_21566' => 'col', 'Cpa.g.sc44.124' => 'cpa', 'Cre07.g320400' => 'cre', 'Cre07.g320450' => 'cre', 'Cre08.g384650' => 'cre', 'Cre09.g393173' => 'cre', 'Cre09.g394325' => 'cre', 'Cre14.g626750' => 'cre', 'Cre16.g679250' => 'cre', 'CsaV3_3G012890' => 'csa', 'CSS0010865' => 'camsi', 'CSS0044338' => 'camsi', 'DCAR_002366' => 'dca', 'DCAR_030687' => 'dca', 'DCAR_030688' => 'dca', 'Dinv14047' => 'din', 'Dinv14048' => 'din', 'Duzib151G0105' => 'dzi', 'Duzib151G0114' => 'dzi', 'Duzib212G1029' => 'dzi', 'ECA232G3536' => 'eca', 'ECA240G0786' => 'eca', 'ECA240G1802' => 'eca', 'ECA240G3760' => 'eca', 'ECA240G3920' => 'eca', 'EL10Ac5g12536' => 'bvu', 'EL10Ac5g12537' => 'bvu', 'EL10Ac5g12538' => 'bvu', 'Eucgr.B01004' => 'egr', 'Eucgr.B01006' => 'egr', 'Eucgr.B01007' => 'egr', 'Eucgr.B01008' => 'egr', 'Eucgr.B01895' => 'egr', 'Eucgr.B01896' => 'egr', 'FAN04G1456' => 'fan', 'FAN08G1769' => 'fan', 'FAN08G2160' => 'fan', 'FAN13G2403' => 'fan', 'FAN13G3303' => 'fan', 'FAN15G2435' => 'fan', 'FAN17G0672' => 'fan', 'FAN17G2441' => 'fan', 'FAN18G1024' => 'fan', 'FAN22G1458' => 'fan', 'FAN24G0037' => 'fan', 'FAN24G0429' => 'fan', 'FAN24G2387' => 'fan', 'FAN27G2746' => 'fan', 'FvH4_2g20400' => 'fve', 'FvH4_2g20420' => 'fve', 'FvH4_2g20430' => 'fve', 'FvH4_4g01270' => 'fve', 'FvH4_4g01290' => 'fve', 'FvH4_4g01300' => 'fve', 'FvH4_4g01310' => 'fve', 'FvH4_4g01330' => 'fve', 'FvH4_5g09070' => 'fve', 'Glyma.10G243800' => 'gma', 'Glyma.20G150600' => 'gma', 'Gohir.A09G219200' => 'ghi', 'Gohir.A09G219300' => 'ghi', 'Gohir.D09G221400' => 'ghi', 'Gohir.D09G221500' => 'ghi', 'Gorai.006G242600' => 'gra', 'Gorai.006G242700' => 'gra', 'GSVIVG01018044001' => 'vvi', 'HanXRQChr03g0083821' => 'han', 'HanXRQChr03g0083841' => 'han', 'HanXRQChr03g0083881' => 'han', 'HanXRQChr03g0083901' => 'han', 'HanXRQChr03g0083921' => 'han', 'HanXRQChr03g0085331' => 'han', 'HanXRQChr03g0085361' => 'han', 'HanXRQChr03g0085411' => 'han', 'HanXRQChr03g0085421' => 'han', 'HanXRQChr03g0085431' => 'han', 'HanXRQChr08g0221991' => 'han', 'HanXRQChr11g0336061' => 'han', 'HanXRQChr11g0336411' => 'han', 'Haze_11234' => 'cav', 'Hma1.2p1_0549F.1_g177010' => 'hma', 'Hma1.2p1_0602F.1_g187630' => 'hma', 'Hund14876' => 'sun', 'Hund14879' => 'sun', 'Lalb_Chr06g0160741' => 'lal', 'Lalb_Chr21g0304781' => 'lal', 'Lj3A726G19' => 'lonja', 'Lj3A726T23' => 'lonja', 'Lj3A726T24' => 'lonja', 'Lj3A726T25' => 'lonja', 'Lj3A727T17' => 'lonja', 'Lj3C726T0' => 'lonja', 'Lj3C726T2' => 'lonja', 'Lj3P725T35' => 'lonja', 'Lj3P727T10' => 'lonja', 'Lj3P727T12' => 'lonja', 'Lj3P727T14' => 'lonja', 'Lj5g0023109' => 'lja', 'Lj6P646T44' => 'lonja', 'Lsat_1_v5_gn_6_75760' => 'lsa', 'Lsat_1_v5_gn_6_75800' => 'lsa', 'Lsat_1_v5_gn_6_75900' => 'lsa', 'Lsat_1_v5_gn_6_76240' => 'lsa', 'Lsat_1_v5_gn_6_76441' => 'lsa', 'Lsat_1_v5_gn_6_76700' => 'lsa', 'Lsat_1_v5_gn_6_76760' => 'lsa', 'Manes.15G033100' => 'mes', 'Mapoly0004s0074' => 'mpo', 'Mapoly0004s0075' => 'mpo', 'Mapoly0004s0163' => 'mpo', 'Mapoly0004s0164' => 'mpo', 'Mapoly0021s0018' => 'mpo', 'Mapoly0041s0136' => 'mpo', 'Mapoly0041s0137' => 'mpo', 'Mapoly0041s0138' => 'mpo', 'Mapoly0041s0139' => 'mpo', 'Mapoly0041s0141' => 'mpo', 'Mapoly0041s0142' => 'mpo', 'Mapoly0041s0143' => 'mpo', 'Mapoly0041s0144' => 'mpo', 'Mapoly0041s0145' => 'mpo', 'Mapoly0047s0106' => 'mpo', 'Mapoly0047s0108' => 'mpo', 'Mapoly0050s0051' => 'mpo', 'Mapoly0050s0052' => 'mpo', 'Mapoly0050s0053' => 'mpo', 'Mapoly0058s0013' => 'mpo', 'Mapoly0091s0078' => 'mpo', 'Mapoly0091s0079' => 'mpo', 'Mapoly0091s0080' => 'mpo', 'Mapoly0091s0081' => 'mpo', 'Mapoly0278s0004' => 'mpo', 'Mapoly0278s0005' => 'mpo', 'Mapoly0278s0006' => 'mpo', 'MBI11_g30648_MAGBIO' => 'mbi', 'MCO03G194' => 'mco', 'MCO03G590' => 'mco', 'MCO07G312' => 'mco', 'MCO10G318' => 'mco', 'MCO12G244' => 'mco', 'MCO13G148' => 'mco', 'MCO13G194' => 'mco', 'MCO16G238' => 'mco', 'MD06G1134100' => 'mdo', 'MD13G1200100' => 'mdo', 'MD13G1200300' => 'mdo', 'MD13G1200600' => 'mdo', 'MD14G1150400' => 'mdo', 'MD16G1200000' => 'mdo', 'Medtr1g102570' => 'mtr', 'Medtr1g102780' => 'mtr', 'Medtr1g102800' => 'mtr', 'Medtr1g102810' => 'mtr', 'Medtr1g102830' => 'mtr', 'MELO3C006499.2' => 'cme', 'Migut.G00385' => 'egut', 'MSTRG.4063' => 'ama', 'Nitab4.5_0000090g0260' => 'nta', 'Nitab4.5_0000977g0030' => 'nta', 'Nitab4.5_0002541g0040' => 'nta', 'Nitab4.5_0007068g0040' => 'nta', 'Nn005s41408' => 'nnu', 'Nn005s41410' => 'nnu', 'Oeu010310.1' => 'oeu', 'Oeu010311.1' => 'oeu', 'Oeu043472.1' => 'oeu', 'Os01g0246400' => 'osa', 'Os04g0267950' => 'osa', 'Os07g0178700' => 'osa', 'Os07g0178800' => 'osa', 'Peaxi162Scf00316g00046' => 'pax', 'Peaxi162Scf00316g00049' => 'pax', 'Peaxi162Scf00316g00059' => 'pax', 'Peaxi162Scf00316g00328' => 'pax', 'Peaxi162Scf00316g00329' => 'pax', 'Peaxi162Scf00316g00411' => 'pax', 'Peaxi162Scf00316g00521' => 'pax', 'Peaxi162Scf00492g00068' => 'pax', 'Peaxi162Scf35631g00002' => 'pax', 'PGR142G3720' => 'pgr', 'PGSC0003DMG400006442' => 'stu', 'Phvul.007G062000' => 'pvu', 'Potri.008G157750' => 'ptr', 'Potri.008G157900' => 'ptr', 'Potri.008G158000' => 'ptr', 'Potri.008G158200' => 'ptr', 'Pp3c11_7280' => 'ppa', 'Pp3c11_7980' => 'ppa', 'Pp3c12_19450' => 'ppa', 'Pp3c14_1480' => 'ppa', 'Pp3c14_1501' => 'ppa', 'Pp3c16_4900' => 'ppa', 'Pp3c16_5010' => 'ppa', 'Pp3c16_5060' => 'ppa', 'Pp3c19_18250' => 'ppa', 'Pp3c23_8530' => 'ppa', 'Pp3c23_8550' => 'ppa', 'Pp3c24_9670' => 'ppa', 'Pp3c2_21390' => 'ppa', 'Pp3c2_31380' => 'ppa', 'Pp3c3_16620' => 'ppa', 'Pp3c3_8090' => 'ppa', 'Pp3c3_8110' => 'ppa', 'Pp3c3_8130' => 'ppa', 'Pp3c3_8150' => 'ppa', 'Pp3c4_14320' => 'ppa', 'Pp3c6_2560' => 'ppa', 'Pp3c9_16700' => 'ppa', 'PRCOL_00000234' => 'pco', 'PRCOL_00000235' => 'pco', 'PRCOL_00000777' => 'pco', 'PRCOL_00002344' => 'pco', 'PRCOL_00002372' => 'pco', 'PRCOL_00006120' => 'pco', 'Prupe.1G021400' => 'ppe', 'Prupe.1G021500' => 'ppe', 'Prupe.1G021600' => 'ppe', 'Prupe.1G021700' => 'ppe', 'Prupe.1G021800' => 'ppe', 'Prupe.5G145100' => 'ppe', 'Psat6g204040' => 'psa', 'Psat6g204800' => 'psa', 'Psat6g204920' => 'psa', 'Psat6g204960' => 'psa', 'Psat6g205080' => 'psa', 'PSO017G0271' => 'pso', 'PSO017G1276' => 'pso', 'PSO017G1429' => 'pso', 'PSO017G1861' => 'pso', 'PSO017G2787' => 'pso', 'PSO017G4466' => 'pso', 'PSO017G5118' => 'pso', 'PSO017G5420' => 'pso', 'PSO063G3678' => 'pso', 'PSO210G0546' => 'pso', 'PSO317G0001' => 'pso', 'PSO357G0512' => 'pso', 'PSO478G2682' => 'pso', 'PSO647G0001' => 'pso', 'PSO675G0001' => 'pso', 'PSO675G2699' => 'pso', 'PSO675G2849' => 'pso', 'PSO675G4991' => 'pso', 'PSO689G0001' => 'pso', 'QL06p000916' => 'qlo', 'QL06p000921' => 'qlo', 'QL06p001398' => 'qlo', 'QL06p001407' => 'qlo', 'QL06p002031' => 'qlo', 'RcHm_v2.0_Chr4g0387791' => 'rch', 'RcHm_v2.0_Chr4g0387801' => 'rch', 'RcHm_v2.0_Chr6g0286501' => 'rch', 'RcHm_v2.0_Chr6g0286511' => 'rch', 'RcHm_v2.0_Chr6g0286521' => 'rch', 'RcHm_v2.0_Chr6g0286531' => 'rch', 'RcHm_v2.0_Chr7g0189141' => 'rch', 'Rhsim02G0028700' => 'rsi', 'Rhsim02G0028800' => 'rsi', 'Rhsim02G0028900' => 'rsi', 'Rhsim02G0029000' => 'rsi', 'Rhsim02G0029100' => 'rsi', 'Rhsim02G0029200' => 'rsi', 'Rhsim02G0029300' => 'rsi', 'Rhsim02G0029400' => 'rsi', 'Rhsim02G0029500' => 'rsi', 'Rhsim02G0029600' => 'rsi', 'RhsimUnG0024000' => 'rsi', 'RhsimUnG0024100' => 'rsi', 'RhsimUnG0024200' => 'rsi', 'RhsimUnG0024300' => 'rsi', 'RhsimUnG0024400' => 'rsi', 'RhsimUnG0024500' => 'rsi', 'RhsimUnG0024700' => 'rsi', 'RhsimUnG0024800' => 'rsi', 'RhsimUnG0024900' => 'rsi', 'RhsimUnG0025100' => 'rsi', 'Sabra08G0120200' => 'sbr', 'Sabra08G0120300' => 'sbr', 'Sabra08G0120500' => 'sbr', 'Sabra08G0120600' => 'sbr', 'Sabra10G0158900' => 'sbr', 'SalBow2G3492' => 'sbo', 'Sc13g0004760' => 'sci', 'Sc13g0004770' => 'sci', 'Sed0003417' => 'sed', 'Sed0019750' => 'sed', 'SEGI_03419' => 'sgi', 'SEGI_05907' => 'sgi', 'SEGI_10682' => 'sgi', 'SEGI_13528' => 'sgi', 'SEGI_16081' => 'sgi', 'SEGI_19370' => 'sgi', 'SEGI_21015' => 'sgi', 'SEGI_21944' => 'sgi', 'SEGI_32906' => 'sgi', 'SEGI_33093' => 'sgi', 'SEGI_36110' => 'sgi', 'SEGI_40397' => 'sgi', 'SGA_v2.0_scaffold191G40426' => 'sas', 'SGA_v2.0_scaffold353G49717' => 'sas', 'SGA_v2.0_scaffold50G18550' => 'sas', 'SMO119G0173' => 'smo', 'SMO172G0002' => 'smo', 'Solyc09g082690.3' => 'sly', 'Solyc09g082700.2' => 'sly', 'Sopen09g031550' => 'spe', 'Sopen09g031560' => 'spe', 'Sp3g20540' => 'spa', 'Sp7g07580' => 'spa', 'TAR134G0002' => 'tar', 'TAR236G0001' => 'tar', 'TAR365G0892' => 'tar', 'TAR636G0166' => 'tar', 'TAR636G0646' => 'tar', 'TAR636G0869' => 'tar', 'TAR636G1317' => 'tar', 'TAR636G1744' => 'tar', 'TAR636G3358' => 'tar', 'TAR636G3436' => 'tar', 'THA.LOC104803047' => 'tha', 'Thecc.04G238900' => 'tca', 'Thhalv10021557m.g' => 'esa', 'Thhalv10026318m.g' => 'esa', 'Thhalv10026335m.g' => 'esa', 'TPR.G17433' => 'tpr', 'TPR.G18915' => 'tpr', 'TPR.G26125' => 'tpr', 'TWI09G0677' => 'twi', 'TWI73G0287' => 'twi', 'unitig_748.g8326' => 'ugi', 'vmacro15370' => 'vma', 'vmacro15371' => 'vma', 'vmacro15372' => 'vma', 'vmacro15373' => 'vma', 'vmacro15374' => 'vma', 'VMungo0720G2826' => 'vmu', 'Zm00001eb116960' => 'zma', 'Zm00001eb301260' => 'zma', 'Zm00001eb301270' => 'zma' ), 'gf_id' => 'HOM05D001460', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001460' ), 'data_identifier' => 'HOM05D001460', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001460', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '433', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p22980' => 'bna', 'A01p32340' => 'bna', 'A03p42970' => 'bna', 'A05p25880' => 'bna', 'Aa31LG8G9320' => 'aar', 'Aa31LG8G9330' => 'aar', 'Aa31LG8G9340' => 'aar', 'Aa31sc221G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1034' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1528' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.829' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2222' => 'aag', 'Ah.12g058830' => 'amhyb', 'Ah.12g058840' => 'amhyb', 'AL3G37160' => 'aly', 'AL7G41310' => 'aly', 'Aqoxy5G00395' => 'aox', 'Aqoxy5G00396' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0C8NZA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5185HY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JZ1PRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MD3LS0' => 'arhy', 'AT3G22840' => 'ath', 'AT4G14690' => 'ath', 'ATR0665G054' => 'atr', 'Atru.chr4.2344' => 'acertr', 'Atru.chr4.2346' => 'acertr', 'Atru.chr4.2347' => 'acertr', 'Atru.chr4.2348' => 'acertr', 'Atru.chr4.2355' => 'acertr', 'Atru.chr4.2356' => 'acertr', 'Atru.chr4.2358' => 'acertr', 'Atru.chr4.2359' => 'acertr', 'Atru.chr4.2360' => 'acertr', 'Atru.chr4.2361' => 'acertr', 'AUR62030476' => 'cqu', 'AUR62030478' => 'cqu', 'AUR62030819' => 'cqu', 'AUR62030820' => 'cqu', 'BcaB03g14648' => 'bca', 'BcaB04g20492' => 'bca', 'BcaB06g26399' => 'bca', 'BcaC01g03416' => 'bca', 'BcaC01g03419' => 'bca', 'BcaC01g03421' => 'bca', 'BcaC01g03424' => 'bca', 'BcaC05g28012' => 'bca', 'BcaC09g49212' => 'bca', 'BcaC09g50140' => 'bca', 'BcaNung00346' => 'bca', 'BolC1t02785H' => 'bol', 'BolC1t04095H' => 'bol', 'BolC3t17545H' => 'bol', 'BolC5t32769H' => 'bol', 'BraA01t02211Z' => 'bra', 'BraA01t03359Z' => 'bra', 'BraA03t13441Z' => 'bra', 'BraA05t21476Z' => 'bra', 'C01p28420' => 'bna', 'C01p41350' => 'bna', 'C03p52750' => 'bna', 'C03p52780' => 'bna', 'C05p40270' => 'bna', 'CAN.G1437.9' => 'can', 'CANSAT78G0035' => 'cansat', 'CANSAT78G1036' => 'cansat', 'CANSAT78G2272' => 'cansat', 'CANSAT78G2478' => 'cansat', 'CARHR098700' => 'chi', 'CARHR221120' => 'chi', 'CARHR221150' => 'chi', 'Carub.0003s2297' => 'cru', 'Carub.0007s2749' => 'cru', 'Carub.0007s2750' => 'cru', 'Carub.0007s2751' => 'cru', 'Ca_10849_v3' => 'car', 'Cc03_g04300' => 'ccan', 'CDE02G3648' => 'cde', 'CDE05G0060' => 'cde', 'CDE05G0692' => 'cde', 'CDE05G2285' => 'cde', 'CDE05G2884' => 'cde', 'CDE05G3072' => 'cde', 'Cfa008439' => 'cfa', 'Cfa008441' => 'cfa', 'Cfa008443' => 'cfa', 'Cfa008448' => 'cfa', 'Ciclev10005974m.g' => 'ccl', 'Ciclev10006006m.g' => 'ccl', 'Ciclev10006775m.g' => 'ccl', 'CiPaw.02G120400' => 'cil', 'CiPaw.02G120500' => 'cil', 'CiPaw.02G120600' => 'cil', 'ClCG05G004850' => 'cla', 'COL.COLO4_21566' => 'col', 'Cpa.g.sc44.124' => 'cpa', 'Cre07.g320400' => 'cre', 'Cre07.g320450' => 'cre', 'Cre08.g384650' => 'cre', 'Cre09.g393173' => 'cre', 'Cre09.g394325' => 'cre', 'Cre14.g626750' => 'cre', 'Cre16.g679250' => 'cre', 'CsaV3_3G012890' => 'csa', 'CSS0010865' => 'camsi', 'CSS0044338' => 'camsi', 'DCAR_002366' => 'dca', 'DCAR_030687' => 'dca', 'DCAR_030688' => 'dca', 'Dinv14047' => 'din', 'Dinv14048' => 'din', 'Duzib151G0105' => 'dzi', 'Duzib151G0114' => 'dzi', 'Duzib212G1029' => 'dzi', 'ECA232G3536' => 'eca', 'ECA240G0786' => 'eca', 'ECA240G1802' => 'eca', 'ECA240G3760' => 'eca', 'ECA240G3920' => 'eca', 'EL10Ac5g12536' => 'bvu', 'EL10Ac5g12537' => 'bvu', 'EL10Ac5g12538' => 'bvu', 'Eucgr.B01004' => 'egr', 'Eucgr.B01006' => 'egr', 'Eucgr.B01007' => 'egr', 'Eucgr.B01008' => 'egr', 'Eucgr.B01895' => 'egr', 'Eucgr.B01896' => 'egr', 'FAN04G1456' => 'fan', 'FAN08G1769' => 'fan', 'FAN08G2160' => 'fan', 'FAN13G2403' => 'fan', 'FAN13G3303' => 'fan', 'FAN15G2435' => 'fan', 'FAN17G0672' => 'fan', 'FAN17G2441' => 'fan', 'FAN18G1024' => 'fan', 'FAN22G1458' => 'fan', 'FAN24G0037' => 'fan', 'FAN24G0429' => 'fan', 'FAN24G2387' => 'fan', 'FAN27G2746' => 'fan', 'FvH4_2g20400' => 'fve', 'FvH4_2g20420' => 'fve', 'FvH4_2g20430' => 'fve', 'FvH4_4g01270' => 'fve', 'FvH4_4g01290' => 'fve', 'FvH4_4g01300' => 'fve', 'FvH4_4g01310' => 'fve', 'FvH4_4g01330' => 'fve', 'FvH4_5g09070' => 'fve', 'Glyma.10G243800' => 'gma', 'Glyma.20G150600' => 'gma', 'Gohir.A09G219200' => 'ghi', 'Gohir.A09G219300' => 'ghi', 'Gohir.D09G221400' => 'ghi', 'Gohir.D09G221500' => 'ghi', 'Gorai.006G242600' => 'gra', 'Gorai.006G242700' => 'gra', 'GSVIVG01018044001' => 'vvi', 'HanXRQChr03g0083821' => 'han', 'HanXRQChr03g0083841' => 'han', 'HanXRQChr03g0083881' => 'han', 'HanXRQChr03g0083901' => 'han', 'HanXRQChr03g0083921' => 'han', 'HanXRQChr03g0085331' => 'han', 'HanXRQChr03g0085361' => 'han', 'HanXRQChr03g0085411' => 'han', 'HanXRQChr03g0085421' => 'han', 'HanXRQChr03g0085431' => 'han', 'HanXRQChr08g0221991' => 'han', 'HanXRQChr11g0336061' => 'han', 'HanXRQChr11g0336411' => 'han', 'Haze_11234' => 'cav', 'Hma1.2p1_0549F.1_g177010' => 'hma', 'Hma1.2p1_0602F.1_g187630' => 'hma', 'Hund14876' => 'sun', 'Hund14879' => 'sun', 'Lalb_Chr06g0160741' => 'lal', 'Lalb_Chr21g0304781' => 'lal', 'Lj3A726G19' => 'lonja', 'Lj3A726T23' => 'lonja', 'Lj3A726T24' => 'lonja', 'Lj3A726T25' => 'lonja', 'Lj3A727T17' => 'lonja', 'Lj3C726T0' => 'lonja', 'Lj3C726T2' => 'lonja', 'Lj3P725T35' => 'lonja', 'Lj3P727T10' => 'lonja', 'Lj3P727T12' => 'lonja', 'Lj3P727T14' => 'lonja', 'Lj5g0023109' => 'lja', 'Lj6P646T44' => 'lonja', 'Lsat_1_v5_gn_6_75760' => 'lsa', 'Lsat_1_v5_gn_6_75800' => 'lsa', 'Lsat_1_v5_gn_6_75900' => 'lsa', 'Lsat_1_v5_gn_6_76240' => 'lsa', 'Lsat_1_v5_gn_6_76441' => 'lsa', 'Lsat_1_v5_gn_6_76700' => 'lsa', 'Lsat_1_v5_gn_6_76760' => 'lsa', 'Manes.15G033100' => 'mes', 'Mapoly0004s0074' => 'mpo', 'Mapoly0004s0075' => 'mpo', 'Mapoly0004s0163' => 'mpo', 'Mapoly0004s0164' => 'mpo', 'Mapoly0021s0018' => 'mpo', 'Mapoly0041s0136' => 'mpo', 'Mapoly0041s0137' => 'mpo', 'Mapoly0041s0138' => 'mpo', 'Mapoly0041s0139' => 'mpo', 'Mapoly0041s0141' => 'mpo', 'Mapoly0041s0142' => 'mpo', 'Mapoly0041s0143' => 'mpo', 'Mapoly0041s0144' => 'mpo', 'Mapoly0041s0145' => 'mpo', 'Mapoly0047s0106' => 'mpo', 'Mapoly0047s0108' => 'mpo', 'Mapoly0050s0051' => 'mpo', 'Mapoly0050s0052' => 'mpo', 'Mapoly0050s0053' => 'mpo', 'Mapoly0058s0013' => 'mpo', 'Mapoly0091s0078' => 'mpo', 'Mapoly0091s0079' => 'mpo', 'Mapoly0091s0080' => 'mpo', 'Mapoly0091s0081' => 'mpo', 'Mapoly0278s0004' => 'mpo', 'Mapoly0278s0005' => 'mpo', 'Mapoly0278s0006' => 'mpo', 'MBI11_g30648_MAGBIO' => 'mbi', 'MCO03G194' => 'mco', 'MCO03G590' => 'mco', 'MCO07G312' => 'mco', 'MCO10G318' => 'mco', 'MCO12G244' => 'mco', 'MCO13G148' => 'mco', 'MCO13G194' => 'mco', 'MCO16G238' => 'mco', 'MD06G1134100' => 'mdo', 'MD13G1200100' => 'mdo', 'MD13G1200300' => 'mdo', 'MD13G1200600' => 'mdo', 'MD14G1150400' => 'mdo', 'MD16G1200000' => 'mdo', 'Medtr1g102570' => 'mtr', 'Medtr1g102780' => 'mtr', 'Medtr1g102800' => 'mtr', 'Medtr1g102810' => 'mtr', 'Medtr1g102830' => 'mtr', 'MELO3C006499.2' => 'cme', 'Migut.G00385' => 'egut', 'MSTRG.4063' => 'ama', 'Nitab4.5_0000090g0260' => 'nta', 'Nitab4.5_0000977g0030' => 'nta', 'Nitab4.5_0002541g0040' => 'nta', 'Nitab4.5_0007068g0040' => 'nta', 'Nn005s41408' => 'nnu', 'Nn005s41410' => 'nnu', 'Oeu010310.1' => 'oeu', 'Oeu010311.1' => 'oeu', 'Oeu043472.1' => 'oeu', 'Os01g0246400' => 'osa', 'Os04g0267950' => 'osa', 'Os07g0178700' => 'osa', 'Os07g0178800' => 'osa', 'Peaxi162Scf00316g00046' => 'pax', 'Peaxi162Scf00316g00049' => 'pax', 'Peaxi162Scf00316g00059' => 'pax', 'Peaxi162Scf00316g00328' => 'pax', 'Peaxi162Scf00316g00329' => 'pax', 'Peaxi162Scf00316g00411' => 'pax', 'Peaxi162Scf00316g00521' => 'pax', 'Peaxi162Scf00492g00068' => 'pax', 'Peaxi162Scf35631g00002' => 'pax', 'PGR142G3720' => 'pgr', 'PGSC0003DMG400006442' => 'stu', 'Phvul.007G062000' => 'pvu', 'Potri.008G157750' => 'ptr', 'Potri.008G157900' => 'ptr', 'Potri.008G158000' => 'ptr', 'Potri.008G158200' => 'ptr', 'Pp3c11_7280' => 'ppa', 'Pp3c11_7980' => 'ppa', 'Pp3c12_19450' => 'ppa', 'Pp3c14_1480' => 'ppa', 'Pp3c14_1501' => 'ppa', 'Pp3c16_4900' => 'ppa', 'Pp3c16_5010' => 'ppa', 'Pp3c16_5060' => 'ppa', 'Pp3c19_18250' => 'ppa', 'Pp3c23_8530' => 'ppa', 'Pp3c23_8550' => 'ppa', 'Pp3c24_9670' => 'ppa', 'Pp3c2_21390' => 'ppa', 'Pp3c2_31380' => 'ppa', 'Pp3c3_16620' => 'ppa', 'Pp3c3_8090' => 'ppa', 'Pp3c3_8110' => 'ppa', 'Pp3c3_8130' => 'ppa', 'Pp3c3_8150' => 'ppa', 'Pp3c4_14320' => 'ppa', 'Pp3c6_2560' => 'ppa', 'Pp3c9_16700' => 'ppa', 'PRCOL_00000234' => 'pco', 'PRCOL_00000235' => 'pco', 'PRCOL_00000777' => 'pco', 'PRCOL_00002344' => 'pco', 'PRCOL_00002372' => 'pco', 'PRCOL_00006120' => 'pco', 'Prupe.1G021400' => 'ppe', 'Prupe.1G021500' => 'ppe', 'Prupe.1G021600' => 'ppe', 'Prupe.1G021700' => 'ppe', 'Prupe.1G021800' => 'ppe', 'Prupe.5G145100' => 'ppe', 'Psat6g204040' => 'psa', 'Psat6g204800' => 'psa', 'Psat6g204920' => 'psa', 'Psat6g204960' => 'psa', 'Psat6g205080' => 'psa', 'PSO017G0271' => 'pso', 'PSO017G1276' => 'pso', 'PSO017G1429' => 'pso', 'PSO017G1861' => 'pso', 'PSO017G2787' => 'pso', 'PSO017G4466' => 'pso', 'PSO017G5118' => 'pso', 'PSO017G5420' => 'pso', 'PSO063G3678' => 'pso', 'PSO210G0546' => 'pso', 'PSO317G0001' => 'pso', 'PSO357G0512' => 'pso', 'PSO478G2682' => 'pso', 'PSO647G0001' => 'pso', 'PSO675G0001' => 'pso', 'PSO675G2699' => 'pso', 'PSO675G2849' => 'pso', 'PSO675G4991' => 'pso', 'PSO689G0001' => 'pso', 'QL06p000916' => 'qlo', 'QL06p000921' => 'qlo', 'QL06p001398' => 'qlo', 'QL06p001407' => 'qlo', 'QL06p002031' => 'qlo', 'RcHm_v2.0_Chr4g0387791' => 'rch', 'RcHm_v2.0_Chr4g0387801' => 'rch', 'RcHm_v2.0_Chr6g0286501' => 'rch', 'RcHm_v2.0_Chr6g0286511' => 'rch', 'RcHm_v2.0_Chr6g0286521' => 'rch', 'RcHm_v2.0_Chr6g0286531' => 'rch', 'RcHm_v2.0_Chr7g0189141' => 'rch', 'Rhsim02G0028700' => 'rsi', 'Rhsim02G0028800' => 'rsi', 'Rhsim02G0028900' => 'rsi', 'Rhsim02G0029000' => 'rsi', 'Rhsim02G0029100' => 'rsi', 'Rhsim02G0029200' => 'rsi', 'Rhsim02G0029300' => 'rsi', 'Rhsim02G0029400' => 'rsi', 'Rhsim02G0029500' => 'rsi', 'Rhsim02G0029600' => 'rsi', 'RhsimUnG0024000' => 'rsi', 'RhsimUnG0024100' => 'rsi', 'RhsimUnG0024200' => 'rsi', 'RhsimUnG0024300' => 'rsi', 'RhsimUnG0024400' => 'rsi', 'RhsimUnG0024500' => 'rsi', 'RhsimUnG0024700' => 'rsi', 'RhsimUnG0024800' => 'rsi', 'RhsimUnG0024900' => 'rsi', 'RhsimUnG0025100' => 'rsi', 'Sabra08G0120200' => 'sbr', 'Sabra08G0120300' => 'sbr', 'Sabra08G0120500' => 'sbr', 'Sabra08G0120600' => 'sbr', 'Sabra10G0158900' => 'sbr', 'SalBow2G3492' => 'sbo', 'Sc13g0004760' => 'sci', 'Sc13g0004770' => 'sci', 'Sed0003417' => 'sed', 'Sed0019750' => 'sed', 'SEGI_03419' => 'sgi', 'SEGI_05907' => 'sgi', 'SEGI_10682' => 'sgi', 'SEGI_13528' => 'sgi', 'SEGI_16081' => 'sgi', 'SEGI_19370' => 'sgi', 'SEGI_21015' => 'sgi', 'SEGI_21944' => 'sgi', 'SEGI_32906' => 'sgi', 'SEGI_33093' => 'sgi', 'SEGI_36110' => 'sgi', 'SEGI_40397' => 'sgi', 'SGA_v2.0_scaffold191G40426' => 'sas', 'SGA_v2.0_scaffold353G49717' => 'sas', 'SGA_v2.0_scaffold50G18550' => 'sas', 'SMO119G0173' => 'smo', 'SMO172G0002' => 'smo', 'Solyc09g082690.3' => 'sly', 'Solyc09g082700.2' => 'sly', 'Sopen09g031550' => 'spe', 'Sopen09g031560' => 'spe', 'Sp3g20540' => 'spa', 'Sp7g07580' => 'spa', 'TAR134G0002' => 'tar', 'TAR236G0001' => 'tar', 'TAR365G0892' => 'tar', 'TAR636G0166' => 'tar', 'TAR636G0646' => 'tar', 'TAR636G0869' => 'tar', 'TAR636G1317' => 'tar', 'TAR636G1744' => 'tar', 'TAR636G3358' => 'tar', 'TAR636G3436' => 'tar', 'THA.LOC104803047' => 'tha', 'Thecc.04G238900' => 'tca', 'Thhalv10021557m.g' => 'esa', 'Thhalv10026318m.g' => 'esa', 'Thhalv10026335m.g' => 'esa', 'TPR.G17433' => 'tpr', 'TPR.G18915' => 'tpr', 'TPR.G26125' => 'tpr', 'TWI09G0677' => 'twi', 'TWI73G0287' => 'twi', 'unitig_748.g8326' => 'ugi', 'vmacro15370' => 'vma', 'vmacro15371' => 'vma', 'vmacro15372' => 'vma', 'vmacro15373' => 'vma', 'vmacro15374' => 'vma', 'VMungo0720G2826' => 'vmu', 'Zm00001eb116960' => 'zma', 'Zm00001eb301260' => 'zma', 'Zm00001eb301270' => 'zma' ) $gf_id = 'HOM05D001460' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001460' ) $data_identifier = 'HOM05D001460' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 4, 'aag' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 2, 'aox' => (int) 2, 'arhy' => (int) 4, 'ath' => (int) 2, 'atr' => (int) 1, 'acertr' => (int) 10, 'cqu' => (int) 4, 'bca' => (int) 11, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 1, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 1, 'ccan' => (int) 1, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 1, 'col' => (int) 1, 'cpa' => (int) 1, 'cre' => (int) 7, 'csa' => (int) 1, 'camsi' => (int) 2, 'dca' => (int) 3, 'din' => (int) 2, 'dzi' => (int) 3, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 14, 'fve' => (int) 9, 'gma' => (int) 2, 'ghi' => (int) 4, 'gra' => (int) 2, 'vvi' => (int) 1, 'han' => (int) 13, 'cav' => (int) 1, 'hma' => (int) 2, 'sun' => (int) 2, 'lal' => (int) 2, 'lonja' => (int) 12, 'lja' => (int) 1, 'lsa' => (int) 7, 'mes' => (int) 1, 'mpo' => (int) 27, 'mbi' => (int) 1, 'mco' => (int) 8, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 1, 'egut' => (int) 1, 'ama' => (int) 1, 'nta' => (int) 4, 'nnu' => (int) 2, 'oeu' => (int) 3, 'osa' => (int) 4, 'pax' => (int) 9, 'pgr' => (int) 1, 'stu' => (int) 1, 'pvu' => (int) 1, 'ptr' => (int) 4, 'ppa' => (int) 22, 'pco' => (int) 6, 'ppe' => (int) 6, 'psa' => (int) 5, 'pso' => (int) 19, 'qlo' => (int) 5, 'rch' => (int) 7, 'rsi' => (int) 20, 'sbr' => (int) 5, 'sbo' => (int) 1, 'sci' => (int) 2, 'sed' => (int) 2, 'sgi' => (int) 12, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 2, 'tar' => (int) 10, 'tha' => (int) 1, 'tca' => (int) 1, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 2, 'ugi' => (int) 1, 'vma' => (int) 5, 'vmu' => (int) 1, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb301270' $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' => 'HOM05D001460', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '433', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p22980' => 'bna', 'A01p32340' => 'bna', 'A03p42970' => 'bna', 'A05p25880' => 'bna', 'Aa31LG8G9320' => 'aar', 'Aa31LG8G9330' => 'aar', 'Aa31LG8G9340' => 'aar', 'Aa31sc221G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1034' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1528' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.829' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2222' => 'aag', 'Ah.12g058830' => 'amhyb', 'Ah.12g058840' => 'amhyb', 'AL3G37160' => 'aly', 'AL7G41310' => 'aly', 'Aqoxy5G00395' => 'aox', 'Aqoxy5G00396' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0C8NZA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5185HY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JZ1PRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MD3LS0' => 'arhy', 'AT3G22840' => 'ath', 'AT4G14690' => 'ath', 'ATR0665G054' => 'atr', 'Atru.chr4.2344' => 'acertr', 'Atru.chr4.2346' => 'acertr', 'Atru.chr4.2347' => 'acertr', 'Atru.chr4.2348' => 'acertr', 'Atru.chr4.2355' => 'acertr', 'Atru.chr4.2356' => 'acertr', 'Atru.chr4.2358' => 'acertr', 'Atru.chr4.2359' => 'acertr', 'Atru.chr4.2360' => 'acertr', 'Atru.chr4.2361' => 'acertr', 'AUR62030476' => 'cqu', 'AUR62030478' => 'cqu', 'AUR62030819' => 'cqu', 'AUR62030820' => 'cqu', 'BcaB03g14648' => 'bca', 'BcaB04g20492' => 'bca', 'BcaB06g26399' => 'bca', 'BcaC01g03416' => 'bca', 'BcaC01g03419' => 'bca', 'BcaC01g03421' => 'bca', 'BcaC01g03424' => 'bca', 'BcaC05g28012' => 'bca', 'BcaC09g49212' => 'bca', 'BcaC09g50140' => 'bca', 'BcaNung00346' => 'bca', 'BolC1t02785H' => 'bol', 'BolC1t04095H' => 'bol', 'BolC3t17545H' => 'bol', 'BolC5t32769H' => 'bol', 'BraA01t02211Z' => 'bra', 'BraA01t03359Z' => 'bra', 'BraA03t13441Z' => 'bra', 'BraA05t21476Z' => 'bra', 'C01p28420' => 'bna', 'C01p41350' => 'bna', 'C03p52750' => 'bna', 'C03p52780' => 'bna', 'C05p40270' => 'bna', 'CAN.G1437.9' => 'can', 'CANSAT78G0035' => 'cansat', 'CANSAT78G1036' => 'cansat', 'CANSAT78G2272' => 'cansat', 'CANSAT78G2478' => 'cansat', 'CARHR098700' => 'chi', 'CARHR221120' => 'chi', 'CARHR221150' => 'chi', 'Carub.0003s2297' => 'cru', 'Carub.0007s2749' => 'cru', 'Carub.0007s2750' => 'cru', 'Carub.0007s2751' => 'cru', 'Ca_10849_v3' => 'car', 'Cc03_g04300' => 'ccan', 'CDE02G3648' => 'cde', 'CDE05G0060' => 'cde', 'CDE05G0692' => 'cde', 'CDE05G2285' => 'cde', 'CDE05G2884' => 'cde', 'CDE05G3072' => 'cde', 'Cfa008439' => 'cfa', 'Cfa008441' => 'cfa', 'Cfa008443' => 'cfa', 'Cfa008448' => 'cfa', 'Ciclev10005974m.g' => 'ccl', 'Ciclev10006006m.g' => 'ccl', 'Ciclev10006775m.g' => 'ccl', 'CiPaw.02G120400' => 'cil', 'CiPaw.02G120500' => 'cil', 'CiPaw.02G120600' => 'cil', 'ClCG05G004850' => 'cla', 'COL.COLO4_21566' => 'col', 'Cpa.g.sc44.124' => 'cpa', 'Cre07.g320400' => 'cre', 'Cre07.g320450' => 'cre', 'Cre08.g384650' => 'cre', 'Cre09.g393173' => 'cre', 'Cre09.g394325' => 'cre', 'Cre14.g626750' => 'cre', 'Cre16.g679250' => 'cre', 'CsaV3_3G012890' => 'csa', 'CSS0010865' => 'camsi', 'CSS0044338' => 'camsi', 'DCAR_002366' => 'dca', 'DCAR_030687' => 'dca', 'DCAR_030688' => 'dca', 'Dinv14047' => 'din', 'Dinv14048' => 'din', 'Duzib151G0105' => 'dzi', 'Duzib151G0114' => 'dzi', 'Duzib212G1029' => 'dzi', 'ECA232G3536' => 'eca', 'ECA240G0786' => 'eca', 'ECA240G1802' => 'eca', 'ECA240G3760' => 'eca', 'ECA240G3920' => 'eca', 'EL10Ac5g12536' => 'bvu', 'EL10Ac5g12537' => 'bvu', 'EL10Ac5g12538' => 'bvu', 'Eucgr.B01004' => 'egr', 'Eucgr.B01006' => 'egr', 'Eucgr.B01007' => 'egr', 'Eucgr.B01008' => 'egr', 'Eucgr.B01895' => 'egr', 'Eucgr.B01896' => 'egr', 'FAN04G1456' => 'fan', 'FAN08G1769' => 'fan', 'FAN08G2160' => 'fan', 'FAN13G2403' => 'fan', 'FAN13G3303' => 'fan', 'FAN15G2435' => 'fan', 'FAN17G0672' => 'fan', 'FAN17G2441' => 'fan', 'FAN18G1024' => 'fan', 'FAN22G1458' => 'fan', 'FAN24G0037' => 'fan', 'FAN24G0429' => 'fan', 'FAN24G2387' => 'fan', 'FAN27G2746' => 'fan', 'FvH4_2g20400' => 'fve', 'FvH4_2g20420' => 'fve', 'FvH4_2g20430' => 'fve', 'FvH4_4g01270' => 'fve', 'FvH4_4g01290' => 'fve', 'FvH4_4g01300' => 'fve', 'FvH4_4g01310' => 'fve', 'FvH4_4g01330' => 'fve', 'FvH4_5g09070' => 'fve', 'Glyma.10G243800' => 'gma', 'Glyma.20G150600' => 'gma', 'Gohir.A09G219200' => 'ghi', 'Gohir.A09G219300' => 'ghi', 'Gohir.D09G221400' => 'ghi', 'Gohir.D09G221500' => 'ghi', 'Gorai.006G242600' => 'gra', 'Gorai.006G242700' => 'gra', 'GSVIVG01018044001' => 'vvi', 'HanXRQChr03g0083821' => 'han', 'HanXRQChr03g0083841' => 'han', 'HanXRQChr03g0083881' => 'han', 'HanXRQChr03g0083901' => 'han', 'HanXRQChr03g0083921' => 'han', 'HanXRQChr03g0085331' => 'han', 'HanXRQChr03g0085361' => 'han', 'HanXRQChr03g0085411' => 'han', 'HanXRQChr03g0085421' => 'han', 'HanXRQChr03g0085431' => 'han', 'HanXRQChr08g0221991' => 'han', 'HanXRQChr11g0336061' => 'han', 'HanXRQChr11g0336411' => 'han', 'Haze_11234' => 'cav', 'Hma1.2p1_0549F.1_g177010' => 'hma', 'Hma1.2p1_0602F.1_g187630' => 'hma', 'Hund14876' => 'sun', 'Hund14879' => 'sun', 'Lalb_Chr06g0160741' => 'lal', 'Lalb_Chr21g0304781' => 'lal', 'Lj3A726G19' => 'lonja', 'Lj3A726T23' => 'lonja', 'Lj3A726T24' => 'lonja', 'Lj3A726T25' => 'lonja', 'Lj3A727T17' => 'lonja', 'Lj3C726T0' => 'lonja', 'Lj3C726T2' => 'lonja', 'Lj3P725T35' => 'lonja', 'Lj3P727T10' => 'lonja', 'Lj3P727T12' => 'lonja', 'Lj3P727T14' => 'lonja', 'Lj5g0023109' => 'lja', 'Lj6P646T44' => 'lonja', 'Lsat_1_v5_gn_6_75760' => 'lsa', 'Lsat_1_v5_gn_6_75800' => 'lsa', 'Lsat_1_v5_gn_6_75900' => 'lsa', 'Lsat_1_v5_gn_6_76240' => 'lsa', 'Lsat_1_v5_gn_6_76441' => 'lsa', 'Lsat_1_v5_gn_6_76700' => 'lsa', 'Lsat_1_v5_gn_6_76760' => 'lsa', 'Manes.15G033100' => 'mes', 'Mapoly0004s0074' => 'mpo', 'Mapoly0004s0075' => 'mpo', 'Mapoly0004s0163' => 'mpo', 'Mapoly0004s0164' => 'mpo', 'Mapoly0021s0018' => 'mpo', 'Mapoly0041s0136' => 'mpo', 'Mapoly0041s0137' => 'mpo', 'Mapoly0041s0138' => 'mpo', 'Mapoly0041s0139' => 'mpo', 'Mapoly0041s0141' => 'mpo', 'Mapoly0041s0142' => 'mpo', 'Mapoly0041s0143' => 'mpo', 'Mapoly0041s0144' => 'mpo', 'Mapoly0041s0145' => 'mpo', 'Mapoly0047s0106' => 'mpo', 'Mapoly0047s0108' => 'mpo', 'Mapoly0050s0051' => 'mpo', 'Mapoly0050s0052' => 'mpo', 'Mapoly0050s0053' => 'mpo', 'Mapoly0058s0013' => 'mpo', 'Mapoly0091s0078' => 'mpo', 'Mapoly0091s0079' => 'mpo', 'Mapoly0091s0080' => 'mpo', 'Mapoly0091s0081' => 'mpo', 'Mapoly0278s0004' => 'mpo', 'Mapoly0278s0005' => 'mpo', 'Mapoly0278s0006' => 'mpo', 'MBI11_g30648_MAGBIO' => 'mbi', 'MCO03G194' => 'mco', 'MCO03G590' => 'mco', 'MCO07G312' => 'mco', 'MCO10G318' => 'mco', 'MCO12G244' => 'mco', 'MCO13G148' => 'mco', 'MCO13G194' => 'mco', 'MCO16G238' => 'mco', 'MD06G1134100' => 'mdo', 'MD13G1200100' => 'mdo', 'MD13G1200300' => 'mdo', 'MD13G1200600' => 'mdo', 'MD14G1150400' => 'mdo', 'MD16G1200000' => 'mdo', 'Medtr1g102570' => 'mtr', 'Medtr1g102780' => 'mtr', 'Medtr1g102800' => 'mtr', 'Medtr1g102810' => 'mtr', 'Medtr1g102830' => 'mtr', 'MELO3C006499.2' => 'cme', 'Migut.G00385' => 'egut', 'MSTRG.4063' => 'ama', 'Nitab4.5_0000090g0260' => 'nta', 'Nitab4.5_0000977g0030' => 'nta', 'Nitab4.5_0002541g0040' => 'nta', 'Nitab4.5_0007068g0040' => 'nta', 'Nn005s41408' => 'nnu', 'Nn005s41410' => 'nnu', 'Oeu010310.1' => 'oeu', 'Oeu010311.1' => 'oeu', 'Oeu043472.1' => 'oeu', 'Os01g0246400' => 'osa', 'Os04g0267950' => 'osa', 'Os07g0178700' => 'osa', 'Os07g0178800' => 'osa', 'Peaxi162Scf00316g00046' => 'pax', 'Peaxi162Scf00316g00049' => 'pax', 'Peaxi162Scf00316g00059' => 'pax', 'Peaxi162Scf00316g00328' => 'pax', 'Peaxi162Scf00316g00329' => 'pax', 'Peaxi162Scf00316g00411' => 'pax', 'Peaxi162Scf00316g00521' => 'pax', 'Peaxi162Scf00492g00068' => 'pax', 'Peaxi162Scf35631g00002' => 'pax', 'PGR142G3720' => 'pgr', 'PGSC0003DMG400006442' => 'stu', 'Phvul.007G062000' => 'pvu', 'Potri.008G157750' => 'ptr', 'Potri.008G157900' => 'ptr', 'Potri.008G158000' => 'ptr', 'Potri.008G158200' => 'ptr', 'Pp3c11_7280' => 'ppa', 'Pp3c11_7980' => 'ppa', 'Pp3c12_19450' => 'ppa', 'Pp3c14_1480' => 'ppa', 'Pp3c14_1501' => 'ppa', 'Pp3c16_4900' => 'ppa', 'Pp3c16_5010' => 'ppa', 'Pp3c16_5060' => 'ppa', 'Pp3c19_18250' => 'ppa', 'Pp3c23_8530' => 'ppa', 'Pp3c23_8550' => 'ppa', 'Pp3c24_9670' => 'ppa', 'Pp3c2_21390' => 'ppa', 'Pp3c2_31380' => 'ppa', 'Pp3c3_16620' => 'ppa', 'Pp3c3_8090' => 'ppa', 'Pp3c3_8110' => 'ppa', 'Pp3c3_8130' => 'ppa', 'Pp3c3_8150' => 'ppa', 'Pp3c4_14320' => 'ppa', 'Pp3c6_2560' => 'ppa', 'Pp3c9_16700' => 'ppa', 'PRCOL_00000234' => 'pco', 'PRCOL_00000235' => 'pco', 'PRCOL_00000777' => 'pco', 'PRCOL_00002344' => 'pco', 'PRCOL_00002372' => 'pco', 'PRCOL_00006120' => 'pco', 'Prupe.1G021400' => 'ppe', 'Prupe.1G021500' => 'ppe', 'Prupe.1G021600' => 'ppe', 'Prupe.1G021700' => 'ppe', 'Prupe.1G021800' => 'ppe', 'Prupe.5G145100' => 'ppe', 'Psat6g204040' => 'psa', 'Psat6g204800' => 'psa', 'Psat6g204920' => 'psa', 'Psat6g204960' => 'psa', 'Psat6g205080' => 'psa', 'PSO017G0271' => 'pso', 'PSO017G1276' => 'pso', 'PSO017G1429' => 'pso', 'PSO017G1861' => 'pso', 'PSO017G2787' => 'pso', 'PSO017G4466' => 'pso', 'PSO017G5118' => 'pso', 'PSO017G5420' => 'pso', 'PSO063G3678' => 'pso', 'PSO210G0546' => 'pso', 'PSO317G0001' => 'pso', 'PSO357G0512' => 'pso', 'PSO478G2682' => 'pso', 'PSO647G0001' => 'pso', 'PSO675G0001' => 'pso', 'PSO675G2699' => 'pso', 'PSO675G2849' => 'pso', 'PSO675G4991' => 'pso', 'PSO689G0001' => 'pso', 'QL06p000916' => 'qlo', 'QL06p000921' => 'qlo', 'QL06p001398' => 'qlo', 'QL06p001407' => 'qlo', 'QL06p002031' => 'qlo', 'RcHm_v2.0_Chr4g0387791' => 'rch', 'RcHm_v2.0_Chr4g0387801' => 'rch', 'RcHm_v2.0_Chr6g0286501' => 'rch', 'RcHm_v2.0_Chr6g0286511' => 'rch', 'RcHm_v2.0_Chr6g0286521' => 'rch', 'RcHm_v2.0_Chr6g0286531' => 'rch', 'RcHm_v2.0_Chr7g0189141' => 'rch', 'Rhsim02G0028700' => 'rsi', 'Rhsim02G0028800' => 'rsi', 'Rhsim02G0028900' => 'rsi', 'Rhsim02G0029000' => 'rsi', 'Rhsim02G0029100' => 'rsi', 'Rhsim02G0029200' => 'rsi', 'Rhsim02G0029300' => 'rsi', 'Rhsim02G0029400' => 'rsi', 'Rhsim02G0029500' => 'rsi', 'Rhsim02G0029600' => 'rsi', 'RhsimUnG0024000' => 'rsi', 'RhsimUnG0024100' => 'rsi', 'RhsimUnG0024200' => 'rsi', 'RhsimUnG0024300' => 'rsi', 'RhsimUnG0024400' => 'rsi', 'RhsimUnG0024500' => 'rsi', 'RhsimUnG0024700' => 'rsi', 'RhsimUnG0024800' => 'rsi', 'RhsimUnG0024900' => 'rsi', 'RhsimUnG0025100' => 'rsi', 'Sabra08G0120200' => 'sbr', 'Sabra08G0120300' => 'sbr', 'Sabra08G0120500' => 'sbr', 'Sabra08G0120600' => 'sbr', 'Sabra10G0158900' => 'sbr', 'SalBow2G3492' => 'sbo', 'Sc13g0004760' => 'sci', 'Sc13g0004770' => 'sci', 'Sed0003417' => 'sed', 'Sed0019750' => 'sed', 'SEGI_03419' => 'sgi', 'SEGI_05907' => 'sgi', 'SEGI_10682' => 'sgi', 'SEGI_13528' => 'sgi', 'SEGI_16081' => 'sgi', 'SEGI_19370' => 'sgi', 'SEGI_21015' => 'sgi', 'SEGI_21944' => 'sgi', 'SEGI_32906' => 'sgi', 'SEGI_33093' => 'sgi', 'SEGI_36110' => 'sgi', 'SEGI_40397' => 'sgi', 'SGA_v2.0_scaffold191G40426' => 'sas', 'SGA_v2.0_scaffold353G49717' => 'sas', 'SGA_v2.0_scaffold50G18550' => 'sas', 'SMO119G0173' => 'smo', 'SMO172G0002' => 'smo', 'Solyc09g082690.3' => 'sly', 'Solyc09g082700.2' => 'sly', 'Sopen09g031550' => 'spe', 'Sopen09g031560' => 'spe', 'Sp3g20540' => 'spa', 'Sp7g07580' => 'spa', 'TAR134G0002' => 'tar', 'TAR236G0001' => 'tar', 'TAR365G0892' => 'tar', 'TAR636G0166' => 'tar', 'TAR636G0646' => 'tar', 'TAR636G0869' => 'tar', 'TAR636G1317' => 'tar', 'TAR636G1744' => 'tar', 'TAR636G3358' => 'tar', 'TAR636G3436' => 'tar', 'THA.LOC104803047' => 'tha', 'Thecc.04G238900' => 'tca', 'Thhalv10021557m.g' => 'esa', 'Thhalv10026318m.g' => 'esa', 'Thhalv10026335m.g' => 'esa', 'TPR.G17433' => 'tpr', 'TPR.G18915' => 'tpr', 'TPR.G26125' => 'tpr', 'TWI09G0677' => 'twi', 'TWI73G0287' => 'twi', 'unitig_748.g8326' => 'ugi', 'vmacro15370' => 'vma', 'vmacro15371' => 'vma', 'vmacro15372' => 'vma', 'vmacro15373' => 'vma', 'vmacro15374' => 'vma', 'VMungo0720G2826' => 'vmu', 'Zm00001eb116960' => 'zma', 'Zm00001eb301260' => 'zma', 'Zm00001eb301270' => 'zma' ), 'gf_id' => 'HOM05D001460', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001460' ), 'data_identifier' => 'HOM05D001460', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001460', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '433', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p22980' => 'bna', 'A01p32340' => 'bna', 'A03p42970' => 'bna', 'A05p25880' => 'bna', 'Aa31LG8G9320' => 'aar', 'Aa31LG8G9330' => 'aar', 'Aa31LG8G9340' => 'aar', 'Aa31sc221G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1034' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1528' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.829' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2222' => 'aag', 'Ah.12g058830' => 'amhyb', 'Ah.12g058840' => 'amhyb', 'AL3G37160' => 'aly', 'AL7G41310' => 'aly', 'Aqoxy5G00395' => 'aox', 'Aqoxy5G00396' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0C8NZA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5185HY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JZ1PRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MD3LS0' => 'arhy', 'AT3G22840' => 'ath', 'AT4G14690' => 'ath', 'ATR0665G054' => 'atr', 'Atru.chr4.2344' => 'acertr', 'Atru.chr4.2346' => 'acertr', 'Atru.chr4.2347' => 'acertr', 'Atru.chr4.2348' => 'acertr', 'Atru.chr4.2355' => 'acertr', 'Atru.chr4.2356' => 'acertr', 'Atru.chr4.2358' => 'acertr', 'Atru.chr4.2359' => 'acertr', 'Atru.chr4.2360' => 'acertr', 'Atru.chr4.2361' => 'acertr', 'AUR62030476' => 'cqu', 'AUR62030478' => 'cqu', 'AUR62030819' => 'cqu', 'AUR62030820' => 'cqu', 'BcaB03g14648' => 'bca', 'BcaB04g20492' => 'bca', 'BcaB06g26399' => 'bca', 'BcaC01g03416' => 'bca', 'BcaC01g03419' => 'bca', 'BcaC01g03421' => 'bca', 'BcaC01g03424' => 'bca', 'BcaC05g28012' => 'bca', 'BcaC09g49212' => 'bca', 'BcaC09g50140' => 'bca', 'BcaNung00346' => 'bca', 'BolC1t02785H' => 'bol', 'BolC1t04095H' => 'bol', 'BolC3t17545H' => 'bol', 'BolC5t32769H' => 'bol', 'BraA01t02211Z' => 'bra', 'BraA01t03359Z' => 'bra', 'BraA03t13441Z' => 'bra', 'BraA05t21476Z' => 'bra', 'C01p28420' => 'bna', 'C01p41350' => 'bna', 'C03p52750' => 'bna', 'C03p52780' => 'bna', 'C05p40270' => 'bna', 'CAN.G1437.9' => 'can', 'CANSAT78G0035' => 'cansat', 'CANSAT78G1036' => 'cansat', 'CANSAT78G2272' => 'cansat', 'CANSAT78G2478' => 'cansat', 'CARHR098700' => 'chi', 'CARHR221120' => 'chi', 'CARHR221150' => 'chi', 'Carub.0003s2297' => 'cru', 'Carub.0007s2749' => 'cru', 'Carub.0007s2750' => 'cru', 'Carub.0007s2751' => 'cru', 'Ca_10849_v3' => 'car', 'Cc03_g04300' => 'ccan', 'CDE02G3648' => 'cde', 'CDE05G0060' => 'cde', 'CDE05G0692' => 'cde', 'CDE05G2285' => 'cde', 'CDE05G2884' => 'cde', 'CDE05G3072' => 'cde', 'Cfa008439' => 'cfa', 'Cfa008441' => 'cfa', 'Cfa008443' => 'cfa', 'Cfa008448' => 'cfa', 'Ciclev10005974m.g' => 'ccl', 'Ciclev10006006m.g' => 'ccl', 'Ciclev10006775m.g' => 'ccl', 'CiPaw.02G120400' => 'cil', 'CiPaw.02G120500' => 'cil', 'CiPaw.02G120600' => 'cil', 'ClCG05G004850' => 'cla', 'COL.COLO4_21566' => 'col', 'Cpa.g.sc44.124' => 'cpa', 'Cre07.g320400' => 'cre', 'Cre07.g320450' => 'cre', 'Cre08.g384650' => 'cre', 'Cre09.g393173' => 'cre', 'Cre09.g394325' => 'cre', 'Cre14.g626750' => 'cre', 'Cre16.g679250' => 'cre', 'CsaV3_3G012890' => 'csa', 'CSS0010865' => 'camsi', 'CSS0044338' => 'camsi', 'DCAR_002366' => 'dca', 'DCAR_030687' => 'dca', 'DCAR_030688' => 'dca', 'Dinv14047' => 'din', 'Dinv14048' => 'din', 'Duzib151G0105' => 'dzi', 'Duzib151G0114' => 'dzi', 'Duzib212G1029' => 'dzi', 'ECA232G3536' => 'eca', 'ECA240G0786' => 'eca', 'ECA240G1802' => 'eca', 'ECA240G3760' => 'eca', 'ECA240G3920' => 'eca', 'EL10Ac5g12536' => 'bvu', 'EL10Ac5g12537' => 'bvu', 'EL10Ac5g12538' => 'bvu', 'Eucgr.B01004' => 'egr', 'Eucgr.B01006' => 'egr', 'Eucgr.B01007' => 'egr', 'Eucgr.B01008' => 'egr', 'Eucgr.B01895' => 'egr', 'Eucgr.B01896' => 'egr', 'FAN04G1456' => 'fan', 'FAN08G1769' => 'fan', 'FAN08G2160' => 'fan', 'FAN13G2403' => 'fan', 'FAN13G3303' => 'fan', 'FAN15G2435' => 'fan', 'FAN17G0672' => 'fan', 'FAN17G2441' => 'fan', 'FAN18G1024' => 'fan', 'FAN22G1458' => 'fan', 'FAN24G0037' => 'fan', 'FAN24G0429' => 'fan', 'FAN24G2387' => 'fan', 'FAN27G2746' => 'fan', 'FvH4_2g20400' => 'fve', 'FvH4_2g20420' => 'fve', 'FvH4_2g20430' => 'fve', 'FvH4_4g01270' => 'fve', 'FvH4_4g01290' => 'fve', 'FvH4_4g01300' => 'fve', 'FvH4_4g01310' => 'fve', 'FvH4_4g01330' => 'fve', 'FvH4_5g09070' => 'fve', 'Glyma.10G243800' => 'gma', 'Glyma.20G150600' => 'gma', 'Gohir.A09G219200' => 'ghi', 'Gohir.A09G219300' => 'ghi', 'Gohir.D09G221400' => 'ghi', 'Gohir.D09G221500' => 'ghi', 'Gorai.006G242600' => 'gra', 'Gorai.006G242700' => 'gra', 'GSVIVG01018044001' => 'vvi', 'HanXRQChr03g0083821' => 'han', 'HanXRQChr03g0083841' => 'han', 'HanXRQChr03g0083881' => 'han', 'HanXRQChr03g0083901' => 'han', 'HanXRQChr03g0083921' => 'han', 'HanXRQChr03g0085331' => 'han', 'HanXRQChr03g0085361' => 'han', 'HanXRQChr03g0085411' => 'han', 'HanXRQChr03g0085421' => 'han', 'HanXRQChr03g0085431' => 'han', 'HanXRQChr08g0221991' => 'han', 'HanXRQChr11g0336061' => 'han', 'HanXRQChr11g0336411' => 'han', 'Haze_11234' => 'cav', 'Hma1.2p1_0549F.1_g177010' => 'hma', 'Hma1.2p1_0602F.1_g187630' => 'hma', 'Hund14876' => 'sun', 'Hund14879' => 'sun', 'Lalb_Chr06g0160741' => 'lal', 'Lalb_Chr21g0304781' => 'lal', 'Lj3A726G19' => 'lonja', 'Lj3A726T23' => 'lonja', 'Lj3A726T24' => 'lonja', 'Lj3A726T25' => 'lonja', 'Lj3A727T17' => 'lonja', 'Lj3C726T0' => 'lonja', 'Lj3C726T2' => 'lonja', 'Lj3P725T35' => 'lonja', 'Lj3P727T10' => 'lonja', 'Lj3P727T12' => 'lonja', 'Lj3P727T14' => 'lonja', 'Lj5g0023109' => 'lja', 'Lj6P646T44' => 'lonja', 'Lsat_1_v5_gn_6_75760' => 'lsa', 'Lsat_1_v5_gn_6_75800' => 'lsa', 'Lsat_1_v5_gn_6_75900' => 'lsa', 'Lsat_1_v5_gn_6_76240' => 'lsa', 'Lsat_1_v5_gn_6_76441' => 'lsa', 'Lsat_1_v5_gn_6_76700' => 'lsa', 'Lsat_1_v5_gn_6_76760' => 'lsa', 'Manes.15G033100' => 'mes', 'Mapoly0004s0074' => 'mpo', 'Mapoly0004s0075' => 'mpo', 'Mapoly0004s0163' => 'mpo', 'Mapoly0004s0164' => 'mpo', 'Mapoly0021s0018' => 'mpo', 'Mapoly0041s0136' => 'mpo', 'Mapoly0041s0137' => 'mpo', 'Mapoly0041s0138' => 'mpo', 'Mapoly0041s0139' => 'mpo', 'Mapoly0041s0141' => 'mpo', 'Mapoly0041s0142' => 'mpo', 'Mapoly0041s0143' => 'mpo', 'Mapoly0041s0144' => 'mpo', 'Mapoly0041s0145' => 'mpo', 'Mapoly0047s0106' => 'mpo', 'Mapoly0047s0108' => 'mpo', 'Mapoly0050s0051' => 'mpo', 'Mapoly0050s0052' => 'mpo', 'Mapoly0050s0053' => 'mpo', 'Mapoly0058s0013' => 'mpo', 'Mapoly0091s0078' => 'mpo', 'Mapoly0091s0079' => 'mpo', 'Mapoly0091s0080' => 'mpo', 'Mapoly0091s0081' => 'mpo', 'Mapoly0278s0004' => 'mpo', 'Mapoly0278s0005' => 'mpo', 'Mapoly0278s0006' => 'mpo', 'MBI11_g30648_MAGBIO' => 'mbi', 'MCO03G194' => 'mco', 'MCO03G590' => 'mco', 'MCO07G312' => 'mco', 'MCO10G318' => 'mco', 'MCO12G244' => 'mco', 'MCO13G148' => 'mco', 'MCO13G194' => 'mco', 'MCO16G238' => 'mco', 'MD06G1134100' => 'mdo', 'MD13G1200100' => 'mdo', 'MD13G1200300' => 'mdo', 'MD13G1200600' => 'mdo', 'MD14G1150400' => 'mdo', 'MD16G1200000' => 'mdo', 'Medtr1g102570' => 'mtr', 'Medtr1g102780' => 'mtr', 'Medtr1g102800' => 'mtr', 'Medtr1g102810' => 'mtr', 'Medtr1g102830' => 'mtr', 'MELO3C006499.2' => 'cme', 'Migut.G00385' => 'egut', 'MSTRG.4063' => 'ama', 'Nitab4.5_0000090g0260' => 'nta', 'Nitab4.5_0000977g0030' => 'nta', 'Nitab4.5_0002541g0040' => 'nta', 'Nitab4.5_0007068g0040' => 'nta', 'Nn005s41408' => 'nnu', 'Nn005s41410' => 'nnu', 'Oeu010310.1' => 'oeu', 'Oeu010311.1' => 'oeu', 'Oeu043472.1' => 'oeu', 'Os01g0246400' => 'osa', 'Os04g0267950' => 'osa', 'Os07g0178700' => 'osa', 'Os07g0178800' => 'osa', 'Peaxi162Scf00316g00046' => 'pax', 'Peaxi162Scf00316g00049' => 'pax', 'Peaxi162Scf00316g00059' => 'pax', 'Peaxi162Scf00316g00328' => 'pax', 'Peaxi162Scf00316g00329' => 'pax', 'Peaxi162Scf00316g00411' => 'pax', 'Peaxi162Scf00316g00521' => 'pax', 'Peaxi162Scf00492g00068' => 'pax', 'Peaxi162Scf35631g00002' => 'pax', 'PGR142G3720' => 'pgr', 'PGSC0003DMG400006442' => 'stu', 'Phvul.007G062000' => 'pvu', 'Potri.008G157750' => 'ptr', 'Potri.008G157900' => 'ptr', 'Potri.008G158000' => 'ptr', 'Potri.008G158200' => 'ptr', 'Pp3c11_7280' => 'ppa', 'Pp3c11_7980' => 'ppa', 'Pp3c12_19450' => 'ppa', 'Pp3c14_1480' => 'ppa', 'Pp3c14_1501' => 'ppa', 'Pp3c16_4900' => 'ppa', 'Pp3c16_5010' => 'ppa', 'Pp3c16_5060' => 'ppa', 'Pp3c19_18250' => 'ppa', 'Pp3c23_8530' => 'ppa', 'Pp3c23_8550' => 'ppa', 'Pp3c24_9670' => 'ppa', 'Pp3c2_21390' => 'ppa', 'Pp3c2_31380' => 'ppa', 'Pp3c3_16620' => 'ppa', 'Pp3c3_8090' => 'ppa', 'Pp3c3_8110' => 'ppa', 'Pp3c3_8130' => 'ppa', 'Pp3c3_8150' => 'ppa', 'Pp3c4_14320' => 'ppa', 'Pp3c6_2560' => 'ppa', 'Pp3c9_16700' => 'ppa', 'PRCOL_00000234' => 'pco', 'PRCOL_00000235' => 'pco', 'PRCOL_00000777' => 'pco', 'PRCOL_00002344' => 'pco', 'PRCOL_00002372' => 'pco', 'PRCOL_00006120' => 'pco', 'Prupe.1G021400' => 'ppe', 'Prupe.1G021500' => 'ppe', 'Prupe.1G021600' => 'ppe', 'Prupe.1G021700' => 'ppe', 'Prupe.1G021800' => 'ppe', 'Prupe.5G145100' => 'ppe', 'Psat6g204040' => 'psa', 'Psat6g204800' => 'psa', 'Psat6g204920' => 'psa', 'Psat6g204960' => 'psa', 'Psat6g205080' => 'psa', 'PSO017G0271' => 'pso', 'PSO017G1276' => 'pso', 'PSO017G1429' => 'pso', 'PSO017G1861' => 'pso', 'PSO017G2787' => 'pso', 'PSO017G4466' => 'pso', 'PSO017G5118' => 'pso', 'PSO017G5420' => 'pso', 'PSO063G3678' => 'pso', 'PSO210G0546' => 'pso', 'PSO317G0001' => 'pso', 'PSO357G0512' => 'pso', 'PSO478G2682' => 'pso', 'PSO647G0001' => 'pso', 'PSO675G0001' => 'pso', 'PSO675G2699' => 'pso', 'PSO675G2849' => 'pso', 'PSO675G4991' => 'pso', 'PSO689G0001' => 'pso', 'QL06p000916' => 'qlo', 'QL06p000921' => 'qlo', 'QL06p001398' => 'qlo', 'QL06p001407' => 'qlo', 'QL06p002031' => 'qlo', 'RcHm_v2.0_Chr4g0387791' => 'rch', 'RcHm_v2.0_Chr4g0387801' => 'rch', 'RcHm_v2.0_Chr6g0286501' => 'rch', 'RcHm_v2.0_Chr6g0286511' => 'rch', 'RcHm_v2.0_Chr6g0286521' => 'rch', 'RcHm_v2.0_Chr6g0286531' => 'rch', 'RcHm_v2.0_Chr7g0189141' => 'rch', 'Rhsim02G0028700' => 'rsi', 'Rhsim02G0028800' => 'rsi', 'Rhsim02G0028900' => 'rsi', 'Rhsim02G0029000' => 'rsi', 'Rhsim02G0029100' => 'rsi', 'Rhsim02G0029200' => 'rsi', 'Rhsim02G0029300' => 'rsi', 'Rhsim02G0029400' => 'rsi', 'Rhsim02G0029500' => 'rsi', 'Rhsim02G0029600' => 'rsi', 'RhsimUnG0024000' => 'rsi', 'RhsimUnG0024100' => 'rsi', 'RhsimUnG0024200' => 'rsi', 'RhsimUnG0024300' => 'rsi', 'RhsimUnG0024400' => 'rsi', 'RhsimUnG0024500' => 'rsi', 'RhsimUnG0024700' => 'rsi', 'RhsimUnG0024800' => 'rsi', 'RhsimUnG0024900' => 'rsi', 'RhsimUnG0025100' => 'rsi', 'Sabra08G0120200' => 'sbr', 'Sabra08G0120300' => 'sbr', 'Sabra08G0120500' => 'sbr', 'Sabra08G0120600' => 'sbr', 'Sabra10G0158900' => 'sbr', 'SalBow2G3492' => 'sbo', 'Sc13g0004760' => 'sci', 'Sc13g0004770' => 'sci', 'Sed0003417' => 'sed', 'Sed0019750' => 'sed', 'SEGI_03419' => 'sgi', 'SEGI_05907' => 'sgi', 'SEGI_10682' => 'sgi', 'SEGI_13528' => 'sgi', 'SEGI_16081' => 'sgi', 'SEGI_19370' => 'sgi', 'SEGI_21015' => 'sgi', 'SEGI_21944' => 'sgi', 'SEGI_32906' => 'sgi', 'SEGI_33093' => 'sgi', 'SEGI_36110' => 'sgi', 'SEGI_40397' => 'sgi', 'SGA_v2.0_scaffold191G40426' => 'sas', 'SGA_v2.0_scaffold353G49717' => 'sas', 'SGA_v2.0_scaffold50G18550' => 'sas', 'SMO119G0173' => 'smo', 'SMO172G0002' => 'smo', 'Solyc09g082690.3' => 'sly', 'Solyc09g082700.2' => 'sly', 'Sopen09g031550' => 'spe', 'Sopen09g031560' => 'spe', 'Sp3g20540' => 'spa', 'Sp7g07580' => 'spa', 'TAR134G0002' => 'tar', 'TAR236G0001' => 'tar', 'TAR365G0892' => 'tar', 'TAR636G0166' => 'tar', 'TAR636G0646' => 'tar', 'TAR636G0869' => 'tar', 'TAR636G1317' => 'tar', 'TAR636G1744' => 'tar', 'TAR636G3358' => 'tar', 'TAR636G3436' => 'tar', 'THA.LOC104803047' => 'tha', 'Thecc.04G238900' => 'tca', 'Thhalv10021557m.g' => 'esa', 'Thhalv10026318m.g' => 'esa', 'Thhalv10026335m.g' => 'esa', 'TPR.G17433' => 'tpr', 'TPR.G18915' => 'tpr', 'TPR.G26125' => 'tpr', 'TWI09G0677' => 'twi', 'TWI73G0287' => 'twi', 'unitig_748.g8326' => 'ugi', 'vmacro15370' => 'vma', 'vmacro15371' => 'vma', 'vmacro15372' => 'vma', 'vmacro15373' => 'vma', 'vmacro15374' => 'vma', 'VMungo0720G2826' => 'vmu', 'Zm00001eb116960' => 'zma', 'Zm00001eb301260' => 'zma', 'Zm00001eb301270' => 'zma' ) $gf_id = 'HOM05D001460' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001460' ) $data_identifier = 'HOM05D001460' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 4, 'aag' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 2, 'aox' => (int) 2, 'arhy' => (int) 4, 'ath' => (int) 2, 'atr' => (int) 1, 'acertr' => (int) 10, 'cqu' => (int) 4, 'bca' => (int) 11, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 1, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 1, 'ccan' => (int) 1, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 1, 'col' => (int) 1, 'cpa' => (int) 1, 'cre' => (int) 7, 'csa' => (int) 1, 'camsi' => (int) 2, 'dca' => (int) 3, 'din' => (int) 2, 'dzi' => (int) 3, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 14, 'fve' => (int) 9, 'gma' => (int) 2, 'ghi' => (int) 4, 'gra' => (int) 2, 'vvi' => (int) 1, 'han' => (int) 13, 'cav' => (int) 1, 'hma' => (int) 2, 'sun' => (int) 2, 'lal' => (int) 2, 'lonja' => (int) 12, 'lja' => (int) 1, 'lsa' => (int) 7, 'mes' => (int) 1, 'mpo' => (int) 27, 'mbi' => (int) 1, 'mco' => (int) 8, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 1, 'egut' => (int) 1, 'ama' => (int) 1, 'nta' => (int) 4, 'nnu' => (int) 2, 'oeu' => (int) 3, 'osa' => (int) 4, 'pax' => (int) 9, 'pgr' => (int) 1, 'stu' => (int) 1, 'pvu' => (int) 1, 'ptr' => (int) 4, 'ppa' => (int) 22, 'pco' => (int) 6, 'ppe' => (int) 6, 'psa' => (int) 5, 'pso' => (int) 19, 'qlo' => (int) 5, 'rch' => (int) 7, 'rsi' => (int) 20, 'sbr' => (int) 5, 'sbo' => (int) 1, 'sci' => (int) 2, 'sed' => (int) 2, 'sgi' => (int) 12, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 2, 'tar' => (int) 10, 'tha' => (int) 1, 'tca' => (int) 1, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 2, 'ugi' => (int) 1, 'vma' => (int) 5, 'vmu' => (int) 1, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb301270' $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' => 'HOM05D001460', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '433', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p22980' => 'bna', 'A01p32340' => 'bna', 'A03p42970' => 'bna', 'A05p25880' => 'bna', 'Aa31LG8G9320' => 'aar', 'Aa31LG8G9330' => 'aar', 'Aa31LG8G9340' => 'aar', 'Aa31sc221G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1034' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1528' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.829' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2222' => 'aag', 'Ah.12g058830' => 'amhyb', 'Ah.12g058840' => 'amhyb', 'AL3G37160' => 'aly', 'AL7G41310' => 'aly', 'Aqoxy5G00395' => 'aox', 'Aqoxy5G00396' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0C8NZA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5185HY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JZ1PRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MD3LS0' => 'arhy', 'AT3G22840' => 'ath', 'AT4G14690' => 'ath', 'ATR0665G054' => 'atr', 'Atru.chr4.2344' => 'acertr', 'Atru.chr4.2346' => 'acertr', 'Atru.chr4.2347' => 'acertr', 'Atru.chr4.2348' => 'acertr', 'Atru.chr4.2355' => 'acertr', 'Atru.chr4.2356' => 'acertr', 'Atru.chr4.2358' => 'acertr', 'Atru.chr4.2359' => 'acertr', 'Atru.chr4.2360' => 'acertr', 'Atru.chr4.2361' => 'acertr', 'AUR62030476' => 'cqu', 'AUR62030478' => 'cqu', 'AUR62030819' => 'cqu', 'AUR62030820' => 'cqu', 'BcaB03g14648' => 'bca', 'BcaB04g20492' => 'bca', 'BcaB06g26399' => 'bca', 'BcaC01g03416' => 'bca', 'BcaC01g03419' => 'bca', 'BcaC01g03421' => 'bca', 'BcaC01g03424' => 'bca', 'BcaC05g28012' => 'bca', 'BcaC09g49212' => 'bca', 'BcaC09g50140' => 'bca', 'BcaNung00346' => 'bca', 'BolC1t02785H' => 'bol', 'BolC1t04095H' => 'bol', 'BolC3t17545H' => 'bol', 'BolC5t32769H' => 'bol', 'BraA01t02211Z' => 'bra', 'BraA01t03359Z' => 'bra', 'BraA03t13441Z' => 'bra', 'BraA05t21476Z' => 'bra', 'C01p28420' => 'bna', 'C01p41350' => 'bna', 'C03p52750' => 'bna', 'C03p52780' => 'bna', 'C05p40270' => 'bna', 'CAN.G1437.9' => 'can', 'CANSAT78G0035' => 'cansat', 'CANSAT78G1036' => 'cansat', 'CANSAT78G2272' => 'cansat', 'CANSAT78G2478' => 'cansat', 'CARHR098700' => 'chi', 'CARHR221120' => 'chi', 'CARHR221150' => 'chi', 'Carub.0003s2297' => 'cru', 'Carub.0007s2749' => 'cru', 'Carub.0007s2750' => 'cru', 'Carub.0007s2751' => 'cru', 'Ca_10849_v3' => 'car', 'Cc03_g04300' => 'ccan', 'CDE02G3648' => 'cde', 'CDE05G0060' => 'cde', 'CDE05G0692' => 'cde', 'CDE05G2285' => 'cde', 'CDE05G2884' => 'cde', 'CDE05G3072' => 'cde', 'Cfa008439' => 'cfa', 'Cfa008441' => 'cfa', 'Cfa008443' => 'cfa', 'Cfa008448' => 'cfa', 'Ciclev10005974m.g' => 'ccl', 'Ciclev10006006m.g' => 'ccl', 'Ciclev10006775m.g' => 'ccl', 'CiPaw.02G120400' => 'cil', 'CiPaw.02G120500' => 'cil', 'CiPaw.02G120600' => 'cil', 'ClCG05G004850' => 'cla', 'COL.COLO4_21566' => 'col', 'Cpa.g.sc44.124' => 'cpa', 'Cre07.g320400' => 'cre', 'Cre07.g320450' => 'cre', 'Cre08.g384650' => 'cre', 'Cre09.g393173' => 'cre', 'Cre09.g394325' => 'cre', 'Cre14.g626750' => 'cre', 'Cre16.g679250' => 'cre', 'CsaV3_3G012890' => 'csa', 'CSS0010865' => 'camsi', 'CSS0044338' => 'camsi', 'DCAR_002366' => 'dca', 'DCAR_030687' => 'dca', 'DCAR_030688' => 'dca', 'Dinv14047' => 'din', 'Dinv14048' => 'din', 'Duzib151G0105' => 'dzi', 'Duzib151G0114' => 'dzi', 'Duzib212G1029' => 'dzi', 'ECA232G3536' => 'eca', 'ECA240G0786' => 'eca', 'ECA240G1802' => 'eca', 'ECA240G3760' => 'eca', 'ECA240G3920' => 'eca', 'EL10Ac5g12536' => 'bvu', 'EL10Ac5g12537' => 'bvu', 'EL10Ac5g12538' => 'bvu', 'Eucgr.B01004' => 'egr', 'Eucgr.B01006' => 'egr', 'Eucgr.B01007' => 'egr', 'Eucgr.B01008' => 'egr', 'Eucgr.B01895' => 'egr', 'Eucgr.B01896' => 'egr', 'FAN04G1456' => 'fan', 'FAN08G1769' => 'fan', 'FAN08G2160' => 'fan', 'FAN13G2403' => 'fan', 'FAN13G3303' => 'fan', 'FAN15G2435' => 'fan', 'FAN17G0672' => 'fan', 'FAN17G2441' => 'fan', 'FAN18G1024' => 'fan', 'FAN22G1458' => 'fan', 'FAN24G0037' => 'fan', 'FAN24G0429' => 'fan', 'FAN24G2387' => 'fan', 'FAN27G2746' => 'fan', 'FvH4_2g20400' => 'fve', 'FvH4_2g20420' => 'fve', 'FvH4_2g20430' => 'fve', 'FvH4_4g01270' => 'fve', 'FvH4_4g01290' => 'fve', 'FvH4_4g01300' => 'fve', 'FvH4_4g01310' => 'fve', 'FvH4_4g01330' => 'fve', 'FvH4_5g09070' => 'fve', 'Glyma.10G243800' => 'gma', 'Glyma.20G150600' => 'gma', 'Gohir.A09G219200' => 'ghi', 'Gohir.A09G219300' => 'ghi', 'Gohir.D09G221400' => 'ghi', 'Gohir.D09G221500' => 'ghi', 'Gorai.006G242600' => 'gra', 'Gorai.006G242700' => 'gra', 'GSVIVG01018044001' => 'vvi', 'HanXRQChr03g0083821' => 'han', 'HanXRQChr03g0083841' => 'han', 'HanXRQChr03g0083881' => 'han', 'HanXRQChr03g0083901' => 'han', 'HanXRQChr03g0083921' => 'han', 'HanXRQChr03g0085331' => 'han', 'HanXRQChr03g0085361' => 'han', 'HanXRQChr03g0085411' => 'han', 'HanXRQChr03g0085421' => 'han', 'HanXRQChr03g0085431' => 'han', 'HanXRQChr08g0221991' => 'han', 'HanXRQChr11g0336061' => 'han', 'HanXRQChr11g0336411' => 'han', 'Haze_11234' => 'cav', 'Hma1.2p1_0549F.1_g177010' => 'hma', 'Hma1.2p1_0602F.1_g187630' => 'hma', 'Hund14876' => 'sun', 'Hund14879' => 'sun', 'Lalb_Chr06g0160741' => 'lal', 'Lalb_Chr21g0304781' => 'lal', 'Lj3A726G19' => 'lonja', 'Lj3A726T23' => 'lonja', 'Lj3A726T24' => 'lonja', 'Lj3A726T25' => 'lonja', 'Lj3A727T17' => 'lonja', 'Lj3C726T0' => 'lonja', 'Lj3C726T2' => 'lonja', 'Lj3P725T35' => 'lonja', 'Lj3P727T10' => 'lonja', 'Lj3P727T12' => 'lonja', 'Lj3P727T14' => 'lonja', 'Lj5g0023109' => 'lja', 'Lj6P646T44' => 'lonja', 'Lsat_1_v5_gn_6_75760' => 'lsa', 'Lsat_1_v5_gn_6_75800' => 'lsa', 'Lsat_1_v5_gn_6_75900' => 'lsa', 'Lsat_1_v5_gn_6_76240' => 'lsa', 'Lsat_1_v5_gn_6_76441' => 'lsa', 'Lsat_1_v5_gn_6_76700' => 'lsa', 'Lsat_1_v5_gn_6_76760' => 'lsa', 'Manes.15G033100' => 'mes', 'Mapoly0004s0074' => 'mpo', 'Mapoly0004s0075' => 'mpo', 'Mapoly0004s0163' => 'mpo', 'Mapoly0004s0164' => 'mpo', 'Mapoly0021s0018' => 'mpo', 'Mapoly0041s0136' => 'mpo', 'Mapoly0041s0137' => 'mpo', 'Mapoly0041s0138' => 'mpo', 'Mapoly0041s0139' => 'mpo', 'Mapoly0041s0141' => 'mpo', 'Mapoly0041s0142' => 'mpo', 'Mapoly0041s0143' => 'mpo', 'Mapoly0041s0144' => 'mpo', 'Mapoly0041s0145' => 'mpo', 'Mapoly0047s0106' => 'mpo', 'Mapoly0047s0108' => 'mpo', 'Mapoly0050s0051' => 'mpo', 'Mapoly0050s0052' => 'mpo', 'Mapoly0050s0053' => 'mpo', 'Mapoly0058s0013' => 'mpo', 'Mapoly0091s0078' => 'mpo', 'Mapoly0091s0079' => 'mpo', 'Mapoly0091s0080' => 'mpo', 'Mapoly0091s0081' => 'mpo', 'Mapoly0278s0004' => 'mpo', 'Mapoly0278s0005' => 'mpo', 'Mapoly0278s0006' => 'mpo', 'MBI11_g30648_MAGBIO' => 'mbi', 'MCO03G194' => 'mco', 'MCO03G590' => 'mco', 'MCO07G312' => 'mco', 'MCO10G318' => 'mco', 'MCO12G244' => 'mco', 'MCO13G148' => 'mco', 'MCO13G194' => 'mco', 'MCO16G238' => 'mco', 'MD06G1134100' => 'mdo', 'MD13G1200100' => 'mdo', 'MD13G1200300' => 'mdo', 'MD13G1200600' => 'mdo', 'MD14G1150400' => 'mdo', 'MD16G1200000' => 'mdo', 'Medtr1g102570' => 'mtr', 'Medtr1g102780' => 'mtr', 'Medtr1g102800' => 'mtr', 'Medtr1g102810' => 'mtr', 'Medtr1g102830' => 'mtr', 'MELO3C006499.2' => 'cme', 'Migut.G00385' => 'egut', 'MSTRG.4063' => 'ama', 'Nitab4.5_0000090g0260' => 'nta', 'Nitab4.5_0000977g0030' => 'nta', 'Nitab4.5_0002541g0040' => 'nta', 'Nitab4.5_0007068g0040' => 'nta', 'Nn005s41408' => 'nnu', 'Nn005s41410' => 'nnu', 'Oeu010310.1' => 'oeu', 'Oeu010311.1' => 'oeu', 'Oeu043472.1' => 'oeu', 'Os01g0246400' => 'osa', 'Os04g0267950' => 'osa', 'Os07g0178700' => 'osa', 'Os07g0178800' => 'osa', 'Peaxi162Scf00316g00046' => 'pax', 'Peaxi162Scf00316g00049' => 'pax', 'Peaxi162Scf00316g00059' => 'pax', 'Peaxi162Scf00316g00328' => 'pax', 'Peaxi162Scf00316g00329' => 'pax', 'Peaxi162Scf00316g00411' => 'pax', 'Peaxi162Scf00316g00521' => 'pax', 'Peaxi162Scf00492g00068' => 'pax', 'Peaxi162Scf35631g00002' => 'pax', 'PGR142G3720' => 'pgr', 'PGSC0003DMG400006442' => 'stu', 'Phvul.007G062000' => 'pvu', 'Potri.008G157750' => 'ptr', 'Potri.008G157900' => 'ptr', 'Potri.008G158000' => 'ptr', 'Potri.008G158200' => 'ptr', 'Pp3c11_7280' => 'ppa', 'Pp3c11_7980' => 'ppa', 'Pp3c12_19450' => 'ppa', 'Pp3c14_1480' => 'ppa', 'Pp3c14_1501' => 'ppa', 'Pp3c16_4900' => 'ppa', 'Pp3c16_5010' => 'ppa', 'Pp3c16_5060' => 'ppa', 'Pp3c19_18250' => 'ppa', 'Pp3c23_8530' => 'ppa', 'Pp3c23_8550' => 'ppa', 'Pp3c24_9670' => 'ppa', 'Pp3c2_21390' => 'ppa', 'Pp3c2_31380' => 'ppa', 'Pp3c3_16620' => 'ppa', 'Pp3c3_8090' => 'ppa', 'Pp3c3_8110' => 'ppa', 'Pp3c3_8130' => 'ppa', 'Pp3c3_8150' => 'ppa', 'Pp3c4_14320' => 'ppa', 'Pp3c6_2560' => 'ppa', 'Pp3c9_16700' => 'ppa', 'PRCOL_00000234' => 'pco', 'PRCOL_00000235' => 'pco', 'PRCOL_00000777' => 'pco', 'PRCOL_00002344' => 'pco', 'PRCOL_00002372' => 'pco', 'PRCOL_00006120' => 'pco', 'Prupe.1G021400' => 'ppe', 'Prupe.1G021500' => 'ppe', 'Prupe.1G021600' => 'ppe', 'Prupe.1G021700' => 'ppe', 'Prupe.1G021800' => 'ppe', 'Prupe.5G145100' => 'ppe', 'Psat6g204040' => 'psa', 'Psat6g204800' => 'psa', 'Psat6g204920' => 'psa', 'Psat6g204960' => 'psa', 'Psat6g205080' => 'psa', 'PSO017G0271' => 'pso', 'PSO017G1276' => 'pso', 'PSO017G1429' => 'pso', 'PSO017G1861' => 'pso', 'PSO017G2787' => 'pso', 'PSO017G4466' => 'pso', 'PSO017G5118' => 'pso', 'PSO017G5420' => 'pso', 'PSO063G3678' => 'pso', 'PSO210G0546' => 'pso', 'PSO317G0001' => 'pso', 'PSO357G0512' => 'pso', 'PSO478G2682' => 'pso', 'PSO647G0001' => 'pso', 'PSO675G0001' => 'pso', 'PSO675G2699' => 'pso', 'PSO675G2849' => 'pso', 'PSO675G4991' => 'pso', 'PSO689G0001' => 'pso', 'QL06p000916' => 'qlo', 'QL06p000921' => 'qlo', 'QL06p001398' => 'qlo', 'QL06p001407' => 'qlo', 'QL06p002031' => 'qlo', 'RcHm_v2.0_Chr4g0387791' => 'rch', 'RcHm_v2.0_Chr4g0387801' => 'rch', 'RcHm_v2.0_Chr6g0286501' => 'rch', 'RcHm_v2.0_Chr6g0286511' => 'rch', 'RcHm_v2.0_Chr6g0286521' => 'rch', 'RcHm_v2.0_Chr6g0286531' => 'rch', 'RcHm_v2.0_Chr7g0189141' => 'rch', 'Rhsim02G0028700' => 'rsi', 'Rhsim02G0028800' => 'rsi', 'Rhsim02G0028900' => 'rsi', 'Rhsim02G0029000' => 'rsi', 'Rhsim02G0029100' => 'rsi', 'Rhsim02G0029200' => 'rsi', 'Rhsim02G0029300' => 'rsi', 'Rhsim02G0029400' => 'rsi', 'Rhsim02G0029500' => 'rsi', 'Rhsim02G0029600' => 'rsi', 'RhsimUnG0024000' => 'rsi', 'RhsimUnG0024100' => 'rsi', 'RhsimUnG0024200' => 'rsi', 'RhsimUnG0024300' => 'rsi', 'RhsimUnG0024400' => 'rsi', 'RhsimUnG0024500' => 'rsi', 'RhsimUnG0024700' => 'rsi', 'RhsimUnG0024800' => 'rsi', 'RhsimUnG0024900' => 'rsi', 'RhsimUnG0025100' => 'rsi', 'Sabra08G0120200' => 'sbr', 'Sabra08G0120300' => 'sbr', 'Sabra08G0120500' => 'sbr', 'Sabra08G0120600' => 'sbr', 'Sabra10G0158900' => 'sbr', 'SalBow2G3492' => 'sbo', 'Sc13g0004760' => 'sci', 'Sc13g0004770' => 'sci', 'Sed0003417' => 'sed', 'Sed0019750' => 'sed', 'SEGI_03419' => 'sgi', 'SEGI_05907' => 'sgi', 'SEGI_10682' => 'sgi', 'SEGI_13528' => 'sgi', 'SEGI_16081' => 'sgi', 'SEGI_19370' => 'sgi', 'SEGI_21015' => 'sgi', 'SEGI_21944' => 'sgi', 'SEGI_32906' => 'sgi', 'SEGI_33093' => 'sgi', 'SEGI_36110' => 'sgi', 'SEGI_40397' => 'sgi', 'SGA_v2.0_scaffold191G40426' => 'sas', 'SGA_v2.0_scaffold353G49717' => 'sas', 'SGA_v2.0_scaffold50G18550' => 'sas', 'SMO119G0173' => 'smo', 'SMO172G0002' => 'smo', 'Solyc09g082690.3' => 'sly', 'Solyc09g082700.2' => 'sly', 'Sopen09g031550' => 'spe', 'Sopen09g031560' => 'spe', 'Sp3g20540' => 'spa', 'Sp7g07580' => 'spa', 'TAR134G0002' => 'tar', 'TAR236G0001' => 'tar', 'TAR365G0892' => 'tar', 'TAR636G0166' => 'tar', 'TAR636G0646' => 'tar', 'TAR636G0869' => 'tar', 'TAR636G1317' => 'tar', 'TAR636G1744' => 'tar', 'TAR636G3358' => 'tar', 'TAR636G3436' => 'tar', 'THA.LOC104803047' => 'tha', 'Thecc.04G238900' => 'tca', 'Thhalv10021557m.g' => 'esa', 'Thhalv10026318m.g' => 'esa', 'Thhalv10026335m.g' => 'esa', 'TPR.G17433' => 'tpr', 'TPR.G18915' => 'tpr', 'TPR.G26125' => 'tpr', 'TWI09G0677' => 'twi', 'TWI73G0287' => 'twi', 'unitig_748.g8326' => 'ugi', 'vmacro15370' => 'vma', 'vmacro15371' => 'vma', 'vmacro15372' => 'vma', 'vmacro15373' => 'vma', 'vmacro15374' => 'vma', 'VMungo0720G2826' => 'vmu', 'Zm00001eb116960' => 'zma', 'Zm00001eb301260' => 'zma', 'Zm00001eb301270' => 'zma' ), 'gf_id' => 'HOM05D001460', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001460' ), 'data_identifier' => 'HOM05D001460', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001460', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '433', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p22980' => 'bna', 'A01p32340' => 'bna', 'A03p42970' => 'bna', 'A05p25880' => 'bna', 'Aa31LG8G9320' => 'aar', 'Aa31LG8G9330' => 'aar', 'Aa31LG8G9340' => 'aar', 'Aa31sc221G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1034' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1528' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.829' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2222' => 'aag', 'Ah.12g058830' => 'amhyb', 'Ah.12g058840' => 'amhyb', 'AL3G37160' => 'aly', 'AL7G41310' => 'aly', 'Aqoxy5G00395' => 'aox', 'Aqoxy5G00396' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0C8NZA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5185HY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JZ1PRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MD3LS0' => 'arhy', 'AT3G22840' => 'ath', 'AT4G14690' => 'ath', 'ATR0665G054' => 'atr', 'Atru.chr4.2344' => 'acertr', 'Atru.chr4.2346' => 'acertr', 'Atru.chr4.2347' => 'acertr', 'Atru.chr4.2348' => 'acertr', 'Atru.chr4.2355' => 'acertr', 'Atru.chr4.2356' => 'acertr', 'Atru.chr4.2358' => 'acertr', 'Atru.chr4.2359' => 'acertr', 'Atru.chr4.2360' => 'acertr', 'Atru.chr4.2361' => 'acertr', 'AUR62030476' => 'cqu', 'AUR62030478' => 'cqu', 'AUR62030819' => 'cqu', 'AUR62030820' => 'cqu', 'BcaB03g14648' => 'bca', 'BcaB04g20492' => 'bca', 'BcaB06g26399' => 'bca', 'BcaC01g03416' => 'bca', 'BcaC01g03419' => 'bca', 'BcaC01g03421' => 'bca', 'BcaC01g03424' => 'bca', 'BcaC05g28012' => 'bca', 'BcaC09g49212' => 'bca', 'BcaC09g50140' => 'bca', 'BcaNung00346' => 'bca', 'BolC1t02785H' => 'bol', 'BolC1t04095H' => 'bol', 'BolC3t17545H' => 'bol', 'BolC5t32769H' => 'bol', 'BraA01t02211Z' => 'bra', 'BraA01t03359Z' => 'bra', 'BraA03t13441Z' => 'bra', 'BraA05t21476Z' => 'bra', 'C01p28420' => 'bna', 'C01p41350' => 'bna', 'C03p52750' => 'bna', 'C03p52780' => 'bna', 'C05p40270' => 'bna', 'CAN.G1437.9' => 'can', 'CANSAT78G0035' => 'cansat', 'CANSAT78G1036' => 'cansat', 'CANSAT78G2272' => 'cansat', 'CANSAT78G2478' => 'cansat', 'CARHR098700' => 'chi', 'CARHR221120' => 'chi', 'CARHR221150' => 'chi', 'Carub.0003s2297' => 'cru', 'Carub.0007s2749' => 'cru', 'Carub.0007s2750' => 'cru', 'Carub.0007s2751' => 'cru', 'Ca_10849_v3' => 'car', 'Cc03_g04300' => 'ccan', 'CDE02G3648' => 'cde', 'CDE05G0060' => 'cde', 'CDE05G0692' => 'cde', 'CDE05G2285' => 'cde', 'CDE05G2884' => 'cde', 'CDE05G3072' => 'cde', 'Cfa008439' => 'cfa', 'Cfa008441' => 'cfa', 'Cfa008443' => 'cfa', 'Cfa008448' => 'cfa', 'Ciclev10005974m.g' => 'ccl', 'Ciclev10006006m.g' => 'ccl', 'Ciclev10006775m.g' => 'ccl', 'CiPaw.02G120400' => 'cil', 'CiPaw.02G120500' => 'cil', 'CiPaw.02G120600' => 'cil', 'ClCG05G004850' => 'cla', 'COL.COLO4_21566' => 'col', 'Cpa.g.sc44.124' => 'cpa', 'Cre07.g320400' => 'cre', 'Cre07.g320450' => 'cre', 'Cre08.g384650' => 'cre', 'Cre09.g393173' => 'cre', 'Cre09.g394325' => 'cre', 'Cre14.g626750' => 'cre', 'Cre16.g679250' => 'cre', 'CsaV3_3G012890' => 'csa', 'CSS0010865' => 'camsi', 'CSS0044338' => 'camsi', 'DCAR_002366' => 'dca', 'DCAR_030687' => 'dca', 'DCAR_030688' => 'dca', 'Dinv14047' => 'din', 'Dinv14048' => 'din', 'Duzib151G0105' => 'dzi', 'Duzib151G0114' => 'dzi', 'Duzib212G1029' => 'dzi', 'ECA232G3536' => 'eca', 'ECA240G0786' => 'eca', 'ECA240G1802' => 'eca', 'ECA240G3760' => 'eca', 'ECA240G3920' => 'eca', 'EL10Ac5g12536' => 'bvu', 'EL10Ac5g12537' => 'bvu', 'EL10Ac5g12538' => 'bvu', 'Eucgr.B01004' => 'egr', 'Eucgr.B01006' => 'egr', 'Eucgr.B01007' => 'egr', 'Eucgr.B01008' => 'egr', 'Eucgr.B01895' => 'egr', 'Eucgr.B01896' => 'egr', 'FAN04G1456' => 'fan', 'FAN08G1769' => 'fan', 'FAN08G2160' => 'fan', 'FAN13G2403' => 'fan', 'FAN13G3303' => 'fan', 'FAN15G2435' => 'fan', 'FAN17G0672' => 'fan', 'FAN17G2441' => 'fan', 'FAN18G1024' => 'fan', 'FAN22G1458' => 'fan', 'FAN24G0037' => 'fan', 'FAN24G0429' => 'fan', 'FAN24G2387' => 'fan', 'FAN27G2746' => 'fan', 'FvH4_2g20400' => 'fve', 'FvH4_2g20420' => 'fve', 'FvH4_2g20430' => 'fve', 'FvH4_4g01270' => 'fve', 'FvH4_4g01290' => 'fve', 'FvH4_4g01300' => 'fve', 'FvH4_4g01310' => 'fve', 'FvH4_4g01330' => 'fve', 'FvH4_5g09070' => 'fve', 'Glyma.10G243800' => 'gma', 'Glyma.20G150600' => 'gma', 'Gohir.A09G219200' => 'ghi', 'Gohir.A09G219300' => 'ghi', 'Gohir.D09G221400' => 'ghi', 'Gohir.D09G221500' => 'ghi', 'Gorai.006G242600' => 'gra', 'Gorai.006G242700' => 'gra', 'GSVIVG01018044001' => 'vvi', 'HanXRQChr03g0083821' => 'han', 'HanXRQChr03g0083841' => 'han', 'HanXRQChr03g0083881' => 'han', 'HanXRQChr03g0083901' => 'han', 'HanXRQChr03g0083921' => 'han', 'HanXRQChr03g0085331' => 'han', 'HanXRQChr03g0085361' => 'han', 'HanXRQChr03g0085411' => 'han', 'HanXRQChr03g0085421' => 'han', 'HanXRQChr03g0085431' => 'han', 'HanXRQChr08g0221991' => 'han', 'HanXRQChr11g0336061' => 'han', 'HanXRQChr11g0336411' => 'han', 'Haze_11234' => 'cav', 'Hma1.2p1_0549F.1_g177010' => 'hma', 'Hma1.2p1_0602F.1_g187630' => 'hma', 'Hund14876' => 'sun', 'Hund14879' => 'sun', 'Lalb_Chr06g0160741' => 'lal', 'Lalb_Chr21g0304781' => 'lal', 'Lj3A726G19' => 'lonja', 'Lj3A726T23' => 'lonja', 'Lj3A726T24' => 'lonja', 'Lj3A726T25' => 'lonja', 'Lj3A727T17' => 'lonja', 'Lj3C726T0' => 'lonja', 'Lj3C726T2' => 'lonja', 'Lj3P725T35' => 'lonja', 'Lj3P727T10' => 'lonja', 'Lj3P727T12' => 'lonja', 'Lj3P727T14' => 'lonja', 'Lj5g0023109' => 'lja', 'Lj6P646T44' => 'lonja', 'Lsat_1_v5_gn_6_75760' => 'lsa', 'Lsat_1_v5_gn_6_75800' => 'lsa', 'Lsat_1_v5_gn_6_75900' => 'lsa', 'Lsat_1_v5_gn_6_76240' => 'lsa', 'Lsat_1_v5_gn_6_76441' => 'lsa', 'Lsat_1_v5_gn_6_76700' => 'lsa', 'Lsat_1_v5_gn_6_76760' => 'lsa', 'Manes.15G033100' => 'mes', 'Mapoly0004s0074' => 'mpo', 'Mapoly0004s0075' => 'mpo', 'Mapoly0004s0163' => 'mpo', 'Mapoly0004s0164' => 'mpo', 'Mapoly0021s0018' => 'mpo', 'Mapoly0041s0136' => 'mpo', 'Mapoly0041s0137' => 'mpo', 'Mapoly0041s0138' => 'mpo', 'Mapoly0041s0139' => 'mpo', 'Mapoly0041s0141' => 'mpo', 'Mapoly0041s0142' => 'mpo', 'Mapoly0041s0143' => 'mpo', 'Mapoly0041s0144' => 'mpo', 'Mapoly0041s0145' => 'mpo', 'Mapoly0047s0106' => 'mpo', 'Mapoly0047s0108' => 'mpo', 'Mapoly0050s0051' => 'mpo', 'Mapoly0050s0052' => 'mpo', 'Mapoly0050s0053' => 'mpo', 'Mapoly0058s0013' => 'mpo', 'Mapoly0091s0078' => 'mpo', 'Mapoly0091s0079' => 'mpo', 'Mapoly0091s0080' => 'mpo', 'Mapoly0091s0081' => 'mpo', 'Mapoly0278s0004' => 'mpo', 'Mapoly0278s0005' => 'mpo', 'Mapoly0278s0006' => 'mpo', 'MBI11_g30648_MAGBIO' => 'mbi', 'MCO03G194' => 'mco', 'MCO03G590' => 'mco', 'MCO07G312' => 'mco', 'MCO10G318' => 'mco', 'MCO12G244' => 'mco', 'MCO13G148' => 'mco', 'MCO13G194' => 'mco', 'MCO16G238' => 'mco', 'MD06G1134100' => 'mdo', 'MD13G1200100' => 'mdo', 'MD13G1200300' => 'mdo', 'MD13G1200600' => 'mdo', 'MD14G1150400' => 'mdo', 'MD16G1200000' => 'mdo', 'Medtr1g102570' => 'mtr', 'Medtr1g102780' => 'mtr', 'Medtr1g102800' => 'mtr', 'Medtr1g102810' => 'mtr', 'Medtr1g102830' => 'mtr', 'MELO3C006499.2' => 'cme', 'Migut.G00385' => 'egut', 'MSTRG.4063' => 'ama', 'Nitab4.5_0000090g0260' => 'nta', 'Nitab4.5_0000977g0030' => 'nta', 'Nitab4.5_0002541g0040' => 'nta', 'Nitab4.5_0007068g0040' => 'nta', 'Nn005s41408' => 'nnu', 'Nn005s41410' => 'nnu', 'Oeu010310.1' => 'oeu', 'Oeu010311.1' => 'oeu', 'Oeu043472.1' => 'oeu', 'Os01g0246400' => 'osa', 'Os04g0267950' => 'osa', 'Os07g0178700' => 'osa', 'Os07g0178800' => 'osa', 'Peaxi162Scf00316g00046' => 'pax', 'Peaxi162Scf00316g00049' => 'pax', 'Peaxi162Scf00316g00059' => 'pax', 'Peaxi162Scf00316g00328' => 'pax', 'Peaxi162Scf00316g00329' => 'pax', 'Peaxi162Scf00316g00411' => 'pax', 'Peaxi162Scf00316g00521' => 'pax', 'Peaxi162Scf00492g00068' => 'pax', 'Peaxi162Scf35631g00002' => 'pax', 'PGR142G3720' => 'pgr', 'PGSC0003DMG400006442' => 'stu', 'Phvul.007G062000' => 'pvu', 'Potri.008G157750' => 'ptr', 'Potri.008G157900' => 'ptr', 'Potri.008G158000' => 'ptr', 'Potri.008G158200' => 'ptr', 'Pp3c11_7280' => 'ppa', 'Pp3c11_7980' => 'ppa', 'Pp3c12_19450' => 'ppa', 'Pp3c14_1480' => 'ppa', 'Pp3c14_1501' => 'ppa', 'Pp3c16_4900' => 'ppa', 'Pp3c16_5010' => 'ppa', 'Pp3c16_5060' => 'ppa', 'Pp3c19_18250' => 'ppa', 'Pp3c23_8530' => 'ppa', 'Pp3c23_8550' => 'ppa', 'Pp3c24_9670' => 'ppa', 'Pp3c2_21390' => 'ppa', 'Pp3c2_31380' => 'ppa', 'Pp3c3_16620' => 'ppa', 'Pp3c3_8090' => 'ppa', 'Pp3c3_8110' => 'ppa', 'Pp3c3_8130' => 'ppa', 'Pp3c3_8150' => 'ppa', 'Pp3c4_14320' => 'ppa', 'Pp3c6_2560' => 'ppa', 'Pp3c9_16700' => 'ppa', 'PRCOL_00000234' => 'pco', 'PRCOL_00000235' => 'pco', 'PRCOL_00000777' => 'pco', 'PRCOL_00002344' => 'pco', 'PRCOL_00002372' => 'pco', 'PRCOL_00006120' => 'pco', 'Prupe.1G021400' => 'ppe', 'Prupe.1G021500' => 'ppe', 'Prupe.1G021600' => 'ppe', 'Prupe.1G021700' => 'ppe', 'Prupe.1G021800' => 'ppe', 'Prupe.5G145100' => 'ppe', 'Psat6g204040' => 'psa', 'Psat6g204800' => 'psa', 'Psat6g204920' => 'psa', 'Psat6g204960' => 'psa', 'Psat6g205080' => 'psa', 'PSO017G0271' => 'pso', 'PSO017G1276' => 'pso', 'PSO017G1429' => 'pso', 'PSO017G1861' => 'pso', 'PSO017G2787' => 'pso', 'PSO017G4466' => 'pso', 'PSO017G5118' => 'pso', 'PSO017G5420' => 'pso', 'PSO063G3678' => 'pso', 'PSO210G0546' => 'pso', 'PSO317G0001' => 'pso', 'PSO357G0512' => 'pso', 'PSO478G2682' => 'pso', 'PSO647G0001' => 'pso', 'PSO675G0001' => 'pso', 'PSO675G2699' => 'pso', 'PSO675G2849' => 'pso', 'PSO675G4991' => 'pso', 'PSO689G0001' => 'pso', 'QL06p000916' => 'qlo', 'QL06p000921' => 'qlo', 'QL06p001398' => 'qlo', 'QL06p001407' => 'qlo', 'QL06p002031' => 'qlo', 'RcHm_v2.0_Chr4g0387791' => 'rch', 'RcHm_v2.0_Chr4g0387801' => 'rch', 'RcHm_v2.0_Chr6g0286501' => 'rch', 'RcHm_v2.0_Chr6g0286511' => 'rch', 'RcHm_v2.0_Chr6g0286521' => 'rch', 'RcHm_v2.0_Chr6g0286531' => 'rch', 'RcHm_v2.0_Chr7g0189141' => 'rch', 'Rhsim02G0028700' => 'rsi', 'Rhsim02G0028800' => 'rsi', 'Rhsim02G0028900' => 'rsi', 'Rhsim02G0029000' => 'rsi', 'Rhsim02G0029100' => 'rsi', 'Rhsim02G0029200' => 'rsi', 'Rhsim02G0029300' => 'rsi', 'Rhsim02G0029400' => 'rsi', 'Rhsim02G0029500' => 'rsi', 'Rhsim02G0029600' => 'rsi', 'RhsimUnG0024000' => 'rsi', 'RhsimUnG0024100' => 'rsi', 'RhsimUnG0024200' => 'rsi', 'RhsimUnG0024300' => 'rsi', 'RhsimUnG0024400' => 'rsi', 'RhsimUnG0024500' => 'rsi', 'RhsimUnG0024700' => 'rsi', 'RhsimUnG0024800' => 'rsi', 'RhsimUnG0024900' => 'rsi', 'RhsimUnG0025100' => 'rsi', 'Sabra08G0120200' => 'sbr', 'Sabra08G0120300' => 'sbr', 'Sabra08G0120500' => 'sbr', 'Sabra08G0120600' => 'sbr', 'Sabra10G0158900' => 'sbr', 'SalBow2G3492' => 'sbo', 'Sc13g0004760' => 'sci', 'Sc13g0004770' => 'sci', 'Sed0003417' => 'sed', 'Sed0019750' => 'sed', 'SEGI_03419' => 'sgi', 'SEGI_05907' => 'sgi', 'SEGI_10682' => 'sgi', 'SEGI_13528' => 'sgi', 'SEGI_16081' => 'sgi', 'SEGI_19370' => 'sgi', 'SEGI_21015' => 'sgi', 'SEGI_21944' => 'sgi', 'SEGI_32906' => 'sgi', 'SEGI_33093' => 'sgi', 'SEGI_36110' => 'sgi', 'SEGI_40397' => 'sgi', 'SGA_v2.0_scaffold191G40426' => 'sas', 'SGA_v2.0_scaffold353G49717' => 'sas', 'SGA_v2.0_scaffold50G18550' => 'sas', 'SMO119G0173' => 'smo', 'SMO172G0002' => 'smo', 'Solyc09g082690.3' => 'sly', 'Solyc09g082700.2' => 'sly', 'Sopen09g031550' => 'spe', 'Sopen09g031560' => 'spe', 'Sp3g20540' => 'spa', 'Sp7g07580' => 'spa', 'TAR134G0002' => 'tar', 'TAR236G0001' => 'tar', 'TAR365G0892' => 'tar', 'TAR636G0166' => 'tar', 'TAR636G0646' => 'tar', 'TAR636G0869' => 'tar', 'TAR636G1317' => 'tar', 'TAR636G1744' => 'tar', 'TAR636G3358' => 'tar', 'TAR636G3436' => 'tar', 'THA.LOC104803047' => 'tha', 'Thecc.04G238900' => 'tca', 'Thhalv10021557m.g' => 'esa', 'Thhalv10026318m.g' => 'esa', 'Thhalv10026335m.g' => 'esa', 'TPR.G17433' => 'tpr', 'TPR.G18915' => 'tpr', 'TPR.G26125' => 'tpr', 'TWI09G0677' => 'twi', 'TWI73G0287' => 'twi', 'unitig_748.g8326' => 'ugi', 'vmacro15370' => 'vma', 'vmacro15371' => 'vma', 'vmacro15372' => 'vma', 'vmacro15373' => 'vma', 'vmacro15374' => 'vma', 'VMungo0720G2826' => 'vmu', 'Zm00001eb116960' => 'zma', 'Zm00001eb301260' => 'zma', 'Zm00001eb301270' => 'zma' ) $gf_id = 'HOM05D001460' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001460' ) $data_identifier = 'HOM05D001460' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 4, 'aag' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 2, 'aox' => (int) 2, 'arhy' => (int) 4, 'ath' => (int) 2, 'atr' => (int) 1, 'acertr' => (int) 10, 'cqu' => (int) 4, 'bca' => (int) 11, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 1, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 1, 'ccan' => (int) 1, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 1, 'col' => (int) 1, 'cpa' => (int) 1, 'cre' => (int) 7, 'csa' => (int) 1, 'camsi' => (int) 2, 'dca' => (int) 3, 'din' => (int) 2, 'dzi' => (int) 3, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 14, 'fve' => (int) 9, 'gma' => (int) 2, 'ghi' => (int) 4, 'gra' => (int) 2, 'vvi' => (int) 1, 'han' => (int) 13, 'cav' => (int) 1, 'hma' => (int) 2, 'sun' => (int) 2, 'lal' => (int) 2, 'lonja' => (int) 12, 'lja' => (int) 1, 'lsa' => (int) 7, 'mes' => (int) 1, 'mpo' => (int) 27, 'mbi' => (int) 1, 'mco' => (int) 8, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 1, 'egut' => (int) 1, 'ama' => (int) 1, 'nta' => (int) 4, 'nnu' => (int) 2, 'oeu' => (int) 3, 'osa' => (int) 4, 'pax' => (int) 9, 'pgr' => (int) 1, 'stu' => (int) 1, 'pvu' => (int) 1, 'ptr' => (int) 4, 'ppa' => (int) 22, 'pco' => (int) 6, 'ppe' => (int) 6, 'psa' => (int) 5, 'pso' => (int) 19, 'qlo' => (int) 5, 'rch' => (int) 7, 'rsi' => (int) 20, 'sbr' => (int) 5, 'sbo' => (int) 1, 'sci' => (int) 2, 'sed' => (int) 2, 'sgi' => (int) 12, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 2, 'tar' => (int) 10, 'tha' => (int) 1, 'tca' => (int) 1, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 2, 'ugi' => (int) 1, 'vma' => (int) 5, 'vmu' => (int) 1, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb301270' $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' => 'HOM05D001460', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '433', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p22980' => 'bna', 'A01p32340' => 'bna', 'A03p42970' => 'bna', 'A05p25880' => 'bna', 'Aa31LG8G9320' => 'aar', 'Aa31LG8G9330' => 'aar', 'Aa31LG8G9340' => 'aar', 'Aa31sc221G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1034' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1528' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.829' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2222' => 'aag', 'Ah.12g058830' => 'amhyb', 'Ah.12g058840' => 'amhyb', 'AL3G37160' => 'aly', 'AL7G41310' => 'aly', 'Aqoxy5G00395' => 'aox', 'Aqoxy5G00396' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0C8NZA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5185HY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JZ1PRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MD3LS0' => 'arhy', 'AT3G22840' => 'ath', 'AT4G14690' => 'ath', 'ATR0665G054' => 'atr', 'Atru.chr4.2344' => 'acertr', 'Atru.chr4.2346' => 'acertr', 'Atru.chr4.2347' => 'acertr', 'Atru.chr4.2348' => 'acertr', 'Atru.chr4.2355' => 'acertr', 'Atru.chr4.2356' => 'acertr', 'Atru.chr4.2358' => 'acertr', 'Atru.chr4.2359' => 'acertr', 'Atru.chr4.2360' => 'acertr', 'Atru.chr4.2361' => 'acertr', 'AUR62030476' => 'cqu', 'AUR62030478' => 'cqu', 'AUR62030819' => 'cqu', 'AUR62030820' => 'cqu', 'BcaB03g14648' => 'bca', 'BcaB04g20492' => 'bca', 'BcaB06g26399' => 'bca', 'BcaC01g03416' => 'bca', 'BcaC01g03419' => 'bca', 'BcaC01g03421' => 'bca', 'BcaC01g03424' => 'bca', 'BcaC05g28012' => 'bca', 'BcaC09g49212' => 'bca', 'BcaC09g50140' => 'bca', 'BcaNung00346' => 'bca', 'BolC1t02785H' => 'bol', 'BolC1t04095H' => 'bol', 'BolC3t17545H' => 'bol', 'BolC5t32769H' => 'bol', 'BraA01t02211Z' => 'bra', 'BraA01t03359Z' => 'bra', 'BraA03t13441Z' => 'bra', 'BraA05t21476Z' => 'bra', 'C01p28420' => 'bna', 'C01p41350' => 'bna', 'C03p52750' => 'bna', 'C03p52780' => 'bna', 'C05p40270' => 'bna', 'CAN.G1437.9' => 'can', 'CANSAT78G0035' => 'cansat', 'CANSAT78G1036' => 'cansat', 'CANSAT78G2272' => 'cansat', 'CANSAT78G2478' => 'cansat', 'CARHR098700' => 'chi', 'CARHR221120' => 'chi', 'CARHR221150' => 'chi', 'Carub.0003s2297' => 'cru', 'Carub.0007s2749' => 'cru', 'Carub.0007s2750' => 'cru', 'Carub.0007s2751' => 'cru', 'Ca_10849_v3' => 'car', 'Cc03_g04300' => 'ccan', 'CDE02G3648' => 'cde', 'CDE05G0060' => 'cde', 'CDE05G0692' => 'cde', 'CDE05G2285' => 'cde', 'CDE05G2884' => 'cde', 'CDE05G3072' => 'cde', 'Cfa008439' => 'cfa', 'Cfa008441' => 'cfa', 'Cfa008443' => 'cfa', 'Cfa008448' => 'cfa', 'Ciclev10005974m.g' => 'ccl', 'Ciclev10006006m.g' => 'ccl', 'Ciclev10006775m.g' => 'ccl', 'CiPaw.02G120400' => 'cil', 'CiPaw.02G120500' => 'cil', 'CiPaw.02G120600' => 'cil', 'ClCG05G004850' => 'cla', 'COL.COLO4_21566' => 'col', 'Cpa.g.sc44.124' => 'cpa', 'Cre07.g320400' => 'cre', 'Cre07.g320450' => 'cre', 'Cre08.g384650' => 'cre', 'Cre09.g393173' => 'cre', 'Cre09.g394325' => 'cre', 'Cre14.g626750' => 'cre', 'Cre16.g679250' => 'cre', 'CsaV3_3G012890' => 'csa', 'CSS0010865' => 'camsi', 'CSS0044338' => 'camsi', 'DCAR_002366' => 'dca', 'DCAR_030687' => 'dca', 'DCAR_030688' => 'dca', 'Dinv14047' => 'din', 'Dinv14048' => 'din', 'Duzib151G0105' => 'dzi', 'Duzib151G0114' => 'dzi', 'Duzib212G1029' => 'dzi', 'ECA232G3536' => 'eca', 'ECA240G0786' => 'eca', 'ECA240G1802' => 'eca', 'ECA240G3760' => 'eca', 'ECA240G3920' => 'eca', 'EL10Ac5g12536' => 'bvu', 'EL10Ac5g12537' => 'bvu', 'EL10Ac5g12538' => 'bvu', 'Eucgr.B01004' => 'egr', 'Eucgr.B01006' => 'egr', 'Eucgr.B01007' => 'egr', 'Eucgr.B01008' => 'egr', 'Eucgr.B01895' => 'egr', 'Eucgr.B01896' => 'egr', 'FAN04G1456' => 'fan', 'FAN08G1769' => 'fan', 'FAN08G2160' => 'fan', 'FAN13G2403' => 'fan', 'FAN13G3303' => 'fan', 'FAN15G2435' => 'fan', 'FAN17G0672' => 'fan', 'FAN17G2441' => 'fan', 'FAN18G1024' => 'fan', 'FAN22G1458' => 'fan', 'FAN24G0037' => 'fan', 'FAN24G0429' => 'fan', 'FAN24G2387' => 'fan', 'FAN27G2746' => 'fan', 'FvH4_2g20400' => 'fve', 'FvH4_2g20420' => 'fve', 'FvH4_2g20430' => 'fve', 'FvH4_4g01270' => 'fve', 'FvH4_4g01290' => 'fve', 'FvH4_4g01300' => 'fve', 'FvH4_4g01310' => 'fve', 'FvH4_4g01330' => 'fve', 'FvH4_5g09070' => 'fve', 'Glyma.10G243800' => 'gma', 'Glyma.20G150600' => 'gma', 'Gohir.A09G219200' => 'ghi', 'Gohir.A09G219300' => 'ghi', 'Gohir.D09G221400' => 'ghi', 'Gohir.D09G221500' => 'ghi', 'Gorai.006G242600' => 'gra', 'Gorai.006G242700' => 'gra', 'GSVIVG01018044001' => 'vvi', 'HanXRQChr03g0083821' => 'han', 'HanXRQChr03g0083841' => 'han', 'HanXRQChr03g0083881' => 'han', 'HanXRQChr03g0083901' => 'han', 'HanXRQChr03g0083921' => 'han', 'HanXRQChr03g0085331' => 'han', 'HanXRQChr03g0085361' => 'han', 'HanXRQChr03g0085411' => 'han', 'HanXRQChr03g0085421' => 'han', 'HanXRQChr03g0085431' => 'han', 'HanXRQChr08g0221991' => 'han', 'HanXRQChr11g0336061' => 'han', 'HanXRQChr11g0336411' => 'han', 'Haze_11234' => 'cav', 'Hma1.2p1_0549F.1_g177010' => 'hma', 'Hma1.2p1_0602F.1_g187630' => 'hma', 'Hund14876' => 'sun', 'Hund14879' => 'sun', 'Lalb_Chr06g0160741' => 'lal', 'Lalb_Chr21g0304781' => 'lal', 'Lj3A726G19' => 'lonja', 'Lj3A726T23' => 'lonja', 'Lj3A726T24' => 'lonja', 'Lj3A726T25' => 'lonja', 'Lj3A727T17' => 'lonja', 'Lj3C726T0' => 'lonja', 'Lj3C726T2' => 'lonja', 'Lj3P725T35' => 'lonja', 'Lj3P727T10' => 'lonja', 'Lj3P727T12' => 'lonja', 'Lj3P727T14' => 'lonja', 'Lj5g0023109' => 'lja', 'Lj6P646T44' => 'lonja', 'Lsat_1_v5_gn_6_75760' => 'lsa', 'Lsat_1_v5_gn_6_75800' => 'lsa', 'Lsat_1_v5_gn_6_75900' => 'lsa', 'Lsat_1_v5_gn_6_76240' => 'lsa', 'Lsat_1_v5_gn_6_76441' => 'lsa', 'Lsat_1_v5_gn_6_76700' => 'lsa', 'Lsat_1_v5_gn_6_76760' => 'lsa', 'Manes.15G033100' => 'mes', 'Mapoly0004s0074' => 'mpo', 'Mapoly0004s0075' => 'mpo', 'Mapoly0004s0163' => 'mpo', 'Mapoly0004s0164' => 'mpo', 'Mapoly0021s0018' => 'mpo', 'Mapoly0041s0136' => 'mpo', 'Mapoly0041s0137' => 'mpo', 'Mapoly0041s0138' => 'mpo', 'Mapoly0041s0139' => 'mpo', 'Mapoly0041s0141' => 'mpo', 'Mapoly0041s0142' => 'mpo', 'Mapoly0041s0143' => 'mpo', 'Mapoly0041s0144' => 'mpo', 'Mapoly0041s0145' => 'mpo', 'Mapoly0047s0106' => 'mpo', 'Mapoly0047s0108' => 'mpo', 'Mapoly0050s0051' => 'mpo', 'Mapoly0050s0052' => 'mpo', 'Mapoly0050s0053' => 'mpo', 'Mapoly0058s0013' => 'mpo', 'Mapoly0091s0078' => 'mpo', 'Mapoly0091s0079' => 'mpo', 'Mapoly0091s0080' => 'mpo', 'Mapoly0091s0081' => 'mpo', 'Mapoly0278s0004' => 'mpo', 'Mapoly0278s0005' => 'mpo', 'Mapoly0278s0006' => 'mpo', 'MBI11_g30648_MAGBIO' => 'mbi', 'MCO03G194' => 'mco', 'MCO03G590' => 'mco', 'MCO07G312' => 'mco', 'MCO10G318' => 'mco', 'MCO12G244' => 'mco', 'MCO13G148' => 'mco', 'MCO13G194' => 'mco', 'MCO16G238' => 'mco', 'MD06G1134100' => 'mdo', 'MD13G1200100' => 'mdo', 'MD13G1200300' => 'mdo', 'MD13G1200600' => 'mdo', 'MD14G1150400' => 'mdo', 'MD16G1200000' => 'mdo', 'Medtr1g102570' => 'mtr', 'Medtr1g102780' => 'mtr', 'Medtr1g102800' => 'mtr', 'Medtr1g102810' => 'mtr', 'Medtr1g102830' => 'mtr', 'MELO3C006499.2' => 'cme', 'Migut.G00385' => 'egut', 'MSTRG.4063' => 'ama', 'Nitab4.5_0000090g0260' => 'nta', 'Nitab4.5_0000977g0030' => 'nta', 'Nitab4.5_0002541g0040' => 'nta', 'Nitab4.5_0007068g0040' => 'nta', 'Nn005s41408' => 'nnu', 'Nn005s41410' => 'nnu', 'Oeu010310.1' => 'oeu', 'Oeu010311.1' => 'oeu', 'Oeu043472.1' => 'oeu', 'Os01g0246400' => 'osa', 'Os04g0267950' => 'osa', 'Os07g0178700' => 'osa', 'Os07g0178800' => 'osa', 'Peaxi162Scf00316g00046' => 'pax', 'Peaxi162Scf00316g00049' => 'pax', 'Peaxi162Scf00316g00059' => 'pax', 'Peaxi162Scf00316g00328' => 'pax', 'Peaxi162Scf00316g00329' => 'pax', 'Peaxi162Scf00316g00411' => 'pax', 'Peaxi162Scf00316g00521' => 'pax', 'Peaxi162Scf00492g00068' => 'pax', 'Peaxi162Scf35631g00002' => 'pax', 'PGR142G3720' => 'pgr', 'PGSC0003DMG400006442' => 'stu', 'Phvul.007G062000' => 'pvu', 'Potri.008G157750' => 'ptr', 'Potri.008G157900' => 'ptr', 'Potri.008G158000' => 'ptr', 'Potri.008G158200' => 'ptr', 'Pp3c11_7280' => 'ppa', 'Pp3c11_7980' => 'ppa', 'Pp3c12_19450' => 'ppa', 'Pp3c14_1480' => 'ppa', 'Pp3c14_1501' => 'ppa', 'Pp3c16_4900' => 'ppa', 'Pp3c16_5010' => 'ppa', 'Pp3c16_5060' => 'ppa', 'Pp3c19_18250' => 'ppa', 'Pp3c23_8530' => 'ppa', 'Pp3c23_8550' => 'ppa', 'Pp3c24_9670' => 'ppa', 'Pp3c2_21390' => 'ppa', 'Pp3c2_31380' => 'ppa', 'Pp3c3_16620' => 'ppa', 'Pp3c3_8090' => 'ppa', 'Pp3c3_8110' => 'ppa', 'Pp3c3_8130' => 'ppa', 'Pp3c3_8150' => 'ppa', 'Pp3c4_14320' => 'ppa', 'Pp3c6_2560' => 'ppa', 'Pp3c9_16700' => 'ppa', 'PRCOL_00000234' => 'pco', 'PRCOL_00000235' => 'pco', 'PRCOL_00000777' => 'pco', 'PRCOL_00002344' => 'pco', 'PRCOL_00002372' => 'pco', 'PRCOL_00006120' => 'pco', 'Prupe.1G021400' => 'ppe', 'Prupe.1G021500' => 'ppe', 'Prupe.1G021600' => 'ppe', 'Prupe.1G021700' => 'ppe', 'Prupe.1G021800' => 'ppe', 'Prupe.5G145100' => 'ppe', 'Psat6g204040' => 'psa', 'Psat6g204800' => 'psa', 'Psat6g204920' => 'psa', 'Psat6g204960' => 'psa', 'Psat6g205080' => 'psa', 'PSO017G0271' => 'pso', 'PSO017G1276' => 'pso', 'PSO017G1429' => 'pso', 'PSO017G1861' => 'pso', 'PSO017G2787' => 'pso', 'PSO017G4466' => 'pso', 'PSO017G5118' => 'pso', 'PSO017G5420' => 'pso', 'PSO063G3678' => 'pso', 'PSO210G0546' => 'pso', 'PSO317G0001' => 'pso', 'PSO357G0512' => 'pso', 'PSO478G2682' => 'pso', 'PSO647G0001' => 'pso', 'PSO675G0001' => 'pso', 'PSO675G2699' => 'pso', 'PSO675G2849' => 'pso', 'PSO675G4991' => 'pso', 'PSO689G0001' => 'pso', 'QL06p000916' => 'qlo', 'QL06p000921' => 'qlo', 'QL06p001398' => 'qlo', 'QL06p001407' => 'qlo', 'QL06p002031' => 'qlo', 'RcHm_v2.0_Chr4g0387791' => 'rch', 'RcHm_v2.0_Chr4g0387801' => 'rch', 'RcHm_v2.0_Chr6g0286501' => 'rch', 'RcHm_v2.0_Chr6g0286511' => 'rch', 'RcHm_v2.0_Chr6g0286521' => 'rch', 'RcHm_v2.0_Chr6g0286531' => 'rch', 'RcHm_v2.0_Chr7g0189141' => 'rch', 'Rhsim02G0028700' => 'rsi', 'Rhsim02G0028800' => 'rsi', 'Rhsim02G0028900' => 'rsi', 'Rhsim02G0029000' => 'rsi', 'Rhsim02G0029100' => 'rsi', 'Rhsim02G0029200' => 'rsi', 'Rhsim02G0029300' => 'rsi', 'Rhsim02G0029400' => 'rsi', 'Rhsim02G0029500' => 'rsi', 'Rhsim02G0029600' => 'rsi', 'RhsimUnG0024000' => 'rsi', 'RhsimUnG0024100' => 'rsi', 'RhsimUnG0024200' => 'rsi', 'RhsimUnG0024300' => 'rsi', 'RhsimUnG0024400' => 'rsi', 'RhsimUnG0024500' => 'rsi', 'RhsimUnG0024700' => 'rsi', 'RhsimUnG0024800' => 'rsi', 'RhsimUnG0024900' => 'rsi', 'RhsimUnG0025100' => 'rsi', 'Sabra08G0120200' => 'sbr', 'Sabra08G0120300' => 'sbr', 'Sabra08G0120500' => 'sbr', 'Sabra08G0120600' => 'sbr', 'Sabra10G0158900' => 'sbr', 'SalBow2G3492' => 'sbo', 'Sc13g0004760' => 'sci', 'Sc13g0004770' => 'sci', 'Sed0003417' => 'sed', 'Sed0019750' => 'sed', 'SEGI_03419' => 'sgi', 'SEGI_05907' => 'sgi', 'SEGI_10682' => 'sgi', 'SEGI_13528' => 'sgi', 'SEGI_16081' => 'sgi', 'SEGI_19370' => 'sgi', 'SEGI_21015' => 'sgi', 'SEGI_21944' => 'sgi', 'SEGI_32906' => 'sgi', 'SEGI_33093' => 'sgi', 'SEGI_36110' => 'sgi', 'SEGI_40397' => 'sgi', 'SGA_v2.0_scaffold191G40426' => 'sas', 'SGA_v2.0_scaffold353G49717' => 'sas', 'SGA_v2.0_scaffold50G18550' => 'sas', 'SMO119G0173' => 'smo', 'SMO172G0002' => 'smo', 'Solyc09g082690.3' => 'sly', 'Solyc09g082700.2' => 'sly', 'Sopen09g031550' => 'spe', 'Sopen09g031560' => 'spe', 'Sp3g20540' => 'spa', 'Sp7g07580' => 'spa', 'TAR134G0002' => 'tar', 'TAR236G0001' => 'tar', 'TAR365G0892' => 'tar', 'TAR636G0166' => 'tar', 'TAR636G0646' => 'tar', 'TAR636G0869' => 'tar', 'TAR636G1317' => 'tar', 'TAR636G1744' => 'tar', 'TAR636G3358' => 'tar', 'TAR636G3436' => 'tar', 'THA.LOC104803047' => 'tha', 'Thecc.04G238900' => 'tca', 'Thhalv10021557m.g' => 'esa', 'Thhalv10026318m.g' => 'esa', 'Thhalv10026335m.g' => 'esa', 'TPR.G17433' => 'tpr', 'TPR.G18915' => 'tpr', 'TPR.G26125' => 'tpr', 'TWI09G0677' => 'twi', 'TWI73G0287' => 'twi', 'unitig_748.g8326' => 'ugi', 'vmacro15370' => 'vma', 'vmacro15371' => 'vma', 'vmacro15372' => 'vma', 'vmacro15373' => 'vma', 'vmacro15374' => 'vma', 'VMungo0720G2826' => 'vmu', 'Zm00001eb116960' => 'zma', 'Zm00001eb301260' => 'zma', 'Zm00001eb301270' => 'zma' ), 'gf_id' => 'HOM05D001460', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001460' ), 'data_identifier' => 'HOM05D001460', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001460', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '433', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p22980' => 'bna', 'A01p32340' => 'bna', 'A03p42970' => 'bna', 'A05p25880' => 'bna', 'Aa31LG8G9320' => 'aar', 'Aa31LG8G9330' => 'aar', 'Aa31LG8G9340' => 'aar', 'Aa31sc221G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1034' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1528' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.829' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2222' => 'aag', 'Ah.12g058830' => 'amhyb', 'Ah.12g058840' => 'amhyb', 'AL3G37160' => 'aly', 'AL7G41310' => 'aly', 'Aqoxy5G00395' => 'aox', 'Aqoxy5G00396' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0C8NZA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5185HY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JZ1PRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MD3LS0' => 'arhy', 'AT3G22840' => 'ath', 'AT4G14690' => 'ath', 'ATR0665G054' => 'atr', 'Atru.chr4.2344' => 'acertr', 'Atru.chr4.2346' => 'acertr', 'Atru.chr4.2347' => 'acertr', 'Atru.chr4.2348' => 'acertr', 'Atru.chr4.2355' => 'acertr', 'Atru.chr4.2356' => 'acertr', 'Atru.chr4.2358' => 'acertr', 'Atru.chr4.2359' => 'acertr', 'Atru.chr4.2360' => 'acertr', 'Atru.chr4.2361' => 'acertr', 'AUR62030476' => 'cqu', 'AUR62030478' => 'cqu', 'AUR62030819' => 'cqu', 'AUR62030820' => 'cqu', 'BcaB03g14648' => 'bca', 'BcaB04g20492' => 'bca', 'BcaB06g26399' => 'bca', 'BcaC01g03416' => 'bca', 'BcaC01g03419' => 'bca', 'BcaC01g03421' => 'bca', 'BcaC01g03424' => 'bca', 'BcaC05g28012' => 'bca', 'BcaC09g49212' => 'bca', 'BcaC09g50140' => 'bca', 'BcaNung00346' => 'bca', 'BolC1t02785H' => 'bol', 'BolC1t04095H' => 'bol', 'BolC3t17545H' => 'bol', 'BolC5t32769H' => 'bol', 'BraA01t02211Z' => 'bra', 'BraA01t03359Z' => 'bra', 'BraA03t13441Z' => 'bra', 'BraA05t21476Z' => 'bra', 'C01p28420' => 'bna', 'C01p41350' => 'bna', 'C03p52750' => 'bna', 'C03p52780' => 'bna', 'C05p40270' => 'bna', 'CAN.G1437.9' => 'can', 'CANSAT78G0035' => 'cansat', 'CANSAT78G1036' => 'cansat', 'CANSAT78G2272' => 'cansat', 'CANSAT78G2478' => 'cansat', 'CARHR098700' => 'chi', 'CARHR221120' => 'chi', 'CARHR221150' => 'chi', 'Carub.0003s2297' => 'cru', 'Carub.0007s2749' => 'cru', 'Carub.0007s2750' => 'cru', 'Carub.0007s2751' => 'cru', 'Ca_10849_v3' => 'car', 'Cc03_g04300' => 'ccan', 'CDE02G3648' => 'cde', 'CDE05G0060' => 'cde', 'CDE05G0692' => 'cde', 'CDE05G2285' => 'cde', 'CDE05G2884' => 'cde', 'CDE05G3072' => 'cde', 'Cfa008439' => 'cfa', 'Cfa008441' => 'cfa', 'Cfa008443' => 'cfa', 'Cfa008448' => 'cfa', 'Ciclev10005974m.g' => 'ccl', 'Ciclev10006006m.g' => 'ccl', 'Ciclev10006775m.g' => 'ccl', 'CiPaw.02G120400' => 'cil', 'CiPaw.02G120500' => 'cil', 'CiPaw.02G120600' => 'cil', 'ClCG05G004850' => 'cla', 'COL.COLO4_21566' => 'col', 'Cpa.g.sc44.124' => 'cpa', 'Cre07.g320400' => 'cre', 'Cre07.g320450' => 'cre', 'Cre08.g384650' => 'cre', 'Cre09.g393173' => 'cre', 'Cre09.g394325' => 'cre', 'Cre14.g626750' => 'cre', 'Cre16.g679250' => 'cre', 'CsaV3_3G012890' => 'csa', 'CSS0010865' => 'camsi', 'CSS0044338' => 'camsi', 'DCAR_002366' => 'dca', 'DCAR_030687' => 'dca', 'DCAR_030688' => 'dca', 'Dinv14047' => 'din', 'Dinv14048' => 'din', 'Duzib151G0105' => 'dzi', 'Duzib151G0114' => 'dzi', 'Duzib212G1029' => 'dzi', 'ECA232G3536' => 'eca', 'ECA240G0786' => 'eca', 'ECA240G1802' => 'eca', 'ECA240G3760' => 'eca', 'ECA240G3920' => 'eca', 'EL10Ac5g12536' => 'bvu', 'EL10Ac5g12537' => 'bvu', 'EL10Ac5g12538' => 'bvu', 'Eucgr.B01004' => 'egr', 'Eucgr.B01006' => 'egr', 'Eucgr.B01007' => 'egr', 'Eucgr.B01008' => 'egr', 'Eucgr.B01895' => 'egr', 'Eucgr.B01896' => 'egr', 'FAN04G1456' => 'fan', 'FAN08G1769' => 'fan', 'FAN08G2160' => 'fan', 'FAN13G2403' => 'fan', 'FAN13G3303' => 'fan', 'FAN15G2435' => 'fan', 'FAN17G0672' => 'fan', 'FAN17G2441' => 'fan', 'FAN18G1024' => 'fan', 'FAN22G1458' => 'fan', 'FAN24G0037' => 'fan', 'FAN24G0429' => 'fan', 'FAN24G2387' => 'fan', 'FAN27G2746' => 'fan', 'FvH4_2g20400' => 'fve', 'FvH4_2g20420' => 'fve', 'FvH4_2g20430' => 'fve', 'FvH4_4g01270' => 'fve', 'FvH4_4g01290' => 'fve', 'FvH4_4g01300' => 'fve', 'FvH4_4g01310' => 'fve', 'FvH4_4g01330' => 'fve', 'FvH4_5g09070' => 'fve', 'Glyma.10G243800' => 'gma', 'Glyma.20G150600' => 'gma', 'Gohir.A09G219200' => 'ghi', 'Gohir.A09G219300' => 'ghi', 'Gohir.D09G221400' => 'ghi', 'Gohir.D09G221500' => 'ghi', 'Gorai.006G242600' => 'gra', 'Gorai.006G242700' => 'gra', 'GSVIVG01018044001' => 'vvi', 'HanXRQChr03g0083821' => 'han', 'HanXRQChr03g0083841' => 'han', 'HanXRQChr03g0083881' => 'han', 'HanXRQChr03g0083901' => 'han', 'HanXRQChr03g0083921' => 'han', 'HanXRQChr03g0085331' => 'han', 'HanXRQChr03g0085361' => 'han', 'HanXRQChr03g0085411' => 'han', 'HanXRQChr03g0085421' => 'han', 'HanXRQChr03g0085431' => 'han', 'HanXRQChr08g0221991' => 'han', 'HanXRQChr11g0336061' => 'han', 'HanXRQChr11g0336411' => 'han', 'Haze_11234' => 'cav', 'Hma1.2p1_0549F.1_g177010' => 'hma', 'Hma1.2p1_0602F.1_g187630' => 'hma', 'Hund14876' => 'sun', 'Hund14879' => 'sun', 'Lalb_Chr06g0160741' => 'lal', 'Lalb_Chr21g0304781' => 'lal', 'Lj3A726G19' => 'lonja', 'Lj3A726T23' => 'lonja', 'Lj3A726T24' => 'lonja', 'Lj3A726T25' => 'lonja', 'Lj3A727T17' => 'lonja', 'Lj3C726T0' => 'lonja', 'Lj3C726T2' => 'lonja', 'Lj3P725T35' => 'lonja', 'Lj3P727T10' => 'lonja', 'Lj3P727T12' => 'lonja', 'Lj3P727T14' => 'lonja', 'Lj5g0023109' => 'lja', 'Lj6P646T44' => 'lonja', 'Lsat_1_v5_gn_6_75760' => 'lsa', 'Lsat_1_v5_gn_6_75800' => 'lsa', 'Lsat_1_v5_gn_6_75900' => 'lsa', 'Lsat_1_v5_gn_6_76240' => 'lsa', 'Lsat_1_v5_gn_6_76441' => 'lsa', 'Lsat_1_v5_gn_6_76700' => 'lsa', 'Lsat_1_v5_gn_6_76760' => 'lsa', 'Manes.15G033100' => 'mes', 'Mapoly0004s0074' => 'mpo', 'Mapoly0004s0075' => 'mpo', 'Mapoly0004s0163' => 'mpo', 'Mapoly0004s0164' => 'mpo', 'Mapoly0021s0018' => 'mpo', 'Mapoly0041s0136' => 'mpo', 'Mapoly0041s0137' => 'mpo', 'Mapoly0041s0138' => 'mpo', 'Mapoly0041s0139' => 'mpo', 'Mapoly0041s0141' => 'mpo', 'Mapoly0041s0142' => 'mpo', 'Mapoly0041s0143' => 'mpo', 'Mapoly0041s0144' => 'mpo', 'Mapoly0041s0145' => 'mpo', 'Mapoly0047s0106' => 'mpo', 'Mapoly0047s0108' => 'mpo', 'Mapoly0050s0051' => 'mpo', 'Mapoly0050s0052' => 'mpo', 'Mapoly0050s0053' => 'mpo', 'Mapoly0058s0013' => 'mpo', 'Mapoly0091s0078' => 'mpo', 'Mapoly0091s0079' => 'mpo', 'Mapoly0091s0080' => 'mpo', 'Mapoly0091s0081' => 'mpo', 'Mapoly0278s0004' => 'mpo', 'Mapoly0278s0005' => 'mpo', 'Mapoly0278s0006' => 'mpo', 'MBI11_g30648_MAGBIO' => 'mbi', 'MCO03G194' => 'mco', 'MCO03G590' => 'mco', 'MCO07G312' => 'mco', 'MCO10G318' => 'mco', 'MCO12G244' => 'mco', 'MCO13G148' => 'mco', 'MCO13G194' => 'mco', 'MCO16G238' => 'mco', 'MD06G1134100' => 'mdo', 'MD13G1200100' => 'mdo', 'MD13G1200300' => 'mdo', 'MD13G1200600' => 'mdo', 'MD14G1150400' => 'mdo', 'MD16G1200000' => 'mdo', 'Medtr1g102570' => 'mtr', 'Medtr1g102780' => 'mtr', 'Medtr1g102800' => 'mtr', 'Medtr1g102810' => 'mtr', 'Medtr1g102830' => 'mtr', 'MELO3C006499.2' => 'cme', 'Migut.G00385' => 'egut', 'MSTRG.4063' => 'ama', 'Nitab4.5_0000090g0260' => 'nta', 'Nitab4.5_0000977g0030' => 'nta', 'Nitab4.5_0002541g0040' => 'nta', 'Nitab4.5_0007068g0040' => 'nta', 'Nn005s41408' => 'nnu', 'Nn005s41410' => 'nnu', 'Oeu010310.1' => 'oeu', 'Oeu010311.1' => 'oeu', 'Oeu043472.1' => 'oeu', 'Os01g0246400' => 'osa', 'Os04g0267950' => 'osa', 'Os07g0178700' => 'osa', 'Os07g0178800' => 'osa', 'Peaxi162Scf00316g00046' => 'pax', 'Peaxi162Scf00316g00049' => 'pax', 'Peaxi162Scf00316g00059' => 'pax', 'Peaxi162Scf00316g00328' => 'pax', 'Peaxi162Scf00316g00329' => 'pax', 'Peaxi162Scf00316g00411' => 'pax', 'Peaxi162Scf00316g00521' => 'pax', 'Peaxi162Scf00492g00068' => 'pax', 'Peaxi162Scf35631g00002' => 'pax', 'PGR142G3720' => 'pgr', 'PGSC0003DMG400006442' => 'stu', 'Phvul.007G062000' => 'pvu', 'Potri.008G157750' => 'ptr', 'Potri.008G157900' => 'ptr', 'Potri.008G158000' => 'ptr', 'Potri.008G158200' => 'ptr', 'Pp3c11_7280' => 'ppa', 'Pp3c11_7980' => 'ppa', 'Pp3c12_19450' => 'ppa', 'Pp3c14_1480' => 'ppa', 'Pp3c14_1501' => 'ppa', 'Pp3c16_4900' => 'ppa', 'Pp3c16_5010' => 'ppa', 'Pp3c16_5060' => 'ppa', 'Pp3c19_18250' => 'ppa', 'Pp3c23_8530' => 'ppa', 'Pp3c23_8550' => 'ppa', 'Pp3c24_9670' => 'ppa', 'Pp3c2_21390' => 'ppa', 'Pp3c2_31380' => 'ppa', 'Pp3c3_16620' => 'ppa', 'Pp3c3_8090' => 'ppa', 'Pp3c3_8110' => 'ppa', 'Pp3c3_8130' => 'ppa', 'Pp3c3_8150' => 'ppa', 'Pp3c4_14320' => 'ppa', 'Pp3c6_2560' => 'ppa', 'Pp3c9_16700' => 'ppa', 'PRCOL_00000234' => 'pco', 'PRCOL_00000235' => 'pco', 'PRCOL_00000777' => 'pco', 'PRCOL_00002344' => 'pco', 'PRCOL_00002372' => 'pco', 'PRCOL_00006120' => 'pco', 'Prupe.1G021400' => 'ppe', 'Prupe.1G021500' => 'ppe', 'Prupe.1G021600' => 'ppe', 'Prupe.1G021700' => 'ppe', 'Prupe.1G021800' => 'ppe', 'Prupe.5G145100' => 'ppe', 'Psat6g204040' => 'psa', 'Psat6g204800' => 'psa', 'Psat6g204920' => 'psa', 'Psat6g204960' => 'psa', 'Psat6g205080' => 'psa', 'PSO017G0271' => 'pso', 'PSO017G1276' => 'pso', 'PSO017G1429' => 'pso', 'PSO017G1861' => 'pso', 'PSO017G2787' => 'pso', 'PSO017G4466' => 'pso', 'PSO017G5118' => 'pso', 'PSO017G5420' => 'pso', 'PSO063G3678' => 'pso', 'PSO210G0546' => 'pso', 'PSO317G0001' => 'pso', 'PSO357G0512' => 'pso', 'PSO478G2682' => 'pso', 'PSO647G0001' => 'pso', 'PSO675G0001' => 'pso', 'PSO675G2699' => 'pso', 'PSO675G2849' => 'pso', 'PSO675G4991' => 'pso', 'PSO689G0001' => 'pso', 'QL06p000916' => 'qlo', 'QL06p000921' => 'qlo', 'QL06p001398' => 'qlo', 'QL06p001407' => 'qlo', 'QL06p002031' => 'qlo', 'RcHm_v2.0_Chr4g0387791' => 'rch', 'RcHm_v2.0_Chr4g0387801' => 'rch', 'RcHm_v2.0_Chr6g0286501' => 'rch', 'RcHm_v2.0_Chr6g0286511' => 'rch', 'RcHm_v2.0_Chr6g0286521' => 'rch', 'RcHm_v2.0_Chr6g0286531' => 'rch', 'RcHm_v2.0_Chr7g0189141' => 'rch', 'Rhsim02G0028700' => 'rsi', 'Rhsim02G0028800' => 'rsi', 'Rhsim02G0028900' => 'rsi', 'Rhsim02G0029000' => 'rsi', 'Rhsim02G0029100' => 'rsi', 'Rhsim02G0029200' => 'rsi', 'Rhsim02G0029300' => 'rsi', 'Rhsim02G0029400' => 'rsi', 'Rhsim02G0029500' => 'rsi', 'Rhsim02G0029600' => 'rsi', 'RhsimUnG0024000' => 'rsi', 'RhsimUnG0024100' => 'rsi', 'RhsimUnG0024200' => 'rsi', 'RhsimUnG0024300' => 'rsi', 'RhsimUnG0024400' => 'rsi', 'RhsimUnG0024500' => 'rsi', 'RhsimUnG0024700' => 'rsi', 'RhsimUnG0024800' => 'rsi', 'RhsimUnG0024900' => 'rsi', 'RhsimUnG0025100' => 'rsi', 'Sabra08G0120200' => 'sbr', 'Sabra08G0120300' => 'sbr', 'Sabra08G0120500' => 'sbr', 'Sabra08G0120600' => 'sbr', 'Sabra10G0158900' => 'sbr', 'SalBow2G3492' => 'sbo', 'Sc13g0004760' => 'sci', 'Sc13g0004770' => 'sci', 'Sed0003417' => 'sed', 'Sed0019750' => 'sed', 'SEGI_03419' => 'sgi', 'SEGI_05907' => 'sgi', 'SEGI_10682' => 'sgi', 'SEGI_13528' => 'sgi', 'SEGI_16081' => 'sgi', 'SEGI_19370' => 'sgi', 'SEGI_21015' => 'sgi', 'SEGI_21944' => 'sgi', 'SEGI_32906' => 'sgi', 'SEGI_33093' => 'sgi', 'SEGI_36110' => 'sgi', 'SEGI_40397' => 'sgi', 'SGA_v2.0_scaffold191G40426' => 'sas', 'SGA_v2.0_scaffold353G49717' => 'sas', 'SGA_v2.0_scaffold50G18550' => 'sas', 'SMO119G0173' => 'smo', 'SMO172G0002' => 'smo', 'Solyc09g082690.3' => 'sly', 'Solyc09g082700.2' => 'sly', 'Sopen09g031550' => 'spe', 'Sopen09g031560' => 'spe', 'Sp3g20540' => 'spa', 'Sp7g07580' => 'spa', 'TAR134G0002' => 'tar', 'TAR236G0001' => 'tar', 'TAR365G0892' => 'tar', 'TAR636G0166' => 'tar', 'TAR636G0646' => 'tar', 'TAR636G0869' => 'tar', 'TAR636G1317' => 'tar', 'TAR636G1744' => 'tar', 'TAR636G3358' => 'tar', 'TAR636G3436' => 'tar', 'THA.LOC104803047' => 'tha', 'Thecc.04G238900' => 'tca', 'Thhalv10021557m.g' => 'esa', 'Thhalv10026318m.g' => 'esa', 'Thhalv10026335m.g' => 'esa', 'TPR.G17433' => 'tpr', 'TPR.G18915' => 'tpr', 'TPR.G26125' => 'tpr', 'TWI09G0677' => 'twi', 'TWI73G0287' => 'twi', 'unitig_748.g8326' => 'ugi', 'vmacro15370' => 'vma', 'vmacro15371' => 'vma', 'vmacro15372' => 'vma', 'vmacro15373' => 'vma', 'vmacro15374' => 'vma', 'VMungo0720G2826' => 'vmu', 'Zm00001eb116960' => 'zma', 'Zm00001eb301260' => 'zma', 'Zm00001eb301270' => 'zma' ) $gf_id = 'HOM05D001460' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001460' ) $data_identifier = 'HOM05D001460' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 4, 'aag' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 2, 'aox' => (int) 2, 'arhy' => (int) 4, 'ath' => (int) 2, 'atr' => (int) 1, 'acertr' => (int) 10, 'cqu' => (int) 4, 'bca' => (int) 11, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 1, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 1, 'ccan' => (int) 1, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 1, 'col' => (int) 1, 'cpa' => (int) 1, 'cre' => (int) 7, 'csa' => (int) 1, 'camsi' => (int) 2, 'dca' => (int) 3, 'din' => (int) 2, 'dzi' => (int) 3, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 14, 'fve' => (int) 9, 'gma' => (int) 2, 'ghi' => (int) 4, 'gra' => (int) 2, 'vvi' => (int) 1, 'han' => (int) 13, 'cav' => (int) 1, 'hma' => (int) 2, 'sun' => (int) 2, 'lal' => (int) 2, 'lonja' => (int) 12, 'lja' => (int) 1, 'lsa' => (int) 7, 'mes' => (int) 1, 'mpo' => (int) 27, 'mbi' => (int) 1, 'mco' => (int) 8, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 1, 'egut' => (int) 1, 'ama' => (int) 1, 'nta' => (int) 4, 'nnu' => (int) 2, 'oeu' => (int) 3, 'osa' => (int) 4, 'pax' => (int) 9, 'pgr' => (int) 1, 'stu' => (int) 1, 'pvu' => (int) 1, 'ptr' => (int) 4, 'ppa' => (int) 22, 'pco' => (int) 6, 'ppe' => (int) 6, 'psa' => (int) 5, 'pso' => (int) 19, 'qlo' => (int) 5, 'rch' => (int) 7, 'rsi' => (int) 20, 'sbr' => (int) 5, 'sbo' => (int) 1, 'sci' => (int) 2, 'sed' => (int) 2, 'sgi' => (int) 12, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 2, 'tar' => (int) 10, 'tha' => (int) 1, 'tca' => (int) 1, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 2, 'ugi' => (int) 1, 'vma' => (int) 5, 'vmu' => (int) 1, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb301270' $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' => 'HOM05D001460', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '433', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p22980' => 'bna', 'A01p32340' => 'bna', 'A03p42970' => 'bna', 'A05p25880' => 'bna', 'Aa31LG8G9320' => 'aar', 'Aa31LG8G9330' => 'aar', 'Aa31LG8G9340' => 'aar', 'Aa31sc221G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1034' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1528' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.829' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2222' => 'aag', 'Ah.12g058830' => 'amhyb', 'Ah.12g058840' => 'amhyb', 'AL3G37160' => 'aly', 'AL7G41310' => 'aly', 'Aqoxy5G00395' => 'aox', 'Aqoxy5G00396' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0C8NZA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5185HY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JZ1PRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MD3LS0' => 'arhy', 'AT3G22840' => 'ath', 'AT4G14690' => 'ath', 'ATR0665G054' => 'atr', 'Atru.chr4.2344' => 'acertr', 'Atru.chr4.2346' => 'acertr', 'Atru.chr4.2347' => 'acertr', 'Atru.chr4.2348' => 'acertr', 'Atru.chr4.2355' => 'acertr', 'Atru.chr4.2356' => 'acertr', 'Atru.chr4.2358' => 'acertr', 'Atru.chr4.2359' => 'acertr', 'Atru.chr4.2360' => 'acertr', 'Atru.chr4.2361' => 'acertr', 'AUR62030476' => 'cqu', 'AUR62030478' => 'cqu', 'AUR62030819' => 'cqu', 'AUR62030820' => 'cqu', 'BcaB03g14648' => 'bca', 'BcaB04g20492' => 'bca', 'BcaB06g26399' => 'bca', 'BcaC01g03416' => 'bca', 'BcaC01g03419' => 'bca', 'BcaC01g03421' => 'bca', 'BcaC01g03424' => 'bca', 'BcaC05g28012' => 'bca', 'BcaC09g49212' => 'bca', 'BcaC09g50140' => 'bca', 'BcaNung00346' => 'bca', 'BolC1t02785H' => 'bol', 'BolC1t04095H' => 'bol', 'BolC3t17545H' => 'bol', 'BolC5t32769H' => 'bol', 'BraA01t02211Z' => 'bra', 'BraA01t03359Z' => 'bra', 'BraA03t13441Z' => 'bra', 'BraA05t21476Z' => 'bra', 'C01p28420' => 'bna', 'C01p41350' => 'bna', 'C03p52750' => 'bna', 'C03p52780' => 'bna', 'C05p40270' => 'bna', 'CAN.G1437.9' => 'can', 'CANSAT78G0035' => 'cansat', 'CANSAT78G1036' => 'cansat', 'CANSAT78G2272' => 'cansat', 'CANSAT78G2478' => 'cansat', 'CARHR098700' => 'chi', 'CARHR221120' => 'chi', 'CARHR221150' => 'chi', 'Carub.0003s2297' => 'cru', 'Carub.0007s2749' => 'cru', 'Carub.0007s2750' => 'cru', 'Carub.0007s2751' => 'cru', 'Ca_10849_v3' => 'car', 'Cc03_g04300' => 'ccan', 'CDE02G3648' => 'cde', 'CDE05G0060' => 'cde', 'CDE05G0692' => 'cde', 'CDE05G2285' => 'cde', 'CDE05G2884' => 'cde', 'CDE05G3072' => 'cde', 'Cfa008439' => 'cfa', 'Cfa008441' => 'cfa', 'Cfa008443' => 'cfa', 'Cfa008448' => 'cfa', 'Ciclev10005974m.g' => 'ccl', 'Ciclev10006006m.g' => 'ccl', 'Ciclev10006775m.g' => 'ccl', 'CiPaw.02G120400' => 'cil', 'CiPaw.02G120500' => 'cil', 'CiPaw.02G120600' => 'cil', 'ClCG05G004850' => 'cla', 'COL.COLO4_21566' => 'col', 'Cpa.g.sc44.124' => 'cpa', 'Cre07.g320400' => 'cre', 'Cre07.g320450' => 'cre', 'Cre08.g384650' => 'cre', 'Cre09.g393173' => 'cre', 'Cre09.g394325' => 'cre', 'Cre14.g626750' => 'cre', 'Cre16.g679250' => 'cre', 'CsaV3_3G012890' => 'csa', 'CSS0010865' => 'camsi', 'CSS0044338' => 'camsi', 'DCAR_002366' => 'dca', 'DCAR_030687' => 'dca', 'DCAR_030688' => 'dca', 'Dinv14047' => 'din', 'Dinv14048' => 'din', 'Duzib151G0105' => 'dzi', 'Duzib151G0114' => 'dzi', 'Duzib212G1029' => 'dzi', 'ECA232G3536' => 'eca', 'ECA240G0786' => 'eca', 'ECA240G1802' => 'eca', 'ECA240G3760' => 'eca', 'ECA240G3920' => 'eca', 'EL10Ac5g12536' => 'bvu', 'EL10Ac5g12537' => 'bvu', 'EL10Ac5g12538' => 'bvu', 'Eucgr.B01004' => 'egr', 'Eucgr.B01006' => 'egr', 'Eucgr.B01007' => 'egr', 'Eucgr.B01008' => 'egr', 'Eucgr.B01895' => 'egr', 'Eucgr.B01896' => 'egr', 'FAN04G1456' => 'fan', 'FAN08G1769' => 'fan', 'FAN08G2160' => 'fan', 'FAN13G2403' => 'fan', 'FAN13G3303' => 'fan', 'FAN15G2435' => 'fan', 'FAN17G0672' => 'fan', 'FAN17G2441' => 'fan', 'FAN18G1024' => 'fan', 'FAN22G1458' => 'fan', 'FAN24G0037' => 'fan', 'FAN24G0429' => 'fan', 'FAN24G2387' => 'fan', 'FAN27G2746' => 'fan', 'FvH4_2g20400' => 'fve', 'FvH4_2g20420' => 'fve', 'FvH4_2g20430' => 'fve', 'FvH4_4g01270' => 'fve', 'FvH4_4g01290' => 'fve', 'FvH4_4g01300' => 'fve', 'FvH4_4g01310' => 'fve', 'FvH4_4g01330' => 'fve', 'FvH4_5g09070' => 'fve', 'Glyma.10G243800' => 'gma', 'Glyma.20G150600' => 'gma', 'Gohir.A09G219200' => 'ghi', 'Gohir.A09G219300' => 'ghi', 'Gohir.D09G221400' => 'ghi', 'Gohir.D09G221500' => 'ghi', 'Gorai.006G242600' => 'gra', 'Gorai.006G242700' => 'gra', 'GSVIVG01018044001' => 'vvi', 'HanXRQChr03g0083821' => 'han', 'HanXRQChr03g0083841' => 'han', 'HanXRQChr03g0083881' => 'han', 'HanXRQChr03g0083901' => 'han', 'HanXRQChr03g0083921' => 'han', 'HanXRQChr03g0085331' => 'han', 'HanXRQChr03g0085361' => 'han', 'HanXRQChr03g0085411' => 'han', 'HanXRQChr03g0085421' => 'han', 'HanXRQChr03g0085431' => 'han', 'HanXRQChr08g0221991' => 'han', 'HanXRQChr11g0336061' => 'han', 'HanXRQChr11g0336411' => 'han', 'Haze_11234' => 'cav', 'Hma1.2p1_0549F.1_g177010' => 'hma', 'Hma1.2p1_0602F.1_g187630' => 'hma', 'Hund14876' => 'sun', 'Hund14879' => 'sun', 'Lalb_Chr06g0160741' => 'lal', 'Lalb_Chr21g0304781' => 'lal', 'Lj3A726G19' => 'lonja', 'Lj3A726T23' => 'lonja', 'Lj3A726T24' => 'lonja', 'Lj3A726T25' => 'lonja', 'Lj3A727T17' => 'lonja', 'Lj3C726T0' => 'lonja', 'Lj3C726T2' => 'lonja', 'Lj3P725T35' => 'lonja', 'Lj3P727T10' => 'lonja', 'Lj3P727T12' => 'lonja', 'Lj3P727T14' => 'lonja', 'Lj5g0023109' => 'lja', 'Lj6P646T44' => 'lonja', 'Lsat_1_v5_gn_6_75760' => 'lsa', 'Lsat_1_v5_gn_6_75800' => 'lsa', 'Lsat_1_v5_gn_6_75900' => 'lsa', 'Lsat_1_v5_gn_6_76240' => 'lsa', 'Lsat_1_v5_gn_6_76441' => 'lsa', 'Lsat_1_v5_gn_6_76700' => 'lsa', 'Lsat_1_v5_gn_6_76760' => 'lsa', 'Manes.15G033100' => 'mes', 'Mapoly0004s0074' => 'mpo', 'Mapoly0004s0075' => 'mpo', 'Mapoly0004s0163' => 'mpo', 'Mapoly0004s0164' => 'mpo', 'Mapoly0021s0018' => 'mpo', 'Mapoly0041s0136' => 'mpo', 'Mapoly0041s0137' => 'mpo', 'Mapoly0041s0138' => 'mpo', 'Mapoly0041s0139' => 'mpo', 'Mapoly0041s0141' => 'mpo', 'Mapoly0041s0142' => 'mpo', 'Mapoly0041s0143' => 'mpo', 'Mapoly0041s0144' => 'mpo', 'Mapoly0041s0145' => 'mpo', 'Mapoly0047s0106' => 'mpo', 'Mapoly0047s0108' => 'mpo', 'Mapoly0050s0051' => 'mpo', 'Mapoly0050s0052' => 'mpo', 'Mapoly0050s0053' => 'mpo', 'Mapoly0058s0013' => 'mpo', 'Mapoly0091s0078' => 'mpo', 'Mapoly0091s0079' => 'mpo', 'Mapoly0091s0080' => 'mpo', 'Mapoly0091s0081' => 'mpo', 'Mapoly0278s0004' => 'mpo', 'Mapoly0278s0005' => 'mpo', 'Mapoly0278s0006' => 'mpo', 'MBI11_g30648_MAGBIO' => 'mbi', 'MCO03G194' => 'mco', 'MCO03G590' => 'mco', 'MCO07G312' => 'mco', 'MCO10G318' => 'mco', 'MCO12G244' => 'mco', 'MCO13G148' => 'mco', 'MCO13G194' => 'mco', 'MCO16G238' => 'mco', 'MD06G1134100' => 'mdo', 'MD13G1200100' => 'mdo', 'MD13G1200300' => 'mdo', 'MD13G1200600' => 'mdo', 'MD14G1150400' => 'mdo', 'MD16G1200000' => 'mdo', 'Medtr1g102570' => 'mtr', 'Medtr1g102780' => 'mtr', 'Medtr1g102800' => 'mtr', 'Medtr1g102810' => 'mtr', 'Medtr1g102830' => 'mtr', 'MELO3C006499.2' => 'cme', 'Migut.G00385' => 'egut', 'MSTRG.4063' => 'ama', 'Nitab4.5_0000090g0260' => 'nta', 'Nitab4.5_0000977g0030' => 'nta', 'Nitab4.5_0002541g0040' => 'nta', 'Nitab4.5_0007068g0040' => 'nta', 'Nn005s41408' => 'nnu', 'Nn005s41410' => 'nnu', 'Oeu010310.1' => 'oeu', 'Oeu010311.1' => 'oeu', 'Oeu043472.1' => 'oeu', 'Os01g0246400' => 'osa', 'Os04g0267950' => 'osa', 'Os07g0178700' => 'osa', 'Os07g0178800' => 'osa', 'Peaxi162Scf00316g00046' => 'pax', 'Peaxi162Scf00316g00049' => 'pax', 'Peaxi162Scf00316g00059' => 'pax', 'Peaxi162Scf00316g00328' => 'pax', 'Peaxi162Scf00316g00329' => 'pax', 'Peaxi162Scf00316g00411' => 'pax', 'Peaxi162Scf00316g00521' => 'pax', 'Peaxi162Scf00492g00068' => 'pax', 'Peaxi162Scf35631g00002' => 'pax', 'PGR142G3720' => 'pgr', 'PGSC0003DMG400006442' => 'stu', 'Phvul.007G062000' => 'pvu', 'Potri.008G157750' => 'ptr', 'Potri.008G157900' => 'ptr', 'Potri.008G158000' => 'ptr', 'Potri.008G158200' => 'ptr', 'Pp3c11_7280' => 'ppa', 'Pp3c11_7980' => 'ppa', 'Pp3c12_19450' => 'ppa', 'Pp3c14_1480' => 'ppa', 'Pp3c14_1501' => 'ppa', 'Pp3c16_4900' => 'ppa', 'Pp3c16_5010' => 'ppa', 'Pp3c16_5060' => 'ppa', 'Pp3c19_18250' => 'ppa', 'Pp3c23_8530' => 'ppa', 'Pp3c23_8550' => 'ppa', 'Pp3c24_9670' => 'ppa', 'Pp3c2_21390' => 'ppa', 'Pp3c2_31380' => 'ppa', 'Pp3c3_16620' => 'ppa', 'Pp3c3_8090' => 'ppa', 'Pp3c3_8110' => 'ppa', 'Pp3c3_8130' => 'ppa', 'Pp3c3_8150' => 'ppa', 'Pp3c4_14320' => 'ppa', 'Pp3c6_2560' => 'ppa', 'Pp3c9_16700' => 'ppa', 'PRCOL_00000234' => 'pco', 'PRCOL_00000235' => 'pco', 'PRCOL_00000777' => 'pco', 'PRCOL_00002344' => 'pco', 'PRCOL_00002372' => 'pco', 'PRCOL_00006120' => 'pco', 'Prupe.1G021400' => 'ppe', 'Prupe.1G021500' => 'ppe', 'Prupe.1G021600' => 'ppe', 'Prupe.1G021700' => 'ppe', 'Prupe.1G021800' => 'ppe', 'Prupe.5G145100' => 'ppe', 'Psat6g204040' => 'psa', 'Psat6g204800' => 'psa', 'Psat6g204920' => 'psa', 'Psat6g204960' => 'psa', 'Psat6g205080' => 'psa', 'PSO017G0271' => 'pso', 'PSO017G1276' => 'pso', 'PSO017G1429' => 'pso', 'PSO017G1861' => 'pso', 'PSO017G2787' => 'pso', 'PSO017G4466' => 'pso', 'PSO017G5118' => 'pso', 'PSO017G5420' => 'pso', 'PSO063G3678' => 'pso', 'PSO210G0546' => 'pso', 'PSO317G0001' => 'pso', 'PSO357G0512' => 'pso', 'PSO478G2682' => 'pso', 'PSO647G0001' => 'pso', 'PSO675G0001' => 'pso', 'PSO675G2699' => 'pso', 'PSO675G2849' => 'pso', 'PSO675G4991' => 'pso', 'PSO689G0001' => 'pso', 'QL06p000916' => 'qlo', 'QL06p000921' => 'qlo', 'QL06p001398' => 'qlo', 'QL06p001407' => 'qlo', 'QL06p002031' => 'qlo', 'RcHm_v2.0_Chr4g0387791' => 'rch', 'RcHm_v2.0_Chr4g0387801' => 'rch', 'RcHm_v2.0_Chr6g0286501' => 'rch', 'RcHm_v2.0_Chr6g0286511' => 'rch', 'RcHm_v2.0_Chr6g0286521' => 'rch', 'RcHm_v2.0_Chr6g0286531' => 'rch', 'RcHm_v2.0_Chr7g0189141' => 'rch', 'Rhsim02G0028700' => 'rsi', 'Rhsim02G0028800' => 'rsi', 'Rhsim02G0028900' => 'rsi', 'Rhsim02G0029000' => 'rsi', 'Rhsim02G0029100' => 'rsi', 'Rhsim02G0029200' => 'rsi', 'Rhsim02G0029300' => 'rsi', 'Rhsim02G0029400' => 'rsi', 'Rhsim02G0029500' => 'rsi', 'Rhsim02G0029600' => 'rsi', 'RhsimUnG0024000' => 'rsi', 'RhsimUnG0024100' => 'rsi', 'RhsimUnG0024200' => 'rsi', 'RhsimUnG0024300' => 'rsi', 'RhsimUnG0024400' => 'rsi', 'RhsimUnG0024500' => 'rsi', 'RhsimUnG0024700' => 'rsi', 'RhsimUnG0024800' => 'rsi', 'RhsimUnG0024900' => 'rsi', 'RhsimUnG0025100' => 'rsi', 'Sabra08G0120200' => 'sbr', 'Sabra08G0120300' => 'sbr', 'Sabra08G0120500' => 'sbr', 'Sabra08G0120600' => 'sbr', 'Sabra10G0158900' => 'sbr', 'SalBow2G3492' => 'sbo', 'Sc13g0004760' => 'sci', 'Sc13g0004770' => 'sci', 'Sed0003417' => 'sed', 'Sed0019750' => 'sed', 'SEGI_03419' => 'sgi', 'SEGI_05907' => 'sgi', 'SEGI_10682' => 'sgi', 'SEGI_13528' => 'sgi', 'SEGI_16081' => 'sgi', 'SEGI_19370' => 'sgi', 'SEGI_21015' => 'sgi', 'SEGI_21944' => 'sgi', 'SEGI_32906' => 'sgi', 'SEGI_33093' => 'sgi', 'SEGI_36110' => 'sgi', 'SEGI_40397' => 'sgi', 'SGA_v2.0_scaffold191G40426' => 'sas', 'SGA_v2.0_scaffold353G49717' => 'sas', 'SGA_v2.0_scaffold50G18550' => 'sas', 'SMO119G0173' => 'smo', 'SMO172G0002' => 'smo', 'Solyc09g082690.3' => 'sly', 'Solyc09g082700.2' => 'sly', 'Sopen09g031550' => 'spe', 'Sopen09g031560' => 'spe', 'Sp3g20540' => 'spa', 'Sp7g07580' => 'spa', 'TAR134G0002' => 'tar', 'TAR236G0001' => 'tar', 'TAR365G0892' => 'tar', 'TAR636G0166' => 'tar', 'TAR636G0646' => 'tar', 'TAR636G0869' => 'tar', 'TAR636G1317' => 'tar', 'TAR636G1744' => 'tar', 'TAR636G3358' => 'tar', 'TAR636G3436' => 'tar', 'THA.LOC104803047' => 'tha', 'Thecc.04G238900' => 'tca', 'Thhalv10021557m.g' => 'esa', 'Thhalv10026318m.g' => 'esa', 'Thhalv10026335m.g' => 'esa', 'TPR.G17433' => 'tpr', 'TPR.G18915' => 'tpr', 'TPR.G26125' => 'tpr', 'TWI09G0677' => 'twi', 'TWI73G0287' => 'twi', 'unitig_748.g8326' => 'ugi', 'vmacro15370' => 'vma', 'vmacro15371' => 'vma', 'vmacro15372' => 'vma', 'vmacro15373' => 'vma', 'vmacro15374' => 'vma', 'VMungo0720G2826' => 'vmu', 'Zm00001eb116960' => 'zma', 'Zm00001eb301260' => 'zma', 'Zm00001eb301270' => 'zma' ), 'gf_id' => 'HOM05D001460', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001460' ), 'data_identifier' => 'HOM05D001460', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001460', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '433', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p22980' => 'bna', 'A01p32340' => 'bna', 'A03p42970' => 'bna', 'A05p25880' => 'bna', 'Aa31LG8G9320' => 'aar', 'Aa31LG8G9330' => 'aar', 'Aa31LG8G9340' => 'aar', 'Aa31sc221G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1034' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1528' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.829' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2222' => 'aag', 'Ah.12g058830' => 'amhyb', 'Ah.12g058840' => 'amhyb', 'AL3G37160' => 'aly', 'AL7G41310' => 'aly', 'Aqoxy5G00395' => 'aox', 'Aqoxy5G00396' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0C8NZA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5185HY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JZ1PRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MD3LS0' => 'arhy', 'AT3G22840' => 'ath', 'AT4G14690' => 'ath', 'ATR0665G054' => 'atr', 'Atru.chr4.2344' => 'acertr', 'Atru.chr4.2346' => 'acertr', 'Atru.chr4.2347' => 'acertr', 'Atru.chr4.2348' => 'acertr', 'Atru.chr4.2355' => 'acertr', 'Atru.chr4.2356' => 'acertr', 'Atru.chr4.2358' => 'acertr', 'Atru.chr4.2359' => 'acertr', 'Atru.chr4.2360' => 'acertr', 'Atru.chr4.2361' => 'acertr', 'AUR62030476' => 'cqu', 'AUR62030478' => 'cqu', 'AUR62030819' => 'cqu', 'AUR62030820' => 'cqu', 'BcaB03g14648' => 'bca', 'BcaB04g20492' => 'bca', 'BcaB06g26399' => 'bca', 'BcaC01g03416' => 'bca', 'BcaC01g03419' => 'bca', 'BcaC01g03421' => 'bca', 'BcaC01g03424' => 'bca', 'BcaC05g28012' => 'bca', 'BcaC09g49212' => 'bca', 'BcaC09g50140' => 'bca', 'BcaNung00346' => 'bca', 'BolC1t02785H' => 'bol', 'BolC1t04095H' => 'bol', 'BolC3t17545H' => 'bol', 'BolC5t32769H' => 'bol', 'BraA01t02211Z' => 'bra', 'BraA01t03359Z' => 'bra', 'BraA03t13441Z' => 'bra', 'BraA05t21476Z' => 'bra', 'C01p28420' => 'bna', 'C01p41350' => 'bna', 'C03p52750' => 'bna', 'C03p52780' => 'bna', 'C05p40270' => 'bna', 'CAN.G1437.9' => 'can', 'CANSAT78G0035' => 'cansat', 'CANSAT78G1036' => 'cansat', 'CANSAT78G2272' => 'cansat', 'CANSAT78G2478' => 'cansat', 'CARHR098700' => 'chi', 'CARHR221120' => 'chi', 'CARHR221150' => 'chi', 'Carub.0003s2297' => 'cru', 'Carub.0007s2749' => 'cru', 'Carub.0007s2750' => 'cru', 'Carub.0007s2751' => 'cru', 'Ca_10849_v3' => 'car', 'Cc03_g04300' => 'ccan', 'CDE02G3648' => 'cde', 'CDE05G0060' => 'cde', 'CDE05G0692' => 'cde', 'CDE05G2285' => 'cde', 'CDE05G2884' => 'cde', 'CDE05G3072' => 'cde', 'Cfa008439' => 'cfa', 'Cfa008441' => 'cfa', 'Cfa008443' => 'cfa', 'Cfa008448' => 'cfa', 'Ciclev10005974m.g' => 'ccl', 'Ciclev10006006m.g' => 'ccl', 'Ciclev10006775m.g' => 'ccl', 'CiPaw.02G120400' => 'cil', 'CiPaw.02G120500' => 'cil', 'CiPaw.02G120600' => 'cil', 'ClCG05G004850' => 'cla', 'COL.COLO4_21566' => 'col', 'Cpa.g.sc44.124' => 'cpa', 'Cre07.g320400' => 'cre', 'Cre07.g320450' => 'cre', 'Cre08.g384650' => 'cre', 'Cre09.g393173' => 'cre', 'Cre09.g394325' => 'cre', 'Cre14.g626750' => 'cre', 'Cre16.g679250' => 'cre', 'CsaV3_3G012890' => 'csa', 'CSS0010865' => 'camsi', 'CSS0044338' => 'camsi', 'DCAR_002366' => 'dca', 'DCAR_030687' => 'dca', 'DCAR_030688' => 'dca', 'Dinv14047' => 'din', 'Dinv14048' => 'din', 'Duzib151G0105' => 'dzi', 'Duzib151G0114' => 'dzi', 'Duzib212G1029' => 'dzi', 'ECA232G3536' => 'eca', 'ECA240G0786' => 'eca', 'ECA240G1802' => 'eca', 'ECA240G3760' => 'eca', 'ECA240G3920' => 'eca', 'EL10Ac5g12536' => 'bvu', 'EL10Ac5g12537' => 'bvu', 'EL10Ac5g12538' => 'bvu', 'Eucgr.B01004' => 'egr', 'Eucgr.B01006' => 'egr', 'Eucgr.B01007' => 'egr', 'Eucgr.B01008' => 'egr', 'Eucgr.B01895' => 'egr', 'Eucgr.B01896' => 'egr', 'FAN04G1456' => 'fan', 'FAN08G1769' => 'fan', 'FAN08G2160' => 'fan', 'FAN13G2403' => 'fan', 'FAN13G3303' => 'fan', 'FAN15G2435' => 'fan', 'FAN17G0672' => 'fan', 'FAN17G2441' => 'fan', 'FAN18G1024' => 'fan', 'FAN22G1458' => 'fan', 'FAN24G0037' => 'fan', 'FAN24G0429' => 'fan', 'FAN24G2387' => 'fan', 'FAN27G2746' => 'fan', 'FvH4_2g20400' => 'fve', 'FvH4_2g20420' => 'fve', 'FvH4_2g20430' => 'fve', 'FvH4_4g01270' => 'fve', 'FvH4_4g01290' => 'fve', 'FvH4_4g01300' => 'fve', 'FvH4_4g01310' => 'fve', 'FvH4_4g01330' => 'fve', 'FvH4_5g09070' => 'fve', 'Glyma.10G243800' => 'gma', 'Glyma.20G150600' => 'gma', 'Gohir.A09G219200' => 'ghi', 'Gohir.A09G219300' => 'ghi', 'Gohir.D09G221400' => 'ghi', 'Gohir.D09G221500' => 'ghi', 'Gorai.006G242600' => 'gra', 'Gorai.006G242700' => 'gra', 'GSVIVG01018044001' => 'vvi', 'HanXRQChr03g0083821' => 'han', 'HanXRQChr03g0083841' => 'han', 'HanXRQChr03g0083881' => 'han', 'HanXRQChr03g0083901' => 'han', 'HanXRQChr03g0083921' => 'han', 'HanXRQChr03g0085331' => 'han', 'HanXRQChr03g0085361' => 'han', 'HanXRQChr03g0085411' => 'han', 'HanXRQChr03g0085421' => 'han', 'HanXRQChr03g0085431' => 'han', 'HanXRQChr08g0221991' => 'han', 'HanXRQChr11g0336061' => 'han', 'HanXRQChr11g0336411' => 'han', 'Haze_11234' => 'cav', 'Hma1.2p1_0549F.1_g177010' => 'hma', 'Hma1.2p1_0602F.1_g187630' => 'hma', 'Hund14876' => 'sun', 'Hund14879' => 'sun', 'Lalb_Chr06g0160741' => 'lal', 'Lalb_Chr21g0304781' => 'lal', 'Lj3A726G19' => 'lonja', 'Lj3A726T23' => 'lonja', 'Lj3A726T24' => 'lonja', 'Lj3A726T25' => 'lonja', 'Lj3A727T17' => 'lonja', 'Lj3C726T0' => 'lonja', 'Lj3C726T2' => 'lonja', 'Lj3P725T35' => 'lonja', 'Lj3P727T10' => 'lonja', 'Lj3P727T12' => 'lonja', 'Lj3P727T14' => 'lonja', 'Lj5g0023109' => 'lja', 'Lj6P646T44' => 'lonja', 'Lsat_1_v5_gn_6_75760' => 'lsa', 'Lsat_1_v5_gn_6_75800' => 'lsa', 'Lsat_1_v5_gn_6_75900' => 'lsa', 'Lsat_1_v5_gn_6_76240' => 'lsa', 'Lsat_1_v5_gn_6_76441' => 'lsa', 'Lsat_1_v5_gn_6_76700' => 'lsa', 'Lsat_1_v5_gn_6_76760' => 'lsa', 'Manes.15G033100' => 'mes', 'Mapoly0004s0074' => 'mpo', 'Mapoly0004s0075' => 'mpo', 'Mapoly0004s0163' => 'mpo', 'Mapoly0004s0164' => 'mpo', 'Mapoly0021s0018' => 'mpo', 'Mapoly0041s0136' => 'mpo', 'Mapoly0041s0137' => 'mpo', 'Mapoly0041s0138' => 'mpo', 'Mapoly0041s0139' => 'mpo', 'Mapoly0041s0141' => 'mpo', 'Mapoly0041s0142' => 'mpo', 'Mapoly0041s0143' => 'mpo', 'Mapoly0041s0144' => 'mpo', 'Mapoly0041s0145' => 'mpo', 'Mapoly0047s0106' => 'mpo', 'Mapoly0047s0108' => 'mpo', 'Mapoly0050s0051' => 'mpo', 'Mapoly0050s0052' => 'mpo', 'Mapoly0050s0053' => 'mpo', 'Mapoly0058s0013' => 'mpo', 'Mapoly0091s0078' => 'mpo', 'Mapoly0091s0079' => 'mpo', 'Mapoly0091s0080' => 'mpo', 'Mapoly0091s0081' => 'mpo', 'Mapoly0278s0004' => 'mpo', 'Mapoly0278s0005' => 'mpo', 'Mapoly0278s0006' => 'mpo', 'MBI11_g30648_MAGBIO' => 'mbi', 'MCO03G194' => 'mco', 'MCO03G590' => 'mco', 'MCO07G312' => 'mco', 'MCO10G318' => 'mco', 'MCO12G244' => 'mco', 'MCO13G148' => 'mco', 'MCO13G194' => 'mco', 'MCO16G238' => 'mco', 'MD06G1134100' => 'mdo', 'MD13G1200100' => 'mdo', 'MD13G1200300' => 'mdo', 'MD13G1200600' => 'mdo', 'MD14G1150400' => 'mdo', 'MD16G1200000' => 'mdo', 'Medtr1g102570' => 'mtr', 'Medtr1g102780' => 'mtr', 'Medtr1g102800' => 'mtr', 'Medtr1g102810' => 'mtr', 'Medtr1g102830' => 'mtr', 'MELO3C006499.2' => 'cme', 'Migut.G00385' => 'egut', 'MSTRG.4063' => 'ama', 'Nitab4.5_0000090g0260' => 'nta', 'Nitab4.5_0000977g0030' => 'nta', 'Nitab4.5_0002541g0040' => 'nta', 'Nitab4.5_0007068g0040' => 'nta', 'Nn005s41408' => 'nnu', 'Nn005s41410' => 'nnu', 'Oeu010310.1' => 'oeu', 'Oeu010311.1' => 'oeu', 'Oeu043472.1' => 'oeu', 'Os01g0246400' => 'osa', 'Os04g0267950' => 'osa', 'Os07g0178700' => 'osa', 'Os07g0178800' => 'osa', 'Peaxi162Scf00316g00046' => 'pax', 'Peaxi162Scf00316g00049' => 'pax', 'Peaxi162Scf00316g00059' => 'pax', 'Peaxi162Scf00316g00328' => 'pax', 'Peaxi162Scf00316g00329' => 'pax', 'Peaxi162Scf00316g00411' => 'pax', 'Peaxi162Scf00316g00521' => 'pax', 'Peaxi162Scf00492g00068' => 'pax', 'Peaxi162Scf35631g00002' => 'pax', 'PGR142G3720' => 'pgr', 'PGSC0003DMG400006442' => 'stu', 'Phvul.007G062000' => 'pvu', 'Potri.008G157750' => 'ptr', 'Potri.008G157900' => 'ptr', 'Potri.008G158000' => 'ptr', 'Potri.008G158200' => 'ptr', 'Pp3c11_7280' => 'ppa', 'Pp3c11_7980' => 'ppa', 'Pp3c12_19450' => 'ppa', 'Pp3c14_1480' => 'ppa', 'Pp3c14_1501' => 'ppa', 'Pp3c16_4900' => 'ppa', 'Pp3c16_5010' => 'ppa', 'Pp3c16_5060' => 'ppa', 'Pp3c19_18250' => 'ppa', 'Pp3c23_8530' => 'ppa', 'Pp3c23_8550' => 'ppa', 'Pp3c24_9670' => 'ppa', 'Pp3c2_21390' => 'ppa', 'Pp3c2_31380' => 'ppa', 'Pp3c3_16620' => 'ppa', 'Pp3c3_8090' => 'ppa', 'Pp3c3_8110' => 'ppa', 'Pp3c3_8130' => 'ppa', 'Pp3c3_8150' => 'ppa', 'Pp3c4_14320' => 'ppa', 'Pp3c6_2560' => 'ppa', 'Pp3c9_16700' => 'ppa', 'PRCOL_00000234' => 'pco', 'PRCOL_00000235' => 'pco', 'PRCOL_00000777' => 'pco', 'PRCOL_00002344' => 'pco', 'PRCOL_00002372' => 'pco', 'PRCOL_00006120' => 'pco', 'Prupe.1G021400' => 'ppe', 'Prupe.1G021500' => 'ppe', 'Prupe.1G021600' => 'ppe', 'Prupe.1G021700' => 'ppe', 'Prupe.1G021800' => 'ppe', 'Prupe.5G145100' => 'ppe', 'Psat6g204040' => 'psa', 'Psat6g204800' => 'psa', 'Psat6g204920' => 'psa', 'Psat6g204960' => 'psa', 'Psat6g205080' => 'psa', 'PSO017G0271' => 'pso', 'PSO017G1276' => 'pso', 'PSO017G1429' => 'pso', 'PSO017G1861' => 'pso', 'PSO017G2787' => 'pso', 'PSO017G4466' => 'pso', 'PSO017G5118' => 'pso', 'PSO017G5420' => 'pso', 'PSO063G3678' => 'pso', 'PSO210G0546' => 'pso', 'PSO317G0001' => 'pso', 'PSO357G0512' => 'pso', 'PSO478G2682' => 'pso', 'PSO647G0001' => 'pso', 'PSO675G0001' => 'pso', 'PSO675G2699' => 'pso', 'PSO675G2849' => 'pso', 'PSO675G4991' => 'pso', 'PSO689G0001' => 'pso', 'QL06p000916' => 'qlo', 'QL06p000921' => 'qlo', 'QL06p001398' => 'qlo', 'QL06p001407' => 'qlo', 'QL06p002031' => 'qlo', 'RcHm_v2.0_Chr4g0387791' => 'rch', 'RcHm_v2.0_Chr4g0387801' => 'rch', 'RcHm_v2.0_Chr6g0286501' => 'rch', 'RcHm_v2.0_Chr6g0286511' => 'rch', 'RcHm_v2.0_Chr6g0286521' => 'rch', 'RcHm_v2.0_Chr6g0286531' => 'rch', 'RcHm_v2.0_Chr7g0189141' => 'rch', 'Rhsim02G0028700' => 'rsi', 'Rhsim02G0028800' => 'rsi', 'Rhsim02G0028900' => 'rsi', 'Rhsim02G0029000' => 'rsi', 'Rhsim02G0029100' => 'rsi', 'Rhsim02G0029200' => 'rsi', 'Rhsim02G0029300' => 'rsi', 'Rhsim02G0029400' => 'rsi', 'Rhsim02G0029500' => 'rsi', 'Rhsim02G0029600' => 'rsi', 'RhsimUnG0024000' => 'rsi', 'RhsimUnG0024100' => 'rsi', 'RhsimUnG0024200' => 'rsi', 'RhsimUnG0024300' => 'rsi', 'RhsimUnG0024400' => 'rsi', 'RhsimUnG0024500' => 'rsi', 'RhsimUnG0024700' => 'rsi', 'RhsimUnG0024800' => 'rsi', 'RhsimUnG0024900' => 'rsi', 'RhsimUnG0025100' => 'rsi', 'Sabra08G0120200' => 'sbr', 'Sabra08G0120300' => 'sbr', 'Sabra08G0120500' => 'sbr', 'Sabra08G0120600' => 'sbr', 'Sabra10G0158900' => 'sbr', 'SalBow2G3492' => 'sbo', 'Sc13g0004760' => 'sci', 'Sc13g0004770' => 'sci', 'Sed0003417' => 'sed', 'Sed0019750' => 'sed', 'SEGI_03419' => 'sgi', 'SEGI_05907' => 'sgi', 'SEGI_10682' => 'sgi', 'SEGI_13528' => 'sgi', 'SEGI_16081' => 'sgi', 'SEGI_19370' => 'sgi', 'SEGI_21015' => 'sgi', 'SEGI_21944' => 'sgi', 'SEGI_32906' => 'sgi', 'SEGI_33093' => 'sgi', 'SEGI_36110' => 'sgi', 'SEGI_40397' => 'sgi', 'SGA_v2.0_scaffold191G40426' => 'sas', 'SGA_v2.0_scaffold353G49717' => 'sas', 'SGA_v2.0_scaffold50G18550' => 'sas', 'SMO119G0173' => 'smo', 'SMO172G0002' => 'smo', 'Solyc09g082690.3' => 'sly', 'Solyc09g082700.2' => 'sly', 'Sopen09g031550' => 'spe', 'Sopen09g031560' => 'spe', 'Sp3g20540' => 'spa', 'Sp7g07580' => 'spa', 'TAR134G0002' => 'tar', 'TAR236G0001' => 'tar', 'TAR365G0892' => 'tar', 'TAR636G0166' => 'tar', 'TAR636G0646' => 'tar', 'TAR636G0869' => 'tar', 'TAR636G1317' => 'tar', 'TAR636G1744' => 'tar', 'TAR636G3358' => 'tar', 'TAR636G3436' => 'tar', 'THA.LOC104803047' => 'tha', 'Thecc.04G238900' => 'tca', 'Thhalv10021557m.g' => 'esa', 'Thhalv10026318m.g' => 'esa', 'Thhalv10026335m.g' => 'esa', 'TPR.G17433' => 'tpr', 'TPR.G18915' => 'tpr', 'TPR.G26125' => 'tpr', 'TWI09G0677' => 'twi', 'TWI73G0287' => 'twi', 'unitig_748.g8326' => 'ugi', 'vmacro15370' => 'vma', 'vmacro15371' => 'vma', 'vmacro15372' => 'vma', 'vmacro15373' => 'vma', 'vmacro15374' => 'vma', 'VMungo0720G2826' => 'vmu', 'Zm00001eb116960' => 'zma', 'Zm00001eb301260' => 'zma', 'Zm00001eb301270' => 'zma' ) $gf_id = 'HOM05D001460' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001460' ) $data_identifier = 'HOM05D001460' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 4, 'aag' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 2, 'aox' => (int) 2, 'arhy' => (int) 4, 'ath' => (int) 2, 'atr' => (int) 1, 'acertr' => (int) 10, 'cqu' => (int) 4, 'bca' => (int) 11, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 1, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 1, 'ccan' => (int) 1, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 1, 'col' => (int) 1, 'cpa' => (int) 1, 'cre' => (int) 7, 'csa' => (int) 1, 'camsi' => (int) 2, 'dca' => (int) 3, 'din' => (int) 2, 'dzi' => (int) 3, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 14, 'fve' => (int) 9, 'gma' => (int) 2, 'ghi' => (int) 4, 'gra' => (int) 2, 'vvi' => (int) 1, 'han' => (int) 13, 'cav' => (int) 1, 'hma' => (int) 2, 'sun' => (int) 2, 'lal' => (int) 2, 'lonja' => (int) 12, 'lja' => (int) 1, 'lsa' => (int) 7, 'mes' => (int) 1, 'mpo' => (int) 27, 'mbi' => (int) 1, 'mco' => (int) 8, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 1, 'egut' => (int) 1, 'ama' => (int) 1, 'nta' => (int) 4, 'nnu' => (int) 2, 'oeu' => (int) 3, 'osa' => (int) 4, 'pax' => (int) 9, 'pgr' => (int) 1, 'stu' => (int) 1, 'pvu' => (int) 1, 'ptr' => (int) 4, 'ppa' => (int) 22, 'pco' => (int) 6, 'ppe' => (int) 6, 'psa' => (int) 5, 'pso' => (int) 19, 'qlo' => (int) 5, 'rch' => (int) 7, 'rsi' => (int) 20, 'sbr' => (int) 5, 'sbo' => (int) 1, 'sci' => (int) 2, 'sed' => (int) 2, 'sgi' => (int) 12, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 2, 'tar' => (int) 10, 'tha' => (int) 1, 'tca' => (int) 1, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 2, 'ugi' => (int) 1, 'vma' => (int) 5, 'vmu' => (int) 1, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb301270' $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' => 'HOM05D001460', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '433', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p22980' => 'bna', 'A01p32340' => 'bna', 'A03p42970' => 'bna', 'A05p25880' => 'bna', 'Aa31LG8G9320' => 'aar', 'Aa31LG8G9330' => 'aar', 'Aa31LG8G9340' => 'aar', 'Aa31sc221G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1034' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1528' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.829' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2222' => 'aag', 'Ah.12g058830' => 'amhyb', 'Ah.12g058840' => 'amhyb', 'AL3G37160' => 'aly', 'AL7G41310' => 'aly', 'Aqoxy5G00395' => 'aox', 'Aqoxy5G00396' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0C8NZA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5185HY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JZ1PRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MD3LS0' => 'arhy', 'AT3G22840' => 'ath', 'AT4G14690' => 'ath', 'ATR0665G054' => 'atr', 'Atru.chr4.2344' => 'acertr', 'Atru.chr4.2346' => 'acertr', 'Atru.chr4.2347' => 'acertr', 'Atru.chr4.2348' => 'acertr', 'Atru.chr4.2355' => 'acertr', 'Atru.chr4.2356' => 'acertr', 'Atru.chr4.2358' => 'acertr', 'Atru.chr4.2359' => 'acertr', 'Atru.chr4.2360' => 'acertr', 'Atru.chr4.2361' => 'acertr', 'AUR62030476' => 'cqu', 'AUR62030478' => 'cqu', 'AUR62030819' => 'cqu', 'AUR62030820' => 'cqu', 'BcaB03g14648' => 'bca', 'BcaB04g20492' => 'bca', 'BcaB06g26399' => 'bca', 'BcaC01g03416' => 'bca', 'BcaC01g03419' => 'bca', 'BcaC01g03421' => 'bca', 'BcaC01g03424' => 'bca', 'BcaC05g28012' => 'bca', 'BcaC09g49212' => 'bca', 'BcaC09g50140' => 'bca', 'BcaNung00346' => 'bca', 'BolC1t02785H' => 'bol', 'BolC1t04095H' => 'bol', 'BolC3t17545H' => 'bol', 'BolC5t32769H' => 'bol', 'BraA01t02211Z' => 'bra', 'BraA01t03359Z' => 'bra', 'BraA03t13441Z' => 'bra', 'BraA05t21476Z' => 'bra', 'C01p28420' => 'bna', 'C01p41350' => 'bna', 'C03p52750' => 'bna', 'C03p52780' => 'bna', 'C05p40270' => 'bna', 'CAN.G1437.9' => 'can', 'CANSAT78G0035' => 'cansat', 'CANSAT78G1036' => 'cansat', 'CANSAT78G2272' => 'cansat', 'CANSAT78G2478' => 'cansat', 'CARHR098700' => 'chi', 'CARHR221120' => 'chi', 'CARHR221150' => 'chi', 'Carub.0003s2297' => 'cru', 'Carub.0007s2749' => 'cru', 'Carub.0007s2750' => 'cru', 'Carub.0007s2751' => 'cru', 'Ca_10849_v3' => 'car', 'Cc03_g04300' => 'ccan', 'CDE02G3648' => 'cde', 'CDE05G0060' => 'cde', 'CDE05G0692' => 'cde', 'CDE05G2285' => 'cde', 'CDE05G2884' => 'cde', 'CDE05G3072' => 'cde', 'Cfa008439' => 'cfa', 'Cfa008441' => 'cfa', 'Cfa008443' => 'cfa', 'Cfa008448' => 'cfa', 'Ciclev10005974m.g' => 'ccl', 'Ciclev10006006m.g' => 'ccl', 'Ciclev10006775m.g' => 'ccl', 'CiPaw.02G120400' => 'cil', 'CiPaw.02G120500' => 'cil', 'CiPaw.02G120600' => 'cil', 'ClCG05G004850' => 'cla', 'COL.COLO4_21566' => 'col', 'Cpa.g.sc44.124' => 'cpa', 'Cre07.g320400' => 'cre', 'Cre07.g320450' => 'cre', 'Cre08.g384650' => 'cre', 'Cre09.g393173' => 'cre', 'Cre09.g394325' => 'cre', 'Cre14.g626750' => 'cre', 'Cre16.g679250' => 'cre', 'CsaV3_3G012890' => 'csa', 'CSS0010865' => 'camsi', 'CSS0044338' => 'camsi', 'DCAR_002366' => 'dca', 'DCAR_030687' => 'dca', 'DCAR_030688' => 'dca', 'Dinv14047' => 'din', 'Dinv14048' => 'din', 'Duzib151G0105' => 'dzi', 'Duzib151G0114' => 'dzi', 'Duzib212G1029' => 'dzi', 'ECA232G3536' => 'eca', 'ECA240G0786' => 'eca', 'ECA240G1802' => 'eca', 'ECA240G3760' => 'eca', 'ECA240G3920' => 'eca', 'EL10Ac5g12536' => 'bvu', 'EL10Ac5g12537' => 'bvu', 'EL10Ac5g12538' => 'bvu', 'Eucgr.B01004' => 'egr', 'Eucgr.B01006' => 'egr', 'Eucgr.B01007' => 'egr', 'Eucgr.B01008' => 'egr', 'Eucgr.B01895' => 'egr', 'Eucgr.B01896' => 'egr', 'FAN04G1456' => 'fan', 'FAN08G1769' => 'fan', 'FAN08G2160' => 'fan', 'FAN13G2403' => 'fan', 'FAN13G3303' => 'fan', 'FAN15G2435' => 'fan', 'FAN17G0672' => 'fan', 'FAN17G2441' => 'fan', 'FAN18G1024' => 'fan', 'FAN22G1458' => 'fan', 'FAN24G0037' => 'fan', 'FAN24G0429' => 'fan', 'FAN24G2387' => 'fan', 'FAN27G2746' => 'fan', 'FvH4_2g20400' => 'fve', 'FvH4_2g20420' => 'fve', 'FvH4_2g20430' => 'fve', 'FvH4_4g01270' => 'fve', 'FvH4_4g01290' => 'fve', 'FvH4_4g01300' => 'fve', 'FvH4_4g01310' => 'fve', 'FvH4_4g01330' => 'fve', 'FvH4_5g09070' => 'fve', 'Glyma.10G243800' => 'gma', 'Glyma.20G150600' => 'gma', 'Gohir.A09G219200' => 'ghi', 'Gohir.A09G219300' => 'ghi', 'Gohir.D09G221400' => 'ghi', 'Gohir.D09G221500' => 'ghi', 'Gorai.006G242600' => 'gra', 'Gorai.006G242700' => 'gra', 'GSVIVG01018044001' => 'vvi', 'HanXRQChr03g0083821' => 'han', 'HanXRQChr03g0083841' => 'han', 'HanXRQChr03g0083881' => 'han', 'HanXRQChr03g0083901' => 'han', 'HanXRQChr03g0083921' => 'han', 'HanXRQChr03g0085331' => 'han', 'HanXRQChr03g0085361' => 'han', 'HanXRQChr03g0085411' => 'han', 'HanXRQChr03g0085421' => 'han', 'HanXRQChr03g0085431' => 'han', 'HanXRQChr08g0221991' => 'han', 'HanXRQChr11g0336061' => 'han', 'HanXRQChr11g0336411' => 'han', 'Haze_11234' => 'cav', 'Hma1.2p1_0549F.1_g177010' => 'hma', 'Hma1.2p1_0602F.1_g187630' => 'hma', 'Hund14876' => 'sun', 'Hund14879' => 'sun', 'Lalb_Chr06g0160741' => 'lal', 'Lalb_Chr21g0304781' => 'lal', 'Lj3A726G19' => 'lonja', 'Lj3A726T23' => 'lonja', 'Lj3A726T24' => 'lonja', 'Lj3A726T25' => 'lonja', 'Lj3A727T17' => 'lonja', 'Lj3C726T0' => 'lonja', 'Lj3C726T2' => 'lonja', 'Lj3P725T35' => 'lonja', 'Lj3P727T10' => 'lonja', 'Lj3P727T12' => 'lonja', 'Lj3P727T14' => 'lonja', 'Lj5g0023109' => 'lja', 'Lj6P646T44' => 'lonja', 'Lsat_1_v5_gn_6_75760' => 'lsa', 'Lsat_1_v5_gn_6_75800' => 'lsa', 'Lsat_1_v5_gn_6_75900' => 'lsa', 'Lsat_1_v5_gn_6_76240' => 'lsa', 'Lsat_1_v5_gn_6_76441' => 'lsa', 'Lsat_1_v5_gn_6_76700' => 'lsa', 'Lsat_1_v5_gn_6_76760' => 'lsa', 'Manes.15G033100' => 'mes', 'Mapoly0004s0074' => 'mpo', 'Mapoly0004s0075' => 'mpo', 'Mapoly0004s0163' => 'mpo', 'Mapoly0004s0164' => 'mpo', 'Mapoly0021s0018' => 'mpo', 'Mapoly0041s0136' => 'mpo', 'Mapoly0041s0137' => 'mpo', 'Mapoly0041s0138' => 'mpo', 'Mapoly0041s0139' => 'mpo', 'Mapoly0041s0141' => 'mpo', 'Mapoly0041s0142' => 'mpo', 'Mapoly0041s0143' => 'mpo', 'Mapoly0041s0144' => 'mpo', 'Mapoly0041s0145' => 'mpo', 'Mapoly0047s0106' => 'mpo', 'Mapoly0047s0108' => 'mpo', 'Mapoly0050s0051' => 'mpo', 'Mapoly0050s0052' => 'mpo', 'Mapoly0050s0053' => 'mpo', 'Mapoly0058s0013' => 'mpo', 'Mapoly0091s0078' => 'mpo', 'Mapoly0091s0079' => 'mpo', 'Mapoly0091s0080' => 'mpo', 'Mapoly0091s0081' => 'mpo', 'Mapoly0278s0004' => 'mpo', 'Mapoly0278s0005' => 'mpo', 'Mapoly0278s0006' => 'mpo', 'MBI11_g30648_MAGBIO' => 'mbi', 'MCO03G194' => 'mco', 'MCO03G590' => 'mco', 'MCO07G312' => 'mco', 'MCO10G318' => 'mco', 'MCO12G244' => 'mco', 'MCO13G148' => 'mco', 'MCO13G194' => 'mco', 'MCO16G238' => 'mco', 'MD06G1134100' => 'mdo', 'MD13G1200100' => 'mdo', 'MD13G1200300' => 'mdo', 'MD13G1200600' => 'mdo', 'MD14G1150400' => 'mdo', 'MD16G1200000' => 'mdo', 'Medtr1g102570' => 'mtr', 'Medtr1g102780' => 'mtr', 'Medtr1g102800' => 'mtr', 'Medtr1g102810' => 'mtr', 'Medtr1g102830' => 'mtr', 'MELO3C006499.2' => 'cme', 'Migut.G00385' => 'egut', 'MSTRG.4063' => 'ama', 'Nitab4.5_0000090g0260' => 'nta', 'Nitab4.5_0000977g0030' => 'nta', 'Nitab4.5_0002541g0040' => 'nta', 'Nitab4.5_0007068g0040' => 'nta', 'Nn005s41408' => 'nnu', 'Nn005s41410' => 'nnu', 'Oeu010310.1' => 'oeu', 'Oeu010311.1' => 'oeu', 'Oeu043472.1' => 'oeu', 'Os01g0246400' => 'osa', 'Os04g0267950' => 'osa', 'Os07g0178700' => 'osa', 'Os07g0178800' => 'osa', 'Peaxi162Scf00316g00046' => 'pax', 'Peaxi162Scf00316g00049' => 'pax', 'Peaxi162Scf00316g00059' => 'pax', 'Peaxi162Scf00316g00328' => 'pax', 'Peaxi162Scf00316g00329' => 'pax', 'Peaxi162Scf00316g00411' => 'pax', 'Peaxi162Scf00316g00521' => 'pax', 'Peaxi162Scf00492g00068' => 'pax', 'Peaxi162Scf35631g00002' => 'pax', 'PGR142G3720' => 'pgr', 'PGSC0003DMG400006442' => 'stu', 'Phvul.007G062000' => 'pvu', 'Potri.008G157750' => 'ptr', 'Potri.008G157900' => 'ptr', 'Potri.008G158000' => 'ptr', 'Potri.008G158200' => 'ptr', 'Pp3c11_7280' => 'ppa', 'Pp3c11_7980' => 'ppa', 'Pp3c12_19450' => 'ppa', 'Pp3c14_1480' => 'ppa', 'Pp3c14_1501' => 'ppa', 'Pp3c16_4900' => 'ppa', 'Pp3c16_5010' => 'ppa', 'Pp3c16_5060' => 'ppa', 'Pp3c19_18250' => 'ppa', 'Pp3c23_8530' => 'ppa', 'Pp3c23_8550' => 'ppa', 'Pp3c24_9670' => 'ppa', 'Pp3c2_21390' => 'ppa', 'Pp3c2_31380' => 'ppa', 'Pp3c3_16620' => 'ppa', 'Pp3c3_8090' => 'ppa', 'Pp3c3_8110' => 'ppa', 'Pp3c3_8130' => 'ppa', 'Pp3c3_8150' => 'ppa', 'Pp3c4_14320' => 'ppa', 'Pp3c6_2560' => 'ppa', 'Pp3c9_16700' => 'ppa', 'PRCOL_00000234' => 'pco', 'PRCOL_00000235' => 'pco', 'PRCOL_00000777' => 'pco', 'PRCOL_00002344' => 'pco', 'PRCOL_00002372' => 'pco', 'PRCOL_00006120' => 'pco', 'Prupe.1G021400' => 'ppe', 'Prupe.1G021500' => 'ppe', 'Prupe.1G021600' => 'ppe', 'Prupe.1G021700' => 'ppe', 'Prupe.1G021800' => 'ppe', 'Prupe.5G145100' => 'ppe', 'Psat6g204040' => 'psa', 'Psat6g204800' => 'psa', 'Psat6g204920' => 'psa', 'Psat6g204960' => 'psa', 'Psat6g205080' => 'psa', 'PSO017G0271' => 'pso', 'PSO017G1276' => 'pso', 'PSO017G1429' => 'pso', 'PSO017G1861' => 'pso', 'PSO017G2787' => 'pso', 'PSO017G4466' => 'pso', 'PSO017G5118' => 'pso', 'PSO017G5420' => 'pso', 'PSO063G3678' => 'pso', 'PSO210G0546' => 'pso', 'PSO317G0001' => 'pso', 'PSO357G0512' => 'pso', 'PSO478G2682' => 'pso', 'PSO647G0001' => 'pso', 'PSO675G0001' => 'pso', 'PSO675G2699' => 'pso', 'PSO675G2849' => 'pso', 'PSO675G4991' => 'pso', 'PSO689G0001' => 'pso', 'QL06p000916' => 'qlo', 'QL06p000921' => 'qlo', 'QL06p001398' => 'qlo', 'QL06p001407' => 'qlo', 'QL06p002031' => 'qlo', 'RcHm_v2.0_Chr4g0387791' => 'rch', 'RcHm_v2.0_Chr4g0387801' => 'rch', 'RcHm_v2.0_Chr6g0286501' => 'rch', 'RcHm_v2.0_Chr6g0286511' => 'rch', 'RcHm_v2.0_Chr6g0286521' => 'rch', 'RcHm_v2.0_Chr6g0286531' => 'rch', 'RcHm_v2.0_Chr7g0189141' => 'rch', 'Rhsim02G0028700' => 'rsi', 'Rhsim02G0028800' => 'rsi', 'Rhsim02G0028900' => 'rsi', 'Rhsim02G0029000' => 'rsi', 'Rhsim02G0029100' => 'rsi', 'Rhsim02G0029200' => 'rsi', 'Rhsim02G0029300' => 'rsi', 'Rhsim02G0029400' => 'rsi', 'Rhsim02G0029500' => 'rsi', 'Rhsim02G0029600' => 'rsi', 'RhsimUnG0024000' => 'rsi', 'RhsimUnG0024100' => 'rsi', 'RhsimUnG0024200' => 'rsi', 'RhsimUnG0024300' => 'rsi', 'RhsimUnG0024400' => 'rsi', 'RhsimUnG0024500' => 'rsi', 'RhsimUnG0024700' => 'rsi', 'RhsimUnG0024800' => 'rsi', 'RhsimUnG0024900' => 'rsi', 'RhsimUnG0025100' => 'rsi', 'Sabra08G0120200' => 'sbr', 'Sabra08G0120300' => 'sbr', 'Sabra08G0120500' => 'sbr', 'Sabra08G0120600' => 'sbr', 'Sabra10G0158900' => 'sbr', 'SalBow2G3492' => 'sbo', 'Sc13g0004760' => 'sci', 'Sc13g0004770' => 'sci', 'Sed0003417' => 'sed', 'Sed0019750' => 'sed', 'SEGI_03419' => 'sgi', 'SEGI_05907' => 'sgi', 'SEGI_10682' => 'sgi', 'SEGI_13528' => 'sgi', 'SEGI_16081' => 'sgi', 'SEGI_19370' => 'sgi', 'SEGI_21015' => 'sgi', 'SEGI_21944' => 'sgi', 'SEGI_32906' => 'sgi', 'SEGI_33093' => 'sgi', 'SEGI_36110' => 'sgi', 'SEGI_40397' => 'sgi', 'SGA_v2.0_scaffold191G40426' => 'sas', 'SGA_v2.0_scaffold353G49717' => 'sas', 'SGA_v2.0_scaffold50G18550' => 'sas', 'SMO119G0173' => 'smo', 'SMO172G0002' => 'smo', 'Solyc09g082690.3' => 'sly', 'Solyc09g082700.2' => 'sly', 'Sopen09g031550' => 'spe', 'Sopen09g031560' => 'spe', 'Sp3g20540' => 'spa', 'Sp7g07580' => 'spa', 'TAR134G0002' => 'tar', 'TAR236G0001' => 'tar', 'TAR365G0892' => 'tar', 'TAR636G0166' => 'tar', 'TAR636G0646' => 'tar', 'TAR636G0869' => 'tar', 'TAR636G1317' => 'tar', 'TAR636G1744' => 'tar', 'TAR636G3358' => 'tar', 'TAR636G3436' => 'tar', 'THA.LOC104803047' => 'tha', 'Thecc.04G238900' => 'tca', 'Thhalv10021557m.g' => 'esa', 'Thhalv10026318m.g' => 'esa', 'Thhalv10026335m.g' => 'esa', 'TPR.G17433' => 'tpr', 'TPR.G18915' => 'tpr', 'TPR.G26125' => 'tpr', 'TWI09G0677' => 'twi', 'TWI73G0287' => 'twi', 'unitig_748.g8326' => 'ugi', 'vmacro15370' => 'vma', 'vmacro15371' => 'vma', 'vmacro15372' => 'vma', 'vmacro15373' => 'vma', 'vmacro15374' => 'vma', 'VMungo0720G2826' => 'vmu', 'Zm00001eb116960' => 'zma', 'Zm00001eb301260' => 'zma', 'Zm00001eb301270' => 'zma' ), 'gf_id' => 'HOM05D001460', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001460' ), 'data_identifier' => 'HOM05D001460', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001460', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '433', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p22980' => 'bna', 'A01p32340' => 'bna', 'A03p42970' => 'bna', 'A05p25880' => 'bna', 'Aa31LG8G9320' => 'aar', 'Aa31LG8G9330' => 'aar', 'Aa31LG8G9340' => 'aar', 'Aa31sc221G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1034' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1528' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.829' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2222' => 'aag', 'Ah.12g058830' => 'amhyb', 'Ah.12g058840' => 'amhyb', 'AL3G37160' => 'aly', 'AL7G41310' => 'aly', 'Aqoxy5G00395' => 'aox', 'Aqoxy5G00396' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0C8NZA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5185HY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JZ1PRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MD3LS0' => 'arhy', 'AT3G22840' => 'ath', 'AT4G14690' => 'ath', 'ATR0665G054' => 'atr', 'Atru.chr4.2344' => 'acertr', 'Atru.chr4.2346' => 'acertr', 'Atru.chr4.2347' => 'acertr', 'Atru.chr4.2348' => 'acertr', 'Atru.chr4.2355' => 'acertr', 'Atru.chr4.2356' => 'acertr', 'Atru.chr4.2358' => 'acertr', 'Atru.chr4.2359' => 'acertr', 'Atru.chr4.2360' => 'acertr', 'Atru.chr4.2361' => 'acertr', 'AUR62030476' => 'cqu', 'AUR62030478' => 'cqu', 'AUR62030819' => 'cqu', 'AUR62030820' => 'cqu', 'BcaB03g14648' => 'bca', 'BcaB04g20492' => 'bca', 'BcaB06g26399' => 'bca', 'BcaC01g03416' => 'bca', 'BcaC01g03419' => 'bca', 'BcaC01g03421' => 'bca', 'BcaC01g03424' => 'bca', 'BcaC05g28012' => 'bca', 'BcaC09g49212' => 'bca', 'BcaC09g50140' => 'bca', 'BcaNung00346' => 'bca', 'BolC1t02785H' => 'bol', 'BolC1t04095H' => 'bol', 'BolC3t17545H' => 'bol', 'BolC5t32769H' => 'bol', 'BraA01t02211Z' => 'bra', 'BraA01t03359Z' => 'bra', 'BraA03t13441Z' => 'bra', 'BraA05t21476Z' => 'bra', 'C01p28420' => 'bna', 'C01p41350' => 'bna', 'C03p52750' => 'bna', 'C03p52780' => 'bna', 'C05p40270' => 'bna', 'CAN.G1437.9' => 'can', 'CANSAT78G0035' => 'cansat', 'CANSAT78G1036' => 'cansat', 'CANSAT78G2272' => 'cansat', 'CANSAT78G2478' => 'cansat', 'CARHR098700' => 'chi', 'CARHR221120' => 'chi', 'CARHR221150' => 'chi', 'Carub.0003s2297' => 'cru', 'Carub.0007s2749' => 'cru', 'Carub.0007s2750' => 'cru', 'Carub.0007s2751' => 'cru', 'Ca_10849_v3' => 'car', 'Cc03_g04300' => 'ccan', 'CDE02G3648' => 'cde', 'CDE05G0060' => 'cde', 'CDE05G0692' => 'cde', 'CDE05G2285' => 'cde', 'CDE05G2884' => 'cde', 'CDE05G3072' => 'cde', 'Cfa008439' => 'cfa', 'Cfa008441' => 'cfa', 'Cfa008443' => 'cfa', 'Cfa008448' => 'cfa', 'Ciclev10005974m.g' => 'ccl', 'Ciclev10006006m.g' => 'ccl', 'Ciclev10006775m.g' => 'ccl', 'CiPaw.02G120400' => 'cil', 'CiPaw.02G120500' => 'cil', 'CiPaw.02G120600' => 'cil', 'ClCG05G004850' => 'cla', 'COL.COLO4_21566' => 'col', 'Cpa.g.sc44.124' => 'cpa', 'Cre07.g320400' => 'cre', 'Cre07.g320450' => 'cre', 'Cre08.g384650' => 'cre', 'Cre09.g393173' => 'cre', 'Cre09.g394325' => 'cre', 'Cre14.g626750' => 'cre', 'Cre16.g679250' => 'cre', 'CsaV3_3G012890' => 'csa', 'CSS0010865' => 'camsi', 'CSS0044338' => 'camsi', 'DCAR_002366' => 'dca', 'DCAR_030687' => 'dca', 'DCAR_030688' => 'dca', 'Dinv14047' => 'din', 'Dinv14048' => 'din', 'Duzib151G0105' => 'dzi', 'Duzib151G0114' => 'dzi', 'Duzib212G1029' => 'dzi', 'ECA232G3536' => 'eca', 'ECA240G0786' => 'eca', 'ECA240G1802' => 'eca', 'ECA240G3760' => 'eca', 'ECA240G3920' => 'eca', 'EL10Ac5g12536' => 'bvu', 'EL10Ac5g12537' => 'bvu', 'EL10Ac5g12538' => 'bvu', 'Eucgr.B01004' => 'egr', 'Eucgr.B01006' => 'egr', 'Eucgr.B01007' => 'egr', 'Eucgr.B01008' => 'egr', 'Eucgr.B01895' => 'egr', 'Eucgr.B01896' => 'egr', 'FAN04G1456' => 'fan', 'FAN08G1769' => 'fan', 'FAN08G2160' => 'fan', 'FAN13G2403' => 'fan', 'FAN13G3303' => 'fan', 'FAN15G2435' => 'fan', 'FAN17G0672' => 'fan', 'FAN17G2441' => 'fan', 'FAN18G1024' => 'fan', 'FAN22G1458' => 'fan', 'FAN24G0037' => 'fan', 'FAN24G0429' => 'fan', 'FAN24G2387' => 'fan', 'FAN27G2746' => 'fan', 'FvH4_2g20400' => 'fve', 'FvH4_2g20420' => 'fve', 'FvH4_2g20430' => 'fve', 'FvH4_4g01270' => 'fve', 'FvH4_4g01290' => 'fve', 'FvH4_4g01300' => 'fve', 'FvH4_4g01310' => 'fve', 'FvH4_4g01330' => 'fve', 'FvH4_5g09070' => 'fve', 'Glyma.10G243800' => 'gma', 'Glyma.20G150600' => 'gma', 'Gohir.A09G219200' => 'ghi', 'Gohir.A09G219300' => 'ghi', 'Gohir.D09G221400' => 'ghi', 'Gohir.D09G221500' => 'ghi', 'Gorai.006G242600' => 'gra', 'Gorai.006G242700' => 'gra', 'GSVIVG01018044001' => 'vvi', 'HanXRQChr03g0083821' => 'han', 'HanXRQChr03g0083841' => 'han', 'HanXRQChr03g0083881' => 'han', 'HanXRQChr03g0083901' => 'han', 'HanXRQChr03g0083921' => 'han', 'HanXRQChr03g0085331' => 'han', 'HanXRQChr03g0085361' => 'han', 'HanXRQChr03g0085411' => 'han', 'HanXRQChr03g0085421' => 'han', 'HanXRQChr03g0085431' => 'han', 'HanXRQChr08g0221991' => 'han', 'HanXRQChr11g0336061' => 'han', 'HanXRQChr11g0336411' => 'han', 'Haze_11234' => 'cav', 'Hma1.2p1_0549F.1_g177010' => 'hma', 'Hma1.2p1_0602F.1_g187630' => 'hma', 'Hund14876' => 'sun', 'Hund14879' => 'sun', 'Lalb_Chr06g0160741' => 'lal', 'Lalb_Chr21g0304781' => 'lal', 'Lj3A726G19' => 'lonja', 'Lj3A726T23' => 'lonja', 'Lj3A726T24' => 'lonja', 'Lj3A726T25' => 'lonja', 'Lj3A727T17' => 'lonja', 'Lj3C726T0' => 'lonja', 'Lj3C726T2' => 'lonja', 'Lj3P725T35' => 'lonja', 'Lj3P727T10' => 'lonja', 'Lj3P727T12' => 'lonja', 'Lj3P727T14' => 'lonja', 'Lj5g0023109' => 'lja', 'Lj6P646T44' => 'lonja', 'Lsat_1_v5_gn_6_75760' => 'lsa', 'Lsat_1_v5_gn_6_75800' => 'lsa', 'Lsat_1_v5_gn_6_75900' => 'lsa', 'Lsat_1_v5_gn_6_76240' => 'lsa', 'Lsat_1_v5_gn_6_76441' => 'lsa', 'Lsat_1_v5_gn_6_76700' => 'lsa', 'Lsat_1_v5_gn_6_76760' => 'lsa', 'Manes.15G033100' => 'mes', 'Mapoly0004s0074' => 'mpo', 'Mapoly0004s0075' => 'mpo', 'Mapoly0004s0163' => 'mpo', 'Mapoly0004s0164' => 'mpo', 'Mapoly0021s0018' => 'mpo', 'Mapoly0041s0136' => 'mpo', 'Mapoly0041s0137' => 'mpo', 'Mapoly0041s0138' => 'mpo', 'Mapoly0041s0139' => 'mpo', 'Mapoly0041s0141' => 'mpo', 'Mapoly0041s0142' => 'mpo', 'Mapoly0041s0143' => 'mpo', 'Mapoly0041s0144' => 'mpo', 'Mapoly0041s0145' => 'mpo', 'Mapoly0047s0106' => 'mpo', 'Mapoly0047s0108' => 'mpo', 'Mapoly0050s0051' => 'mpo', 'Mapoly0050s0052' => 'mpo', 'Mapoly0050s0053' => 'mpo', 'Mapoly0058s0013' => 'mpo', 'Mapoly0091s0078' => 'mpo', 'Mapoly0091s0079' => 'mpo', 'Mapoly0091s0080' => 'mpo', 'Mapoly0091s0081' => 'mpo', 'Mapoly0278s0004' => 'mpo', 'Mapoly0278s0005' => 'mpo', 'Mapoly0278s0006' => 'mpo', 'MBI11_g30648_MAGBIO' => 'mbi', 'MCO03G194' => 'mco', 'MCO03G590' => 'mco', 'MCO07G312' => 'mco', 'MCO10G318' => 'mco', 'MCO12G244' => 'mco', 'MCO13G148' => 'mco', 'MCO13G194' => 'mco', 'MCO16G238' => 'mco', 'MD06G1134100' => 'mdo', 'MD13G1200100' => 'mdo', 'MD13G1200300' => 'mdo', 'MD13G1200600' => 'mdo', 'MD14G1150400' => 'mdo', 'MD16G1200000' => 'mdo', 'Medtr1g102570' => 'mtr', 'Medtr1g102780' => 'mtr', 'Medtr1g102800' => 'mtr', 'Medtr1g102810' => 'mtr', 'Medtr1g102830' => 'mtr', 'MELO3C006499.2' => 'cme', 'Migut.G00385' => 'egut', 'MSTRG.4063' => 'ama', 'Nitab4.5_0000090g0260' => 'nta', 'Nitab4.5_0000977g0030' => 'nta', 'Nitab4.5_0002541g0040' => 'nta', 'Nitab4.5_0007068g0040' => 'nta', 'Nn005s41408' => 'nnu', 'Nn005s41410' => 'nnu', 'Oeu010310.1' => 'oeu', 'Oeu010311.1' => 'oeu', 'Oeu043472.1' => 'oeu', 'Os01g0246400' => 'osa', 'Os04g0267950' => 'osa', 'Os07g0178700' => 'osa', 'Os07g0178800' => 'osa', 'Peaxi162Scf00316g00046' => 'pax', 'Peaxi162Scf00316g00049' => 'pax', 'Peaxi162Scf00316g00059' => 'pax', 'Peaxi162Scf00316g00328' => 'pax', 'Peaxi162Scf00316g00329' => 'pax', 'Peaxi162Scf00316g00411' => 'pax', 'Peaxi162Scf00316g00521' => 'pax', 'Peaxi162Scf00492g00068' => 'pax', 'Peaxi162Scf35631g00002' => 'pax', 'PGR142G3720' => 'pgr', 'PGSC0003DMG400006442' => 'stu', 'Phvul.007G062000' => 'pvu', 'Potri.008G157750' => 'ptr', 'Potri.008G157900' => 'ptr', 'Potri.008G158000' => 'ptr', 'Potri.008G158200' => 'ptr', 'Pp3c11_7280' => 'ppa', 'Pp3c11_7980' => 'ppa', 'Pp3c12_19450' => 'ppa', 'Pp3c14_1480' => 'ppa', 'Pp3c14_1501' => 'ppa', 'Pp3c16_4900' => 'ppa', 'Pp3c16_5010' => 'ppa', 'Pp3c16_5060' => 'ppa', 'Pp3c19_18250' => 'ppa', 'Pp3c23_8530' => 'ppa', 'Pp3c23_8550' => 'ppa', 'Pp3c24_9670' => 'ppa', 'Pp3c2_21390' => 'ppa', 'Pp3c2_31380' => 'ppa', 'Pp3c3_16620' => 'ppa', 'Pp3c3_8090' => 'ppa', 'Pp3c3_8110' => 'ppa', 'Pp3c3_8130' => 'ppa', 'Pp3c3_8150' => 'ppa', 'Pp3c4_14320' => 'ppa', 'Pp3c6_2560' => 'ppa', 'Pp3c9_16700' => 'ppa', 'PRCOL_00000234' => 'pco', 'PRCOL_00000235' => 'pco', 'PRCOL_00000777' => 'pco', 'PRCOL_00002344' => 'pco', 'PRCOL_00002372' => 'pco', 'PRCOL_00006120' => 'pco', 'Prupe.1G021400' => 'ppe', 'Prupe.1G021500' => 'ppe', 'Prupe.1G021600' => 'ppe', 'Prupe.1G021700' => 'ppe', 'Prupe.1G021800' => 'ppe', 'Prupe.5G145100' => 'ppe', 'Psat6g204040' => 'psa', 'Psat6g204800' => 'psa', 'Psat6g204920' => 'psa', 'Psat6g204960' => 'psa', 'Psat6g205080' => 'psa', 'PSO017G0271' => 'pso', 'PSO017G1276' => 'pso', 'PSO017G1429' => 'pso', 'PSO017G1861' => 'pso', 'PSO017G2787' => 'pso', 'PSO017G4466' => 'pso', 'PSO017G5118' => 'pso', 'PSO017G5420' => 'pso', 'PSO063G3678' => 'pso', 'PSO210G0546' => 'pso', 'PSO317G0001' => 'pso', 'PSO357G0512' => 'pso', 'PSO478G2682' => 'pso', 'PSO647G0001' => 'pso', 'PSO675G0001' => 'pso', 'PSO675G2699' => 'pso', 'PSO675G2849' => 'pso', 'PSO675G4991' => 'pso', 'PSO689G0001' => 'pso', 'QL06p000916' => 'qlo', 'QL06p000921' => 'qlo', 'QL06p001398' => 'qlo', 'QL06p001407' => 'qlo', 'QL06p002031' => 'qlo', 'RcHm_v2.0_Chr4g0387791' => 'rch', 'RcHm_v2.0_Chr4g0387801' => 'rch', 'RcHm_v2.0_Chr6g0286501' => 'rch', 'RcHm_v2.0_Chr6g0286511' => 'rch', 'RcHm_v2.0_Chr6g0286521' => 'rch', 'RcHm_v2.0_Chr6g0286531' => 'rch', 'RcHm_v2.0_Chr7g0189141' => 'rch', 'Rhsim02G0028700' => 'rsi', 'Rhsim02G0028800' => 'rsi', 'Rhsim02G0028900' => 'rsi', 'Rhsim02G0029000' => 'rsi', 'Rhsim02G0029100' => 'rsi', 'Rhsim02G0029200' => 'rsi', 'Rhsim02G0029300' => 'rsi', 'Rhsim02G0029400' => 'rsi', 'Rhsim02G0029500' => 'rsi', 'Rhsim02G0029600' => 'rsi', 'RhsimUnG0024000' => 'rsi', 'RhsimUnG0024100' => 'rsi', 'RhsimUnG0024200' => 'rsi', 'RhsimUnG0024300' => 'rsi', 'RhsimUnG0024400' => 'rsi', 'RhsimUnG0024500' => 'rsi', 'RhsimUnG0024700' => 'rsi', 'RhsimUnG0024800' => 'rsi', 'RhsimUnG0024900' => 'rsi', 'RhsimUnG0025100' => 'rsi', 'Sabra08G0120200' => 'sbr', 'Sabra08G0120300' => 'sbr', 'Sabra08G0120500' => 'sbr', 'Sabra08G0120600' => 'sbr', 'Sabra10G0158900' => 'sbr', 'SalBow2G3492' => 'sbo', 'Sc13g0004760' => 'sci', 'Sc13g0004770' => 'sci', 'Sed0003417' => 'sed', 'Sed0019750' => 'sed', 'SEGI_03419' => 'sgi', 'SEGI_05907' => 'sgi', 'SEGI_10682' => 'sgi', 'SEGI_13528' => 'sgi', 'SEGI_16081' => 'sgi', 'SEGI_19370' => 'sgi', 'SEGI_21015' => 'sgi', 'SEGI_21944' => 'sgi', 'SEGI_32906' => 'sgi', 'SEGI_33093' => 'sgi', 'SEGI_36110' => 'sgi', 'SEGI_40397' => 'sgi', 'SGA_v2.0_scaffold191G40426' => 'sas', 'SGA_v2.0_scaffold353G49717' => 'sas', 'SGA_v2.0_scaffold50G18550' => 'sas', 'SMO119G0173' => 'smo', 'SMO172G0002' => 'smo', 'Solyc09g082690.3' => 'sly', 'Solyc09g082700.2' => 'sly', 'Sopen09g031550' => 'spe', 'Sopen09g031560' => 'spe', 'Sp3g20540' => 'spa', 'Sp7g07580' => 'spa', 'TAR134G0002' => 'tar', 'TAR236G0001' => 'tar', 'TAR365G0892' => 'tar', 'TAR636G0166' => 'tar', 'TAR636G0646' => 'tar', 'TAR636G0869' => 'tar', 'TAR636G1317' => 'tar', 'TAR636G1744' => 'tar', 'TAR636G3358' => 'tar', 'TAR636G3436' => 'tar', 'THA.LOC104803047' => 'tha', 'Thecc.04G238900' => 'tca', 'Thhalv10021557m.g' => 'esa', 'Thhalv10026318m.g' => 'esa', 'Thhalv10026335m.g' => 'esa', 'TPR.G17433' => 'tpr', 'TPR.G18915' => 'tpr', 'TPR.G26125' => 'tpr', 'TWI09G0677' => 'twi', 'TWI73G0287' => 'twi', 'unitig_748.g8326' => 'ugi', 'vmacro15370' => 'vma', 'vmacro15371' => 'vma', 'vmacro15372' => 'vma', 'vmacro15373' => 'vma', 'vmacro15374' => 'vma', 'VMungo0720G2826' => 'vmu', 'Zm00001eb116960' => 'zma', 'Zm00001eb301260' => 'zma', 'Zm00001eb301270' => 'zma' ) $gf_id = 'HOM05D001460' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001460' ) $data_identifier = 'HOM05D001460' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 4, 'aag' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 2, 'aox' => (int) 2, 'arhy' => (int) 4, 'ath' => (int) 2, 'atr' => (int) 1, 'acertr' => (int) 10, 'cqu' => (int) 4, 'bca' => (int) 11, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 1, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 1, 'ccan' => (int) 1, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 1, 'col' => (int) 1, 'cpa' => (int) 1, 'cre' => (int) 7, 'csa' => (int) 1, 'camsi' => (int) 2, 'dca' => (int) 3, 'din' => (int) 2, 'dzi' => (int) 3, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 14, 'fve' => (int) 9, 'gma' => (int) 2, 'ghi' => (int) 4, 'gra' => (int) 2, 'vvi' => (int) 1, 'han' => (int) 13, 'cav' => (int) 1, 'hma' => (int) 2, 'sun' => (int) 2, 'lal' => (int) 2, 'lonja' => (int) 12, 'lja' => (int) 1, 'lsa' => (int) 7, 'mes' => (int) 1, 'mpo' => (int) 27, 'mbi' => (int) 1, 'mco' => (int) 8, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 1, 'egut' => (int) 1, 'ama' => (int) 1, 'nta' => (int) 4, 'nnu' => (int) 2, 'oeu' => (int) 3, 'osa' => (int) 4, 'pax' => (int) 9, 'pgr' => (int) 1, 'stu' => (int) 1, 'pvu' => (int) 1, 'ptr' => (int) 4, 'ppa' => (int) 22, 'pco' => (int) 6, 'ppe' => (int) 6, 'psa' => (int) 5, 'pso' => (int) 19, 'qlo' => (int) 5, 'rch' => (int) 7, 'rsi' => (int) 20, 'sbr' => (int) 5, 'sbo' => (int) 1, 'sci' => (int) 2, 'sed' => (int) 2, 'sgi' => (int) 12, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 2, 'tar' => (int) 10, 'tha' => (int) 1, 'tca' => (int) 1, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 2, 'ugi' => (int) 1, 'vma' => (int) 5, 'vmu' => (int) 1, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb301270' $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' => 'HOM05D001460', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '433', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p22980' => 'bna', 'A01p32340' => 'bna', 'A03p42970' => 'bna', 'A05p25880' => 'bna', 'Aa31LG8G9320' => 'aar', 'Aa31LG8G9330' => 'aar', 'Aa31LG8G9340' => 'aar', 'Aa31sc221G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1034' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1528' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.829' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2222' => 'aag', 'Ah.12g058830' => 'amhyb', 'Ah.12g058840' => 'amhyb', 'AL3G37160' => 'aly', 'AL7G41310' => 'aly', 'Aqoxy5G00395' => 'aox', 'Aqoxy5G00396' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0C8NZA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5185HY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JZ1PRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MD3LS0' => 'arhy', 'AT3G22840' => 'ath', 'AT4G14690' => 'ath', 'ATR0665G054' => 'atr', 'Atru.chr4.2344' => 'acertr', 'Atru.chr4.2346' => 'acertr', 'Atru.chr4.2347' => 'acertr', 'Atru.chr4.2348' => 'acertr', 'Atru.chr4.2355' => 'acertr', 'Atru.chr4.2356' => 'acertr', 'Atru.chr4.2358' => 'acertr', 'Atru.chr4.2359' => 'acertr', 'Atru.chr4.2360' => 'acertr', 'Atru.chr4.2361' => 'acertr', 'AUR62030476' => 'cqu', 'AUR62030478' => 'cqu', 'AUR62030819' => 'cqu', 'AUR62030820' => 'cqu', 'BcaB03g14648' => 'bca', 'BcaB04g20492' => 'bca', 'BcaB06g26399' => 'bca', 'BcaC01g03416' => 'bca', 'BcaC01g03419' => 'bca', 'BcaC01g03421' => 'bca', 'BcaC01g03424' => 'bca', 'BcaC05g28012' => 'bca', 'BcaC09g49212' => 'bca', 'BcaC09g50140' => 'bca', 'BcaNung00346' => 'bca', 'BolC1t02785H' => 'bol', 'BolC1t04095H' => 'bol', 'BolC3t17545H' => 'bol', 'BolC5t32769H' => 'bol', 'BraA01t02211Z' => 'bra', 'BraA01t03359Z' => 'bra', 'BraA03t13441Z' => 'bra', 'BraA05t21476Z' => 'bra', 'C01p28420' => 'bna', 'C01p41350' => 'bna', 'C03p52750' => 'bna', 'C03p52780' => 'bna', 'C05p40270' => 'bna', 'CAN.G1437.9' => 'can', 'CANSAT78G0035' => 'cansat', 'CANSAT78G1036' => 'cansat', 'CANSAT78G2272' => 'cansat', 'CANSAT78G2478' => 'cansat', 'CARHR098700' => 'chi', 'CARHR221120' => 'chi', 'CARHR221150' => 'chi', 'Carub.0003s2297' => 'cru', 'Carub.0007s2749' => 'cru', 'Carub.0007s2750' => 'cru', 'Carub.0007s2751' => 'cru', 'Ca_10849_v3' => 'car', 'Cc03_g04300' => 'ccan', 'CDE02G3648' => 'cde', 'CDE05G0060' => 'cde', 'CDE05G0692' => 'cde', 'CDE05G2285' => 'cde', 'CDE05G2884' => 'cde', 'CDE05G3072' => 'cde', 'Cfa008439' => 'cfa', 'Cfa008441' => 'cfa', 'Cfa008443' => 'cfa', 'Cfa008448' => 'cfa', 'Ciclev10005974m.g' => 'ccl', 'Ciclev10006006m.g' => 'ccl', 'Ciclev10006775m.g' => 'ccl', 'CiPaw.02G120400' => 'cil', 'CiPaw.02G120500' => 'cil', 'CiPaw.02G120600' => 'cil', 'ClCG05G004850' => 'cla', 'COL.COLO4_21566' => 'col', 'Cpa.g.sc44.124' => 'cpa', 'Cre07.g320400' => 'cre', 'Cre07.g320450' => 'cre', 'Cre08.g384650' => 'cre', 'Cre09.g393173' => 'cre', 'Cre09.g394325' => 'cre', 'Cre14.g626750' => 'cre', 'Cre16.g679250' => 'cre', 'CsaV3_3G012890' => 'csa', 'CSS0010865' => 'camsi', 'CSS0044338' => 'camsi', 'DCAR_002366' => 'dca', 'DCAR_030687' => 'dca', 'DCAR_030688' => 'dca', 'Dinv14047' => 'din', 'Dinv14048' => 'din', 'Duzib151G0105' => 'dzi', 'Duzib151G0114' => 'dzi', 'Duzib212G1029' => 'dzi', 'ECA232G3536' => 'eca', 'ECA240G0786' => 'eca', 'ECA240G1802' => 'eca', 'ECA240G3760' => 'eca', 'ECA240G3920' => 'eca', 'EL10Ac5g12536' => 'bvu', 'EL10Ac5g12537' => 'bvu', 'EL10Ac5g12538' => 'bvu', 'Eucgr.B01004' => 'egr', 'Eucgr.B01006' => 'egr', 'Eucgr.B01007' => 'egr', 'Eucgr.B01008' => 'egr', 'Eucgr.B01895' => 'egr', 'Eucgr.B01896' => 'egr', 'FAN04G1456' => 'fan', 'FAN08G1769' => 'fan', 'FAN08G2160' => 'fan', 'FAN13G2403' => 'fan', 'FAN13G3303' => 'fan', 'FAN15G2435' => 'fan', 'FAN17G0672' => 'fan', 'FAN17G2441' => 'fan', 'FAN18G1024' => 'fan', 'FAN22G1458' => 'fan', 'FAN24G0037' => 'fan', 'FAN24G0429' => 'fan', 'FAN24G2387' => 'fan', 'FAN27G2746' => 'fan', 'FvH4_2g20400' => 'fve', 'FvH4_2g20420' => 'fve', 'FvH4_2g20430' => 'fve', 'FvH4_4g01270' => 'fve', 'FvH4_4g01290' => 'fve', 'FvH4_4g01300' => 'fve', 'FvH4_4g01310' => 'fve', 'FvH4_4g01330' => 'fve', 'FvH4_5g09070' => 'fve', 'Glyma.10G243800' => 'gma', 'Glyma.20G150600' => 'gma', 'Gohir.A09G219200' => 'ghi', 'Gohir.A09G219300' => 'ghi', 'Gohir.D09G221400' => 'ghi', 'Gohir.D09G221500' => 'ghi', 'Gorai.006G242600' => 'gra', 'Gorai.006G242700' => 'gra', 'GSVIVG01018044001' => 'vvi', 'HanXRQChr03g0083821' => 'han', 'HanXRQChr03g0083841' => 'han', 'HanXRQChr03g0083881' => 'han', 'HanXRQChr03g0083901' => 'han', 'HanXRQChr03g0083921' => 'han', 'HanXRQChr03g0085331' => 'han', 'HanXRQChr03g0085361' => 'han', 'HanXRQChr03g0085411' => 'han', 'HanXRQChr03g0085421' => 'han', 'HanXRQChr03g0085431' => 'han', 'HanXRQChr08g0221991' => 'han', 'HanXRQChr11g0336061' => 'han', 'HanXRQChr11g0336411' => 'han', 'Haze_11234' => 'cav', 'Hma1.2p1_0549F.1_g177010' => 'hma', 'Hma1.2p1_0602F.1_g187630' => 'hma', 'Hund14876' => 'sun', 'Hund14879' => 'sun', 'Lalb_Chr06g0160741' => 'lal', 'Lalb_Chr21g0304781' => 'lal', 'Lj3A726G19' => 'lonja', 'Lj3A726T23' => 'lonja', 'Lj3A726T24' => 'lonja', 'Lj3A726T25' => 'lonja', 'Lj3A727T17' => 'lonja', 'Lj3C726T0' => 'lonja', 'Lj3C726T2' => 'lonja', 'Lj3P725T35' => 'lonja', 'Lj3P727T10' => 'lonja', 'Lj3P727T12' => 'lonja', 'Lj3P727T14' => 'lonja', 'Lj5g0023109' => 'lja', 'Lj6P646T44' => 'lonja', 'Lsat_1_v5_gn_6_75760' => 'lsa', 'Lsat_1_v5_gn_6_75800' => 'lsa', 'Lsat_1_v5_gn_6_75900' => 'lsa', 'Lsat_1_v5_gn_6_76240' => 'lsa', 'Lsat_1_v5_gn_6_76441' => 'lsa', 'Lsat_1_v5_gn_6_76700' => 'lsa', 'Lsat_1_v5_gn_6_76760' => 'lsa', 'Manes.15G033100' => 'mes', 'Mapoly0004s0074' => 'mpo', 'Mapoly0004s0075' => 'mpo', 'Mapoly0004s0163' => 'mpo', 'Mapoly0004s0164' => 'mpo', 'Mapoly0021s0018' => 'mpo', 'Mapoly0041s0136' => 'mpo', 'Mapoly0041s0137' => 'mpo', 'Mapoly0041s0138' => 'mpo', 'Mapoly0041s0139' => 'mpo', 'Mapoly0041s0141' => 'mpo', 'Mapoly0041s0142' => 'mpo', 'Mapoly0041s0143' => 'mpo', 'Mapoly0041s0144' => 'mpo', 'Mapoly0041s0145' => 'mpo', 'Mapoly0047s0106' => 'mpo', 'Mapoly0047s0108' => 'mpo', 'Mapoly0050s0051' => 'mpo', 'Mapoly0050s0052' => 'mpo', 'Mapoly0050s0053' => 'mpo', 'Mapoly0058s0013' => 'mpo', 'Mapoly0091s0078' => 'mpo', 'Mapoly0091s0079' => 'mpo', 'Mapoly0091s0080' => 'mpo', 'Mapoly0091s0081' => 'mpo', 'Mapoly0278s0004' => 'mpo', 'Mapoly0278s0005' => 'mpo', 'Mapoly0278s0006' => 'mpo', 'MBI11_g30648_MAGBIO' => 'mbi', 'MCO03G194' => 'mco', 'MCO03G590' => 'mco', 'MCO07G312' => 'mco', 'MCO10G318' => 'mco', 'MCO12G244' => 'mco', 'MCO13G148' => 'mco', 'MCO13G194' => 'mco', 'MCO16G238' => 'mco', 'MD06G1134100' => 'mdo', 'MD13G1200100' => 'mdo', 'MD13G1200300' => 'mdo', 'MD13G1200600' => 'mdo', 'MD14G1150400' => 'mdo', 'MD16G1200000' => 'mdo', 'Medtr1g102570' => 'mtr', 'Medtr1g102780' => 'mtr', 'Medtr1g102800' => 'mtr', 'Medtr1g102810' => 'mtr', 'Medtr1g102830' => 'mtr', 'MELO3C006499.2' => 'cme', 'Migut.G00385' => 'egut', 'MSTRG.4063' => 'ama', 'Nitab4.5_0000090g0260' => 'nta', 'Nitab4.5_0000977g0030' => 'nta', 'Nitab4.5_0002541g0040' => 'nta', 'Nitab4.5_0007068g0040' => 'nta', 'Nn005s41408' => 'nnu', 'Nn005s41410' => 'nnu', 'Oeu010310.1' => 'oeu', 'Oeu010311.1' => 'oeu', 'Oeu043472.1' => 'oeu', 'Os01g0246400' => 'osa', 'Os04g0267950' => 'osa', 'Os07g0178700' => 'osa', 'Os07g0178800' => 'osa', 'Peaxi162Scf00316g00046' => 'pax', 'Peaxi162Scf00316g00049' => 'pax', 'Peaxi162Scf00316g00059' => 'pax', 'Peaxi162Scf00316g00328' => 'pax', 'Peaxi162Scf00316g00329' => 'pax', 'Peaxi162Scf00316g00411' => 'pax', 'Peaxi162Scf00316g00521' => 'pax', 'Peaxi162Scf00492g00068' => 'pax', 'Peaxi162Scf35631g00002' => 'pax', 'PGR142G3720' => 'pgr', 'PGSC0003DMG400006442' => 'stu', 'Phvul.007G062000' => 'pvu', 'Potri.008G157750' => 'ptr', 'Potri.008G157900' => 'ptr', 'Potri.008G158000' => 'ptr', 'Potri.008G158200' => 'ptr', 'Pp3c11_7280' => 'ppa', 'Pp3c11_7980' => 'ppa', 'Pp3c12_19450' => 'ppa', 'Pp3c14_1480' => 'ppa', 'Pp3c14_1501' => 'ppa', 'Pp3c16_4900' => 'ppa', 'Pp3c16_5010' => 'ppa', 'Pp3c16_5060' => 'ppa', 'Pp3c19_18250' => 'ppa', 'Pp3c23_8530' => 'ppa', 'Pp3c23_8550' => 'ppa', 'Pp3c24_9670' => 'ppa', 'Pp3c2_21390' => 'ppa', 'Pp3c2_31380' => 'ppa', 'Pp3c3_16620' => 'ppa', 'Pp3c3_8090' => 'ppa', 'Pp3c3_8110' => 'ppa', 'Pp3c3_8130' => 'ppa', 'Pp3c3_8150' => 'ppa', 'Pp3c4_14320' => 'ppa', 'Pp3c6_2560' => 'ppa', 'Pp3c9_16700' => 'ppa', 'PRCOL_00000234' => 'pco', 'PRCOL_00000235' => 'pco', 'PRCOL_00000777' => 'pco', 'PRCOL_00002344' => 'pco', 'PRCOL_00002372' => 'pco', 'PRCOL_00006120' => 'pco', 'Prupe.1G021400' => 'ppe', 'Prupe.1G021500' => 'ppe', 'Prupe.1G021600' => 'ppe', 'Prupe.1G021700' => 'ppe', 'Prupe.1G021800' => 'ppe', 'Prupe.5G145100' => 'ppe', 'Psat6g204040' => 'psa', 'Psat6g204800' => 'psa', 'Psat6g204920' => 'psa', 'Psat6g204960' => 'psa', 'Psat6g205080' => 'psa', 'PSO017G0271' => 'pso', 'PSO017G1276' => 'pso', 'PSO017G1429' => 'pso', 'PSO017G1861' => 'pso', 'PSO017G2787' => 'pso', 'PSO017G4466' => 'pso', 'PSO017G5118' => 'pso', 'PSO017G5420' => 'pso', 'PSO063G3678' => 'pso', 'PSO210G0546' => 'pso', 'PSO317G0001' => 'pso', 'PSO357G0512' => 'pso', 'PSO478G2682' => 'pso', 'PSO647G0001' => 'pso', 'PSO675G0001' => 'pso', 'PSO675G2699' => 'pso', 'PSO675G2849' => 'pso', 'PSO675G4991' => 'pso', 'PSO689G0001' => 'pso', 'QL06p000916' => 'qlo', 'QL06p000921' => 'qlo', 'QL06p001398' => 'qlo', 'QL06p001407' => 'qlo', 'QL06p002031' => 'qlo', 'RcHm_v2.0_Chr4g0387791' => 'rch', 'RcHm_v2.0_Chr4g0387801' => 'rch', 'RcHm_v2.0_Chr6g0286501' => 'rch', 'RcHm_v2.0_Chr6g0286511' => 'rch', 'RcHm_v2.0_Chr6g0286521' => 'rch', 'RcHm_v2.0_Chr6g0286531' => 'rch', 'RcHm_v2.0_Chr7g0189141' => 'rch', 'Rhsim02G0028700' => 'rsi', 'Rhsim02G0028800' => 'rsi', 'Rhsim02G0028900' => 'rsi', 'Rhsim02G0029000' => 'rsi', 'Rhsim02G0029100' => 'rsi', 'Rhsim02G0029200' => 'rsi', 'Rhsim02G0029300' => 'rsi', 'Rhsim02G0029400' => 'rsi', 'Rhsim02G0029500' => 'rsi', 'Rhsim02G0029600' => 'rsi', 'RhsimUnG0024000' => 'rsi', 'RhsimUnG0024100' => 'rsi', 'RhsimUnG0024200' => 'rsi', 'RhsimUnG0024300' => 'rsi', 'RhsimUnG0024400' => 'rsi', 'RhsimUnG0024500' => 'rsi', 'RhsimUnG0024700' => 'rsi', 'RhsimUnG0024800' => 'rsi', 'RhsimUnG0024900' => 'rsi', 'RhsimUnG0025100' => 'rsi', 'Sabra08G0120200' => 'sbr', 'Sabra08G0120300' => 'sbr', 'Sabra08G0120500' => 'sbr', 'Sabra08G0120600' => 'sbr', 'Sabra10G0158900' => 'sbr', 'SalBow2G3492' => 'sbo', 'Sc13g0004760' => 'sci', 'Sc13g0004770' => 'sci', 'Sed0003417' => 'sed', 'Sed0019750' => 'sed', 'SEGI_03419' => 'sgi', 'SEGI_05907' => 'sgi', 'SEGI_10682' => 'sgi', 'SEGI_13528' => 'sgi', 'SEGI_16081' => 'sgi', 'SEGI_19370' => 'sgi', 'SEGI_21015' => 'sgi', 'SEGI_21944' => 'sgi', 'SEGI_32906' => 'sgi', 'SEGI_33093' => 'sgi', 'SEGI_36110' => 'sgi', 'SEGI_40397' => 'sgi', 'SGA_v2.0_scaffold191G40426' => 'sas', 'SGA_v2.0_scaffold353G49717' => 'sas', 'SGA_v2.0_scaffold50G18550' => 'sas', 'SMO119G0173' => 'smo', 'SMO172G0002' => 'smo', 'Solyc09g082690.3' => 'sly', 'Solyc09g082700.2' => 'sly', 'Sopen09g031550' => 'spe', 'Sopen09g031560' => 'spe', 'Sp3g20540' => 'spa', 'Sp7g07580' => 'spa', 'TAR134G0002' => 'tar', 'TAR236G0001' => 'tar', 'TAR365G0892' => 'tar', 'TAR636G0166' => 'tar', 'TAR636G0646' => 'tar', 'TAR636G0869' => 'tar', 'TAR636G1317' => 'tar', 'TAR636G1744' => 'tar', 'TAR636G3358' => 'tar', 'TAR636G3436' => 'tar', 'THA.LOC104803047' => 'tha', 'Thecc.04G238900' => 'tca', 'Thhalv10021557m.g' => 'esa', 'Thhalv10026318m.g' => 'esa', 'Thhalv10026335m.g' => 'esa', 'TPR.G17433' => 'tpr', 'TPR.G18915' => 'tpr', 'TPR.G26125' => 'tpr', 'TWI09G0677' => 'twi', 'TWI73G0287' => 'twi', 'unitig_748.g8326' => 'ugi', 'vmacro15370' => 'vma', 'vmacro15371' => 'vma', 'vmacro15372' => 'vma', 'vmacro15373' => 'vma', 'vmacro15374' => 'vma', 'VMungo0720G2826' => 'vmu', 'Zm00001eb116960' => 'zma', 'Zm00001eb301260' => 'zma', 'Zm00001eb301270' => 'zma' ), 'gf_id' => 'HOM05D001460', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001460' ), 'data_identifier' => 'HOM05D001460', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001460', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '433', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p22980' => 'bna', 'A01p32340' => 'bna', 'A03p42970' => 'bna', 'A05p25880' => 'bna', 'Aa31LG8G9320' => 'aar', 'Aa31LG8G9330' => 'aar', 'Aa31LG8G9340' => 'aar', 'Aa31sc221G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1034' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1528' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.829' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2222' => 'aag', 'Ah.12g058830' => 'amhyb', 'Ah.12g058840' => 'amhyb', 'AL3G37160' => 'aly', 'AL7G41310' => 'aly', 'Aqoxy5G00395' => 'aox', 'Aqoxy5G00396' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0C8NZA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5185HY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JZ1PRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MD3LS0' => 'arhy', 'AT3G22840' => 'ath', 'AT4G14690' => 'ath', 'ATR0665G054' => 'atr', 'Atru.chr4.2344' => 'acertr', 'Atru.chr4.2346' => 'acertr', 'Atru.chr4.2347' => 'acertr', 'Atru.chr4.2348' => 'acertr', 'Atru.chr4.2355' => 'acertr', 'Atru.chr4.2356' => 'acertr', 'Atru.chr4.2358' => 'acertr', 'Atru.chr4.2359' => 'acertr', 'Atru.chr4.2360' => 'acertr', 'Atru.chr4.2361' => 'acertr', 'AUR62030476' => 'cqu', 'AUR62030478' => 'cqu', 'AUR62030819' => 'cqu', 'AUR62030820' => 'cqu', 'BcaB03g14648' => 'bca', 'BcaB04g20492' => 'bca', 'BcaB06g26399' => 'bca', 'BcaC01g03416' => 'bca', 'BcaC01g03419' => 'bca', 'BcaC01g03421' => 'bca', 'BcaC01g03424' => 'bca', 'BcaC05g28012' => 'bca', 'BcaC09g49212' => 'bca', 'BcaC09g50140' => 'bca', 'BcaNung00346' => 'bca', 'BolC1t02785H' => 'bol', 'BolC1t04095H' => 'bol', 'BolC3t17545H' => 'bol', 'BolC5t32769H' => 'bol', 'BraA01t02211Z' => 'bra', 'BraA01t03359Z' => 'bra', 'BraA03t13441Z' => 'bra', 'BraA05t21476Z' => 'bra', 'C01p28420' => 'bna', 'C01p41350' => 'bna', 'C03p52750' => 'bna', 'C03p52780' => 'bna', 'C05p40270' => 'bna', 'CAN.G1437.9' => 'can', 'CANSAT78G0035' => 'cansat', 'CANSAT78G1036' => 'cansat', 'CANSAT78G2272' => 'cansat', 'CANSAT78G2478' => 'cansat', 'CARHR098700' => 'chi', 'CARHR221120' => 'chi', 'CARHR221150' => 'chi', 'Carub.0003s2297' => 'cru', 'Carub.0007s2749' => 'cru', 'Carub.0007s2750' => 'cru', 'Carub.0007s2751' => 'cru', 'Ca_10849_v3' => 'car', 'Cc03_g04300' => 'ccan', 'CDE02G3648' => 'cde', 'CDE05G0060' => 'cde', 'CDE05G0692' => 'cde', 'CDE05G2285' => 'cde', 'CDE05G2884' => 'cde', 'CDE05G3072' => 'cde', 'Cfa008439' => 'cfa', 'Cfa008441' => 'cfa', 'Cfa008443' => 'cfa', 'Cfa008448' => 'cfa', 'Ciclev10005974m.g' => 'ccl', 'Ciclev10006006m.g' => 'ccl', 'Ciclev10006775m.g' => 'ccl', 'CiPaw.02G120400' => 'cil', 'CiPaw.02G120500' => 'cil', 'CiPaw.02G120600' => 'cil', 'ClCG05G004850' => 'cla', 'COL.COLO4_21566' => 'col', 'Cpa.g.sc44.124' => 'cpa', 'Cre07.g320400' => 'cre', 'Cre07.g320450' => 'cre', 'Cre08.g384650' => 'cre', 'Cre09.g393173' => 'cre', 'Cre09.g394325' => 'cre', 'Cre14.g626750' => 'cre', 'Cre16.g679250' => 'cre', 'CsaV3_3G012890' => 'csa', 'CSS0010865' => 'camsi', 'CSS0044338' => 'camsi', 'DCAR_002366' => 'dca', 'DCAR_030687' => 'dca', 'DCAR_030688' => 'dca', 'Dinv14047' => 'din', 'Dinv14048' => 'din', 'Duzib151G0105' => 'dzi', 'Duzib151G0114' => 'dzi', 'Duzib212G1029' => 'dzi', 'ECA232G3536' => 'eca', 'ECA240G0786' => 'eca', 'ECA240G1802' => 'eca', 'ECA240G3760' => 'eca', 'ECA240G3920' => 'eca', 'EL10Ac5g12536' => 'bvu', 'EL10Ac5g12537' => 'bvu', 'EL10Ac5g12538' => 'bvu', 'Eucgr.B01004' => 'egr', 'Eucgr.B01006' => 'egr', 'Eucgr.B01007' => 'egr', 'Eucgr.B01008' => 'egr', 'Eucgr.B01895' => 'egr', 'Eucgr.B01896' => 'egr', 'FAN04G1456' => 'fan', 'FAN08G1769' => 'fan', 'FAN08G2160' => 'fan', 'FAN13G2403' => 'fan', 'FAN13G3303' => 'fan', 'FAN15G2435' => 'fan', 'FAN17G0672' => 'fan', 'FAN17G2441' => 'fan', 'FAN18G1024' => 'fan', 'FAN22G1458' => 'fan', 'FAN24G0037' => 'fan', 'FAN24G0429' => 'fan', 'FAN24G2387' => 'fan', 'FAN27G2746' => 'fan', 'FvH4_2g20400' => 'fve', 'FvH4_2g20420' => 'fve', 'FvH4_2g20430' => 'fve', 'FvH4_4g01270' => 'fve', 'FvH4_4g01290' => 'fve', 'FvH4_4g01300' => 'fve', 'FvH4_4g01310' => 'fve', 'FvH4_4g01330' => 'fve', 'FvH4_5g09070' => 'fve', 'Glyma.10G243800' => 'gma', 'Glyma.20G150600' => 'gma', 'Gohir.A09G219200' => 'ghi', 'Gohir.A09G219300' => 'ghi', 'Gohir.D09G221400' => 'ghi', 'Gohir.D09G221500' => 'ghi', 'Gorai.006G242600' => 'gra', 'Gorai.006G242700' => 'gra', 'GSVIVG01018044001' => 'vvi', 'HanXRQChr03g0083821' => 'han', 'HanXRQChr03g0083841' => 'han', 'HanXRQChr03g0083881' => 'han', 'HanXRQChr03g0083901' => 'han', 'HanXRQChr03g0083921' => 'han', 'HanXRQChr03g0085331' => 'han', 'HanXRQChr03g0085361' => 'han', 'HanXRQChr03g0085411' => 'han', 'HanXRQChr03g0085421' => 'han', 'HanXRQChr03g0085431' => 'han', 'HanXRQChr08g0221991' => 'han', 'HanXRQChr11g0336061' => 'han', 'HanXRQChr11g0336411' => 'han', 'Haze_11234' => 'cav', 'Hma1.2p1_0549F.1_g177010' => 'hma', 'Hma1.2p1_0602F.1_g187630' => 'hma', 'Hund14876' => 'sun', 'Hund14879' => 'sun', 'Lalb_Chr06g0160741' => 'lal', 'Lalb_Chr21g0304781' => 'lal', 'Lj3A726G19' => 'lonja', 'Lj3A726T23' => 'lonja', 'Lj3A726T24' => 'lonja', 'Lj3A726T25' => 'lonja', 'Lj3A727T17' => 'lonja', 'Lj3C726T0' => 'lonja', 'Lj3C726T2' => 'lonja', 'Lj3P725T35' => 'lonja', 'Lj3P727T10' => 'lonja', 'Lj3P727T12' => 'lonja', 'Lj3P727T14' => 'lonja', 'Lj5g0023109' => 'lja', 'Lj6P646T44' => 'lonja', 'Lsat_1_v5_gn_6_75760' => 'lsa', 'Lsat_1_v5_gn_6_75800' => 'lsa', 'Lsat_1_v5_gn_6_75900' => 'lsa', 'Lsat_1_v5_gn_6_76240' => 'lsa', 'Lsat_1_v5_gn_6_76441' => 'lsa', 'Lsat_1_v5_gn_6_76700' => 'lsa', 'Lsat_1_v5_gn_6_76760' => 'lsa', 'Manes.15G033100' => 'mes', 'Mapoly0004s0074' => 'mpo', 'Mapoly0004s0075' => 'mpo', 'Mapoly0004s0163' => 'mpo', 'Mapoly0004s0164' => 'mpo', 'Mapoly0021s0018' => 'mpo', 'Mapoly0041s0136' => 'mpo', 'Mapoly0041s0137' => 'mpo', 'Mapoly0041s0138' => 'mpo', 'Mapoly0041s0139' => 'mpo', 'Mapoly0041s0141' => 'mpo', 'Mapoly0041s0142' => 'mpo', 'Mapoly0041s0143' => 'mpo', 'Mapoly0041s0144' => 'mpo', 'Mapoly0041s0145' => 'mpo', 'Mapoly0047s0106' => 'mpo', 'Mapoly0047s0108' => 'mpo', 'Mapoly0050s0051' => 'mpo', 'Mapoly0050s0052' => 'mpo', 'Mapoly0050s0053' => 'mpo', 'Mapoly0058s0013' => 'mpo', 'Mapoly0091s0078' => 'mpo', 'Mapoly0091s0079' => 'mpo', 'Mapoly0091s0080' => 'mpo', 'Mapoly0091s0081' => 'mpo', 'Mapoly0278s0004' => 'mpo', 'Mapoly0278s0005' => 'mpo', 'Mapoly0278s0006' => 'mpo', 'MBI11_g30648_MAGBIO' => 'mbi', 'MCO03G194' => 'mco', 'MCO03G590' => 'mco', 'MCO07G312' => 'mco', 'MCO10G318' => 'mco', 'MCO12G244' => 'mco', 'MCO13G148' => 'mco', 'MCO13G194' => 'mco', 'MCO16G238' => 'mco', 'MD06G1134100' => 'mdo', 'MD13G1200100' => 'mdo', 'MD13G1200300' => 'mdo', 'MD13G1200600' => 'mdo', 'MD14G1150400' => 'mdo', 'MD16G1200000' => 'mdo', 'Medtr1g102570' => 'mtr', 'Medtr1g102780' => 'mtr', 'Medtr1g102800' => 'mtr', 'Medtr1g102810' => 'mtr', 'Medtr1g102830' => 'mtr', 'MELO3C006499.2' => 'cme', 'Migut.G00385' => 'egut', 'MSTRG.4063' => 'ama', 'Nitab4.5_0000090g0260' => 'nta', 'Nitab4.5_0000977g0030' => 'nta', 'Nitab4.5_0002541g0040' => 'nta', 'Nitab4.5_0007068g0040' => 'nta', 'Nn005s41408' => 'nnu', 'Nn005s41410' => 'nnu', 'Oeu010310.1' => 'oeu', 'Oeu010311.1' => 'oeu', 'Oeu043472.1' => 'oeu', 'Os01g0246400' => 'osa', 'Os04g0267950' => 'osa', 'Os07g0178700' => 'osa', 'Os07g0178800' => 'osa', 'Peaxi162Scf00316g00046' => 'pax', 'Peaxi162Scf00316g00049' => 'pax', 'Peaxi162Scf00316g00059' => 'pax', 'Peaxi162Scf00316g00328' => 'pax', 'Peaxi162Scf00316g00329' => 'pax', 'Peaxi162Scf00316g00411' => 'pax', 'Peaxi162Scf00316g00521' => 'pax', 'Peaxi162Scf00492g00068' => 'pax', 'Peaxi162Scf35631g00002' => 'pax', 'PGR142G3720' => 'pgr', 'PGSC0003DMG400006442' => 'stu', 'Phvul.007G062000' => 'pvu', 'Potri.008G157750' => 'ptr', 'Potri.008G157900' => 'ptr', 'Potri.008G158000' => 'ptr', 'Potri.008G158200' => 'ptr', 'Pp3c11_7280' => 'ppa', 'Pp3c11_7980' => 'ppa', 'Pp3c12_19450' => 'ppa', 'Pp3c14_1480' => 'ppa', 'Pp3c14_1501' => 'ppa', 'Pp3c16_4900' => 'ppa', 'Pp3c16_5010' => 'ppa', 'Pp3c16_5060' => 'ppa', 'Pp3c19_18250' => 'ppa', 'Pp3c23_8530' => 'ppa', 'Pp3c23_8550' => 'ppa', 'Pp3c24_9670' => 'ppa', 'Pp3c2_21390' => 'ppa', 'Pp3c2_31380' => 'ppa', 'Pp3c3_16620' => 'ppa', 'Pp3c3_8090' => 'ppa', 'Pp3c3_8110' => 'ppa', 'Pp3c3_8130' => 'ppa', 'Pp3c3_8150' => 'ppa', 'Pp3c4_14320' => 'ppa', 'Pp3c6_2560' => 'ppa', 'Pp3c9_16700' => 'ppa', 'PRCOL_00000234' => 'pco', 'PRCOL_00000235' => 'pco', 'PRCOL_00000777' => 'pco', 'PRCOL_00002344' => 'pco', 'PRCOL_00002372' => 'pco', 'PRCOL_00006120' => 'pco', 'Prupe.1G021400' => 'ppe', 'Prupe.1G021500' => 'ppe', 'Prupe.1G021600' => 'ppe', 'Prupe.1G021700' => 'ppe', 'Prupe.1G021800' => 'ppe', 'Prupe.5G145100' => 'ppe', 'Psat6g204040' => 'psa', 'Psat6g204800' => 'psa', 'Psat6g204920' => 'psa', 'Psat6g204960' => 'psa', 'Psat6g205080' => 'psa', 'PSO017G0271' => 'pso', 'PSO017G1276' => 'pso', 'PSO017G1429' => 'pso', 'PSO017G1861' => 'pso', 'PSO017G2787' => 'pso', 'PSO017G4466' => 'pso', 'PSO017G5118' => 'pso', 'PSO017G5420' => 'pso', 'PSO063G3678' => 'pso', 'PSO210G0546' => 'pso', 'PSO317G0001' => 'pso', 'PSO357G0512' => 'pso', 'PSO478G2682' => 'pso', 'PSO647G0001' => 'pso', 'PSO675G0001' => 'pso', 'PSO675G2699' => 'pso', 'PSO675G2849' => 'pso', 'PSO675G4991' => 'pso', 'PSO689G0001' => 'pso', 'QL06p000916' => 'qlo', 'QL06p000921' => 'qlo', 'QL06p001398' => 'qlo', 'QL06p001407' => 'qlo', 'QL06p002031' => 'qlo', 'RcHm_v2.0_Chr4g0387791' => 'rch', 'RcHm_v2.0_Chr4g0387801' => 'rch', 'RcHm_v2.0_Chr6g0286501' => 'rch', 'RcHm_v2.0_Chr6g0286511' => 'rch', 'RcHm_v2.0_Chr6g0286521' => 'rch', 'RcHm_v2.0_Chr6g0286531' => 'rch', 'RcHm_v2.0_Chr7g0189141' => 'rch', 'Rhsim02G0028700' => 'rsi', 'Rhsim02G0028800' => 'rsi', 'Rhsim02G0028900' => 'rsi', 'Rhsim02G0029000' => 'rsi', 'Rhsim02G0029100' => 'rsi', 'Rhsim02G0029200' => 'rsi', 'Rhsim02G0029300' => 'rsi', 'Rhsim02G0029400' => 'rsi', 'Rhsim02G0029500' => 'rsi', 'Rhsim02G0029600' => 'rsi', 'RhsimUnG0024000' => 'rsi', 'RhsimUnG0024100' => 'rsi', 'RhsimUnG0024200' => 'rsi', 'RhsimUnG0024300' => 'rsi', 'RhsimUnG0024400' => 'rsi', 'RhsimUnG0024500' => 'rsi', 'RhsimUnG0024700' => 'rsi', 'RhsimUnG0024800' => 'rsi', 'RhsimUnG0024900' => 'rsi', 'RhsimUnG0025100' => 'rsi', 'Sabra08G0120200' => 'sbr', 'Sabra08G0120300' => 'sbr', 'Sabra08G0120500' => 'sbr', 'Sabra08G0120600' => 'sbr', 'Sabra10G0158900' => 'sbr', 'SalBow2G3492' => 'sbo', 'Sc13g0004760' => 'sci', 'Sc13g0004770' => 'sci', 'Sed0003417' => 'sed', 'Sed0019750' => 'sed', 'SEGI_03419' => 'sgi', 'SEGI_05907' => 'sgi', 'SEGI_10682' => 'sgi', 'SEGI_13528' => 'sgi', 'SEGI_16081' => 'sgi', 'SEGI_19370' => 'sgi', 'SEGI_21015' => 'sgi', 'SEGI_21944' => 'sgi', 'SEGI_32906' => 'sgi', 'SEGI_33093' => 'sgi', 'SEGI_36110' => 'sgi', 'SEGI_40397' => 'sgi', 'SGA_v2.0_scaffold191G40426' => 'sas', 'SGA_v2.0_scaffold353G49717' => 'sas', 'SGA_v2.0_scaffold50G18550' => 'sas', 'SMO119G0173' => 'smo', 'SMO172G0002' => 'smo', 'Solyc09g082690.3' => 'sly', 'Solyc09g082700.2' => 'sly', 'Sopen09g031550' => 'spe', 'Sopen09g031560' => 'spe', 'Sp3g20540' => 'spa', 'Sp7g07580' => 'spa', 'TAR134G0002' => 'tar', 'TAR236G0001' => 'tar', 'TAR365G0892' => 'tar', 'TAR636G0166' => 'tar', 'TAR636G0646' => 'tar', 'TAR636G0869' => 'tar', 'TAR636G1317' => 'tar', 'TAR636G1744' => 'tar', 'TAR636G3358' => 'tar', 'TAR636G3436' => 'tar', 'THA.LOC104803047' => 'tha', 'Thecc.04G238900' => 'tca', 'Thhalv10021557m.g' => 'esa', 'Thhalv10026318m.g' => 'esa', 'Thhalv10026335m.g' => 'esa', 'TPR.G17433' => 'tpr', 'TPR.G18915' => 'tpr', 'TPR.G26125' => 'tpr', 'TWI09G0677' => 'twi', 'TWI73G0287' => 'twi', 'unitig_748.g8326' => 'ugi', 'vmacro15370' => 'vma', 'vmacro15371' => 'vma', 'vmacro15372' => 'vma', 'vmacro15373' => 'vma', 'vmacro15374' => 'vma', 'VMungo0720G2826' => 'vmu', 'Zm00001eb116960' => 'zma', 'Zm00001eb301260' => 'zma', 'Zm00001eb301270' => 'zma' ) $gf_id = 'HOM05D001460' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001460' ) $data_identifier = 'HOM05D001460' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 4, 'aag' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 2, 'aox' => (int) 2, 'arhy' => (int) 4, 'ath' => (int) 2, 'atr' => (int) 1, 'acertr' => (int) 10, 'cqu' => (int) 4, 'bca' => (int) 11, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 1, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 1, 'ccan' => (int) 1, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 1, 'col' => (int) 1, 'cpa' => (int) 1, 'cre' => (int) 7, 'csa' => (int) 1, 'camsi' => (int) 2, 'dca' => (int) 3, 'din' => (int) 2, 'dzi' => (int) 3, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 14, 'fve' => (int) 9, 'gma' => (int) 2, 'ghi' => (int) 4, 'gra' => (int) 2, 'vvi' => (int) 1, 'han' => (int) 13, 'cav' => (int) 1, 'hma' => (int) 2, 'sun' => (int) 2, 'lal' => (int) 2, 'lonja' => (int) 12, 'lja' => (int) 1, 'lsa' => (int) 7, 'mes' => (int) 1, 'mpo' => (int) 27, 'mbi' => (int) 1, 'mco' => (int) 8, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 1, 'egut' => (int) 1, 'ama' => (int) 1, 'nta' => (int) 4, 'nnu' => (int) 2, 'oeu' => (int) 3, 'osa' => (int) 4, 'pax' => (int) 9, 'pgr' => (int) 1, 'stu' => (int) 1, 'pvu' => (int) 1, 'ptr' => (int) 4, 'ppa' => (int) 22, 'pco' => (int) 6, 'ppe' => (int) 6, 'psa' => (int) 5, 'pso' => (int) 19, 'qlo' => (int) 5, 'rch' => (int) 7, 'rsi' => (int) 20, 'sbr' => (int) 5, 'sbo' => (int) 1, 'sci' => (int) 2, 'sed' => (int) 2, 'sgi' => (int) 12, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 2, 'tar' => (int) 10, 'tha' => (int) 1, 'tca' => (int) 1, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 2, 'ugi' => (int) 1, 'vma' => (int) 5, 'vmu' => (int) 1, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb301270' $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' => 'HOM05D001460', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '433', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p22980' => 'bna', 'A01p32340' => 'bna', 'A03p42970' => 'bna', 'A05p25880' => 'bna', 'Aa31LG8G9320' => 'aar', 'Aa31LG8G9330' => 'aar', 'Aa31LG8G9340' => 'aar', 'Aa31sc221G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1034' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1528' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.829' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2222' => 'aag', 'Ah.12g058830' => 'amhyb', 'Ah.12g058840' => 'amhyb', 'AL3G37160' => 'aly', 'AL7G41310' => 'aly', 'Aqoxy5G00395' => 'aox', 'Aqoxy5G00396' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0C8NZA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5185HY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JZ1PRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MD3LS0' => 'arhy', 'AT3G22840' => 'ath', 'AT4G14690' => 'ath', 'ATR0665G054' => 'atr', 'Atru.chr4.2344' => 'acertr', 'Atru.chr4.2346' => 'acertr', 'Atru.chr4.2347' => 'acertr', 'Atru.chr4.2348' => 'acertr', 'Atru.chr4.2355' => 'acertr', 'Atru.chr4.2356' => 'acertr', 'Atru.chr4.2358' => 'acertr', 'Atru.chr4.2359' => 'acertr', 'Atru.chr4.2360' => 'acertr', 'Atru.chr4.2361' => 'acertr', 'AUR62030476' => 'cqu', 'AUR62030478' => 'cqu', 'AUR62030819' => 'cqu', 'AUR62030820' => 'cqu', 'BcaB03g14648' => 'bca', 'BcaB04g20492' => 'bca', 'BcaB06g26399' => 'bca', 'BcaC01g03416' => 'bca', 'BcaC01g03419' => 'bca', 'BcaC01g03421' => 'bca', 'BcaC01g03424' => 'bca', 'BcaC05g28012' => 'bca', 'BcaC09g49212' => 'bca', 'BcaC09g50140' => 'bca', 'BcaNung00346' => 'bca', 'BolC1t02785H' => 'bol', 'BolC1t04095H' => 'bol', 'BolC3t17545H' => 'bol', 'BolC5t32769H' => 'bol', 'BraA01t02211Z' => 'bra', 'BraA01t03359Z' => 'bra', 'BraA03t13441Z' => 'bra', 'BraA05t21476Z' => 'bra', 'C01p28420' => 'bna', 'C01p41350' => 'bna', 'C03p52750' => 'bna', 'C03p52780' => 'bna', 'C05p40270' => 'bna', 'CAN.G1437.9' => 'can', 'CANSAT78G0035' => 'cansat', 'CANSAT78G1036' => 'cansat', 'CANSAT78G2272' => 'cansat', 'CANSAT78G2478' => 'cansat', 'CARHR098700' => 'chi', 'CARHR221120' => 'chi', 'CARHR221150' => 'chi', 'Carub.0003s2297' => 'cru', 'Carub.0007s2749' => 'cru', 'Carub.0007s2750' => 'cru', 'Carub.0007s2751' => 'cru', 'Ca_10849_v3' => 'car', 'Cc03_g04300' => 'ccan', 'CDE02G3648' => 'cde', 'CDE05G0060' => 'cde', 'CDE05G0692' => 'cde', 'CDE05G2285' => 'cde', 'CDE05G2884' => 'cde', 'CDE05G3072' => 'cde', 'Cfa008439' => 'cfa', 'Cfa008441' => 'cfa', 'Cfa008443' => 'cfa', 'Cfa008448' => 'cfa', 'Ciclev10005974m.g' => 'ccl', 'Ciclev10006006m.g' => 'ccl', 'Ciclev10006775m.g' => 'ccl', 'CiPaw.02G120400' => 'cil', 'CiPaw.02G120500' => 'cil', 'CiPaw.02G120600' => 'cil', 'ClCG05G004850' => 'cla', 'COL.COLO4_21566' => 'col', 'Cpa.g.sc44.124' => 'cpa', 'Cre07.g320400' => 'cre', 'Cre07.g320450' => 'cre', 'Cre08.g384650' => 'cre', 'Cre09.g393173' => 'cre', 'Cre09.g394325' => 'cre', 'Cre14.g626750' => 'cre', 'Cre16.g679250' => 'cre', 'CsaV3_3G012890' => 'csa', 'CSS0010865' => 'camsi', 'CSS0044338' => 'camsi', 'DCAR_002366' => 'dca', 'DCAR_030687' => 'dca', 'DCAR_030688' => 'dca', 'Dinv14047' => 'din', 'Dinv14048' => 'din', 'Duzib151G0105' => 'dzi', 'Duzib151G0114' => 'dzi', 'Duzib212G1029' => 'dzi', 'ECA232G3536' => 'eca', 'ECA240G0786' => 'eca', 'ECA240G1802' => 'eca', 'ECA240G3760' => 'eca', 'ECA240G3920' => 'eca', 'EL10Ac5g12536' => 'bvu', 'EL10Ac5g12537' => 'bvu', 'EL10Ac5g12538' => 'bvu', 'Eucgr.B01004' => 'egr', 'Eucgr.B01006' => 'egr', 'Eucgr.B01007' => 'egr', 'Eucgr.B01008' => 'egr', 'Eucgr.B01895' => 'egr', 'Eucgr.B01896' => 'egr', 'FAN04G1456' => 'fan', 'FAN08G1769' => 'fan', 'FAN08G2160' => 'fan', 'FAN13G2403' => 'fan', 'FAN13G3303' => 'fan', 'FAN15G2435' => 'fan', 'FAN17G0672' => 'fan', 'FAN17G2441' => 'fan', 'FAN18G1024' => 'fan', 'FAN22G1458' => 'fan', 'FAN24G0037' => 'fan', 'FAN24G0429' => 'fan', 'FAN24G2387' => 'fan', 'FAN27G2746' => 'fan', 'FvH4_2g20400' => 'fve', 'FvH4_2g20420' => 'fve', 'FvH4_2g20430' => 'fve', 'FvH4_4g01270' => 'fve', 'FvH4_4g01290' => 'fve', 'FvH4_4g01300' => 'fve', 'FvH4_4g01310' => 'fve', 'FvH4_4g01330' => 'fve', 'FvH4_5g09070' => 'fve', 'Glyma.10G243800' => 'gma', 'Glyma.20G150600' => 'gma', 'Gohir.A09G219200' => 'ghi', 'Gohir.A09G219300' => 'ghi', 'Gohir.D09G221400' => 'ghi', 'Gohir.D09G221500' => 'ghi', 'Gorai.006G242600' => 'gra', 'Gorai.006G242700' => 'gra', 'GSVIVG01018044001' => 'vvi', 'HanXRQChr03g0083821' => 'han', 'HanXRQChr03g0083841' => 'han', 'HanXRQChr03g0083881' => 'han', 'HanXRQChr03g0083901' => 'han', 'HanXRQChr03g0083921' => 'han', 'HanXRQChr03g0085331' => 'han', 'HanXRQChr03g0085361' => 'han', 'HanXRQChr03g0085411' => 'han', 'HanXRQChr03g0085421' => 'han', 'HanXRQChr03g0085431' => 'han', 'HanXRQChr08g0221991' => 'han', 'HanXRQChr11g0336061' => 'han', 'HanXRQChr11g0336411' => 'han', 'Haze_11234' => 'cav', 'Hma1.2p1_0549F.1_g177010' => 'hma', 'Hma1.2p1_0602F.1_g187630' => 'hma', 'Hund14876' => 'sun', 'Hund14879' => 'sun', 'Lalb_Chr06g0160741' => 'lal', 'Lalb_Chr21g0304781' => 'lal', 'Lj3A726G19' => 'lonja', 'Lj3A726T23' => 'lonja', 'Lj3A726T24' => 'lonja', 'Lj3A726T25' => 'lonja', 'Lj3A727T17' => 'lonja', 'Lj3C726T0' => 'lonja', 'Lj3C726T2' => 'lonja', 'Lj3P725T35' => 'lonja', 'Lj3P727T10' => 'lonja', 'Lj3P727T12' => 'lonja', 'Lj3P727T14' => 'lonja', 'Lj5g0023109' => 'lja', 'Lj6P646T44' => 'lonja', 'Lsat_1_v5_gn_6_75760' => 'lsa', 'Lsat_1_v5_gn_6_75800' => 'lsa', 'Lsat_1_v5_gn_6_75900' => 'lsa', 'Lsat_1_v5_gn_6_76240' => 'lsa', 'Lsat_1_v5_gn_6_76441' => 'lsa', 'Lsat_1_v5_gn_6_76700' => 'lsa', 'Lsat_1_v5_gn_6_76760' => 'lsa', 'Manes.15G033100' => 'mes', 'Mapoly0004s0074' => 'mpo', 'Mapoly0004s0075' => 'mpo', 'Mapoly0004s0163' => 'mpo', 'Mapoly0004s0164' => 'mpo', 'Mapoly0021s0018' => 'mpo', 'Mapoly0041s0136' => 'mpo', 'Mapoly0041s0137' => 'mpo', 'Mapoly0041s0138' => 'mpo', 'Mapoly0041s0139' => 'mpo', 'Mapoly0041s0141' => 'mpo', 'Mapoly0041s0142' => 'mpo', 'Mapoly0041s0143' => 'mpo', 'Mapoly0041s0144' => 'mpo', 'Mapoly0041s0145' => 'mpo', 'Mapoly0047s0106' => 'mpo', 'Mapoly0047s0108' => 'mpo', 'Mapoly0050s0051' => 'mpo', 'Mapoly0050s0052' => 'mpo', 'Mapoly0050s0053' => 'mpo', 'Mapoly0058s0013' => 'mpo', 'Mapoly0091s0078' => 'mpo', 'Mapoly0091s0079' => 'mpo', 'Mapoly0091s0080' => 'mpo', 'Mapoly0091s0081' => 'mpo', 'Mapoly0278s0004' => 'mpo', 'Mapoly0278s0005' => 'mpo', 'Mapoly0278s0006' => 'mpo', 'MBI11_g30648_MAGBIO' => 'mbi', 'MCO03G194' => 'mco', 'MCO03G590' => 'mco', 'MCO07G312' => 'mco', 'MCO10G318' => 'mco', 'MCO12G244' => 'mco', 'MCO13G148' => 'mco', 'MCO13G194' => 'mco', 'MCO16G238' => 'mco', 'MD06G1134100' => 'mdo', 'MD13G1200100' => 'mdo', 'MD13G1200300' => 'mdo', 'MD13G1200600' => 'mdo', 'MD14G1150400' => 'mdo', 'MD16G1200000' => 'mdo', 'Medtr1g102570' => 'mtr', 'Medtr1g102780' => 'mtr', 'Medtr1g102800' => 'mtr', 'Medtr1g102810' => 'mtr', 'Medtr1g102830' => 'mtr', 'MELO3C006499.2' => 'cme', 'Migut.G00385' => 'egut', 'MSTRG.4063' => 'ama', 'Nitab4.5_0000090g0260' => 'nta', 'Nitab4.5_0000977g0030' => 'nta', 'Nitab4.5_0002541g0040' => 'nta', 'Nitab4.5_0007068g0040' => 'nta', 'Nn005s41408' => 'nnu', 'Nn005s41410' => 'nnu', 'Oeu010310.1' => 'oeu', 'Oeu010311.1' => 'oeu', 'Oeu043472.1' => 'oeu', 'Os01g0246400' => 'osa', 'Os04g0267950' => 'osa', 'Os07g0178700' => 'osa', 'Os07g0178800' => 'osa', 'Peaxi162Scf00316g00046' => 'pax', 'Peaxi162Scf00316g00049' => 'pax', 'Peaxi162Scf00316g00059' => 'pax', 'Peaxi162Scf00316g00328' => 'pax', 'Peaxi162Scf00316g00329' => 'pax', 'Peaxi162Scf00316g00411' => 'pax', 'Peaxi162Scf00316g00521' => 'pax', 'Peaxi162Scf00492g00068' => 'pax', 'Peaxi162Scf35631g00002' => 'pax', 'PGR142G3720' => 'pgr', 'PGSC0003DMG400006442' => 'stu', 'Phvul.007G062000' => 'pvu', 'Potri.008G157750' => 'ptr', 'Potri.008G157900' => 'ptr', 'Potri.008G158000' => 'ptr', 'Potri.008G158200' => 'ptr', 'Pp3c11_7280' => 'ppa', 'Pp3c11_7980' => 'ppa', 'Pp3c12_19450' => 'ppa', 'Pp3c14_1480' => 'ppa', 'Pp3c14_1501' => 'ppa', 'Pp3c16_4900' => 'ppa', 'Pp3c16_5010' => 'ppa', 'Pp3c16_5060' => 'ppa', 'Pp3c19_18250' => 'ppa', 'Pp3c23_8530' => 'ppa', 'Pp3c23_8550' => 'ppa', 'Pp3c24_9670' => 'ppa', 'Pp3c2_21390' => 'ppa', 'Pp3c2_31380' => 'ppa', 'Pp3c3_16620' => 'ppa', 'Pp3c3_8090' => 'ppa', 'Pp3c3_8110' => 'ppa', 'Pp3c3_8130' => 'ppa', 'Pp3c3_8150' => 'ppa', 'Pp3c4_14320' => 'ppa', 'Pp3c6_2560' => 'ppa', 'Pp3c9_16700' => 'ppa', 'PRCOL_00000234' => 'pco', 'PRCOL_00000235' => 'pco', 'PRCOL_00000777' => 'pco', 'PRCOL_00002344' => 'pco', 'PRCOL_00002372' => 'pco', 'PRCOL_00006120' => 'pco', 'Prupe.1G021400' => 'ppe', 'Prupe.1G021500' => 'ppe', 'Prupe.1G021600' => 'ppe', 'Prupe.1G021700' => 'ppe', 'Prupe.1G021800' => 'ppe', 'Prupe.5G145100' => 'ppe', 'Psat6g204040' => 'psa', 'Psat6g204800' => 'psa', 'Psat6g204920' => 'psa', 'Psat6g204960' => 'psa', 'Psat6g205080' => 'psa', 'PSO017G0271' => 'pso', 'PSO017G1276' => 'pso', 'PSO017G1429' => 'pso', 'PSO017G1861' => 'pso', 'PSO017G2787' => 'pso', 'PSO017G4466' => 'pso', 'PSO017G5118' => 'pso', 'PSO017G5420' => 'pso', 'PSO063G3678' => 'pso', 'PSO210G0546' => 'pso', 'PSO317G0001' => 'pso', 'PSO357G0512' => 'pso', 'PSO478G2682' => 'pso', 'PSO647G0001' => 'pso', 'PSO675G0001' => 'pso', 'PSO675G2699' => 'pso', 'PSO675G2849' => 'pso', 'PSO675G4991' => 'pso', 'PSO689G0001' => 'pso', 'QL06p000916' => 'qlo', 'QL06p000921' => 'qlo', 'QL06p001398' => 'qlo', 'QL06p001407' => 'qlo', 'QL06p002031' => 'qlo', 'RcHm_v2.0_Chr4g0387791' => 'rch', 'RcHm_v2.0_Chr4g0387801' => 'rch', 'RcHm_v2.0_Chr6g0286501' => 'rch', 'RcHm_v2.0_Chr6g0286511' => 'rch', 'RcHm_v2.0_Chr6g0286521' => 'rch', 'RcHm_v2.0_Chr6g0286531' => 'rch', 'RcHm_v2.0_Chr7g0189141' => 'rch', 'Rhsim02G0028700' => 'rsi', 'Rhsim02G0028800' => 'rsi', 'Rhsim02G0028900' => 'rsi', 'Rhsim02G0029000' => 'rsi', 'Rhsim02G0029100' => 'rsi', 'Rhsim02G0029200' => 'rsi', 'Rhsim02G0029300' => 'rsi', 'Rhsim02G0029400' => 'rsi', 'Rhsim02G0029500' => 'rsi', 'Rhsim02G0029600' => 'rsi', 'RhsimUnG0024000' => 'rsi', 'RhsimUnG0024100' => 'rsi', 'RhsimUnG0024200' => 'rsi', 'RhsimUnG0024300' => 'rsi', 'RhsimUnG0024400' => 'rsi', 'RhsimUnG0024500' => 'rsi', 'RhsimUnG0024700' => 'rsi', 'RhsimUnG0024800' => 'rsi', 'RhsimUnG0024900' => 'rsi', 'RhsimUnG0025100' => 'rsi', 'Sabra08G0120200' => 'sbr', 'Sabra08G0120300' => 'sbr', 'Sabra08G0120500' => 'sbr', 'Sabra08G0120600' => 'sbr', 'Sabra10G0158900' => 'sbr', 'SalBow2G3492' => 'sbo', 'Sc13g0004760' => 'sci', 'Sc13g0004770' => 'sci', 'Sed0003417' => 'sed', 'Sed0019750' => 'sed', 'SEGI_03419' => 'sgi', 'SEGI_05907' => 'sgi', 'SEGI_10682' => 'sgi', 'SEGI_13528' => 'sgi', 'SEGI_16081' => 'sgi', 'SEGI_19370' => 'sgi', 'SEGI_21015' => 'sgi', 'SEGI_21944' => 'sgi', 'SEGI_32906' => 'sgi', 'SEGI_33093' => 'sgi', 'SEGI_36110' => 'sgi', 'SEGI_40397' => 'sgi', 'SGA_v2.0_scaffold191G40426' => 'sas', 'SGA_v2.0_scaffold353G49717' => 'sas', 'SGA_v2.0_scaffold50G18550' => 'sas', 'SMO119G0173' => 'smo', 'SMO172G0002' => 'smo', 'Solyc09g082690.3' => 'sly', 'Solyc09g082700.2' => 'sly', 'Sopen09g031550' => 'spe', 'Sopen09g031560' => 'spe', 'Sp3g20540' => 'spa', 'Sp7g07580' => 'spa', 'TAR134G0002' => 'tar', 'TAR236G0001' => 'tar', 'TAR365G0892' => 'tar', 'TAR636G0166' => 'tar', 'TAR636G0646' => 'tar', 'TAR636G0869' => 'tar', 'TAR636G1317' => 'tar', 'TAR636G1744' => 'tar', 'TAR636G3358' => 'tar', 'TAR636G3436' => 'tar', 'THA.LOC104803047' => 'tha', 'Thecc.04G238900' => 'tca', 'Thhalv10021557m.g' => 'esa', 'Thhalv10026318m.g' => 'esa', 'Thhalv10026335m.g' => 'esa', 'TPR.G17433' => 'tpr', 'TPR.G18915' => 'tpr', 'TPR.G26125' => 'tpr', 'TWI09G0677' => 'twi', 'TWI73G0287' => 'twi', 'unitig_748.g8326' => 'ugi', 'vmacro15370' => 'vma', 'vmacro15371' => 'vma', 'vmacro15372' => 'vma', 'vmacro15373' => 'vma', 'vmacro15374' => 'vma', 'VMungo0720G2826' => 'vmu', 'Zm00001eb116960' => 'zma', 'Zm00001eb301260' => 'zma', 'Zm00001eb301270' => 'zma' ), 'gf_id' => 'HOM05D001460', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001460' ), 'data_identifier' => 'HOM05D001460', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001460', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '433', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p22980' => 'bna', 'A01p32340' => 'bna', 'A03p42970' => 'bna', 'A05p25880' => 'bna', 'Aa31LG8G9320' => 'aar', 'Aa31LG8G9330' => 'aar', 'Aa31LG8G9340' => 'aar', 'Aa31sc221G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1034' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1528' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.829' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2222' => 'aag', 'Ah.12g058830' => 'amhyb', 'Ah.12g058840' => 'amhyb', 'AL3G37160' => 'aly', 'AL7G41310' => 'aly', 'Aqoxy5G00395' => 'aox', 'Aqoxy5G00396' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0C8NZA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5185HY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JZ1PRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MD3LS0' => 'arhy', 'AT3G22840' => 'ath', 'AT4G14690' => 'ath', 'ATR0665G054' => 'atr', 'Atru.chr4.2344' => 'acertr', 'Atru.chr4.2346' => 'acertr', 'Atru.chr4.2347' => 'acertr', 'Atru.chr4.2348' => 'acertr', 'Atru.chr4.2355' => 'acertr', 'Atru.chr4.2356' => 'acertr', 'Atru.chr4.2358' => 'acertr', 'Atru.chr4.2359' => 'acertr', 'Atru.chr4.2360' => 'acertr', 'Atru.chr4.2361' => 'acertr', 'AUR62030476' => 'cqu', 'AUR62030478' => 'cqu', 'AUR62030819' => 'cqu', 'AUR62030820' => 'cqu', 'BcaB03g14648' => 'bca', 'BcaB04g20492' => 'bca', 'BcaB06g26399' => 'bca', 'BcaC01g03416' => 'bca', 'BcaC01g03419' => 'bca', 'BcaC01g03421' => 'bca', 'BcaC01g03424' => 'bca', 'BcaC05g28012' => 'bca', 'BcaC09g49212' => 'bca', 'BcaC09g50140' => 'bca', 'BcaNung00346' => 'bca', 'BolC1t02785H' => 'bol', 'BolC1t04095H' => 'bol', 'BolC3t17545H' => 'bol', 'BolC5t32769H' => 'bol', 'BraA01t02211Z' => 'bra', 'BraA01t03359Z' => 'bra', 'BraA03t13441Z' => 'bra', 'BraA05t21476Z' => 'bra', 'C01p28420' => 'bna', 'C01p41350' => 'bna', 'C03p52750' => 'bna', 'C03p52780' => 'bna', 'C05p40270' => 'bna', 'CAN.G1437.9' => 'can', 'CANSAT78G0035' => 'cansat', 'CANSAT78G1036' => 'cansat', 'CANSAT78G2272' => 'cansat', 'CANSAT78G2478' => 'cansat', 'CARHR098700' => 'chi', 'CARHR221120' => 'chi', 'CARHR221150' => 'chi', 'Carub.0003s2297' => 'cru', 'Carub.0007s2749' => 'cru', 'Carub.0007s2750' => 'cru', 'Carub.0007s2751' => 'cru', 'Ca_10849_v3' => 'car', 'Cc03_g04300' => 'ccan', 'CDE02G3648' => 'cde', 'CDE05G0060' => 'cde', 'CDE05G0692' => 'cde', 'CDE05G2285' => 'cde', 'CDE05G2884' => 'cde', 'CDE05G3072' => 'cde', 'Cfa008439' => 'cfa', 'Cfa008441' => 'cfa', 'Cfa008443' => 'cfa', 'Cfa008448' => 'cfa', 'Ciclev10005974m.g' => 'ccl', 'Ciclev10006006m.g' => 'ccl', 'Ciclev10006775m.g' => 'ccl', 'CiPaw.02G120400' => 'cil', 'CiPaw.02G120500' => 'cil', 'CiPaw.02G120600' => 'cil', 'ClCG05G004850' => 'cla', 'COL.COLO4_21566' => 'col', 'Cpa.g.sc44.124' => 'cpa', 'Cre07.g320400' => 'cre', 'Cre07.g320450' => 'cre', 'Cre08.g384650' => 'cre', 'Cre09.g393173' => 'cre', 'Cre09.g394325' => 'cre', 'Cre14.g626750' => 'cre', 'Cre16.g679250' => 'cre', 'CsaV3_3G012890' => 'csa', 'CSS0010865' => 'camsi', 'CSS0044338' => 'camsi', 'DCAR_002366' => 'dca', 'DCAR_030687' => 'dca', 'DCAR_030688' => 'dca', 'Dinv14047' => 'din', 'Dinv14048' => 'din', 'Duzib151G0105' => 'dzi', 'Duzib151G0114' => 'dzi', 'Duzib212G1029' => 'dzi', 'ECA232G3536' => 'eca', 'ECA240G0786' => 'eca', 'ECA240G1802' => 'eca', 'ECA240G3760' => 'eca', 'ECA240G3920' => 'eca', 'EL10Ac5g12536' => 'bvu', 'EL10Ac5g12537' => 'bvu', 'EL10Ac5g12538' => 'bvu', 'Eucgr.B01004' => 'egr', 'Eucgr.B01006' => 'egr', 'Eucgr.B01007' => 'egr', 'Eucgr.B01008' => 'egr', 'Eucgr.B01895' => 'egr', 'Eucgr.B01896' => 'egr', 'FAN04G1456' => 'fan', 'FAN08G1769' => 'fan', 'FAN08G2160' => 'fan', 'FAN13G2403' => 'fan', 'FAN13G3303' => 'fan', 'FAN15G2435' => 'fan', 'FAN17G0672' => 'fan', 'FAN17G2441' => 'fan', 'FAN18G1024' => 'fan', 'FAN22G1458' => 'fan', 'FAN24G0037' => 'fan', 'FAN24G0429' => 'fan', 'FAN24G2387' => 'fan', 'FAN27G2746' => 'fan', 'FvH4_2g20400' => 'fve', 'FvH4_2g20420' => 'fve', 'FvH4_2g20430' => 'fve', 'FvH4_4g01270' => 'fve', 'FvH4_4g01290' => 'fve', 'FvH4_4g01300' => 'fve', 'FvH4_4g01310' => 'fve', 'FvH4_4g01330' => 'fve', 'FvH4_5g09070' => 'fve', 'Glyma.10G243800' => 'gma', 'Glyma.20G150600' => 'gma', 'Gohir.A09G219200' => 'ghi', 'Gohir.A09G219300' => 'ghi', 'Gohir.D09G221400' => 'ghi', 'Gohir.D09G221500' => 'ghi', 'Gorai.006G242600' => 'gra', 'Gorai.006G242700' => 'gra', 'GSVIVG01018044001' => 'vvi', 'HanXRQChr03g0083821' => 'han', 'HanXRQChr03g0083841' => 'han', 'HanXRQChr03g0083881' => 'han', 'HanXRQChr03g0083901' => 'han', 'HanXRQChr03g0083921' => 'han', 'HanXRQChr03g0085331' => 'han', 'HanXRQChr03g0085361' => 'han', 'HanXRQChr03g0085411' => 'han', 'HanXRQChr03g0085421' => 'han', 'HanXRQChr03g0085431' => 'han', 'HanXRQChr08g0221991' => 'han', 'HanXRQChr11g0336061' => 'han', 'HanXRQChr11g0336411' => 'han', 'Haze_11234' => 'cav', 'Hma1.2p1_0549F.1_g177010' => 'hma', 'Hma1.2p1_0602F.1_g187630' => 'hma', 'Hund14876' => 'sun', 'Hund14879' => 'sun', 'Lalb_Chr06g0160741' => 'lal', 'Lalb_Chr21g0304781' => 'lal', 'Lj3A726G19' => 'lonja', 'Lj3A726T23' => 'lonja', 'Lj3A726T24' => 'lonja', 'Lj3A726T25' => 'lonja', 'Lj3A727T17' => 'lonja', 'Lj3C726T0' => 'lonja', 'Lj3C726T2' => 'lonja', 'Lj3P725T35' => 'lonja', 'Lj3P727T10' => 'lonja', 'Lj3P727T12' => 'lonja', 'Lj3P727T14' => 'lonja', 'Lj5g0023109' => 'lja', 'Lj6P646T44' => 'lonja', 'Lsat_1_v5_gn_6_75760' => 'lsa', 'Lsat_1_v5_gn_6_75800' => 'lsa', 'Lsat_1_v5_gn_6_75900' => 'lsa', 'Lsat_1_v5_gn_6_76240' => 'lsa', 'Lsat_1_v5_gn_6_76441' => 'lsa', 'Lsat_1_v5_gn_6_76700' => 'lsa', 'Lsat_1_v5_gn_6_76760' => 'lsa', 'Manes.15G033100' => 'mes', 'Mapoly0004s0074' => 'mpo', 'Mapoly0004s0075' => 'mpo', 'Mapoly0004s0163' => 'mpo', 'Mapoly0004s0164' => 'mpo', 'Mapoly0021s0018' => 'mpo', 'Mapoly0041s0136' => 'mpo', 'Mapoly0041s0137' => 'mpo', 'Mapoly0041s0138' => 'mpo', 'Mapoly0041s0139' => 'mpo', 'Mapoly0041s0141' => 'mpo', 'Mapoly0041s0142' => 'mpo', 'Mapoly0041s0143' => 'mpo', 'Mapoly0041s0144' => 'mpo', 'Mapoly0041s0145' => 'mpo', 'Mapoly0047s0106' => 'mpo', 'Mapoly0047s0108' => 'mpo', 'Mapoly0050s0051' => 'mpo', 'Mapoly0050s0052' => 'mpo', 'Mapoly0050s0053' => 'mpo', 'Mapoly0058s0013' => 'mpo', 'Mapoly0091s0078' => 'mpo', 'Mapoly0091s0079' => 'mpo', 'Mapoly0091s0080' => 'mpo', 'Mapoly0091s0081' => 'mpo', 'Mapoly0278s0004' => 'mpo', 'Mapoly0278s0005' => 'mpo', 'Mapoly0278s0006' => 'mpo', 'MBI11_g30648_MAGBIO' => 'mbi', 'MCO03G194' => 'mco', 'MCO03G590' => 'mco', 'MCO07G312' => 'mco', 'MCO10G318' => 'mco', 'MCO12G244' => 'mco', 'MCO13G148' => 'mco', 'MCO13G194' => 'mco', 'MCO16G238' => 'mco', 'MD06G1134100' => 'mdo', 'MD13G1200100' => 'mdo', 'MD13G1200300' => 'mdo', 'MD13G1200600' => 'mdo', 'MD14G1150400' => 'mdo', 'MD16G1200000' => 'mdo', 'Medtr1g102570' => 'mtr', 'Medtr1g102780' => 'mtr', 'Medtr1g102800' => 'mtr', 'Medtr1g102810' => 'mtr', 'Medtr1g102830' => 'mtr', 'MELO3C006499.2' => 'cme', 'Migut.G00385' => 'egut', 'MSTRG.4063' => 'ama', 'Nitab4.5_0000090g0260' => 'nta', 'Nitab4.5_0000977g0030' => 'nta', 'Nitab4.5_0002541g0040' => 'nta', 'Nitab4.5_0007068g0040' => 'nta', 'Nn005s41408' => 'nnu', 'Nn005s41410' => 'nnu', 'Oeu010310.1' => 'oeu', 'Oeu010311.1' => 'oeu', 'Oeu043472.1' => 'oeu', 'Os01g0246400' => 'osa', 'Os04g0267950' => 'osa', 'Os07g0178700' => 'osa', 'Os07g0178800' => 'osa', 'Peaxi162Scf00316g00046' => 'pax', 'Peaxi162Scf00316g00049' => 'pax', 'Peaxi162Scf00316g00059' => 'pax', 'Peaxi162Scf00316g00328' => 'pax', 'Peaxi162Scf00316g00329' => 'pax', 'Peaxi162Scf00316g00411' => 'pax', 'Peaxi162Scf00316g00521' => 'pax', 'Peaxi162Scf00492g00068' => 'pax', 'Peaxi162Scf35631g00002' => 'pax', 'PGR142G3720' => 'pgr', 'PGSC0003DMG400006442' => 'stu', 'Phvul.007G062000' => 'pvu', 'Potri.008G157750' => 'ptr', 'Potri.008G157900' => 'ptr', 'Potri.008G158000' => 'ptr', 'Potri.008G158200' => 'ptr', 'Pp3c11_7280' => 'ppa', 'Pp3c11_7980' => 'ppa', 'Pp3c12_19450' => 'ppa', 'Pp3c14_1480' => 'ppa', 'Pp3c14_1501' => 'ppa', 'Pp3c16_4900' => 'ppa', 'Pp3c16_5010' => 'ppa', 'Pp3c16_5060' => 'ppa', 'Pp3c19_18250' => 'ppa', 'Pp3c23_8530' => 'ppa', 'Pp3c23_8550' => 'ppa', 'Pp3c24_9670' => 'ppa', 'Pp3c2_21390' => 'ppa', 'Pp3c2_31380' => 'ppa', 'Pp3c3_16620' => 'ppa', 'Pp3c3_8090' => 'ppa', 'Pp3c3_8110' => 'ppa', 'Pp3c3_8130' => 'ppa', 'Pp3c3_8150' => 'ppa', 'Pp3c4_14320' => 'ppa', 'Pp3c6_2560' => 'ppa', 'Pp3c9_16700' => 'ppa', 'PRCOL_00000234' => 'pco', 'PRCOL_00000235' => 'pco', 'PRCOL_00000777' => 'pco', 'PRCOL_00002344' => 'pco', 'PRCOL_00002372' => 'pco', 'PRCOL_00006120' => 'pco', 'Prupe.1G021400' => 'ppe', 'Prupe.1G021500' => 'ppe', 'Prupe.1G021600' => 'ppe', 'Prupe.1G021700' => 'ppe', 'Prupe.1G021800' => 'ppe', 'Prupe.5G145100' => 'ppe', 'Psat6g204040' => 'psa', 'Psat6g204800' => 'psa', 'Psat6g204920' => 'psa', 'Psat6g204960' => 'psa', 'Psat6g205080' => 'psa', 'PSO017G0271' => 'pso', 'PSO017G1276' => 'pso', 'PSO017G1429' => 'pso', 'PSO017G1861' => 'pso', 'PSO017G2787' => 'pso', 'PSO017G4466' => 'pso', 'PSO017G5118' => 'pso', 'PSO017G5420' => 'pso', 'PSO063G3678' => 'pso', 'PSO210G0546' => 'pso', 'PSO317G0001' => 'pso', 'PSO357G0512' => 'pso', 'PSO478G2682' => 'pso', 'PSO647G0001' => 'pso', 'PSO675G0001' => 'pso', 'PSO675G2699' => 'pso', 'PSO675G2849' => 'pso', 'PSO675G4991' => 'pso', 'PSO689G0001' => 'pso', 'QL06p000916' => 'qlo', 'QL06p000921' => 'qlo', 'QL06p001398' => 'qlo', 'QL06p001407' => 'qlo', 'QL06p002031' => 'qlo', 'RcHm_v2.0_Chr4g0387791' => 'rch', 'RcHm_v2.0_Chr4g0387801' => 'rch', 'RcHm_v2.0_Chr6g0286501' => 'rch', 'RcHm_v2.0_Chr6g0286511' => 'rch', 'RcHm_v2.0_Chr6g0286521' => 'rch', 'RcHm_v2.0_Chr6g0286531' => 'rch', 'RcHm_v2.0_Chr7g0189141' => 'rch', 'Rhsim02G0028700' => 'rsi', 'Rhsim02G0028800' => 'rsi', 'Rhsim02G0028900' => 'rsi', 'Rhsim02G0029000' => 'rsi', 'Rhsim02G0029100' => 'rsi', 'Rhsim02G0029200' => 'rsi', 'Rhsim02G0029300' => 'rsi', 'Rhsim02G0029400' => 'rsi', 'Rhsim02G0029500' => 'rsi', 'Rhsim02G0029600' => 'rsi', 'RhsimUnG0024000' => 'rsi', 'RhsimUnG0024100' => 'rsi', 'RhsimUnG0024200' => 'rsi', 'RhsimUnG0024300' => 'rsi', 'RhsimUnG0024400' => 'rsi', 'RhsimUnG0024500' => 'rsi', 'RhsimUnG0024700' => 'rsi', 'RhsimUnG0024800' => 'rsi', 'RhsimUnG0024900' => 'rsi', 'RhsimUnG0025100' => 'rsi', 'Sabra08G0120200' => 'sbr', 'Sabra08G0120300' => 'sbr', 'Sabra08G0120500' => 'sbr', 'Sabra08G0120600' => 'sbr', 'Sabra10G0158900' => 'sbr', 'SalBow2G3492' => 'sbo', 'Sc13g0004760' => 'sci', 'Sc13g0004770' => 'sci', 'Sed0003417' => 'sed', 'Sed0019750' => 'sed', 'SEGI_03419' => 'sgi', 'SEGI_05907' => 'sgi', 'SEGI_10682' => 'sgi', 'SEGI_13528' => 'sgi', 'SEGI_16081' => 'sgi', 'SEGI_19370' => 'sgi', 'SEGI_21015' => 'sgi', 'SEGI_21944' => 'sgi', 'SEGI_32906' => 'sgi', 'SEGI_33093' => 'sgi', 'SEGI_36110' => 'sgi', 'SEGI_40397' => 'sgi', 'SGA_v2.0_scaffold191G40426' => 'sas', 'SGA_v2.0_scaffold353G49717' => 'sas', 'SGA_v2.0_scaffold50G18550' => 'sas', 'SMO119G0173' => 'smo', 'SMO172G0002' => 'smo', 'Solyc09g082690.3' => 'sly', 'Solyc09g082700.2' => 'sly', 'Sopen09g031550' => 'spe', 'Sopen09g031560' => 'spe', 'Sp3g20540' => 'spa', 'Sp7g07580' => 'spa', 'TAR134G0002' => 'tar', 'TAR236G0001' => 'tar', 'TAR365G0892' => 'tar', 'TAR636G0166' => 'tar', 'TAR636G0646' => 'tar', 'TAR636G0869' => 'tar', 'TAR636G1317' => 'tar', 'TAR636G1744' => 'tar', 'TAR636G3358' => 'tar', 'TAR636G3436' => 'tar', 'THA.LOC104803047' => 'tha', 'Thecc.04G238900' => 'tca', 'Thhalv10021557m.g' => 'esa', 'Thhalv10026318m.g' => 'esa', 'Thhalv10026335m.g' => 'esa', 'TPR.G17433' => 'tpr', 'TPR.G18915' => 'tpr', 'TPR.G26125' => 'tpr', 'TWI09G0677' => 'twi', 'TWI73G0287' => 'twi', 'unitig_748.g8326' => 'ugi', 'vmacro15370' => 'vma', 'vmacro15371' => 'vma', 'vmacro15372' => 'vma', 'vmacro15373' => 'vma', 'vmacro15374' => 'vma', 'VMungo0720G2826' => 'vmu', 'Zm00001eb116960' => 'zma', 'Zm00001eb301260' => 'zma', 'Zm00001eb301270' => 'zma' ) $gf_id = 'HOM05D001460' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001460' ) $data_identifier = 'HOM05D001460' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 4, 'aag' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 2, 'aox' => (int) 2, 'arhy' => (int) 4, 'ath' => (int) 2, 'atr' => (int) 1, 'acertr' => (int) 10, 'cqu' => (int) 4, 'bca' => (int) 11, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 1, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 1, 'ccan' => (int) 1, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 1, 'col' => (int) 1, 'cpa' => (int) 1, 'cre' => (int) 7, 'csa' => (int) 1, 'camsi' => (int) 2, 'dca' => (int) 3, 'din' => (int) 2, 'dzi' => (int) 3, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 14, 'fve' => (int) 9, 'gma' => (int) 2, 'ghi' => (int) 4, 'gra' => (int) 2, 'vvi' => (int) 1, 'han' => (int) 13, 'cav' => (int) 1, 'hma' => (int) 2, 'sun' => (int) 2, 'lal' => (int) 2, 'lonja' => (int) 12, 'lja' => (int) 1, 'lsa' => (int) 7, 'mes' => (int) 1, 'mpo' => (int) 27, 'mbi' => (int) 1, 'mco' => (int) 8, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 1, 'egut' => (int) 1, 'ama' => (int) 1, 'nta' => (int) 4, 'nnu' => (int) 2, 'oeu' => (int) 3, 'osa' => (int) 4, 'pax' => (int) 9, 'pgr' => (int) 1, 'stu' => (int) 1, 'pvu' => (int) 1, 'ptr' => (int) 4, 'ppa' => (int) 22, 'pco' => (int) 6, 'ppe' => (int) 6, 'psa' => (int) 5, 'pso' => (int) 19, 'qlo' => (int) 5, 'rch' => (int) 7, 'rsi' => (int) 20, 'sbr' => (int) 5, 'sbo' => (int) 1, 'sci' => (int) 2, 'sed' => (int) 2, 'sgi' => (int) 12, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 2, 'tar' => (int) 10, 'tha' => (int) 1, 'tca' => (int) 1, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 2, 'ugi' => (int) 1, 'vma' => (int) 5, 'vmu' => (int) 1, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb301270' $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' => 'HOM05D001460', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '433', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p22980' => 'bna', 'A01p32340' => 'bna', 'A03p42970' => 'bna', 'A05p25880' => 'bna', 'Aa31LG8G9320' => 'aar', 'Aa31LG8G9330' => 'aar', 'Aa31LG8G9340' => 'aar', 'Aa31sc221G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1034' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1528' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.829' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2222' => 'aag', 'Ah.12g058830' => 'amhyb', 'Ah.12g058840' => 'amhyb', 'AL3G37160' => 'aly', 'AL7G41310' => 'aly', 'Aqoxy5G00395' => 'aox', 'Aqoxy5G00396' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0C8NZA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5185HY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JZ1PRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MD3LS0' => 'arhy', 'AT3G22840' => 'ath', 'AT4G14690' => 'ath', 'ATR0665G054' => 'atr', 'Atru.chr4.2344' => 'acertr', 'Atru.chr4.2346' => 'acertr', 'Atru.chr4.2347' => 'acertr', 'Atru.chr4.2348' => 'acertr', 'Atru.chr4.2355' => 'acertr', 'Atru.chr4.2356' => 'acertr', 'Atru.chr4.2358' => 'acertr', 'Atru.chr4.2359' => 'acertr', 'Atru.chr4.2360' => 'acertr', 'Atru.chr4.2361' => 'acertr', 'AUR62030476' => 'cqu', 'AUR62030478' => 'cqu', 'AUR62030819' => 'cqu', 'AUR62030820' => 'cqu', 'BcaB03g14648' => 'bca', 'BcaB04g20492' => 'bca', 'BcaB06g26399' => 'bca', 'BcaC01g03416' => 'bca', 'BcaC01g03419' => 'bca', 'BcaC01g03421' => 'bca', 'BcaC01g03424' => 'bca', 'BcaC05g28012' => 'bca', 'BcaC09g49212' => 'bca', 'BcaC09g50140' => 'bca', 'BcaNung00346' => 'bca', 'BolC1t02785H' => 'bol', 'BolC1t04095H' => 'bol', 'BolC3t17545H' => 'bol', 'BolC5t32769H' => 'bol', 'BraA01t02211Z' => 'bra', 'BraA01t03359Z' => 'bra', 'BraA03t13441Z' => 'bra', 'BraA05t21476Z' => 'bra', 'C01p28420' => 'bna', 'C01p41350' => 'bna', 'C03p52750' => 'bna', 'C03p52780' => 'bna', 'C05p40270' => 'bna', 'CAN.G1437.9' => 'can', 'CANSAT78G0035' => 'cansat', 'CANSAT78G1036' => 'cansat', 'CANSAT78G2272' => 'cansat', 'CANSAT78G2478' => 'cansat', 'CARHR098700' => 'chi', 'CARHR221120' => 'chi', 'CARHR221150' => 'chi', 'Carub.0003s2297' => 'cru', 'Carub.0007s2749' => 'cru', 'Carub.0007s2750' => 'cru', 'Carub.0007s2751' => 'cru', 'Ca_10849_v3' => 'car', 'Cc03_g04300' => 'ccan', 'CDE02G3648' => 'cde', 'CDE05G0060' => 'cde', 'CDE05G0692' => 'cde', 'CDE05G2285' => 'cde', 'CDE05G2884' => 'cde', 'CDE05G3072' => 'cde', 'Cfa008439' => 'cfa', 'Cfa008441' => 'cfa', 'Cfa008443' => 'cfa', 'Cfa008448' => 'cfa', 'Ciclev10005974m.g' => 'ccl', 'Ciclev10006006m.g' => 'ccl', 'Ciclev10006775m.g' => 'ccl', 'CiPaw.02G120400' => 'cil', 'CiPaw.02G120500' => 'cil', 'CiPaw.02G120600' => 'cil', 'ClCG05G004850' => 'cla', 'COL.COLO4_21566' => 'col', 'Cpa.g.sc44.124' => 'cpa', 'Cre07.g320400' => 'cre', 'Cre07.g320450' => 'cre', 'Cre08.g384650' => 'cre', 'Cre09.g393173' => 'cre', 'Cre09.g394325' => 'cre', 'Cre14.g626750' => 'cre', 'Cre16.g679250' => 'cre', 'CsaV3_3G012890' => 'csa', 'CSS0010865' => 'camsi', 'CSS0044338' => 'camsi', 'DCAR_002366' => 'dca', 'DCAR_030687' => 'dca', 'DCAR_030688' => 'dca', 'Dinv14047' => 'din', 'Dinv14048' => 'din', 'Duzib151G0105' => 'dzi', 'Duzib151G0114' => 'dzi', 'Duzib212G1029' => 'dzi', 'ECA232G3536' => 'eca', 'ECA240G0786' => 'eca', 'ECA240G1802' => 'eca', 'ECA240G3760' => 'eca', 'ECA240G3920' => 'eca', 'EL10Ac5g12536' => 'bvu', 'EL10Ac5g12537' => 'bvu', 'EL10Ac5g12538' => 'bvu', 'Eucgr.B01004' => 'egr', 'Eucgr.B01006' => 'egr', 'Eucgr.B01007' => 'egr', 'Eucgr.B01008' => 'egr', 'Eucgr.B01895' => 'egr', 'Eucgr.B01896' => 'egr', 'FAN04G1456' => 'fan', 'FAN08G1769' => 'fan', 'FAN08G2160' => 'fan', 'FAN13G2403' => 'fan', 'FAN13G3303' => 'fan', 'FAN15G2435' => 'fan', 'FAN17G0672' => 'fan', 'FAN17G2441' => 'fan', 'FAN18G1024' => 'fan', 'FAN22G1458' => 'fan', 'FAN24G0037' => 'fan', 'FAN24G0429' => 'fan', 'FAN24G2387' => 'fan', 'FAN27G2746' => 'fan', 'FvH4_2g20400' => 'fve', 'FvH4_2g20420' => 'fve', 'FvH4_2g20430' => 'fve', 'FvH4_4g01270' => 'fve', 'FvH4_4g01290' => 'fve', 'FvH4_4g01300' => 'fve', 'FvH4_4g01310' => 'fve', 'FvH4_4g01330' => 'fve', 'FvH4_5g09070' => 'fve', 'Glyma.10G243800' => 'gma', 'Glyma.20G150600' => 'gma', 'Gohir.A09G219200' => 'ghi', 'Gohir.A09G219300' => 'ghi', 'Gohir.D09G221400' => 'ghi', 'Gohir.D09G221500' => 'ghi', 'Gorai.006G242600' => 'gra', 'Gorai.006G242700' => 'gra', 'GSVIVG01018044001' => 'vvi', 'HanXRQChr03g0083821' => 'han', 'HanXRQChr03g0083841' => 'han', 'HanXRQChr03g0083881' => 'han', 'HanXRQChr03g0083901' => 'han', 'HanXRQChr03g0083921' => 'han', 'HanXRQChr03g0085331' => 'han', 'HanXRQChr03g0085361' => 'han', 'HanXRQChr03g0085411' => 'han', 'HanXRQChr03g0085421' => 'han', 'HanXRQChr03g0085431' => 'han', 'HanXRQChr08g0221991' => 'han', 'HanXRQChr11g0336061' => 'han', 'HanXRQChr11g0336411' => 'han', 'Haze_11234' => 'cav', 'Hma1.2p1_0549F.1_g177010' => 'hma', 'Hma1.2p1_0602F.1_g187630' => 'hma', 'Hund14876' => 'sun', 'Hund14879' => 'sun', 'Lalb_Chr06g0160741' => 'lal', 'Lalb_Chr21g0304781' => 'lal', 'Lj3A726G19' => 'lonja', 'Lj3A726T23' => 'lonja', 'Lj3A726T24' => 'lonja', 'Lj3A726T25' => 'lonja', 'Lj3A727T17' => 'lonja', 'Lj3C726T0' => 'lonja', 'Lj3C726T2' => 'lonja', 'Lj3P725T35' => 'lonja', 'Lj3P727T10' => 'lonja', 'Lj3P727T12' => 'lonja', 'Lj3P727T14' => 'lonja', 'Lj5g0023109' => 'lja', 'Lj6P646T44' => 'lonja', 'Lsat_1_v5_gn_6_75760' => 'lsa', 'Lsat_1_v5_gn_6_75800' => 'lsa', 'Lsat_1_v5_gn_6_75900' => 'lsa', 'Lsat_1_v5_gn_6_76240' => 'lsa', 'Lsat_1_v5_gn_6_76441' => 'lsa', 'Lsat_1_v5_gn_6_76700' => 'lsa', 'Lsat_1_v5_gn_6_76760' => 'lsa', 'Manes.15G033100' => 'mes', 'Mapoly0004s0074' => 'mpo', 'Mapoly0004s0075' => 'mpo', 'Mapoly0004s0163' => 'mpo', 'Mapoly0004s0164' => 'mpo', 'Mapoly0021s0018' => 'mpo', 'Mapoly0041s0136' => 'mpo', 'Mapoly0041s0137' => 'mpo', 'Mapoly0041s0138' => 'mpo', 'Mapoly0041s0139' => 'mpo', 'Mapoly0041s0141' => 'mpo', 'Mapoly0041s0142' => 'mpo', 'Mapoly0041s0143' => 'mpo', 'Mapoly0041s0144' => 'mpo', 'Mapoly0041s0145' => 'mpo', 'Mapoly0047s0106' => 'mpo', 'Mapoly0047s0108' => 'mpo', 'Mapoly0050s0051' => 'mpo', 'Mapoly0050s0052' => 'mpo', 'Mapoly0050s0053' => 'mpo', 'Mapoly0058s0013' => 'mpo', 'Mapoly0091s0078' => 'mpo', 'Mapoly0091s0079' => 'mpo', 'Mapoly0091s0080' => 'mpo', 'Mapoly0091s0081' => 'mpo', 'Mapoly0278s0004' => 'mpo', 'Mapoly0278s0005' => 'mpo', 'Mapoly0278s0006' => 'mpo', 'MBI11_g30648_MAGBIO' => 'mbi', 'MCO03G194' => 'mco', 'MCO03G590' => 'mco', 'MCO07G312' => 'mco', 'MCO10G318' => 'mco', 'MCO12G244' => 'mco', 'MCO13G148' => 'mco', 'MCO13G194' => 'mco', 'MCO16G238' => 'mco', 'MD06G1134100' => 'mdo', 'MD13G1200100' => 'mdo', 'MD13G1200300' => 'mdo', 'MD13G1200600' => 'mdo', 'MD14G1150400' => 'mdo', 'MD16G1200000' => 'mdo', 'Medtr1g102570' => 'mtr', 'Medtr1g102780' => 'mtr', 'Medtr1g102800' => 'mtr', 'Medtr1g102810' => 'mtr', 'Medtr1g102830' => 'mtr', 'MELO3C006499.2' => 'cme', 'Migut.G00385' => 'egut', 'MSTRG.4063' => 'ama', 'Nitab4.5_0000090g0260' => 'nta', 'Nitab4.5_0000977g0030' => 'nta', 'Nitab4.5_0002541g0040' => 'nta', 'Nitab4.5_0007068g0040' => 'nta', 'Nn005s41408' => 'nnu', 'Nn005s41410' => 'nnu', 'Oeu010310.1' => 'oeu', 'Oeu010311.1' => 'oeu', 'Oeu043472.1' => 'oeu', 'Os01g0246400' => 'osa', 'Os04g0267950' => 'osa', 'Os07g0178700' => 'osa', 'Os07g0178800' => 'osa', 'Peaxi162Scf00316g00046' => 'pax', 'Peaxi162Scf00316g00049' => 'pax', 'Peaxi162Scf00316g00059' => 'pax', 'Peaxi162Scf00316g00328' => 'pax', 'Peaxi162Scf00316g00329' => 'pax', 'Peaxi162Scf00316g00411' => 'pax', 'Peaxi162Scf00316g00521' => 'pax', 'Peaxi162Scf00492g00068' => 'pax', 'Peaxi162Scf35631g00002' => 'pax', 'PGR142G3720' => 'pgr', 'PGSC0003DMG400006442' => 'stu', 'Phvul.007G062000' => 'pvu', 'Potri.008G157750' => 'ptr', 'Potri.008G157900' => 'ptr', 'Potri.008G158000' => 'ptr', 'Potri.008G158200' => 'ptr', 'Pp3c11_7280' => 'ppa', 'Pp3c11_7980' => 'ppa', 'Pp3c12_19450' => 'ppa', 'Pp3c14_1480' => 'ppa', 'Pp3c14_1501' => 'ppa', 'Pp3c16_4900' => 'ppa', 'Pp3c16_5010' => 'ppa', 'Pp3c16_5060' => 'ppa', 'Pp3c19_18250' => 'ppa', 'Pp3c23_8530' => 'ppa', 'Pp3c23_8550' => 'ppa', 'Pp3c24_9670' => 'ppa', 'Pp3c2_21390' => 'ppa', 'Pp3c2_31380' => 'ppa', 'Pp3c3_16620' => 'ppa', 'Pp3c3_8090' => 'ppa', 'Pp3c3_8110' => 'ppa', 'Pp3c3_8130' => 'ppa', 'Pp3c3_8150' => 'ppa', 'Pp3c4_14320' => 'ppa', 'Pp3c6_2560' => 'ppa', 'Pp3c9_16700' => 'ppa', 'PRCOL_00000234' => 'pco', 'PRCOL_00000235' => 'pco', 'PRCOL_00000777' => 'pco', 'PRCOL_00002344' => 'pco', 'PRCOL_00002372' => 'pco', 'PRCOL_00006120' => 'pco', 'Prupe.1G021400' => 'ppe', 'Prupe.1G021500' => 'ppe', 'Prupe.1G021600' => 'ppe', 'Prupe.1G021700' => 'ppe', 'Prupe.1G021800' => 'ppe', 'Prupe.5G145100' => 'ppe', 'Psat6g204040' => 'psa', 'Psat6g204800' => 'psa', 'Psat6g204920' => 'psa', 'Psat6g204960' => 'psa', 'Psat6g205080' => 'psa', 'PSO017G0271' => 'pso', 'PSO017G1276' => 'pso', 'PSO017G1429' => 'pso', 'PSO017G1861' => 'pso', 'PSO017G2787' => 'pso', 'PSO017G4466' => 'pso', 'PSO017G5118' => 'pso', 'PSO017G5420' => 'pso', 'PSO063G3678' => 'pso', 'PSO210G0546' => 'pso', 'PSO317G0001' => 'pso', 'PSO357G0512' => 'pso', 'PSO478G2682' => 'pso', 'PSO647G0001' => 'pso', 'PSO675G0001' => 'pso', 'PSO675G2699' => 'pso', 'PSO675G2849' => 'pso', 'PSO675G4991' => 'pso', 'PSO689G0001' => 'pso', 'QL06p000916' => 'qlo', 'QL06p000921' => 'qlo', 'QL06p001398' => 'qlo', 'QL06p001407' => 'qlo', 'QL06p002031' => 'qlo', 'RcHm_v2.0_Chr4g0387791' => 'rch', 'RcHm_v2.0_Chr4g0387801' => 'rch', 'RcHm_v2.0_Chr6g0286501' => 'rch', 'RcHm_v2.0_Chr6g0286511' => 'rch', 'RcHm_v2.0_Chr6g0286521' => 'rch', 'RcHm_v2.0_Chr6g0286531' => 'rch', 'RcHm_v2.0_Chr7g0189141' => 'rch', 'Rhsim02G0028700' => 'rsi', 'Rhsim02G0028800' => 'rsi', 'Rhsim02G0028900' => 'rsi', 'Rhsim02G0029000' => 'rsi', 'Rhsim02G0029100' => 'rsi', 'Rhsim02G0029200' => 'rsi', 'Rhsim02G0029300' => 'rsi', 'Rhsim02G0029400' => 'rsi', 'Rhsim02G0029500' => 'rsi', 'Rhsim02G0029600' => 'rsi', 'RhsimUnG0024000' => 'rsi', 'RhsimUnG0024100' => 'rsi', 'RhsimUnG0024200' => 'rsi', 'RhsimUnG0024300' => 'rsi', 'RhsimUnG0024400' => 'rsi', 'RhsimUnG0024500' => 'rsi', 'RhsimUnG0024700' => 'rsi', 'RhsimUnG0024800' => 'rsi', 'RhsimUnG0024900' => 'rsi', 'RhsimUnG0025100' => 'rsi', 'Sabra08G0120200' => 'sbr', 'Sabra08G0120300' => 'sbr', 'Sabra08G0120500' => 'sbr', 'Sabra08G0120600' => 'sbr', 'Sabra10G0158900' => 'sbr', 'SalBow2G3492' => 'sbo', 'Sc13g0004760' => 'sci', 'Sc13g0004770' => 'sci', 'Sed0003417' => 'sed', 'Sed0019750' => 'sed', 'SEGI_03419' => 'sgi', 'SEGI_05907' => 'sgi', 'SEGI_10682' => 'sgi', 'SEGI_13528' => 'sgi', 'SEGI_16081' => 'sgi', 'SEGI_19370' => 'sgi', 'SEGI_21015' => 'sgi', 'SEGI_21944' => 'sgi', 'SEGI_32906' => 'sgi', 'SEGI_33093' => 'sgi', 'SEGI_36110' => 'sgi', 'SEGI_40397' => 'sgi', 'SGA_v2.0_scaffold191G40426' => 'sas', 'SGA_v2.0_scaffold353G49717' => 'sas', 'SGA_v2.0_scaffold50G18550' => 'sas', 'SMO119G0173' => 'smo', 'SMO172G0002' => 'smo', 'Solyc09g082690.3' => 'sly', 'Solyc09g082700.2' => 'sly', 'Sopen09g031550' => 'spe', 'Sopen09g031560' => 'spe', 'Sp3g20540' => 'spa', 'Sp7g07580' => 'spa', 'TAR134G0002' => 'tar', 'TAR236G0001' => 'tar', 'TAR365G0892' => 'tar', 'TAR636G0166' => 'tar', 'TAR636G0646' => 'tar', 'TAR636G0869' => 'tar', 'TAR636G1317' => 'tar', 'TAR636G1744' => 'tar', 'TAR636G3358' => 'tar', 'TAR636G3436' => 'tar', 'THA.LOC104803047' => 'tha', 'Thecc.04G238900' => 'tca', 'Thhalv10021557m.g' => 'esa', 'Thhalv10026318m.g' => 'esa', 'Thhalv10026335m.g' => 'esa', 'TPR.G17433' => 'tpr', 'TPR.G18915' => 'tpr', 'TPR.G26125' => 'tpr', 'TWI09G0677' => 'twi', 'TWI73G0287' => 'twi', 'unitig_748.g8326' => 'ugi', 'vmacro15370' => 'vma', 'vmacro15371' => 'vma', 'vmacro15372' => 'vma', 'vmacro15373' => 'vma', 'vmacro15374' => 'vma', 'VMungo0720G2826' => 'vmu', 'Zm00001eb116960' => 'zma', 'Zm00001eb301260' => 'zma', 'Zm00001eb301270' => 'zma' ), 'gf_id' => 'HOM05D001460', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001460' ), 'data_identifier' => 'HOM05D001460', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001460', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '433', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p22980' => 'bna', 'A01p32340' => 'bna', 'A03p42970' => 'bna', 'A05p25880' => 'bna', 'Aa31LG8G9320' => 'aar', 'Aa31LG8G9330' => 'aar', 'Aa31LG8G9340' => 'aar', 'Aa31sc221G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1034' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1528' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.829' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2222' => 'aag', 'Ah.12g058830' => 'amhyb', 'Ah.12g058840' => 'amhyb', 'AL3G37160' => 'aly', 'AL7G41310' => 'aly', 'Aqoxy5G00395' => 'aox', 'Aqoxy5G00396' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0C8NZA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5185HY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JZ1PRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MD3LS0' => 'arhy', 'AT3G22840' => 'ath', 'AT4G14690' => 'ath', 'ATR0665G054' => 'atr', 'Atru.chr4.2344' => 'acertr', 'Atru.chr4.2346' => 'acertr', 'Atru.chr4.2347' => 'acertr', 'Atru.chr4.2348' => 'acertr', 'Atru.chr4.2355' => 'acertr', 'Atru.chr4.2356' => 'acertr', 'Atru.chr4.2358' => 'acertr', 'Atru.chr4.2359' => 'acertr', 'Atru.chr4.2360' => 'acertr', 'Atru.chr4.2361' => 'acertr', 'AUR62030476' => 'cqu', 'AUR62030478' => 'cqu', 'AUR62030819' => 'cqu', 'AUR62030820' => 'cqu', 'BcaB03g14648' => 'bca', 'BcaB04g20492' => 'bca', 'BcaB06g26399' => 'bca', 'BcaC01g03416' => 'bca', 'BcaC01g03419' => 'bca', 'BcaC01g03421' => 'bca', 'BcaC01g03424' => 'bca', 'BcaC05g28012' => 'bca', 'BcaC09g49212' => 'bca', 'BcaC09g50140' => 'bca', 'BcaNung00346' => 'bca', 'BolC1t02785H' => 'bol', 'BolC1t04095H' => 'bol', 'BolC3t17545H' => 'bol', 'BolC5t32769H' => 'bol', 'BraA01t02211Z' => 'bra', 'BraA01t03359Z' => 'bra', 'BraA03t13441Z' => 'bra', 'BraA05t21476Z' => 'bra', 'C01p28420' => 'bna', 'C01p41350' => 'bna', 'C03p52750' => 'bna', 'C03p52780' => 'bna', 'C05p40270' => 'bna', 'CAN.G1437.9' => 'can', 'CANSAT78G0035' => 'cansat', 'CANSAT78G1036' => 'cansat', 'CANSAT78G2272' => 'cansat', 'CANSAT78G2478' => 'cansat', 'CARHR098700' => 'chi', 'CARHR221120' => 'chi', 'CARHR221150' => 'chi', 'Carub.0003s2297' => 'cru', 'Carub.0007s2749' => 'cru', 'Carub.0007s2750' => 'cru', 'Carub.0007s2751' => 'cru', 'Ca_10849_v3' => 'car', 'Cc03_g04300' => 'ccan', 'CDE02G3648' => 'cde', 'CDE05G0060' => 'cde', 'CDE05G0692' => 'cde', 'CDE05G2285' => 'cde', 'CDE05G2884' => 'cde', 'CDE05G3072' => 'cde', 'Cfa008439' => 'cfa', 'Cfa008441' => 'cfa', 'Cfa008443' => 'cfa', 'Cfa008448' => 'cfa', 'Ciclev10005974m.g' => 'ccl', 'Ciclev10006006m.g' => 'ccl', 'Ciclev10006775m.g' => 'ccl', 'CiPaw.02G120400' => 'cil', 'CiPaw.02G120500' => 'cil', 'CiPaw.02G120600' => 'cil', 'ClCG05G004850' => 'cla', 'COL.COLO4_21566' => 'col', 'Cpa.g.sc44.124' => 'cpa', 'Cre07.g320400' => 'cre', 'Cre07.g320450' => 'cre', 'Cre08.g384650' => 'cre', 'Cre09.g393173' => 'cre', 'Cre09.g394325' => 'cre', 'Cre14.g626750' => 'cre', 'Cre16.g679250' => 'cre', 'CsaV3_3G012890' => 'csa', 'CSS0010865' => 'camsi', 'CSS0044338' => 'camsi', 'DCAR_002366' => 'dca', 'DCAR_030687' => 'dca', 'DCAR_030688' => 'dca', 'Dinv14047' => 'din', 'Dinv14048' => 'din', 'Duzib151G0105' => 'dzi', 'Duzib151G0114' => 'dzi', 'Duzib212G1029' => 'dzi', 'ECA232G3536' => 'eca', 'ECA240G0786' => 'eca', 'ECA240G1802' => 'eca', 'ECA240G3760' => 'eca', 'ECA240G3920' => 'eca', 'EL10Ac5g12536' => 'bvu', 'EL10Ac5g12537' => 'bvu', 'EL10Ac5g12538' => 'bvu', 'Eucgr.B01004' => 'egr', 'Eucgr.B01006' => 'egr', 'Eucgr.B01007' => 'egr', 'Eucgr.B01008' => 'egr', 'Eucgr.B01895' => 'egr', 'Eucgr.B01896' => 'egr', 'FAN04G1456' => 'fan', 'FAN08G1769' => 'fan', 'FAN08G2160' => 'fan', 'FAN13G2403' => 'fan', 'FAN13G3303' => 'fan', 'FAN15G2435' => 'fan', 'FAN17G0672' => 'fan', 'FAN17G2441' => 'fan', 'FAN18G1024' => 'fan', 'FAN22G1458' => 'fan', 'FAN24G0037' => 'fan', 'FAN24G0429' => 'fan', 'FAN24G2387' => 'fan', 'FAN27G2746' => 'fan', 'FvH4_2g20400' => 'fve', 'FvH4_2g20420' => 'fve', 'FvH4_2g20430' => 'fve', 'FvH4_4g01270' => 'fve', 'FvH4_4g01290' => 'fve', 'FvH4_4g01300' => 'fve', 'FvH4_4g01310' => 'fve', 'FvH4_4g01330' => 'fve', 'FvH4_5g09070' => 'fve', 'Glyma.10G243800' => 'gma', 'Glyma.20G150600' => 'gma', 'Gohir.A09G219200' => 'ghi', 'Gohir.A09G219300' => 'ghi', 'Gohir.D09G221400' => 'ghi', 'Gohir.D09G221500' => 'ghi', 'Gorai.006G242600' => 'gra', 'Gorai.006G242700' => 'gra', 'GSVIVG01018044001' => 'vvi', 'HanXRQChr03g0083821' => 'han', 'HanXRQChr03g0083841' => 'han', 'HanXRQChr03g0083881' => 'han', 'HanXRQChr03g0083901' => 'han', 'HanXRQChr03g0083921' => 'han', 'HanXRQChr03g0085331' => 'han', 'HanXRQChr03g0085361' => 'han', 'HanXRQChr03g0085411' => 'han', 'HanXRQChr03g0085421' => 'han', 'HanXRQChr03g0085431' => 'han', 'HanXRQChr08g0221991' => 'han', 'HanXRQChr11g0336061' => 'han', 'HanXRQChr11g0336411' => 'han', 'Haze_11234' => 'cav', 'Hma1.2p1_0549F.1_g177010' => 'hma', 'Hma1.2p1_0602F.1_g187630' => 'hma', 'Hund14876' => 'sun', 'Hund14879' => 'sun', 'Lalb_Chr06g0160741' => 'lal', 'Lalb_Chr21g0304781' => 'lal', 'Lj3A726G19' => 'lonja', 'Lj3A726T23' => 'lonja', 'Lj3A726T24' => 'lonja', 'Lj3A726T25' => 'lonja', 'Lj3A727T17' => 'lonja', 'Lj3C726T0' => 'lonja', 'Lj3C726T2' => 'lonja', 'Lj3P725T35' => 'lonja', 'Lj3P727T10' => 'lonja', 'Lj3P727T12' => 'lonja', 'Lj3P727T14' => 'lonja', 'Lj5g0023109' => 'lja', 'Lj6P646T44' => 'lonja', 'Lsat_1_v5_gn_6_75760' => 'lsa', 'Lsat_1_v5_gn_6_75800' => 'lsa', 'Lsat_1_v5_gn_6_75900' => 'lsa', 'Lsat_1_v5_gn_6_76240' => 'lsa', 'Lsat_1_v5_gn_6_76441' => 'lsa', 'Lsat_1_v5_gn_6_76700' => 'lsa', 'Lsat_1_v5_gn_6_76760' => 'lsa', 'Manes.15G033100' => 'mes', 'Mapoly0004s0074' => 'mpo', 'Mapoly0004s0075' => 'mpo', 'Mapoly0004s0163' => 'mpo', 'Mapoly0004s0164' => 'mpo', 'Mapoly0021s0018' => 'mpo', 'Mapoly0041s0136' => 'mpo', 'Mapoly0041s0137' => 'mpo', 'Mapoly0041s0138' => 'mpo', 'Mapoly0041s0139' => 'mpo', 'Mapoly0041s0141' => 'mpo', 'Mapoly0041s0142' => 'mpo', 'Mapoly0041s0143' => 'mpo', 'Mapoly0041s0144' => 'mpo', 'Mapoly0041s0145' => 'mpo', 'Mapoly0047s0106' => 'mpo', 'Mapoly0047s0108' => 'mpo', 'Mapoly0050s0051' => 'mpo', 'Mapoly0050s0052' => 'mpo', 'Mapoly0050s0053' => 'mpo', 'Mapoly0058s0013' => 'mpo', 'Mapoly0091s0078' => 'mpo', 'Mapoly0091s0079' => 'mpo', 'Mapoly0091s0080' => 'mpo', 'Mapoly0091s0081' => 'mpo', 'Mapoly0278s0004' => 'mpo', 'Mapoly0278s0005' => 'mpo', 'Mapoly0278s0006' => 'mpo', 'MBI11_g30648_MAGBIO' => 'mbi', 'MCO03G194' => 'mco', 'MCO03G590' => 'mco', 'MCO07G312' => 'mco', 'MCO10G318' => 'mco', 'MCO12G244' => 'mco', 'MCO13G148' => 'mco', 'MCO13G194' => 'mco', 'MCO16G238' => 'mco', 'MD06G1134100' => 'mdo', 'MD13G1200100' => 'mdo', 'MD13G1200300' => 'mdo', 'MD13G1200600' => 'mdo', 'MD14G1150400' => 'mdo', 'MD16G1200000' => 'mdo', 'Medtr1g102570' => 'mtr', 'Medtr1g102780' => 'mtr', 'Medtr1g102800' => 'mtr', 'Medtr1g102810' => 'mtr', 'Medtr1g102830' => 'mtr', 'MELO3C006499.2' => 'cme', 'Migut.G00385' => 'egut', 'MSTRG.4063' => 'ama', 'Nitab4.5_0000090g0260' => 'nta', 'Nitab4.5_0000977g0030' => 'nta', 'Nitab4.5_0002541g0040' => 'nta', 'Nitab4.5_0007068g0040' => 'nta', 'Nn005s41408' => 'nnu', 'Nn005s41410' => 'nnu', 'Oeu010310.1' => 'oeu', 'Oeu010311.1' => 'oeu', 'Oeu043472.1' => 'oeu', 'Os01g0246400' => 'osa', 'Os04g0267950' => 'osa', 'Os07g0178700' => 'osa', 'Os07g0178800' => 'osa', 'Peaxi162Scf00316g00046' => 'pax', 'Peaxi162Scf00316g00049' => 'pax', 'Peaxi162Scf00316g00059' => 'pax', 'Peaxi162Scf00316g00328' => 'pax', 'Peaxi162Scf00316g00329' => 'pax', 'Peaxi162Scf00316g00411' => 'pax', 'Peaxi162Scf00316g00521' => 'pax', 'Peaxi162Scf00492g00068' => 'pax', 'Peaxi162Scf35631g00002' => 'pax', 'PGR142G3720' => 'pgr', 'PGSC0003DMG400006442' => 'stu', 'Phvul.007G062000' => 'pvu', 'Potri.008G157750' => 'ptr', 'Potri.008G157900' => 'ptr', 'Potri.008G158000' => 'ptr', 'Potri.008G158200' => 'ptr', 'Pp3c11_7280' => 'ppa', 'Pp3c11_7980' => 'ppa', 'Pp3c12_19450' => 'ppa', 'Pp3c14_1480' => 'ppa', 'Pp3c14_1501' => 'ppa', 'Pp3c16_4900' => 'ppa', 'Pp3c16_5010' => 'ppa', 'Pp3c16_5060' => 'ppa', 'Pp3c19_18250' => 'ppa', 'Pp3c23_8530' => 'ppa', 'Pp3c23_8550' => 'ppa', 'Pp3c24_9670' => 'ppa', 'Pp3c2_21390' => 'ppa', 'Pp3c2_31380' => 'ppa', 'Pp3c3_16620' => 'ppa', 'Pp3c3_8090' => 'ppa', 'Pp3c3_8110' => 'ppa', 'Pp3c3_8130' => 'ppa', 'Pp3c3_8150' => 'ppa', 'Pp3c4_14320' => 'ppa', 'Pp3c6_2560' => 'ppa', 'Pp3c9_16700' => 'ppa', 'PRCOL_00000234' => 'pco', 'PRCOL_00000235' => 'pco', 'PRCOL_00000777' => 'pco', 'PRCOL_00002344' => 'pco', 'PRCOL_00002372' => 'pco', 'PRCOL_00006120' => 'pco', 'Prupe.1G021400' => 'ppe', 'Prupe.1G021500' => 'ppe', 'Prupe.1G021600' => 'ppe', 'Prupe.1G021700' => 'ppe', 'Prupe.1G021800' => 'ppe', 'Prupe.5G145100' => 'ppe', 'Psat6g204040' => 'psa', 'Psat6g204800' => 'psa', 'Psat6g204920' => 'psa', 'Psat6g204960' => 'psa', 'Psat6g205080' => 'psa', 'PSO017G0271' => 'pso', 'PSO017G1276' => 'pso', 'PSO017G1429' => 'pso', 'PSO017G1861' => 'pso', 'PSO017G2787' => 'pso', 'PSO017G4466' => 'pso', 'PSO017G5118' => 'pso', 'PSO017G5420' => 'pso', 'PSO063G3678' => 'pso', 'PSO210G0546' => 'pso', 'PSO317G0001' => 'pso', 'PSO357G0512' => 'pso', 'PSO478G2682' => 'pso', 'PSO647G0001' => 'pso', 'PSO675G0001' => 'pso', 'PSO675G2699' => 'pso', 'PSO675G2849' => 'pso', 'PSO675G4991' => 'pso', 'PSO689G0001' => 'pso', 'QL06p000916' => 'qlo', 'QL06p000921' => 'qlo', 'QL06p001398' => 'qlo', 'QL06p001407' => 'qlo', 'QL06p002031' => 'qlo', 'RcHm_v2.0_Chr4g0387791' => 'rch', 'RcHm_v2.0_Chr4g0387801' => 'rch', 'RcHm_v2.0_Chr6g0286501' => 'rch', 'RcHm_v2.0_Chr6g0286511' => 'rch', 'RcHm_v2.0_Chr6g0286521' => 'rch', 'RcHm_v2.0_Chr6g0286531' => 'rch', 'RcHm_v2.0_Chr7g0189141' => 'rch', 'Rhsim02G0028700' => 'rsi', 'Rhsim02G0028800' => 'rsi', 'Rhsim02G0028900' => 'rsi', 'Rhsim02G0029000' => 'rsi', 'Rhsim02G0029100' => 'rsi', 'Rhsim02G0029200' => 'rsi', 'Rhsim02G0029300' => 'rsi', 'Rhsim02G0029400' => 'rsi', 'Rhsim02G0029500' => 'rsi', 'Rhsim02G0029600' => 'rsi', 'RhsimUnG0024000' => 'rsi', 'RhsimUnG0024100' => 'rsi', 'RhsimUnG0024200' => 'rsi', 'RhsimUnG0024300' => 'rsi', 'RhsimUnG0024400' => 'rsi', 'RhsimUnG0024500' => 'rsi', 'RhsimUnG0024700' => 'rsi', 'RhsimUnG0024800' => 'rsi', 'RhsimUnG0024900' => 'rsi', 'RhsimUnG0025100' => 'rsi', 'Sabra08G0120200' => 'sbr', 'Sabra08G0120300' => 'sbr', 'Sabra08G0120500' => 'sbr', 'Sabra08G0120600' => 'sbr', 'Sabra10G0158900' => 'sbr', 'SalBow2G3492' => 'sbo', 'Sc13g0004760' => 'sci', 'Sc13g0004770' => 'sci', 'Sed0003417' => 'sed', 'Sed0019750' => 'sed', 'SEGI_03419' => 'sgi', 'SEGI_05907' => 'sgi', 'SEGI_10682' => 'sgi', 'SEGI_13528' => 'sgi', 'SEGI_16081' => 'sgi', 'SEGI_19370' => 'sgi', 'SEGI_21015' => 'sgi', 'SEGI_21944' => 'sgi', 'SEGI_32906' => 'sgi', 'SEGI_33093' => 'sgi', 'SEGI_36110' => 'sgi', 'SEGI_40397' => 'sgi', 'SGA_v2.0_scaffold191G40426' => 'sas', 'SGA_v2.0_scaffold353G49717' => 'sas', 'SGA_v2.0_scaffold50G18550' => 'sas', 'SMO119G0173' => 'smo', 'SMO172G0002' => 'smo', 'Solyc09g082690.3' => 'sly', 'Solyc09g082700.2' => 'sly', 'Sopen09g031550' => 'spe', 'Sopen09g031560' => 'spe', 'Sp3g20540' => 'spa', 'Sp7g07580' => 'spa', 'TAR134G0002' => 'tar', 'TAR236G0001' => 'tar', 'TAR365G0892' => 'tar', 'TAR636G0166' => 'tar', 'TAR636G0646' => 'tar', 'TAR636G0869' => 'tar', 'TAR636G1317' => 'tar', 'TAR636G1744' => 'tar', 'TAR636G3358' => 'tar', 'TAR636G3436' => 'tar', 'THA.LOC104803047' => 'tha', 'Thecc.04G238900' => 'tca', 'Thhalv10021557m.g' => 'esa', 'Thhalv10026318m.g' => 'esa', 'Thhalv10026335m.g' => 'esa', 'TPR.G17433' => 'tpr', 'TPR.G18915' => 'tpr', 'TPR.G26125' => 'tpr', 'TWI09G0677' => 'twi', 'TWI73G0287' => 'twi', 'unitig_748.g8326' => 'ugi', 'vmacro15370' => 'vma', 'vmacro15371' => 'vma', 'vmacro15372' => 'vma', 'vmacro15373' => 'vma', 'vmacro15374' => 'vma', 'VMungo0720G2826' => 'vmu', 'Zm00001eb116960' => 'zma', 'Zm00001eb301260' => 'zma', 'Zm00001eb301270' => 'zma' ) $gf_id = 'HOM05D001460' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001460' ) $data_identifier = 'HOM05D001460' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 4, 'aag' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 2, 'aox' => (int) 2, 'arhy' => (int) 4, 'ath' => (int) 2, 'atr' => (int) 1, 'acertr' => (int) 10, 'cqu' => (int) 4, 'bca' => (int) 11, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 1, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 1, 'ccan' => (int) 1, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 1, 'col' => (int) 1, 'cpa' => (int) 1, 'cre' => (int) 7, 'csa' => (int) 1, 'camsi' => (int) 2, 'dca' => (int) 3, 'din' => (int) 2, 'dzi' => (int) 3, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 14, 'fve' => (int) 9, 'gma' => (int) 2, 'ghi' => (int) 4, 'gra' => (int) 2, 'vvi' => (int) 1, 'han' => (int) 13, 'cav' => (int) 1, 'hma' => (int) 2, 'sun' => (int) 2, 'lal' => (int) 2, 'lonja' => (int) 12, 'lja' => (int) 1, 'lsa' => (int) 7, 'mes' => (int) 1, 'mpo' => (int) 27, 'mbi' => (int) 1, 'mco' => (int) 8, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 1, 'egut' => (int) 1, 'ama' => (int) 1, 'nta' => (int) 4, 'nnu' => (int) 2, 'oeu' => (int) 3, 'osa' => (int) 4, 'pax' => (int) 9, 'pgr' => (int) 1, 'stu' => (int) 1, 'pvu' => (int) 1, 'ptr' => (int) 4, 'ppa' => (int) 22, 'pco' => (int) 6, 'ppe' => (int) 6, 'psa' => (int) 5, 'pso' => (int) 19, 'qlo' => (int) 5, 'rch' => (int) 7, 'rsi' => (int) 20, 'sbr' => (int) 5, 'sbo' => (int) 1, 'sci' => (int) 2, 'sed' => (int) 2, 'sgi' => (int) 12, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 2, 'tar' => (int) 10, 'tha' => (int) 1, 'tca' => (int) 1, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 2, 'ugi' => (int) 1, 'vma' => (int) 5, 'vmu' => (int) 1, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb301270' $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' => 'HOM05D001460', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '433', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p22980' => 'bna', 'A01p32340' => 'bna', 'A03p42970' => 'bna', 'A05p25880' => 'bna', 'Aa31LG8G9320' => 'aar', 'Aa31LG8G9330' => 'aar', 'Aa31LG8G9340' => 'aar', 'Aa31sc221G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1034' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1528' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.829' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2222' => 'aag', 'Ah.12g058830' => 'amhyb', 'Ah.12g058840' => 'amhyb', 'AL3G37160' => 'aly', 'AL7G41310' => 'aly', 'Aqoxy5G00395' => 'aox', 'Aqoxy5G00396' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0C8NZA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5185HY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JZ1PRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MD3LS0' => 'arhy', 'AT3G22840' => 'ath', 'AT4G14690' => 'ath', 'ATR0665G054' => 'atr', 'Atru.chr4.2344' => 'acertr', 'Atru.chr4.2346' => 'acertr', 'Atru.chr4.2347' => 'acertr', 'Atru.chr4.2348' => 'acertr', 'Atru.chr4.2355' => 'acertr', 'Atru.chr4.2356' => 'acertr', 'Atru.chr4.2358' => 'acertr', 'Atru.chr4.2359' => 'acertr', 'Atru.chr4.2360' => 'acertr', 'Atru.chr4.2361' => 'acertr', 'AUR62030476' => 'cqu', 'AUR62030478' => 'cqu', 'AUR62030819' => 'cqu', 'AUR62030820' => 'cqu', 'BcaB03g14648' => 'bca', 'BcaB04g20492' => 'bca', 'BcaB06g26399' => 'bca', 'BcaC01g03416' => 'bca', 'BcaC01g03419' => 'bca', 'BcaC01g03421' => 'bca', 'BcaC01g03424' => 'bca', 'BcaC05g28012' => 'bca', 'BcaC09g49212' => 'bca', 'BcaC09g50140' => 'bca', 'BcaNung00346' => 'bca', 'BolC1t02785H' => 'bol', 'BolC1t04095H' => 'bol', 'BolC3t17545H' => 'bol', 'BolC5t32769H' => 'bol', 'BraA01t02211Z' => 'bra', 'BraA01t03359Z' => 'bra', 'BraA03t13441Z' => 'bra', 'BraA05t21476Z' => 'bra', 'C01p28420' => 'bna', 'C01p41350' => 'bna', 'C03p52750' => 'bna', 'C03p52780' => 'bna', 'C05p40270' => 'bna', 'CAN.G1437.9' => 'can', 'CANSAT78G0035' => 'cansat', 'CANSAT78G1036' => 'cansat', 'CANSAT78G2272' => 'cansat', 'CANSAT78G2478' => 'cansat', 'CARHR098700' => 'chi', 'CARHR221120' => 'chi', 'CARHR221150' => 'chi', 'Carub.0003s2297' => 'cru', 'Carub.0007s2749' => 'cru', 'Carub.0007s2750' => 'cru', 'Carub.0007s2751' => 'cru', 'Ca_10849_v3' => 'car', 'Cc03_g04300' => 'ccan', 'CDE02G3648' => 'cde', 'CDE05G0060' => 'cde', 'CDE05G0692' => 'cde', 'CDE05G2285' => 'cde', 'CDE05G2884' => 'cde', 'CDE05G3072' => 'cde', 'Cfa008439' => 'cfa', 'Cfa008441' => 'cfa', 'Cfa008443' => 'cfa', 'Cfa008448' => 'cfa', 'Ciclev10005974m.g' => 'ccl', 'Ciclev10006006m.g' => 'ccl', 'Ciclev10006775m.g' => 'ccl', 'CiPaw.02G120400' => 'cil', 'CiPaw.02G120500' => 'cil', 'CiPaw.02G120600' => 'cil', 'ClCG05G004850' => 'cla', 'COL.COLO4_21566' => 'col', 'Cpa.g.sc44.124' => 'cpa', 'Cre07.g320400' => 'cre', 'Cre07.g320450' => 'cre', 'Cre08.g384650' => 'cre', 'Cre09.g393173' => 'cre', 'Cre09.g394325' => 'cre', 'Cre14.g626750' => 'cre', 'Cre16.g679250' => 'cre', 'CsaV3_3G012890' => 'csa', 'CSS0010865' => 'camsi', 'CSS0044338' => 'camsi', 'DCAR_002366' => 'dca', 'DCAR_030687' => 'dca', 'DCAR_030688' => 'dca', 'Dinv14047' => 'din', 'Dinv14048' => 'din', 'Duzib151G0105' => 'dzi', 'Duzib151G0114' => 'dzi', 'Duzib212G1029' => 'dzi', 'ECA232G3536' => 'eca', 'ECA240G0786' => 'eca', 'ECA240G1802' => 'eca', 'ECA240G3760' => 'eca', 'ECA240G3920' => 'eca', 'EL10Ac5g12536' => 'bvu', 'EL10Ac5g12537' => 'bvu', 'EL10Ac5g12538' => 'bvu', 'Eucgr.B01004' => 'egr', 'Eucgr.B01006' => 'egr', 'Eucgr.B01007' => 'egr', 'Eucgr.B01008' => 'egr', 'Eucgr.B01895' => 'egr', 'Eucgr.B01896' => 'egr', 'FAN04G1456' => 'fan', 'FAN08G1769' => 'fan', 'FAN08G2160' => 'fan', 'FAN13G2403' => 'fan', 'FAN13G3303' => 'fan', 'FAN15G2435' => 'fan', 'FAN17G0672' => 'fan', 'FAN17G2441' => 'fan', 'FAN18G1024' => 'fan', 'FAN22G1458' => 'fan', 'FAN24G0037' => 'fan', 'FAN24G0429' => 'fan', 'FAN24G2387' => 'fan', 'FAN27G2746' => 'fan', 'FvH4_2g20400' => 'fve', 'FvH4_2g20420' => 'fve', 'FvH4_2g20430' => 'fve', 'FvH4_4g01270' => 'fve', 'FvH4_4g01290' => 'fve', 'FvH4_4g01300' => 'fve', 'FvH4_4g01310' => 'fve', 'FvH4_4g01330' => 'fve', 'FvH4_5g09070' => 'fve', 'Glyma.10G243800' => 'gma', 'Glyma.20G150600' => 'gma', 'Gohir.A09G219200' => 'ghi', 'Gohir.A09G219300' => 'ghi', 'Gohir.D09G221400' => 'ghi', 'Gohir.D09G221500' => 'ghi', 'Gorai.006G242600' => 'gra', 'Gorai.006G242700' => 'gra', 'GSVIVG01018044001' => 'vvi', 'HanXRQChr03g0083821' => 'han', 'HanXRQChr03g0083841' => 'han', 'HanXRQChr03g0083881' => 'han', 'HanXRQChr03g0083901' => 'han', 'HanXRQChr03g0083921' => 'han', 'HanXRQChr03g0085331' => 'han', 'HanXRQChr03g0085361' => 'han', 'HanXRQChr03g0085411' => 'han', 'HanXRQChr03g0085421' => 'han', 'HanXRQChr03g0085431' => 'han', 'HanXRQChr08g0221991' => 'han', 'HanXRQChr11g0336061' => 'han', 'HanXRQChr11g0336411' => 'han', 'Haze_11234' => 'cav', 'Hma1.2p1_0549F.1_g177010' => 'hma', 'Hma1.2p1_0602F.1_g187630' => 'hma', 'Hund14876' => 'sun', 'Hund14879' => 'sun', 'Lalb_Chr06g0160741' => 'lal', 'Lalb_Chr21g0304781' => 'lal', 'Lj3A726G19' => 'lonja', 'Lj3A726T23' => 'lonja', 'Lj3A726T24' => 'lonja', 'Lj3A726T25' => 'lonja', 'Lj3A727T17' => 'lonja', 'Lj3C726T0' => 'lonja', 'Lj3C726T2' => 'lonja', 'Lj3P725T35' => 'lonja', 'Lj3P727T10' => 'lonja', 'Lj3P727T12' => 'lonja', 'Lj3P727T14' => 'lonja', 'Lj5g0023109' => 'lja', 'Lj6P646T44' => 'lonja', 'Lsat_1_v5_gn_6_75760' => 'lsa', 'Lsat_1_v5_gn_6_75800' => 'lsa', 'Lsat_1_v5_gn_6_75900' => 'lsa', 'Lsat_1_v5_gn_6_76240' => 'lsa', 'Lsat_1_v5_gn_6_76441' => 'lsa', 'Lsat_1_v5_gn_6_76700' => 'lsa', 'Lsat_1_v5_gn_6_76760' => 'lsa', 'Manes.15G033100' => 'mes', 'Mapoly0004s0074' => 'mpo', 'Mapoly0004s0075' => 'mpo', 'Mapoly0004s0163' => 'mpo', 'Mapoly0004s0164' => 'mpo', 'Mapoly0021s0018' => 'mpo', 'Mapoly0041s0136' => 'mpo', 'Mapoly0041s0137' => 'mpo', 'Mapoly0041s0138' => 'mpo', 'Mapoly0041s0139' => 'mpo', 'Mapoly0041s0141' => 'mpo', 'Mapoly0041s0142' => 'mpo', 'Mapoly0041s0143' => 'mpo', 'Mapoly0041s0144' => 'mpo', 'Mapoly0041s0145' => 'mpo', 'Mapoly0047s0106' => 'mpo', 'Mapoly0047s0108' => 'mpo', 'Mapoly0050s0051' => 'mpo', 'Mapoly0050s0052' => 'mpo', 'Mapoly0050s0053' => 'mpo', 'Mapoly0058s0013' => 'mpo', 'Mapoly0091s0078' => 'mpo', 'Mapoly0091s0079' => 'mpo', 'Mapoly0091s0080' => 'mpo', 'Mapoly0091s0081' => 'mpo', 'Mapoly0278s0004' => 'mpo', 'Mapoly0278s0005' => 'mpo', 'Mapoly0278s0006' => 'mpo', 'MBI11_g30648_MAGBIO' => 'mbi', 'MCO03G194' => 'mco', 'MCO03G590' => 'mco', 'MCO07G312' => 'mco', 'MCO10G318' => 'mco', 'MCO12G244' => 'mco', 'MCO13G148' => 'mco', 'MCO13G194' => 'mco', 'MCO16G238' => 'mco', 'MD06G1134100' => 'mdo', 'MD13G1200100' => 'mdo', 'MD13G1200300' => 'mdo', 'MD13G1200600' => 'mdo', 'MD14G1150400' => 'mdo', 'MD16G1200000' => 'mdo', 'Medtr1g102570' => 'mtr', 'Medtr1g102780' => 'mtr', 'Medtr1g102800' => 'mtr', 'Medtr1g102810' => 'mtr', 'Medtr1g102830' => 'mtr', 'MELO3C006499.2' => 'cme', 'Migut.G00385' => 'egut', 'MSTRG.4063' => 'ama', 'Nitab4.5_0000090g0260' => 'nta', 'Nitab4.5_0000977g0030' => 'nta', 'Nitab4.5_0002541g0040' => 'nta', 'Nitab4.5_0007068g0040' => 'nta', 'Nn005s41408' => 'nnu', 'Nn005s41410' => 'nnu', 'Oeu010310.1' => 'oeu', 'Oeu010311.1' => 'oeu', 'Oeu043472.1' => 'oeu', 'Os01g0246400' => 'osa', 'Os04g0267950' => 'osa', 'Os07g0178700' => 'osa', 'Os07g0178800' => 'osa', 'Peaxi162Scf00316g00046' => 'pax', 'Peaxi162Scf00316g00049' => 'pax', 'Peaxi162Scf00316g00059' => 'pax', 'Peaxi162Scf00316g00328' => 'pax', 'Peaxi162Scf00316g00329' => 'pax', 'Peaxi162Scf00316g00411' => 'pax', 'Peaxi162Scf00316g00521' => 'pax', 'Peaxi162Scf00492g00068' => 'pax', 'Peaxi162Scf35631g00002' => 'pax', 'PGR142G3720' => 'pgr', 'PGSC0003DMG400006442' => 'stu', 'Phvul.007G062000' => 'pvu', 'Potri.008G157750' => 'ptr', 'Potri.008G157900' => 'ptr', 'Potri.008G158000' => 'ptr', 'Potri.008G158200' => 'ptr', 'Pp3c11_7280' => 'ppa', 'Pp3c11_7980' => 'ppa', 'Pp3c12_19450' => 'ppa', 'Pp3c14_1480' => 'ppa', 'Pp3c14_1501' => 'ppa', 'Pp3c16_4900' => 'ppa', 'Pp3c16_5010' => 'ppa', 'Pp3c16_5060' => 'ppa', 'Pp3c19_18250' => 'ppa', 'Pp3c23_8530' => 'ppa', 'Pp3c23_8550' => 'ppa', 'Pp3c24_9670' => 'ppa', 'Pp3c2_21390' => 'ppa', 'Pp3c2_31380' => 'ppa', 'Pp3c3_16620' => 'ppa', 'Pp3c3_8090' => 'ppa', 'Pp3c3_8110' => 'ppa', 'Pp3c3_8130' => 'ppa', 'Pp3c3_8150' => 'ppa', 'Pp3c4_14320' => 'ppa', 'Pp3c6_2560' => 'ppa', 'Pp3c9_16700' => 'ppa', 'PRCOL_00000234' => 'pco', 'PRCOL_00000235' => 'pco', 'PRCOL_00000777' => 'pco', 'PRCOL_00002344' => 'pco', 'PRCOL_00002372' => 'pco', 'PRCOL_00006120' => 'pco', 'Prupe.1G021400' => 'ppe', 'Prupe.1G021500' => 'ppe', 'Prupe.1G021600' => 'ppe', 'Prupe.1G021700' => 'ppe', 'Prupe.1G021800' => 'ppe', 'Prupe.5G145100' => 'ppe', 'Psat6g204040' => 'psa', 'Psat6g204800' => 'psa', 'Psat6g204920' => 'psa', 'Psat6g204960' => 'psa', 'Psat6g205080' => 'psa', 'PSO017G0271' => 'pso', 'PSO017G1276' => 'pso', 'PSO017G1429' => 'pso', 'PSO017G1861' => 'pso', 'PSO017G2787' => 'pso', 'PSO017G4466' => 'pso', 'PSO017G5118' => 'pso', 'PSO017G5420' => 'pso', 'PSO063G3678' => 'pso', 'PSO210G0546' => 'pso', 'PSO317G0001' => 'pso', 'PSO357G0512' => 'pso', 'PSO478G2682' => 'pso', 'PSO647G0001' => 'pso', 'PSO675G0001' => 'pso', 'PSO675G2699' => 'pso', 'PSO675G2849' => 'pso', 'PSO675G4991' => 'pso', 'PSO689G0001' => 'pso', 'QL06p000916' => 'qlo', 'QL06p000921' => 'qlo', 'QL06p001398' => 'qlo', 'QL06p001407' => 'qlo', 'QL06p002031' => 'qlo', 'RcHm_v2.0_Chr4g0387791' => 'rch', 'RcHm_v2.0_Chr4g0387801' => 'rch', 'RcHm_v2.0_Chr6g0286501' => 'rch', 'RcHm_v2.0_Chr6g0286511' => 'rch', 'RcHm_v2.0_Chr6g0286521' => 'rch', 'RcHm_v2.0_Chr6g0286531' => 'rch', 'RcHm_v2.0_Chr7g0189141' => 'rch', 'Rhsim02G0028700' => 'rsi', 'Rhsim02G0028800' => 'rsi', 'Rhsim02G0028900' => 'rsi', 'Rhsim02G0029000' => 'rsi', 'Rhsim02G0029100' => 'rsi', 'Rhsim02G0029200' => 'rsi', 'Rhsim02G0029300' => 'rsi', 'Rhsim02G0029400' => 'rsi', 'Rhsim02G0029500' => 'rsi', 'Rhsim02G0029600' => 'rsi', 'RhsimUnG0024000' => 'rsi', 'RhsimUnG0024100' => 'rsi', 'RhsimUnG0024200' => 'rsi', 'RhsimUnG0024300' => 'rsi', 'RhsimUnG0024400' => 'rsi', 'RhsimUnG0024500' => 'rsi', 'RhsimUnG0024700' => 'rsi', 'RhsimUnG0024800' => 'rsi', 'RhsimUnG0024900' => 'rsi', 'RhsimUnG0025100' => 'rsi', 'Sabra08G0120200' => 'sbr', 'Sabra08G0120300' => 'sbr', 'Sabra08G0120500' => 'sbr', 'Sabra08G0120600' => 'sbr', 'Sabra10G0158900' => 'sbr', 'SalBow2G3492' => 'sbo', 'Sc13g0004760' => 'sci', 'Sc13g0004770' => 'sci', 'Sed0003417' => 'sed', 'Sed0019750' => 'sed', 'SEGI_03419' => 'sgi', 'SEGI_05907' => 'sgi', 'SEGI_10682' => 'sgi', 'SEGI_13528' => 'sgi', 'SEGI_16081' => 'sgi', 'SEGI_19370' => 'sgi', 'SEGI_21015' => 'sgi', 'SEGI_21944' => 'sgi', 'SEGI_32906' => 'sgi', 'SEGI_33093' => 'sgi', 'SEGI_36110' => 'sgi', 'SEGI_40397' => 'sgi', 'SGA_v2.0_scaffold191G40426' => 'sas', 'SGA_v2.0_scaffold353G49717' => 'sas', 'SGA_v2.0_scaffold50G18550' => 'sas', 'SMO119G0173' => 'smo', 'SMO172G0002' => 'smo', 'Solyc09g082690.3' => 'sly', 'Solyc09g082700.2' => 'sly', 'Sopen09g031550' => 'spe', 'Sopen09g031560' => 'spe', 'Sp3g20540' => 'spa', 'Sp7g07580' => 'spa', 'TAR134G0002' => 'tar', 'TAR236G0001' => 'tar', 'TAR365G0892' => 'tar', 'TAR636G0166' => 'tar', 'TAR636G0646' => 'tar', 'TAR636G0869' => 'tar', 'TAR636G1317' => 'tar', 'TAR636G1744' => 'tar', 'TAR636G3358' => 'tar', 'TAR636G3436' => 'tar', 'THA.LOC104803047' => 'tha', 'Thecc.04G238900' => 'tca', 'Thhalv10021557m.g' => 'esa', 'Thhalv10026318m.g' => 'esa', 'Thhalv10026335m.g' => 'esa', 'TPR.G17433' => 'tpr', 'TPR.G18915' => 'tpr', 'TPR.G26125' => 'tpr', 'TWI09G0677' => 'twi', 'TWI73G0287' => 'twi', 'unitig_748.g8326' => 'ugi', 'vmacro15370' => 'vma', 'vmacro15371' => 'vma', 'vmacro15372' => 'vma', 'vmacro15373' => 'vma', 'vmacro15374' => 'vma', 'VMungo0720G2826' => 'vmu', 'Zm00001eb116960' => 'zma', 'Zm00001eb301260' => 'zma', 'Zm00001eb301270' => 'zma' ), 'gf_id' => 'HOM05D001460', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001460' ), 'data_identifier' => 'HOM05D001460', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001460', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '433', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p22980' => 'bna', 'A01p32340' => 'bna', 'A03p42970' => 'bna', 'A05p25880' => 'bna', 'Aa31LG8G9320' => 'aar', 'Aa31LG8G9330' => 'aar', 'Aa31LG8G9340' => 'aar', 'Aa31sc221G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1034' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1528' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.829' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2222' => 'aag', 'Ah.12g058830' => 'amhyb', 'Ah.12g058840' => 'amhyb', 'AL3G37160' => 'aly', 'AL7G41310' => 'aly', 'Aqoxy5G00395' => 'aox', 'Aqoxy5G00396' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0C8NZA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5185HY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JZ1PRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MD3LS0' => 'arhy', 'AT3G22840' => 'ath', 'AT4G14690' => 'ath', 'ATR0665G054' => 'atr', 'Atru.chr4.2344' => 'acertr', 'Atru.chr4.2346' => 'acertr', 'Atru.chr4.2347' => 'acertr', 'Atru.chr4.2348' => 'acertr', 'Atru.chr4.2355' => 'acertr', 'Atru.chr4.2356' => 'acertr', 'Atru.chr4.2358' => 'acertr', 'Atru.chr4.2359' => 'acertr', 'Atru.chr4.2360' => 'acertr', 'Atru.chr4.2361' => 'acertr', 'AUR62030476' => 'cqu', 'AUR62030478' => 'cqu', 'AUR62030819' => 'cqu', 'AUR62030820' => 'cqu', 'BcaB03g14648' => 'bca', 'BcaB04g20492' => 'bca', 'BcaB06g26399' => 'bca', 'BcaC01g03416' => 'bca', 'BcaC01g03419' => 'bca', 'BcaC01g03421' => 'bca', 'BcaC01g03424' => 'bca', 'BcaC05g28012' => 'bca', 'BcaC09g49212' => 'bca', 'BcaC09g50140' => 'bca', 'BcaNung00346' => 'bca', 'BolC1t02785H' => 'bol', 'BolC1t04095H' => 'bol', 'BolC3t17545H' => 'bol', 'BolC5t32769H' => 'bol', 'BraA01t02211Z' => 'bra', 'BraA01t03359Z' => 'bra', 'BraA03t13441Z' => 'bra', 'BraA05t21476Z' => 'bra', 'C01p28420' => 'bna', 'C01p41350' => 'bna', 'C03p52750' => 'bna', 'C03p52780' => 'bna', 'C05p40270' => 'bna', 'CAN.G1437.9' => 'can', 'CANSAT78G0035' => 'cansat', 'CANSAT78G1036' => 'cansat', 'CANSAT78G2272' => 'cansat', 'CANSAT78G2478' => 'cansat', 'CARHR098700' => 'chi', 'CARHR221120' => 'chi', 'CARHR221150' => 'chi', 'Carub.0003s2297' => 'cru', 'Carub.0007s2749' => 'cru', 'Carub.0007s2750' => 'cru', 'Carub.0007s2751' => 'cru', 'Ca_10849_v3' => 'car', 'Cc03_g04300' => 'ccan', 'CDE02G3648' => 'cde', 'CDE05G0060' => 'cde', 'CDE05G0692' => 'cde', 'CDE05G2285' => 'cde', 'CDE05G2884' => 'cde', 'CDE05G3072' => 'cde', 'Cfa008439' => 'cfa', 'Cfa008441' => 'cfa', 'Cfa008443' => 'cfa', 'Cfa008448' => 'cfa', 'Ciclev10005974m.g' => 'ccl', 'Ciclev10006006m.g' => 'ccl', 'Ciclev10006775m.g' => 'ccl', 'CiPaw.02G120400' => 'cil', 'CiPaw.02G120500' => 'cil', 'CiPaw.02G120600' => 'cil', 'ClCG05G004850' => 'cla', 'COL.COLO4_21566' => 'col', 'Cpa.g.sc44.124' => 'cpa', 'Cre07.g320400' => 'cre', 'Cre07.g320450' => 'cre', 'Cre08.g384650' => 'cre', 'Cre09.g393173' => 'cre', 'Cre09.g394325' => 'cre', 'Cre14.g626750' => 'cre', 'Cre16.g679250' => 'cre', 'CsaV3_3G012890' => 'csa', 'CSS0010865' => 'camsi', 'CSS0044338' => 'camsi', 'DCAR_002366' => 'dca', 'DCAR_030687' => 'dca', 'DCAR_030688' => 'dca', 'Dinv14047' => 'din', 'Dinv14048' => 'din', 'Duzib151G0105' => 'dzi', 'Duzib151G0114' => 'dzi', 'Duzib212G1029' => 'dzi', 'ECA232G3536' => 'eca', 'ECA240G0786' => 'eca', 'ECA240G1802' => 'eca', 'ECA240G3760' => 'eca', 'ECA240G3920' => 'eca', 'EL10Ac5g12536' => 'bvu', 'EL10Ac5g12537' => 'bvu', 'EL10Ac5g12538' => 'bvu', 'Eucgr.B01004' => 'egr', 'Eucgr.B01006' => 'egr', 'Eucgr.B01007' => 'egr', 'Eucgr.B01008' => 'egr', 'Eucgr.B01895' => 'egr', 'Eucgr.B01896' => 'egr', 'FAN04G1456' => 'fan', 'FAN08G1769' => 'fan', 'FAN08G2160' => 'fan', 'FAN13G2403' => 'fan', 'FAN13G3303' => 'fan', 'FAN15G2435' => 'fan', 'FAN17G0672' => 'fan', 'FAN17G2441' => 'fan', 'FAN18G1024' => 'fan', 'FAN22G1458' => 'fan', 'FAN24G0037' => 'fan', 'FAN24G0429' => 'fan', 'FAN24G2387' => 'fan', 'FAN27G2746' => 'fan', 'FvH4_2g20400' => 'fve', 'FvH4_2g20420' => 'fve', 'FvH4_2g20430' => 'fve', 'FvH4_4g01270' => 'fve', 'FvH4_4g01290' => 'fve', 'FvH4_4g01300' => 'fve', 'FvH4_4g01310' => 'fve', 'FvH4_4g01330' => 'fve', 'FvH4_5g09070' => 'fve', 'Glyma.10G243800' => 'gma', 'Glyma.20G150600' => 'gma', 'Gohir.A09G219200' => 'ghi', 'Gohir.A09G219300' => 'ghi', 'Gohir.D09G221400' => 'ghi', 'Gohir.D09G221500' => 'ghi', 'Gorai.006G242600' => 'gra', 'Gorai.006G242700' => 'gra', 'GSVIVG01018044001' => 'vvi', 'HanXRQChr03g0083821' => 'han', 'HanXRQChr03g0083841' => 'han', 'HanXRQChr03g0083881' => 'han', 'HanXRQChr03g0083901' => 'han', 'HanXRQChr03g0083921' => 'han', 'HanXRQChr03g0085331' => 'han', 'HanXRQChr03g0085361' => 'han', 'HanXRQChr03g0085411' => 'han', 'HanXRQChr03g0085421' => 'han', 'HanXRQChr03g0085431' => 'han', 'HanXRQChr08g0221991' => 'han', 'HanXRQChr11g0336061' => 'han', 'HanXRQChr11g0336411' => 'han', 'Haze_11234' => 'cav', 'Hma1.2p1_0549F.1_g177010' => 'hma', 'Hma1.2p1_0602F.1_g187630' => 'hma', 'Hund14876' => 'sun', 'Hund14879' => 'sun', 'Lalb_Chr06g0160741' => 'lal', 'Lalb_Chr21g0304781' => 'lal', 'Lj3A726G19' => 'lonja', 'Lj3A726T23' => 'lonja', 'Lj3A726T24' => 'lonja', 'Lj3A726T25' => 'lonja', 'Lj3A727T17' => 'lonja', 'Lj3C726T0' => 'lonja', 'Lj3C726T2' => 'lonja', 'Lj3P725T35' => 'lonja', 'Lj3P727T10' => 'lonja', 'Lj3P727T12' => 'lonja', 'Lj3P727T14' => 'lonja', 'Lj5g0023109' => 'lja', 'Lj6P646T44' => 'lonja', 'Lsat_1_v5_gn_6_75760' => 'lsa', 'Lsat_1_v5_gn_6_75800' => 'lsa', 'Lsat_1_v5_gn_6_75900' => 'lsa', 'Lsat_1_v5_gn_6_76240' => 'lsa', 'Lsat_1_v5_gn_6_76441' => 'lsa', 'Lsat_1_v5_gn_6_76700' => 'lsa', 'Lsat_1_v5_gn_6_76760' => 'lsa', 'Manes.15G033100' => 'mes', 'Mapoly0004s0074' => 'mpo', 'Mapoly0004s0075' => 'mpo', 'Mapoly0004s0163' => 'mpo', 'Mapoly0004s0164' => 'mpo', 'Mapoly0021s0018' => 'mpo', 'Mapoly0041s0136' => 'mpo', 'Mapoly0041s0137' => 'mpo', 'Mapoly0041s0138' => 'mpo', 'Mapoly0041s0139' => 'mpo', 'Mapoly0041s0141' => 'mpo', 'Mapoly0041s0142' => 'mpo', 'Mapoly0041s0143' => 'mpo', 'Mapoly0041s0144' => 'mpo', 'Mapoly0041s0145' => 'mpo', 'Mapoly0047s0106' => 'mpo', 'Mapoly0047s0108' => 'mpo', 'Mapoly0050s0051' => 'mpo', 'Mapoly0050s0052' => 'mpo', 'Mapoly0050s0053' => 'mpo', 'Mapoly0058s0013' => 'mpo', 'Mapoly0091s0078' => 'mpo', 'Mapoly0091s0079' => 'mpo', 'Mapoly0091s0080' => 'mpo', 'Mapoly0091s0081' => 'mpo', 'Mapoly0278s0004' => 'mpo', 'Mapoly0278s0005' => 'mpo', 'Mapoly0278s0006' => 'mpo', 'MBI11_g30648_MAGBIO' => 'mbi', 'MCO03G194' => 'mco', 'MCO03G590' => 'mco', 'MCO07G312' => 'mco', 'MCO10G318' => 'mco', 'MCO12G244' => 'mco', 'MCO13G148' => 'mco', 'MCO13G194' => 'mco', 'MCO16G238' => 'mco', 'MD06G1134100' => 'mdo', 'MD13G1200100' => 'mdo', 'MD13G1200300' => 'mdo', 'MD13G1200600' => 'mdo', 'MD14G1150400' => 'mdo', 'MD16G1200000' => 'mdo', 'Medtr1g102570' => 'mtr', 'Medtr1g102780' => 'mtr', 'Medtr1g102800' => 'mtr', 'Medtr1g102810' => 'mtr', 'Medtr1g102830' => 'mtr', 'MELO3C006499.2' => 'cme', 'Migut.G00385' => 'egut', 'MSTRG.4063' => 'ama', 'Nitab4.5_0000090g0260' => 'nta', 'Nitab4.5_0000977g0030' => 'nta', 'Nitab4.5_0002541g0040' => 'nta', 'Nitab4.5_0007068g0040' => 'nta', 'Nn005s41408' => 'nnu', 'Nn005s41410' => 'nnu', 'Oeu010310.1' => 'oeu', 'Oeu010311.1' => 'oeu', 'Oeu043472.1' => 'oeu', 'Os01g0246400' => 'osa', 'Os04g0267950' => 'osa', 'Os07g0178700' => 'osa', 'Os07g0178800' => 'osa', 'Peaxi162Scf00316g00046' => 'pax', 'Peaxi162Scf00316g00049' => 'pax', 'Peaxi162Scf00316g00059' => 'pax', 'Peaxi162Scf00316g00328' => 'pax', 'Peaxi162Scf00316g00329' => 'pax', 'Peaxi162Scf00316g00411' => 'pax', 'Peaxi162Scf00316g00521' => 'pax', 'Peaxi162Scf00492g00068' => 'pax', 'Peaxi162Scf35631g00002' => 'pax', 'PGR142G3720' => 'pgr', 'PGSC0003DMG400006442' => 'stu', 'Phvul.007G062000' => 'pvu', 'Potri.008G157750' => 'ptr', 'Potri.008G157900' => 'ptr', 'Potri.008G158000' => 'ptr', 'Potri.008G158200' => 'ptr', 'Pp3c11_7280' => 'ppa', 'Pp3c11_7980' => 'ppa', 'Pp3c12_19450' => 'ppa', 'Pp3c14_1480' => 'ppa', 'Pp3c14_1501' => 'ppa', 'Pp3c16_4900' => 'ppa', 'Pp3c16_5010' => 'ppa', 'Pp3c16_5060' => 'ppa', 'Pp3c19_18250' => 'ppa', 'Pp3c23_8530' => 'ppa', 'Pp3c23_8550' => 'ppa', 'Pp3c24_9670' => 'ppa', 'Pp3c2_21390' => 'ppa', 'Pp3c2_31380' => 'ppa', 'Pp3c3_16620' => 'ppa', 'Pp3c3_8090' => 'ppa', 'Pp3c3_8110' => 'ppa', 'Pp3c3_8130' => 'ppa', 'Pp3c3_8150' => 'ppa', 'Pp3c4_14320' => 'ppa', 'Pp3c6_2560' => 'ppa', 'Pp3c9_16700' => 'ppa', 'PRCOL_00000234' => 'pco', 'PRCOL_00000235' => 'pco', 'PRCOL_00000777' => 'pco', 'PRCOL_00002344' => 'pco', 'PRCOL_00002372' => 'pco', 'PRCOL_00006120' => 'pco', 'Prupe.1G021400' => 'ppe', 'Prupe.1G021500' => 'ppe', 'Prupe.1G021600' => 'ppe', 'Prupe.1G021700' => 'ppe', 'Prupe.1G021800' => 'ppe', 'Prupe.5G145100' => 'ppe', 'Psat6g204040' => 'psa', 'Psat6g204800' => 'psa', 'Psat6g204920' => 'psa', 'Psat6g204960' => 'psa', 'Psat6g205080' => 'psa', 'PSO017G0271' => 'pso', 'PSO017G1276' => 'pso', 'PSO017G1429' => 'pso', 'PSO017G1861' => 'pso', 'PSO017G2787' => 'pso', 'PSO017G4466' => 'pso', 'PSO017G5118' => 'pso', 'PSO017G5420' => 'pso', 'PSO063G3678' => 'pso', 'PSO210G0546' => 'pso', 'PSO317G0001' => 'pso', 'PSO357G0512' => 'pso', 'PSO478G2682' => 'pso', 'PSO647G0001' => 'pso', 'PSO675G0001' => 'pso', 'PSO675G2699' => 'pso', 'PSO675G2849' => 'pso', 'PSO675G4991' => 'pso', 'PSO689G0001' => 'pso', 'QL06p000916' => 'qlo', 'QL06p000921' => 'qlo', 'QL06p001398' => 'qlo', 'QL06p001407' => 'qlo', 'QL06p002031' => 'qlo', 'RcHm_v2.0_Chr4g0387791' => 'rch', 'RcHm_v2.0_Chr4g0387801' => 'rch', 'RcHm_v2.0_Chr6g0286501' => 'rch', 'RcHm_v2.0_Chr6g0286511' => 'rch', 'RcHm_v2.0_Chr6g0286521' => 'rch', 'RcHm_v2.0_Chr6g0286531' => 'rch', 'RcHm_v2.0_Chr7g0189141' => 'rch', 'Rhsim02G0028700' => 'rsi', 'Rhsim02G0028800' => 'rsi', 'Rhsim02G0028900' => 'rsi', 'Rhsim02G0029000' => 'rsi', 'Rhsim02G0029100' => 'rsi', 'Rhsim02G0029200' => 'rsi', 'Rhsim02G0029300' => 'rsi', 'Rhsim02G0029400' => 'rsi', 'Rhsim02G0029500' => 'rsi', 'Rhsim02G0029600' => 'rsi', 'RhsimUnG0024000' => 'rsi', 'RhsimUnG0024100' => 'rsi', 'RhsimUnG0024200' => 'rsi', 'RhsimUnG0024300' => 'rsi', 'RhsimUnG0024400' => 'rsi', 'RhsimUnG0024500' => 'rsi', 'RhsimUnG0024700' => 'rsi', 'RhsimUnG0024800' => 'rsi', 'RhsimUnG0024900' => 'rsi', 'RhsimUnG0025100' => 'rsi', 'Sabra08G0120200' => 'sbr', 'Sabra08G0120300' => 'sbr', 'Sabra08G0120500' => 'sbr', 'Sabra08G0120600' => 'sbr', 'Sabra10G0158900' => 'sbr', 'SalBow2G3492' => 'sbo', 'Sc13g0004760' => 'sci', 'Sc13g0004770' => 'sci', 'Sed0003417' => 'sed', 'Sed0019750' => 'sed', 'SEGI_03419' => 'sgi', 'SEGI_05907' => 'sgi', 'SEGI_10682' => 'sgi', 'SEGI_13528' => 'sgi', 'SEGI_16081' => 'sgi', 'SEGI_19370' => 'sgi', 'SEGI_21015' => 'sgi', 'SEGI_21944' => 'sgi', 'SEGI_32906' => 'sgi', 'SEGI_33093' => 'sgi', 'SEGI_36110' => 'sgi', 'SEGI_40397' => 'sgi', 'SGA_v2.0_scaffold191G40426' => 'sas', 'SGA_v2.0_scaffold353G49717' => 'sas', 'SGA_v2.0_scaffold50G18550' => 'sas', 'SMO119G0173' => 'smo', 'SMO172G0002' => 'smo', 'Solyc09g082690.3' => 'sly', 'Solyc09g082700.2' => 'sly', 'Sopen09g031550' => 'spe', 'Sopen09g031560' => 'spe', 'Sp3g20540' => 'spa', 'Sp7g07580' => 'spa', 'TAR134G0002' => 'tar', 'TAR236G0001' => 'tar', 'TAR365G0892' => 'tar', 'TAR636G0166' => 'tar', 'TAR636G0646' => 'tar', 'TAR636G0869' => 'tar', 'TAR636G1317' => 'tar', 'TAR636G1744' => 'tar', 'TAR636G3358' => 'tar', 'TAR636G3436' => 'tar', 'THA.LOC104803047' => 'tha', 'Thecc.04G238900' => 'tca', 'Thhalv10021557m.g' => 'esa', 'Thhalv10026318m.g' => 'esa', 'Thhalv10026335m.g' => 'esa', 'TPR.G17433' => 'tpr', 'TPR.G18915' => 'tpr', 'TPR.G26125' => 'tpr', 'TWI09G0677' => 'twi', 'TWI73G0287' => 'twi', 'unitig_748.g8326' => 'ugi', 'vmacro15370' => 'vma', 'vmacro15371' => 'vma', 'vmacro15372' => 'vma', 'vmacro15373' => 'vma', 'vmacro15374' => 'vma', 'VMungo0720G2826' => 'vmu', 'Zm00001eb116960' => 'zma', 'Zm00001eb301260' => 'zma', 'Zm00001eb301270' => 'zma' ) $gf_id = 'HOM05D001460' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001460' ) $data_identifier = 'HOM05D001460' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 4, 'aag' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 2, 'aox' => (int) 2, 'arhy' => (int) 4, 'ath' => (int) 2, 'atr' => (int) 1, 'acertr' => (int) 10, 'cqu' => (int) 4, 'bca' => (int) 11, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 1, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 1, 'ccan' => (int) 1, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 1, 'col' => (int) 1, 'cpa' => (int) 1, 'cre' => (int) 7, 'csa' => (int) 1, 'camsi' => (int) 2, 'dca' => (int) 3, 'din' => (int) 2, 'dzi' => (int) 3, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 14, 'fve' => (int) 9, 'gma' => (int) 2, 'ghi' => (int) 4, 'gra' => (int) 2, 'vvi' => (int) 1, 'han' => (int) 13, 'cav' => (int) 1, 'hma' => (int) 2, 'sun' => (int) 2, 'lal' => (int) 2, 'lonja' => (int) 12, 'lja' => (int) 1, 'lsa' => (int) 7, 'mes' => (int) 1, 'mpo' => (int) 27, 'mbi' => (int) 1, 'mco' => (int) 8, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 1, 'egut' => (int) 1, 'ama' => (int) 1, 'nta' => (int) 4, 'nnu' => (int) 2, 'oeu' => (int) 3, 'osa' => (int) 4, 'pax' => (int) 9, 'pgr' => (int) 1, 'stu' => (int) 1, 'pvu' => (int) 1, 'ptr' => (int) 4, 'ppa' => (int) 22, 'pco' => (int) 6, 'ppe' => (int) 6, 'psa' => (int) 5, 'pso' => (int) 19, 'qlo' => (int) 5, 'rch' => (int) 7, 'rsi' => (int) 20, 'sbr' => (int) 5, 'sbo' => (int) 1, 'sci' => (int) 2, 'sed' => (int) 2, 'sgi' => (int) 12, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 2, 'tar' => (int) 10, 'tha' => (int) 1, 'tca' => (int) 1, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 2, 'ugi' => (int) 1, 'vma' => (int) 5, 'vmu' => (int) 1, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb301270' $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' => 'HOM05D001460', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '433', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p22980' => 'bna', 'A01p32340' => 'bna', 'A03p42970' => 'bna', 'A05p25880' => 'bna', 'Aa31LG8G9320' => 'aar', 'Aa31LG8G9330' => 'aar', 'Aa31LG8G9340' => 'aar', 'Aa31sc221G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1034' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1528' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.829' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2222' => 'aag', 'Ah.12g058830' => 'amhyb', 'Ah.12g058840' => 'amhyb', 'AL3G37160' => 'aly', 'AL7G41310' => 'aly', 'Aqoxy5G00395' => 'aox', 'Aqoxy5G00396' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0C8NZA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5185HY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JZ1PRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MD3LS0' => 'arhy', 'AT3G22840' => 'ath', 'AT4G14690' => 'ath', 'ATR0665G054' => 'atr', 'Atru.chr4.2344' => 'acertr', 'Atru.chr4.2346' => 'acertr', 'Atru.chr4.2347' => 'acertr', 'Atru.chr4.2348' => 'acertr', 'Atru.chr4.2355' => 'acertr', 'Atru.chr4.2356' => 'acertr', 'Atru.chr4.2358' => 'acertr', 'Atru.chr4.2359' => 'acertr', 'Atru.chr4.2360' => 'acertr', 'Atru.chr4.2361' => 'acertr', 'AUR62030476' => 'cqu', 'AUR62030478' => 'cqu', 'AUR62030819' => 'cqu', 'AUR62030820' => 'cqu', 'BcaB03g14648' => 'bca', 'BcaB04g20492' => 'bca', 'BcaB06g26399' => 'bca', 'BcaC01g03416' => 'bca', 'BcaC01g03419' => 'bca', 'BcaC01g03421' => 'bca', 'BcaC01g03424' => 'bca', 'BcaC05g28012' => 'bca', 'BcaC09g49212' => 'bca', 'BcaC09g50140' => 'bca', 'BcaNung00346' => 'bca', 'BolC1t02785H' => 'bol', 'BolC1t04095H' => 'bol', 'BolC3t17545H' => 'bol', 'BolC5t32769H' => 'bol', 'BraA01t02211Z' => 'bra', 'BraA01t03359Z' => 'bra', 'BraA03t13441Z' => 'bra', 'BraA05t21476Z' => 'bra', 'C01p28420' => 'bna', 'C01p41350' => 'bna', 'C03p52750' => 'bna', 'C03p52780' => 'bna', 'C05p40270' => 'bna', 'CAN.G1437.9' => 'can', 'CANSAT78G0035' => 'cansat', 'CANSAT78G1036' => 'cansat', 'CANSAT78G2272' => 'cansat', 'CANSAT78G2478' => 'cansat', 'CARHR098700' => 'chi', 'CARHR221120' => 'chi', 'CARHR221150' => 'chi', 'Carub.0003s2297' => 'cru', 'Carub.0007s2749' => 'cru', 'Carub.0007s2750' => 'cru', 'Carub.0007s2751' => 'cru', 'Ca_10849_v3' => 'car', 'Cc03_g04300' => 'ccan', 'CDE02G3648' => 'cde', 'CDE05G0060' => 'cde', 'CDE05G0692' => 'cde', 'CDE05G2285' => 'cde', 'CDE05G2884' => 'cde', 'CDE05G3072' => 'cde', 'Cfa008439' => 'cfa', 'Cfa008441' => 'cfa', 'Cfa008443' => 'cfa', 'Cfa008448' => 'cfa', 'Ciclev10005974m.g' => 'ccl', 'Ciclev10006006m.g' => 'ccl', 'Ciclev10006775m.g' => 'ccl', 'CiPaw.02G120400' => 'cil', 'CiPaw.02G120500' => 'cil', 'CiPaw.02G120600' => 'cil', 'ClCG05G004850' => 'cla', 'COL.COLO4_21566' => 'col', 'Cpa.g.sc44.124' => 'cpa', 'Cre07.g320400' => 'cre', 'Cre07.g320450' => 'cre', 'Cre08.g384650' => 'cre', 'Cre09.g393173' => 'cre', 'Cre09.g394325' => 'cre', 'Cre14.g626750' => 'cre', 'Cre16.g679250' => 'cre', 'CsaV3_3G012890' => 'csa', 'CSS0010865' => 'camsi', 'CSS0044338' => 'camsi', 'DCAR_002366' => 'dca', 'DCAR_030687' => 'dca', 'DCAR_030688' => 'dca', 'Dinv14047' => 'din', 'Dinv14048' => 'din', 'Duzib151G0105' => 'dzi', 'Duzib151G0114' => 'dzi', 'Duzib212G1029' => 'dzi', 'ECA232G3536' => 'eca', 'ECA240G0786' => 'eca', 'ECA240G1802' => 'eca', 'ECA240G3760' => 'eca', 'ECA240G3920' => 'eca', 'EL10Ac5g12536' => 'bvu', 'EL10Ac5g12537' => 'bvu', 'EL10Ac5g12538' => 'bvu', 'Eucgr.B01004' => 'egr', 'Eucgr.B01006' => 'egr', 'Eucgr.B01007' => 'egr', 'Eucgr.B01008' => 'egr', 'Eucgr.B01895' => 'egr', 'Eucgr.B01896' => 'egr', 'FAN04G1456' => 'fan', 'FAN08G1769' => 'fan', 'FAN08G2160' => 'fan', 'FAN13G2403' => 'fan', 'FAN13G3303' => 'fan', 'FAN15G2435' => 'fan', 'FAN17G0672' => 'fan', 'FAN17G2441' => 'fan', 'FAN18G1024' => 'fan', 'FAN22G1458' => 'fan', 'FAN24G0037' => 'fan', 'FAN24G0429' => 'fan', 'FAN24G2387' => 'fan', 'FAN27G2746' => 'fan', 'FvH4_2g20400' => 'fve', 'FvH4_2g20420' => 'fve', 'FvH4_2g20430' => 'fve', 'FvH4_4g01270' => 'fve', 'FvH4_4g01290' => 'fve', 'FvH4_4g01300' => 'fve', 'FvH4_4g01310' => 'fve', 'FvH4_4g01330' => 'fve', 'FvH4_5g09070' => 'fve', 'Glyma.10G243800' => 'gma', 'Glyma.20G150600' => 'gma', 'Gohir.A09G219200' => 'ghi', 'Gohir.A09G219300' => 'ghi', 'Gohir.D09G221400' => 'ghi', 'Gohir.D09G221500' => 'ghi', 'Gorai.006G242600' => 'gra', 'Gorai.006G242700' => 'gra', 'GSVIVG01018044001' => 'vvi', 'HanXRQChr03g0083821' => 'han', 'HanXRQChr03g0083841' => 'han', 'HanXRQChr03g0083881' => 'han', 'HanXRQChr03g0083901' => 'han', 'HanXRQChr03g0083921' => 'han', 'HanXRQChr03g0085331' => 'han', 'HanXRQChr03g0085361' => 'han', 'HanXRQChr03g0085411' => 'han', 'HanXRQChr03g0085421' => 'han', 'HanXRQChr03g0085431' => 'han', 'HanXRQChr08g0221991' => 'han', 'HanXRQChr11g0336061' => 'han', 'HanXRQChr11g0336411' => 'han', 'Haze_11234' => 'cav', 'Hma1.2p1_0549F.1_g177010' => 'hma', 'Hma1.2p1_0602F.1_g187630' => 'hma', 'Hund14876' => 'sun', 'Hund14879' => 'sun', 'Lalb_Chr06g0160741' => 'lal', 'Lalb_Chr21g0304781' => 'lal', 'Lj3A726G19' => 'lonja', 'Lj3A726T23' => 'lonja', 'Lj3A726T24' => 'lonja', 'Lj3A726T25' => 'lonja', 'Lj3A727T17' => 'lonja', 'Lj3C726T0' => 'lonja', 'Lj3C726T2' => 'lonja', 'Lj3P725T35' => 'lonja', 'Lj3P727T10' => 'lonja', 'Lj3P727T12' => 'lonja', 'Lj3P727T14' => 'lonja', 'Lj5g0023109' => 'lja', 'Lj6P646T44' => 'lonja', 'Lsat_1_v5_gn_6_75760' => 'lsa', 'Lsat_1_v5_gn_6_75800' => 'lsa', 'Lsat_1_v5_gn_6_75900' => 'lsa', 'Lsat_1_v5_gn_6_76240' => 'lsa', 'Lsat_1_v5_gn_6_76441' => 'lsa', 'Lsat_1_v5_gn_6_76700' => 'lsa', 'Lsat_1_v5_gn_6_76760' => 'lsa', 'Manes.15G033100' => 'mes', 'Mapoly0004s0074' => 'mpo', 'Mapoly0004s0075' => 'mpo', 'Mapoly0004s0163' => 'mpo', 'Mapoly0004s0164' => 'mpo', 'Mapoly0021s0018' => 'mpo', 'Mapoly0041s0136' => 'mpo', 'Mapoly0041s0137' => 'mpo', 'Mapoly0041s0138' => 'mpo', 'Mapoly0041s0139' => 'mpo', 'Mapoly0041s0141' => 'mpo', 'Mapoly0041s0142' => 'mpo', 'Mapoly0041s0143' => 'mpo', 'Mapoly0041s0144' => 'mpo', 'Mapoly0041s0145' => 'mpo', 'Mapoly0047s0106' => 'mpo', 'Mapoly0047s0108' => 'mpo', 'Mapoly0050s0051' => 'mpo', 'Mapoly0050s0052' => 'mpo', 'Mapoly0050s0053' => 'mpo', 'Mapoly0058s0013' => 'mpo', 'Mapoly0091s0078' => 'mpo', 'Mapoly0091s0079' => 'mpo', 'Mapoly0091s0080' => 'mpo', 'Mapoly0091s0081' => 'mpo', 'Mapoly0278s0004' => 'mpo', 'Mapoly0278s0005' => 'mpo', 'Mapoly0278s0006' => 'mpo', 'MBI11_g30648_MAGBIO' => 'mbi', 'MCO03G194' => 'mco', 'MCO03G590' => 'mco', 'MCO07G312' => 'mco', 'MCO10G318' => 'mco', 'MCO12G244' => 'mco', 'MCO13G148' => 'mco', 'MCO13G194' => 'mco', 'MCO16G238' => 'mco', 'MD06G1134100' => 'mdo', 'MD13G1200100' => 'mdo', 'MD13G1200300' => 'mdo', 'MD13G1200600' => 'mdo', 'MD14G1150400' => 'mdo', 'MD16G1200000' => 'mdo', 'Medtr1g102570' => 'mtr', 'Medtr1g102780' => 'mtr', 'Medtr1g102800' => 'mtr', 'Medtr1g102810' => 'mtr', 'Medtr1g102830' => 'mtr', 'MELO3C006499.2' => 'cme', 'Migut.G00385' => 'egut', 'MSTRG.4063' => 'ama', 'Nitab4.5_0000090g0260' => 'nta', 'Nitab4.5_0000977g0030' => 'nta', 'Nitab4.5_0002541g0040' => 'nta', 'Nitab4.5_0007068g0040' => 'nta', 'Nn005s41408' => 'nnu', 'Nn005s41410' => 'nnu', 'Oeu010310.1' => 'oeu', 'Oeu010311.1' => 'oeu', 'Oeu043472.1' => 'oeu', 'Os01g0246400' => 'osa', 'Os04g0267950' => 'osa', 'Os07g0178700' => 'osa', 'Os07g0178800' => 'osa', 'Peaxi162Scf00316g00046' => 'pax', 'Peaxi162Scf00316g00049' => 'pax', 'Peaxi162Scf00316g00059' => 'pax', 'Peaxi162Scf00316g00328' => 'pax', 'Peaxi162Scf00316g00329' => 'pax', 'Peaxi162Scf00316g00411' => 'pax', 'Peaxi162Scf00316g00521' => 'pax', 'Peaxi162Scf00492g00068' => 'pax', 'Peaxi162Scf35631g00002' => 'pax', 'PGR142G3720' => 'pgr', 'PGSC0003DMG400006442' => 'stu', 'Phvul.007G062000' => 'pvu', 'Potri.008G157750' => 'ptr', 'Potri.008G157900' => 'ptr', 'Potri.008G158000' => 'ptr', 'Potri.008G158200' => 'ptr', 'Pp3c11_7280' => 'ppa', 'Pp3c11_7980' => 'ppa', 'Pp3c12_19450' => 'ppa', 'Pp3c14_1480' => 'ppa', 'Pp3c14_1501' => 'ppa', 'Pp3c16_4900' => 'ppa', 'Pp3c16_5010' => 'ppa', 'Pp3c16_5060' => 'ppa', 'Pp3c19_18250' => 'ppa', 'Pp3c23_8530' => 'ppa', 'Pp3c23_8550' => 'ppa', 'Pp3c24_9670' => 'ppa', 'Pp3c2_21390' => 'ppa', 'Pp3c2_31380' => 'ppa', 'Pp3c3_16620' => 'ppa', 'Pp3c3_8090' => 'ppa', 'Pp3c3_8110' => 'ppa', 'Pp3c3_8130' => 'ppa', 'Pp3c3_8150' => 'ppa', 'Pp3c4_14320' => 'ppa', 'Pp3c6_2560' => 'ppa', 'Pp3c9_16700' => 'ppa', 'PRCOL_00000234' => 'pco', 'PRCOL_00000235' => 'pco', 'PRCOL_00000777' => 'pco', 'PRCOL_00002344' => 'pco', 'PRCOL_00002372' => 'pco', 'PRCOL_00006120' => 'pco', 'Prupe.1G021400' => 'ppe', 'Prupe.1G021500' => 'ppe', 'Prupe.1G021600' => 'ppe', 'Prupe.1G021700' => 'ppe', 'Prupe.1G021800' => 'ppe', 'Prupe.5G145100' => 'ppe', 'Psat6g204040' => 'psa', 'Psat6g204800' => 'psa', 'Psat6g204920' => 'psa', 'Psat6g204960' => 'psa', 'Psat6g205080' => 'psa', 'PSO017G0271' => 'pso', 'PSO017G1276' => 'pso', 'PSO017G1429' => 'pso', 'PSO017G1861' => 'pso', 'PSO017G2787' => 'pso', 'PSO017G4466' => 'pso', 'PSO017G5118' => 'pso', 'PSO017G5420' => 'pso', 'PSO063G3678' => 'pso', 'PSO210G0546' => 'pso', 'PSO317G0001' => 'pso', 'PSO357G0512' => 'pso', 'PSO478G2682' => 'pso', 'PSO647G0001' => 'pso', 'PSO675G0001' => 'pso', 'PSO675G2699' => 'pso', 'PSO675G2849' => 'pso', 'PSO675G4991' => 'pso', 'PSO689G0001' => 'pso', 'QL06p000916' => 'qlo', 'QL06p000921' => 'qlo', 'QL06p001398' => 'qlo', 'QL06p001407' => 'qlo', 'QL06p002031' => 'qlo', 'RcHm_v2.0_Chr4g0387791' => 'rch', 'RcHm_v2.0_Chr4g0387801' => 'rch', 'RcHm_v2.0_Chr6g0286501' => 'rch', 'RcHm_v2.0_Chr6g0286511' => 'rch', 'RcHm_v2.0_Chr6g0286521' => 'rch', 'RcHm_v2.0_Chr6g0286531' => 'rch', 'RcHm_v2.0_Chr7g0189141' => 'rch', 'Rhsim02G0028700' => 'rsi', 'Rhsim02G0028800' => 'rsi', 'Rhsim02G0028900' => 'rsi', 'Rhsim02G0029000' => 'rsi', 'Rhsim02G0029100' => 'rsi', 'Rhsim02G0029200' => 'rsi', 'Rhsim02G0029300' => 'rsi', 'Rhsim02G0029400' => 'rsi', 'Rhsim02G0029500' => 'rsi', 'Rhsim02G0029600' => 'rsi', 'RhsimUnG0024000' => 'rsi', 'RhsimUnG0024100' => 'rsi', 'RhsimUnG0024200' => 'rsi', 'RhsimUnG0024300' => 'rsi', 'RhsimUnG0024400' => 'rsi', 'RhsimUnG0024500' => 'rsi', 'RhsimUnG0024700' => 'rsi', 'RhsimUnG0024800' => 'rsi', 'RhsimUnG0024900' => 'rsi', 'RhsimUnG0025100' => 'rsi', 'Sabra08G0120200' => 'sbr', 'Sabra08G0120300' => 'sbr', 'Sabra08G0120500' => 'sbr', 'Sabra08G0120600' => 'sbr', 'Sabra10G0158900' => 'sbr', 'SalBow2G3492' => 'sbo', 'Sc13g0004760' => 'sci', 'Sc13g0004770' => 'sci', 'Sed0003417' => 'sed', 'Sed0019750' => 'sed', 'SEGI_03419' => 'sgi', 'SEGI_05907' => 'sgi', 'SEGI_10682' => 'sgi', 'SEGI_13528' => 'sgi', 'SEGI_16081' => 'sgi', 'SEGI_19370' => 'sgi', 'SEGI_21015' => 'sgi', 'SEGI_21944' => 'sgi', 'SEGI_32906' => 'sgi', 'SEGI_33093' => 'sgi', 'SEGI_36110' => 'sgi', 'SEGI_40397' => 'sgi', 'SGA_v2.0_scaffold191G40426' => 'sas', 'SGA_v2.0_scaffold353G49717' => 'sas', 'SGA_v2.0_scaffold50G18550' => 'sas', 'SMO119G0173' => 'smo', 'SMO172G0002' => 'smo', 'Solyc09g082690.3' => 'sly', 'Solyc09g082700.2' => 'sly', 'Sopen09g031550' => 'spe', 'Sopen09g031560' => 'spe', 'Sp3g20540' => 'spa', 'Sp7g07580' => 'spa', 'TAR134G0002' => 'tar', 'TAR236G0001' => 'tar', 'TAR365G0892' => 'tar', 'TAR636G0166' => 'tar', 'TAR636G0646' => 'tar', 'TAR636G0869' => 'tar', 'TAR636G1317' => 'tar', 'TAR636G1744' => 'tar', 'TAR636G3358' => 'tar', 'TAR636G3436' => 'tar', 'THA.LOC104803047' => 'tha', 'Thecc.04G238900' => 'tca', 'Thhalv10021557m.g' => 'esa', 'Thhalv10026318m.g' => 'esa', 'Thhalv10026335m.g' => 'esa', 'TPR.G17433' => 'tpr', 'TPR.G18915' => 'tpr', 'TPR.G26125' => 'tpr', 'TWI09G0677' => 'twi', 'TWI73G0287' => 'twi', 'unitig_748.g8326' => 'ugi', 'vmacro15370' => 'vma', 'vmacro15371' => 'vma', 'vmacro15372' => 'vma', 'vmacro15373' => 'vma', 'vmacro15374' => 'vma', 'VMungo0720G2826' => 'vmu', 'Zm00001eb116960' => 'zma', 'Zm00001eb301260' => 'zma', 'Zm00001eb301270' => 'zma' ), 'gf_id' => 'HOM05D001460', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001460' ), 'data_identifier' => 'HOM05D001460', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001460', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '433', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p22980' => 'bna', 'A01p32340' => 'bna', 'A03p42970' => 'bna', 'A05p25880' => 'bna', 'Aa31LG8G9320' => 'aar', 'Aa31LG8G9330' => 'aar', 'Aa31LG8G9340' => 'aar', 'Aa31sc221G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1034' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1528' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.829' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2222' => 'aag', 'Ah.12g058830' => 'amhyb', 'Ah.12g058840' => 'amhyb', 'AL3G37160' => 'aly', 'AL7G41310' => 'aly', 'Aqoxy5G00395' => 'aox', 'Aqoxy5G00396' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0C8NZA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5185HY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JZ1PRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MD3LS0' => 'arhy', 'AT3G22840' => 'ath', 'AT4G14690' => 'ath', 'ATR0665G054' => 'atr', 'Atru.chr4.2344' => 'acertr', 'Atru.chr4.2346' => 'acertr', 'Atru.chr4.2347' => 'acertr', 'Atru.chr4.2348' => 'acertr', 'Atru.chr4.2355' => 'acertr', 'Atru.chr4.2356' => 'acertr', 'Atru.chr4.2358' => 'acertr', 'Atru.chr4.2359' => 'acertr', 'Atru.chr4.2360' => 'acertr', 'Atru.chr4.2361' => 'acertr', 'AUR62030476' => 'cqu', 'AUR62030478' => 'cqu', 'AUR62030819' => 'cqu', 'AUR62030820' => 'cqu', 'BcaB03g14648' => 'bca', 'BcaB04g20492' => 'bca', 'BcaB06g26399' => 'bca', 'BcaC01g03416' => 'bca', 'BcaC01g03419' => 'bca', 'BcaC01g03421' => 'bca', 'BcaC01g03424' => 'bca', 'BcaC05g28012' => 'bca', 'BcaC09g49212' => 'bca', 'BcaC09g50140' => 'bca', 'BcaNung00346' => 'bca', 'BolC1t02785H' => 'bol', 'BolC1t04095H' => 'bol', 'BolC3t17545H' => 'bol', 'BolC5t32769H' => 'bol', 'BraA01t02211Z' => 'bra', 'BraA01t03359Z' => 'bra', 'BraA03t13441Z' => 'bra', 'BraA05t21476Z' => 'bra', 'C01p28420' => 'bna', 'C01p41350' => 'bna', 'C03p52750' => 'bna', 'C03p52780' => 'bna', 'C05p40270' => 'bna', 'CAN.G1437.9' => 'can', 'CANSAT78G0035' => 'cansat', 'CANSAT78G1036' => 'cansat', 'CANSAT78G2272' => 'cansat', 'CANSAT78G2478' => 'cansat', 'CARHR098700' => 'chi', 'CARHR221120' => 'chi', 'CARHR221150' => 'chi', 'Carub.0003s2297' => 'cru', 'Carub.0007s2749' => 'cru', 'Carub.0007s2750' => 'cru', 'Carub.0007s2751' => 'cru', 'Ca_10849_v3' => 'car', 'Cc03_g04300' => 'ccan', 'CDE02G3648' => 'cde', 'CDE05G0060' => 'cde', 'CDE05G0692' => 'cde', 'CDE05G2285' => 'cde', 'CDE05G2884' => 'cde', 'CDE05G3072' => 'cde', 'Cfa008439' => 'cfa', 'Cfa008441' => 'cfa', 'Cfa008443' => 'cfa', 'Cfa008448' => 'cfa', 'Ciclev10005974m.g' => 'ccl', 'Ciclev10006006m.g' => 'ccl', 'Ciclev10006775m.g' => 'ccl', 'CiPaw.02G120400' => 'cil', 'CiPaw.02G120500' => 'cil', 'CiPaw.02G120600' => 'cil', 'ClCG05G004850' => 'cla', 'COL.COLO4_21566' => 'col', 'Cpa.g.sc44.124' => 'cpa', 'Cre07.g320400' => 'cre', 'Cre07.g320450' => 'cre', 'Cre08.g384650' => 'cre', 'Cre09.g393173' => 'cre', 'Cre09.g394325' => 'cre', 'Cre14.g626750' => 'cre', 'Cre16.g679250' => 'cre', 'CsaV3_3G012890' => 'csa', 'CSS0010865' => 'camsi', 'CSS0044338' => 'camsi', 'DCAR_002366' => 'dca', 'DCAR_030687' => 'dca', 'DCAR_030688' => 'dca', 'Dinv14047' => 'din', 'Dinv14048' => 'din', 'Duzib151G0105' => 'dzi', 'Duzib151G0114' => 'dzi', 'Duzib212G1029' => 'dzi', 'ECA232G3536' => 'eca', 'ECA240G0786' => 'eca', 'ECA240G1802' => 'eca', 'ECA240G3760' => 'eca', 'ECA240G3920' => 'eca', 'EL10Ac5g12536' => 'bvu', 'EL10Ac5g12537' => 'bvu', 'EL10Ac5g12538' => 'bvu', 'Eucgr.B01004' => 'egr', 'Eucgr.B01006' => 'egr', 'Eucgr.B01007' => 'egr', 'Eucgr.B01008' => 'egr', 'Eucgr.B01895' => 'egr', 'Eucgr.B01896' => 'egr', 'FAN04G1456' => 'fan', 'FAN08G1769' => 'fan', 'FAN08G2160' => 'fan', 'FAN13G2403' => 'fan', 'FAN13G3303' => 'fan', 'FAN15G2435' => 'fan', 'FAN17G0672' => 'fan', 'FAN17G2441' => 'fan', 'FAN18G1024' => 'fan', 'FAN22G1458' => 'fan', 'FAN24G0037' => 'fan', 'FAN24G0429' => 'fan', 'FAN24G2387' => 'fan', 'FAN27G2746' => 'fan', 'FvH4_2g20400' => 'fve', 'FvH4_2g20420' => 'fve', 'FvH4_2g20430' => 'fve', 'FvH4_4g01270' => 'fve', 'FvH4_4g01290' => 'fve', 'FvH4_4g01300' => 'fve', 'FvH4_4g01310' => 'fve', 'FvH4_4g01330' => 'fve', 'FvH4_5g09070' => 'fve', 'Glyma.10G243800' => 'gma', 'Glyma.20G150600' => 'gma', 'Gohir.A09G219200' => 'ghi', 'Gohir.A09G219300' => 'ghi', 'Gohir.D09G221400' => 'ghi', 'Gohir.D09G221500' => 'ghi', 'Gorai.006G242600' => 'gra', 'Gorai.006G242700' => 'gra', 'GSVIVG01018044001' => 'vvi', 'HanXRQChr03g0083821' => 'han', 'HanXRQChr03g0083841' => 'han', 'HanXRQChr03g0083881' => 'han', 'HanXRQChr03g0083901' => 'han', 'HanXRQChr03g0083921' => 'han', 'HanXRQChr03g0085331' => 'han', 'HanXRQChr03g0085361' => 'han', 'HanXRQChr03g0085411' => 'han', 'HanXRQChr03g0085421' => 'han', 'HanXRQChr03g0085431' => 'han', 'HanXRQChr08g0221991' => 'han', 'HanXRQChr11g0336061' => 'han', 'HanXRQChr11g0336411' => 'han', 'Haze_11234' => 'cav', 'Hma1.2p1_0549F.1_g177010' => 'hma', 'Hma1.2p1_0602F.1_g187630' => 'hma', 'Hund14876' => 'sun', 'Hund14879' => 'sun', 'Lalb_Chr06g0160741' => 'lal', 'Lalb_Chr21g0304781' => 'lal', 'Lj3A726G19' => 'lonja', 'Lj3A726T23' => 'lonja', 'Lj3A726T24' => 'lonja', 'Lj3A726T25' => 'lonja', 'Lj3A727T17' => 'lonja', 'Lj3C726T0' => 'lonja', 'Lj3C726T2' => 'lonja', 'Lj3P725T35' => 'lonja', 'Lj3P727T10' => 'lonja', 'Lj3P727T12' => 'lonja', 'Lj3P727T14' => 'lonja', 'Lj5g0023109' => 'lja', 'Lj6P646T44' => 'lonja', 'Lsat_1_v5_gn_6_75760' => 'lsa', 'Lsat_1_v5_gn_6_75800' => 'lsa', 'Lsat_1_v5_gn_6_75900' => 'lsa', 'Lsat_1_v5_gn_6_76240' => 'lsa', 'Lsat_1_v5_gn_6_76441' => 'lsa', 'Lsat_1_v5_gn_6_76700' => 'lsa', 'Lsat_1_v5_gn_6_76760' => 'lsa', 'Manes.15G033100' => 'mes', 'Mapoly0004s0074' => 'mpo', 'Mapoly0004s0075' => 'mpo', 'Mapoly0004s0163' => 'mpo', 'Mapoly0004s0164' => 'mpo', 'Mapoly0021s0018' => 'mpo', 'Mapoly0041s0136' => 'mpo', 'Mapoly0041s0137' => 'mpo', 'Mapoly0041s0138' => 'mpo', 'Mapoly0041s0139' => 'mpo', 'Mapoly0041s0141' => 'mpo', 'Mapoly0041s0142' => 'mpo', 'Mapoly0041s0143' => 'mpo', 'Mapoly0041s0144' => 'mpo', 'Mapoly0041s0145' => 'mpo', 'Mapoly0047s0106' => 'mpo', 'Mapoly0047s0108' => 'mpo', 'Mapoly0050s0051' => 'mpo', 'Mapoly0050s0052' => 'mpo', 'Mapoly0050s0053' => 'mpo', 'Mapoly0058s0013' => 'mpo', 'Mapoly0091s0078' => 'mpo', 'Mapoly0091s0079' => 'mpo', 'Mapoly0091s0080' => 'mpo', 'Mapoly0091s0081' => 'mpo', 'Mapoly0278s0004' => 'mpo', 'Mapoly0278s0005' => 'mpo', 'Mapoly0278s0006' => 'mpo', 'MBI11_g30648_MAGBIO' => 'mbi', 'MCO03G194' => 'mco', 'MCO03G590' => 'mco', 'MCO07G312' => 'mco', 'MCO10G318' => 'mco', 'MCO12G244' => 'mco', 'MCO13G148' => 'mco', 'MCO13G194' => 'mco', 'MCO16G238' => 'mco', 'MD06G1134100' => 'mdo', 'MD13G1200100' => 'mdo', 'MD13G1200300' => 'mdo', 'MD13G1200600' => 'mdo', 'MD14G1150400' => 'mdo', 'MD16G1200000' => 'mdo', 'Medtr1g102570' => 'mtr', 'Medtr1g102780' => 'mtr', 'Medtr1g102800' => 'mtr', 'Medtr1g102810' => 'mtr', 'Medtr1g102830' => 'mtr', 'MELO3C006499.2' => 'cme', 'Migut.G00385' => 'egut', 'MSTRG.4063' => 'ama', 'Nitab4.5_0000090g0260' => 'nta', 'Nitab4.5_0000977g0030' => 'nta', 'Nitab4.5_0002541g0040' => 'nta', 'Nitab4.5_0007068g0040' => 'nta', 'Nn005s41408' => 'nnu', 'Nn005s41410' => 'nnu', 'Oeu010310.1' => 'oeu', 'Oeu010311.1' => 'oeu', 'Oeu043472.1' => 'oeu', 'Os01g0246400' => 'osa', 'Os04g0267950' => 'osa', 'Os07g0178700' => 'osa', 'Os07g0178800' => 'osa', 'Peaxi162Scf00316g00046' => 'pax', 'Peaxi162Scf00316g00049' => 'pax', 'Peaxi162Scf00316g00059' => 'pax', 'Peaxi162Scf00316g00328' => 'pax', 'Peaxi162Scf00316g00329' => 'pax', 'Peaxi162Scf00316g00411' => 'pax', 'Peaxi162Scf00316g00521' => 'pax', 'Peaxi162Scf00492g00068' => 'pax', 'Peaxi162Scf35631g00002' => 'pax', 'PGR142G3720' => 'pgr', 'PGSC0003DMG400006442' => 'stu', 'Phvul.007G062000' => 'pvu', 'Potri.008G157750' => 'ptr', 'Potri.008G157900' => 'ptr', 'Potri.008G158000' => 'ptr', 'Potri.008G158200' => 'ptr', 'Pp3c11_7280' => 'ppa', 'Pp3c11_7980' => 'ppa', 'Pp3c12_19450' => 'ppa', 'Pp3c14_1480' => 'ppa', 'Pp3c14_1501' => 'ppa', 'Pp3c16_4900' => 'ppa', 'Pp3c16_5010' => 'ppa', 'Pp3c16_5060' => 'ppa', 'Pp3c19_18250' => 'ppa', 'Pp3c23_8530' => 'ppa', 'Pp3c23_8550' => 'ppa', 'Pp3c24_9670' => 'ppa', 'Pp3c2_21390' => 'ppa', 'Pp3c2_31380' => 'ppa', 'Pp3c3_16620' => 'ppa', 'Pp3c3_8090' => 'ppa', 'Pp3c3_8110' => 'ppa', 'Pp3c3_8130' => 'ppa', 'Pp3c3_8150' => 'ppa', 'Pp3c4_14320' => 'ppa', 'Pp3c6_2560' => 'ppa', 'Pp3c9_16700' => 'ppa', 'PRCOL_00000234' => 'pco', 'PRCOL_00000235' => 'pco', 'PRCOL_00000777' => 'pco', 'PRCOL_00002344' => 'pco', 'PRCOL_00002372' => 'pco', 'PRCOL_00006120' => 'pco', 'Prupe.1G021400' => 'ppe', 'Prupe.1G021500' => 'ppe', 'Prupe.1G021600' => 'ppe', 'Prupe.1G021700' => 'ppe', 'Prupe.1G021800' => 'ppe', 'Prupe.5G145100' => 'ppe', 'Psat6g204040' => 'psa', 'Psat6g204800' => 'psa', 'Psat6g204920' => 'psa', 'Psat6g204960' => 'psa', 'Psat6g205080' => 'psa', 'PSO017G0271' => 'pso', 'PSO017G1276' => 'pso', 'PSO017G1429' => 'pso', 'PSO017G1861' => 'pso', 'PSO017G2787' => 'pso', 'PSO017G4466' => 'pso', 'PSO017G5118' => 'pso', 'PSO017G5420' => 'pso', 'PSO063G3678' => 'pso', 'PSO210G0546' => 'pso', 'PSO317G0001' => 'pso', 'PSO357G0512' => 'pso', 'PSO478G2682' => 'pso', 'PSO647G0001' => 'pso', 'PSO675G0001' => 'pso', 'PSO675G2699' => 'pso', 'PSO675G2849' => 'pso', 'PSO675G4991' => 'pso', 'PSO689G0001' => 'pso', 'QL06p000916' => 'qlo', 'QL06p000921' => 'qlo', 'QL06p001398' => 'qlo', 'QL06p001407' => 'qlo', 'QL06p002031' => 'qlo', 'RcHm_v2.0_Chr4g0387791' => 'rch', 'RcHm_v2.0_Chr4g0387801' => 'rch', 'RcHm_v2.0_Chr6g0286501' => 'rch', 'RcHm_v2.0_Chr6g0286511' => 'rch', 'RcHm_v2.0_Chr6g0286521' => 'rch', 'RcHm_v2.0_Chr6g0286531' => 'rch', 'RcHm_v2.0_Chr7g0189141' => 'rch', 'Rhsim02G0028700' => 'rsi', 'Rhsim02G0028800' => 'rsi', 'Rhsim02G0028900' => 'rsi', 'Rhsim02G0029000' => 'rsi', 'Rhsim02G0029100' => 'rsi', 'Rhsim02G0029200' => 'rsi', 'Rhsim02G0029300' => 'rsi', 'Rhsim02G0029400' => 'rsi', 'Rhsim02G0029500' => 'rsi', 'Rhsim02G0029600' => 'rsi', 'RhsimUnG0024000' => 'rsi', 'RhsimUnG0024100' => 'rsi', 'RhsimUnG0024200' => 'rsi', 'RhsimUnG0024300' => 'rsi', 'RhsimUnG0024400' => 'rsi', 'RhsimUnG0024500' => 'rsi', 'RhsimUnG0024700' => 'rsi', 'RhsimUnG0024800' => 'rsi', 'RhsimUnG0024900' => 'rsi', 'RhsimUnG0025100' => 'rsi', 'Sabra08G0120200' => 'sbr', 'Sabra08G0120300' => 'sbr', 'Sabra08G0120500' => 'sbr', 'Sabra08G0120600' => 'sbr', 'Sabra10G0158900' => 'sbr', 'SalBow2G3492' => 'sbo', 'Sc13g0004760' => 'sci', 'Sc13g0004770' => 'sci', 'Sed0003417' => 'sed', 'Sed0019750' => 'sed', 'SEGI_03419' => 'sgi', 'SEGI_05907' => 'sgi', 'SEGI_10682' => 'sgi', 'SEGI_13528' => 'sgi', 'SEGI_16081' => 'sgi', 'SEGI_19370' => 'sgi', 'SEGI_21015' => 'sgi', 'SEGI_21944' => 'sgi', 'SEGI_32906' => 'sgi', 'SEGI_33093' => 'sgi', 'SEGI_36110' => 'sgi', 'SEGI_40397' => 'sgi', 'SGA_v2.0_scaffold191G40426' => 'sas', 'SGA_v2.0_scaffold353G49717' => 'sas', 'SGA_v2.0_scaffold50G18550' => 'sas', 'SMO119G0173' => 'smo', 'SMO172G0002' => 'smo', 'Solyc09g082690.3' => 'sly', 'Solyc09g082700.2' => 'sly', 'Sopen09g031550' => 'spe', 'Sopen09g031560' => 'spe', 'Sp3g20540' => 'spa', 'Sp7g07580' => 'spa', 'TAR134G0002' => 'tar', 'TAR236G0001' => 'tar', 'TAR365G0892' => 'tar', 'TAR636G0166' => 'tar', 'TAR636G0646' => 'tar', 'TAR636G0869' => 'tar', 'TAR636G1317' => 'tar', 'TAR636G1744' => 'tar', 'TAR636G3358' => 'tar', 'TAR636G3436' => 'tar', 'THA.LOC104803047' => 'tha', 'Thecc.04G238900' => 'tca', 'Thhalv10021557m.g' => 'esa', 'Thhalv10026318m.g' => 'esa', 'Thhalv10026335m.g' => 'esa', 'TPR.G17433' => 'tpr', 'TPR.G18915' => 'tpr', 'TPR.G26125' => 'tpr', 'TWI09G0677' => 'twi', 'TWI73G0287' => 'twi', 'unitig_748.g8326' => 'ugi', 'vmacro15370' => 'vma', 'vmacro15371' => 'vma', 'vmacro15372' => 'vma', 'vmacro15373' => 'vma', 'vmacro15374' => 'vma', 'VMungo0720G2826' => 'vmu', 'Zm00001eb116960' => 'zma', 'Zm00001eb301260' => 'zma', 'Zm00001eb301270' => 'zma' ) $gf_id = 'HOM05D001460' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001460' ) $data_identifier = 'HOM05D001460' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 4, 'aag' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 2, 'aox' => (int) 2, 'arhy' => (int) 4, 'ath' => (int) 2, 'atr' => (int) 1, 'acertr' => (int) 10, 'cqu' => (int) 4, 'bca' => (int) 11, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 1, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 1, 'ccan' => (int) 1, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 1, 'col' => (int) 1, 'cpa' => (int) 1, 'cre' => (int) 7, 'csa' => (int) 1, 'camsi' => (int) 2, 'dca' => (int) 3, 'din' => (int) 2, 'dzi' => (int) 3, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 14, 'fve' => (int) 9, 'gma' => (int) 2, 'ghi' => (int) 4, 'gra' => (int) 2, 'vvi' => (int) 1, 'han' => (int) 13, 'cav' => (int) 1, 'hma' => (int) 2, 'sun' => (int) 2, 'lal' => (int) 2, 'lonja' => (int) 12, 'lja' => (int) 1, 'lsa' => (int) 7, 'mes' => (int) 1, 'mpo' => (int) 27, 'mbi' => (int) 1, 'mco' => (int) 8, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 1, 'egut' => (int) 1, 'ama' => (int) 1, 'nta' => (int) 4, 'nnu' => (int) 2, 'oeu' => (int) 3, 'osa' => (int) 4, 'pax' => (int) 9, 'pgr' => (int) 1, 'stu' => (int) 1, 'pvu' => (int) 1, 'ptr' => (int) 4, 'ppa' => (int) 22, 'pco' => (int) 6, 'ppe' => (int) 6, 'psa' => (int) 5, 'pso' => (int) 19, 'qlo' => (int) 5, 'rch' => (int) 7, 'rsi' => (int) 20, 'sbr' => (int) 5, 'sbo' => (int) 1, 'sci' => (int) 2, 'sed' => (int) 2, 'sgi' => (int) 12, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 2, 'tar' => (int) 10, 'tha' => (int) 1, 'tca' => (int) 1, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 2, 'ugi' => (int) 1, 'vma' => (int) 5, 'vmu' => (int) 1, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb301270' $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' => 'HOM05D001460', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '433', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p22980' => 'bna', 'A01p32340' => 'bna', 'A03p42970' => 'bna', 'A05p25880' => 'bna', 'Aa31LG8G9320' => 'aar', 'Aa31LG8G9330' => 'aar', 'Aa31LG8G9340' => 'aar', 'Aa31sc221G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1034' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1528' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.829' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2222' => 'aag', 'Ah.12g058830' => 'amhyb', 'Ah.12g058840' => 'amhyb', 'AL3G37160' => 'aly', 'AL7G41310' => 'aly', 'Aqoxy5G00395' => 'aox', 'Aqoxy5G00396' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0C8NZA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5185HY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JZ1PRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MD3LS0' => 'arhy', 'AT3G22840' => 'ath', 'AT4G14690' => 'ath', 'ATR0665G054' => 'atr', 'Atru.chr4.2344' => 'acertr', 'Atru.chr4.2346' => 'acertr', 'Atru.chr4.2347' => 'acertr', 'Atru.chr4.2348' => 'acertr', 'Atru.chr4.2355' => 'acertr', 'Atru.chr4.2356' => 'acertr', 'Atru.chr4.2358' => 'acertr', 'Atru.chr4.2359' => 'acertr', 'Atru.chr4.2360' => 'acertr', 'Atru.chr4.2361' => 'acertr', 'AUR62030476' => 'cqu', 'AUR62030478' => 'cqu', 'AUR62030819' => 'cqu', 'AUR62030820' => 'cqu', 'BcaB03g14648' => 'bca', 'BcaB04g20492' => 'bca', 'BcaB06g26399' => 'bca', 'BcaC01g03416' => 'bca', 'BcaC01g03419' => 'bca', 'BcaC01g03421' => 'bca', 'BcaC01g03424' => 'bca', 'BcaC05g28012' => 'bca', 'BcaC09g49212' => 'bca', 'BcaC09g50140' => 'bca', 'BcaNung00346' => 'bca', 'BolC1t02785H' => 'bol', 'BolC1t04095H' => 'bol', 'BolC3t17545H' => 'bol', 'BolC5t32769H' => 'bol', 'BraA01t02211Z' => 'bra', 'BraA01t03359Z' => 'bra', 'BraA03t13441Z' => 'bra', 'BraA05t21476Z' => 'bra', 'C01p28420' => 'bna', 'C01p41350' => 'bna', 'C03p52750' => 'bna', 'C03p52780' => 'bna', 'C05p40270' => 'bna', 'CAN.G1437.9' => 'can', 'CANSAT78G0035' => 'cansat', 'CANSAT78G1036' => 'cansat', 'CANSAT78G2272' => 'cansat', 'CANSAT78G2478' => 'cansat', 'CARHR098700' => 'chi', 'CARHR221120' => 'chi', 'CARHR221150' => 'chi', 'Carub.0003s2297' => 'cru', 'Carub.0007s2749' => 'cru', 'Carub.0007s2750' => 'cru', 'Carub.0007s2751' => 'cru', 'Ca_10849_v3' => 'car', 'Cc03_g04300' => 'ccan', 'CDE02G3648' => 'cde', 'CDE05G0060' => 'cde', 'CDE05G0692' => 'cde', 'CDE05G2285' => 'cde', 'CDE05G2884' => 'cde', 'CDE05G3072' => 'cde', 'Cfa008439' => 'cfa', 'Cfa008441' => 'cfa', 'Cfa008443' => 'cfa', 'Cfa008448' => 'cfa', 'Ciclev10005974m.g' => 'ccl', 'Ciclev10006006m.g' => 'ccl', 'Ciclev10006775m.g' => 'ccl', 'CiPaw.02G120400' => 'cil', 'CiPaw.02G120500' => 'cil', 'CiPaw.02G120600' => 'cil', 'ClCG05G004850' => 'cla', 'COL.COLO4_21566' => 'col', 'Cpa.g.sc44.124' => 'cpa', 'Cre07.g320400' => 'cre', 'Cre07.g320450' => 'cre', 'Cre08.g384650' => 'cre', 'Cre09.g393173' => 'cre', 'Cre09.g394325' => 'cre', 'Cre14.g626750' => 'cre', 'Cre16.g679250' => 'cre', 'CsaV3_3G012890' => 'csa', 'CSS0010865' => 'camsi', 'CSS0044338' => 'camsi', 'DCAR_002366' => 'dca', 'DCAR_030687' => 'dca', 'DCAR_030688' => 'dca', 'Dinv14047' => 'din', 'Dinv14048' => 'din', 'Duzib151G0105' => 'dzi', 'Duzib151G0114' => 'dzi', 'Duzib212G1029' => 'dzi', 'ECA232G3536' => 'eca', 'ECA240G0786' => 'eca', 'ECA240G1802' => 'eca', 'ECA240G3760' => 'eca', 'ECA240G3920' => 'eca', 'EL10Ac5g12536' => 'bvu', 'EL10Ac5g12537' => 'bvu', 'EL10Ac5g12538' => 'bvu', 'Eucgr.B01004' => 'egr', 'Eucgr.B01006' => 'egr', 'Eucgr.B01007' => 'egr', 'Eucgr.B01008' => 'egr', 'Eucgr.B01895' => 'egr', 'Eucgr.B01896' => 'egr', 'FAN04G1456' => 'fan', 'FAN08G1769' => 'fan', 'FAN08G2160' => 'fan', 'FAN13G2403' => 'fan', 'FAN13G3303' => 'fan', 'FAN15G2435' => 'fan', 'FAN17G0672' => 'fan', 'FAN17G2441' => 'fan', 'FAN18G1024' => 'fan', 'FAN22G1458' => 'fan', 'FAN24G0037' => 'fan', 'FAN24G0429' => 'fan', 'FAN24G2387' => 'fan', 'FAN27G2746' => 'fan', 'FvH4_2g20400' => 'fve', 'FvH4_2g20420' => 'fve', 'FvH4_2g20430' => 'fve', 'FvH4_4g01270' => 'fve', 'FvH4_4g01290' => 'fve', 'FvH4_4g01300' => 'fve', 'FvH4_4g01310' => 'fve', 'FvH4_4g01330' => 'fve', 'FvH4_5g09070' => 'fve', 'Glyma.10G243800' => 'gma', 'Glyma.20G150600' => 'gma', 'Gohir.A09G219200' => 'ghi', 'Gohir.A09G219300' => 'ghi', 'Gohir.D09G221400' => 'ghi', 'Gohir.D09G221500' => 'ghi', 'Gorai.006G242600' => 'gra', 'Gorai.006G242700' => 'gra', 'GSVIVG01018044001' => 'vvi', 'HanXRQChr03g0083821' => 'han', 'HanXRQChr03g0083841' => 'han', 'HanXRQChr03g0083881' => 'han', 'HanXRQChr03g0083901' => 'han', 'HanXRQChr03g0083921' => 'han', 'HanXRQChr03g0085331' => 'han', 'HanXRQChr03g0085361' => 'han', 'HanXRQChr03g0085411' => 'han', 'HanXRQChr03g0085421' => 'han', 'HanXRQChr03g0085431' => 'han', 'HanXRQChr08g0221991' => 'han', 'HanXRQChr11g0336061' => 'han', 'HanXRQChr11g0336411' => 'han', 'Haze_11234' => 'cav', 'Hma1.2p1_0549F.1_g177010' => 'hma', 'Hma1.2p1_0602F.1_g187630' => 'hma', 'Hund14876' => 'sun', 'Hund14879' => 'sun', 'Lalb_Chr06g0160741' => 'lal', 'Lalb_Chr21g0304781' => 'lal', 'Lj3A726G19' => 'lonja', 'Lj3A726T23' => 'lonja', 'Lj3A726T24' => 'lonja', 'Lj3A726T25' => 'lonja', 'Lj3A727T17' => 'lonja', 'Lj3C726T0' => 'lonja', 'Lj3C726T2' => 'lonja', 'Lj3P725T35' => 'lonja', 'Lj3P727T10' => 'lonja', 'Lj3P727T12' => 'lonja', 'Lj3P727T14' => 'lonja', 'Lj5g0023109' => 'lja', 'Lj6P646T44' => 'lonja', 'Lsat_1_v5_gn_6_75760' => 'lsa', 'Lsat_1_v5_gn_6_75800' => 'lsa', 'Lsat_1_v5_gn_6_75900' => 'lsa', 'Lsat_1_v5_gn_6_76240' => 'lsa', 'Lsat_1_v5_gn_6_76441' => 'lsa', 'Lsat_1_v5_gn_6_76700' => 'lsa', 'Lsat_1_v5_gn_6_76760' => 'lsa', 'Manes.15G033100' => 'mes', 'Mapoly0004s0074' => 'mpo', 'Mapoly0004s0075' => 'mpo', 'Mapoly0004s0163' => 'mpo', 'Mapoly0004s0164' => 'mpo', 'Mapoly0021s0018' => 'mpo', 'Mapoly0041s0136' => 'mpo', 'Mapoly0041s0137' => 'mpo', 'Mapoly0041s0138' => 'mpo', 'Mapoly0041s0139' => 'mpo', 'Mapoly0041s0141' => 'mpo', 'Mapoly0041s0142' => 'mpo', 'Mapoly0041s0143' => 'mpo', 'Mapoly0041s0144' => 'mpo', 'Mapoly0041s0145' => 'mpo', 'Mapoly0047s0106' => 'mpo', 'Mapoly0047s0108' => 'mpo', 'Mapoly0050s0051' => 'mpo', 'Mapoly0050s0052' => 'mpo', 'Mapoly0050s0053' => 'mpo', 'Mapoly0058s0013' => 'mpo', 'Mapoly0091s0078' => 'mpo', 'Mapoly0091s0079' => 'mpo', 'Mapoly0091s0080' => 'mpo', 'Mapoly0091s0081' => 'mpo', 'Mapoly0278s0004' => 'mpo', 'Mapoly0278s0005' => 'mpo', 'Mapoly0278s0006' => 'mpo', 'MBI11_g30648_MAGBIO' => 'mbi', 'MCO03G194' => 'mco', 'MCO03G590' => 'mco', 'MCO07G312' => 'mco', 'MCO10G318' => 'mco', 'MCO12G244' => 'mco', 'MCO13G148' => 'mco', 'MCO13G194' => 'mco', 'MCO16G238' => 'mco', 'MD06G1134100' => 'mdo', 'MD13G1200100' => 'mdo', 'MD13G1200300' => 'mdo', 'MD13G1200600' => 'mdo', 'MD14G1150400' => 'mdo', 'MD16G1200000' => 'mdo', 'Medtr1g102570' => 'mtr', 'Medtr1g102780' => 'mtr', 'Medtr1g102800' => 'mtr', 'Medtr1g102810' => 'mtr', 'Medtr1g102830' => 'mtr', 'MELO3C006499.2' => 'cme', 'Migut.G00385' => 'egut', 'MSTRG.4063' => 'ama', 'Nitab4.5_0000090g0260' => 'nta', 'Nitab4.5_0000977g0030' => 'nta', 'Nitab4.5_0002541g0040' => 'nta', 'Nitab4.5_0007068g0040' => 'nta', 'Nn005s41408' => 'nnu', 'Nn005s41410' => 'nnu', 'Oeu010310.1' => 'oeu', 'Oeu010311.1' => 'oeu', 'Oeu043472.1' => 'oeu', 'Os01g0246400' => 'osa', 'Os04g0267950' => 'osa', 'Os07g0178700' => 'osa', 'Os07g0178800' => 'osa', 'Peaxi162Scf00316g00046' => 'pax', 'Peaxi162Scf00316g00049' => 'pax', 'Peaxi162Scf00316g00059' => 'pax', 'Peaxi162Scf00316g00328' => 'pax', 'Peaxi162Scf00316g00329' => 'pax', 'Peaxi162Scf00316g00411' => 'pax', 'Peaxi162Scf00316g00521' => 'pax', 'Peaxi162Scf00492g00068' => 'pax', 'Peaxi162Scf35631g00002' => 'pax', 'PGR142G3720' => 'pgr', 'PGSC0003DMG400006442' => 'stu', 'Phvul.007G062000' => 'pvu', 'Potri.008G157750' => 'ptr', 'Potri.008G157900' => 'ptr', 'Potri.008G158000' => 'ptr', 'Potri.008G158200' => 'ptr', 'Pp3c11_7280' => 'ppa', 'Pp3c11_7980' => 'ppa', 'Pp3c12_19450' => 'ppa', 'Pp3c14_1480' => 'ppa', 'Pp3c14_1501' => 'ppa', 'Pp3c16_4900' => 'ppa', 'Pp3c16_5010' => 'ppa', 'Pp3c16_5060' => 'ppa', 'Pp3c19_18250' => 'ppa', 'Pp3c23_8530' => 'ppa', 'Pp3c23_8550' => 'ppa', 'Pp3c24_9670' => 'ppa', 'Pp3c2_21390' => 'ppa', 'Pp3c2_31380' => 'ppa', 'Pp3c3_16620' => 'ppa', 'Pp3c3_8090' => 'ppa', 'Pp3c3_8110' => 'ppa', 'Pp3c3_8130' => 'ppa', 'Pp3c3_8150' => 'ppa', 'Pp3c4_14320' => 'ppa', 'Pp3c6_2560' => 'ppa', 'Pp3c9_16700' => 'ppa', 'PRCOL_00000234' => 'pco', 'PRCOL_00000235' => 'pco', 'PRCOL_00000777' => 'pco', 'PRCOL_00002344' => 'pco', 'PRCOL_00002372' => 'pco', 'PRCOL_00006120' => 'pco', 'Prupe.1G021400' => 'ppe', 'Prupe.1G021500' => 'ppe', 'Prupe.1G021600' => 'ppe', 'Prupe.1G021700' => 'ppe', 'Prupe.1G021800' => 'ppe', 'Prupe.5G145100' => 'ppe', 'Psat6g204040' => 'psa', 'Psat6g204800' => 'psa', 'Psat6g204920' => 'psa', 'Psat6g204960' => 'psa', 'Psat6g205080' => 'psa', 'PSO017G0271' => 'pso', 'PSO017G1276' => 'pso', 'PSO017G1429' => 'pso', 'PSO017G1861' => 'pso', 'PSO017G2787' => 'pso', 'PSO017G4466' => 'pso', 'PSO017G5118' => 'pso', 'PSO017G5420' => 'pso', 'PSO063G3678' => 'pso', 'PSO210G0546' => 'pso', 'PSO317G0001' => 'pso', 'PSO357G0512' => 'pso', 'PSO478G2682' => 'pso', 'PSO647G0001' => 'pso', 'PSO675G0001' => 'pso', 'PSO675G2699' => 'pso', 'PSO675G2849' => 'pso', 'PSO675G4991' => 'pso', 'PSO689G0001' => 'pso', 'QL06p000916' => 'qlo', 'QL06p000921' => 'qlo', 'QL06p001398' => 'qlo', 'QL06p001407' => 'qlo', 'QL06p002031' => 'qlo', 'RcHm_v2.0_Chr4g0387791' => 'rch', 'RcHm_v2.0_Chr4g0387801' => 'rch', 'RcHm_v2.0_Chr6g0286501' => 'rch', 'RcHm_v2.0_Chr6g0286511' => 'rch', 'RcHm_v2.0_Chr6g0286521' => 'rch', 'RcHm_v2.0_Chr6g0286531' => 'rch', 'RcHm_v2.0_Chr7g0189141' => 'rch', 'Rhsim02G0028700' => 'rsi', 'Rhsim02G0028800' => 'rsi', 'Rhsim02G0028900' => 'rsi', 'Rhsim02G0029000' => 'rsi', 'Rhsim02G0029100' => 'rsi', 'Rhsim02G0029200' => 'rsi', 'Rhsim02G0029300' => 'rsi', 'Rhsim02G0029400' => 'rsi', 'Rhsim02G0029500' => 'rsi', 'Rhsim02G0029600' => 'rsi', 'RhsimUnG0024000' => 'rsi', 'RhsimUnG0024100' => 'rsi', 'RhsimUnG0024200' => 'rsi', 'RhsimUnG0024300' => 'rsi', 'RhsimUnG0024400' => 'rsi', 'RhsimUnG0024500' => 'rsi', 'RhsimUnG0024700' => 'rsi', 'RhsimUnG0024800' => 'rsi', 'RhsimUnG0024900' => 'rsi', 'RhsimUnG0025100' => 'rsi', 'Sabra08G0120200' => 'sbr', 'Sabra08G0120300' => 'sbr', 'Sabra08G0120500' => 'sbr', 'Sabra08G0120600' => 'sbr', 'Sabra10G0158900' => 'sbr', 'SalBow2G3492' => 'sbo', 'Sc13g0004760' => 'sci', 'Sc13g0004770' => 'sci', 'Sed0003417' => 'sed', 'Sed0019750' => 'sed', 'SEGI_03419' => 'sgi', 'SEGI_05907' => 'sgi', 'SEGI_10682' => 'sgi', 'SEGI_13528' => 'sgi', 'SEGI_16081' => 'sgi', 'SEGI_19370' => 'sgi', 'SEGI_21015' => 'sgi', 'SEGI_21944' => 'sgi', 'SEGI_32906' => 'sgi', 'SEGI_33093' => 'sgi', 'SEGI_36110' => 'sgi', 'SEGI_40397' => 'sgi', 'SGA_v2.0_scaffold191G40426' => 'sas', 'SGA_v2.0_scaffold353G49717' => 'sas', 'SGA_v2.0_scaffold50G18550' => 'sas', 'SMO119G0173' => 'smo', 'SMO172G0002' => 'smo', 'Solyc09g082690.3' => 'sly', 'Solyc09g082700.2' => 'sly', 'Sopen09g031550' => 'spe', 'Sopen09g031560' => 'spe', 'Sp3g20540' => 'spa', 'Sp7g07580' => 'spa', 'TAR134G0002' => 'tar', 'TAR236G0001' => 'tar', 'TAR365G0892' => 'tar', 'TAR636G0166' => 'tar', 'TAR636G0646' => 'tar', 'TAR636G0869' => 'tar', 'TAR636G1317' => 'tar', 'TAR636G1744' => 'tar', 'TAR636G3358' => 'tar', 'TAR636G3436' => 'tar', 'THA.LOC104803047' => 'tha', 'Thecc.04G238900' => 'tca', 'Thhalv10021557m.g' => 'esa', 'Thhalv10026318m.g' => 'esa', 'Thhalv10026335m.g' => 'esa', 'TPR.G17433' => 'tpr', 'TPR.G18915' => 'tpr', 'TPR.G26125' => 'tpr', 'TWI09G0677' => 'twi', 'TWI73G0287' => 'twi', 'unitig_748.g8326' => 'ugi', 'vmacro15370' => 'vma', 'vmacro15371' => 'vma', 'vmacro15372' => 'vma', 'vmacro15373' => 'vma', 'vmacro15374' => 'vma', 'VMungo0720G2826' => 'vmu', 'Zm00001eb116960' => 'zma', 'Zm00001eb301260' => 'zma', 'Zm00001eb301270' => 'zma' ), 'gf_id' => 'HOM05D001460', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001460' ), 'data_identifier' => 'HOM05D001460', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001460', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '433', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p22980' => 'bna', 'A01p32340' => 'bna', 'A03p42970' => 'bna', 'A05p25880' => 'bna', 'Aa31LG8G9320' => 'aar', 'Aa31LG8G9330' => 'aar', 'Aa31LG8G9340' => 'aar', 'Aa31sc221G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1034' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1528' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.829' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2222' => 'aag', 'Ah.12g058830' => 'amhyb', 'Ah.12g058840' => 'amhyb', 'AL3G37160' => 'aly', 'AL7G41310' => 'aly', 'Aqoxy5G00395' => 'aox', 'Aqoxy5G00396' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0C8NZA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5185HY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JZ1PRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MD3LS0' => 'arhy', 'AT3G22840' => 'ath', 'AT4G14690' => 'ath', 'ATR0665G054' => 'atr', 'Atru.chr4.2344' => 'acertr', 'Atru.chr4.2346' => 'acertr', 'Atru.chr4.2347' => 'acertr', 'Atru.chr4.2348' => 'acertr', 'Atru.chr4.2355' => 'acertr', 'Atru.chr4.2356' => 'acertr', 'Atru.chr4.2358' => 'acertr', 'Atru.chr4.2359' => 'acertr', 'Atru.chr4.2360' => 'acertr', 'Atru.chr4.2361' => 'acertr', 'AUR62030476' => 'cqu', 'AUR62030478' => 'cqu', 'AUR62030819' => 'cqu', 'AUR62030820' => 'cqu', 'BcaB03g14648' => 'bca', 'BcaB04g20492' => 'bca', 'BcaB06g26399' => 'bca', 'BcaC01g03416' => 'bca', 'BcaC01g03419' => 'bca', 'BcaC01g03421' => 'bca', 'BcaC01g03424' => 'bca', 'BcaC05g28012' => 'bca', 'BcaC09g49212' => 'bca', 'BcaC09g50140' => 'bca', 'BcaNung00346' => 'bca', 'BolC1t02785H' => 'bol', 'BolC1t04095H' => 'bol', 'BolC3t17545H' => 'bol', 'BolC5t32769H' => 'bol', 'BraA01t02211Z' => 'bra', 'BraA01t03359Z' => 'bra', 'BraA03t13441Z' => 'bra', 'BraA05t21476Z' => 'bra', 'C01p28420' => 'bna', 'C01p41350' => 'bna', 'C03p52750' => 'bna', 'C03p52780' => 'bna', 'C05p40270' => 'bna', 'CAN.G1437.9' => 'can', 'CANSAT78G0035' => 'cansat', 'CANSAT78G1036' => 'cansat', 'CANSAT78G2272' => 'cansat', 'CANSAT78G2478' => 'cansat', 'CARHR098700' => 'chi', 'CARHR221120' => 'chi', 'CARHR221150' => 'chi', 'Carub.0003s2297' => 'cru', 'Carub.0007s2749' => 'cru', 'Carub.0007s2750' => 'cru', 'Carub.0007s2751' => 'cru', 'Ca_10849_v3' => 'car', 'Cc03_g04300' => 'ccan', 'CDE02G3648' => 'cde', 'CDE05G0060' => 'cde', 'CDE05G0692' => 'cde', 'CDE05G2285' => 'cde', 'CDE05G2884' => 'cde', 'CDE05G3072' => 'cde', 'Cfa008439' => 'cfa', 'Cfa008441' => 'cfa', 'Cfa008443' => 'cfa', 'Cfa008448' => 'cfa', 'Ciclev10005974m.g' => 'ccl', 'Ciclev10006006m.g' => 'ccl', 'Ciclev10006775m.g' => 'ccl', 'CiPaw.02G120400' => 'cil', 'CiPaw.02G120500' => 'cil', 'CiPaw.02G120600' => 'cil', 'ClCG05G004850' => 'cla', 'COL.COLO4_21566' => 'col', 'Cpa.g.sc44.124' => 'cpa', 'Cre07.g320400' => 'cre', 'Cre07.g320450' => 'cre', 'Cre08.g384650' => 'cre', 'Cre09.g393173' => 'cre', 'Cre09.g394325' => 'cre', 'Cre14.g626750' => 'cre', 'Cre16.g679250' => 'cre', 'CsaV3_3G012890' => 'csa', 'CSS0010865' => 'camsi', 'CSS0044338' => 'camsi', 'DCAR_002366' => 'dca', 'DCAR_030687' => 'dca', 'DCAR_030688' => 'dca', 'Dinv14047' => 'din', 'Dinv14048' => 'din', 'Duzib151G0105' => 'dzi', 'Duzib151G0114' => 'dzi', 'Duzib212G1029' => 'dzi', 'ECA232G3536' => 'eca', 'ECA240G0786' => 'eca', 'ECA240G1802' => 'eca', 'ECA240G3760' => 'eca', 'ECA240G3920' => 'eca', 'EL10Ac5g12536' => 'bvu', 'EL10Ac5g12537' => 'bvu', 'EL10Ac5g12538' => 'bvu', 'Eucgr.B01004' => 'egr', 'Eucgr.B01006' => 'egr', 'Eucgr.B01007' => 'egr', 'Eucgr.B01008' => 'egr', 'Eucgr.B01895' => 'egr', 'Eucgr.B01896' => 'egr', 'FAN04G1456' => 'fan', 'FAN08G1769' => 'fan', 'FAN08G2160' => 'fan', 'FAN13G2403' => 'fan', 'FAN13G3303' => 'fan', 'FAN15G2435' => 'fan', 'FAN17G0672' => 'fan', 'FAN17G2441' => 'fan', 'FAN18G1024' => 'fan', 'FAN22G1458' => 'fan', 'FAN24G0037' => 'fan', 'FAN24G0429' => 'fan', 'FAN24G2387' => 'fan', 'FAN27G2746' => 'fan', 'FvH4_2g20400' => 'fve', 'FvH4_2g20420' => 'fve', 'FvH4_2g20430' => 'fve', 'FvH4_4g01270' => 'fve', 'FvH4_4g01290' => 'fve', 'FvH4_4g01300' => 'fve', 'FvH4_4g01310' => 'fve', 'FvH4_4g01330' => 'fve', 'FvH4_5g09070' => 'fve', 'Glyma.10G243800' => 'gma', 'Glyma.20G150600' => 'gma', 'Gohir.A09G219200' => 'ghi', 'Gohir.A09G219300' => 'ghi', 'Gohir.D09G221400' => 'ghi', 'Gohir.D09G221500' => 'ghi', 'Gorai.006G242600' => 'gra', 'Gorai.006G242700' => 'gra', 'GSVIVG01018044001' => 'vvi', 'HanXRQChr03g0083821' => 'han', 'HanXRQChr03g0083841' => 'han', 'HanXRQChr03g0083881' => 'han', 'HanXRQChr03g0083901' => 'han', 'HanXRQChr03g0083921' => 'han', 'HanXRQChr03g0085331' => 'han', 'HanXRQChr03g0085361' => 'han', 'HanXRQChr03g0085411' => 'han', 'HanXRQChr03g0085421' => 'han', 'HanXRQChr03g0085431' => 'han', 'HanXRQChr08g0221991' => 'han', 'HanXRQChr11g0336061' => 'han', 'HanXRQChr11g0336411' => 'han', 'Haze_11234' => 'cav', 'Hma1.2p1_0549F.1_g177010' => 'hma', 'Hma1.2p1_0602F.1_g187630' => 'hma', 'Hund14876' => 'sun', 'Hund14879' => 'sun', 'Lalb_Chr06g0160741' => 'lal', 'Lalb_Chr21g0304781' => 'lal', 'Lj3A726G19' => 'lonja', 'Lj3A726T23' => 'lonja', 'Lj3A726T24' => 'lonja', 'Lj3A726T25' => 'lonja', 'Lj3A727T17' => 'lonja', 'Lj3C726T0' => 'lonja', 'Lj3C726T2' => 'lonja', 'Lj3P725T35' => 'lonja', 'Lj3P727T10' => 'lonja', 'Lj3P727T12' => 'lonja', 'Lj3P727T14' => 'lonja', 'Lj5g0023109' => 'lja', 'Lj6P646T44' => 'lonja', 'Lsat_1_v5_gn_6_75760' => 'lsa', 'Lsat_1_v5_gn_6_75800' => 'lsa', 'Lsat_1_v5_gn_6_75900' => 'lsa', 'Lsat_1_v5_gn_6_76240' => 'lsa', 'Lsat_1_v5_gn_6_76441' => 'lsa', 'Lsat_1_v5_gn_6_76700' => 'lsa', 'Lsat_1_v5_gn_6_76760' => 'lsa', 'Manes.15G033100' => 'mes', 'Mapoly0004s0074' => 'mpo', 'Mapoly0004s0075' => 'mpo', 'Mapoly0004s0163' => 'mpo', 'Mapoly0004s0164' => 'mpo', 'Mapoly0021s0018' => 'mpo', 'Mapoly0041s0136' => 'mpo', 'Mapoly0041s0137' => 'mpo', 'Mapoly0041s0138' => 'mpo', 'Mapoly0041s0139' => 'mpo', 'Mapoly0041s0141' => 'mpo', 'Mapoly0041s0142' => 'mpo', 'Mapoly0041s0143' => 'mpo', 'Mapoly0041s0144' => 'mpo', 'Mapoly0041s0145' => 'mpo', 'Mapoly0047s0106' => 'mpo', 'Mapoly0047s0108' => 'mpo', 'Mapoly0050s0051' => 'mpo', 'Mapoly0050s0052' => 'mpo', 'Mapoly0050s0053' => 'mpo', 'Mapoly0058s0013' => 'mpo', 'Mapoly0091s0078' => 'mpo', 'Mapoly0091s0079' => 'mpo', 'Mapoly0091s0080' => 'mpo', 'Mapoly0091s0081' => 'mpo', 'Mapoly0278s0004' => 'mpo', 'Mapoly0278s0005' => 'mpo', 'Mapoly0278s0006' => 'mpo', 'MBI11_g30648_MAGBIO' => 'mbi', 'MCO03G194' => 'mco', 'MCO03G590' => 'mco', 'MCO07G312' => 'mco', 'MCO10G318' => 'mco', 'MCO12G244' => 'mco', 'MCO13G148' => 'mco', 'MCO13G194' => 'mco', 'MCO16G238' => 'mco', 'MD06G1134100' => 'mdo', 'MD13G1200100' => 'mdo', 'MD13G1200300' => 'mdo', 'MD13G1200600' => 'mdo', 'MD14G1150400' => 'mdo', 'MD16G1200000' => 'mdo', 'Medtr1g102570' => 'mtr', 'Medtr1g102780' => 'mtr', 'Medtr1g102800' => 'mtr', 'Medtr1g102810' => 'mtr', 'Medtr1g102830' => 'mtr', 'MELO3C006499.2' => 'cme', 'Migut.G00385' => 'egut', 'MSTRG.4063' => 'ama', 'Nitab4.5_0000090g0260' => 'nta', 'Nitab4.5_0000977g0030' => 'nta', 'Nitab4.5_0002541g0040' => 'nta', 'Nitab4.5_0007068g0040' => 'nta', 'Nn005s41408' => 'nnu', 'Nn005s41410' => 'nnu', 'Oeu010310.1' => 'oeu', 'Oeu010311.1' => 'oeu', 'Oeu043472.1' => 'oeu', 'Os01g0246400' => 'osa', 'Os04g0267950' => 'osa', 'Os07g0178700' => 'osa', 'Os07g0178800' => 'osa', 'Peaxi162Scf00316g00046' => 'pax', 'Peaxi162Scf00316g00049' => 'pax', 'Peaxi162Scf00316g00059' => 'pax', 'Peaxi162Scf00316g00328' => 'pax', 'Peaxi162Scf00316g00329' => 'pax', 'Peaxi162Scf00316g00411' => 'pax', 'Peaxi162Scf00316g00521' => 'pax', 'Peaxi162Scf00492g00068' => 'pax', 'Peaxi162Scf35631g00002' => 'pax', 'PGR142G3720' => 'pgr', 'PGSC0003DMG400006442' => 'stu', 'Phvul.007G062000' => 'pvu', 'Potri.008G157750' => 'ptr', 'Potri.008G157900' => 'ptr', 'Potri.008G158000' => 'ptr', 'Potri.008G158200' => 'ptr', 'Pp3c11_7280' => 'ppa', 'Pp3c11_7980' => 'ppa', 'Pp3c12_19450' => 'ppa', 'Pp3c14_1480' => 'ppa', 'Pp3c14_1501' => 'ppa', 'Pp3c16_4900' => 'ppa', 'Pp3c16_5010' => 'ppa', 'Pp3c16_5060' => 'ppa', 'Pp3c19_18250' => 'ppa', 'Pp3c23_8530' => 'ppa', 'Pp3c23_8550' => 'ppa', 'Pp3c24_9670' => 'ppa', 'Pp3c2_21390' => 'ppa', 'Pp3c2_31380' => 'ppa', 'Pp3c3_16620' => 'ppa', 'Pp3c3_8090' => 'ppa', 'Pp3c3_8110' => 'ppa', 'Pp3c3_8130' => 'ppa', 'Pp3c3_8150' => 'ppa', 'Pp3c4_14320' => 'ppa', 'Pp3c6_2560' => 'ppa', 'Pp3c9_16700' => 'ppa', 'PRCOL_00000234' => 'pco', 'PRCOL_00000235' => 'pco', 'PRCOL_00000777' => 'pco', 'PRCOL_00002344' => 'pco', 'PRCOL_00002372' => 'pco', 'PRCOL_00006120' => 'pco', 'Prupe.1G021400' => 'ppe', 'Prupe.1G021500' => 'ppe', 'Prupe.1G021600' => 'ppe', 'Prupe.1G021700' => 'ppe', 'Prupe.1G021800' => 'ppe', 'Prupe.5G145100' => 'ppe', 'Psat6g204040' => 'psa', 'Psat6g204800' => 'psa', 'Psat6g204920' => 'psa', 'Psat6g204960' => 'psa', 'Psat6g205080' => 'psa', 'PSO017G0271' => 'pso', 'PSO017G1276' => 'pso', 'PSO017G1429' => 'pso', 'PSO017G1861' => 'pso', 'PSO017G2787' => 'pso', 'PSO017G4466' => 'pso', 'PSO017G5118' => 'pso', 'PSO017G5420' => 'pso', 'PSO063G3678' => 'pso', 'PSO210G0546' => 'pso', 'PSO317G0001' => 'pso', 'PSO357G0512' => 'pso', 'PSO478G2682' => 'pso', 'PSO647G0001' => 'pso', 'PSO675G0001' => 'pso', 'PSO675G2699' => 'pso', 'PSO675G2849' => 'pso', 'PSO675G4991' => 'pso', 'PSO689G0001' => 'pso', 'QL06p000916' => 'qlo', 'QL06p000921' => 'qlo', 'QL06p001398' => 'qlo', 'QL06p001407' => 'qlo', 'QL06p002031' => 'qlo', 'RcHm_v2.0_Chr4g0387791' => 'rch', 'RcHm_v2.0_Chr4g0387801' => 'rch', 'RcHm_v2.0_Chr6g0286501' => 'rch', 'RcHm_v2.0_Chr6g0286511' => 'rch', 'RcHm_v2.0_Chr6g0286521' => 'rch', 'RcHm_v2.0_Chr6g0286531' => 'rch', 'RcHm_v2.0_Chr7g0189141' => 'rch', 'Rhsim02G0028700' => 'rsi', 'Rhsim02G0028800' => 'rsi', 'Rhsim02G0028900' => 'rsi', 'Rhsim02G0029000' => 'rsi', 'Rhsim02G0029100' => 'rsi', 'Rhsim02G0029200' => 'rsi', 'Rhsim02G0029300' => 'rsi', 'Rhsim02G0029400' => 'rsi', 'Rhsim02G0029500' => 'rsi', 'Rhsim02G0029600' => 'rsi', 'RhsimUnG0024000' => 'rsi', 'RhsimUnG0024100' => 'rsi', 'RhsimUnG0024200' => 'rsi', 'RhsimUnG0024300' => 'rsi', 'RhsimUnG0024400' => 'rsi', 'RhsimUnG0024500' => 'rsi', 'RhsimUnG0024700' => 'rsi', 'RhsimUnG0024800' => 'rsi', 'RhsimUnG0024900' => 'rsi', 'RhsimUnG0025100' => 'rsi', 'Sabra08G0120200' => 'sbr', 'Sabra08G0120300' => 'sbr', 'Sabra08G0120500' => 'sbr', 'Sabra08G0120600' => 'sbr', 'Sabra10G0158900' => 'sbr', 'SalBow2G3492' => 'sbo', 'Sc13g0004760' => 'sci', 'Sc13g0004770' => 'sci', 'Sed0003417' => 'sed', 'Sed0019750' => 'sed', 'SEGI_03419' => 'sgi', 'SEGI_05907' => 'sgi', 'SEGI_10682' => 'sgi', 'SEGI_13528' => 'sgi', 'SEGI_16081' => 'sgi', 'SEGI_19370' => 'sgi', 'SEGI_21015' => 'sgi', 'SEGI_21944' => 'sgi', 'SEGI_32906' => 'sgi', 'SEGI_33093' => 'sgi', 'SEGI_36110' => 'sgi', 'SEGI_40397' => 'sgi', 'SGA_v2.0_scaffold191G40426' => 'sas', 'SGA_v2.0_scaffold353G49717' => 'sas', 'SGA_v2.0_scaffold50G18550' => 'sas', 'SMO119G0173' => 'smo', 'SMO172G0002' => 'smo', 'Solyc09g082690.3' => 'sly', 'Solyc09g082700.2' => 'sly', 'Sopen09g031550' => 'spe', 'Sopen09g031560' => 'spe', 'Sp3g20540' => 'spa', 'Sp7g07580' => 'spa', 'TAR134G0002' => 'tar', 'TAR236G0001' => 'tar', 'TAR365G0892' => 'tar', 'TAR636G0166' => 'tar', 'TAR636G0646' => 'tar', 'TAR636G0869' => 'tar', 'TAR636G1317' => 'tar', 'TAR636G1744' => 'tar', 'TAR636G3358' => 'tar', 'TAR636G3436' => 'tar', 'THA.LOC104803047' => 'tha', 'Thecc.04G238900' => 'tca', 'Thhalv10021557m.g' => 'esa', 'Thhalv10026318m.g' => 'esa', 'Thhalv10026335m.g' => 'esa', 'TPR.G17433' => 'tpr', 'TPR.G18915' => 'tpr', 'TPR.G26125' => 'tpr', 'TWI09G0677' => 'twi', 'TWI73G0287' => 'twi', 'unitig_748.g8326' => 'ugi', 'vmacro15370' => 'vma', 'vmacro15371' => 'vma', 'vmacro15372' => 'vma', 'vmacro15373' => 'vma', 'vmacro15374' => 'vma', 'VMungo0720G2826' => 'vmu', 'Zm00001eb116960' => 'zma', 'Zm00001eb301260' => 'zma', 'Zm00001eb301270' => 'zma' ) $gf_id = 'HOM05D001460' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001460' ) $data_identifier = 'HOM05D001460' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 4, 'aag' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 2, 'aox' => (int) 2, 'arhy' => (int) 4, 'ath' => (int) 2, 'atr' => (int) 1, 'acertr' => (int) 10, 'cqu' => (int) 4, 'bca' => (int) 11, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 1, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 1, 'ccan' => (int) 1, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 1, 'col' => (int) 1, 'cpa' => (int) 1, 'cre' => (int) 7, 'csa' => (int) 1, 'camsi' => (int) 2, 'dca' => (int) 3, 'din' => (int) 2, 'dzi' => (int) 3, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 14, 'fve' => (int) 9, 'gma' => (int) 2, 'ghi' => (int) 4, 'gra' => (int) 2, 'vvi' => (int) 1, 'han' => (int) 13, 'cav' => (int) 1, 'hma' => (int) 2, 'sun' => (int) 2, 'lal' => (int) 2, 'lonja' => (int) 12, 'lja' => (int) 1, 'lsa' => (int) 7, 'mes' => (int) 1, 'mpo' => (int) 27, 'mbi' => (int) 1, 'mco' => (int) 8, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 1, 'egut' => (int) 1, 'ama' => (int) 1, 'nta' => (int) 4, 'nnu' => (int) 2, 'oeu' => (int) 3, 'osa' => (int) 4, 'pax' => (int) 9, 'pgr' => (int) 1, 'stu' => (int) 1, 'pvu' => (int) 1, 'ptr' => (int) 4, 'ppa' => (int) 22, 'pco' => (int) 6, 'ppe' => (int) 6, 'psa' => (int) 5, 'pso' => (int) 19, 'qlo' => (int) 5, 'rch' => (int) 7, 'rsi' => (int) 20, 'sbr' => (int) 5, 'sbo' => (int) 1, 'sci' => (int) 2, 'sed' => (int) 2, 'sgi' => (int) 12, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 2, 'tar' => (int) 10, 'tha' => (int) 1, 'tca' => (int) 1, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 2, 'ugi' => (int) 1, 'vma' => (int) 5, 'vmu' => (int) 1, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb301270' $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' => 'HOM05D001460', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '433', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p22980' => 'bna', 'A01p32340' => 'bna', 'A03p42970' => 'bna', 'A05p25880' => 'bna', 'Aa31LG8G9320' => 'aar', 'Aa31LG8G9330' => 'aar', 'Aa31LG8G9340' => 'aar', 'Aa31sc221G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1034' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1528' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.829' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2222' => 'aag', 'Ah.12g058830' => 'amhyb', 'Ah.12g058840' => 'amhyb', 'AL3G37160' => 'aly', 'AL7G41310' => 'aly', 'Aqoxy5G00395' => 'aox', 'Aqoxy5G00396' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0C8NZA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5185HY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JZ1PRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MD3LS0' => 'arhy', 'AT3G22840' => 'ath', 'AT4G14690' => 'ath', 'ATR0665G054' => 'atr', 'Atru.chr4.2344' => 'acertr', 'Atru.chr4.2346' => 'acertr', 'Atru.chr4.2347' => 'acertr', 'Atru.chr4.2348' => 'acertr', 'Atru.chr4.2355' => 'acertr', 'Atru.chr4.2356' => 'acertr', 'Atru.chr4.2358' => 'acertr', 'Atru.chr4.2359' => 'acertr', 'Atru.chr4.2360' => 'acertr', 'Atru.chr4.2361' => 'acertr', 'AUR62030476' => 'cqu', 'AUR62030478' => 'cqu', 'AUR62030819' => 'cqu', 'AUR62030820' => 'cqu', 'BcaB03g14648' => 'bca', 'BcaB04g20492' => 'bca', 'BcaB06g26399' => 'bca', 'BcaC01g03416' => 'bca', 'BcaC01g03419' => 'bca', 'BcaC01g03421' => 'bca', 'BcaC01g03424' => 'bca', 'BcaC05g28012' => 'bca', 'BcaC09g49212' => 'bca', 'BcaC09g50140' => 'bca', 'BcaNung00346' => 'bca', 'BolC1t02785H' => 'bol', 'BolC1t04095H' => 'bol', 'BolC3t17545H' => 'bol', 'BolC5t32769H' => 'bol', 'BraA01t02211Z' => 'bra', 'BraA01t03359Z' => 'bra', 'BraA03t13441Z' => 'bra', 'BraA05t21476Z' => 'bra', 'C01p28420' => 'bna', 'C01p41350' => 'bna', 'C03p52750' => 'bna', 'C03p52780' => 'bna', 'C05p40270' => 'bna', 'CAN.G1437.9' => 'can', 'CANSAT78G0035' => 'cansat', 'CANSAT78G1036' => 'cansat', 'CANSAT78G2272' => 'cansat', 'CANSAT78G2478' => 'cansat', 'CARHR098700' => 'chi', 'CARHR221120' => 'chi', 'CARHR221150' => 'chi', 'Carub.0003s2297' => 'cru', 'Carub.0007s2749' => 'cru', 'Carub.0007s2750' => 'cru', 'Carub.0007s2751' => 'cru', 'Ca_10849_v3' => 'car', 'Cc03_g04300' => 'ccan', 'CDE02G3648' => 'cde', 'CDE05G0060' => 'cde', 'CDE05G0692' => 'cde', 'CDE05G2285' => 'cde', 'CDE05G2884' => 'cde', 'CDE05G3072' => 'cde', 'Cfa008439' => 'cfa', 'Cfa008441' => 'cfa', 'Cfa008443' => 'cfa', 'Cfa008448' => 'cfa', 'Ciclev10005974m.g' => 'ccl', 'Ciclev10006006m.g' => 'ccl', 'Ciclev10006775m.g' => 'ccl', 'CiPaw.02G120400' => 'cil', 'CiPaw.02G120500' => 'cil', 'CiPaw.02G120600' => 'cil', 'ClCG05G004850' => 'cla', 'COL.COLO4_21566' => 'col', 'Cpa.g.sc44.124' => 'cpa', 'Cre07.g320400' => 'cre', 'Cre07.g320450' => 'cre', 'Cre08.g384650' => 'cre', 'Cre09.g393173' => 'cre', 'Cre09.g394325' => 'cre', 'Cre14.g626750' => 'cre', 'Cre16.g679250' => 'cre', 'CsaV3_3G012890' => 'csa', 'CSS0010865' => 'camsi', 'CSS0044338' => 'camsi', 'DCAR_002366' => 'dca', 'DCAR_030687' => 'dca', 'DCAR_030688' => 'dca', 'Dinv14047' => 'din', 'Dinv14048' => 'din', 'Duzib151G0105' => 'dzi', 'Duzib151G0114' => 'dzi', 'Duzib212G1029' => 'dzi', 'ECA232G3536' => 'eca', 'ECA240G0786' => 'eca', 'ECA240G1802' => 'eca', 'ECA240G3760' => 'eca', 'ECA240G3920' => 'eca', 'EL10Ac5g12536' => 'bvu', 'EL10Ac5g12537' => 'bvu', 'EL10Ac5g12538' => 'bvu', 'Eucgr.B01004' => 'egr', 'Eucgr.B01006' => 'egr', 'Eucgr.B01007' => 'egr', 'Eucgr.B01008' => 'egr', 'Eucgr.B01895' => 'egr', 'Eucgr.B01896' => 'egr', 'FAN04G1456' => 'fan', 'FAN08G1769' => 'fan', 'FAN08G2160' => 'fan', 'FAN13G2403' => 'fan', 'FAN13G3303' => 'fan', 'FAN15G2435' => 'fan', 'FAN17G0672' => 'fan', 'FAN17G2441' => 'fan', 'FAN18G1024' => 'fan', 'FAN22G1458' => 'fan', 'FAN24G0037' => 'fan', 'FAN24G0429' => 'fan', 'FAN24G2387' => 'fan', 'FAN27G2746' => 'fan', 'FvH4_2g20400' => 'fve', 'FvH4_2g20420' => 'fve', 'FvH4_2g20430' => 'fve', 'FvH4_4g01270' => 'fve', 'FvH4_4g01290' => 'fve', 'FvH4_4g01300' => 'fve', 'FvH4_4g01310' => 'fve', 'FvH4_4g01330' => 'fve', 'FvH4_5g09070' => 'fve', 'Glyma.10G243800' => 'gma', 'Glyma.20G150600' => 'gma', 'Gohir.A09G219200' => 'ghi', 'Gohir.A09G219300' => 'ghi', 'Gohir.D09G221400' => 'ghi', 'Gohir.D09G221500' => 'ghi', 'Gorai.006G242600' => 'gra', 'Gorai.006G242700' => 'gra', 'GSVIVG01018044001' => 'vvi', 'HanXRQChr03g0083821' => 'han', 'HanXRQChr03g0083841' => 'han', 'HanXRQChr03g0083881' => 'han', 'HanXRQChr03g0083901' => 'han', 'HanXRQChr03g0083921' => 'han', 'HanXRQChr03g0085331' => 'han', 'HanXRQChr03g0085361' => 'han', 'HanXRQChr03g0085411' => 'han', 'HanXRQChr03g0085421' => 'han', 'HanXRQChr03g0085431' => 'han', 'HanXRQChr08g0221991' => 'han', 'HanXRQChr11g0336061' => 'han', 'HanXRQChr11g0336411' => 'han', 'Haze_11234' => 'cav', 'Hma1.2p1_0549F.1_g177010' => 'hma', 'Hma1.2p1_0602F.1_g187630' => 'hma', 'Hund14876' => 'sun', 'Hund14879' => 'sun', 'Lalb_Chr06g0160741' => 'lal', 'Lalb_Chr21g0304781' => 'lal', 'Lj3A726G19' => 'lonja', 'Lj3A726T23' => 'lonja', 'Lj3A726T24' => 'lonja', 'Lj3A726T25' => 'lonja', 'Lj3A727T17' => 'lonja', 'Lj3C726T0' => 'lonja', 'Lj3C726T2' => 'lonja', 'Lj3P725T35' => 'lonja', 'Lj3P727T10' => 'lonja', 'Lj3P727T12' => 'lonja', 'Lj3P727T14' => 'lonja', 'Lj5g0023109' => 'lja', 'Lj6P646T44' => 'lonja', 'Lsat_1_v5_gn_6_75760' => 'lsa', 'Lsat_1_v5_gn_6_75800' => 'lsa', 'Lsat_1_v5_gn_6_75900' => 'lsa', 'Lsat_1_v5_gn_6_76240' => 'lsa', 'Lsat_1_v5_gn_6_76441' => 'lsa', 'Lsat_1_v5_gn_6_76700' => 'lsa', 'Lsat_1_v5_gn_6_76760' => 'lsa', 'Manes.15G033100' => 'mes', 'Mapoly0004s0074' => 'mpo', 'Mapoly0004s0075' => 'mpo', 'Mapoly0004s0163' => 'mpo', 'Mapoly0004s0164' => 'mpo', 'Mapoly0021s0018' => 'mpo', 'Mapoly0041s0136' => 'mpo', 'Mapoly0041s0137' => 'mpo', 'Mapoly0041s0138' => 'mpo', 'Mapoly0041s0139' => 'mpo', 'Mapoly0041s0141' => 'mpo', 'Mapoly0041s0142' => 'mpo', 'Mapoly0041s0143' => 'mpo', 'Mapoly0041s0144' => 'mpo', 'Mapoly0041s0145' => 'mpo', 'Mapoly0047s0106' => 'mpo', 'Mapoly0047s0108' => 'mpo', 'Mapoly0050s0051' => 'mpo', 'Mapoly0050s0052' => 'mpo', 'Mapoly0050s0053' => 'mpo', 'Mapoly0058s0013' => 'mpo', 'Mapoly0091s0078' => 'mpo', 'Mapoly0091s0079' => 'mpo', 'Mapoly0091s0080' => 'mpo', 'Mapoly0091s0081' => 'mpo', 'Mapoly0278s0004' => 'mpo', 'Mapoly0278s0005' => 'mpo', 'Mapoly0278s0006' => 'mpo', 'MBI11_g30648_MAGBIO' => 'mbi', 'MCO03G194' => 'mco', 'MCO03G590' => 'mco', 'MCO07G312' => 'mco', 'MCO10G318' => 'mco', 'MCO12G244' => 'mco', 'MCO13G148' => 'mco', 'MCO13G194' => 'mco', 'MCO16G238' => 'mco', 'MD06G1134100' => 'mdo', 'MD13G1200100' => 'mdo', 'MD13G1200300' => 'mdo', 'MD13G1200600' => 'mdo', 'MD14G1150400' => 'mdo', 'MD16G1200000' => 'mdo', 'Medtr1g102570' => 'mtr', 'Medtr1g102780' => 'mtr', 'Medtr1g102800' => 'mtr', 'Medtr1g102810' => 'mtr', 'Medtr1g102830' => 'mtr', 'MELO3C006499.2' => 'cme', 'Migut.G00385' => 'egut', 'MSTRG.4063' => 'ama', 'Nitab4.5_0000090g0260' => 'nta', 'Nitab4.5_0000977g0030' => 'nta', 'Nitab4.5_0002541g0040' => 'nta', 'Nitab4.5_0007068g0040' => 'nta', 'Nn005s41408' => 'nnu', 'Nn005s41410' => 'nnu', 'Oeu010310.1' => 'oeu', 'Oeu010311.1' => 'oeu', 'Oeu043472.1' => 'oeu', 'Os01g0246400' => 'osa', 'Os04g0267950' => 'osa', 'Os07g0178700' => 'osa', 'Os07g0178800' => 'osa', 'Peaxi162Scf00316g00046' => 'pax', 'Peaxi162Scf00316g00049' => 'pax', 'Peaxi162Scf00316g00059' => 'pax', 'Peaxi162Scf00316g00328' => 'pax', 'Peaxi162Scf00316g00329' => 'pax', 'Peaxi162Scf00316g00411' => 'pax', 'Peaxi162Scf00316g00521' => 'pax', 'Peaxi162Scf00492g00068' => 'pax', 'Peaxi162Scf35631g00002' => 'pax', 'PGR142G3720' => 'pgr', 'PGSC0003DMG400006442' => 'stu', 'Phvul.007G062000' => 'pvu', 'Potri.008G157750' => 'ptr', 'Potri.008G157900' => 'ptr', 'Potri.008G158000' => 'ptr', 'Potri.008G158200' => 'ptr', 'Pp3c11_7280' => 'ppa', 'Pp3c11_7980' => 'ppa', 'Pp3c12_19450' => 'ppa', 'Pp3c14_1480' => 'ppa', 'Pp3c14_1501' => 'ppa', 'Pp3c16_4900' => 'ppa', 'Pp3c16_5010' => 'ppa', 'Pp3c16_5060' => 'ppa', 'Pp3c19_18250' => 'ppa', 'Pp3c23_8530' => 'ppa', 'Pp3c23_8550' => 'ppa', 'Pp3c24_9670' => 'ppa', 'Pp3c2_21390' => 'ppa', 'Pp3c2_31380' => 'ppa', 'Pp3c3_16620' => 'ppa', 'Pp3c3_8090' => 'ppa', 'Pp3c3_8110' => 'ppa', 'Pp3c3_8130' => 'ppa', 'Pp3c3_8150' => 'ppa', 'Pp3c4_14320' => 'ppa', 'Pp3c6_2560' => 'ppa', 'Pp3c9_16700' => 'ppa', 'PRCOL_00000234' => 'pco', 'PRCOL_00000235' => 'pco', 'PRCOL_00000777' => 'pco', 'PRCOL_00002344' => 'pco', 'PRCOL_00002372' => 'pco', 'PRCOL_00006120' => 'pco', 'Prupe.1G021400' => 'ppe', 'Prupe.1G021500' => 'ppe', 'Prupe.1G021600' => 'ppe', 'Prupe.1G021700' => 'ppe', 'Prupe.1G021800' => 'ppe', 'Prupe.5G145100' => 'ppe', 'Psat6g204040' => 'psa', 'Psat6g204800' => 'psa', 'Psat6g204920' => 'psa', 'Psat6g204960' => 'psa', 'Psat6g205080' => 'psa', 'PSO017G0271' => 'pso', 'PSO017G1276' => 'pso', 'PSO017G1429' => 'pso', 'PSO017G1861' => 'pso', 'PSO017G2787' => 'pso', 'PSO017G4466' => 'pso', 'PSO017G5118' => 'pso', 'PSO017G5420' => 'pso', 'PSO063G3678' => 'pso', 'PSO210G0546' => 'pso', 'PSO317G0001' => 'pso', 'PSO357G0512' => 'pso', 'PSO478G2682' => 'pso', 'PSO647G0001' => 'pso', 'PSO675G0001' => 'pso', 'PSO675G2699' => 'pso', 'PSO675G2849' => 'pso', 'PSO675G4991' => 'pso', 'PSO689G0001' => 'pso', 'QL06p000916' => 'qlo', 'QL06p000921' => 'qlo', 'QL06p001398' => 'qlo', 'QL06p001407' => 'qlo', 'QL06p002031' => 'qlo', 'RcHm_v2.0_Chr4g0387791' => 'rch', 'RcHm_v2.0_Chr4g0387801' => 'rch', 'RcHm_v2.0_Chr6g0286501' => 'rch', 'RcHm_v2.0_Chr6g0286511' => 'rch', 'RcHm_v2.0_Chr6g0286521' => 'rch', 'RcHm_v2.0_Chr6g0286531' => 'rch', 'RcHm_v2.0_Chr7g0189141' => 'rch', 'Rhsim02G0028700' => 'rsi', 'Rhsim02G0028800' => 'rsi', 'Rhsim02G0028900' => 'rsi', 'Rhsim02G0029000' => 'rsi', 'Rhsim02G0029100' => 'rsi', 'Rhsim02G0029200' => 'rsi', 'Rhsim02G0029300' => 'rsi', 'Rhsim02G0029400' => 'rsi', 'Rhsim02G0029500' => 'rsi', 'Rhsim02G0029600' => 'rsi', 'RhsimUnG0024000' => 'rsi', 'RhsimUnG0024100' => 'rsi', 'RhsimUnG0024200' => 'rsi', 'RhsimUnG0024300' => 'rsi', 'RhsimUnG0024400' => 'rsi', 'RhsimUnG0024500' => 'rsi', 'RhsimUnG0024700' => 'rsi', 'RhsimUnG0024800' => 'rsi', 'RhsimUnG0024900' => 'rsi', 'RhsimUnG0025100' => 'rsi', 'Sabra08G0120200' => 'sbr', 'Sabra08G0120300' => 'sbr', 'Sabra08G0120500' => 'sbr', 'Sabra08G0120600' => 'sbr', 'Sabra10G0158900' => 'sbr', 'SalBow2G3492' => 'sbo', 'Sc13g0004760' => 'sci', 'Sc13g0004770' => 'sci', 'Sed0003417' => 'sed', 'Sed0019750' => 'sed', 'SEGI_03419' => 'sgi', 'SEGI_05907' => 'sgi', 'SEGI_10682' => 'sgi', 'SEGI_13528' => 'sgi', 'SEGI_16081' => 'sgi', 'SEGI_19370' => 'sgi', 'SEGI_21015' => 'sgi', 'SEGI_21944' => 'sgi', 'SEGI_32906' => 'sgi', 'SEGI_33093' => 'sgi', 'SEGI_36110' => 'sgi', 'SEGI_40397' => 'sgi', 'SGA_v2.0_scaffold191G40426' => 'sas', 'SGA_v2.0_scaffold353G49717' => 'sas', 'SGA_v2.0_scaffold50G18550' => 'sas', 'SMO119G0173' => 'smo', 'SMO172G0002' => 'smo', 'Solyc09g082690.3' => 'sly', 'Solyc09g082700.2' => 'sly', 'Sopen09g031550' => 'spe', 'Sopen09g031560' => 'spe', 'Sp3g20540' => 'spa', 'Sp7g07580' => 'spa', 'TAR134G0002' => 'tar', 'TAR236G0001' => 'tar', 'TAR365G0892' => 'tar', 'TAR636G0166' => 'tar', 'TAR636G0646' => 'tar', 'TAR636G0869' => 'tar', 'TAR636G1317' => 'tar', 'TAR636G1744' => 'tar', 'TAR636G3358' => 'tar', 'TAR636G3436' => 'tar', 'THA.LOC104803047' => 'tha', 'Thecc.04G238900' => 'tca', 'Thhalv10021557m.g' => 'esa', 'Thhalv10026318m.g' => 'esa', 'Thhalv10026335m.g' => 'esa', 'TPR.G17433' => 'tpr', 'TPR.G18915' => 'tpr', 'TPR.G26125' => 'tpr', 'TWI09G0677' => 'twi', 'TWI73G0287' => 'twi', 'unitig_748.g8326' => 'ugi', 'vmacro15370' => 'vma', 'vmacro15371' => 'vma', 'vmacro15372' => 'vma', 'vmacro15373' => 'vma', 'vmacro15374' => 'vma', 'VMungo0720G2826' => 'vmu', 'Zm00001eb116960' => 'zma', 'Zm00001eb301260' => 'zma', 'Zm00001eb301270' => 'zma' ), 'gf_id' => 'HOM05D001460', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001460' ), 'data_identifier' => 'HOM05D001460', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001460', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '433', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p22980' => 'bna', 'A01p32340' => 'bna', 'A03p42970' => 'bna', 'A05p25880' => 'bna', 'Aa31LG8G9320' => 'aar', 'Aa31LG8G9330' => 'aar', 'Aa31LG8G9340' => 'aar', 'Aa31sc221G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1034' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1528' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.829' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2222' => 'aag', 'Ah.12g058830' => 'amhyb', 'Ah.12g058840' => 'amhyb', 'AL3G37160' => 'aly', 'AL7G41310' => 'aly', 'Aqoxy5G00395' => 'aox', 'Aqoxy5G00396' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0C8NZA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5185HY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JZ1PRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MD3LS0' => 'arhy', 'AT3G22840' => 'ath', 'AT4G14690' => 'ath', 'ATR0665G054' => 'atr', 'Atru.chr4.2344' => 'acertr', 'Atru.chr4.2346' => 'acertr', 'Atru.chr4.2347' => 'acertr', 'Atru.chr4.2348' => 'acertr', 'Atru.chr4.2355' => 'acertr', 'Atru.chr4.2356' => 'acertr', 'Atru.chr4.2358' => 'acertr', 'Atru.chr4.2359' => 'acertr', 'Atru.chr4.2360' => 'acertr', 'Atru.chr4.2361' => 'acertr', 'AUR62030476' => 'cqu', 'AUR62030478' => 'cqu', 'AUR62030819' => 'cqu', 'AUR62030820' => 'cqu', 'BcaB03g14648' => 'bca', 'BcaB04g20492' => 'bca', 'BcaB06g26399' => 'bca', 'BcaC01g03416' => 'bca', 'BcaC01g03419' => 'bca', 'BcaC01g03421' => 'bca', 'BcaC01g03424' => 'bca', 'BcaC05g28012' => 'bca', 'BcaC09g49212' => 'bca', 'BcaC09g50140' => 'bca', 'BcaNung00346' => 'bca', 'BolC1t02785H' => 'bol', 'BolC1t04095H' => 'bol', 'BolC3t17545H' => 'bol', 'BolC5t32769H' => 'bol', 'BraA01t02211Z' => 'bra', 'BraA01t03359Z' => 'bra', 'BraA03t13441Z' => 'bra', 'BraA05t21476Z' => 'bra', 'C01p28420' => 'bna', 'C01p41350' => 'bna', 'C03p52750' => 'bna', 'C03p52780' => 'bna', 'C05p40270' => 'bna', 'CAN.G1437.9' => 'can', 'CANSAT78G0035' => 'cansat', 'CANSAT78G1036' => 'cansat', 'CANSAT78G2272' => 'cansat', 'CANSAT78G2478' => 'cansat', 'CARHR098700' => 'chi', 'CARHR221120' => 'chi', 'CARHR221150' => 'chi', 'Carub.0003s2297' => 'cru', 'Carub.0007s2749' => 'cru', 'Carub.0007s2750' => 'cru', 'Carub.0007s2751' => 'cru', 'Ca_10849_v3' => 'car', 'Cc03_g04300' => 'ccan', 'CDE02G3648' => 'cde', 'CDE05G0060' => 'cde', 'CDE05G0692' => 'cde', 'CDE05G2285' => 'cde', 'CDE05G2884' => 'cde', 'CDE05G3072' => 'cde', 'Cfa008439' => 'cfa', 'Cfa008441' => 'cfa', 'Cfa008443' => 'cfa', 'Cfa008448' => 'cfa', 'Ciclev10005974m.g' => 'ccl', 'Ciclev10006006m.g' => 'ccl', 'Ciclev10006775m.g' => 'ccl', 'CiPaw.02G120400' => 'cil', 'CiPaw.02G120500' => 'cil', 'CiPaw.02G120600' => 'cil', 'ClCG05G004850' => 'cla', 'COL.COLO4_21566' => 'col', 'Cpa.g.sc44.124' => 'cpa', 'Cre07.g320400' => 'cre', 'Cre07.g320450' => 'cre', 'Cre08.g384650' => 'cre', 'Cre09.g393173' => 'cre', 'Cre09.g394325' => 'cre', 'Cre14.g626750' => 'cre', 'Cre16.g679250' => 'cre', 'CsaV3_3G012890' => 'csa', 'CSS0010865' => 'camsi', 'CSS0044338' => 'camsi', 'DCAR_002366' => 'dca', 'DCAR_030687' => 'dca', 'DCAR_030688' => 'dca', 'Dinv14047' => 'din', 'Dinv14048' => 'din', 'Duzib151G0105' => 'dzi', 'Duzib151G0114' => 'dzi', 'Duzib212G1029' => 'dzi', 'ECA232G3536' => 'eca', 'ECA240G0786' => 'eca', 'ECA240G1802' => 'eca', 'ECA240G3760' => 'eca', 'ECA240G3920' => 'eca', 'EL10Ac5g12536' => 'bvu', 'EL10Ac5g12537' => 'bvu', 'EL10Ac5g12538' => 'bvu', 'Eucgr.B01004' => 'egr', 'Eucgr.B01006' => 'egr', 'Eucgr.B01007' => 'egr', 'Eucgr.B01008' => 'egr', 'Eucgr.B01895' => 'egr', 'Eucgr.B01896' => 'egr', 'FAN04G1456' => 'fan', 'FAN08G1769' => 'fan', 'FAN08G2160' => 'fan', 'FAN13G2403' => 'fan', 'FAN13G3303' => 'fan', 'FAN15G2435' => 'fan', 'FAN17G0672' => 'fan', 'FAN17G2441' => 'fan', 'FAN18G1024' => 'fan', 'FAN22G1458' => 'fan', 'FAN24G0037' => 'fan', 'FAN24G0429' => 'fan', 'FAN24G2387' => 'fan', 'FAN27G2746' => 'fan', 'FvH4_2g20400' => 'fve', 'FvH4_2g20420' => 'fve', 'FvH4_2g20430' => 'fve', 'FvH4_4g01270' => 'fve', 'FvH4_4g01290' => 'fve', 'FvH4_4g01300' => 'fve', 'FvH4_4g01310' => 'fve', 'FvH4_4g01330' => 'fve', 'FvH4_5g09070' => 'fve', 'Glyma.10G243800' => 'gma', 'Glyma.20G150600' => 'gma', 'Gohir.A09G219200' => 'ghi', 'Gohir.A09G219300' => 'ghi', 'Gohir.D09G221400' => 'ghi', 'Gohir.D09G221500' => 'ghi', 'Gorai.006G242600' => 'gra', 'Gorai.006G242700' => 'gra', 'GSVIVG01018044001' => 'vvi', 'HanXRQChr03g0083821' => 'han', 'HanXRQChr03g0083841' => 'han', 'HanXRQChr03g0083881' => 'han', 'HanXRQChr03g0083901' => 'han', 'HanXRQChr03g0083921' => 'han', 'HanXRQChr03g0085331' => 'han', 'HanXRQChr03g0085361' => 'han', 'HanXRQChr03g0085411' => 'han', 'HanXRQChr03g0085421' => 'han', 'HanXRQChr03g0085431' => 'han', 'HanXRQChr08g0221991' => 'han', 'HanXRQChr11g0336061' => 'han', 'HanXRQChr11g0336411' => 'han', 'Haze_11234' => 'cav', 'Hma1.2p1_0549F.1_g177010' => 'hma', 'Hma1.2p1_0602F.1_g187630' => 'hma', 'Hund14876' => 'sun', 'Hund14879' => 'sun', 'Lalb_Chr06g0160741' => 'lal', 'Lalb_Chr21g0304781' => 'lal', 'Lj3A726G19' => 'lonja', 'Lj3A726T23' => 'lonja', 'Lj3A726T24' => 'lonja', 'Lj3A726T25' => 'lonja', 'Lj3A727T17' => 'lonja', 'Lj3C726T0' => 'lonja', 'Lj3C726T2' => 'lonja', 'Lj3P725T35' => 'lonja', 'Lj3P727T10' => 'lonja', 'Lj3P727T12' => 'lonja', 'Lj3P727T14' => 'lonja', 'Lj5g0023109' => 'lja', 'Lj6P646T44' => 'lonja', 'Lsat_1_v5_gn_6_75760' => 'lsa', 'Lsat_1_v5_gn_6_75800' => 'lsa', 'Lsat_1_v5_gn_6_75900' => 'lsa', 'Lsat_1_v5_gn_6_76240' => 'lsa', 'Lsat_1_v5_gn_6_76441' => 'lsa', 'Lsat_1_v5_gn_6_76700' => 'lsa', 'Lsat_1_v5_gn_6_76760' => 'lsa', 'Manes.15G033100' => 'mes', 'Mapoly0004s0074' => 'mpo', 'Mapoly0004s0075' => 'mpo', 'Mapoly0004s0163' => 'mpo', 'Mapoly0004s0164' => 'mpo', 'Mapoly0021s0018' => 'mpo', 'Mapoly0041s0136' => 'mpo', 'Mapoly0041s0137' => 'mpo', 'Mapoly0041s0138' => 'mpo', 'Mapoly0041s0139' => 'mpo', 'Mapoly0041s0141' => 'mpo', 'Mapoly0041s0142' => 'mpo', 'Mapoly0041s0143' => 'mpo', 'Mapoly0041s0144' => 'mpo', 'Mapoly0041s0145' => 'mpo', 'Mapoly0047s0106' => 'mpo', 'Mapoly0047s0108' => 'mpo', 'Mapoly0050s0051' => 'mpo', 'Mapoly0050s0052' => 'mpo', 'Mapoly0050s0053' => 'mpo', 'Mapoly0058s0013' => 'mpo', 'Mapoly0091s0078' => 'mpo', 'Mapoly0091s0079' => 'mpo', 'Mapoly0091s0080' => 'mpo', 'Mapoly0091s0081' => 'mpo', 'Mapoly0278s0004' => 'mpo', 'Mapoly0278s0005' => 'mpo', 'Mapoly0278s0006' => 'mpo', 'MBI11_g30648_MAGBIO' => 'mbi', 'MCO03G194' => 'mco', 'MCO03G590' => 'mco', 'MCO07G312' => 'mco', 'MCO10G318' => 'mco', 'MCO12G244' => 'mco', 'MCO13G148' => 'mco', 'MCO13G194' => 'mco', 'MCO16G238' => 'mco', 'MD06G1134100' => 'mdo', 'MD13G1200100' => 'mdo', 'MD13G1200300' => 'mdo', 'MD13G1200600' => 'mdo', 'MD14G1150400' => 'mdo', 'MD16G1200000' => 'mdo', 'Medtr1g102570' => 'mtr', 'Medtr1g102780' => 'mtr', 'Medtr1g102800' => 'mtr', 'Medtr1g102810' => 'mtr', 'Medtr1g102830' => 'mtr', 'MELO3C006499.2' => 'cme', 'Migut.G00385' => 'egut', 'MSTRG.4063' => 'ama', 'Nitab4.5_0000090g0260' => 'nta', 'Nitab4.5_0000977g0030' => 'nta', 'Nitab4.5_0002541g0040' => 'nta', 'Nitab4.5_0007068g0040' => 'nta', 'Nn005s41408' => 'nnu', 'Nn005s41410' => 'nnu', 'Oeu010310.1' => 'oeu', 'Oeu010311.1' => 'oeu', 'Oeu043472.1' => 'oeu', 'Os01g0246400' => 'osa', 'Os04g0267950' => 'osa', 'Os07g0178700' => 'osa', 'Os07g0178800' => 'osa', 'Peaxi162Scf00316g00046' => 'pax', 'Peaxi162Scf00316g00049' => 'pax', 'Peaxi162Scf00316g00059' => 'pax', 'Peaxi162Scf00316g00328' => 'pax', 'Peaxi162Scf00316g00329' => 'pax', 'Peaxi162Scf00316g00411' => 'pax', 'Peaxi162Scf00316g00521' => 'pax', 'Peaxi162Scf00492g00068' => 'pax', 'Peaxi162Scf35631g00002' => 'pax', 'PGR142G3720' => 'pgr', 'PGSC0003DMG400006442' => 'stu', 'Phvul.007G062000' => 'pvu', 'Potri.008G157750' => 'ptr', 'Potri.008G157900' => 'ptr', 'Potri.008G158000' => 'ptr', 'Potri.008G158200' => 'ptr', 'Pp3c11_7280' => 'ppa', 'Pp3c11_7980' => 'ppa', 'Pp3c12_19450' => 'ppa', 'Pp3c14_1480' => 'ppa', 'Pp3c14_1501' => 'ppa', 'Pp3c16_4900' => 'ppa', 'Pp3c16_5010' => 'ppa', 'Pp3c16_5060' => 'ppa', 'Pp3c19_18250' => 'ppa', 'Pp3c23_8530' => 'ppa', 'Pp3c23_8550' => 'ppa', 'Pp3c24_9670' => 'ppa', 'Pp3c2_21390' => 'ppa', 'Pp3c2_31380' => 'ppa', 'Pp3c3_16620' => 'ppa', 'Pp3c3_8090' => 'ppa', 'Pp3c3_8110' => 'ppa', 'Pp3c3_8130' => 'ppa', 'Pp3c3_8150' => 'ppa', 'Pp3c4_14320' => 'ppa', 'Pp3c6_2560' => 'ppa', 'Pp3c9_16700' => 'ppa', 'PRCOL_00000234' => 'pco', 'PRCOL_00000235' => 'pco', 'PRCOL_00000777' => 'pco', 'PRCOL_00002344' => 'pco', 'PRCOL_00002372' => 'pco', 'PRCOL_00006120' => 'pco', 'Prupe.1G021400' => 'ppe', 'Prupe.1G021500' => 'ppe', 'Prupe.1G021600' => 'ppe', 'Prupe.1G021700' => 'ppe', 'Prupe.1G021800' => 'ppe', 'Prupe.5G145100' => 'ppe', 'Psat6g204040' => 'psa', 'Psat6g204800' => 'psa', 'Psat6g204920' => 'psa', 'Psat6g204960' => 'psa', 'Psat6g205080' => 'psa', 'PSO017G0271' => 'pso', 'PSO017G1276' => 'pso', 'PSO017G1429' => 'pso', 'PSO017G1861' => 'pso', 'PSO017G2787' => 'pso', 'PSO017G4466' => 'pso', 'PSO017G5118' => 'pso', 'PSO017G5420' => 'pso', 'PSO063G3678' => 'pso', 'PSO210G0546' => 'pso', 'PSO317G0001' => 'pso', 'PSO357G0512' => 'pso', 'PSO478G2682' => 'pso', 'PSO647G0001' => 'pso', 'PSO675G0001' => 'pso', 'PSO675G2699' => 'pso', 'PSO675G2849' => 'pso', 'PSO675G4991' => 'pso', 'PSO689G0001' => 'pso', 'QL06p000916' => 'qlo', 'QL06p000921' => 'qlo', 'QL06p001398' => 'qlo', 'QL06p001407' => 'qlo', 'QL06p002031' => 'qlo', 'RcHm_v2.0_Chr4g0387791' => 'rch', 'RcHm_v2.0_Chr4g0387801' => 'rch', 'RcHm_v2.0_Chr6g0286501' => 'rch', 'RcHm_v2.0_Chr6g0286511' => 'rch', 'RcHm_v2.0_Chr6g0286521' => 'rch', 'RcHm_v2.0_Chr6g0286531' => 'rch', 'RcHm_v2.0_Chr7g0189141' => 'rch', 'Rhsim02G0028700' => 'rsi', 'Rhsim02G0028800' => 'rsi', 'Rhsim02G0028900' => 'rsi', 'Rhsim02G0029000' => 'rsi', 'Rhsim02G0029100' => 'rsi', 'Rhsim02G0029200' => 'rsi', 'Rhsim02G0029300' => 'rsi', 'Rhsim02G0029400' => 'rsi', 'Rhsim02G0029500' => 'rsi', 'Rhsim02G0029600' => 'rsi', 'RhsimUnG0024000' => 'rsi', 'RhsimUnG0024100' => 'rsi', 'RhsimUnG0024200' => 'rsi', 'RhsimUnG0024300' => 'rsi', 'RhsimUnG0024400' => 'rsi', 'RhsimUnG0024500' => 'rsi', 'RhsimUnG0024700' => 'rsi', 'RhsimUnG0024800' => 'rsi', 'RhsimUnG0024900' => 'rsi', 'RhsimUnG0025100' => 'rsi', 'Sabra08G0120200' => 'sbr', 'Sabra08G0120300' => 'sbr', 'Sabra08G0120500' => 'sbr', 'Sabra08G0120600' => 'sbr', 'Sabra10G0158900' => 'sbr', 'SalBow2G3492' => 'sbo', 'Sc13g0004760' => 'sci', 'Sc13g0004770' => 'sci', 'Sed0003417' => 'sed', 'Sed0019750' => 'sed', 'SEGI_03419' => 'sgi', 'SEGI_05907' => 'sgi', 'SEGI_10682' => 'sgi', 'SEGI_13528' => 'sgi', 'SEGI_16081' => 'sgi', 'SEGI_19370' => 'sgi', 'SEGI_21015' => 'sgi', 'SEGI_21944' => 'sgi', 'SEGI_32906' => 'sgi', 'SEGI_33093' => 'sgi', 'SEGI_36110' => 'sgi', 'SEGI_40397' => 'sgi', 'SGA_v2.0_scaffold191G40426' => 'sas', 'SGA_v2.0_scaffold353G49717' => 'sas', 'SGA_v2.0_scaffold50G18550' => 'sas', 'SMO119G0173' => 'smo', 'SMO172G0002' => 'smo', 'Solyc09g082690.3' => 'sly', 'Solyc09g082700.2' => 'sly', 'Sopen09g031550' => 'spe', 'Sopen09g031560' => 'spe', 'Sp3g20540' => 'spa', 'Sp7g07580' => 'spa', 'TAR134G0002' => 'tar', 'TAR236G0001' => 'tar', 'TAR365G0892' => 'tar', 'TAR636G0166' => 'tar', 'TAR636G0646' => 'tar', 'TAR636G0869' => 'tar', 'TAR636G1317' => 'tar', 'TAR636G1744' => 'tar', 'TAR636G3358' => 'tar', 'TAR636G3436' => 'tar', 'THA.LOC104803047' => 'tha', 'Thecc.04G238900' => 'tca', 'Thhalv10021557m.g' => 'esa', 'Thhalv10026318m.g' => 'esa', 'Thhalv10026335m.g' => 'esa', 'TPR.G17433' => 'tpr', 'TPR.G18915' => 'tpr', 'TPR.G26125' => 'tpr', 'TWI09G0677' => 'twi', 'TWI73G0287' => 'twi', 'unitig_748.g8326' => 'ugi', 'vmacro15370' => 'vma', 'vmacro15371' => 'vma', 'vmacro15372' => 'vma', 'vmacro15373' => 'vma', 'vmacro15374' => 'vma', 'VMungo0720G2826' => 'vmu', 'Zm00001eb116960' => 'zma', 'Zm00001eb301260' => 'zma', 'Zm00001eb301270' => 'zma' ) $gf_id = 'HOM05D001460' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001460' ) $data_identifier = 'HOM05D001460' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 4, 'aag' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 2, 'aox' => (int) 2, 'arhy' => (int) 4, 'ath' => (int) 2, 'atr' => (int) 1, 'acertr' => (int) 10, 'cqu' => (int) 4, 'bca' => (int) 11, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 1, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 1, 'ccan' => (int) 1, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 1, 'col' => (int) 1, 'cpa' => (int) 1, 'cre' => (int) 7, 'csa' => (int) 1, 'camsi' => (int) 2, 'dca' => (int) 3, 'din' => (int) 2, 'dzi' => (int) 3, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 14, 'fve' => (int) 9, 'gma' => (int) 2, 'ghi' => (int) 4, 'gra' => (int) 2, 'vvi' => (int) 1, 'han' => (int) 13, 'cav' => (int) 1, 'hma' => (int) 2, 'sun' => (int) 2, 'lal' => (int) 2, 'lonja' => (int) 12, 'lja' => (int) 1, 'lsa' => (int) 7, 'mes' => (int) 1, 'mpo' => (int) 27, 'mbi' => (int) 1, 'mco' => (int) 8, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 1, 'egut' => (int) 1, 'ama' => (int) 1, 'nta' => (int) 4, 'nnu' => (int) 2, 'oeu' => (int) 3, 'osa' => (int) 4, 'pax' => (int) 9, 'pgr' => (int) 1, 'stu' => (int) 1, 'pvu' => (int) 1, 'ptr' => (int) 4, 'ppa' => (int) 22, 'pco' => (int) 6, 'ppe' => (int) 6, 'psa' => (int) 5, 'pso' => (int) 19, 'qlo' => (int) 5, 'rch' => (int) 7, 'rsi' => (int) 20, 'sbr' => (int) 5, 'sbo' => (int) 1, 'sci' => (int) 2, 'sed' => (int) 2, 'sgi' => (int) 12, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 2, 'tar' => (int) 10, 'tha' => (int) 1, 'tca' => (int) 1, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 2, 'ugi' => (int) 1, 'vma' => (int) 5, 'vmu' => (int) 1, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb301270' $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' => 'HOM05D001460', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '433', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p22980' => 'bna', 'A01p32340' => 'bna', 'A03p42970' => 'bna', 'A05p25880' => 'bna', 'Aa31LG8G9320' => 'aar', 'Aa31LG8G9330' => 'aar', 'Aa31LG8G9340' => 'aar', 'Aa31sc221G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1034' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1528' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.829' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2222' => 'aag', 'Ah.12g058830' => 'amhyb', 'Ah.12g058840' => 'amhyb', 'AL3G37160' => 'aly', 'AL7G41310' => 'aly', 'Aqoxy5G00395' => 'aox', 'Aqoxy5G00396' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0C8NZA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5185HY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JZ1PRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MD3LS0' => 'arhy', 'AT3G22840' => 'ath', 'AT4G14690' => 'ath', 'ATR0665G054' => 'atr', 'Atru.chr4.2344' => 'acertr', 'Atru.chr4.2346' => 'acertr', 'Atru.chr4.2347' => 'acertr', 'Atru.chr4.2348' => 'acertr', 'Atru.chr4.2355' => 'acertr', 'Atru.chr4.2356' => 'acertr', 'Atru.chr4.2358' => 'acertr', 'Atru.chr4.2359' => 'acertr', 'Atru.chr4.2360' => 'acertr', 'Atru.chr4.2361' => 'acertr', 'AUR62030476' => 'cqu', 'AUR62030478' => 'cqu', 'AUR62030819' => 'cqu', 'AUR62030820' => 'cqu', 'BcaB03g14648' => 'bca', 'BcaB04g20492' => 'bca', 'BcaB06g26399' => 'bca', 'BcaC01g03416' => 'bca', 'BcaC01g03419' => 'bca', 'BcaC01g03421' => 'bca', 'BcaC01g03424' => 'bca', 'BcaC05g28012' => 'bca', 'BcaC09g49212' => 'bca', 'BcaC09g50140' => 'bca', 'BcaNung00346' => 'bca', 'BolC1t02785H' => 'bol', 'BolC1t04095H' => 'bol', 'BolC3t17545H' => 'bol', 'BolC5t32769H' => 'bol', 'BraA01t02211Z' => 'bra', 'BraA01t03359Z' => 'bra', 'BraA03t13441Z' => 'bra', 'BraA05t21476Z' => 'bra', 'C01p28420' => 'bna', 'C01p41350' => 'bna', 'C03p52750' => 'bna', 'C03p52780' => 'bna', 'C05p40270' => 'bna', 'CAN.G1437.9' => 'can', 'CANSAT78G0035' => 'cansat', 'CANSAT78G1036' => 'cansat', 'CANSAT78G2272' => 'cansat', 'CANSAT78G2478' => 'cansat', 'CARHR098700' => 'chi', 'CARHR221120' => 'chi', 'CARHR221150' => 'chi', 'Carub.0003s2297' => 'cru', 'Carub.0007s2749' => 'cru', 'Carub.0007s2750' => 'cru', 'Carub.0007s2751' => 'cru', 'Ca_10849_v3' => 'car', 'Cc03_g04300' => 'ccan', 'CDE02G3648' => 'cde', 'CDE05G0060' => 'cde', 'CDE05G0692' => 'cde', 'CDE05G2285' => 'cde', 'CDE05G2884' => 'cde', 'CDE05G3072' => 'cde', 'Cfa008439' => 'cfa', 'Cfa008441' => 'cfa', 'Cfa008443' => 'cfa', 'Cfa008448' => 'cfa', 'Ciclev10005974m.g' => 'ccl', 'Ciclev10006006m.g' => 'ccl', 'Ciclev10006775m.g' => 'ccl', 'CiPaw.02G120400' => 'cil', 'CiPaw.02G120500' => 'cil', 'CiPaw.02G120600' => 'cil', 'ClCG05G004850' => 'cla', 'COL.COLO4_21566' => 'col', 'Cpa.g.sc44.124' => 'cpa', 'Cre07.g320400' => 'cre', 'Cre07.g320450' => 'cre', 'Cre08.g384650' => 'cre', 'Cre09.g393173' => 'cre', 'Cre09.g394325' => 'cre', 'Cre14.g626750' => 'cre', 'Cre16.g679250' => 'cre', 'CsaV3_3G012890' => 'csa', 'CSS0010865' => 'camsi', 'CSS0044338' => 'camsi', 'DCAR_002366' => 'dca', 'DCAR_030687' => 'dca', 'DCAR_030688' => 'dca', 'Dinv14047' => 'din', 'Dinv14048' => 'din', 'Duzib151G0105' => 'dzi', 'Duzib151G0114' => 'dzi', 'Duzib212G1029' => 'dzi', 'ECA232G3536' => 'eca', 'ECA240G0786' => 'eca', 'ECA240G1802' => 'eca', 'ECA240G3760' => 'eca', 'ECA240G3920' => 'eca', 'EL10Ac5g12536' => 'bvu', 'EL10Ac5g12537' => 'bvu', 'EL10Ac5g12538' => 'bvu', 'Eucgr.B01004' => 'egr', 'Eucgr.B01006' => 'egr', 'Eucgr.B01007' => 'egr', 'Eucgr.B01008' => 'egr', 'Eucgr.B01895' => 'egr', 'Eucgr.B01896' => 'egr', 'FAN04G1456' => 'fan', 'FAN08G1769' => 'fan', 'FAN08G2160' => 'fan', 'FAN13G2403' => 'fan', 'FAN13G3303' => 'fan', 'FAN15G2435' => 'fan', 'FAN17G0672' => 'fan', 'FAN17G2441' => 'fan', 'FAN18G1024' => 'fan', 'FAN22G1458' => 'fan', 'FAN24G0037' => 'fan', 'FAN24G0429' => 'fan', 'FAN24G2387' => 'fan', 'FAN27G2746' => 'fan', 'FvH4_2g20400' => 'fve', 'FvH4_2g20420' => 'fve', 'FvH4_2g20430' => 'fve', 'FvH4_4g01270' => 'fve', 'FvH4_4g01290' => 'fve', 'FvH4_4g01300' => 'fve', 'FvH4_4g01310' => 'fve', 'FvH4_4g01330' => 'fve', 'FvH4_5g09070' => 'fve', 'Glyma.10G243800' => 'gma', 'Glyma.20G150600' => 'gma', 'Gohir.A09G219200' => 'ghi', 'Gohir.A09G219300' => 'ghi', 'Gohir.D09G221400' => 'ghi', 'Gohir.D09G221500' => 'ghi', 'Gorai.006G242600' => 'gra', 'Gorai.006G242700' => 'gra', 'GSVIVG01018044001' => 'vvi', 'HanXRQChr03g0083821' => 'han', 'HanXRQChr03g0083841' => 'han', 'HanXRQChr03g0083881' => 'han', 'HanXRQChr03g0083901' => 'han', 'HanXRQChr03g0083921' => 'han', 'HanXRQChr03g0085331' => 'han', 'HanXRQChr03g0085361' => 'han', 'HanXRQChr03g0085411' => 'han', 'HanXRQChr03g0085421' => 'han', 'HanXRQChr03g0085431' => 'han', 'HanXRQChr08g0221991' => 'han', 'HanXRQChr11g0336061' => 'han', 'HanXRQChr11g0336411' => 'han', 'Haze_11234' => 'cav', 'Hma1.2p1_0549F.1_g177010' => 'hma', 'Hma1.2p1_0602F.1_g187630' => 'hma', 'Hund14876' => 'sun', 'Hund14879' => 'sun', 'Lalb_Chr06g0160741' => 'lal', 'Lalb_Chr21g0304781' => 'lal', 'Lj3A726G19' => 'lonja', 'Lj3A726T23' => 'lonja', 'Lj3A726T24' => 'lonja', 'Lj3A726T25' => 'lonja', 'Lj3A727T17' => 'lonja', 'Lj3C726T0' => 'lonja', 'Lj3C726T2' => 'lonja', 'Lj3P725T35' => 'lonja', 'Lj3P727T10' => 'lonja', 'Lj3P727T12' => 'lonja', 'Lj3P727T14' => 'lonja', 'Lj5g0023109' => 'lja', 'Lj6P646T44' => 'lonja', 'Lsat_1_v5_gn_6_75760' => 'lsa', 'Lsat_1_v5_gn_6_75800' => 'lsa', 'Lsat_1_v5_gn_6_75900' => 'lsa', 'Lsat_1_v5_gn_6_76240' => 'lsa', 'Lsat_1_v5_gn_6_76441' => 'lsa', 'Lsat_1_v5_gn_6_76700' => 'lsa', 'Lsat_1_v5_gn_6_76760' => 'lsa', 'Manes.15G033100' => 'mes', 'Mapoly0004s0074' => 'mpo', 'Mapoly0004s0075' => 'mpo', 'Mapoly0004s0163' => 'mpo', 'Mapoly0004s0164' => 'mpo', 'Mapoly0021s0018' => 'mpo', 'Mapoly0041s0136' => 'mpo', 'Mapoly0041s0137' => 'mpo', 'Mapoly0041s0138' => 'mpo', 'Mapoly0041s0139' => 'mpo', 'Mapoly0041s0141' => 'mpo', 'Mapoly0041s0142' => 'mpo', 'Mapoly0041s0143' => 'mpo', 'Mapoly0041s0144' => 'mpo', 'Mapoly0041s0145' => 'mpo', 'Mapoly0047s0106' => 'mpo', 'Mapoly0047s0108' => 'mpo', 'Mapoly0050s0051' => 'mpo', 'Mapoly0050s0052' => 'mpo', 'Mapoly0050s0053' => 'mpo', 'Mapoly0058s0013' => 'mpo', 'Mapoly0091s0078' => 'mpo', 'Mapoly0091s0079' => 'mpo', 'Mapoly0091s0080' => 'mpo', 'Mapoly0091s0081' => 'mpo', 'Mapoly0278s0004' => 'mpo', 'Mapoly0278s0005' => 'mpo', 'Mapoly0278s0006' => 'mpo', 'MBI11_g30648_MAGBIO' => 'mbi', 'MCO03G194' => 'mco', 'MCO03G590' => 'mco', 'MCO07G312' => 'mco', 'MCO10G318' => 'mco', 'MCO12G244' => 'mco', 'MCO13G148' => 'mco', 'MCO13G194' => 'mco', 'MCO16G238' => 'mco', 'MD06G1134100' => 'mdo', 'MD13G1200100' => 'mdo', 'MD13G1200300' => 'mdo', 'MD13G1200600' => 'mdo', 'MD14G1150400' => 'mdo', 'MD16G1200000' => 'mdo', 'Medtr1g102570' => 'mtr', 'Medtr1g102780' => 'mtr', 'Medtr1g102800' => 'mtr', 'Medtr1g102810' => 'mtr', 'Medtr1g102830' => 'mtr', 'MELO3C006499.2' => 'cme', 'Migut.G00385' => 'egut', 'MSTRG.4063' => 'ama', 'Nitab4.5_0000090g0260' => 'nta', 'Nitab4.5_0000977g0030' => 'nta', 'Nitab4.5_0002541g0040' => 'nta', 'Nitab4.5_0007068g0040' => 'nta', 'Nn005s41408' => 'nnu', 'Nn005s41410' => 'nnu', 'Oeu010310.1' => 'oeu', 'Oeu010311.1' => 'oeu', 'Oeu043472.1' => 'oeu', 'Os01g0246400' => 'osa', 'Os04g0267950' => 'osa', 'Os07g0178700' => 'osa', 'Os07g0178800' => 'osa', 'Peaxi162Scf00316g00046' => 'pax', 'Peaxi162Scf00316g00049' => 'pax', 'Peaxi162Scf00316g00059' => 'pax', 'Peaxi162Scf00316g00328' => 'pax', 'Peaxi162Scf00316g00329' => 'pax', 'Peaxi162Scf00316g00411' => 'pax', 'Peaxi162Scf00316g00521' => 'pax', 'Peaxi162Scf00492g00068' => 'pax', 'Peaxi162Scf35631g00002' => 'pax', 'PGR142G3720' => 'pgr', 'PGSC0003DMG400006442' => 'stu', 'Phvul.007G062000' => 'pvu', 'Potri.008G157750' => 'ptr', 'Potri.008G157900' => 'ptr', 'Potri.008G158000' => 'ptr', 'Potri.008G158200' => 'ptr', 'Pp3c11_7280' => 'ppa', 'Pp3c11_7980' => 'ppa', 'Pp3c12_19450' => 'ppa', 'Pp3c14_1480' => 'ppa', 'Pp3c14_1501' => 'ppa', 'Pp3c16_4900' => 'ppa', 'Pp3c16_5010' => 'ppa', 'Pp3c16_5060' => 'ppa', 'Pp3c19_18250' => 'ppa', 'Pp3c23_8530' => 'ppa', 'Pp3c23_8550' => 'ppa', 'Pp3c24_9670' => 'ppa', 'Pp3c2_21390' => 'ppa', 'Pp3c2_31380' => 'ppa', 'Pp3c3_16620' => 'ppa', 'Pp3c3_8090' => 'ppa', 'Pp3c3_8110' => 'ppa', 'Pp3c3_8130' => 'ppa', 'Pp3c3_8150' => 'ppa', 'Pp3c4_14320' => 'ppa', 'Pp3c6_2560' => 'ppa', 'Pp3c9_16700' => 'ppa', 'PRCOL_00000234' => 'pco', 'PRCOL_00000235' => 'pco', 'PRCOL_00000777' => 'pco', 'PRCOL_00002344' => 'pco', 'PRCOL_00002372' => 'pco', 'PRCOL_00006120' => 'pco', 'Prupe.1G021400' => 'ppe', 'Prupe.1G021500' => 'ppe', 'Prupe.1G021600' => 'ppe', 'Prupe.1G021700' => 'ppe', 'Prupe.1G021800' => 'ppe', 'Prupe.5G145100' => 'ppe', 'Psat6g204040' => 'psa', 'Psat6g204800' => 'psa', 'Psat6g204920' => 'psa', 'Psat6g204960' => 'psa', 'Psat6g205080' => 'psa', 'PSO017G0271' => 'pso', 'PSO017G1276' => 'pso', 'PSO017G1429' => 'pso', 'PSO017G1861' => 'pso', 'PSO017G2787' => 'pso', 'PSO017G4466' => 'pso', 'PSO017G5118' => 'pso', 'PSO017G5420' => 'pso', 'PSO063G3678' => 'pso', 'PSO210G0546' => 'pso', 'PSO317G0001' => 'pso', 'PSO357G0512' => 'pso', 'PSO478G2682' => 'pso', 'PSO647G0001' => 'pso', 'PSO675G0001' => 'pso', 'PSO675G2699' => 'pso', 'PSO675G2849' => 'pso', 'PSO675G4991' => 'pso', 'PSO689G0001' => 'pso', 'QL06p000916' => 'qlo', 'QL06p000921' => 'qlo', 'QL06p001398' => 'qlo', 'QL06p001407' => 'qlo', 'QL06p002031' => 'qlo', 'RcHm_v2.0_Chr4g0387791' => 'rch', 'RcHm_v2.0_Chr4g0387801' => 'rch', 'RcHm_v2.0_Chr6g0286501' => 'rch', 'RcHm_v2.0_Chr6g0286511' => 'rch', 'RcHm_v2.0_Chr6g0286521' => 'rch', 'RcHm_v2.0_Chr6g0286531' => 'rch', 'RcHm_v2.0_Chr7g0189141' => 'rch', 'Rhsim02G0028700' => 'rsi', 'Rhsim02G0028800' => 'rsi', 'Rhsim02G0028900' => 'rsi', 'Rhsim02G0029000' => 'rsi', 'Rhsim02G0029100' => 'rsi', 'Rhsim02G0029200' => 'rsi', 'Rhsim02G0029300' => 'rsi', 'Rhsim02G0029400' => 'rsi', 'Rhsim02G0029500' => 'rsi', 'Rhsim02G0029600' => 'rsi', 'RhsimUnG0024000' => 'rsi', 'RhsimUnG0024100' => 'rsi', 'RhsimUnG0024200' => 'rsi', 'RhsimUnG0024300' => 'rsi', 'RhsimUnG0024400' => 'rsi', 'RhsimUnG0024500' => 'rsi', 'RhsimUnG0024700' => 'rsi', 'RhsimUnG0024800' => 'rsi', 'RhsimUnG0024900' => 'rsi', 'RhsimUnG0025100' => 'rsi', 'Sabra08G0120200' => 'sbr', 'Sabra08G0120300' => 'sbr', 'Sabra08G0120500' => 'sbr', 'Sabra08G0120600' => 'sbr', 'Sabra10G0158900' => 'sbr', 'SalBow2G3492' => 'sbo', 'Sc13g0004760' => 'sci', 'Sc13g0004770' => 'sci', 'Sed0003417' => 'sed', 'Sed0019750' => 'sed', 'SEGI_03419' => 'sgi', 'SEGI_05907' => 'sgi', 'SEGI_10682' => 'sgi', 'SEGI_13528' => 'sgi', 'SEGI_16081' => 'sgi', 'SEGI_19370' => 'sgi', 'SEGI_21015' => 'sgi', 'SEGI_21944' => 'sgi', 'SEGI_32906' => 'sgi', 'SEGI_33093' => 'sgi', 'SEGI_36110' => 'sgi', 'SEGI_40397' => 'sgi', 'SGA_v2.0_scaffold191G40426' => 'sas', 'SGA_v2.0_scaffold353G49717' => 'sas', 'SGA_v2.0_scaffold50G18550' => 'sas', 'SMO119G0173' => 'smo', 'SMO172G0002' => 'smo', 'Solyc09g082690.3' => 'sly', 'Solyc09g082700.2' => 'sly', 'Sopen09g031550' => 'spe', 'Sopen09g031560' => 'spe', 'Sp3g20540' => 'spa', 'Sp7g07580' => 'spa', 'TAR134G0002' => 'tar', 'TAR236G0001' => 'tar', 'TAR365G0892' => 'tar', 'TAR636G0166' => 'tar', 'TAR636G0646' => 'tar', 'TAR636G0869' => 'tar', 'TAR636G1317' => 'tar', 'TAR636G1744' => 'tar', 'TAR636G3358' => 'tar', 'TAR636G3436' => 'tar', 'THA.LOC104803047' => 'tha', 'Thecc.04G238900' => 'tca', 'Thhalv10021557m.g' => 'esa', 'Thhalv10026318m.g' => 'esa', 'Thhalv10026335m.g' => 'esa', 'TPR.G17433' => 'tpr', 'TPR.G18915' => 'tpr', 'TPR.G26125' => 'tpr', 'TWI09G0677' => 'twi', 'TWI73G0287' => 'twi', 'unitig_748.g8326' => 'ugi', 'vmacro15370' => 'vma', 'vmacro15371' => 'vma', 'vmacro15372' => 'vma', 'vmacro15373' => 'vma', 'vmacro15374' => 'vma', 'VMungo0720G2826' => 'vmu', 'Zm00001eb116960' => 'zma', 'Zm00001eb301260' => 'zma', 'Zm00001eb301270' => 'zma' ), 'gf_id' => 'HOM05D001460', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001460' ), 'data_identifier' => 'HOM05D001460', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001460', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '433', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p22980' => 'bna', 'A01p32340' => 'bna', 'A03p42970' => 'bna', 'A05p25880' => 'bna', 'Aa31LG8G9320' => 'aar', 'Aa31LG8G9330' => 'aar', 'Aa31LG8G9340' => 'aar', 'Aa31sc221G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1034' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1528' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.829' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2222' => 'aag', 'Ah.12g058830' => 'amhyb', 'Ah.12g058840' => 'amhyb', 'AL3G37160' => 'aly', 'AL7G41310' => 'aly', 'Aqoxy5G00395' => 'aox', 'Aqoxy5G00396' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0C8NZA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5185HY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JZ1PRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MD3LS0' => 'arhy', 'AT3G22840' => 'ath', 'AT4G14690' => 'ath', 'ATR0665G054' => 'atr', 'Atru.chr4.2344' => 'acertr', 'Atru.chr4.2346' => 'acertr', 'Atru.chr4.2347' => 'acertr', 'Atru.chr4.2348' => 'acertr', 'Atru.chr4.2355' => 'acertr', 'Atru.chr4.2356' => 'acertr', 'Atru.chr4.2358' => 'acertr', 'Atru.chr4.2359' => 'acertr', 'Atru.chr4.2360' => 'acertr', 'Atru.chr4.2361' => 'acertr', 'AUR62030476' => 'cqu', 'AUR62030478' => 'cqu', 'AUR62030819' => 'cqu', 'AUR62030820' => 'cqu', 'BcaB03g14648' => 'bca', 'BcaB04g20492' => 'bca', 'BcaB06g26399' => 'bca', 'BcaC01g03416' => 'bca', 'BcaC01g03419' => 'bca', 'BcaC01g03421' => 'bca', 'BcaC01g03424' => 'bca', 'BcaC05g28012' => 'bca', 'BcaC09g49212' => 'bca', 'BcaC09g50140' => 'bca', 'BcaNung00346' => 'bca', 'BolC1t02785H' => 'bol', 'BolC1t04095H' => 'bol', 'BolC3t17545H' => 'bol', 'BolC5t32769H' => 'bol', 'BraA01t02211Z' => 'bra', 'BraA01t03359Z' => 'bra', 'BraA03t13441Z' => 'bra', 'BraA05t21476Z' => 'bra', 'C01p28420' => 'bna', 'C01p41350' => 'bna', 'C03p52750' => 'bna', 'C03p52780' => 'bna', 'C05p40270' => 'bna', 'CAN.G1437.9' => 'can', 'CANSAT78G0035' => 'cansat', 'CANSAT78G1036' => 'cansat', 'CANSAT78G2272' => 'cansat', 'CANSAT78G2478' => 'cansat', 'CARHR098700' => 'chi', 'CARHR221120' => 'chi', 'CARHR221150' => 'chi', 'Carub.0003s2297' => 'cru', 'Carub.0007s2749' => 'cru', 'Carub.0007s2750' => 'cru', 'Carub.0007s2751' => 'cru', 'Ca_10849_v3' => 'car', 'Cc03_g04300' => 'ccan', 'CDE02G3648' => 'cde', 'CDE05G0060' => 'cde', 'CDE05G0692' => 'cde', 'CDE05G2285' => 'cde', 'CDE05G2884' => 'cde', 'CDE05G3072' => 'cde', 'Cfa008439' => 'cfa', 'Cfa008441' => 'cfa', 'Cfa008443' => 'cfa', 'Cfa008448' => 'cfa', 'Ciclev10005974m.g' => 'ccl', 'Ciclev10006006m.g' => 'ccl', 'Ciclev10006775m.g' => 'ccl', 'CiPaw.02G120400' => 'cil', 'CiPaw.02G120500' => 'cil', 'CiPaw.02G120600' => 'cil', 'ClCG05G004850' => 'cla', 'COL.COLO4_21566' => 'col', 'Cpa.g.sc44.124' => 'cpa', 'Cre07.g320400' => 'cre', 'Cre07.g320450' => 'cre', 'Cre08.g384650' => 'cre', 'Cre09.g393173' => 'cre', 'Cre09.g394325' => 'cre', 'Cre14.g626750' => 'cre', 'Cre16.g679250' => 'cre', 'CsaV3_3G012890' => 'csa', 'CSS0010865' => 'camsi', 'CSS0044338' => 'camsi', 'DCAR_002366' => 'dca', 'DCAR_030687' => 'dca', 'DCAR_030688' => 'dca', 'Dinv14047' => 'din', 'Dinv14048' => 'din', 'Duzib151G0105' => 'dzi', 'Duzib151G0114' => 'dzi', 'Duzib212G1029' => 'dzi', 'ECA232G3536' => 'eca', 'ECA240G0786' => 'eca', 'ECA240G1802' => 'eca', 'ECA240G3760' => 'eca', 'ECA240G3920' => 'eca', 'EL10Ac5g12536' => 'bvu', 'EL10Ac5g12537' => 'bvu', 'EL10Ac5g12538' => 'bvu', 'Eucgr.B01004' => 'egr', 'Eucgr.B01006' => 'egr', 'Eucgr.B01007' => 'egr', 'Eucgr.B01008' => 'egr', 'Eucgr.B01895' => 'egr', 'Eucgr.B01896' => 'egr', 'FAN04G1456' => 'fan', 'FAN08G1769' => 'fan', 'FAN08G2160' => 'fan', 'FAN13G2403' => 'fan', 'FAN13G3303' => 'fan', 'FAN15G2435' => 'fan', 'FAN17G0672' => 'fan', 'FAN17G2441' => 'fan', 'FAN18G1024' => 'fan', 'FAN22G1458' => 'fan', 'FAN24G0037' => 'fan', 'FAN24G0429' => 'fan', 'FAN24G2387' => 'fan', 'FAN27G2746' => 'fan', 'FvH4_2g20400' => 'fve', 'FvH4_2g20420' => 'fve', 'FvH4_2g20430' => 'fve', 'FvH4_4g01270' => 'fve', 'FvH4_4g01290' => 'fve', 'FvH4_4g01300' => 'fve', 'FvH4_4g01310' => 'fve', 'FvH4_4g01330' => 'fve', 'FvH4_5g09070' => 'fve', 'Glyma.10G243800' => 'gma', 'Glyma.20G150600' => 'gma', 'Gohir.A09G219200' => 'ghi', 'Gohir.A09G219300' => 'ghi', 'Gohir.D09G221400' => 'ghi', 'Gohir.D09G221500' => 'ghi', 'Gorai.006G242600' => 'gra', 'Gorai.006G242700' => 'gra', 'GSVIVG01018044001' => 'vvi', 'HanXRQChr03g0083821' => 'han', 'HanXRQChr03g0083841' => 'han', 'HanXRQChr03g0083881' => 'han', 'HanXRQChr03g0083901' => 'han', 'HanXRQChr03g0083921' => 'han', 'HanXRQChr03g0085331' => 'han', 'HanXRQChr03g0085361' => 'han', 'HanXRQChr03g0085411' => 'han', 'HanXRQChr03g0085421' => 'han', 'HanXRQChr03g0085431' => 'han', 'HanXRQChr08g0221991' => 'han', 'HanXRQChr11g0336061' => 'han', 'HanXRQChr11g0336411' => 'han', 'Haze_11234' => 'cav', 'Hma1.2p1_0549F.1_g177010' => 'hma', 'Hma1.2p1_0602F.1_g187630' => 'hma', 'Hund14876' => 'sun', 'Hund14879' => 'sun', 'Lalb_Chr06g0160741' => 'lal', 'Lalb_Chr21g0304781' => 'lal', 'Lj3A726G19' => 'lonja', 'Lj3A726T23' => 'lonja', 'Lj3A726T24' => 'lonja', 'Lj3A726T25' => 'lonja', 'Lj3A727T17' => 'lonja', 'Lj3C726T0' => 'lonja', 'Lj3C726T2' => 'lonja', 'Lj3P725T35' => 'lonja', 'Lj3P727T10' => 'lonja', 'Lj3P727T12' => 'lonja', 'Lj3P727T14' => 'lonja', 'Lj5g0023109' => 'lja', 'Lj6P646T44' => 'lonja', 'Lsat_1_v5_gn_6_75760' => 'lsa', 'Lsat_1_v5_gn_6_75800' => 'lsa', 'Lsat_1_v5_gn_6_75900' => 'lsa', 'Lsat_1_v5_gn_6_76240' => 'lsa', 'Lsat_1_v5_gn_6_76441' => 'lsa', 'Lsat_1_v5_gn_6_76700' => 'lsa', 'Lsat_1_v5_gn_6_76760' => 'lsa', 'Manes.15G033100' => 'mes', 'Mapoly0004s0074' => 'mpo', 'Mapoly0004s0075' => 'mpo', 'Mapoly0004s0163' => 'mpo', 'Mapoly0004s0164' => 'mpo', 'Mapoly0021s0018' => 'mpo', 'Mapoly0041s0136' => 'mpo', 'Mapoly0041s0137' => 'mpo', 'Mapoly0041s0138' => 'mpo', 'Mapoly0041s0139' => 'mpo', 'Mapoly0041s0141' => 'mpo', 'Mapoly0041s0142' => 'mpo', 'Mapoly0041s0143' => 'mpo', 'Mapoly0041s0144' => 'mpo', 'Mapoly0041s0145' => 'mpo', 'Mapoly0047s0106' => 'mpo', 'Mapoly0047s0108' => 'mpo', 'Mapoly0050s0051' => 'mpo', 'Mapoly0050s0052' => 'mpo', 'Mapoly0050s0053' => 'mpo', 'Mapoly0058s0013' => 'mpo', 'Mapoly0091s0078' => 'mpo', 'Mapoly0091s0079' => 'mpo', 'Mapoly0091s0080' => 'mpo', 'Mapoly0091s0081' => 'mpo', 'Mapoly0278s0004' => 'mpo', 'Mapoly0278s0005' => 'mpo', 'Mapoly0278s0006' => 'mpo', 'MBI11_g30648_MAGBIO' => 'mbi', 'MCO03G194' => 'mco', 'MCO03G590' => 'mco', 'MCO07G312' => 'mco', 'MCO10G318' => 'mco', 'MCO12G244' => 'mco', 'MCO13G148' => 'mco', 'MCO13G194' => 'mco', 'MCO16G238' => 'mco', 'MD06G1134100' => 'mdo', 'MD13G1200100' => 'mdo', 'MD13G1200300' => 'mdo', 'MD13G1200600' => 'mdo', 'MD14G1150400' => 'mdo', 'MD16G1200000' => 'mdo', 'Medtr1g102570' => 'mtr', 'Medtr1g102780' => 'mtr', 'Medtr1g102800' => 'mtr', 'Medtr1g102810' => 'mtr', 'Medtr1g102830' => 'mtr', 'MELO3C006499.2' => 'cme', 'Migut.G00385' => 'egut', 'MSTRG.4063' => 'ama', 'Nitab4.5_0000090g0260' => 'nta', 'Nitab4.5_0000977g0030' => 'nta', 'Nitab4.5_0002541g0040' => 'nta', 'Nitab4.5_0007068g0040' => 'nta', 'Nn005s41408' => 'nnu', 'Nn005s41410' => 'nnu', 'Oeu010310.1' => 'oeu', 'Oeu010311.1' => 'oeu', 'Oeu043472.1' => 'oeu', 'Os01g0246400' => 'osa', 'Os04g0267950' => 'osa', 'Os07g0178700' => 'osa', 'Os07g0178800' => 'osa', 'Peaxi162Scf00316g00046' => 'pax', 'Peaxi162Scf00316g00049' => 'pax', 'Peaxi162Scf00316g00059' => 'pax', 'Peaxi162Scf00316g00328' => 'pax', 'Peaxi162Scf00316g00329' => 'pax', 'Peaxi162Scf00316g00411' => 'pax', 'Peaxi162Scf00316g00521' => 'pax', 'Peaxi162Scf00492g00068' => 'pax', 'Peaxi162Scf35631g00002' => 'pax', 'PGR142G3720' => 'pgr', 'PGSC0003DMG400006442' => 'stu', 'Phvul.007G062000' => 'pvu', 'Potri.008G157750' => 'ptr', 'Potri.008G157900' => 'ptr', 'Potri.008G158000' => 'ptr', 'Potri.008G158200' => 'ptr', 'Pp3c11_7280' => 'ppa', 'Pp3c11_7980' => 'ppa', 'Pp3c12_19450' => 'ppa', 'Pp3c14_1480' => 'ppa', 'Pp3c14_1501' => 'ppa', 'Pp3c16_4900' => 'ppa', 'Pp3c16_5010' => 'ppa', 'Pp3c16_5060' => 'ppa', 'Pp3c19_18250' => 'ppa', 'Pp3c23_8530' => 'ppa', 'Pp3c23_8550' => 'ppa', 'Pp3c24_9670' => 'ppa', 'Pp3c2_21390' => 'ppa', 'Pp3c2_31380' => 'ppa', 'Pp3c3_16620' => 'ppa', 'Pp3c3_8090' => 'ppa', 'Pp3c3_8110' => 'ppa', 'Pp3c3_8130' => 'ppa', 'Pp3c3_8150' => 'ppa', 'Pp3c4_14320' => 'ppa', 'Pp3c6_2560' => 'ppa', 'Pp3c9_16700' => 'ppa', 'PRCOL_00000234' => 'pco', 'PRCOL_00000235' => 'pco', 'PRCOL_00000777' => 'pco', 'PRCOL_00002344' => 'pco', 'PRCOL_00002372' => 'pco', 'PRCOL_00006120' => 'pco', 'Prupe.1G021400' => 'ppe', 'Prupe.1G021500' => 'ppe', 'Prupe.1G021600' => 'ppe', 'Prupe.1G021700' => 'ppe', 'Prupe.1G021800' => 'ppe', 'Prupe.5G145100' => 'ppe', 'Psat6g204040' => 'psa', 'Psat6g204800' => 'psa', 'Psat6g204920' => 'psa', 'Psat6g204960' => 'psa', 'Psat6g205080' => 'psa', 'PSO017G0271' => 'pso', 'PSO017G1276' => 'pso', 'PSO017G1429' => 'pso', 'PSO017G1861' => 'pso', 'PSO017G2787' => 'pso', 'PSO017G4466' => 'pso', 'PSO017G5118' => 'pso', 'PSO017G5420' => 'pso', 'PSO063G3678' => 'pso', 'PSO210G0546' => 'pso', 'PSO317G0001' => 'pso', 'PSO357G0512' => 'pso', 'PSO478G2682' => 'pso', 'PSO647G0001' => 'pso', 'PSO675G0001' => 'pso', 'PSO675G2699' => 'pso', 'PSO675G2849' => 'pso', 'PSO675G4991' => 'pso', 'PSO689G0001' => 'pso', 'QL06p000916' => 'qlo', 'QL06p000921' => 'qlo', 'QL06p001398' => 'qlo', 'QL06p001407' => 'qlo', 'QL06p002031' => 'qlo', 'RcHm_v2.0_Chr4g0387791' => 'rch', 'RcHm_v2.0_Chr4g0387801' => 'rch', 'RcHm_v2.0_Chr6g0286501' => 'rch', 'RcHm_v2.0_Chr6g0286511' => 'rch', 'RcHm_v2.0_Chr6g0286521' => 'rch', 'RcHm_v2.0_Chr6g0286531' => 'rch', 'RcHm_v2.0_Chr7g0189141' => 'rch', 'Rhsim02G0028700' => 'rsi', 'Rhsim02G0028800' => 'rsi', 'Rhsim02G0028900' => 'rsi', 'Rhsim02G0029000' => 'rsi', 'Rhsim02G0029100' => 'rsi', 'Rhsim02G0029200' => 'rsi', 'Rhsim02G0029300' => 'rsi', 'Rhsim02G0029400' => 'rsi', 'Rhsim02G0029500' => 'rsi', 'Rhsim02G0029600' => 'rsi', 'RhsimUnG0024000' => 'rsi', 'RhsimUnG0024100' => 'rsi', 'RhsimUnG0024200' => 'rsi', 'RhsimUnG0024300' => 'rsi', 'RhsimUnG0024400' => 'rsi', 'RhsimUnG0024500' => 'rsi', 'RhsimUnG0024700' => 'rsi', 'RhsimUnG0024800' => 'rsi', 'RhsimUnG0024900' => 'rsi', 'RhsimUnG0025100' => 'rsi', 'Sabra08G0120200' => 'sbr', 'Sabra08G0120300' => 'sbr', 'Sabra08G0120500' => 'sbr', 'Sabra08G0120600' => 'sbr', 'Sabra10G0158900' => 'sbr', 'SalBow2G3492' => 'sbo', 'Sc13g0004760' => 'sci', 'Sc13g0004770' => 'sci', 'Sed0003417' => 'sed', 'Sed0019750' => 'sed', 'SEGI_03419' => 'sgi', 'SEGI_05907' => 'sgi', 'SEGI_10682' => 'sgi', 'SEGI_13528' => 'sgi', 'SEGI_16081' => 'sgi', 'SEGI_19370' => 'sgi', 'SEGI_21015' => 'sgi', 'SEGI_21944' => 'sgi', 'SEGI_32906' => 'sgi', 'SEGI_33093' => 'sgi', 'SEGI_36110' => 'sgi', 'SEGI_40397' => 'sgi', 'SGA_v2.0_scaffold191G40426' => 'sas', 'SGA_v2.0_scaffold353G49717' => 'sas', 'SGA_v2.0_scaffold50G18550' => 'sas', 'SMO119G0173' => 'smo', 'SMO172G0002' => 'smo', 'Solyc09g082690.3' => 'sly', 'Solyc09g082700.2' => 'sly', 'Sopen09g031550' => 'spe', 'Sopen09g031560' => 'spe', 'Sp3g20540' => 'spa', 'Sp7g07580' => 'spa', 'TAR134G0002' => 'tar', 'TAR236G0001' => 'tar', 'TAR365G0892' => 'tar', 'TAR636G0166' => 'tar', 'TAR636G0646' => 'tar', 'TAR636G0869' => 'tar', 'TAR636G1317' => 'tar', 'TAR636G1744' => 'tar', 'TAR636G3358' => 'tar', 'TAR636G3436' => 'tar', 'THA.LOC104803047' => 'tha', 'Thecc.04G238900' => 'tca', 'Thhalv10021557m.g' => 'esa', 'Thhalv10026318m.g' => 'esa', 'Thhalv10026335m.g' => 'esa', 'TPR.G17433' => 'tpr', 'TPR.G18915' => 'tpr', 'TPR.G26125' => 'tpr', 'TWI09G0677' => 'twi', 'TWI73G0287' => 'twi', 'unitig_748.g8326' => 'ugi', 'vmacro15370' => 'vma', 'vmacro15371' => 'vma', 'vmacro15372' => 'vma', 'vmacro15373' => 'vma', 'vmacro15374' => 'vma', 'VMungo0720G2826' => 'vmu', 'Zm00001eb116960' => 'zma', 'Zm00001eb301260' => 'zma', 'Zm00001eb301270' => 'zma' ) $gf_id = 'HOM05D001460' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001460' ) $data_identifier = 'HOM05D001460' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 4, 'aag' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 2, 'aox' => (int) 2, 'arhy' => (int) 4, 'ath' => (int) 2, 'atr' => (int) 1, 'acertr' => (int) 10, 'cqu' => (int) 4, 'bca' => (int) 11, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 1, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 1, 'ccan' => (int) 1, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 1, 'col' => (int) 1, 'cpa' => (int) 1, 'cre' => (int) 7, 'csa' => (int) 1, 'camsi' => (int) 2, 'dca' => (int) 3, 'din' => (int) 2, 'dzi' => (int) 3, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 14, 'fve' => (int) 9, 'gma' => (int) 2, 'ghi' => (int) 4, 'gra' => (int) 2, 'vvi' => (int) 1, 'han' => (int) 13, 'cav' => (int) 1, 'hma' => (int) 2, 'sun' => (int) 2, 'lal' => (int) 2, 'lonja' => (int) 12, 'lja' => (int) 1, 'lsa' => (int) 7, 'mes' => (int) 1, 'mpo' => (int) 27, 'mbi' => (int) 1, 'mco' => (int) 8, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 1, 'egut' => (int) 1, 'ama' => (int) 1, 'nta' => (int) 4, 'nnu' => (int) 2, 'oeu' => (int) 3, 'osa' => (int) 4, 'pax' => (int) 9, 'pgr' => (int) 1, 'stu' => (int) 1, 'pvu' => (int) 1, 'ptr' => (int) 4, 'ppa' => (int) 22, 'pco' => (int) 6, 'ppe' => (int) 6, 'psa' => (int) 5, 'pso' => (int) 19, 'qlo' => (int) 5, 'rch' => (int) 7, 'rsi' => (int) 20, 'sbr' => (int) 5, 'sbo' => (int) 1, 'sci' => (int) 2, 'sed' => (int) 2, 'sgi' => (int) 12, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 2, 'tar' => (int) 10, 'tha' => (int) 1, 'tca' => (int) 1, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 2, 'ugi' => (int) 1, 'vma' => (int) 5, 'vmu' => (int) 1, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb301270' $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' => 'HOM05D001460', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '433', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p22980' => 'bna', 'A01p32340' => 'bna', 'A03p42970' => 'bna', 'A05p25880' => 'bna', 'Aa31LG8G9320' => 'aar', 'Aa31LG8G9330' => 'aar', 'Aa31LG8G9340' => 'aar', 'Aa31sc221G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1034' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1528' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.829' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2222' => 'aag', 'Ah.12g058830' => 'amhyb', 'Ah.12g058840' => 'amhyb', 'AL3G37160' => 'aly', 'AL7G41310' => 'aly', 'Aqoxy5G00395' => 'aox', 'Aqoxy5G00396' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0C8NZA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5185HY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JZ1PRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MD3LS0' => 'arhy', 'AT3G22840' => 'ath', 'AT4G14690' => 'ath', 'ATR0665G054' => 'atr', 'Atru.chr4.2344' => 'acertr', 'Atru.chr4.2346' => 'acertr', 'Atru.chr4.2347' => 'acertr', 'Atru.chr4.2348' => 'acertr', 'Atru.chr4.2355' => 'acertr', 'Atru.chr4.2356' => 'acertr', 'Atru.chr4.2358' => 'acertr', 'Atru.chr4.2359' => 'acertr', 'Atru.chr4.2360' => 'acertr', 'Atru.chr4.2361' => 'acertr', 'AUR62030476' => 'cqu', 'AUR62030478' => 'cqu', 'AUR62030819' => 'cqu', 'AUR62030820' => 'cqu', 'BcaB03g14648' => 'bca', 'BcaB04g20492' => 'bca', 'BcaB06g26399' => 'bca', 'BcaC01g03416' => 'bca', 'BcaC01g03419' => 'bca', 'BcaC01g03421' => 'bca', 'BcaC01g03424' => 'bca', 'BcaC05g28012' => 'bca', 'BcaC09g49212' => 'bca', 'BcaC09g50140' => 'bca', 'BcaNung00346' => 'bca', 'BolC1t02785H' => 'bol', 'BolC1t04095H' => 'bol', 'BolC3t17545H' => 'bol', 'BolC5t32769H' => 'bol', 'BraA01t02211Z' => 'bra', 'BraA01t03359Z' => 'bra', 'BraA03t13441Z' => 'bra', 'BraA05t21476Z' => 'bra', 'C01p28420' => 'bna', 'C01p41350' => 'bna', 'C03p52750' => 'bna', 'C03p52780' => 'bna', 'C05p40270' => 'bna', 'CAN.G1437.9' => 'can', 'CANSAT78G0035' => 'cansat', 'CANSAT78G1036' => 'cansat', 'CANSAT78G2272' => 'cansat', 'CANSAT78G2478' => 'cansat', 'CARHR098700' => 'chi', 'CARHR221120' => 'chi', 'CARHR221150' => 'chi', 'Carub.0003s2297' => 'cru', 'Carub.0007s2749' => 'cru', 'Carub.0007s2750' => 'cru', 'Carub.0007s2751' => 'cru', 'Ca_10849_v3' => 'car', 'Cc03_g04300' => 'ccan', 'CDE02G3648' => 'cde', 'CDE05G0060' => 'cde', 'CDE05G0692' => 'cde', 'CDE05G2285' => 'cde', 'CDE05G2884' => 'cde', 'CDE05G3072' => 'cde', 'Cfa008439' => 'cfa', 'Cfa008441' => 'cfa', 'Cfa008443' => 'cfa', 'Cfa008448' => 'cfa', 'Ciclev10005974m.g' => 'ccl', 'Ciclev10006006m.g' => 'ccl', 'Ciclev10006775m.g' => 'ccl', 'CiPaw.02G120400' => 'cil', 'CiPaw.02G120500' => 'cil', 'CiPaw.02G120600' => 'cil', 'ClCG05G004850' => 'cla', 'COL.COLO4_21566' => 'col', 'Cpa.g.sc44.124' => 'cpa', 'Cre07.g320400' => 'cre', 'Cre07.g320450' => 'cre', 'Cre08.g384650' => 'cre', 'Cre09.g393173' => 'cre', 'Cre09.g394325' => 'cre', 'Cre14.g626750' => 'cre', 'Cre16.g679250' => 'cre', 'CsaV3_3G012890' => 'csa', 'CSS0010865' => 'camsi', 'CSS0044338' => 'camsi', 'DCAR_002366' => 'dca', 'DCAR_030687' => 'dca', 'DCAR_030688' => 'dca', 'Dinv14047' => 'din', 'Dinv14048' => 'din', 'Duzib151G0105' => 'dzi', 'Duzib151G0114' => 'dzi', 'Duzib212G1029' => 'dzi', 'ECA232G3536' => 'eca', 'ECA240G0786' => 'eca', 'ECA240G1802' => 'eca', 'ECA240G3760' => 'eca', 'ECA240G3920' => 'eca', 'EL10Ac5g12536' => 'bvu', 'EL10Ac5g12537' => 'bvu', 'EL10Ac5g12538' => 'bvu', 'Eucgr.B01004' => 'egr', 'Eucgr.B01006' => 'egr', 'Eucgr.B01007' => 'egr', 'Eucgr.B01008' => 'egr', 'Eucgr.B01895' => 'egr', 'Eucgr.B01896' => 'egr', 'FAN04G1456' => 'fan', 'FAN08G1769' => 'fan', 'FAN08G2160' => 'fan', 'FAN13G2403' => 'fan', 'FAN13G3303' => 'fan', 'FAN15G2435' => 'fan', 'FAN17G0672' => 'fan', 'FAN17G2441' => 'fan', 'FAN18G1024' => 'fan', 'FAN22G1458' => 'fan', 'FAN24G0037' => 'fan', 'FAN24G0429' => 'fan', 'FAN24G2387' => 'fan', 'FAN27G2746' => 'fan', 'FvH4_2g20400' => 'fve', 'FvH4_2g20420' => 'fve', 'FvH4_2g20430' => 'fve', 'FvH4_4g01270' => 'fve', 'FvH4_4g01290' => 'fve', 'FvH4_4g01300' => 'fve', 'FvH4_4g01310' => 'fve', 'FvH4_4g01330' => 'fve', 'FvH4_5g09070' => 'fve', 'Glyma.10G243800' => 'gma', 'Glyma.20G150600' => 'gma', 'Gohir.A09G219200' => 'ghi', 'Gohir.A09G219300' => 'ghi', 'Gohir.D09G221400' => 'ghi', 'Gohir.D09G221500' => 'ghi', 'Gorai.006G242600' => 'gra', 'Gorai.006G242700' => 'gra', 'GSVIVG01018044001' => 'vvi', 'HanXRQChr03g0083821' => 'han', 'HanXRQChr03g0083841' => 'han', 'HanXRQChr03g0083881' => 'han', 'HanXRQChr03g0083901' => 'han', 'HanXRQChr03g0083921' => 'han', 'HanXRQChr03g0085331' => 'han', 'HanXRQChr03g0085361' => 'han', 'HanXRQChr03g0085411' => 'han', 'HanXRQChr03g0085421' => 'han', 'HanXRQChr03g0085431' => 'han', 'HanXRQChr08g0221991' => 'han', 'HanXRQChr11g0336061' => 'han', 'HanXRQChr11g0336411' => 'han', 'Haze_11234' => 'cav', 'Hma1.2p1_0549F.1_g177010' => 'hma', 'Hma1.2p1_0602F.1_g187630' => 'hma', 'Hund14876' => 'sun', 'Hund14879' => 'sun', 'Lalb_Chr06g0160741' => 'lal', 'Lalb_Chr21g0304781' => 'lal', 'Lj3A726G19' => 'lonja', 'Lj3A726T23' => 'lonja', 'Lj3A726T24' => 'lonja', 'Lj3A726T25' => 'lonja', 'Lj3A727T17' => 'lonja', 'Lj3C726T0' => 'lonja', 'Lj3C726T2' => 'lonja', 'Lj3P725T35' => 'lonja', 'Lj3P727T10' => 'lonja', 'Lj3P727T12' => 'lonja', 'Lj3P727T14' => 'lonja', 'Lj5g0023109' => 'lja', 'Lj6P646T44' => 'lonja', 'Lsat_1_v5_gn_6_75760' => 'lsa', 'Lsat_1_v5_gn_6_75800' => 'lsa', 'Lsat_1_v5_gn_6_75900' => 'lsa', 'Lsat_1_v5_gn_6_76240' => 'lsa', 'Lsat_1_v5_gn_6_76441' => 'lsa', 'Lsat_1_v5_gn_6_76700' => 'lsa', 'Lsat_1_v5_gn_6_76760' => 'lsa', 'Manes.15G033100' => 'mes', 'Mapoly0004s0074' => 'mpo', 'Mapoly0004s0075' => 'mpo', 'Mapoly0004s0163' => 'mpo', 'Mapoly0004s0164' => 'mpo', 'Mapoly0021s0018' => 'mpo', 'Mapoly0041s0136' => 'mpo', 'Mapoly0041s0137' => 'mpo', 'Mapoly0041s0138' => 'mpo', 'Mapoly0041s0139' => 'mpo', 'Mapoly0041s0141' => 'mpo', 'Mapoly0041s0142' => 'mpo', 'Mapoly0041s0143' => 'mpo', 'Mapoly0041s0144' => 'mpo', 'Mapoly0041s0145' => 'mpo', 'Mapoly0047s0106' => 'mpo', 'Mapoly0047s0108' => 'mpo', 'Mapoly0050s0051' => 'mpo', 'Mapoly0050s0052' => 'mpo', 'Mapoly0050s0053' => 'mpo', 'Mapoly0058s0013' => 'mpo', 'Mapoly0091s0078' => 'mpo', 'Mapoly0091s0079' => 'mpo', 'Mapoly0091s0080' => 'mpo', 'Mapoly0091s0081' => 'mpo', 'Mapoly0278s0004' => 'mpo', 'Mapoly0278s0005' => 'mpo', 'Mapoly0278s0006' => 'mpo', 'MBI11_g30648_MAGBIO' => 'mbi', 'MCO03G194' => 'mco', 'MCO03G590' => 'mco', 'MCO07G312' => 'mco', 'MCO10G318' => 'mco', 'MCO12G244' => 'mco', 'MCO13G148' => 'mco', 'MCO13G194' => 'mco', 'MCO16G238' => 'mco', 'MD06G1134100' => 'mdo', 'MD13G1200100' => 'mdo', 'MD13G1200300' => 'mdo', 'MD13G1200600' => 'mdo', 'MD14G1150400' => 'mdo', 'MD16G1200000' => 'mdo', 'Medtr1g102570' => 'mtr', 'Medtr1g102780' => 'mtr', 'Medtr1g102800' => 'mtr', 'Medtr1g102810' => 'mtr', 'Medtr1g102830' => 'mtr', 'MELO3C006499.2' => 'cme', 'Migut.G00385' => 'egut', 'MSTRG.4063' => 'ama', 'Nitab4.5_0000090g0260' => 'nta', 'Nitab4.5_0000977g0030' => 'nta', 'Nitab4.5_0002541g0040' => 'nta', 'Nitab4.5_0007068g0040' => 'nta', 'Nn005s41408' => 'nnu', 'Nn005s41410' => 'nnu', 'Oeu010310.1' => 'oeu', 'Oeu010311.1' => 'oeu', 'Oeu043472.1' => 'oeu', 'Os01g0246400' => 'osa', 'Os04g0267950' => 'osa', 'Os07g0178700' => 'osa', 'Os07g0178800' => 'osa', 'Peaxi162Scf00316g00046' => 'pax', 'Peaxi162Scf00316g00049' => 'pax', 'Peaxi162Scf00316g00059' => 'pax', 'Peaxi162Scf00316g00328' => 'pax', 'Peaxi162Scf00316g00329' => 'pax', 'Peaxi162Scf00316g00411' => 'pax', 'Peaxi162Scf00316g00521' => 'pax', 'Peaxi162Scf00492g00068' => 'pax', 'Peaxi162Scf35631g00002' => 'pax', 'PGR142G3720' => 'pgr', 'PGSC0003DMG400006442' => 'stu', 'Phvul.007G062000' => 'pvu', 'Potri.008G157750' => 'ptr', 'Potri.008G157900' => 'ptr', 'Potri.008G158000' => 'ptr', 'Potri.008G158200' => 'ptr', 'Pp3c11_7280' => 'ppa', 'Pp3c11_7980' => 'ppa', 'Pp3c12_19450' => 'ppa', 'Pp3c14_1480' => 'ppa', 'Pp3c14_1501' => 'ppa', 'Pp3c16_4900' => 'ppa', 'Pp3c16_5010' => 'ppa', 'Pp3c16_5060' => 'ppa', 'Pp3c19_18250' => 'ppa', 'Pp3c23_8530' => 'ppa', 'Pp3c23_8550' => 'ppa', 'Pp3c24_9670' => 'ppa', 'Pp3c2_21390' => 'ppa', 'Pp3c2_31380' => 'ppa', 'Pp3c3_16620' => 'ppa', 'Pp3c3_8090' => 'ppa', 'Pp3c3_8110' => 'ppa', 'Pp3c3_8130' => 'ppa', 'Pp3c3_8150' => 'ppa', 'Pp3c4_14320' => 'ppa', 'Pp3c6_2560' => 'ppa', 'Pp3c9_16700' => 'ppa', 'PRCOL_00000234' => 'pco', 'PRCOL_00000235' => 'pco', 'PRCOL_00000777' => 'pco', 'PRCOL_00002344' => 'pco', 'PRCOL_00002372' => 'pco', 'PRCOL_00006120' => 'pco', 'Prupe.1G021400' => 'ppe', 'Prupe.1G021500' => 'ppe', 'Prupe.1G021600' => 'ppe', 'Prupe.1G021700' => 'ppe', 'Prupe.1G021800' => 'ppe', 'Prupe.5G145100' => 'ppe', 'Psat6g204040' => 'psa', 'Psat6g204800' => 'psa', 'Psat6g204920' => 'psa', 'Psat6g204960' => 'psa', 'Psat6g205080' => 'psa', 'PSO017G0271' => 'pso', 'PSO017G1276' => 'pso', 'PSO017G1429' => 'pso', 'PSO017G1861' => 'pso', 'PSO017G2787' => 'pso', 'PSO017G4466' => 'pso', 'PSO017G5118' => 'pso', 'PSO017G5420' => 'pso', 'PSO063G3678' => 'pso', 'PSO210G0546' => 'pso', 'PSO317G0001' => 'pso', 'PSO357G0512' => 'pso', 'PSO478G2682' => 'pso', 'PSO647G0001' => 'pso', 'PSO675G0001' => 'pso', 'PSO675G2699' => 'pso', 'PSO675G2849' => 'pso', 'PSO675G4991' => 'pso', 'PSO689G0001' => 'pso', 'QL06p000916' => 'qlo', 'QL06p000921' => 'qlo', 'QL06p001398' => 'qlo', 'QL06p001407' => 'qlo', 'QL06p002031' => 'qlo', 'RcHm_v2.0_Chr4g0387791' => 'rch', 'RcHm_v2.0_Chr4g0387801' => 'rch', 'RcHm_v2.0_Chr6g0286501' => 'rch', 'RcHm_v2.0_Chr6g0286511' => 'rch', 'RcHm_v2.0_Chr6g0286521' => 'rch', 'RcHm_v2.0_Chr6g0286531' => 'rch', 'RcHm_v2.0_Chr7g0189141' => 'rch', 'Rhsim02G0028700' => 'rsi', 'Rhsim02G0028800' => 'rsi', 'Rhsim02G0028900' => 'rsi', 'Rhsim02G0029000' => 'rsi', 'Rhsim02G0029100' => 'rsi', 'Rhsim02G0029200' => 'rsi', 'Rhsim02G0029300' => 'rsi', 'Rhsim02G0029400' => 'rsi', 'Rhsim02G0029500' => 'rsi', 'Rhsim02G0029600' => 'rsi', 'RhsimUnG0024000' => 'rsi', 'RhsimUnG0024100' => 'rsi', 'RhsimUnG0024200' => 'rsi', 'RhsimUnG0024300' => 'rsi', 'RhsimUnG0024400' => 'rsi', 'RhsimUnG0024500' => 'rsi', 'RhsimUnG0024700' => 'rsi', 'RhsimUnG0024800' => 'rsi', 'RhsimUnG0024900' => 'rsi', 'RhsimUnG0025100' => 'rsi', 'Sabra08G0120200' => 'sbr', 'Sabra08G0120300' => 'sbr', 'Sabra08G0120500' => 'sbr', 'Sabra08G0120600' => 'sbr', 'Sabra10G0158900' => 'sbr', 'SalBow2G3492' => 'sbo', 'Sc13g0004760' => 'sci', 'Sc13g0004770' => 'sci', 'Sed0003417' => 'sed', 'Sed0019750' => 'sed', 'SEGI_03419' => 'sgi', 'SEGI_05907' => 'sgi', 'SEGI_10682' => 'sgi', 'SEGI_13528' => 'sgi', 'SEGI_16081' => 'sgi', 'SEGI_19370' => 'sgi', 'SEGI_21015' => 'sgi', 'SEGI_21944' => 'sgi', 'SEGI_32906' => 'sgi', 'SEGI_33093' => 'sgi', 'SEGI_36110' => 'sgi', 'SEGI_40397' => 'sgi', 'SGA_v2.0_scaffold191G40426' => 'sas', 'SGA_v2.0_scaffold353G49717' => 'sas', 'SGA_v2.0_scaffold50G18550' => 'sas', 'SMO119G0173' => 'smo', 'SMO172G0002' => 'smo', 'Solyc09g082690.3' => 'sly', 'Solyc09g082700.2' => 'sly', 'Sopen09g031550' => 'spe', 'Sopen09g031560' => 'spe', 'Sp3g20540' => 'spa', 'Sp7g07580' => 'spa', 'TAR134G0002' => 'tar', 'TAR236G0001' => 'tar', 'TAR365G0892' => 'tar', 'TAR636G0166' => 'tar', 'TAR636G0646' => 'tar', 'TAR636G0869' => 'tar', 'TAR636G1317' => 'tar', 'TAR636G1744' => 'tar', 'TAR636G3358' => 'tar', 'TAR636G3436' => 'tar', 'THA.LOC104803047' => 'tha', 'Thecc.04G238900' => 'tca', 'Thhalv10021557m.g' => 'esa', 'Thhalv10026318m.g' => 'esa', 'Thhalv10026335m.g' => 'esa', 'TPR.G17433' => 'tpr', 'TPR.G18915' => 'tpr', 'TPR.G26125' => 'tpr', 'TWI09G0677' => 'twi', 'TWI73G0287' => 'twi', 'unitig_748.g8326' => 'ugi', 'vmacro15370' => 'vma', 'vmacro15371' => 'vma', 'vmacro15372' => 'vma', 'vmacro15373' => 'vma', 'vmacro15374' => 'vma', 'VMungo0720G2826' => 'vmu', 'Zm00001eb116960' => 'zma', 'Zm00001eb301260' => 'zma', 'Zm00001eb301270' => 'zma' ), 'gf_id' => 'HOM05D001460', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001460' ), 'data_identifier' => 'HOM05D001460', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001460', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '433', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p22980' => 'bna', 'A01p32340' => 'bna', 'A03p42970' => 'bna', 'A05p25880' => 'bna', 'Aa31LG8G9320' => 'aar', 'Aa31LG8G9330' => 'aar', 'Aa31LG8G9340' => 'aar', 'Aa31sc221G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1034' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1528' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.829' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2222' => 'aag', 'Ah.12g058830' => 'amhyb', 'Ah.12g058840' => 'amhyb', 'AL3G37160' => 'aly', 'AL7G41310' => 'aly', 'Aqoxy5G00395' => 'aox', 'Aqoxy5G00396' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0C8NZA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5185HY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JZ1PRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MD3LS0' => 'arhy', 'AT3G22840' => 'ath', 'AT4G14690' => 'ath', 'ATR0665G054' => 'atr', 'Atru.chr4.2344' => 'acertr', 'Atru.chr4.2346' => 'acertr', 'Atru.chr4.2347' => 'acertr', 'Atru.chr4.2348' => 'acertr', 'Atru.chr4.2355' => 'acertr', 'Atru.chr4.2356' => 'acertr', 'Atru.chr4.2358' => 'acertr', 'Atru.chr4.2359' => 'acertr', 'Atru.chr4.2360' => 'acertr', 'Atru.chr4.2361' => 'acertr', 'AUR62030476' => 'cqu', 'AUR62030478' => 'cqu', 'AUR62030819' => 'cqu', 'AUR62030820' => 'cqu', 'BcaB03g14648' => 'bca', 'BcaB04g20492' => 'bca', 'BcaB06g26399' => 'bca', 'BcaC01g03416' => 'bca', 'BcaC01g03419' => 'bca', 'BcaC01g03421' => 'bca', 'BcaC01g03424' => 'bca', 'BcaC05g28012' => 'bca', 'BcaC09g49212' => 'bca', 'BcaC09g50140' => 'bca', 'BcaNung00346' => 'bca', 'BolC1t02785H' => 'bol', 'BolC1t04095H' => 'bol', 'BolC3t17545H' => 'bol', 'BolC5t32769H' => 'bol', 'BraA01t02211Z' => 'bra', 'BraA01t03359Z' => 'bra', 'BraA03t13441Z' => 'bra', 'BraA05t21476Z' => 'bra', 'C01p28420' => 'bna', 'C01p41350' => 'bna', 'C03p52750' => 'bna', 'C03p52780' => 'bna', 'C05p40270' => 'bna', 'CAN.G1437.9' => 'can', 'CANSAT78G0035' => 'cansat', 'CANSAT78G1036' => 'cansat', 'CANSAT78G2272' => 'cansat', 'CANSAT78G2478' => 'cansat', 'CARHR098700' => 'chi', 'CARHR221120' => 'chi', 'CARHR221150' => 'chi', 'Carub.0003s2297' => 'cru', 'Carub.0007s2749' => 'cru', 'Carub.0007s2750' => 'cru', 'Carub.0007s2751' => 'cru', 'Ca_10849_v3' => 'car', 'Cc03_g04300' => 'ccan', 'CDE02G3648' => 'cde', 'CDE05G0060' => 'cde', 'CDE05G0692' => 'cde', 'CDE05G2285' => 'cde', 'CDE05G2884' => 'cde', 'CDE05G3072' => 'cde', 'Cfa008439' => 'cfa', 'Cfa008441' => 'cfa', 'Cfa008443' => 'cfa', 'Cfa008448' => 'cfa', 'Ciclev10005974m.g' => 'ccl', 'Ciclev10006006m.g' => 'ccl', 'Ciclev10006775m.g' => 'ccl', 'CiPaw.02G120400' => 'cil', 'CiPaw.02G120500' => 'cil', 'CiPaw.02G120600' => 'cil', 'ClCG05G004850' => 'cla', 'COL.COLO4_21566' => 'col', 'Cpa.g.sc44.124' => 'cpa', 'Cre07.g320400' => 'cre', 'Cre07.g320450' => 'cre', 'Cre08.g384650' => 'cre', 'Cre09.g393173' => 'cre', 'Cre09.g394325' => 'cre', 'Cre14.g626750' => 'cre', 'Cre16.g679250' => 'cre', 'CsaV3_3G012890' => 'csa', 'CSS0010865' => 'camsi', 'CSS0044338' => 'camsi', 'DCAR_002366' => 'dca', 'DCAR_030687' => 'dca', 'DCAR_030688' => 'dca', 'Dinv14047' => 'din', 'Dinv14048' => 'din', 'Duzib151G0105' => 'dzi', 'Duzib151G0114' => 'dzi', 'Duzib212G1029' => 'dzi', 'ECA232G3536' => 'eca', 'ECA240G0786' => 'eca', 'ECA240G1802' => 'eca', 'ECA240G3760' => 'eca', 'ECA240G3920' => 'eca', 'EL10Ac5g12536' => 'bvu', 'EL10Ac5g12537' => 'bvu', 'EL10Ac5g12538' => 'bvu', 'Eucgr.B01004' => 'egr', 'Eucgr.B01006' => 'egr', 'Eucgr.B01007' => 'egr', 'Eucgr.B01008' => 'egr', 'Eucgr.B01895' => 'egr', 'Eucgr.B01896' => 'egr', 'FAN04G1456' => 'fan', 'FAN08G1769' => 'fan', 'FAN08G2160' => 'fan', 'FAN13G2403' => 'fan', 'FAN13G3303' => 'fan', 'FAN15G2435' => 'fan', 'FAN17G0672' => 'fan', 'FAN17G2441' => 'fan', 'FAN18G1024' => 'fan', 'FAN22G1458' => 'fan', 'FAN24G0037' => 'fan', 'FAN24G0429' => 'fan', 'FAN24G2387' => 'fan', 'FAN27G2746' => 'fan', 'FvH4_2g20400' => 'fve', 'FvH4_2g20420' => 'fve', 'FvH4_2g20430' => 'fve', 'FvH4_4g01270' => 'fve', 'FvH4_4g01290' => 'fve', 'FvH4_4g01300' => 'fve', 'FvH4_4g01310' => 'fve', 'FvH4_4g01330' => 'fve', 'FvH4_5g09070' => 'fve', 'Glyma.10G243800' => 'gma', 'Glyma.20G150600' => 'gma', 'Gohir.A09G219200' => 'ghi', 'Gohir.A09G219300' => 'ghi', 'Gohir.D09G221400' => 'ghi', 'Gohir.D09G221500' => 'ghi', 'Gorai.006G242600' => 'gra', 'Gorai.006G242700' => 'gra', 'GSVIVG01018044001' => 'vvi', 'HanXRQChr03g0083821' => 'han', 'HanXRQChr03g0083841' => 'han', 'HanXRQChr03g0083881' => 'han', 'HanXRQChr03g0083901' => 'han', 'HanXRQChr03g0083921' => 'han', 'HanXRQChr03g0085331' => 'han', 'HanXRQChr03g0085361' => 'han', 'HanXRQChr03g0085411' => 'han', 'HanXRQChr03g0085421' => 'han', 'HanXRQChr03g0085431' => 'han', 'HanXRQChr08g0221991' => 'han', 'HanXRQChr11g0336061' => 'han', 'HanXRQChr11g0336411' => 'han', 'Haze_11234' => 'cav', 'Hma1.2p1_0549F.1_g177010' => 'hma', 'Hma1.2p1_0602F.1_g187630' => 'hma', 'Hund14876' => 'sun', 'Hund14879' => 'sun', 'Lalb_Chr06g0160741' => 'lal', 'Lalb_Chr21g0304781' => 'lal', 'Lj3A726G19' => 'lonja', 'Lj3A726T23' => 'lonja', 'Lj3A726T24' => 'lonja', 'Lj3A726T25' => 'lonja', 'Lj3A727T17' => 'lonja', 'Lj3C726T0' => 'lonja', 'Lj3C726T2' => 'lonja', 'Lj3P725T35' => 'lonja', 'Lj3P727T10' => 'lonja', 'Lj3P727T12' => 'lonja', 'Lj3P727T14' => 'lonja', 'Lj5g0023109' => 'lja', 'Lj6P646T44' => 'lonja', 'Lsat_1_v5_gn_6_75760' => 'lsa', 'Lsat_1_v5_gn_6_75800' => 'lsa', 'Lsat_1_v5_gn_6_75900' => 'lsa', 'Lsat_1_v5_gn_6_76240' => 'lsa', 'Lsat_1_v5_gn_6_76441' => 'lsa', 'Lsat_1_v5_gn_6_76700' => 'lsa', 'Lsat_1_v5_gn_6_76760' => 'lsa', 'Manes.15G033100' => 'mes', 'Mapoly0004s0074' => 'mpo', 'Mapoly0004s0075' => 'mpo', 'Mapoly0004s0163' => 'mpo', 'Mapoly0004s0164' => 'mpo', 'Mapoly0021s0018' => 'mpo', 'Mapoly0041s0136' => 'mpo', 'Mapoly0041s0137' => 'mpo', 'Mapoly0041s0138' => 'mpo', 'Mapoly0041s0139' => 'mpo', 'Mapoly0041s0141' => 'mpo', 'Mapoly0041s0142' => 'mpo', 'Mapoly0041s0143' => 'mpo', 'Mapoly0041s0144' => 'mpo', 'Mapoly0041s0145' => 'mpo', 'Mapoly0047s0106' => 'mpo', 'Mapoly0047s0108' => 'mpo', 'Mapoly0050s0051' => 'mpo', 'Mapoly0050s0052' => 'mpo', 'Mapoly0050s0053' => 'mpo', 'Mapoly0058s0013' => 'mpo', 'Mapoly0091s0078' => 'mpo', 'Mapoly0091s0079' => 'mpo', 'Mapoly0091s0080' => 'mpo', 'Mapoly0091s0081' => 'mpo', 'Mapoly0278s0004' => 'mpo', 'Mapoly0278s0005' => 'mpo', 'Mapoly0278s0006' => 'mpo', 'MBI11_g30648_MAGBIO' => 'mbi', 'MCO03G194' => 'mco', 'MCO03G590' => 'mco', 'MCO07G312' => 'mco', 'MCO10G318' => 'mco', 'MCO12G244' => 'mco', 'MCO13G148' => 'mco', 'MCO13G194' => 'mco', 'MCO16G238' => 'mco', 'MD06G1134100' => 'mdo', 'MD13G1200100' => 'mdo', 'MD13G1200300' => 'mdo', 'MD13G1200600' => 'mdo', 'MD14G1150400' => 'mdo', 'MD16G1200000' => 'mdo', 'Medtr1g102570' => 'mtr', 'Medtr1g102780' => 'mtr', 'Medtr1g102800' => 'mtr', 'Medtr1g102810' => 'mtr', 'Medtr1g102830' => 'mtr', 'MELO3C006499.2' => 'cme', 'Migut.G00385' => 'egut', 'MSTRG.4063' => 'ama', 'Nitab4.5_0000090g0260' => 'nta', 'Nitab4.5_0000977g0030' => 'nta', 'Nitab4.5_0002541g0040' => 'nta', 'Nitab4.5_0007068g0040' => 'nta', 'Nn005s41408' => 'nnu', 'Nn005s41410' => 'nnu', 'Oeu010310.1' => 'oeu', 'Oeu010311.1' => 'oeu', 'Oeu043472.1' => 'oeu', 'Os01g0246400' => 'osa', 'Os04g0267950' => 'osa', 'Os07g0178700' => 'osa', 'Os07g0178800' => 'osa', 'Peaxi162Scf00316g00046' => 'pax', 'Peaxi162Scf00316g00049' => 'pax', 'Peaxi162Scf00316g00059' => 'pax', 'Peaxi162Scf00316g00328' => 'pax', 'Peaxi162Scf00316g00329' => 'pax', 'Peaxi162Scf00316g00411' => 'pax', 'Peaxi162Scf00316g00521' => 'pax', 'Peaxi162Scf00492g00068' => 'pax', 'Peaxi162Scf35631g00002' => 'pax', 'PGR142G3720' => 'pgr', 'PGSC0003DMG400006442' => 'stu', 'Phvul.007G062000' => 'pvu', 'Potri.008G157750' => 'ptr', 'Potri.008G157900' => 'ptr', 'Potri.008G158000' => 'ptr', 'Potri.008G158200' => 'ptr', 'Pp3c11_7280' => 'ppa', 'Pp3c11_7980' => 'ppa', 'Pp3c12_19450' => 'ppa', 'Pp3c14_1480' => 'ppa', 'Pp3c14_1501' => 'ppa', 'Pp3c16_4900' => 'ppa', 'Pp3c16_5010' => 'ppa', 'Pp3c16_5060' => 'ppa', 'Pp3c19_18250' => 'ppa', 'Pp3c23_8530' => 'ppa', 'Pp3c23_8550' => 'ppa', 'Pp3c24_9670' => 'ppa', 'Pp3c2_21390' => 'ppa', 'Pp3c2_31380' => 'ppa', 'Pp3c3_16620' => 'ppa', 'Pp3c3_8090' => 'ppa', 'Pp3c3_8110' => 'ppa', 'Pp3c3_8130' => 'ppa', 'Pp3c3_8150' => 'ppa', 'Pp3c4_14320' => 'ppa', 'Pp3c6_2560' => 'ppa', 'Pp3c9_16700' => 'ppa', 'PRCOL_00000234' => 'pco', 'PRCOL_00000235' => 'pco', 'PRCOL_00000777' => 'pco', 'PRCOL_00002344' => 'pco', 'PRCOL_00002372' => 'pco', 'PRCOL_00006120' => 'pco', 'Prupe.1G021400' => 'ppe', 'Prupe.1G021500' => 'ppe', 'Prupe.1G021600' => 'ppe', 'Prupe.1G021700' => 'ppe', 'Prupe.1G021800' => 'ppe', 'Prupe.5G145100' => 'ppe', 'Psat6g204040' => 'psa', 'Psat6g204800' => 'psa', 'Psat6g204920' => 'psa', 'Psat6g204960' => 'psa', 'Psat6g205080' => 'psa', 'PSO017G0271' => 'pso', 'PSO017G1276' => 'pso', 'PSO017G1429' => 'pso', 'PSO017G1861' => 'pso', 'PSO017G2787' => 'pso', 'PSO017G4466' => 'pso', 'PSO017G5118' => 'pso', 'PSO017G5420' => 'pso', 'PSO063G3678' => 'pso', 'PSO210G0546' => 'pso', 'PSO317G0001' => 'pso', 'PSO357G0512' => 'pso', 'PSO478G2682' => 'pso', 'PSO647G0001' => 'pso', 'PSO675G0001' => 'pso', 'PSO675G2699' => 'pso', 'PSO675G2849' => 'pso', 'PSO675G4991' => 'pso', 'PSO689G0001' => 'pso', 'QL06p000916' => 'qlo', 'QL06p000921' => 'qlo', 'QL06p001398' => 'qlo', 'QL06p001407' => 'qlo', 'QL06p002031' => 'qlo', 'RcHm_v2.0_Chr4g0387791' => 'rch', 'RcHm_v2.0_Chr4g0387801' => 'rch', 'RcHm_v2.0_Chr6g0286501' => 'rch', 'RcHm_v2.0_Chr6g0286511' => 'rch', 'RcHm_v2.0_Chr6g0286521' => 'rch', 'RcHm_v2.0_Chr6g0286531' => 'rch', 'RcHm_v2.0_Chr7g0189141' => 'rch', 'Rhsim02G0028700' => 'rsi', 'Rhsim02G0028800' => 'rsi', 'Rhsim02G0028900' => 'rsi', 'Rhsim02G0029000' => 'rsi', 'Rhsim02G0029100' => 'rsi', 'Rhsim02G0029200' => 'rsi', 'Rhsim02G0029300' => 'rsi', 'Rhsim02G0029400' => 'rsi', 'Rhsim02G0029500' => 'rsi', 'Rhsim02G0029600' => 'rsi', 'RhsimUnG0024000' => 'rsi', 'RhsimUnG0024100' => 'rsi', 'RhsimUnG0024200' => 'rsi', 'RhsimUnG0024300' => 'rsi', 'RhsimUnG0024400' => 'rsi', 'RhsimUnG0024500' => 'rsi', 'RhsimUnG0024700' => 'rsi', 'RhsimUnG0024800' => 'rsi', 'RhsimUnG0024900' => 'rsi', 'RhsimUnG0025100' => 'rsi', 'Sabra08G0120200' => 'sbr', 'Sabra08G0120300' => 'sbr', 'Sabra08G0120500' => 'sbr', 'Sabra08G0120600' => 'sbr', 'Sabra10G0158900' => 'sbr', 'SalBow2G3492' => 'sbo', 'Sc13g0004760' => 'sci', 'Sc13g0004770' => 'sci', 'Sed0003417' => 'sed', 'Sed0019750' => 'sed', 'SEGI_03419' => 'sgi', 'SEGI_05907' => 'sgi', 'SEGI_10682' => 'sgi', 'SEGI_13528' => 'sgi', 'SEGI_16081' => 'sgi', 'SEGI_19370' => 'sgi', 'SEGI_21015' => 'sgi', 'SEGI_21944' => 'sgi', 'SEGI_32906' => 'sgi', 'SEGI_33093' => 'sgi', 'SEGI_36110' => 'sgi', 'SEGI_40397' => 'sgi', 'SGA_v2.0_scaffold191G40426' => 'sas', 'SGA_v2.0_scaffold353G49717' => 'sas', 'SGA_v2.0_scaffold50G18550' => 'sas', 'SMO119G0173' => 'smo', 'SMO172G0002' => 'smo', 'Solyc09g082690.3' => 'sly', 'Solyc09g082700.2' => 'sly', 'Sopen09g031550' => 'spe', 'Sopen09g031560' => 'spe', 'Sp3g20540' => 'spa', 'Sp7g07580' => 'spa', 'TAR134G0002' => 'tar', 'TAR236G0001' => 'tar', 'TAR365G0892' => 'tar', 'TAR636G0166' => 'tar', 'TAR636G0646' => 'tar', 'TAR636G0869' => 'tar', 'TAR636G1317' => 'tar', 'TAR636G1744' => 'tar', 'TAR636G3358' => 'tar', 'TAR636G3436' => 'tar', 'THA.LOC104803047' => 'tha', 'Thecc.04G238900' => 'tca', 'Thhalv10021557m.g' => 'esa', 'Thhalv10026318m.g' => 'esa', 'Thhalv10026335m.g' => 'esa', 'TPR.G17433' => 'tpr', 'TPR.G18915' => 'tpr', 'TPR.G26125' => 'tpr', 'TWI09G0677' => 'twi', 'TWI73G0287' => 'twi', 'unitig_748.g8326' => 'ugi', 'vmacro15370' => 'vma', 'vmacro15371' => 'vma', 'vmacro15372' => 'vma', 'vmacro15373' => 'vma', 'vmacro15374' => 'vma', 'VMungo0720G2826' => 'vmu', 'Zm00001eb116960' => 'zma', 'Zm00001eb301260' => 'zma', 'Zm00001eb301270' => 'zma' ) $gf_id = 'HOM05D001460' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001460' ) $data_identifier = 'HOM05D001460' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 4, 'aag' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 2, 'aox' => (int) 2, 'arhy' => (int) 4, 'ath' => (int) 2, 'atr' => (int) 1, 'acertr' => (int) 10, 'cqu' => (int) 4, 'bca' => (int) 11, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 1, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 1, 'ccan' => (int) 1, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 1, 'col' => (int) 1, 'cpa' => (int) 1, 'cre' => (int) 7, 'csa' => (int) 1, 'camsi' => (int) 2, 'dca' => (int) 3, 'din' => (int) 2, 'dzi' => (int) 3, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 14, 'fve' => (int) 9, 'gma' => (int) 2, 'ghi' => (int) 4, 'gra' => (int) 2, 'vvi' => (int) 1, 'han' => (int) 13, 'cav' => (int) 1, 'hma' => (int) 2, 'sun' => (int) 2, 'lal' => (int) 2, 'lonja' => (int) 12, 'lja' => (int) 1, 'lsa' => (int) 7, 'mes' => (int) 1, 'mpo' => (int) 27, 'mbi' => (int) 1, 'mco' => (int) 8, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 1, 'egut' => (int) 1, 'ama' => (int) 1, 'nta' => (int) 4, 'nnu' => (int) 2, 'oeu' => (int) 3, 'osa' => (int) 4, 'pax' => (int) 9, 'pgr' => (int) 1, 'stu' => (int) 1, 'pvu' => (int) 1, 'ptr' => (int) 4, 'ppa' => (int) 22, 'pco' => (int) 6, 'ppe' => (int) 6, 'psa' => (int) 5, 'pso' => (int) 19, 'qlo' => (int) 5, 'rch' => (int) 7, 'rsi' => (int) 20, 'sbr' => (int) 5, 'sbo' => (int) 1, 'sci' => (int) 2, 'sed' => (int) 2, 'sgi' => (int) 12, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 2, 'tar' => (int) 10, 'tha' => (int) 1, 'tca' => (int) 1, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 2, 'ugi' => (int) 1, 'vma' => (int) 5, 'vmu' => (int) 1, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb301270' $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' => 'HOM05D001460', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '433', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p22980' => 'bna', 'A01p32340' => 'bna', 'A03p42970' => 'bna', 'A05p25880' => 'bna', 'Aa31LG8G9320' => 'aar', 'Aa31LG8G9330' => 'aar', 'Aa31LG8G9340' => 'aar', 'Aa31sc221G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1034' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1528' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.829' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2222' => 'aag', 'Ah.12g058830' => 'amhyb', 'Ah.12g058840' => 'amhyb', 'AL3G37160' => 'aly', 'AL7G41310' => 'aly', 'Aqoxy5G00395' => 'aox', 'Aqoxy5G00396' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0C8NZA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5185HY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JZ1PRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MD3LS0' => 'arhy', 'AT3G22840' => 'ath', 'AT4G14690' => 'ath', 'ATR0665G054' => 'atr', 'Atru.chr4.2344' => 'acertr', 'Atru.chr4.2346' => 'acertr', 'Atru.chr4.2347' => 'acertr', 'Atru.chr4.2348' => 'acertr', 'Atru.chr4.2355' => 'acertr', 'Atru.chr4.2356' => 'acertr', 'Atru.chr4.2358' => 'acertr', 'Atru.chr4.2359' => 'acertr', 'Atru.chr4.2360' => 'acertr', 'Atru.chr4.2361' => 'acertr', 'AUR62030476' => 'cqu', 'AUR62030478' => 'cqu', 'AUR62030819' => 'cqu', 'AUR62030820' => 'cqu', 'BcaB03g14648' => 'bca', 'BcaB04g20492' => 'bca', 'BcaB06g26399' => 'bca', 'BcaC01g03416' => 'bca', 'BcaC01g03419' => 'bca', 'BcaC01g03421' => 'bca', 'BcaC01g03424' => 'bca', 'BcaC05g28012' => 'bca', 'BcaC09g49212' => 'bca', 'BcaC09g50140' => 'bca', 'BcaNung00346' => 'bca', 'BolC1t02785H' => 'bol', 'BolC1t04095H' => 'bol', 'BolC3t17545H' => 'bol', 'BolC5t32769H' => 'bol', 'BraA01t02211Z' => 'bra', 'BraA01t03359Z' => 'bra', 'BraA03t13441Z' => 'bra', 'BraA05t21476Z' => 'bra', 'C01p28420' => 'bna', 'C01p41350' => 'bna', 'C03p52750' => 'bna', 'C03p52780' => 'bna', 'C05p40270' => 'bna', 'CAN.G1437.9' => 'can', 'CANSAT78G0035' => 'cansat', 'CANSAT78G1036' => 'cansat', 'CANSAT78G2272' => 'cansat', 'CANSAT78G2478' => 'cansat', 'CARHR098700' => 'chi', 'CARHR221120' => 'chi', 'CARHR221150' => 'chi', 'Carub.0003s2297' => 'cru', 'Carub.0007s2749' => 'cru', 'Carub.0007s2750' => 'cru', 'Carub.0007s2751' => 'cru', 'Ca_10849_v3' => 'car', 'Cc03_g04300' => 'ccan', 'CDE02G3648' => 'cde', 'CDE05G0060' => 'cde', 'CDE05G0692' => 'cde', 'CDE05G2285' => 'cde', 'CDE05G2884' => 'cde', 'CDE05G3072' => 'cde', 'Cfa008439' => 'cfa', 'Cfa008441' => 'cfa', 'Cfa008443' => 'cfa', 'Cfa008448' => 'cfa', 'Ciclev10005974m.g' => 'ccl', 'Ciclev10006006m.g' => 'ccl', 'Ciclev10006775m.g' => 'ccl', 'CiPaw.02G120400' => 'cil', 'CiPaw.02G120500' => 'cil', 'CiPaw.02G120600' => 'cil', 'ClCG05G004850' => 'cla', 'COL.COLO4_21566' => 'col', 'Cpa.g.sc44.124' => 'cpa', 'Cre07.g320400' => 'cre', 'Cre07.g320450' => 'cre', 'Cre08.g384650' => 'cre', 'Cre09.g393173' => 'cre', 'Cre09.g394325' => 'cre', 'Cre14.g626750' => 'cre', 'Cre16.g679250' => 'cre', 'CsaV3_3G012890' => 'csa', 'CSS0010865' => 'camsi', 'CSS0044338' => 'camsi', 'DCAR_002366' => 'dca', 'DCAR_030687' => 'dca', 'DCAR_030688' => 'dca', 'Dinv14047' => 'din', 'Dinv14048' => 'din', 'Duzib151G0105' => 'dzi', 'Duzib151G0114' => 'dzi', 'Duzib212G1029' => 'dzi', 'ECA232G3536' => 'eca', 'ECA240G0786' => 'eca', 'ECA240G1802' => 'eca', 'ECA240G3760' => 'eca', 'ECA240G3920' => 'eca', 'EL10Ac5g12536' => 'bvu', 'EL10Ac5g12537' => 'bvu', 'EL10Ac5g12538' => 'bvu', 'Eucgr.B01004' => 'egr', 'Eucgr.B01006' => 'egr', 'Eucgr.B01007' => 'egr', 'Eucgr.B01008' => 'egr', 'Eucgr.B01895' => 'egr', 'Eucgr.B01896' => 'egr', 'FAN04G1456' => 'fan', 'FAN08G1769' => 'fan', 'FAN08G2160' => 'fan', 'FAN13G2403' => 'fan', 'FAN13G3303' => 'fan', 'FAN15G2435' => 'fan', 'FAN17G0672' => 'fan', 'FAN17G2441' => 'fan', 'FAN18G1024' => 'fan', 'FAN22G1458' => 'fan', 'FAN24G0037' => 'fan', 'FAN24G0429' => 'fan', 'FAN24G2387' => 'fan', 'FAN27G2746' => 'fan', 'FvH4_2g20400' => 'fve', 'FvH4_2g20420' => 'fve', 'FvH4_2g20430' => 'fve', 'FvH4_4g01270' => 'fve', 'FvH4_4g01290' => 'fve', 'FvH4_4g01300' => 'fve', 'FvH4_4g01310' => 'fve', 'FvH4_4g01330' => 'fve', 'FvH4_5g09070' => 'fve', 'Glyma.10G243800' => 'gma', 'Glyma.20G150600' => 'gma', 'Gohir.A09G219200' => 'ghi', 'Gohir.A09G219300' => 'ghi', 'Gohir.D09G221400' => 'ghi', 'Gohir.D09G221500' => 'ghi', 'Gorai.006G242600' => 'gra', 'Gorai.006G242700' => 'gra', 'GSVIVG01018044001' => 'vvi', 'HanXRQChr03g0083821' => 'han', 'HanXRQChr03g0083841' => 'han', 'HanXRQChr03g0083881' => 'han', 'HanXRQChr03g0083901' => 'han', 'HanXRQChr03g0083921' => 'han', 'HanXRQChr03g0085331' => 'han', 'HanXRQChr03g0085361' => 'han', 'HanXRQChr03g0085411' => 'han', 'HanXRQChr03g0085421' => 'han', 'HanXRQChr03g0085431' => 'han', 'HanXRQChr08g0221991' => 'han', 'HanXRQChr11g0336061' => 'han', 'HanXRQChr11g0336411' => 'han', 'Haze_11234' => 'cav', 'Hma1.2p1_0549F.1_g177010' => 'hma', 'Hma1.2p1_0602F.1_g187630' => 'hma', 'Hund14876' => 'sun', 'Hund14879' => 'sun', 'Lalb_Chr06g0160741' => 'lal', 'Lalb_Chr21g0304781' => 'lal', 'Lj3A726G19' => 'lonja', 'Lj3A726T23' => 'lonja', 'Lj3A726T24' => 'lonja', 'Lj3A726T25' => 'lonja', 'Lj3A727T17' => 'lonja', 'Lj3C726T0' => 'lonja', 'Lj3C726T2' => 'lonja', 'Lj3P725T35' => 'lonja', 'Lj3P727T10' => 'lonja', 'Lj3P727T12' => 'lonja', 'Lj3P727T14' => 'lonja', 'Lj5g0023109' => 'lja', 'Lj6P646T44' => 'lonja', 'Lsat_1_v5_gn_6_75760' => 'lsa', 'Lsat_1_v5_gn_6_75800' => 'lsa', 'Lsat_1_v5_gn_6_75900' => 'lsa', 'Lsat_1_v5_gn_6_76240' => 'lsa', 'Lsat_1_v5_gn_6_76441' => 'lsa', 'Lsat_1_v5_gn_6_76700' => 'lsa', 'Lsat_1_v5_gn_6_76760' => 'lsa', 'Manes.15G033100' => 'mes', 'Mapoly0004s0074' => 'mpo', 'Mapoly0004s0075' => 'mpo', 'Mapoly0004s0163' => 'mpo', 'Mapoly0004s0164' => 'mpo', 'Mapoly0021s0018' => 'mpo', 'Mapoly0041s0136' => 'mpo', 'Mapoly0041s0137' => 'mpo', 'Mapoly0041s0138' => 'mpo', 'Mapoly0041s0139' => 'mpo', 'Mapoly0041s0141' => 'mpo', 'Mapoly0041s0142' => 'mpo', 'Mapoly0041s0143' => 'mpo', 'Mapoly0041s0144' => 'mpo', 'Mapoly0041s0145' => 'mpo', 'Mapoly0047s0106' => 'mpo', 'Mapoly0047s0108' => 'mpo', 'Mapoly0050s0051' => 'mpo', 'Mapoly0050s0052' => 'mpo', 'Mapoly0050s0053' => 'mpo', 'Mapoly0058s0013' => 'mpo', 'Mapoly0091s0078' => 'mpo', 'Mapoly0091s0079' => 'mpo', 'Mapoly0091s0080' => 'mpo', 'Mapoly0091s0081' => 'mpo', 'Mapoly0278s0004' => 'mpo', 'Mapoly0278s0005' => 'mpo', 'Mapoly0278s0006' => 'mpo', 'MBI11_g30648_MAGBIO' => 'mbi', 'MCO03G194' => 'mco', 'MCO03G590' => 'mco', 'MCO07G312' => 'mco', 'MCO10G318' => 'mco', 'MCO12G244' => 'mco', 'MCO13G148' => 'mco', 'MCO13G194' => 'mco', 'MCO16G238' => 'mco', 'MD06G1134100' => 'mdo', 'MD13G1200100' => 'mdo', 'MD13G1200300' => 'mdo', 'MD13G1200600' => 'mdo', 'MD14G1150400' => 'mdo', 'MD16G1200000' => 'mdo', 'Medtr1g102570' => 'mtr', 'Medtr1g102780' => 'mtr', 'Medtr1g102800' => 'mtr', 'Medtr1g102810' => 'mtr', 'Medtr1g102830' => 'mtr', 'MELO3C006499.2' => 'cme', 'Migut.G00385' => 'egut', 'MSTRG.4063' => 'ama', 'Nitab4.5_0000090g0260' => 'nta', 'Nitab4.5_0000977g0030' => 'nta', 'Nitab4.5_0002541g0040' => 'nta', 'Nitab4.5_0007068g0040' => 'nta', 'Nn005s41408' => 'nnu', 'Nn005s41410' => 'nnu', 'Oeu010310.1' => 'oeu', 'Oeu010311.1' => 'oeu', 'Oeu043472.1' => 'oeu', 'Os01g0246400' => 'osa', 'Os04g0267950' => 'osa', 'Os07g0178700' => 'osa', 'Os07g0178800' => 'osa', 'Peaxi162Scf00316g00046' => 'pax', 'Peaxi162Scf00316g00049' => 'pax', 'Peaxi162Scf00316g00059' => 'pax', 'Peaxi162Scf00316g00328' => 'pax', 'Peaxi162Scf00316g00329' => 'pax', 'Peaxi162Scf00316g00411' => 'pax', 'Peaxi162Scf00316g00521' => 'pax', 'Peaxi162Scf00492g00068' => 'pax', 'Peaxi162Scf35631g00002' => 'pax', 'PGR142G3720' => 'pgr', 'PGSC0003DMG400006442' => 'stu', 'Phvul.007G062000' => 'pvu', 'Potri.008G157750' => 'ptr', 'Potri.008G157900' => 'ptr', 'Potri.008G158000' => 'ptr', 'Potri.008G158200' => 'ptr', 'Pp3c11_7280' => 'ppa', 'Pp3c11_7980' => 'ppa', 'Pp3c12_19450' => 'ppa', 'Pp3c14_1480' => 'ppa', 'Pp3c14_1501' => 'ppa', 'Pp3c16_4900' => 'ppa', 'Pp3c16_5010' => 'ppa', 'Pp3c16_5060' => 'ppa', 'Pp3c19_18250' => 'ppa', 'Pp3c23_8530' => 'ppa', 'Pp3c23_8550' => 'ppa', 'Pp3c24_9670' => 'ppa', 'Pp3c2_21390' => 'ppa', 'Pp3c2_31380' => 'ppa', 'Pp3c3_16620' => 'ppa', 'Pp3c3_8090' => 'ppa', 'Pp3c3_8110' => 'ppa', 'Pp3c3_8130' => 'ppa', 'Pp3c3_8150' => 'ppa', 'Pp3c4_14320' => 'ppa', 'Pp3c6_2560' => 'ppa', 'Pp3c9_16700' => 'ppa', 'PRCOL_00000234' => 'pco', 'PRCOL_00000235' => 'pco', 'PRCOL_00000777' => 'pco', 'PRCOL_00002344' => 'pco', 'PRCOL_00002372' => 'pco', 'PRCOL_00006120' => 'pco', 'Prupe.1G021400' => 'ppe', 'Prupe.1G021500' => 'ppe', 'Prupe.1G021600' => 'ppe', 'Prupe.1G021700' => 'ppe', 'Prupe.1G021800' => 'ppe', 'Prupe.5G145100' => 'ppe', 'Psat6g204040' => 'psa', 'Psat6g204800' => 'psa', 'Psat6g204920' => 'psa', 'Psat6g204960' => 'psa', 'Psat6g205080' => 'psa', 'PSO017G0271' => 'pso', 'PSO017G1276' => 'pso', 'PSO017G1429' => 'pso', 'PSO017G1861' => 'pso', 'PSO017G2787' => 'pso', 'PSO017G4466' => 'pso', 'PSO017G5118' => 'pso', 'PSO017G5420' => 'pso', 'PSO063G3678' => 'pso', 'PSO210G0546' => 'pso', 'PSO317G0001' => 'pso', 'PSO357G0512' => 'pso', 'PSO478G2682' => 'pso', 'PSO647G0001' => 'pso', 'PSO675G0001' => 'pso', 'PSO675G2699' => 'pso', 'PSO675G2849' => 'pso', 'PSO675G4991' => 'pso', 'PSO689G0001' => 'pso', 'QL06p000916' => 'qlo', 'QL06p000921' => 'qlo', 'QL06p001398' => 'qlo', 'QL06p001407' => 'qlo', 'QL06p002031' => 'qlo', 'RcHm_v2.0_Chr4g0387791' => 'rch', 'RcHm_v2.0_Chr4g0387801' => 'rch', 'RcHm_v2.0_Chr6g0286501' => 'rch', 'RcHm_v2.0_Chr6g0286511' => 'rch', 'RcHm_v2.0_Chr6g0286521' => 'rch', 'RcHm_v2.0_Chr6g0286531' => 'rch', 'RcHm_v2.0_Chr7g0189141' => 'rch', 'Rhsim02G0028700' => 'rsi', 'Rhsim02G0028800' => 'rsi', 'Rhsim02G0028900' => 'rsi', 'Rhsim02G0029000' => 'rsi', 'Rhsim02G0029100' => 'rsi', 'Rhsim02G0029200' => 'rsi', 'Rhsim02G0029300' => 'rsi', 'Rhsim02G0029400' => 'rsi', 'Rhsim02G0029500' => 'rsi', 'Rhsim02G0029600' => 'rsi', 'RhsimUnG0024000' => 'rsi', 'RhsimUnG0024100' => 'rsi', 'RhsimUnG0024200' => 'rsi', 'RhsimUnG0024300' => 'rsi', 'RhsimUnG0024400' => 'rsi', 'RhsimUnG0024500' => 'rsi', 'RhsimUnG0024700' => 'rsi', 'RhsimUnG0024800' => 'rsi', 'RhsimUnG0024900' => 'rsi', 'RhsimUnG0025100' => 'rsi', 'Sabra08G0120200' => 'sbr', 'Sabra08G0120300' => 'sbr', 'Sabra08G0120500' => 'sbr', 'Sabra08G0120600' => 'sbr', 'Sabra10G0158900' => 'sbr', 'SalBow2G3492' => 'sbo', 'Sc13g0004760' => 'sci', 'Sc13g0004770' => 'sci', 'Sed0003417' => 'sed', 'Sed0019750' => 'sed', 'SEGI_03419' => 'sgi', 'SEGI_05907' => 'sgi', 'SEGI_10682' => 'sgi', 'SEGI_13528' => 'sgi', 'SEGI_16081' => 'sgi', 'SEGI_19370' => 'sgi', 'SEGI_21015' => 'sgi', 'SEGI_21944' => 'sgi', 'SEGI_32906' => 'sgi', 'SEGI_33093' => 'sgi', 'SEGI_36110' => 'sgi', 'SEGI_40397' => 'sgi', 'SGA_v2.0_scaffold191G40426' => 'sas', 'SGA_v2.0_scaffold353G49717' => 'sas', 'SGA_v2.0_scaffold50G18550' => 'sas', 'SMO119G0173' => 'smo', 'SMO172G0002' => 'smo', 'Solyc09g082690.3' => 'sly', 'Solyc09g082700.2' => 'sly', 'Sopen09g031550' => 'spe', 'Sopen09g031560' => 'spe', 'Sp3g20540' => 'spa', 'Sp7g07580' => 'spa', 'TAR134G0002' => 'tar', 'TAR236G0001' => 'tar', 'TAR365G0892' => 'tar', 'TAR636G0166' => 'tar', 'TAR636G0646' => 'tar', 'TAR636G0869' => 'tar', 'TAR636G1317' => 'tar', 'TAR636G1744' => 'tar', 'TAR636G3358' => 'tar', 'TAR636G3436' => 'tar', 'THA.LOC104803047' => 'tha', 'Thecc.04G238900' => 'tca', 'Thhalv10021557m.g' => 'esa', 'Thhalv10026318m.g' => 'esa', 'Thhalv10026335m.g' => 'esa', 'TPR.G17433' => 'tpr', 'TPR.G18915' => 'tpr', 'TPR.G26125' => 'tpr', 'TWI09G0677' => 'twi', 'TWI73G0287' => 'twi', 'unitig_748.g8326' => 'ugi', 'vmacro15370' => 'vma', 'vmacro15371' => 'vma', 'vmacro15372' => 'vma', 'vmacro15373' => 'vma', 'vmacro15374' => 'vma', 'VMungo0720G2826' => 'vmu', 'Zm00001eb116960' => 'zma', 'Zm00001eb301260' => 'zma', 'Zm00001eb301270' => 'zma' ), 'gf_id' => 'HOM05D001460', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001460' ), 'data_identifier' => 'HOM05D001460', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001460', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '433', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p22980' => 'bna', 'A01p32340' => 'bna', 'A03p42970' => 'bna', 'A05p25880' => 'bna', 'Aa31LG8G9320' => 'aar', 'Aa31LG8G9330' => 'aar', 'Aa31LG8G9340' => 'aar', 'Aa31sc221G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1034' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1528' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.829' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2222' => 'aag', 'Ah.12g058830' => 'amhyb', 'Ah.12g058840' => 'amhyb', 'AL3G37160' => 'aly', 'AL7G41310' => 'aly', 'Aqoxy5G00395' => 'aox', 'Aqoxy5G00396' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0C8NZA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5185HY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JZ1PRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MD3LS0' => 'arhy', 'AT3G22840' => 'ath', 'AT4G14690' => 'ath', 'ATR0665G054' => 'atr', 'Atru.chr4.2344' => 'acertr', 'Atru.chr4.2346' => 'acertr', 'Atru.chr4.2347' => 'acertr', 'Atru.chr4.2348' => 'acertr', 'Atru.chr4.2355' => 'acertr', 'Atru.chr4.2356' => 'acertr', 'Atru.chr4.2358' => 'acertr', 'Atru.chr4.2359' => 'acertr', 'Atru.chr4.2360' => 'acertr', 'Atru.chr4.2361' => 'acertr', 'AUR62030476' => 'cqu', 'AUR62030478' => 'cqu', 'AUR62030819' => 'cqu', 'AUR62030820' => 'cqu', 'BcaB03g14648' => 'bca', 'BcaB04g20492' => 'bca', 'BcaB06g26399' => 'bca', 'BcaC01g03416' => 'bca', 'BcaC01g03419' => 'bca', 'BcaC01g03421' => 'bca', 'BcaC01g03424' => 'bca', 'BcaC05g28012' => 'bca', 'BcaC09g49212' => 'bca', 'BcaC09g50140' => 'bca', 'BcaNung00346' => 'bca', 'BolC1t02785H' => 'bol', 'BolC1t04095H' => 'bol', 'BolC3t17545H' => 'bol', 'BolC5t32769H' => 'bol', 'BraA01t02211Z' => 'bra', 'BraA01t03359Z' => 'bra', 'BraA03t13441Z' => 'bra', 'BraA05t21476Z' => 'bra', 'C01p28420' => 'bna', 'C01p41350' => 'bna', 'C03p52750' => 'bna', 'C03p52780' => 'bna', 'C05p40270' => 'bna', 'CAN.G1437.9' => 'can', 'CANSAT78G0035' => 'cansat', 'CANSAT78G1036' => 'cansat', 'CANSAT78G2272' => 'cansat', 'CANSAT78G2478' => 'cansat', 'CARHR098700' => 'chi', 'CARHR221120' => 'chi', 'CARHR221150' => 'chi', 'Carub.0003s2297' => 'cru', 'Carub.0007s2749' => 'cru', 'Carub.0007s2750' => 'cru', 'Carub.0007s2751' => 'cru', 'Ca_10849_v3' => 'car', 'Cc03_g04300' => 'ccan', 'CDE02G3648' => 'cde', 'CDE05G0060' => 'cde', 'CDE05G0692' => 'cde', 'CDE05G2285' => 'cde', 'CDE05G2884' => 'cde', 'CDE05G3072' => 'cde', 'Cfa008439' => 'cfa', 'Cfa008441' => 'cfa', 'Cfa008443' => 'cfa', 'Cfa008448' => 'cfa', 'Ciclev10005974m.g' => 'ccl', 'Ciclev10006006m.g' => 'ccl', 'Ciclev10006775m.g' => 'ccl', 'CiPaw.02G120400' => 'cil', 'CiPaw.02G120500' => 'cil', 'CiPaw.02G120600' => 'cil', 'ClCG05G004850' => 'cla', 'COL.COLO4_21566' => 'col', 'Cpa.g.sc44.124' => 'cpa', 'Cre07.g320400' => 'cre', 'Cre07.g320450' => 'cre', 'Cre08.g384650' => 'cre', 'Cre09.g393173' => 'cre', 'Cre09.g394325' => 'cre', 'Cre14.g626750' => 'cre', 'Cre16.g679250' => 'cre', 'CsaV3_3G012890' => 'csa', 'CSS0010865' => 'camsi', 'CSS0044338' => 'camsi', 'DCAR_002366' => 'dca', 'DCAR_030687' => 'dca', 'DCAR_030688' => 'dca', 'Dinv14047' => 'din', 'Dinv14048' => 'din', 'Duzib151G0105' => 'dzi', 'Duzib151G0114' => 'dzi', 'Duzib212G1029' => 'dzi', 'ECA232G3536' => 'eca', 'ECA240G0786' => 'eca', 'ECA240G1802' => 'eca', 'ECA240G3760' => 'eca', 'ECA240G3920' => 'eca', 'EL10Ac5g12536' => 'bvu', 'EL10Ac5g12537' => 'bvu', 'EL10Ac5g12538' => 'bvu', 'Eucgr.B01004' => 'egr', 'Eucgr.B01006' => 'egr', 'Eucgr.B01007' => 'egr', 'Eucgr.B01008' => 'egr', 'Eucgr.B01895' => 'egr', 'Eucgr.B01896' => 'egr', 'FAN04G1456' => 'fan', 'FAN08G1769' => 'fan', 'FAN08G2160' => 'fan', 'FAN13G2403' => 'fan', 'FAN13G3303' => 'fan', 'FAN15G2435' => 'fan', 'FAN17G0672' => 'fan', 'FAN17G2441' => 'fan', 'FAN18G1024' => 'fan', 'FAN22G1458' => 'fan', 'FAN24G0037' => 'fan', 'FAN24G0429' => 'fan', 'FAN24G2387' => 'fan', 'FAN27G2746' => 'fan', 'FvH4_2g20400' => 'fve', 'FvH4_2g20420' => 'fve', 'FvH4_2g20430' => 'fve', 'FvH4_4g01270' => 'fve', 'FvH4_4g01290' => 'fve', 'FvH4_4g01300' => 'fve', 'FvH4_4g01310' => 'fve', 'FvH4_4g01330' => 'fve', 'FvH4_5g09070' => 'fve', 'Glyma.10G243800' => 'gma', 'Glyma.20G150600' => 'gma', 'Gohir.A09G219200' => 'ghi', 'Gohir.A09G219300' => 'ghi', 'Gohir.D09G221400' => 'ghi', 'Gohir.D09G221500' => 'ghi', 'Gorai.006G242600' => 'gra', 'Gorai.006G242700' => 'gra', 'GSVIVG01018044001' => 'vvi', 'HanXRQChr03g0083821' => 'han', 'HanXRQChr03g0083841' => 'han', 'HanXRQChr03g0083881' => 'han', 'HanXRQChr03g0083901' => 'han', 'HanXRQChr03g0083921' => 'han', 'HanXRQChr03g0085331' => 'han', 'HanXRQChr03g0085361' => 'han', 'HanXRQChr03g0085411' => 'han', 'HanXRQChr03g0085421' => 'han', 'HanXRQChr03g0085431' => 'han', 'HanXRQChr08g0221991' => 'han', 'HanXRQChr11g0336061' => 'han', 'HanXRQChr11g0336411' => 'han', 'Haze_11234' => 'cav', 'Hma1.2p1_0549F.1_g177010' => 'hma', 'Hma1.2p1_0602F.1_g187630' => 'hma', 'Hund14876' => 'sun', 'Hund14879' => 'sun', 'Lalb_Chr06g0160741' => 'lal', 'Lalb_Chr21g0304781' => 'lal', 'Lj3A726G19' => 'lonja', 'Lj3A726T23' => 'lonja', 'Lj3A726T24' => 'lonja', 'Lj3A726T25' => 'lonja', 'Lj3A727T17' => 'lonja', 'Lj3C726T0' => 'lonja', 'Lj3C726T2' => 'lonja', 'Lj3P725T35' => 'lonja', 'Lj3P727T10' => 'lonja', 'Lj3P727T12' => 'lonja', 'Lj3P727T14' => 'lonja', 'Lj5g0023109' => 'lja', 'Lj6P646T44' => 'lonja', 'Lsat_1_v5_gn_6_75760' => 'lsa', 'Lsat_1_v5_gn_6_75800' => 'lsa', 'Lsat_1_v5_gn_6_75900' => 'lsa', 'Lsat_1_v5_gn_6_76240' => 'lsa', 'Lsat_1_v5_gn_6_76441' => 'lsa', 'Lsat_1_v5_gn_6_76700' => 'lsa', 'Lsat_1_v5_gn_6_76760' => 'lsa', 'Manes.15G033100' => 'mes', 'Mapoly0004s0074' => 'mpo', 'Mapoly0004s0075' => 'mpo', 'Mapoly0004s0163' => 'mpo', 'Mapoly0004s0164' => 'mpo', 'Mapoly0021s0018' => 'mpo', 'Mapoly0041s0136' => 'mpo', 'Mapoly0041s0137' => 'mpo', 'Mapoly0041s0138' => 'mpo', 'Mapoly0041s0139' => 'mpo', 'Mapoly0041s0141' => 'mpo', 'Mapoly0041s0142' => 'mpo', 'Mapoly0041s0143' => 'mpo', 'Mapoly0041s0144' => 'mpo', 'Mapoly0041s0145' => 'mpo', 'Mapoly0047s0106' => 'mpo', 'Mapoly0047s0108' => 'mpo', 'Mapoly0050s0051' => 'mpo', 'Mapoly0050s0052' => 'mpo', 'Mapoly0050s0053' => 'mpo', 'Mapoly0058s0013' => 'mpo', 'Mapoly0091s0078' => 'mpo', 'Mapoly0091s0079' => 'mpo', 'Mapoly0091s0080' => 'mpo', 'Mapoly0091s0081' => 'mpo', 'Mapoly0278s0004' => 'mpo', 'Mapoly0278s0005' => 'mpo', 'Mapoly0278s0006' => 'mpo', 'MBI11_g30648_MAGBIO' => 'mbi', 'MCO03G194' => 'mco', 'MCO03G590' => 'mco', 'MCO07G312' => 'mco', 'MCO10G318' => 'mco', 'MCO12G244' => 'mco', 'MCO13G148' => 'mco', 'MCO13G194' => 'mco', 'MCO16G238' => 'mco', 'MD06G1134100' => 'mdo', 'MD13G1200100' => 'mdo', 'MD13G1200300' => 'mdo', 'MD13G1200600' => 'mdo', 'MD14G1150400' => 'mdo', 'MD16G1200000' => 'mdo', 'Medtr1g102570' => 'mtr', 'Medtr1g102780' => 'mtr', 'Medtr1g102800' => 'mtr', 'Medtr1g102810' => 'mtr', 'Medtr1g102830' => 'mtr', 'MELO3C006499.2' => 'cme', 'Migut.G00385' => 'egut', 'MSTRG.4063' => 'ama', 'Nitab4.5_0000090g0260' => 'nta', 'Nitab4.5_0000977g0030' => 'nta', 'Nitab4.5_0002541g0040' => 'nta', 'Nitab4.5_0007068g0040' => 'nta', 'Nn005s41408' => 'nnu', 'Nn005s41410' => 'nnu', 'Oeu010310.1' => 'oeu', 'Oeu010311.1' => 'oeu', 'Oeu043472.1' => 'oeu', 'Os01g0246400' => 'osa', 'Os04g0267950' => 'osa', 'Os07g0178700' => 'osa', 'Os07g0178800' => 'osa', 'Peaxi162Scf00316g00046' => 'pax', 'Peaxi162Scf00316g00049' => 'pax', 'Peaxi162Scf00316g00059' => 'pax', 'Peaxi162Scf00316g00328' => 'pax', 'Peaxi162Scf00316g00329' => 'pax', 'Peaxi162Scf00316g00411' => 'pax', 'Peaxi162Scf00316g00521' => 'pax', 'Peaxi162Scf00492g00068' => 'pax', 'Peaxi162Scf35631g00002' => 'pax', 'PGR142G3720' => 'pgr', 'PGSC0003DMG400006442' => 'stu', 'Phvul.007G062000' => 'pvu', 'Potri.008G157750' => 'ptr', 'Potri.008G157900' => 'ptr', 'Potri.008G158000' => 'ptr', 'Potri.008G158200' => 'ptr', 'Pp3c11_7280' => 'ppa', 'Pp3c11_7980' => 'ppa', 'Pp3c12_19450' => 'ppa', 'Pp3c14_1480' => 'ppa', 'Pp3c14_1501' => 'ppa', 'Pp3c16_4900' => 'ppa', 'Pp3c16_5010' => 'ppa', 'Pp3c16_5060' => 'ppa', 'Pp3c19_18250' => 'ppa', 'Pp3c23_8530' => 'ppa', 'Pp3c23_8550' => 'ppa', 'Pp3c24_9670' => 'ppa', 'Pp3c2_21390' => 'ppa', 'Pp3c2_31380' => 'ppa', 'Pp3c3_16620' => 'ppa', 'Pp3c3_8090' => 'ppa', 'Pp3c3_8110' => 'ppa', 'Pp3c3_8130' => 'ppa', 'Pp3c3_8150' => 'ppa', 'Pp3c4_14320' => 'ppa', 'Pp3c6_2560' => 'ppa', 'Pp3c9_16700' => 'ppa', 'PRCOL_00000234' => 'pco', 'PRCOL_00000235' => 'pco', 'PRCOL_00000777' => 'pco', 'PRCOL_00002344' => 'pco', 'PRCOL_00002372' => 'pco', 'PRCOL_00006120' => 'pco', 'Prupe.1G021400' => 'ppe', 'Prupe.1G021500' => 'ppe', 'Prupe.1G021600' => 'ppe', 'Prupe.1G021700' => 'ppe', 'Prupe.1G021800' => 'ppe', 'Prupe.5G145100' => 'ppe', 'Psat6g204040' => 'psa', 'Psat6g204800' => 'psa', 'Psat6g204920' => 'psa', 'Psat6g204960' => 'psa', 'Psat6g205080' => 'psa', 'PSO017G0271' => 'pso', 'PSO017G1276' => 'pso', 'PSO017G1429' => 'pso', 'PSO017G1861' => 'pso', 'PSO017G2787' => 'pso', 'PSO017G4466' => 'pso', 'PSO017G5118' => 'pso', 'PSO017G5420' => 'pso', 'PSO063G3678' => 'pso', 'PSO210G0546' => 'pso', 'PSO317G0001' => 'pso', 'PSO357G0512' => 'pso', 'PSO478G2682' => 'pso', 'PSO647G0001' => 'pso', 'PSO675G0001' => 'pso', 'PSO675G2699' => 'pso', 'PSO675G2849' => 'pso', 'PSO675G4991' => 'pso', 'PSO689G0001' => 'pso', 'QL06p000916' => 'qlo', 'QL06p000921' => 'qlo', 'QL06p001398' => 'qlo', 'QL06p001407' => 'qlo', 'QL06p002031' => 'qlo', 'RcHm_v2.0_Chr4g0387791' => 'rch', 'RcHm_v2.0_Chr4g0387801' => 'rch', 'RcHm_v2.0_Chr6g0286501' => 'rch', 'RcHm_v2.0_Chr6g0286511' => 'rch', 'RcHm_v2.0_Chr6g0286521' => 'rch', 'RcHm_v2.0_Chr6g0286531' => 'rch', 'RcHm_v2.0_Chr7g0189141' => 'rch', 'Rhsim02G0028700' => 'rsi', 'Rhsim02G0028800' => 'rsi', 'Rhsim02G0028900' => 'rsi', 'Rhsim02G0029000' => 'rsi', 'Rhsim02G0029100' => 'rsi', 'Rhsim02G0029200' => 'rsi', 'Rhsim02G0029300' => 'rsi', 'Rhsim02G0029400' => 'rsi', 'Rhsim02G0029500' => 'rsi', 'Rhsim02G0029600' => 'rsi', 'RhsimUnG0024000' => 'rsi', 'RhsimUnG0024100' => 'rsi', 'RhsimUnG0024200' => 'rsi', 'RhsimUnG0024300' => 'rsi', 'RhsimUnG0024400' => 'rsi', 'RhsimUnG0024500' => 'rsi', 'RhsimUnG0024700' => 'rsi', 'RhsimUnG0024800' => 'rsi', 'RhsimUnG0024900' => 'rsi', 'RhsimUnG0025100' => 'rsi', 'Sabra08G0120200' => 'sbr', 'Sabra08G0120300' => 'sbr', 'Sabra08G0120500' => 'sbr', 'Sabra08G0120600' => 'sbr', 'Sabra10G0158900' => 'sbr', 'SalBow2G3492' => 'sbo', 'Sc13g0004760' => 'sci', 'Sc13g0004770' => 'sci', 'Sed0003417' => 'sed', 'Sed0019750' => 'sed', 'SEGI_03419' => 'sgi', 'SEGI_05907' => 'sgi', 'SEGI_10682' => 'sgi', 'SEGI_13528' => 'sgi', 'SEGI_16081' => 'sgi', 'SEGI_19370' => 'sgi', 'SEGI_21015' => 'sgi', 'SEGI_21944' => 'sgi', 'SEGI_32906' => 'sgi', 'SEGI_33093' => 'sgi', 'SEGI_36110' => 'sgi', 'SEGI_40397' => 'sgi', 'SGA_v2.0_scaffold191G40426' => 'sas', 'SGA_v2.0_scaffold353G49717' => 'sas', 'SGA_v2.0_scaffold50G18550' => 'sas', 'SMO119G0173' => 'smo', 'SMO172G0002' => 'smo', 'Solyc09g082690.3' => 'sly', 'Solyc09g082700.2' => 'sly', 'Sopen09g031550' => 'spe', 'Sopen09g031560' => 'spe', 'Sp3g20540' => 'spa', 'Sp7g07580' => 'spa', 'TAR134G0002' => 'tar', 'TAR236G0001' => 'tar', 'TAR365G0892' => 'tar', 'TAR636G0166' => 'tar', 'TAR636G0646' => 'tar', 'TAR636G0869' => 'tar', 'TAR636G1317' => 'tar', 'TAR636G1744' => 'tar', 'TAR636G3358' => 'tar', 'TAR636G3436' => 'tar', 'THA.LOC104803047' => 'tha', 'Thecc.04G238900' => 'tca', 'Thhalv10021557m.g' => 'esa', 'Thhalv10026318m.g' => 'esa', 'Thhalv10026335m.g' => 'esa', 'TPR.G17433' => 'tpr', 'TPR.G18915' => 'tpr', 'TPR.G26125' => 'tpr', 'TWI09G0677' => 'twi', 'TWI73G0287' => 'twi', 'unitig_748.g8326' => 'ugi', 'vmacro15370' => 'vma', 'vmacro15371' => 'vma', 'vmacro15372' => 'vma', 'vmacro15373' => 'vma', 'vmacro15374' => 'vma', 'VMungo0720G2826' => 'vmu', 'Zm00001eb116960' => 'zma', 'Zm00001eb301260' => 'zma', 'Zm00001eb301270' => 'zma' ) $gf_id = 'HOM05D001460' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001460' ) $data_identifier = 'HOM05D001460' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 4, 'aag' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 2, 'aox' => (int) 2, 'arhy' => (int) 4, 'ath' => (int) 2, 'atr' => (int) 1, 'acertr' => (int) 10, 'cqu' => (int) 4, 'bca' => (int) 11, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 1, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 1, 'ccan' => (int) 1, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 1, 'col' => (int) 1, 'cpa' => (int) 1, 'cre' => (int) 7, 'csa' => (int) 1, 'camsi' => (int) 2, 'dca' => (int) 3, 'din' => (int) 2, 'dzi' => (int) 3, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 14, 'fve' => (int) 9, 'gma' => (int) 2, 'ghi' => (int) 4, 'gra' => (int) 2, 'vvi' => (int) 1, 'han' => (int) 13, 'cav' => (int) 1, 'hma' => (int) 2, 'sun' => (int) 2, 'lal' => (int) 2, 'lonja' => (int) 12, 'lja' => (int) 1, 'lsa' => (int) 7, 'mes' => (int) 1, 'mpo' => (int) 27, 'mbi' => (int) 1, 'mco' => (int) 8, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 1, 'egut' => (int) 1, 'ama' => (int) 1, 'nta' => (int) 4, 'nnu' => (int) 2, 'oeu' => (int) 3, 'osa' => (int) 4, 'pax' => (int) 9, 'pgr' => (int) 1, 'stu' => (int) 1, 'pvu' => (int) 1, 'ptr' => (int) 4, 'ppa' => (int) 22, 'pco' => (int) 6, 'ppe' => (int) 6, 'psa' => (int) 5, 'pso' => (int) 19, 'qlo' => (int) 5, 'rch' => (int) 7, 'rsi' => (int) 20, 'sbr' => (int) 5, 'sbo' => (int) 1, 'sci' => (int) 2, 'sed' => (int) 2, 'sgi' => (int) 12, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 2, 'tar' => (int) 10, 'tha' => (int) 1, 'tca' => (int) 1, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 2, 'ugi' => (int) 1, 'vma' => (int) 5, 'vmu' => (int) 1, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb301270' $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' => 'HOM05D001460', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '433', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p22980' => 'bna', 'A01p32340' => 'bna', 'A03p42970' => 'bna', 'A05p25880' => 'bna', 'Aa31LG8G9320' => 'aar', 'Aa31LG8G9330' => 'aar', 'Aa31LG8G9340' => 'aar', 'Aa31sc221G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1034' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1528' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.829' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2222' => 'aag', 'Ah.12g058830' => 'amhyb', 'Ah.12g058840' => 'amhyb', 'AL3G37160' => 'aly', 'AL7G41310' => 'aly', 'Aqoxy5G00395' => 'aox', 'Aqoxy5G00396' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0C8NZA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5185HY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JZ1PRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MD3LS0' => 'arhy', 'AT3G22840' => 'ath', 'AT4G14690' => 'ath', 'ATR0665G054' => 'atr', 'Atru.chr4.2344' => 'acertr', 'Atru.chr4.2346' => 'acertr', 'Atru.chr4.2347' => 'acertr', 'Atru.chr4.2348' => 'acertr', 'Atru.chr4.2355' => 'acertr', 'Atru.chr4.2356' => 'acertr', 'Atru.chr4.2358' => 'acertr', 'Atru.chr4.2359' => 'acertr', 'Atru.chr4.2360' => 'acertr', 'Atru.chr4.2361' => 'acertr', 'AUR62030476' => 'cqu', 'AUR62030478' => 'cqu', 'AUR62030819' => 'cqu', 'AUR62030820' => 'cqu', 'BcaB03g14648' => 'bca', 'BcaB04g20492' => 'bca', 'BcaB06g26399' => 'bca', 'BcaC01g03416' => 'bca', 'BcaC01g03419' => 'bca', 'BcaC01g03421' => 'bca', 'BcaC01g03424' => 'bca', 'BcaC05g28012' => 'bca', 'BcaC09g49212' => 'bca', 'BcaC09g50140' => 'bca', 'BcaNung00346' => 'bca', 'BolC1t02785H' => 'bol', 'BolC1t04095H' => 'bol', 'BolC3t17545H' => 'bol', 'BolC5t32769H' => 'bol', 'BraA01t02211Z' => 'bra', 'BraA01t03359Z' => 'bra', 'BraA03t13441Z' => 'bra', 'BraA05t21476Z' => 'bra', 'C01p28420' => 'bna', 'C01p41350' => 'bna', 'C03p52750' => 'bna', 'C03p52780' => 'bna', 'C05p40270' => 'bna', 'CAN.G1437.9' => 'can', 'CANSAT78G0035' => 'cansat', 'CANSAT78G1036' => 'cansat', 'CANSAT78G2272' => 'cansat', 'CANSAT78G2478' => 'cansat', 'CARHR098700' => 'chi', 'CARHR221120' => 'chi', 'CARHR221150' => 'chi', 'Carub.0003s2297' => 'cru', 'Carub.0007s2749' => 'cru', 'Carub.0007s2750' => 'cru', 'Carub.0007s2751' => 'cru', 'Ca_10849_v3' => 'car', 'Cc03_g04300' => 'ccan', 'CDE02G3648' => 'cde', 'CDE05G0060' => 'cde', 'CDE05G0692' => 'cde', 'CDE05G2285' => 'cde', 'CDE05G2884' => 'cde', 'CDE05G3072' => 'cde', 'Cfa008439' => 'cfa', 'Cfa008441' => 'cfa', 'Cfa008443' => 'cfa', 'Cfa008448' => 'cfa', 'Ciclev10005974m.g' => 'ccl', 'Ciclev10006006m.g' => 'ccl', 'Ciclev10006775m.g' => 'ccl', 'CiPaw.02G120400' => 'cil', 'CiPaw.02G120500' => 'cil', 'CiPaw.02G120600' => 'cil', 'ClCG05G004850' => 'cla', 'COL.COLO4_21566' => 'col', 'Cpa.g.sc44.124' => 'cpa', 'Cre07.g320400' => 'cre', 'Cre07.g320450' => 'cre', 'Cre08.g384650' => 'cre', 'Cre09.g393173' => 'cre', 'Cre09.g394325' => 'cre', 'Cre14.g626750' => 'cre', 'Cre16.g679250' => 'cre', 'CsaV3_3G012890' => 'csa', 'CSS0010865' => 'camsi', 'CSS0044338' => 'camsi', 'DCAR_002366' => 'dca', 'DCAR_030687' => 'dca', 'DCAR_030688' => 'dca', 'Dinv14047' => 'din', 'Dinv14048' => 'din', 'Duzib151G0105' => 'dzi', 'Duzib151G0114' => 'dzi', 'Duzib212G1029' => 'dzi', 'ECA232G3536' => 'eca', 'ECA240G0786' => 'eca', 'ECA240G1802' => 'eca', 'ECA240G3760' => 'eca', 'ECA240G3920' => 'eca', 'EL10Ac5g12536' => 'bvu', 'EL10Ac5g12537' => 'bvu', 'EL10Ac5g12538' => 'bvu', 'Eucgr.B01004' => 'egr', 'Eucgr.B01006' => 'egr', 'Eucgr.B01007' => 'egr', 'Eucgr.B01008' => 'egr', 'Eucgr.B01895' => 'egr', 'Eucgr.B01896' => 'egr', 'FAN04G1456' => 'fan', 'FAN08G1769' => 'fan', 'FAN08G2160' => 'fan', 'FAN13G2403' => 'fan', 'FAN13G3303' => 'fan', 'FAN15G2435' => 'fan', 'FAN17G0672' => 'fan', 'FAN17G2441' => 'fan', 'FAN18G1024' => 'fan', 'FAN22G1458' => 'fan', 'FAN24G0037' => 'fan', 'FAN24G0429' => 'fan', 'FAN24G2387' => 'fan', 'FAN27G2746' => 'fan', 'FvH4_2g20400' => 'fve', 'FvH4_2g20420' => 'fve', 'FvH4_2g20430' => 'fve', 'FvH4_4g01270' => 'fve', 'FvH4_4g01290' => 'fve', 'FvH4_4g01300' => 'fve', 'FvH4_4g01310' => 'fve', 'FvH4_4g01330' => 'fve', 'FvH4_5g09070' => 'fve', 'Glyma.10G243800' => 'gma', 'Glyma.20G150600' => 'gma', 'Gohir.A09G219200' => 'ghi', 'Gohir.A09G219300' => 'ghi', 'Gohir.D09G221400' => 'ghi', 'Gohir.D09G221500' => 'ghi', 'Gorai.006G242600' => 'gra', 'Gorai.006G242700' => 'gra', 'GSVIVG01018044001' => 'vvi', 'HanXRQChr03g0083821' => 'han', 'HanXRQChr03g0083841' => 'han', 'HanXRQChr03g0083881' => 'han', 'HanXRQChr03g0083901' => 'han', 'HanXRQChr03g0083921' => 'han', 'HanXRQChr03g0085331' => 'han', 'HanXRQChr03g0085361' => 'han', 'HanXRQChr03g0085411' => 'han', 'HanXRQChr03g0085421' => 'han', 'HanXRQChr03g0085431' => 'han', 'HanXRQChr08g0221991' => 'han', 'HanXRQChr11g0336061' => 'han', 'HanXRQChr11g0336411' => 'han', 'Haze_11234' => 'cav', 'Hma1.2p1_0549F.1_g177010' => 'hma', 'Hma1.2p1_0602F.1_g187630' => 'hma', 'Hund14876' => 'sun', 'Hund14879' => 'sun', 'Lalb_Chr06g0160741' => 'lal', 'Lalb_Chr21g0304781' => 'lal', 'Lj3A726G19' => 'lonja', 'Lj3A726T23' => 'lonja', 'Lj3A726T24' => 'lonja', 'Lj3A726T25' => 'lonja', 'Lj3A727T17' => 'lonja', 'Lj3C726T0' => 'lonja', 'Lj3C726T2' => 'lonja', 'Lj3P725T35' => 'lonja', 'Lj3P727T10' => 'lonja', 'Lj3P727T12' => 'lonja', 'Lj3P727T14' => 'lonja', 'Lj5g0023109' => 'lja', 'Lj6P646T44' => 'lonja', 'Lsat_1_v5_gn_6_75760' => 'lsa', 'Lsat_1_v5_gn_6_75800' => 'lsa', 'Lsat_1_v5_gn_6_75900' => 'lsa', 'Lsat_1_v5_gn_6_76240' => 'lsa', 'Lsat_1_v5_gn_6_76441' => 'lsa', 'Lsat_1_v5_gn_6_76700' => 'lsa', 'Lsat_1_v5_gn_6_76760' => 'lsa', 'Manes.15G033100' => 'mes', 'Mapoly0004s0074' => 'mpo', 'Mapoly0004s0075' => 'mpo', 'Mapoly0004s0163' => 'mpo', 'Mapoly0004s0164' => 'mpo', 'Mapoly0021s0018' => 'mpo', 'Mapoly0041s0136' => 'mpo', 'Mapoly0041s0137' => 'mpo', 'Mapoly0041s0138' => 'mpo', 'Mapoly0041s0139' => 'mpo', 'Mapoly0041s0141' => 'mpo', 'Mapoly0041s0142' => 'mpo', 'Mapoly0041s0143' => 'mpo', 'Mapoly0041s0144' => 'mpo', 'Mapoly0041s0145' => 'mpo', 'Mapoly0047s0106' => 'mpo', 'Mapoly0047s0108' => 'mpo', 'Mapoly0050s0051' => 'mpo', 'Mapoly0050s0052' => 'mpo', 'Mapoly0050s0053' => 'mpo', 'Mapoly0058s0013' => 'mpo', 'Mapoly0091s0078' => 'mpo', 'Mapoly0091s0079' => 'mpo', 'Mapoly0091s0080' => 'mpo', 'Mapoly0091s0081' => 'mpo', 'Mapoly0278s0004' => 'mpo', 'Mapoly0278s0005' => 'mpo', 'Mapoly0278s0006' => 'mpo', 'MBI11_g30648_MAGBIO' => 'mbi', 'MCO03G194' => 'mco', 'MCO03G590' => 'mco', 'MCO07G312' => 'mco', 'MCO10G318' => 'mco', 'MCO12G244' => 'mco', 'MCO13G148' => 'mco', 'MCO13G194' => 'mco', 'MCO16G238' => 'mco', 'MD06G1134100' => 'mdo', 'MD13G1200100' => 'mdo', 'MD13G1200300' => 'mdo', 'MD13G1200600' => 'mdo', 'MD14G1150400' => 'mdo', 'MD16G1200000' => 'mdo', 'Medtr1g102570' => 'mtr', 'Medtr1g102780' => 'mtr', 'Medtr1g102800' => 'mtr', 'Medtr1g102810' => 'mtr', 'Medtr1g102830' => 'mtr', 'MELO3C006499.2' => 'cme', 'Migut.G00385' => 'egut', 'MSTRG.4063' => 'ama', 'Nitab4.5_0000090g0260' => 'nta', 'Nitab4.5_0000977g0030' => 'nta', 'Nitab4.5_0002541g0040' => 'nta', 'Nitab4.5_0007068g0040' => 'nta', 'Nn005s41408' => 'nnu', 'Nn005s41410' => 'nnu', 'Oeu010310.1' => 'oeu', 'Oeu010311.1' => 'oeu', 'Oeu043472.1' => 'oeu', 'Os01g0246400' => 'osa', 'Os04g0267950' => 'osa', 'Os07g0178700' => 'osa', 'Os07g0178800' => 'osa', 'Peaxi162Scf00316g00046' => 'pax', 'Peaxi162Scf00316g00049' => 'pax', 'Peaxi162Scf00316g00059' => 'pax', 'Peaxi162Scf00316g00328' => 'pax', 'Peaxi162Scf00316g00329' => 'pax', 'Peaxi162Scf00316g00411' => 'pax', 'Peaxi162Scf00316g00521' => 'pax', 'Peaxi162Scf00492g00068' => 'pax', 'Peaxi162Scf35631g00002' => 'pax', 'PGR142G3720' => 'pgr', 'PGSC0003DMG400006442' => 'stu', 'Phvul.007G062000' => 'pvu', 'Potri.008G157750' => 'ptr', 'Potri.008G157900' => 'ptr', 'Potri.008G158000' => 'ptr', 'Potri.008G158200' => 'ptr', 'Pp3c11_7280' => 'ppa', 'Pp3c11_7980' => 'ppa', 'Pp3c12_19450' => 'ppa', 'Pp3c14_1480' => 'ppa', 'Pp3c14_1501' => 'ppa', 'Pp3c16_4900' => 'ppa', 'Pp3c16_5010' => 'ppa', 'Pp3c16_5060' => 'ppa', 'Pp3c19_18250' => 'ppa', 'Pp3c23_8530' => 'ppa', 'Pp3c23_8550' => 'ppa', 'Pp3c24_9670' => 'ppa', 'Pp3c2_21390' => 'ppa', 'Pp3c2_31380' => 'ppa', 'Pp3c3_16620' => 'ppa', 'Pp3c3_8090' => 'ppa', 'Pp3c3_8110' => 'ppa', 'Pp3c3_8130' => 'ppa', 'Pp3c3_8150' => 'ppa', 'Pp3c4_14320' => 'ppa', 'Pp3c6_2560' => 'ppa', 'Pp3c9_16700' => 'ppa', 'PRCOL_00000234' => 'pco', 'PRCOL_00000235' => 'pco', 'PRCOL_00000777' => 'pco', 'PRCOL_00002344' => 'pco', 'PRCOL_00002372' => 'pco', 'PRCOL_00006120' => 'pco', 'Prupe.1G021400' => 'ppe', 'Prupe.1G021500' => 'ppe', 'Prupe.1G021600' => 'ppe', 'Prupe.1G021700' => 'ppe', 'Prupe.1G021800' => 'ppe', 'Prupe.5G145100' => 'ppe', 'Psat6g204040' => 'psa', 'Psat6g204800' => 'psa', 'Psat6g204920' => 'psa', 'Psat6g204960' => 'psa', 'Psat6g205080' => 'psa', 'PSO017G0271' => 'pso', 'PSO017G1276' => 'pso', 'PSO017G1429' => 'pso', 'PSO017G1861' => 'pso', 'PSO017G2787' => 'pso', 'PSO017G4466' => 'pso', 'PSO017G5118' => 'pso', 'PSO017G5420' => 'pso', 'PSO063G3678' => 'pso', 'PSO210G0546' => 'pso', 'PSO317G0001' => 'pso', 'PSO357G0512' => 'pso', 'PSO478G2682' => 'pso', 'PSO647G0001' => 'pso', 'PSO675G0001' => 'pso', 'PSO675G2699' => 'pso', 'PSO675G2849' => 'pso', 'PSO675G4991' => 'pso', 'PSO689G0001' => 'pso', 'QL06p000916' => 'qlo', 'QL06p000921' => 'qlo', 'QL06p001398' => 'qlo', 'QL06p001407' => 'qlo', 'QL06p002031' => 'qlo', 'RcHm_v2.0_Chr4g0387791' => 'rch', 'RcHm_v2.0_Chr4g0387801' => 'rch', 'RcHm_v2.0_Chr6g0286501' => 'rch', 'RcHm_v2.0_Chr6g0286511' => 'rch', 'RcHm_v2.0_Chr6g0286521' => 'rch', 'RcHm_v2.0_Chr6g0286531' => 'rch', 'RcHm_v2.0_Chr7g0189141' => 'rch', 'Rhsim02G0028700' => 'rsi', 'Rhsim02G0028800' => 'rsi', 'Rhsim02G0028900' => 'rsi', 'Rhsim02G0029000' => 'rsi', 'Rhsim02G0029100' => 'rsi', 'Rhsim02G0029200' => 'rsi', 'Rhsim02G0029300' => 'rsi', 'Rhsim02G0029400' => 'rsi', 'Rhsim02G0029500' => 'rsi', 'Rhsim02G0029600' => 'rsi', 'RhsimUnG0024000' => 'rsi', 'RhsimUnG0024100' => 'rsi', 'RhsimUnG0024200' => 'rsi', 'RhsimUnG0024300' => 'rsi', 'RhsimUnG0024400' => 'rsi', 'RhsimUnG0024500' => 'rsi', 'RhsimUnG0024700' => 'rsi', 'RhsimUnG0024800' => 'rsi', 'RhsimUnG0024900' => 'rsi', 'RhsimUnG0025100' => 'rsi', 'Sabra08G0120200' => 'sbr', 'Sabra08G0120300' => 'sbr', 'Sabra08G0120500' => 'sbr', 'Sabra08G0120600' => 'sbr', 'Sabra10G0158900' => 'sbr', 'SalBow2G3492' => 'sbo', 'Sc13g0004760' => 'sci', 'Sc13g0004770' => 'sci', 'Sed0003417' => 'sed', 'Sed0019750' => 'sed', 'SEGI_03419' => 'sgi', 'SEGI_05907' => 'sgi', 'SEGI_10682' => 'sgi', 'SEGI_13528' => 'sgi', 'SEGI_16081' => 'sgi', 'SEGI_19370' => 'sgi', 'SEGI_21015' => 'sgi', 'SEGI_21944' => 'sgi', 'SEGI_32906' => 'sgi', 'SEGI_33093' => 'sgi', 'SEGI_36110' => 'sgi', 'SEGI_40397' => 'sgi', 'SGA_v2.0_scaffold191G40426' => 'sas', 'SGA_v2.0_scaffold353G49717' => 'sas', 'SGA_v2.0_scaffold50G18550' => 'sas', 'SMO119G0173' => 'smo', 'SMO172G0002' => 'smo', 'Solyc09g082690.3' => 'sly', 'Solyc09g082700.2' => 'sly', 'Sopen09g031550' => 'spe', 'Sopen09g031560' => 'spe', 'Sp3g20540' => 'spa', 'Sp7g07580' => 'spa', 'TAR134G0002' => 'tar', 'TAR236G0001' => 'tar', 'TAR365G0892' => 'tar', 'TAR636G0166' => 'tar', 'TAR636G0646' => 'tar', 'TAR636G0869' => 'tar', 'TAR636G1317' => 'tar', 'TAR636G1744' => 'tar', 'TAR636G3358' => 'tar', 'TAR636G3436' => 'tar', 'THA.LOC104803047' => 'tha', 'Thecc.04G238900' => 'tca', 'Thhalv10021557m.g' => 'esa', 'Thhalv10026318m.g' => 'esa', 'Thhalv10026335m.g' => 'esa', 'TPR.G17433' => 'tpr', 'TPR.G18915' => 'tpr', 'TPR.G26125' => 'tpr', 'TWI09G0677' => 'twi', 'TWI73G0287' => 'twi', 'unitig_748.g8326' => 'ugi', 'vmacro15370' => 'vma', 'vmacro15371' => 'vma', 'vmacro15372' => 'vma', 'vmacro15373' => 'vma', 'vmacro15374' => 'vma', 'VMungo0720G2826' => 'vmu', 'Zm00001eb116960' => 'zma', 'Zm00001eb301260' => 'zma', 'Zm00001eb301270' => 'zma' ), 'gf_id' => 'HOM05D001460', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001460' ), 'data_identifier' => 'HOM05D001460', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001460', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '433', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p22980' => 'bna', 'A01p32340' => 'bna', 'A03p42970' => 'bna', 'A05p25880' => 'bna', 'Aa31LG8G9320' => 'aar', 'Aa31LG8G9330' => 'aar', 'Aa31LG8G9340' => 'aar', 'Aa31sc221G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1034' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1528' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.829' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2222' => 'aag', 'Ah.12g058830' => 'amhyb', 'Ah.12g058840' => 'amhyb', 'AL3G37160' => 'aly', 'AL7G41310' => 'aly', 'Aqoxy5G00395' => 'aox', 'Aqoxy5G00396' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0C8NZA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5185HY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JZ1PRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MD3LS0' => 'arhy', 'AT3G22840' => 'ath', 'AT4G14690' => 'ath', 'ATR0665G054' => 'atr', 'Atru.chr4.2344' => 'acertr', 'Atru.chr4.2346' => 'acertr', 'Atru.chr4.2347' => 'acertr', 'Atru.chr4.2348' => 'acertr', 'Atru.chr4.2355' => 'acertr', 'Atru.chr4.2356' => 'acertr', 'Atru.chr4.2358' => 'acertr', 'Atru.chr4.2359' => 'acertr', 'Atru.chr4.2360' => 'acertr', 'Atru.chr4.2361' => 'acertr', 'AUR62030476' => 'cqu', 'AUR62030478' => 'cqu', 'AUR62030819' => 'cqu', 'AUR62030820' => 'cqu', 'BcaB03g14648' => 'bca', 'BcaB04g20492' => 'bca', 'BcaB06g26399' => 'bca', 'BcaC01g03416' => 'bca', 'BcaC01g03419' => 'bca', 'BcaC01g03421' => 'bca', 'BcaC01g03424' => 'bca', 'BcaC05g28012' => 'bca', 'BcaC09g49212' => 'bca', 'BcaC09g50140' => 'bca', 'BcaNung00346' => 'bca', 'BolC1t02785H' => 'bol', 'BolC1t04095H' => 'bol', 'BolC3t17545H' => 'bol', 'BolC5t32769H' => 'bol', 'BraA01t02211Z' => 'bra', 'BraA01t03359Z' => 'bra', 'BraA03t13441Z' => 'bra', 'BraA05t21476Z' => 'bra', 'C01p28420' => 'bna', 'C01p41350' => 'bna', 'C03p52750' => 'bna', 'C03p52780' => 'bna', 'C05p40270' => 'bna', 'CAN.G1437.9' => 'can', 'CANSAT78G0035' => 'cansat', 'CANSAT78G1036' => 'cansat', 'CANSAT78G2272' => 'cansat', 'CANSAT78G2478' => 'cansat', 'CARHR098700' => 'chi', 'CARHR221120' => 'chi', 'CARHR221150' => 'chi', 'Carub.0003s2297' => 'cru', 'Carub.0007s2749' => 'cru', 'Carub.0007s2750' => 'cru', 'Carub.0007s2751' => 'cru', 'Ca_10849_v3' => 'car', 'Cc03_g04300' => 'ccan', 'CDE02G3648' => 'cde', 'CDE05G0060' => 'cde', 'CDE05G0692' => 'cde', 'CDE05G2285' => 'cde', 'CDE05G2884' => 'cde', 'CDE05G3072' => 'cde', 'Cfa008439' => 'cfa', 'Cfa008441' => 'cfa', 'Cfa008443' => 'cfa', 'Cfa008448' => 'cfa', 'Ciclev10005974m.g' => 'ccl', 'Ciclev10006006m.g' => 'ccl', 'Ciclev10006775m.g' => 'ccl', 'CiPaw.02G120400' => 'cil', 'CiPaw.02G120500' => 'cil', 'CiPaw.02G120600' => 'cil', 'ClCG05G004850' => 'cla', 'COL.COLO4_21566' => 'col', 'Cpa.g.sc44.124' => 'cpa', 'Cre07.g320400' => 'cre', 'Cre07.g320450' => 'cre', 'Cre08.g384650' => 'cre', 'Cre09.g393173' => 'cre', 'Cre09.g394325' => 'cre', 'Cre14.g626750' => 'cre', 'Cre16.g679250' => 'cre', 'CsaV3_3G012890' => 'csa', 'CSS0010865' => 'camsi', 'CSS0044338' => 'camsi', 'DCAR_002366' => 'dca', 'DCAR_030687' => 'dca', 'DCAR_030688' => 'dca', 'Dinv14047' => 'din', 'Dinv14048' => 'din', 'Duzib151G0105' => 'dzi', 'Duzib151G0114' => 'dzi', 'Duzib212G1029' => 'dzi', 'ECA232G3536' => 'eca', 'ECA240G0786' => 'eca', 'ECA240G1802' => 'eca', 'ECA240G3760' => 'eca', 'ECA240G3920' => 'eca', 'EL10Ac5g12536' => 'bvu', 'EL10Ac5g12537' => 'bvu', 'EL10Ac5g12538' => 'bvu', 'Eucgr.B01004' => 'egr', 'Eucgr.B01006' => 'egr', 'Eucgr.B01007' => 'egr', 'Eucgr.B01008' => 'egr', 'Eucgr.B01895' => 'egr', 'Eucgr.B01896' => 'egr', 'FAN04G1456' => 'fan', 'FAN08G1769' => 'fan', 'FAN08G2160' => 'fan', 'FAN13G2403' => 'fan', 'FAN13G3303' => 'fan', 'FAN15G2435' => 'fan', 'FAN17G0672' => 'fan', 'FAN17G2441' => 'fan', 'FAN18G1024' => 'fan', 'FAN22G1458' => 'fan', 'FAN24G0037' => 'fan', 'FAN24G0429' => 'fan', 'FAN24G2387' => 'fan', 'FAN27G2746' => 'fan', 'FvH4_2g20400' => 'fve', 'FvH4_2g20420' => 'fve', 'FvH4_2g20430' => 'fve', 'FvH4_4g01270' => 'fve', 'FvH4_4g01290' => 'fve', 'FvH4_4g01300' => 'fve', 'FvH4_4g01310' => 'fve', 'FvH4_4g01330' => 'fve', 'FvH4_5g09070' => 'fve', 'Glyma.10G243800' => 'gma', 'Glyma.20G150600' => 'gma', 'Gohir.A09G219200' => 'ghi', 'Gohir.A09G219300' => 'ghi', 'Gohir.D09G221400' => 'ghi', 'Gohir.D09G221500' => 'ghi', 'Gorai.006G242600' => 'gra', 'Gorai.006G242700' => 'gra', 'GSVIVG01018044001' => 'vvi', 'HanXRQChr03g0083821' => 'han', 'HanXRQChr03g0083841' => 'han', 'HanXRQChr03g0083881' => 'han', 'HanXRQChr03g0083901' => 'han', 'HanXRQChr03g0083921' => 'han', 'HanXRQChr03g0085331' => 'han', 'HanXRQChr03g0085361' => 'han', 'HanXRQChr03g0085411' => 'han', 'HanXRQChr03g0085421' => 'han', 'HanXRQChr03g0085431' => 'han', 'HanXRQChr08g0221991' => 'han', 'HanXRQChr11g0336061' => 'han', 'HanXRQChr11g0336411' => 'han', 'Haze_11234' => 'cav', 'Hma1.2p1_0549F.1_g177010' => 'hma', 'Hma1.2p1_0602F.1_g187630' => 'hma', 'Hund14876' => 'sun', 'Hund14879' => 'sun', 'Lalb_Chr06g0160741' => 'lal', 'Lalb_Chr21g0304781' => 'lal', 'Lj3A726G19' => 'lonja', 'Lj3A726T23' => 'lonja', 'Lj3A726T24' => 'lonja', 'Lj3A726T25' => 'lonja', 'Lj3A727T17' => 'lonja', 'Lj3C726T0' => 'lonja', 'Lj3C726T2' => 'lonja', 'Lj3P725T35' => 'lonja', 'Lj3P727T10' => 'lonja', 'Lj3P727T12' => 'lonja', 'Lj3P727T14' => 'lonja', 'Lj5g0023109' => 'lja', 'Lj6P646T44' => 'lonja', 'Lsat_1_v5_gn_6_75760' => 'lsa', 'Lsat_1_v5_gn_6_75800' => 'lsa', 'Lsat_1_v5_gn_6_75900' => 'lsa', 'Lsat_1_v5_gn_6_76240' => 'lsa', 'Lsat_1_v5_gn_6_76441' => 'lsa', 'Lsat_1_v5_gn_6_76700' => 'lsa', 'Lsat_1_v5_gn_6_76760' => 'lsa', 'Manes.15G033100' => 'mes', 'Mapoly0004s0074' => 'mpo', 'Mapoly0004s0075' => 'mpo', 'Mapoly0004s0163' => 'mpo', 'Mapoly0004s0164' => 'mpo', 'Mapoly0021s0018' => 'mpo', 'Mapoly0041s0136' => 'mpo', 'Mapoly0041s0137' => 'mpo', 'Mapoly0041s0138' => 'mpo', 'Mapoly0041s0139' => 'mpo', 'Mapoly0041s0141' => 'mpo', 'Mapoly0041s0142' => 'mpo', 'Mapoly0041s0143' => 'mpo', 'Mapoly0041s0144' => 'mpo', 'Mapoly0041s0145' => 'mpo', 'Mapoly0047s0106' => 'mpo', 'Mapoly0047s0108' => 'mpo', 'Mapoly0050s0051' => 'mpo', 'Mapoly0050s0052' => 'mpo', 'Mapoly0050s0053' => 'mpo', 'Mapoly0058s0013' => 'mpo', 'Mapoly0091s0078' => 'mpo', 'Mapoly0091s0079' => 'mpo', 'Mapoly0091s0080' => 'mpo', 'Mapoly0091s0081' => 'mpo', 'Mapoly0278s0004' => 'mpo', 'Mapoly0278s0005' => 'mpo', 'Mapoly0278s0006' => 'mpo', 'MBI11_g30648_MAGBIO' => 'mbi', 'MCO03G194' => 'mco', 'MCO03G590' => 'mco', 'MCO07G312' => 'mco', 'MCO10G318' => 'mco', 'MCO12G244' => 'mco', 'MCO13G148' => 'mco', 'MCO13G194' => 'mco', 'MCO16G238' => 'mco', 'MD06G1134100' => 'mdo', 'MD13G1200100' => 'mdo', 'MD13G1200300' => 'mdo', 'MD13G1200600' => 'mdo', 'MD14G1150400' => 'mdo', 'MD16G1200000' => 'mdo', 'Medtr1g102570' => 'mtr', 'Medtr1g102780' => 'mtr', 'Medtr1g102800' => 'mtr', 'Medtr1g102810' => 'mtr', 'Medtr1g102830' => 'mtr', 'MELO3C006499.2' => 'cme', 'Migut.G00385' => 'egut', 'MSTRG.4063' => 'ama', 'Nitab4.5_0000090g0260' => 'nta', 'Nitab4.5_0000977g0030' => 'nta', 'Nitab4.5_0002541g0040' => 'nta', 'Nitab4.5_0007068g0040' => 'nta', 'Nn005s41408' => 'nnu', 'Nn005s41410' => 'nnu', 'Oeu010310.1' => 'oeu', 'Oeu010311.1' => 'oeu', 'Oeu043472.1' => 'oeu', 'Os01g0246400' => 'osa', 'Os04g0267950' => 'osa', 'Os07g0178700' => 'osa', 'Os07g0178800' => 'osa', 'Peaxi162Scf00316g00046' => 'pax', 'Peaxi162Scf00316g00049' => 'pax', 'Peaxi162Scf00316g00059' => 'pax', 'Peaxi162Scf00316g00328' => 'pax', 'Peaxi162Scf00316g00329' => 'pax', 'Peaxi162Scf00316g00411' => 'pax', 'Peaxi162Scf00316g00521' => 'pax', 'Peaxi162Scf00492g00068' => 'pax', 'Peaxi162Scf35631g00002' => 'pax', 'PGR142G3720' => 'pgr', 'PGSC0003DMG400006442' => 'stu', 'Phvul.007G062000' => 'pvu', 'Potri.008G157750' => 'ptr', 'Potri.008G157900' => 'ptr', 'Potri.008G158000' => 'ptr', 'Potri.008G158200' => 'ptr', 'Pp3c11_7280' => 'ppa', 'Pp3c11_7980' => 'ppa', 'Pp3c12_19450' => 'ppa', 'Pp3c14_1480' => 'ppa', 'Pp3c14_1501' => 'ppa', 'Pp3c16_4900' => 'ppa', 'Pp3c16_5010' => 'ppa', 'Pp3c16_5060' => 'ppa', 'Pp3c19_18250' => 'ppa', 'Pp3c23_8530' => 'ppa', 'Pp3c23_8550' => 'ppa', 'Pp3c24_9670' => 'ppa', 'Pp3c2_21390' => 'ppa', 'Pp3c2_31380' => 'ppa', 'Pp3c3_16620' => 'ppa', 'Pp3c3_8090' => 'ppa', 'Pp3c3_8110' => 'ppa', 'Pp3c3_8130' => 'ppa', 'Pp3c3_8150' => 'ppa', 'Pp3c4_14320' => 'ppa', 'Pp3c6_2560' => 'ppa', 'Pp3c9_16700' => 'ppa', 'PRCOL_00000234' => 'pco', 'PRCOL_00000235' => 'pco', 'PRCOL_00000777' => 'pco', 'PRCOL_00002344' => 'pco', 'PRCOL_00002372' => 'pco', 'PRCOL_00006120' => 'pco', 'Prupe.1G021400' => 'ppe', 'Prupe.1G021500' => 'ppe', 'Prupe.1G021600' => 'ppe', 'Prupe.1G021700' => 'ppe', 'Prupe.1G021800' => 'ppe', 'Prupe.5G145100' => 'ppe', 'Psat6g204040' => 'psa', 'Psat6g204800' => 'psa', 'Psat6g204920' => 'psa', 'Psat6g204960' => 'psa', 'Psat6g205080' => 'psa', 'PSO017G0271' => 'pso', 'PSO017G1276' => 'pso', 'PSO017G1429' => 'pso', 'PSO017G1861' => 'pso', 'PSO017G2787' => 'pso', 'PSO017G4466' => 'pso', 'PSO017G5118' => 'pso', 'PSO017G5420' => 'pso', 'PSO063G3678' => 'pso', 'PSO210G0546' => 'pso', 'PSO317G0001' => 'pso', 'PSO357G0512' => 'pso', 'PSO478G2682' => 'pso', 'PSO647G0001' => 'pso', 'PSO675G0001' => 'pso', 'PSO675G2699' => 'pso', 'PSO675G2849' => 'pso', 'PSO675G4991' => 'pso', 'PSO689G0001' => 'pso', 'QL06p000916' => 'qlo', 'QL06p000921' => 'qlo', 'QL06p001398' => 'qlo', 'QL06p001407' => 'qlo', 'QL06p002031' => 'qlo', 'RcHm_v2.0_Chr4g0387791' => 'rch', 'RcHm_v2.0_Chr4g0387801' => 'rch', 'RcHm_v2.0_Chr6g0286501' => 'rch', 'RcHm_v2.0_Chr6g0286511' => 'rch', 'RcHm_v2.0_Chr6g0286521' => 'rch', 'RcHm_v2.0_Chr6g0286531' => 'rch', 'RcHm_v2.0_Chr7g0189141' => 'rch', 'Rhsim02G0028700' => 'rsi', 'Rhsim02G0028800' => 'rsi', 'Rhsim02G0028900' => 'rsi', 'Rhsim02G0029000' => 'rsi', 'Rhsim02G0029100' => 'rsi', 'Rhsim02G0029200' => 'rsi', 'Rhsim02G0029300' => 'rsi', 'Rhsim02G0029400' => 'rsi', 'Rhsim02G0029500' => 'rsi', 'Rhsim02G0029600' => 'rsi', 'RhsimUnG0024000' => 'rsi', 'RhsimUnG0024100' => 'rsi', 'RhsimUnG0024200' => 'rsi', 'RhsimUnG0024300' => 'rsi', 'RhsimUnG0024400' => 'rsi', 'RhsimUnG0024500' => 'rsi', 'RhsimUnG0024700' => 'rsi', 'RhsimUnG0024800' => 'rsi', 'RhsimUnG0024900' => 'rsi', 'RhsimUnG0025100' => 'rsi', 'Sabra08G0120200' => 'sbr', 'Sabra08G0120300' => 'sbr', 'Sabra08G0120500' => 'sbr', 'Sabra08G0120600' => 'sbr', 'Sabra10G0158900' => 'sbr', 'SalBow2G3492' => 'sbo', 'Sc13g0004760' => 'sci', 'Sc13g0004770' => 'sci', 'Sed0003417' => 'sed', 'Sed0019750' => 'sed', 'SEGI_03419' => 'sgi', 'SEGI_05907' => 'sgi', 'SEGI_10682' => 'sgi', 'SEGI_13528' => 'sgi', 'SEGI_16081' => 'sgi', 'SEGI_19370' => 'sgi', 'SEGI_21015' => 'sgi', 'SEGI_21944' => 'sgi', 'SEGI_32906' => 'sgi', 'SEGI_33093' => 'sgi', 'SEGI_36110' => 'sgi', 'SEGI_40397' => 'sgi', 'SGA_v2.0_scaffold191G40426' => 'sas', 'SGA_v2.0_scaffold353G49717' => 'sas', 'SGA_v2.0_scaffold50G18550' => 'sas', 'SMO119G0173' => 'smo', 'SMO172G0002' => 'smo', 'Solyc09g082690.3' => 'sly', 'Solyc09g082700.2' => 'sly', 'Sopen09g031550' => 'spe', 'Sopen09g031560' => 'spe', 'Sp3g20540' => 'spa', 'Sp7g07580' => 'spa', 'TAR134G0002' => 'tar', 'TAR236G0001' => 'tar', 'TAR365G0892' => 'tar', 'TAR636G0166' => 'tar', 'TAR636G0646' => 'tar', 'TAR636G0869' => 'tar', 'TAR636G1317' => 'tar', 'TAR636G1744' => 'tar', 'TAR636G3358' => 'tar', 'TAR636G3436' => 'tar', 'THA.LOC104803047' => 'tha', 'Thecc.04G238900' => 'tca', 'Thhalv10021557m.g' => 'esa', 'Thhalv10026318m.g' => 'esa', 'Thhalv10026335m.g' => 'esa', 'TPR.G17433' => 'tpr', 'TPR.G18915' => 'tpr', 'TPR.G26125' => 'tpr', 'TWI09G0677' => 'twi', 'TWI73G0287' => 'twi', 'unitig_748.g8326' => 'ugi', 'vmacro15370' => 'vma', 'vmacro15371' => 'vma', 'vmacro15372' => 'vma', 'vmacro15373' => 'vma', 'vmacro15374' => 'vma', 'VMungo0720G2826' => 'vmu', 'Zm00001eb116960' => 'zma', 'Zm00001eb301260' => 'zma', 'Zm00001eb301270' => 'zma' ) $gf_id = 'HOM05D001460' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001460' ) $data_identifier = 'HOM05D001460' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 4, 'aag' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 2, 'aox' => (int) 2, 'arhy' => (int) 4, 'ath' => (int) 2, 'atr' => (int) 1, 'acertr' => (int) 10, 'cqu' => (int) 4, 'bca' => (int) 11, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 1, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 1, 'ccan' => (int) 1, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 1, 'col' => (int) 1, 'cpa' => (int) 1, 'cre' => (int) 7, 'csa' => (int) 1, 'camsi' => (int) 2, 'dca' => (int) 3, 'din' => (int) 2, 'dzi' => (int) 3, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 14, 'fve' => (int) 9, 'gma' => (int) 2, 'ghi' => (int) 4, 'gra' => (int) 2, 'vvi' => (int) 1, 'han' => (int) 13, 'cav' => (int) 1, 'hma' => (int) 2, 'sun' => (int) 2, 'lal' => (int) 2, 'lonja' => (int) 12, 'lja' => (int) 1, 'lsa' => (int) 7, 'mes' => (int) 1, 'mpo' => (int) 27, 'mbi' => (int) 1, 'mco' => (int) 8, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 1, 'egut' => (int) 1, 'ama' => (int) 1, 'nta' => (int) 4, 'nnu' => (int) 2, 'oeu' => (int) 3, 'osa' => (int) 4, 'pax' => (int) 9, 'pgr' => (int) 1, 'stu' => (int) 1, 'pvu' => (int) 1, 'ptr' => (int) 4, 'ppa' => (int) 22, 'pco' => (int) 6, 'ppe' => (int) 6, 'psa' => (int) 5, 'pso' => (int) 19, 'qlo' => (int) 5, 'rch' => (int) 7, 'rsi' => (int) 20, 'sbr' => (int) 5, 'sbo' => (int) 1, 'sci' => (int) 2, 'sed' => (int) 2, 'sgi' => (int) 12, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 2, 'tar' => (int) 10, 'tha' => (int) 1, 'tca' => (int) 1, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 2, 'ugi' => (int) 1, 'vma' => (int) 5, 'vmu' => (int) 1, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb301270' $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' => 'HOM05D001460', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '433', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p22980' => 'bna', 'A01p32340' => 'bna', 'A03p42970' => 'bna', 'A05p25880' => 'bna', 'Aa31LG8G9320' => 'aar', 'Aa31LG8G9330' => 'aar', 'Aa31LG8G9340' => 'aar', 'Aa31sc221G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1034' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1528' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.829' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2222' => 'aag', 'Ah.12g058830' => 'amhyb', 'Ah.12g058840' => 'amhyb', 'AL3G37160' => 'aly', 'AL7G41310' => 'aly', 'Aqoxy5G00395' => 'aox', 'Aqoxy5G00396' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0C8NZA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5185HY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JZ1PRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MD3LS0' => 'arhy', 'AT3G22840' => 'ath', 'AT4G14690' => 'ath', 'ATR0665G054' => 'atr', 'Atru.chr4.2344' => 'acertr', 'Atru.chr4.2346' => 'acertr', 'Atru.chr4.2347' => 'acertr', 'Atru.chr4.2348' => 'acertr', 'Atru.chr4.2355' => 'acertr', 'Atru.chr4.2356' => 'acertr', 'Atru.chr4.2358' => 'acertr', 'Atru.chr4.2359' => 'acertr', 'Atru.chr4.2360' => 'acertr', 'Atru.chr4.2361' => 'acertr', 'AUR62030476' => 'cqu', 'AUR62030478' => 'cqu', 'AUR62030819' => 'cqu', 'AUR62030820' => 'cqu', 'BcaB03g14648' => 'bca', 'BcaB04g20492' => 'bca', 'BcaB06g26399' => 'bca', 'BcaC01g03416' => 'bca', 'BcaC01g03419' => 'bca', 'BcaC01g03421' => 'bca', 'BcaC01g03424' => 'bca', 'BcaC05g28012' => 'bca', 'BcaC09g49212' => 'bca', 'BcaC09g50140' => 'bca', 'BcaNung00346' => 'bca', 'BolC1t02785H' => 'bol', 'BolC1t04095H' => 'bol', 'BolC3t17545H' => 'bol', 'BolC5t32769H' => 'bol', 'BraA01t02211Z' => 'bra', 'BraA01t03359Z' => 'bra', 'BraA03t13441Z' => 'bra', 'BraA05t21476Z' => 'bra', 'C01p28420' => 'bna', 'C01p41350' => 'bna', 'C03p52750' => 'bna', 'C03p52780' => 'bna', 'C05p40270' => 'bna', 'CAN.G1437.9' => 'can', 'CANSAT78G0035' => 'cansat', 'CANSAT78G1036' => 'cansat', 'CANSAT78G2272' => 'cansat', 'CANSAT78G2478' => 'cansat', 'CARHR098700' => 'chi', 'CARHR221120' => 'chi', 'CARHR221150' => 'chi', 'Carub.0003s2297' => 'cru', 'Carub.0007s2749' => 'cru', 'Carub.0007s2750' => 'cru', 'Carub.0007s2751' => 'cru', 'Ca_10849_v3' => 'car', 'Cc03_g04300' => 'ccan', 'CDE02G3648' => 'cde', 'CDE05G0060' => 'cde', 'CDE05G0692' => 'cde', 'CDE05G2285' => 'cde', 'CDE05G2884' => 'cde', 'CDE05G3072' => 'cde', 'Cfa008439' => 'cfa', 'Cfa008441' => 'cfa', 'Cfa008443' => 'cfa', 'Cfa008448' => 'cfa', 'Ciclev10005974m.g' => 'ccl', 'Ciclev10006006m.g' => 'ccl', 'Ciclev10006775m.g' => 'ccl', 'CiPaw.02G120400' => 'cil', 'CiPaw.02G120500' => 'cil', 'CiPaw.02G120600' => 'cil', 'ClCG05G004850' => 'cla', 'COL.COLO4_21566' => 'col', 'Cpa.g.sc44.124' => 'cpa', 'Cre07.g320400' => 'cre', 'Cre07.g320450' => 'cre', 'Cre08.g384650' => 'cre', 'Cre09.g393173' => 'cre', 'Cre09.g394325' => 'cre', 'Cre14.g626750' => 'cre', 'Cre16.g679250' => 'cre', 'CsaV3_3G012890' => 'csa', 'CSS0010865' => 'camsi', 'CSS0044338' => 'camsi', 'DCAR_002366' => 'dca', 'DCAR_030687' => 'dca', 'DCAR_030688' => 'dca', 'Dinv14047' => 'din', 'Dinv14048' => 'din', 'Duzib151G0105' => 'dzi', 'Duzib151G0114' => 'dzi', 'Duzib212G1029' => 'dzi', 'ECA232G3536' => 'eca', 'ECA240G0786' => 'eca', 'ECA240G1802' => 'eca', 'ECA240G3760' => 'eca', 'ECA240G3920' => 'eca', 'EL10Ac5g12536' => 'bvu', 'EL10Ac5g12537' => 'bvu', 'EL10Ac5g12538' => 'bvu', 'Eucgr.B01004' => 'egr', 'Eucgr.B01006' => 'egr', 'Eucgr.B01007' => 'egr', 'Eucgr.B01008' => 'egr', 'Eucgr.B01895' => 'egr', 'Eucgr.B01896' => 'egr', 'FAN04G1456' => 'fan', 'FAN08G1769' => 'fan', 'FAN08G2160' => 'fan', 'FAN13G2403' => 'fan', 'FAN13G3303' => 'fan', 'FAN15G2435' => 'fan', 'FAN17G0672' => 'fan', 'FAN17G2441' => 'fan', 'FAN18G1024' => 'fan', 'FAN22G1458' => 'fan', 'FAN24G0037' => 'fan', 'FAN24G0429' => 'fan', 'FAN24G2387' => 'fan', 'FAN27G2746' => 'fan', 'FvH4_2g20400' => 'fve', 'FvH4_2g20420' => 'fve', 'FvH4_2g20430' => 'fve', 'FvH4_4g01270' => 'fve', 'FvH4_4g01290' => 'fve', 'FvH4_4g01300' => 'fve', 'FvH4_4g01310' => 'fve', 'FvH4_4g01330' => 'fve', 'FvH4_5g09070' => 'fve', 'Glyma.10G243800' => 'gma', 'Glyma.20G150600' => 'gma', 'Gohir.A09G219200' => 'ghi', 'Gohir.A09G219300' => 'ghi', 'Gohir.D09G221400' => 'ghi', 'Gohir.D09G221500' => 'ghi', 'Gorai.006G242600' => 'gra', 'Gorai.006G242700' => 'gra', 'GSVIVG01018044001' => 'vvi', 'HanXRQChr03g0083821' => 'han', 'HanXRQChr03g0083841' => 'han', 'HanXRQChr03g0083881' => 'han', 'HanXRQChr03g0083901' => 'han', 'HanXRQChr03g0083921' => 'han', 'HanXRQChr03g0085331' => 'han', 'HanXRQChr03g0085361' => 'han', 'HanXRQChr03g0085411' => 'han', 'HanXRQChr03g0085421' => 'han', 'HanXRQChr03g0085431' => 'han', 'HanXRQChr08g0221991' => 'han', 'HanXRQChr11g0336061' => 'han', 'HanXRQChr11g0336411' => 'han', 'Haze_11234' => 'cav', 'Hma1.2p1_0549F.1_g177010' => 'hma', 'Hma1.2p1_0602F.1_g187630' => 'hma', 'Hund14876' => 'sun', 'Hund14879' => 'sun', 'Lalb_Chr06g0160741' => 'lal', 'Lalb_Chr21g0304781' => 'lal', 'Lj3A726G19' => 'lonja', 'Lj3A726T23' => 'lonja', 'Lj3A726T24' => 'lonja', 'Lj3A726T25' => 'lonja', 'Lj3A727T17' => 'lonja', 'Lj3C726T0' => 'lonja', 'Lj3C726T2' => 'lonja', 'Lj3P725T35' => 'lonja', 'Lj3P727T10' => 'lonja', 'Lj3P727T12' => 'lonja', 'Lj3P727T14' => 'lonja', 'Lj5g0023109' => 'lja', 'Lj6P646T44' => 'lonja', 'Lsat_1_v5_gn_6_75760' => 'lsa', 'Lsat_1_v5_gn_6_75800' => 'lsa', 'Lsat_1_v5_gn_6_75900' => 'lsa', 'Lsat_1_v5_gn_6_76240' => 'lsa', 'Lsat_1_v5_gn_6_76441' => 'lsa', 'Lsat_1_v5_gn_6_76700' => 'lsa', 'Lsat_1_v5_gn_6_76760' => 'lsa', 'Manes.15G033100' => 'mes', 'Mapoly0004s0074' => 'mpo', 'Mapoly0004s0075' => 'mpo', 'Mapoly0004s0163' => 'mpo', 'Mapoly0004s0164' => 'mpo', 'Mapoly0021s0018' => 'mpo', 'Mapoly0041s0136' => 'mpo', 'Mapoly0041s0137' => 'mpo', 'Mapoly0041s0138' => 'mpo', 'Mapoly0041s0139' => 'mpo', 'Mapoly0041s0141' => 'mpo', 'Mapoly0041s0142' => 'mpo', 'Mapoly0041s0143' => 'mpo', 'Mapoly0041s0144' => 'mpo', 'Mapoly0041s0145' => 'mpo', 'Mapoly0047s0106' => 'mpo', 'Mapoly0047s0108' => 'mpo', 'Mapoly0050s0051' => 'mpo', 'Mapoly0050s0052' => 'mpo', 'Mapoly0050s0053' => 'mpo', 'Mapoly0058s0013' => 'mpo', 'Mapoly0091s0078' => 'mpo', 'Mapoly0091s0079' => 'mpo', 'Mapoly0091s0080' => 'mpo', 'Mapoly0091s0081' => 'mpo', 'Mapoly0278s0004' => 'mpo', 'Mapoly0278s0005' => 'mpo', 'Mapoly0278s0006' => 'mpo', 'MBI11_g30648_MAGBIO' => 'mbi', 'MCO03G194' => 'mco', 'MCO03G590' => 'mco', 'MCO07G312' => 'mco', 'MCO10G318' => 'mco', 'MCO12G244' => 'mco', 'MCO13G148' => 'mco', 'MCO13G194' => 'mco', 'MCO16G238' => 'mco', 'MD06G1134100' => 'mdo', 'MD13G1200100' => 'mdo', 'MD13G1200300' => 'mdo', 'MD13G1200600' => 'mdo', 'MD14G1150400' => 'mdo', 'MD16G1200000' => 'mdo', 'Medtr1g102570' => 'mtr', 'Medtr1g102780' => 'mtr', 'Medtr1g102800' => 'mtr', 'Medtr1g102810' => 'mtr', 'Medtr1g102830' => 'mtr', 'MELO3C006499.2' => 'cme', 'Migut.G00385' => 'egut', 'MSTRG.4063' => 'ama', 'Nitab4.5_0000090g0260' => 'nta', 'Nitab4.5_0000977g0030' => 'nta', 'Nitab4.5_0002541g0040' => 'nta', 'Nitab4.5_0007068g0040' => 'nta', 'Nn005s41408' => 'nnu', 'Nn005s41410' => 'nnu', 'Oeu010310.1' => 'oeu', 'Oeu010311.1' => 'oeu', 'Oeu043472.1' => 'oeu', 'Os01g0246400' => 'osa', 'Os04g0267950' => 'osa', 'Os07g0178700' => 'osa', 'Os07g0178800' => 'osa', 'Peaxi162Scf00316g00046' => 'pax', 'Peaxi162Scf00316g00049' => 'pax', 'Peaxi162Scf00316g00059' => 'pax', 'Peaxi162Scf00316g00328' => 'pax', 'Peaxi162Scf00316g00329' => 'pax', 'Peaxi162Scf00316g00411' => 'pax', 'Peaxi162Scf00316g00521' => 'pax', 'Peaxi162Scf00492g00068' => 'pax', 'Peaxi162Scf35631g00002' => 'pax', 'PGR142G3720' => 'pgr', 'PGSC0003DMG400006442' => 'stu', 'Phvul.007G062000' => 'pvu', 'Potri.008G157750' => 'ptr', 'Potri.008G157900' => 'ptr', 'Potri.008G158000' => 'ptr', 'Potri.008G158200' => 'ptr', 'Pp3c11_7280' => 'ppa', 'Pp3c11_7980' => 'ppa', 'Pp3c12_19450' => 'ppa', 'Pp3c14_1480' => 'ppa', 'Pp3c14_1501' => 'ppa', 'Pp3c16_4900' => 'ppa', 'Pp3c16_5010' => 'ppa', 'Pp3c16_5060' => 'ppa', 'Pp3c19_18250' => 'ppa', 'Pp3c23_8530' => 'ppa', 'Pp3c23_8550' => 'ppa', 'Pp3c24_9670' => 'ppa', 'Pp3c2_21390' => 'ppa', 'Pp3c2_31380' => 'ppa', 'Pp3c3_16620' => 'ppa', 'Pp3c3_8090' => 'ppa', 'Pp3c3_8110' => 'ppa', 'Pp3c3_8130' => 'ppa', 'Pp3c3_8150' => 'ppa', 'Pp3c4_14320' => 'ppa', 'Pp3c6_2560' => 'ppa', 'Pp3c9_16700' => 'ppa', 'PRCOL_00000234' => 'pco', 'PRCOL_00000235' => 'pco', 'PRCOL_00000777' => 'pco', 'PRCOL_00002344' => 'pco', 'PRCOL_00002372' => 'pco', 'PRCOL_00006120' => 'pco', 'Prupe.1G021400' => 'ppe', 'Prupe.1G021500' => 'ppe', 'Prupe.1G021600' => 'ppe', 'Prupe.1G021700' => 'ppe', 'Prupe.1G021800' => 'ppe', 'Prupe.5G145100' => 'ppe', 'Psat6g204040' => 'psa', 'Psat6g204800' => 'psa', 'Psat6g204920' => 'psa', 'Psat6g204960' => 'psa', 'Psat6g205080' => 'psa', 'PSO017G0271' => 'pso', 'PSO017G1276' => 'pso', 'PSO017G1429' => 'pso', 'PSO017G1861' => 'pso', 'PSO017G2787' => 'pso', 'PSO017G4466' => 'pso', 'PSO017G5118' => 'pso', 'PSO017G5420' => 'pso', 'PSO063G3678' => 'pso', 'PSO210G0546' => 'pso', 'PSO317G0001' => 'pso', 'PSO357G0512' => 'pso', 'PSO478G2682' => 'pso', 'PSO647G0001' => 'pso', 'PSO675G0001' => 'pso', 'PSO675G2699' => 'pso', 'PSO675G2849' => 'pso', 'PSO675G4991' => 'pso', 'PSO689G0001' => 'pso', 'QL06p000916' => 'qlo', 'QL06p000921' => 'qlo', 'QL06p001398' => 'qlo', 'QL06p001407' => 'qlo', 'QL06p002031' => 'qlo', 'RcHm_v2.0_Chr4g0387791' => 'rch', 'RcHm_v2.0_Chr4g0387801' => 'rch', 'RcHm_v2.0_Chr6g0286501' => 'rch', 'RcHm_v2.0_Chr6g0286511' => 'rch', 'RcHm_v2.0_Chr6g0286521' => 'rch', 'RcHm_v2.0_Chr6g0286531' => 'rch', 'RcHm_v2.0_Chr7g0189141' => 'rch', 'Rhsim02G0028700' => 'rsi', 'Rhsim02G0028800' => 'rsi', 'Rhsim02G0028900' => 'rsi', 'Rhsim02G0029000' => 'rsi', 'Rhsim02G0029100' => 'rsi', 'Rhsim02G0029200' => 'rsi', 'Rhsim02G0029300' => 'rsi', 'Rhsim02G0029400' => 'rsi', 'Rhsim02G0029500' => 'rsi', 'Rhsim02G0029600' => 'rsi', 'RhsimUnG0024000' => 'rsi', 'RhsimUnG0024100' => 'rsi', 'RhsimUnG0024200' => 'rsi', 'RhsimUnG0024300' => 'rsi', 'RhsimUnG0024400' => 'rsi', 'RhsimUnG0024500' => 'rsi', 'RhsimUnG0024700' => 'rsi', 'RhsimUnG0024800' => 'rsi', 'RhsimUnG0024900' => 'rsi', 'RhsimUnG0025100' => 'rsi', 'Sabra08G0120200' => 'sbr', 'Sabra08G0120300' => 'sbr', 'Sabra08G0120500' => 'sbr', 'Sabra08G0120600' => 'sbr', 'Sabra10G0158900' => 'sbr', 'SalBow2G3492' => 'sbo', 'Sc13g0004760' => 'sci', 'Sc13g0004770' => 'sci', 'Sed0003417' => 'sed', 'Sed0019750' => 'sed', 'SEGI_03419' => 'sgi', 'SEGI_05907' => 'sgi', 'SEGI_10682' => 'sgi', 'SEGI_13528' => 'sgi', 'SEGI_16081' => 'sgi', 'SEGI_19370' => 'sgi', 'SEGI_21015' => 'sgi', 'SEGI_21944' => 'sgi', 'SEGI_32906' => 'sgi', 'SEGI_33093' => 'sgi', 'SEGI_36110' => 'sgi', 'SEGI_40397' => 'sgi', 'SGA_v2.0_scaffold191G40426' => 'sas', 'SGA_v2.0_scaffold353G49717' => 'sas', 'SGA_v2.0_scaffold50G18550' => 'sas', 'SMO119G0173' => 'smo', 'SMO172G0002' => 'smo', 'Solyc09g082690.3' => 'sly', 'Solyc09g082700.2' => 'sly', 'Sopen09g031550' => 'spe', 'Sopen09g031560' => 'spe', 'Sp3g20540' => 'spa', 'Sp7g07580' => 'spa', 'TAR134G0002' => 'tar', 'TAR236G0001' => 'tar', 'TAR365G0892' => 'tar', 'TAR636G0166' => 'tar', 'TAR636G0646' => 'tar', 'TAR636G0869' => 'tar', 'TAR636G1317' => 'tar', 'TAR636G1744' => 'tar', 'TAR636G3358' => 'tar', 'TAR636G3436' => 'tar', 'THA.LOC104803047' => 'tha', 'Thecc.04G238900' => 'tca', 'Thhalv10021557m.g' => 'esa', 'Thhalv10026318m.g' => 'esa', 'Thhalv10026335m.g' => 'esa', 'TPR.G17433' => 'tpr', 'TPR.G18915' => 'tpr', 'TPR.G26125' => 'tpr', 'TWI09G0677' => 'twi', 'TWI73G0287' => 'twi', 'unitig_748.g8326' => 'ugi', 'vmacro15370' => 'vma', 'vmacro15371' => 'vma', 'vmacro15372' => 'vma', 'vmacro15373' => 'vma', 'vmacro15374' => 'vma', 'VMungo0720G2826' => 'vmu', 'Zm00001eb116960' => 'zma', 'Zm00001eb301260' => 'zma', 'Zm00001eb301270' => 'zma' ), 'gf_id' => 'HOM05D001460', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001460' ), 'data_identifier' => 'HOM05D001460', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001460', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '433', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p22980' => 'bna', 'A01p32340' => 'bna', 'A03p42970' => 'bna', 'A05p25880' => 'bna', 'Aa31LG8G9320' => 'aar', 'Aa31LG8G9330' => 'aar', 'Aa31LG8G9340' => 'aar', 'Aa31sc221G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1034' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1528' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.829' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2222' => 'aag', 'Ah.12g058830' => 'amhyb', 'Ah.12g058840' => 'amhyb', 'AL3G37160' => 'aly', 'AL7G41310' => 'aly', 'Aqoxy5G00395' => 'aox', 'Aqoxy5G00396' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0C8NZA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5185HY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JZ1PRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MD3LS0' => 'arhy', 'AT3G22840' => 'ath', 'AT4G14690' => 'ath', 'ATR0665G054' => 'atr', 'Atru.chr4.2344' => 'acertr', 'Atru.chr4.2346' => 'acertr', 'Atru.chr4.2347' => 'acertr', 'Atru.chr4.2348' => 'acertr', 'Atru.chr4.2355' => 'acertr', 'Atru.chr4.2356' => 'acertr', 'Atru.chr4.2358' => 'acertr', 'Atru.chr4.2359' => 'acertr', 'Atru.chr4.2360' => 'acertr', 'Atru.chr4.2361' => 'acertr', 'AUR62030476' => 'cqu', 'AUR62030478' => 'cqu', 'AUR62030819' => 'cqu', 'AUR62030820' => 'cqu', 'BcaB03g14648' => 'bca', 'BcaB04g20492' => 'bca', 'BcaB06g26399' => 'bca', 'BcaC01g03416' => 'bca', 'BcaC01g03419' => 'bca', 'BcaC01g03421' => 'bca', 'BcaC01g03424' => 'bca', 'BcaC05g28012' => 'bca', 'BcaC09g49212' => 'bca', 'BcaC09g50140' => 'bca', 'BcaNung00346' => 'bca', 'BolC1t02785H' => 'bol', 'BolC1t04095H' => 'bol', 'BolC3t17545H' => 'bol', 'BolC5t32769H' => 'bol', 'BraA01t02211Z' => 'bra', 'BraA01t03359Z' => 'bra', 'BraA03t13441Z' => 'bra', 'BraA05t21476Z' => 'bra', 'C01p28420' => 'bna', 'C01p41350' => 'bna', 'C03p52750' => 'bna', 'C03p52780' => 'bna', 'C05p40270' => 'bna', 'CAN.G1437.9' => 'can', 'CANSAT78G0035' => 'cansat', 'CANSAT78G1036' => 'cansat', 'CANSAT78G2272' => 'cansat', 'CANSAT78G2478' => 'cansat', 'CARHR098700' => 'chi', 'CARHR221120' => 'chi', 'CARHR221150' => 'chi', 'Carub.0003s2297' => 'cru', 'Carub.0007s2749' => 'cru', 'Carub.0007s2750' => 'cru', 'Carub.0007s2751' => 'cru', 'Ca_10849_v3' => 'car', 'Cc03_g04300' => 'ccan', 'CDE02G3648' => 'cde', 'CDE05G0060' => 'cde', 'CDE05G0692' => 'cde', 'CDE05G2285' => 'cde', 'CDE05G2884' => 'cde', 'CDE05G3072' => 'cde', 'Cfa008439' => 'cfa', 'Cfa008441' => 'cfa', 'Cfa008443' => 'cfa', 'Cfa008448' => 'cfa', 'Ciclev10005974m.g' => 'ccl', 'Ciclev10006006m.g' => 'ccl', 'Ciclev10006775m.g' => 'ccl', 'CiPaw.02G120400' => 'cil', 'CiPaw.02G120500' => 'cil', 'CiPaw.02G120600' => 'cil', 'ClCG05G004850' => 'cla', 'COL.COLO4_21566' => 'col', 'Cpa.g.sc44.124' => 'cpa', 'Cre07.g320400' => 'cre', 'Cre07.g320450' => 'cre', 'Cre08.g384650' => 'cre', 'Cre09.g393173' => 'cre', 'Cre09.g394325' => 'cre', 'Cre14.g626750' => 'cre', 'Cre16.g679250' => 'cre', 'CsaV3_3G012890' => 'csa', 'CSS0010865' => 'camsi', 'CSS0044338' => 'camsi', 'DCAR_002366' => 'dca', 'DCAR_030687' => 'dca', 'DCAR_030688' => 'dca', 'Dinv14047' => 'din', 'Dinv14048' => 'din', 'Duzib151G0105' => 'dzi', 'Duzib151G0114' => 'dzi', 'Duzib212G1029' => 'dzi', 'ECA232G3536' => 'eca', 'ECA240G0786' => 'eca', 'ECA240G1802' => 'eca', 'ECA240G3760' => 'eca', 'ECA240G3920' => 'eca', 'EL10Ac5g12536' => 'bvu', 'EL10Ac5g12537' => 'bvu', 'EL10Ac5g12538' => 'bvu', 'Eucgr.B01004' => 'egr', 'Eucgr.B01006' => 'egr', 'Eucgr.B01007' => 'egr', 'Eucgr.B01008' => 'egr', 'Eucgr.B01895' => 'egr', 'Eucgr.B01896' => 'egr', 'FAN04G1456' => 'fan', 'FAN08G1769' => 'fan', 'FAN08G2160' => 'fan', 'FAN13G2403' => 'fan', 'FAN13G3303' => 'fan', 'FAN15G2435' => 'fan', 'FAN17G0672' => 'fan', 'FAN17G2441' => 'fan', 'FAN18G1024' => 'fan', 'FAN22G1458' => 'fan', 'FAN24G0037' => 'fan', 'FAN24G0429' => 'fan', 'FAN24G2387' => 'fan', 'FAN27G2746' => 'fan', 'FvH4_2g20400' => 'fve', 'FvH4_2g20420' => 'fve', 'FvH4_2g20430' => 'fve', 'FvH4_4g01270' => 'fve', 'FvH4_4g01290' => 'fve', 'FvH4_4g01300' => 'fve', 'FvH4_4g01310' => 'fve', 'FvH4_4g01330' => 'fve', 'FvH4_5g09070' => 'fve', 'Glyma.10G243800' => 'gma', 'Glyma.20G150600' => 'gma', 'Gohir.A09G219200' => 'ghi', 'Gohir.A09G219300' => 'ghi', 'Gohir.D09G221400' => 'ghi', 'Gohir.D09G221500' => 'ghi', 'Gorai.006G242600' => 'gra', 'Gorai.006G242700' => 'gra', 'GSVIVG01018044001' => 'vvi', 'HanXRQChr03g0083821' => 'han', 'HanXRQChr03g0083841' => 'han', 'HanXRQChr03g0083881' => 'han', 'HanXRQChr03g0083901' => 'han', 'HanXRQChr03g0083921' => 'han', 'HanXRQChr03g0085331' => 'han', 'HanXRQChr03g0085361' => 'han', 'HanXRQChr03g0085411' => 'han', 'HanXRQChr03g0085421' => 'han', 'HanXRQChr03g0085431' => 'han', 'HanXRQChr08g0221991' => 'han', 'HanXRQChr11g0336061' => 'han', 'HanXRQChr11g0336411' => 'han', 'Haze_11234' => 'cav', 'Hma1.2p1_0549F.1_g177010' => 'hma', 'Hma1.2p1_0602F.1_g187630' => 'hma', 'Hund14876' => 'sun', 'Hund14879' => 'sun', 'Lalb_Chr06g0160741' => 'lal', 'Lalb_Chr21g0304781' => 'lal', 'Lj3A726G19' => 'lonja', 'Lj3A726T23' => 'lonja', 'Lj3A726T24' => 'lonja', 'Lj3A726T25' => 'lonja', 'Lj3A727T17' => 'lonja', 'Lj3C726T0' => 'lonja', 'Lj3C726T2' => 'lonja', 'Lj3P725T35' => 'lonja', 'Lj3P727T10' => 'lonja', 'Lj3P727T12' => 'lonja', 'Lj3P727T14' => 'lonja', 'Lj5g0023109' => 'lja', 'Lj6P646T44' => 'lonja', 'Lsat_1_v5_gn_6_75760' => 'lsa', 'Lsat_1_v5_gn_6_75800' => 'lsa', 'Lsat_1_v5_gn_6_75900' => 'lsa', 'Lsat_1_v5_gn_6_76240' => 'lsa', 'Lsat_1_v5_gn_6_76441' => 'lsa', 'Lsat_1_v5_gn_6_76700' => 'lsa', 'Lsat_1_v5_gn_6_76760' => 'lsa', 'Manes.15G033100' => 'mes', 'Mapoly0004s0074' => 'mpo', 'Mapoly0004s0075' => 'mpo', 'Mapoly0004s0163' => 'mpo', 'Mapoly0004s0164' => 'mpo', 'Mapoly0021s0018' => 'mpo', 'Mapoly0041s0136' => 'mpo', 'Mapoly0041s0137' => 'mpo', 'Mapoly0041s0138' => 'mpo', 'Mapoly0041s0139' => 'mpo', 'Mapoly0041s0141' => 'mpo', 'Mapoly0041s0142' => 'mpo', 'Mapoly0041s0143' => 'mpo', 'Mapoly0041s0144' => 'mpo', 'Mapoly0041s0145' => 'mpo', 'Mapoly0047s0106' => 'mpo', 'Mapoly0047s0108' => 'mpo', 'Mapoly0050s0051' => 'mpo', 'Mapoly0050s0052' => 'mpo', 'Mapoly0050s0053' => 'mpo', 'Mapoly0058s0013' => 'mpo', 'Mapoly0091s0078' => 'mpo', 'Mapoly0091s0079' => 'mpo', 'Mapoly0091s0080' => 'mpo', 'Mapoly0091s0081' => 'mpo', 'Mapoly0278s0004' => 'mpo', 'Mapoly0278s0005' => 'mpo', 'Mapoly0278s0006' => 'mpo', 'MBI11_g30648_MAGBIO' => 'mbi', 'MCO03G194' => 'mco', 'MCO03G590' => 'mco', 'MCO07G312' => 'mco', 'MCO10G318' => 'mco', 'MCO12G244' => 'mco', 'MCO13G148' => 'mco', 'MCO13G194' => 'mco', 'MCO16G238' => 'mco', 'MD06G1134100' => 'mdo', 'MD13G1200100' => 'mdo', 'MD13G1200300' => 'mdo', 'MD13G1200600' => 'mdo', 'MD14G1150400' => 'mdo', 'MD16G1200000' => 'mdo', 'Medtr1g102570' => 'mtr', 'Medtr1g102780' => 'mtr', 'Medtr1g102800' => 'mtr', 'Medtr1g102810' => 'mtr', 'Medtr1g102830' => 'mtr', 'MELO3C006499.2' => 'cme', 'Migut.G00385' => 'egut', 'MSTRG.4063' => 'ama', 'Nitab4.5_0000090g0260' => 'nta', 'Nitab4.5_0000977g0030' => 'nta', 'Nitab4.5_0002541g0040' => 'nta', 'Nitab4.5_0007068g0040' => 'nta', 'Nn005s41408' => 'nnu', 'Nn005s41410' => 'nnu', 'Oeu010310.1' => 'oeu', 'Oeu010311.1' => 'oeu', 'Oeu043472.1' => 'oeu', 'Os01g0246400' => 'osa', 'Os04g0267950' => 'osa', 'Os07g0178700' => 'osa', 'Os07g0178800' => 'osa', 'Peaxi162Scf00316g00046' => 'pax', 'Peaxi162Scf00316g00049' => 'pax', 'Peaxi162Scf00316g00059' => 'pax', 'Peaxi162Scf00316g00328' => 'pax', 'Peaxi162Scf00316g00329' => 'pax', 'Peaxi162Scf00316g00411' => 'pax', 'Peaxi162Scf00316g00521' => 'pax', 'Peaxi162Scf00492g00068' => 'pax', 'Peaxi162Scf35631g00002' => 'pax', 'PGR142G3720' => 'pgr', 'PGSC0003DMG400006442' => 'stu', 'Phvul.007G062000' => 'pvu', 'Potri.008G157750' => 'ptr', 'Potri.008G157900' => 'ptr', 'Potri.008G158000' => 'ptr', 'Potri.008G158200' => 'ptr', 'Pp3c11_7280' => 'ppa', 'Pp3c11_7980' => 'ppa', 'Pp3c12_19450' => 'ppa', 'Pp3c14_1480' => 'ppa', 'Pp3c14_1501' => 'ppa', 'Pp3c16_4900' => 'ppa', 'Pp3c16_5010' => 'ppa', 'Pp3c16_5060' => 'ppa', 'Pp3c19_18250' => 'ppa', 'Pp3c23_8530' => 'ppa', 'Pp3c23_8550' => 'ppa', 'Pp3c24_9670' => 'ppa', 'Pp3c2_21390' => 'ppa', 'Pp3c2_31380' => 'ppa', 'Pp3c3_16620' => 'ppa', 'Pp3c3_8090' => 'ppa', 'Pp3c3_8110' => 'ppa', 'Pp3c3_8130' => 'ppa', 'Pp3c3_8150' => 'ppa', 'Pp3c4_14320' => 'ppa', 'Pp3c6_2560' => 'ppa', 'Pp3c9_16700' => 'ppa', 'PRCOL_00000234' => 'pco', 'PRCOL_00000235' => 'pco', 'PRCOL_00000777' => 'pco', 'PRCOL_00002344' => 'pco', 'PRCOL_00002372' => 'pco', 'PRCOL_00006120' => 'pco', 'Prupe.1G021400' => 'ppe', 'Prupe.1G021500' => 'ppe', 'Prupe.1G021600' => 'ppe', 'Prupe.1G021700' => 'ppe', 'Prupe.1G021800' => 'ppe', 'Prupe.5G145100' => 'ppe', 'Psat6g204040' => 'psa', 'Psat6g204800' => 'psa', 'Psat6g204920' => 'psa', 'Psat6g204960' => 'psa', 'Psat6g205080' => 'psa', 'PSO017G0271' => 'pso', 'PSO017G1276' => 'pso', 'PSO017G1429' => 'pso', 'PSO017G1861' => 'pso', 'PSO017G2787' => 'pso', 'PSO017G4466' => 'pso', 'PSO017G5118' => 'pso', 'PSO017G5420' => 'pso', 'PSO063G3678' => 'pso', 'PSO210G0546' => 'pso', 'PSO317G0001' => 'pso', 'PSO357G0512' => 'pso', 'PSO478G2682' => 'pso', 'PSO647G0001' => 'pso', 'PSO675G0001' => 'pso', 'PSO675G2699' => 'pso', 'PSO675G2849' => 'pso', 'PSO675G4991' => 'pso', 'PSO689G0001' => 'pso', 'QL06p000916' => 'qlo', 'QL06p000921' => 'qlo', 'QL06p001398' => 'qlo', 'QL06p001407' => 'qlo', 'QL06p002031' => 'qlo', 'RcHm_v2.0_Chr4g0387791' => 'rch', 'RcHm_v2.0_Chr4g0387801' => 'rch', 'RcHm_v2.0_Chr6g0286501' => 'rch', 'RcHm_v2.0_Chr6g0286511' => 'rch', 'RcHm_v2.0_Chr6g0286521' => 'rch', 'RcHm_v2.0_Chr6g0286531' => 'rch', 'RcHm_v2.0_Chr7g0189141' => 'rch', 'Rhsim02G0028700' => 'rsi', 'Rhsim02G0028800' => 'rsi', 'Rhsim02G0028900' => 'rsi', 'Rhsim02G0029000' => 'rsi', 'Rhsim02G0029100' => 'rsi', 'Rhsim02G0029200' => 'rsi', 'Rhsim02G0029300' => 'rsi', 'Rhsim02G0029400' => 'rsi', 'Rhsim02G0029500' => 'rsi', 'Rhsim02G0029600' => 'rsi', 'RhsimUnG0024000' => 'rsi', 'RhsimUnG0024100' => 'rsi', 'RhsimUnG0024200' => 'rsi', 'RhsimUnG0024300' => 'rsi', 'RhsimUnG0024400' => 'rsi', 'RhsimUnG0024500' => 'rsi', 'RhsimUnG0024700' => 'rsi', 'RhsimUnG0024800' => 'rsi', 'RhsimUnG0024900' => 'rsi', 'RhsimUnG0025100' => 'rsi', 'Sabra08G0120200' => 'sbr', 'Sabra08G0120300' => 'sbr', 'Sabra08G0120500' => 'sbr', 'Sabra08G0120600' => 'sbr', 'Sabra10G0158900' => 'sbr', 'SalBow2G3492' => 'sbo', 'Sc13g0004760' => 'sci', 'Sc13g0004770' => 'sci', 'Sed0003417' => 'sed', 'Sed0019750' => 'sed', 'SEGI_03419' => 'sgi', 'SEGI_05907' => 'sgi', 'SEGI_10682' => 'sgi', 'SEGI_13528' => 'sgi', 'SEGI_16081' => 'sgi', 'SEGI_19370' => 'sgi', 'SEGI_21015' => 'sgi', 'SEGI_21944' => 'sgi', 'SEGI_32906' => 'sgi', 'SEGI_33093' => 'sgi', 'SEGI_36110' => 'sgi', 'SEGI_40397' => 'sgi', 'SGA_v2.0_scaffold191G40426' => 'sas', 'SGA_v2.0_scaffold353G49717' => 'sas', 'SGA_v2.0_scaffold50G18550' => 'sas', 'SMO119G0173' => 'smo', 'SMO172G0002' => 'smo', 'Solyc09g082690.3' => 'sly', 'Solyc09g082700.2' => 'sly', 'Sopen09g031550' => 'spe', 'Sopen09g031560' => 'spe', 'Sp3g20540' => 'spa', 'Sp7g07580' => 'spa', 'TAR134G0002' => 'tar', 'TAR236G0001' => 'tar', 'TAR365G0892' => 'tar', 'TAR636G0166' => 'tar', 'TAR636G0646' => 'tar', 'TAR636G0869' => 'tar', 'TAR636G1317' => 'tar', 'TAR636G1744' => 'tar', 'TAR636G3358' => 'tar', 'TAR636G3436' => 'tar', 'THA.LOC104803047' => 'tha', 'Thecc.04G238900' => 'tca', 'Thhalv10021557m.g' => 'esa', 'Thhalv10026318m.g' => 'esa', 'Thhalv10026335m.g' => 'esa', 'TPR.G17433' => 'tpr', 'TPR.G18915' => 'tpr', 'TPR.G26125' => 'tpr', 'TWI09G0677' => 'twi', 'TWI73G0287' => 'twi', 'unitig_748.g8326' => 'ugi', 'vmacro15370' => 'vma', 'vmacro15371' => 'vma', 'vmacro15372' => 'vma', 'vmacro15373' => 'vma', 'vmacro15374' => 'vma', 'VMungo0720G2826' => 'vmu', 'Zm00001eb116960' => 'zma', 'Zm00001eb301260' => 'zma', 'Zm00001eb301270' => 'zma' ) $gf_id = 'HOM05D001460' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001460' ) $data_identifier = 'HOM05D001460' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 4, 'aag' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 2, 'aox' => (int) 2, 'arhy' => (int) 4, 'ath' => (int) 2, 'atr' => (int) 1, 'acertr' => (int) 10, 'cqu' => (int) 4, 'bca' => (int) 11, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 1, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 1, 'ccan' => (int) 1, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 1, 'col' => (int) 1, 'cpa' => (int) 1, 'cre' => (int) 7, 'csa' => (int) 1, 'camsi' => (int) 2, 'dca' => (int) 3, 'din' => (int) 2, 'dzi' => (int) 3, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 14, 'fve' => (int) 9, 'gma' => (int) 2, 'ghi' => (int) 4, 'gra' => (int) 2, 'vvi' => (int) 1, 'han' => (int) 13, 'cav' => (int) 1, 'hma' => (int) 2, 'sun' => (int) 2, 'lal' => (int) 2, 'lonja' => (int) 12, 'lja' => (int) 1, 'lsa' => (int) 7, 'mes' => (int) 1, 'mpo' => (int) 27, 'mbi' => (int) 1, 'mco' => (int) 8, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 1, 'egut' => (int) 1, 'ama' => (int) 1, 'nta' => (int) 4, 'nnu' => (int) 2, 'oeu' => (int) 3, 'osa' => (int) 4, 'pax' => (int) 9, 'pgr' => (int) 1, 'stu' => (int) 1, 'pvu' => (int) 1, 'ptr' => (int) 4, 'ppa' => (int) 22, 'pco' => (int) 6, 'ppe' => (int) 6, 'psa' => (int) 5, 'pso' => (int) 19, 'qlo' => (int) 5, 'rch' => (int) 7, 'rsi' => (int) 20, 'sbr' => (int) 5, 'sbo' => (int) 1, 'sci' => (int) 2, 'sed' => (int) 2, 'sgi' => (int) 12, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 2, 'tar' => (int) 10, 'tha' => (int) 1, 'tca' => (int) 1, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 2, 'ugi' => (int) 1, 'vma' => (int) 5, 'vmu' => (int) 1, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb301270' $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' => 'HOM05D001460', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '433', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p22980' => 'bna', 'A01p32340' => 'bna', 'A03p42970' => 'bna', 'A05p25880' => 'bna', 'Aa31LG8G9320' => 'aar', 'Aa31LG8G9330' => 'aar', 'Aa31LG8G9340' => 'aar', 'Aa31sc221G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1034' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1528' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.829' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2222' => 'aag', 'Ah.12g058830' => 'amhyb', 'Ah.12g058840' => 'amhyb', 'AL3G37160' => 'aly', 'AL7G41310' => 'aly', 'Aqoxy5G00395' => 'aox', 'Aqoxy5G00396' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0C8NZA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5185HY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JZ1PRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MD3LS0' => 'arhy', 'AT3G22840' => 'ath', 'AT4G14690' => 'ath', 'ATR0665G054' => 'atr', 'Atru.chr4.2344' => 'acertr', 'Atru.chr4.2346' => 'acertr', 'Atru.chr4.2347' => 'acertr', 'Atru.chr4.2348' => 'acertr', 'Atru.chr4.2355' => 'acertr', 'Atru.chr4.2356' => 'acertr', 'Atru.chr4.2358' => 'acertr', 'Atru.chr4.2359' => 'acertr', 'Atru.chr4.2360' => 'acertr', 'Atru.chr4.2361' => 'acertr', 'AUR62030476' => 'cqu', 'AUR62030478' => 'cqu', 'AUR62030819' => 'cqu', 'AUR62030820' => 'cqu', 'BcaB03g14648' => 'bca', 'BcaB04g20492' => 'bca', 'BcaB06g26399' => 'bca', 'BcaC01g03416' => 'bca', 'BcaC01g03419' => 'bca', 'BcaC01g03421' => 'bca', 'BcaC01g03424' => 'bca', 'BcaC05g28012' => 'bca', 'BcaC09g49212' => 'bca', 'BcaC09g50140' => 'bca', 'BcaNung00346' => 'bca', 'BolC1t02785H' => 'bol', 'BolC1t04095H' => 'bol', 'BolC3t17545H' => 'bol', 'BolC5t32769H' => 'bol', 'BraA01t02211Z' => 'bra', 'BraA01t03359Z' => 'bra', 'BraA03t13441Z' => 'bra', 'BraA05t21476Z' => 'bra', 'C01p28420' => 'bna', 'C01p41350' => 'bna', 'C03p52750' => 'bna', 'C03p52780' => 'bna', 'C05p40270' => 'bna', 'CAN.G1437.9' => 'can', 'CANSAT78G0035' => 'cansat', 'CANSAT78G1036' => 'cansat', 'CANSAT78G2272' => 'cansat', 'CANSAT78G2478' => 'cansat', 'CARHR098700' => 'chi', 'CARHR221120' => 'chi', 'CARHR221150' => 'chi', 'Carub.0003s2297' => 'cru', 'Carub.0007s2749' => 'cru', 'Carub.0007s2750' => 'cru', 'Carub.0007s2751' => 'cru', 'Ca_10849_v3' => 'car', 'Cc03_g04300' => 'ccan', 'CDE02G3648' => 'cde', 'CDE05G0060' => 'cde', 'CDE05G0692' => 'cde', 'CDE05G2285' => 'cde', 'CDE05G2884' => 'cde', 'CDE05G3072' => 'cde', 'Cfa008439' => 'cfa', 'Cfa008441' => 'cfa', 'Cfa008443' => 'cfa', 'Cfa008448' => 'cfa', 'Ciclev10005974m.g' => 'ccl', 'Ciclev10006006m.g' => 'ccl', 'Ciclev10006775m.g' => 'ccl', 'CiPaw.02G120400' => 'cil', 'CiPaw.02G120500' => 'cil', 'CiPaw.02G120600' => 'cil', 'ClCG05G004850' => 'cla', 'COL.COLO4_21566' => 'col', 'Cpa.g.sc44.124' => 'cpa', 'Cre07.g320400' => 'cre', 'Cre07.g320450' => 'cre', 'Cre08.g384650' => 'cre', 'Cre09.g393173' => 'cre', 'Cre09.g394325' => 'cre', 'Cre14.g626750' => 'cre', 'Cre16.g679250' => 'cre', 'CsaV3_3G012890' => 'csa', 'CSS0010865' => 'camsi', 'CSS0044338' => 'camsi', 'DCAR_002366' => 'dca', 'DCAR_030687' => 'dca', 'DCAR_030688' => 'dca', 'Dinv14047' => 'din', 'Dinv14048' => 'din', 'Duzib151G0105' => 'dzi', 'Duzib151G0114' => 'dzi', 'Duzib212G1029' => 'dzi', 'ECA232G3536' => 'eca', 'ECA240G0786' => 'eca', 'ECA240G1802' => 'eca', 'ECA240G3760' => 'eca', 'ECA240G3920' => 'eca', 'EL10Ac5g12536' => 'bvu', 'EL10Ac5g12537' => 'bvu', 'EL10Ac5g12538' => 'bvu', 'Eucgr.B01004' => 'egr', 'Eucgr.B01006' => 'egr', 'Eucgr.B01007' => 'egr', 'Eucgr.B01008' => 'egr', 'Eucgr.B01895' => 'egr', 'Eucgr.B01896' => 'egr', 'FAN04G1456' => 'fan', 'FAN08G1769' => 'fan', 'FAN08G2160' => 'fan', 'FAN13G2403' => 'fan', 'FAN13G3303' => 'fan', 'FAN15G2435' => 'fan', 'FAN17G0672' => 'fan', 'FAN17G2441' => 'fan', 'FAN18G1024' => 'fan', 'FAN22G1458' => 'fan', 'FAN24G0037' => 'fan', 'FAN24G0429' => 'fan', 'FAN24G2387' => 'fan', 'FAN27G2746' => 'fan', 'FvH4_2g20400' => 'fve', 'FvH4_2g20420' => 'fve', 'FvH4_2g20430' => 'fve', 'FvH4_4g01270' => 'fve', 'FvH4_4g01290' => 'fve', 'FvH4_4g01300' => 'fve', 'FvH4_4g01310' => 'fve', 'FvH4_4g01330' => 'fve', 'FvH4_5g09070' => 'fve', 'Glyma.10G243800' => 'gma', 'Glyma.20G150600' => 'gma', 'Gohir.A09G219200' => 'ghi', 'Gohir.A09G219300' => 'ghi', 'Gohir.D09G221400' => 'ghi', 'Gohir.D09G221500' => 'ghi', 'Gorai.006G242600' => 'gra', 'Gorai.006G242700' => 'gra', 'GSVIVG01018044001' => 'vvi', 'HanXRQChr03g0083821' => 'han', 'HanXRQChr03g0083841' => 'han', 'HanXRQChr03g0083881' => 'han', 'HanXRQChr03g0083901' => 'han', 'HanXRQChr03g0083921' => 'han', 'HanXRQChr03g0085331' => 'han', 'HanXRQChr03g0085361' => 'han', 'HanXRQChr03g0085411' => 'han', 'HanXRQChr03g0085421' => 'han', 'HanXRQChr03g0085431' => 'han', 'HanXRQChr08g0221991' => 'han', 'HanXRQChr11g0336061' => 'han', 'HanXRQChr11g0336411' => 'han', 'Haze_11234' => 'cav', 'Hma1.2p1_0549F.1_g177010' => 'hma', 'Hma1.2p1_0602F.1_g187630' => 'hma', 'Hund14876' => 'sun', 'Hund14879' => 'sun', 'Lalb_Chr06g0160741' => 'lal', 'Lalb_Chr21g0304781' => 'lal', 'Lj3A726G19' => 'lonja', 'Lj3A726T23' => 'lonja', 'Lj3A726T24' => 'lonja', 'Lj3A726T25' => 'lonja', 'Lj3A727T17' => 'lonja', 'Lj3C726T0' => 'lonja', 'Lj3C726T2' => 'lonja', 'Lj3P725T35' => 'lonja', 'Lj3P727T10' => 'lonja', 'Lj3P727T12' => 'lonja', 'Lj3P727T14' => 'lonja', 'Lj5g0023109' => 'lja', 'Lj6P646T44' => 'lonja', 'Lsat_1_v5_gn_6_75760' => 'lsa', 'Lsat_1_v5_gn_6_75800' => 'lsa', 'Lsat_1_v5_gn_6_75900' => 'lsa', 'Lsat_1_v5_gn_6_76240' => 'lsa', 'Lsat_1_v5_gn_6_76441' => 'lsa', 'Lsat_1_v5_gn_6_76700' => 'lsa', 'Lsat_1_v5_gn_6_76760' => 'lsa', 'Manes.15G033100' => 'mes', 'Mapoly0004s0074' => 'mpo', 'Mapoly0004s0075' => 'mpo', 'Mapoly0004s0163' => 'mpo', 'Mapoly0004s0164' => 'mpo', 'Mapoly0021s0018' => 'mpo', 'Mapoly0041s0136' => 'mpo', 'Mapoly0041s0137' => 'mpo', 'Mapoly0041s0138' => 'mpo', 'Mapoly0041s0139' => 'mpo', 'Mapoly0041s0141' => 'mpo', 'Mapoly0041s0142' => 'mpo', 'Mapoly0041s0143' => 'mpo', 'Mapoly0041s0144' => 'mpo', 'Mapoly0041s0145' => 'mpo', 'Mapoly0047s0106' => 'mpo', 'Mapoly0047s0108' => 'mpo', 'Mapoly0050s0051' => 'mpo', 'Mapoly0050s0052' => 'mpo', 'Mapoly0050s0053' => 'mpo', 'Mapoly0058s0013' => 'mpo', 'Mapoly0091s0078' => 'mpo', 'Mapoly0091s0079' => 'mpo', 'Mapoly0091s0080' => 'mpo', 'Mapoly0091s0081' => 'mpo', 'Mapoly0278s0004' => 'mpo', 'Mapoly0278s0005' => 'mpo', 'Mapoly0278s0006' => 'mpo', 'MBI11_g30648_MAGBIO' => 'mbi', 'MCO03G194' => 'mco', 'MCO03G590' => 'mco', 'MCO07G312' => 'mco', 'MCO10G318' => 'mco', 'MCO12G244' => 'mco', 'MCO13G148' => 'mco', 'MCO13G194' => 'mco', 'MCO16G238' => 'mco', 'MD06G1134100' => 'mdo', 'MD13G1200100' => 'mdo', 'MD13G1200300' => 'mdo', 'MD13G1200600' => 'mdo', 'MD14G1150400' => 'mdo', 'MD16G1200000' => 'mdo', 'Medtr1g102570' => 'mtr', 'Medtr1g102780' => 'mtr', 'Medtr1g102800' => 'mtr', 'Medtr1g102810' => 'mtr', 'Medtr1g102830' => 'mtr', 'MELO3C006499.2' => 'cme', 'Migut.G00385' => 'egut', 'MSTRG.4063' => 'ama', 'Nitab4.5_0000090g0260' => 'nta', 'Nitab4.5_0000977g0030' => 'nta', 'Nitab4.5_0002541g0040' => 'nta', 'Nitab4.5_0007068g0040' => 'nta', 'Nn005s41408' => 'nnu', 'Nn005s41410' => 'nnu', 'Oeu010310.1' => 'oeu', 'Oeu010311.1' => 'oeu', 'Oeu043472.1' => 'oeu', 'Os01g0246400' => 'osa', 'Os04g0267950' => 'osa', 'Os07g0178700' => 'osa', 'Os07g0178800' => 'osa', 'Peaxi162Scf00316g00046' => 'pax', 'Peaxi162Scf00316g00049' => 'pax', 'Peaxi162Scf00316g00059' => 'pax', 'Peaxi162Scf00316g00328' => 'pax', 'Peaxi162Scf00316g00329' => 'pax', 'Peaxi162Scf00316g00411' => 'pax', 'Peaxi162Scf00316g00521' => 'pax', 'Peaxi162Scf00492g00068' => 'pax', 'Peaxi162Scf35631g00002' => 'pax', 'PGR142G3720' => 'pgr', 'PGSC0003DMG400006442' => 'stu', 'Phvul.007G062000' => 'pvu', 'Potri.008G157750' => 'ptr', 'Potri.008G157900' => 'ptr', 'Potri.008G158000' => 'ptr', 'Potri.008G158200' => 'ptr', 'Pp3c11_7280' => 'ppa', 'Pp3c11_7980' => 'ppa', 'Pp3c12_19450' => 'ppa', 'Pp3c14_1480' => 'ppa', 'Pp3c14_1501' => 'ppa', 'Pp3c16_4900' => 'ppa', 'Pp3c16_5010' => 'ppa', 'Pp3c16_5060' => 'ppa', 'Pp3c19_18250' => 'ppa', 'Pp3c23_8530' => 'ppa', 'Pp3c23_8550' => 'ppa', 'Pp3c24_9670' => 'ppa', 'Pp3c2_21390' => 'ppa', 'Pp3c2_31380' => 'ppa', 'Pp3c3_16620' => 'ppa', 'Pp3c3_8090' => 'ppa', 'Pp3c3_8110' => 'ppa', 'Pp3c3_8130' => 'ppa', 'Pp3c3_8150' => 'ppa', 'Pp3c4_14320' => 'ppa', 'Pp3c6_2560' => 'ppa', 'Pp3c9_16700' => 'ppa', 'PRCOL_00000234' => 'pco', 'PRCOL_00000235' => 'pco', 'PRCOL_00000777' => 'pco', 'PRCOL_00002344' => 'pco', 'PRCOL_00002372' => 'pco', 'PRCOL_00006120' => 'pco', 'Prupe.1G021400' => 'ppe', 'Prupe.1G021500' => 'ppe', 'Prupe.1G021600' => 'ppe', 'Prupe.1G021700' => 'ppe', 'Prupe.1G021800' => 'ppe', 'Prupe.5G145100' => 'ppe', 'Psat6g204040' => 'psa', 'Psat6g204800' => 'psa', 'Psat6g204920' => 'psa', 'Psat6g204960' => 'psa', 'Psat6g205080' => 'psa', 'PSO017G0271' => 'pso', 'PSO017G1276' => 'pso', 'PSO017G1429' => 'pso', 'PSO017G1861' => 'pso', 'PSO017G2787' => 'pso', 'PSO017G4466' => 'pso', 'PSO017G5118' => 'pso', 'PSO017G5420' => 'pso', 'PSO063G3678' => 'pso', 'PSO210G0546' => 'pso', 'PSO317G0001' => 'pso', 'PSO357G0512' => 'pso', 'PSO478G2682' => 'pso', 'PSO647G0001' => 'pso', 'PSO675G0001' => 'pso', 'PSO675G2699' => 'pso', 'PSO675G2849' => 'pso', 'PSO675G4991' => 'pso', 'PSO689G0001' => 'pso', 'QL06p000916' => 'qlo', 'QL06p000921' => 'qlo', 'QL06p001398' => 'qlo', 'QL06p001407' => 'qlo', 'QL06p002031' => 'qlo', 'RcHm_v2.0_Chr4g0387791' => 'rch', 'RcHm_v2.0_Chr4g0387801' => 'rch', 'RcHm_v2.0_Chr6g0286501' => 'rch', 'RcHm_v2.0_Chr6g0286511' => 'rch', 'RcHm_v2.0_Chr6g0286521' => 'rch', 'RcHm_v2.0_Chr6g0286531' => 'rch', 'RcHm_v2.0_Chr7g0189141' => 'rch', 'Rhsim02G0028700' => 'rsi', 'Rhsim02G0028800' => 'rsi', 'Rhsim02G0028900' => 'rsi', 'Rhsim02G0029000' => 'rsi', 'Rhsim02G0029100' => 'rsi', 'Rhsim02G0029200' => 'rsi', 'Rhsim02G0029300' => 'rsi', 'Rhsim02G0029400' => 'rsi', 'Rhsim02G0029500' => 'rsi', 'Rhsim02G0029600' => 'rsi', 'RhsimUnG0024000' => 'rsi', 'RhsimUnG0024100' => 'rsi', 'RhsimUnG0024200' => 'rsi', 'RhsimUnG0024300' => 'rsi', 'RhsimUnG0024400' => 'rsi', 'RhsimUnG0024500' => 'rsi', 'RhsimUnG0024700' => 'rsi', 'RhsimUnG0024800' => 'rsi', 'RhsimUnG0024900' => 'rsi', 'RhsimUnG0025100' => 'rsi', 'Sabra08G0120200' => 'sbr', 'Sabra08G0120300' => 'sbr', 'Sabra08G0120500' => 'sbr', 'Sabra08G0120600' => 'sbr', 'Sabra10G0158900' => 'sbr', 'SalBow2G3492' => 'sbo', 'Sc13g0004760' => 'sci', 'Sc13g0004770' => 'sci', 'Sed0003417' => 'sed', 'Sed0019750' => 'sed', 'SEGI_03419' => 'sgi', 'SEGI_05907' => 'sgi', 'SEGI_10682' => 'sgi', 'SEGI_13528' => 'sgi', 'SEGI_16081' => 'sgi', 'SEGI_19370' => 'sgi', 'SEGI_21015' => 'sgi', 'SEGI_21944' => 'sgi', 'SEGI_32906' => 'sgi', 'SEGI_33093' => 'sgi', 'SEGI_36110' => 'sgi', 'SEGI_40397' => 'sgi', 'SGA_v2.0_scaffold191G40426' => 'sas', 'SGA_v2.0_scaffold353G49717' => 'sas', 'SGA_v2.0_scaffold50G18550' => 'sas', 'SMO119G0173' => 'smo', 'SMO172G0002' => 'smo', 'Solyc09g082690.3' => 'sly', 'Solyc09g082700.2' => 'sly', 'Sopen09g031550' => 'spe', 'Sopen09g031560' => 'spe', 'Sp3g20540' => 'spa', 'Sp7g07580' => 'spa', 'TAR134G0002' => 'tar', 'TAR236G0001' => 'tar', 'TAR365G0892' => 'tar', 'TAR636G0166' => 'tar', 'TAR636G0646' => 'tar', 'TAR636G0869' => 'tar', 'TAR636G1317' => 'tar', 'TAR636G1744' => 'tar', 'TAR636G3358' => 'tar', 'TAR636G3436' => 'tar', 'THA.LOC104803047' => 'tha', 'Thecc.04G238900' => 'tca', 'Thhalv10021557m.g' => 'esa', 'Thhalv10026318m.g' => 'esa', 'Thhalv10026335m.g' => 'esa', 'TPR.G17433' => 'tpr', 'TPR.G18915' => 'tpr', 'TPR.G26125' => 'tpr', 'TWI09G0677' => 'twi', 'TWI73G0287' => 'twi', 'unitig_748.g8326' => 'ugi', 'vmacro15370' => 'vma', 'vmacro15371' => 'vma', 'vmacro15372' => 'vma', 'vmacro15373' => 'vma', 'vmacro15374' => 'vma', 'VMungo0720G2826' => 'vmu', 'Zm00001eb116960' => 'zma', 'Zm00001eb301260' => 'zma', 'Zm00001eb301270' => 'zma' ), 'gf_id' => 'HOM05D001460', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001460' ), 'data_identifier' => 'HOM05D001460', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001460', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '433', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p22980' => 'bna', 'A01p32340' => 'bna', 'A03p42970' => 'bna', 'A05p25880' => 'bna', 'Aa31LG8G9320' => 'aar', 'Aa31LG8G9330' => 'aar', 'Aa31LG8G9340' => 'aar', 'Aa31sc221G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1034' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1528' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.829' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2222' => 'aag', 'Ah.12g058830' => 'amhyb', 'Ah.12g058840' => 'amhyb', 'AL3G37160' => 'aly', 'AL7G41310' => 'aly', 'Aqoxy5G00395' => 'aox', 'Aqoxy5G00396' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0C8NZA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5185HY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JZ1PRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MD3LS0' => 'arhy', 'AT3G22840' => 'ath', 'AT4G14690' => 'ath', 'ATR0665G054' => 'atr', 'Atru.chr4.2344' => 'acertr', 'Atru.chr4.2346' => 'acertr', 'Atru.chr4.2347' => 'acertr', 'Atru.chr4.2348' => 'acertr', 'Atru.chr4.2355' => 'acertr', 'Atru.chr4.2356' => 'acertr', 'Atru.chr4.2358' => 'acertr', 'Atru.chr4.2359' => 'acertr', 'Atru.chr4.2360' => 'acertr', 'Atru.chr4.2361' => 'acertr', 'AUR62030476' => 'cqu', 'AUR62030478' => 'cqu', 'AUR62030819' => 'cqu', 'AUR62030820' => 'cqu', 'BcaB03g14648' => 'bca', 'BcaB04g20492' => 'bca', 'BcaB06g26399' => 'bca', 'BcaC01g03416' => 'bca', 'BcaC01g03419' => 'bca', 'BcaC01g03421' => 'bca', 'BcaC01g03424' => 'bca', 'BcaC05g28012' => 'bca', 'BcaC09g49212' => 'bca', 'BcaC09g50140' => 'bca', 'BcaNung00346' => 'bca', 'BolC1t02785H' => 'bol', 'BolC1t04095H' => 'bol', 'BolC3t17545H' => 'bol', 'BolC5t32769H' => 'bol', 'BraA01t02211Z' => 'bra', 'BraA01t03359Z' => 'bra', 'BraA03t13441Z' => 'bra', 'BraA05t21476Z' => 'bra', 'C01p28420' => 'bna', 'C01p41350' => 'bna', 'C03p52750' => 'bna', 'C03p52780' => 'bna', 'C05p40270' => 'bna', 'CAN.G1437.9' => 'can', 'CANSAT78G0035' => 'cansat', 'CANSAT78G1036' => 'cansat', 'CANSAT78G2272' => 'cansat', 'CANSAT78G2478' => 'cansat', 'CARHR098700' => 'chi', 'CARHR221120' => 'chi', 'CARHR221150' => 'chi', 'Carub.0003s2297' => 'cru', 'Carub.0007s2749' => 'cru', 'Carub.0007s2750' => 'cru', 'Carub.0007s2751' => 'cru', 'Ca_10849_v3' => 'car', 'Cc03_g04300' => 'ccan', 'CDE02G3648' => 'cde', 'CDE05G0060' => 'cde', 'CDE05G0692' => 'cde', 'CDE05G2285' => 'cde', 'CDE05G2884' => 'cde', 'CDE05G3072' => 'cde', 'Cfa008439' => 'cfa', 'Cfa008441' => 'cfa', 'Cfa008443' => 'cfa', 'Cfa008448' => 'cfa', 'Ciclev10005974m.g' => 'ccl', 'Ciclev10006006m.g' => 'ccl', 'Ciclev10006775m.g' => 'ccl', 'CiPaw.02G120400' => 'cil', 'CiPaw.02G120500' => 'cil', 'CiPaw.02G120600' => 'cil', 'ClCG05G004850' => 'cla', 'COL.COLO4_21566' => 'col', 'Cpa.g.sc44.124' => 'cpa', 'Cre07.g320400' => 'cre', 'Cre07.g320450' => 'cre', 'Cre08.g384650' => 'cre', 'Cre09.g393173' => 'cre', 'Cre09.g394325' => 'cre', 'Cre14.g626750' => 'cre', 'Cre16.g679250' => 'cre', 'CsaV3_3G012890' => 'csa', 'CSS0010865' => 'camsi', 'CSS0044338' => 'camsi', 'DCAR_002366' => 'dca', 'DCAR_030687' => 'dca', 'DCAR_030688' => 'dca', 'Dinv14047' => 'din', 'Dinv14048' => 'din', 'Duzib151G0105' => 'dzi', 'Duzib151G0114' => 'dzi', 'Duzib212G1029' => 'dzi', 'ECA232G3536' => 'eca', 'ECA240G0786' => 'eca', 'ECA240G1802' => 'eca', 'ECA240G3760' => 'eca', 'ECA240G3920' => 'eca', 'EL10Ac5g12536' => 'bvu', 'EL10Ac5g12537' => 'bvu', 'EL10Ac5g12538' => 'bvu', 'Eucgr.B01004' => 'egr', 'Eucgr.B01006' => 'egr', 'Eucgr.B01007' => 'egr', 'Eucgr.B01008' => 'egr', 'Eucgr.B01895' => 'egr', 'Eucgr.B01896' => 'egr', 'FAN04G1456' => 'fan', 'FAN08G1769' => 'fan', 'FAN08G2160' => 'fan', 'FAN13G2403' => 'fan', 'FAN13G3303' => 'fan', 'FAN15G2435' => 'fan', 'FAN17G0672' => 'fan', 'FAN17G2441' => 'fan', 'FAN18G1024' => 'fan', 'FAN22G1458' => 'fan', 'FAN24G0037' => 'fan', 'FAN24G0429' => 'fan', 'FAN24G2387' => 'fan', 'FAN27G2746' => 'fan', 'FvH4_2g20400' => 'fve', 'FvH4_2g20420' => 'fve', 'FvH4_2g20430' => 'fve', 'FvH4_4g01270' => 'fve', 'FvH4_4g01290' => 'fve', 'FvH4_4g01300' => 'fve', 'FvH4_4g01310' => 'fve', 'FvH4_4g01330' => 'fve', 'FvH4_5g09070' => 'fve', 'Glyma.10G243800' => 'gma', 'Glyma.20G150600' => 'gma', 'Gohir.A09G219200' => 'ghi', 'Gohir.A09G219300' => 'ghi', 'Gohir.D09G221400' => 'ghi', 'Gohir.D09G221500' => 'ghi', 'Gorai.006G242600' => 'gra', 'Gorai.006G242700' => 'gra', 'GSVIVG01018044001' => 'vvi', 'HanXRQChr03g0083821' => 'han', 'HanXRQChr03g0083841' => 'han', 'HanXRQChr03g0083881' => 'han', 'HanXRQChr03g0083901' => 'han', 'HanXRQChr03g0083921' => 'han', 'HanXRQChr03g0085331' => 'han', 'HanXRQChr03g0085361' => 'han', 'HanXRQChr03g0085411' => 'han', 'HanXRQChr03g0085421' => 'han', 'HanXRQChr03g0085431' => 'han', 'HanXRQChr08g0221991' => 'han', 'HanXRQChr11g0336061' => 'han', 'HanXRQChr11g0336411' => 'han', 'Haze_11234' => 'cav', 'Hma1.2p1_0549F.1_g177010' => 'hma', 'Hma1.2p1_0602F.1_g187630' => 'hma', 'Hund14876' => 'sun', 'Hund14879' => 'sun', 'Lalb_Chr06g0160741' => 'lal', 'Lalb_Chr21g0304781' => 'lal', 'Lj3A726G19' => 'lonja', 'Lj3A726T23' => 'lonja', 'Lj3A726T24' => 'lonja', 'Lj3A726T25' => 'lonja', 'Lj3A727T17' => 'lonja', 'Lj3C726T0' => 'lonja', 'Lj3C726T2' => 'lonja', 'Lj3P725T35' => 'lonja', 'Lj3P727T10' => 'lonja', 'Lj3P727T12' => 'lonja', 'Lj3P727T14' => 'lonja', 'Lj5g0023109' => 'lja', 'Lj6P646T44' => 'lonja', 'Lsat_1_v5_gn_6_75760' => 'lsa', 'Lsat_1_v5_gn_6_75800' => 'lsa', 'Lsat_1_v5_gn_6_75900' => 'lsa', 'Lsat_1_v5_gn_6_76240' => 'lsa', 'Lsat_1_v5_gn_6_76441' => 'lsa', 'Lsat_1_v5_gn_6_76700' => 'lsa', 'Lsat_1_v5_gn_6_76760' => 'lsa', 'Manes.15G033100' => 'mes', 'Mapoly0004s0074' => 'mpo', 'Mapoly0004s0075' => 'mpo', 'Mapoly0004s0163' => 'mpo', 'Mapoly0004s0164' => 'mpo', 'Mapoly0021s0018' => 'mpo', 'Mapoly0041s0136' => 'mpo', 'Mapoly0041s0137' => 'mpo', 'Mapoly0041s0138' => 'mpo', 'Mapoly0041s0139' => 'mpo', 'Mapoly0041s0141' => 'mpo', 'Mapoly0041s0142' => 'mpo', 'Mapoly0041s0143' => 'mpo', 'Mapoly0041s0144' => 'mpo', 'Mapoly0041s0145' => 'mpo', 'Mapoly0047s0106' => 'mpo', 'Mapoly0047s0108' => 'mpo', 'Mapoly0050s0051' => 'mpo', 'Mapoly0050s0052' => 'mpo', 'Mapoly0050s0053' => 'mpo', 'Mapoly0058s0013' => 'mpo', 'Mapoly0091s0078' => 'mpo', 'Mapoly0091s0079' => 'mpo', 'Mapoly0091s0080' => 'mpo', 'Mapoly0091s0081' => 'mpo', 'Mapoly0278s0004' => 'mpo', 'Mapoly0278s0005' => 'mpo', 'Mapoly0278s0006' => 'mpo', 'MBI11_g30648_MAGBIO' => 'mbi', 'MCO03G194' => 'mco', 'MCO03G590' => 'mco', 'MCO07G312' => 'mco', 'MCO10G318' => 'mco', 'MCO12G244' => 'mco', 'MCO13G148' => 'mco', 'MCO13G194' => 'mco', 'MCO16G238' => 'mco', 'MD06G1134100' => 'mdo', 'MD13G1200100' => 'mdo', 'MD13G1200300' => 'mdo', 'MD13G1200600' => 'mdo', 'MD14G1150400' => 'mdo', 'MD16G1200000' => 'mdo', 'Medtr1g102570' => 'mtr', 'Medtr1g102780' => 'mtr', 'Medtr1g102800' => 'mtr', 'Medtr1g102810' => 'mtr', 'Medtr1g102830' => 'mtr', 'MELO3C006499.2' => 'cme', 'Migut.G00385' => 'egut', 'MSTRG.4063' => 'ama', 'Nitab4.5_0000090g0260' => 'nta', 'Nitab4.5_0000977g0030' => 'nta', 'Nitab4.5_0002541g0040' => 'nta', 'Nitab4.5_0007068g0040' => 'nta', 'Nn005s41408' => 'nnu', 'Nn005s41410' => 'nnu', 'Oeu010310.1' => 'oeu', 'Oeu010311.1' => 'oeu', 'Oeu043472.1' => 'oeu', 'Os01g0246400' => 'osa', 'Os04g0267950' => 'osa', 'Os07g0178700' => 'osa', 'Os07g0178800' => 'osa', 'Peaxi162Scf00316g00046' => 'pax', 'Peaxi162Scf00316g00049' => 'pax', 'Peaxi162Scf00316g00059' => 'pax', 'Peaxi162Scf00316g00328' => 'pax', 'Peaxi162Scf00316g00329' => 'pax', 'Peaxi162Scf00316g00411' => 'pax', 'Peaxi162Scf00316g00521' => 'pax', 'Peaxi162Scf00492g00068' => 'pax', 'Peaxi162Scf35631g00002' => 'pax', 'PGR142G3720' => 'pgr', 'PGSC0003DMG400006442' => 'stu', 'Phvul.007G062000' => 'pvu', 'Potri.008G157750' => 'ptr', 'Potri.008G157900' => 'ptr', 'Potri.008G158000' => 'ptr', 'Potri.008G158200' => 'ptr', 'Pp3c11_7280' => 'ppa', 'Pp3c11_7980' => 'ppa', 'Pp3c12_19450' => 'ppa', 'Pp3c14_1480' => 'ppa', 'Pp3c14_1501' => 'ppa', 'Pp3c16_4900' => 'ppa', 'Pp3c16_5010' => 'ppa', 'Pp3c16_5060' => 'ppa', 'Pp3c19_18250' => 'ppa', 'Pp3c23_8530' => 'ppa', 'Pp3c23_8550' => 'ppa', 'Pp3c24_9670' => 'ppa', 'Pp3c2_21390' => 'ppa', 'Pp3c2_31380' => 'ppa', 'Pp3c3_16620' => 'ppa', 'Pp3c3_8090' => 'ppa', 'Pp3c3_8110' => 'ppa', 'Pp3c3_8130' => 'ppa', 'Pp3c3_8150' => 'ppa', 'Pp3c4_14320' => 'ppa', 'Pp3c6_2560' => 'ppa', 'Pp3c9_16700' => 'ppa', 'PRCOL_00000234' => 'pco', 'PRCOL_00000235' => 'pco', 'PRCOL_00000777' => 'pco', 'PRCOL_00002344' => 'pco', 'PRCOL_00002372' => 'pco', 'PRCOL_00006120' => 'pco', 'Prupe.1G021400' => 'ppe', 'Prupe.1G021500' => 'ppe', 'Prupe.1G021600' => 'ppe', 'Prupe.1G021700' => 'ppe', 'Prupe.1G021800' => 'ppe', 'Prupe.5G145100' => 'ppe', 'Psat6g204040' => 'psa', 'Psat6g204800' => 'psa', 'Psat6g204920' => 'psa', 'Psat6g204960' => 'psa', 'Psat6g205080' => 'psa', 'PSO017G0271' => 'pso', 'PSO017G1276' => 'pso', 'PSO017G1429' => 'pso', 'PSO017G1861' => 'pso', 'PSO017G2787' => 'pso', 'PSO017G4466' => 'pso', 'PSO017G5118' => 'pso', 'PSO017G5420' => 'pso', 'PSO063G3678' => 'pso', 'PSO210G0546' => 'pso', 'PSO317G0001' => 'pso', 'PSO357G0512' => 'pso', 'PSO478G2682' => 'pso', 'PSO647G0001' => 'pso', 'PSO675G0001' => 'pso', 'PSO675G2699' => 'pso', 'PSO675G2849' => 'pso', 'PSO675G4991' => 'pso', 'PSO689G0001' => 'pso', 'QL06p000916' => 'qlo', 'QL06p000921' => 'qlo', 'QL06p001398' => 'qlo', 'QL06p001407' => 'qlo', 'QL06p002031' => 'qlo', 'RcHm_v2.0_Chr4g0387791' => 'rch', 'RcHm_v2.0_Chr4g0387801' => 'rch', 'RcHm_v2.0_Chr6g0286501' => 'rch', 'RcHm_v2.0_Chr6g0286511' => 'rch', 'RcHm_v2.0_Chr6g0286521' => 'rch', 'RcHm_v2.0_Chr6g0286531' => 'rch', 'RcHm_v2.0_Chr7g0189141' => 'rch', 'Rhsim02G0028700' => 'rsi', 'Rhsim02G0028800' => 'rsi', 'Rhsim02G0028900' => 'rsi', 'Rhsim02G0029000' => 'rsi', 'Rhsim02G0029100' => 'rsi', 'Rhsim02G0029200' => 'rsi', 'Rhsim02G0029300' => 'rsi', 'Rhsim02G0029400' => 'rsi', 'Rhsim02G0029500' => 'rsi', 'Rhsim02G0029600' => 'rsi', 'RhsimUnG0024000' => 'rsi', 'RhsimUnG0024100' => 'rsi', 'RhsimUnG0024200' => 'rsi', 'RhsimUnG0024300' => 'rsi', 'RhsimUnG0024400' => 'rsi', 'RhsimUnG0024500' => 'rsi', 'RhsimUnG0024700' => 'rsi', 'RhsimUnG0024800' => 'rsi', 'RhsimUnG0024900' => 'rsi', 'RhsimUnG0025100' => 'rsi', 'Sabra08G0120200' => 'sbr', 'Sabra08G0120300' => 'sbr', 'Sabra08G0120500' => 'sbr', 'Sabra08G0120600' => 'sbr', 'Sabra10G0158900' => 'sbr', 'SalBow2G3492' => 'sbo', 'Sc13g0004760' => 'sci', 'Sc13g0004770' => 'sci', 'Sed0003417' => 'sed', 'Sed0019750' => 'sed', 'SEGI_03419' => 'sgi', 'SEGI_05907' => 'sgi', 'SEGI_10682' => 'sgi', 'SEGI_13528' => 'sgi', 'SEGI_16081' => 'sgi', 'SEGI_19370' => 'sgi', 'SEGI_21015' => 'sgi', 'SEGI_21944' => 'sgi', 'SEGI_32906' => 'sgi', 'SEGI_33093' => 'sgi', 'SEGI_36110' => 'sgi', 'SEGI_40397' => 'sgi', 'SGA_v2.0_scaffold191G40426' => 'sas', 'SGA_v2.0_scaffold353G49717' => 'sas', 'SGA_v2.0_scaffold50G18550' => 'sas', 'SMO119G0173' => 'smo', 'SMO172G0002' => 'smo', 'Solyc09g082690.3' => 'sly', 'Solyc09g082700.2' => 'sly', 'Sopen09g031550' => 'spe', 'Sopen09g031560' => 'spe', 'Sp3g20540' => 'spa', 'Sp7g07580' => 'spa', 'TAR134G0002' => 'tar', 'TAR236G0001' => 'tar', 'TAR365G0892' => 'tar', 'TAR636G0166' => 'tar', 'TAR636G0646' => 'tar', 'TAR636G0869' => 'tar', 'TAR636G1317' => 'tar', 'TAR636G1744' => 'tar', 'TAR636G3358' => 'tar', 'TAR636G3436' => 'tar', 'THA.LOC104803047' => 'tha', 'Thecc.04G238900' => 'tca', 'Thhalv10021557m.g' => 'esa', 'Thhalv10026318m.g' => 'esa', 'Thhalv10026335m.g' => 'esa', 'TPR.G17433' => 'tpr', 'TPR.G18915' => 'tpr', 'TPR.G26125' => 'tpr', 'TWI09G0677' => 'twi', 'TWI73G0287' => 'twi', 'unitig_748.g8326' => 'ugi', 'vmacro15370' => 'vma', 'vmacro15371' => 'vma', 'vmacro15372' => 'vma', 'vmacro15373' => 'vma', 'vmacro15374' => 'vma', 'VMungo0720G2826' => 'vmu', 'Zm00001eb116960' => 'zma', 'Zm00001eb301260' => 'zma', 'Zm00001eb301270' => 'zma' ) $gf_id = 'HOM05D001460' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001460' ) $data_identifier = 'HOM05D001460' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 4, 'aag' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 2, 'aox' => (int) 2, 'arhy' => (int) 4, 'ath' => (int) 2, 'atr' => (int) 1, 'acertr' => (int) 10, 'cqu' => (int) 4, 'bca' => (int) 11, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 1, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 1, 'ccan' => (int) 1, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 1, 'col' => (int) 1, 'cpa' => (int) 1, 'cre' => (int) 7, 'csa' => (int) 1, 'camsi' => (int) 2, 'dca' => (int) 3, 'din' => (int) 2, 'dzi' => (int) 3, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 14, 'fve' => (int) 9, 'gma' => (int) 2, 'ghi' => (int) 4, 'gra' => (int) 2, 'vvi' => (int) 1, 'han' => (int) 13, 'cav' => (int) 1, 'hma' => (int) 2, 'sun' => (int) 2, 'lal' => (int) 2, 'lonja' => (int) 12, 'lja' => (int) 1, 'lsa' => (int) 7, 'mes' => (int) 1, 'mpo' => (int) 27, 'mbi' => (int) 1, 'mco' => (int) 8, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 1, 'egut' => (int) 1, 'ama' => (int) 1, 'nta' => (int) 4, 'nnu' => (int) 2, 'oeu' => (int) 3, 'osa' => (int) 4, 'pax' => (int) 9, 'pgr' => (int) 1, 'stu' => (int) 1, 'pvu' => (int) 1, 'ptr' => (int) 4, 'ppa' => (int) 22, 'pco' => (int) 6, 'ppe' => (int) 6, 'psa' => (int) 5, 'pso' => (int) 19, 'qlo' => (int) 5, 'rch' => (int) 7, 'rsi' => (int) 20, 'sbr' => (int) 5, 'sbo' => (int) 1, 'sci' => (int) 2, 'sed' => (int) 2, 'sgi' => (int) 12, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 2, 'tar' => (int) 10, 'tha' => (int) 1, 'tca' => (int) 1, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 2, 'ugi' => (int) 1, 'vma' => (int) 5, 'vmu' => (int) 1, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb301270' $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' => 'HOM05D001460', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '433', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p22980' => 'bna', 'A01p32340' => 'bna', 'A03p42970' => 'bna', 'A05p25880' => 'bna', 'Aa31LG8G9320' => 'aar', 'Aa31LG8G9330' => 'aar', 'Aa31LG8G9340' => 'aar', 'Aa31sc221G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1034' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1528' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.829' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2222' => 'aag', 'Ah.12g058830' => 'amhyb', 'Ah.12g058840' => 'amhyb', 'AL3G37160' => 'aly', 'AL7G41310' => 'aly', 'Aqoxy5G00395' => 'aox', 'Aqoxy5G00396' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0C8NZA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5185HY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JZ1PRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MD3LS0' => 'arhy', 'AT3G22840' => 'ath', 'AT4G14690' => 'ath', 'ATR0665G054' => 'atr', 'Atru.chr4.2344' => 'acertr', 'Atru.chr4.2346' => 'acertr', 'Atru.chr4.2347' => 'acertr', 'Atru.chr4.2348' => 'acertr', 'Atru.chr4.2355' => 'acertr', 'Atru.chr4.2356' => 'acertr', 'Atru.chr4.2358' => 'acertr', 'Atru.chr4.2359' => 'acertr', 'Atru.chr4.2360' => 'acertr', 'Atru.chr4.2361' => 'acertr', 'AUR62030476' => 'cqu', 'AUR62030478' => 'cqu', 'AUR62030819' => 'cqu', 'AUR62030820' => 'cqu', 'BcaB03g14648' => 'bca', 'BcaB04g20492' => 'bca', 'BcaB06g26399' => 'bca', 'BcaC01g03416' => 'bca', 'BcaC01g03419' => 'bca', 'BcaC01g03421' => 'bca', 'BcaC01g03424' => 'bca', 'BcaC05g28012' => 'bca', 'BcaC09g49212' => 'bca', 'BcaC09g50140' => 'bca', 'BcaNung00346' => 'bca', 'BolC1t02785H' => 'bol', 'BolC1t04095H' => 'bol', 'BolC3t17545H' => 'bol', 'BolC5t32769H' => 'bol', 'BraA01t02211Z' => 'bra', 'BraA01t03359Z' => 'bra', 'BraA03t13441Z' => 'bra', 'BraA05t21476Z' => 'bra', 'C01p28420' => 'bna', 'C01p41350' => 'bna', 'C03p52750' => 'bna', 'C03p52780' => 'bna', 'C05p40270' => 'bna', 'CAN.G1437.9' => 'can', 'CANSAT78G0035' => 'cansat', 'CANSAT78G1036' => 'cansat', 'CANSAT78G2272' => 'cansat', 'CANSAT78G2478' => 'cansat', 'CARHR098700' => 'chi', 'CARHR221120' => 'chi', 'CARHR221150' => 'chi', 'Carub.0003s2297' => 'cru', 'Carub.0007s2749' => 'cru', 'Carub.0007s2750' => 'cru', 'Carub.0007s2751' => 'cru', 'Ca_10849_v3' => 'car', 'Cc03_g04300' => 'ccan', 'CDE02G3648' => 'cde', 'CDE05G0060' => 'cde', 'CDE05G0692' => 'cde', 'CDE05G2285' => 'cde', 'CDE05G2884' => 'cde', 'CDE05G3072' => 'cde', 'Cfa008439' => 'cfa', 'Cfa008441' => 'cfa', 'Cfa008443' => 'cfa', 'Cfa008448' => 'cfa', 'Ciclev10005974m.g' => 'ccl', 'Ciclev10006006m.g' => 'ccl', 'Ciclev10006775m.g' => 'ccl', 'CiPaw.02G120400' => 'cil', 'CiPaw.02G120500' => 'cil', 'CiPaw.02G120600' => 'cil', 'ClCG05G004850' => 'cla', 'COL.COLO4_21566' => 'col', 'Cpa.g.sc44.124' => 'cpa', 'Cre07.g320400' => 'cre', 'Cre07.g320450' => 'cre', 'Cre08.g384650' => 'cre', 'Cre09.g393173' => 'cre', 'Cre09.g394325' => 'cre', 'Cre14.g626750' => 'cre', 'Cre16.g679250' => 'cre', 'CsaV3_3G012890' => 'csa', 'CSS0010865' => 'camsi', 'CSS0044338' => 'camsi', 'DCAR_002366' => 'dca', 'DCAR_030687' => 'dca', 'DCAR_030688' => 'dca', 'Dinv14047' => 'din', 'Dinv14048' => 'din', 'Duzib151G0105' => 'dzi', 'Duzib151G0114' => 'dzi', 'Duzib212G1029' => 'dzi', 'ECA232G3536' => 'eca', 'ECA240G0786' => 'eca', 'ECA240G1802' => 'eca', 'ECA240G3760' => 'eca', 'ECA240G3920' => 'eca', 'EL10Ac5g12536' => 'bvu', 'EL10Ac5g12537' => 'bvu', 'EL10Ac5g12538' => 'bvu', 'Eucgr.B01004' => 'egr', 'Eucgr.B01006' => 'egr', 'Eucgr.B01007' => 'egr', 'Eucgr.B01008' => 'egr', 'Eucgr.B01895' => 'egr', 'Eucgr.B01896' => 'egr', 'FAN04G1456' => 'fan', 'FAN08G1769' => 'fan', 'FAN08G2160' => 'fan', 'FAN13G2403' => 'fan', 'FAN13G3303' => 'fan', 'FAN15G2435' => 'fan', 'FAN17G0672' => 'fan', 'FAN17G2441' => 'fan', 'FAN18G1024' => 'fan', 'FAN22G1458' => 'fan', 'FAN24G0037' => 'fan', 'FAN24G0429' => 'fan', 'FAN24G2387' => 'fan', 'FAN27G2746' => 'fan', 'FvH4_2g20400' => 'fve', 'FvH4_2g20420' => 'fve', 'FvH4_2g20430' => 'fve', 'FvH4_4g01270' => 'fve', 'FvH4_4g01290' => 'fve', 'FvH4_4g01300' => 'fve', 'FvH4_4g01310' => 'fve', 'FvH4_4g01330' => 'fve', 'FvH4_5g09070' => 'fve', 'Glyma.10G243800' => 'gma', 'Glyma.20G150600' => 'gma', 'Gohir.A09G219200' => 'ghi', 'Gohir.A09G219300' => 'ghi', 'Gohir.D09G221400' => 'ghi', 'Gohir.D09G221500' => 'ghi', 'Gorai.006G242600' => 'gra', 'Gorai.006G242700' => 'gra', 'GSVIVG01018044001' => 'vvi', 'HanXRQChr03g0083821' => 'han', 'HanXRQChr03g0083841' => 'han', 'HanXRQChr03g0083881' => 'han', 'HanXRQChr03g0083901' => 'han', 'HanXRQChr03g0083921' => 'han', 'HanXRQChr03g0085331' => 'han', 'HanXRQChr03g0085361' => 'han', 'HanXRQChr03g0085411' => 'han', 'HanXRQChr03g0085421' => 'han', 'HanXRQChr03g0085431' => 'han', 'HanXRQChr08g0221991' => 'han', 'HanXRQChr11g0336061' => 'han', 'HanXRQChr11g0336411' => 'han', 'Haze_11234' => 'cav', 'Hma1.2p1_0549F.1_g177010' => 'hma', 'Hma1.2p1_0602F.1_g187630' => 'hma', 'Hund14876' => 'sun', 'Hund14879' => 'sun', 'Lalb_Chr06g0160741' => 'lal', 'Lalb_Chr21g0304781' => 'lal', 'Lj3A726G19' => 'lonja', 'Lj3A726T23' => 'lonja', 'Lj3A726T24' => 'lonja', 'Lj3A726T25' => 'lonja', 'Lj3A727T17' => 'lonja', 'Lj3C726T0' => 'lonja', 'Lj3C726T2' => 'lonja', 'Lj3P725T35' => 'lonja', 'Lj3P727T10' => 'lonja', 'Lj3P727T12' => 'lonja', 'Lj3P727T14' => 'lonja', 'Lj5g0023109' => 'lja', 'Lj6P646T44' => 'lonja', 'Lsat_1_v5_gn_6_75760' => 'lsa', 'Lsat_1_v5_gn_6_75800' => 'lsa', 'Lsat_1_v5_gn_6_75900' => 'lsa', 'Lsat_1_v5_gn_6_76240' => 'lsa', 'Lsat_1_v5_gn_6_76441' => 'lsa', 'Lsat_1_v5_gn_6_76700' => 'lsa', 'Lsat_1_v5_gn_6_76760' => 'lsa', 'Manes.15G033100' => 'mes', 'Mapoly0004s0074' => 'mpo', 'Mapoly0004s0075' => 'mpo', 'Mapoly0004s0163' => 'mpo', 'Mapoly0004s0164' => 'mpo', 'Mapoly0021s0018' => 'mpo', 'Mapoly0041s0136' => 'mpo', 'Mapoly0041s0137' => 'mpo', 'Mapoly0041s0138' => 'mpo', 'Mapoly0041s0139' => 'mpo', 'Mapoly0041s0141' => 'mpo', 'Mapoly0041s0142' => 'mpo', 'Mapoly0041s0143' => 'mpo', 'Mapoly0041s0144' => 'mpo', 'Mapoly0041s0145' => 'mpo', 'Mapoly0047s0106' => 'mpo', 'Mapoly0047s0108' => 'mpo', 'Mapoly0050s0051' => 'mpo', 'Mapoly0050s0052' => 'mpo', 'Mapoly0050s0053' => 'mpo', 'Mapoly0058s0013' => 'mpo', 'Mapoly0091s0078' => 'mpo', 'Mapoly0091s0079' => 'mpo', 'Mapoly0091s0080' => 'mpo', 'Mapoly0091s0081' => 'mpo', 'Mapoly0278s0004' => 'mpo', 'Mapoly0278s0005' => 'mpo', 'Mapoly0278s0006' => 'mpo', 'MBI11_g30648_MAGBIO' => 'mbi', 'MCO03G194' => 'mco', 'MCO03G590' => 'mco', 'MCO07G312' => 'mco', 'MCO10G318' => 'mco', 'MCO12G244' => 'mco', 'MCO13G148' => 'mco', 'MCO13G194' => 'mco', 'MCO16G238' => 'mco', 'MD06G1134100' => 'mdo', 'MD13G1200100' => 'mdo', 'MD13G1200300' => 'mdo', 'MD13G1200600' => 'mdo', 'MD14G1150400' => 'mdo', 'MD16G1200000' => 'mdo', 'Medtr1g102570' => 'mtr', 'Medtr1g102780' => 'mtr', 'Medtr1g102800' => 'mtr', 'Medtr1g102810' => 'mtr', 'Medtr1g102830' => 'mtr', 'MELO3C006499.2' => 'cme', 'Migut.G00385' => 'egut', 'MSTRG.4063' => 'ama', 'Nitab4.5_0000090g0260' => 'nta', 'Nitab4.5_0000977g0030' => 'nta', 'Nitab4.5_0002541g0040' => 'nta', 'Nitab4.5_0007068g0040' => 'nta', 'Nn005s41408' => 'nnu', 'Nn005s41410' => 'nnu', 'Oeu010310.1' => 'oeu', 'Oeu010311.1' => 'oeu', 'Oeu043472.1' => 'oeu', 'Os01g0246400' => 'osa', 'Os04g0267950' => 'osa', 'Os07g0178700' => 'osa', 'Os07g0178800' => 'osa', 'Peaxi162Scf00316g00046' => 'pax', 'Peaxi162Scf00316g00049' => 'pax', 'Peaxi162Scf00316g00059' => 'pax', 'Peaxi162Scf00316g00328' => 'pax', 'Peaxi162Scf00316g00329' => 'pax', 'Peaxi162Scf00316g00411' => 'pax', 'Peaxi162Scf00316g00521' => 'pax', 'Peaxi162Scf00492g00068' => 'pax', 'Peaxi162Scf35631g00002' => 'pax', 'PGR142G3720' => 'pgr', 'PGSC0003DMG400006442' => 'stu', 'Phvul.007G062000' => 'pvu', 'Potri.008G157750' => 'ptr', 'Potri.008G157900' => 'ptr', 'Potri.008G158000' => 'ptr', 'Potri.008G158200' => 'ptr', 'Pp3c11_7280' => 'ppa', 'Pp3c11_7980' => 'ppa', 'Pp3c12_19450' => 'ppa', 'Pp3c14_1480' => 'ppa', 'Pp3c14_1501' => 'ppa', 'Pp3c16_4900' => 'ppa', 'Pp3c16_5010' => 'ppa', 'Pp3c16_5060' => 'ppa', 'Pp3c19_18250' => 'ppa', 'Pp3c23_8530' => 'ppa', 'Pp3c23_8550' => 'ppa', 'Pp3c24_9670' => 'ppa', 'Pp3c2_21390' => 'ppa', 'Pp3c2_31380' => 'ppa', 'Pp3c3_16620' => 'ppa', 'Pp3c3_8090' => 'ppa', 'Pp3c3_8110' => 'ppa', 'Pp3c3_8130' => 'ppa', 'Pp3c3_8150' => 'ppa', 'Pp3c4_14320' => 'ppa', 'Pp3c6_2560' => 'ppa', 'Pp3c9_16700' => 'ppa', 'PRCOL_00000234' => 'pco', 'PRCOL_00000235' => 'pco', 'PRCOL_00000777' => 'pco', 'PRCOL_00002344' => 'pco', 'PRCOL_00002372' => 'pco', 'PRCOL_00006120' => 'pco', 'Prupe.1G021400' => 'ppe', 'Prupe.1G021500' => 'ppe', 'Prupe.1G021600' => 'ppe', 'Prupe.1G021700' => 'ppe', 'Prupe.1G021800' => 'ppe', 'Prupe.5G145100' => 'ppe', 'Psat6g204040' => 'psa', 'Psat6g204800' => 'psa', 'Psat6g204920' => 'psa', 'Psat6g204960' => 'psa', 'Psat6g205080' => 'psa', 'PSO017G0271' => 'pso', 'PSO017G1276' => 'pso', 'PSO017G1429' => 'pso', 'PSO017G1861' => 'pso', 'PSO017G2787' => 'pso', 'PSO017G4466' => 'pso', 'PSO017G5118' => 'pso', 'PSO017G5420' => 'pso', 'PSO063G3678' => 'pso', 'PSO210G0546' => 'pso', 'PSO317G0001' => 'pso', 'PSO357G0512' => 'pso', 'PSO478G2682' => 'pso', 'PSO647G0001' => 'pso', 'PSO675G0001' => 'pso', 'PSO675G2699' => 'pso', 'PSO675G2849' => 'pso', 'PSO675G4991' => 'pso', 'PSO689G0001' => 'pso', 'QL06p000916' => 'qlo', 'QL06p000921' => 'qlo', 'QL06p001398' => 'qlo', 'QL06p001407' => 'qlo', 'QL06p002031' => 'qlo', 'RcHm_v2.0_Chr4g0387791' => 'rch', 'RcHm_v2.0_Chr4g0387801' => 'rch', 'RcHm_v2.0_Chr6g0286501' => 'rch', 'RcHm_v2.0_Chr6g0286511' => 'rch', 'RcHm_v2.0_Chr6g0286521' => 'rch', 'RcHm_v2.0_Chr6g0286531' => 'rch', 'RcHm_v2.0_Chr7g0189141' => 'rch', 'Rhsim02G0028700' => 'rsi', 'Rhsim02G0028800' => 'rsi', 'Rhsim02G0028900' => 'rsi', 'Rhsim02G0029000' => 'rsi', 'Rhsim02G0029100' => 'rsi', 'Rhsim02G0029200' => 'rsi', 'Rhsim02G0029300' => 'rsi', 'Rhsim02G0029400' => 'rsi', 'Rhsim02G0029500' => 'rsi', 'Rhsim02G0029600' => 'rsi', 'RhsimUnG0024000' => 'rsi', 'RhsimUnG0024100' => 'rsi', 'RhsimUnG0024200' => 'rsi', 'RhsimUnG0024300' => 'rsi', 'RhsimUnG0024400' => 'rsi', 'RhsimUnG0024500' => 'rsi', 'RhsimUnG0024700' => 'rsi', 'RhsimUnG0024800' => 'rsi', 'RhsimUnG0024900' => 'rsi', 'RhsimUnG0025100' => 'rsi', 'Sabra08G0120200' => 'sbr', 'Sabra08G0120300' => 'sbr', 'Sabra08G0120500' => 'sbr', 'Sabra08G0120600' => 'sbr', 'Sabra10G0158900' => 'sbr', 'SalBow2G3492' => 'sbo', 'Sc13g0004760' => 'sci', 'Sc13g0004770' => 'sci', 'Sed0003417' => 'sed', 'Sed0019750' => 'sed', 'SEGI_03419' => 'sgi', 'SEGI_05907' => 'sgi', 'SEGI_10682' => 'sgi', 'SEGI_13528' => 'sgi', 'SEGI_16081' => 'sgi', 'SEGI_19370' => 'sgi', 'SEGI_21015' => 'sgi', 'SEGI_21944' => 'sgi', 'SEGI_32906' => 'sgi', 'SEGI_33093' => 'sgi', 'SEGI_36110' => 'sgi', 'SEGI_40397' => 'sgi', 'SGA_v2.0_scaffold191G40426' => 'sas', 'SGA_v2.0_scaffold353G49717' => 'sas', 'SGA_v2.0_scaffold50G18550' => 'sas', 'SMO119G0173' => 'smo', 'SMO172G0002' => 'smo', 'Solyc09g082690.3' => 'sly', 'Solyc09g082700.2' => 'sly', 'Sopen09g031550' => 'spe', 'Sopen09g031560' => 'spe', 'Sp3g20540' => 'spa', 'Sp7g07580' => 'spa', 'TAR134G0002' => 'tar', 'TAR236G0001' => 'tar', 'TAR365G0892' => 'tar', 'TAR636G0166' => 'tar', 'TAR636G0646' => 'tar', 'TAR636G0869' => 'tar', 'TAR636G1317' => 'tar', 'TAR636G1744' => 'tar', 'TAR636G3358' => 'tar', 'TAR636G3436' => 'tar', 'THA.LOC104803047' => 'tha', 'Thecc.04G238900' => 'tca', 'Thhalv10021557m.g' => 'esa', 'Thhalv10026318m.g' => 'esa', 'Thhalv10026335m.g' => 'esa', 'TPR.G17433' => 'tpr', 'TPR.G18915' => 'tpr', 'TPR.G26125' => 'tpr', 'TWI09G0677' => 'twi', 'TWI73G0287' => 'twi', 'unitig_748.g8326' => 'ugi', 'vmacro15370' => 'vma', 'vmacro15371' => 'vma', 'vmacro15372' => 'vma', 'vmacro15373' => 'vma', 'vmacro15374' => 'vma', 'VMungo0720G2826' => 'vmu', 'Zm00001eb116960' => 'zma', 'Zm00001eb301260' => 'zma', 'Zm00001eb301270' => 'zma' ), 'gf_id' => 'HOM05D001460', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001460' ), 'data_identifier' => 'HOM05D001460', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001460', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '433', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p22980' => 'bna', 'A01p32340' => 'bna', 'A03p42970' => 'bna', 'A05p25880' => 'bna', 'Aa31LG8G9320' => 'aar', 'Aa31LG8G9330' => 'aar', 'Aa31LG8G9340' => 'aar', 'Aa31sc221G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1034' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1528' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.829' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2222' => 'aag', 'Ah.12g058830' => 'amhyb', 'Ah.12g058840' => 'amhyb', 'AL3G37160' => 'aly', 'AL7G41310' => 'aly', 'Aqoxy5G00395' => 'aox', 'Aqoxy5G00396' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0C8NZA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5185HY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JZ1PRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MD3LS0' => 'arhy', 'AT3G22840' => 'ath', 'AT4G14690' => 'ath', 'ATR0665G054' => 'atr', 'Atru.chr4.2344' => 'acertr', 'Atru.chr4.2346' => 'acertr', 'Atru.chr4.2347' => 'acertr', 'Atru.chr4.2348' => 'acertr', 'Atru.chr4.2355' => 'acertr', 'Atru.chr4.2356' => 'acertr', 'Atru.chr4.2358' => 'acertr', 'Atru.chr4.2359' => 'acertr', 'Atru.chr4.2360' => 'acertr', 'Atru.chr4.2361' => 'acertr', 'AUR62030476' => 'cqu', 'AUR62030478' => 'cqu', 'AUR62030819' => 'cqu', 'AUR62030820' => 'cqu', 'BcaB03g14648' => 'bca', 'BcaB04g20492' => 'bca', 'BcaB06g26399' => 'bca', 'BcaC01g03416' => 'bca', 'BcaC01g03419' => 'bca', 'BcaC01g03421' => 'bca', 'BcaC01g03424' => 'bca', 'BcaC05g28012' => 'bca', 'BcaC09g49212' => 'bca', 'BcaC09g50140' => 'bca', 'BcaNung00346' => 'bca', 'BolC1t02785H' => 'bol', 'BolC1t04095H' => 'bol', 'BolC3t17545H' => 'bol', 'BolC5t32769H' => 'bol', 'BraA01t02211Z' => 'bra', 'BraA01t03359Z' => 'bra', 'BraA03t13441Z' => 'bra', 'BraA05t21476Z' => 'bra', 'C01p28420' => 'bna', 'C01p41350' => 'bna', 'C03p52750' => 'bna', 'C03p52780' => 'bna', 'C05p40270' => 'bna', 'CAN.G1437.9' => 'can', 'CANSAT78G0035' => 'cansat', 'CANSAT78G1036' => 'cansat', 'CANSAT78G2272' => 'cansat', 'CANSAT78G2478' => 'cansat', 'CARHR098700' => 'chi', 'CARHR221120' => 'chi', 'CARHR221150' => 'chi', 'Carub.0003s2297' => 'cru', 'Carub.0007s2749' => 'cru', 'Carub.0007s2750' => 'cru', 'Carub.0007s2751' => 'cru', 'Ca_10849_v3' => 'car', 'Cc03_g04300' => 'ccan', 'CDE02G3648' => 'cde', 'CDE05G0060' => 'cde', 'CDE05G0692' => 'cde', 'CDE05G2285' => 'cde', 'CDE05G2884' => 'cde', 'CDE05G3072' => 'cde', 'Cfa008439' => 'cfa', 'Cfa008441' => 'cfa', 'Cfa008443' => 'cfa', 'Cfa008448' => 'cfa', 'Ciclev10005974m.g' => 'ccl', 'Ciclev10006006m.g' => 'ccl', 'Ciclev10006775m.g' => 'ccl', 'CiPaw.02G120400' => 'cil', 'CiPaw.02G120500' => 'cil', 'CiPaw.02G120600' => 'cil', 'ClCG05G004850' => 'cla', 'COL.COLO4_21566' => 'col', 'Cpa.g.sc44.124' => 'cpa', 'Cre07.g320400' => 'cre', 'Cre07.g320450' => 'cre', 'Cre08.g384650' => 'cre', 'Cre09.g393173' => 'cre', 'Cre09.g394325' => 'cre', 'Cre14.g626750' => 'cre', 'Cre16.g679250' => 'cre', 'CsaV3_3G012890' => 'csa', 'CSS0010865' => 'camsi', 'CSS0044338' => 'camsi', 'DCAR_002366' => 'dca', 'DCAR_030687' => 'dca', 'DCAR_030688' => 'dca', 'Dinv14047' => 'din', 'Dinv14048' => 'din', 'Duzib151G0105' => 'dzi', 'Duzib151G0114' => 'dzi', 'Duzib212G1029' => 'dzi', 'ECA232G3536' => 'eca', 'ECA240G0786' => 'eca', 'ECA240G1802' => 'eca', 'ECA240G3760' => 'eca', 'ECA240G3920' => 'eca', 'EL10Ac5g12536' => 'bvu', 'EL10Ac5g12537' => 'bvu', 'EL10Ac5g12538' => 'bvu', 'Eucgr.B01004' => 'egr', 'Eucgr.B01006' => 'egr', 'Eucgr.B01007' => 'egr', 'Eucgr.B01008' => 'egr', 'Eucgr.B01895' => 'egr', 'Eucgr.B01896' => 'egr', 'FAN04G1456' => 'fan', 'FAN08G1769' => 'fan', 'FAN08G2160' => 'fan', 'FAN13G2403' => 'fan', 'FAN13G3303' => 'fan', 'FAN15G2435' => 'fan', 'FAN17G0672' => 'fan', 'FAN17G2441' => 'fan', 'FAN18G1024' => 'fan', 'FAN22G1458' => 'fan', 'FAN24G0037' => 'fan', 'FAN24G0429' => 'fan', 'FAN24G2387' => 'fan', 'FAN27G2746' => 'fan', 'FvH4_2g20400' => 'fve', 'FvH4_2g20420' => 'fve', 'FvH4_2g20430' => 'fve', 'FvH4_4g01270' => 'fve', 'FvH4_4g01290' => 'fve', 'FvH4_4g01300' => 'fve', 'FvH4_4g01310' => 'fve', 'FvH4_4g01330' => 'fve', 'FvH4_5g09070' => 'fve', 'Glyma.10G243800' => 'gma', 'Glyma.20G150600' => 'gma', 'Gohir.A09G219200' => 'ghi', 'Gohir.A09G219300' => 'ghi', 'Gohir.D09G221400' => 'ghi', 'Gohir.D09G221500' => 'ghi', 'Gorai.006G242600' => 'gra', 'Gorai.006G242700' => 'gra', 'GSVIVG01018044001' => 'vvi', 'HanXRQChr03g0083821' => 'han', 'HanXRQChr03g0083841' => 'han', 'HanXRQChr03g0083881' => 'han', 'HanXRQChr03g0083901' => 'han', 'HanXRQChr03g0083921' => 'han', 'HanXRQChr03g0085331' => 'han', 'HanXRQChr03g0085361' => 'han', 'HanXRQChr03g0085411' => 'han', 'HanXRQChr03g0085421' => 'han', 'HanXRQChr03g0085431' => 'han', 'HanXRQChr08g0221991' => 'han', 'HanXRQChr11g0336061' => 'han', 'HanXRQChr11g0336411' => 'han', 'Haze_11234' => 'cav', 'Hma1.2p1_0549F.1_g177010' => 'hma', 'Hma1.2p1_0602F.1_g187630' => 'hma', 'Hund14876' => 'sun', 'Hund14879' => 'sun', 'Lalb_Chr06g0160741' => 'lal', 'Lalb_Chr21g0304781' => 'lal', 'Lj3A726G19' => 'lonja', 'Lj3A726T23' => 'lonja', 'Lj3A726T24' => 'lonja', 'Lj3A726T25' => 'lonja', 'Lj3A727T17' => 'lonja', 'Lj3C726T0' => 'lonja', 'Lj3C726T2' => 'lonja', 'Lj3P725T35' => 'lonja', 'Lj3P727T10' => 'lonja', 'Lj3P727T12' => 'lonja', 'Lj3P727T14' => 'lonja', 'Lj5g0023109' => 'lja', 'Lj6P646T44' => 'lonja', 'Lsat_1_v5_gn_6_75760' => 'lsa', 'Lsat_1_v5_gn_6_75800' => 'lsa', 'Lsat_1_v5_gn_6_75900' => 'lsa', 'Lsat_1_v5_gn_6_76240' => 'lsa', 'Lsat_1_v5_gn_6_76441' => 'lsa', 'Lsat_1_v5_gn_6_76700' => 'lsa', 'Lsat_1_v5_gn_6_76760' => 'lsa', 'Manes.15G033100' => 'mes', 'Mapoly0004s0074' => 'mpo', 'Mapoly0004s0075' => 'mpo', 'Mapoly0004s0163' => 'mpo', 'Mapoly0004s0164' => 'mpo', 'Mapoly0021s0018' => 'mpo', 'Mapoly0041s0136' => 'mpo', 'Mapoly0041s0137' => 'mpo', 'Mapoly0041s0138' => 'mpo', 'Mapoly0041s0139' => 'mpo', 'Mapoly0041s0141' => 'mpo', 'Mapoly0041s0142' => 'mpo', 'Mapoly0041s0143' => 'mpo', 'Mapoly0041s0144' => 'mpo', 'Mapoly0041s0145' => 'mpo', 'Mapoly0047s0106' => 'mpo', 'Mapoly0047s0108' => 'mpo', 'Mapoly0050s0051' => 'mpo', 'Mapoly0050s0052' => 'mpo', 'Mapoly0050s0053' => 'mpo', 'Mapoly0058s0013' => 'mpo', 'Mapoly0091s0078' => 'mpo', 'Mapoly0091s0079' => 'mpo', 'Mapoly0091s0080' => 'mpo', 'Mapoly0091s0081' => 'mpo', 'Mapoly0278s0004' => 'mpo', 'Mapoly0278s0005' => 'mpo', 'Mapoly0278s0006' => 'mpo', 'MBI11_g30648_MAGBIO' => 'mbi', 'MCO03G194' => 'mco', 'MCO03G590' => 'mco', 'MCO07G312' => 'mco', 'MCO10G318' => 'mco', 'MCO12G244' => 'mco', 'MCO13G148' => 'mco', 'MCO13G194' => 'mco', 'MCO16G238' => 'mco', 'MD06G1134100' => 'mdo', 'MD13G1200100' => 'mdo', 'MD13G1200300' => 'mdo', 'MD13G1200600' => 'mdo', 'MD14G1150400' => 'mdo', 'MD16G1200000' => 'mdo', 'Medtr1g102570' => 'mtr', 'Medtr1g102780' => 'mtr', 'Medtr1g102800' => 'mtr', 'Medtr1g102810' => 'mtr', 'Medtr1g102830' => 'mtr', 'MELO3C006499.2' => 'cme', 'Migut.G00385' => 'egut', 'MSTRG.4063' => 'ama', 'Nitab4.5_0000090g0260' => 'nta', 'Nitab4.5_0000977g0030' => 'nta', 'Nitab4.5_0002541g0040' => 'nta', 'Nitab4.5_0007068g0040' => 'nta', 'Nn005s41408' => 'nnu', 'Nn005s41410' => 'nnu', 'Oeu010310.1' => 'oeu', 'Oeu010311.1' => 'oeu', 'Oeu043472.1' => 'oeu', 'Os01g0246400' => 'osa', 'Os04g0267950' => 'osa', 'Os07g0178700' => 'osa', 'Os07g0178800' => 'osa', 'Peaxi162Scf00316g00046' => 'pax', 'Peaxi162Scf00316g00049' => 'pax', 'Peaxi162Scf00316g00059' => 'pax', 'Peaxi162Scf00316g00328' => 'pax', 'Peaxi162Scf00316g00329' => 'pax', 'Peaxi162Scf00316g00411' => 'pax', 'Peaxi162Scf00316g00521' => 'pax', 'Peaxi162Scf00492g00068' => 'pax', 'Peaxi162Scf35631g00002' => 'pax', 'PGR142G3720' => 'pgr', 'PGSC0003DMG400006442' => 'stu', 'Phvul.007G062000' => 'pvu', 'Potri.008G157750' => 'ptr', 'Potri.008G157900' => 'ptr', 'Potri.008G158000' => 'ptr', 'Potri.008G158200' => 'ptr', 'Pp3c11_7280' => 'ppa', 'Pp3c11_7980' => 'ppa', 'Pp3c12_19450' => 'ppa', 'Pp3c14_1480' => 'ppa', 'Pp3c14_1501' => 'ppa', 'Pp3c16_4900' => 'ppa', 'Pp3c16_5010' => 'ppa', 'Pp3c16_5060' => 'ppa', 'Pp3c19_18250' => 'ppa', 'Pp3c23_8530' => 'ppa', 'Pp3c23_8550' => 'ppa', 'Pp3c24_9670' => 'ppa', 'Pp3c2_21390' => 'ppa', 'Pp3c2_31380' => 'ppa', 'Pp3c3_16620' => 'ppa', 'Pp3c3_8090' => 'ppa', 'Pp3c3_8110' => 'ppa', 'Pp3c3_8130' => 'ppa', 'Pp3c3_8150' => 'ppa', 'Pp3c4_14320' => 'ppa', 'Pp3c6_2560' => 'ppa', 'Pp3c9_16700' => 'ppa', 'PRCOL_00000234' => 'pco', 'PRCOL_00000235' => 'pco', 'PRCOL_00000777' => 'pco', 'PRCOL_00002344' => 'pco', 'PRCOL_00002372' => 'pco', 'PRCOL_00006120' => 'pco', 'Prupe.1G021400' => 'ppe', 'Prupe.1G021500' => 'ppe', 'Prupe.1G021600' => 'ppe', 'Prupe.1G021700' => 'ppe', 'Prupe.1G021800' => 'ppe', 'Prupe.5G145100' => 'ppe', 'Psat6g204040' => 'psa', 'Psat6g204800' => 'psa', 'Psat6g204920' => 'psa', 'Psat6g204960' => 'psa', 'Psat6g205080' => 'psa', 'PSO017G0271' => 'pso', 'PSO017G1276' => 'pso', 'PSO017G1429' => 'pso', 'PSO017G1861' => 'pso', 'PSO017G2787' => 'pso', 'PSO017G4466' => 'pso', 'PSO017G5118' => 'pso', 'PSO017G5420' => 'pso', 'PSO063G3678' => 'pso', 'PSO210G0546' => 'pso', 'PSO317G0001' => 'pso', 'PSO357G0512' => 'pso', 'PSO478G2682' => 'pso', 'PSO647G0001' => 'pso', 'PSO675G0001' => 'pso', 'PSO675G2699' => 'pso', 'PSO675G2849' => 'pso', 'PSO675G4991' => 'pso', 'PSO689G0001' => 'pso', 'QL06p000916' => 'qlo', 'QL06p000921' => 'qlo', 'QL06p001398' => 'qlo', 'QL06p001407' => 'qlo', 'QL06p002031' => 'qlo', 'RcHm_v2.0_Chr4g0387791' => 'rch', 'RcHm_v2.0_Chr4g0387801' => 'rch', 'RcHm_v2.0_Chr6g0286501' => 'rch', 'RcHm_v2.0_Chr6g0286511' => 'rch', 'RcHm_v2.0_Chr6g0286521' => 'rch', 'RcHm_v2.0_Chr6g0286531' => 'rch', 'RcHm_v2.0_Chr7g0189141' => 'rch', 'Rhsim02G0028700' => 'rsi', 'Rhsim02G0028800' => 'rsi', 'Rhsim02G0028900' => 'rsi', 'Rhsim02G0029000' => 'rsi', 'Rhsim02G0029100' => 'rsi', 'Rhsim02G0029200' => 'rsi', 'Rhsim02G0029300' => 'rsi', 'Rhsim02G0029400' => 'rsi', 'Rhsim02G0029500' => 'rsi', 'Rhsim02G0029600' => 'rsi', 'RhsimUnG0024000' => 'rsi', 'RhsimUnG0024100' => 'rsi', 'RhsimUnG0024200' => 'rsi', 'RhsimUnG0024300' => 'rsi', 'RhsimUnG0024400' => 'rsi', 'RhsimUnG0024500' => 'rsi', 'RhsimUnG0024700' => 'rsi', 'RhsimUnG0024800' => 'rsi', 'RhsimUnG0024900' => 'rsi', 'RhsimUnG0025100' => 'rsi', 'Sabra08G0120200' => 'sbr', 'Sabra08G0120300' => 'sbr', 'Sabra08G0120500' => 'sbr', 'Sabra08G0120600' => 'sbr', 'Sabra10G0158900' => 'sbr', 'SalBow2G3492' => 'sbo', 'Sc13g0004760' => 'sci', 'Sc13g0004770' => 'sci', 'Sed0003417' => 'sed', 'Sed0019750' => 'sed', 'SEGI_03419' => 'sgi', 'SEGI_05907' => 'sgi', 'SEGI_10682' => 'sgi', 'SEGI_13528' => 'sgi', 'SEGI_16081' => 'sgi', 'SEGI_19370' => 'sgi', 'SEGI_21015' => 'sgi', 'SEGI_21944' => 'sgi', 'SEGI_32906' => 'sgi', 'SEGI_33093' => 'sgi', 'SEGI_36110' => 'sgi', 'SEGI_40397' => 'sgi', 'SGA_v2.0_scaffold191G40426' => 'sas', 'SGA_v2.0_scaffold353G49717' => 'sas', 'SGA_v2.0_scaffold50G18550' => 'sas', 'SMO119G0173' => 'smo', 'SMO172G0002' => 'smo', 'Solyc09g082690.3' => 'sly', 'Solyc09g082700.2' => 'sly', 'Sopen09g031550' => 'spe', 'Sopen09g031560' => 'spe', 'Sp3g20540' => 'spa', 'Sp7g07580' => 'spa', 'TAR134G0002' => 'tar', 'TAR236G0001' => 'tar', 'TAR365G0892' => 'tar', 'TAR636G0166' => 'tar', 'TAR636G0646' => 'tar', 'TAR636G0869' => 'tar', 'TAR636G1317' => 'tar', 'TAR636G1744' => 'tar', 'TAR636G3358' => 'tar', 'TAR636G3436' => 'tar', 'THA.LOC104803047' => 'tha', 'Thecc.04G238900' => 'tca', 'Thhalv10021557m.g' => 'esa', 'Thhalv10026318m.g' => 'esa', 'Thhalv10026335m.g' => 'esa', 'TPR.G17433' => 'tpr', 'TPR.G18915' => 'tpr', 'TPR.G26125' => 'tpr', 'TWI09G0677' => 'twi', 'TWI73G0287' => 'twi', 'unitig_748.g8326' => 'ugi', 'vmacro15370' => 'vma', 'vmacro15371' => 'vma', 'vmacro15372' => 'vma', 'vmacro15373' => 'vma', 'vmacro15374' => 'vma', 'VMungo0720G2826' => 'vmu', 'Zm00001eb116960' => 'zma', 'Zm00001eb301260' => 'zma', 'Zm00001eb301270' => 'zma' ) $gf_id = 'HOM05D001460' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001460' ) $data_identifier = 'HOM05D001460' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 4, 'aag' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 2, 'aox' => (int) 2, 'arhy' => (int) 4, 'ath' => (int) 2, 'atr' => (int) 1, 'acertr' => (int) 10, 'cqu' => (int) 4, 'bca' => (int) 11, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 1, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 1, 'ccan' => (int) 1, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 1, 'col' => (int) 1, 'cpa' => (int) 1, 'cre' => (int) 7, 'csa' => (int) 1, 'camsi' => (int) 2, 'dca' => (int) 3, 'din' => (int) 2, 'dzi' => (int) 3, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 14, 'fve' => (int) 9, 'gma' => (int) 2, 'ghi' => (int) 4, 'gra' => (int) 2, 'vvi' => (int) 1, 'han' => (int) 13, 'cav' => (int) 1, 'hma' => (int) 2, 'sun' => (int) 2, 'lal' => (int) 2, 'lonja' => (int) 12, 'lja' => (int) 1, 'lsa' => (int) 7, 'mes' => (int) 1, 'mpo' => (int) 27, 'mbi' => (int) 1, 'mco' => (int) 8, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 1, 'egut' => (int) 1, 'ama' => (int) 1, 'nta' => (int) 4, 'nnu' => (int) 2, 'oeu' => (int) 3, 'osa' => (int) 4, 'pax' => (int) 9, 'pgr' => (int) 1, 'stu' => (int) 1, 'pvu' => (int) 1, 'ptr' => (int) 4, 'ppa' => (int) 22, 'pco' => (int) 6, 'ppe' => (int) 6, 'psa' => (int) 5, 'pso' => (int) 19, 'qlo' => (int) 5, 'rch' => (int) 7, 'rsi' => (int) 20, 'sbr' => (int) 5, 'sbo' => (int) 1, 'sci' => (int) 2, 'sed' => (int) 2, 'sgi' => (int) 12, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 2, 'tar' => (int) 10, 'tha' => (int) 1, 'tca' => (int) 1, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 2, 'ugi' => (int) 1, 'vma' => (int) 5, 'vmu' => (int) 1, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb301270' $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' => 'HOM05D001460', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '433', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p22980' => 'bna', 'A01p32340' => 'bna', 'A03p42970' => 'bna', 'A05p25880' => 'bna', 'Aa31LG8G9320' => 'aar', 'Aa31LG8G9330' => 'aar', 'Aa31LG8G9340' => 'aar', 'Aa31sc221G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1034' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1528' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.829' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2222' => 'aag', 'Ah.12g058830' => 'amhyb', 'Ah.12g058840' => 'amhyb', 'AL3G37160' => 'aly', 'AL7G41310' => 'aly', 'Aqoxy5G00395' => 'aox', 'Aqoxy5G00396' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0C8NZA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5185HY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JZ1PRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MD3LS0' => 'arhy', 'AT3G22840' => 'ath', 'AT4G14690' => 'ath', 'ATR0665G054' => 'atr', 'Atru.chr4.2344' => 'acertr', 'Atru.chr4.2346' => 'acertr', 'Atru.chr4.2347' => 'acertr', 'Atru.chr4.2348' => 'acertr', 'Atru.chr4.2355' => 'acertr', 'Atru.chr4.2356' => 'acertr', 'Atru.chr4.2358' => 'acertr', 'Atru.chr4.2359' => 'acertr', 'Atru.chr4.2360' => 'acertr', 'Atru.chr4.2361' => 'acertr', 'AUR62030476' => 'cqu', 'AUR62030478' => 'cqu', 'AUR62030819' => 'cqu', 'AUR62030820' => 'cqu', 'BcaB03g14648' => 'bca', 'BcaB04g20492' => 'bca', 'BcaB06g26399' => 'bca', 'BcaC01g03416' => 'bca', 'BcaC01g03419' => 'bca', 'BcaC01g03421' => 'bca', 'BcaC01g03424' => 'bca', 'BcaC05g28012' => 'bca', 'BcaC09g49212' => 'bca', 'BcaC09g50140' => 'bca', 'BcaNung00346' => 'bca', 'BolC1t02785H' => 'bol', 'BolC1t04095H' => 'bol', 'BolC3t17545H' => 'bol', 'BolC5t32769H' => 'bol', 'BraA01t02211Z' => 'bra', 'BraA01t03359Z' => 'bra', 'BraA03t13441Z' => 'bra', 'BraA05t21476Z' => 'bra', 'C01p28420' => 'bna', 'C01p41350' => 'bna', 'C03p52750' => 'bna', 'C03p52780' => 'bna', 'C05p40270' => 'bna', 'CAN.G1437.9' => 'can', 'CANSAT78G0035' => 'cansat', 'CANSAT78G1036' => 'cansat', 'CANSAT78G2272' => 'cansat', 'CANSAT78G2478' => 'cansat', 'CARHR098700' => 'chi', 'CARHR221120' => 'chi', 'CARHR221150' => 'chi', 'Carub.0003s2297' => 'cru', 'Carub.0007s2749' => 'cru', 'Carub.0007s2750' => 'cru', 'Carub.0007s2751' => 'cru', 'Ca_10849_v3' => 'car', 'Cc03_g04300' => 'ccan', 'CDE02G3648' => 'cde', 'CDE05G0060' => 'cde', 'CDE05G0692' => 'cde', 'CDE05G2285' => 'cde', 'CDE05G2884' => 'cde', 'CDE05G3072' => 'cde', 'Cfa008439' => 'cfa', 'Cfa008441' => 'cfa', 'Cfa008443' => 'cfa', 'Cfa008448' => 'cfa', 'Ciclev10005974m.g' => 'ccl', 'Ciclev10006006m.g' => 'ccl', 'Ciclev10006775m.g' => 'ccl', 'CiPaw.02G120400' => 'cil', 'CiPaw.02G120500' => 'cil', 'CiPaw.02G120600' => 'cil', 'ClCG05G004850' => 'cla', 'COL.COLO4_21566' => 'col', 'Cpa.g.sc44.124' => 'cpa', 'Cre07.g320400' => 'cre', 'Cre07.g320450' => 'cre', 'Cre08.g384650' => 'cre', 'Cre09.g393173' => 'cre', 'Cre09.g394325' => 'cre', 'Cre14.g626750' => 'cre', 'Cre16.g679250' => 'cre', 'CsaV3_3G012890' => 'csa', 'CSS0010865' => 'camsi', 'CSS0044338' => 'camsi', 'DCAR_002366' => 'dca', 'DCAR_030687' => 'dca', 'DCAR_030688' => 'dca', 'Dinv14047' => 'din', 'Dinv14048' => 'din', 'Duzib151G0105' => 'dzi', 'Duzib151G0114' => 'dzi', 'Duzib212G1029' => 'dzi', 'ECA232G3536' => 'eca', 'ECA240G0786' => 'eca', 'ECA240G1802' => 'eca', 'ECA240G3760' => 'eca', 'ECA240G3920' => 'eca', 'EL10Ac5g12536' => 'bvu', 'EL10Ac5g12537' => 'bvu', 'EL10Ac5g12538' => 'bvu', 'Eucgr.B01004' => 'egr', 'Eucgr.B01006' => 'egr', 'Eucgr.B01007' => 'egr', 'Eucgr.B01008' => 'egr', 'Eucgr.B01895' => 'egr', 'Eucgr.B01896' => 'egr', 'FAN04G1456' => 'fan', 'FAN08G1769' => 'fan', 'FAN08G2160' => 'fan', 'FAN13G2403' => 'fan', 'FAN13G3303' => 'fan', 'FAN15G2435' => 'fan', 'FAN17G0672' => 'fan', 'FAN17G2441' => 'fan', 'FAN18G1024' => 'fan', 'FAN22G1458' => 'fan', 'FAN24G0037' => 'fan', 'FAN24G0429' => 'fan', 'FAN24G2387' => 'fan', 'FAN27G2746' => 'fan', 'FvH4_2g20400' => 'fve', 'FvH4_2g20420' => 'fve', 'FvH4_2g20430' => 'fve', 'FvH4_4g01270' => 'fve', 'FvH4_4g01290' => 'fve', 'FvH4_4g01300' => 'fve', 'FvH4_4g01310' => 'fve', 'FvH4_4g01330' => 'fve', 'FvH4_5g09070' => 'fve', 'Glyma.10G243800' => 'gma', 'Glyma.20G150600' => 'gma', 'Gohir.A09G219200' => 'ghi', 'Gohir.A09G219300' => 'ghi', 'Gohir.D09G221400' => 'ghi', 'Gohir.D09G221500' => 'ghi', 'Gorai.006G242600' => 'gra', 'Gorai.006G242700' => 'gra', 'GSVIVG01018044001' => 'vvi', 'HanXRQChr03g0083821' => 'han', 'HanXRQChr03g0083841' => 'han', 'HanXRQChr03g0083881' => 'han', 'HanXRQChr03g0083901' => 'han', 'HanXRQChr03g0083921' => 'han', 'HanXRQChr03g0085331' => 'han', 'HanXRQChr03g0085361' => 'han', 'HanXRQChr03g0085411' => 'han', 'HanXRQChr03g0085421' => 'han', 'HanXRQChr03g0085431' => 'han', 'HanXRQChr08g0221991' => 'han', 'HanXRQChr11g0336061' => 'han', 'HanXRQChr11g0336411' => 'han', 'Haze_11234' => 'cav', 'Hma1.2p1_0549F.1_g177010' => 'hma', 'Hma1.2p1_0602F.1_g187630' => 'hma', 'Hund14876' => 'sun', 'Hund14879' => 'sun', 'Lalb_Chr06g0160741' => 'lal', 'Lalb_Chr21g0304781' => 'lal', 'Lj3A726G19' => 'lonja', 'Lj3A726T23' => 'lonja', 'Lj3A726T24' => 'lonja', 'Lj3A726T25' => 'lonja', 'Lj3A727T17' => 'lonja', 'Lj3C726T0' => 'lonja', 'Lj3C726T2' => 'lonja', 'Lj3P725T35' => 'lonja', 'Lj3P727T10' => 'lonja', 'Lj3P727T12' => 'lonja', 'Lj3P727T14' => 'lonja', 'Lj5g0023109' => 'lja', 'Lj6P646T44' => 'lonja', 'Lsat_1_v5_gn_6_75760' => 'lsa', 'Lsat_1_v5_gn_6_75800' => 'lsa', 'Lsat_1_v5_gn_6_75900' => 'lsa', 'Lsat_1_v5_gn_6_76240' => 'lsa', 'Lsat_1_v5_gn_6_76441' => 'lsa', 'Lsat_1_v5_gn_6_76700' => 'lsa', 'Lsat_1_v5_gn_6_76760' => 'lsa', 'Manes.15G033100' => 'mes', 'Mapoly0004s0074' => 'mpo', 'Mapoly0004s0075' => 'mpo', 'Mapoly0004s0163' => 'mpo', 'Mapoly0004s0164' => 'mpo', 'Mapoly0021s0018' => 'mpo', 'Mapoly0041s0136' => 'mpo', 'Mapoly0041s0137' => 'mpo', 'Mapoly0041s0138' => 'mpo', 'Mapoly0041s0139' => 'mpo', 'Mapoly0041s0141' => 'mpo', 'Mapoly0041s0142' => 'mpo', 'Mapoly0041s0143' => 'mpo', 'Mapoly0041s0144' => 'mpo', 'Mapoly0041s0145' => 'mpo', 'Mapoly0047s0106' => 'mpo', 'Mapoly0047s0108' => 'mpo', 'Mapoly0050s0051' => 'mpo', 'Mapoly0050s0052' => 'mpo', 'Mapoly0050s0053' => 'mpo', 'Mapoly0058s0013' => 'mpo', 'Mapoly0091s0078' => 'mpo', 'Mapoly0091s0079' => 'mpo', 'Mapoly0091s0080' => 'mpo', 'Mapoly0091s0081' => 'mpo', 'Mapoly0278s0004' => 'mpo', 'Mapoly0278s0005' => 'mpo', 'Mapoly0278s0006' => 'mpo', 'MBI11_g30648_MAGBIO' => 'mbi', 'MCO03G194' => 'mco', 'MCO03G590' => 'mco', 'MCO07G312' => 'mco', 'MCO10G318' => 'mco', 'MCO12G244' => 'mco', 'MCO13G148' => 'mco', 'MCO13G194' => 'mco', 'MCO16G238' => 'mco', 'MD06G1134100' => 'mdo', 'MD13G1200100' => 'mdo', 'MD13G1200300' => 'mdo', 'MD13G1200600' => 'mdo', 'MD14G1150400' => 'mdo', 'MD16G1200000' => 'mdo', 'Medtr1g102570' => 'mtr', 'Medtr1g102780' => 'mtr', 'Medtr1g102800' => 'mtr', 'Medtr1g102810' => 'mtr', 'Medtr1g102830' => 'mtr', 'MELO3C006499.2' => 'cme', 'Migut.G00385' => 'egut', 'MSTRG.4063' => 'ama', 'Nitab4.5_0000090g0260' => 'nta', 'Nitab4.5_0000977g0030' => 'nta', 'Nitab4.5_0002541g0040' => 'nta', 'Nitab4.5_0007068g0040' => 'nta', 'Nn005s41408' => 'nnu', 'Nn005s41410' => 'nnu', 'Oeu010310.1' => 'oeu', 'Oeu010311.1' => 'oeu', 'Oeu043472.1' => 'oeu', 'Os01g0246400' => 'osa', 'Os04g0267950' => 'osa', 'Os07g0178700' => 'osa', 'Os07g0178800' => 'osa', 'Peaxi162Scf00316g00046' => 'pax', 'Peaxi162Scf00316g00049' => 'pax', 'Peaxi162Scf00316g00059' => 'pax', 'Peaxi162Scf00316g00328' => 'pax', 'Peaxi162Scf00316g00329' => 'pax', 'Peaxi162Scf00316g00411' => 'pax', 'Peaxi162Scf00316g00521' => 'pax', 'Peaxi162Scf00492g00068' => 'pax', 'Peaxi162Scf35631g00002' => 'pax', 'PGR142G3720' => 'pgr', 'PGSC0003DMG400006442' => 'stu', 'Phvul.007G062000' => 'pvu', 'Potri.008G157750' => 'ptr', 'Potri.008G157900' => 'ptr', 'Potri.008G158000' => 'ptr', 'Potri.008G158200' => 'ptr', 'Pp3c11_7280' => 'ppa', 'Pp3c11_7980' => 'ppa', 'Pp3c12_19450' => 'ppa', 'Pp3c14_1480' => 'ppa', 'Pp3c14_1501' => 'ppa', 'Pp3c16_4900' => 'ppa', 'Pp3c16_5010' => 'ppa', 'Pp3c16_5060' => 'ppa', 'Pp3c19_18250' => 'ppa', 'Pp3c23_8530' => 'ppa', 'Pp3c23_8550' => 'ppa', 'Pp3c24_9670' => 'ppa', 'Pp3c2_21390' => 'ppa', 'Pp3c2_31380' => 'ppa', 'Pp3c3_16620' => 'ppa', 'Pp3c3_8090' => 'ppa', 'Pp3c3_8110' => 'ppa', 'Pp3c3_8130' => 'ppa', 'Pp3c3_8150' => 'ppa', 'Pp3c4_14320' => 'ppa', 'Pp3c6_2560' => 'ppa', 'Pp3c9_16700' => 'ppa', 'PRCOL_00000234' => 'pco', 'PRCOL_00000235' => 'pco', 'PRCOL_00000777' => 'pco', 'PRCOL_00002344' => 'pco', 'PRCOL_00002372' => 'pco', 'PRCOL_00006120' => 'pco', 'Prupe.1G021400' => 'ppe', 'Prupe.1G021500' => 'ppe', 'Prupe.1G021600' => 'ppe', 'Prupe.1G021700' => 'ppe', 'Prupe.1G021800' => 'ppe', 'Prupe.5G145100' => 'ppe', 'Psat6g204040' => 'psa', 'Psat6g204800' => 'psa', 'Psat6g204920' => 'psa', 'Psat6g204960' => 'psa', 'Psat6g205080' => 'psa', 'PSO017G0271' => 'pso', 'PSO017G1276' => 'pso', 'PSO017G1429' => 'pso', 'PSO017G1861' => 'pso', 'PSO017G2787' => 'pso', 'PSO017G4466' => 'pso', 'PSO017G5118' => 'pso', 'PSO017G5420' => 'pso', 'PSO063G3678' => 'pso', 'PSO210G0546' => 'pso', 'PSO317G0001' => 'pso', 'PSO357G0512' => 'pso', 'PSO478G2682' => 'pso', 'PSO647G0001' => 'pso', 'PSO675G0001' => 'pso', 'PSO675G2699' => 'pso', 'PSO675G2849' => 'pso', 'PSO675G4991' => 'pso', 'PSO689G0001' => 'pso', 'QL06p000916' => 'qlo', 'QL06p000921' => 'qlo', 'QL06p001398' => 'qlo', 'QL06p001407' => 'qlo', 'QL06p002031' => 'qlo', 'RcHm_v2.0_Chr4g0387791' => 'rch', 'RcHm_v2.0_Chr4g0387801' => 'rch', 'RcHm_v2.0_Chr6g0286501' => 'rch', 'RcHm_v2.0_Chr6g0286511' => 'rch', 'RcHm_v2.0_Chr6g0286521' => 'rch', 'RcHm_v2.0_Chr6g0286531' => 'rch', 'RcHm_v2.0_Chr7g0189141' => 'rch', 'Rhsim02G0028700' => 'rsi', 'Rhsim02G0028800' => 'rsi', 'Rhsim02G0028900' => 'rsi', 'Rhsim02G0029000' => 'rsi', 'Rhsim02G0029100' => 'rsi', 'Rhsim02G0029200' => 'rsi', 'Rhsim02G0029300' => 'rsi', 'Rhsim02G0029400' => 'rsi', 'Rhsim02G0029500' => 'rsi', 'Rhsim02G0029600' => 'rsi', 'RhsimUnG0024000' => 'rsi', 'RhsimUnG0024100' => 'rsi', 'RhsimUnG0024200' => 'rsi', 'RhsimUnG0024300' => 'rsi', 'RhsimUnG0024400' => 'rsi', 'RhsimUnG0024500' => 'rsi', 'RhsimUnG0024700' => 'rsi', 'RhsimUnG0024800' => 'rsi', 'RhsimUnG0024900' => 'rsi', 'RhsimUnG0025100' => 'rsi', 'Sabra08G0120200' => 'sbr', 'Sabra08G0120300' => 'sbr', 'Sabra08G0120500' => 'sbr', 'Sabra08G0120600' => 'sbr', 'Sabra10G0158900' => 'sbr', 'SalBow2G3492' => 'sbo', 'Sc13g0004760' => 'sci', 'Sc13g0004770' => 'sci', 'Sed0003417' => 'sed', 'Sed0019750' => 'sed', 'SEGI_03419' => 'sgi', 'SEGI_05907' => 'sgi', 'SEGI_10682' => 'sgi', 'SEGI_13528' => 'sgi', 'SEGI_16081' => 'sgi', 'SEGI_19370' => 'sgi', 'SEGI_21015' => 'sgi', 'SEGI_21944' => 'sgi', 'SEGI_32906' => 'sgi', 'SEGI_33093' => 'sgi', 'SEGI_36110' => 'sgi', 'SEGI_40397' => 'sgi', 'SGA_v2.0_scaffold191G40426' => 'sas', 'SGA_v2.0_scaffold353G49717' => 'sas', 'SGA_v2.0_scaffold50G18550' => 'sas', 'SMO119G0173' => 'smo', 'SMO172G0002' => 'smo', 'Solyc09g082690.3' => 'sly', 'Solyc09g082700.2' => 'sly', 'Sopen09g031550' => 'spe', 'Sopen09g031560' => 'spe', 'Sp3g20540' => 'spa', 'Sp7g07580' => 'spa', 'TAR134G0002' => 'tar', 'TAR236G0001' => 'tar', 'TAR365G0892' => 'tar', 'TAR636G0166' => 'tar', 'TAR636G0646' => 'tar', 'TAR636G0869' => 'tar', 'TAR636G1317' => 'tar', 'TAR636G1744' => 'tar', 'TAR636G3358' => 'tar', 'TAR636G3436' => 'tar', 'THA.LOC104803047' => 'tha', 'Thecc.04G238900' => 'tca', 'Thhalv10021557m.g' => 'esa', 'Thhalv10026318m.g' => 'esa', 'Thhalv10026335m.g' => 'esa', 'TPR.G17433' => 'tpr', 'TPR.G18915' => 'tpr', 'TPR.G26125' => 'tpr', 'TWI09G0677' => 'twi', 'TWI73G0287' => 'twi', 'unitig_748.g8326' => 'ugi', 'vmacro15370' => 'vma', 'vmacro15371' => 'vma', 'vmacro15372' => 'vma', 'vmacro15373' => 'vma', 'vmacro15374' => 'vma', 'VMungo0720G2826' => 'vmu', 'Zm00001eb116960' => 'zma', 'Zm00001eb301260' => 'zma', 'Zm00001eb301270' => 'zma' ), 'gf_id' => 'HOM05D001460', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001460' ), 'data_identifier' => 'HOM05D001460', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001460', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '433', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p22980' => 'bna', 'A01p32340' => 'bna', 'A03p42970' => 'bna', 'A05p25880' => 'bna', 'Aa31LG8G9320' => 'aar', 'Aa31LG8G9330' => 'aar', 'Aa31LG8G9340' => 'aar', 'Aa31sc221G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1034' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1528' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.829' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2222' => 'aag', 'Ah.12g058830' => 'amhyb', 'Ah.12g058840' => 'amhyb', 'AL3G37160' => 'aly', 'AL7G41310' => 'aly', 'Aqoxy5G00395' => 'aox', 'Aqoxy5G00396' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0C8NZA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5185HY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JZ1PRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MD3LS0' => 'arhy', 'AT3G22840' => 'ath', 'AT4G14690' => 'ath', 'ATR0665G054' => 'atr', 'Atru.chr4.2344' => 'acertr', 'Atru.chr4.2346' => 'acertr', 'Atru.chr4.2347' => 'acertr', 'Atru.chr4.2348' => 'acertr', 'Atru.chr4.2355' => 'acertr', 'Atru.chr4.2356' => 'acertr', 'Atru.chr4.2358' => 'acertr', 'Atru.chr4.2359' => 'acertr', 'Atru.chr4.2360' => 'acertr', 'Atru.chr4.2361' => 'acertr', 'AUR62030476' => 'cqu', 'AUR62030478' => 'cqu', 'AUR62030819' => 'cqu', 'AUR62030820' => 'cqu', 'BcaB03g14648' => 'bca', 'BcaB04g20492' => 'bca', 'BcaB06g26399' => 'bca', 'BcaC01g03416' => 'bca', 'BcaC01g03419' => 'bca', 'BcaC01g03421' => 'bca', 'BcaC01g03424' => 'bca', 'BcaC05g28012' => 'bca', 'BcaC09g49212' => 'bca', 'BcaC09g50140' => 'bca', 'BcaNung00346' => 'bca', 'BolC1t02785H' => 'bol', 'BolC1t04095H' => 'bol', 'BolC3t17545H' => 'bol', 'BolC5t32769H' => 'bol', 'BraA01t02211Z' => 'bra', 'BraA01t03359Z' => 'bra', 'BraA03t13441Z' => 'bra', 'BraA05t21476Z' => 'bra', 'C01p28420' => 'bna', 'C01p41350' => 'bna', 'C03p52750' => 'bna', 'C03p52780' => 'bna', 'C05p40270' => 'bna', 'CAN.G1437.9' => 'can', 'CANSAT78G0035' => 'cansat', 'CANSAT78G1036' => 'cansat', 'CANSAT78G2272' => 'cansat', 'CANSAT78G2478' => 'cansat', 'CARHR098700' => 'chi', 'CARHR221120' => 'chi', 'CARHR221150' => 'chi', 'Carub.0003s2297' => 'cru', 'Carub.0007s2749' => 'cru', 'Carub.0007s2750' => 'cru', 'Carub.0007s2751' => 'cru', 'Ca_10849_v3' => 'car', 'Cc03_g04300' => 'ccan', 'CDE02G3648' => 'cde', 'CDE05G0060' => 'cde', 'CDE05G0692' => 'cde', 'CDE05G2285' => 'cde', 'CDE05G2884' => 'cde', 'CDE05G3072' => 'cde', 'Cfa008439' => 'cfa', 'Cfa008441' => 'cfa', 'Cfa008443' => 'cfa', 'Cfa008448' => 'cfa', 'Ciclev10005974m.g' => 'ccl', 'Ciclev10006006m.g' => 'ccl', 'Ciclev10006775m.g' => 'ccl', 'CiPaw.02G120400' => 'cil', 'CiPaw.02G120500' => 'cil', 'CiPaw.02G120600' => 'cil', 'ClCG05G004850' => 'cla', 'COL.COLO4_21566' => 'col', 'Cpa.g.sc44.124' => 'cpa', 'Cre07.g320400' => 'cre', 'Cre07.g320450' => 'cre', 'Cre08.g384650' => 'cre', 'Cre09.g393173' => 'cre', 'Cre09.g394325' => 'cre', 'Cre14.g626750' => 'cre', 'Cre16.g679250' => 'cre', 'CsaV3_3G012890' => 'csa', 'CSS0010865' => 'camsi', 'CSS0044338' => 'camsi', 'DCAR_002366' => 'dca', 'DCAR_030687' => 'dca', 'DCAR_030688' => 'dca', 'Dinv14047' => 'din', 'Dinv14048' => 'din', 'Duzib151G0105' => 'dzi', 'Duzib151G0114' => 'dzi', 'Duzib212G1029' => 'dzi', 'ECA232G3536' => 'eca', 'ECA240G0786' => 'eca', 'ECA240G1802' => 'eca', 'ECA240G3760' => 'eca', 'ECA240G3920' => 'eca', 'EL10Ac5g12536' => 'bvu', 'EL10Ac5g12537' => 'bvu', 'EL10Ac5g12538' => 'bvu', 'Eucgr.B01004' => 'egr', 'Eucgr.B01006' => 'egr', 'Eucgr.B01007' => 'egr', 'Eucgr.B01008' => 'egr', 'Eucgr.B01895' => 'egr', 'Eucgr.B01896' => 'egr', 'FAN04G1456' => 'fan', 'FAN08G1769' => 'fan', 'FAN08G2160' => 'fan', 'FAN13G2403' => 'fan', 'FAN13G3303' => 'fan', 'FAN15G2435' => 'fan', 'FAN17G0672' => 'fan', 'FAN17G2441' => 'fan', 'FAN18G1024' => 'fan', 'FAN22G1458' => 'fan', 'FAN24G0037' => 'fan', 'FAN24G0429' => 'fan', 'FAN24G2387' => 'fan', 'FAN27G2746' => 'fan', 'FvH4_2g20400' => 'fve', 'FvH4_2g20420' => 'fve', 'FvH4_2g20430' => 'fve', 'FvH4_4g01270' => 'fve', 'FvH4_4g01290' => 'fve', 'FvH4_4g01300' => 'fve', 'FvH4_4g01310' => 'fve', 'FvH4_4g01330' => 'fve', 'FvH4_5g09070' => 'fve', 'Glyma.10G243800' => 'gma', 'Glyma.20G150600' => 'gma', 'Gohir.A09G219200' => 'ghi', 'Gohir.A09G219300' => 'ghi', 'Gohir.D09G221400' => 'ghi', 'Gohir.D09G221500' => 'ghi', 'Gorai.006G242600' => 'gra', 'Gorai.006G242700' => 'gra', 'GSVIVG01018044001' => 'vvi', 'HanXRQChr03g0083821' => 'han', 'HanXRQChr03g0083841' => 'han', 'HanXRQChr03g0083881' => 'han', 'HanXRQChr03g0083901' => 'han', 'HanXRQChr03g0083921' => 'han', 'HanXRQChr03g0085331' => 'han', 'HanXRQChr03g0085361' => 'han', 'HanXRQChr03g0085411' => 'han', 'HanXRQChr03g0085421' => 'han', 'HanXRQChr03g0085431' => 'han', 'HanXRQChr08g0221991' => 'han', 'HanXRQChr11g0336061' => 'han', 'HanXRQChr11g0336411' => 'han', 'Haze_11234' => 'cav', 'Hma1.2p1_0549F.1_g177010' => 'hma', 'Hma1.2p1_0602F.1_g187630' => 'hma', 'Hund14876' => 'sun', 'Hund14879' => 'sun', 'Lalb_Chr06g0160741' => 'lal', 'Lalb_Chr21g0304781' => 'lal', 'Lj3A726G19' => 'lonja', 'Lj3A726T23' => 'lonja', 'Lj3A726T24' => 'lonja', 'Lj3A726T25' => 'lonja', 'Lj3A727T17' => 'lonja', 'Lj3C726T0' => 'lonja', 'Lj3C726T2' => 'lonja', 'Lj3P725T35' => 'lonja', 'Lj3P727T10' => 'lonja', 'Lj3P727T12' => 'lonja', 'Lj3P727T14' => 'lonja', 'Lj5g0023109' => 'lja', 'Lj6P646T44' => 'lonja', 'Lsat_1_v5_gn_6_75760' => 'lsa', 'Lsat_1_v5_gn_6_75800' => 'lsa', 'Lsat_1_v5_gn_6_75900' => 'lsa', 'Lsat_1_v5_gn_6_76240' => 'lsa', 'Lsat_1_v5_gn_6_76441' => 'lsa', 'Lsat_1_v5_gn_6_76700' => 'lsa', 'Lsat_1_v5_gn_6_76760' => 'lsa', 'Manes.15G033100' => 'mes', 'Mapoly0004s0074' => 'mpo', 'Mapoly0004s0075' => 'mpo', 'Mapoly0004s0163' => 'mpo', 'Mapoly0004s0164' => 'mpo', 'Mapoly0021s0018' => 'mpo', 'Mapoly0041s0136' => 'mpo', 'Mapoly0041s0137' => 'mpo', 'Mapoly0041s0138' => 'mpo', 'Mapoly0041s0139' => 'mpo', 'Mapoly0041s0141' => 'mpo', 'Mapoly0041s0142' => 'mpo', 'Mapoly0041s0143' => 'mpo', 'Mapoly0041s0144' => 'mpo', 'Mapoly0041s0145' => 'mpo', 'Mapoly0047s0106' => 'mpo', 'Mapoly0047s0108' => 'mpo', 'Mapoly0050s0051' => 'mpo', 'Mapoly0050s0052' => 'mpo', 'Mapoly0050s0053' => 'mpo', 'Mapoly0058s0013' => 'mpo', 'Mapoly0091s0078' => 'mpo', 'Mapoly0091s0079' => 'mpo', 'Mapoly0091s0080' => 'mpo', 'Mapoly0091s0081' => 'mpo', 'Mapoly0278s0004' => 'mpo', 'Mapoly0278s0005' => 'mpo', 'Mapoly0278s0006' => 'mpo', 'MBI11_g30648_MAGBIO' => 'mbi', 'MCO03G194' => 'mco', 'MCO03G590' => 'mco', 'MCO07G312' => 'mco', 'MCO10G318' => 'mco', 'MCO12G244' => 'mco', 'MCO13G148' => 'mco', 'MCO13G194' => 'mco', 'MCO16G238' => 'mco', 'MD06G1134100' => 'mdo', 'MD13G1200100' => 'mdo', 'MD13G1200300' => 'mdo', 'MD13G1200600' => 'mdo', 'MD14G1150400' => 'mdo', 'MD16G1200000' => 'mdo', 'Medtr1g102570' => 'mtr', 'Medtr1g102780' => 'mtr', 'Medtr1g102800' => 'mtr', 'Medtr1g102810' => 'mtr', 'Medtr1g102830' => 'mtr', 'MELO3C006499.2' => 'cme', 'Migut.G00385' => 'egut', 'MSTRG.4063' => 'ama', 'Nitab4.5_0000090g0260' => 'nta', 'Nitab4.5_0000977g0030' => 'nta', 'Nitab4.5_0002541g0040' => 'nta', 'Nitab4.5_0007068g0040' => 'nta', 'Nn005s41408' => 'nnu', 'Nn005s41410' => 'nnu', 'Oeu010310.1' => 'oeu', 'Oeu010311.1' => 'oeu', 'Oeu043472.1' => 'oeu', 'Os01g0246400' => 'osa', 'Os04g0267950' => 'osa', 'Os07g0178700' => 'osa', 'Os07g0178800' => 'osa', 'Peaxi162Scf00316g00046' => 'pax', 'Peaxi162Scf00316g00049' => 'pax', 'Peaxi162Scf00316g00059' => 'pax', 'Peaxi162Scf00316g00328' => 'pax', 'Peaxi162Scf00316g00329' => 'pax', 'Peaxi162Scf00316g00411' => 'pax', 'Peaxi162Scf00316g00521' => 'pax', 'Peaxi162Scf00492g00068' => 'pax', 'Peaxi162Scf35631g00002' => 'pax', 'PGR142G3720' => 'pgr', 'PGSC0003DMG400006442' => 'stu', 'Phvul.007G062000' => 'pvu', 'Potri.008G157750' => 'ptr', 'Potri.008G157900' => 'ptr', 'Potri.008G158000' => 'ptr', 'Potri.008G158200' => 'ptr', 'Pp3c11_7280' => 'ppa', 'Pp3c11_7980' => 'ppa', 'Pp3c12_19450' => 'ppa', 'Pp3c14_1480' => 'ppa', 'Pp3c14_1501' => 'ppa', 'Pp3c16_4900' => 'ppa', 'Pp3c16_5010' => 'ppa', 'Pp3c16_5060' => 'ppa', 'Pp3c19_18250' => 'ppa', 'Pp3c23_8530' => 'ppa', 'Pp3c23_8550' => 'ppa', 'Pp3c24_9670' => 'ppa', 'Pp3c2_21390' => 'ppa', 'Pp3c2_31380' => 'ppa', 'Pp3c3_16620' => 'ppa', 'Pp3c3_8090' => 'ppa', 'Pp3c3_8110' => 'ppa', 'Pp3c3_8130' => 'ppa', 'Pp3c3_8150' => 'ppa', 'Pp3c4_14320' => 'ppa', 'Pp3c6_2560' => 'ppa', 'Pp3c9_16700' => 'ppa', 'PRCOL_00000234' => 'pco', 'PRCOL_00000235' => 'pco', 'PRCOL_00000777' => 'pco', 'PRCOL_00002344' => 'pco', 'PRCOL_00002372' => 'pco', 'PRCOL_00006120' => 'pco', 'Prupe.1G021400' => 'ppe', 'Prupe.1G021500' => 'ppe', 'Prupe.1G021600' => 'ppe', 'Prupe.1G021700' => 'ppe', 'Prupe.1G021800' => 'ppe', 'Prupe.5G145100' => 'ppe', 'Psat6g204040' => 'psa', 'Psat6g204800' => 'psa', 'Psat6g204920' => 'psa', 'Psat6g204960' => 'psa', 'Psat6g205080' => 'psa', 'PSO017G0271' => 'pso', 'PSO017G1276' => 'pso', 'PSO017G1429' => 'pso', 'PSO017G1861' => 'pso', 'PSO017G2787' => 'pso', 'PSO017G4466' => 'pso', 'PSO017G5118' => 'pso', 'PSO017G5420' => 'pso', 'PSO063G3678' => 'pso', 'PSO210G0546' => 'pso', 'PSO317G0001' => 'pso', 'PSO357G0512' => 'pso', 'PSO478G2682' => 'pso', 'PSO647G0001' => 'pso', 'PSO675G0001' => 'pso', 'PSO675G2699' => 'pso', 'PSO675G2849' => 'pso', 'PSO675G4991' => 'pso', 'PSO689G0001' => 'pso', 'QL06p000916' => 'qlo', 'QL06p000921' => 'qlo', 'QL06p001398' => 'qlo', 'QL06p001407' => 'qlo', 'QL06p002031' => 'qlo', 'RcHm_v2.0_Chr4g0387791' => 'rch', 'RcHm_v2.0_Chr4g0387801' => 'rch', 'RcHm_v2.0_Chr6g0286501' => 'rch', 'RcHm_v2.0_Chr6g0286511' => 'rch', 'RcHm_v2.0_Chr6g0286521' => 'rch', 'RcHm_v2.0_Chr6g0286531' => 'rch', 'RcHm_v2.0_Chr7g0189141' => 'rch', 'Rhsim02G0028700' => 'rsi', 'Rhsim02G0028800' => 'rsi', 'Rhsim02G0028900' => 'rsi', 'Rhsim02G0029000' => 'rsi', 'Rhsim02G0029100' => 'rsi', 'Rhsim02G0029200' => 'rsi', 'Rhsim02G0029300' => 'rsi', 'Rhsim02G0029400' => 'rsi', 'Rhsim02G0029500' => 'rsi', 'Rhsim02G0029600' => 'rsi', 'RhsimUnG0024000' => 'rsi', 'RhsimUnG0024100' => 'rsi', 'RhsimUnG0024200' => 'rsi', 'RhsimUnG0024300' => 'rsi', 'RhsimUnG0024400' => 'rsi', 'RhsimUnG0024500' => 'rsi', 'RhsimUnG0024700' => 'rsi', 'RhsimUnG0024800' => 'rsi', 'RhsimUnG0024900' => 'rsi', 'RhsimUnG0025100' => 'rsi', 'Sabra08G0120200' => 'sbr', 'Sabra08G0120300' => 'sbr', 'Sabra08G0120500' => 'sbr', 'Sabra08G0120600' => 'sbr', 'Sabra10G0158900' => 'sbr', 'SalBow2G3492' => 'sbo', 'Sc13g0004760' => 'sci', 'Sc13g0004770' => 'sci', 'Sed0003417' => 'sed', 'Sed0019750' => 'sed', 'SEGI_03419' => 'sgi', 'SEGI_05907' => 'sgi', 'SEGI_10682' => 'sgi', 'SEGI_13528' => 'sgi', 'SEGI_16081' => 'sgi', 'SEGI_19370' => 'sgi', 'SEGI_21015' => 'sgi', 'SEGI_21944' => 'sgi', 'SEGI_32906' => 'sgi', 'SEGI_33093' => 'sgi', 'SEGI_36110' => 'sgi', 'SEGI_40397' => 'sgi', 'SGA_v2.0_scaffold191G40426' => 'sas', 'SGA_v2.0_scaffold353G49717' => 'sas', 'SGA_v2.0_scaffold50G18550' => 'sas', 'SMO119G0173' => 'smo', 'SMO172G0002' => 'smo', 'Solyc09g082690.3' => 'sly', 'Solyc09g082700.2' => 'sly', 'Sopen09g031550' => 'spe', 'Sopen09g031560' => 'spe', 'Sp3g20540' => 'spa', 'Sp7g07580' => 'spa', 'TAR134G0002' => 'tar', 'TAR236G0001' => 'tar', 'TAR365G0892' => 'tar', 'TAR636G0166' => 'tar', 'TAR636G0646' => 'tar', 'TAR636G0869' => 'tar', 'TAR636G1317' => 'tar', 'TAR636G1744' => 'tar', 'TAR636G3358' => 'tar', 'TAR636G3436' => 'tar', 'THA.LOC104803047' => 'tha', 'Thecc.04G238900' => 'tca', 'Thhalv10021557m.g' => 'esa', 'Thhalv10026318m.g' => 'esa', 'Thhalv10026335m.g' => 'esa', 'TPR.G17433' => 'tpr', 'TPR.G18915' => 'tpr', 'TPR.G26125' => 'tpr', 'TWI09G0677' => 'twi', 'TWI73G0287' => 'twi', 'unitig_748.g8326' => 'ugi', 'vmacro15370' => 'vma', 'vmacro15371' => 'vma', 'vmacro15372' => 'vma', 'vmacro15373' => 'vma', 'vmacro15374' => 'vma', 'VMungo0720G2826' => 'vmu', 'Zm00001eb116960' => 'zma', 'Zm00001eb301260' => 'zma', 'Zm00001eb301270' => 'zma' ) $gf_id = 'HOM05D001460' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001460' ) $data_identifier = 'HOM05D001460' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 4, 'aag' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 2, 'aox' => (int) 2, 'arhy' => (int) 4, 'ath' => (int) 2, 'atr' => (int) 1, 'acertr' => (int) 10, 'cqu' => (int) 4, 'bca' => (int) 11, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 1, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 1, 'ccan' => (int) 1, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 1, 'col' => (int) 1, 'cpa' => (int) 1, 'cre' => (int) 7, 'csa' => (int) 1, 'camsi' => (int) 2, 'dca' => (int) 3, 'din' => (int) 2, 'dzi' => (int) 3, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 14, 'fve' => (int) 9, 'gma' => (int) 2, 'ghi' => (int) 4, 'gra' => (int) 2, 'vvi' => (int) 1, 'han' => (int) 13, 'cav' => (int) 1, 'hma' => (int) 2, 'sun' => (int) 2, 'lal' => (int) 2, 'lonja' => (int) 12, 'lja' => (int) 1, 'lsa' => (int) 7, 'mes' => (int) 1, 'mpo' => (int) 27, 'mbi' => (int) 1, 'mco' => (int) 8, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 1, 'egut' => (int) 1, 'ama' => (int) 1, 'nta' => (int) 4, 'nnu' => (int) 2, 'oeu' => (int) 3, 'osa' => (int) 4, 'pax' => (int) 9, 'pgr' => (int) 1, 'stu' => (int) 1, 'pvu' => (int) 1, 'ptr' => (int) 4, 'ppa' => (int) 22, 'pco' => (int) 6, 'ppe' => (int) 6, 'psa' => (int) 5, 'pso' => (int) 19, 'qlo' => (int) 5, 'rch' => (int) 7, 'rsi' => (int) 20, 'sbr' => (int) 5, 'sbo' => (int) 1, 'sci' => (int) 2, 'sed' => (int) 2, 'sgi' => (int) 12, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 2, 'tar' => (int) 10, 'tha' => (int) 1, 'tca' => (int) 1, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 2, 'ugi' => (int) 1, 'vma' => (int) 5, 'vmu' => (int) 1, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb301270' $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' => 'HOM05D001460', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '433', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p22980' => 'bna', 'A01p32340' => 'bna', 'A03p42970' => 'bna', 'A05p25880' => 'bna', 'Aa31LG8G9320' => 'aar', 'Aa31LG8G9330' => 'aar', 'Aa31LG8G9340' => 'aar', 'Aa31sc221G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1034' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1528' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.829' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2222' => 'aag', 'Ah.12g058830' => 'amhyb', 'Ah.12g058840' => 'amhyb', 'AL3G37160' => 'aly', 'AL7G41310' => 'aly', 'Aqoxy5G00395' => 'aox', 'Aqoxy5G00396' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0C8NZA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5185HY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JZ1PRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MD3LS0' => 'arhy', 'AT3G22840' => 'ath', 'AT4G14690' => 'ath', 'ATR0665G054' => 'atr', 'Atru.chr4.2344' => 'acertr', 'Atru.chr4.2346' => 'acertr', 'Atru.chr4.2347' => 'acertr', 'Atru.chr4.2348' => 'acertr', 'Atru.chr4.2355' => 'acertr', 'Atru.chr4.2356' => 'acertr', 'Atru.chr4.2358' => 'acertr', 'Atru.chr4.2359' => 'acertr', 'Atru.chr4.2360' => 'acertr', 'Atru.chr4.2361' => 'acertr', 'AUR62030476' => 'cqu', 'AUR62030478' => 'cqu', 'AUR62030819' => 'cqu', 'AUR62030820' => 'cqu', 'BcaB03g14648' => 'bca', 'BcaB04g20492' => 'bca', 'BcaB06g26399' => 'bca', 'BcaC01g03416' => 'bca', 'BcaC01g03419' => 'bca', 'BcaC01g03421' => 'bca', 'BcaC01g03424' => 'bca', 'BcaC05g28012' => 'bca', 'BcaC09g49212' => 'bca', 'BcaC09g50140' => 'bca', 'BcaNung00346' => 'bca', 'BolC1t02785H' => 'bol', 'BolC1t04095H' => 'bol', 'BolC3t17545H' => 'bol', 'BolC5t32769H' => 'bol', 'BraA01t02211Z' => 'bra', 'BraA01t03359Z' => 'bra', 'BraA03t13441Z' => 'bra', 'BraA05t21476Z' => 'bra', 'C01p28420' => 'bna', 'C01p41350' => 'bna', 'C03p52750' => 'bna', 'C03p52780' => 'bna', 'C05p40270' => 'bna', 'CAN.G1437.9' => 'can', 'CANSAT78G0035' => 'cansat', 'CANSAT78G1036' => 'cansat', 'CANSAT78G2272' => 'cansat', 'CANSAT78G2478' => 'cansat', 'CARHR098700' => 'chi', 'CARHR221120' => 'chi', 'CARHR221150' => 'chi', 'Carub.0003s2297' => 'cru', 'Carub.0007s2749' => 'cru', 'Carub.0007s2750' => 'cru', 'Carub.0007s2751' => 'cru', 'Ca_10849_v3' => 'car', 'Cc03_g04300' => 'ccan', 'CDE02G3648' => 'cde', 'CDE05G0060' => 'cde', 'CDE05G0692' => 'cde', 'CDE05G2285' => 'cde', 'CDE05G2884' => 'cde', 'CDE05G3072' => 'cde', 'Cfa008439' => 'cfa', 'Cfa008441' => 'cfa', 'Cfa008443' => 'cfa', 'Cfa008448' => 'cfa', 'Ciclev10005974m.g' => 'ccl', 'Ciclev10006006m.g' => 'ccl', 'Ciclev10006775m.g' => 'ccl', 'CiPaw.02G120400' => 'cil', 'CiPaw.02G120500' => 'cil', 'CiPaw.02G120600' => 'cil', 'ClCG05G004850' => 'cla', 'COL.COLO4_21566' => 'col', 'Cpa.g.sc44.124' => 'cpa', 'Cre07.g320400' => 'cre', 'Cre07.g320450' => 'cre', 'Cre08.g384650' => 'cre', 'Cre09.g393173' => 'cre', 'Cre09.g394325' => 'cre', 'Cre14.g626750' => 'cre', 'Cre16.g679250' => 'cre', 'CsaV3_3G012890' => 'csa', 'CSS0010865' => 'camsi', 'CSS0044338' => 'camsi', 'DCAR_002366' => 'dca', 'DCAR_030687' => 'dca', 'DCAR_030688' => 'dca', 'Dinv14047' => 'din', 'Dinv14048' => 'din', 'Duzib151G0105' => 'dzi', 'Duzib151G0114' => 'dzi', 'Duzib212G1029' => 'dzi', 'ECA232G3536' => 'eca', 'ECA240G0786' => 'eca', 'ECA240G1802' => 'eca', 'ECA240G3760' => 'eca', 'ECA240G3920' => 'eca', 'EL10Ac5g12536' => 'bvu', 'EL10Ac5g12537' => 'bvu', 'EL10Ac5g12538' => 'bvu', 'Eucgr.B01004' => 'egr', 'Eucgr.B01006' => 'egr', 'Eucgr.B01007' => 'egr', 'Eucgr.B01008' => 'egr', 'Eucgr.B01895' => 'egr', 'Eucgr.B01896' => 'egr', 'FAN04G1456' => 'fan', 'FAN08G1769' => 'fan', 'FAN08G2160' => 'fan', 'FAN13G2403' => 'fan', 'FAN13G3303' => 'fan', 'FAN15G2435' => 'fan', 'FAN17G0672' => 'fan', 'FAN17G2441' => 'fan', 'FAN18G1024' => 'fan', 'FAN22G1458' => 'fan', 'FAN24G0037' => 'fan', 'FAN24G0429' => 'fan', 'FAN24G2387' => 'fan', 'FAN27G2746' => 'fan', 'FvH4_2g20400' => 'fve', 'FvH4_2g20420' => 'fve', 'FvH4_2g20430' => 'fve', 'FvH4_4g01270' => 'fve', 'FvH4_4g01290' => 'fve', 'FvH4_4g01300' => 'fve', 'FvH4_4g01310' => 'fve', 'FvH4_4g01330' => 'fve', 'FvH4_5g09070' => 'fve', 'Glyma.10G243800' => 'gma', 'Glyma.20G150600' => 'gma', 'Gohir.A09G219200' => 'ghi', 'Gohir.A09G219300' => 'ghi', 'Gohir.D09G221400' => 'ghi', 'Gohir.D09G221500' => 'ghi', 'Gorai.006G242600' => 'gra', 'Gorai.006G242700' => 'gra', 'GSVIVG01018044001' => 'vvi', 'HanXRQChr03g0083821' => 'han', 'HanXRQChr03g0083841' => 'han', 'HanXRQChr03g0083881' => 'han', 'HanXRQChr03g0083901' => 'han', 'HanXRQChr03g0083921' => 'han', 'HanXRQChr03g0085331' => 'han', 'HanXRQChr03g0085361' => 'han', 'HanXRQChr03g0085411' => 'han', 'HanXRQChr03g0085421' => 'han', 'HanXRQChr03g0085431' => 'han', 'HanXRQChr08g0221991' => 'han', 'HanXRQChr11g0336061' => 'han', 'HanXRQChr11g0336411' => 'han', 'Haze_11234' => 'cav', 'Hma1.2p1_0549F.1_g177010' => 'hma', 'Hma1.2p1_0602F.1_g187630' => 'hma', 'Hund14876' => 'sun', 'Hund14879' => 'sun', 'Lalb_Chr06g0160741' => 'lal', 'Lalb_Chr21g0304781' => 'lal', 'Lj3A726G19' => 'lonja', 'Lj3A726T23' => 'lonja', 'Lj3A726T24' => 'lonja', 'Lj3A726T25' => 'lonja', 'Lj3A727T17' => 'lonja', 'Lj3C726T0' => 'lonja', 'Lj3C726T2' => 'lonja', 'Lj3P725T35' => 'lonja', 'Lj3P727T10' => 'lonja', 'Lj3P727T12' => 'lonja', 'Lj3P727T14' => 'lonja', 'Lj5g0023109' => 'lja', 'Lj6P646T44' => 'lonja', 'Lsat_1_v5_gn_6_75760' => 'lsa', 'Lsat_1_v5_gn_6_75800' => 'lsa', 'Lsat_1_v5_gn_6_75900' => 'lsa', 'Lsat_1_v5_gn_6_76240' => 'lsa', 'Lsat_1_v5_gn_6_76441' => 'lsa', 'Lsat_1_v5_gn_6_76700' => 'lsa', 'Lsat_1_v5_gn_6_76760' => 'lsa', 'Manes.15G033100' => 'mes', 'Mapoly0004s0074' => 'mpo', 'Mapoly0004s0075' => 'mpo', 'Mapoly0004s0163' => 'mpo', 'Mapoly0004s0164' => 'mpo', 'Mapoly0021s0018' => 'mpo', 'Mapoly0041s0136' => 'mpo', 'Mapoly0041s0137' => 'mpo', 'Mapoly0041s0138' => 'mpo', 'Mapoly0041s0139' => 'mpo', 'Mapoly0041s0141' => 'mpo', 'Mapoly0041s0142' => 'mpo', 'Mapoly0041s0143' => 'mpo', 'Mapoly0041s0144' => 'mpo', 'Mapoly0041s0145' => 'mpo', 'Mapoly0047s0106' => 'mpo', 'Mapoly0047s0108' => 'mpo', 'Mapoly0050s0051' => 'mpo', 'Mapoly0050s0052' => 'mpo', 'Mapoly0050s0053' => 'mpo', 'Mapoly0058s0013' => 'mpo', 'Mapoly0091s0078' => 'mpo', 'Mapoly0091s0079' => 'mpo', 'Mapoly0091s0080' => 'mpo', 'Mapoly0091s0081' => 'mpo', 'Mapoly0278s0004' => 'mpo', 'Mapoly0278s0005' => 'mpo', 'Mapoly0278s0006' => 'mpo', 'MBI11_g30648_MAGBIO' => 'mbi', 'MCO03G194' => 'mco', 'MCO03G590' => 'mco', 'MCO07G312' => 'mco', 'MCO10G318' => 'mco', 'MCO12G244' => 'mco', 'MCO13G148' => 'mco', 'MCO13G194' => 'mco', 'MCO16G238' => 'mco', 'MD06G1134100' => 'mdo', 'MD13G1200100' => 'mdo', 'MD13G1200300' => 'mdo', 'MD13G1200600' => 'mdo', 'MD14G1150400' => 'mdo', 'MD16G1200000' => 'mdo', 'Medtr1g102570' => 'mtr', 'Medtr1g102780' => 'mtr', 'Medtr1g102800' => 'mtr', 'Medtr1g102810' => 'mtr', 'Medtr1g102830' => 'mtr', 'MELO3C006499.2' => 'cme', 'Migut.G00385' => 'egut', 'MSTRG.4063' => 'ama', 'Nitab4.5_0000090g0260' => 'nta', 'Nitab4.5_0000977g0030' => 'nta', 'Nitab4.5_0002541g0040' => 'nta', 'Nitab4.5_0007068g0040' => 'nta', 'Nn005s41408' => 'nnu', 'Nn005s41410' => 'nnu', 'Oeu010310.1' => 'oeu', 'Oeu010311.1' => 'oeu', 'Oeu043472.1' => 'oeu', 'Os01g0246400' => 'osa', 'Os04g0267950' => 'osa', 'Os07g0178700' => 'osa', 'Os07g0178800' => 'osa', 'Peaxi162Scf00316g00046' => 'pax', 'Peaxi162Scf00316g00049' => 'pax', 'Peaxi162Scf00316g00059' => 'pax', 'Peaxi162Scf00316g00328' => 'pax', 'Peaxi162Scf00316g00329' => 'pax', 'Peaxi162Scf00316g00411' => 'pax', 'Peaxi162Scf00316g00521' => 'pax', 'Peaxi162Scf00492g00068' => 'pax', 'Peaxi162Scf35631g00002' => 'pax', 'PGR142G3720' => 'pgr', 'PGSC0003DMG400006442' => 'stu', 'Phvul.007G062000' => 'pvu', 'Potri.008G157750' => 'ptr', 'Potri.008G157900' => 'ptr', 'Potri.008G158000' => 'ptr', 'Potri.008G158200' => 'ptr', 'Pp3c11_7280' => 'ppa', 'Pp3c11_7980' => 'ppa', 'Pp3c12_19450' => 'ppa', 'Pp3c14_1480' => 'ppa', 'Pp3c14_1501' => 'ppa', 'Pp3c16_4900' => 'ppa', 'Pp3c16_5010' => 'ppa', 'Pp3c16_5060' => 'ppa', 'Pp3c19_18250' => 'ppa', 'Pp3c23_8530' => 'ppa', 'Pp3c23_8550' => 'ppa', 'Pp3c24_9670' => 'ppa', 'Pp3c2_21390' => 'ppa', 'Pp3c2_31380' => 'ppa', 'Pp3c3_16620' => 'ppa', 'Pp3c3_8090' => 'ppa', 'Pp3c3_8110' => 'ppa', 'Pp3c3_8130' => 'ppa', 'Pp3c3_8150' => 'ppa', 'Pp3c4_14320' => 'ppa', 'Pp3c6_2560' => 'ppa', 'Pp3c9_16700' => 'ppa', 'PRCOL_00000234' => 'pco', 'PRCOL_00000235' => 'pco', 'PRCOL_00000777' => 'pco', 'PRCOL_00002344' => 'pco', 'PRCOL_00002372' => 'pco', 'PRCOL_00006120' => 'pco', 'Prupe.1G021400' => 'ppe', 'Prupe.1G021500' => 'ppe', 'Prupe.1G021600' => 'ppe', 'Prupe.1G021700' => 'ppe', 'Prupe.1G021800' => 'ppe', 'Prupe.5G145100' => 'ppe', 'Psat6g204040' => 'psa', 'Psat6g204800' => 'psa', 'Psat6g204920' => 'psa', 'Psat6g204960' => 'psa', 'Psat6g205080' => 'psa', 'PSO017G0271' => 'pso', 'PSO017G1276' => 'pso', 'PSO017G1429' => 'pso', 'PSO017G1861' => 'pso', 'PSO017G2787' => 'pso', 'PSO017G4466' => 'pso', 'PSO017G5118' => 'pso', 'PSO017G5420' => 'pso', 'PSO063G3678' => 'pso', 'PSO210G0546' => 'pso', 'PSO317G0001' => 'pso', 'PSO357G0512' => 'pso', 'PSO478G2682' => 'pso', 'PSO647G0001' => 'pso', 'PSO675G0001' => 'pso', 'PSO675G2699' => 'pso', 'PSO675G2849' => 'pso', 'PSO675G4991' => 'pso', 'PSO689G0001' => 'pso', 'QL06p000916' => 'qlo', 'QL06p000921' => 'qlo', 'QL06p001398' => 'qlo', 'QL06p001407' => 'qlo', 'QL06p002031' => 'qlo', 'RcHm_v2.0_Chr4g0387791' => 'rch', 'RcHm_v2.0_Chr4g0387801' => 'rch', 'RcHm_v2.0_Chr6g0286501' => 'rch', 'RcHm_v2.0_Chr6g0286511' => 'rch', 'RcHm_v2.0_Chr6g0286521' => 'rch', 'RcHm_v2.0_Chr6g0286531' => 'rch', 'RcHm_v2.0_Chr7g0189141' => 'rch', 'Rhsim02G0028700' => 'rsi', 'Rhsim02G0028800' => 'rsi', 'Rhsim02G0028900' => 'rsi', 'Rhsim02G0029000' => 'rsi', 'Rhsim02G0029100' => 'rsi', 'Rhsim02G0029200' => 'rsi', 'Rhsim02G0029300' => 'rsi', 'Rhsim02G0029400' => 'rsi', 'Rhsim02G0029500' => 'rsi', 'Rhsim02G0029600' => 'rsi', 'RhsimUnG0024000' => 'rsi', 'RhsimUnG0024100' => 'rsi', 'RhsimUnG0024200' => 'rsi', 'RhsimUnG0024300' => 'rsi', 'RhsimUnG0024400' => 'rsi', 'RhsimUnG0024500' => 'rsi', 'RhsimUnG0024700' => 'rsi', 'RhsimUnG0024800' => 'rsi', 'RhsimUnG0024900' => 'rsi', 'RhsimUnG0025100' => 'rsi', 'Sabra08G0120200' => 'sbr', 'Sabra08G0120300' => 'sbr', 'Sabra08G0120500' => 'sbr', 'Sabra08G0120600' => 'sbr', 'Sabra10G0158900' => 'sbr', 'SalBow2G3492' => 'sbo', 'Sc13g0004760' => 'sci', 'Sc13g0004770' => 'sci', 'Sed0003417' => 'sed', 'Sed0019750' => 'sed', 'SEGI_03419' => 'sgi', 'SEGI_05907' => 'sgi', 'SEGI_10682' => 'sgi', 'SEGI_13528' => 'sgi', 'SEGI_16081' => 'sgi', 'SEGI_19370' => 'sgi', 'SEGI_21015' => 'sgi', 'SEGI_21944' => 'sgi', 'SEGI_32906' => 'sgi', 'SEGI_33093' => 'sgi', 'SEGI_36110' => 'sgi', 'SEGI_40397' => 'sgi', 'SGA_v2.0_scaffold191G40426' => 'sas', 'SGA_v2.0_scaffold353G49717' => 'sas', 'SGA_v2.0_scaffold50G18550' => 'sas', 'SMO119G0173' => 'smo', 'SMO172G0002' => 'smo', 'Solyc09g082690.3' => 'sly', 'Solyc09g082700.2' => 'sly', 'Sopen09g031550' => 'spe', 'Sopen09g031560' => 'spe', 'Sp3g20540' => 'spa', 'Sp7g07580' => 'spa', 'TAR134G0002' => 'tar', 'TAR236G0001' => 'tar', 'TAR365G0892' => 'tar', 'TAR636G0166' => 'tar', 'TAR636G0646' => 'tar', 'TAR636G0869' => 'tar', 'TAR636G1317' => 'tar', 'TAR636G1744' => 'tar', 'TAR636G3358' => 'tar', 'TAR636G3436' => 'tar', 'THA.LOC104803047' => 'tha', 'Thecc.04G238900' => 'tca', 'Thhalv10021557m.g' => 'esa', 'Thhalv10026318m.g' => 'esa', 'Thhalv10026335m.g' => 'esa', 'TPR.G17433' => 'tpr', 'TPR.G18915' => 'tpr', 'TPR.G26125' => 'tpr', 'TWI09G0677' => 'twi', 'TWI73G0287' => 'twi', 'unitig_748.g8326' => 'ugi', 'vmacro15370' => 'vma', 'vmacro15371' => 'vma', 'vmacro15372' => 'vma', 'vmacro15373' => 'vma', 'vmacro15374' => 'vma', 'VMungo0720G2826' => 'vmu', 'Zm00001eb116960' => 'zma', 'Zm00001eb301260' => 'zma', 'Zm00001eb301270' => 'zma' ), 'gf_id' => 'HOM05D001460', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001460' ), 'data_identifier' => 'HOM05D001460', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001460', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '433', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p22980' => 'bna', 'A01p32340' => 'bna', 'A03p42970' => 'bna', 'A05p25880' => 'bna', 'Aa31LG8G9320' => 'aar', 'Aa31LG8G9330' => 'aar', 'Aa31LG8G9340' => 'aar', 'Aa31sc221G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1034' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1528' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.829' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2222' => 'aag', 'Ah.12g058830' => 'amhyb', 'Ah.12g058840' => 'amhyb', 'AL3G37160' => 'aly', 'AL7G41310' => 'aly', 'Aqoxy5G00395' => 'aox', 'Aqoxy5G00396' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0C8NZA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5185HY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JZ1PRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MD3LS0' => 'arhy', 'AT3G22840' => 'ath', 'AT4G14690' => 'ath', 'ATR0665G054' => 'atr', 'Atru.chr4.2344' => 'acertr', 'Atru.chr4.2346' => 'acertr', 'Atru.chr4.2347' => 'acertr', 'Atru.chr4.2348' => 'acertr', 'Atru.chr4.2355' => 'acertr', 'Atru.chr4.2356' => 'acertr', 'Atru.chr4.2358' => 'acertr', 'Atru.chr4.2359' => 'acertr', 'Atru.chr4.2360' => 'acertr', 'Atru.chr4.2361' => 'acertr', 'AUR62030476' => 'cqu', 'AUR62030478' => 'cqu', 'AUR62030819' => 'cqu', 'AUR62030820' => 'cqu', 'BcaB03g14648' => 'bca', 'BcaB04g20492' => 'bca', 'BcaB06g26399' => 'bca', 'BcaC01g03416' => 'bca', 'BcaC01g03419' => 'bca', 'BcaC01g03421' => 'bca', 'BcaC01g03424' => 'bca', 'BcaC05g28012' => 'bca', 'BcaC09g49212' => 'bca', 'BcaC09g50140' => 'bca', 'BcaNung00346' => 'bca', 'BolC1t02785H' => 'bol', 'BolC1t04095H' => 'bol', 'BolC3t17545H' => 'bol', 'BolC5t32769H' => 'bol', 'BraA01t02211Z' => 'bra', 'BraA01t03359Z' => 'bra', 'BraA03t13441Z' => 'bra', 'BraA05t21476Z' => 'bra', 'C01p28420' => 'bna', 'C01p41350' => 'bna', 'C03p52750' => 'bna', 'C03p52780' => 'bna', 'C05p40270' => 'bna', 'CAN.G1437.9' => 'can', 'CANSAT78G0035' => 'cansat', 'CANSAT78G1036' => 'cansat', 'CANSAT78G2272' => 'cansat', 'CANSAT78G2478' => 'cansat', 'CARHR098700' => 'chi', 'CARHR221120' => 'chi', 'CARHR221150' => 'chi', 'Carub.0003s2297' => 'cru', 'Carub.0007s2749' => 'cru', 'Carub.0007s2750' => 'cru', 'Carub.0007s2751' => 'cru', 'Ca_10849_v3' => 'car', 'Cc03_g04300' => 'ccan', 'CDE02G3648' => 'cde', 'CDE05G0060' => 'cde', 'CDE05G0692' => 'cde', 'CDE05G2285' => 'cde', 'CDE05G2884' => 'cde', 'CDE05G3072' => 'cde', 'Cfa008439' => 'cfa', 'Cfa008441' => 'cfa', 'Cfa008443' => 'cfa', 'Cfa008448' => 'cfa', 'Ciclev10005974m.g' => 'ccl', 'Ciclev10006006m.g' => 'ccl', 'Ciclev10006775m.g' => 'ccl', 'CiPaw.02G120400' => 'cil', 'CiPaw.02G120500' => 'cil', 'CiPaw.02G120600' => 'cil', 'ClCG05G004850' => 'cla', 'COL.COLO4_21566' => 'col', 'Cpa.g.sc44.124' => 'cpa', 'Cre07.g320400' => 'cre', 'Cre07.g320450' => 'cre', 'Cre08.g384650' => 'cre', 'Cre09.g393173' => 'cre', 'Cre09.g394325' => 'cre', 'Cre14.g626750' => 'cre', 'Cre16.g679250' => 'cre', 'CsaV3_3G012890' => 'csa', 'CSS0010865' => 'camsi', 'CSS0044338' => 'camsi', 'DCAR_002366' => 'dca', 'DCAR_030687' => 'dca', 'DCAR_030688' => 'dca', 'Dinv14047' => 'din', 'Dinv14048' => 'din', 'Duzib151G0105' => 'dzi', 'Duzib151G0114' => 'dzi', 'Duzib212G1029' => 'dzi', 'ECA232G3536' => 'eca', 'ECA240G0786' => 'eca', 'ECA240G1802' => 'eca', 'ECA240G3760' => 'eca', 'ECA240G3920' => 'eca', 'EL10Ac5g12536' => 'bvu', 'EL10Ac5g12537' => 'bvu', 'EL10Ac5g12538' => 'bvu', 'Eucgr.B01004' => 'egr', 'Eucgr.B01006' => 'egr', 'Eucgr.B01007' => 'egr', 'Eucgr.B01008' => 'egr', 'Eucgr.B01895' => 'egr', 'Eucgr.B01896' => 'egr', 'FAN04G1456' => 'fan', 'FAN08G1769' => 'fan', 'FAN08G2160' => 'fan', 'FAN13G2403' => 'fan', 'FAN13G3303' => 'fan', 'FAN15G2435' => 'fan', 'FAN17G0672' => 'fan', 'FAN17G2441' => 'fan', 'FAN18G1024' => 'fan', 'FAN22G1458' => 'fan', 'FAN24G0037' => 'fan', 'FAN24G0429' => 'fan', 'FAN24G2387' => 'fan', 'FAN27G2746' => 'fan', 'FvH4_2g20400' => 'fve', 'FvH4_2g20420' => 'fve', 'FvH4_2g20430' => 'fve', 'FvH4_4g01270' => 'fve', 'FvH4_4g01290' => 'fve', 'FvH4_4g01300' => 'fve', 'FvH4_4g01310' => 'fve', 'FvH4_4g01330' => 'fve', 'FvH4_5g09070' => 'fve', 'Glyma.10G243800' => 'gma', 'Glyma.20G150600' => 'gma', 'Gohir.A09G219200' => 'ghi', 'Gohir.A09G219300' => 'ghi', 'Gohir.D09G221400' => 'ghi', 'Gohir.D09G221500' => 'ghi', 'Gorai.006G242600' => 'gra', 'Gorai.006G242700' => 'gra', 'GSVIVG01018044001' => 'vvi', 'HanXRQChr03g0083821' => 'han', 'HanXRQChr03g0083841' => 'han', 'HanXRQChr03g0083881' => 'han', 'HanXRQChr03g0083901' => 'han', 'HanXRQChr03g0083921' => 'han', 'HanXRQChr03g0085331' => 'han', 'HanXRQChr03g0085361' => 'han', 'HanXRQChr03g0085411' => 'han', 'HanXRQChr03g0085421' => 'han', 'HanXRQChr03g0085431' => 'han', 'HanXRQChr08g0221991' => 'han', 'HanXRQChr11g0336061' => 'han', 'HanXRQChr11g0336411' => 'han', 'Haze_11234' => 'cav', 'Hma1.2p1_0549F.1_g177010' => 'hma', 'Hma1.2p1_0602F.1_g187630' => 'hma', 'Hund14876' => 'sun', 'Hund14879' => 'sun', 'Lalb_Chr06g0160741' => 'lal', 'Lalb_Chr21g0304781' => 'lal', 'Lj3A726G19' => 'lonja', 'Lj3A726T23' => 'lonja', 'Lj3A726T24' => 'lonja', 'Lj3A726T25' => 'lonja', 'Lj3A727T17' => 'lonja', 'Lj3C726T0' => 'lonja', 'Lj3C726T2' => 'lonja', 'Lj3P725T35' => 'lonja', 'Lj3P727T10' => 'lonja', 'Lj3P727T12' => 'lonja', 'Lj3P727T14' => 'lonja', 'Lj5g0023109' => 'lja', 'Lj6P646T44' => 'lonja', 'Lsat_1_v5_gn_6_75760' => 'lsa', 'Lsat_1_v5_gn_6_75800' => 'lsa', 'Lsat_1_v5_gn_6_75900' => 'lsa', 'Lsat_1_v5_gn_6_76240' => 'lsa', 'Lsat_1_v5_gn_6_76441' => 'lsa', 'Lsat_1_v5_gn_6_76700' => 'lsa', 'Lsat_1_v5_gn_6_76760' => 'lsa', 'Manes.15G033100' => 'mes', 'Mapoly0004s0074' => 'mpo', 'Mapoly0004s0075' => 'mpo', 'Mapoly0004s0163' => 'mpo', 'Mapoly0004s0164' => 'mpo', 'Mapoly0021s0018' => 'mpo', 'Mapoly0041s0136' => 'mpo', 'Mapoly0041s0137' => 'mpo', 'Mapoly0041s0138' => 'mpo', 'Mapoly0041s0139' => 'mpo', 'Mapoly0041s0141' => 'mpo', 'Mapoly0041s0142' => 'mpo', 'Mapoly0041s0143' => 'mpo', 'Mapoly0041s0144' => 'mpo', 'Mapoly0041s0145' => 'mpo', 'Mapoly0047s0106' => 'mpo', 'Mapoly0047s0108' => 'mpo', 'Mapoly0050s0051' => 'mpo', 'Mapoly0050s0052' => 'mpo', 'Mapoly0050s0053' => 'mpo', 'Mapoly0058s0013' => 'mpo', 'Mapoly0091s0078' => 'mpo', 'Mapoly0091s0079' => 'mpo', 'Mapoly0091s0080' => 'mpo', 'Mapoly0091s0081' => 'mpo', 'Mapoly0278s0004' => 'mpo', 'Mapoly0278s0005' => 'mpo', 'Mapoly0278s0006' => 'mpo', 'MBI11_g30648_MAGBIO' => 'mbi', 'MCO03G194' => 'mco', 'MCO03G590' => 'mco', 'MCO07G312' => 'mco', 'MCO10G318' => 'mco', 'MCO12G244' => 'mco', 'MCO13G148' => 'mco', 'MCO13G194' => 'mco', 'MCO16G238' => 'mco', 'MD06G1134100' => 'mdo', 'MD13G1200100' => 'mdo', 'MD13G1200300' => 'mdo', 'MD13G1200600' => 'mdo', 'MD14G1150400' => 'mdo', 'MD16G1200000' => 'mdo', 'Medtr1g102570' => 'mtr', 'Medtr1g102780' => 'mtr', 'Medtr1g102800' => 'mtr', 'Medtr1g102810' => 'mtr', 'Medtr1g102830' => 'mtr', 'MELO3C006499.2' => 'cme', 'Migut.G00385' => 'egut', 'MSTRG.4063' => 'ama', 'Nitab4.5_0000090g0260' => 'nta', 'Nitab4.5_0000977g0030' => 'nta', 'Nitab4.5_0002541g0040' => 'nta', 'Nitab4.5_0007068g0040' => 'nta', 'Nn005s41408' => 'nnu', 'Nn005s41410' => 'nnu', 'Oeu010310.1' => 'oeu', 'Oeu010311.1' => 'oeu', 'Oeu043472.1' => 'oeu', 'Os01g0246400' => 'osa', 'Os04g0267950' => 'osa', 'Os07g0178700' => 'osa', 'Os07g0178800' => 'osa', 'Peaxi162Scf00316g00046' => 'pax', 'Peaxi162Scf00316g00049' => 'pax', 'Peaxi162Scf00316g00059' => 'pax', 'Peaxi162Scf00316g00328' => 'pax', 'Peaxi162Scf00316g00329' => 'pax', 'Peaxi162Scf00316g00411' => 'pax', 'Peaxi162Scf00316g00521' => 'pax', 'Peaxi162Scf00492g00068' => 'pax', 'Peaxi162Scf35631g00002' => 'pax', 'PGR142G3720' => 'pgr', 'PGSC0003DMG400006442' => 'stu', 'Phvul.007G062000' => 'pvu', 'Potri.008G157750' => 'ptr', 'Potri.008G157900' => 'ptr', 'Potri.008G158000' => 'ptr', 'Potri.008G158200' => 'ptr', 'Pp3c11_7280' => 'ppa', 'Pp3c11_7980' => 'ppa', 'Pp3c12_19450' => 'ppa', 'Pp3c14_1480' => 'ppa', 'Pp3c14_1501' => 'ppa', 'Pp3c16_4900' => 'ppa', 'Pp3c16_5010' => 'ppa', 'Pp3c16_5060' => 'ppa', 'Pp3c19_18250' => 'ppa', 'Pp3c23_8530' => 'ppa', 'Pp3c23_8550' => 'ppa', 'Pp3c24_9670' => 'ppa', 'Pp3c2_21390' => 'ppa', 'Pp3c2_31380' => 'ppa', 'Pp3c3_16620' => 'ppa', 'Pp3c3_8090' => 'ppa', 'Pp3c3_8110' => 'ppa', 'Pp3c3_8130' => 'ppa', 'Pp3c3_8150' => 'ppa', 'Pp3c4_14320' => 'ppa', 'Pp3c6_2560' => 'ppa', 'Pp3c9_16700' => 'ppa', 'PRCOL_00000234' => 'pco', 'PRCOL_00000235' => 'pco', 'PRCOL_00000777' => 'pco', 'PRCOL_00002344' => 'pco', 'PRCOL_00002372' => 'pco', 'PRCOL_00006120' => 'pco', 'Prupe.1G021400' => 'ppe', 'Prupe.1G021500' => 'ppe', 'Prupe.1G021600' => 'ppe', 'Prupe.1G021700' => 'ppe', 'Prupe.1G021800' => 'ppe', 'Prupe.5G145100' => 'ppe', 'Psat6g204040' => 'psa', 'Psat6g204800' => 'psa', 'Psat6g204920' => 'psa', 'Psat6g204960' => 'psa', 'Psat6g205080' => 'psa', 'PSO017G0271' => 'pso', 'PSO017G1276' => 'pso', 'PSO017G1429' => 'pso', 'PSO017G1861' => 'pso', 'PSO017G2787' => 'pso', 'PSO017G4466' => 'pso', 'PSO017G5118' => 'pso', 'PSO017G5420' => 'pso', 'PSO063G3678' => 'pso', 'PSO210G0546' => 'pso', 'PSO317G0001' => 'pso', 'PSO357G0512' => 'pso', 'PSO478G2682' => 'pso', 'PSO647G0001' => 'pso', 'PSO675G0001' => 'pso', 'PSO675G2699' => 'pso', 'PSO675G2849' => 'pso', 'PSO675G4991' => 'pso', 'PSO689G0001' => 'pso', 'QL06p000916' => 'qlo', 'QL06p000921' => 'qlo', 'QL06p001398' => 'qlo', 'QL06p001407' => 'qlo', 'QL06p002031' => 'qlo', 'RcHm_v2.0_Chr4g0387791' => 'rch', 'RcHm_v2.0_Chr4g0387801' => 'rch', 'RcHm_v2.0_Chr6g0286501' => 'rch', 'RcHm_v2.0_Chr6g0286511' => 'rch', 'RcHm_v2.0_Chr6g0286521' => 'rch', 'RcHm_v2.0_Chr6g0286531' => 'rch', 'RcHm_v2.0_Chr7g0189141' => 'rch', 'Rhsim02G0028700' => 'rsi', 'Rhsim02G0028800' => 'rsi', 'Rhsim02G0028900' => 'rsi', 'Rhsim02G0029000' => 'rsi', 'Rhsim02G0029100' => 'rsi', 'Rhsim02G0029200' => 'rsi', 'Rhsim02G0029300' => 'rsi', 'Rhsim02G0029400' => 'rsi', 'Rhsim02G0029500' => 'rsi', 'Rhsim02G0029600' => 'rsi', 'RhsimUnG0024000' => 'rsi', 'RhsimUnG0024100' => 'rsi', 'RhsimUnG0024200' => 'rsi', 'RhsimUnG0024300' => 'rsi', 'RhsimUnG0024400' => 'rsi', 'RhsimUnG0024500' => 'rsi', 'RhsimUnG0024700' => 'rsi', 'RhsimUnG0024800' => 'rsi', 'RhsimUnG0024900' => 'rsi', 'RhsimUnG0025100' => 'rsi', 'Sabra08G0120200' => 'sbr', 'Sabra08G0120300' => 'sbr', 'Sabra08G0120500' => 'sbr', 'Sabra08G0120600' => 'sbr', 'Sabra10G0158900' => 'sbr', 'SalBow2G3492' => 'sbo', 'Sc13g0004760' => 'sci', 'Sc13g0004770' => 'sci', 'Sed0003417' => 'sed', 'Sed0019750' => 'sed', 'SEGI_03419' => 'sgi', 'SEGI_05907' => 'sgi', 'SEGI_10682' => 'sgi', 'SEGI_13528' => 'sgi', 'SEGI_16081' => 'sgi', 'SEGI_19370' => 'sgi', 'SEGI_21015' => 'sgi', 'SEGI_21944' => 'sgi', 'SEGI_32906' => 'sgi', 'SEGI_33093' => 'sgi', 'SEGI_36110' => 'sgi', 'SEGI_40397' => 'sgi', 'SGA_v2.0_scaffold191G40426' => 'sas', 'SGA_v2.0_scaffold353G49717' => 'sas', 'SGA_v2.0_scaffold50G18550' => 'sas', 'SMO119G0173' => 'smo', 'SMO172G0002' => 'smo', 'Solyc09g082690.3' => 'sly', 'Solyc09g082700.2' => 'sly', 'Sopen09g031550' => 'spe', 'Sopen09g031560' => 'spe', 'Sp3g20540' => 'spa', 'Sp7g07580' => 'spa', 'TAR134G0002' => 'tar', 'TAR236G0001' => 'tar', 'TAR365G0892' => 'tar', 'TAR636G0166' => 'tar', 'TAR636G0646' => 'tar', 'TAR636G0869' => 'tar', 'TAR636G1317' => 'tar', 'TAR636G1744' => 'tar', 'TAR636G3358' => 'tar', 'TAR636G3436' => 'tar', 'THA.LOC104803047' => 'tha', 'Thecc.04G238900' => 'tca', 'Thhalv10021557m.g' => 'esa', 'Thhalv10026318m.g' => 'esa', 'Thhalv10026335m.g' => 'esa', 'TPR.G17433' => 'tpr', 'TPR.G18915' => 'tpr', 'TPR.G26125' => 'tpr', 'TWI09G0677' => 'twi', 'TWI73G0287' => 'twi', 'unitig_748.g8326' => 'ugi', 'vmacro15370' => 'vma', 'vmacro15371' => 'vma', 'vmacro15372' => 'vma', 'vmacro15373' => 'vma', 'vmacro15374' => 'vma', 'VMungo0720G2826' => 'vmu', 'Zm00001eb116960' => 'zma', 'Zm00001eb301260' => 'zma', 'Zm00001eb301270' => 'zma' ) $gf_id = 'HOM05D001460' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001460' ) $data_identifier = 'HOM05D001460' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 4, 'aag' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 2, 'aox' => (int) 2, 'arhy' => (int) 4, 'ath' => (int) 2, 'atr' => (int) 1, 'acertr' => (int) 10, 'cqu' => (int) 4, 'bca' => (int) 11, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 1, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 1, 'ccan' => (int) 1, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 1, 'col' => (int) 1, 'cpa' => (int) 1, 'cre' => (int) 7, 'csa' => (int) 1, 'camsi' => (int) 2, 'dca' => (int) 3, 'din' => (int) 2, 'dzi' => (int) 3, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 14, 'fve' => (int) 9, 'gma' => (int) 2, 'ghi' => (int) 4, 'gra' => (int) 2, 'vvi' => (int) 1, 'han' => (int) 13, 'cav' => (int) 1, 'hma' => (int) 2, 'sun' => (int) 2, 'lal' => (int) 2, 'lonja' => (int) 12, 'lja' => (int) 1, 'lsa' => (int) 7, 'mes' => (int) 1, 'mpo' => (int) 27, 'mbi' => (int) 1, 'mco' => (int) 8, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 1, 'egut' => (int) 1, 'ama' => (int) 1, 'nta' => (int) 4, 'nnu' => (int) 2, 'oeu' => (int) 3, 'osa' => (int) 4, 'pax' => (int) 9, 'pgr' => (int) 1, 'stu' => (int) 1, 'pvu' => (int) 1, 'ptr' => (int) 4, 'ppa' => (int) 22, 'pco' => (int) 6, 'ppe' => (int) 6, 'psa' => (int) 5, 'pso' => (int) 19, 'qlo' => (int) 5, 'rch' => (int) 7, 'rsi' => (int) 20, 'sbr' => (int) 5, 'sbo' => (int) 1, 'sci' => (int) 2, 'sed' => (int) 2, 'sgi' => (int) 12, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 2, 'tar' => (int) 10, 'tha' => (int) 1, 'tca' => (int) 1, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 2, 'ugi' => (int) 1, 'vma' => (int) 5, 'vmu' => (int) 1, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb301270' $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' => 'HOM05D001460', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '433', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p22980' => 'bna', 'A01p32340' => 'bna', 'A03p42970' => 'bna', 'A05p25880' => 'bna', 'Aa31LG8G9320' => 'aar', 'Aa31LG8G9330' => 'aar', 'Aa31LG8G9340' => 'aar', 'Aa31sc221G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1034' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1528' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.829' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2222' => 'aag', 'Ah.12g058830' => 'amhyb', 'Ah.12g058840' => 'amhyb', 'AL3G37160' => 'aly', 'AL7G41310' => 'aly', 'Aqoxy5G00395' => 'aox', 'Aqoxy5G00396' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0C8NZA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5185HY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JZ1PRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MD3LS0' => 'arhy', 'AT3G22840' => 'ath', 'AT4G14690' => 'ath', 'ATR0665G054' => 'atr', 'Atru.chr4.2344' => 'acertr', 'Atru.chr4.2346' => 'acertr', 'Atru.chr4.2347' => 'acertr', 'Atru.chr4.2348' => 'acertr', 'Atru.chr4.2355' => 'acertr', 'Atru.chr4.2356' => 'acertr', 'Atru.chr4.2358' => 'acertr', 'Atru.chr4.2359' => 'acertr', 'Atru.chr4.2360' => 'acertr', 'Atru.chr4.2361' => 'acertr', 'AUR62030476' => 'cqu', 'AUR62030478' => 'cqu', 'AUR62030819' => 'cqu', 'AUR62030820' => 'cqu', 'BcaB03g14648' => 'bca', 'BcaB04g20492' => 'bca', 'BcaB06g26399' => 'bca', 'BcaC01g03416' => 'bca', 'BcaC01g03419' => 'bca', 'BcaC01g03421' => 'bca', 'BcaC01g03424' => 'bca', 'BcaC05g28012' => 'bca', 'BcaC09g49212' => 'bca', 'BcaC09g50140' => 'bca', 'BcaNung00346' => 'bca', 'BolC1t02785H' => 'bol', 'BolC1t04095H' => 'bol', 'BolC3t17545H' => 'bol', 'BolC5t32769H' => 'bol', 'BraA01t02211Z' => 'bra', 'BraA01t03359Z' => 'bra', 'BraA03t13441Z' => 'bra', 'BraA05t21476Z' => 'bra', 'C01p28420' => 'bna', 'C01p41350' => 'bna', 'C03p52750' => 'bna', 'C03p52780' => 'bna', 'C05p40270' => 'bna', 'CAN.G1437.9' => 'can', 'CANSAT78G0035' => 'cansat', 'CANSAT78G1036' => 'cansat', 'CANSAT78G2272' => 'cansat', 'CANSAT78G2478' => 'cansat', 'CARHR098700' => 'chi', 'CARHR221120' => 'chi', 'CARHR221150' => 'chi', 'Carub.0003s2297' => 'cru', 'Carub.0007s2749' => 'cru', 'Carub.0007s2750' => 'cru', 'Carub.0007s2751' => 'cru', 'Ca_10849_v3' => 'car', 'Cc03_g04300' => 'ccan', 'CDE02G3648' => 'cde', 'CDE05G0060' => 'cde', 'CDE05G0692' => 'cde', 'CDE05G2285' => 'cde', 'CDE05G2884' => 'cde', 'CDE05G3072' => 'cde', 'Cfa008439' => 'cfa', 'Cfa008441' => 'cfa', 'Cfa008443' => 'cfa', 'Cfa008448' => 'cfa', 'Ciclev10005974m.g' => 'ccl', 'Ciclev10006006m.g' => 'ccl', 'Ciclev10006775m.g' => 'ccl', 'CiPaw.02G120400' => 'cil', 'CiPaw.02G120500' => 'cil', 'CiPaw.02G120600' => 'cil', 'ClCG05G004850' => 'cla', 'COL.COLO4_21566' => 'col', 'Cpa.g.sc44.124' => 'cpa', 'Cre07.g320400' => 'cre', 'Cre07.g320450' => 'cre', 'Cre08.g384650' => 'cre', 'Cre09.g393173' => 'cre', 'Cre09.g394325' => 'cre', 'Cre14.g626750' => 'cre', 'Cre16.g679250' => 'cre', 'CsaV3_3G012890' => 'csa', 'CSS0010865' => 'camsi', 'CSS0044338' => 'camsi', 'DCAR_002366' => 'dca', 'DCAR_030687' => 'dca', 'DCAR_030688' => 'dca', 'Dinv14047' => 'din', 'Dinv14048' => 'din', 'Duzib151G0105' => 'dzi', 'Duzib151G0114' => 'dzi', 'Duzib212G1029' => 'dzi', 'ECA232G3536' => 'eca', 'ECA240G0786' => 'eca', 'ECA240G1802' => 'eca', 'ECA240G3760' => 'eca', 'ECA240G3920' => 'eca', 'EL10Ac5g12536' => 'bvu', 'EL10Ac5g12537' => 'bvu', 'EL10Ac5g12538' => 'bvu', 'Eucgr.B01004' => 'egr', 'Eucgr.B01006' => 'egr', 'Eucgr.B01007' => 'egr', 'Eucgr.B01008' => 'egr', 'Eucgr.B01895' => 'egr', 'Eucgr.B01896' => 'egr', 'FAN04G1456' => 'fan', 'FAN08G1769' => 'fan', 'FAN08G2160' => 'fan', 'FAN13G2403' => 'fan', 'FAN13G3303' => 'fan', 'FAN15G2435' => 'fan', 'FAN17G0672' => 'fan', 'FAN17G2441' => 'fan', 'FAN18G1024' => 'fan', 'FAN22G1458' => 'fan', 'FAN24G0037' => 'fan', 'FAN24G0429' => 'fan', 'FAN24G2387' => 'fan', 'FAN27G2746' => 'fan', 'FvH4_2g20400' => 'fve', 'FvH4_2g20420' => 'fve', 'FvH4_2g20430' => 'fve', 'FvH4_4g01270' => 'fve', 'FvH4_4g01290' => 'fve', 'FvH4_4g01300' => 'fve', 'FvH4_4g01310' => 'fve', 'FvH4_4g01330' => 'fve', 'FvH4_5g09070' => 'fve', 'Glyma.10G243800' => 'gma', 'Glyma.20G150600' => 'gma', 'Gohir.A09G219200' => 'ghi', 'Gohir.A09G219300' => 'ghi', 'Gohir.D09G221400' => 'ghi', 'Gohir.D09G221500' => 'ghi', 'Gorai.006G242600' => 'gra', 'Gorai.006G242700' => 'gra', 'GSVIVG01018044001' => 'vvi', 'HanXRQChr03g0083821' => 'han', 'HanXRQChr03g0083841' => 'han', 'HanXRQChr03g0083881' => 'han', 'HanXRQChr03g0083901' => 'han', 'HanXRQChr03g0083921' => 'han', 'HanXRQChr03g0085331' => 'han', 'HanXRQChr03g0085361' => 'han', 'HanXRQChr03g0085411' => 'han', 'HanXRQChr03g0085421' => 'han', 'HanXRQChr03g0085431' => 'han', 'HanXRQChr08g0221991' => 'han', 'HanXRQChr11g0336061' => 'han', 'HanXRQChr11g0336411' => 'han', 'Haze_11234' => 'cav', 'Hma1.2p1_0549F.1_g177010' => 'hma', 'Hma1.2p1_0602F.1_g187630' => 'hma', 'Hund14876' => 'sun', 'Hund14879' => 'sun', 'Lalb_Chr06g0160741' => 'lal', 'Lalb_Chr21g0304781' => 'lal', 'Lj3A726G19' => 'lonja', 'Lj3A726T23' => 'lonja', 'Lj3A726T24' => 'lonja', 'Lj3A726T25' => 'lonja', 'Lj3A727T17' => 'lonja', 'Lj3C726T0' => 'lonja', 'Lj3C726T2' => 'lonja', 'Lj3P725T35' => 'lonja', 'Lj3P727T10' => 'lonja', 'Lj3P727T12' => 'lonja', 'Lj3P727T14' => 'lonja', 'Lj5g0023109' => 'lja', 'Lj6P646T44' => 'lonja', 'Lsat_1_v5_gn_6_75760' => 'lsa', 'Lsat_1_v5_gn_6_75800' => 'lsa', 'Lsat_1_v5_gn_6_75900' => 'lsa', 'Lsat_1_v5_gn_6_76240' => 'lsa', 'Lsat_1_v5_gn_6_76441' => 'lsa', 'Lsat_1_v5_gn_6_76700' => 'lsa', 'Lsat_1_v5_gn_6_76760' => 'lsa', 'Manes.15G033100' => 'mes', 'Mapoly0004s0074' => 'mpo', 'Mapoly0004s0075' => 'mpo', 'Mapoly0004s0163' => 'mpo', 'Mapoly0004s0164' => 'mpo', 'Mapoly0021s0018' => 'mpo', 'Mapoly0041s0136' => 'mpo', 'Mapoly0041s0137' => 'mpo', 'Mapoly0041s0138' => 'mpo', 'Mapoly0041s0139' => 'mpo', 'Mapoly0041s0141' => 'mpo', 'Mapoly0041s0142' => 'mpo', 'Mapoly0041s0143' => 'mpo', 'Mapoly0041s0144' => 'mpo', 'Mapoly0041s0145' => 'mpo', 'Mapoly0047s0106' => 'mpo', 'Mapoly0047s0108' => 'mpo', 'Mapoly0050s0051' => 'mpo', 'Mapoly0050s0052' => 'mpo', 'Mapoly0050s0053' => 'mpo', 'Mapoly0058s0013' => 'mpo', 'Mapoly0091s0078' => 'mpo', 'Mapoly0091s0079' => 'mpo', 'Mapoly0091s0080' => 'mpo', 'Mapoly0091s0081' => 'mpo', 'Mapoly0278s0004' => 'mpo', 'Mapoly0278s0005' => 'mpo', 'Mapoly0278s0006' => 'mpo', 'MBI11_g30648_MAGBIO' => 'mbi', 'MCO03G194' => 'mco', 'MCO03G590' => 'mco', 'MCO07G312' => 'mco', 'MCO10G318' => 'mco', 'MCO12G244' => 'mco', 'MCO13G148' => 'mco', 'MCO13G194' => 'mco', 'MCO16G238' => 'mco', 'MD06G1134100' => 'mdo', 'MD13G1200100' => 'mdo', 'MD13G1200300' => 'mdo', 'MD13G1200600' => 'mdo', 'MD14G1150400' => 'mdo', 'MD16G1200000' => 'mdo', 'Medtr1g102570' => 'mtr', 'Medtr1g102780' => 'mtr', 'Medtr1g102800' => 'mtr', 'Medtr1g102810' => 'mtr', 'Medtr1g102830' => 'mtr', 'MELO3C006499.2' => 'cme', 'Migut.G00385' => 'egut', 'MSTRG.4063' => 'ama', 'Nitab4.5_0000090g0260' => 'nta', 'Nitab4.5_0000977g0030' => 'nta', 'Nitab4.5_0002541g0040' => 'nta', 'Nitab4.5_0007068g0040' => 'nta', 'Nn005s41408' => 'nnu', 'Nn005s41410' => 'nnu', 'Oeu010310.1' => 'oeu', 'Oeu010311.1' => 'oeu', 'Oeu043472.1' => 'oeu', 'Os01g0246400' => 'osa', 'Os04g0267950' => 'osa', 'Os07g0178700' => 'osa', 'Os07g0178800' => 'osa', 'Peaxi162Scf00316g00046' => 'pax', 'Peaxi162Scf00316g00049' => 'pax', 'Peaxi162Scf00316g00059' => 'pax', 'Peaxi162Scf00316g00328' => 'pax', 'Peaxi162Scf00316g00329' => 'pax', 'Peaxi162Scf00316g00411' => 'pax', 'Peaxi162Scf00316g00521' => 'pax', 'Peaxi162Scf00492g00068' => 'pax', 'Peaxi162Scf35631g00002' => 'pax', 'PGR142G3720' => 'pgr', 'PGSC0003DMG400006442' => 'stu', 'Phvul.007G062000' => 'pvu', 'Potri.008G157750' => 'ptr', 'Potri.008G157900' => 'ptr', 'Potri.008G158000' => 'ptr', 'Potri.008G158200' => 'ptr', 'Pp3c11_7280' => 'ppa', 'Pp3c11_7980' => 'ppa', 'Pp3c12_19450' => 'ppa', 'Pp3c14_1480' => 'ppa', 'Pp3c14_1501' => 'ppa', 'Pp3c16_4900' => 'ppa', 'Pp3c16_5010' => 'ppa', 'Pp3c16_5060' => 'ppa', 'Pp3c19_18250' => 'ppa', 'Pp3c23_8530' => 'ppa', 'Pp3c23_8550' => 'ppa', 'Pp3c24_9670' => 'ppa', 'Pp3c2_21390' => 'ppa', 'Pp3c2_31380' => 'ppa', 'Pp3c3_16620' => 'ppa', 'Pp3c3_8090' => 'ppa', 'Pp3c3_8110' => 'ppa', 'Pp3c3_8130' => 'ppa', 'Pp3c3_8150' => 'ppa', 'Pp3c4_14320' => 'ppa', 'Pp3c6_2560' => 'ppa', 'Pp3c9_16700' => 'ppa', 'PRCOL_00000234' => 'pco', 'PRCOL_00000235' => 'pco', 'PRCOL_00000777' => 'pco', 'PRCOL_00002344' => 'pco', 'PRCOL_00002372' => 'pco', 'PRCOL_00006120' => 'pco', 'Prupe.1G021400' => 'ppe', 'Prupe.1G021500' => 'ppe', 'Prupe.1G021600' => 'ppe', 'Prupe.1G021700' => 'ppe', 'Prupe.1G021800' => 'ppe', 'Prupe.5G145100' => 'ppe', 'Psat6g204040' => 'psa', 'Psat6g204800' => 'psa', 'Psat6g204920' => 'psa', 'Psat6g204960' => 'psa', 'Psat6g205080' => 'psa', 'PSO017G0271' => 'pso', 'PSO017G1276' => 'pso', 'PSO017G1429' => 'pso', 'PSO017G1861' => 'pso', 'PSO017G2787' => 'pso', 'PSO017G4466' => 'pso', 'PSO017G5118' => 'pso', 'PSO017G5420' => 'pso', 'PSO063G3678' => 'pso', 'PSO210G0546' => 'pso', 'PSO317G0001' => 'pso', 'PSO357G0512' => 'pso', 'PSO478G2682' => 'pso', 'PSO647G0001' => 'pso', 'PSO675G0001' => 'pso', 'PSO675G2699' => 'pso', 'PSO675G2849' => 'pso', 'PSO675G4991' => 'pso', 'PSO689G0001' => 'pso', 'QL06p000916' => 'qlo', 'QL06p000921' => 'qlo', 'QL06p001398' => 'qlo', 'QL06p001407' => 'qlo', 'QL06p002031' => 'qlo', 'RcHm_v2.0_Chr4g0387791' => 'rch', 'RcHm_v2.0_Chr4g0387801' => 'rch', 'RcHm_v2.0_Chr6g0286501' => 'rch', 'RcHm_v2.0_Chr6g0286511' => 'rch', 'RcHm_v2.0_Chr6g0286521' => 'rch', 'RcHm_v2.0_Chr6g0286531' => 'rch', 'RcHm_v2.0_Chr7g0189141' => 'rch', 'Rhsim02G0028700' => 'rsi', 'Rhsim02G0028800' => 'rsi', 'Rhsim02G0028900' => 'rsi', 'Rhsim02G0029000' => 'rsi', 'Rhsim02G0029100' => 'rsi', 'Rhsim02G0029200' => 'rsi', 'Rhsim02G0029300' => 'rsi', 'Rhsim02G0029400' => 'rsi', 'Rhsim02G0029500' => 'rsi', 'Rhsim02G0029600' => 'rsi', 'RhsimUnG0024000' => 'rsi', 'RhsimUnG0024100' => 'rsi', 'RhsimUnG0024200' => 'rsi', 'RhsimUnG0024300' => 'rsi', 'RhsimUnG0024400' => 'rsi', 'RhsimUnG0024500' => 'rsi', 'RhsimUnG0024700' => 'rsi', 'RhsimUnG0024800' => 'rsi', 'RhsimUnG0024900' => 'rsi', 'RhsimUnG0025100' => 'rsi', 'Sabra08G0120200' => 'sbr', 'Sabra08G0120300' => 'sbr', 'Sabra08G0120500' => 'sbr', 'Sabra08G0120600' => 'sbr', 'Sabra10G0158900' => 'sbr', 'SalBow2G3492' => 'sbo', 'Sc13g0004760' => 'sci', 'Sc13g0004770' => 'sci', 'Sed0003417' => 'sed', 'Sed0019750' => 'sed', 'SEGI_03419' => 'sgi', 'SEGI_05907' => 'sgi', 'SEGI_10682' => 'sgi', 'SEGI_13528' => 'sgi', 'SEGI_16081' => 'sgi', 'SEGI_19370' => 'sgi', 'SEGI_21015' => 'sgi', 'SEGI_21944' => 'sgi', 'SEGI_32906' => 'sgi', 'SEGI_33093' => 'sgi', 'SEGI_36110' => 'sgi', 'SEGI_40397' => 'sgi', 'SGA_v2.0_scaffold191G40426' => 'sas', 'SGA_v2.0_scaffold353G49717' => 'sas', 'SGA_v2.0_scaffold50G18550' => 'sas', 'SMO119G0173' => 'smo', 'SMO172G0002' => 'smo', 'Solyc09g082690.3' => 'sly', 'Solyc09g082700.2' => 'sly', 'Sopen09g031550' => 'spe', 'Sopen09g031560' => 'spe', 'Sp3g20540' => 'spa', 'Sp7g07580' => 'spa', 'TAR134G0002' => 'tar', 'TAR236G0001' => 'tar', 'TAR365G0892' => 'tar', 'TAR636G0166' => 'tar', 'TAR636G0646' => 'tar', 'TAR636G0869' => 'tar', 'TAR636G1317' => 'tar', 'TAR636G1744' => 'tar', 'TAR636G3358' => 'tar', 'TAR636G3436' => 'tar', 'THA.LOC104803047' => 'tha', 'Thecc.04G238900' => 'tca', 'Thhalv10021557m.g' => 'esa', 'Thhalv10026318m.g' => 'esa', 'Thhalv10026335m.g' => 'esa', 'TPR.G17433' => 'tpr', 'TPR.G18915' => 'tpr', 'TPR.G26125' => 'tpr', 'TWI09G0677' => 'twi', 'TWI73G0287' => 'twi', 'unitig_748.g8326' => 'ugi', 'vmacro15370' => 'vma', 'vmacro15371' => 'vma', 'vmacro15372' => 'vma', 'vmacro15373' => 'vma', 'vmacro15374' => 'vma', 'VMungo0720G2826' => 'vmu', 'Zm00001eb116960' => 'zma', 'Zm00001eb301260' => 'zma', 'Zm00001eb301270' => 'zma' ), 'gf_id' => 'HOM05D001460', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001460' ), 'data_identifier' => 'HOM05D001460', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001460', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '433', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p22980' => 'bna', 'A01p32340' => 'bna', 'A03p42970' => 'bna', 'A05p25880' => 'bna', 'Aa31LG8G9320' => 'aar', 'Aa31LG8G9330' => 'aar', 'Aa31LG8G9340' => 'aar', 'Aa31sc221G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1034' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1528' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.829' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2222' => 'aag', 'Ah.12g058830' => 'amhyb', 'Ah.12g058840' => 'amhyb', 'AL3G37160' => 'aly', 'AL7G41310' => 'aly', 'Aqoxy5G00395' => 'aox', 'Aqoxy5G00396' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0C8NZA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5185HY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JZ1PRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MD3LS0' => 'arhy', 'AT3G22840' => 'ath', 'AT4G14690' => 'ath', 'ATR0665G054' => 'atr', 'Atru.chr4.2344' => 'acertr', 'Atru.chr4.2346' => 'acertr', 'Atru.chr4.2347' => 'acertr', 'Atru.chr4.2348' => 'acertr', 'Atru.chr4.2355' => 'acertr', 'Atru.chr4.2356' => 'acertr', 'Atru.chr4.2358' => 'acertr', 'Atru.chr4.2359' => 'acertr', 'Atru.chr4.2360' => 'acertr', 'Atru.chr4.2361' => 'acertr', 'AUR62030476' => 'cqu', 'AUR62030478' => 'cqu', 'AUR62030819' => 'cqu', 'AUR62030820' => 'cqu', 'BcaB03g14648' => 'bca', 'BcaB04g20492' => 'bca', 'BcaB06g26399' => 'bca', 'BcaC01g03416' => 'bca', 'BcaC01g03419' => 'bca', 'BcaC01g03421' => 'bca', 'BcaC01g03424' => 'bca', 'BcaC05g28012' => 'bca', 'BcaC09g49212' => 'bca', 'BcaC09g50140' => 'bca', 'BcaNung00346' => 'bca', 'BolC1t02785H' => 'bol', 'BolC1t04095H' => 'bol', 'BolC3t17545H' => 'bol', 'BolC5t32769H' => 'bol', 'BraA01t02211Z' => 'bra', 'BraA01t03359Z' => 'bra', 'BraA03t13441Z' => 'bra', 'BraA05t21476Z' => 'bra', 'C01p28420' => 'bna', 'C01p41350' => 'bna', 'C03p52750' => 'bna', 'C03p52780' => 'bna', 'C05p40270' => 'bna', 'CAN.G1437.9' => 'can', 'CANSAT78G0035' => 'cansat', 'CANSAT78G1036' => 'cansat', 'CANSAT78G2272' => 'cansat', 'CANSAT78G2478' => 'cansat', 'CARHR098700' => 'chi', 'CARHR221120' => 'chi', 'CARHR221150' => 'chi', 'Carub.0003s2297' => 'cru', 'Carub.0007s2749' => 'cru', 'Carub.0007s2750' => 'cru', 'Carub.0007s2751' => 'cru', 'Ca_10849_v3' => 'car', 'Cc03_g04300' => 'ccan', 'CDE02G3648' => 'cde', 'CDE05G0060' => 'cde', 'CDE05G0692' => 'cde', 'CDE05G2285' => 'cde', 'CDE05G2884' => 'cde', 'CDE05G3072' => 'cde', 'Cfa008439' => 'cfa', 'Cfa008441' => 'cfa', 'Cfa008443' => 'cfa', 'Cfa008448' => 'cfa', 'Ciclev10005974m.g' => 'ccl', 'Ciclev10006006m.g' => 'ccl', 'Ciclev10006775m.g' => 'ccl', 'CiPaw.02G120400' => 'cil', 'CiPaw.02G120500' => 'cil', 'CiPaw.02G120600' => 'cil', 'ClCG05G004850' => 'cla', 'COL.COLO4_21566' => 'col', 'Cpa.g.sc44.124' => 'cpa', 'Cre07.g320400' => 'cre', 'Cre07.g320450' => 'cre', 'Cre08.g384650' => 'cre', 'Cre09.g393173' => 'cre', 'Cre09.g394325' => 'cre', 'Cre14.g626750' => 'cre', 'Cre16.g679250' => 'cre', 'CsaV3_3G012890' => 'csa', 'CSS0010865' => 'camsi', 'CSS0044338' => 'camsi', 'DCAR_002366' => 'dca', 'DCAR_030687' => 'dca', 'DCAR_030688' => 'dca', 'Dinv14047' => 'din', 'Dinv14048' => 'din', 'Duzib151G0105' => 'dzi', 'Duzib151G0114' => 'dzi', 'Duzib212G1029' => 'dzi', 'ECA232G3536' => 'eca', 'ECA240G0786' => 'eca', 'ECA240G1802' => 'eca', 'ECA240G3760' => 'eca', 'ECA240G3920' => 'eca', 'EL10Ac5g12536' => 'bvu', 'EL10Ac5g12537' => 'bvu', 'EL10Ac5g12538' => 'bvu', 'Eucgr.B01004' => 'egr', 'Eucgr.B01006' => 'egr', 'Eucgr.B01007' => 'egr', 'Eucgr.B01008' => 'egr', 'Eucgr.B01895' => 'egr', 'Eucgr.B01896' => 'egr', 'FAN04G1456' => 'fan', 'FAN08G1769' => 'fan', 'FAN08G2160' => 'fan', 'FAN13G2403' => 'fan', 'FAN13G3303' => 'fan', 'FAN15G2435' => 'fan', 'FAN17G0672' => 'fan', 'FAN17G2441' => 'fan', 'FAN18G1024' => 'fan', 'FAN22G1458' => 'fan', 'FAN24G0037' => 'fan', 'FAN24G0429' => 'fan', 'FAN24G2387' => 'fan', 'FAN27G2746' => 'fan', 'FvH4_2g20400' => 'fve', 'FvH4_2g20420' => 'fve', 'FvH4_2g20430' => 'fve', 'FvH4_4g01270' => 'fve', 'FvH4_4g01290' => 'fve', 'FvH4_4g01300' => 'fve', 'FvH4_4g01310' => 'fve', 'FvH4_4g01330' => 'fve', 'FvH4_5g09070' => 'fve', 'Glyma.10G243800' => 'gma', 'Glyma.20G150600' => 'gma', 'Gohir.A09G219200' => 'ghi', 'Gohir.A09G219300' => 'ghi', 'Gohir.D09G221400' => 'ghi', 'Gohir.D09G221500' => 'ghi', 'Gorai.006G242600' => 'gra', 'Gorai.006G242700' => 'gra', 'GSVIVG01018044001' => 'vvi', 'HanXRQChr03g0083821' => 'han', 'HanXRQChr03g0083841' => 'han', 'HanXRQChr03g0083881' => 'han', 'HanXRQChr03g0083901' => 'han', 'HanXRQChr03g0083921' => 'han', 'HanXRQChr03g0085331' => 'han', 'HanXRQChr03g0085361' => 'han', 'HanXRQChr03g0085411' => 'han', 'HanXRQChr03g0085421' => 'han', 'HanXRQChr03g0085431' => 'han', 'HanXRQChr08g0221991' => 'han', 'HanXRQChr11g0336061' => 'han', 'HanXRQChr11g0336411' => 'han', 'Haze_11234' => 'cav', 'Hma1.2p1_0549F.1_g177010' => 'hma', 'Hma1.2p1_0602F.1_g187630' => 'hma', 'Hund14876' => 'sun', 'Hund14879' => 'sun', 'Lalb_Chr06g0160741' => 'lal', 'Lalb_Chr21g0304781' => 'lal', 'Lj3A726G19' => 'lonja', 'Lj3A726T23' => 'lonja', 'Lj3A726T24' => 'lonja', 'Lj3A726T25' => 'lonja', 'Lj3A727T17' => 'lonja', 'Lj3C726T0' => 'lonja', 'Lj3C726T2' => 'lonja', 'Lj3P725T35' => 'lonja', 'Lj3P727T10' => 'lonja', 'Lj3P727T12' => 'lonja', 'Lj3P727T14' => 'lonja', 'Lj5g0023109' => 'lja', 'Lj6P646T44' => 'lonja', 'Lsat_1_v5_gn_6_75760' => 'lsa', 'Lsat_1_v5_gn_6_75800' => 'lsa', 'Lsat_1_v5_gn_6_75900' => 'lsa', 'Lsat_1_v5_gn_6_76240' => 'lsa', 'Lsat_1_v5_gn_6_76441' => 'lsa', 'Lsat_1_v5_gn_6_76700' => 'lsa', 'Lsat_1_v5_gn_6_76760' => 'lsa', 'Manes.15G033100' => 'mes', 'Mapoly0004s0074' => 'mpo', 'Mapoly0004s0075' => 'mpo', 'Mapoly0004s0163' => 'mpo', 'Mapoly0004s0164' => 'mpo', 'Mapoly0021s0018' => 'mpo', 'Mapoly0041s0136' => 'mpo', 'Mapoly0041s0137' => 'mpo', 'Mapoly0041s0138' => 'mpo', 'Mapoly0041s0139' => 'mpo', 'Mapoly0041s0141' => 'mpo', 'Mapoly0041s0142' => 'mpo', 'Mapoly0041s0143' => 'mpo', 'Mapoly0041s0144' => 'mpo', 'Mapoly0041s0145' => 'mpo', 'Mapoly0047s0106' => 'mpo', 'Mapoly0047s0108' => 'mpo', 'Mapoly0050s0051' => 'mpo', 'Mapoly0050s0052' => 'mpo', 'Mapoly0050s0053' => 'mpo', 'Mapoly0058s0013' => 'mpo', 'Mapoly0091s0078' => 'mpo', 'Mapoly0091s0079' => 'mpo', 'Mapoly0091s0080' => 'mpo', 'Mapoly0091s0081' => 'mpo', 'Mapoly0278s0004' => 'mpo', 'Mapoly0278s0005' => 'mpo', 'Mapoly0278s0006' => 'mpo', 'MBI11_g30648_MAGBIO' => 'mbi', 'MCO03G194' => 'mco', 'MCO03G590' => 'mco', 'MCO07G312' => 'mco', 'MCO10G318' => 'mco', 'MCO12G244' => 'mco', 'MCO13G148' => 'mco', 'MCO13G194' => 'mco', 'MCO16G238' => 'mco', 'MD06G1134100' => 'mdo', 'MD13G1200100' => 'mdo', 'MD13G1200300' => 'mdo', 'MD13G1200600' => 'mdo', 'MD14G1150400' => 'mdo', 'MD16G1200000' => 'mdo', 'Medtr1g102570' => 'mtr', 'Medtr1g102780' => 'mtr', 'Medtr1g102800' => 'mtr', 'Medtr1g102810' => 'mtr', 'Medtr1g102830' => 'mtr', 'MELO3C006499.2' => 'cme', 'Migut.G00385' => 'egut', 'MSTRG.4063' => 'ama', 'Nitab4.5_0000090g0260' => 'nta', 'Nitab4.5_0000977g0030' => 'nta', 'Nitab4.5_0002541g0040' => 'nta', 'Nitab4.5_0007068g0040' => 'nta', 'Nn005s41408' => 'nnu', 'Nn005s41410' => 'nnu', 'Oeu010310.1' => 'oeu', 'Oeu010311.1' => 'oeu', 'Oeu043472.1' => 'oeu', 'Os01g0246400' => 'osa', 'Os04g0267950' => 'osa', 'Os07g0178700' => 'osa', 'Os07g0178800' => 'osa', 'Peaxi162Scf00316g00046' => 'pax', 'Peaxi162Scf00316g00049' => 'pax', 'Peaxi162Scf00316g00059' => 'pax', 'Peaxi162Scf00316g00328' => 'pax', 'Peaxi162Scf00316g00329' => 'pax', 'Peaxi162Scf00316g00411' => 'pax', 'Peaxi162Scf00316g00521' => 'pax', 'Peaxi162Scf00492g00068' => 'pax', 'Peaxi162Scf35631g00002' => 'pax', 'PGR142G3720' => 'pgr', 'PGSC0003DMG400006442' => 'stu', 'Phvul.007G062000' => 'pvu', 'Potri.008G157750' => 'ptr', 'Potri.008G157900' => 'ptr', 'Potri.008G158000' => 'ptr', 'Potri.008G158200' => 'ptr', 'Pp3c11_7280' => 'ppa', 'Pp3c11_7980' => 'ppa', 'Pp3c12_19450' => 'ppa', 'Pp3c14_1480' => 'ppa', 'Pp3c14_1501' => 'ppa', 'Pp3c16_4900' => 'ppa', 'Pp3c16_5010' => 'ppa', 'Pp3c16_5060' => 'ppa', 'Pp3c19_18250' => 'ppa', 'Pp3c23_8530' => 'ppa', 'Pp3c23_8550' => 'ppa', 'Pp3c24_9670' => 'ppa', 'Pp3c2_21390' => 'ppa', 'Pp3c2_31380' => 'ppa', 'Pp3c3_16620' => 'ppa', 'Pp3c3_8090' => 'ppa', 'Pp3c3_8110' => 'ppa', 'Pp3c3_8130' => 'ppa', 'Pp3c3_8150' => 'ppa', 'Pp3c4_14320' => 'ppa', 'Pp3c6_2560' => 'ppa', 'Pp3c9_16700' => 'ppa', 'PRCOL_00000234' => 'pco', 'PRCOL_00000235' => 'pco', 'PRCOL_00000777' => 'pco', 'PRCOL_00002344' => 'pco', 'PRCOL_00002372' => 'pco', 'PRCOL_00006120' => 'pco', 'Prupe.1G021400' => 'ppe', 'Prupe.1G021500' => 'ppe', 'Prupe.1G021600' => 'ppe', 'Prupe.1G021700' => 'ppe', 'Prupe.1G021800' => 'ppe', 'Prupe.5G145100' => 'ppe', 'Psat6g204040' => 'psa', 'Psat6g204800' => 'psa', 'Psat6g204920' => 'psa', 'Psat6g204960' => 'psa', 'Psat6g205080' => 'psa', 'PSO017G0271' => 'pso', 'PSO017G1276' => 'pso', 'PSO017G1429' => 'pso', 'PSO017G1861' => 'pso', 'PSO017G2787' => 'pso', 'PSO017G4466' => 'pso', 'PSO017G5118' => 'pso', 'PSO017G5420' => 'pso', 'PSO063G3678' => 'pso', 'PSO210G0546' => 'pso', 'PSO317G0001' => 'pso', 'PSO357G0512' => 'pso', 'PSO478G2682' => 'pso', 'PSO647G0001' => 'pso', 'PSO675G0001' => 'pso', 'PSO675G2699' => 'pso', 'PSO675G2849' => 'pso', 'PSO675G4991' => 'pso', 'PSO689G0001' => 'pso', 'QL06p000916' => 'qlo', 'QL06p000921' => 'qlo', 'QL06p001398' => 'qlo', 'QL06p001407' => 'qlo', 'QL06p002031' => 'qlo', 'RcHm_v2.0_Chr4g0387791' => 'rch', 'RcHm_v2.0_Chr4g0387801' => 'rch', 'RcHm_v2.0_Chr6g0286501' => 'rch', 'RcHm_v2.0_Chr6g0286511' => 'rch', 'RcHm_v2.0_Chr6g0286521' => 'rch', 'RcHm_v2.0_Chr6g0286531' => 'rch', 'RcHm_v2.0_Chr7g0189141' => 'rch', 'Rhsim02G0028700' => 'rsi', 'Rhsim02G0028800' => 'rsi', 'Rhsim02G0028900' => 'rsi', 'Rhsim02G0029000' => 'rsi', 'Rhsim02G0029100' => 'rsi', 'Rhsim02G0029200' => 'rsi', 'Rhsim02G0029300' => 'rsi', 'Rhsim02G0029400' => 'rsi', 'Rhsim02G0029500' => 'rsi', 'Rhsim02G0029600' => 'rsi', 'RhsimUnG0024000' => 'rsi', 'RhsimUnG0024100' => 'rsi', 'RhsimUnG0024200' => 'rsi', 'RhsimUnG0024300' => 'rsi', 'RhsimUnG0024400' => 'rsi', 'RhsimUnG0024500' => 'rsi', 'RhsimUnG0024700' => 'rsi', 'RhsimUnG0024800' => 'rsi', 'RhsimUnG0024900' => 'rsi', 'RhsimUnG0025100' => 'rsi', 'Sabra08G0120200' => 'sbr', 'Sabra08G0120300' => 'sbr', 'Sabra08G0120500' => 'sbr', 'Sabra08G0120600' => 'sbr', 'Sabra10G0158900' => 'sbr', 'SalBow2G3492' => 'sbo', 'Sc13g0004760' => 'sci', 'Sc13g0004770' => 'sci', 'Sed0003417' => 'sed', 'Sed0019750' => 'sed', 'SEGI_03419' => 'sgi', 'SEGI_05907' => 'sgi', 'SEGI_10682' => 'sgi', 'SEGI_13528' => 'sgi', 'SEGI_16081' => 'sgi', 'SEGI_19370' => 'sgi', 'SEGI_21015' => 'sgi', 'SEGI_21944' => 'sgi', 'SEGI_32906' => 'sgi', 'SEGI_33093' => 'sgi', 'SEGI_36110' => 'sgi', 'SEGI_40397' => 'sgi', 'SGA_v2.0_scaffold191G40426' => 'sas', 'SGA_v2.0_scaffold353G49717' => 'sas', 'SGA_v2.0_scaffold50G18550' => 'sas', 'SMO119G0173' => 'smo', 'SMO172G0002' => 'smo', 'Solyc09g082690.3' => 'sly', 'Solyc09g082700.2' => 'sly', 'Sopen09g031550' => 'spe', 'Sopen09g031560' => 'spe', 'Sp3g20540' => 'spa', 'Sp7g07580' => 'spa', 'TAR134G0002' => 'tar', 'TAR236G0001' => 'tar', 'TAR365G0892' => 'tar', 'TAR636G0166' => 'tar', 'TAR636G0646' => 'tar', 'TAR636G0869' => 'tar', 'TAR636G1317' => 'tar', 'TAR636G1744' => 'tar', 'TAR636G3358' => 'tar', 'TAR636G3436' => 'tar', 'THA.LOC104803047' => 'tha', 'Thecc.04G238900' => 'tca', 'Thhalv10021557m.g' => 'esa', 'Thhalv10026318m.g' => 'esa', 'Thhalv10026335m.g' => 'esa', 'TPR.G17433' => 'tpr', 'TPR.G18915' => 'tpr', 'TPR.G26125' => 'tpr', 'TWI09G0677' => 'twi', 'TWI73G0287' => 'twi', 'unitig_748.g8326' => 'ugi', 'vmacro15370' => 'vma', 'vmacro15371' => 'vma', 'vmacro15372' => 'vma', 'vmacro15373' => 'vma', 'vmacro15374' => 'vma', 'VMungo0720G2826' => 'vmu', 'Zm00001eb116960' => 'zma', 'Zm00001eb301260' => 'zma', 'Zm00001eb301270' => 'zma' ) $gf_id = 'HOM05D001460' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001460' ) $data_identifier = 'HOM05D001460' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 4, 'aag' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 2, 'aox' => (int) 2, 'arhy' => (int) 4, 'ath' => (int) 2, 'atr' => (int) 1, 'acertr' => (int) 10, 'cqu' => (int) 4, 'bca' => (int) 11, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 1, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 1, 'ccan' => (int) 1, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 1, 'col' => (int) 1, 'cpa' => (int) 1, 'cre' => (int) 7, 'csa' => (int) 1, 'camsi' => (int) 2, 'dca' => (int) 3, 'din' => (int) 2, 'dzi' => (int) 3, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 14, 'fve' => (int) 9, 'gma' => (int) 2, 'ghi' => (int) 4, 'gra' => (int) 2, 'vvi' => (int) 1, 'han' => (int) 13, 'cav' => (int) 1, 'hma' => (int) 2, 'sun' => (int) 2, 'lal' => (int) 2, 'lonja' => (int) 12, 'lja' => (int) 1, 'lsa' => (int) 7, 'mes' => (int) 1, 'mpo' => (int) 27, 'mbi' => (int) 1, 'mco' => (int) 8, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 1, 'egut' => (int) 1, 'ama' => (int) 1, 'nta' => (int) 4, 'nnu' => (int) 2, 'oeu' => (int) 3, 'osa' => (int) 4, 'pax' => (int) 9, 'pgr' => (int) 1, 'stu' => (int) 1, 'pvu' => (int) 1, 'ptr' => (int) 4, 'ppa' => (int) 22, 'pco' => (int) 6, 'ppe' => (int) 6, 'psa' => (int) 5, 'pso' => (int) 19, 'qlo' => (int) 5, 'rch' => (int) 7, 'rsi' => (int) 20, 'sbr' => (int) 5, 'sbo' => (int) 1, 'sci' => (int) 2, 'sed' => (int) 2, 'sgi' => (int) 12, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 2, 'tar' => (int) 10, 'tha' => (int) 1, 'tca' => (int) 1, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 2, 'ugi' => (int) 1, 'vma' => (int) 5, 'vmu' => (int) 1, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb301270' $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' => 'HOM05D001460', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '433', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p22980' => 'bna', 'A01p32340' => 'bna', 'A03p42970' => 'bna', 'A05p25880' => 'bna', 'Aa31LG8G9320' => 'aar', 'Aa31LG8G9330' => 'aar', 'Aa31LG8G9340' => 'aar', 'Aa31sc221G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1034' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1528' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.829' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2222' => 'aag', 'Ah.12g058830' => 'amhyb', 'Ah.12g058840' => 'amhyb', 'AL3G37160' => 'aly', 'AL7G41310' => 'aly', 'Aqoxy5G00395' => 'aox', 'Aqoxy5G00396' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0C8NZA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5185HY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JZ1PRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MD3LS0' => 'arhy', 'AT3G22840' => 'ath', 'AT4G14690' => 'ath', 'ATR0665G054' => 'atr', 'Atru.chr4.2344' => 'acertr', 'Atru.chr4.2346' => 'acertr', 'Atru.chr4.2347' => 'acertr', 'Atru.chr4.2348' => 'acertr', 'Atru.chr4.2355' => 'acertr', 'Atru.chr4.2356' => 'acertr', 'Atru.chr4.2358' => 'acertr', 'Atru.chr4.2359' => 'acertr', 'Atru.chr4.2360' => 'acertr', 'Atru.chr4.2361' => 'acertr', 'AUR62030476' => 'cqu', 'AUR62030478' => 'cqu', 'AUR62030819' => 'cqu', 'AUR62030820' => 'cqu', 'BcaB03g14648' => 'bca', 'BcaB04g20492' => 'bca', 'BcaB06g26399' => 'bca', 'BcaC01g03416' => 'bca', 'BcaC01g03419' => 'bca', 'BcaC01g03421' => 'bca', 'BcaC01g03424' => 'bca', 'BcaC05g28012' => 'bca', 'BcaC09g49212' => 'bca', 'BcaC09g50140' => 'bca', 'BcaNung00346' => 'bca', 'BolC1t02785H' => 'bol', 'BolC1t04095H' => 'bol', 'BolC3t17545H' => 'bol', 'BolC5t32769H' => 'bol', 'BraA01t02211Z' => 'bra', 'BraA01t03359Z' => 'bra', 'BraA03t13441Z' => 'bra', 'BraA05t21476Z' => 'bra', 'C01p28420' => 'bna', 'C01p41350' => 'bna', 'C03p52750' => 'bna', 'C03p52780' => 'bna', 'C05p40270' => 'bna', 'CAN.G1437.9' => 'can', 'CANSAT78G0035' => 'cansat', 'CANSAT78G1036' => 'cansat', 'CANSAT78G2272' => 'cansat', 'CANSAT78G2478' => 'cansat', 'CARHR098700' => 'chi', 'CARHR221120' => 'chi', 'CARHR221150' => 'chi', 'Carub.0003s2297' => 'cru', 'Carub.0007s2749' => 'cru', 'Carub.0007s2750' => 'cru', 'Carub.0007s2751' => 'cru', 'Ca_10849_v3' => 'car', 'Cc03_g04300' => 'ccan', 'CDE02G3648' => 'cde', 'CDE05G0060' => 'cde', 'CDE05G0692' => 'cde', 'CDE05G2285' => 'cde', 'CDE05G2884' => 'cde', 'CDE05G3072' => 'cde', 'Cfa008439' => 'cfa', 'Cfa008441' => 'cfa', 'Cfa008443' => 'cfa', 'Cfa008448' => 'cfa', 'Ciclev10005974m.g' => 'ccl', 'Ciclev10006006m.g' => 'ccl', 'Ciclev10006775m.g' => 'ccl', 'CiPaw.02G120400' => 'cil', 'CiPaw.02G120500' => 'cil', 'CiPaw.02G120600' => 'cil', 'ClCG05G004850' => 'cla', 'COL.COLO4_21566' => 'col', 'Cpa.g.sc44.124' => 'cpa', 'Cre07.g320400' => 'cre', 'Cre07.g320450' => 'cre', 'Cre08.g384650' => 'cre', 'Cre09.g393173' => 'cre', 'Cre09.g394325' => 'cre', 'Cre14.g626750' => 'cre', 'Cre16.g679250' => 'cre', 'CsaV3_3G012890' => 'csa', 'CSS0010865' => 'camsi', 'CSS0044338' => 'camsi', 'DCAR_002366' => 'dca', 'DCAR_030687' => 'dca', 'DCAR_030688' => 'dca', 'Dinv14047' => 'din', 'Dinv14048' => 'din', 'Duzib151G0105' => 'dzi', 'Duzib151G0114' => 'dzi', 'Duzib212G1029' => 'dzi', 'ECA232G3536' => 'eca', 'ECA240G0786' => 'eca', 'ECA240G1802' => 'eca', 'ECA240G3760' => 'eca', 'ECA240G3920' => 'eca', 'EL10Ac5g12536' => 'bvu', 'EL10Ac5g12537' => 'bvu', 'EL10Ac5g12538' => 'bvu', 'Eucgr.B01004' => 'egr', 'Eucgr.B01006' => 'egr', 'Eucgr.B01007' => 'egr', 'Eucgr.B01008' => 'egr', 'Eucgr.B01895' => 'egr', 'Eucgr.B01896' => 'egr', 'FAN04G1456' => 'fan', 'FAN08G1769' => 'fan', 'FAN08G2160' => 'fan', 'FAN13G2403' => 'fan', 'FAN13G3303' => 'fan', 'FAN15G2435' => 'fan', 'FAN17G0672' => 'fan', 'FAN17G2441' => 'fan', 'FAN18G1024' => 'fan', 'FAN22G1458' => 'fan', 'FAN24G0037' => 'fan', 'FAN24G0429' => 'fan', 'FAN24G2387' => 'fan', 'FAN27G2746' => 'fan', 'FvH4_2g20400' => 'fve', 'FvH4_2g20420' => 'fve', 'FvH4_2g20430' => 'fve', 'FvH4_4g01270' => 'fve', 'FvH4_4g01290' => 'fve', 'FvH4_4g01300' => 'fve', 'FvH4_4g01310' => 'fve', 'FvH4_4g01330' => 'fve', 'FvH4_5g09070' => 'fve', 'Glyma.10G243800' => 'gma', 'Glyma.20G150600' => 'gma', 'Gohir.A09G219200' => 'ghi', 'Gohir.A09G219300' => 'ghi', 'Gohir.D09G221400' => 'ghi', 'Gohir.D09G221500' => 'ghi', 'Gorai.006G242600' => 'gra', 'Gorai.006G242700' => 'gra', 'GSVIVG01018044001' => 'vvi', 'HanXRQChr03g0083821' => 'han', 'HanXRQChr03g0083841' => 'han', 'HanXRQChr03g0083881' => 'han', 'HanXRQChr03g0083901' => 'han', 'HanXRQChr03g0083921' => 'han', 'HanXRQChr03g0085331' => 'han', 'HanXRQChr03g0085361' => 'han', 'HanXRQChr03g0085411' => 'han', 'HanXRQChr03g0085421' => 'han', 'HanXRQChr03g0085431' => 'han', 'HanXRQChr08g0221991' => 'han', 'HanXRQChr11g0336061' => 'han', 'HanXRQChr11g0336411' => 'han', 'Haze_11234' => 'cav', 'Hma1.2p1_0549F.1_g177010' => 'hma', 'Hma1.2p1_0602F.1_g187630' => 'hma', 'Hund14876' => 'sun', 'Hund14879' => 'sun', 'Lalb_Chr06g0160741' => 'lal', 'Lalb_Chr21g0304781' => 'lal', 'Lj3A726G19' => 'lonja', 'Lj3A726T23' => 'lonja', 'Lj3A726T24' => 'lonja', 'Lj3A726T25' => 'lonja', 'Lj3A727T17' => 'lonja', 'Lj3C726T0' => 'lonja', 'Lj3C726T2' => 'lonja', 'Lj3P725T35' => 'lonja', 'Lj3P727T10' => 'lonja', 'Lj3P727T12' => 'lonja', 'Lj3P727T14' => 'lonja', 'Lj5g0023109' => 'lja', 'Lj6P646T44' => 'lonja', 'Lsat_1_v5_gn_6_75760' => 'lsa', 'Lsat_1_v5_gn_6_75800' => 'lsa', 'Lsat_1_v5_gn_6_75900' => 'lsa', 'Lsat_1_v5_gn_6_76240' => 'lsa', 'Lsat_1_v5_gn_6_76441' => 'lsa', 'Lsat_1_v5_gn_6_76700' => 'lsa', 'Lsat_1_v5_gn_6_76760' => 'lsa', 'Manes.15G033100' => 'mes', 'Mapoly0004s0074' => 'mpo', 'Mapoly0004s0075' => 'mpo', 'Mapoly0004s0163' => 'mpo', 'Mapoly0004s0164' => 'mpo', 'Mapoly0021s0018' => 'mpo', 'Mapoly0041s0136' => 'mpo', 'Mapoly0041s0137' => 'mpo', 'Mapoly0041s0138' => 'mpo', 'Mapoly0041s0139' => 'mpo', 'Mapoly0041s0141' => 'mpo', 'Mapoly0041s0142' => 'mpo', 'Mapoly0041s0143' => 'mpo', 'Mapoly0041s0144' => 'mpo', 'Mapoly0041s0145' => 'mpo', 'Mapoly0047s0106' => 'mpo', 'Mapoly0047s0108' => 'mpo', 'Mapoly0050s0051' => 'mpo', 'Mapoly0050s0052' => 'mpo', 'Mapoly0050s0053' => 'mpo', 'Mapoly0058s0013' => 'mpo', 'Mapoly0091s0078' => 'mpo', 'Mapoly0091s0079' => 'mpo', 'Mapoly0091s0080' => 'mpo', 'Mapoly0091s0081' => 'mpo', 'Mapoly0278s0004' => 'mpo', 'Mapoly0278s0005' => 'mpo', 'Mapoly0278s0006' => 'mpo', 'MBI11_g30648_MAGBIO' => 'mbi', 'MCO03G194' => 'mco', 'MCO03G590' => 'mco', 'MCO07G312' => 'mco', 'MCO10G318' => 'mco', 'MCO12G244' => 'mco', 'MCO13G148' => 'mco', 'MCO13G194' => 'mco', 'MCO16G238' => 'mco', 'MD06G1134100' => 'mdo', 'MD13G1200100' => 'mdo', 'MD13G1200300' => 'mdo', 'MD13G1200600' => 'mdo', 'MD14G1150400' => 'mdo', 'MD16G1200000' => 'mdo', 'Medtr1g102570' => 'mtr', 'Medtr1g102780' => 'mtr', 'Medtr1g102800' => 'mtr', 'Medtr1g102810' => 'mtr', 'Medtr1g102830' => 'mtr', 'MELO3C006499.2' => 'cme', 'Migut.G00385' => 'egut', 'MSTRG.4063' => 'ama', 'Nitab4.5_0000090g0260' => 'nta', 'Nitab4.5_0000977g0030' => 'nta', 'Nitab4.5_0002541g0040' => 'nta', 'Nitab4.5_0007068g0040' => 'nta', 'Nn005s41408' => 'nnu', 'Nn005s41410' => 'nnu', 'Oeu010310.1' => 'oeu', 'Oeu010311.1' => 'oeu', 'Oeu043472.1' => 'oeu', 'Os01g0246400' => 'osa', 'Os04g0267950' => 'osa', 'Os07g0178700' => 'osa', 'Os07g0178800' => 'osa', 'Peaxi162Scf00316g00046' => 'pax', 'Peaxi162Scf00316g00049' => 'pax', 'Peaxi162Scf00316g00059' => 'pax', 'Peaxi162Scf00316g00328' => 'pax', 'Peaxi162Scf00316g00329' => 'pax', 'Peaxi162Scf00316g00411' => 'pax', 'Peaxi162Scf00316g00521' => 'pax', 'Peaxi162Scf00492g00068' => 'pax', 'Peaxi162Scf35631g00002' => 'pax', 'PGR142G3720' => 'pgr', 'PGSC0003DMG400006442' => 'stu', 'Phvul.007G062000' => 'pvu', 'Potri.008G157750' => 'ptr', 'Potri.008G157900' => 'ptr', 'Potri.008G158000' => 'ptr', 'Potri.008G158200' => 'ptr', 'Pp3c11_7280' => 'ppa', 'Pp3c11_7980' => 'ppa', 'Pp3c12_19450' => 'ppa', 'Pp3c14_1480' => 'ppa', 'Pp3c14_1501' => 'ppa', 'Pp3c16_4900' => 'ppa', 'Pp3c16_5010' => 'ppa', 'Pp3c16_5060' => 'ppa', 'Pp3c19_18250' => 'ppa', 'Pp3c23_8530' => 'ppa', 'Pp3c23_8550' => 'ppa', 'Pp3c24_9670' => 'ppa', 'Pp3c2_21390' => 'ppa', 'Pp3c2_31380' => 'ppa', 'Pp3c3_16620' => 'ppa', 'Pp3c3_8090' => 'ppa', 'Pp3c3_8110' => 'ppa', 'Pp3c3_8130' => 'ppa', 'Pp3c3_8150' => 'ppa', 'Pp3c4_14320' => 'ppa', 'Pp3c6_2560' => 'ppa', 'Pp3c9_16700' => 'ppa', 'PRCOL_00000234' => 'pco', 'PRCOL_00000235' => 'pco', 'PRCOL_00000777' => 'pco', 'PRCOL_00002344' => 'pco', 'PRCOL_00002372' => 'pco', 'PRCOL_00006120' => 'pco', 'Prupe.1G021400' => 'ppe', 'Prupe.1G021500' => 'ppe', 'Prupe.1G021600' => 'ppe', 'Prupe.1G021700' => 'ppe', 'Prupe.1G021800' => 'ppe', 'Prupe.5G145100' => 'ppe', 'Psat6g204040' => 'psa', 'Psat6g204800' => 'psa', 'Psat6g204920' => 'psa', 'Psat6g204960' => 'psa', 'Psat6g205080' => 'psa', 'PSO017G0271' => 'pso', 'PSO017G1276' => 'pso', 'PSO017G1429' => 'pso', 'PSO017G1861' => 'pso', 'PSO017G2787' => 'pso', 'PSO017G4466' => 'pso', 'PSO017G5118' => 'pso', 'PSO017G5420' => 'pso', 'PSO063G3678' => 'pso', 'PSO210G0546' => 'pso', 'PSO317G0001' => 'pso', 'PSO357G0512' => 'pso', 'PSO478G2682' => 'pso', 'PSO647G0001' => 'pso', 'PSO675G0001' => 'pso', 'PSO675G2699' => 'pso', 'PSO675G2849' => 'pso', 'PSO675G4991' => 'pso', 'PSO689G0001' => 'pso', 'QL06p000916' => 'qlo', 'QL06p000921' => 'qlo', 'QL06p001398' => 'qlo', 'QL06p001407' => 'qlo', 'QL06p002031' => 'qlo', 'RcHm_v2.0_Chr4g0387791' => 'rch', 'RcHm_v2.0_Chr4g0387801' => 'rch', 'RcHm_v2.0_Chr6g0286501' => 'rch', 'RcHm_v2.0_Chr6g0286511' => 'rch', 'RcHm_v2.0_Chr6g0286521' => 'rch', 'RcHm_v2.0_Chr6g0286531' => 'rch', 'RcHm_v2.0_Chr7g0189141' => 'rch', 'Rhsim02G0028700' => 'rsi', 'Rhsim02G0028800' => 'rsi', 'Rhsim02G0028900' => 'rsi', 'Rhsim02G0029000' => 'rsi', 'Rhsim02G0029100' => 'rsi', 'Rhsim02G0029200' => 'rsi', 'Rhsim02G0029300' => 'rsi', 'Rhsim02G0029400' => 'rsi', 'Rhsim02G0029500' => 'rsi', 'Rhsim02G0029600' => 'rsi', 'RhsimUnG0024000' => 'rsi', 'RhsimUnG0024100' => 'rsi', 'RhsimUnG0024200' => 'rsi', 'RhsimUnG0024300' => 'rsi', 'RhsimUnG0024400' => 'rsi', 'RhsimUnG0024500' => 'rsi', 'RhsimUnG0024700' => 'rsi', 'RhsimUnG0024800' => 'rsi', 'RhsimUnG0024900' => 'rsi', 'RhsimUnG0025100' => 'rsi', 'Sabra08G0120200' => 'sbr', 'Sabra08G0120300' => 'sbr', 'Sabra08G0120500' => 'sbr', 'Sabra08G0120600' => 'sbr', 'Sabra10G0158900' => 'sbr', 'SalBow2G3492' => 'sbo', 'Sc13g0004760' => 'sci', 'Sc13g0004770' => 'sci', 'Sed0003417' => 'sed', 'Sed0019750' => 'sed', 'SEGI_03419' => 'sgi', 'SEGI_05907' => 'sgi', 'SEGI_10682' => 'sgi', 'SEGI_13528' => 'sgi', 'SEGI_16081' => 'sgi', 'SEGI_19370' => 'sgi', 'SEGI_21015' => 'sgi', 'SEGI_21944' => 'sgi', 'SEGI_32906' => 'sgi', 'SEGI_33093' => 'sgi', 'SEGI_36110' => 'sgi', 'SEGI_40397' => 'sgi', 'SGA_v2.0_scaffold191G40426' => 'sas', 'SGA_v2.0_scaffold353G49717' => 'sas', 'SGA_v2.0_scaffold50G18550' => 'sas', 'SMO119G0173' => 'smo', 'SMO172G0002' => 'smo', 'Solyc09g082690.3' => 'sly', 'Solyc09g082700.2' => 'sly', 'Sopen09g031550' => 'spe', 'Sopen09g031560' => 'spe', 'Sp3g20540' => 'spa', 'Sp7g07580' => 'spa', 'TAR134G0002' => 'tar', 'TAR236G0001' => 'tar', 'TAR365G0892' => 'tar', 'TAR636G0166' => 'tar', 'TAR636G0646' => 'tar', 'TAR636G0869' => 'tar', 'TAR636G1317' => 'tar', 'TAR636G1744' => 'tar', 'TAR636G3358' => 'tar', 'TAR636G3436' => 'tar', 'THA.LOC104803047' => 'tha', 'Thecc.04G238900' => 'tca', 'Thhalv10021557m.g' => 'esa', 'Thhalv10026318m.g' => 'esa', 'Thhalv10026335m.g' => 'esa', 'TPR.G17433' => 'tpr', 'TPR.G18915' => 'tpr', 'TPR.G26125' => 'tpr', 'TWI09G0677' => 'twi', 'TWI73G0287' => 'twi', 'unitig_748.g8326' => 'ugi', 'vmacro15370' => 'vma', 'vmacro15371' => 'vma', 'vmacro15372' => 'vma', 'vmacro15373' => 'vma', 'vmacro15374' => 'vma', 'VMungo0720G2826' => 'vmu', 'Zm00001eb116960' => 'zma', 'Zm00001eb301260' => 'zma', 'Zm00001eb301270' => 'zma' ), 'gf_id' => 'HOM05D001460', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001460' ), 'data_identifier' => 'HOM05D001460', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001460', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '433', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p22980' => 'bna', 'A01p32340' => 'bna', 'A03p42970' => 'bna', 'A05p25880' => 'bna', 'Aa31LG8G9320' => 'aar', 'Aa31LG8G9330' => 'aar', 'Aa31LG8G9340' => 'aar', 'Aa31sc221G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1034' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1528' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.829' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2222' => 'aag', 'Ah.12g058830' => 'amhyb', 'Ah.12g058840' => 'amhyb', 'AL3G37160' => 'aly', 'AL7G41310' => 'aly', 'Aqoxy5G00395' => 'aox', 'Aqoxy5G00396' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0C8NZA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5185HY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JZ1PRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MD3LS0' => 'arhy', 'AT3G22840' => 'ath', 'AT4G14690' => 'ath', 'ATR0665G054' => 'atr', 'Atru.chr4.2344' => 'acertr', 'Atru.chr4.2346' => 'acertr', 'Atru.chr4.2347' => 'acertr', 'Atru.chr4.2348' => 'acertr', 'Atru.chr4.2355' => 'acertr', 'Atru.chr4.2356' => 'acertr', 'Atru.chr4.2358' => 'acertr', 'Atru.chr4.2359' => 'acertr', 'Atru.chr4.2360' => 'acertr', 'Atru.chr4.2361' => 'acertr', 'AUR62030476' => 'cqu', 'AUR62030478' => 'cqu', 'AUR62030819' => 'cqu', 'AUR62030820' => 'cqu', 'BcaB03g14648' => 'bca', 'BcaB04g20492' => 'bca', 'BcaB06g26399' => 'bca', 'BcaC01g03416' => 'bca', 'BcaC01g03419' => 'bca', 'BcaC01g03421' => 'bca', 'BcaC01g03424' => 'bca', 'BcaC05g28012' => 'bca', 'BcaC09g49212' => 'bca', 'BcaC09g50140' => 'bca', 'BcaNung00346' => 'bca', 'BolC1t02785H' => 'bol', 'BolC1t04095H' => 'bol', 'BolC3t17545H' => 'bol', 'BolC5t32769H' => 'bol', 'BraA01t02211Z' => 'bra', 'BraA01t03359Z' => 'bra', 'BraA03t13441Z' => 'bra', 'BraA05t21476Z' => 'bra', 'C01p28420' => 'bna', 'C01p41350' => 'bna', 'C03p52750' => 'bna', 'C03p52780' => 'bna', 'C05p40270' => 'bna', 'CAN.G1437.9' => 'can', 'CANSAT78G0035' => 'cansat', 'CANSAT78G1036' => 'cansat', 'CANSAT78G2272' => 'cansat', 'CANSAT78G2478' => 'cansat', 'CARHR098700' => 'chi', 'CARHR221120' => 'chi', 'CARHR221150' => 'chi', 'Carub.0003s2297' => 'cru', 'Carub.0007s2749' => 'cru', 'Carub.0007s2750' => 'cru', 'Carub.0007s2751' => 'cru', 'Ca_10849_v3' => 'car', 'Cc03_g04300' => 'ccan', 'CDE02G3648' => 'cde', 'CDE05G0060' => 'cde', 'CDE05G0692' => 'cde', 'CDE05G2285' => 'cde', 'CDE05G2884' => 'cde', 'CDE05G3072' => 'cde', 'Cfa008439' => 'cfa', 'Cfa008441' => 'cfa', 'Cfa008443' => 'cfa', 'Cfa008448' => 'cfa', 'Ciclev10005974m.g' => 'ccl', 'Ciclev10006006m.g' => 'ccl', 'Ciclev10006775m.g' => 'ccl', 'CiPaw.02G120400' => 'cil', 'CiPaw.02G120500' => 'cil', 'CiPaw.02G120600' => 'cil', 'ClCG05G004850' => 'cla', 'COL.COLO4_21566' => 'col', 'Cpa.g.sc44.124' => 'cpa', 'Cre07.g320400' => 'cre', 'Cre07.g320450' => 'cre', 'Cre08.g384650' => 'cre', 'Cre09.g393173' => 'cre', 'Cre09.g394325' => 'cre', 'Cre14.g626750' => 'cre', 'Cre16.g679250' => 'cre', 'CsaV3_3G012890' => 'csa', 'CSS0010865' => 'camsi', 'CSS0044338' => 'camsi', 'DCAR_002366' => 'dca', 'DCAR_030687' => 'dca', 'DCAR_030688' => 'dca', 'Dinv14047' => 'din', 'Dinv14048' => 'din', 'Duzib151G0105' => 'dzi', 'Duzib151G0114' => 'dzi', 'Duzib212G1029' => 'dzi', 'ECA232G3536' => 'eca', 'ECA240G0786' => 'eca', 'ECA240G1802' => 'eca', 'ECA240G3760' => 'eca', 'ECA240G3920' => 'eca', 'EL10Ac5g12536' => 'bvu', 'EL10Ac5g12537' => 'bvu', 'EL10Ac5g12538' => 'bvu', 'Eucgr.B01004' => 'egr', 'Eucgr.B01006' => 'egr', 'Eucgr.B01007' => 'egr', 'Eucgr.B01008' => 'egr', 'Eucgr.B01895' => 'egr', 'Eucgr.B01896' => 'egr', 'FAN04G1456' => 'fan', 'FAN08G1769' => 'fan', 'FAN08G2160' => 'fan', 'FAN13G2403' => 'fan', 'FAN13G3303' => 'fan', 'FAN15G2435' => 'fan', 'FAN17G0672' => 'fan', 'FAN17G2441' => 'fan', 'FAN18G1024' => 'fan', 'FAN22G1458' => 'fan', 'FAN24G0037' => 'fan', 'FAN24G0429' => 'fan', 'FAN24G2387' => 'fan', 'FAN27G2746' => 'fan', 'FvH4_2g20400' => 'fve', 'FvH4_2g20420' => 'fve', 'FvH4_2g20430' => 'fve', 'FvH4_4g01270' => 'fve', 'FvH4_4g01290' => 'fve', 'FvH4_4g01300' => 'fve', 'FvH4_4g01310' => 'fve', 'FvH4_4g01330' => 'fve', 'FvH4_5g09070' => 'fve', 'Glyma.10G243800' => 'gma', 'Glyma.20G150600' => 'gma', 'Gohir.A09G219200' => 'ghi', 'Gohir.A09G219300' => 'ghi', 'Gohir.D09G221400' => 'ghi', 'Gohir.D09G221500' => 'ghi', 'Gorai.006G242600' => 'gra', 'Gorai.006G242700' => 'gra', 'GSVIVG01018044001' => 'vvi', 'HanXRQChr03g0083821' => 'han', 'HanXRQChr03g0083841' => 'han', 'HanXRQChr03g0083881' => 'han', 'HanXRQChr03g0083901' => 'han', 'HanXRQChr03g0083921' => 'han', 'HanXRQChr03g0085331' => 'han', 'HanXRQChr03g0085361' => 'han', 'HanXRQChr03g0085411' => 'han', 'HanXRQChr03g0085421' => 'han', 'HanXRQChr03g0085431' => 'han', 'HanXRQChr08g0221991' => 'han', 'HanXRQChr11g0336061' => 'han', 'HanXRQChr11g0336411' => 'han', 'Haze_11234' => 'cav', 'Hma1.2p1_0549F.1_g177010' => 'hma', 'Hma1.2p1_0602F.1_g187630' => 'hma', 'Hund14876' => 'sun', 'Hund14879' => 'sun', 'Lalb_Chr06g0160741' => 'lal', 'Lalb_Chr21g0304781' => 'lal', 'Lj3A726G19' => 'lonja', 'Lj3A726T23' => 'lonja', 'Lj3A726T24' => 'lonja', 'Lj3A726T25' => 'lonja', 'Lj3A727T17' => 'lonja', 'Lj3C726T0' => 'lonja', 'Lj3C726T2' => 'lonja', 'Lj3P725T35' => 'lonja', 'Lj3P727T10' => 'lonja', 'Lj3P727T12' => 'lonja', 'Lj3P727T14' => 'lonja', 'Lj5g0023109' => 'lja', 'Lj6P646T44' => 'lonja', 'Lsat_1_v5_gn_6_75760' => 'lsa', 'Lsat_1_v5_gn_6_75800' => 'lsa', 'Lsat_1_v5_gn_6_75900' => 'lsa', 'Lsat_1_v5_gn_6_76240' => 'lsa', 'Lsat_1_v5_gn_6_76441' => 'lsa', 'Lsat_1_v5_gn_6_76700' => 'lsa', 'Lsat_1_v5_gn_6_76760' => 'lsa', 'Manes.15G033100' => 'mes', 'Mapoly0004s0074' => 'mpo', 'Mapoly0004s0075' => 'mpo', 'Mapoly0004s0163' => 'mpo', 'Mapoly0004s0164' => 'mpo', 'Mapoly0021s0018' => 'mpo', 'Mapoly0041s0136' => 'mpo', 'Mapoly0041s0137' => 'mpo', 'Mapoly0041s0138' => 'mpo', 'Mapoly0041s0139' => 'mpo', 'Mapoly0041s0141' => 'mpo', 'Mapoly0041s0142' => 'mpo', 'Mapoly0041s0143' => 'mpo', 'Mapoly0041s0144' => 'mpo', 'Mapoly0041s0145' => 'mpo', 'Mapoly0047s0106' => 'mpo', 'Mapoly0047s0108' => 'mpo', 'Mapoly0050s0051' => 'mpo', 'Mapoly0050s0052' => 'mpo', 'Mapoly0050s0053' => 'mpo', 'Mapoly0058s0013' => 'mpo', 'Mapoly0091s0078' => 'mpo', 'Mapoly0091s0079' => 'mpo', 'Mapoly0091s0080' => 'mpo', 'Mapoly0091s0081' => 'mpo', 'Mapoly0278s0004' => 'mpo', 'Mapoly0278s0005' => 'mpo', 'Mapoly0278s0006' => 'mpo', 'MBI11_g30648_MAGBIO' => 'mbi', 'MCO03G194' => 'mco', 'MCO03G590' => 'mco', 'MCO07G312' => 'mco', 'MCO10G318' => 'mco', 'MCO12G244' => 'mco', 'MCO13G148' => 'mco', 'MCO13G194' => 'mco', 'MCO16G238' => 'mco', 'MD06G1134100' => 'mdo', 'MD13G1200100' => 'mdo', 'MD13G1200300' => 'mdo', 'MD13G1200600' => 'mdo', 'MD14G1150400' => 'mdo', 'MD16G1200000' => 'mdo', 'Medtr1g102570' => 'mtr', 'Medtr1g102780' => 'mtr', 'Medtr1g102800' => 'mtr', 'Medtr1g102810' => 'mtr', 'Medtr1g102830' => 'mtr', 'MELO3C006499.2' => 'cme', 'Migut.G00385' => 'egut', 'MSTRG.4063' => 'ama', 'Nitab4.5_0000090g0260' => 'nta', 'Nitab4.5_0000977g0030' => 'nta', 'Nitab4.5_0002541g0040' => 'nta', 'Nitab4.5_0007068g0040' => 'nta', 'Nn005s41408' => 'nnu', 'Nn005s41410' => 'nnu', 'Oeu010310.1' => 'oeu', 'Oeu010311.1' => 'oeu', 'Oeu043472.1' => 'oeu', 'Os01g0246400' => 'osa', 'Os04g0267950' => 'osa', 'Os07g0178700' => 'osa', 'Os07g0178800' => 'osa', 'Peaxi162Scf00316g00046' => 'pax', 'Peaxi162Scf00316g00049' => 'pax', 'Peaxi162Scf00316g00059' => 'pax', 'Peaxi162Scf00316g00328' => 'pax', 'Peaxi162Scf00316g00329' => 'pax', 'Peaxi162Scf00316g00411' => 'pax', 'Peaxi162Scf00316g00521' => 'pax', 'Peaxi162Scf00492g00068' => 'pax', 'Peaxi162Scf35631g00002' => 'pax', 'PGR142G3720' => 'pgr', 'PGSC0003DMG400006442' => 'stu', 'Phvul.007G062000' => 'pvu', 'Potri.008G157750' => 'ptr', 'Potri.008G157900' => 'ptr', 'Potri.008G158000' => 'ptr', 'Potri.008G158200' => 'ptr', 'Pp3c11_7280' => 'ppa', 'Pp3c11_7980' => 'ppa', 'Pp3c12_19450' => 'ppa', 'Pp3c14_1480' => 'ppa', 'Pp3c14_1501' => 'ppa', 'Pp3c16_4900' => 'ppa', 'Pp3c16_5010' => 'ppa', 'Pp3c16_5060' => 'ppa', 'Pp3c19_18250' => 'ppa', 'Pp3c23_8530' => 'ppa', 'Pp3c23_8550' => 'ppa', 'Pp3c24_9670' => 'ppa', 'Pp3c2_21390' => 'ppa', 'Pp3c2_31380' => 'ppa', 'Pp3c3_16620' => 'ppa', 'Pp3c3_8090' => 'ppa', 'Pp3c3_8110' => 'ppa', 'Pp3c3_8130' => 'ppa', 'Pp3c3_8150' => 'ppa', 'Pp3c4_14320' => 'ppa', 'Pp3c6_2560' => 'ppa', 'Pp3c9_16700' => 'ppa', 'PRCOL_00000234' => 'pco', 'PRCOL_00000235' => 'pco', 'PRCOL_00000777' => 'pco', 'PRCOL_00002344' => 'pco', 'PRCOL_00002372' => 'pco', 'PRCOL_00006120' => 'pco', 'Prupe.1G021400' => 'ppe', 'Prupe.1G021500' => 'ppe', 'Prupe.1G021600' => 'ppe', 'Prupe.1G021700' => 'ppe', 'Prupe.1G021800' => 'ppe', 'Prupe.5G145100' => 'ppe', 'Psat6g204040' => 'psa', 'Psat6g204800' => 'psa', 'Psat6g204920' => 'psa', 'Psat6g204960' => 'psa', 'Psat6g205080' => 'psa', 'PSO017G0271' => 'pso', 'PSO017G1276' => 'pso', 'PSO017G1429' => 'pso', 'PSO017G1861' => 'pso', 'PSO017G2787' => 'pso', 'PSO017G4466' => 'pso', 'PSO017G5118' => 'pso', 'PSO017G5420' => 'pso', 'PSO063G3678' => 'pso', 'PSO210G0546' => 'pso', 'PSO317G0001' => 'pso', 'PSO357G0512' => 'pso', 'PSO478G2682' => 'pso', 'PSO647G0001' => 'pso', 'PSO675G0001' => 'pso', 'PSO675G2699' => 'pso', 'PSO675G2849' => 'pso', 'PSO675G4991' => 'pso', 'PSO689G0001' => 'pso', 'QL06p000916' => 'qlo', 'QL06p000921' => 'qlo', 'QL06p001398' => 'qlo', 'QL06p001407' => 'qlo', 'QL06p002031' => 'qlo', 'RcHm_v2.0_Chr4g0387791' => 'rch', 'RcHm_v2.0_Chr4g0387801' => 'rch', 'RcHm_v2.0_Chr6g0286501' => 'rch', 'RcHm_v2.0_Chr6g0286511' => 'rch', 'RcHm_v2.0_Chr6g0286521' => 'rch', 'RcHm_v2.0_Chr6g0286531' => 'rch', 'RcHm_v2.0_Chr7g0189141' => 'rch', 'Rhsim02G0028700' => 'rsi', 'Rhsim02G0028800' => 'rsi', 'Rhsim02G0028900' => 'rsi', 'Rhsim02G0029000' => 'rsi', 'Rhsim02G0029100' => 'rsi', 'Rhsim02G0029200' => 'rsi', 'Rhsim02G0029300' => 'rsi', 'Rhsim02G0029400' => 'rsi', 'Rhsim02G0029500' => 'rsi', 'Rhsim02G0029600' => 'rsi', 'RhsimUnG0024000' => 'rsi', 'RhsimUnG0024100' => 'rsi', 'RhsimUnG0024200' => 'rsi', 'RhsimUnG0024300' => 'rsi', 'RhsimUnG0024400' => 'rsi', 'RhsimUnG0024500' => 'rsi', 'RhsimUnG0024700' => 'rsi', 'RhsimUnG0024800' => 'rsi', 'RhsimUnG0024900' => 'rsi', 'RhsimUnG0025100' => 'rsi', 'Sabra08G0120200' => 'sbr', 'Sabra08G0120300' => 'sbr', 'Sabra08G0120500' => 'sbr', 'Sabra08G0120600' => 'sbr', 'Sabra10G0158900' => 'sbr', 'SalBow2G3492' => 'sbo', 'Sc13g0004760' => 'sci', 'Sc13g0004770' => 'sci', 'Sed0003417' => 'sed', 'Sed0019750' => 'sed', 'SEGI_03419' => 'sgi', 'SEGI_05907' => 'sgi', 'SEGI_10682' => 'sgi', 'SEGI_13528' => 'sgi', 'SEGI_16081' => 'sgi', 'SEGI_19370' => 'sgi', 'SEGI_21015' => 'sgi', 'SEGI_21944' => 'sgi', 'SEGI_32906' => 'sgi', 'SEGI_33093' => 'sgi', 'SEGI_36110' => 'sgi', 'SEGI_40397' => 'sgi', 'SGA_v2.0_scaffold191G40426' => 'sas', 'SGA_v2.0_scaffold353G49717' => 'sas', 'SGA_v2.0_scaffold50G18550' => 'sas', 'SMO119G0173' => 'smo', 'SMO172G0002' => 'smo', 'Solyc09g082690.3' => 'sly', 'Solyc09g082700.2' => 'sly', 'Sopen09g031550' => 'spe', 'Sopen09g031560' => 'spe', 'Sp3g20540' => 'spa', 'Sp7g07580' => 'spa', 'TAR134G0002' => 'tar', 'TAR236G0001' => 'tar', 'TAR365G0892' => 'tar', 'TAR636G0166' => 'tar', 'TAR636G0646' => 'tar', 'TAR636G0869' => 'tar', 'TAR636G1317' => 'tar', 'TAR636G1744' => 'tar', 'TAR636G3358' => 'tar', 'TAR636G3436' => 'tar', 'THA.LOC104803047' => 'tha', 'Thecc.04G238900' => 'tca', 'Thhalv10021557m.g' => 'esa', 'Thhalv10026318m.g' => 'esa', 'Thhalv10026335m.g' => 'esa', 'TPR.G17433' => 'tpr', 'TPR.G18915' => 'tpr', 'TPR.G26125' => 'tpr', 'TWI09G0677' => 'twi', 'TWI73G0287' => 'twi', 'unitig_748.g8326' => 'ugi', 'vmacro15370' => 'vma', 'vmacro15371' => 'vma', 'vmacro15372' => 'vma', 'vmacro15373' => 'vma', 'vmacro15374' => 'vma', 'VMungo0720G2826' => 'vmu', 'Zm00001eb116960' => 'zma', 'Zm00001eb301260' => 'zma', 'Zm00001eb301270' => 'zma' ) $gf_id = 'HOM05D001460' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001460' ) $data_identifier = 'HOM05D001460' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 4, 'aag' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 2, 'aox' => (int) 2, 'arhy' => (int) 4, 'ath' => (int) 2, 'atr' => (int) 1, 'acertr' => (int) 10, 'cqu' => (int) 4, 'bca' => (int) 11, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 1, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 1, 'ccan' => (int) 1, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 1, 'col' => (int) 1, 'cpa' => (int) 1, 'cre' => (int) 7, 'csa' => (int) 1, 'camsi' => (int) 2, 'dca' => (int) 3, 'din' => (int) 2, 'dzi' => (int) 3, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 14, 'fve' => (int) 9, 'gma' => (int) 2, 'ghi' => (int) 4, 'gra' => (int) 2, 'vvi' => (int) 1, 'han' => (int) 13, 'cav' => (int) 1, 'hma' => (int) 2, 'sun' => (int) 2, 'lal' => (int) 2, 'lonja' => (int) 12, 'lja' => (int) 1, 'lsa' => (int) 7, 'mes' => (int) 1, 'mpo' => (int) 27, 'mbi' => (int) 1, 'mco' => (int) 8, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 1, 'egut' => (int) 1, 'ama' => (int) 1, 'nta' => (int) 4, 'nnu' => (int) 2, 'oeu' => (int) 3, 'osa' => (int) 4, 'pax' => (int) 9, 'pgr' => (int) 1, 'stu' => (int) 1, 'pvu' => (int) 1, 'ptr' => (int) 4, 'ppa' => (int) 22, 'pco' => (int) 6, 'ppe' => (int) 6, 'psa' => (int) 5, 'pso' => (int) 19, 'qlo' => (int) 5, 'rch' => (int) 7, 'rsi' => (int) 20, 'sbr' => (int) 5, 'sbo' => (int) 1, 'sci' => (int) 2, 'sed' => (int) 2, 'sgi' => (int) 12, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 2, 'tar' => (int) 10, 'tha' => (int) 1, 'tca' => (int) 1, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 2, 'ugi' => (int) 1, 'vma' => (int) 5, 'vmu' => (int) 1, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb301270' $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' => 'HOM05D001460', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '433', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p22980' => 'bna', 'A01p32340' => 'bna', 'A03p42970' => 'bna', 'A05p25880' => 'bna', 'Aa31LG8G9320' => 'aar', 'Aa31LG8G9330' => 'aar', 'Aa31LG8G9340' => 'aar', 'Aa31sc221G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1034' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1528' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.829' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2222' => 'aag', 'Ah.12g058830' => 'amhyb', 'Ah.12g058840' => 'amhyb', 'AL3G37160' => 'aly', 'AL7G41310' => 'aly', 'Aqoxy5G00395' => 'aox', 'Aqoxy5G00396' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0C8NZA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5185HY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JZ1PRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MD3LS0' => 'arhy', 'AT3G22840' => 'ath', 'AT4G14690' => 'ath', 'ATR0665G054' => 'atr', 'Atru.chr4.2344' => 'acertr', 'Atru.chr4.2346' => 'acertr', 'Atru.chr4.2347' => 'acertr', 'Atru.chr4.2348' => 'acertr', 'Atru.chr4.2355' => 'acertr', 'Atru.chr4.2356' => 'acertr', 'Atru.chr4.2358' => 'acertr', 'Atru.chr4.2359' => 'acertr', 'Atru.chr4.2360' => 'acertr', 'Atru.chr4.2361' => 'acertr', 'AUR62030476' => 'cqu', 'AUR62030478' => 'cqu', 'AUR62030819' => 'cqu', 'AUR62030820' => 'cqu', 'BcaB03g14648' => 'bca', 'BcaB04g20492' => 'bca', 'BcaB06g26399' => 'bca', 'BcaC01g03416' => 'bca', 'BcaC01g03419' => 'bca', 'BcaC01g03421' => 'bca', 'BcaC01g03424' => 'bca', 'BcaC05g28012' => 'bca', 'BcaC09g49212' => 'bca', 'BcaC09g50140' => 'bca', 'BcaNung00346' => 'bca', 'BolC1t02785H' => 'bol', 'BolC1t04095H' => 'bol', 'BolC3t17545H' => 'bol', 'BolC5t32769H' => 'bol', 'BraA01t02211Z' => 'bra', 'BraA01t03359Z' => 'bra', 'BraA03t13441Z' => 'bra', 'BraA05t21476Z' => 'bra', 'C01p28420' => 'bna', 'C01p41350' => 'bna', 'C03p52750' => 'bna', 'C03p52780' => 'bna', 'C05p40270' => 'bna', 'CAN.G1437.9' => 'can', 'CANSAT78G0035' => 'cansat', 'CANSAT78G1036' => 'cansat', 'CANSAT78G2272' => 'cansat', 'CANSAT78G2478' => 'cansat', 'CARHR098700' => 'chi', 'CARHR221120' => 'chi', 'CARHR221150' => 'chi', 'Carub.0003s2297' => 'cru', 'Carub.0007s2749' => 'cru', 'Carub.0007s2750' => 'cru', 'Carub.0007s2751' => 'cru', 'Ca_10849_v3' => 'car', 'Cc03_g04300' => 'ccan', 'CDE02G3648' => 'cde', 'CDE05G0060' => 'cde', 'CDE05G0692' => 'cde', 'CDE05G2285' => 'cde', 'CDE05G2884' => 'cde', 'CDE05G3072' => 'cde', 'Cfa008439' => 'cfa', 'Cfa008441' => 'cfa', 'Cfa008443' => 'cfa', 'Cfa008448' => 'cfa', 'Ciclev10005974m.g' => 'ccl', 'Ciclev10006006m.g' => 'ccl', 'Ciclev10006775m.g' => 'ccl', 'CiPaw.02G120400' => 'cil', 'CiPaw.02G120500' => 'cil', 'CiPaw.02G120600' => 'cil', 'ClCG05G004850' => 'cla', 'COL.COLO4_21566' => 'col', 'Cpa.g.sc44.124' => 'cpa', 'Cre07.g320400' => 'cre', 'Cre07.g320450' => 'cre', 'Cre08.g384650' => 'cre', 'Cre09.g393173' => 'cre', 'Cre09.g394325' => 'cre', 'Cre14.g626750' => 'cre', 'Cre16.g679250' => 'cre', 'CsaV3_3G012890' => 'csa', 'CSS0010865' => 'camsi', 'CSS0044338' => 'camsi', 'DCAR_002366' => 'dca', 'DCAR_030687' => 'dca', 'DCAR_030688' => 'dca', 'Dinv14047' => 'din', 'Dinv14048' => 'din', 'Duzib151G0105' => 'dzi', 'Duzib151G0114' => 'dzi', 'Duzib212G1029' => 'dzi', 'ECA232G3536' => 'eca', 'ECA240G0786' => 'eca', 'ECA240G1802' => 'eca', 'ECA240G3760' => 'eca', 'ECA240G3920' => 'eca', 'EL10Ac5g12536' => 'bvu', 'EL10Ac5g12537' => 'bvu', 'EL10Ac5g12538' => 'bvu', 'Eucgr.B01004' => 'egr', 'Eucgr.B01006' => 'egr', 'Eucgr.B01007' => 'egr', 'Eucgr.B01008' => 'egr', 'Eucgr.B01895' => 'egr', 'Eucgr.B01896' => 'egr', 'FAN04G1456' => 'fan', 'FAN08G1769' => 'fan', 'FAN08G2160' => 'fan', 'FAN13G2403' => 'fan', 'FAN13G3303' => 'fan', 'FAN15G2435' => 'fan', 'FAN17G0672' => 'fan', 'FAN17G2441' => 'fan', 'FAN18G1024' => 'fan', 'FAN22G1458' => 'fan', 'FAN24G0037' => 'fan', 'FAN24G0429' => 'fan', 'FAN24G2387' => 'fan', 'FAN27G2746' => 'fan', 'FvH4_2g20400' => 'fve', 'FvH4_2g20420' => 'fve', 'FvH4_2g20430' => 'fve', 'FvH4_4g01270' => 'fve', 'FvH4_4g01290' => 'fve', 'FvH4_4g01300' => 'fve', 'FvH4_4g01310' => 'fve', 'FvH4_4g01330' => 'fve', 'FvH4_5g09070' => 'fve', 'Glyma.10G243800' => 'gma', 'Glyma.20G150600' => 'gma', 'Gohir.A09G219200' => 'ghi', 'Gohir.A09G219300' => 'ghi', 'Gohir.D09G221400' => 'ghi', 'Gohir.D09G221500' => 'ghi', 'Gorai.006G242600' => 'gra', 'Gorai.006G242700' => 'gra', 'GSVIVG01018044001' => 'vvi', 'HanXRQChr03g0083821' => 'han', 'HanXRQChr03g0083841' => 'han', 'HanXRQChr03g0083881' => 'han', 'HanXRQChr03g0083901' => 'han', 'HanXRQChr03g0083921' => 'han', 'HanXRQChr03g0085331' => 'han', 'HanXRQChr03g0085361' => 'han', 'HanXRQChr03g0085411' => 'han', 'HanXRQChr03g0085421' => 'han', 'HanXRQChr03g0085431' => 'han', 'HanXRQChr08g0221991' => 'han', 'HanXRQChr11g0336061' => 'han', 'HanXRQChr11g0336411' => 'han', 'Haze_11234' => 'cav', 'Hma1.2p1_0549F.1_g177010' => 'hma', 'Hma1.2p1_0602F.1_g187630' => 'hma', 'Hund14876' => 'sun', 'Hund14879' => 'sun', 'Lalb_Chr06g0160741' => 'lal', 'Lalb_Chr21g0304781' => 'lal', 'Lj3A726G19' => 'lonja', 'Lj3A726T23' => 'lonja', 'Lj3A726T24' => 'lonja', 'Lj3A726T25' => 'lonja', 'Lj3A727T17' => 'lonja', 'Lj3C726T0' => 'lonja', 'Lj3C726T2' => 'lonja', 'Lj3P725T35' => 'lonja', 'Lj3P727T10' => 'lonja', 'Lj3P727T12' => 'lonja', 'Lj3P727T14' => 'lonja', 'Lj5g0023109' => 'lja', 'Lj6P646T44' => 'lonja', 'Lsat_1_v5_gn_6_75760' => 'lsa', 'Lsat_1_v5_gn_6_75800' => 'lsa', 'Lsat_1_v5_gn_6_75900' => 'lsa', 'Lsat_1_v5_gn_6_76240' => 'lsa', 'Lsat_1_v5_gn_6_76441' => 'lsa', 'Lsat_1_v5_gn_6_76700' => 'lsa', 'Lsat_1_v5_gn_6_76760' => 'lsa', 'Manes.15G033100' => 'mes', 'Mapoly0004s0074' => 'mpo', 'Mapoly0004s0075' => 'mpo', 'Mapoly0004s0163' => 'mpo', 'Mapoly0004s0164' => 'mpo', 'Mapoly0021s0018' => 'mpo', 'Mapoly0041s0136' => 'mpo', 'Mapoly0041s0137' => 'mpo', 'Mapoly0041s0138' => 'mpo', 'Mapoly0041s0139' => 'mpo', 'Mapoly0041s0141' => 'mpo', 'Mapoly0041s0142' => 'mpo', 'Mapoly0041s0143' => 'mpo', 'Mapoly0041s0144' => 'mpo', 'Mapoly0041s0145' => 'mpo', 'Mapoly0047s0106' => 'mpo', 'Mapoly0047s0108' => 'mpo', 'Mapoly0050s0051' => 'mpo', 'Mapoly0050s0052' => 'mpo', 'Mapoly0050s0053' => 'mpo', 'Mapoly0058s0013' => 'mpo', 'Mapoly0091s0078' => 'mpo', 'Mapoly0091s0079' => 'mpo', 'Mapoly0091s0080' => 'mpo', 'Mapoly0091s0081' => 'mpo', 'Mapoly0278s0004' => 'mpo', 'Mapoly0278s0005' => 'mpo', 'Mapoly0278s0006' => 'mpo', 'MBI11_g30648_MAGBIO' => 'mbi', 'MCO03G194' => 'mco', 'MCO03G590' => 'mco', 'MCO07G312' => 'mco', 'MCO10G318' => 'mco', 'MCO12G244' => 'mco', 'MCO13G148' => 'mco', 'MCO13G194' => 'mco', 'MCO16G238' => 'mco', 'MD06G1134100' => 'mdo', 'MD13G1200100' => 'mdo', 'MD13G1200300' => 'mdo', 'MD13G1200600' => 'mdo', 'MD14G1150400' => 'mdo', 'MD16G1200000' => 'mdo', 'Medtr1g102570' => 'mtr', 'Medtr1g102780' => 'mtr', 'Medtr1g102800' => 'mtr', 'Medtr1g102810' => 'mtr', 'Medtr1g102830' => 'mtr', 'MELO3C006499.2' => 'cme', 'Migut.G00385' => 'egut', 'MSTRG.4063' => 'ama', 'Nitab4.5_0000090g0260' => 'nta', 'Nitab4.5_0000977g0030' => 'nta', 'Nitab4.5_0002541g0040' => 'nta', 'Nitab4.5_0007068g0040' => 'nta', 'Nn005s41408' => 'nnu', 'Nn005s41410' => 'nnu', 'Oeu010310.1' => 'oeu', 'Oeu010311.1' => 'oeu', 'Oeu043472.1' => 'oeu', 'Os01g0246400' => 'osa', 'Os04g0267950' => 'osa', 'Os07g0178700' => 'osa', 'Os07g0178800' => 'osa', 'Peaxi162Scf00316g00046' => 'pax', 'Peaxi162Scf00316g00049' => 'pax', 'Peaxi162Scf00316g00059' => 'pax', 'Peaxi162Scf00316g00328' => 'pax', 'Peaxi162Scf00316g00329' => 'pax', 'Peaxi162Scf00316g00411' => 'pax', 'Peaxi162Scf00316g00521' => 'pax', 'Peaxi162Scf00492g00068' => 'pax', 'Peaxi162Scf35631g00002' => 'pax', 'PGR142G3720' => 'pgr', 'PGSC0003DMG400006442' => 'stu', 'Phvul.007G062000' => 'pvu', 'Potri.008G157750' => 'ptr', 'Potri.008G157900' => 'ptr', 'Potri.008G158000' => 'ptr', 'Potri.008G158200' => 'ptr', 'Pp3c11_7280' => 'ppa', 'Pp3c11_7980' => 'ppa', 'Pp3c12_19450' => 'ppa', 'Pp3c14_1480' => 'ppa', 'Pp3c14_1501' => 'ppa', 'Pp3c16_4900' => 'ppa', 'Pp3c16_5010' => 'ppa', 'Pp3c16_5060' => 'ppa', 'Pp3c19_18250' => 'ppa', 'Pp3c23_8530' => 'ppa', 'Pp3c23_8550' => 'ppa', 'Pp3c24_9670' => 'ppa', 'Pp3c2_21390' => 'ppa', 'Pp3c2_31380' => 'ppa', 'Pp3c3_16620' => 'ppa', 'Pp3c3_8090' => 'ppa', 'Pp3c3_8110' => 'ppa', 'Pp3c3_8130' => 'ppa', 'Pp3c3_8150' => 'ppa', 'Pp3c4_14320' => 'ppa', 'Pp3c6_2560' => 'ppa', 'Pp3c9_16700' => 'ppa', 'PRCOL_00000234' => 'pco', 'PRCOL_00000235' => 'pco', 'PRCOL_00000777' => 'pco', 'PRCOL_00002344' => 'pco', 'PRCOL_00002372' => 'pco', 'PRCOL_00006120' => 'pco', 'Prupe.1G021400' => 'ppe', 'Prupe.1G021500' => 'ppe', 'Prupe.1G021600' => 'ppe', 'Prupe.1G021700' => 'ppe', 'Prupe.1G021800' => 'ppe', 'Prupe.5G145100' => 'ppe', 'Psat6g204040' => 'psa', 'Psat6g204800' => 'psa', 'Psat6g204920' => 'psa', 'Psat6g204960' => 'psa', 'Psat6g205080' => 'psa', 'PSO017G0271' => 'pso', 'PSO017G1276' => 'pso', 'PSO017G1429' => 'pso', 'PSO017G1861' => 'pso', 'PSO017G2787' => 'pso', 'PSO017G4466' => 'pso', 'PSO017G5118' => 'pso', 'PSO017G5420' => 'pso', 'PSO063G3678' => 'pso', 'PSO210G0546' => 'pso', 'PSO317G0001' => 'pso', 'PSO357G0512' => 'pso', 'PSO478G2682' => 'pso', 'PSO647G0001' => 'pso', 'PSO675G0001' => 'pso', 'PSO675G2699' => 'pso', 'PSO675G2849' => 'pso', 'PSO675G4991' => 'pso', 'PSO689G0001' => 'pso', 'QL06p000916' => 'qlo', 'QL06p000921' => 'qlo', 'QL06p001398' => 'qlo', 'QL06p001407' => 'qlo', 'QL06p002031' => 'qlo', 'RcHm_v2.0_Chr4g0387791' => 'rch', 'RcHm_v2.0_Chr4g0387801' => 'rch', 'RcHm_v2.0_Chr6g0286501' => 'rch', 'RcHm_v2.0_Chr6g0286511' => 'rch', 'RcHm_v2.0_Chr6g0286521' => 'rch', 'RcHm_v2.0_Chr6g0286531' => 'rch', 'RcHm_v2.0_Chr7g0189141' => 'rch', 'Rhsim02G0028700' => 'rsi', 'Rhsim02G0028800' => 'rsi', 'Rhsim02G0028900' => 'rsi', 'Rhsim02G0029000' => 'rsi', 'Rhsim02G0029100' => 'rsi', 'Rhsim02G0029200' => 'rsi', 'Rhsim02G0029300' => 'rsi', 'Rhsim02G0029400' => 'rsi', 'Rhsim02G0029500' => 'rsi', 'Rhsim02G0029600' => 'rsi', 'RhsimUnG0024000' => 'rsi', 'RhsimUnG0024100' => 'rsi', 'RhsimUnG0024200' => 'rsi', 'RhsimUnG0024300' => 'rsi', 'RhsimUnG0024400' => 'rsi', 'RhsimUnG0024500' => 'rsi', 'RhsimUnG0024700' => 'rsi', 'RhsimUnG0024800' => 'rsi', 'RhsimUnG0024900' => 'rsi', 'RhsimUnG0025100' => 'rsi', 'Sabra08G0120200' => 'sbr', 'Sabra08G0120300' => 'sbr', 'Sabra08G0120500' => 'sbr', 'Sabra08G0120600' => 'sbr', 'Sabra10G0158900' => 'sbr', 'SalBow2G3492' => 'sbo', 'Sc13g0004760' => 'sci', 'Sc13g0004770' => 'sci', 'Sed0003417' => 'sed', 'Sed0019750' => 'sed', 'SEGI_03419' => 'sgi', 'SEGI_05907' => 'sgi', 'SEGI_10682' => 'sgi', 'SEGI_13528' => 'sgi', 'SEGI_16081' => 'sgi', 'SEGI_19370' => 'sgi', 'SEGI_21015' => 'sgi', 'SEGI_21944' => 'sgi', 'SEGI_32906' => 'sgi', 'SEGI_33093' => 'sgi', 'SEGI_36110' => 'sgi', 'SEGI_40397' => 'sgi', 'SGA_v2.0_scaffold191G40426' => 'sas', 'SGA_v2.0_scaffold353G49717' => 'sas', 'SGA_v2.0_scaffold50G18550' => 'sas', 'SMO119G0173' => 'smo', 'SMO172G0002' => 'smo', 'Solyc09g082690.3' => 'sly', 'Solyc09g082700.2' => 'sly', 'Sopen09g031550' => 'spe', 'Sopen09g031560' => 'spe', 'Sp3g20540' => 'spa', 'Sp7g07580' => 'spa', 'TAR134G0002' => 'tar', 'TAR236G0001' => 'tar', 'TAR365G0892' => 'tar', 'TAR636G0166' => 'tar', 'TAR636G0646' => 'tar', 'TAR636G0869' => 'tar', 'TAR636G1317' => 'tar', 'TAR636G1744' => 'tar', 'TAR636G3358' => 'tar', 'TAR636G3436' => 'tar', 'THA.LOC104803047' => 'tha', 'Thecc.04G238900' => 'tca', 'Thhalv10021557m.g' => 'esa', 'Thhalv10026318m.g' => 'esa', 'Thhalv10026335m.g' => 'esa', 'TPR.G17433' => 'tpr', 'TPR.G18915' => 'tpr', 'TPR.G26125' => 'tpr', 'TWI09G0677' => 'twi', 'TWI73G0287' => 'twi', 'unitig_748.g8326' => 'ugi', 'vmacro15370' => 'vma', 'vmacro15371' => 'vma', 'vmacro15372' => 'vma', 'vmacro15373' => 'vma', 'vmacro15374' => 'vma', 'VMungo0720G2826' => 'vmu', 'Zm00001eb116960' => 'zma', 'Zm00001eb301260' => 'zma', 'Zm00001eb301270' => 'zma' ), 'gf_id' => 'HOM05D001460', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001460' ), 'data_identifier' => 'HOM05D001460', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001460', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '433', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p22980' => 'bna', 'A01p32340' => 'bna', 'A03p42970' => 'bna', 'A05p25880' => 'bna', 'Aa31LG8G9320' => 'aar', 'Aa31LG8G9330' => 'aar', 'Aa31LG8G9340' => 'aar', 'Aa31sc221G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1034' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1528' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.829' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2222' => 'aag', 'Ah.12g058830' => 'amhyb', 'Ah.12g058840' => 'amhyb', 'AL3G37160' => 'aly', 'AL7G41310' => 'aly', 'Aqoxy5G00395' => 'aox', 'Aqoxy5G00396' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0C8NZA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5185HY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JZ1PRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MD3LS0' => 'arhy', 'AT3G22840' => 'ath', 'AT4G14690' => 'ath', 'ATR0665G054' => 'atr', 'Atru.chr4.2344' => 'acertr', 'Atru.chr4.2346' => 'acertr', 'Atru.chr4.2347' => 'acertr', 'Atru.chr4.2348' => 'acertr', 'Atru.chr4.2355' => 'acertr', 'Atru.chr4.2356' => 'acertr', 'Atru.chr4.2358' => 'acertr', 'Atru.chr4.2359' => 'acertr', 'Atru.chr4.2360' => 'acertr', 'Atru.chr4.2361' => 'acertr', 'AUR62030476' => 'cqu', 'AUR62030478' => 'cqu', 'AUR62030819' => 'cqu', 'AUR62030820' => 'cqu', 'BcaB03g14648' => 'bca', 'BcaB04g20492' => 'bca', 'BcaB06g26399' => 'bca', 'BcaC01g03416' => 'bca', 'BcaC01g03419' => 'bca', 'BcaC01g03421' => 'bca', 'BcaC01g03424' => 'bca', 'BcaC05g28012' => 'bca', 'BcaC09g49212' => 'bca', 'BcaC09g50140' => 'bca', 'BcaNung00346' => 'bca', 'BolC1t02785H' => 'bol', 'BolC1t04095H' => 'bol', 'BolC3t17545H' => 'bol', 'BolC5t32769H' => 'bol', 'BraA01t02211Z' => 'bra', 'BraA01t03359Z' => 'bra', 'BraA03t13441Z' => 'bra', 'BraA05t21476Z' => 'bra', 'C01p28420' => 'bna', 'C01p41350' => 'bna', 'C03p52750' => 'bna', 'C03p52780' => 'bna', 'C05p40270' => 'bna', 'CAN.G1437.9' => 'can', 'CANSAT78G0035' => 'cansat', 'CANSAT78G1036' => 'cansat', 'CANSAT78G2272' => 'cansat', 'CANSAT78G2478' => 'cansat', 'CARHR098700' => 'chi', 'CARHR221120' => 'chi', 'CARHR221150' => 'chi', 'Carub.0003s2297' => 'cru', 'Carub.0007s2749' => 'cru', 'Carub.0007s2750' => 'cru', 'Carub.0007s2751' => 'cru', 'Ca_10849_v3' => 'car', 'Cc03_g04300' => 'ccan', 'CDE02G3648' => 'cde', 'CDE05G0060' => 'cde', 'CDE05G0692' => 'cde', 'CDE05G2285' => 'cde', 'CDE05G2884' => 'cde', 'CDE05G3072' => 'cde', 'Cfa008439' => 'cfa', 'Cfa008441' => 'cfa', 'Cfa008443' => 'cfa', 'Cfa008448' => 'cfa', 'Ciclev10005974m.g' => 'ccl', 'Ciclev10006006m.g' => 'ccl', 'Ciclev10006775m.g' => 'ccl', 'CiPaw.02G120400' => 'cil', 'CiPaw.02G120500' => 'cil', 'CiPaw.02G120600' => 'cil', 'ClCG05G004850' => 'cla', 'COL.COLO4_21566' => 'col', 'Cpa.g.sc44.124' => 'cpa', 'Cre07.g320400' => 'cre', 'Cre07.g320450' => 'cre', 'Cre08.g384650' => 'cre', 'Cre09.g393173' => 'cre', 'Cre09.g394325' => 'cre', 'Cre14.g626750' => 'cre', 'Cre16.g679250' => 'cre', 'CsaV3_3G012890' => 'csa', 'CSS0010865' => 'camsi', 'CSS0044338' => 'camsi', 'DCAR_002366' => 'dca', 'DCAR_030687' => 'dca', 'DCAR_030688' => 'dca', 'Dinv14047' => 'din', 'Dinv14048' => 'din', 'Duzib151G0105' => 'dzi', 'Duzib151G0114' => 'dzi', 'Duzib212G1029' => 'dzi', 'ECA232G3536' => 'eca', 'ECA240G0786' => 'eca', 'ECA240G1802' => 'eca', 'ECA240G3760' => 'eca', 'ECA240G3920' => 'eca', 'EL10Ac5g12536' => 'bvu', 'EL10Ac5g12537' => 'bvu', 'EL10Ac5g12538' => 'bvu', 'Eucgr.B01004' => 'egr', 'Eucgr.B01006' => 'egr', 'Eucgr.B01007' => 'egr', 'Eucgr.B01008' => 'egr', 'Eucgr.B01895' => 'egr', 'Eucgr.B01896' => 'egr', 'FAN04G1456' => 'fan', 'FAN08G1769' => 'fan', 'FAN08G2160' => 'fan', 'FAN13G2403' => 'fan', 'FAN13G3303' => 'fan', 'FAN15G2435' => 'fan', 'FAN17G0672' => 'fan', 'FAN17G2441' => 'fan', 'FAN18G1024' => 'fan', 'FAN22G1458' => 'fan', 'FAN24G0037' => 'fan', 'FAN24G0429' => 'fan', 'FAN24G2387' => 'fan', 'FAN27G2746' => 'fan', 'FvH4_2g20400' => 'fve', 'FvH4_2g20420' => 'fve', 'FvH4_2g20430' => 'fve', 'FvH4_4g01270' => 'fve', 'FvH4_4g01290' => 'fve', 'FvH4_4g01300' => 'fve', 'FvH4_4g01310' => 'fve', 'FvH4_4g01330' => 'fve', 'FvH4_5g09070' => 'fve', 'Glyma.10G243800' => 'gma', 'Glyma.20G150600' => 'gma', 'Gohir.A09G219200' => 'ghi', 'Gohir.A09G219300' => 'ghi', 'Gohir.D09G221400' => 'ghi', 'Gohir.D09G221500' => 'ghi', 'Gorai.006G242600' => 'gra', 'Gorai.006G242700' => 'gra', 'GSVIVG01018044001' => 'vvi', 'HanXRQChr03g0083821' => 'han', 'HanXRQChr03g0083841' => 'han', 'HanXRQChr03g0083881' => 'han', 'HanXRQChr03g0083901' => 'han', 'HanXRQChr03g0083921' => 'han', 'HanXRQChr03g0085331' => 'han', 'HanXRQChr03g0085361' => 'han', 'HanXRQChr03g0085411' => 'han', 'HanXRQChr03g0085421' => 'han', 'HanXRQChr03g0085431' => 'han', 'HanXRQChr08g0221991' => 'han', 'HanXRQChr11g0336061' => 'han', 'HanXRQChr11g0336411' => 'han', 'Haze_11234' => 'cav', 'Hma1.2p1_0549F.1_g177010' => 'hma', 'Hma1.2p1_0602F.1_g187630' => 'hma', 'Hund14876' => 'sun', 'Hund14879' => 'sun', 'Lalb_Chr06g0160741' => 'lal', 'Lalb_Chr21g0304781' => 'lal', 'Lj3A726G19' => 'lonja', 'Lj3A726T23' => 'lonja', 'Lj3A726T24' => 'lonja', 'Lj3A726T25' => 'lonja', 'Lj3A727T17' => 'lonja', 'Lj3C726T0' => 'lonja', 'Lj3C726T2' => 'lonja', 'Lj3P725T35' => 'lonja', 'Lj3P727T10' => 'lonja', 'Lj3P727T12' => 'lonja', 'Lj3P727T14' => 'lonja', 'Lj5g0023109' => 'lja', 'Lj6P646T44' => 'lonja', 'Lsat_1_v5_gn_6_75760' => 'lsa', 'Lsat_1_v5_gn_6_75800' => 'lsa', 'Lsat_1_v5_gn_6_75900' => 'lsa', 'Lsat_1_v5_gn_6_76240' => 'lsa', 'Lsat_1_v5_gn_6_76441' => 'lsa', 'Lsat_1_v5_gn_6_76700' => 'lsa', 'Lsat_1_v5_gn_6_76760' => 'lsa', 'Manes.15G033100' => 'mes', 'Mapoly0004s0074' => 'mpo', 'Mapoly0004s0075' => 'mpo', 'Mapoly0004s0163' => 'mpo', 'Mapoly0004s0164' => 'mpo', 'Mapoly0021s0018' => 'mpo', 'Mapoly0041s0136' => 'mpo', 'Mapoly0041s0137' => 'mpo', 'Mapoly0041s0138' => 'mpo', 'Mapoly0041s0139' => 'mpo', 'Mapoly0041s0141' => 'mpo', 'Mapoly0041s0142' => 'mpo', 'Mapoly0041s0143' => 'mpo', 'Mapoly0041s0144' => 'mpo', 'Mapoly0041s0145' => 'mpo', 'Mapoly0047s0106' => 'mpo', 'Mapoly0047s0108' => 'mpo', 'Mapoly0050s0051' => 'mpo', 'Mapoly0050s0052' => 'mpo', 'Mapoly0050s0053' => 'mpo', 'Mapoly0058s0013' => 'mpo', 'Mapoly0091s0078' => 'mpo', 'Mapoly0091s0079' => 'mpo', 'Mapoly0091s0080' => 'mpo', 'Mapoly0091s0081' => 'mpo', 'Mapoly0278s0004' => 'mpo', 'Mapoly0278s0005' => 'mpo', 'Mapoly0278s0006' => 'mpo', 'MBI11_g30648_MAGBIO' => 'mbi', 'MCO03G194' => 'mco', 'MCO03G590' => 'mco', 'MCO07G312' => 'mco', 'MCO10G318' => 'mco', 'MCO12G244' => 'mco', 'MCO13G148' => 'mco', 'MCO13G194' => 'mco', 'MCO16G238' => 'mco', 'MD06G1134100' => 'mdo', 'MD13G1200100' => 'mdo', 'MD13G1200300' => 'mdo', 'MD13G1200600' => 'mdo', 'MD14G1150400' => 'mdo', 'MD16G1200000' => 'mdo', 'Medtr1g102570' => 'mtr', 'Medtr1g102780' => 'mtr', 'Medtr1g102800' => 'mtr', 'Medtr1g102810' => 'mtr', 'Medtr1g102830' => 'mtr', 'MELO3C006499.2' => 'cme', 'Migut.G00385' => 'egut', 'MSTRG.4063' => 'ama', 'Nitab4.5_0000090g0260' => 'nta', 'Nitab4.5_0000977g0030' => 'nta', 'Nitab4.5_0002541g0040' => 'nta', 'Nitab4.5_0007068g0040' => 'nta', 'Nn005s41408' => 'nnu', 'Nn005s41410' => 'nnu', 'Oeu010310.1' => 'oeu', 'Oeu010311.1' => 'oeu', 'Oeu043472.1' => 'oeu', 'Os01g0246400' => 'osa', 'Os04g0267950' => 'osa', 'Os07g0178700' => 'osa', 'Os07g0178800' => 'osa', 'Peaxi162Scf00316g00046' => 'pax', 'Peaxi162Scf00316g00049' => 'pax', 'Peaxi162Scf00316g00059' => 'pax', 'Peaxi162Scf00316g00328' => 'pax', 'Peaxi162Scf00316g00329' => 'pax', 'Peaxi162Scf00316g00411' => 'pax', 'Peaxi162Scf00316g00521' => 'pax', 'Peaxi162Scf00492g00068' => 'pax', 'Peaxi162Scf35631g00002' => 'pax', 'PGR142G3720' => 'pgr', 'PGSC0003DMG400006442' => 'stu', 'Phvul.007G062000' => 'pvu', 'Potri.008G157750' => 'ptr', 'Potri.008G157900' => 'ptr', 'Potri.008G158000' => 'ptr', 'Potri.008G158200' => 'ptr', 'Pp3c11_7280' => 'ppa', 'Pp3c11_7980' => 'ppa', 'Pp3c12_19450' => 'ppa', 'Pp3c14_1480' => 'ppa', 'Pp3c14_1501' => 'ppa', 'Pp3c16_4900' => 'ppa', 'Pp3c16_5010' => 'ppa', 'Pp3c16_5060' => 'ppa', 'Pp3c19_18250' => 'ppa', 'Pp3c23_8530' => 'ppa', 'Pp3c23_8550' => 'ppa', 'Pp3c24_9670' => 'ppa', 'Pp3c2_21390' => 'ppa', 'Pp3c2_31380' => 'ppa', 'Pp3c3_16620' => 'ppa', 'Pp3c3_8090' => 'ppa', 'Pp3c3_8110' => 'ppa', 'Pp3c3_8130' => 'ppa', 'Pp3c3_8150' => 'ppa', 'Pp3c4_14320' => 'ppa', 'Pp3c6_2560' => 'ppa', 'Pp3c9_16700' => 'ppa', 'PRCOL_00000234' => 'pco', 'PRCOL_00000235' => 'pco', 'PRCOL_00000777' => 'pco', 'PRCOL_00002344' => 'pco', 'PRCOL_00002372' => 'pco', 'PRCOL_00006120' => 'pco', 'Prupe.1G021400' => 'ppe', 'Prupe.1G021500' => 'ppe', 'Prupe.1G021600' => 'ppe', 'Prupe.1G021700' => 'ppe', 'Prupe.1G021800' => 'ppe', 'Prupe.5G145100' => 'ppe', 'Psat6g204040' => 'psa', 'Psat6g204800' => 'psa', 'Psat6g204920' => 'psa', 'Psat6g204960' => 'psa', 'Psat6g205080' => 'psa', 'PSO017G0271' => 'pso', 'PSO017G1276' => 'pso', 'PSO017G1429' => 'pso', 'PSO017G1861' => 'pso', 'PSO017G2787' => 'pso', 'PSO017G4466' => 'pso', 'PSO017G5118' => 'pso', 'PSO017G5420' => 'pso', 'PSO063G3678' => 'pso', 'PSO210G0546' => 'pso', 'PSO317G0001' => 'pso', 'PSO357G0512' => 'pso', 'PSO478G2682' => 'pso', 'PSO647G0001' => 'pso', 'PSO675G0001' => 'pso', 'PSO675G2699' => 'pso', 'PSO675G2849' => 'pso', 'PSO675G4991' => 'pso', 'PSO689G0001' => 'pso', 'QL06p000916' => 'qlo', 'QL06p000921' => 'qlo', 'QL06p001398' => 'qlo', 'QL06p001407' => 'qlo', 'QL06p002031' => 'qlo', 'RcHm_v2.0_Chr4g0387791' => 'rch', 'RcHm_v2.0_Chr4g0387801' => 'rch', 'RcHm_v2.0_Chr6g0286501' => 'rch', 'RcHm_v2.0_Chr6g0286511' => 'rch', 'RcHm_v2.0_Chr6g0286521' => 'rch', 'RcHm_v2.0_Chr6g0286531' => 'rch', 'RcHm_v2.0_Chr7g0189141' => 'rch', 'Rhsim02G0028700' => 'rsi', 'Rhsim02G0028800' => 'rsi', 'Rhsim02G0028900' => 'rsi', 'Rhsim02G0029000' => 'rsi', 'Rhsim02G0029100' => 'rsi', 'Rhsim02G0029200' => 'rsi', 'Rhsim02G0029300' => 'rsi', 'Rhsim02G0029400' => 'rsi', 'Rhsim02G0029500' => 'rsi', 'Rhsim02G0029600' => 'rsi', 'RhsimUnG0024000' => 'rsi', 'RhsimUnG0024100' => 'rsi', 'RhsimUnG0024200' => 'rsi', 'RhsimUnG0024300' => 'rsi', 'RhsimUnG0024400' => 'rsi', 'RhsimUnG0024500' => 'rsi', 'RhsimUnG0024700' => 'rsi', 'RhsimUnG0024800' => 'rsi', 'RhsimUnG0024900' => 'rsi', 'RhsimUnG0025100' => 'rsi', 'Sabra08G0120200' => 'sbr', 'Sabra08G0120300' => 'sbr', 'Sabra08G0120500' => 'sbr', 'Sabra08G0120600' => 'sbr', 'Sabra10G0158900' => 'sbr', 'SalBow2G3492' => 'sbo', 'Sc13g0004760' => 'sci', 'Sc13g0004770' => 'sci', 'Sed0003417' => 'sed', 'Sed0019750' => 'sed', 'SEGI_03419' => 'sgi', 'SEGI_05907' => 'sgi', 'SEGI_10682' => 'sgi', 'SEGI_13528' => 'sgi', 'SEGI_16081' => 'sgi', 'SEGI_19370' => 'sgi', 'SEGI_21015' => 'sgi', 'SEGI_21944' => 'sgi', 'SEGI_32906' => 'sgi', 'SEGI_33093' => 'sgi', 'SEGI_36110' => 'sgi', 'SEGI_40397' => 'sgi', 'SGA_v2.0_scaffold191G40426' => 'sas', 'SGA_v2.0_scaffold353G49717' => 'sas', 'SGA_v2.0_scaffold50G18550' => 'sas', 'SMO119G0173' => 'smo', 'SMO172G0002' => 'smo', 'Solyc09g082690.3' => 'sly', 'Solyc09g082700.2' => 'sly', 'Sopen09g031550' => 'spe', 'Sopen09g031560' => 'spe', 'Sp3g20540' => 'spa', 'Sp7g07580' => 'spa', 'TAR134G0002' => 'tar', 'TAR236G0001' => 'tar', 'TAR365G0892' => 'tar', 'TAR636G0166' => 'tar', 'TAR636G0646' => 'tar', 'TAR636G0869' => 'tar', 'TAR636G1317' => 'tar', 'TAR636G1744' => 'tar', 'TAR636G3358' => 'tar', 'TAR636G3436' => 'tar', 'THA.LOC104803047' => 'tha', 'Thecc.04G238900' => 'tca', 'Thhalv10021557m.g' => 'esa', 'Thhalv10026318m.g' => 'esa', 'Thhalv10026335m.g' => 'esa', 'TPR.G17433' => 'tpr', 'TPR.G18915' => 'tpr', 'TPR.G26125' => 'tpr', 'TWI09G0677' => 'twi', 'TWI73G0287' => 'twi', 'unitig_748.g8326' => 'ugi', 'vmacro15370' => 'vma', 'vmacro15371' => 'vma', 'vmacro15372' => 'vma', 'vmacro15373' => 'vma', 'vmacro15374' => 'vma', 'VMungo0720G2826' => 'vmu', 'Zm00001eb116960' => 'zma', 'Zm00001eb301260' => 'zma', 'Zm00001eb301270' => 'zma' ) $gf_id = 'HOM05D001460' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001460' ) $data_identifier = 'HOM05D001460' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 4, 'aag' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 2, 'aox' => (int) 2, 'arhy' => (int) 4, 'ath' => (int) 2, 'atr' => (int) 1, 'acertr' => (int) 10, 'cqu' => (int) 4, 'bca' => (int) 11, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 1, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 1, 'ccan' => (int) 1, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 1, 'col' => (int) 1, 'cpa' => (int) 1, 'cre' => (int) 7, 'csa' => (int) 1, 'camsi' => (int) 2, 'dca' => (int) 3, 'din' => (int) 2, 'dzi' => (int) 3, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 14, 'fve' => (int) 9, 'gma' => (int) 2, 'ghi' => (int) 4, 'gra' => (int) 2, 'vvi' => (int) 1, 'han' => (int) 13, 'cav' => (int) 1, 'hma' => (int) 2, 'sun' => (int) 2, 'lal' => (int) 2, 'lonja' => (int) 12, 'lja' => (int) 1, 'lsa' => (int) 7, 'mes' => (int) 1, 'mpo' => (int) 27, 'mbi' => (int) 1, 'mco' => (int) 8, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 1, 'egut' => (int) 1, 'ama' => (int) 1, 'nta' => (int) 4, 'nnu' => (int) 2, 'oeu' => (int) 3, 'osa' => (int) 4, 'pax' => (int) 9, 'pgr' => (int) 1, 'stu' => (int) 1, 'pvu' => (int) 1, 'ptr' => (int) 4, 'ppa' => (int) 22, 'pco' => (int) 6, 'ppe' => (int) 6, 'psa' => (int) 5, 'pso' => (int) 19, 'qlo' => (int) 5, 'rch' => (int) 7, 'rsi' => (int) 20, 'sbr' => (int) 5, 'sbo' => (int) 1, 'sci' => (int) 2, 'sed' => (int) 2, 'sgi' => (int) 12, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 2, 'tar' => (int) 10, 'tha' => (int) 1, 'tca' => (int) 1, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 2, 'ugi' => (int) 1, 'vma' => (int) 5, 'vmu' => (int) 1, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb301270' $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' => 'HOM05D001460', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '433', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p22980' => 'bna', 'A01p32340' => 'bna', 'A03p42970' => 'bna', 'A05p25880' => 'bna', 'Aa31LG8G9320' => 'aar', 'Aa31LG8G9330' => 'aar', 'Aa31LG8G9340' => 'aar', 'Aa31sc221G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1034' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1528' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.829' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2222' => 'aag', 'Ah.12g058830' => 'amhyb', 'Ah.12g058840' => 'amhyb', 'AL3G37160' => 'aly', 'AL7G41310' => 'aly', 'Aqoxy5G00395' => 'aox', 'Aqoxy5G00396' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0C8NZA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5185HY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JZ1PRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MD3LS0' => 'arhy', 'AT3G22840' => 'ath', 'AT4G14690' => 'ath', 'ATR0665G054' => 'atr', 'Atru.chr4.2344' => 'acertr', 'Atru.chr4.2346' => 'acertr', 'Atru.chr4.2347' => 'acertr', 'Atru.chr4.2348' => 'acertr', 'Atru.chr4.2355' => 'acertr', 'Atru.chr4.2356' => 'acertr', 'Atru.chr4.2358' => 'acertr', 'Atru.chr4.2359' => 'acertr', 'Atru.chr4.2360' => 'acertr', 'Atru.chr4.2361' => 'acertr', 'AUR62030476' => 'cqu', 'AUR62030478' => 'cqu', 'AUR62030819' => 'cqu', 'AUR62030820' => 'cqu', 'BcaB03g14648' => 'bca', 'BcaB04g20492' => 'bca', 'BcaB06g26399' => 'bca', 'BcaC01g03416' => 'bca', 'BcaC01g03419' => 'bca', 'BcaC01g03421' => 'bca', 'BcaC01g03424' => 'bca', 'BcaC05g28012' => 'bca', 'BcaC09g49212' => 'bca', 'BcaC09g50140' => 'bca', 'BcaNung00346' => 'bca', 'BolC1t02785H' => 'bol', 'BolC1t04095H' => 'bol', 'BolC3t17545H' => 'bol', 'BolC5t32769H' => 'bol', 'BraA01t02211Z' => 'bra', 'BraA01t03359Z' => 'bra', 'BraA03t13441Z' => 'bra', 'BraA05t21476Z' => 'bra', 'C01p28420' => 'bna', 'C01p41350' => 'bna', 'C03p52750' => 'bna', 'C03p52780' => 'bna', 'C05p40270' => 'bna', 'CAN.G1437.9' => 'can', 'CANSAT78G0035' => 'cansat', 'CANSAT78G1036' => 'cansat', 'CANSAT78G2272' => 'cansat', 'CANSAT78G2478' => 'cansat', 'CARHR098700' => 'chi', 'CARHR221120' => 'chi', 'CARHR221150' => 'chi', 'Carub.0003s2297' => 'cru', 'Carub.0007s2749' => 'cru', 'Carub.0007s2750' => 'cru', 'Carub.0007s2751' => 'cru', 'Ca_10849_v3' => 'car', 'Cc03_g04300' => 'ccan', 'CDE02G3648' => 'cde', 'CDE05G0060' => 'cde', 'CDE05G0692' => 'cde', 'CDE05G2285' => 'cde', 'CDE05G2884' => 'cde', 'CDE05G3072' => 'cde', 'Cfa008439' => 'cfa', 'Cfa008441' => 'cfa', 'Cfa008443' => 'cfa', 'Cfa008448' => 'cfa', 'Ciclev10005974m.g' => 'ccl', 'Ciclev10006006m.g' => 'ccl', 'Ciclev10006775m.g' => 'ccl', 'CiPaw.02G120400' => 'cil', 'CiPaw.02G120500' => 'cil', 'CiPaw.02G120600' => 'cil', 'ClCG05G004850' => 'cla', 'COL.COLO4_21566' => 'col', 'Cpa.g.sc44.124' => 'cpa', 'Cre07.g320400' => 'cre', 'Cre07.g320450' => 'cre', 'Cre08.g384650' => 'cre', 'Cre09.g393173' => 'cre', 'Cre09.g394325' => 'cre', 'Cre14.g626750' => 'cre', 'Cre16.g679250' => 'cre', 'CsaV3_3G012890' => 'csa', 'CSS0010865' => 'camsi', 'CSS0044338' => 'camsi', 'DCAR_002366' => 'dca', 'DCAR_030687' => 'dca', 'DCAR_030688' => 'dca', 'Dinv14047' => 'din', 'Dinv14048' => 'din', 'Duzib151G0105' => 'dzi', 'Duzib151G0114' => 'dzi', 'Duzib212G1029' => 'dzi', 'ECA232G3536' => 'eca', 'ECA240G0786' => 'eca', 'ECA240G1802' => 'eca', 'ECA240G3760' => 'eca', 'ECA240G3920' => 'eca', 'EL10Ac5g12536' => 'bvu', 'EL10Ac5g12537' => 'bvu', 'EL10Ac5g12538' => 'bvu', 'Eucgr.B01004' => 'egr', 'Eucgr.B01006' => 'egr', 'Eucgr.B01007' => 'egr', 'Eucgr.B01008' => 'egr', 'Eucgr.B01895' => 'egr', 'Eucgr.B01896' => 'egr', 'FAN04G1456' => 'fan', 'FAN08G1769' => 'fan', 'FAN08G2160' => 'fan', 'FAN13G2403' => 'fan', 'FAN13G3303' => 'fan', 'FAN15G2435' => 'fan', 'FAN17G0672' => 'fan', 'FAN17G2441' => 'fan', 'FAN18G1024' => 'fan', 'FAN22G1458' => 'fan', 'FAN24G0037' => 'fan', 'FAN24G0429' => 'fan', 'FAN24G2387' => 'fan', 'FAN27G2746' => 'fan', 'FvH4_2g20400' => 'fve', 'FvH4_2g20420' => 'fve', 'FvH4_2g20430' => 'fve', 'FvH4_4g01270' => 'fve', 'FvH4_4g01290' => 'fve', 'FvH4_4g01300' => 'fve', 'FvH4_4g01310' => 'fve', 'FvH4_4g01330' => 'fve', 'FvH4_5g09070' => 'fve', 'Glyma.10G243800' => 'gma', 'Glyma.20G150600' => 'gma', 'Gohir.A09G219200' => 'ghi', 'Gohir.A09G219300' => 'ghi', 'Gohir.D09G221400' => 'ghi', 'Gohir.D09G221500' => 'ghi', 'Gorai.006G242600' => 'gra', 'Gorai.006G242700' => 'gra', 'GSVIVG01018044001' => 'vvi', 'HanXRQChr03g0083821' => 'han', 'HanXRQChr03g0083841' => 'han', 'HanXRQChr03g0083881' => 'han', 'HanXRQChr03g0083901' => 'han', 'HanXRQChr03g0083921' => 'han', 'HanXRQChr03g0085331' => 'han', 'HanXRQChr03g0085361' => 'han', 'HanXRQChr03g0085411' => 'han', 'HanXRQChr03g0085421' => 'han', 'HanXRQChr03g0085431' => 'han', 'HanXRQChr08g0221991' => 'han', 'HanXRQChr11g0336061' => 'han', 'HanXRQChr11g0336411' => 'han', 'Haze_11234' => 'cav', 'Hma1.2p1_0549F.1_g177010' => 'hma', 'Hma1.2p1_0602F.1_g187630' => 'hma', 'Hund14876' => 'sun', 'Hund14879' => 'sun', 'Lalb_Chr06g0160741' => 'lal', 'Lalb_Chr21g0304781' => 'lal', 'Lj3A726G19' => 'lonja', 'Lj3A726T23' => 'lonja', 'Lj3A726T24' => 'lonja', 'Lj3A726T25' => 'lonja', 'Lj3A727T17' => 'lonja', 'Lj3C726T0' => 'lonja', 'Lj3C726T2' => 'lonja', 'Lj3P725T35' => 'lonja', 'Lj3P727T10' => 'lonja', 'Lj3P727T12' => 'lonja', 'Lj3P727T14' => 'lonja', 'Lj5g0023109' => 'lja', 'Lj6P646T44' => 'lonja', 'Lsat_1_v5_gn_6_75760' => 'lsa', 'Lsat_1_v5_gn_6_75800' => 'lsa', 'Lsat_1_v5_gn_6_75900' => 'lsa', 'Lsat_1_v5_gn_6_76240' => 'lsa', 'Lsat_1_v5_gn_6_76441' => 'lsa', 'Lsat_1_v5_gn_6_76700' => 'lsa', 'Lsat_1_v5_gn_6_76760' => 'lsa', 'Manes.15G033100' => 'mes', 'Mapoly0004s0074' => 'mpo', 'Mapoly0004s0075' => 'mpo', 'Mapoly0004s0163' => 'mpo', 'Mapoly0004s0164' => 'mpo', 'Mapoly0021s0018' => 'mpo', 'Mapoly0041s0136' => 'mpo', 'Mapoly0041s0137' => 'mpo', 'Mapoly0041s0138' => 'mpo', 'Mapoly0041s0139' => 'mpo', 'Mapoly0041s0141' => 'mpo', 'Mapoly0041s0142' => 'mpo', 'Mapoly0041s0143' => 'mpo', 'Mapoly0041s0144' => 'mpo', 'Mapoly0041s0145' => 'mpo', 'Mapoly0047s0106' => 'mpo', 'Mapoly0047s0108' => 'mpo', 'Mapoly0050s0051' => 'mpo', 'Mapoly0050s0052' => 'mpo', 'Mapoly0050s0053' => 'mpo', 'Mapoly0058s0013' => 'mpo', 'Mapoly0091s0078' => 'mpo', 'Mapoly0091s0079' => 'mpo', 'Mapoly0091s0080' => 'mpo', 'Mapoly0091s0081' => 'mpo', 'Mapoly0278s0004' => 'mpo', 'Mapoly0278s0005' => 'mpo', 'Mapoly0278s0006' => 'mpo', 'MBI11_g30648_MAGBIO' => 'mbi', 'MCO03G194' => 'mco', 'MCO03G590' => 'mco', 'MCO07G312' => 'mco', 'MCO10G318' => 'mco', 'MCO12G244' => 'mco', 'MCO13G148' => 'mco', 'MCO13G194' => 'mco', 'MCO16G238' => 'mco', 'MD06G1134100' => 'mdo', 'MD13G1200100' => 'mdo', 'MD13G1200300' => 'mdo', 'MD13G1200600' => 'mdo', 'MD14G1150400' => 'mdo', 'MD16G1200000' => 'mdo', 'Medtr1g102570' => 'mtr', 'Medtr1g102780' => 'mtr', 'Medtr1g102800' => 'mtr', 'Medtr1g102810' => 'mtr', 'Medtr1g102830' => 'mtr', 'MELO3C006499.2' => 'cme', 'Migut.G00385' => 'egut', 'MSTRG.4063' => 'ama', 'Nitab4.5_0000090g0260' => 'nta', 'Nitab4.5_0000977g0030' => 'nta', 'Nitab4.5_0002541g0040' => 'nta', 'Nitab4.5_0007068g0040' => 'nta', 'Nn005s41408' => 'nnu', 'Nn005s41410' => 'nnu', 'Oeu010310.1' => 'oeu', 'Oeu010311.1' => 'oeu', 'Oeu043472.1' => 'oeu', 'Os01g0246400' => 'osa', 'Os04g0267950' => 'osa', 'Os07g0178700' => 'osa', 'Os07g0178800' => 'osa', 'Peaxi162Scf00316g00046' => 'pax', 'Peaxi162Scf00316g00049' => 'pax', 'Peaxi162Scf00316g00059' => 'pax', 'Peaxi162Scf00316g00328' => 'pax', 'Peaxi162Scf00316g00329' => 'pax', 'Peaxi162Scf00316g00411' => 'pax', 'Peaxi162Scf00316g00521' => 'pax', 'Peaxi162Scf00492g00068' => 'pax', 'Peaxi162Scf35631g00002' => 'pax', 'PGR142G3720' => 'pgr', 'PGSC0003DMG400006442' => 'stu', 'Phvul.007G062000' => 'pvu', 'Potri.008G157750' => 'ptr', 'Potri.008G157900' => 'ptr', 'Potri.008G158000' => 'ptr', 'Potri.008G158200' => 'ptr', 'Pp3c11_7280' => 'ppa', 'Pp3c11_7980' => 'ppa', 'Pp3c12_19450' => 'ppa', 'Pp3c14_1480' => 'ppa', 'Pp3c14_1501' => 'ppa', 'Pp3c16_4900' => 'ppa', 'Pp3c16_5010' => 'ppa', 'Pp3c16_5060' => 'ppa', 'Pp3c19_18250' => 'ppa', 'Pp3c23_8530' => 'ppa', 'Pp3c23_8550' => 'ppa', 'Pp3c24_9670' => 'ppa', 'Pp3c2_21390' => 'ppa', 'Pp3c2_31380' => 'ppa', 'Pp3c3_16620' => 'ppa', 'Pp3c3_8090' => 'ppa', 'Pp3c3_8110' => 'ppa', 'Pp3c3_8130' => 'ppa', 'Pp3c3_8150' => 'ppa', 'Pp3c4_14320' => 'ppa', 'Pp3c6_2560' => 'ppa', 'Pp3c9_16700' => 'ppa', 'PRCOL_00000234' => 'pco', 'PRCOL_00000235' => 'pco', 'PRCOL_00000777' => 'pco', 'PRCOL_00002344' => 'pco', 'PRCOL_00002372' => 'pco', 'PRCOL_00006120' => 'pco', 'Prupe.1G021400' => 'ppe', 'Prupe.1G021500' => 'ppe', 'Prupe.1G021600' => 'ppe', 'Prupe.1G021700' => 'ppe', 'Prupe.1G021800' => 'ppe', 'Prupe.5G145100' => 'ppe', 'Psat6g204040' => 'psa', 'Psat6g204800' => 'psa', 'Psat6g204920' => 'psa', 'Psat6g204960' => 'psa', 'Psat6g205080' => 'psa', 'PSO017G0271' => 'pso', 'PSO017G1276' => 'pso', 'PSO017G1429' => 'pso', 'PSO017G1861' => 'pso', 'PSO017G2787' => 'pso', 'PSO017G4466' => 'pso', 'PSO017G5118' => 'pso', 'PSO017G5420' => 'pso', 'PSO063G3678' => 'pso', 'PSO210G0546' => 'pso', 'PSO317G0001' => 'pso', 'PSO357G0512' => 'pso', 'PSO478G2682' => 'pso', 'PSO647G0001' => 'pso', 'PSO675G0001' => 'pso', 'PSO675G2699' => 'pso', 'PSO675G2849' => 'pso', 'PSO675G4991' => 'pso', 'PSO689G0001' => 'pso', 'QL06p000916' => 'qlo', 'QL06p000921' => 'qlo', 'QL06p001398' => 'qlo', 'QL06p001407' => 'qlo', 'QL06p002031' => 'qlo', 'RcHm_v2.0_Chr4g0387791' => 'rch', 'RcHm_v2.0_Chr4g0387801' => 'rch', 'RcHm_v2.0_Chr6g0286501' => 'rch', 'RcHm_v2.0_Chr6g0286511' => 'rch', 'RcHm_v2.0_Chr6g0286521' => 'rch', 'RcHm_v2.0_Chr6g0286531' => 'rch', 'RcHm_v2.0_Chr7g0189141' => 'rch', 'Rhsim02G0028700' => 'rsi', 'Rhsim02G0028800' => 'rsi', 'Rhsim02G0028900' => 'rsi', 'Rhsim02G0029000' => 'rsi', 'Rhsim02G0029100' => 'rsi', 'Rhsim02G0029200' => 'rsi', 'Rhsim02G0029300' => 'rsi', 'Rhsim02G0029400' => 'rsi', 'Rhsim02G0029500' => 'rsi', 'Rhsim02G0029600' => 'rsi', 'RhsimUnG0024000' => 'rsi', 'RhsimUnG0024100' => 'rsi', 'RhsimUnG0024200' => 'rsi', 'RhsimUnG0024300' => 'rsi', 'RhsimUnG0024400' => 'rsi', 'RhsimUnG0024500' => 'rsi', 'RhsimUnG0024700' => 'rsi', 'RhsimUnG0024800' => 'rsi', 'RhsimUnG0024900' => 'rsi', 'RhsimUnG0025100' => 'rsi', 'Sabra08G0120200' => 'sbr', 'Sabra08G0120300' => 'sbr', 'Sabra08G0120500' => 'sbr', 'Sabra08G0120600' => 'sbr', 'Sabra10G0158900' => 'sbr', 'SalBow2G3492' => 'sbo', 'Sc13g0004760' => 'sci', 'Sc13g0004770' => 'sci', 'Sed0003417' => 'sed', 'Sed0019750' => 'sed', 'SEGI_03419' => 'sgi', 'SEGI_05907' => 'sgi', 'SEGI_10682' => 'sgi', 'SEGI_13528' => 'sgi', 'SEGI_16081' => 'sgi', 'SEGI_19370' => 'sgi', 'SEGI_21015' => 'sgi', 'SEGI_21944' => 'sgi', 'SEGI_32906' => 'sgi', 'SEGI_33093' => 'sgi', 'SEGI_36110' => 'sgi', 'SEGI_40397' => 'sgi', 'SGA_v2.0_scaffold191G40426' => 'sas', 'SGA_v2.0_scaffold353G49717' => 'sas', 'SGA_v2.0_scaffold50G18550' => 'sas', 'SMO119G0173' => 'smo', 'SMO172G0002' => 'smo', 'Solyc09g082690.3' => 'sly', 'Solyc09g082700.2' => 'sly', 'Sopen09g031550' => 'spe', 'Sopen09g031560' => 'spe', 'Sp3g20540' => 'spa', 'Sp7g07580' => 'spa', 'TAR134G0002' => 'tar', 'TAR236G0001' => 'tar', 'TAR365G0892' => 'tar', 'TAR636G0166' => 'tar', 'TAR636G0646' => 'tar', 'TAR636G0869' => 'tar', 'TAR636G1317' => 'tar', 'TAR636G1744' => 'tar', 'TAR636G3358' => 'tar', 'TAR636G3436' => 'tar', 'THA.LOC104803047' => 'tha', 'Thecc.04G238900' => 'tca', 'Thhalv10021557m.g' => 'esa', 'Thhalv10026318m.g' => 'esa', 'Thhalv10026335m.g' => 'esa', 'TPR.G17433' => 'tpr', 'TPR.G18915' => 'tpr', 'TPR.G26125' => 'tpr', 'TWI09G0677' => 'twi', 'TWI73G0287' => 'twi', 'unitig_748.g8326' => 'ugi', 'vmacro15370' => 'vma', 'vmacro15371' => 'vma', 'vmacro15372' => 'vma', 'vmacro15373' => 'vma', 'vmacro15374' => 'vma', 'VMungo0720G2826' => 'vmu', 'Zm00001eb116960' => 'zma', 'Zm00001eb301260' => 'zma', 'Zm00001eb301270' => 'zma' ), 'gf_id' => 'HOM05D001460', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001460' ), 'data_identifier' => 'HOM05D001460', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001460', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '433', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p22980' => 'bna', 'A01p32340' => 'bna', 'A03p42970' => 'bna', 'A05p25880' => 'bna', 'Aa31LG8G9320' => 'aar', 'Aa31LG8G9330' => 'aar', 'Aa31LG8G9340' => 'aar', 'Aa31sc221G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1034' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1528' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.829' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2222' => 'aag', 'Ah.12g058830' => 'amhyb', 'Ah.12g058840' => 'amhyb', 'AL3G37160' => 'aly', 'AL7G41310' => 'aly', 'Aqoxy5G00395' => 'aox', 'Aqoxy5G00396' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0C8NZA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5185HY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JZ1PRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MD3LS0' => 'arhy', 'AT3G22840' => 'ath', 'AT4G14690' => 'ath', 'ATR0665G054' => 'atr', 'Atru.chr4.2344' => 'acertr', 'Atru.chr4.2346' => 'acertr', 'Atru.chr4.2347' => 'acertr', 'Atru.chr4.2348' => 'acertr', 'Atru.chr4.2355' => 'acertr', 'Atru.chr4.2356' => 'acertr', 'Atru.chr4.2358' => 'acertr', 'Atru.chr4.2359' => 'acertr', 'Atru.chr4.2360' => 'acertr', 'Atru.chr4.2361' => 'acertr', 'AUR62030476' => 'cqu', 'AUR62030478' => 'cqu', 'AUR62030819' => 'cqu', 'AUR62030820' => 'cqu', 'BcaB03g14648' => 'bca', 'BcaB04g20492' => 'bca', 'BcaB06g26399' => 'bca', 'BcaC01g03416' => 'bca', 'BcaC01g03419' => 'bca', 'BcaC01g03421' => 'bca', 'BcaC01g03424' => 'bca', 'BcaC05g28012' => 'bca', 'BcaC09g49212' => 'bca', 'BcaC09g50140' => 'bca', 'BcaNung00346' => 'bca', 'BolC1t02785H' => 'bol', 'BolC1t04095H' => 'bol', 'BolC3t17545H' => 'bol', 'BolC5t32769H' => 'bol', 'BraA01t02211Z' => 'bra', 'BraA01t03359Z' => 'bra', 'BraA03t13441Z' => 'bra', 'BraA05t21476Z' => 'bra', 'C01p28420' => 'bna', 'C01p41350' => 'bna', 'C03p52750' => 'bna', 'C03p52780' => 'bna', 'C05p40270' => 'bna', 'CAN.G1437.9' => 'can', 'CANSAT78G0035' => 'cansat', 'CANSAT78G1036' => 'cansat', 'CANSAT78G2272' => 'cansat', 'CANSAT78G2478' => 'cansat', 'CARHR098700' => 'chi', 'CARHR221120' => 'chi', 'CARHR221150' => 'chi', 'Carub.0003s2297' => 'cru', 'Carub.0007s2749' => 'cru', 'Carub.0007s2750' => 'cru', 'Carub.0007s2751' => 'cru', 'Ca_10849_v3' => 'car', 'Cc03_g04300' => 'ccan', 'CDE02G3648' => 'cde', 'CDE05G0060' => 'cde', 'CDE05G0692' => 'cde', 'CDE05G2285' => 'cde', 'CDE05G2884' => 'cde', 'CDE05G3072' => 'cde', 'Cfa008439' => 'cfa', 'Cfa008441' => 'cfa', 'Cfa008443' => 'cfa', 'Cfa008448' => 'cfa', 'Ciclev10005974m.g' => 'ccl', 'Ciclev10006006m.g' => 'ccl', 'Ciclev10006775m.g' => 'ccl', 'CiPaw.02G120400' => 'cil', 'CiPaw.02G120500' => 'cil', 'CiPaw.02G120600' => 'cil', 'ClCG05G004850' => 'cla', 'COL.COLO4_21566' => 'col', 'Cpa.g.sc44.124' => 'cpa', 'Cre07.g320400' => 'cre', 'Cre07.g320450' => 'cre', 'Cre08.g384650' => 'cre', 'Cre09.g393173' => 'cre', 'Cre09.g394325' => 'cre', 'Cre14.g626750' => 'cre', 'Cre16.g679250' => 'cre', 'CsaV3_3G012890' => 'csa', 'CSS0010865' => 'camsi', 'CSS0044338' => 'camsi', 'DCAR_002366' => 'dca', 'DCAR_030687' => 'dca', 'DCAR_030688' => 'dca', 'Dinv14047' => 'din', 'Dinv14048' => 'din', 'Duzib151G0105' => 'dzi', 'Duzib151G0114' => 'dzi', 'Duzib212G1029' => 'dzi', 'ECA232G3536' => 'eca', 'ECA240G0786' => 'eca', 'ECA240G1802' => 'eca', 'ECA240G3760' => 'eca', 'ECA240G3920' => 'eca', 'EL10Ac5g12536' => 'bvu', 'EL10Ac5g12537' => 'bvu', 'EL10Ac5g12538' => 'bvu', 'Eucgr.B01004' => 'egr', 'Eucgr.B01006' => 'egr', 'Eucgr.B01007' => 'egr', 'Eucgr.B01008' => 'egr', 'Eucgr.B01895' => 'egr', 'Eucgr.B01896' => 'egr', 'FAN04G1456' => 'fan', 'FAN08G1769' => 'fan', 'FAN08G2160' => 'fan', 'FAN13G2403' => 'fan', 'FAN13G3303' => 'fan', 'FAN15G2435' => 'fan', 'FAN17G0672' => 'fan', 'FAN17G2441' => 'fan', 'FAN18G1024' => 'fan', 'FAN22G1458' => 'fan', 'FAN24G0037' => 'fan', 'FAN24G0429' => 'fan', 'FAN24G2387' => 'fan', 'FAN27G2746' => 'fan', 'FvH4_2g20400' => 'fve', 'FvH4_2g20420' => 'fve', 'FvH4_2g20430' => 'fve', 'FvH4_4g01270' => 'fve', 'FvH4_4g01290' => 'fve', 'FvH4_4g01300' => 'fve', 'FvH4_4g01310' => 'fve', 'FvH4_4g01330' => 'fve', 'FvH4_5g09070' => 'fve', 'Glyma.10G243800' => 'gma', 'Glyma.20G150600' => 'gma', 'Gohir.A09G219200' => 'ghi', 'Gohir.A09G219300' => 'ghi', 'Gohir.D09G221400' => 'ghi', 'Gohir.D09G221500' => 'ghi', 'Gorai.006G242600' => 'gra', 'Gorai.006G242700' => 'gra', 'GSVIVG01018044001' => 'vvi', 'HanXRQChr03g0083821' => 'han', 'HanXRQChr03g0083841' => 'han', 'HanXRQChr03g0083881' => 'han', 'HanXRQChr03g0083901' => 'han', 'HanXRQChr03g0083921' => 'han', 'HanXRQChr03g0085331' => 'han', 'HanXRQChr03g0085361' => 'han', 'HanXRQChr03g0085411' => 'han', 'HanXRQChr03g0085421' => 'han', 'HanXRQChr03g0085431' => 'han', 'HanXRQChr08g0221991' => 'han', 'HanXRQChr11g0336061' => 'han', 'HanXRQChr11g0336411' => 'han', 'Haze_11234' => 'cav', 'Hma1.2p1_0549F.1_g177010' => 'hma', 'Hma1.2p1_0602F.1_g187630' => 'hma', 'Hund14876' => 'sun', 'Hund14879' => 'sun', 'Lalb_Chr06g0160741' => 'lal', 'Lalb_Chr21g0304781' => 'lal', 'Lj3A726G19' => 'lonja', 'Lj3A726T23' => 'lonja', 'Lj3A726T24' => 'lonja', 'Lj3A726T25' => 'lonja', 'Lj3A727T17' => 'lonja', 'Lj3C726T0' => 'lonja', 'Lj3C726T2' => 'lonja', 'Lj3P725T35' => 'lonja', 'Lj3P727T10' => 'lonja', 'Lj3P727T12' => 'lonja', 'Lj3P727T14' => 'lonja', 'Lj5g0023109' => 'lja', 'Lj6P646T44' => 'lonja', 'Lsat_1_v5_gn_6_75760' => 'lsa', 'Lsat_1_v5_gn_6_75800' => 'lsa', 'Lsat_1_v5_gn_6_75900' => 'lsa', 'Lsat_1_v5_gn_6_76240' => 'lsa', 'Lsat_1_v5_gn_6_76441' => 'lsa', 'Lsat_1_v5_gn_6_76700' => 'lsa', 'Lsat_1_v5_gn_6_76760' => 'lsa', 'Manes.15G033100' => 'mes', 'Mapoly0004s0074' => 'mpo', 'Mapoly0004s0075' => 'mpo', 'Mapoly0004s0163' => 'mpo', 'Mapoly0004s0164' => 'mpo', 'Mapoly0021s0018' => 'mpo', 'Mapoly0041s0136' => 'mpo', 'Mapoly0041s0137' => 'mpo', 'Mapoly0041s0138' => 'mpo', 'Mapoly0041s0139' => 'mpo', 'Mapoly0041s0141' => 'mpo', 'Mapoly0041s0142' => 'mpo', 'Mapoly0041s0143' => 'mpo', 'Mapoly0041s0144' => 'mpo', 'Mapoly0041s0145' => 'mpo', 'Mapoly0047s0106' => 'mpo', 'Mapoly0047s0108' => 'mpo', 'Mapoly0050s0051' => 'mpo', 'Mapoly0050s0052' => 'mpo', 'Mapoly0050s0053' => 'mpo', 'Mapoly0058s0013' => 'mpo', 'Mapoly0091s0078' => 'mpo', 'Mapoly0091s0079' => 'mpo', 'Mapoly0091s0080' => 'mpo', 'Mapoly0091s0081' => 'mpo', 'Mapoly0278s0004' => 'mpo', 'Mapoly0278s0005' => 'mpo', 'Mapoly0278s0006' => 'mpo', 'MBI11_g30648_MAGBIO' => 'mbi', 'MCO03G194' => 'mco', 'MCO03G590' => 'mco', 'MCO07G312' => 'mco', 'MCO10G318' => 'mco', 'MCO12G244' => 'mco', 'MCO13G148' => 'mco', 'MCO13G194' => 'mco', 'MCO16G238' => 'mco', 'MD06G1134100' => 'mdo', 'MD13G1200100' => 'mdo', 'MD13G1200300' => 'mdo', 'MD13G1200600' => 'mdo', 'MD14G1150400' => 'mdo', 'MD16G1200000' => 'mdo', 'Medtr1g102570' => 'mtr', 'Medtr1g102780' => 'mtr', 'Medtr1g102800' => 'mtr', 'Medtr1g102810' => 'mtr', 'Medtr1g102830' => 'mtr', 'MELO3C006499.2' => 'cme', 'Migut.G00385' => 'egut', 'MSTRG.4063' => 'ama', 'Nitab4.5_0000090g0260' => 'nta', 'Nitab4.5_0000977g0030' => 'nta', 'Nitab4.5_0002541g0040' => 'nta', 'Nitab4.5_0007068g0040' => 'nta', 'Nn005s41408' => 'nnu', 'Nn005s41410' => 'nnu', 'Oeu010310.1' => 'oeu', 'Oeu010311.1' => 'oeu', 'Oeu043472.1' => 'oeu', 'Os01g0246400' => 'osa', 'Os04g0267950' => 'osa', 'Os07g0178700' => 'osa', 'Os07g0178800' => 'osa', 'Peaxi162Scf00316g00046' => 'pax', 'Peaxi162Scf00316g00049' => 'pax', 'Peaxi162Scf00316g00059' => 'pax', 'Peaxi162Scf00316g00328' => 'pax', 'Peaxi162Scf00316g00329' => 'pax', 'Peaxi162Scf00316g00411' => 'pax', 'Peaxi162Scf00316g00521' => 'pax', 'Peaxi162Scf00492g00068' => 'pax', 'Peaxi162Scf35631g00002' => 'pax', 'PGR142G3720' => 'pgr', 'PGSC0003DMG400006442' => 'stu', 'Phvul.007G062000' => 'pvu', 'Potri.008G157750' => 'ptr', 'Potri.008G157900' => 'ptr', 'Potri.008G158000' => 'ptr', 'Potri.008G158200' => 'ptr', 'Pp3c11_7280' => 'ppa', 'Pp3c11_7980' => 'ppa', 'Pp3c12_19450' => 'ppa', 'Pp3c14_1480' => 'ppa', 'Pp3c14_1501' => 'ppa', 'Pp3c16_4900' => 'ppa', 'Pp3c16_5010' => 'ppa', 'Pp3c16_5060' => 'ppa', 'Pp3c19_18250' => 'ppa', 'Pp3c23_8530' => 'ppa', 'Pp3c23_8550' => 'ppa', 'Pp3c24_9670' => 'ppa', 'Pp3c2_21390' => 'ppa', 'Pp3c2_31380' => 'ppa', 'Pp3c3_16620' => 'ppa', 'Pp3c3_8090' => 'ppa', 'Pp3c3_8110' => 'ppa', 'Pp3c3_8130' => 'ppa', 'Pp3c3_8150' => 'ppa', 'Pp3c4_14320' => 'ppa', 'Pp3c6_2560' => 'ppa', 'Pp3c9_16700' => 'ppa', 'PRCOL_00000234' => 'pco', 'PRCOL_00000235' => 'pco', 'PRCOL_00000777' => 'pco', 'PRCOL_00002344' => 'pco', 'PRCOL_00002372' => 'pco', 'PRCOL_00006120' => 'pco', 'Prupe.1G021400' => 'ppe', 'Prupe.1G021500' => 'ppe', 'Prupe.1G021600' => 'ppe', 'Prupe.1G021700' => 'ppe', 'Prupe.1G021800' => 'ppe', 'Prupe.5G145100' => 'ppe', 'Psat6g204040' => 'psa', 'Psat6g204800' => 'psa', 'Psat6g204920' => 'psa', 'Psat6g204960' => 'psa', 'Psat6g205080' => 'psa', 'PSO017G0271' => 'pso', 'PSO017G1276' => 'pso', 'PSO017G1429' => 'pso', 'PSO017G1861' => 'pso', 'PSO017G2787' => 'pso', 'PSO017G4466' => 'pso', 'PSO017G5118' => 'pso', 'PSO017G5420' => 'pso', 'PSO063G3678' => 'pso', 'PSO210G0546' => 'pso', 'PSO317G0001' => 'pso', 'PSO357G0512' => 'pso', 'PSO478G2682' => 'pso', 'PSO647G0001' => 'pso', 'PSO675G0001' => 'pso', 'PSO675G2699' => 'pso', 'PSO675G2849' => 'pso', 'PSO675G4991' => 'pso', 'PSO689G0001' => 'pso', 'QL06p000916' => 'qlo', 'QL06p000921' => 'qlo', 'QL06p001398' => 'qlo', 'QL06p001407' => 'qlo', 'QL06p002031' => 'qlo', 'RcHm_v2.0_Chr4g0387791' => 'rch', 'RcHm_v2.0_Chr4g0387801' => 'rch', 'RcHm_v2.0_Chr6g0286501' => 'rch', 'RcHm_v2.0_Chr6g0286511' => 'rch', 'RcHm_v2.0_Chr6g0286521' => 'rch', 'RcHm_v2.0_Chr6g0286531' => 'rch', 'RcHm_v2.0_Chr7g0189141' => 'rch', 'Rhsim02G0028700' => 'rsi', 'Rhsim02G0028800' => 'rsi', 'Rhsim02G0028900' => 'rsi', 'Rhsim02G0029000' => 'rsi', 'Rhsim02G0029100' => 'rsi', 'Rhsim02G0029200' => 'rsi', 'Rhsim02G0029300' => 'rsi', 'Rhsim02G0029400' => 'rsi', 'Rhsim02G0029500' => 'rsi', 'Rhsim02G0029600' => 'rsi', 'RhsimUnG0024000' => 'rsi', 'RhsimUnG0024100' => 'rsi', 'RhsimUnG0024200' => 'rsi', 'RhsimUnG0024300' => 'rsi', 'RhsimUnG0024400' => 'rsi', 'RhsimUnG0024500' => 'rsi', 'RhsimUnG0024700' => 'rsi', 'RhsimUnG0024800' => 'rsi', 'RhsimUnG0024900' => 'rsi', 'RhsimUnG0025100' => 'rsi', 'Sabra08G0120200' => 'sbr', 'Sabra08G0120300' => 'sbr', 'Sabra08G0120500' => 'sbr', 'Sabra08G0120600' => 'sbr', 'Sabra10G0158900' => 'sbr', 'SalBow2G3492' => 'sbo', 'Sc13g0004760' => 'sci', 'Sc13g0004770' => 'sci', 'Sed0003417' => 'sed', 'Sed0019750' => 'sed', 'SEGI_03419' => 'sgi', 'SEGI_05907' => 'sgi', 'SEGI_10682' => 'sgi', 'SEGI_13528' => 'sgi', 'SEGI_16081' => 'sgi', 'SEGI_19370' => 'sgi', 'SEGI_21015' => 'sgi', 'SEGI_21944' => 'sgi', 'SEGI_32906' => 'sgi', 'SEGI_33093' => 'sgi', 'SEGI_36110' => 'sgi', 'SEGI_40397' => 'sgi', 'SGA_v2.0_scaffold191G40426' => 'sas', 'SGA_v2.0_scaffold353G49717' => 'sas', 'SGA_v2.0_scaffold50G18550' => 'sas', 'SMO119G0173' => 'smo', 'SMO172G0002' => 'smo', 'Solyc09g082690.3' => 'sly', 'Solyc09g082700.2' => 'sly', 'Sopen09g031550' => 'spe', 'Sopen09g031560' => 'spe', 'Sp3g20540' => 'spa', 'Sp7g07580' => 'spa', 'TAR134G0002' => 'tar', 'TAR236G0001' => 'tar', 'TAR365G0892' => 'tar', 'TAR636G0166' => 'tar', 'TAR636G0646' => 'tar', 'TAR636G0869' => 'tar', 'TAR636G1317' => 'tar', 'TAR636G1744' => 'tar', 'TAR636G3358' => 'tar', 'TAR636G3436' => 'tar', 'THA.LOC104803047' => 'tha', 'Thecc.04G238900' => 'tca', 'Thhalv10021557m.g' => 'esa', 'Thhalv10026318m.g' => 'esa', 'Thhalv10026335m.g' => 'esa', 'TPR.G17433' => 'tpr', 'TPR.G18915' => 'tpr', 'TPR.G26125' => 'tpr', 'TWI09G0677' => 'twi', 'TWI73G0287' => 'twi', 'unitig_748.g8326' => 'ugi', 'vmacro15370' => 'vma', 'vmacro15371' => 'vma', 'vmacro15372' => 'vma', 'vmacro15373' => 'vma', 'vmacro15374' => 'vma', 'VMungo0720G2826' => 'vmu', 'Zm00001eb116960' => 'zma', 'Zm00001eb301260' => 'zma', 'Zm00001eb301270' => 'zma' ) $gf_id = 'HOM05D001460' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001460' ) $data_identifier = 'HOM05D001460' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 4, 'aag' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 2, 'aox' => (int) 2, 'arhy' => (int) 4, 'ath' => (int) 2, 'atr' => (int) 1, 'acertr' => (int) 10, 'cqu' => (int) 4, 'bca' => (int) 11, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 1, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 1, 'ccan' => (int) 1, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 1, 'col' => (int) 1, 'cpa' => (int) 1, 'cre' => (int) 7, 'csa' => (int) 1, 'camsi' => (int) 2, 'dca' => (int) 3, 'din' => (int) 2, 'dzi' => (int) 3, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 14, 'fve' => (int) 9, 'gma' => (int) 2, 'ghi' => (int) 4, 'gra' => (int) 2, 'vvi' => (int) 1, 'han' => (int) 13, 'cav' => (int) 1, 'hma' => (int) 2, 'sun' => (int) 2, 'lal' => (int) 2, 'lonja' => (int) 12, 'lja' => (int) 1, 'lsa' => (int) 7, 'mes' => (int) 1, 'mpo' => (int) 27, 'mbi' => (int) 1, 'mco' => (int) 8, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 1, 'egut' => (int) 1, 'ama' => (int) 1, 'nta' => (int) 4, 'nnu' => (int) 2, 'oeu' => (int) 3, 'osa' => (int) 4, 'pax' => (int) 9, 'pgr' => (int) 1, 'stu' => (int) 1, 'pvu' => (int) 1, 'ptr' => (int) 4, 'ppa' => (int) 22, 'pco' => (int) 6, 'ppe' => (int) 6, 'psa' => (int) 5, 'pso' => (int) 19, 'qlo' => (int) 5, 'rch' => (int) 7, 'rsi' => (int) 20, 'sbr' => (int) 5, 'sbo' => (int) 1, 'sci' => (int) 2, 'sed' => (int) 2, 'sgi' => (int) 12, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 2, 'tar' => (int) 10, 'tha' => (int) 1, 'tca' => (int) 1, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 2, 'ugi' => (int) 1, 'vma' => (int) 5, 'vmu' => (int) 1, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb301270' $species_info = array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ) $local_species = 'spa' $disabled = '' $selected = '' $num_hits = (int) 0include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001460', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '433', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p22980' => 'bna', 'A01p32340' => 'bna', 'A03p42970' => 'bna', 'A05p25880' => 'bna', 'Aa31LG8G9320' => 'aar', 'Aa31LG8G9330' => 'aar', 'Aa31LG8G9340' => 'aar', 'Aa31sc221G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1034' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1528' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.829' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2222' => 'aag', 'Ah.12g058830' => 'amhyb', 'Ah.12g058840' => 'amhyb', 'AL3G37160' => 'aly', 'AL7G41310' => 'aly', 'Aqoxy5G00395' => 'aox', 'Aqoxy5G00396' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0C8NZA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5185HY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JZ1PRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MD3LS0' => 'arhy', 'AT3G22840' => 'ath', 'AT4G14690' => 'ath', 'ATR0665G054' => 'atr', 'Atru.chr4.2344' => 'acertr', 'Atru.chr4.2346' => 'acertr', 'Atru.chr4.2347' => 'acertr', 'Atru.chr4.2348' => 'acertr', 'Atru.chr4.2355' => 'acertr', 'Atru.chr4.2356' => 'acertr', 'Atru.chr4.2358' => 'acertr', 'Atru.chr4.2359' => 'acertr', 'Atru.chr4.2360' => 'acertr', 'Atru.chr4.2361' => 'acertr', 'AUR62030476' => 'cqu', 'AUR62030478' => 'cqu', 'AUR62030819' => 'cqu', 'AUR62030820' => 'cqu', 'BcaB03g14648' => 'bca', 'BcaB04g20492' => 'bca', 'BcaB06g26399' => 'bca', 'BcaC01g03416' => 'bca', 'BcaC01g03419' => 'bca', 'BcaC01g03421' => 'bca', 'BcaC01g03424' => 'bca', 'BcaC05g28012' => 'bca', 'BcaC09g49212' => 'bca', 'BcaC09g50140' => 'bca', 'BcaNung00346' => 'bca', 'BolC1t02785H' => 'bol', 'BolC1t04095H' => 'bol', 'BolC3t17545H' => 'bol', 'BolC5t32769H' => 'bol', 'BraA01t02211Z' => 'bra', 'BraA01t03359Z' => 'bra', 'BraA03t13441Z' => 'bra', 'BraA05t21476Z' => 'bra', 'C01p28420' => 'bna', 'C01p41350' => 'bna', 'C03p52750' => 'bna', 'C03p52780' => 'bna', 'C05p40270' => 'bna', 'CAN.G1437.9' => 'can', 'CANSAT78G0035' => 'cansat', 'CANSAT78G1036' => 'cansat', 'CANSAT78G2272' => 'cansat', 'CANSAT78G2478' => 'cansat', 'CARHR098700' => 'chi', 'CARHR221120' => 'chi', 'CARHR221150' => 'chi', 'Carub.0003s2297' => 'cru', 'Carub.0007s2749' => 'cru', 'Carub.0007s2750' => 'cru', 'Carub.0007s2751' => 'cru', 'Ca_10849_v3' => 'car', 'Cc03_g04300' => 'ccan', 'CDE02G3648' => 'cde', 'CDE05G0060' => 'cde', 'CDE05G0692' => 'cde', 'CDE05G2285' => 'cde', 'CDE05G2884' => 'cde', 'CDE05G3072' => 'cde', 'Cfa008439' => 'cfa', 'Cfa008441' => 'cfa', 'Cfa008443' => 'cfa', 'Cfa008448' => 'cfa', 'Ciclev10005974m.g' => 'ccl', 'Ciclev10006006m.g' => 'ccl', 'Ciclev10006775m.g' => 'ccl', 'CiPaw.02G120400' => 'cil', 'CiPaw.02G120500' => 'cil', 'CiPaw.02G120600' => 'cil', 'ClCG05G004850' => 'cla', 'COL.COLO4_21566' => 'col', 'Cpa.g.sc44.124' => 'cpa', 'Cre07.g320400' => 'cre', 'Cre07.g320450' => 'cre', 'Cre08.g384650' => 'cre', 'Cre09.g393173' => 'cre', 'Cre09.g394325' => 'cre', 'Cre14.g626750' => 'cre', 'Cre16.g679250' => 'cre', 'CsaV3_3G012890' => 'csa', 'CSS0010865' => 'camsi', 'CSS0044338' => 'camsi', 'DCAR_002366' => 'dca', 'DCAR_030687' => 'dca', 'DCAR_030688' => 'dca', 'Dinv14047' => 'din', 'Dinv14048' => 'din', 'Duzib151G0105' => 'dzi', 'Duzib151G0114' => 'dzi', 'Duzib212G1029' => 'dzi', 'ECA232G3536' => 'eca', 'ECA240G0786' => 'eca', 'ECA240G1802' => 'eca', 'ECA240G3760' => 'eca', 'ECA240G3920' => 'eca', 'EL10Ac5g12536' => 'bvu', 'EL10Ac5g12537' => 'bvu', 'EL10Ac5g12538' => 'bvu', 'Eucgr.B01004' => 'egr', 'Eucgr.B01006' => 'egr', 'Eucgr.B01007' => 'egr', 'Eucgr.B01008' => 'egr', 'Eucgr.B01895' => 'egr', 'Eucgr.B01896' => 'egr', 'FAN04G1456' => 'fan', 'FAN08G1769' => 'fan', 'FAN08G2160' => 'fan', 'FAN13G2403' => 'fan', 'FAN13G3303' => 'fan', 'FAN15G2435' => 'fan', 'FAN17G0672' => 'fan', 'FAN17G2441' => 'fan', 'FAN18G1024' => 'fan', 'FAN22G1458' => 'fan', 'FAN24G0037' => 'fan', 'FAN24G0429' => 'fan', 'FAN24G2387' => 'fan', 'FAN27G2746' => 'fan', 'FvH4_2g20400' => 'fve', 'FvH4_2g20420' => 'fve', 'FvH4_2g20430' => 'fve', 'FvH4_4g01270' => 'fve', 'FvH4_4g01290' => 'fve', 'FvH4_4g01300' => 'fve', 'FvH4_4g01310' => 'fve', 'FvH4_4g01330' => 'fve', 'FvH4_5g09070' => 'fve', 'Glyma.10G243800' => 'gma', 'Glyma.20G150600' => 'gma', 'Gohir.A09G219200' => 'ghi', 'Gohir.A09G219300' => 'ghi', 'Gohir.D09G221400' => 'ghi', 'Gohir.D09G221500' => 'ghi', 'Gorai.006G242600' => 'gra', 'Gorai.006G242700' => 'gra', 'GSVIVG01018044001' => 'vvi', 'HanXRQChr03g0083821' => 'han', 'HanXRQChr03g0083841' => 'han', 'HanXRQChr03g0083881' => 'han', 'HanXRQChr03g0083901' => 'han', 'HanXRQChr03g0083921' => 'han', 'HanXRQChr03g0085331' => 'han', 'HanXRQChr03g0085361' => 'han', 'HanXRQChr03g0085411' => 'han', 'HanXRQChr03g0085421' => 'han', 'HanXRQChr03g0085431' => 'han', 'HanXRQChr08g0221991' => 'han', 'HanXRQChr11g0336061' => 'han', 'HanXRQChr11g0336411' => 'han', 'Haze_11234' => 'cav', 'Hma1.2p1_0549F.1_g177010' => 'hma', 'Hma1.2p1_0602F.1_g187630' => 'hma', 'Hund14876' => 'sun', 'Hund14879' => 'sun', 'Lalb_Chr06g0160741' => 'lal', 'Lalb_Chr21g0304781' => 'lal', 'Lj3A726G19' => 'lonja', 'Lj3A726T23' => 'lonja', 'Lj3A726T24' => 'lonja', 'Lj3A726T25' => 'lonja', 'Lj3A727T17' => 'lonja', 'Lj3C726T0' => 'lonja', 'Lj3C726T2' => 'lonja', 'Lj3P725T35' => 'lonja', 'Lj3P727T10' => 'lonja', 'Lj3P727T12' => 'lonja', 'Lj3P727T14' => 'lonja', 'Lj5g0023109' => 'lja', 'Lj6P646T44' => 'lonja', 'Lsat_1_v5_gn_6_75760' => 'lsa', 'Lsat_1_v5_gn_6_75800' => 'lsa', 'Lsat_1_v5_gn_6_75900' => 'lsa', 'Lsat_1_v5_gn_6_76240' => 'lsa', 'Lsat_1_v5_gn_6_76441' => 'lsa', 'Lsat_1_v5_gn_6_76700' => 'lsa', 'Lsat_1_v5_gn_6_76760' => 'lsa', 'Manes.15G033100' => 'mes', 'Mapoly0004s0074' => 'mpo', 'Mapoly0004s0075' => 'mpo', 'Mapoly0004s0163' => 'mpo', 'Mapoly0004s0164' => 'mpo', 'Mapoly0021s0018' => 'mpo', 'Mapoly0041s0136' => 'mpo', 'Mapoly0041s0137' => 'mpo', 'Mapoly0041s0138' => 'mpo', 'Mapoly0041s0139' => 'mpo', 'Mapoly0041s0141' => 'mpo', 'Mapoly0041s0142' => 'mpo', 'Mapoly0041s0143' => 'mpo', 'Mapoly0041s0144' => 'mpo', 'Mapoly0041s0145' => 'mpo', 'Mapoly0047s0106' => 'mpo', 'Mapoly0047s0108' => 'mpo', 'Mapoly0050s0051' => 'mpo', 'Mapoly0050s0052' => 'mpo', 'Mapoly0050s0053' => 'mpo', 'Mapoly0058s0013' => 'mpo', 'Mapoly0091s0078' => 'mpo', 'Mapoly0091s0079' => 'mpo', 'Mapoly0091s0080' => 'mpo', 'Mapoly0091s0081' => 'mpo', 'Mapoly0278s0004' => 'mpo', 'Mapoly0278s0005' => 'mpo', 'Mapoly0278s0006' => 'mpo', 'MBI11_g30648_MAGBIO' => 'mbi', 'MCO03G194' => 'mco', 'MCO03G590' => 'mco', 'MCO07G312' => 'mco', 'MCO10G318' => 'mco', 'MCO12G244' => 'mco', 'MCO13G148' => 'mco', 'MCO13G194' => 'mco', 'MCO16G238' => 'mco', 'MD06G1134100' => 'mdo', 'MD13G1200100' => 'mdo', 'MD13G1200300' => 'mdo', 'MD13G1200600' => 'mdo', 'MD14G1150400' => 'mdo', 'MD16G1200000' => 'mdo', 'Medtr1g102570' => 'mtr', 'Medtr1g102780' => 'mtr', 'Medtr1g102800' => 'mtr', 'Medtr1g102810' => 'mtr', 'Medtr1g102830' => 'mtr', 'MELO3C006499.2' => 'cme', 'Migut.G00385' => 'egut', 'MSTRG.4063' => 'ama', 'Nitab4.5_0000090g0260' => 'nta', 'Nitab4.5_0000977g0030' => 'nta', 'Nitab4.5_0002541g0040' => 'nta', 'Nitab4.5_0007068g0040' => 'nta', 'Nn005s41408' => 'nnu', 'Nn005s41410' => 'nnu', 'Oeu010310.1' => 'oeu', 'Oeu010311.1' => 'oeu', 'Oeu043472.1' => 'oeu', 'Os01g0246400' => 'osa', 'Os04g0267950' => 'osa', 'Os07g0178700' => 'osa', 'Os07g0178800' => 'osa', 'Peaxi162Scf00316g00046' => 'pax', 'Peaxi162Scf00316g00049' => 'pax', 'Peaxi162Scf00316g00059' => 'pax', 'Peaxi162Scf00316g00328' => 'pax', 'Peaxi162Scf00316g00329' => 'pax', 'Peaxi162Scf00316g00411' => 'pax', 'Peaxi162Scf00316g00521' => 'pax', 'Peaxi162Scf00492g00068' => 'pax', 'Peaxi162Scf35631g00002' => 'pax', 'PGR142G3720' => 'pgr', 'PGSC0003DMG400006442' => 'stu', 'Phvul.007G062000' => 'pvu', 'Potri.008G157750' => 'ptr', 'Potri.008G157900' => 'ptr', 'Potri.008G158000' => 'ptr', 'Potri.008G158200' => 'ptr', 'Pp3c11_7280' => 'ppa', 'Pp3c11_7980' => 'ppa', 'Pp3c12_19450' => 'ppa', 'Pp3c14_1480' => 'ppa', 'Pp3c14_1501' => 'ppa', 'Pp3c16_4900' => 'ppa', 'Pp3c16_5010' => 'ppa', 'Pp3c16_5060' => 'ppa', 'Pp3c19_18250' => 'ppa', 'Pp3c23_8530' => 'ppa', 'Pp3c23_8550' => 'ppa', 'Pp3c24_9670' => 'ppa', 'Pp3c2_21390' => 'ppa', 'Pp3c2_31380' => 'ppa', 'Pp3c3_16620' => 'ppa', 'Pp3c3_8090' => 'ppa', 'Pp3c3_8110' => 'ppa', 'Pp3c3_8130' => 'ppa', 'Pp3c3_8150' => 'ppa', 'Pp3c4_14320' => 'ppa', 'Pp3c6_2560' => 'ppa', 'Pp3c9_16700' => 'ppa', 'PRCOL_00000234' => 'pco', 'PRCOL_00000235' => 'pco', 'PRCOL_00000777' => 'pco', 'PRCOL_00002344' => 'pco', 'PRCOL_00002372' => 'pco', 'PRCOL_00006120' => 'pco', 'Prupe.1G021400' => 'ppe', 'Prupe.1G021500' => 'ppe', 'Prupe.1G021600' => 'ppe', 'Prupe.1G021700' => 'ppe', 'Prupe.1G021800' => 'ppe', 'Prupe.5G145100' => 'ppe', 'Psat6g204040' => 'psa', 'Psat6g204800' => 'psa', 'Psat6g204920' => 'psa', 'Psat6g204960' => 'psa', 'Psat6g205080' => 'psa', 'PSO017G0271' => 'pso', 'PSO017G1276' => 'pso', 'PSO017G1429' => 'pso', 'PSO017G1861' => 'pso', 'PSO017G2787' => 'pso', 'PSO017G4466' => 'pso', 'PSO017G5118' => 'pso', 'PSO017G5420' => 'pso', 'PSO063G3678' => 'pso', 'PSO210G0546' => 'pso', 'PSO317G0001' => 'pso', 'PSO357G0512' => 'pso', 'PSO478G2682' => 'pso', 'PSO647G0001' => 'pso', 'PSO675G0001' => 'pso', 'PSO675G2699' => 'pso', 'PSO675G2849' => 'pso', 'PSO675G4991' => 'pso', 'PSO689G0001' => 'pso', 'QL06p000916' => 'qlo', 'QL06p000921' => 'qlo', 'QL06p001398' => 'qlo', 'QL06p001407' => 'qlo', 'QL06p002031' => 'qlo', 'RcHm_v2.0_Chr4g0387791' => 'rch', 'RcHm_v2.0_Chr4g0387801' => 'rch', 'RcHm_v2.0_Chr6g0286501' => 'rch', 'RcHm_v2.0_Chr6g0286511' => 'rch', 'RcHm_v2.0_Chr6g0286521' => 'rch', 'RcHm_v2.0_Chr6g0286531' => 'rch', 'RcHm_v2.0_Chr7g0189141' => 'rch', 'Rhsim02G0028700' => 'rsi', 'Rhsim02G0028800' => 'rsi', 'Rhsim02G0028900' => 'rsi', 'Rhsim02G0029000' => 'rsi', 'Rhsim02G0029100' => 'rsi', 'Rhsim02G0029200' => 'rsi', 'Rhsim02G0029300' => 'rsi', 'Rhsim02G0029400' => 'rsi', 'Rhsim02G0029500' => 'rsi', 'Rhsim02G0029600' => 'rsi', 'RhsimUnG0024000' => 'rsi', 'RhsimUnG0024100' => 'rsi', 'RhsimUnG0024200' => 'rsi', 'RhsimUnG0024300' => 'rsi', 'RhsimUnG0024400' => 'rsi', 'RhsimUnG0024500' => 'rsi', 'RhsimUnG0024700' => 'rsi', 'RhsimUnG0024800' => 'rsi', 'RhsimUnG0024900' => 'rsi', 'RhsimUnG0025100' => 'rsi', 'Sabra08G0120200' => 'sbr', 'Sabra08G0120300' => 'sbr', 'Sabra08G0120500' => 'sbr', 'Sabra08G0120600' => 'sbr', 'Sabra10G0158900' => 'sbr', 'SalBow2G3492' => 'sbo', 'Sc13g0004760' => 'sci', 'Sc13g0004770' => 'sci', 'Sed0003417' => 'sed', 'Sed0019750' => 'sed', 'SEGI_03419' => 'sgi', 'SEGI_05907' => 'sgi', 'SEGI_10682' => 'sgi', 'SEGI_13528' => 'sgi', 'SEGI_16081' => 'sgi', 'SEGI_19370' => 'sgi', 'SEGI_21015' => 'sgi', 'SEGI_21944' => 'sgi', 'SEGI_32906' => 'sgi', 'SEGI_33093' => 'sgi', 'SEGI_36110' => 'sgi', 'SEGI_40397' => 'sgi', 'SGA_v2.0_scaffold191G40426' => 'sas', 'SGA_v2.0_scaffold353G49717' => 'sas', 'SGA_v2.0_scaffold50G18550' => 'sas', 'SMO119G0173' => 'smo', 'SMO172G0002' => 'smo', 'Solyc09g082690.3' => 'sly', 'Solyc09g082700.2' => 'sly', 'Sopen09g031550' => 'spe', 'Sopen09g031560' => 'spe', 'Sp3g20540' => 'spa', 'Sp7g07580' => 'spa', 'TAR134G0002' => 'tar', 'TAR236G0001' => 'tar', 'TAR365G0892' => 'tar', 'TAR636G0166' => 'tar', 'TAR636G0646' => 'tar', 'TAR636G0869' => 'tar', 'TAR636G1317' => 'tar', 'TAR636G1744' => 'tar', 'TAR636G3358' => 'tar', 'TAR636G3436' => 'tar', 'THA.LOC104803047' => 'tha', 'Thecc.04G238900' => 'tca', 'Thhalv10021557m.g' => 'esa', 'Thhalv10026318m.g' => 'esa', 'Thhalv10026335m.g' => 'esa', 'TPR.G17433' => 'tpr', 'TPR.G18915' => 'tpr', 'TPR.G26125' => 'tpr', 'TWI09G0677' => 'twi', 'TWI73G0287' => 'twi', 'unitig_748.g8326' => 'ugi', 'vmacro15370' => 'vma', 'vmacro15371' => 'vma', 'vmacro15372' => 'vma', 'vmacro15373' => 'vma', 'vmacro15374' => 'vma', 'VMungo0720G2826' => 'vmu', 'Zm00001eb116960' => 'zma', 'Zm00001eb301260' => 'zma', 'Zm00001eb301270' => 'zma' ), 'gf_id' => 'HOM05D001460', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001460' ), 'data_identifier' => 'HOM05D001460', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001460', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '433', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p22980' => 'bna', 'A01p32340' => 'bna', 'A03p42970' => 'bna', 'A05p25880' => 'bna', 'Aa31LG8G9320' => 'aar', 'Aa31LG8G9330' => 'aar', 'Aa31LG8G9340' => 'aar', 'Aa31sc221G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1034' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1528' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.829' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2222' => 'aag', 'Ah.12g058830' => 'amhyb', 'Ah.12g058840' => 'amhyb', 'AL3G37160' => 'aly', 'AL7G41310' => 'aly', 'Aqoxy5G00395' => 'aox', 'Aqoxy5G00396' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0C8NZA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5185HY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JZ1PRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MD3LS0' => 'arhy', 'AT3G22840' => 'ath', 'AT4G14690' => 'ath', 'ATR0665G054' => 'atr', 'Atru.chr4.2344' => 'acertr', 'Atru.chr4.2346' => 'acertr', 'Atru.chr4.2347' => 'acertr', 'Atru.chr4.2348' => 'acertr', 'Atru.chr4.2355' => 'acertr', 'Atru.chr4.2356' => 'acertr', 'Atru.chr4.2358' => 'acertr', 'Atru.chr4.2359' => 'acertr', 'Atru.chr4.2360' => 'acertr', 'Atru.chr4.2361' => 'acertr', 'AUR62030476' => 'cqu', 'AUR62030478' => 'cqu', 'AUR62030819' => 'cqu', 'AUR62030820' => 'cqu', 'BcaB03g14648' => 'bca', 'BcaB04g20492' => 'bca', 'BcaB06g26399' => 'bca', 'BcaC01g03416' => 'bca', 'BcaC01g03419' => 'bca', 'BcaC01g03421' => 'bca', 'BcaC01g03424' => 'bca', 'BcaC05g28012' => 'bca', 'BcaC09g49212' => 'bca', 'BcaC09g50140' => 'bca', 'BcaNung00346' => 'bca', 'BolC1t02785H' => 'bol', 'BolC1t04095H' => 'bol', 'BolC3t17545H' => 'bol', 'BolC5t32769H' => 'bol', 'BraA01t02211Z' => 'bra', 'BraA01t03359Z' => 'bra', 'BraA03t13441Z' => 'bra', 'BraA05t21476Z' => 'bra', 'C01p28420' => 'bna', 'C01p41350' => 'bna', 'C03p52750' => 'bna', 'C03p52780' => 'bna', 'C05p40270' => 'bna', 'CAN.G1437.9' => 'can', 'CANSAT78G0035' => 'cansat', 'CANSAT78G1036' => 'cansat', 'CANSAT78G2272' => 'cansat', 'CANSAT78G2478' => 'cansat', 'CARHR098700' => 'chi', 'CARHR221120' => 'chi', 'CARHR221150' => 'chi', 'Carub.0003s2297' => 'cru', 'Carub.0007s2749' => 'cru', 'Carub.0007s2750' => 'cru', 'Carub.0007s2751' => 'cru', 'Ca_10849_v3' => 'car', 'Cc03_g04300' => 'ccan', 'CDE02G3648' => 'cde', 'CDE05G0060' => 'cde', 'CDE05G0692' => 'cde', 'CDE05G2285' => 'cde', 'CDE05G2884' => 'cde', 'CDE05G3072' => 'cde', 'Cfa008439' => 'cfa', 'Cfa008441' => 'cfa', 'Cfa008443' => 'cfa', 'Cfa008448' => 'cfa', 'Ciclev10005974m.g' => 'ccl', 'Ciclev10006006m.g' => 'ccl', 'Ciclev10006775m.g' => 'ccl', 'CiPaw.02G120400' => 'cil', 'CiPaw.02G120500' => 'cil', 'CiPaw.02G120600' => 'cil', 'ClCG05G004850' => 'cla', 'COL.COLO4_21566' => 'col', 'Cpa.g.sc44.124' => 'cpa', 'Cre07.g320400' => 'cre', 'Cre07.g320450' => 'cre', 'Cre08.g384650' => 'cre', 'Cre09.g393173' => 'cre', 'Cre09.g394325' => 'cre', 'Cre14.g626750' => 'cre', 'Cre16.g679250' => 'cre', 'CsaV3_3G012890' => 'csa', 'CSS0010865' => 'camsi', 'CSS0044338' => 'camsi', 'DCAR_002366' => 'dca', 'DCAR_030687' => 'dca', 'DCAR_030688' => 'dca', 'Dinv14047' => 'din', 'Dinv14048' => 'din', 'Duzib151G0105' => 'dzi', 'Duzib151G0114' => 'dzi', 'Duzib212G1029' => 'dzi', 'ECA232G3536' => 'eca', 'ECA240G0786' => 'eca', 'ECA240G1802' => 'eca', 'ECA240G3760' => 'eca', 'ECA240G3920' => 'eca', 'EL10Ac5g12536' => 'bvu', 'EL10Ac5g12537' => 'bvu', 'EL10Ac5g12538' => 'bvu', 'Eucgr.B01004' => 'egr', 'Eucgr.B01006' => 'egr', 'Eucgr.B01007' => 'egr', 'Eucgr.B01008' => 'egr', 'Eucgr.B01895' => 'egr', 'Eucgr.B01896' => 'egr', 'FAN04G1456' => 'fan', 'FAN08G1769' => 'fan', 'FAN08G2160' => 'fan', 'FAN13G2403' => 'fan', 'FAN13G3303' => 'fan', 'FAN15G2435' => 'fan', 'FAN17G0672' => 'fan', 'FAN17G2441' => 'fan', 'FAN18G1024' => 'fan', 'FAN22G1458' => 'fan', 'FAN24G0037' => 'fan', 'FAN24G0429' => 'fan', 'FAN24G2387' => 'fan', 'FAN27G2746' => 'fan', 'FvH4_2g20400' => 'fve', 'FvH4_2g20420' => 'fve', 'FvH4_2g20430' => 'fve', 'FvH4_4g01270' => 'fve', 'FvH4_4g01290' => 'fve', 'FvH4_4g01300' => 'fve', 'FvH4_4g01310' => 'fve', 'FvH4_4g01330' => 'fve', 'FvH4_5g09070' => 'fve', 'Glyma.10G243800' => 'gma', 'Glyma.20G150600' => 'gma', 'Gohir.A09G219200' => 'ghi', 'Gohir.A09G219300' => 'ghi', 'Gohir.D09G221400' => 'ghi', 'Gohir.D09G221500' => 'ghi', 'Gorai.006G242600' => 'gra', 'Gorai.006G242700' => 'gra', 'GSVIVG01018044001' => 'vvi', 'HanXRQChr03g0083821' => 'han', 'HanXRQChr03g0083841' => 'han', 'HanXRQChr03g0083881' => 'han', 'HanXRQChr03g0083901' => 'han', 'HanXRQChr03g0083921' => 'han', 'HanXRQChr03g0085331' => 'han', 'HanXRQChr03g0085361' => 'han', 'HanXRQChr03g0085411' => 'han', 'HanXRQChr03g0085421' => 'han', 'HanXRQChr03g0085431' => 'han', 'HanXRQChr08g0221991' => 'han', 'HanXRQChr11g0336061' => 'han', 'HanXRQChr11g0336411' => 'han', 'Haze_11234' => 'cav', 'Hma1.2p1_0549F.1_g177010' => 'hma', 'Hma1.2p1_0602F.1_g187630' => 'hma', 'Hund14876' => 'sun', 'Hund14879' => 'sun', 'Lalb_Chr06g0160741' => 'lal', 'Lalb_Chr21g0304781' => 'lal', 'Lj3A726G19' => 'lonja', 'Lj3A726T23' => 'lonja', 'Lj3A726T24' => 'lonja', 'Lj3A726T25' => 'lonja', 'Lj3A727T17' => 'lonja', 'Lj3C726T0' => 'lonja', 'Lj3C726T2' => 'lonja', 'Lj3P725T35' => 'lonja', 'Lj3P727T10' => 'lonja', 'Lj3P727T12' => 'lonja', 'Lj3P727T14' => 'lonja', 'Lj5g0023109' => 'lja', 'Lj6P646T44' => 'lonja', 'Lsat_1_v5_gn_6_75760' => 'lsa', 'Lsat_1_v5_gn_6_75800' => 'lsa', 'Lsat_1_v5_gn_6_75900' => 'lsa', 'Lsat_1_v5_gn_6_76240' => 'lsa', 'Lsat_1_v5_gn_6_76441' => 'lsa', 'Lsat_1_v5_gn_6_76700' => 'lsa', 'Lsat_1_v5_gn_6_76760' => 'lsa', 'Manes.15G033100' => 'mes', 'Mapoly0004s0074' => 'mpo', 'Mapoly0004s0075' => 'mpo', 'Mapoly0004s0163' => 'mpo', 'Mapoly0004s0164' => 'mpo', 'Mapoly0021s0018' => 'mpo', 'Mapoly0041s0136' => 'mpo', 'Mapoly0041s0137' => 'mpo', 'Mapoly0041s0138' => 'mpo', 'Mapoly0041s0139' => 'mpo', 'Mapoly0041s0141' => 'mpo', 'Mapoly0041s0142' => 'mpo', 'Mapoly0041s0143' => 'mpo', 'Mapoly0041s0144' => 'mpo', 'Mapoly0041s0145' => 'mpo', 'Mapoly0047s0106' => 'mpo', 'Mapoly0047s0108' => 'mpo', 'Mapoly0050s0051' => 'mpo', 'Mapoly0050s0052' => 'mpo', 'Mapoly0050s0053' => 'mpo', 'Mapoly0058s0013' => 'mpo', 'Mapoly0091s0078' => 'mpo', 'Mapoly0091s0079' => 'mpo', 'Mapoly0091s0080' => 'mpo', 'Mapoly0091s0081' => 'mpo', 'Mapoly0278s0004' => 'mpo', 'Mapoly0278s0005' => 'mpo', 'Mapoly0278s0006' => 'mpo', 'MBI11_g30648_MAGBIO' => 'mbi', 'MCO03G194' => 'mco', 'MCO03G590' => 'mco', 'MCO07G312' => 'mco', 'MCO10G318' => 'mco', 'MCO12G244' => 'mco', 'MCO13G148' => 'mco', 'MCO13G194' => 'mco', 'MCO16G238' => 'mco', 'MD06G1134100' => 'mdo', 'MD13G1200100' => 'mdo', 'MD13G1200300' => 'mdo', 'MD13G1200600' => 'mdo', 'MD14G1150400' => 'mdo', 'MD16G1200000' => 'mdo', 'Medtr1g102570' => 'mtr', 'Medtr1g102780' => 'mtr', 'Medtr1g102800' => 'mtr', 'Medtr1g102810' => 'mtr', 'Medtr1g102830' => 'mtr', 'MELO3C006499.2' => 'cme', 'Migut.G00385' => 'egut', 'MSTRG.4063' => 'ama', 'Nitab4.5_0000090g0260' => 'nta', 'Nitab4.5_0000977g0030' => 'nta', 'Nitab4.5_0002541g0040' => 'nta', 'Nitab4.5_0007068g0040' => 'nta', 'Nn005s41408' => 'nnu', 'Nn005s41410' => 'nnu', 'Oeu010310.1' => 'oeu', 'Oeu010311.1' => 'oeu', 'Oeu043472.1' => 'oeu', 'Os01g0246400' => 'osa', 'Os04g0267950' => 'osa', 'Os07g0178700' => 'osa', 'Os07g0178800' => 'osa', 'Peaxi162Scf00316g00046' => 'pax', 'Peaxi162Scf00316g00049' => 'pax', 'Peaxi162Scf00316g00059' => 'pax', 'Peaxi162Scf00316g00328' => 'pax', 'Peaxi162Scf00316g00329' => 'pax', 'Peaxi162Scf00316g00411' => 'pax', 'Peaxi162Scf00316g00521' => 'pax', 'Peaxi162Scf00492g00068' => 'pax', 'Peaxi162Scf35631g00002' => 'pax', 'PGR142G3720' => 'pgr', 'PGSC0003DMG400006442' => 'stu', 'Phvul.007G062000' => 'pvu', 'Potri.008G157750' => 'ptr', 'Potri.008G157900' => 'ptr', 'Potri.008G158000' => 'ptr', 'Potri.008G158200' => 'ptr', 'Pp3c11_7280' => 'ppa', 'Pp3c11_7980' => 'ppa', 'Pp3c12_19450' => 'ppa', 'Pp3c14_1480' => 'ppa', 'Pp3c14_1501' => 'ppa', 'Pp3c16_4900' => 'ppa', 'Pp3c16_5010' => 'ppa', 'Pp3c16_5060' => 'ppa', 'Pp3c19_18250' => 'ppa', 'Pp3c23_8530' => 'ppa', 'Pp3c23_8550' => 'ppa', 'Pp3c24_9670' => 'ppa', 'Pp3c2_21390' => 'ppa', 'Pp3c2_31380' => 'ppa', 'Pp3c3_16620' => 'ppa', 'Pp3c3_8090' => 'ppa', 'Pp3c3_8110' => 'ppa', 'Pp3c3_8130' => 'ppa', 'Pp3c3_8150' => 'ppa', 'Pp3c4_14320' => 'ppa', 'Pp3c6_2560' => 'ppa', 'Pp3c9_16700' => 'ppa', 'PRCOL_00000234' => 'pco', 'PRCOL_00000235' => 'pco', 'PRCOL_00000777' => 'pco', 'PRCOL_00002344' => 'pco', 'PRCOL_00002372' => 'pco', 'PRCOL_00006120' => 'pco', 'Prupe.1G021400' => 'ppe', 'Prupe.1G021500' => 'ppe', 'Prupe.1G021600' => 'ppe', 'Prupe.1G021700' => 'ppe', 'Prupe.1G021800' => 'ppe', 'Prupe.5G145100' => 'ppe', 'Psat6g204040' => 'psa', 'Psat6g204800' => 'psa', 'Psat6g204920' => 'psa', 'Psat6g204960' => 'psa', 'Psat6g205080' => 'psa', 'PSO017G0271' => 'pso', 'PSO017G1276' => 'pso', 'PSO017G1429' => 'pso', 'PSO017G1861' => 'pso', 'PSO017G2787' => 'pso', 'PSO017G4466' => 'pso', 'PSO017G5118' => 'pso', 'PSO017G5420' => 'pso', 'PSO063G3678' => 'pso', 'PSO210G0546' => 'pso', 'PSO317G0001' => 'pso', 'PSO357G0512' => 'pso', 'PSO478G2682' => 'pso', 'PSO647G0001' => 'pso', 'PSO675G0001' => 'pso', 'PSO675G2699' => 'pso', 'PSO675G2849' => 'pso', 'PSO675G4991' => 'pso', 'PSO689G0001' => 'pso', 'QL06p000916' => 'qlo', 'QL06p000921' => 'qlo', 'QL06p001398' => 'qlo', 'QL06p001407' => 'qlo', 'QL06p002031' => 'qlo', 'RcHm_v2.0_Chr4g0387791' => 'rch', 'RcHm_v2.0_Chr4g0387801' => 'rch', 'RcHm_v2.0_Chr6g0286501' => 'rch', 'RcHm_v2.0_Chr6g0286511' => 'rch', 'RcHm_v2.0_Chr6g0286521' => 'rch', 'RcHm_v2.0_Chr6g0286531' => 'rch', 'RcHm_v2.0_Chr7g0189141' => 'rch', 'Rhsim02G0028700' => 'rsi', 'Rhsim02G0028800' => 'rsi', 'Rhsim02G0028900' => 'rsi', 'Rhsim02G0029000' => 'rsi', 'Rhsim02G0029100' => 'rsi', 'Rhsim02G0029200' => 'rsi', 'Rhsim02G0029300' => 'rsi', 'Rhsim02G0029400' => 'rsi', 'Rhsim02G0029500' => 'rsi', 'Rhsim02G0029600' => 'rsi', 'RhsimUnG0024000' => 'rsi', 'RhsimUnG0024100' => 'rsi', 'RhsimUnG0024200' => 'rsi', 'RhsimUnG0024300' => 'rsi', 'RhsimUnG0024400' => 'rsi', 'RhsimUnG0024500' => 'rsi', 'RhsimUnG0024700' => 'rsi', 'RhsimUnG0024800' => 'rsi', 'RhsimUnG0024900' => 'rsi', 'RhsimUnG0025100' => 'rsi', 'Sabra08G0120200' => 'sbr', 'Sabra08G0120300' => 'sbr', 'Sabra08G0120500' => 'sbr', 'Sabra08G0120600' => 'sbr', 'Sabra10G0158900' => 'sbr', 'SalBow2G3492' => 'sbo', 'Sc13g0004760' => 'sci', 'Sc13g0004770' => 'sci', 'Sed0003417' => 'sed', 'Sed0019750' => 'sed', 'SEGI_03419' => 'sgi', 'SEGI_05907' => 'sgi', 'SEGI_10682' => 'sgi', 'SEGI_13528' => 'sgi', 'SEGI_16081' => 'sgi', 'SEGI_19370' => 'sgi', 'SEGI_21015' => 'sgi', 'SEGI_21944' => 'sgi', 'SEGI_32906' => 'sgi', 'SEGI_33093' => 'sgi', 'SEGI_36110' => 'sgi', 'SEGI_40397' => 'sgi', 'SGA_v2.0_scaffold191G40426' => 'sas', 'SGA_v2.0_scaffold353G49717' => 'sas', 'SGA_v2.0_scaffold50G18550' => 'sas', 'SMO119G0173' => 'smo', 'SMO172G0002' => 'smo', 'Solyc09g082690.3' => 'sly', 'Solyc09g082700.2' => 'sly', 'Sopen09g031550' => 'spe', 'Sopen09g031560' => 'spe', 'Sp3g20540' => 'spa', 'Sp7g07580' => 'spa', 'TAR134G0002' => 'tar', 'TAR236G0001' => 'tar', 'TAR365G0892' => 'tar', 'TAR636G0166' => 'tar', 'TAR636G0646' => 'tar', 'TAR636G0869' => 'tar', 'TAR636G1317' => 'tar', 'TAR636G1744' => 'tar', 'TAR636G3358' => 'tar', 'TAR636G3436' => 'tar', 'THA.LOC104803047' => 'tha', 'Thecc.04G238900' => 'tca', 'Thhalv10021557m.g' => 'esa', 'Thhalv10026318m.g' => 'esa', 'Thhalv10026335m.g' => 'esa', 'TPR.G17433' => 'tpr', 'TPR.G18915' => 'tpr', 'TPR.G26125' => 'tpr', 'TWI09G0677' => 'twi', 'TWI73G0287' => 'twi', 'unitig_748.g8326' => 'ugi', 'vmacro15370' => 'vma', 'vmacro15371' => 'vma', 'vmacro15372' => 'vma', 'vmacro15373' => 'vma', 'vmacro15374' => 'vma', 'VMungo0720G2826' => 'vmu', 'Zm00001eb116960' => 'zma', 'Zm00001eb301260' => 'zma', 'Zm00001eb301270' => 'zma' ) $gf_id = 'HOM05D001460' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001460' ) $data_identifier = 'HOM05D001460' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 4, 'aag' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 2, 'aox' => (int) 2, 'arhy' => (int) 4, 'ath' => (int) 2, 'atr' => (int) 1, 'acertr' => (int) 10, 'cqu' => (int) 4, 'bca' => (int) 11, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 1, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 1, 'ccan' => (int) 1, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 1, 'col' => (int) 1, 'cpa' => (int) 1, 'cre' => (int) 7, 'csa' => (int) 1, 'camsi' => (int) 2, 'dca' => (int) 3, 'din' => (int) 2, 'dzi' => (int) 3, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 14, 'fve' => (int) 9, 'gma' => (int) 2, 'ghi' => (int) 4, 'gra' => (int) 2, 'vvi' => (int) 1, 'han' => (int) 13, 'cav' => (int) 1, 'hma' => (int) 2, 'sun' => (int) 2, 'lal' => (int) 2, 'lonja' => (int) 12, 'lja' => (int) 1, 'lsa' => (int) 7, 'mes' => (int) 1, 'mpo' => (int) 27, 'mbi' => (int) 1, 'mco' => (int) 8, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 1, 'egut' => (int) 1, 'ama' => (int) 1, 'nta' => (int) 4, 'nnu' => (int) 2, 'oeu' => (int) 3, 'osa' => (int) 4, 'pax' => (int) 9, 'pgr' => (int) 1, 'stu' => (int) 1, 'pvu' => (int) 1, 'ptr' => (int) 4, 'ppa' => (int) 22, 'pco' => (int) 6, 'ppe' => (int) 6, 'psa' => (int) 5, 'pso' => (int) 19, 'qlo' => (int) 5, 'rch' => (int) 7, 'rsi' => (int) 20, 'sbr' => (int) 5, 'sbo' => (int) 1, 'sci' => (int) 2, 'sed' => (int) 2, 'sgi' => (int) 12, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 2, 'tar' => (int) 10, 'tha' => (int) 1, 'tca' => (int) 1, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 2, 'ugi' => (int) 1, 'vma' => (int) 5, 'vmu' => (int) 1, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb301270' $species_info = array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ) $local_species = 'spa' $disabled = '' $selected = '' $num_hits = (int) 0
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001460', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '433', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p22980' => 'bna', 'A01p32340' => 'bna', 'A03p42970' => 'bna', 'A05p25880' => 'bna', 'Aa31LG8G9320' => 'aar', 'Aa31LG8G9330' => 'aar', 'Aa31LG8G9340' => 'aar', 'Aa31sc221G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1034' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1528' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.829' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2222' => 'aag', 'Ah.12g058830' => 'amhyb', 'Ah.12g058840' => 'amhyb', 'AL3G37160' => 'aly', 'AL7G41310' => 'aly', 'Aqoxy5G00395' => 'aox', 'Aqoxy5G00396' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0C8NZA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5185HY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JZ1PRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MD3LS0' => 'arhy', 'AT3G22840' => 'ath', 'AT4G14690' => 'ath', 'ATR0665G054' => 'atr', 'Atru.chr4.2344' => 'acertr', 'Atru.chr4.2346' => 'acertr', 'Atru.chr4.2347' => 'acertr', 'Atru.chr4.2348' => 'acertr', 'Atru.chr4.2355' => 'acertr', 'Atru.chr4.2356' => 'acertr', 'Atru.chr4.2358' => 'acertr', 'Atru.chr4.2359' => 'acertr', 'Atru.chr4.2360' => 'acertr', 'Atru.chr4.2361' => 'acertr', 'AUR62030476' => 'cqu', 'AUR62030478' => 'cqu', 'AUR62030819' => 'cqu', 'AUR62030820' => 'cqu', 'BcaB03g14648' => 'bca', 'BcaB04g20492' => 'bca', 'BcaB06g26399' => 'bca', 'BcaC01g03416' => 'bca', 'BcaC01g03419' => 'bca', 'BcaC01g03421' => 'bca', 'BcaC01g03424' => 'bca', 'BcaC05g28012' => 'bca', 'BcaC09g49212' => 'bca', 'BcaC09g50140' => 'bca', 'BcaNung00346' => 'bca', 'BolC1t02785H' => 'bol', 'BolC1t04095H' => 'bol', 'BolC3t17545H' => 'bol', 'BolC5t32769H' => 'bol', 'BraA01t02211Z' => 'bra', 'BraA01t03359Z' => 'bra', 'BraA03t13441Z' => 'bra', 'BraA05t21476Z' => 'bra', 'C01p28420' => 'bna', 'C01p41350' => 'bna', 'C03p52750' => 'bna', 'C03p52780' => 'bna', 'C05p40270' => 'bna', 'CAN.G1437.9' => 'can', 'CANSAT78G0035' => 'cansat', 'CANSAT78G1036' => 'cansat', 'CANSAT78G2272' => 'cansat', 'CANSAT78G2478' => 'cansat', 'CARHR098700' => 'chi', 'CARHR221120' => 'chi', 'CARHR221150' => 'chi', 'Carub.0003s2297' => 'cru', 'Carub.0007s2749' => 'cru', 'Carub.0007s2750' => 'cru', 'Carub.0007s2751' => 'cru', 'Ca_10849_v3' => 'car', 'Cc03_g04300' => 'ccan', 'CDE02G3648' => 'cde', 'CDE05G0060' => 'cde', 'CDE05G0692' => 'cde', 'CDE05G2285' => 'cde', 'CDE05G2884' => 'cde', 'CDE05G3072' => 'cde', 'Cfa008439' => 'cfa', 'Cfa008441' => 'cfa', 'Cfa008443' => 'cfa', 'Cfa008448' => 'cfa', 'Ciclev10005974m.g' => 'ccl', 'Ciclev10006006m.g' => 'ccl', 'Ciclev10006775m.g' => 'ccl', 'CiPaw.02G120400' => 'cil', 'CiPaw.02G120500' => 'cil', 'CiPaw.02G120600' => 'cil', 'ClCG05G004850' => 'cla', 'COL.COLO4_21566' => 'col', 'Cpa.g.sc44.124' => 'cpa', 'Cre07.g320400' => 'cre', 'Cre07.g320450' => 'cre', 'Cre08.g384650' => 'cre', 'Cre09.g393173' => 'cre', 'Cre09.g394325' => 'cre', 'Cre14.g626750' => 'cre', 'Cre16.g679250' => 'cre', 'CsaV3_3G012890' => 'csa', 'CSS0010865' => 'camsi', 'CSS0044338' => 'camsi', 'DCAR_002366' => 'dca', 'DCAR_030687' => 'dca', 'DCAR_030688' => 'dca', 'Dinv14047' => 'din', 'Dinv14048' => 'din', 'Duzib151G0105' => 'dzi', 'Duzib151G0114' => 'dzi', 'Duzib212G1029' => 'dzi', 'ECA232G3536' => 'eca', 'ECA240G0786' => 'eca', 'ECA240G1802' => 'eca', 'ECA240G3760' => 'eca', 'ECA240G3920' => 'eca', 'EL10Ac5g12536' => 'bvu', 'EL10Ac5g12537' => 'bvu', 'EL10Ac5g12538' => 'bvu', 'Eucgr.B01004' => 'egr', 'Eucgr.B01006' => 'egr', 'Eucgr.B01007' => 'egr', 'Eucgr.B01008' => 'egr', 'Eucgr.B01895' => 'egr', 'Eucgr.B01896' => 'egr', 'FAN04G1456' => 'fan', 'FAN08G1769' => 'fan', 'FAN08G2160' => 'fan', 'FAN13G2403' => 'fan', 'FAN13G3303' => 'fan', 'FAN15G2435' => 'fan', 'FAN17G0672' => 'fan', 'FAN17G2441' => 'fan', 'FAN18G1024' => 'fan', 'FAN22G1458' => 'fan', 'FAN24G0037' => 'fan', 'FAN24G0429' => 'fan', 'FAN24G2387' => 'fan', 'FAN27G2746' => 'fan', 'FvH4_2g20400' => 'fve', 'FvH4_2g20420' => 'fve', 'FvH4_2g20430' => 'fve', 'FvH4_4g01270' => 'fve', 'FvH4_4g01290' => 'fve', 'FvH4_4g01300' => 'fve', 'FvH4_4g01310' => 'fve', 'FvH4_4g01330' => 'fve', 'FvH4_5g09070' => 'fve', 'Glyma.10G243800' => 'gma', 'Glyma.20G150600' => 'gma', 'Gohir.A09G219200' => 'ghi', 'Gohir.A09G219300' => 'ghi', 'Gohir.D09G221400' => 'ghi', 'Gohir.D09G221500' => 'ghi', 'Gorai.006G242600' => 'gra', 'Gorai.006G242700' => 'gra', 'GSVIVG01018044001' => 'vvi', 'HanXRQChr03g0083821' => 'han', 'HanXRQChr03g0083841' => 'han', 'HanXRQChr03g0083881' => 'han', 'HanXRQChr03g0083901' => 'han', 'HanXRQChr03g0083921' => 'han', 'HanXRQChr03g0085331' => 'han', 'HanXRQChr03g0085361' => 'han', 'HanXRQChr03g0085411' => 'han', 'HanXRQChr03g0085421' => 'han', 'HanXRQChr03g0085431' => 'han', 'HanXRQChr08g0221991' => 'han', 'HanXRQChr11g0336061' => 'han', 'HanXRQChr11g0336411' => 'han', 'Haze_11234' => 'cav', 'Hma1.2p1_0549F.1_g177010' => 'hma', 'Hma1.2p1_0602F.1_g187630' => 'hma', 'Hund14876' => 'sun', 'Hund14879' => 'sun', 'Lalb_Chr06g0160741' => 'lal', 'Lalb_Chr21g0304781' => 'lal', 'Lj3A726G19' => 'lonja', 'Lj3A726T23' => 'lonja', 'Lj3A726T24' => 'lonja', 'Lj3A726T25' => 'lonja', 'Lj3A727T17' => 'lonja', 'Lj3C726T0' => 'lonja', 'Lj3C726T2' => 'lonja', 'Lj3P725T35' => 'lonja', 'Lj3P727T10' => 'lonja', 'Lj3P727T12' => 'lonja', 'Lj3P727T14' => 'lonja', 'Lj5g0023109' => 'lja', 'Lj6P646T44' => 'lonja', 'Lsat_1_v5_gn_6_75760' => 'lsa', 'Lsat_1_v5_gn_6_75800' => 'lsa', 'Lsat_1_v5_gn_6_75900' => 'lsa', 'Lsat_1_v5_gn_6_76240' => 'lsa', 'Lsat_1_v5_gn_6_76441' => 'lsa', 'Lsat_1_v5_gn_6_76700' => 'lsa', 'Lsat_1_v5_gn_6_76760' => 'lsa', 'Manes.15G033100' => 'mes', 'Mapoly0004s0074' => 'mpo', 'Mapoly0004s0075' => 'mpo', 'Mapoly0004s0163' => 'mpo', 'Mapoly0004s0164' => 'mpo', 'Mapoly0021s0018' => 'mpo', 'Mapoly0041s0136' => 'mpo', 'Mapoly0041s0137' => 'mpo', 'Mapoly0041s0138' => 'mpo', 'Mapoly0041s0139' => 'mpo', 'Mapoly0041s0141' => 'mpo', 'Mapoly0041s0142' => 'mpo', 'Mapoly0041s0143' => 'mpo', 'Mapoly0041s0144' => 'mpo', 'Mapoly0041s0145' => 'mpo', 'Mapoly0047s0106' => 'mpo', 'Mapoly0047s0108' => 'mpo', 'Mapoly0050s0051' => 'mpo', 'Mapoly0050s0052' => 'mpo', 'Mapoly0050s0053' => 'mpo', 'Mapoly0058s0013' => 'mpo', 'Mapoly0091s0078' => 'mpo', 'Mapoly0091s0079' => 'mpo', 'Mapoly0091s0080' => 'mpo', 'Mapoly0091s0081' => 'mpo', 'Mapoly0278s0004' => 'mpo', 'Mapoly0278s0005' => 'mpo', 'Mapoly0278s0006' => 'mpo', 'MBI11_g30648_MAGBIO' => 'mbi', 'MCO03G194' => 'mco', 'MCO03G590' => 'mco', 'MCO07G312' => 'mco', 'MCO10G318' => 'mco', 'MCO12G244' => 'mco', 'MCO13G148' => 'mco', 'MCO13G194' => 'mco', 'MCO16G238' => 'mco', 'MD06G1134100' => 'mdo', 'MD13G1200100' => 'mdo', 'MD13G1200300' => 'mdo', 'MD13G1200600' => 'mdo', 'MD14G1150400' => 'mdo', 'MD16G1200000' => 'mdo', 'Medtr1g102570' => 'mtr', 'Medtr1g102780' => 'mtr', 'Medtr1g102800' => 'mtr', 'Medtr1g102810' => 'mtr', 'Medtr1g102830' => 'mtr', 'MELO3C006499.2' => 'cme', 'Migut.G00385' => 'egut', 'MSTRG.4063' => 'ama', 'Nitab4.5_0000090g0260' => 'nta', 'Nitab4.5_0000977g0030' => 'nta', 'Nitab4.5_0002541g0040' => 'nta', 'Nitab4.5_0007068g0040' => 'nta', 'Nn005s41408' => 'nnu', 'Nn005s41410' => 'nnu', 'Oeu010310.1' => 'oeu', 'Oeu010311.1' => 'oeu', 'Oeu043472.1' => 'oeu', 'Os01g0246400' => 'osa', 'Os04g0267950' => 'osa', 'Os07g0178700' => 'osa', 'Os07g0178800' => 'osa', 'Peaxi162Scf00316g00046' => 'pax', 'Peaxi162Scf00316g00049' => 'pax', 'Peaxi162Scf00316g00059' => 'pax', 'Peaxi162Scf00316g00328' => 'pax', 'Peaxi162Scf00316g00329' => 'pax', 'Peaxi162Scf00316g00411' => 'pax', 'Peaxi162Scf00316g00521' => 'pax', 'Peaxi162Scf00492g00068' => 'pax', 'Peaxi162Scf35631g00002' => 'pax', 'PGR142G3720' => 'pgr', 'PGSC0003DMG400006442' => 'stu', 'Phvul.007G062000' => 'pvu', 'Potri.008G157750' => 'ptr', 'Potri.008G157900' => 'ptr', 'Potri.008G158000' => 'ptr', 'Potri.008G158200' => 'ptr', 'Pp3c11_7280' => 'ppa', 'Pp3c11_7980' => 'ppa', 'Pp3c12_19450' => 'ppa', 'Pp3c14_1480' => 'ppa', 'Pp3c14_1501' => 'ppa', 'Pp3c16_4900' => 'ppa', 'Pp3c16_5010' => 'ppa', 'Pp3c16_5060' => 'ppa', 'Pp3c19_18250' => 'ppa', 'Pp3c23_8530' => 'ppa', 'Pp3c23_8550' => 'ppa', 'Pp3c24_9670' => 'ppa', 'Pp3c2_21390' => 'ppa', 'Pp3c2_31380' => 'ppa', 'Pp3c3_16620' => 'ppa', 'Pp3c3_8090' => 'ppa', 'Pp3c3_8110' => 'ppa', 'Pp3c3_8130' => 'ppa', 'Pp3c3_8150' => 'ppa', 'Pp3c4_14320' => 'ppa', 'Pp3c6_2560' => 'ppa', 'Pp3c9_16700' => 'ppa', 'PRCOL_00000234' => 'pco', 'PRCOL_00000235' => 'pco', 'PRCOL_00000777' => 'pco', 'PRCOL_00002344' => 'pco', 'PRCOL_00002372' => 'pco', 'PRCOL_00006120' => 'pco', 'Prupe.1G021400' => 'ppe', 'Prupe.1G021500' => 'ppe', 'Prupe.1G021600' => 'ppe', 'Prupe.1G021700' => 'ppe', 'Prupe.1G021800' => 'ppe', 'Prupe.5G145100' => 'ppe', 'Psat6g204040' => 'psa', 'Psat6g204800' => 'psa', 'Psat6g204920' => 'psa', 'Psat6g204960' => 'psa', 'Psat6g205080' => 'psa', 'PSO017G0271' => 'pso', 'PSO017G1276' => 'pso', 'PSO017G1429' => 'pso', 'PSO017G1861' => 'pso', 'PSO017G2787' => 'pso', 'PSO017G4466' => 'pso', 'PSO017G5118' => 'pso', 'PSO017G5420' => 'pso', 'PSO063G3678' => 'pso', 'PSO210G0546' => 'pso', 'PSO317G0001' => 'pso', 'PSO357G0512' => 'pso', 'PSO478G2682' => 'pso', 'PSO647G0001' => 'pso', 'PSO675G0001' => 'pso', 'PSO675G2699' => 'pso', 'PSO675G2849' => 'pso', 'PSO675G4991' => 'pso', 'PSO689G0001' => 'pso', 'QL06p000916' => 'qlo', 'QL06p000921' => 'qlo', 'QL06p001398' => 'qlo', 'QL06p001407' => 'qlo', 'QL06p002031' => 'qlo', 'RcHm_v2.0_Chr4g0387791' => 'rch', 'RcHm_v2.0_Chr4g0387801' => 'rch', 'RcHm_v2.0_Chr6g0286501' => 'rch', 'RcHm_v2.0_Chr6g0286511' => 'rch', 'RcHm_v2.0_Chr6g0286521' => 'rch', 'RcHm_v2.0_Chr6g0286531' => 'rch', 'RcHm_v2.0_Chr7g0189141' => 'rch', 'Rhsim02G0028700' => 'rsi', 'Rhsim02G0028800' => 'rsi', 'Rhsim02G0028900' => 'rsi', 'Rhsim02G0029000' => 'rsi', 'Rhsim02G0029100' => 'rsi', 'Rhsim02G0029200' => 'rsi', 'Rhsim02G0029300' => 'rsi', 'Rhsim02G0029400' => 'rsi', 'Rhsim02G0029500' => 'rsi', 'Rhsim02G0029600' => 'rsi', 'RhsimUnG0024000' => 'rsi', 'RhsimUnG0024100' => 'rsi', 'RhsimUnG0024200' => 'rsi', 'RhsimUnG0024300' => 'rsi', 'RhsimUnG0024400' => 'rsi', 'RhsimUnG0024500' => 'rsi', 'RhsimUnG0024700' => 'rsi', 'RhsimUnG0024800' => 'rsi', 'RhsimUnG0024900' => 'rsi', 'RhsimUnG0025100' => 'rsi', 'Sabra08G0120200' => 'sbr', 'Sabra08G0120300' => 'sbr', 'Sabra08G0120500' => 'sbr', 'Sabra08G0120600' => 'sbr', 'Sabra10G0158900' => 'sbr', 'SalBow2G3492' => 'sbo', 'Sc13g0004760' => 'sci', 'Sc13g0004770' => 'sci', 'Sed0003417' => 'sed', 'Sed0019750' => 'sed', 'SEGI_03419' => 'sgi', 'SEGI_05907' => 'sgi', 'SEGI_10682' => 'sgi', 'SEGI_13528' => 'sgi', 'SEGI_16081' => 'sgi', 'SEGI_19370' => 'sgi', 'SEGI_21015' => 'sgi', 'SEGI_21944' => 'sgi', 'SEGI_32906' => 'sgi', 'SEGI_33093' => 'sgi', 'SEGI_36110' => 'sgi', 'SEGI_40397' => 'sgi', 'SGA_v2.0_scaffold191G40426' => 'sas', 'SGA_v2.0_scaffold353G49717' => 'sas', 'SGA_v2.0_scaffold50G18550' => 'sas', 'SMO119G0173' => 'smo', 'SMO172G0002' => 'smo', 'Solyc09g082690.3' => 'sly', 'Solyc09g082700.2' => 'sly', 'Sopen09g031550' => 'spe', 'Sopen09g031560' => 'spe', 'Sp3g20540' => 'spa', 'Sp7g07580' => 'spa', 'TAR134G0002' => 'tar', 'TAR236G0001' => 'tar', 'TAR365G0892' => 'tar', 'TAR636G0166' => 'tar', 'TAR636G0646' => 'tar', 'TAR636G0869' => 'tar', 'TAR636G1317' => 'tar', 'TAR636G1744' => 'tar', 'TAR636G3358' => 'tar', 'TAR636G3436' => 'tar', 'THA.LOC104803047' => 'tha', 'Thecc.04G238900' => 'tca', 'Thhalv10021557m.g' => 'esa', 'Thhalv10026318m.g' => 'esa', 'Thhalv10026335m.g' => 'esa', 'TPR.G17433' => 'tpr', 'TPR.G18915' => 'tpr', 'TPR.G26125' => 'tpr', 'TWI09G0677' => 'twi', 'TWI73G0287' => 'twi', 'unitig_748.g8326' => 'ugi', 'vmacro15370' => 'vma', 'vmacro15371' => 'vma', 'vmacro15372' => 'vma', 'vmacro15373' => 'vma', 'vmacro15374' => 'vma', 'VMungo0720G2826' => 'vmu', 'Zm00001eb116960' => 'zma', 'Zm00001eb301260' => 'zma', 'Zm00001eb301270' => 'zma' ), 'gf_id' => 'HOM05D001460', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001460' ), 'data_identifier' => 'HOM05D001460', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001460', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '433', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p22980' => 'bna', 'A01p32340' => 'bna', 'A03p42970' => 'bna', 'A05p25880' => 'bna', 'Aa31LG8G9320' => 'aar', 'Aa31LG8G9330' => 'aar', 'Aa31LG8G9340' => 'aar', 'Aa31sc221G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1034' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1528' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.829' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2222' => 'aag', 'Ah.12g058830' => 'amhyb', 'Ah.12g058840' => 'amhyb', 'AL3G37160' => 'aly', 'AL7G41310' => 'aly', 'Aqoxy5G00395' => 'aox', 'Aqoxy5G00396' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0C8NZA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5185HY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JZ1PRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MD3LS0' => 'arhy', 'AT3G22840' => 'ath', 'AT4G14690' => 'ath', 'ATR0665G054' => 'atr', 'Atru.chr4.2344' => 'acertr', 'Atru.chr4.2346' => 'acertr', 'Atru.chr4.2347' => 'acertr', 'Atru.chr4.2348' => 'acertr', 'Atru.chr4.2355' => 'acertr', 'Atru.chr4.2356' => 'acertr', 'Atru.chr4.2358' => 'acertr', 'Atru.chr4.2359' => 'acertr', 'Atru.chr4.2360' => 'acertr', 'Atru.chr4.2361' => 'acertr', 'AUR62030476' => 'cqu', 'AUR62030478' => 'cqu', 'AUR62030819' => 'cqu', 'AUR62030820' => 'cqu', 'BcaB03g14648' => 'bca', 'BcaB04g20492' => 'bca', 'BcaB06g26399' => 'bca', 'BcaC01g03416' => 'bca', 'BcaC01g03419' => 'bca', 'BcaC01g03421' => 'bca', 'BcaC01g03424' => 'bca', 'BcaC05g28012' => 'bca', 'BcaC09g49212' => 'bca', 'BcaC09g50140' => 'bca', 'BcaNung00346' => 'bca', 'BolC1t02785H' => 'bol', 'BolC1t04095H' => 'bol', 'BolC3t17545H' => 'bol', 'BolC5t32769H' => 'bol', 'BraA01t02211Z' => 'bra', 'BraA01t03359Z' => 'bra', 'BraA03t13441Z' => 'bra', 'BraA05t21476Z' => 'bra', 'C01p28420' => 'bna', 'C01p41350' => 'bna', 'C03p52750' => 'bna', 'C03p52780' => 'bna', 'C05p40270' => 'bna', 'CAN.G1437.9' => 'can', 'CANSAT78G0035' => 'cansat', 'CANSAT78G1036' => 'cansat', 'CANSAT78G2272' => 'cansat', 'CANSAT78G2478' => 'cansat', 'CARHR098700' => 'chi', 'CARHR221120' => 'chi', 'CARHR221150' => 'chi', 'Carub.0003s2297' => 'cru', 'Carub.0007s2749' => 'cru', 'Carub.0007s2750' => 'cru', 'Carub.0007s2751' => 'cru', 'Ca_10849_v3' => 'car', 'Cc03_g04300' => 'ccan', 'CDE02G3648' => 'cde', 'CDE05G0060' => 'cde', 'CDE05G0692' => 'cde', 'CDE05G2285' => 'cde', 'CDE05G2884' => 'cde', 'CDE05G3072' => 'cde', 'Cfa008439' => 'cfa', 'Cfa008441' => 'cfa', 'Cfa008443' => 'cfa', 'Cfa008448' => 'cfa', 'Ciclev10005974m.g' => 'ccl', 'Ciclev10006006m.g' => 'ccl', 'Ciclev10006775m.g' => 'ccl', 'CiPaw.02G120400' => 'cil', 'CiPaw.02G120500' => 'cil', 'CiPaw.02G120600' => 'cil', 'ClCG05G004850' => 'cla', 'COL.COLO4_21566' => 'col', 'Cpa.g.sc44.124' => 'cpa', 'Cre07.g320400' => 'cre', 'Cre07.g320450' => 'cre', 'Cre08.g384650' => 'cre', 'Cre09.g393173' => 'cre', 'Cre09.g394325' => 'cre', 'Cre14.g626750' => 'cre', 'Cre16.g679250' => 'cre', 'CsaV3_3G012890' => 'csa', 'CSS0010865' => 'camsi', 'CSS0044338' => 'camsi', 'DCAR_002366' => 'dca', 'DCAR_030687' => 'dca', 'DCAR_030688' => 'dca', 'Dinv14047' => 'din', 'Dinv14048' => 'din', 'Duzib151G0105' => 'dzi', 'Duzib151G0114' => 'dzi', 'Duzib212G1029' => 'dzi', 'ECA232G3536' => 'eca', 'ECA240G0786' => 'eca', 'ECA240G1802' => 'eca', 'ECA240G3760' => 'eca', 'ECA240G3920' => 'eca', 'EL10Ac5g12536' => 'bvu', 'EL10Ac5g12537' => 'bvu', 'EL10Ac5g12538' => 'bvu', 'Eucgr.B01004' => 'egr', 'Eucgr.B01006' => 'egr', 'Eucgr.B01007' => 'egr', 'Eucgr.B01008' => 'egr', 'Eucgr.B01895' => 'egr', 'Eucgr.B01896' => 'egr', 'FAN04G1456' => 'fan', 'FAN08G1769' => 'fan', 'FAN08G2160' => 'fan', 'FAN13G2403' => 'fan', 'FAN13G3303' => 'fan', 'FAN15G2435' => 'fan', 'FAN17G0672' => 'fan', 'FAN17G2441' => 'fan', 'FAN18G1024' => 'fan', 'FAN22G1458' => 'fan', 'FAN24G0037' => 'fan', 'FAN24G0429' => 'fan', 'FAN24G2387' => 'fan', 'FAN27G2746' => 'fan', 'FvH4_2g20400' => 'fve', 'FvH4_2g20420' => 'fve', 'FvH4_2g20430' => 'fve', 'FvH4_4g01270' => 'fve', 'FvH4_4g01290' => 'fve', 'FvH4_4g01300' => 'fve', 'FvH4_4g01310' => 'fve', 'FvH4_4g01330' => 'fve', 'FvH4_5g09070' => 'fve', 'Glyma.10G243800' => 'gma', 'Glyma.20G150600' => 'gma', 'Gohir.A09G219200' => 'ghi', 'Gohir.A09G219300' => 'ghi', 'Gohir.D09G221400' => 'ghi', 'Gohir.D09G221500' => 'ghi', 'Gorai.006G242600' => 'gra', 'Gorai.006G242700' => 'gra', 'GSVIVG01018044001' => 'vvi', 'HanXRQChr03g0083821' => 'han', 'HanXRQChr03g0083841' => 'han', 'HanXRQChr03g0083881' => 'han', 'HanXRQChr03g0083901' => 'han', 'HanXRQChr03g0083921' => 'han', 'HanXRQChr03g0085331' => 'han', 'HanXRQChr03g0085361' => 'han', 'HanXRQChr03g0085411' => 'han', 'HanXRQChr03g0085421' => 'han', 'HanXRQChr03g0085431' => 'han', 'HanXRQChr08g0221991' => 'han', 'HanXRQChr11g0336061' => 'han', 'HanXRQChr11g0336411' => 'han', 'Haze_11234' => 'cav', 'Hma1.2p1_0549F.1_g177010' => 'hma', 'Hma1.2p1_0602F.1_g187630' => 'hma', 'Hund14876' => 'sun', 'Hund14879' => 'sun', 'Lalb_Chr06g0160741' => 'lal', 'Lalb_Chr21g0304781' => 'lal', 'Lj3A726G19' => 'lonja', 'Lj3A726T23' => 'lonja', 'Lj3A726T24' => 'lonja', 'Lj3A726T25' => 'lonja', 'Lj3A727T17' => 'lonja', 'Lj3C726T0' => 'lonja', 'Lj3C726T2' => 'lonja', 'Lj3P725T35' => 'lonja', 'Lj3P727T10' => 'lonja', 'Lj3P727T12' => 'lonja', 'Lj3P727T14' => 'lonja', 'Lj5g0023109' => 'lja', 'Lj6P646T44' => 'lonja', 'Lsat_1_v5_gn_6_75760' => 'lsa', 'Lsat_1_v5_gn_6_75800' => 'lsa', 'Lsat_1_v5_gn_6_75900' => 'lsa', 'Lsat_1_v5_gn_6_76240' => 'lsa', 'Lsat_1_v5_gn_6_76441' => 'lsa', 'Lsat_1_v5_gn_6_76700' => 'lsa', 'Lsat_1_v5_gn_6_76760' => 'lsa', 'Manes.15G033100' => 'mes', 'Mapoly0004s0074' => 'mpo', 'Mapoly0004s0075' => 'mpo', 'Mapoly0004s0163' => 'mpo', 'Mapoly0004s0164' => 'mpo', 'Mapoly0021s0018' => 'mpo', 'Mapoly0041s0136' => 'mpo', 'Mapoly0041s0137' => 'mpo', 'Mapoly0041s0138' => 'mpo', 'Mapoly0041s0139' => 'mpo', 'Mapoly0041s0141' => 'mpo', 'Mapoly0041s0142' => 'mpo', 'Mapoly0041s0143' => 'mpo', 'Mapoly0041s0144' => 'mpo', 'Mapoly0041s0145' => 'mpo', 'Mapoly0047s0106' => 'mpo', 'Mapoly0047s0108' => 'mpo', 'Mapoly0050s0051' => 'mpo', 'Mapoly0050s0052' => 'mpo', 'Mapoly0050s0053' => 'mpo', 'Mapoly0058s0013' => 'mpo', 'Mapoly0091s0078' => 'mpo', 'Mapoly0091s0079' => 'mpo', 'Mapoly0091s0080' => 'mpo', 'Mapoly0091s0081' => 'mpo', 'Mapoly0278s0004' => 'mpo', 'Mapoly0278s0005' => 'mpo', 'Mapoly0278s0006' => 'mpo', 'MBI11_g30648_MAGBIO' => 'mbi', 'MCO03G194' => 'mco', 'MCO03G590' => 'mco', 'MCO07G312' => 'mco', 'MCO10G318' => 'mco', 'MCO12G244' => 'mco', 'MCO13G148' => 'mco', 'MCO13G194' => 'mco', 'MCO16G238' => 'mco', 'MD06G1134100' => 'mdo', 'MD13G1200100' => 'mdo', 'MD13G1200300' => 'mdo', 'MD13G1200600' => 'mdo', 'MD14G1150400' => 'mdo', 'MD16G1200000' => 'mdo', 'Medtr1g102570' => 'mtr', 'Medtr1g102780' => 'mtr', 'Medtr1g102800' => 'mtr', 'Medtr1g102810' => 'mtr', 'Medtr1g102830' => 'mtr', 'MELO3C006499.2' => 'cme', 'Migut.G00385' => 'egut', 'MSTRG.4063' => 'ama', 'Nitab4.5_0000090g0260' => 'nta', 'Nitab4.5_0000977g0030' => 'nta', 'Nitab4.5_0002541g0040' => 'nta', 'Nitab4.5_0007068g0040' => 'nta', 'Nn005s41408' => 'nnu', 'Nn005s41410' => 'nnu', 'Oeu010310.1' => 'oeu', 'Oeu010311.1' => 'oeu', 'Oeu043472.1' => 'oeu', 'Os01g0246400' => 'osa', 'Os04g0267950' => 'osa', 'Os07g0178700' => 'osa', 'Os07g0178800' => 'osa', 'Peaxi162Scf00316g00046' => 'pax', 'Peaxi162Scf00316g00049' => 'pax', 'Peaxi162Scf00316g00059' => 'pax', 'Peaxi162Scf00316g00328' => 'pax', 'Peaxi162Scf00316g00329' => 'pax', 'Peaxi162Scf00316g00411' => 'pax', 'Peaxi162Scf00316g00521' => 'pax', 'Peaxi162Scf00492g00068' => 'pax', 'Peaxi162Scf35631g00002' => 'pax', 'PGR142G3720' => 'pgr', 'PGSC0003DMG400006442' => 'stu', 'Phvul.007G062000' => 'pvu', 'Potri.008G157750' => 'ptr', 'Potri.008G157900' => 'ptr', 'Potri.008G158000' => 'ptr', 'Potri.008G158200' => 'ptr', 'Pp3c11_7280' => 'ppa', 'Pp3c11_7980' => 'ppa', 'Pp3c12_19450' => 'ppa', 'Pp3c14_1480' => 'ppa', 'Pp3c14_1501' => 'ppa', 'Pp3c16_4900' => 'ppa', 'Pp3c16_5010' => 'ppa', 'Pp3c16_5060' => 'ppa', 'Pp3c19_18250' => 'ppa', 'Pp3c23_8530' => 'ppa', 'Pp3c23_8550' => 'ppa', 'Pp3c24_9670' => 'ppa', 'Pp3c2_21390' => 'ppa', 'Pp3c2_31380' => 'ppa', 'Pp3c3_16620' => 'ppa', 'Pp3c3_8090' => 'ppa', 'Pp3c3_8110' => 'ppa', 'Pp3c3_8130' => 'ppa', 'Pp3c3_8150' => 'ppa', 'Pp3c4_14320' => 'ppa', 'Pp3c6_2560' => 'ppa', 'Pp3c9_16700' => 'ppa', 'PRCOL_00000234' => 'pco', 'PRCOL_00000235' => 'pco', 'PRCOL_00000777' => 'pco', 'PRCOL_00002344' => 'pco', 'PRCOL_00002372' => 'pco', 'PRCOL_00006120' => 'pco', 'Prupe.1G021400' => 'ppe', 'Prupe.1G021500' => 'ppe', 'Prupe.1G021600' => 'ppe', 'Prupe.1G021700' => 'ppe', 'Prupe.1G021800' => 'ppe', 'Prupe.5G145100' => 'ppe', 'Psat6g204040' => 'psa', 'Psat6g204800' => 'psa', 'Psat6g204920' => 'psa', 'Psat6g204960' => 'psa', 'Psat6g205080' => 'psa', 'PSO017G0271' => 'pso', 'PSO017G1276' => 'pso', 'PSO017G1429' => 'pso', 'PSO017G1861' => 'pso', 'PSO017G2787' => 'pso', 'PSO017G4466' => 'pso', 'PSO017G5118' => 'pso', 'PSO017G5420' => 'pso', 'PSO063G3678' => 'pso', 'PSO210G0546' => 'pso', 'PSO317G0001' => 'pso', 'PSO357G0512' => 'pso', 'PSO478G2682' => 'pso', 'PSO647G0001' => 'pso', 'PSO675G0001' => 'pso', 'PSO675G2699' => 'pso', 'PSO675G2849' => 'pso', 'PSO675G4991' => 'pso', 'PSO689G0001' => 'pso', 'QL06p000916' => 'qlo', 'QL06p000921' => 'qlo', 'QL06p001398' => 'qlo', 'QL06p001407' => 'qlo', 'QL06p002031' => 'qlo', 'RcHm_v2.0_Chr4g0387791' => 'rch', 'RcHm_v2.0_Chr4g0387801' => 'rch', 'RcHm_v2.0_Chr6g0286501' => 'rch', 'RcHm_v2.0_Chr6g0286511' => 'rch', 'RcHm_v2.0_Chr6g0286521' => 'rch', 'RcHm_v2.0_Chr6g0286531' => 'rch', 'RcHm_v2.0_Chr7g0189141' => 'rch', 'Rhsim02G0028700' => 'rsi', 'Rhsim02G0028800' => 'rsi', 'Rhsim02G0028900' => 'rsi', 'Rhsim02G0029000' => 'rsi', 'Rhsim02G0029100' => 'rsi', 'Rhsim02G0029200' => 'rsi', 'Rhsim02G0029300' => 'rsi', 'Rhsim02G0029400' => 'rsi', 'Rhsim02G0029500' => 'rsi', 'Rhsim02G0029600' => 'rsi', 'RhsimUnG0024000' => 'rsi', 'RhsimUnG0024100' => 'rsi', 'RhsimUnG0024200' => 'rsi', 'RhsimUnG0024300' => 'rsi', 'RhsimUnG0024400' => 'rsi', 'RhsimUnG0024500' => 'rsi', 'RhsimUnG0024700' => 'rsi', 'RhsimUnG0024800' => 'rsi', 'RhsimUnG0024900' => 'rsi', 'RhsimUnG0025100' => 'rsi', 'Sabra08G0120200' => 'sbr', 'Sabra08G0120300' => 'sbr', 'Sabra08G0120500' => 'sbr', 'Sabra08G0120600' => 'sbr', 'Sabra10G0158900' => 'sbr', 'SalBow2G3492' => 'sbo', 'Sc13g0004760' => 'sci', 'Sc13g0004770' => 'sci', 'Sed0003417' => 'sed', 'Sed0019750' => 'sed', 'SEGI_03419' => 'sgi', 'SEGI_05907' => 'sgi', 'SEGI_10682' => 'sgi', 'SEGI_13528' => 'sgi', 'SEGI_16081' => 'sgi', 'SEGI_19370' => 'sgi', 'SEGI_21015' => 'sgi', 'SEGI_21944' => 'sgi', 'SEGI_32906' => 'sgi', 'SEGI_33093' => 'sgi', 'SEGI_36110' => 'sgi', 'SEGI_40397' => 'sgi', 'SGA_v2.0_scaffold191G40426' => 'sas', 'SGA_v2.0_scaffold353G49717' => 'sas', 'SGA_v2.0_scaffold50G18550' => 'sas', 'SMO119G0173' => 'smo', 'SMO172G0002' => 'smo', 'Solyc09g082690.3' => 'sly', 'Solyc09g082700.2' => 'sly', 'Sopen09g031550' => 'spe', 'Sopen09g031560' => 'spe', 'Sp3g20540' => 'spa', 'Sp7g07580' => 'spa', 'TAR134G0002' => 'tar', 'TAR236G0001' => 'tar', 'TAR365G0892' => 'tar', 'TAR636G0166' => 'tar', 'TAR636G0646' => 'tar', 'TAR636G0869' => 'tar', 'TAR636G1317' => 'tar', 'TAR636G1744' => 'tar', 'TAR636G3358' => 'tar', 'TAR636G3436' => 'tar', 'THA.LOC104803047' => 'tha', 'Thecc.04G238900' => 'tca', 'Thhalv10021557m.g' => 'esa', 'Thhalv10026318m.g' => 'esa', 'Thhalv10026335m.g' => 'esa', 'TPR.G17433' => 'tpr', 'TPR.G18915' => 'tpr', 'TPR.G26125' => 'tpr', 'TWI09G0677' => 'twi', 'TWI73G0287' => 'twi', 'unitig_748.g8326' => 'ugi', 'vmacro15370' => 'vma', 'vmacro15371' => 'vma', 'vmacro15372' => 'vma', 'vmacro15373' => 'vma', 'vmacro15374' => 'vma', 'VMungo0720G2826' => 'vmu', 'Zm00001eb116960' => 'zma', 'Zm00001eb301260' => 'zma', 'Zm00001eb301270' => 'zma' ) $gf_id = 'HOM05D001460' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001460' ) $data_identifier = 'HOM05D001460' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 4, 'aag' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 2, 'aox' => (int) 2, 'arhy' => (int) 4, 'ath' => (int) 2, 'atr' => (int) 1, 'acertr' => (int) 10, 'cqu' => (int) 4, 'bca' => (int) 11, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 1, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 1, 'ccan' => (int) 1, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 1, 'col' => (int) 1, 'cpa' => (int) 1, 'cre' => (int) 7, 'csa' => (int) 1, 'camsi' => (int) 2, 'dca' => (int) 3, 'din' => (int) 2, 'dzi' => (int) 3, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 14, 'fve' => (int) 9, 'gma' => (int) 2, 'ghi' => (int) 4, 'gra' => (int) 2, 'vvi' => (int) 1, 'han' => (int) 13, 'cav' => (int) 1, 'hma' => (int) 2, 'sun' => (int) 2, 'lal' => (int) 2, 'lonja' => (int) 12, 'lja' => (int) 1, 'lsa' => (int) 7, 'mes' => (int) 1, 'mpo' => (int) 27, 'mbi' => (int) 1, 'mco' => (int) 8, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 1, 'egut' => (int) 1, 'ama' => (int) 1, 'nta' => (int) 4, 'nnu' => (int) 2, 'oeu' => (int) 3, 'osa' => (int) 4, 'pax' => (int) 9, 'pgr' => (int) 1, 'stu' => (int) 1, 'pvu' => (int) 1, 'ptr' => (int) 4, 'ppa' => (int) 22, 'pco' => (int) 6, 'ppe' => (int) 6, 'psa' => (int) 5, 'pso' => (int) 19, 'qlo' => (int) 5, 'rch' => (int) 7, 'rsi' => (int) 20, 'sbr' => (int) 5, 'sbo' => (int) 1, 'sci' => (int) 2, 'sed' => (int) 2, 'sgi' => (int) 12, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 2, 'tar' => (int) 10, 'tha' => (int) 1, 'tca' => (int) 1, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 2, 'ugi' => (int) 1, 'vma' => (int) 5, 'vmu' => (int) 1, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb301270' $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' => 'HOM05D001460', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '433', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p22980' => 'bna', 'A01p32340' => 'bna', 'A03p42970' => 'bna', 'A05p25880' => 'bna', 'Aa31LG8G9320' => 'aar', 'Aa31LG8G9330' => 'aar', 'Aa31LG8G9340' => 'aar', 'Aa31sc221G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1034' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1528' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.829' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2222' => 'aag', 'Ah.12g058830' => 'amhyb', 'Ah.12g058840' => 'amhyb', 'AL3G37160' => 'aly', 'AL7G41310' => 'aly', 'Aqoxy5G00395' => 'aox', 'Aqoxy5G00396' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0C8NZA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5185HY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JZ1PRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MD3LS0' => 'arhy', 'AT3G22840' => 'ath', 'AT4G14690' => 'ath', 'ATR0665G054' => 'atr', 'Atru.chr4.2344' => 'acertr', 'Atru.chr4.2346' => 'acertr', 'Atru.chr4.2347' => 'acertr', 'Atru.chr4.2348' => 'acertr', 'Atru.chr4.2355' => 'acertr', 'Atru.chr4.2356' => 'acertr', 'Atru.chr4.2358' => 'acertr', 'Atru.chr4.2359' => 'acertr', 'Atru.chr4.2360' => 'acertr', 'Atru.chr4.2361' => 'acertr', 'AUR62030476' => 'cqu', 'AUR62030478' => 'cqu', 'AUR62030819' => 'cqu', 'AUR62030820' => 'cqu', 'BcaB03g14648' => 'bca', 'BcaB04g20492' => 'bca', 'BcaB06g26399' => 'bca', 'BcaC01g03416' => 'bca', 'BcaC01g03419' => 'bca', 'BcaC01g03421' => 'bca', 'BcaC01g03424' => 'bca', 'BcaC05g28012' => 'bca', 'BcaC09g49212' => 'bca', 'BcaC09g50140' => 'bca', 'BcaNung00346' => 'bca', 'BolC1t02785H' => 'bol', 'BolC1t04095H' => 'bol', 'BolC3t17545H' => 'bol', 'BolC5t32769H' => 'bol', 'BraA01t02211Z' => 'bra', 'BraA01t03359Z' => 'bra', 'BraA03t13441Z' => 'bra', 'BraA05t21476Z' => 'bra', 'C01p28420' => 'bna', 'C01p41350' => 'bna', 'C03p52750' => 'bna', 'C03p52780' => 'bna', 'C05p40270' => 'bna', 'CAN.G1437.9' => 'can', 'CANSAT78G0035' => 'cansat', 'CANSAT78G1036' => 'cansat', 'CANSAT78G2272' => 'cansat', 'CANSAT78G2478' => 'cansat', 'CARHR098700' => 'chi', 'CARHR221120' => 'chi', 'CARHR221150' => 'chi', 'Carub.0003s2297' => 'cru', 'Carub.0007s2749' => 'cru', 'Carub.0007s2750' => 'cru', 'Carub.0007s2751' => 'cru', 'Ca_10849_v3' => 'car', 'Cc03_g04300' => 'ccan', 'CDE02G3648' => 'cde', 'CDE05G0060' => 'cde', 'CDE05G0692' => 'cde', 'CDE05G2285' => 'cde', 'CDE05G2884' => 'cde', 'CDE05G3072' => 'cde', 'Cfa008439' => 'cfa', 'Cfa008441' => 'cfa', 'Cfa008443' => 'cfa', 'Cfa008448' => 'cfa', 'Ciclev10005974m.g' => 'ccl', 'Ciclev10006006m.g' => 'ccl', 'Ciclev10006775m.g' => 'ccl', 'CiPaw.02G120400' => 'cil', 'CiPaw.02G120500' => 'cil', 'CiPaw.02G120600' => 'cil', 'ClCG05G004850' => 'cla', 'COL.COLO4_21566' => 'col', 'Cpa.g.sc44.124' => 'cpa', 'Cre07.g320400' => 'cre', 'Cre07.g320450' => 'cre', 'Cre08.g384650' => 'cre', 'Cre09.g393173' => 'cre', 'Cre09.g394325' => 'cre', 'Cre14.g626750' => 'cre', 'Cre16.g679250' => 'cre', 'CsaV3_3G012890' => 'csa', 'CSS0010865' => 'camsi', 'CSS0044338' => 'camsi', 'DCAR_002366' => 'dca', 'DCAR_030687' => 'dca', 'DCAR_030688' => 'dca', 'Dinv14047' => 'din', 'Dinv14048' => 'din', 'Duzib151G0105' => 'dzi', 'Duzib151G0114' => 'dzi', 'Duzib212G1029' => 'dzi', 'ECA232G3536' => 'eca', 'ECA240G0786' => 'eca', 'ECA240G1802' => 'eca', 'ECA240G3760' => 'eca', 'ECA240G3920' => 'eca', 'EL10Ac5g12536' => 'bvu', 'EL10Ac5g12537' => 'bvu', 'EL10Ac5g12538' => 'bvu', 'Eucgr.B01004' => 'egr', 'Eucgr.B01006' => 'egr', 'Eucgr.B01007' => 'egr', 'Eucgr.B01008' => 'egr', 'Eucgr.B01895' => 'egr', 'Eucgr.B01896' => 'egr', 'FAN04G1456' => 'fan', 'FAN08G1769' => 'fan', 'FAN08G2160' => 'fan', 'FAN13G2403' => 'fan', 'FAN13G3303' => 'fan', 'FAN15G2435' => 'fan', 'FAN17G0672' => 'fan', 'FAN17G2441' => 'fan', 'FAN18G1024' => 'fan', 'FAN22G1458' => 'fan', 'FAN24G0037' => 'fan', 'FAN24G0429' => 'fan', 'FAN24G2387' => 'fan', 'FAN27G2746' => 'fan', 'FvH4_2g20400' => 'fve', 'FvH4_2g20420' => 'fve', 'FvH4_2g20430' => 'fve', 'FvH4_4g01270' => 'fve', 'FvH4_4g01290' => 'fve', 'FvH4_4g01300' => 'fve', 'FvH4_4g01310' => 'fve', 'FvH4_4g01330' => 'fve', 'FvH4_5g09070' => 'fve', 'Glyma.10G243800' => 'gma', 'Glyma.20G150600' => 'gma', 'Gohir.A09G219200' => 'ghi', 'Gohir.A09G219300' => 'ghi', 'Gohir.D09G221400' => 'ghi', 'Gohir.D09G221500' => 'ghi', 'Gorai.006G242600' => 'gra', 'Gorai.006G242700' => 'gra', 'GSVIVG01018044001' => 'vvi', 'HanXRQChr03g0083821' => 'han', 'HanXRQChr03g0083841' => 'han', 'HanXRQChr03g0083881' => 'han', 'HanXRQChr03g0083901' => 'han', 'HanXRQChr03g0083921' => 'han', 'HanXRQChr03g0085331' => 'han', 'HanXRQChr03g0085361' => 'han', 'HanXRQChr03g0085411' => 'han', 'HanXRQChr03g0085421' => 'han', 'HanXRQChr03g0085431' => 'han', 'HanXRQChr08g0221991' => 'han', 'HanXRQChr11g0336061' => 'han', 'HanXRQChr11g0336411' => 'han', 'Haze_11234' => 'cav', 'Hma1.2p1_0549F.1_g177010' => 'hma', 'Hma1.2p1_0602F.1_g187630' => 'hma', 'Hund14876' => 'sun', 'Hund14879' => 'sun', 'Lalb_Chr06g0160741' => 'lal', 'Lalb_Chr21g0304781' => 'lal', 'Lj3A726G19' => 'lonja', 'Lj3A726T23' => 'lonja', 'Lj3A726T24' => 'lonja', 'Lj3A726T25' => 'lonja', 'Lj3A727T17' => 'lonja', 'Lj3C726T0' => 'lonja', 'Lj3C726T2' => 'lonja', 'Lj3P725T35' => 'lonja', 'Lj3P727T10' => 'lonja', 'Lj3P727T12' => 'lonja', 'Lj3P727T14' => 'lonja', 'Lj5g0023109' => 'lja', 'Lj6P646T44' => 'lonja', 'Lsat_1_v5_gn_6_75760' => 'lsa', 'Lsat_1_v5_gn_6_75800' => 'lsa', 'Lsat_1_v5_gn_6_75900' => 'lsa', 'Lsat_1_v5_gn_6_76240' => 'lsa', 'Lsat_1_v5_gn_6_76441' => 'lsa', 'Lsat_1_v5_gn_6_76700' => 'lsa', 'Lsat_1_v5_gn_6_76760' => 'lsa', 'Manes.15G033100' => 'mes', 'Mapoly0004s0074' => 'mpo', 'Mapoly0004s0075' => 'mpo', 'Mapoly0004s0163' => 'mpo', 'Mapoly0004s0164' => 'mpo', 'Mapoly0021s0018' => 'mpo', 'Mapoly0041s0136' => 'mpo', 'Mapoly0041s0137' => 'mpo', 'Mapoly0041s0138' => 'mpo', 'Mapoly0041s0139' => 'mpo', 'Mapoly0041s0141' => 'mpo', 'Mapoly0041s0142' => 'mpo', 'Mapoly0041s0143' => 'mpo', 'Mapoly0041s0144' => 'mpo', 'Mapoly0041s0145' => 'mpo', 'Mapoly0047s0106' => 'mpo', 'Mapoly0047s0108' => 'mpo', 'Mapoly0050s0051' => 'mpo', 'Mapoly0050s0052' => 'mpo', 'Mapoly0050s0053' => 'mpo', 'Mapoly0058s0013' => 'mpo', 'Mapoly0091s0078' => 'mpo', 'Mapoly0091s0079' => 'mpo', 'Mapoly0091s0080' => 'mpo', 'Mapoly0091s0081' => 'mpo', 'Mapoly0278s0004' => 'mpo', 'Mapoly0278s0005' => 'mpo', 'Mapoly0278s0006' => 'mpo', 'MBI11_g30648_MAGBIO' => 'mbi', 'MCO03G194' => 'mco', 'MCO03G590' => 'mco', 'MCO07G312' => 'mco', 'MCO10G318' => 'mco', 'MCO12G244' => 'mco', 'MCO13G148' => 'mco', 'MCO13G194' => 'mco', 'MCO16G238' => 'mco', 'MD06G1134100' => 'mdo', 'MD13G1200100' => 'mdo', 'MD13G1200300' => 'mdo', 'MD13G1200600' => 'mdo', 'MD14G1150400' => 'mdo', 'MD16G1200000' => 'mdo', 'Medtr1g102570' => 'mtr', 'Medtr1g102780' => 'mtr', 'Medtr1g102800' => 'mtr', 'Medtr1g102810' => 'mtr', 'Medtr1g102830' => 'mtr', 'MELO3C006499.2' => 'cme', 'Migut.G00385' => 'egut', 'MSTRG.4063' => 'ama', 'Nitab4.5_0000090g0260' => 'nta', 'Nitab4.5_0000977g0030' => 'nta', 'Nitab4.5_0002541g0040' => 'nta', 'Nitab4.5_0007068g0040' => 'nta', 'Nn005s41408' => 'nnu', 'Nn005s41410' => 'nnu', 'Oeu010310.1' => 'oeu', 'Oeu010311.1' => 'oeu', 'Oeu043472.1' => 'oeu', 'Os01g0246400' => 'osa', 'Os04g0267950' => 'osa', 'Os07g0178700' => 'osa', 'Os07g0178800' => 'osa', 'Peaxi162Scf00316g00046' => 'pax', 'Peaxi162Scf00316g00049' => 'pax', 'Peaxi162Scf00316g00059' => 'pax', 'Peaxi162Scf00316g00328' => 'pax', 'Peaxi162Scf00316g00329' => 'pax', 'Peaxi162Scf00316g00411' => 'pax', 'Peaxi162Scf00316g00521' => 'pax', 'Peaxi162Scf00492g00068' => 'pax', 'Peaxi162Scf35631g00002' => 'pax', 'PGR142G3720' => 'pgr', 'PGSC0003DMG400006442' => 'stu', 'Phvul.007G062000' => 'pvu', 'Potri.008G157750' => 'ptr', 'Potri.008G157900' => 'ptr', 'Potri.008G158000' => 'ptr', 'Potri.008G158200' => 'ptr', 'Pp3c11_7280' => 'ppa', 'Pp3c11_7980' => 'ppa', 'Pp3c12_19450' => 'ppa', 'Pp3c14_1480' => 'ppa', 'Pp3c14_1501' => 'ppa', 'Pp3c16_4900' => 'ppa', 'Pp3c16_5010' => 'ppa', 'Pp3c16_5060' => 'ppa', 'Pp3c19_18250' => 'ppa', 'Pp3c23_8530' => 'ppa', 'Pp3c23_8550' => 'ppa', 'Pp3c24_9670' => 'ppa', 'Pp3c2_21390' => 'ppa', 'Pp3c2_31380' => 'ppa', 'Pp3c3_16620' => 'ppa', 'Pp3c3_8090' => 'ppa', 'Pp3c3_8110' => 'ppa', 'Pp3c3_8130' => 'ppa', 'Pp3c3_8150' => 'ppa', 'Pp3c4_14320' => 'ppa', 'Pp3c6_2560' => 'ppa', 'Pp3c9_16700' => 'ppa', 'PRCOL_00000234' => 'pco', 'PRCOL_00000235' => 'pco', 'PRCOL_00000777' => 'pco', 'PRCOL_00002344' => 'pco', 'PRCOL_00002372' => 'pco', 'PRCOL_00006120' => 'pco', 'Prupe.1G021400' => 'ppe', 'Prupe.1G021500' => 'ppe', 'Prupe.1G021600' => 'ppe', 'Prupe.1G021700' => 'ppe', 'Prupe.1G021800' => 'ppe', 'Prupe.5G145100' => 'ppe', 'Psat6g204040' => 'psa', 'Psat6g204800' => 'psa', 'Psat6g204920' => 'psa', 'Psat6g204960' => 'psa', 'Psat6g205080' => 'psa', 'PSO017G0271' => 'pso', 'PSO017G1276' => 'pso', 'PSO017G1429' => 'pso', 'PSO017G1861' => 'pso', 'PSO017G2787' => 'pso', 'PSO017G4466' => 'pso', 'PSO017G5118' => 'pso', 'PSO017G5420' => 'pso', 'PSO063G3678' => 'pso', 'PSO210G0546' => 'pso', 'PSO317G0001' => 'pso', 'PSO357G0512' => 'pso', 'PSO478G2682' => 'pso', 'PSO647G0001' => 'pso', 'PSO675G0001' => 'pso', 'PSO675G2699' => 'pso', 'PSO675G2849' => 'pso', 'PSO675G4991' => 'pso', 'PSO689G0001' => 'pso', 'QL06p000916' => 'qlo', 'QL06p000921' => 'qlo', 'QL06p001398' => 'qlo', 'QL06p001407' => 'qlo', 'QL06p002031' => 'qlo', 'RcHm_v2.0_Chr4g0387791' => 'rch', 'RcHm_v2.0_Chr4g0387801' => 'rch', 'RcHm_v2.0_Chr6g0286501' => 'rch', 'RcHm_v2.0_Chr6g0286511' => 'rch', 'RcHm_v2.0_Chr6g0286521' => 'rch', 'RcHm_v2.0_Chr6g0286531' => 'rch', 'RcHm_v2.0_Chr7g0189141' => 'rch', 'Rhsim02G0028700' => 'rsi', 'Rhsim02G0028800' => 'rsi', 'Rhsim02G0028900' => 'rsi', 'Rhsim02G0029000' => 'rsi', 'Rhsim02G0029100' => 'rsi', 'Rhsim02G0029200' => 'rsi', 'Rhsim02G0029300' => 'rsi', 'Rhsim02G0029400' => 'rsi', 'Rhsim02G0029500' => 'rsi', 'Rhsim02G0029600' => 'rsi', 'RhsimUnG0024000' => 'rsi', 'RhsimUnG0024100' => 'rsi', 'RhsimUnG0024200' => 'rsi', 'RhsimUnG0024300' => 'rsi', 'RhsimUnG0024400' => 'rsi', 'RhsimUnG0024500' => 'rsi', 'RhsimUnG0024700' => 'rsi', 'RhsimUnG0024800' => 'rsi', 'RhsimUnG0024900' => 'rsi', 'RhsimUnG0025100' => 'rsi', 'Sabra08G0120200' => 'sbr', 'Sabra08G0120300' => 'sbr', 'Sabra08G0120500' => 'sbr', 'Sabra08G0120600' => 'sbr', 'Sabra10G0158900' => 'sbr', 'SalBow2G3492' => 'sbo', 'Sc13g0004760' => 'sci', 'Sc13g0004770' => 'sci', 'Sed0003417' => 'sed', 'Sed0019750' => 'sed', 'SEGI_03419' => 'sgi', 'SEGI_05907' => 'sgi', 'SEGI_10682' => 'sgi', 'SEGI_13528' => 'sgi', 'SEGI_16081' => 'sgi', 'SEGI_19370' => 'sgi', 'SEGI_21015' => 'sgi', 'SEGI_21944' => 'sgi', 'SEGI_32906' => 'sgi', 'SEGI_33093' => 'sgi', 'SEGI_36110' => 'sgi', 'SEGI_40397' => 'sgi', 'SGA_v2.0_scaffold191G40426' => 'sas', 'SGA_v2.0_scaffold353G49717' => 'sas', 'SGA_v2.0_scaffold50G18550' => 'sas', 'SMO119G0173' => 'smo', 'SMO172G0002' => 'smo', 'Solyc09g082690.3' => 'sly', 'Solyc09g082700.2' => 'sly', 'Sopen09g031550' => 'spe', 'Sopen09g031560' => 'spe', 'Sp3g20540' => 'spa', 'Sp7g07580' => 'spa', 'TAR134G0002' => 'tar', 'TAR236G0001' => 'tar', 'TAR365G0892' => 'tar', 'TAR636G0166' => 'tar', 'TAR636G0646' => 'tar', 'TAR636G0869' => 'tar', 'TAR636G1317' => 'tar', 'TAR636G1744' => 'tar', 'TAR636G3358' => 'tar', 'TAR636G3436' => 'tar', 'THA.LOC104803047' => 'tha', 'Thecc.04G238900' => 'tca', 'Thhalv10021557m.g' => 'esa', 'Thhalv10026318m.g' => 'esa', 'Thhalv10026335m.g' => 'esa', 'TPR.G17433' => 'tpr', 'TPR.G18915' => 'tpr', 'TPR.G26125' => 'tpr', 'TWI09G0677' => 'twi', 'TWI73G0287' => 'twi', 'unitig_748.g8326' => 'ugi', 'vmacro15370' => 'vma', 'vmacro15371' => 'vma', 'vmacro15372' => 'vma', 'vmacro15373' => 'vma', 'vmacro15374' => 'vma', 'VMungo0720G2826' => 'vmu', 'Zm00001eb116960' => 'zma', 'Zm00001eb301260' => 'zma', 'Zm00001eb301270' => 'zma' ), 'gf_id' => 'HOM05D001460', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001460' ), 'data_identifier' => 'HOM05D001460', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001460', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '433', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p22980' => 'bna', 'A01p32340' => 'bna', 'A03p42970' => 'bna', 'A05p25880' => 'bna', 'Aa31LG8G9320' => 'aar', 'Aa31LG8G9330' => 'aar', 'Aa31LG8G9340' => 'aar', 'Aa31sc221G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1034' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1528' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.829' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2222' => 'aag', 'Ah.12g058830' => 'amhyb', 'Ah.12g058840' => 'amhyb', 'AL3G37160' => 'aly', 'AL7G41310' => 'aly', 'Aqoxy5G00395' => 'aox', 'Aqoxy5G00396' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0C8NZA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5185HY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JZ1PRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MD3LS0' => 'arhy', 'AT3G22840' => 'ath', 'AT4G14690' => 'ath', 'ATR0665G054' => 'atr', 'Atru.chr4.2344' => 'acertr', 'Atru.chr4.2346' => 'acertr', 'Atru.chr4.2347' => 'acertr', 'Atru.chr4.2348' => 'acertr', 'Atru.chr4.2355' => 'acertr', 'Atru.chr4.2356' => 'acertr', 'Atru.chr4.2358' => 'acertr', 'Atru.chr4.2359' => 'acertr', 'Atru.chr4.2360' => 'acertr', 'Atru.chr4.2361' => 'acertr', 'AUR62030476' => 'cqu', 'AUR62030478' => 'cqu', 'AUR62030819' => 'cqu', 'AUR62030820' => 'cqu', 'BcaB03g14648' => 'bca', 'BcaB04g20492' => 'bca', 'BcaB06g26399' => 'bca', 'BcaC01g03416' => 'bca', 'BcaC01g03419' => 'bca', 'BcaC01g03421' => 'bca', 'BcaC01g03424' => 'bca', 'BcaC05g28012' => 'bca', 'BcaC09g49212' => 'bca', 'BcaC09g50140' => 'bca', 'BcaNung00346' => 'bca', 'BolC1t02785H' => 'bol', 'BolC1t04095H' => 'bol', 'BolC3t17545H' => 'bol', 'BolC5t32769H' => 'bol', 'BraA01t02211Z' => 'bra', 'BraA01t03359Z' => 'bra', 'BraA03t13441Z' => 'bra', 'BraA05t21476Z' => 'bra', 'C01p28420' => 'bna', 'C01p41350' => 'bna', 'C03p52750' => 'bna', 'C03p52780' => 'bna', 'C05p40270' => 'bna', 'CAN.G1437.9' => 'can', 'CANSAT78G0035' => 'cansat', 'CANSAT78G1036' => 'cansat', 'CANSAT78G2272' => 'cansat', 'CANSAT78G2478' => 'cansat', 'CARHR098700' => 'chi', 'CARHR221120' => 'chi', 'CARHR221150' => 'chi', 'Carub.0003s2297' => 'cru', 'Carub.0007s2749' => 'cru', 'Carub.0007s2750' => 'cru', 'Carub.0007s2751' => 'cru', 'Ca_10849_v3' => 'car', 'Cc03_g04300' => 'ccan', 'CDE02G3648' => 'cde', 'CDE05G0060' => 'cde', 'CDE05G0692' => 'cde', 'CDE05G2285' => 'cde', 'CDE05G2884' => 'cde', 'CDE05G3072' => 'cde', 'Cfa008439' => 'cfa', 'Cfa008441' => 'cfa', 'Cfa008443' => 'cfa', 'Cfa008448' => 'cfa', 'Ciclev10005974m.g' => 'ccl', 'Ciclev10006006m.g' => 'ccl', 'Ciclev10006775m.g' => 'ccl', 'CiPaw.02G120400' => 'cil', 'CiPaw.02G120500' => 'cil', 'CiPaw.02G120600' => 'cil', 'ClCG05G004850' => 'cla', 'COL.COLO4_21566' => 'col', 'Cpa.g.sc44.124' => 'cpa', 'Cre07.g320400' => 'cre', 'Cre07.g320450' => 'cre', 'Cre08.g384650' => 'cre', 'Cre09.g393173' => 'cre', 'Cre09.g394325' => 'cre', 'Cre14.g626750' => 'cre', 'Cre16.g679250' => 'cre', 'CsaV3_3G012890' => 'csa', 'CSS0010865' => 'camsi', 'CSS0044338' => 'camsi', 'DCAR_002366' => 'dca', 'DCAR_030687' => 'dca', 'DCAR_030688' => 'dca', 'Dinv14047' => 'din', 'Dinv14048' => 'din', 'Duzib151G0105' => 'dzi', 'Duzib151G0114' => 'dzi', 'Duzib212G1029' => 'dzi', 'ECA232G3536' => 'eca', 'ECA240G0786' => 'eca', 'ECA240G1802' => 'eca', 'ECA240G3760' => 'eca', 'ECA240G3920' => 'eca', 'EL10Ac5g12536' => 'bvu', 'EL10Ac5g12537' => 'bvu', 'EL10Ac5g12538' => 'bvu', 'Eucgr.B01004' => 'egr', 'Eucgr.B01006' => 'egr', 'Eucgr.B01007' => 'egr', 'Eucgr.B01008' => 'egr', 'Eucgr.B01895' => 'egr', 'Eucgr.B01896' => 'egr', 'FAN04G1456' => 'fan', 'FAN08G1769' => 'fan', 'FAN08G2160' => 'fan', 'FAN13G2403' => 'fan', 'FAN13G3303' => 'fan', 'FAN15G2435' => 'fan', 'FAN17G0672' => 'fan', 'FAN17G2441' => 'fan', 'FAN18G1024' => 'fan', 'FAN22G1458' => 'fan', 'FAN24G0037' => 'fan', 'FAN24G0429' => 'fan', 'FAN24G2387' => 'fan', 'FAN27G2746' => 'fan', 'FvH4_2g20400' => 'fve', 'FvH4_2g20420' => 'fve', 'FvH4_2g20430' => 'fve', 'FvH4_4g01270' => 'fve', 'FvH4_4g01290' => 'fve', 'FvH4_4g01300' => 'fve', 'FvH4_4g01310' => 'fve', 'FvH4_4g01330' => 'fve', 'FvH4_5g09070' => 'fve', 'Glyma.10G243800' => 'gma', 'Glyma.20G150600' => 'gma', 'Gohir.A09G219200' => 'ghi', 'Gohir.A09G219300' => 'ghi', 'Gohir.D09G221400' => 'ghi', 'Gohir.D09G221500' => 'ghi', 'Gorai.006G242600' => 'gra', 'Gorai.006G242700' => 'gra', 'GSVIVG01018044001' => 'vvi', 'HanXRQChr03g0083821' => 'han', 'HanXRQChr03g0083841' => 'han', 'HanXRQChr03g0083881' => 'han', 'HanXRQChr03g0083901' => 'han', 'HanXRQChr03g0083921' => 'han', 'HanXRQChr03g0085331' => 'han', 'HanXRQChr03g0085361' => 'han', 'HanXRQChr03g0085411' => 'han', 'HanXRQChr03g0085421' => 'han', 'HanXRQChr03g0085431' => 'han', 'HanXRQChr08g0221991' => 'han', 'HanXRQChr11g0336061' => 'han', 'HanXRQChr11g0336411' => 'han', 'Haze_11234' => 'cav', 'Hma1.2p1_0549F.1_g177010' => 'hma', 'Hma1.2p1_0602F.1_g187630' => 'hma', 'Hund14876' => 'sun', 'Hund14879' => 'sun', 'Lalb_Chr06g0160741' => 'lal', 'Lalb_Chr21g0304781' => 'lal', 'Lj3A726G19' => 'lonja', 'Lj3A726T23' => 'lonja', 'Lj3A726T24' => 'lonja', 'Lj3A726T25' => 'lonja', 'Lj3A727T17' => 'lonja', 'Lj3C726T0' => 'lonja', 'Lj3C726T2' => 'lonja', 'Lj3P725T35' => 'lonja', 'Lj3P727T10' => 'lonja', 'Lj3P727T12' => 'lonja', 'Lj3P727T14' => 'lonja', 'Lj5g0023109' => 'lja', 'Lj6P646T44' => 'lonja', 'Lsat_1_v5_gn_6_75760' => 'lsa', 'Lsat_1_v5_gn_6_75800' => 'lsa', 'Lsat_1_v5_gn_6_75900' => 'lsa', 'Lsat_1_v5_gn_6_76240' => 'lsa', 'Lsat_1_v5_gn_6_76441' => 'lsa', 'Lsat_1_v5_gn_6_76700' => 'lsa', 'Lsat_1_v5_gn_6_76760' => 'lsa', 'Manes.15G033100' => 'mes', 'Mapoly0004s0074' => 'mpo', 'Mapoly0004s0075' => 'mpo', 'Mapoly0004s0163' => 'mpo', 'Mapoly0004s0164' => 'mpo', 'Mapoly0021s0018' => 'mpo', 'Mapoly0041s0136' => 'mpo', 'Mapoly0041s0137' => 'mpo', 'Mapoly0041s0138' => 'mpo', 'Mapoly0041s0139' => 'mpo', 'Mapoly0041s0141' => 'mpo', 'Mapoly0041s0142' => 'mpo', 'Mapoly0041s0143' => 'mpo', 'Mapoly0041s0144' => 'mpo', 'Mapoly0041s0145' => 'mpo', 'Mapoly0047s0106' => 'mpo', 'Mapoly0047s0108' => 'mpo', 'Mapoly0050s0051' => 'mpo', 'Mapoly0050s0052' => 'mpo', 'Mapoly0050s0053' => 'mpo', 'Mapoly0058s0013' => 'mpo', 'Mapoly0091s0078' => 'mpo', 'Mapoly0091s0079' => 'mpo', 'Mapoly0091s0080' => 'mpo', 'Mapoly0091s0081' => 'mpo', 'Mapoly0278s0004' => 'mpo', 'Mapoly0278s0005' => 'mpo', 'Mapoly0278s0006' => 'mpo', 'MBI11_g30648_MAGBIO' => 'mbi', 'MCO03G194' => 'mco', 'MCO03G590' => 'mco', 'MCO07G312' => 'mco', 'MCO10G318' => 'mco', 'MCO12G244' => 'mco', 'MCO13G148' => 'mco', 'MCO13G194' => 'mco', 'MCO16G238' => 'mco', 'MD06G1134100' => 'mdo', 'MD13G1200100' => 'mdo', 'MD13G1200300' => 'mdo', 'MD13G1200600' => 'mdo', 'MD14G1150400' => 'mdo', 'MD16G1200000' => 'mdo', 'Medtr1g102570' => 'mtr', 'Medtr1g102780' => 'mtr', 'Medtr1g102800' => 'mtr', 'Medtr1g102810' => 'mtr', 'Medtr1g102830' => 'mtr', 'MELO3C006499.2' => 'cme', 'Migut.G00385' => 'egut', 'MSTRG.4063' => 'ama', 'Nitab4.5_0000090g0260' => 'nta', 'Nitab4.5_0000977g0030' => 'nta', 'Nitab4.5_0002541g0040' => 'nta', 'Nitab4.5_0007068g0040' => 'nta', 'Nn005s41408' => 'nnu', 'Nn005s41410' => 'nnu', 'Oeu010310.1' => 'oeu', 'Oeu010311.1' => 'oeu', 'Oeu043472.1' => 'oeu', 'Os01g0246400' => 'osa', 'Os04g0267950' => 'osa', 'Os07g0178700' => 'osa', 'Os07g0178800' => 'osa', 'Peaxi162Scf00316g00046' => 'pax', 'Peaxi162Scf00316g00049' => 'pax', 'Peaxi162Scf00316g00059' => 'pax', 'Peaxi162Scf00316g00328' => 'pax', 'Peaxi162Scf00316g00329' => 'pax', 'Peaxi162Scf00316g00411' => 'pax', 'Peaxi162Scf00316g00521' => 'pax', 'Peaxi162Scf00492g00068' => 'pax', 'Peaxi162Scf35631g00002' => 'pax', 'PGR142G3720' => 'pgr', 'PGSC0003DMG400006442' => 'stu', 'Phvul.007G062000' => 'pvu', 'Potri.008G157750' => 'ptr', 'Potri.008G157900' => 'ptr', 'Potri.008G158000' => 'ptr', 'Potri.008G158200' => 'ptr', 'Pp3c11_7280' => 'ppa', 'Pp3c11_7980' => 'ppa', 'Pp3c12_19450' => 'ppa', 'Pp3c14_1480' => 'ppa', 'Pp3c14_1501' => 'ppa', 'Pp3c16_4900' => 'ppa', 'Pp3c16_5010' => 'ppa', 'Pp3c16_5060' => 'ppa', 'Pp3c19_18250' => 'ppa', 'Pp3c23_8530' => 'ppa', 'Pp3c23_8550' => 'ppa', 'Pp3c24_9670' => 'ppa', 'Pp3c2_21390' => 'ppa', 'Pp3c2_31380' => 'ppa', 'Pp3c3_16620' => 'ppa', 'Pp3c3_8090' => 'ppa', 'Pp3c3_8110' => 'ppa', 'Pp3c3_8130' => 'ppa', 'Pp3c3_8150' => 'ppa', 'Pp3c4_14320' => 'ppa', 'Pp3c6_2560' => 'ppa', 'Pp3c9_16700' => 'ppa', 'PRCOL_00000234' => 'pco', 'PRCOL_00000235' => 'pco', 'PRCOL_00000777' => 'pco', 'PRCOL_00002344' => 'pco', 'PRCOL_00002372' => 'pco', 'PRCOL_00006120' => 'pco', 'Prupe.1G021400' => 'ppe', 'Prupe.1G021500' => 'ppe', 'Prupe.1G021600' => 'ppe', 'Prupe.1G021700' => 'ppe', 'Prupe.1G021800' => 'ppe', 'Prupe.5G145100' => 'ppe', 'Psat6g204040' => 'psa', 'Psat6g204800' => 'psa', 'Psat6g204920' => 'psa', 'Psat6g204960' => 'psa', 'Psat6g205080' => 'psa', 'PSO017G0271' => 'pso', 'PSO017G1276' => 'pso', 'PSO017G1429' => 'pso', 'PSO017G1861' => 'pso', 'PSO017G2787' => 'pso', 'PSO017G4466' => 'pso', 'PSO017G5118' => 'pso', 'PSO017G5420' => 'pso', 'PSO063G3678' => 'pso', 'PSO210G0546' => 'pso', 'PSO317G0001' => 'pso', 'PSO357G0512' => 'pso', 'PSO478G2682' => 'pso', 'PSO647G0001' => 'pso', 'PSO675G0001' => 'pso', 'PSO675G2699' => 'pso', 'PSO675G2849' => 'pso', 'PSO675G4991' => 'pso', 'PSO689G0001' => 'pso', 'QL06p000916' => 'qlo', 'QL06p000921' => 'qlo', 'QL06p001398' => 'qlo', 'QL06p001407' => 'qlo', 'QL06p002031' => 'qlo', 'RcHm_v2.0_Chr4g0387791' => 'rch', 'RcHm_v2.0_Chr4g0387801' => 'rch', 'RcHm_v2.0_Chr6g0286501' => 'rch', 'RcHm_v2.0_Chr6g0286511' => 'rch', 'RcHm_v2.0_Chr6g0286521' => 'rch', 'RcHm_v2.0_Chr6g0286531' => 'rch', 'RcHm_v2.0_Chr7g0189141' => 'rch', 'Rhsim02G0028700' => 'rsi', 'Rhsim02G0028800' => 'rsi', 'Rhsim02G0028900' => 'rsi', 'Rhsim02G0029000' => 'rsi', 'Rhsim02G0029100' => 'rsi', 'Rhsim02G0029200' => 'rsi', 'Rhsim02G0029300' => 'rsi', 'Rhsim02G0029400' => 'rsi', 'Rhsim02G0029500' => 'rsi', 'Rhsim02G0029600' => 'rsi', 'RhsimUnG0024000' => 'rsi', 'RhsimUnG0024100' => 'rsi', 'RhsimUnG0024200' => 'rsi', 'RhsimUnG0024300' => 'rsi', 'RhsimUnG0024400' => 'rsi', 'RhsimUnG0024500' => 'rsi', 'RhsimUnG0024700' => 'rsi', 'RhsimUnG0024800' => 'rsi', 'RhsimUnG0024900' => 'rsi', 'RhsimUnG0025100' => 'rsi', 'Sabra08G0120200' => 'sbr', 'Sabra08G0120300' => 'sbr', 'Sabra08G0120500' => 'sbr', 'Sabra08G0120600' => 'sbr', 'Sabra10G0158900' => 'sbr', 'SalBow2G3492' => 'sbo', 'Sc13g0004760' => 'sci', 'Sc13g0004770' => 'sci', 'Sed0003417' => 'sed', 'Sed0019750' => 'sed', 'SEGI_03419' => 'sgi', 'SEGI_05907' => 'sgi', 'SEGI_10682' => 'sgi', 'SEGI_13528' => 'sgi', 'SEGI_16081' => 'sgi', 'SEGI_19370' => 'sgi', 'SEGI_21015' => 'sgi', 'SEGI_21944' => 'sgi', 'SEGI_32906' => 'sgi', 'SEGI_33093' => 'sgi', 'SEGI_36110' => 'sgi', 'SEGI_40397' => 'sgi', 'SGA_v2.0_scaffold191G40426' => 'sas', 'SGA_v2.0_scaffold353G49717' => 'sas', 'SGA_v2.0_scaffold50G18550' => 'sas', 'SMO119G0173' => 'smo', 'SMO172G0002' => 'smo', 'Solyc09g082690.3' => 'sly', 'Solyc09g082700.2' => 'sly', 'Sopen09g031550' => 'spe', 'Sopen09g031560' => 'spe', 'Sp3g20540' => 'spa', 'Sp7g07580' => 'spa', 'TAR134G0002' => 'tar', 'TAR236G0001' => 'tar', 'TAR365G0892' => 'tar', 'TAR636G0166' => 'tar', 'TAR636G0646' => 'tar', 'TAR636G0869' => 'tar', 'TAR636G1317' => 'tar', 'TAR636G1744' => 'tar', 'TAR636G3358' => 'tar', 'TAR636G3436' => 'tar', 'THA.LOC104803047' => 'tha', 'Thecc.04G238900' => 'tca', 'Thhalv10021557m.g' => 'esa', 'Thhalv10026318m.g' => 'esa', 'Thhalv10026335m.g' => 'esa', 'TPR.G17433' => 'tpr', 'TPR.G18915' => 'tpr', 'TPR.G26125' => 'tpr', 'TWI09G0677' => 'twi', 'TWI73G0287' => 'twi', 'unitig_748.g8326' => 'ugi', 'vmacro15370' => 'vma', 'vmacro15371' => 'vma', 'vmacro15372' => 'vma', 'vmacro15373' => 'vma', 'vmacro15374' => 'vma', 'VMungo0720G2826' => 'vmu', 'Zm00001eb116960' => 'zma', 'Zm00001eb301260' => 'zma', 'Zm00001eb301270' => 'zma' ) $gf_id = 'HOM05D001460' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001460' ) $data_identifier = 'HOM05D001460' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 4, 'aag' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 2, 'aox' => (int) 2, 'arhy' => (int) 4, 'ath' => (int) 2, 'atr' => (int) 1, 'acertr' => (int) 10, 'cqu' => (int) 4, 'bca' => (int) 11, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 1, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 1, 'ccan' => (int) 1, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 1, 'col' => (int) 1, 'cpa' => (int) 1, 'cre' => (int) 7, 'csa' => (int) 1, 'camsi' => (int) 2, 'dca' => (int) 3, 'din' => (int) 2, 'dzi' => (int) 3, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 14, 'fve' => (int) 9, 'gma' => (int) 2, 'ghi' => (int) 4, 'gra' => (int) 2, 'vvi' => (int) 1, 'han' => (int) 13, 'cav' => (int) 1, 'hma' => (int) 2, 'sun' => (int) 2, 'lal' => (int) 2, 'lonja' => (int) 12, 'lja' => (int) 1, 'lsa' => (int) 7, 'mes' => (int) 1, 'mpo' => (int) 27, 'mbi' => (int) 1, 'mco' => (int) 8, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 1, 'egut' => (int) 1, 'ama' => (int) 1, 'nta' => (int) 4, 'nnu' => (int) 2, 'oeu' => (int) 3, 'osa' => (int) 4, 'pax' => (int) 9, 'pgr' => (int) 1, 'stu' => (int) 1, 'pvu' => (int) 1, 'ptr' => (int) 4, 'ppa' => (int) 22, 'pco' => (int) 6, 'ppe' => (int) 6, 'psa' => (int) 5, 'pso' => (int) 19, 'qlo' => (int) 5, 'rch' => (int) 7, 'rsi' => (int) 20, 'sbr' => (int) 5, 'sbo' => (int) 1, 'sci' => (int) 2, 'sed' => (int) 2, 'sgi' => (int) 12, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 2, 'tar' => (int) 10, 'tha' => (int) 1, 'tca' => (int) 1, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 2, 'ugi' => (int) 1, 'vma' => (int) 5, 'vmu' => (int) 1, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb301270' $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' => 'HOM05D001460', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '433', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p22980' => 'bna', 'A01p32340' => 'bna', 'A03p42970' => 'bna', 'A05p25880' => 'bna', 'Aa31LG8G9320' => 'aar', 'Aa31LG8G9330' => 'aar', 'Aa31LG8G9340' => 'aar', 'Aa31sc221G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1034' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1528' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.829' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2222' => 'aag', 'Ah.12g058830' => 'amhyb', 'Ah.12g058840' => 'amhyb', 'AL3G37160' => 'aly', 'AL7G41310' => 'aly', 'Aqoxy5G00395' => 'aox', 'Aqoxy5G00396' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0C8NZA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5185HY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JZ1PRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MD3LS0' => 'arhy', 'AT3G22840' => 'ath', 'AT4G14690' => 'ath', 'ATR0665G054' => 'atr', 'Atru.chr4.2344' => 'acertr', 'Atru.chr4.2346' => 'acertr', 'Atru.chr4.2347' => 'acertr', 'Atru.chr4.2348' => 'acertr', 'Atru.chr4.2355' => 'acertr', 'Atru.chr4.2356' => 'acertr', 'Atru.chr4.2358' => 'acertr', 'Atru.chr4.2359' => 'acertr', 'Atru.chr4.2360' => 'acertr', 'Atru.chr4.2361' => 'acertr', 'AUR62030476' => 'cqu', 'AUR62030478' => 'cqu', 'AUR62030819' => 'cqu', 'AUR62030820' => 'cqu', 'BcaB03g14648' => 'bca', 'BcaB04g20492' => 'bca', 'BcaB06g26399' => 'bca', 'BcaC01g03416' => 'bca', 'BcaC01g03419' => 'bca', 'BcaC01g03421' => 'bca', 'BcaC01g03424' => 'bca', 'BcaC05g28012' => 'bca', 'BcaC09g49212' => 'bca', 'BcaC09g50140' => 'bca', 'BcaNung00346' => 'bca', 'BolC1t02785H' => 'bol', 'BolC1t04095H' => 'bol', 'BolC3t17545H' => 'bol', 'BolC5t32769H' => 'bol', 'BraA01t02211Z' => 'bra', 'BraA01t03359Z' => 'bra', 'BraA03t13441Z' => 'bra', 'BraA05t21476Z' => 'bra', 'C01p28420' => 'bna', 'C01p41350' => 'bna', 'C03p52750' => 'bna', 'C03p52780' => 'bna', 'C05p40270' => 'bna', 'CAN.G1437.9' => 'can', 'CANSAT78G0035' => 'cansat', 'CANSAT78G1036' => 'cansat', 'CANSAT78G2272' => 'cansat', 'CANSAT78G2478' => 'cansat', 'CARHR098700' => 'chi', 'CARHR221120' => 'chi', 'CARHR221150' => 'chi', 'Carub.0003s2297' => 'cru', 'Carub.0007s2749' => 'cru', 'Carub.0007s2750' => 'cru', 'Carub.0007s2751' => 'cru', 'Ca_10849_v3' => 'car', 'Cc03_g04300' => 'ccan', 'CDE02G3648' => 'cde', 'CDE05G0060' => 'cde', 'CDE05G0692' => 'cde', 'CDE05G2285' => 'cde', 'CDE05G2884' => 'cde', 'CDE05G3072' => 'cde', 'Cfa008439' => 'cfa', 'Cfa008441' => 'cfa', 'Cfa008443' => 'cfa', 'Cfa008448' => 'cfa', 'Ciclev10005974m.g' => 'ccl', 'Ciclev10006006m.g' => 'ccl', 'Ciclev10006775m.g' => 'ccl', 'CiPaw.02G120400' => 'cil', 'CiPaw.02G120500' => 'cil', 'CiPaw.02G120600' => 'cil', 'ClCG05G004850' => 'cla', 'COL.COLO4_21566' => 'col', 'Cpa.g.sc44.124' => 'cpa', 'Cre07.g320400' => 'cre', 'Cre07.g320450' => 'cre', 'Cre08.g384650' => 'cre', 'Cre09.g393173' => 'cre', 'Cre09.g394325' => 'cre', 'Cre14.g626750' => 'cre', 'Cre16.g679250' => 'cre', 'CsaV3_3G012890' => 'csa', 'CSS0010865' => 'camsi', 'CSS0044338' => 'camsi', 'DCAR_002366' => 'dca', 'DCAR_030687' => 'dca', 'DCAR_030688' => 'dca', 'Dinv14047' => 'din', 'Dinv14048' => 'din', 'Duzib151G0105' => 'dzi', 'Duzib151G0114' => 'dzi', 'Duzib212G1029' => 'dzi', 'ECA232G3536' => 'eca', 'ECA240G0786' => 'eca', 'ECA240G1802' => 'eca', 'ECA240G3760' => 'eca', 'ECA240G3920' => 'eca', 'EL10Ac5g12536' => 'bvu', 'EL10Ac5g12537' => 'bvu', 'EL10Ac5g12538' => 'bvu', 'Eucgr.B01004' => 'egr', 'Eucgr.B01006' => 'egr', 'Eucgr.B01007' => 'egr', 'Eucgr.B01008' => 'egr', 'Eucgr.B01895' => 'egr', 'Eucgr.B01896' => 'egr', 'FAN04G1456' => 'fan', 'FAN08G1769' => 'fan', 'FAN08G2160' => 'fan', 'FAN13G2403' => 'fan', 'FAN13G3303' => 'fan', 'FAN15G2435' => 'fan', 'FAN17G0672' => 'fan', 'FAN17G2441' => 'fan', 'FAN18G1024' => 'fan', 'FAN22G1458' => 'fan', 'FAN24G0037' => 'fan', 'FAN24G0429' => 'fan', 'FAN24G2387' => 'fan', 'FAN27G2746' => 'fan', 'FvH4_2g20400' => 'fve', 'FvH4_2g20420' => 'fve', 'FvH4_2g20430' => 'fve', 'FvH4_4g01270' => 'fve', 'FvH4_4g01290' => 'fve', 'FvH4_4g01300' => 'fve', 'FvH4_4g01310' => 'fve', 'FvH4_4g01330' => 'fve', 'FvH4_5g09070' => 'fve', 'Glyma.10G243800' => 'gma', 'Glyma.20G150600' => 'gma', 'Gohir.A09G219200' => 'ghi', 'Gohir.A09G219300' => 'ghi', 'Gohir.D09G221400' => 'ghi', 'Gohir.D09G221500' => 'ghi', 'Gorai.006G242600' => 'gra', 'Gorai.006G242700' => 'gra', 'GSVIVG01018044001' => 'vvi', 'HanXRQChr03g0083821' => 'han', 'HanXRQChr03g0083841' => 'han', 'HanXRQChr03g0083881' => 'han', 'HanXRQChr03g0083901' => 'han', 'HanXRQChr03g0083921' => 'han', 'HanXRQChr03g0085331' => 'han', 'HanXRQChr03g0085361' => 'han', 'HanXRQChr03g0085411' => 'han', 'HanXRQChr03g0085421' => 'han', 'HanXRQChr03g0085431' => 'han', 'HanXRQChr08g0221991' => 'han', 'HanXRQChr11g0336061' => 'han', 'HanXRQChr11g0336411' => 'han', 'Haze_11234' => 'cav', 'Hma1.2p1_0549F.1_g177010' => 'hma', 'Hma1.2p1_0602F.1_g187630' => 'hma', 'Hund14876' => 'sun', 'Hund14879' => 'sun', 'Lalb_Chr06g0160741' => 'lal', 'Lalb_Chr21g0304781' => 'lal', 'Lj3A726G19' => 'lonja', 'Lj3A726T23' => 'lonja', 'Lj3A726T24' => 'lonja', 'Lj3A726T25' => 'lonja', 'Lj3A727T17' => 'lonja', 'Lj3C726T0' => 'lonja', 'Lj3C726T2' => 'lonja', 'Lj3P725T35' => 'lonja', 'Lj3P727T10' => 'lonja', 'Lj3P727T12' => 'lonja', 'Lj3P727T14' => 'lonja', 'Lj5g0023109' => 'lja', 'Lj6P646T44' => 'lonja', 'Lsat_1_v5_gn_6_75760' => 'lsa', 'Lsat_1_v5_gn_6_75800' => 'lsa', 'Lsat_1_v5_gn_6_75900' => 'lsa', 'Lsat_1_v5_gn_6_76240' => 'lsa', 'Lsat_1_v5_gn_6_76441' => 'lsa', 'Lsat_1_v5_gn_6_76700' => 'lsa', 'Lsat_1_v5_gn_6_76760' => 'lsa', 'Manes.15G033100' => 'mes', 'Mapoly0004s0074' => 'mpo', 'Mapoly0004s0075' => 'mpo', 'Mapoly0004s0163' => 'mpo', 'Mapoly0004s0164' => 'mpo', 'Mapoly0021s0018' => 'mpo', 'Mapoly0041s0136' => 'mpo', 'Mapoly0041s0137' => 'mpo', 'Mapoly0041s0138' => 'mpo', 'Mapoly0041s0139' => 'mpo', 'Mapoly0041s0141' => 'mpo', 'Mapoly0041s0142' => 'mpo', 'Mapoly0041s0143' => 'mpo', 'Mapoly0041s0144' => 'mpo', 'Mapoly0041s0145' => 'mpo', 'Mapoly0047s0106' => 'mpo', 'Mapoly0047s0108' => 'mpo', 'Mapoly0050s0051' => 'mpo', 'Mapoly0050s0052' => 'mpo', 'Mapoly0050s0053' => 'mpo', 'Mapoly0058s0013' => 'mpo', 'Mapoly0091s0078' => 'mpo', 'Mapoly0091s0079' => 'mpo', 'Mapoly0091s0080' => 'mpo', 'Mapoly0091s0081' => 'mpo', 'Mapoly0278s0004' => 'mpo', 'Mapoly0278s0005' => 'mpo', 'Mapoly0278s0006' => 'mpo', 'MBI11_g30648_MAGBIO' => 'mbi', 'MCO03G194' => 'mco', 'MCO03G590' => 'mco', 'MCO07G312' => 'mco', 'MCO10G318' => 'mco', 'MCO12G244' => 'mco', 'MCO13G148' => 'mco', 'MCO13G194' => 'mco', 'MCO16G238' => 'mco', 'MD06G1134100' => 'mdo', 'MD13G1200100' => 'mdo', 'MD13G1200300' => 'mdo', 'MD13G1200600' => 'mdo', 'MD14G1150400' => 'mdo', 'MD16G1200000' => 'mdo', 'Medtr1g102570' => 'mtr', 'Medtr1g102780' => 'mtr', 'Medtr1g102800' => 'mtr', 'Medtr1g102810' => 'mtr', 'Medtr1g102830' => 'mtr', 'MELO3C006499.2' => 'cme', 'Migut.G00385' => 'egut', 'MSTRG.4063' => 'ama', 'Nitab4.5_0000090g0260' => 'nta', 'Nitab4.5_0000977g0030' => 'nta', 'Nitab4.5_0002541g0040' => 'nta', 'Nitab4.5_0007068g0040' => 'nta', 'Nn005s41408' => 'nnu', 'Nn005s41410' => 'nnu', 'Oeu010310.1' => 'oeu', 'Oeu010311.1' => 'oeu', 'Oeu043472.1' => 'oeu', 'Os01g0246400' => 'osa', 'Os04g0267950' => 'osa', 'Os07g0178700' => 'osa', 'Os07g0178800' => 'osa', 'Peaxi162Scf00316g00046' => 'pax', 'Peaxi162Scf00316g00049' => 'pax', 'Peaxi162Scf00316g00059' => 'pax', 'Peaxi162Scf00316g00328' => 'pax', 'Peaxi162Scf00316g00329' => 'pax', 'Peaxi162Scf00316g00411' => 'pax', 'Peaxi162Scf00316g00521' => 'pax', 'Peaxi162Scf00492g00068' => 'pax', 'Peaxi162Scf35631g00002' => 'pax', 'PGR142G3720' => 'pgr', 'PGSC0003DMG400006442' => 'stu', 'Phvul.007G062000' => 'pvu', 'Potri.008G157750' => 'ptr', 'Potri.008G157900' => 'ptr', 'Potri.008G158000' => 'ptr', 'Potri.008G158200' => 'ptr', 'Pp3c11_7280' => 'ppa', 'Pp3c11_7980' => 'ppa', 'Pp3c12_19450' => 'ppa', 'Pp3c14_1480' => 'ppa', 'Pp3c14_1501' => 'ppa', 'Pp3c16_4900' => 'ppa', 'Pp3c16_5010' => 'ppa', 'Pp3c16_5060' => 'ppa', 'Pp3c19_18250' => 'ppa', 'Pp3c23_8530' => 'ppa', 'Pp3c23_8550' => 'ppa', 'Pp3c24_9670' => 'ppa', 'Pp3c2_21390' => 'ppa', 'Pp3c2_31380' => 'ppa', 'Pp3c3_16620' => 'ppa', 'Pp3c3_8090' => 'ppa', 'Pp3c3_8110' => 'ppa', 'Pp3c3_8130' => 'ppa', 'Pp3c3_8150' => 'ppa', 'Pp3c4_14320' => 'ppa', 'Pp3c6_2560' => 'ppa', 'Pp3c9_16700' => 'ppa', 'PRCOL_00000234' => 'pco', 'PRCOL_00000235' => 'pco', 'PRCOL_00000777' => 'pco', 'PRCOL_00002344' => 'pco', 'PRCOL_00002372' => 'pco', 'PRCOL_00006120' => 'pco', 'Prupe.1G021400' => 'ppe', 'Prupe.1G021500' => 'ppe', 'Prupe.1G021600' => 'ppe', 'Prupe.1G021700' => 'ppe', 'Prupe.1G021800' => 'ppe', 'Prupe.5G145100' => 'ppe', 'Psat6g204040' => 'psa', 'Psat6g204800' => 'psa', 'Psat6g204920' => 'psa', 'Psat6g204960' => 'psa', 'Psat6g205080' => 'psa', 'PSO017G0271' => 'pso', 'PSO017G1276' => 'pso', 'PSO017G1429' => 'pso', 'PSO017G1861' => 'pso', 'PSO017G2787' => 'pso', 'PSO017G4466' => 'pso', 'PSO017G5118' => 'pso', 'PSO017G5420' => 'pso', 'PSO063G3678' => 'pso', 'PSO210G0546' => 'pso', 'PSO317G0001' => 'pso', 'PSO357G0512' => 'pso', 'PSO478G2682' => 'pso', 'PSO647G0001' => 'pso', 'PSO675G0001' => 'pso', 'PSO675G2699' => 'pso', 'PSO675G2849' => 'pso', 'PSO675G4991' => 'pso', 'PSO689G0001' => 'pso', 'QL06p000916' => 'qlo', 'QL06p000921' => 'qlo', 'QL06p001398' => 'qlo', 'QL06p001407' => 'qlo', 'QL06p002031' => 'qlo', 'RcHm_v2.0_Chr4g0387791' => 'rch', 'RcHm_v2.0_Chr4g0387801' => 'rch', 'RcHm_v2.0_Chr6g0286501' => 'rch', 'RcHm_v2.0_Chr6g0286511' => 'rch', 'RcHm_v2.0_Chr6g0286521' => 'rch', 'RcHm_v2.0_Chr6g0286531' => 'rch', 'RcHm_v2.0_Chr7g0189141' => 'rch', 'Rhsim02G0028700' => 'rsi', 'Rhsim02G0028800' => 'rsi', 'Rhsim02G0028900' => 'rsi', 'Rhsim02G0029000' => 'rsi', 'Rhsim02G0029100' => 'rsi', 'Rhsim02G0029200' => 'rsi', 'Rhsim02G0029300' => 'rsi', 'Rhsim02G0029400' => 'rsi', 'Rhsim02G0029500' => 'rsi', 'Rhsim02G0029600' => 'rsi', 'RhsimUnG0024000' => 'rsi', 'RhsimUnG0024100' => 'rsi', 'RhsimUnG0024200' => 'rsi', 'RhsimUnG0024300' => 'rsi', 'RhsimUnG0024400' => 'rsi', 'RhsimUnG0024500' => 'rsi', 'RhsimUnG0024700' => 'rsi', 'RhsimUnG0024800' => 'rsi', 'RhsimUnG0024900' => 'rsi', 'RhsimUnG0025100' => 'rsi', 'Sabra08G0120200' => 'sbr', 'Sabra08G0120300' => 'sbr', 'Sabra08G0120500' => 'sbr', 'Sabra08G0120600' => 'sbr', 'Sabra10G0158900' => 'sbr', 'SalBow2G3492' => 'sbo', 'Sc13g0004760' => 'sci', 'Sc13g0004770' => 'sci', 'Sed0003417' => 'sed', 'Sed0019750' => 'sed', 'SEGI_03419' => 'sgi', 'SEGI_05907' => 'sgi', 'SEGI_10682' => 'sgi', 'SEGI_13528' => 'sgi', 'SEGI_16081' => 'sgi', 'SEGI_19370' => 'sgi', 'SEGI_21015' => 'sgi', 'SEGI_21944' => 'sgi', 'SEGI_32906' => 'sgi', 'SEGI_33093' => 'sgi', 'SEGI_36110' => 'sgi', 'SEGI_40397' => 'sgi', 'SGA_v2.0_scaffold191G40426' => 'sas', 'SGA_v2.0_scaffold353G49717' => 'sas', 'SGA_v2.0_scaffold50G18550' => 'sas', 'SMO119G0173' => 'smo', 'SMO172G0002' => 'smo', 'Solyc09g082690.3' => 'sly', 'Solyc09g082700.2' => 'sly', 'Sopen09g031550' => 'spe', 'Sopen09g031560' => 'spe', 'Sp3g20540' => 'spa', 'Sp7g07580' => 'spa', 'TAR134G0002' => 'tar', 'TAR236G0001' => 'tar', 'TAR365G0892' => 'tar', 'TAR636G0166' => 'tar', 'TAR636G0646' => 'tar', 'TAR636G0869' => 'tar', 'TAR636G1317' => 'tar', 'TAR636G1744' => 'tar', 'TAR636G3358' => 'tar', 'TAR636G3436' => 'tar', 'THA.LOC104803047' => 'tha', 'Thecc.04G238900' => 'tca', 'Thhalv10021557m.g' => 'esa', 'Thhalv10026318m.g' => 'esa', 'Thhalv10026335m.g' => 'esa', 'TPR.G17433' => 'tpr', 'TPR.G18915' => 'tpr', 'TPR.G26125' => 'tpr', 'TWI09G0677' => 'twi', 'TWI73G0287' => 'twi', 'unitig_748.g8326' => 'ugi', 'vmacro15370' => 'vma', 'vmacro15371' => 'vma', 'vmacro15372' => 'vma', 'vmacro15373' => 'vma', 'vmacro15374' => 'vma', 'VMungo0720G2826' => 'vmu', 'Zm00001eb116960' => 'zma', 'Zm00001eb301260' => 'zma', 'Zm00001eb301270' => 'zma' ), 'gf_id' => 'HOM05D001460', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001460' ), 'data_identifier' => 'HOM05D001460', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001460', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '433', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p22980' => 'bna', 'A01p32340' => 'bna', 'A03p42970' => 'bna', 'A05p25880' => 'bna', 'Aa31LG8G9320' => 'aar', 'Aa31LG8G9330' => 'aar', 'Aa31LG8G9340' => 'aar', 'Aa31sc221G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1034' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1528' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.829' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2222' => 'aag', 'Ah.12g058830' => 'amhyb', 'Ah.12g058840' => 'amhyb', 'AL3G37160' => 'aly', 'AL7G41310' => 'aly', 'Aqoxy5G00395' => 'aox', 'Aqoxy5G00396' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0C8NZA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5185HY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JZ1PRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MD3LS0' => 'arhy', 'AT3G22840' => 'ath', 'AT4G14690' => 'ath', 'ATR0665G054' => 'atr', 'Atru.chr4.2344' => 'acertr', 'Atru.chr4.2346' => 'acertr', 'Atru.chr4.2347' => 'acertr', 'Atru.chr4.2348' => 'acertr', 'Atru.chr4.2355' => 'acertr', 'Atru.chr4.2356' => 'acertr', 'Atru.chr4.2358' => 'acertr', 'Atru.chr4.2359' => 'acertr', 'Atru.chr4.2360' => 'acertr', 'Atru.chr4.2361' => 'acertr', 'AUR62030476' => 'cqu', 'AUR62030478' => 'cqu', 'AUR62030819' => 'cqu', 'AUR62030820' => 'cqu', 'BcaB03g14648' => 'bca', 'BcaB04g20492' => 'bca', 'BcaB06g26399' => 'bca', 'BcaC01g03416' => 'bca', 'BcaC01g03419' => 'bca', 'BcaC01g03421' => 'bca', 'BcaC01g03424' => 'bca', 'BcaC05g28012' => 'bca', 'BcaC09g49212' => 'bca', 'BcaC09g50140' => 'bca', 'BcaNung00346' => 'bca', 'BolC1t02785H' => 'bol', 'BolC1t04095H' => 'bol', 'BolC3t17545H' => 'bol', 'BolC5t32769H' => 'bol', 'BraA01t02211Z' => 'bra', 'BraA01t03359Z' => 'bra', 'BraA03t13441Z' => 'bra', 'BraA05t21476Z' => 'bra', 'C01p28420' => 'bna', 'C01p41350' => 'bna', 'C03p52750' => 'bna', 'C03p52780' => 'bna', 'C05p40270' => 'bna', 'CAN.G1437.9' => 'can', 'CANSAT78G0035' => 'cansat', 'CANSAT78G1036' => 'cansat', 'CANSAT78G2272' => 'cansat', 'CANSAT78G2478' => 'cansat', 'CARHR098700' => 'chi', 'CARHR221120' => 'chi', 'CARHR221150' => 'chi', 'Carub.0003s2297' => 'cru', 'Carub.0007s2749' => 'cru', 'Carub.0007s2750' => 'cru', 'Carub.0007s2751' => 'cru', 'Ca_10849_v3' => 'car', 'Cc03_g04300' => 'ccan', 'CDE02G3648' => 'cde', 'CDE05G0060' => 'cde', 'CDE05G0692' => 'cde', 'CDE05G2285' => 'cde', 'CDE05G2884' => 'cde', 'CDE05G3072' => 'cde', 'Cfa008439' => 'cfa', 'Cfa008441' => 'cfa', 'Cfa008443' => 'cfa', 'Cfa008448' => 'cfa', 'Ciclev10005974m.g' => 'ccl', 'Ciclev10006006m.g' => 'ccl', 'Ciclev10006775m.g' => 'ccl', 'CiPaw.02G120400' => 'cil', 'CiPaw.02G120500' => 'cil', 'CiPaw.02G120600' => 'cil', 'ClCG05G004850' => 'cla', 'COL.COLO4_21566' => 'col', 'Cpa.g.sc44.124' => 'cpa', 'Cre07.g320400' => 'cre', 'Cre07.g320450' => 'cre', 'Cre08.g384650' => 'cre', 'Cre09.g393173' => 'cre', 'Cre09.g394325' => 'cre', 'Cre14.g626750' => 'cre', 'Cre16.g679250' => 'cre', 'CsaV3_3G012890' => 'csa', 'CSS0010865' => 'camsi', 'CSS0044338' => 'camsi', 'DCAR_002366' => 'dca', 'DCAR_030687' => 'dca', 'DCAR_030688' => 'dca', 'Dinv14047' => 'din', 'Dinv14048' => 'din', 'Duzib151G0105' => 'dzi', 'Duzib151G0114' => 'dzi', 'Duzib212G1029' => 'dzi', 'ECA232G3536' => 'eca', 'ECA240G0786' => 'eca', 'ECA240G1802' => 'eca', 'ECA240G3760' => 'eca', 'ECA240G3920' => 'eca', 'EL10Ac5g12536' => 'bvu', 'EL10Ac5g12537' => 'bvu', 'EL10Ac5g12538' => 'bvu', 'Eucgr.B01004' => 'egr', 'Eucgr.B01006' => 'egr', 'Eucgr.B01007' => 'egr', 'Eucgr.B01008' => 'egr', 'Eucgr.B01895' => 'egr', 'Eucgr.B01896' => 'egr', 'FAN04G1456' => 'fan', 'FAN08G1769' => 'fan', 'FAN08G2160' => 'fan', 'FAN13G2403' => 'fan', 'FAN13G3303' => 'fan', 'FAN15G2435' => 'fan', 'FAN17G0672' => 'fan', 'FAN17G2441' => 'fan', 'FAN18G1024' => 'fan', 'FAN22G1458' => 'fan', 'FAN24G0037' => 'fan', 'FAN24G0429' => 'fan', 'FAN24G2387' => 'fan', 'FAN27G2746' => 'fan', 'FvH4_2g20400' => 'fve', 'FvH4_2g20420' => 'fve', 'FvH4_2g20430' => 'fve', 'FvH4_4g01270' => 'fve', 'FvH4_4g01290' => 'fve', 'FvH4_4g01300' => 'fve', 'FvH4_4g01310' => 'fve', 'FvH4_4g01330' => 'fve', 'FvH4_5g09070' => 'fve', 'Glyma.10G243800' => 'gma', 'Glyma.20G150600' => 'gma', 'Gohir.A09G219200' => 'ghi', 'Gohir.A09G219300' => 'ghi', 'Gohir.D09G221400' => 'ghi', 'Gohir.D09G221500' => 'ghi', 'Gorai.006G242600' => 'gra', 'Gorai.006G242700' => 'gra', 'GSVIVG01018044001' => 'vvi', 'HanXRQChr03g0083821' => 'han', 'HanXRQChr03g0083841' => 'han', 'HanXRQChr03g0083881' => 'han', 'HanXRQChr03g0083901' => 'han', 'HanXRQChr03g0083921' => 'han', 'HanXRQChr03g0085331' => 'han', 'HanXRQChr03g0085361' => 'han', 'HanXRQChr03g0085411' => 'han', 'HanXRQChr03g0085421' => 'han', 'HanXRQChr03g0085431' => 'han', 'HanXRQChr08g0221991' => 'han', 'HanXRQChr11g0336061' => 'han', 'HanXRQChr11g0336411' => 'han', 'Haze_11234' => 'cav', 'Hma1.2p1_0549F.1_g177010' => 'hma', 'Hma1.2p1_0602F.1_g187630' => 'hma', 'Hund14876' => 'sun', 'Hund14879' => 'sun', 'Lalb_Chr06g0160741' => 'lal', 'Lalb_Chr21g0304781' => 'lal', 'Lj3A726G19' => 'lonja', 'Lj3A726T23' => 'lonja', 'Lj3A726T24' => 'lonja', 'Lj3A726T25' => 'lonja', 'Lj3A727T17' => 'lonja', 'Lj3C726T0' => 'lonja', 'Lj3C726T2' => 'lonja', 'Lj3P725T35' => 'lonja', 'Lj3P727T10' => 'lonja', 'Lj3P727T12' => 'lonja', 'Lj3P727T14' => 'lonja', 'Lj5g0023109' => 'lja', 'Lj6P646T44' => 'lonja', 'Lsat_1_v5_gn_6_75760' => 'lsa', 'Lsat_1_v5_gn_6_75800' => 'lsa', 'Lsat_1_v5_gn_6_75900' => 'lsa', 'Lsat_1_v5_gn_6_76240' => 'lsa', 'Lsat_1_v5_gn_6_76441' => 'lsa', 'Lsat_1_v5_gn_6_76700' => 'lsa', 'Lsat_1_v5_gn_6_76760' => 'lsa', 'Manes.15G033100' => 'mes', 'Mapoly0004s0074' => 'mpo', 'Mapoly0004s0075' => 'mpo', 'Mapoly0004s0163' => 'mpo', 'Mapoly0004s0164' => 'mpo', 'Mapoly0021s0018' => 'mpo', 'Mapoly0041s0136' => 'mpo', 'Mapoly0041s0137' => 'mpo', 'Mapoly0041s0138' => 'mpo', 'Mapoly0041s0139' => 'mpo', 'Mapoly0041s0141' => 'mpo', 'Mapoly0041s0142' => 'mpo', 'Mapoly0041s0143' => 'mpo', 'Mapoly0041s0144' => 'mpo', 'Mapoly0041s0145' => 'mpo', 'Mapoly0047s0106' => 'mpo', 'Mapoly0047s0108' => 'mpo', 'Mapoly0050s0051' => 'mpo', 'Mapoly0050s0052' => 'mpo', 'Mapoly0050s0053' => 'mpo', 'Mapoly0058s0013' => 'mpo', 'Mapoly0091s0078' => 'mpo', 'Mapoly0091s0079' => 'mpo', 'Mapoly0091s0080' => 'mpo', 'Mapoly0091s0081' => 'mpo', 'Mapoly0278s0004' => 'mpo', 'Mapoly0278s0005' => 'mpo', 'Mapoly0278s0006' => 'mpo', 'MBI11_g30648_MAGBIO' => 'mbi', 'MCO03G194' => 'mco', 'MCO03G590' => 'mco', 'MCO07G312' => 'mco', 'MCO10G318' => 'mco', 'MCO12G244' => 'mco', 'MCO13G148' => 'mco', 'MCO13G194' => 'mco', 'MCO16G238' => 'mco', 'MD06G1134100' => 'mdo', 'MD13G1200100' => 'mdo', 'MD13G1200300' => 'mdo', 'MD13G1200600' => 'mdo', 'MD14G1150400' => 'mdo', 'MD16G1200000' => 'mdo', 'Medtr1g102570' => 'mtr', 'Medtr1g102780' => 'mtr', 'Medtr1g102800' => 'mtr', 'Medtr1g102810' => 'mtr', 'Medtr1g102830' => 'mtr', 'MELO3C006499.2' => 'cme', 'Migut.G00385' => 'egut', 'MSTRG.4063' => 'ama', 'Nitab4.5_0000090g0260' => 'nta', 'Nitab4.5_0000977g0030' => 'nta', 'Nitab4.5_0002541g0040' => 'nta', 'Nitab4.5_0007068g0040' => 'nta', 'Nn005s41408' => 'nnu', 'Nn005s41410' => 'nnu', 'Oeu010310.1' => 'oeu', 'Oeu010311.1' => 'oeu', 'Oeu043472.1' => 'oeu', 'Os01g0246400' => 'osa', 'Os04g0267950' => 'osa', 'Os07g0178700' => 'osa', 'Os07g0178800' => 'osa', 'Peaxi162Scf00316g00046' => 'pax', 'Peaxi162Scf00316g00049' => 'pax', 'Peaxi162Scf00316g00059' => 'pax', 'Peaxi162Scf00316g00328' => 'pax', 'Peaxi162Scf00316g00329' => 'pax', 'Peaxi162Scf00316g00411' => 'pax', 'Peaxi162Scf00316g00521' => 'pax', 'Peaxi162Scf00492g00068' => 'pax', 'Peaxi162Scf35631g00002' => 'pax', 'PGR142G3720' => 'pgr', 'PGSC0003DMG400006442' => 'stu', 'Phvul.007G062000' => 'pvu', 'Potri.008G157750' => 'ptr', 'Potri.008G157900' => 'ptr', 'Potri.008G158000' => 'ptr', 'Potri.008G158200' => 'ptr', 'Pp3c11_7280' => 'ppa', 'Pp3c11_7980' => 'ppa', 'Pp3c12_19450' => 'ppa', 'Pp3c14_1480' => 'ppa', 'Pp3c14_1501' => 'ppa', 'Pp3c16_4900' => 'ppa', 'Pp3c16_5010' => 'ppa', 'Pp3c16_5060' => 'ppa', 'Pp3c19_18250' => 'ppa', 'Pp3c23_8530' => 'ppa', 'Pp3c23_8550' => 'ppa', 'Pp3c24_9670' => 'ppa', 'Pp3c2_21390' => 'ppa', 'Pp3c2_31380' => 'ppa', 'Pp3c3_16620' => 'ppa', 'Pp3c3_8090' => 'ppa', 'Pp3c3_8110' => 'ppa', 'Pp3c3_8130' => 'ppa', 'Pp3c3_8150' => 'ppa', 'Pp3c4_14320' => 'ppa', 'Pp3c6_2560' => 'ppa', 'Pp3c9_16700' => 'ppa', 'PRCOL_00000234' => 'pco', 'PRCOL_00000235' => 'pco', 'PRCOL_00000777' => 'pco', 'PRCOL_00002344' => 'pco', 'PRCOL_00002372' => 'pco', 'PRCOL_00006120' => 'pco', 'Prupe.1G021400' => 'ppe', 'Prupe.1G021500' => 'ppe', 'Prupe.1G021600' => 'ppe', 'Prupe.1G021700' => 'ppe', 'Prupe.1G021800' => 'ppe', 'Prupe.5G145100' => 'ppe', 'Psat6g204040' => 'psa', 'Psat6g204800' => 'psa', 'Psat6g204920' => 'psa', 'Psat6g204960' => 'psa', 'Psat6g205080' => 'psa', 'PSO017G0271' => 'pso', 'PSO017G1276' => 'pso', 'PSO017G1429' => 'pso', 'PSO017G1861' => 'pso', 'PSO017G2787' => 'pso', 'PSO017G4466' => 'pso', 'PSO017G5118' => 'pso', 'PSO017G5420' => 'pso', 'PSO063G3678' => 'pso', 'PSO210G0546' => 'pso', 'PSO317G0001' => 'pso', 'PSO357G0512' => 'pso', 'PSO478G2682' => 'pso', 'PSO647G0001' => 'pso', 'PSO675G0001' => 'pso', 'PSO675G2699' => 'pso', 'PSO675G2849' => 'pso', 'PSO675G4991' => 'pso', 'PSO689G0001' => 'pso', 'QL06p000916' => 'qlo', 'QL06p000921' => 'qlo', 'QL06p001398' => 'qlo', 'QL06p001407' => 'qlo', 'QL06p002031' => 'qlo', 'RcHm_v2.0_Chr4g0387791' => 'rch', 'RcHm_v2.0_Chr4g0387801' => 'rch', 'RcHm_v2.0_Chr6g0286501' => 'rch', 'RcHm_v2.0_Chr6g0286511' => 'rch', 'RcHm_v2.0_Chr6g0286521' => 'rch', 'RcHm_v2.0_Chr6g0286531' => 'rch', 'RcHm_v2.0_Chr7g0189141' => 'rch', 'Rhsim02G0028700' => 'rsi', 'Rhsim02G0028800' => 'rsi', 'Rhsim02G0028900' => 'rsi', 'Rhsim02G0029000' => 'rsi', 'Rhsim02G0029100' => 'rsi', 'Rhsim02G0029200' => 'rsi', 'Rhsim02G0029300' => 'rsi', 'Rhsim02G0029400' => 'rsi', 'Rhsim02G0029500' => 'rsi', 'Rhsim02G0029600' => 'rsi', 'RhsimUnG0024000' => 'rsi', 'RhsimUnG0024100' => 'rsi', 'RhsimUnG0024200' => 'rsi', 'RhsimUnG0024300' => 'rsi', 'RhsimUnG0024400' => 'rsi', 'RhsimUnG0024500' => 'rsi', 'RhsimUnG0024700' => 'rsi', 'RhsimUnG0024800' => 'rsi', 'RhsimUnG0024900' => 'rsi', 'RhsimUnG0025100' => 'rsi', 'Sabra08G0120200' => 'sbr', 'Sabra08G0120300' => 'sbr', 'Sabra08G0120500' => 'sbr', 'Sabra08G0120600' => 'sbr', 'Sabra10G0158900' => 'sbr', 'SalBow2G3492' => 'sbo', 'Sc13g0004760' => 'sci', 'Sc13g0004770' => 'sci', 'Sed0003417' => 'sed', 'Sed0019750' => 'sed', 'SEGI_03419' => 'sgi', 'SEGI_05907' => 'sgi', 'SEGI_10682' => 'sgi', 'SEGI_13528' => 'sgi', 'SEGI_16081' => 'sgi', 'SEGI_19370' => 'sgi', 'SEGI_21015' => 'sgi', 'SEGI_21944' => 'sgi', 'SEGI_32906' => 'sgi', 'SEGI_33093' => 'sgi', 'SEGI_36110' => 'sgi', 'SEGI_40397' => 'sgi', 'SGA_v2.0_scaffold191G40426' => 'sas', 'SGA_v2.0_scaffold353G49717' => 'sas', 'SGA_v2.0_scaffold50G18550' => 'sas', 'SMO119G0173' => 'smo', 'SMO172G0002' => 'smo', 'Solyc09g082690.3' => 'sly', 'Solyc09g082700.2' => 'sly', 'Sopen09g031550' => 'spe', 'Sopen09g031560' => 'spe', 'Sp3g20540' => 'spa', 'Sp7g07580' => 'spa', 'TAR134G0002' => 'tar', 'TAR236G0001' => 'tar', 'TAR365G0892' => 'tar', 'TAR636G0166' => 'tar', 'TAR636G0646' => 'tar', 'TAR636G0869' => 'tar', 'TAR636G1317' => 'tar', 'TAR636G1744' => 'tar', 'TAR636G3358' => 'tar', 'TAR636G3436' => 'tar', 'THA.LOC104803047' => 'tha', 'Thecc.04G238900' => 'tca', 'Thhalv10021557m.g' => 'esa', 'Thhalv10026318m.g' => 'esa', 'Thhalv10026335m.g' => 'esa', 'TPR.G17433' => 'tpr', 'TPR.G18915' => 'tpr', 'TPR.G26125' => 'tpr', 'TWI09G0677' => 'twi', 'TWI73G0287' => 'twi', 'unitig_748.g8326' => 'ugi', 'vmacro15370' => 'vma', 'vmacro15371' => 'vma', 'vmacro15372' => 'vma', 'vmacro15373' => 'vma', 'vmacro15374' => 'vma', 'VMungo0720G2826' => 'vmu', 'Zm00001eb116960' => 'zma', 'Zm00001eb301260' => 'zma', 'Zm00001eb301270' => 'zma' ) $gf_id = 'HOM05D001460' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001460' ) $data_identifier = 'HOM05D001460' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 4, 'aag' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 2, 'aox' => (int) 2, 'arhy' => (int) 4, 'ath' => (int) 2, 'atr' => (int) 1, 'acertr' => (int) 10, 'cqu' => (int) 4, 'bca' => (int) 11, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 1, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 1, 'ccan' => (int) 1, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 1, 'col' => (int) 1, 'cpa' => (int) 1, 'cre' => (int) 7, 'csa' => (int) 1, 'camsi' => (int) 2, 'dca' => (int) 3, 'din' => (int) 2, 'dzi' => (int) 3, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 14, 'fve' => (int) 9, 'gma' => (int) 2, 'ghi' => (int) 4, 'gra' => (int) 2, 'vvi' => (int) 1, 'han' => (int) 13, 'cav' => (int) 1, 'hma' => (int) 2, 'sun' => (int) 2, 'lal' => (int) 2, 'lonja' => (int) 12, 'lja' => (int) 1, 'lsa' => (int) 7, 'mes' => (int) 1, 'mpo' => (int) 27, 'mbi' => (int) 1, 'mco' => (int) 8, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 1, 'egut' => (int) 1, 'ama' => (int) 1, 'nta' => (int) 4, 'nnu' => (int) 2, 'oeu' => (int) 3, 'osa' => (int) 4, 'pax' => (int) 9, 'pgr' => (int) 1, 'stu' => (int) 1, 'pvu' => (int) 1, 'ptr' => (int) 4, 'ppa' => (int) 22, 'pco' => (int) 6, 'ppe' => (int) 6, 'psa' => (int) 5, 'pso' => (int) 19, 'qlo' => (int) 5, 'rch' => (int) 7, 'rsi' => (int) 20, 'sbr' => (int) 5, 'sbo' => (int) 1, 'sci' => (int) 2, 'sed' => (int) 2, 'sgi' => (int) 12, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 2, 'tar' => (int) 10, 'tha' => (int) 1, 'tca' => (int) 1, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 2, 'ugi' => (int) 1, 'vma' => (int) 5, 'vmu' => (int) 1, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb301270' $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' => 'HOM05D001460', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '433', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p22980' => 'bna', 'A01p32340' => 'bna', 'A03p42970' => 'bna', 'A05p25880' => 'bna', 'Aa31LG8G9320' => 'aar', 'Aa31LG8G9330' => 'aar', 'Aa31LG8G9340' => 'aar', 'Aa31sc221G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1034' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1528' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.829' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2222' => 'aag', 'Ah.12g058830' => 'amhyb', 'Ah.12g058840' => 'amhyb', 'AL3G37160' => 'aly', 'AL7G41310' => 'aly', 'Aqoxy5G00395' => 'aox', 'Aqoxy5G00396' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0C8NZA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5185HY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JZ1PRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MD3LS0' => 'arhy', 'AT3G22840' => 'ath', 'AT4G14690' => 'ath', 'ATR0665G054' => 'atr', 'Atru.chr4.2344' => 'acertr', 'Atru.chr4.2346' => 'acertr', 'Atru.chr4.2347' => 'acertr', 'Atru.chr4.2348' => 'acertr', 'Atru.chr4.2355' => 'acertr', 'Atru.chr4.2356' => 'acertr', 'Atru.chr4.2358' => 'acertr', 'Atru.chr4.2359' => 'acertr', 'Atru.chr4.2360' => 'acertr', 'Atru.chr4.2361' => 'acertr', 'AUR62030476' => 'cqu', 'AUR62030478' => 'cqu', 'AUR62030819' => 'cqu', 'AUR62030820' => 'cqu', 'BcaB03g14648' => 'bca', 'BcaB04g20492' => 'bca', 'BcaB06g26399' => 'bca', 'BcaC01g03416' => 'bca', 'BcaC01g03419' => 'bca', 'BcaC01g03421' => 'bca', 'BcaC01g03424' => 'bca', 'BcaC05g28012' => 'bca', 'BcaC09g49212' => 'bca', 'BcaC09g50140' => 'bca', 'BcaNung00346' => 'bca', 'BolC1t02785H' => 'bol', 'BolC1t04095H' => 'bol', 'BolC3t17545H' => 'bol', 'BolC5t32769H' => 'bol', 'BraA01t02211Z' => 'bra', 'BraA01t03359Z' => 'bra', 'BraA03t13441Z' => 'bra', 'BraA05t21476Z' => 'bra', 'C01p28420' => 'bna', 'C01p41350' => 'bna', 'C03p52750' => 'bna', 'C03p52780' => 'bna', 'C05p40270' => 'bna', 'CAN.G1437.9' => 'can', 'CANSAT78G0035' => 'cansat', 'CANSAT78G1036' => 'cansat', 'CANSAT78G2272' => 'cansat', 'CANSAT78G2478' => 'cansat', 'CARHR098700' => 'chi', 'CARHR221120' => 'chi', 'CARHR221150' => 'chi', 'Carub.0003s2297' => 'cru', 'Carub.0007s2749' => 'cru', 'Carub.0007s2750' => 'cru', 'Carub.0007s2751' => 'cru', 'Ca_10849_v3' => 'car', 'Cc03_g04300' => 'ccan', 'CDE02G3648' => 'cde', 'CDE05G0060' => 'cde', 'CDE05G0692' => 'cde', 'CDE05G2285' => 'cde', 'CDE05G2884' => 'cde', 'CDE05G3072' => 'cde', 'Cfa008439' => 'cfa', 'Cfa008441' => 'cfa', 'Cfa008443' => 'cfa', 'Cfa008448' => 'cfa', 'Ciclev10005974m.g' => 'ccl', 'Ciclev10006006m.g' => 'ccl', 'Ciclev10006775m.g' => 'ccl', 'CiPaw.02G120400' => 'cil', 'CiPaw.02G120500' => 'cil', 'CiPaw.02G120600' => 'cil', 'ClCG05G004850' => 'cla', 'COL.COLO4_21566' => 'col', 'Cpa.g.sc44.124' => 'cpa', 'Cre07.g320400' => 'cre', 'Cre07.g320450' => 'cre', 'Cre08.g384650' => 'cre', 'Cre09.g393173' => 'cre', 'Cre09.g394325' => 'cre', 'Cre14.g626750' => 'cre', 'Cre16.g679250' => 'cre', 'CsaV3_3G012890' => 'csa', 'CSS0010865' => 'camsi', 'CSS0044338' => 'camsi', 'DCAR_002366' => 'dca', 'DCAR_030687' => 'dca', 'DCAR_030688' => 'dca', 'Dinv14047' => 'din', 'Dinv14048' => 'din', 'Duzib151G0105' => 'dzi', 'Duzib151G0114' => 'dzi', 'Duzib212G1029' => 'dzi', 'ECA232G3536' => 'eca', 'ECA240G0786' => 'eca', 'ECA240G1802' => 'eca', 'ECA240G3760' => 'eca', 'ECA240G3920' => 'eca', 'EL10Ac5g12536' => 'bvu', 'EL10Ac5g12537' => 'bvu', 'EL10Ac5g12538' => 'bvu', 'Eucgr.B01004' => 'egr', 'Eucgr.B01006' => 'egr', 'Eucgr.B01007' => 'egr', 'Eucgr.B01008' => 'egr', 'Eucgr.B01895' => 'egr', 'Eucgr.B01896' => 'egr', 'FAN04G1456' => 'fan', 'FAN08G1769' => 'fan', 'FAN08G2160' => 'fan', 'FAN13G2403' => 'fan', 'FAN13G3303' => 'fan', 'FAN15G2435' => 'fan', 'FAN17G0672' => 'fan', 'FAN17G2441' => 'fan', 'FAN18G1024' => 'fan', 'FAN22G1458' => 'fan', 'FAN24G0037' => 'fan', 'FAN24G0429' => 'fan', 'FAN24G2387' => 'fan', 'FAN27G2746' => 'fan', 'FvH4_2g20400' => 'fve', 'FvH4_2g20420' => 'fve', 'FvH4_2g20430' => 'fve', 'FvH4_4g01270' => 'fve', 'FvH4_4g01290' => 'fve', 'FvH4_4g01300' => 'fve', 'FvH4_4g01310' => 'fve', 'FvH4_4g01330' => 'fve', 'FvH4_5g09070' => 'fve', 'Glyma.10G243800' => 'gma', 'Glyma.20G150600' => 'gma', 'Gohir.A09G219200' => 'ghi', 'Gohir.A09G219300' => 'ghi', 'Gohir.D09G221400' => 'ghi', 'Gohir.D09G221500' => 'ghi', 'Gorai.006G242600' => 'gra', 'Gorai.006G242700' => 'gra', 'GSVIVG01018044001' => 'vvi', 'HanXRQChr03g0083821' => 'han', 'HanXRQChr03g0083841' => 'han', 'HanXRQChr03g0083881' => 'han', 'HanXRQChr03g0083901' => 'han', 'HanXRQChr03g0083921' => 'han', 'HanXRQChr03g0085331' => 'han', 'HanXRQChr03g0085361' => 'han', 'HanXRQChr03g0085411' => 'han', 'HanXRQChr03g0085421' => 'han', 'HanXRQChr03g0085431' => 'han', 'HanXRQChr08g0221991' => 'han', 'HanXRQChr11g0336061' => 'han', 'HanXRQChr11g0336411' => 'han', 'Haze_11234' => 'cav', 'Hma1.2p1_0549F.1_g177010' => 'hma', 'Hma1.2p1_0602F.1_g187630' => 'hma', 'Hund14876' => 'sun', 'Hund14879' => 'sun', 'Lalb_Chr06g0160741' => 'lal', 'Lalb_Chr21g0304781' => 'lal', 'Lj3A726G19' => 'lonja', 'Lj3A726T23' => 'lonja', 'Lj3A726T24' => 'lonja', 'Lj3A726T25' => 'lonja', 'Lj3A727T17' => 'lonja', 'Lj3C726T0' => 'lonja', 'Lj3C726T2' => 'lonja', 'Lj3P725T35' => 'lonja', 'Lj3P727T10' => 'lonja', 'Lj3P727T12' => 'lonja', 'Lj3P727T14' => 'lonja', 'Lj5g0023109' => 'lja', 'Lj6P646T44' => 'lonja', 'Lsat_1_v5_gn_6_75760' => 'lsa', 'Lsat_1_v5_gn_6_75800' => 'lsa', 'Lsat_1_v5_gn_6_75900' => 'lsa', 'Lsat_1_v5_gn_6_76240' => 'lsa', 'Lsat_1_v5_gn_6_76441' => 'lsa', 'Lsat_1_v5_gn_6_76700' => 'lsa', 'Lsat_1_v5_gn_6_76760' => 'lsa', 'Manes.15G033100' => 'mes', 'Mapoly0004s0074' => 'mpo', 'Mapoly0004s0075' => 'mpo', 'Mapoly0004s0163' => 'mpo', 'Mapoly0004s0164' => 'mpo', 'Mapoly0021s0018' => 'mpo', 'Mapoly0041s0136' => 'mpo', 'Mapoly0041s0137' => 'mpo', 'Mapoly0041s0138' => 'mpo', 'Mapoly0041s0139' => 'mpo', 'Mapoly0041s0141' => 'mpo', 'Mapoly0041s0142' => 'mpo', 'Mapoly0041s0143' => 'mpo', 'Mapoly0041s0144' => 'mpo', 'Mapoly0041s0145' => 'mpo', 'Mapoly0047s0106' => 'mpo', 'Mapoly0047s0108' => 'mpo', 'Mapoly0050s0051' => 'mpo', 'Mapoly0050s0052' => 'mpo', 'Mapoly0050s0053' => 'mpo', 'Mapoly0058s0013' => 'mpo', 'Mapoly0091s0078' => 'mpo', 'Mapoly0091s0079' => 'mpo', 'Mapoly0091s0080' => 'mpo', 'Mapoly0091s0081' => 'mpo', 'Mapoly0278s0004' => 'mpo', 'Mapoly0278s0005' => 'mpo', 'Mapoly0278s0006' => 'mpo', 'MBI11_g30648_MAGBIO' => 'mbi', 'MCO03G194' => 'mco', 'MCO03G590' => 'mco', 'MCO07G312' => 'mco', 'MCO10G318' => 'mco', 'MCO12G244' => 'mco', 'MCO13G148' => 'mco', 'MCO13G194' => 'mco', 'MCO16G238' => 'mco', 'MD06G1134100' => 'mdo', 'MD13G1200100' => 'mdo', 'MD13G1200300' => 'mdo', 'MD13G1200600' => 'mdo', 'MD14G1150400' => 'mdo', 'MD16G1200000' => 'mdo', 'Medtr1g102570' => 'mtr', 'Medtr1g102780' => 'mtr', 'Medtr1g102800' => 'mtr', 'Medtr1g102810' => 'mtr', 'Medtr1g102830' => 'mtr', 'MELO3C006499.2' => 'cme', 'Migut.G00385' => 'egut', 'MSTRG.4063' => 'ama', 'Nitab4.5_0000090g0260' => 'nta', 'Nitab4.5_0000977g0030' => 'nta', 'Nitab4.5_0002541g0040' => 'nta', 'Nitab4.5_0007068g0040' => 'nta', 'Nn005s41408' => 'nnu', 'Nn005s41410' => 'nnu', 'Oeu010310.1' => 'oeu', 'Oeu010311.1' => 'oeu', 'Oeu043472.1' => 'oeu', 'Os01g0246400' => 'osa', 'Os04g0267950' => 'osa', 'Os07g0178700' => 'osa', 'Os07g0178800' => 'osa', 'Peaxi162Scf00316g00046' => 'pax', 'Peaxi162Scf00316g00049' => 'pax', 'Peaxi162Scf00316g00059' => 'pax', 'Peaxi162Scf00316g00328' => 'pax', 'Peaxi162Scf00316g00329' => 'pax', 'Peaxi162Scf00316g00411' => 'pax', 'Peaxi162Scf00316g00521' => 'pax', 'Peaxi162Scf00492g00068' => 'pax', 'Peaxi162Scf35631g00002' => 'pax', 'PGR142G3720' => 'pgr', 'PGSC0003DMG400006442' => 'stu', 'Phvul.007G062000' => 'pvu', 'Potri.008G157750' => 'ptr', 'Potri.008G157900' => 'ptr', 'Potri.008G158000' => 'ptr', 'Potri.008G158200' => 'ptr', 'Pp3c11_7280' => 'ppa', 'Pp3c11_7980' => 'ppa', 'Pp3c12_19450' => 'ppa', 'Pp3c14_1480' => 'ppa', 'Pp3c14_1501' => 'ppa', 'Pp3c16_4900' => 'ppa', 'Pp3c16_5010' => 'ppa', 'Pp3c16_5060' => 'ppa', 'Pp3c19_18250' => 'ppa', 'Pp3c23_8530' => 'ppa', 'Pp3c23_8550' => 'ppa', 'Pp3c24_9670' => 'ppa', 'Pp3c2_21390' => 'ppa', 'Pp3c2_31380' => 'ppa', 'Pp3c3_16620' => 'ppa', 'Pp3c3_8090' => 'ppa', 'Pp3c3_8110' => 'ppa', 'Pp3c3_8130' => 'ppa', 'Pp3c3_8150' => 'ppa', 'Pp3c4_14320' => 'ppa', 'Pp3c6_2560' => 'ppa', 'Pp3c9_16700' => 'ppa', 'PRCOL_00000234' => 'pco', 'PRCOL_00000235' => 'pco', 'PRCOL_00000777' => 'pco', 'PRCOL_00002344' => 'pco', 'PRCOL_00002372' => 'pco', 'PRCOL_00006120' => 'pco', 'Prupe.1G021400' => 'ppe', 'Prupe.1G021500' => 'ppe', 'Prupe.1G021600' => 'ppe', 'Prupe.1G021700' => 'ppe', 'Prupe.1G021800' => 'ppe', 'Prupe.5G145100' => 'ppe', 'Psat6g204040' => 'psa', 'Psat6g204800' => 'psa', 'Psat6g204920' => 'psa', 'Psat6g204960' => 'psa', 'Psat6g205080' => 'psa', 'PSO017G0271' => 'pso', 'PSO017G1276' => 'pso', 'PSO017G1429' => 'pso', 'PSO017G1861' => 'pso', 'PSO017G2787' => 'pso', 'PSO017G4466' => 'pso', 'PSO017G5118' => 'pso', 'PSO017G5420' => 'pso', 'PSO063G3678' => 'pso', 'PSO210G0546' => 'pso', 'PSO317G0001' => 'pso', 'PSO357G0512' => 'pso', 'PSO478G2682' => 'pso', 'PSO647G0001' => 'pso', 'PSO675G0001' => 'pso', 'PSO675G2699' => 'pso', 'PSO675G2849' => 'pso', 'PSO675G4991' => 'pso', 'PSO689G0001' => 'pso', 'QL06p000916' => 'qlo', 'QL06p000921' => 'qlo', 'QL06p001398' => 'qlo', 'QL06p001407' => 'qlo', 'QL06p002031' => 'qlo', 'RcHm_v2.0_Chr4g0387791' => 'rch', 'RcHm_v2.0_Chr4g0387801' => 'rch', 'RcHm_v2.0_Chr6g0286501' => 'rch', 'RcHm_v2.0_Chr6g0286511' => 'rch', 'RcHm_v2.0_Chr6g0286521' => 'rch', 'RcHm_v2.0_Chr6g0286531' => 'rch', 'RcHm_v2.0_Chr7g0189141' => 'rch', 'Rhsim02G0028700' => 'rsi', 'Rhsim02G0028800' => 'rsi', 'Rhsim02G0028900' => 'rsi', 'Rhsim02G0029000' => 'rsi', 'Rhsim02G0029100' => 'rsi', 'Rhsim02G0029200' => 'rsi', 'Rhsim02G0029300' => 'rsi', 'Rhsim02G0029400' => 'rsi', 'Rhsim02G0029500' => 'rsi', 'Rhsim02G0029600' => 'rsi', 'RhsimUnG0024000' => 'rsi', 'RhsimUnG0024100' => 'rsi', 'RhsimUnG0024200' => 'rsi', 'RhsimUnG0024300' => 'rsi', 'RhsimUnG0024400' => 'rsi', 'RhsimUnG0024500' => 'rsi', 'RhsimUnG0024700' => 'rsi', 'RhsimUnG0024800' => 'rsi', 'RhsimUnG0024900' => 'rsi', 'RhsimUnG0025100' => 'rsi', 'Sabra08G0120200' => 'sbr', 'Sabra08G0120300' => 'sbr', 'Sabra08G0120500' => 'sbr', 'Sabra08G0120600' => 'sbr', 'Sabra10G0158900' => 'sbr', 'SalBow2G3492' => 'sbo', 'Sc13g0004760' => 'sci', 'Sc13g0004770' => 'sci', 'Sed0003417' => 'sed', 'Sed0019750' => 'sed', 'SEGI_03419' => 'sgi', 'SEGI_05907' => 'sgi', 'SEGI_10682' => 'sgi', 'SEGI_13528' => 'sgi', 'SEGI_16081' => 'sgi', 'SEGI_19370' => 'sgi', 'SEGI_21015' => 'sgi', 'SEGI_21944' => 'sgi', 'SEGI_32906' => 'sgi', 'SEGI_33093' => 'sgi', 'SEGI_36110' => 'sgi', 'SEGI_40397' => 'sgi', 'SGA_v2.0_scaffold191G40426' => 'sas', 'SGA_v2.0_scaffold353G49717' => 'sas', 'SGA_v2.0_scaffold50G18550' => 'sas', 'SMO119G0173' => 'smo', 'SMO172G0002' => 'smo', 'Solyc09g082690.3' => 'sly', 'Solyc09g082700.2' => 'sly', 'Sopen09g031550' => 'spe', 'Sopen09g031560' => 'spe', 'Sp3g20540' => 'spa', 'Sp7g07580' => 'spa', 'TAR134G0002' => 'tar', 'TAR236G0001' => 'tar', 'TAR365G0892' => 'tar', 'TAR636G0166' => 'tar', 'TAR636G0646' => 'tar', 'TAR636G0869' => 'tar', 'TAR636G1317' => 'tar', 'TAR636G1744' => 'tar', 'TAR636G3358' => 'tar', 'TAR636G3436' => 'tar', 'THA.LOC104803047' => 'tha', 'Thecc.04G238900' => 'tca', 'Thhalv10021557m.g' => 'esa', 'Thhalv10026318m.g' => 'esa', 'Thhalv10026335m.g' => 'esa', 'TPR.G17433' => 'tpr', 'TPR.G18915' => 'tpr', 'TPR.G26125' => 'tpr', 'TWI09G0677' => 'twi', 'TWI73G0287' => 'twi', 'unitig_748.g8326' => 'ugi', 'vmacro15370' => 'vma', 'vmacro15371' => 'vma', 'vmacro15372' => 'vma', 'vmacro15373' => 'vma', 'vmacro15374' => 'vma', 'VMungo0720G2826' => 'vmu', 'Zm00001eb116960' => 'zma', 'Zm00001eb301260' => 'zma', 'Zm00001eb301270' => 'zma' ), 'gf_id' => 'HOM05D001460', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001460' ), 'data_identifier' => 'HOM05D001460', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001460', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '433', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p22980' => 'bna', 'A01p32340' => 'bna', 'A03p42970' => 'bna', 'A05p25880' => 'bna', 'Aa31LG8G9320' => 'aar', 'Aa31LG8G9330' => 'aar', 'Aa31LG8G9340' => 'aar', 'Aa31sc221G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1034' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1528' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.829' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2222' => 'aag', 'Ah.12g058830' => 'amhyb', 'Ah.12g058840' => 'amhyb', 'AL3G37160' => 'aly', 'AL7G41310' => 'aly', 'Aqoxy5G00395' => 'aox', 'Aqoxy5G00396' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0C8NZA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5185HY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JZ1PRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MD3LS0' => 'arhy', 'AT3G22840' => 'ath', 'AT4G14690' => 'ath', 'ATR0665G054' => 'atr', 'Atru.chr4.2344' => 'acertr', 'Atru.chr4.2346' => 'acertr', 'Atru.chr4.2347' => 'acertr', 'Atru.chr4.2348' => 'acertr', 'Atru.chr4.2355' => 'acertr', 'Atru.chr4.2356' => 'acertr', 'Atru.chr4.2358' => 'acertr', 'Atru.chr4.2359' => 'acertr', 'Atru.chr4.2360' => 'acertr', 'Atru.chr4.2361' => 'acertr', 'AUR62030476' => 'cqu', 'AUR62030478' => 'cqu', 'AUR62030819' => 'cqu', 'AUR62030820' => 'cqu', 'BcaB03g14648' => 'bca', 'BcaB04g20492' => 'bca', 'BcaB06g26399' => 'bca', 'BcaC01g03416' => 'bca', 'BcaC01g03419' => 'bca', 'BcaC01g03421' => 'bca', 'BcaC01g03424' => 'bca', 'BcaC05g28012' => 'bca', 'BcaC09g49212' => 'bca', 'BcaC09g50140' => 'bca', 'BcaNung00346' => 'bca', 'BolC1t02785H' => 'bol', 'BolC1t04095H' => 'bol', 'BolC3t17545H' => 'bol', 'BolC5t32769H' => 'bol', 'BraA01t02211Z' => 'bra', 'BraA01t03359Z' => 'bra', 'BraA03t13441Z' => 'bra', 'BraA05t21476Z' => 'bra', 'C01p28420' => 'bna', 'C01p41350' => 'bna', 'C03p52750' => 'bna', 'C03p52780' => 'bna', 'C05p40270' => 'bna', 'CAN.G1437.9' => 'can', 'CANSAT78G0035' => 'cansat', 'CANSAT78G1036' => 'cansat', 'CANSAT78G2272' => 'cansat', 'CANSAT78G2478' => 'cansat', 'CARHR098700' => 'chi', 'CARHR221120' => 'chi', 'CARHR221150' => 'chi', 'Carub.0003s2297' => 'cru', 'Carub.0007s2749' => 'cru', 'Carub.0007s2750' => 'cru', 'Carub.0007s2751' => 'cru', 'Ca_10849_v3' => 'car', 'Cc03_g04300' => 'ccan', 'CDE02G3648' => 'cde', 'CDE05G0060' => 'cde', 'CDE05G0692' => 'cde', 'CDE05G2285' => 'cde', 'CDE05G2884' => 'cde', 'CDE05G3072' => 'cde', 'Cfa008439' => 'cfa', 'Cfa008441' => 'cfa', 'Cfa008443' => 'cfa', 'Cfa008448' => 'cfa', 'Ciclev10005974m.g' => 'ccl', 'Ciclev10006006m.g' => 'ccl', 'Ciclev10006775m.g' => 'ccl', 'CiPaw.02G120400' => 'cil', 'CiPaw.02G120500' => 'cil', 'CiPaw.02G120600' => 'cil', 'ClCG05G004850' => 'cla', 'COL.COLO4_21566' => 'col', 'Cpa.g.sc44.124' => 'cpa', 'Cre07.g320400' => 'cre', 'Cre07.g320450' => 'cre', 'Cre08.g384650' => 'cre', 'Cre09.g393173' => 'cre', 'Cre09.g394325' => 'cre', 'Cre14.g626750' => 'cre', 'Cre16.g679250' => 'cre', 'CsaV3_3G012890' => 'csa', 'CSS0010865' => 'camsi', 'CSS0044338' => 'camsi', 'DCAR_002366' => 'dca', 'DCAR_030687' => 'dca', 'DCAR_030688' => 'dca', 'Dinv14047' => 'din', 'Dinv14048' => 'din', 'Duzib151G0105' => 'dzi', 'Duzib151G0114' => 'dzi', 'Duzib212G1029' => 'dzi', 'ECA232G3536' => 'eca', 'ECA240G0786' => 'eca', 'ECA240G1802' => 'eca', 'ECA240G3760' => 'eca', 'ECA240G3920' => 'eca', 'EL10Ac5g12536' => 'bvu', 'EL10Ac5g12537' => 'bvu', 'EL10Ac5g12538' => 'bvu', 'Eucgr.B01004' => 'egr', 'Eucgr.B01006' => 'egr', 'Eucgr.B01007' => 'egr', 'Eucgr.B01008' => 'egr', 'Eucgr.B01895' => 'egr', 'Eucgr.B01896' => 'egr', 'FAN04G1456' => 'fan', 'FAN08G1769' => 'fan', 'FAN08G2160' => 'fan', 'FAN13G2403' => 'fan', 'FAN13G3303' => 'fan', 'FAN15G2435' => 'fan', 'FAN17G0672' => 'fan', 'FAN17G2441' => 'fan', 'FAN18G1024' => 'fan', 'FAN22G1458' => 'fan', 'FAN24G0037' => 'fan', 'FAN24G0429' => 'fan', 'FAN24G2387' => 'fan', 'FAN27G2746' => 'fan', 'FvH4_2g20400' => 'fve', 'FvH4_2g20420' => 'fve', 'FvH4_2g20430' => 'fve', 'FvH4_4g01270' => 'fve', 'FvH4_4g01290' => 'fve', 'FvH4_4g01300' => 'fve', 'FvH4_4g01310' => 'fve', 'FvH4_4g01330' => 'fve', 'FvH4_5g09070' => 'fve', 'Glyma.10G243800' => 'gma', 'Glyma.20G150600' => 'gma', 'Gohir.A09G219200' => 'ghi', 'Gohir.A09G219300' => 'ghi', 'Gohir.D09G221400' => 'ghi', 'Gohir.D09G221500' => 'ghi', 'Gorai.006G242600' => 'gra', 'Gorai.006G242700' => 'gra', 'GSVIVG01018044001' => 'vvi', 'HanXRQChr03g0083821' => 'han', 'HanXRQChr03g0083841' => 'han', 'HanXRQChr03g0083881' => 'han', 'HanXRQChr03g0083901' => 'han', 'HanXRQChr03g0083921' => 'han', 'HanXRQChr03g0085331' => 'han', 'HanXRQChr03g0085361' => 'han', 'HanXRQChr03g0085411' => 'han', 'HanXRQChr03g0085421' => 'han', 'HanXRQChr03g0085431' => 'han', 'HanXRQChr08g0221991' => 'han', 'HanXRQChr11g0336061' => 'han', 'HanXRQChr11g0336411' => 'han', 'Haze_11234' => 'cav', 'Hma1.2p1_0549F.1_g177010' => 'hma', 'Hma1.2p1_0602F.1_g187630' => 'hma', 'Hund14876' => 'sun', 'Hund14879' => 'sun', 'Lalb_Chr06g0160741' => 'lal', 'Lalb_Chr21g0304781' => 'lal', 'Lj3A726G19' => 'lonja', 'Lj3A726T23' => 'lonja', 'Lj3A726T24' => 'lonja', 'Lj3A726T25' => 'lonja', 'Lj3A727T17' => 'lonja', 'Lj3C726T0' => 'lonja', 'Lj3C726T2' => 'lonja', 'Lj3P725T35' => 'lonja', 'Lj3P727T10' => 'lonja', 'Lj3P727T12' => 'lonja', 'Lj3P727T14' => 'lonja', 'Lj5g0023109' => 'lja', 'Lj6P646T44' => 'lonja', 'Lsat_1_v5_gn_6_75760' => 'lsa', 'Lsat_1_v5_gn_6_75800' => 'lsa', 'Lsat_1_v5_gn_6_75900' => 'lsa', 'Lsat_1_v5_gn_6_76240' => 'lsa', 'Lsat_1_v5_gn_6_76441' => 'lsa', 'Lsat_1_v5_gn_6_76700' => 'lsa', 'Lsat_1_v5_gn_6_76760' => 'lsa', 'Manes.15G033100' => 'mes', 'Mapoly0004s0074' => 'mpo', 'Mapoly0004s0075' => 'mpo', 'Mapoly0004s0163' => 'mpo', 'Mapoly0004s0164' => 'mpo', 'Mapoly0021s0018' => 'mpo', 'Mapoly0041s0136' => 'mpo', 'Mapoly0041s0137' => 'mpo', 'Mapoly0041s0138' => 'mpo', 'Mapoly0041s0139' => 'mpo', 'Mapoly0041s0141' => 'mpo', 'Mapoly0041s0142' => 'mpo', 'Mapoly0041s0143' => 'mpo', 'Mapoly0041s0144' => 'mpo', 'Mapoly0041s0145' => 'mpo', 'Mapoly0047s0106' => 'mpo', 'Mapoly0047s0108' => 'mpo', 'Mapoly0050s0051' => 'mpo', 'Mapoly0050s0052' => 'mpo', 'Mapoly0050s0053' => 'mpo', 'Mapoly0058s0013' => 'mpo', 'Mapoly0091s0078' => 'mpo', 'Mapoly0091s0079' => 'mpo', 'Mapoly0091s0080' => 'mpo', 'Mapoly0091s0081' => 'mpo', 'Mapoly0278s0004' => 'mpo', 'Mapoly0278s0005' => 'mpo', 'Mapoly0278s0006' => 'mpo', 'MBI11_g30648_MAGBIO' => 'mbi', 'MCO03G194' => 'mco', 'MCO03G590' => 'mco', 'MCO07G312' => 'mco', 'MCO10G318' => 'mco', 'MCO12G244' => 'mco', 'MCO13G148' => 'mco', 'MCO13G194' => 'mco', 'MCO16G238' => 'mco', 'MD06G1134100' => 'mdo', 'MD13G1200100' => 'mdo', 'MD13G1200300' => 'mdo', 'MD13G1200600' => 'mdo', 'MD14G1150400' => 'mdo', 'MD16G1200000' => 'mdo', 'Medtr1g102570' => 'mtr', 'Medtr1g102780' => 'mtr', 'Medtr1g102800' => 'mtr', 'Medtr1g102810' => 'mtr', 'Medtr1g102830' => 'mtr', 'MELO3C006499.2' => 'cme', 'Migut.G00385' => 'egut', 'MSTRG.4063' => 'ama', 'Nitab4.5_0000090g0260' => 'nta', 'Nitab4.5_0000977g0030' => 'nta', 'Nitab4.5_0002541g0040' => 'nta', 'Nitab4.5_0007068g0040' => 'nta', 'Nn005s41408' => 'nnu', 'Nn005s41410' => 'nnu', 'Oeu010310.1' => 'oeu', 'Oeu010311.1' => 'oeu', 'Oeu043472.1' => 'oeu', 'Os01g0246400' => 'osa', 'Os04g0267950' => 'osa', 'Os07g0178700' => 'osa', 'Os07g0178800' => 'osa', 'Peaxi162Scf00316g00046' => 'pax', 'Peaxi162Scf00316g00049' => 'pax', 'Peaxi162Scf00316g00059' => 'pax', 'Peaxi162Scf00316g00328' => 'pax', 'Peaxi162Scf00316g00329' => 'pax', 'Peaxi162Scf00316g00411' => 'pax', 'Peaxi162Scf00316g00521' => 'pax', 'Peaxi162Scf00492g00068' => 'pax', 'Peaxi162Scf35631g00002' => 'pax', 'PGR142G3720' => 'pgr', 'PGSC0003DMG400006442' => 'stu', 'Phvul.007G062000' => 'pvu', 'Potri.008G157750' => 'ptr', 'Potri.008G157900' => 'ptr', 'Potri.008G158000' => 'ptr', 'Potri.008G158200' => 'ptr', 'Pp3c11_7280' => 'ppa', 'Pp3c11_7980' => 'ppa', 'Pp3c12_19450' => 'ppa', 'Pp3c14_1480' => 'ppa', 'Pp3c14_1501' => 'ppa', 'Pp3c16_4900' => 'ppa', 'Pp3c16_5010' => 'ppa', 'Pp3c16_5060' => 'ppa', 'Pp3c19_18250' => 'ppa', 'Pp3c23_8530' => 'ppa', 'Pp3c23_8550' => 'ppa', 'Pp3c24_9670' => 'ppa', 'Pp3c2_21390' => 'ppa', 'Pp3c2_31380' => 'ppa', 'Pp3c3_16620' => 'ppa', 'Pp3c3_8090' => 'ppa', 'Pp3c3_8110' => 'ppa', 'Pp3c3_8130' => 'ppa', 'Pp3c3_8150' => 'ppa', 'Pp3c4_14320' => 'ppa', 'Pp3c6_2560' => 'ppa', 'Pp3c9_16700' => 'ppa', 'PRCOL_00000234' => 'pco', 'PRCOL_00000235' => 'pco', 'PRCOL_00000777' => 'pco', 'PRCOL_00002344' => 'pco', 'PRCOL_00002372' => 'pco', 'PRCOL_00006120' => 'pco', 'Prupe.1G021400' => 'ppe', 'Prupe.1G021500' => 'ppe', 'Prupe.1G021600' => 'ppe', 'Prupe.1G021700' => 'ppe', 'Prupe.1G021800' => 'ppe', 'Prupe.5G145100' => 'ppe', 'Psat6g204040' => 'psa', 'Psat6g204800' => 'psa', 'Psat6g204920' => 'psa', 'Psat6g204960' => 'psa', 'Psat6g205080' => 'psa', 'PSO017G0271' => 'pso', 'PSO017G1276' => 'pso', 'PSO017G1429' => 'pso', 'PSO017G1861' => 'pso', 'PSO017G2787' => 'pso', 'PSO017G4466' => 'pso', 'PSO017G5118' => 'pso', 'PSO017G5420' => 'pso', 'PSO063G3678' => 'pso', 'PSO210G0546' => 'pso', 'PSO317G0001' => 'pso', 'PSO357G0512' => 'pso', 'PSO478G2682' => 'pso', 'PSO647G0001' => 'pso', 'PSO675G0001' => 'pso', 'PSO675G2699' => 'pso', 'PSO675G2849' => 'pso', 'PSO675G4991' => 'pso', 'PSO689G0001' => 'pso', 'QL06p000916' => 'qlo', 'QL06p000921' => 'qlo', 'QL06p001398' => 'qlo', 'QL06p001407' => 'qlo', 'QL06p002031' => 'qlo', 'RcHm_v2.0_Chr4g0387791' => 'rch', 'RcHm_v2.0_Chr4g0387801' => 'rch', 'RcHm_v2.0_Chr6g0286501' => 'rch', 'RcHm_v2.0_Chr6g0286511' => 'rch', 'RcHm_v2.0_Chr6g0286521' => 'rch', 'RcHm_v2.0_Chr6g0286531' => 'rch', 'RcHm_v2.0_Chr7g0189141' => 'rch', 'Rhsim02G0028700' => 'rsi', 'Rhsim02G0028800' => 'rsi', 'Rhsim02G0028900' => 'rsi', 'Rhsim02G0029000' => 'rsi', 'Rhsim02G0029100' => 'rsi', 'Rhsim02G0029200' => 'rsi', 'Rhsim02G0029300' => 'rsi', 'Rhsim02G0029400' => 'rsi', 'Rhsim02G0029500' => 'rsi', 'Rhsim02G0029600' => 'rsi', 'RhsimUnG0024000' => 'rsi', 'RhsimUnG0024100' => 'rsi', 'RhsimUnG0024200' => 'rsi', 'RhsimUnG0024300' => 'rsi', 'RhsimUnG0024400' => 'rsi', 'RhsimUnG0024500' => 'rsi', 'RhsimUnG0024700' => 'rsi', 'RhsimUnG0024800' => 'rsi', 'RhsimUnG0024900' => 'rsi', 'RhsimUnG0025100' => 'rsi', 'Sabra08G0120200' => 'sbr', 'Sabra08G0120300' => 'sbr', 'Sabra08G0120500' => 'sbr', 'Sabra08G0120600' => 'sbr', 'Sabra10G0158900' => 'sbr', 'SalBow2G3492' => 'sbo', 'Sc13g0004760' => 'sci', 'Sc13g0004770' => 'sci', 'Sed0003417' => 'sed', 'Sed0019750' => 'sed', 'SEGI_03419' => 'sgi', 'SEGI_05907' => 'sgi', 'SEGI_10682' => 'sgi', 'SEGI_13528' => 'sgi', 'SEGI_16081' => 'sgi', 'SEGI_19370' => 'sgi', 'SEGI_21015' => 'sgi', 'SEGI_21944' => 'sgi', 'SEGI_32906' => 'sgi', 'SEGI_33093' => 'sgi', 'SEGI_36110' => 'sgi', 'SEGI_40397' => 'sgi', 'SGA_v2.0_scaffold191G40426' => 'sas', 'SGA_v2.0_scaffold353G49717' => 'sas', 'SGA_v2.0_scaffold50G18550' => 'sas', 'SMO119G0173' => 'smo', 'SMO172G0002' => 'smo', 'Solyc09g082690.3' => 'sly', 'Solyc09g082700.2' => 'sly', 'Sopen09g031550' => 'spe', 'Sopen09g031560' => 'spe', 'Sp3g20540' => 'spa', 'Sp7g07580' => 'spa', 'TAR134G0002' => 'tar', 'TAR236G0001' => 'tar', 'TAR365G0892' => 'tar', 'TAR636G0166' => 'tar', 'TAR636G0646' => 'tar', 'TAR636G0869' => 'tar', 'TAR636G1317' => 'tar', 'TAR636G1744' => 'tar', 'TAR636G3358' => 'tar', 'TAR636G3436' => 'tar', 'THA.LOC104803047' => 'tha', 'Thecc.04G238900' => 'tca', 'Thhalv10021557m.g' => 'esa', 'Thhalv10026318m.g' => 'esa', 'Thhalv10026335m.g' => 'esa', 'TPR.G17433' => 'tpr', 'TPR.G18915' => 'tpr', 'TPR.G26125' => 'tpr', 'TWI09G0677' => 'twi', 'TWI73G0287' => 'twi', 'unitig_748.g8326' => 'ugi', 'vmacro15370' => 'vma', 'vmacro15371' => 'vma', 'vmacro15372' => 'vma', 'vmacro15373' => 'vma', 'vmacro15374' => 'vma', 'VMungo0720G2826' => 'vmu', 'Zm00001eb116960' => 'zma', 'Zm00001eb301260' => 'zma', 'Zm00001eb301270' => 'zma' ) $gf_id = 'HOM05D001460' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001460' ) $data_identifier = 'HOM05D001460' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 4, 'aag' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 2, 'aox' => (int) 2, 'arhy' => (int) 4, 'ath' => (int) 2, 'atr' => (int) 1, 'acertr' => (int) 10, 'cqu' => (int) 4, 'bca' => (int) 11, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 1, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 1, 'ccan' => (int) 1, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 1, 'col' => (int) 1, 'cpa' => (int) 1, 'cre' => (int) 7, 'csa' => (int) 1, 'camsi' => (int) 2, 'dca' => (int) 3, 'din' => (int) 2, 'dzi' => (int) 3, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 14, 'fve' => (int) 9, 'gma' => (int) 2, 'ghi' => (int) 4, 'gra' => (int) 2, 'vvi' => (int) 1, 'han' => (int) 13, 'cav' => (int) 1, 'hma' => (int) 2, 'sun' => (int) 2, 'lal' => (int) 2, 'lonja' => (int) 12, 'lja' => (int) 1, 'lsa' => (int) 7, 'mes' => (int) 1, 'mpo' => (int) 27, 'mbi' => (int) 1, 'mco' => (int) 8, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 1, 'egut' => (int) 1, 'ama' => (int) 1, 'nta' => (int) 4, 'nnu' => (int) 2, 'oeu' => (int) 3, 'osa' => (int) 4, 'pax' => (int) 9, 'pgr' => (int) 1, 'stu' => (int) 1, 'pvu' => (int) 1, 'ptr' => (int) 4, 'ppa' => (int) 22, 'pco' => (int) 6, 'ppe' => (int) 6, 'psa' => (int) 5, 'pso' => (int) 19, 'qlo' => (int) 5, 'rch' => (int) 7, 'rsi' => (int) 20, 'sbr' => (int) 5, 'sbo' => (int) 1, 'sci' => (int) 2, 'sed' => (int) 2, 'sgi' => (int) 12, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 2, 'tar' => (int) 10, 'tha' => (int) 1, 'tca' => (int) 1, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 2, 'ugi' => (int) 1, 'vma' => (int) 5, 'vmu' => (int) 1, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb301270' $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' => 'HOM05D001460', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '433', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p22980' => 'bna', 'A01p32340' => 'bna', 'A03p42970' => 'bna', 'A05p25880' => 'bna', 'Aa31LG8G9320' => 'aar', 'Aa31LG8G9330' => 'aar', 'Aa31LG8G9340' => 'aar', 'Aa31sc221G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1034' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1528' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.829' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2222' => 'aag', 'Ah.12g058830' => 'amhyb', 'Ah.12g058840' => 'amhyb', 'AL3G37160' => 'aly', 'AL7G41310' => 'aly', 'Aqoxy5G00395' => 'aox', 'Aqoxy5G00396' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0C8NZA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5185HY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JZ1PRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MD3LS0' => 'arhy', 'AT3G22840' => 'ath', 'AT4G14690' => 'ath', 'ATR0665G054' => 'atr', 'Atru.chr4.2344' => 'acertr', 'Atru.chr4.2346' => 'acertr', 'Atru.chr4.2347' => 'acertr', 'Atru.chr4.2348' => 'acertr', 'Atru.chr4.2355' => 'acertr', 'Atru.chr4.2356' => 'acertr', 'Atru.chr4.2358' => 'acertr', 'Atru.chr4.2359' => 'acertr', 'Atru.chr4.2360' => 'acertr', 'Atru.chr4.2361' => 'acertr', 'AUR62030476' => 'cqu', 'AUR62030478' => 'cqu', 'AUR62030819' => 'cqu', 'AUR62030820' => 'cqu', 'BcaB03g14648' => 'bca', 'BcaB04g20492' => 'bca', 'BcaB06g26399' => 'bca', 'BcaC01g03416' => 'bca', 'BcaC01g03419' => 'bca', 'BcaC01g03421' => 'bca', 'BcaC01g03424' => 'bca', 'BcaC05g28012' => 'bca', 'BcaC09g49212' => 'bca', 'BcaC09g50140' => 'bca', 'BcaNung00346' => 'bca', 'BolC1t02785H' => 'bol', 'BolC1t04095H' => 'bol', 'BolC3t17545H' => 'bol', 'BolC5t32769H' => 'bol', 'BraA01t02211Z' => 'bra', 'BraA01t03359Z' => 'bra', 'BraA03t13441Z' => 'bra', 'BraA05t21476Z' => 'bra', 'C01p28420' => 'bna', 'C01p41350' => 'bna', 'C03p52750' => 'bna', 'C03p52780' => 'bna', 'C05p40270' => 'bna', 'CAN.G1437.9' => 'can', 'CANSAT78G0035' => 'cansat', 'CANSAT78G1036' => 'cansat', 'CANSAT78G2272' => 'cansat', 'CANSAT78G2478' => 'cansat', 'CARHR098700' => 'chi', 'CARHR221120' => 'chi', 'CARHR221150' => 'chi', 'Carub.0003s2297' => 'cru', 'Carub.0007s2749' => 'cru', 'Carub.0007s2750' => 'cru', 'Carub.0007s2751' => 'cru', 'Ca_10849_v3' => 'car', 'Cc03_g04300' => 'ccan', 'CDE02G3648' => 'cde', 'CDE05G0060' => 'cde', 'CDE05G0692' => 'cde', 'CDE05G2285' => 'cde', 'CDE05G2884' => 'cde', 'CDE05G3072' => 'cde', 'Cfa008439' => 'cfa', 'Cfa008441' => 'cfa', 'Cfa008443' => 'cfa', 'Cfa008448' => 'cfa', 'Ciclev10005974m.g' => 'ccl', 'Ciclev10006006m.g' => 'ccl', 'Ciclev10006775m.g' => 'ccl', 'CiPaw.02G120400' => 'cil', 'CiPaw.02G120500' => 'cil', 'CiPaw.02G120600' => 'cil', 'ClCG05G004850' => 'cla', 'COL.COLO4_21566' => 'col', 'Cpa.g.sc44.124' => 'cpa', 'Cre07.g320400' => 'cre', 'Cre07.g320450' => 'cre', 'Cre08.g384650' => 'cre', 'Cre09.g393173' => 'cre', 'Cre09.g394325' => 'cre', 'Cre14.g626750' => 'cre', 'Cre16.g679250' => 'cre', 'CsaV3_3G012890' => 'csa', 'CSS0010865' => 'camsi', 'CSS0044338' => 'camsi', 'DCAR_002366' => 'dca', 'DCAR_030687' => 'dca', 'DCAR_030688' => 'dca', 'Dinv14047' => 'din', 'Dinv14048' => 'din', 'Duzib151G0105' => 'dzi', 'Duzib151G0114' => 'dzi', 'Duzib212G1029' => 'dzi', 'ECA232G3536' => 'eca', 'ECA240G0786' => 'eca', 'ECA240G1802' => 'eca', 'ECA240G3760' => 'eca', 'ECA240G3920' => 'eca', 'EL10Ac5g12536' => 'bvu', 'EL10Ac5g12537' => 'bvu', 'EL10Ac5g12538' => 'bvu', 'Eucgr.B01004' => 'egr', 'Eucgr.B01006' => 'egr', 'Eucgr.B01007' => 'egr', 'Eucgr.B01008' => 'egr', 'Eucgr.B01895' => 'egr', 'Eucgr.B01896' => 'egr', 'FAN04G1456' => 'fan', 'FAN08G1769' => 'fan', 'FAN08G2160' => 'fan', 'FAN13G2403' => 'fan', 'FAN13G3303' => 'fan', 'FAN15G2435' => 'fan', 'FAN17G0672' => 'fan', 'FAN17G2441' => 'fan', 'FAN18G1024' => 'fan', 'FAN22G1458' => 'fan', 'FAN24G0037' => 'fan', 'FAN24G0429' => 'fan', 'FAN24G2387' => 'fan', 'FAN27G2746' => 'fan', 'FvH4_2g20400' => 'fve', 'FvH4_2g20420' => 'fve', 'FvH4_2g20430' => 'fve', 'FvH4_4g01270' => 'fve', 'FvH4_4g01290' => 'fve', 'FvH4_4g01300' => 'fve', 'FvH4_4g01310' => 'fve', 'FvH4_4g01330' => 'fve', 'FvH4_5g09070' => 'fve', 'Glyma.10G243800' => 'gma', 'Glyma.20G150600' => 'gma', 'Gohir.A09G219200' => 'ghi', 'Gohir.A09G219300' => 'ghi', 'Gohir.D09G221400' => 'ghi', 'Gohir.D09G221500' => 'ghi', 'Gorai.006G242600' => 'gra', 'Gorai.006G242700' => 'gra', 'GSVIVG01018044001' => 'vvi', 'HanXRQChr03g0083821' => 'han', 'HanXRQChr03g0083841' => 'han', 'HanXRQChr03g0083881' => 'han', 'HanXRQChr03g0083901' => 'han', 'HanXRQChr03g0083921' => 'han', 'HanXRQChr03g0085331' => 'han', 'HanXRQChr03g0085361' => 'han', 'HanXRQChr03g0085411' => 'han', 'HanXRQChr03g0085421' => 'han', 'HanXRQChr03g0085431' => 'han', 'HanXRQChr08g0221991' => 'han', 'HanXRQChr11g0336061' => 'han', 'HanXRQChr11g0336411' => 'han', 'Haze_11234' => 'cav', 'Hma1.2p1_0549F.1_g177010' => 'hma', 'Hma1.2p1_0602F.1_g187630' => 'hma', 'Hund14876' => 'sun', 'Hund14879' => 'sun', 'Lalb_Chr06g0160741' => 'lal', 'Lalb_Chr21g0304781' => 'lal', 'Lj3A726G19' => 'lonja', 'Lj3A726T23' => 'lonja', 'Lj3A726T24' => 'lonja', 'Lj3A726T25' => 'lonja', 'Lj3A727T17' => 'lonja', 'Lj3C726T0' => 'lonja', 'Lj3C726T2' => 'lonja', 'Lj3P725T35' => 'lonja', 'Lj3P727T10' => 'lonja', 'Lj3P727T12' => 'lonja', 'Lj3P727T14' => 'lonja', 'Lj5g0023109' => 'lja', 'Lj6P646T44' => 'lonja', 'Lsat_1_v5_gn_6_75760' => 'lsa', 'Lsat_1_v5_gn_6_75800' => 'lsa', 'Lsat_1_v5_gn_6_75900' => 'lsa', 'Lsat_1_v5_gn_6_76240' => 'lsa', 'Lsat_1_v5_gn_6_76441' => 'lsa', 'Lsat_1_v5_gn_6_76700' => 'lsa', 'Lsat_1_v5_gn_6_76760' => 'lsa', 'Manes.15G033100' => 'mes', 'Mapoly0004s0074' => 'mpo', 'Mapoly0004s0075' => 'mpo', 'Mapoly0004s0163' => 'mpo', 'Mapoly0004s0164' => 'mpo', 'Mapoly0021s0018' => 'mpo', 'Mapoly0041s0136' => 'mpo', 'Mapoly0041s0137' => 'mpo', 'Mapoly0041s0138' => 'mpo', 'Mapoly0041s0139' => 'mpo', 'Mapoly0041s0141' => 'mpo', 'Mapoly0041s0142' => 'mpo', 'Mapoly0041s0143' => 'mpo', 'Mapoly0041s0144' => 'mpo', 'Mapoly0041s0145' => 'mpo', 'Mapoly0047s0106' => 'mpo', 'Mapoly0047s0108' => 'mpo', 'Mapoly0050s0051' => 'mpo', 'Mapoly0050s0052' => 'mpo', 'Mapoly0050s0053' => 'mpo', 'Mapoly0058s0013' => 'mpo', 'Mapoly0091s0078' => 'mpo', 'Mapoly0091s0079' => 'mpo', 'Mapoly0091s0080' => 'mpo', 'Mapoly0091s0081' => 'mpo', 'Mapoly0278s0004' => 'mpo', 'Mapoly0278s0005' => 'mpo', 'Mapoly0278s0006' => 'mpo', 'MBI11_g30648_MAGBIO' => 'mbi', 'MCO03G194' => 'mco', 'MCO03G590' => 'mco', 'MCO07G312' => 'mco', 'MCO10G318' => 'mco', 'MCO12G244' => 'mco', 'MCO13G148' => 'mco', 'MCO13G194' => 'mco', 'MCO16G238' => 'mco', 'MD06G1134100' => 'mdo', 'MD13G1200100' => 'mdo', 'MD13G1200300' => 'mdo', 'MD13G1200600' => 'mdo', 'MD14G1150400' => 'mdo', 'MD16G1200000' => 'mdo', 'Medtr1g102570' => 'mtr', 'Medtr1g102780' => 'mtr', 'Medtr1g102800' => 'mtr', 'Medtr1g102810' => 'mtr', 'Medtr1g102830' => 'mtr', 'MELO3C006499.2' => 'cme', 'Migut.G00385' => 'egut', 'MSTRG.4063' => 'ama', 'Nitab4.5_0000090g0260' => 'nta', 'Nitab4.5_0000977g0030' => 'nta', 'Nitab4.5_0002541g0040' => 'nta', 'Nitab4.5_0007068g0040' => 'nta', 'Nn005s41408' => 'nnu', 'Nn005s41410' => 'nnu', 'Oeu010310.1' => 'oeu', 'Oeu010311.1' => 'oeu', 'Oeu043472.1' => 'oeu', 'Os01g0246400' => 'osa', 'Os04g0267950' => 'osa', 'Os07g0178700' => 'osa', 'Os07g0178800' => 'osa', 'Peaxi162Scf00316g00046' => 'pax', 'Peaxi162Scf00316g00049' => 'pax', 'Peaxi162Scf00316g00059' => 'pax', 'Peaxi162Scf00316g00328' => 'pax', 'Peaxi162Scf00316g00329' => 'pax', 'Peaxi162Scf00316g00411' => 'pax', 'Peaxi162Scf00316g00521' => 'pax', 'Peaxi162Scf00492g00068' => 'pax', 'Peaxi162Scf35631g00002' => 'pax', 'PGR142G3720' => 'pgr', 'PGSC0003DMG400006442' => 'stu', 'Phvul.007G062000' => 'pvu', 'Potri.008G157750' => 'ptr', 'Potri.008G157900' => 'ptr', 'Potri.008G158000' => 'ptr', 'Potri.008G158200' => 'ptr', 'Pp3c11_7280' => 'ppa', 'Pp3c11_7980' => 'ppa', 'Pp3c12_19450' => 'ppa', 'Pp3c14_1480' => 'ppa', 'Pp3c14_1501' => 'ppa', 'Pp3c16_4900' => 'ppa', 'Pp3c16_5010' => 'ppa', 'Pp3c16_5060' => 'ppa', 'Pp3c19_18250' => 'ppa', 'Pp3c23_8530' => 'ppa', 'Pp3c23_8550' => 'ppa', 'Pp3c24_9670' => 'ppa', 'Pp3c2_21390' => 'ppa', 'Pp3c2_31380' => 'ppa', 'Pp3c3_16620' => 'ppa', 'Pp3c3_8090' => 'ppa', 'Pp3c3_8110' => 'ppa', 'Pp3c3_8130' => 'ppa', 'Pp3c3_8150' => 'ppa', 'Pp3c4_14320' => 'ppa', 'Pp3c6_2560' => 'ppa', 'Pp3c9_16700' => 'ppa', 'PRCOL_00000234' => 'pco', 'PRCOL_00000235' => 'pco', 'PRCOL_00000777' => 'pco', 'PRCOL_00002344' => 'pco', 'PRCOL_00002372' => 'pco', 'PRCOL_00006120' => 'pco', 'Prupe.1G021400' => 'ppe', 'Prupe.1G021500' => 'ppe', 'Prupe.1G021600' => 'ppe', 'Prupe.1G021700' => 'ppe', 'Prupe.1G021800' => 'ppe', 'Prupe.5G145100' => 'ppe', 'Psat6g204040' => 'psa', 'Psat6g204800' => 'psa', 'Psat6g204920' => 'psa', 'Psat6g204960' => 'psa', 'Psat6g205080' => 'psa', 'PSO017G0271' => 'pso', 'PSO017G1276' => 'pso', 'PSO017G1429' => 'pso', 'PSO017G1861' => 'pso', 'PSO017G2787' => 'pso', 'PSO017G4466' => 'pso', 'PSO017G5118' => 'pso', 'PSO017G5420' => 'pso', 'PSO063G3678' => 'pso', 'PSO210G0546' => 'pso', 'PSO317G0001' => 'pso', 'PSO357G0512' => 'pso', 'PSO478G2682' => 'pso', 'PSO647G0001' => 'pso', 'PSO675G0001' => 'pso', 'PSO675G2699' => 'pso', 'PSO675G2849' => 'pso', 'PSO675G4991' => 'pso', 'PSO689G0001' => 'pso', 'QL06p000916' => 'qlo', 'QL06p000921' => 'qlo', 'QL06p001398' => 'qlo', 'QL06p001407' => 'qlo', 'QL06p002031' => 'qlo', 'RcHm_v2.0_Chr4g0387791' => 'rch', 'RcHm_v2.0_Chr4g0387801' => 'rch', 'RcHm_v2.0_Chr6g0286501' => 'rch', 'RcHm_v2.0_Chr6g0286511' => 'rch', 'RcHm_v2.0_Chr6g0286521' => 'rch', 'RcHm_v2.0_Chr6g0286531' => 'rch', 'RcHm_v2.0_Chr7g0189141' => 'rch', 'Rhsim02G0028700' => 'rsi', 'Rhsim02G0028800' => 'rsi', 'Rhsim02G0028900' => 'rsi', 'Rhsim02G0029000' => 'rsi', 'Rhsim02G0029100' => 'rsi', 'Rhsim02G0029200' => 'rsi', 'Rhsim02G0029300' => 'rsi', 'Rhsim02G0029400' => 'rsi', 'Rhsim02G0029500' => 'rsi', 'Rhsim02G0029600' => 'rsi', 'RhsimUnG0024000' => 'rsi', 'RhsimUnG0024100' => 'rsi', 'RhsimUnG0024200' => 'rsi', 'RhsimUnG0024300' => 'rsi', 'RhsimUnG0024400' => 'rsi', 'RhsimUnG0024500' => 'rsi', 'RhsimUnG0024700' => 'rsi', 'RhsimUnG0024800' => 'rsi', 'RhsimUnG0024900' => 'rsi', 'RhsimUnG0025100' => 'rsi', 'Sabra08G0120200' => 'sbr', 'Sabra08G0120300' => 'sbr', 'Sabra08G0120500' => 'sbr', 'Sabra08G0120600' => 'sbr', 'Sabra10G0158900' => 'sbr', 'SalBow2G3492' => 'sbo', 'Sc13g0004760' => 'sci', 'Sc13g0004770' => 'sci', 'Sed0003417' => 'sed', 'Sed0019750' => 'sed', 'SEGI_03419' => 'sgi', 'SEGI_05907' => 'sgi', 'SEGI_10682' => 'sgi', 'SEGI_13528' => 'sgi', 'SEGI_16081' => 'sgi', 'SEGI_19370' => 'sgi', 'SEGI_21015' => 'sgi', 'SEGI_21944' => 'sgi', 'SEGI_32906' => 'sgi', 'SEGI_33093' => 'sgi', 'SEGI_36110' => 'sgi', 'SEGI_40397' => 'sgi', 'SGA_v2.0_scaffold191G40426' => 'sas', 'SGA_v2.0_scaffold353G49717' => 'sas', 'SGA_v2.0_scaffold50G18550' => 'sas', 'SMO119G0173' => 'smo', 'SMO172G0002' => 'smo', 'Solyc09g082690.3' => 'sly', 'Solyc09g082700.2' => 'sly', 'Sopen09g031550' => 'spe', 'Sopen09g031560' => 'spe', 'Sp3g20540' => 'spa', 'Sp7g07580' => 'spa', 'TAR134G0002' => 'tar', 'TAR236G0001' => 'tar', 'TAR365G0892' => 'tar', 'TAR636G0166' => 'tar', 'TAR636G0646' => 'tar', 'TAR636G0869' => 'tar', 'TAR636G1317' => 'tar', 'TAR636G1744' => 'tar', 'TAR636G3358' => 'tar', 'TAR636G3436' => 'tar', 'THA.LOC104803047' => 'tha', 'Thecc.04G238900' => 'tca', 'Thhalv10021557m.g' => 'esa', 'Thhalv10026318m.g' => 'esa', 'Thhalv10026335m.g' => 'esa', 'TPR.G17433' => 'tpr', 'TPR.G18915' => 'tpr', 'TPR.G26125' => 'tpr', 'TWI09G0677' => 'twi', 'TWI73G0287' => 'twi', 'unitig_748.g8326' => 'ugi', 'vmacro15370' => 'vma', 'vmacro15371' => 'vma', 'vmacro15372' => 'vma', 'vmacro15373' => 'vma', 'vmacro15374' => 'vma', 'VMungo0720G2826' => 'vmu', 'Zm00001eb116960' => 'zma', 'Zm00001eb301260' => 'zma', 'Zm00001eb301270' => 'zma' ), 'gf_id' => 'HOM05D001460', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001460' ), 'data_identifier' => 'HOM05D001460', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001460', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '433', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p22980' => 'bna', 'A01p32340' => 'bna', 'A03p42970' => 'bna', 'A05p25880' => 'bna', 'Aa31LG8G9320' => 'aar', 'Aa31LG8G9330' => 'aar', 'Aa31LG8G9340' => 'aar', 'Aa31sc221G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1034' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1528' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.829' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2222' => 'aag', 'Ah.12g058830' => 'amhyb', 'Ah.12g058840' => 'amhyb', 'AL3G37160' => 'aly', 'AL7G41310' => 'aly', 'Aqoxy5G00395' => 'aox', 'Aqoxy5G00396' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0C8NZA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5185HY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JZ1PRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MD3LS0' => 'arhy', 'AT3G22840' => 'ath', 'AT4G14690' => 'ath', 'ATR0665G054' => 'atr', 'Atru.chr4.2344' => 'acertr', 'Atru.chr4.2346' => 'acertr', 'Atru.chr4.2347' => 'acertr', 'Atru.chr4.2348' => 'acertr', 'Atru.chr4.2355' => 'acertr', 'Atru.chr4.2356' => 'acertr', 'Atru.chr4.2358' => 'acertr', 'Atru.chr4.2359' => 'acertr', 'Atru.chr4.2360' => 'acertr', 'Atru.chr4.2361' => 'acertr', 'AUR62030476' => 'cqu', 'AUR62030478' => 'cqu', 'AUR62030819' => 'cqu', 'AUR62030820' => 'cqu', 'BcaB03g14648' => 'bca', 'BcaB04g20492' => 'bca', 'BcaB06g26399' => 'bca', 'BcaC01g03416' => 'bca', 'BcaC01g03419' => 'bca', 'BcaC01g03421' => 'bca', 'BcaC01g03424' => 'bca', 'BcaC05g28012' => 'bca', 'BcaC09g49212' => 'bca', 'BcaC09g50140' => 'bca', 'BcaNung00346' => 'bca', 'BolC1t02785H' => 'bol', 'BolC1t04095H' => 'bol', 'BolC3t17545H' => 'bol', 'BolC5t32769H' => 'bol', 'BraA01t02211Z' => 'bra', 'BraA01t03359Z' => 'bra', 'BraA03t13441Z' => 'bra', 'BraA05t21476Z' => 'bra', 'C01p28420' => 'bna', 'C01p41350' => 'bna', 'C03p52750' => 'bna', 'C03p52780' => 'bna', 'C05p40270' => 'bna', 'CAN.G1437.9' => 'can', 'CANSAT78G0035' => 'cansat', 'CANSAT78G1036' => 'cansat', 'CANSAT78G2272' => 'cansat', 'CANSAT78G2478' => 'cansat', 'CARHR098700' => 'chi', 'CARHR221120' => 'chi', 'CARHR221150' => 'chi', 'Carub.0003s2297' => 'cru', 'Carub.0007s2749' => 'cru', 'Carub.0007s2750' => 'cru', 'Carub.0007s2751' => 'cru', 'Ca_10849_v3' => 'car', 'Cc03_g04300' => 'ccan', 'CDE02G3648' => 'cde', 'CDE05G0060' => 'cde', 'CDE05G0692' => 'cde', 'CDE05G2285' => 'cde', 'CDE05G2884' => 'cde', 'CDE05G3072' => 'cde', 'Cfa008439' => 'cfa', 'Cfa008441' => 'cfa', 'Cfa008443' => 'cfa', 'Cfa008448' => 'cfa', 'Ciclev10005974m.g' => 'ccl', 'Ciclev10006006m.g' => 'ccl', 'Ciclev10006775m.g' => 'ccl', 'CiPaw.02G120400' => 'cil', 'CiPaw.02G120500' => 'cil', 'CiPaw.02G120600' => 'cil', 'ClCG05G004850' => 'cla', 'COL.COLO4_21566' => 'col', 'Cpa.g.sc44.124' => 'cpa', 'Cre07.g320400' => 'cre', 'Cre07.g320450' => 'cre', 'Cre08.g384650' => 'cre', 'Cre09.g393173' => 'cre', 'Cre09.g394325' => 'cre', 'Cre14.g626750' => 'cre', 'Cre16.g679250' => 'cre', 'CsaV3_3G012890' => 'csa', 'CSS0010865' => 'camsi', 'CSS0044338' => 'camsi', 'DCAR_002366' => 'dca', 'DCAR_030687' => 'dca', 'DCAR_030688' => 'dca', 'Dinv14047' => 'din', 'Dinv14048' => 'din', 'Duzib151G0105' => 'dzi', 'Duzib151G0114' => 'dzi', 'Duzib212G1029' => 'dzi', 'ECA232G3536' => 'eca', 'ECA240G0786' => 'eca', 'ECA240G1802' => 'eca', 'ECA240G3760' => 'eca', 'ECA240G3920' => 'eca', 'EL10Ac5g12536' => 'bvu', 'EL10Ac5g12537' => 'bvu', 'EL10Ac5g12538' => 'bvu', 'Eucgr.B01004' => 'egr', 'Eucgr.B01006' => 'egr', 'Eucgr.B01007' => 'egr', 'Eucgr.B01008' => 'egr', 'Eucgr.B01895' => 'egr', 'Eucgr.B01896' => 'egr', 'FAN04G1456' => 'fan', 'FAN08G1769' => 'fan', 'FAN08G2160' => 'fan', 'FAN13G2403' => 'fan', 'FAN13G3303' => 'fan', 'FAN15G2435' => 'fan', 'FAN17G0672' => 'fan', 'FAN17G2441' => 'fan', 'FAN18G1024' => 'fan', 'FAN22G1458' => 'fan', 'FAN24G0037' => 'fan', 'FAN24G0429' => 'fan', 'FAN24G2387' => 'fan', 'FAN27G2746' => 'fan', 'FvH4_2g20400' => 'fve', 'FvH4_2g20420' => 'fve', 'FvH4_2g20430' => 'fve', 'FvH4_4g01270' => 'fve', 'FvH4_4g01290' => 'fve', 'FvH4_4g01300' => 'fve', 'FvH4_4g01310' => 'fve', 'FvH4_4g01330' => 'fve', 'FvH4_5g09070' => 'fve', 'Glyma.10G243800' => 'gma', 'Glyma.20G150600' => 'gma', 'Gohir.A09G219200' => 'ghi', 'Gohir.A09G219300' => 'ghi', 'Gohir.D09G221400' => 'ghi', 'Gohir.D09G221500' => 'ghi', 'Gorai.006G242600' => 'gra', 'Gorai.006G242700' => 'gra', 'GSVIVG01018044001' => 'vvi', 'HanXRQChr03g0083821' => 'han', 'HanXRQChr03g0083841' => 'han', 'HanXRQChr03g0083881' => 'han', 'HanXRQChr03g0083901' => 'han', 'HanXRQChr03g0083921' => 'han', 'HanXRQChr03g0085331' => 'han', 'HanXRQChr03g0085361' => 'han', 'HanXRQChr03g0085411' => 'han', 'HanXRQChr03g0085421' => 'han', 'HanXRQChr03g0085431' => 'han', 'HanXRQChr08g0221991' => 'han', 'HanXRQChr11g0336061' => 'han', 'HanXRQChr11g0336411' => 'han', 'Haze_11234' => 'cav', 'Hma1.2p1_0549F.1_g177010' => 'hma', 'Hma1.2p1_0602F.1_g187630' => 'hma', 'Hund14876' => 'sun', 'Hund14879' => 'sun', 'Lalb_Chr06g0160741' => 'lal', 'Lalb_Chr21g0304781' => 'lal', 'Lj3A726G19' => 'lonja', 'Lj3A726T23' => 'lonja', 'Lj3A726T24' => 'lonja', 'Lj3A726T25' => 'lonja', 'Lj3A727T17' => 'lonja', 'Lj3C726T0' => 'lonja', 'Lj3C726T2' => 'lonja', 'Lj3P725T35' => 'lonja', 'Lj3P727T10' => 'lonja', 'Lj3P727T12' => 'lonja', 'Lj3P727T14' => 'lonja', 'Lj5g0023109' => 'lja', 'Lj6P646T44' => 'lonja', 'Lsat_1_v5_gn_6_75760' => 'lsa', 'Lsat_1_v5_gn_6_75800' => 'lsa', 'Lsat_1_v5_gn_6_75900' => 'lsa', 'Lsat_1_v5_gn_6_76240' => 'lsa', 'Lsat_1_v5_gn_6_76441' => 'lsa', 'Lsat_1_v5_gn_6_76700' => 'lsa', 'Lsat_1_v5_gn_6_76760' => 'lsa', 'Manes.15G033100' => 'mes', 'Mapoly0004s0074' => 'mpo', 'Mapoly0004s0075' => 'mpo', 'Mapoly0004s0163' => 'mpo', 'Mapoly0004s0164' => 'mpo', 'Mapoly0021s0018' => 'mpo', 'Mapoly0041s0136' => 'mpo', 'Mapoly0041s0137' => 'mpo', 'Mapoly0041s0138' => 'mpo', 'Mapoly0041s0139' => 'mpo', 'Mapoly0041s0141' => 'mpo', 'Mapoly0041s0142' => 'mpo', 'Mapoly0041s0143' => 'mpo', 'Mapoly0041s0144' => 'mpo', 'Mapoly0041s0145' => 'mpo', 'Mapoly0047s0106' => 'mpo', 'Mapoly0047s0108' => 'mpo', 'Mapoly0050s0051' => 'mpo', 'Mapoly0050s0052' => 'mpo', 'Mapoly0050s0053' => 'mpo', 'Mapoly0058s0013' => 'mpo', 'Mapoly0091s0078' => 'mpo', 'Mapoly0091s0079' => 'mpo', 'Mapoly0091s0080' => 'mpo', 'Mapoly0091s0081' => 'mpo', 'Mapoly0278s0004' => 'mpo', 'Mapoly0278s0005' => 'mpo', 'Mapoly0278s0006' => 'mpo', 'MBI11_g30648_MAGBIO' => 'mbi', 'MCO03G194' => 'mco', 'MCO03G590' => 'mco', 'MCO07G312' => 'mco', 'MCO10G318' => 'mco', 'MCO12G244' => 'mco', 'MCO13G148' => 'mco', 'MCO13G194' => 'mco', 'MCO16G238' => 'mco', 'MD06G1134100' => 'mdo', 'MD13G1200100' => 'mdo', 'MD13G1200300' => 'mdo', 'MD13G1200600' => 'mdo', 'MD14G1150400' => 'mdo', 'MD16G1200000' => 'mdo', 'Medtr1g102570' => 'mtr', 'Medtr1g102780' => 'mtr', 'Medtr1g102800' => 'mtr', 'Medtr1g102810' => 'mtr', 'Medtr1g102830' => 'mtr', 'MELO3C006499.2' => 'cme', 'Migut.G00385' => 'egut', 'MSTRG.4063' => 'ama', 'Nitab4.5_0000090g0260' => 'nta', 'Nitab4.5_0000977g0030' => 'nta', 'Nitab4.5_0002541g0040' => 'nta', 'Nitab4.5_0007068g0040' => 'nta', 'Nn005s41408' => 'nnu', 'Nn005s41410' => 'nnu', 'Oeu010310.1' => 'oeu', 'Oeu010311.1' => 'oeu', 'Oeu043472.1' => 'oeu', 'Os01g0246400' => 'osa', 'Os04g0267950' => 'osa', 'Os07g0178700' => 'osa', 'Os07g0178800' => 'osa', 'Peaxi162Scf00316g00046' => 'pax', 'Peaxi162Scf00316g00049' => 'pax', 'Peaxi162Scf00316g00059' => 'pax', 'Peaxi162Scf00316g00328' => 'pax', 'Peaxi162Scf00316g00329' => 'pax', 'Peaxi162Scf00316g00411' => 'pax', 'Peaxi162Scf00316g00521' => 'pax', 'Peaxi162Scf00492g00068' => 'pax', 'Peaxi162Scf35631g00002' => 'pax', 'PGR142G3720' => 'pgr', 'PGSC0003DMG400006442' => 'stu', 'Phvul.007G062000' => 'pvu', 'Potri.008G157750' => 'ptr', 'Potri.008G157900' => 'ptr', 'Potri.008G158000' => 'ptr', 'Potri.008G158200' => 'ptr', 'Pp3c11_7280' => 'ppa', 'Pp3c11_7980' => 'ppa', 'Pp3c12_19450' => 'ppa', 'Pp3c14_1480' => 'ppa', 'Pp3c14_1501' => 'ppa', 'Pp3c16_4900' => 'ppa', 'Pp3c16_5010' => 'ppa', 'Pp3c16_5060' => 'ppa', 'Pp3c19_18250' => 'ppa', 'Pp3c23_8530' => 'ppa', 'Pp3c23_8550' => 'ppa', 'Pp3c24_9670' => 'ppa', 'Pp3c2_21390' => 'ppa', 'Pp3c2_31380' => 'ppa', 'Pp3c3_16620' => 'ppa', 'Pp3c3_8090' => 'ppa', 'Pp3c3_8110' => 'ppa', 'Pp3c3_8130' => 'ppa', 'Pp3c3_8150' => 'ppa', 'Pp3c4_14320' => 'ppa', 'Pp3c6_2560' => 'ppa', 'Pp3c9_16700' => 'ppa', 'PRCOL_00000234' => 'pco', 'PRCOL_00000235' => 'pco', 'PRCOL_00000777' => 'pco', 'PRCOL_00002344' => 'pco', 'PRCOL_00002372' => 'pco', 'PRCOL_00006120' => 'pco', 'Prupe.1G021400' => 'ppe', 'Prupe.1G021500' => 'ppe', 'Prupe.1G021600' => 'ppe', 'Prupe.1G021700' => 'ppe', 'Prupe.1G021800' => 'ppe', 'Prupe.5G145100' => 'ppe', 'Psat6g204040' => 'psa', 'Psat6g204800' => 'psa', 'Psat6g204920' => 'psa', 'Psat6g204960' => 'psa', 'Psat6g205080' => 'psa', 'PSO017G0271' => 'pso', 'PSO017G1276' => 'pso', 'PSO017G1429' => 'pso', 'PSO017G1861' => 'pso', 'PSO017G2787' => 'pso', 'PSO017G4466' => 'pso', 'PSO017G5118' => 'pso', 'PSO017G5420' => 'pso', 'PSO063G3678' => 'pso', 'PSO210G0546' => 'pso', 'PSO317G0001' => 'pso', 'PSO357G0512' => 'pso', 'PSO478G2682' => 'pso', 'PSO647G0001' => 'pso', 'PSO675G0001' => 'pso', 'PSO675G2699' => 'pso', 'PSO675G2849' => 'pso', 'PSO675G4991' => 'pso', 'PSO689G0001' => 'pso', 'QL06p000916' => 'qlo', 'QL06p000921' => 'qlo', 'QL06p001398' => 'qlo', 'QL06p001407' => 'qlo', 'QL06p002031' => 'qlo', 'RcHm_v2.0_Chr4g0387791' => 'rch', 'RcHm_v2.0_Chr4g0387801' => 'rch', 'RcHm_v2.0_Chr6g0286501' => 'rch', 'RcHm_v2.0_Chr6g0286511' => 'rch', 'RcHm_v2.0_Chr6g0286521' => 'rch', 'RcHm_v2.0_Chr6g0286531' => 'rch', 'RcHm_v2.0_Chr7g0189141' => 'rch', 'Rhsim02G0028700' => 'rsi', 'Rhsim02G0028800' => 'rsi', 'Rhsim02G0028900' => 'rsi', 'Rhsim02G0029000' => 'rsi', 'Rhsim02G0029100' => 'rsi', 'Rhsim02G0029200' => 'rsi', 'Rhsim02G0029300' => 'rsi', 'Rhsim02G0029400' => 'rsi', 'Rhsim02G0029500' => 'rsi', 'Rhsim02G0029600' => 'rsi', 'RhsimUnG0024000' => 'rsi', 'RhsimUnG0024100' => 'rsi', 'RhsimUnG0024200' => 'rsi', 'RhsimUnG0024300' => 'rsi', 'RhsimUnG0024400' => 'rsi', 'RhsimUnG0024500' => 'rsi', 'RhsimUnG0024700' => 'rsi', 'RhsimUnG0024800' => 'rsi', 'RhsimUnG0024900' => 'rsi', 'RhsimUnG0025100' => 'rsi', 'Sabra08G0120200' => 'sbr', 'Sabra08G0120300' => 'sbr', 'Sabra08G0120500' => 'sbr', 'Sabra08G0120600' => 'sbr', 'Sabra10G0158900' => 'sbr', 'SalBow2G3492' => 'sbo', 'Sc13g0004760' => 'sci', 'Sc13g0004770' => 'sci', 'Sed0003417' => 'sed', 'Sed0019750' => 'sed', 'SEGI_03419' => 'sgi', 'SEGI_05907' => 'sgi', 'SEGI_10682' => 'sgi', 'SEGI_13528' => 'sgi', 'SEGI_16081' => 'sgi', 'SEGI_19370' => 'sgi', 'SEGI_21015' => 'sgi', 'SEGI_21944' => 'sgi', 'SEGI_32906' => 'sgi', 'SEGI_33093' => 'sgi', 'SEGI_36110' => 'sgi', 'SEGI_40397' => 'sgi', 'SGA_v2.0_scaffold191G40426' => 'sas', 'SGA_v2.0_scaffold353G49717' => 'sas', 'SGA_v2.0_scaffold50G18550' => 'sas', 'SMO119G0173' => 'smo', 'SMO172G0002' => 'smo', 'Solyc09g082690.3' => 'sly', 'Solyc09g082700.2' => 'sly', 'Sopen09g031550' => 'spe', 'Sopen09g031560' => 'spe', 'Sp3g20540' => 'spa', 'Sp7g07580' => 'spa', 'TAR134G0002' => 'tar', 'TAR236G0001' => 'tar', 'TAR365G0892' => 'tar', 'TAR636G0166' => 'tar', 'TAR636G0646' => 'tar', 'TAR636G0869' => 'tar', 'TAR636G1317' => 'tar', 'TAR636G1744' => 'tar', 'TAR636G3358' => 'tar', 'TAR636G3436' => 'tar', 'THA.LOC104803047' => 'tha', 'Thecc.04G238900' => 'tca', 'Thhalv10021557m.g' => 'esa', 'Thhalv10026318m.g' => 'esa', 'Thhalv10026335m.g' => 'esa', 'TPR.G17433' => 'tpr', 'TPR.G18915' => 'tpr', 'TPR.G26125' => 'tpr', 'TWI09G0677' => 'twi', 'TWI73G0287' => 'twi', 'unitig_748.g8326' => 'ugi', 'vmacro15370' => 'vma', 'vmacro15371' => 'vma', 'vmacro15372' => 'vma', 'vmacro15373' => 'vma', 'vmacro15374' => 'vma', 'VMungo0720G2826' => 'vmu', 'Zm00001eb116960' => 'zma', 'Zm00001eb301260' => 'zma', 'Zm00001eb301270' => 'zma' ) $gf_id = 'HOM05D001460' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001460' ) $data_identifier = 'HOM05D001460' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 4, 'aag' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 2, 'aox' => (int) 2, 'arhy' => (int) 4, 'ath' => (int) 2, 'atr' => (int) 1, 'acertr' => (int) 10, 'cqu' => (int) 4, 'bca' => (int) 11, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 1, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 1, 'ccan' => (int) 1, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 1, 'col' => (int) 1, 'cpa' => (int) 1, 'cre' => (int) 7, 'csa' => (int) 1, 'camsi' => (int) 2, 'dca' => (int) 3, 'din' => (int) 2, 'dzi' => (int) 3, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 14, 'fve' => (int) 9, 'gma' => (int) 2, 'ghi' => (int) 4, 'gra' => (int) 2, 'vvi' => (int) 1, 'han' => (int) 13, 'cav' => (int) 1, 'hma' => (int) 2, 'sun' => (int) 2, 'lal' => (int) 2, 'lonja' => (int) 12, 'lja' => (int) 1, 'lsa' => (int) 7, 'mes' => (int) 1, 'mpo' => (int) 27, 'mbi' => (int) 1, 'mco' => (int) 8, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 1, 'egut' => (int) 1, 'ama' => (int) 1, 'nta' => (int) 4, 'nnu' => (int) 2, 'oeu' => (int) 3, 'osa' => (int) 4, 'pax' => (int) 9, 'pgr' => (int) 1, 'stu' => (int) 1, 'pvu' => (int) 1, 'ptr' => (int) 4, 'ppa' => (int) 22, 'pco' => (int) 6, 'ppe' => (int) 6, 'psa' => (int) 5, 'pso' => (int) 19, 'qlo' => (int) 5, 'rch' => (int) 7, 'rsi' => (int) 20, 'sbr' => (int) 5, 'sbo' => (int) 1, 'sci' => (int) 2, 'sed' => (int) 2, 'sgi' => (int) 12, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 2, 'tar' => (int) 10, 'tha' => (int) 1, 'tca' => (int) 1, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 2, 'ugi' => (int) 1, 'vma' => (int) 5, 'vmu' => (int) 1, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb301270' $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' => 'HOM05D001460', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '433', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p22980' => 'bna', 'A01p32340' => 'bna', 'A03p42970' => 'bna', 'A05p25880' => 'bna', 'Aa31LG8G9320' => 'aar', 'Aa31LG8G9330' => 'aar', 'Aa31LG8G9340' => 'aar', 'Aa31sc221G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1034' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1528' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.829' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2222' => 'aag', 'Ah.12g058830' => 'amhyb', 'Ah.12g058840' => 'amhyb', 'AL3G37160' => 'aly', 'AL7G41310' => 'aly', 'Aqoxy5G00395' => 'aox', 'Aqoxy5G00396' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0C8NZA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5185HY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JZ1PRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MD3LS0' => 'arhy', 'AT3G22840' => 'ath', 'AT4G14690' => 'ath', 'ATR0665G054' => 'atr', 'Atru.chr4.2344' => 'acertr', 'Atru.chr4.2346' => 'acertr', 'Atru.chr4.2347' => 'acertr', 'Atru.chr4.2348' => 'acertr', 'Atru.chr4.2355' => 'acertr', 'Atru.chr4.2356' => 'acertr', 'Atru.chr4.2358' => 'acertr', 'Atru.chr4.2359' => 'acertr', 'Atru.chr4.2360' => 'acertr', 'Atru.chr4.2361' => 'acertr', 'AUR62030476' => 'cqu', 'AUR62030478' => 'cqu', 'AUR62030819' => 'cqu', 'AUR62030820' => 'cqu', 'BcaB03g14648' => 'bca', 'BcaB04g20492' => 'bca', 'BcaB06g26399' => 'bca', 'BcaC01g03416' => 'bca', 'BcaC01g03419' => 'bca', 'BcaC01g03421' => 'bca', 'BcaC01g03424' => 'bca', 'BcaC05g28012' => 'bca', 'BcaC09g49212' => 'bca', 'BcaC09g50140' => 'bca', 'BcaNung00346' => 'bca', 'BolC1t02785H' => 'bol', 'BolC1t04095H' => 'bol', 'BolC3t17545H' => 'bol', 'BolC5t32769H' => 'bol', 'BraA01t02211Z' => 'bra', 'BraA01t03359Z' => 'bra', 'BraA03t13441Z' => 'bra', 'BraA05t21476Z' => 'bra', 'C01p28420' => 'bna', 'C01p41350' => 'bna', 'C03p52750' => 'bna', 'C03p52780' => 'bna', 'C05p40270' => 'bna', 'CAN.G1437.9' => 'can', 'CANSAT78G0035' => 'cansat', 'CANSAT78G1036' => 'cansat', 'CANSAT78G2272' => 'cansat', 'CANSAT78G2478' => 'cansat', 'CARHR098700' => 'chi', 'CARHR221120' => 'chi', 'CARHR221150' => 'chi', 'Carub.0003s2297' => 'cru', 'Carub.0007s2749' => 'cru', 'Carub.0007s2750' => 'cru', 'Carub.0007s2751' => 'cru', 'Ca_10849_v3' => 'car', 'Cc03_g04300' => 'ccan', 'CDE02G3648' => 'cde', 'CDE05G0060' => 'cde', 'CDE05G0692' => 'cde', 'CDE05G2285' => 'cde', 'CDE05G2884' => 'cde', 'CDE05G3072' => 'cde', 'Cfa008439' => 'cfa', 'Cfa008441' => 'cfa', 'Cfa008443' => 'cfa', 'Cfa008448' => 'cfa', 'Ciclev10005974m.g' => 'ccl', 'Ciclev10006006m.g' => 'ccl', 'Ciclev10006775m.g' => 'ccl', 'CiPaw.02G120400' => 'cil', 'CiPaw.02G120500' => 'cil', 'CiPaw.02G120600' => 'cil', 'ClCG05G004850' => 'cla', 'COL.COLO4_21566' => 'col', 'Cpa.g.sc44.124' => 'cpa', 'Cre07.g320400' => 'cre', 'Cre07.g320450' => 'cre', 'Cre08.g384650' => 'cre', 'Cre09.g393173' => 'cre', 'Cre09.g394325' => 'cre', 'Cre14.g626750' => 'cre', 'Cre16.g679250' => 'cre', 'CsaV3_3G012890' => 'csa', 'CSS0010865' => 'camsi', 'CSS0044338' => 'camsi', 'DCAR_002366' => 'dca', 'DCAR_030687' => 'dca', 'DCAR_030688' => 'dca', 'Dinv14047' => 'din', 'Dinv14048' => 'din', 'Duzib151G0105' => 'dzi', 'Duzib151G0114' => 'dzi', 'Duzib212G1029' => 'dzi', 'ECA232G3536' => 'eca', 'ECA240G0786' => 'eca', 'ECA240G1802' => 'eca', 'ECA240G3760' => 'eca', 'ECA240G3920' => 'eca', 'EL10Ac5g12536' => 'bvu', 'EL10Ac5g12537' => 'bvu', 'EL10Ac5g12538' => 'bvu', 'Eucgr.B01004' => 'egr', 'Eucgr.B01006' => 'egr', 'Eucgr.B01007' => 'egr', 'Eucgr.B01008' => 'egr', 'Eucgr.B01895' => 'egr', 'Eucgr.B01896' => 'egr', 'FAN04G1456' => 'fan', 'FAN08G1769' => 'fan', 'FAN08G2160' => 'fan', 'FAN13G2403' => 'fan', 'FAN13G3303' => 'fan', 'FAN15G2435' => 'fan', 'FAN17G0672' => 'fan', 'FAN17G2441' => 'fan', 'FAN18G1024' => 'fan', 'FAN22G1458' => 'fan', 'FAN24G0037' => 'fan', 'FAN24G0429' => 'fan', 'FAN24G2387' => 'fan', 'FAN27G2746' => 'fan', 'FvH4_2g20400' => 'fve', 'FvH4_2g20420' => 'fve', 'FvH4_2g20430' => 'fve', 'FvH4_4g01270' => 'fve', 'FvH4_4g01290' => 'fve', 'FvH4_4g01300' => 'fve', 'FvH4_4g01310' => 'fve', 'FvH4_4g01330' => 'fve', 'FvH4_5g09070' => 'fve', 'Glyma.10G243800' => 'gma', 'Glyma.20G150600' => 'gma', 'Gohir.A09G219200' => 'ghi', 'Gohir.A09G219300' => 'ghi', 'Gohir.D09G221400' => 'ghi', 'Gohir.D09G221500' => 'ghi', 'Gorai.006G242600' => 'gra', 'Gorai.006G242700' => 'gra', 'GSVIVG01018044001' => 'vvi', 'HanXRQChr03g0083821' => 'han', 'HanXRQChr03g0083841' => 'han', 'HanXRQChr03g0083881' => 'han', 'HanXRQChr03g0083901' => 'han', 'HanXRQChr03g0083921' => 'han', 'HanXRQChr03g0085331' => 'han', 'HanXRQChr03g0085361' => 'han', 'HanXRQChr03g0085411' => 'han', 'HanXRQChr03g0085421' => 'han', 'HanXRQChr03g0085431' => 'han', 'HanXRQChr08g0221991' => 'han', 'HanXRQChr11g0336061' => 'han', 'HanXRQChr11g0336411' => 'han', 'Haze_11234' => 'cav', 'Hma1.2p1_0549F.1_g177010' => 'hma', 'Hma1.2p1_0602F.1_g187630' => 'hma', 'Hund14876' => 'sun', 'Hund14879' => 'sun', 'Lalb_Chr06g0160741' => 'lal', 'Lalb_Chr21g0304781' => 'lal', 'Lj3A726G19' => 'lonja', 'Lj3A726T23' => 'lonja', 'Lj3A726T24' => 'lonja', 'Lj3A726T25' => 'lonja', 'Lj3A727T17' => 'lonja', 'Lj3C726T0' => 'lonja', 'Lj3C726T2' => 'lonja', 'Lj3P725T35' => 'lonja', 'Lj3P727T10' => 'lonja', 'Lj3P727T12' => 'lonja', 'Lj3P727T14' => 'lonja', 'Lj5g0023109' => 'lja', 'Lj6P646T44' => 'lonja', 'Lsat_1_v5_gn_6_75760' => 'lsa', 'Lsat_1_v5_gn_6_75800' => 'lsa', 'Lsat_1_v5_gn_6_75900' => 'lsa', 'Lsat_1_v5_gn_6_76240' => 'lsa', 'Lsat_1_v5_gn_6_76441' => 'lsa', 'Lsat_1_v5_gn_6_76700' => 'lsa', 'Lsat_1_v5_gn_6_76760' => 'lsa', 'Manes.15G033100' => 'mes', 'Mapoly0004s0074' => 'mpo', 'Mapoly0004s0075' => 'mpo', 'Mapoly0004s0163' => 'mpo', 'Mapoly0004s0164' => 'mpo', 'Mapoly0021s0018' => 'mpo', 'Mapoly0041s0136' => 'mpo', 'Mapoly0041s0137' => 'mpo', 'Mapoly0041s0138' => 'mpo', 'Mapoly0041s0139' => 'mpo', 'Mapoly0041s0141' => 'mpo', 'Mapoly0041s0142' => 'mpo', 'Mapoly0041s0143' => 'mpo', 'Mapoly0041s0144' => 'mpo', 'Mapoly0041s0145' => 'mpo', 'Mapoly0047s0106' => 'mpo', 'Mapoly0047s0108' => 'mpo', 'Mapoly0050s0051' => 'mpo', 'Mapoly0050s0052' => 'mpo', 'Mapoly0050s0053' => 'mpo', 'Mapoly0058s0013' => 'mpo', 'Mapoly0091s0078' => 'mpo', 'Mapoly0091s0079' => 'mpo', 'Mapoly0091s0080' => 'mpo', 'Mapoly0091s0081' => 'mpo', 'Mapoly0278s0004' => 'mpo', 'Mapoly0278s0005' => 'mpo', 'Mapoly0278s0006' => 'mpo', 'MBI11_g30648_MAGBIO' => 'mbi', 'MCO03G194' => 'mco', 'MCO03G590' => 'mco', 'MCO07G312' => 'mco', 'MCO10G318' => 'mco', 'MCO12G244' => 'mco', 'MCO13G148' => 'mco', 'MCO13G194' => 'mco', 'MCO16G238' => 'mco', 'MD06G1134100' => 'mdo', 'MD13G1200100' => 'mdo', 'MD13G1200300' => 'mdo', 'MD13G1200600' => 'mdo', 'MD14G1150400' => 'mdo', 'MD16G1200000' => 'mdo', 'Medtr1g102570' => 'mtr', 'Medtr1g102780' => 'mtr', 'Medtr1g102800' => 'mtr', 'Medtr1g102810' => 'mtr', 'Medtr1g102830' => 'mtr', 'MELO3C006499.2' => 'cme', 'Migut.G00385' => 'egut', 'MSTRG.4063' => 'ama', 'Nitab4.5_0000090g0260' => 'nta', 'Nitab4.5_0000977g0030' => 'nta', 'Nitab4.5_0002541g0040' => 'nta', 'Nitab4.5_0007068g0040' => 'nta', 'Nn005s41408' => 'nnu', 'Nn005s41410' => 'nnu', 'Oeu010310.1' => 'oeu', 'Oeu010311.1' => 'oeu', 'Oeu043472.1' => 'oeu', 'Os01g0246400' => 'osa', 'Os04g0267950' => 'osa', 'Os07g0178700' => 'osa', 'Os07g0178800' => 'osa', 'Peaxi162Scf00316g00046' => 'pax', 'Peaxi162Scf00316g00049' => 'pax', 'Peaxi162Scf00316g00059' => 'pax', 'Peaxi162Scf00316g00328' => 'pax', 'Peaxi162Scf00316g00329' => 'pax', 'Peaxi162Scf00316g00411' => 'pax', 'Peaxi162Scf00316g00521' => 'pax', 'Peaxi162Scf00492g00068' => 'pax', 'Peaxi162Scf35631g00002' => 'pax', 'PGR142G3720' => 'pgr', 'PGSC0003DMG400006442' => 'stu', 'Phvul.007G062000' => 'pvu', 'Potri.008G157750' => 'ptr', 'Potri.008G157900' => 'ptr', 'Potri.008G158000' => 'ptr', 'Potri.008G158200' => 'ptr', 'Pp3c11_7280' => 'ppa', 'Pp3c11_7980' => 'ppa', 'Pp3c12_19450' => 'ppa', 'Pp3c14_1480' => 'ppa', 'Pp3c14_1501' => 'ppa', 'Pp3c16_4900' => 'ppa', 'Pp3c16_5010' => 'ppa', 'Pp3c16_5060' => 'ppa', 'Pp3c19_18250' => 'ppa', 'Pp3c23_8530' => 'ppa', 'Pp3c23_8550' => 'ppa', 'Pp3c24_9670' => 'ppa', 'Pp3c2_21390' => 'ppa', 'Pp3c2_31380' => 'ppa', 'Pp3c3_16620' => 'ppa', 'Pp3c3_8090' => 'ppa', 'Pp3c3_8110' => 'ppa', 'Pp3c3_8130' => 'ppa', 'Pp3c3_8150' => 'ppa', 'Pp3c4_14320' => 'ppa', 'Pp3c6_2560' => 'ppa', 'Pp3c9_16700' => 'ppa', 'PRCOL_00000234' => 'pco', 'PRCOL_00000235' => 'pco', 'PRCOL_00000777' => 'pco', 'PRCOL_00002344' => 'pco', 'PRCOL_00002372' => 'pco', 'PRCOL_00006120' => 'pco', 'Prupe.1G021400' => 'ppe', 'Prupe.1G021500' => 'ppe', 'Prupe.1G021600' => 'ppe', 'Prupe.1G021700' => 'ppe', 'Prupe.1G021800' => 'ppe', 'Prupe.5G145100' => 'ppe', 'Psat6g204040' => 'psa', 'Psat6g204800' => 'psa', 'Psat6g204920' => 'psa', 'Psat6g204960' => 'psa', 'Psat6g205080' => 'psa', 'PSO017G0271' => 'pso', 'PSO017G1276' => 'pso', 'PSO017G1429' => 'pso', 'PSO017G1861' => 'pso', 'PSO017G2787' => 'pso', 'PSO017G4466' => 'pso', 'PSO017G5118' => 'pso', 'PSO017G5420' => 'pso', 'PSO063G3678' => 'pso', 'PSO210G0546' => 'pso', 'PSO317G0001' => 'pso', 'PSO357G0512' => 'pso', 'PSO478G2682' => 'pso', 'PSO647G0001' => 'pso', 'PSO675G0001' => 'pso', 'PSO675G2699' => 'pso', 'PSO675G2849' => 'pso', 'PSO675G4991' => 'pso', 'PSO689G0001' => 'pso', 'QL06p000916' => 'qlo', 'QL06p000921' => 'qlo', 'QL06p001398' => 'qlo', 'QL06p001407' => 'qlo', 'QL06p002031' => 'qlo', 'RcHm_v2.0_Chr4g0387791' => 'rch', 'RcHm_v2.0_Chr4g0387801' => 'rch', 'RcHm_v2.0_Chr6g0286501' => 'rch', 'RcHm_v2.0_Chr6g0286511' => 'rch', 'RcHm_v2.0_Chr6g0286521' => 'rch', 'RcHm_v2.0_Chr6g0286531' => 'rch', 'RcHm_v2.0_Chr7g0189141' => 'rch', 'Rhsim02G0028700' => 'rsi', 'Rhsim02G0028800' => 'rsi', 'Rhsim02G0028900' => 'rsi', 'Rhsim02G0029000' => 'rsi', 'Rhsim02G0029100' => 'rsi', 'Rhsim02G0029200' => 'rsi', 'Rhsim02G0029300' => 'rsi', 'Rhsim02G0029400' => 'rsi', 'Rhsim02G0029500' => 'rsi', 'Rhsim02G0029600' => 'rsi', 'RhsimUnG0024000' => 'rsi', 'RhsimUnG0024100' => 'rsi', 'RhsimUnG0024200' => 'rsi', 'RhsimUnG0024300' => 'rsi', 'RhsimUnG0024400' => 'rsi', 'RhsimUnG0024500' => 'rsi', 'RhsimUnG0024700' => 'rsi', 'RhsimUnG0024800' => 'rsi', 'RhsimUnG0024900' => 'rsi', 'RhsimUnG0025100' => 'rsi', 'Sabra08G0120200' => 'sbr', 'Sabra08G0120300' => 'sbr', 'Sabra08G0120500' => 'sbr', 'Sabra08G0120600' => 'sbr', 'Sabra10G0158900' => 'sbr', 'SalBow2G3492' => 'sbo', 'Sc13g0004760' => 'sci', 'Sc13g0004770' => 'sci', 'Sed0003417' => 'sed', 'Sed0019750' => 'sed', 'SEGI_03419' => 'sgi', 'SEGI_05907' => 'sgi', 'SEGI_10682' => 'sgi', 'SEGI_13528' => 'sgi', 'SEGI_16081' => 'sgi', 'SEGI_19370' => 'sgi', 'SEGI_21015' => 'sgi', 'SEGI_21944' => 'sgi', 'SEGI_32906' => 'sgi', 'SEGI_33093' => 'sgi', 'SEGI_36110' => 'sgi', 'SEGI_40397' => 'sgi', 'SGA_v2.0_scaffold191G40426' => 'sas', 'SGA_v2.0_scaffold353G49717' => 'sas', 'SGA_v2.0_scaffold50G18550' => 'sas', 'SMO119G0173' => 'smo', 'SMO172G0002' => 'smo', 'Solyc09g082690.3' => 'sly', 'Solyc09g082700.2' => 'sly', 'Sopen09g031550' => 'spe', 'Sopen09g031560' => 'spe', 'Sp3g20540' => 'spa', 'Sp7g07580' => 'spa', 'TAR134G0002' => 'tar', 'TAR236G0001' => 'tar', 'TAR365G0892' => 'tar', 'TAR636G0166' => 'tar', 'TAR636G0646' => 'tar', 'TAR636G0869' => 'tar', 'TAR636G1317' => 'tar', 'TAR636G1744' => 'tar', 'TAR636G3358' => 'tar', 'TAR636G3436' => 'tar', 'THA.LOC104803047' => 'tha', 'Thecc.04G238900' => 'tca', 'Thhalv10021557m.g' => 'esa', 'Thhalv10026318m.g' => 'esa', 'Thhalv10026335m.g' => 'esa', 'TPR.G17433' => 'tpr', 'TPR.G18915' => 'tpr', 'TPR.G26125' => 'tpr', 'TWI09G0677' => 'twi', 'TWI73G0287' => 'twi', 'unitig_748.g8326' => 'ugi', 'vmacro15370' => 'vma', 'vmacro15371' => 'vma', 'vmacro15372' => 'vma', 'vmacro15373' => 'vma', 'vmacro15374' => 'vma', 'VMungo0720G2826' => 'vmu', 'Zm00001eb116960' => 'zma', 'Zm00001eb301260' => 'zma', 'Zm00001eb301270' => 'zma' ), 'gf_id' => 'HOM05D001460', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001460' ), 'data_identifier' => 'HOM05D001460', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001460', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '433', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p22980' => 'bna', 'A01p32340' => 'bna', 'A03p42970' => 'bna', 'A05p25880' => 'bna', 'Aa31LG8G9320' => 'aar', 'Aa31LG8G9330' => 'aar', 'Aa31LG8G9340' => 'aar', 'Aa31sc221G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1034' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1528' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.829' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2222' => 'aag', 'Ah.12g058830' => 'amhyb', 'Ah.12g058840' => 'amhyb', 'AL3G37160' => 'aly', 'AL7G41310' => 'aly', 'Aqoxy5G00395' => 'aox', 'Aqoxy5G00396' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0C8NZA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5185HY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JZ1PRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MD3LS0' => 'arhy', 'AT3G22840' => 'ath', 'AT4G14690' => 'ath', 'ATR0665G054' => 'atr', 'Atru.chr4.2344' => 'acertr', 'Atru.chr4.2346' => 'acertr', 'Atru.chr4.2347' => 'acertr', 'Atru.chr4.2348' => 'acertr', 'Atru.chr4.2355' => 'acertr', 'Atru.chr4.2356' => 'acertr', 'Atru.chr4.2358' => 'acertr', 'Atru.chr4.2359' => 'acertr', 'Atru.chr4.2360' => 'acertr', 'Atru.chr4.2361' => 'acertr', 'AUR62030476' => 'cqu', 'AUR62030478' => 'cqu', 'AUR62030819' => 'cqu', 'AUR62030820' => 'cqu', 'BcaB03g14648' => 'bca', 'BcaB04g20492' => 'bca', 'BcaB06g26399' => 'bca', 'BcaC01g03416' => 'bca', 'BcaC01g03419' => 'bca', 'BcaC01g03421' => 'bca', 'BcaC01g03424' => 'bca', 'BcaC05g28012' => 'bca', 'BcaC09g49212' => 'bca', 'BcaC09g50140' => 'bca', 'BcaNung00346' => 'bca', 'BolC1t02785H' => 'bol', 'BolC1t04095H' => 'bol', 'BolC3t17545H' => 'bol', 'BolC5t32769H' => 'bol', 'BraA01t02211Z' => 'bra', 'BraA01t03359Z' => 'bra', 'BraA03t13441Z' => 'bra', 'BraA05t21476Z' => 'bra', 'C01p28420' => 'bna', 'C01p41350' => 'bna', 'C03p52750' => 'bna', 'C03p52780' => 'bna', 'C05p40270' => 'bna', 'CAN.G1437.9' => 'can', 'CANSAT78G0035' => 'cansat', 'CANSAT78G1036' => 'cansat', 'CANSAT78G2272' => 'cansat', 'CANSAT78G2478' => 'cansat', 'CARHR098700' => 'chi', 'CARHR221120' => 'chi', 'CARHR221150' => 'chi', 'Carub.0003s2297' => 'cru', 'Carub.0007s2749' => 'cru', 'Carub.0007s2750' => 'cru', 'Carub.0007s2751' => 'cru', 'Ca_10849_v3' => 'car', 'Cc03_g04300' => 'ccan', 'CDE02G3648' => 'cde', 'CDE05G0060' => 'cde', 'CDE05G0692' => 'cde', 'CDE05G2285' => 'cde', 'CDE05G2884' => 'cde', 'CDE05G3072' => 'cde', 'Cfa008439' => 'cfa', 'Cfa008441' => 'cfa', 'Cfa008443' => 'cfa', 'Cfa008448' => 'cfa', 'Ciclev10005974m.g' => 'ccl', 'Ciclev10006006m.g' => 'ccl', 'Ciclev10006775m.g' => 'ccl', 'CiPaw.02G120400' => 'cil', 'CiPaw.02G120500' => 'cil', 'CiPaw.02G120600' => 'cil', 'ClCG05G004850' => 'cla', 'COL.COLO4_21566' => 'col', 'Cpa.g.sc44.124' => 'cpa', 'Cre07.g320400' => 'cre', 'Cre07.g320450' => 'cre', 'Cre08.g384650' => 'cre', 'Cre09.g393173' => 'cre', 'Cre09.g394325' => 'cre', 'Cre14.g626750' => 'cre', 'Cre16.g679250' => 'cre', 'CsaV3_3G012890' => 'csa', 'CSS0010865' => 'camsi', 'CSS0044338' => 'camsi', 'DCAR_002366' => 'dca', 'DCAR_030687' => 'dca', 'DCAR_030688' => 'dca', 'Dinv14047' => 'din', 'Dinv14048' => 'din', 'Duzib151G0105' => 'dzi', 'Duzib151G0114' => 'dzi', 'Duzib212G1029' => 'dzi', 'ECA232G3536' => 'eca', 'ECA240G0786' => 'eca', 'ECA240G1802' => 'eca', 'ECA240G3760' => 'eca', 'ECA240G3920' => 'eca', 'EL10Ac5g12536' => 'bvu', 'EL10Ac5g12537' => 'bvu', 'EL10Ac5g12538' => 'bvu', 'Eucgr.B01004' => 'egr', 'Eucgr.B01006' => 'egr', 'Eucgr.B01007' => 'egr', 'Eucgr.B01008' => 'egr', 'Eucgr.B01895' => 'egr', 'Eucgr.B01896' => 'egr', 'FAN04G1456' => 'fan', 'FAN08G1769' => 'fan', 'FAN08G2160' => 'fan', 'FAN13G2403' => 'fan', 'FAN13G3303' => 'fan', 'FAN15G2435' => 'fan', 'FAN17G0672' => 'fan', 'FAN17G2441' => 'fan', 'FAN18G1024' => 'fan', 'FAN22G1458' => 'fan', 'FAN24G0037' => 'fan', 'FAN24G0429' => 'fan', 'FAN24G2387' => 'fan', 'FAN27G2746' => 'fan', 'FvH4_2g20400' => 'fve', 'FvH4_2g20420' => 'fve', 'FvH4_2g20430' => 'fve', 'FvH4_4g01270' => 'fve', 'FvH4_4g01290' => 'fve', 'FvH4_4g01300' => 'fve', 'FvH4_4g01310' => 'fve', 'FvH4_4g01330' => 'fve', 'FvH4_5g09070' => 'fve', 'Glyma.10G243800' => 'gma', 'Glyma.20G150600' => 'gma', 'Gohir.A09G219200' => 'ghi', 'Gohir.A09G219300' => 'ghi', 'Gohir.D09G221400' => 'ghi', 'Gohir.D09G221500' => 'ghi', 'Gorai.006G242600' => 'gra', 'Gorai.006G242700' => 'gra', 'GSVIVG01018044001' => 'vvi', 'HanXRQChr03g0083821' => 'han', 'HanXRQChr03g0083841' => 'han', 'HanXRQChr03g0083881' => 'han', 'HanXRQChr03g0083901' => 'han', 'HanXRQChr03g0083921' => 'han', 'HanXRQChr03g0085331' => 'han', 'HanXRQChr03g0085361' => 'han', 'HanXRQChr03g0085411' => 'han', 'HanXRQChr03g0085421' => 'han', 'HanXRQChr03g0085431' => 'han', 'HanXRQChr08g0221991' => 'han', 'HanXRQChr11g0336061' => 'han', 'HanXRQChr11g0336411' => 'han', 'Haze_11234' => 'cav', 'Hma1.2p1_0549F.1_g177010' => 'hma', 'Hma1.2p1_0602F.1_g187630' => 'hma', 'Hund14876' => 'sun', 'Hund14879' => 'sun', 'Lalb_Chr06g0160741' => 'lal', 'Lalb_Chr21g0304781' => 'lal', 'Lj3A726G19' => 'lonja', 'Lj3A726T23' => 'lonja', 'Lj3A726T24' => 'lonja', 'Lj3A726T25' => 'lonja', 'Lj3A727T17' => 'lonja', 'Lj3C726T0' => 'lonja', 'Lj3C726T2' => 'lonja', 'Lj3P725T35' => 'lonja', 'Lj3P727T10' => 'lonja', 'Lj3P727T12' => 'lonja', 'Lj3P727T14' => 'lonja', 'Lj5g0023109' => 'lja', 'Lj6P646T44' => 'lonja', 'Lsat_1_v5_gn_6_75760' => 'lsa', 'Lsat_1_v5_gn_6_75800' => 'lsa', 'Lsat_1_v5_gn_6_75900' => 'lsa', 'Lsat_1_v5_gn_6_76240' => 'lsa', 'Lsat_1_v5_gn_6_76441' => 'lsa', 'Lsat_1_v5_gn_6_76700' => 'lsa', 'Lsat_1_v5_gn_6_76760' => 'lsa', 'Manes.15G033100' => 'mes', 'Mapoly0004s0074' => 'mpo', 'Mapoly0004s0075' => 'mpo', 'Mapoly0004s0163' => 'mpo', 'Mapoly0004s0164' => 'mpo', 'Mapoly0021s0018' => 'mpo', 'Mapoly0041s0136' => 'mpo', 'Mapoly0041s0137' => 'mpo', 'Mapoly0041s0138' => 'mpo', 'Mapoly0041s0139' => 'mpo', 'Mapoly0041s0141' => 'mpo', 'Mapoly0041s0142' => 'mpo', 'Mapoly0041s0143' => 'mpo', 'Mapoly0041s0144' => 'mpo', 'Mapoly0041s0145' => 'mpo', 'Mapoly0047s0106' => 'mpo', 'Mapoly0047s0108' => 'mpo', 'Mapoly0050s0051' => 'mpo', 'Mapoly0050s0052' => 'mpo', 'Mapoly0050s0053' => 'mpo', 'Mapoly0058s0013' => 'mpo', 'Mapoly0091s0078' => 'mpo', 'Mapoly0091s0079' => 'mpo', 'Mapoly0091s0080' => 'mpo', 'Mapoly0091s0081' => 'mpo', 'Mapoly0278s0004' => 'mpo', 'Mapoly0278s0005' => 'mpo', 'Mapoly0278s0006' => 'mpo', 'MBI11_g30648_MAGBIO' => 'mbi', 'MCO03G194' => 'mco', 'MCO03G590' => 'mco', 'MCO07G312' => 'mco', 'MCO10G318' => 'mco', 'MCO12G244' => 'mco', 'MCO13G148' => 'mco', 'MCO13G194' => 'mco', 'MCO16G238' => 'mco', 'MD06G1134100' => 'mdo', 'MD13G1200100' => 'mdo', 'MD13G1200300' => 'mdo', 'MD13G1200600' => 'mdo', 'MD14G1150400' => 'mdo', 'MD16G1200000' => 'mdo', 'Medtr1g102570' => 'mtr', 'Medtr1g102780' => 'mtr', 'Medtr1g102800' => 'mtr', 'Medtr1g102810' => 'mtr', 'Medtr1g102830' => 'mtr', 'MELO3C006499.2' => 'cme', 'Migut.G00385' => 'egut', 'MSTRG.4063' => 'ama', 'Nitab4.5_0000090g0260' => 'nta', 'Nitab4.5_0000977g0030' => 'nta', 'Nitab4.5_0002541g0040' => 'nta', 'Nitab4.5_0007068g0040' => 'nta', 'Nn005s41408' => 'nnu', 'Nn005s41410' => 'nnu', 'Oeu010310.1' => 'oeu', 'Oeu010311.1' => 'oeu', 'Oeu043472.1' => 'oeu', 'Os01g0246400' => 'osa', 'Os04g0267950' => 'osa', 'Os07g0178700' => 'osa', 'Os07g0178800' => 'osa', 'Peaxi162Scf00316g00046' => 'pax', 'Peaxi162Scf00316g00049' => 'pax', 'Peaxi162Scf00316g00059' => 'pax', 'Peaxi162Scf00316g00328' => 'pax', 'Peaxi162Scf00316g00329' => 'pax', 'Peaxi162Scf00316g00411' => 'pax', 'Peaxi162Scf00316g00521' => 'pax', 'Peaxi162Scf00492g00068' => 'pax', 'Peaxi162Scf35631g00002' => 'pax', 'PGR142G3720' => 'pgr', 'PGSC0003DMG400006442' => 'stu', 'Phvul.007G062000' => 'pvu', 'Potri.008G157750' => 'ptr', 'Potri.008G157900' => 'ptr', 'Potri.008G158000' => 'ptr', 'Potri.008G158200' => 'ptr', 'Pp3c11_7280' => 'ppa', 'Pp3c11_7980' => 'ppa', 'Pp3c12_19450' => 'ppa', 'Pp3c14_1480' => 'ppa', 'Pp3c14_1501' => 'ppa', 'Pp3c16_4900' => 'ppa', 'Pp3c16_5010' => 'ppa', 'Pp3c16_5060' => 'ppa', 'Pp3c19_18250' => 'ppa', 'Pp3c23_8530' => 'ppa', 'Pp3c23_8550' => 'ppa', 'Pp3c24_9670' => 'ppa', 'Pp3c2_21390' => 'ppa', 'Pp3c2_31380' => 'ppa', 'Pp3c3_16620' => 'ppa', 'Pp3c3_8090' => 'ppa', 'Pp3c3_8110' => 'ppa', 'Pp3c3_8130' => 'ppa', 'Pp3c3_8150' => 'ppa', 'Pp3c4_14320' => 'ppa', 'Pp3c6_2560' => 'ppa', 'Pp3c9_16700' => 'ppa', 'PRCOL_00000234' => 'pco', 'PRCOL_00000235' => 'pco', 'PRCOL_00000777' => 'pco', 'PRCOL_00002344' => 'pco', 'PRCOL_00002372' => 'pco', 'PRCOL_00006120' => 'pco', 'Prupe.1G021400' => 'ppe', 'Prupe.1G021500' => 'ppe', 'Prupe.1G021600' => 'ppe', 'Prupe.1G021700' => 'ppe', 'Prupe.1G021800' => 'ppe', 'Prupe.5G145100' => 'ppe', 'Psat6g204040' => 'psa', 'Psat6g204800' => 'psa', 'Psat6g204920' => 'psa', 'Psat6g204960' => 'psa', 'Psat6g205080' => 'psa', 'PSO017G0271' => 'pso', 'PSO017G1276' => 'pso', 'PSO017G1429' => 'pso', 'PSO017G1861' => 'pso', 'PSO017G2787' => 'pso', 'PSO017G4466' => 'pso', 'PSO017G5118' => 'pso', 'PSO017G5420' => 'pso', 'PSO063G3678' => 'pso', 'PSO210G0546' => 'pso', 'PSO317G0001' => 'pso', 'PSO357G0512' => 'pso', 'PSO478G2682' => 'pso', 'PSO647G0001' => 'pso', 'PSO675G0001' => 'pso', 'PSO675G2699' => 'pso', 'PSO675G2849' => 'pso', 'PSO675G4991' => 'pso', 'PSO689G0001' => 'pso', 'QL06p000916' => 'qlo', 'QL06p000921' => 'qlo', 'QL06p001398' => 'qlo', 'QL06p001407' => 'qlo', 'QL06p002031' => 'qlo', 'RcHm_v2.0_Chr4g0387791' => 'rch', 'RcHm_v2.0_Chr4g0387801' => 'rch', 'RcHm_v2.0_Chr6g0286501' => 'rch', 'RcHm_v2.0_Chr6g0286511' => 'rch', 'RcHm_v2.0_Chr6g0286521' => 'rch', 'RcHm_v2.0_Chr6g0286531' => 'rch', 'RcHm_v2.0_Chr7g0189141' => 'rch', 'Rhsim02G0028700' => 'rsi', 'Rhsim02G0028800' => 'rsi', 'Rhsim02G0028900' => 'rsi', 'Rhsim02G0029000' => 'rsi', 'Rhsim02G0029100' => 'rsi', 'Rhsim02G0029200' => 'rsi', 'Rhsim02G0029300' => 'rsi', 'Rhsim02G0029400' => 'rsi', 'Rhsim02G0029500' => 'rsi', 'Rhsim02G0029600' => 'rsi', 'RhsimUnG0024000' => 'rsi', 'RhsimUnG0024100' => 'rsi', 'RhsimUnG0024200' => 'rsi', 'RhsimUnG0024300' => 'rsi', 'RhsimUnG0024400' => 'rsi', 'RhsimUnG0024500' => 'rsi', 'RhsimUnG0024700' => 'rsi', 'RhsimUnG0024800' => 'rsi', 'RhsimUnG0024900' => 'rsi', 'RhsimUnG0025100' => 'rsi', 'Sabra08G0120200' => 'sbr', 'Sabra08G0120300' => 'sbr', 'Sabra08G0120500' => 'sbr', 'Sabra08G0120600' => 'sbr', 'Sabra10G0158900' => 'sbr', 'SalBow2G3492' => 'sbo', 'Sc13g0004760' => 'sci', 'Sc13g0004770' => 'sci', 'Sed0003417' => 'sed', 'Sed0019750' => 'sed', 'SEGI_03419' => 'sgi', 'SEGI_05907' => 'sgi', 'SEGI_10682' => 'sgi', 'SEGI_13528' => 'sgi', 'SEGI_16081' => 'sgi', 'SEGI_19370' => 'sgi', 'SEGI_21015' => 'sgi', 'SEGI_21944' => 'sgi', 'SEGI_32906' => 'sgi', 'SEGI_33093' => 'sgi', 'SEGI_36110' => 'sgi', 'SEGI_40397' => 'sgi', 'SGA_v2.0_scaffold191G40426' => 'sas', 'SGA_v2.0_scaffold353G49717' => 'sas', 'SGA_v2.0_scaffold50G18550' => 'sas', 'SMO119G0173' => 'smo', 'SMO172G0002' => 'smo', 'Solyc09g082690.3' => 'sly', 'Solyc09g082700.2' => 'sly', 'Sopen09g031550' => 'spe', 'Sopen09g031560' => 'spe', 'Sp3g20540' => 'spa', 'Sp7g07580' => 'spa', 'TAR134G0002' => 'tar', 'TAR236G0001' => 'tar', 'TAR365G0892' => 'tar', 'TAR636G0166' => 'tar', 'TAR636G0646' => 'tar', 'TAR636G0869' => 'tar', 'TAR636G1317' => 'tar', 'TAR636G1744' => 'tar', 'TAR636G3358' => 'tar', 'TAR636G3436' => 'tar', 'THA.LOC104803047' => 'tha', 'Thecc.04G238900' => 'tca', 'Thhalv10021557m.g' => 'esa', 'Thhalv10026318m.g' => 'esa', 'Thhalv10026335m.g' => 'esa', 'TPR.G17433' => 'tpr', 'TPR.G18915' => 'tpr', 'TPR.G26125' => 'tpr', 'TWI09G0677' => 'twi', 'TWI73G0287' => 'twi', 'unitig_748.g8326' => 'ugi', 'vmacro15370' => 'vma', 'vmacro15371' => 'vma', 'vmacro15372' => 'vma', 'vmacro15373' => 'vma', 'vmacro15374' => 'vma', 'VMungo0720G2826' => 'vmu', 'Zm00001eb116960' => 'zma', 'Zm00001eb301260' => 'zma', 'Zm00001eb301270' => 'zma' ) $gf_id = 'HOM05D001460' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001460' ) $data_identifier = 'HOM05D001460' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 4, 'aag' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 2, 'aox' => (int) 2, 'arhy' => (int) 4, 'ath' => (int) 2, 'atr' => (int) 1, 'acertr' => (int) 10, 'cqu' => (int) 4, 'bca' => (int) 11, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 1, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 1, 'ccan' => (int) 1, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 1, 'col' => (int) 1, 'cpa' => (int) 1, 'cre' => (int) 7, 'csa' => (int) 1, 'camsi' => (int) 2, 'dca' => (int) 3, 'din' => (int) 2, 'dzi' => (int) 3, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 14, 'fve' => (int) 9, 'gma' => (int) 2, 'ghi' => (int) 4, 'gra' => (int) 2, 'vvi' => (int) 1, 'han' => (int) 13, 'cav' => (int) 1, 'hma' => (int) 2, 'sun' => (int) 2, 'lal' => (int) 2, 'lonja' => (int) 12, 'lja' => (int) 1, 'lsa' => (int) 7, 'mes' => (int) 1, 'mpo' => (int) 27, 'mbi' => (int) 1, 'mco' => (int) 8, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 1, 'egut' => (int) 1, 'ama' => (int) 1, 'nta' => (int) 4, 'nnu' => (int) 2, 'oeu' => (int) 3, 'osa' => (int) 4, 'pax' => (int) 9, 'pgr' => (int) 1, 'stu' => (int) 1, 'pvu' => (int) 1, 'ptr' => (int) 4, 'ppa' => (int) 22, 'pco' => (int) 6, 'ppe' => (int) 6, 'psa' => (int) 5, 'pso' => (int) 19, 'qlo' => (int) 5, 'rch' => (int) 7, 'rsi' => (int) 20, 'sbr' => (int) 5, 'sbo' => (int) 1, 'sci' => (int) 2, 'sed' => (int) 2, 'sgi' => (int) 12, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 2, 'tar' => (int) 10, 'tha' => (int) 1, 'tca' => (int) 1, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 2, 'ugi' => (int) 1, 'vma' => (int) 5, 'vmu' => (int) 1, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb301270' $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' => 'HOM05D001460', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '433', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p22980' => 'bna', 'A01p32340' => 'bna', 'A03p42970' => 'bna', 'A05p25880' => 'bna', 'Aa31LG8G9320' => 'aar', 'Aa31LG8G9330' => 'aar', 'Aa31LG8G9340' => 'aar', 'Aa31sc221G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1034' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1528' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.829' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2222' => 'aag', 'Ah.12g058830' => 'amhyb', 'Ah.12g058840' => 'amhyb', 'AL3G37160' => 'aly', 'AL7G41310' => 'aly', 'Aqoxy5G00395' => 'aox', 'Aqoxy5G00396' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0C8NZA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5185HY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JZ1PRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MD3LS0' => 'arhy', 'AT3G22840' => 'ath', 'AT4G14690' => 'ath', 'ATR0665G054' => 'atr', 'Atru.chr4.2344' => 'acertr', 'Atru.chr4.2346' => 'acertr', 'Atru.chr4.2347' => 'acertr', 'Atru.chr4.2348' => 'acertr', 'Atru.chr4.2355' => 'acertr', 'Atru.chr4.2356' => 'acertr', 'Atru.chr4.2358' => 'acertr', 'Atru.chr4.2359' => 'acertr', 'Atru.chr4.2360' => 'acertr', 'Atru.chr4.2361' => 'acertr', 'AUR62030476' => 'cqu', 'AUR62030478' => 'cqu', 'AUR62030819' => 'cqu', 'AUR62030820' => 'cqu', 'BcaB03g14648' => 'bca', 'BcaB04g20492' => 'bca', 'BcaB06g26399' => 'bca', 'BcaC01g03416' => 'bca', 'BcaC01g03419' => 'bca', 'BcaC01g03421' => 'bca', 'BcaC01g03424' => 'bca', 'BcaC05g28012' => 'bca', 'BcaC09g49212' => 'bca', 'BcaC09g50140' => 'bca', 'BcaNung00346' => 'bca', 'BolC1t02785H' => 'bol', 'BolC1t04095H' => 'bol', 'BolC3t17545H' => 'bol', 'BolC5t32769H' => 'bol', 'BraA01t02211Z' => 'bra', 'BraA01t03359Z' => 'bra', 'BraA03t13441Z' => 'bra', 'BraA05t21476Z' => 'bra', 'C01p28420' => 'bna', 'C01p41350' => 'bna', 'C03p52750' => 'bna', 'C03p52780' => 'bna', 'C05p40270' => 'bna', 'CAN.G1437.9' => 'can', 'CANSAT78G0035' => 'cansat', 'CANSAT78G1036' => 'cansat', 'CANSAT78G2272' => 'cansat', 'CANSAT78G2478' => 'cansat', 'CARHR098700' => 'chi', 'CARHR221120' => 'chi', 'CARHR221150' => 'chi', 'Carub.0003s2297' => 'cru', 'Carub.0007s2749' => 'cru', 'Carub.0007s2750' => 'cru', 'Carub.0007s2751' => 'cru', 'Ca_10849_v3' => 'car', 'Cc03_g04300' => 'ccan', 'CDE02G3648' => 'cde', 'CDE05G0060' => 'cde', 'CDE05G0692' => 'cde', 'CDE05G2285' => 'cde', 'CDE05G2884' => 'cde', 'CDE05G3072' => 'cde', 'Cfa008439' => 'cfa', 'Cfa008441' => 'cfa', 'Cfa008443' => 'cfa', 'Cfa008448' => 'cfa', 'Ciclev10005974m.g' => 'ccl', 'Ciclev10006006m.g' => 'ccl', 'Ciclev10006775m.g' => 'ccl', 'CiPaw.02G120400' => 'cil', 'CiPaw.02G120500' => 'cil', 'CiPaw.02G120600' => 'cil', 'ClCG05G004850' => 'cla', 'COL.COLO4_21566' => 'col', 'Cpa.g.sc44.124' => 'cpa', 'Cre07.g320400' => 'cre', 'Cre07.g320450' => 'cre', 'Cre08.g384650' => 'cre', 'Cre09.g393173' => 'cre', 'Cre09.g394325' => 'cre', 'Cre14.g626750' => 'cre', 'Cre16.g679250' => 'cre', 'CsaV3_3G012890' => 'csa', 'CSS0010865' => 'camsi', 'CSS0044338' => 'camsi', 'DCAR_002366' => 'dca', 'DCAR_030687' => 'dca', 'DCAR_030688' => 'dca', 'Dinv14047' => 'din', 'Dinv14048' => 'din', 'Duzib151G0105' => 'dzi', 'Duzib151G0114' => 'dzi', 'Duzib212G1029' => 'dzi', 'ECA232G3536' => 'eca', 'ECA240G0786' => 'eca', 'ECA240G1802' => 'eca', 'ECA240G3760' => 'eca', 'ECA240G3920' => 'eca', 'EL10Ac5g12536' => 'bvu', 'EL10Ac5g12537' => 'bvu', 'EL10Ac5g12538' => 'bvu', 'Eucgr.B01004' => 'egr', 'Eucgr.B01006' => 'egr', 'Eucgr.B01007' => 'egr', 'Eucgr.B01008' => 'egr', 'Eucgr.B01895' => 'egr', 'Eucgr.B01896' => 'egr', 'FAN04G1456' => 'fan', 'FAN08G1769' => 'fan', 'FAN08G2160' => 'fan', 'FAN13G2403' => 'fan', 'FAN13G3303' => 'fan', 'FAN15G2435' => 'fan', 'FAN17G0672' => 'fan', 'FAN17G2441' => 'fan', 'FAN18G1024' => 'fan', 'FAN22G1458' => 'fan', 'FAN24G0037' => 'fan', 'FAN24G0429' => 'fan', 'FAN24G2387' => 'fan', 'FAN27G2746' => 'fan', 'FvH4_2g20400' => 'fve', 'FvH4_2g20420' => 'fve', 'FvH4_2g20430' => 'fve', 'FvH4_4g01270' => 'fve', 'FvH4_4g01290' => 'fve', 'FvH4_4g01300' => 'fve', 'FvH4_4g01310' => 'fve', 'FvH4_4g01330' => 'fve', 'FvH4_5g09070' => 'fve', 'Glyma.10G243800' => 'gma', 'Glyma.20G150600' => 'gma', 'Gohir.A09G219200' => 'ghi', 'Gohir.A09G219300' => 'ghi', 'Gohir.D09G221400' => 'ghi', 'Gohir.D09G221500' => 'ghi', 'Gorai.006G242600' => 'gra', 'Gorai.006G242700' => 'gra', 'GSVIVG01018044001' => 'vvi', 'HanXRQChr03g0083821' => 'han', 'HanXRQChr03g0083841' => 'han', 'HanXRQChr03g0083881' => 'han', 'HanXRQChr03g0083901' => 'han', 'HanXRQChr03g0083921' => 'han', 'HanXRQChr03g0085331' => 'han', 'HanXRQChr03g0085361' => 'han', 'HanXRQChr03g0085411' => 'han', 'HanXRQChr03g0085421' => 'han', 'HanXRQChr03g0085431' => 'han', 'HanXRQChr08g0221991' => 'han', 'HanXRQChr11g0336061' => 'han', 'HanXRQChr11g0336411' => 'han', 'Haze_11234' => 'cav', 'Hma1.2p1_0549F.1_g177010' => 'hma', 'Hma1.2p1_0602F.1_g187630' => 'hma', 'Hund14876' => 'sun', 'Hund14879' => 'sun', 'Lalb_Chr06g0160741' => 'lal', 'Lalb_Chr21g0304781' => 'lal', 'Lj3A726G19' => 'lonja', 'Lj3A726T23' => 'lonja', 'Lj3A726T24' => 'lonja', 'Lj3A726T25' => 'lonja', 'Lj3A727T17' => 'lonja', 'Lj3C726T0' => 'lonja', 'Lj3C726T2' => 'lonja', 'Lj3P725T35' => 'lonja', 'Lj3P727T10' => 'lonja', 'Lj3P727T12' => 'lonja', 'Lj3P727T14' => 'lonja', 'Lj5g0023109' => 'lja', 'Lj6P646T44' => 'lonja', 'Lsat_1_v5_gn_6_75760' => 'lsa', 'Lsat_1_v5_gn_6_75800' => 'lsa', 'Lsat_1_v5_gn_6_75900' => 'lsa', 'Lsat_1_v5_gn_6_76240' => 'lsa', 'Lsat_1_v5_gn_6_76441' => 'lsa', 'Lsat_1_v5_gn_6_76700' => 'lsa', 'Lsat_1_v5_gn_6_76760' => 'lsa', 'Manes.15G033100' => 'mes', 'Mapoly0004s0074' => 'mpo', 'Mapoly0004s0075' => 'mpo', 'Mapoly0004s0163' => 'mpo', 'Mapoly0004s0164' => 'mpo', 'Mapoly0021s0018' => 'mpo', 'Mapoly0041s0136' => 'mpo', 'Mapoly0041s0137' => 'mpo', 'Mapoly0041s0138' => 'mpo', 'Mapoly0041s0139' => 'mpo', 'Mapoly0041s0141' => 'mpo', 'Mapoly0041s0142' => 'mpo', 'Mapoly0041s0143' => 'mpo', 'Mapoly0041s0144' => 'mpo', 'Mapoly0041s0145' => 'mpo', 'Mapoly0047s0106' => 'mpo', 'Mapoly0047s0108' => 'mpo', 'Mapoly0050s0051' => 'mpo', 'Mapoly0050s0052' => 'mpo', 'Mapoly0050s0053' => 'mpo', 'Mapoly0058s0013' => 'mpo', 'Mapoly0091s0078' => 'mpo', 'Mapoly0091s0079' => 'mpo', 'Mapoly0091s0080' => 'mpo', 'Mapoly0091s0081' => 'mpo', 'Mapoly0278s0004' => 'mpo', 'Mapoly0278s0005' => 'mpo', 'Mapoly0278s0006' => 'mpo', 'MBI11_g30648_MAGBIO' => 'mbi', 'MCO03G194' => 'mco', 'MCO03G590' => 'mco', 'MCO07G312' => 'mco', 'MCO10G318' => 'mco', 'MCO12G244' => 'mco', 'MCO13G148' => 'mco', 'MCO13G194' => 'mco', 'MCO16G238' => 'mco', 'MD06G1134100' => 'mdo', 'MD13G1200100' => 'mdo', 'MD13G1200300' => 'mdo', 'MD13G1200600' => 'mdo', 'MD14G1150400' => 'mdo', 'MD16G1200000' => 'mdo', 'Medtr1g102570' => 'mtr', 'Medtr1g102780' => 'mtr', 'Medtr1g102800' => 'mtr', 'Medtr1g102810' => 'mtr', 'Medtr1g102830' => 'mtr', 'MELO3C006499.2' => 'cme', 'Migut.G00385' => 'egut', 'MSTRG.4063' => 'ama', 'Nitab4.5_0000090g0260' => 'nta', 'Nitab4.5_0000977g0030' => 'nta', 'Nitab4.5_0002541g0040' => 'nta', 'Nitab4.5_0007068g0040' => 'nta', 'Nn005s41408' => 'nnu', 'Nn005s41410' => 'nnu', 'Oeu010310.1' => 'oeu', 'Oeu010311.1' => 'oeu', 'Oeu043472.1' => 'oeu', 'Os01g0246400' => 'osa', 'Os04g0267950' => 'osa', 'Os07g0178700' => 'osa', 'Os07g0178800' => 'osa', 'Peaxi162Scf00316g00046' => 'pax', 'Peaxi162Scf00316g00049' => 'pax', 'Peaxi162Scf00316g00059' => 'pax', 'Peaxi162Scf00316g00328' => 'pax', 'Peaxi162Scf00316g00329' => 'pax', 'Peaxi162Scf00316g00411' => 'pax', 'Peaxi162Scf00316g00521' => 'pax', 'Peaxi162Scf00492g00068' => 'pax', 'Peaxi162Scf35631g00002' => 'pax', 'PGR142G3720' => 'pgr', 'PGSC0003DMG400006442' => 'stu', 'Phvul.007G062000' => 'pvu', 'Potri.008G157750' => 'ptr', 'Potri.008G157900' => 'ptr', 'Potri.008G158000' => 'ptr', 'Potri.008G158200' => 'ptr', 'Pp3c11_7280' => 'ppa', 'Pp3c11_7980' => 'ppa', 'Pp3c12_19450' => 'ppa', 'Pp3c14_1480' => 'ppa', 'Pp3c14_1501' => 'ppa', 'Pp3c16_4900' => 'ppa', 'Pp3c16_5010' => 'ppa', 'Pp3c16_5060' => 'ppa', 'Pp3c19_18250' => 'ppa', 'Pp3c23_8530' => 'ppa', 'Pp3c23_8550' => 'ppa', 'Pp3c24_9670' => 'ppa', 'Pp3c2_21390' => 'ppa', 'Pp3c2_31380' => 'ppa', 'Pp3c3_16620' => 'ppa', 'Pp3c3_8090' => 'ppa', 'Pp3c3_8110' => 'ppa', 'Pp3c3_8130' => 'ppa', 'Pp3c3_8150' => 'ppa', 'Pp3c4_14320' => 'ppa', 'Pp3c6_2560' => 'ppa', 'Pp3c9_16700' => 'ppa', 'PRCOL_00000234' => 'pco', 'PRCOL_00000235' => 'pco', 'PRCOL_00000777' => 'pco', 'PRCOL_00002344' => 'pco', 'PRCOL_00002372' => 'pco', 'PRCOL_00006120' => 'pco', 'Prupe.1G021400' => 'ppe', 'Prupe.1G021500' => 'ppe', 'Prupe.1G021600' => 'ppe', 'Prupe.1G021700' => 'ppe', 'Prupe.1G021800' => 'ppe', 'Prupe.5G145100' => 'ppe', 'Psat6g204040' => 'psa', 'Psat6g204800' => 'psa', 'Psat6g204920' => 'psa', 'Psat6g204960' => 'psa', 'Psat6g205080' => 'psa', 'PSO017G0271' => 'pso', 'PSO017G1276' => 'pso', 'PSO017G1429' => 'pso', 'PSO017G1861' => 'pso', 'PSO017G2787' => 'pso', 'PSO017G4466' => 'pso', 'PSO017G5118' => 'pso', 'PSO017G5420' => 'pso', 'PSO063G3678' => 'pso', 'PSO210G0546' => 'pso', 'PSO317G0001' => 'pso', 'PSO357G0512' => 'pso', 'PSO478G2682' => 'pso', 'PSO647G0001' => 'pso', 'PSO675G0001' => 'pso', 'PSO675G2699' => 'pso', 'PSO675G2849' => 'pso', 'PSO675G4991' => 'pso', 'PSO689G0001' => 'pso', 'QL06p000916' => 'qlo', 'QL06p000921' => 'qlo', 'QL06p001398' => 'qlo', 'QL06p001407' => 'qlo', 'QL06p002031' => 'qlo', 'RcHm_v2.0_Chr4g0387791' => 'rch', 'RcHm_v2.0_Chr4g0387801' => 'rch', 'RcHm_v2.0_Chr6g0286501' => 'rch', 'RcHm_v2.0_Chr6g0286511' => 'rch', 'RcHm_v2.0_Chr6g0286521' => 'rch', 'RcHm_v2.0_Chr6g0286531' => 'rch', 'RcHm_v2.0_Chr7g0189141' => 'rch', 'Rhsim02G0028700' => 'rsi', 'Rhsim02G0028800' => 'rsi', 'Rhsim02G0028900' => 'rsi', 'Rhsim02G0029000' => 'rsi', 'Rhsim02G0029100' => 'rsi', 'Rhsim02G0029200' => 'rsi', 'Rhsim02G0029300' => 'rsi', 'Rhsim02G0029400' => 'rsi', 'Rhsim02G0029500' => 'rsi', 'Rhsim02G0029600' => 'rsi', 'RhsimUnG0024000' => 'rsi', 'RhsimUnG0024100' => 'rsi', 'RhsimUnG0024200' => 'rsi', 'RhsimUnG0024300' => 'rsi', 'RhsimUnG0024400' => 'rsi', 'RhsimUnG0024500' => 'rsi', 'RhsimUnG0024700' => 'rsi', 'RhsimUnG0024800' => 'rsi', 'RhsimUnG0024900' => 'rsi', 'RhsimUnG0025100' => 'rsi', 'Sabra08G0120200' => 'sbr', 'Sabra08G0120300' => 'sbr', 'Sabra08G0120500' => 'sbr', 'Sabra08G0120600' => 'sbr', 'Sabra10G0158900' => 'sbr', 'SalBow2G3492' => 'sbo', 'Sc13g0004760' => 'sci', 'Sc13g0004770' => 'sci', 'Sed0003417' => 'sed', 'Sed0019750' => 'sed', 'SEGI_03419' => 'sgi', 'SEGI_05907' => 'sgi', 'SEGI_10682' => 'sgi', 'SEGI_13528' => 'sgi', 'SEGI_16081' => 'sgi', 'SEGI_19370' => 'sgi', 'SEGI_21015' => 'sgi', 'SEGI_21944' => 'sgi', 'SEGI_32906' => 'sgi', 'SEGI_33093' => 'sgi', 'SEGI_36110' => 'sgi', 'SEGI_40397' => 'sgi', 'SGA_v2.0_scaffold191G40426' => 'sas', 'SGA_v2.0_scaffold353G49717' => 'sas', 'SGA_v2.0_scaffold50G18550' => 'sas', 'SMO119G0173' => 'smo', 'SMO172G0002' => 'smo', 'Solyc09g082690.3' => 'sly', 'Solyc09g082700.2' => 'sly', 'Sopen09g031550' => 'spe', 'Sopen09g031560' => 'spe', 'Sp3g20540' => 'spa', 'Sp7g07580' => 'spa', 'TAR134G0002' => 'tar', 'TAR236G0001' => 'tar', 'TAR365G0892' => 'tar', 'TAR636G0166' => 'tar', 'TAR636G0646' => 'tar', 'TAR636G0869' => 'tar', 'TAR636G1317' => 'tar', 'TAR636G1744' => 'tar', 'TAR636G3358' => 'tar', 'TAR636G3436' => 'tar', 'THA.LOC104803047' => 'tha', 'Thecc.04G238900' => 'tca', 'Thhalv10021557m.g' => 'esa', 'Thhalv10026318m.g' => 'esa', 'Thhalv10026335m.g' => 'esa', 'TPR.G17433' => 'tpr', 'TPR.G18915' => 'tpr', 'TPR.G26125' => 'tpr', 'TWI09G0677' => 'twi', 'TWI73G0287' => 'twi', 'unitig_748.g8326' => 'ugi', 'vmacro15370' => 'vma', 'vmacro15371' => 'vma', 'vmacro15372' => 'vma', 'vmacro15373' => 'vma', 'vmacro15374' => 'vma', 'VMungo0720G2826' => 'vmu', 'Zm00001eb116960' => 'zma', 'Zm00001eb301260' => 'zma', 'Zm00001eb301270' => 'zma' ), 'gf_id' => 'HOM05D001460', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001460' ), 'data_identifier' => 'HOM05D001460', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001460', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '433', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p22980' => 'bna', 'A01p32340' => 'bna', 'A03p42970' => 'bna', 'A05p25880' => 'bna', 'Aa31LG8G9320' => 'aar', 'Aa31LG8G9330' => 'aar', 'Aa31LG8G9340' => 'aar', 'Aa31sc221G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1034' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1528' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.829' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2222' => 'aag', 'Ah.12g058830' => 'amhyb', 'Ah.12g058840' => 'amhyb', 'AL3G37160' => 'aly', 'AL7G41310' => 'aly', 'Aqoxy5G00395' => 'aox', 'Aqoxy5G00396' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0C8NZA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5185HY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JZ1PRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MD3LS0' => 'arhy', 'AT3G22840' => 'ath', 'AT4G14690' => 'ath', 'ATR0665G054' => 'atr', 'Atru.chr4.2344' => 'acertr', 'Atru.chr4.2346' => 'acertr', 'Atru.chr4.2347' => 'acertr', 'Atru.chr4.2348' => 'acertr', 'Atru.chr4.2355' => 'acertr', 'Atru.chr4.2356' => 'acertr', 'Atru.chr4.2358' => 'acertr', 'Atru.chr4.2359' => 'acertr', 'Atru.chr4.2360' => 'acertr', 'Atru.chr4.2361' => 'acertr', 'AUR62030476' => 'cqu', 'AUR62030478' => 'cqu', 'AUR62030819' => 'cqu', 'AUR62030820' => 'cqu', 'BcaB03g14648' => 'bca', 'BcaB04g20492' => 'bca', 'BcaB06g26399' => 'bca', 'BcaC01g03416' => 'bca', 'BcaC01g03419' => 'bca', 'BcaC01g03421' => 'bca', 'BcaC01g03424' => 'bca', 'BcaC05g28012' => 'bca', 'BcaC09g49212' => 'bca', 'BcaC09g50140' => 'bca', 'BcaNung00346' => 'bca', 'BolC1t02785H' => 'bol', 'BolC1t04095H' => 'bol', 'BolC3t17545H' => 'bol', 'BolC5t32769H' => 'bol', 'BraA01t02211Z' => 'bra', 'BraA01t03359Z' => 'bra', 'BraA03t13441Z' => 'bra', 'BraA05t21476Z' => 'bra', 'C01p28420' => 'bna', 'C01p41350' => 'bna', 'C03p52750' => 'bna', 'C03p52780' => 'bna', 'C05p40270' => 'bna', 'CAN.G1437.9' => 'can', 'CANSAT78G0035' => 'cansat', 'CANSAT78G1036' => 'cansat', 'CANSAT78G2272' => 'cansat', 'CANSAT78G2478' => 'cansat', 'CARHR098700' => 'chi', 'CARHR221120' => 'chi', 'CARHR221150' => 'chi', 'Carub.0003s2297' => 'cru', 'Carub.0007s2749' => 'cru', 'Carub.0007s2750' => 'cru', 'Carub.0007s2751' => 'cru', 'Ca_10849_v3' => 'car', 'Cc03_g04300' => 'ccan', 'CDE02G3648' => 'cde', 'CDE05G0060' => 'cde', 'CDE05G0692' => 'cde', 'CDE05G2285' => 'cde', 'CDE05G2884' => 'cde', 'CDE05G3072' => 'cde', 'Cfa008439' => 'cfa', 'Cfa008441' => 'cfa', 'Cfa008443' => 'cfa', 'Cfa008448' => 'cfa', 'Ciclev10005974m.g' => 'ccl', 'Ciclev10006006m.g' => 'ccl', 'Ciclev10006775m.g' => 'ccl', 'CiPaw.02G120400' => 'cil', 'CiPaw.02G120500' => 'cil', 'CiPaw.02G120600' => 'cil', 'ClCG05G004850' => 'cla', 'COL.COLO4_21566' => 'col', 'Cpa.g.sc44.124' => 'cpa', 'Cre07.g320400' => 'cre', 'Cre07.g320450' => 'cre', 'Cre08.g384650' => 'cre', 'Cre09.g393173' => 'cre', 'Cre09.g394325' => 'cre', 'Cre14.g626750' => 'cre', 'Cre16.g679250' => 'cre', 'CsaV3_3G012890' => 'csa', 'CSS0010865' => 'camsi', 'CSS0044338' => 'camsi', 'DCAR_002366' => 'dca', 'DCAR_030687' => 'dca', 'DCAR_030688' => 'dca', 'Dinv14047' => 'din', 'Dinv14048' => 'din', 'Duzib151G0105' => 'dzi', 'Duzib151G0114' => 'dzi', 'Duzib212G1029' => 'dzi', 'ECA232G3536' => 'eca', 'ECA240G0786' => 'eca', 'ECA240G1802' => 'eca', 'ECA240G3760' => 'eca', 'ECA240G3920' => 'eca', 'EL10Ac5g12536' => 'bvu', 'EL10Ac5g12537' => 'bvu', 'EL10Ac5g12538' => 'bvu', 'Eucgr.B01004' => 'egr', 'Eucgr.B01006' => 'egr', 'Eucgr.B01007' => 'egr', 'Eucgr.B01008' => 'egr', 'Eucgr.B01895' => 'egr', 'Eucgr.B01896' => 'egr', 'FAN04G1456' => 'fan', 'FAN08G1769' => 'fan', 'FAN08G2160' => 'fan', 'FAN13G2403' => 'fan', 'FAN13G3303' => 'fan', 'FAN15G2435' => 'fan', 'FAN17G0672' => 'fan', 'FAN17G2441' => 'fan', 'FAN18G1024' => 'fan', 'FAN22G1458' => 'fan', 'FAN24G0037' => 'fan', 'FAN24G0429' => 'fan', 'FAN24G2387' => 'fan', 'FAN27G2746' => 'fan', 'FvH4_2g20400' => 'fve', 'FvH4_2g20420' => 'fve', 'FvH4_2g20430' => 'fve', 'FvH4_4g01270' => 'fve', 'FvH4_4g01290' => 'fve', 'FvH4_4g01300' => 'fve', 'FvH4_4g01310' => 'fve', 'FvH4_4g01330' => 'fve', 'FvH4_5g09070' => 'fve', 'Glyma.10G243800' => 'gma', 'Glyma.20G150600' => 'gma', 'Gohir.A09G219200' => 'ghi', 'Gohir.A09G219300' => 'ghi', 'Gohir.D09G221400' => 'ghi', 'Gohir.D09G221500' => 'ghi', 'Gorai.006G242600' => 'gra', 'Gorai.006G242700' => 'gra', 'GSVIVG01018044001' => 'vvi', 'HanXRQChr03g0083821' => 'han', 'HanXRQChr03g0083841' => 'han', 'HanXRQChr03g0083881' => 'han', 'HanXRQChr03g0083901' => 'han', 'HanXRQChr03g0083921' => 'han', 'HanXRQChr03g0085331' => 'han', 'HanXRQChr03g0085361' => 'han', 'HanXRQChr03g0085411' => 'han', 'HanXRQChr03g0085421' => 'han', 'HanXRQChr03g0085431' => 'han', 'HanXRQChr08g0221991' => 'han', 'HanXRQChr11g0336061' => 'han', 'HanXRQChr11g0336411' => 'han', 'Haze_11234' => 'cav', 'Hma1.2p1_0549F.1_g177010' => 'hma', 'Hma1.2p1_0602F.1_g187630' => 'hma', 'Hund14876' => 'sun', 'Hund14879' => 'sun', 'Lalb_Chr06g0160741' => 'lal', 'Lalb_Chr21g0304781' => 'lal', 'Lj3A726G19' => 'lonja', 'Lj3A726T23' => 'lonja', 'Lj3A726T24' => 'lonja', 'Lj3A726T25' => 'lonja', 'Lj3A727T17' => 'lonja', 'Lj3C726T0' => 'lonja', 'Lj3C726T2' => 'lonja', 'Lj3P725T35' => 'lonja', 'Lj3P727T10' => 'lonja', 'Lj3P727T12' => 'lonja', 'Lj3P727T14' => 'lonja', 'Lj5g0023109' => 'lja', 'Lj6P646T44' => 'lonja', 'Lsat_1_v5_gn_6_75760' => 'lsa', 'Lsat_1_v5_gn_6_75800' => 'lsa', 'Lsat_1_v5_gn_6_75900' => 'lsa', 'Lsat_1_v5_gn_6_76240' => 'lsa', 'Lsat_1_v5_gn_6_76441' => 'lsa', 'Lsat_1_v5_gn_6_76700' => 'lsa', 'Lsat_1_v5_gn_6_76760' => 'lsa', 'Manes.15G033100' => 'mes', 'Mapoly0004s0074' => 'mpo', 'Mapoly0004s0075' => 'mpo', 'Mapoly0004s0163' => 'mpo', 'Mapoly0004s0164' => 'mpo', 'Mapoly0021s0018' => 'mpo', 'Mapoly0041s0136' => 'mpo', 'Mapoly0041s0137' => 'mpo', 'Mapoly0041s0138' => 'mpo', 'Mapoly0041s0139' => 'mpo', 'Mapoly0041s0141' => 'mpo', 'Mapoly0041s0142' => 'mpo', 'Mapoly0041s0143' => 'mpo', 'Mapoly0041s0144' => 'mpo', 'Mapoly0041s0145' => 'mpo', 'Mapoly0047s0106' => 'mpo', 'Mapoly0047s0108' => 'mpo', 'Mapoly0050s0051' => 'mpo', 'Mapoly0050s0052' => 'mpo', 'Mapoly0050s0053' => 'mpo', 'Mapoly0058s0013' => 'mpo', 'Mapoly0091s0078' => 'mpo', 'Mapoly0091s0079' => 'mpo', 'Mapoly0091s0080' => 'mpo', 'Mapoly0091s0081' => 'mpo', 'Mapoly0278s0004' => 'mpo', 'Mapoly0278s0005' => 'mpo', 'Mapoly0278s0006' => 'mpo', 'MBI11_g30648_MAGBIO' => 'mbi', 'MCO03G194' => 'mco', 'MCO03G590' => 'mco', 'MCO07G312' => 'mco', 'MCO10G318' => 'mco', 'MCO12G244' => 'mco', 'MCO13G148' => 'mco', 'MCO13G194' => 'mco', 'MCO16G238' => 'mco', 'MD06G1134100' => 'mdo', 'MD13G1200100' => 'mdo', 'MD13G1200300' => 'mdo', 'MD13G1200600' => 'mdo', 'MD14G1150400' => 'mdo', 'MD16G1200000' => 'mdo', 'Medtr1g102570' => 'mtr', 'Medtr1g102780' => 'mtr', 'Medtr1g102800' => 'mtr', 'Medtr1g102810' => 'mtr', 'Medtr1g102830' => 'mtr', 'MELO3C006499.2' => 'cme', 'Migut.G00385' => 'egut', 'MSTRG.4063' => 'ama', 'Nitab4.5_0000090g0260' => 'nta', 'Nitab4.5_0000977g0030' => 'nta', 'Nitab4.5_0002541g0040' => 'nta', 'Nitab4.5_0007068g0040' => 'nta', 'Nn005s41408' => 'nnu', 'Nn005s41410' => 'nnu', 'Oeu010310.1' => 'oeu', 'Oeu010311.1' => 'oeu', 'Oeu043472.1' => 'oeu', 'Os01g0246400' => 'osa', 'Os04g0267950' => 'osa', 'Os07g0178700' => 'osa', 'Os07g0178800' => 'osa', 'Peaxi162Scf00316g00046' => 'pax', 'Peaxi162Scf00316g00049' => 'pax', 'Peaxi162Scf00316g00059' => 'pax', 'Peaxi162Scf00316g00328' => 'pax', 'Peaxi162Scf00316g00329' => 'pax', 'Peaxi162Scf00316g00411' => 'pax', 'Peaxi162Scf00316g00521' => 'pax', 'Peaxi162Scf00492g00068' => 'pax', 'Peaxi162Scf35631g00002' => 'pax', 'PGR142G3720' => 'pgr', 'PGSC0003DMG400006442' => 'stu', 'Phvul.007G062000' => 'pvu', 'Potri.008G157750' => 'ptr', 'Potri.008G157900' => 'ptr', 'Potri.008G158000' => 'ptr', 'Potri.008G158200' => 'ptr', 'Pp3c11_7280' => 'ppa', 'Pp3c11_7980' => 'ppa', 'Pp3c12_19450' => 'ppa', 'Pp3c14_1480' => 'ppa', 'Pp3c14_1501' => 'ppa', 'Pp3c16_4900' => 'ppa', 'Pp3c16_5010' => 'ppa', 'Pp3c16_5060' => 'ppa', 'Pp3c19_18250' => 'ppa', 'Pp3c23_8530' => 'ppa', 'Pp3c23_8550' => 'ppa', 'Pp3c24_9670' => 'ppa', 'Pp3c2_21390' => 'ppa', 'Pp3c2_31380' => 'ppa', 'Pp3c3_16620' => 'ppa', 'Pp3c3_8090' => 'ppa', 'Pp3c3_8110' => 'ppa', 'Pp3c3_8130' => 'ppa', 'Pp3c3_8150' => 'ppa', 'Pp3c4_14320' => 'ppa', 'Pp3c6_2560' => 'ppa', 'Pp3c9_16700' => 'ppa', 'PRCOL_00000234' => 'pco', 'PRCOL_00000235' => 'pco', 'PRCOL_00000777' => 'pco', 'PRCOL_00002344' => 'pco', 'PRCOL_00002372' => 'pco', 'PRCOL_00006120' => 'pco', 'Prupe.1G021400' => 'ppe', 'Prupe.1G021500' => 'ppe', 'Prupe.1G021600' => 'ppe', 'Prupe.1G021700' => 'ppe', 'Prupe.1G021800' => 'ppe', 'Prupe.5G145100' => 'ppe', 'Psat6g204040' => 'psa', 'Psat6g204800' => 'psa', 'Psat6g204920' => 'psa', 'Psat6g204960' => 'psa', 'Psat6g205080' => 'psa', 'PSO017G0271' => 'pso', 'PSO017G1276' => 'pso', 'PSO017G1429' => 'pso', 'PSO017G1861' => 'pso', 'PSO017G2787' => 'pso', 'PSO017G4466' => 'pso', 'PSO017G5118' => 'pso', 'PSO017G5420' => 'pso', 'PSO063G3678' => 'pso', 'PSO210G0546' => 'pso', 'PSO317G0001' => 'pso', 'PSO357G0512' => 'pso', 'PSO478G2682' => 'pso', 'PSO647G0001' => 'pso', 'PSO675G0001' => 'pso', 'PSO675G2699' => 'pso', 'PSO675G2849' => 'pso', 'PSO675G4991' => 'pso', 'PSO689G0001' => 'pso', 'QL06p000916' => 'qlo', 'QL06p000921' => 'qlo', 'QL06p001398' => 'qlo', 'QL06p001407' => 'qlo', 'QL06p002031' => 'qlo', 'RcHm_v2.0_Chr4g0387791' => 'rch', 'RcHm_v2.0_Chr4g0387801' => 'rch', 'RcHm_v2.0_Chr6g0286501' => 'rch', 'RcHm_v2.0_Chr6g0286511' => 'rch', 'RcHm_v2.0_Chr6g0286521' => 'rch', 'RcHm_v2.0_Chr6g0286531' => 'rch', 'RcHm_v2.0_Chr7g0189141' => 'rch', 'Rhsim02G0028700' => 'rsi', 'Rhsim02G0028800' => 'rsi', 'Rhsim02G0028900' => 'rsi', 'Rhsim02G0029000' => 'rsi', 'Rhsim02G0029100' => 'rsi', 'Rhsim02G0029200' => 'rsi', 'Rhsim02G0029300' => 'rsi', 'Rhsim02G0029400' => 'rsi', 'Rhsim02G0029500' => 'rsi', 'Rhsim02G0029600' => 'rsi', 'RhsimUnG0024000' => 'rsi', 'RhsimUnG0024100' => 'rsi', 'RhsimUnG0024200' => 'rsi', 'RhsimUnG0024300' => 'rsi', 'RhsimUnG0024400' => 'rsi', 'RhsimUnG0024500' => 'rsi', 'RhsimUnG0024700' => 'rsi', 'RhsimUnG0024800' => 'rsi', 'RhsimUnG0024900' => 'rsi', 'RhsimUnG0025100' => 'rsi', 'Sabra08G0120200' => 'sbr', 'Sabra08G0120300' => 'sbr', 'Sabra08G0120500' => 'sbr', 'Sabra08G0120600' => 'sbr', 'Sabra10G0158900' => 'sbr', 'SalBow2G3492' => 'sbo', 'Sc13g0004760' => 'sci', 'Sc13g0004770' => 'sci', 'Sed0003417' => 'sed', 'Sed0019750' => 'sed', 'SEGI_03419' => 'sgi', 'SEGI_05907' => 'sgi', 'SEGI_10682' => 'sgi', 'SEGI_13528' => 'sgi', 'SEGI_16081' => 'sgi', 'SEGI_19370' => 'sgi', 'SEGI_21015' => 'sgi', 'SEGI_21944' => 'sgi', 'SEGI_32906' => 'sgi', 'SEGI_33093' => 'sgi', 'SEGI_36110' => 'sgi', 'SEGI_40397' => 'sgi', 'SGA_v2.0_scaffold191G40426' => 'sas', 'SGA_v2.0_scaffold353G49717' => 'sas', 'SGA_v2.0_scaffold50G18550' => 'sas', 'SMO119G0173' => 'smo', 'SMO172G0002' => 'smo', 'Solyc09g082690.3' => 'sly', 'Solyc09g082700.2' => 'sly', 'Sopen09g031550' => 'spe', 'Sopen09g031560' => 'spe', 'Sp3g20540' => 'spa', 'Sp7g07580' => 'spa', 'TAR134G0002' => 'tar', 'TAR236G0001' => 'tar', 'TAR365G0892' => 'tar', 'TAR636G0166' => 'tar', 'TAR636G0646' => 'tar', 'TAR636G0869' => 'tar', 'TAR636G1317' => 'tar', 'TAR636G1744' => 'tar', 'TAR636G3358' => 'tar', 'TAR636G3436' => 'tar', 'THA.LOC104803047' => 'tha', 'Thecc.04G238900' => 'tca', 'Thhalv10021557m.g' => 'esa', 'Thhalv10026318m.g' => 'esa', 'Thhalv10026335m.g' => 'esa', 'TPR.G17433' => 'tpr', 'TPR.G18915' => 'tpr', 'TPR.G26125' => 'tpr', 'TWI09G0677' => 'twi', 'TWI73G0287' => 'twi', 'unitig_748.g8326' => 'ugi', 'vmacro15370' => 'vma', 'vmacro15371' => 'vma', 'vmacro15372' => 'vma', 'vmacro15373' => 'vma', 'vmacro15374' => 'vma', 'VMungo0720G2826' => 'vmu', 'Zm00001eb116960' => 'zma', 'Zm00001eb301260' => 'zma', 'Zm00001eb301270' => 'zma' ) $gf_id = 'HOM05D001460' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001460' ) $data_identifier = 'HOM05D001460' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 4, 'aag' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 2, 'aox' => (int) 2, 'arhy' => (int) 4, 'ath' => (int) 2, 'atr' => (int) 1, 'acertr' => (int) 10, 'cqu' => (int) 4, 'bca' => (int) 11, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 1, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 1, 'ccan' => (int) 1, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 1, 'col' => (int) 1, 'cpa' => (int) 1, 'cre' => (int) 7, 'csa' => (int) 1, 'camsi' => (int) 2, 'dca' => (int) 3, 'din' => (int) 2, 'dzi' => (int) 3, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 14, 'fve' => (int) 9, 'gma' => (int) 2, 'ghi' => (int) 4, 'gra' => (int) 2, 'vvi' => (int) 1, 'han' => (int) 13, 'cav' => (int) 1, 'hma' => (int) 2, 'sun' => (int) 2, 'lal' => (int) 2, 'lonja' => (int) 12, 'lja' => (int) 1, 'lsa' => (int) 7, 'mes' => (int) 1, 'mpo' => (int) 27, 'mbi' => (int) 1, 'mco' => (int) 8, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 1, 'egut' => (int) 1, 'ama' => (int) 1, 'nta' => (int) 4, 'nnu' => (int) 2, 'oeu' => (int) 3, 'osa' => (int) 4, 'pax' => (int) 9, 'pgr' => (int) 1, 'stu' => (int) 1, 'pvu' => (int) 1, 'ptr' => (int) 4, 'ppa' => (int) 22, 'pco' => (int) 6, 'ppe' => (int) 6, 'psa' => (int) 5, 'pso' => (int) 19, 'qlo' => (int) 5, 'rch' => (int) 7, 'rsi' => (int) 20, 'sbr' => (int) 5, 'sbo' => (int) 1, 'sci' => (int) 2, 'sed' => (int) 2, 'sgi' => (int) 12, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 2, 'tar' => (int) 10, 'tha' => (int) 1, 'tca' => (int) 1, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 2, 'ugi' => (int) 1, 'vma' => (int) 5, 'vmu' => (int) 1, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb301270' $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' => 'HOM05D001460', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '433', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p22980' => 'bna', 'A01p32340' => 'bna', 'A03p42970' => 'bna', 'A05p25880' => 'bna', 'Aa31LG8G9320' => 'aar', 'Aa31LG8G9330' => 'aar', 'Aa31LG8G9340' => 'aar', 'Aa31sc221G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1034' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1528' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.829' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2222' => 'aag', 'Ah.12g058830' => 'amhyb', 'Ah.12g058840' => 'amhyb', 'AL3G37160' => 'aly', 'AL7G41310' => 'aly', 'Aqoxy5G00395' => 'aox', 'Aqoxy5G00396' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0C8NZA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5185HY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JZ1PRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MD3LS0' => 'arhy', 'AT3G22840' => 'ath', 'AT4G14690' => 'ath', 'ATR0665G054' => 'atr', 'Atru.chr4.2344' => 'acertr', 'Atru.chr4.2346' => 'acertr', 'Atru.chr4.2347' => 'acertr', 'Atru.chr4.2348' => 'acertr', 'Atru.chr4.2355' => 'acertr', 'Atru.chr4.2356' => 'acertr', 'Atru.chr4.2358' => 'acertr', 'Atru.chr4.2359' => 'acertr', 'Atru.chr4.2360' => 'acertr', 'Atru.chr4.2361' => 'acertr', 'AUR62030476' => 'cqu', 'AUR62030478' => 'cqu', 'AUR62030819' => 'cqu', 'AUR62030820' => 'cqu', 'BcaB03g14648' => 'bca', 'BcaB04g20492' => 'bca', 'BcaB06g26399' => 'bca', 'BcaC01g03416' => 'bca', 'BcaC01g03419' => 'bca', 'BcaC01g03421' => 'bca', 'BcaC01g03424' => 'bca', 'BcaC05g28012' => 'bca', 'BcaC09g49212' => 'bca', 'BcaC09g50140' => 'bca', 'BcaNung00346' => 'bca', 'BolC1t02785H' => 'bol', 'BolC1t04095H' => 'bol', 'BolC3t17545H' => 'bol', 'BolC5t32769H' => 'bol', 'BraA01t02211Z' => 'bra', 'BraA01t03359Z' => 'bra', 'BraA03t13441Z' => 'bra', 'BraA05t21476Z' => 'bra', 'C01p28420' => 'bna', 'C01p41350' => 'bna', 'C03p52750' => 'bna', 'C03p52780' => 'bna', 'C05p40270' => 'bna', 'CAN.G1437.9' => 'can', 'CANSAT78G0035' => 'cansat', 'CANSAT78G1036' => 'cansat', 'CANSAT78G2272' => 'cansat', 'CANSAT78G2478' => 'cansat', 'CARHR098700' => 'chi', 'CARHR221120' => 'chi', 'CARHR221150' => 'chi', 'Carub.0003s2297' => 'cru', 'Carub.0007s2749' => 'cru', 'Carub.0007s2750' => 'cru', 'Carub.0007s2751' => 'cru', 'Ca_10849_v3' => 'car', 'Cc03_g04300' => 'ccan', 'CDE02G3648' => 'cde', 'CDE05G0060' => 'cde', 'CDE05G0692' => 'cde', 'CDE05G2285' => 'cde', 'CDE05G2884' => 'cde', 'CDE05G3072' => 'cde', 'Cfa008439' => 'cfa', 'Cfa008441' => 'cfa', 'Cfa008443' => 'cfa', 'Cfa008448' => 'cfa', 'Ciclev10005974m.g' => 'ccl', 'Ciclev10006006m.g' => 'ccl', 'Ciclev10006775m.g' => 'ccl', 'CiPaw.02G120400' => 'cil', 'CiPaw.02G120500' => 'cil', 'CiPaw.02G120600' => 'cil', 'ClCG05G004850' => 'cla', 'COL.COLO4_21566' => 'col', 'Cpa.g.sc44.124' => 'cpa', 'Cre07.g320400' => 'cre', 'Cre07.g320450' => 'cre', 'Cre08.g384650' => 'cre', 'Cre09.g393173' => 'cre', 'Cre09.g394325' => 'cre', 'Cre14.g626750' => 'cre', 'Cre16.g679250' => 'cre', 'CsaV3_3G012890' => 'csa', 'CSS0010865' => 'camsi', 'CSS0044338' => 'camsi', 'DCAR_002366' => 'dca', 'DCAR_030687' => 'dca', 'DCAR_030688' => 'dca', 'Dinv14047' => 'din', 'Dinv14048' => 'din', 'Duzib151G0105' => 'dzi', 'Duzib151G0114' => 'dzi', 'Duzib212G1029' => 'dzi', 'ECA232G3536' => 'eca', 'ECA240G0786' => 'eca', 'ECA240G1802' => 'eca', 'ECA240G3760' => 'eca', 'ECA240G3920' => 'eca', 'EL10Ac5g12536' => 'bvu', 'EL10Ac5g12537' => 'bvu', 'EL10Ac5g12538' => 'bvu', 'Eucgr.B01004' => 'egr', 'Eucgr.B01006' => 'egr', 'Eucgr.B01007' => 'egr', 'Eucgr.B01008' => 'egr', 'Eucgr.B01895' => 'egr', 'Eucgr.B01896' => 'egr', 'FAN04G1456' => 'fan', 'FAN08G1769' => 'fan', 'FAN08G2160' => 'fan', 'FAN13G2403' => 'fan', 'FAN13G3303' => 'fan', 'FAN15G2435' => 'fan', 'FAN17G0672' => 'fan', 'FAN17G2441' => 'fan', 'FAN18G1024' => 'fan', 'FAN22G1458' => 'fan', 'FAN24G0037' => 'fan', 'FAN24G0429' => 'fan', 'FAN24G2387' => 'fan', 'FAN27G2746' => 'fan', 'FvH4_2g20400' => 'fve', 'FvH4_2g20420' => 'fve', 'FvH4_2g20430' => 'fve', 'FvH4_4g01270' => 'fve', 'FvH4_4g01290' => 'fve', 'FvH4_4g01300' => 'fve', 'FvH4_4g01310' => 'fve', 'FvH4_4g01330' => 'fve', 'FvH4_5g09070' => 'fve', 'Glyma.10G243800' => 'gma', 'Glyma.20G150600' => 'gma', 'Gohir.A09G219200' => 'ghi', 'Gohir.A09G219300' => 'ghi', 'Gohir.D09G221400' => 'ghi', 'Gohir.D09G221500' => 'ghi', 'Gorai.006G242600' => 'gra', 'Gorai.006G242700' => 'gra', 'GSVIVG01018044001' => 'vvi', 'HanXRQChr03g0083821' => 'han', 'HanXRQChr03g0083841' => 'han', 'HanXRQChr03g0083881' => 'han', 'HanXRQChr03g0083901' => 'han', 'HanXRQChr03g0083921' => 'han', 'HanXRQChr03g0085331' => 'han', 'HanXRQChr03g0085361' => 'han', 'HanXRQChr03g0085411' => 'han', 'HanXRQChr03g0085421' => 'han', 'HanXRQChr03g0085431' => 'han', 'HanXRQChr08g0221991' => 'han', 'HanXRQChr11g0336061' => 'han', 'HanXRQChr11g0336411' => 'han', 'Haze_11234' => 'cav', 'Hma1.2p1_0549F.1_g177010' => 'hma', 'Hma1.2p1_0602F.1_g187630' => 'hma', 'Hund14876' => 'sun', 'Hund14879' => 'sun', 'Lalb_Chr06g0160741' => 'lal', 'Lalb_Chr21g0304781' => 'lal', 'Lj3A726G19' => 'lonja', 'Lj3A726T23' => 'lonja', 'Lj3A726T24' => 'lonja', 'Lj3A726T25' => 'lonja', 'Lj3A727T17' => 'lonja', 'Lj3C726T0' => 'lonja', 'Lj3C726T2' => 'lonja', 'Lj3P725T35' => 'lonja', 'Lj3P727T10' => 'lonja', 'Lj3P727T12' => 'lonja', 'Lj3P727T14' => 'lonja', 'Lj5g0023109' => 'lja', 'Lj6P646T44' => 'lonja', 'Lsat_1_v5_gn_6_75760' => 'lsa', 'Lsat_1_v5_gn_6_75800' => 'lsa', 'Lsat_1_v5_gn_6_75900' => 'lsa', 'Lsat_1_v5_gn_6_76240' => 'lsa', 'Lsat_1_v5_gn_6_76441' => 'lsa', 'Lsat_1_v5_gn_6_76700' => 'lsa', 'Lsat_1_v5_gn_6_76760' => 'lsa', 'Manes.15G033100' => 'mes', 'Mapoly0004s0074' => 'mpo', 'Mapoly0004s0075' => 'mpo', 'Mapoly0004s0163' => 'mpo', 'Mapoly0004s0164' => 'mpo', 'Mapoly0021s0018' => 'mpo', 'Mapoly0041s0136' => 'mpo', 'Mapoly0041s0137' => 'mpo', 'Mapoly0041s0138' => 'mpo', 'Mapoly0041s0139' => 'mpo', 'Mapoly0041s0141' => 'mpo', 'Mapoly0041s0142' => 'mpo', 'Mapoly0041s0143' => 'mpo', 'Mapoly0041s0144' => 'mpo', 'Mapoly0041s0145' => 'mpo', 'Mapoly0047s0106' => 'mpo', 'Mapoly0047s0108' => 'mpo', 'Mapoly0050s0051' => 'mpo', 'Mapoly0050s0052' => 'mpo', 'Mapoly0050s0053' => 'mpo', 'Mapoly0058s0013' => 'mpo', 'Mapoly0091s0078' => 'mpo', 'Mapoly0091s0079' => 'mpo', 'Mapoly0091s0080' => 'mpo', 'Mapoly0091s0081' => 'mpo', 'Mapoly0278s0004' => 'mpo', 'Mapoly0278s0005' => 'mpo', 'Mapoly0278s0006' => 'mpo', 'MBI11_g30648_MAGBIO' => 'mbi', 'MCO03G194' => 'mco', 'MCO03G590' => 'mco', 'MCO07G312' => 'mco', 'MCO10G318' => 'mco', 'MCO12G244' => 'mco', 'MCO13G148' => 'mco', 'MCO13G194' => 'mco', 'MCO16G238' => 'mco', 'MD06G1134100' => 'mdo', 'MD13G1200100' => 'mdo', 'MD13G1200300' => 'mdo', 'MD13G1200600' => 'mdo', 'MD14G1150400' => 'mdo', 'MD16G1200000' => 'mdo', 'Medtr1g102570' => 'mtr', 'Medtr1g102780' => 'mtr', 'Medtr1g102800' => 'mtr', 'Medtr1g102810' => 'mtr', 'Medtr1g102830' => 'mtr', 'MELO3C006499.2' => 'cme', 'Migut.G00385' => 'egut', 'MSTRG.4063' => 'ama', 'Nitab4.5_0000090g0260' => 'nta', 'Nitab4.5_0000977g0030' => 'nta', 'Nitab4.5_0002541g0040' => 'nta', 'Nitab4.5_0007068g0040' => 'nta', 'Nn005s41408' => 'nnu', 'Nn005s41410' => 'nnu', 'Oeu010310.1' => 'oeu', 'Oeu010311.1' => 'oeu', 'Oeu043472.1' => 'oeu', 'Os01g0246400' => 'osa', 'Os04g0267950' => 'osa', 'Os07g0178700' => 'osa', 'Os07g0178800' => 'osa', 'Peaxi162Scf00316g00046' => 'pax', 'Peaxi162Scf00316g00049' => 'pax', 'Peaxi162Scf00316g00059' => 'pax', 'Peaxi162Scf00316g00328' => 'pax', 'Peaxi162Scf00316g00329' => 'pax', 'Peaxi162Scf00316g00411' => 'pax', 'Peaxi162Scf00316g00521' => 'pax', 'Peaxi162Scf00492g00068' => 'pax', 'Peaxi162Scf35631g00002' => 'pax', 'PGR142G3720' => 'pgr', 'PGSC0003DMG400006442' => 'stu', 'Phvul.007G062000' => 'pvu', 'Potri.008G157750' => 'ptr', 'Potri.008G157900' => 'ptr', 'Potri.008G158000' => 'ptr', 'Potri.008G158200' => 'ptr', 'Pp3c11_7280' => 'ppa', 'Pp3c11_7980' => 'ppa', 'Pp3c12_19450' => 'ppa', 'Pp3c14_1480' => 'ppa', 'Pp3c14_1501' => 'ppa', 'Pp3c16_4900' => 'ppa', 'Pp3c16_5010' => 'ppa', 'Pp3c16_5060' => 'ppa', 'Pp3c19_18250' => 'ppa', 'Pp3c23_8530' => 'ppa', 'Pp3c23_8550' => 'ppa', 'Pp3c24_9670' => 'ppa', 'Pp3c2_21390' => 'ppa', 'Pp3c2_31380' => 'ppa', 'Pp3c3_16620' => 'ppa', 'Pp3c3_8090' => 'ppa', 'Pp3c3_8110' => 'ppa', 'Pp3c3_8130' => 'ppa', 'Pp3c3_8150' => 'ppa', 'Pp3c4_14320' => 'ppa', 'Pp3c6_2560' => 'ppa', 'Pp3c9_16700' => 'ppa', 'PRCOL_00000234' => 'pco', 'PRCOL_00000235' => 'pco', 'PRCOL_00000777' => 'pco', 'PRCOL_00002344' => 'pco', 'PRCOL_00002372' => 'pco', 'PRCOL_00006120' => 'pco', 'Prupe.1G021400' => 'ppe', 'Prupe.1G021500' => 'ppe', 'Prupe.1G021600' => 'ppe', 'Prupe.1G021700' => 'ppe', 'Prupe.1G021800' => 'ppe', 'Prupe.5G145100' => 'ppe', 'Psat6g204040' => 'psa', 'Psat6g204800' => 'psa', 'Psat6g204920' => 'psa', 'Psat6g204960' => 'psa', 'Psat6g205080' => 'psa', 'PSO017G0271' => 'pso', 'PSO017G1276' => 'pso', 'PSO017G1429' => 'pso', 'PSO017G1861' => 'pso', 'PSO017G2787' => 'pso', 'PSO017G4466' => 'pso', 'PSO017G5118' => 'pso', 'PSO017G5420' => 'pso', 'PSO063G3678' => 'pso', 'PSO210G0546' => 'pso', 'PSO317G0001' => 'pso', 'PSO357G0512' => 'pso', 'PSO478G2682' => 'pso', 'PSO647G0001' => 'pso', 'PSO675G0001' => 'pso', 'PSO675G2699' => 'pso', 'PSO675G2849' => 'pso', 'PSO675G4991' => 'pso', 'PSO689G0001' => 'pso', 'QL06p000916' => 'qlo', 'QL06p000921' => 'qlo', 'QL06p001398' => 'qlo', 'QL06p001407' => 'qlo', 'QL06p002031' => 'qlo', 'RcHm_v2.0_Chr4g0387791' => 'rch', 'RcHm_v2.0_Chr4g0387801' => 'rch', 'RcHm_v2.0_Chr6g0286501' => 'rch', 'RcHm_v2.0_Chr6g0286511' => 'rch', 'RcHm_v2.0_Chr6g0286521' => 'rch', 'RcHm_v2.0_Chr6g0286531' => 'rch', 'RcHm_v2.0_Chr7g0189141' => 'rch', 'Rhsim02G0028700' => 'rsi', 'Rhsim02G0028800' => 'rsi', 'Rhsim02G0028900' => 'rsi', 'Rhsim02G0029000' => 'rsi', 'Rhsim02G0029100' => 'rsi', 'Rhsim02G0029200' => 'rsi', 'Rhsim02G0029300' => 'rsi', 'Rhsim02G0029400' => 'rsi', 'Rhsim02G0029500' => 'rsi', 'Rhsim02G0029600' => 'rsi', 'RhsimUnG0024000' => 'rsi', 'RhsimUnG0024100' => 'rsi', 'RhsimUnG0024200' => 'rsi', 'RhsimUnG0024300' => 'rsi', 'RhsimUnG0024400' => 'rsi', 'RhsimUnG0024500' => 'rsi', 'RhsimUnG0024700' => 'rsi', 'RhsimUnG0024800' => 'rsi', 'RhsimUnG0024900' => 'rsi', 'RhsimUnG0025100' => 'rsi', 'Sabra08G0120200' => 'sbr', 'Sabra08G0120300' => 'sbr', 'Sabra08G0120500' => 'sbr', 'Sabra08G0120600' => 'sbr', 'Sabra10G0158900' => 'sbr', 'SalBow2G3492' => 'sbo', 'Sc13g0004760' => 'sci', 'Sc13g0004770' => 'sci', 'Sed0003417' => 'sed', 'Sed0019750' => 'sed', 'SEGI_03419' => 'sgi', 'SEGI_05907' => 'sgi', 'SEGI_10682' => 'sgi', 'SEGI_13528' => 'sgi', 'SEGI_16081' => 'sgi', 'SEGI_19370' => 'sgi', 'SEGI_21015' => 'sgi', 'SEGI_21944' => 'sgi', 'SEGI_32906' => 'sgi', 'SEGI_33093' => 'sgi', 'SEGI_36110' => 'sgi', 'SEGI_40397' => 'sgi', 'SGA_v2.0_scaffold191G40426' => 'sas', 'SGA_v2.0_scaffold353G49717' => 'sas', 'SGA_v2.0_scaffold50G18550' => 'sas', 'SMO119G0173' => 'smo', 'SMO172G0002' => 'smo', 'Solyc09g082690.3' => 'sly', 'Solyc09g082700.2' => 'sly', 'Sopen09g031550' => 'spe', 'Sopen09g031560' => 'spe', 'Sp3g20540' => 'spa', 'Sp7g07580' => 'spa', 'TAR134G0002' => 'tar', 'TAR236G0001' => 'tar', 'TAR365G0892' => 'tar', 'TAR636G0166' => 'tar', 'TAR636G0646' => 'tar', 'TAR636G0869' => 'tar', 'TAR636G1317' => 'tar', 'TAR636G1744' => 'tar', 'TAR636G3358' => 'tar', 'TAR636G3436' => 'tar', 'THA.LOC104803047' => 'tha', 'Thecc.04G238900' => 'tca', 'Thhalv10021557m.g' => 'esa', 'Thhalv10026318m.g' => 'esa', 'Thhalv10026335m.g' => 'esa', 'TPR.G17433' => 'tpr', 'TPR.G18915' => 'tpr', 'TPR.G26125' => 'tpr', 'TWI09G0677' => 'twi', 'TWI73G0287' => 'twi', 'unitig_748.g8326' => 'ugi', 'vmacro15370' => 'vma', 'vmacro15371' => 'vma', 'vmacro15372' => 'vma', 'vmacro15373' => 'vma', 'vmacro15374' => 'vma', 'VMungo0720G2826' => 'vmu', 'Zm00001eb116960' => 'zma', 'Zm00001eb301260' => 'zma', 'Zm00001eb301270' => 'zma' ), 'gf_id' => 'HOM05D001460', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001460' ), 'data_identifier' => 'HOM05D001460', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001460', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '433', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p22980' => 'bna', 'A01p32340' => 'bna', 'A03p42970' => 'bna', 'A05p25880' => 'bna', 'Aa31LG8G9320' => 'aar', 'Aa31LG8G9330' => 'aar', 'Aa31LG8G9340' => 'aar', 'Aa31sc221G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1034' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1528' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.829' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2222' => 'aag', 'Ah.12g058830' => 'amhyb', 'Ah.12g058840' => 'amhyb', 'AL3G37160' => 'aly', 'AL7G41310' => 'aly', 'Aqoxy5G00395' => 'aox', 'Aqoxy5G00396' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0C8NZA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5185HY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JZ1PRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MD3LS0' => 'arhy', 'AT3G22840' => 'ath', 'AT4G14690' => 'ath', 'ATR0665G054' => 'atr', 'Atru.chr4.2344' => 'acertr', 'Atru.chr4.2346' => 'acertr', 'Atru.chr4.2347' => 'acertr', 'Atru.chr4.2348' => 'acertr', 'Atru.chr4.2355' => 'acertr', 'Atru.chr4.2356' => 'acertr', 'Atru.chr4.2358' => 'acertr', 'Atru.chr4.2359' => 'acertr', 'Atru.chr4.2360' => 'acertr', 'Atru.chr4.2361' => 'acertr', 'AUR62030476' => 'cqu', 'AUR62030478' => 'cqu', 'AUR62030819' => 'cqu', 'AUR62030820' => 'cqu', 'BcaB03g14648' => 'bca', 'BcaB04g20492' => 'bca', 'BcaB06g26399' => 'bca', 'BcaC01g03416' => 'bca', 'BcaC01g03419' => 'bca', 'BcaC01g03421' => 'bca', 'BcaC01g03424' => 'bca', 'BcaC05g28012' => 'bca', 'BcaC09g49212' => 'bca', 'BcaC09g50140' => 'bca', 'BcaNung00346' => 'bca', 'BolC1t02785H' => 'bol', 'BolC1t04095H' => 'bol', 'BolC3t17545H' => 'bol', 'BolC5t32769H' => 'bol', 'BraA01t02211Z' => 'bra', 'BraA01t03359Z' => 'bra', 'BraA03t13441Z' => 'bra', 'BraA05t21476Z' => 'bra', 'C01p28420' => 'bna', 'C01p41350' => 'bna', 'C03p52750' => 'bna', 'C03p52780' => 'bna', 'C05p40270' => 'bna', 'CAN.G1437.9' => 'can', 'CANSAT78G0035' => 'cansat', 'CANSAT78G1036' => 'cansat', 'CANSAT78G2272' => 'cansat', 'CANSAT78G2478' => 'cansat', 'CARHR098700' => 'chi', 'CARHR221120' => 'chi', 'CARHR221150' => 'chi', 'Carub.0003s2297' => 'cru', 'Carub.0007s2749' => 'cru', 'Carub.0007s2750' => 'cru', 'Carub.0007s2751' => 'cru', 'Ca_10849_v3' => 'car', 'Cc03_g04300' => 'ccan', 'CDE02G3648' => 'cde', 'CDE05G0060' => 'cde', 'CDE05G0692' => 'cde', 'CDE05G2285' => 'cde', 'CDE05G2884' => 'cde', 'CDE05G3072' => 'cde', 'Cfa008439' => 'cfa', 'Cfa008441' => 'cfa', 'Cfa008443' => 'cfa', 'Cfa008448' => 'cfa', 'Ciclev10005974m.g' => 'ccl', 'Ciclev10006006m.g' => 'ccl', 'Ciclev10006775m.g' => 'ccl', 'CiPaw.02G120400' => 'cil', 'CiPaw.02G120500' => 'cil', 'CiPaw.02G120600' => 'cil', 'ClCG05G004850' => 'cla', 'COL.COLO4_21566' => 'col', 'Cpa.g.sc44.124' => 'cpa', 'Cre07.g320400' => 'cre', 'Cre07.g320450' => 'cre', 'Cre08.g384650' => 'cre', 'Cre09.g393173' => 'cre', 'Cre09.g394325' => 'cre', 'Cre14.g626750' => 'cre', 'Cre16.g679250' => 'cre', 'CsaV3_3G012890' => 'csa', 'CSS0010865' => 'camsi', 'CSS0044338' => 'camsi', 'DCAR_002366' => 'dca', 'DCAR_030687' => 'dca', 'DCAR_030688' => 'dca', 'Dinv14047' => 'din', 'Dinv14048' => 'din', 'Duzib151G0105' => 'dzi', 'Duzib151G0114' => 'dzi', 'Duzib212G1029' => 'dzi', 'ECA232G3536' => 'eca', 'ECA240G0786' => 'eca', 'ECA240G1802' => 'eca', 'ECA240G3760' => 'eca', 'ECA240G3920' => 'eca', 'EL10Ac5g12536' => 'bvu', 'EL10Ac5g12537' => 'bvu', 'EL10Ac5g12538' => 'bvu', 'Eucgr.B01004' => 'egr', 'Eucgr.B01006' => 'egr', 'Eucgr.B01007' => 'egr', 'Eucgr.B01008' => 'egr', 'Eucgr.B01895' => 'egr', 'Eucgr.B01896' => 'egr', 'FAN04G1456' => 'fan', 'FAN08G1769' => 'fan', 'FAN08G2160' => 'fan', 'FAN13G2403' => 'fan', 'FAN13G3303' => 'fan', 'FAN15G2435' => 'fan', 'FAN17G0672' => 'fan', 'FAN17G2441' => 'fan', 'FAN18G1024' => 'fan', 'FAN22G1458' => 'fan', 'FAN24G0037' => 'fan', 'FAN24G0429' => 'fan', 'FAN24G2387' => 'fan', 'FAN27G2746' => 'fan', 'FvH4_2g20400' => 'fve', 'FvH4_2g20420' => 'fve', 'FvH4_2g20430' => 'fve', 'FvH4_4g01270' => 'fve', 'FvH4_4g01290' => 'fve', 'FvH4_4g01300' => 'fve', 'FvH4_4g01310' => 'fve', 'FvH4_4g01330' => 'fve', 'FvH4_5g09070' => 'fve', 'Glyma.10G243800' => 'gma', 'Glyma.20G150600' => 'gma', 'Gohir.A09G219200' => 'ghi', 'Gohir.A09G219300' => 'ghi', 'Gohir.D09G221400' => 'ghi', 'Gohir.D09G221500' => 'ghi', 'Gorai.006G242600' => 'gra', 'Gorai.006G242700' => 'gra', 'GSVIVG01018044001' => 'vvi', 'HanXRQChr03g0083821' => 'han', 'HanXRQChr03g0083841' => 'han', 'HanXRQChr03g0083881' => 'han', 'HanXRQChr03g0083901' => 'han', 'HanXRQChr03g0083921' => 'han', 'HanXRQChr03g0085331' => 'han', 'HanXRQChr03g0085361' => 'han', 'HanXRQChr03g0085411' => 'han', 'HanXRQChr03g0085421' => 'han', 'HanXRQChr03g0085431' => 'han', 'HanXRQChr08g0221991' => 'han', 'HanXRQChr11g0336061' => 'han', 'HanXRQChr11g0336411' => 'han', 'Haze_11234' => 'cav', 'Hma1.2p1_0549F.1_g177010' => 'hma', 'Hma1.2p1_0602F.1_g187630' => 'hma', 'Hund14876' => 'sun', 'Hund14879' => 'sun', 'Lalb_Chr06g0160741' => 'lal', 'Lalb_Chr21g0304781' => 'lal', 'Lj3A726G19' => 'lonja', 'Lj3A726T23' => 'lonja', 'Lj3A726T24' => 'lonja', 'Lj3A726T25' => 'lonja', 'Lj3A727T17' => 'lonja', 'Lj3C726T0' => 'lonja', 'Lj3C726T2' => 'lonja', 'Lj3P725T35' => 'lonja', 'Lj3P727T10' => 'lonja', 'Lj3P727T12' => 'lonja', 'Lj3P727T14' => 'lonja', 'Lj5g0023109' => 'lja', 'Lj6P646T44' => 'lonja', 'Lsat_1_v5_gn_6_75760' => 'lsa', 'Lsat_1_v5_gn_6_75800' => 'lsa', 'Lsat_1_v5_gn_6_75900' => 'lsa', 'Lsat_1_v5_gn_6_76240' => 'lsa', 'Lsat_1_v5_gn_6_76441' => 'lsa', 'Lsat_1_v5_gn_6_76700' => 'lsa', 'Lsat_1_v5_gn_6_76760' => 'lsa', 'Manes.15G033100' => 'mes', 'Mapoly0004s0074' => 'mpo', 'Mapoly0004s0075' => 'mpo', 'Mapoly0004s0163' => 'mpo', 'Mapoly0004s0164' => 'mpo', 'Mapoly0021s0018' => 'mpo', 'Mapoly0041s0136' => 'mpo', 'Mapoly0041s0137' => 'mpo', 'Mapoly0041s0138' => 'mpo', 'Mapoly0041s0139' => 'mpo', 'Mapoly0041s0141' => 'mpo', 'Mapoly0041s0142' => 'mpo', 'Mapoly0041s0143' => 'mpo', 'Mapoly0041s0144' => 'mpo', 'Mapoly0041s0145' => 'mpo', 'Mapoly0047s0106' => 'mpo', 'Mapoly0047s0108' => 'mpo', 'Mapoly0050s0051' => 'mpo', 'Mapoly0050s0052' => 'mpo', 'Mapoly0050s0053' => 'mpo', 'Mapoly0058s0013' => 'mpo', 'Mapoly0091s0078' => 'mpo', 'Mapoly0091s0079' => 'mpo', 'Mapoly0091s0080' => 'mpo', 'Mapoly0091s0081' => 'mpo', 'Mapoly0278s0004' => 'mpo', 'Mapoly0278s0005' => 'mpo', 'Mapoly0278s0006' => 'mpo', 'MBI11_g30648_MAGBIO' => 'mbi', 'MCO03G194' => 'mco', 'MCO03G590' => 'mco', 'MCO07G312' => 'mco', 'MCO10G318' => 'mco', 'MCO12G244' => 'mco', 'MCO13G148' => 'mco', 'MCO13G194' => 'mco', 'MCO16G238' => 'mco', 'MD06G1134100' => 'mdo', 'MD13G1200100' => 'mdo', 'MD13G1200300' => 'mdo', 'MD13G1200600' => 'mdo', 'MD14G1150400' => 'mdo', 'MD16G1200000' => 'mdo', 'Medtr1g102570' => 'mtr', 'Medtr1g102780' => 'mtr', 'Medtr1g102800' => 'mtr', 'Medtr1g102810' => 'mtr', 'Medtr1g102830' => 'mtr', 'MELO3C006499.2' => 'cme', 'Migut.G00385' => 'egut', 'MSTRG.4063' => 'ama', 'Nitab4.5_0000090g0260' => 'nta', 'Nitab4.5_0000977g0030' => 'nta', 'Nitab4.5_0002541g0040' => 'nta', 'Nitab4.5_0007068g0040' => 'nta', 'Nn005s41408' => 'nnu', 'Nn005s41410' => 'nnu', 'Oeu010310.1' => 'oeu', 'Oeu010311.1' => 'oeu', 'Oeu043472.1' => 'oeu', 'Os01g0246400' => 'osa', 'Os04g0267950' => 'osa', 'Os07g0178700' => 'osa', 'Os07g0178800' => 'osa', 'Peaxi162Scf00316g00046' => 'pax', 'Peaxi162Scf00316g00049' => 'pax', 'Peaxi162Scf00316g00059' => 'pax', 'Peaxi162Scf00316g00328' => 'pax', 'Peaxi162Scf00316g00329' => 'pax', 'Peaxi162Scf00316g00411' => 'pax', 'Peaxi162Scf00316g00521' => 'pax', 'Peaxi162Scf00492g00068' => 'pax', 'Peaxi162Scf35631g00002' => 'pax', 'PGR142G3720' => 'pgr', 'PGSC0003DMG400006442' => 'stu', 'Phvul.007G062000' => 'pvu', 'Potri.008G157750' => 'ptr', 'Potri.008G157900' => 'ptr', 'Potri.008G158000' => 'ptr', 'Potri.008G158200' => 'ptr', 'Pp3c11_7280' => 'ppa', 'Pp3c11_7980' => 'ppa', 'Pp3c12_19450' => 'ppa', 'Pp3c14_1480' => 'ppa', 'Pp3c14_1501' => 'ppa', 'Pp3c16_4900' => 'ppa', 'Pp3c16_5010' => 'ppa', 'Pp3c16_5060' => 'ppa', 'Pp3c19_18250' => 'ppa', 'Pp3c23_8530' => 'ppa', 'Pp3c23_8550' => 'ppa', 'Pp3c24_9670' => 'ppa', 'Pp3c2_21390' => 'ppa', 'Pp3c2_31380' => 'ppa', 'Pp3c3_16620' => 'ppa', 'Pp3c3_8090' => 'ppa', 'Pp3c3_8110' => 'ppa', 'Pp3c3_8130' => 'ppa', 'Pp3c3_8150' => 'ppa', 'Pp3c4_14320' => 'ppa', 'Pp3c6_2560' => 'ppa', 'Pp3c9_16700' => 'ppa', 'PRCOL_00000234' => 'pco', 'PRCOL_00000235' => 'pco', 'PRCOL_00000777' => 'pco', 'PRCOL_00002344' => 'pco', 'PRCOL_00002372' => 'pco', 'PRCOL_00006120' => 'pco', 'Prupe.1G021400' => 'ppe', 'Prupe.1G021500' => 'ppe', 'Prupe.1G021600' => 'ppe', 'Prupe.1G021700' => 'ppe', 'Prupe.1G021800' => 'ppe', 'Prupe.5G145100' => 'ppe', 'Psat6g204040' => 'psa', 'Psat6g204800' => 'psa', 'Psat6g204920' => 'psa', 'Psat6g204960' => 'psa', 'Psat6g205080' => 'psa', 'PSO017G0271' => 'pso', 'PSO017G1276' => 'pso', 'PSO017G1429' => 'pso', 'PSO017G1861' => 'pso', 'PSO017G2787' => 'pso', 'PSO017G4466' => 'pso', 'PSO017G5118' => 'pso', 'PSO017G5420' => 'pso', 'PSO063G3678' => 'pso', 'PSO210G0546' => 'pso', 'PSO317G0001' => 'pso', 'PSO357G0512' => 'pso', 'PSO478G2682' => 'pso', 'PSO647G0001' => 'pso', 'PSO675G0001' => 'pso', 'PSO675G2699' => 'pso', 'PSO675G2849' => 'pso', 'PSO675G4991' => 'pso', 'PSO689G0001' => 'pso', 'QL06p000916' => 'qlo', 'QL06p000921' => 'qlo', 'QL06p001398' => 'qlo', 'QL06p001407' => 'qlo', 'QL06p002031' => 'qlo', 'RcHm_v2.0_Chr4g0387791' => 'rch', 'RcHm_v2.0_Chr4g0387801' => 'rch', 'RcHm_v2.0_Chr6g0286501' => 'rch', 'RcHm_v2.0_Chr6g0286511' => 'rch', 'RcHm_v2.0_Chr6g0286521' => 'rch', 'RcHm_v2.0_Chr6g0286531' => 'rch', 'RcHm_v2.0_Chr7g0189141' => 'rch', 'Rhsim02G0028700' => 'rsi', 'Rhsim02G0028800' => 'rsi', 'Rhsim02G0028900' => 'rsi', 'Rhsim02G0029000' => 'rsi', 'Rhsim02G0029100' => 'rsi', 'Rhsim02G0029200' => 'rsi', 'Rhsim02G0029300' => 'rsi', 'Rhsim02G0029400' => 'rsi', 'Rhsim02G0029500' => 'rsi', 'Rhsim02G0029600' => 'rsi', 'RhsimUnG0024000' => 'rsi', 'RhsimUnG0024100' => 'rsi', 'RhsimUnG0024200' => 'rsi', 'RhsimUnG0024300' => 'rsi', 'RhsimUnG0024400' => 'rsi', 'RhsimUnG0024500' => 'rsi', 'RhsimUnG0024700' => 'rsi', 'RhsimUnG0024800' => 'rsi', 'RhsimUnG0024900' => 'rsi', 'RhsimUnG0025100' => 'rsi', 'Sabra08G0120200' => 'sbr', 'Sabra08G0120300' => 'sbr', 'Sabra08G0120500' => 'sbr', 'Sabra08G0120600' => 'sbr', 'Sabra10G0158900' => 'sbr', 'SalBow2G3492' => 'sbo', 'Sc13g0004760' => 'sci', 'Sc13g0004770' => 'sci', 'Sed0003417' => 'sed', 'Sed0019750' => 'sed', 'SEGI_03419' => 'sgi', 'SEGI_05907' => 'sgi', 'SEGI_10682' => 'sgi', 'SEGI_13528' => 'sgi', 'SEGI_16081' => 'sgi', 'SEGI_19370' => 'sgi', 'SEGI_21015' => 'sgi', 'SEGI_21944' => 'sgi', 'SEGI_32906' => 'sgi', 'SEGI_33093' => 'sgi', 'SEGI_36110' => 'sgi', 'SEGI_40397' => 'sgi', 'SGA_v2.0_scaffold191G40426' => 'sas', 'SGA_v2.0_scaffold353G49717' => 'sas', 'SGA_v2.0_scaffold50G18550' => 'sas', 'SMO119G0173' => 'smo', 'SMO172G0002' => 'smo', 'Solyc09g082690.3' => 'sly', 'Solyc09g082700.2' => 'sly', 'Sopen09g031550' => 'spe', 'Sopen09g031560' => 'spe', 'Sp3g20540' => 'spa', 'Sp7g07580' => 'spa', 'TAR134G0002' => 'tar', 'TAR236G0001' => 'tar', 'TAR365G0892' => 'tar', 'TAR636G0166' => 'tar', 'TAR636G0646' => 'tar', 'TAR636G0869' => 'tar', 'TAR636G1317' => 'tar', 'TAR636G1744' => 'tar', 'TAR636G3358' => 'tar', 'TAR636G3436' => 'tar', 'THA.LOC104803047' => 'tha', 'Thecc.04G238900' => 'tca', 'Thhalv10021557m.g' => 'esa', 'Thhalv10026318m.g' => 'esa', 'Thhalv10026335m.g' => 'esa', 'TPR.G17433' => 'tpr', 'TPR.G18915' => 'tpr', 'TPR.G26125' => 'tpr', 'TWI09G0677' => 'twi', 'TWI73G0287' => 'twi', 'unitig_748.g8326' => 'ugi', 'vmacro15370' => 'vma', 'vmacro15371' => 'vma', 'vmacro15372' => 'vma', 'vmacro15373' => 'vma', 'vmacro15374' => 'vma', 'VMungo0720G2826' => 'vmu', 'Zm00001eb116960' => 'zma', 'Zm00001eb301260' => 'zma', 'Zm00001eb301270' => 'zma' ) $gf_id = 'HOM05D001460' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001460' ) $data_identifier = 'HOM05D001460' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 4, 'aag' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 2, 'aox' => (int) 2, 'arhy' => (int) 4, 'ath' => (int) 2, 'atr' => (int) 1, 'acertr' => (int) 10, 'cqu' => (int) 4, 'bca' => (int) 11, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 1, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 1, 'ccan' => (int) 1, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 1, 'col' => (int) 1, 'cpa' => (int) 1, 'cre' => (int) 7, 'csa' => (int) 1, 'camsi' => (int) 2, 'dca' => (int) 3, 'din' => (int) 2, 'dzi' => (int) 3, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 14, 'fve' => (int) 9, 'gma' => (int) 2, 'ghi' => (int) 4, 'gra' => (int) 2, 'vvi' => (int) 1, 'han' => (int) 13, 'cav' => (int) 1, 'hma' => (int) 2, 'sun' => (int) 2, 'lal' => (int) 2, 'lonja' => (int) 12, 'lja' => (int) 1, 'lsa' => (int) 7, 'mes' => (int) 1, 'mpo' => (int) 27, 'mbi' => (int) 1, 'mco' => (int) 8, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 1, 'egut' => (int) 1, 'ama' => (int) 1, 'nta' => (int) 4, 'nnu' => (int) 2, 'oeu' => (int) 3, 'osa' => (int) 4, 'pax' => (int) 9, 'pgr' => (int) 1, 'stu' => (int) 1, 'pvu' => (int) 1, 'ptr' => (int) 4, 'ppa' => (int) 22, 'pco' => (int) 6, 'ppe' => (int) 6, 'psa' => (int) 5, 'pso' => (int) 19, 'qlo' => (int) 5, 'rch' => (int) 7, 'rsi' => (int) 20, 'sbr' => (int) 5, 'sbo' => (int) 1, 'sci' => (int) 2, 'sed' => (int) 2, 'sgi' => (int) 12, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 2, 'tar' => (int) 10, 'tha' => (int) 1, 'tca' => (int) 1, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 2, 'ugi' => (int) 1, 'vma' => (int) 5, 'vmu' => (int) 1, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb301270' $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' => 'HOM05D001460', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '433', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p22980' => 'bna', 'A01p32340' => 'bna', 'A03p42970' => 'bna', 'A05p25880' => 'bna', 'Aa31LG8G9320' => 'aar', 'Aa31LG8G9330' => 'aar', 'Aa31LG8G9340' => 'aar', 'Aa31sc221G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1034' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1528' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.829' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2222' => 'aag', 'Ah.12g058830' => 'amhyb', 'Ah.12g058840' => 'amhyb', 'AL3G37160' => 'aly', 'AL7G41310' => 'aly', 'Aqoxy5G00395' => 'aox', 'Aqoxy5G00396' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0C8NZA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5185HY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JZ1PRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MD3LS0' => 'arhy', 'AT3G22840' => 'ath', 'AT4G14690' => 'ath', 'ATR0665G054' => 'atr', 'Atru.chr4.2344' => 'acertr', 'Atru.chr4.2346' => 'acertr', 'Atru.chr4.2347' => 'acertr', 'Atru.chr4.2348' => 'acertr', 'Atru.chr4.2355' => 'acertr', 'Atru.chr4.2356' => 'acertr', 'Atru.chr4.2358' => 'acertr', 'Atru.chr4.2359' => 'acertr', 'Atru.chr4.2360' => 'acertr', 'Atru.chr4.2361' => 'acertr', 'AUR62030476' => 'cqu', 'AUR62030478' => 'cqu', 'AUR62030819' => 'cqu', 'AUR62030820' => 'cqu', 'BcaB03g14648' => 'bca', 'BcaB04g20492' => 'bca', 'BcaB06g26399' => 'bca', 'BcaC01g03416' => 'bca', 'BcaC01g03419' => 'bca', 'BcaC01g03421' => 'bca', 'BcaC01g03424' => 'bca', 'BcaC05g28012' => 'bca', 'BcaC09g49212' => 'bca', 'BcaC09g50140' => 'bca', 'BcaNung00346' => 'bca', 'BolC1t02785H' => 'bol', 'BolC1t04095H' => 'bol', 'BolC3t17545H' => 'bol', 'BolC5t32769H' => 'bol', 'BraA01t02211Z' => 'bra', 'BraA01t03359Z' => 'bra', 'BraA03t13441Z' => 'bra', 'BraA05t21476Z' => 'bra', 'C01p28420' => 'bna', 'C01p41350' => 'bna', 'C03p52750' => 'bna', 'C03p52780' => 'bna', 'C05p40270' => 'bna', 'CAN.G1437.9' => 'can', 'CANSAT78G0035' => 'cansat', 'CANSAT78G1036' => 'cansat', 'CANSAT78G2272' => 'cansat', 'CANSAT78G2478' => 'cansat', 'CARHR098700' => 'chi', 'CARHR221120' => 'chi', 'CARHR221150' => 'chi', 'Carub.0003s2297' => 'cru', 'Carub.0007s2749' => 'cru', 'Carub.0007s2750' => 'cru', 'Carub.0007s2751' => 'cru', 'Ca_10849_v3' => 'car', 'Cc03_g04300' => 'ccan', 'CDE02G3648' => 'cde', 'CDE05G0060' => 'cde', 'CDE05G0692' => 'cde', 'CDE05G2285' => 'cde', 'CDE05G2884' => 'cde', 'CDE05G3072' => 'cde', 'Cfa008439' => 'cfa', 'Cfa008441' => 'cfa', 'Cfa008443' => 'cfa', 'Cfa008448' => 'cfa', 'Ciclev10005974m.g' => 'ccl', 'Ciclev10006006m.g' => 'ccl', 'Ciclev10006775m.g' => 'ccl', 'CiPaw.02G120400' => 'cil', 'CiPaw.02G120500' => 'cil', 'CiPaw.02G120600' => 'cil', 'ClCG05G004850' => 'cla', 'COL.COLO4_21566' => 'col', 'Cpa.g.sc44.124' => 'cpa', 'Cre07.g320400' => 'cre', 'Cre07.g320450' => 'cre', 'Cre08.g384650' => 'cre', 'Cre09.g393173' => 'cre', 'Cre09.g394325' => 'cre', 'Cre14.g626750' => 'cre', 'Cre16.g679250' => 'cre', 'CsaV3_3G012890' => 'csa', 'CSS0010865' => 'camsi', 'CSS0044338' => 'camsi', 'DCAR_002366' => 'dca', 'DCAR_030687' => 'dca', 'DCAR_030688' => 'dca', 'Dinv14047' => 'din', 'Dinv14048' => 'din', 'Duzib151G0105' => 'dzi', 'Duzib151G0114' => 'dzi', 'Duzib212G1029' => 'dzi', 'ECA232G3536' => 'eca', 'ECA240G0786' => 'eca', 'ECA240G1802' => 'eca', 'ECA240G3760' => 'eca', 'ECA240G3920' => 'eca', 'EL10Ac5g12536' => 'bvu', 'EL10Ac5g12537' => 'bvu', 'EL10Ac5g12538' => 'bvu', 'Eucgr.B01004' => 'egr', 'Eucgr.B01006' => 'egr', 'Eucgr.B01007' => 'egr', 'Eucgr.B01008' => 'egr', 'Eucgr.B01895' => 'egr', 'Eucgr.B01896' => 'egr', 'FAN04G1456' => 'fan', 'FAN08G1769' => 'fan', 'FAN08G2160' => 'fan', 'FAN13G2403' => 'fan', 'FAN13G3303' => 'fan', 'FAN15G2435' => 'fan', 'FAN17G0672' => 'fan', 'FAN17G2441' => 'fan', 'FAN18G1024' => 'fan', 'FAN22G1458' => 'fan', 'FAN24G0037' => 'fan', 'FAN24G0429' => 'fan', 'FAN24G2387' => 'fan', 'FAN27G2746' => 'fan', 'FvH4_2g20400' => 'fve', 'FvH4_2g20420' => 'fve', 'FvH4_2g20430' => 'fve', 'FvH4_4g01270' => 'fve', 'FvH4_4g01290' => 'fve', 'FvH4_4g01300' => 'fve', 'FvH4_4g01310' => 'fve', 'FvH4_4g01330' => 'fve', 'FvH4_5g09070' => 'fve', 'Glyma.10G243800' => 'gma', 'Glyma.20G150600' => 'gma', 'Gohir.A09G219200' => 'ghi', 'Gohir.A09G219300' => 'ghi', 'Gohir.D09G221400' => 'ghi', 'Gohir.D09G221500' => 'ghi', 'Gorai.006G242600' => 'gra', 'Gorai.006G242700' => 'gra', 'GSVIVG01018044001' => 'vvi', 'HanXRQChr03g0083821' => 'han', 'HanXRQChr03g0083841' => 'han', 'HanXRQChr03g0083881' => 'han', 'HanXRQChr03g0083901' => 'han', 'HanXRQChr03g0083921' => 'han', 'HanXRQChr03g0085331' => 'han', 'HanXRQChr03g0085361' => 'han', 'HanXRQChr03g0085411' => 'han', 'HanXRQChr03g0085421' => 'han', 'HanXRQChr03g0085431' => 'han', 'HanXRQChr08g0221991' => 'han', 'HanXRQChr11g0336061' => 'han', 'HanXRQChr11g0336411' => 'han', 'Haze_11234' => 'cav', 'Hma1.2p1_0549F.1_g177010' => 'hma', 'Hma1.2p1_0602F.1_g187630' => 'hma', 'Hund14876' => 'sun', 'Hund14879' => 'sun', 'Lalb_Chr06g0160741' => 'lal', 'Lalb_Chr21g0304781' => 'lal', 'Lj3A726G19' => 'lonja', 'Lj3A726T23' => 'lonja', 'Lj3A726T24' => 'lonja', 'Lj3A726T25' => 'lonja', 'Lj3A727T17' => 'lonja', 'Lj3C726T0' => 'lonja', 'Lj3C726T2' => 'lonja', 'Lj3P725T35' => 'lonja', 'Lj3P727T10' => 'lonja', 'Lj3P727T12' => 'lonja', 'Lj3P727T14' => 'lonja', 'Lj5g0023109' => 'lja', 'Lj6P646T44' => 'lonja', 'Lsat_1_v5_gn_6_75760' => 'lsa', 'Lsat_1_v5_gn_6_75800' => 'lsa', 'Lsat_1_v5_gn_6_75900' => 'lsa', 'Lsat_1_v5_gn_6_76240' => 'lsa', 'Lsat_1_v5_gn_6_76441' => 'lsa', 'Lsat_1_v5_gn_6_76700' => 'lsa', 'Lsat_1_v5_gn_6_76760' => 'lsa', 'Manes.15G033100' => 'mes', 'Mapoly0004s0074' => 'mpo', 'Mapoly0004s0075' => 'mpo', 'Mapoly0004s0163' => 'mpo', 'Mapoly0004s0164' => 'mpo', 'Mapoly0021s0018' => 'mpo', 'Mapoly0041s0136' => 'mpo', 'Mapoly0041s0137' => 'mpo', 'Mapoly0041s0138' => 'mpo', 'Mapoly0041s0139' => 'mpo', 'Mapoly0041s0141' => 'mpo', 'Mapoly0041s0142' => 'mpo', 'Mapoly0041s0143' => 'mpo', 'Mapoly0041s0144' => 'mpo', 'Mapoly0041s0145' => 'mpo', 'Mapoly0047s0106' => 'mpo', 'Mapoly0047s0108' => 'mpo', 'Mapoly0050s0051' => 'mpo', 'Mapoly0050s0052' => 'mpo', 'Mapoly0050s0053' => 'mpo', 'Mapoly0058s0013' => 'mpo', 'Mapoly0091s0078' => 'mpo', 'Mapoly0091s0079' => 'mpo', 'Mapoly0091s0080' => 'mpo', 'Mapoly0091s0081' => 'mpo', 'Mapoly0278s0004' => 'mpo', 'Mapoly0278s0005' => 'mpo', 'Mapoly0278s0006' => 'mpo', 'MBI11_g30648_MAGBIO' => 'mbi', 'MCO03G194' => 'mco', 'MCO03G590' => 'mco', 'MCO07G312' => 'mco', 'MCO10G318' => 'mco', 'MCO12G244' => 'mco', 'MCO13G148' => 'mco', 'MCO13G194' => 'mco', 'MCO16G238' => 'mco', 'MD06G1134100' => 'mdo', 'MD13G1200100' => 'mdo', 'MD13G1200300' => 'mdo', 'MD13G1200600' => 'mdo', 'MD14G1150400' => 'mdo', 'MD16G1200000' => 'mdo', 'Medtr1g102570' => 'mtr', 'Medtr1g102780' => 'mtr', 'Medtr1g102800' => 'mtr', 'Medtr1g102810' => 'mtr', 'Medtr1g102830' => 'mtr', 'MELO3C006499.2' => 'cme', 'Migut.G00385' => 'egut', 'MSTRG.4063' => 'ama', 'Nitab4.5_0000090g0260' => 'nta', 'Nitab4.5_0000977g0030' => 'nta', 'Nitab4.5_0002541g0040' => 'nta', 'Nitab4.5_0007068g0040' => 'nta', 'Nn005s41408' => 'nnu', 'Nn005s41410' => 'nnu', 'Oeu010310.1' => 'oeu', 'Oeu010311.1' => 'oeu', 'Oeu043472.1' => 'oeu', 'Os01g0246400' => 'osa', 'Os04g0267950' => 'osa', 'Os07g0178700' => 'osa', 'Os07g0178800' => 'osa', 'Peaxi162Scf00316g00046' => 'pax', 'Peaxi162Scf00316g00049' => 'pax', 'Peaxi162Scf00316g00059' => 'pax', 'Peaxi162Scf00316g00328' => 'pax', 'Peaxi162Scf00316g00329' => 'pax', 'Peaxi162Scf00316g00411' => 'pax', 'Peaxi162Scf00316g00521' => 'pax', 'Peaxi162Scf00492g00068' => 'pax', 'Peaxi162Scf35631g00002' => 'pax', 'PGR142G3720' => 'pgr', 'PGSC0003DMG400006442' => 'stu', 'Phvul.007G062000' => 'pvu', 'Potri.008G157750' => 'ptr', 'Potri.008G157900' => 'ptr', 'Potri.008G158000' => 'ptr', 'Potri.008G158200' => 'ptr', 'Pp3c11_7280' => 'ppa', 'Pp3c11_7980' => 'ppa', 'Pp3c12_19450' => 'ppa', 'Pp3c14_1480' => 'ppa', 'Pp3c14_1501' => 'ppa', 'Pp3c16_4900' => 'ppa', 'Pp3c16_5010' => 'ppa', 'Pp3c16_5060' => 'ppa', 'Pp3c19_18250' => 'ppa', 'Pp3c23_8530' => 'ppa', 'Pp3c23_8550' => 'ppa', 'Pp3c24_9670' => 'ppa', 'Pp3c2_21390' => 'ppa', 'Pp3c2_31380' => 'ppa', 'Pp3c3_16620' => 'ppa', 'Pp3c3_8090' => 'ppa', 'Pp3c3_8110' => 'ppa', 'Pp3c3_8130' => 'ppa', 'Pp3c3_8150' => 'ppa', 'Pp3c4_14320' => 'ppa', 'Pp3c6_2560' => 'ppa', 'Pp3c9_16700' => 'ppa', 'PRCOL_00000234' => 'pco', 'PRCOL_00000235' => 'pco', 'PRCOL_00000777' => 'pco', 'PRCOL_00002344' => 'pco', 'PRCOL_00002372' => 'pco', 'PRCOL_00006120' => 'pco', 'Prupe.1G021400' => 'ppe', 'Prupe.1G021500' => 'ppe', 'Prupe.1G021600' => 'ppe', 'Prupe.1G021700' => 'ppe', 'Prupe.1G021800' => 'ppe', 'Prupe.5G145100' => 'ppe', 'Psat6g204040' => 'psa', 'Psat6g204800' => 'psa', 'Psat6g204920' => 'psa', 'Psat6g204960' => 'psa', 'Psat6g205080' => 'psa', 'PSO017G0271' => 'pso', 'PSO017G1276' => 'pso', 'PSO017G1429' => 'pso', 'PSO017G1861' => 'pso', 'PSO017G2787' => 'pso', 'PSO017G4466' => 'pso', 'PSO017G5118' => 'pso', 'PSO017G5420' => 'pso', 'PSO063G3678' => 'pso', 'PSO210G0546' => 'pso', 'PSO317G0001' => 'pso', 'PSO357G0512' => 'pso', 'PSO478G2682' => 'pso', 'PSO647G0001' => 'pso', 'PSO675G0001' => 'pso', 'PSO675G2699' => 'pso', 'PSO675G2849' => 'pso', 'PSO675G4991' => 'pso', 'PSO689G0001' => 'pso', 'QL06p000916' => 'qlo', 'QL06p000921' => 'qlo', 'QL06p001398' => 'qlo', 'QL06p001407' => 'qlo', 'QL06p002031' => 'qlo', 'RcHm_v2.0_Chr4g0387791' => 'rch', 'RcHm_v2.0_Chr4g0387801' => 'rch', 'RcHm_v2.0_Chr6g0286501' => 'rch', 'RcHm_v2.0_Chr6g0286511' => 'rch', 'RcHm_v2.0_Chr6g0286521' => 'rch', 'RcHm_v2.0_Chr6g0286531' => 'rch', 'RcHm_v2.0_Chr7g0189141' => 'rch', 'Rhsim02G0028700' => 'rsi', 'Rhsim02G0028800' => 'rsi', 'Rhsim02G0028900' => 'rsi', 'Rhsim02G0029000' => 'rsi', 'Rhsim02G0029100' => 'rsi', 'Rhsim02G0029200' => 'rsi', 'Rhsim02G0029300' => 'rsi', 'Rhsim02G0029400' => 'rsi', 'Rhsim02G0029500' => 'rsi', 'Rhsim02G0029600' => 'rsi', 'RhsimUnG0024000' => 'rsi', 'RhsimUnG0024100' => 'rsi', 'RhsimUnG0024200' => 'rsi', 'RhsimUnG0024300' => 'rsi', 'RhsimUnG0024400' => 'rsi', 'RhsimUnG0024500' => 'rsi', 'RhsimUnG0024700' => 'rsi', 'RhsimUnG0024800' => 'rsi', 'RhsimUnG0024900' => 'rsi', 'RhsimUnG0025100' => 'rsi', 'Sabra08G0120200' => 'sbr', 'Sabra08G0120300' => 'sbr', 'Sabra08G0120500' => 'sbr', 'Sabra08G0120600' => 'sbr', 'Sabra10G0158900' => 'sbr', 'SalBow2G3492' => 'sbo', 'Sc13g0004760' => 'sci', 'Sc13g0004770' => 'sci', 'Sed0003417' => 'sed', 'Sed0019750' => 'sed', 'SEGI_03419' => 'sgi', 'SEGI_05907' => 'sgi', 'SEGI_10682' => 'sgi', 'SEGI_13528' => 'sgi', 'SEGI_16081' => 'sgi', 'SEGI_19370' => 'sgi', 'SEGI_21015' => 'sgi', 'SEGI_21944' => 'sgi', 'SEGI_32906' => 'sgi', 'SEGI_33093' => 'sgi', 'SEGI_36110' => 'sgi', 'SEGI_40397' => 'sgi', 'SGA_v2.0_scaffold191G40426' => 'sas', 'SGA_v2.0_scaffold353G49717' => 'sas', 'SGA_v2.0_scaffold50G18550' => 'sas', 'SMO119G0173' => 'smo', 'SMO172G0002' => 'smo', 'Solyc09g082690.3' => 'sly', 'Solyc09g082700.2' => 'sly', 'Sopen09g031550' => 'spe', 'Sopen09g031560' => 'spe', 'Sp3g20540' => 'spa', 'Sp7g07580' => 'spa', 'TAR134G0002' => 'tar', 'TAR236G0001' => 'tar', 'TAR365G0892' => 'tar', 'TAR636G0166' => 'tar', 'TAR636G0646' => 'tar', 'TAR636G0869' => 'tar', 'TAR636G1317' => 'tar', 'TAR636G1744' => 'tar', 'TAR636G3358' => 'tar', 'TAR636G3436' => 'tar', 'THA.LOC104803047' => 'tha', 'Thecc.04G238900' => 'tca', 'Thhalv10021557m.g' => 'esa', 'Thhalv10026318m.g' => 'esa', 'Thhalv10026335m.g' => 'esa', 'TPR.G17433' => 'tpr', 'TPR.G18915' => 'tpr', 'TPR.G26125' => 'tpr', 'TWI09G0677' => 'twi', 'TWI73G0287' => 'twi', 'unitig_748.g8326' => 'ugi', 'vmacro15370' => 'vma', 'vmacro15371' => 'vma', 'vmacro15372' => 'vma', 'vmacro15373' => 'vma', 'vmacro15374' => 'vma', 'VMungo0720G2826' => 'vmu', 'Zm00001eb116960' => 'zma', 'Zm00001eb301260' => 'zma', 'Zm00001eb301270' => 'zma' ), 'gf_id' => 'HOM05D001460', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001460' ), 'data_identifier' => 'HOM05D001460', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001460', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '433', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p22980' => 'bna', 'A01p32340' => 'bna', 'A03p42970' => 'bna', 'A05p25880' => 'bna', 'Aa31LG8G9320' => 'aar', 'Aa31LG8G9330' => 'aar', 'Aa31LG8G9340' => 'aar', 'Aa31sc221G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1034' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1528' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.829' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2222' => 'aag', 'Ah.12g058830' => 'amhyb', 'Ah.12g058840' => 'amhyb', 'AL3G37160' => 'aly', 'AL7G41310' => 'aly', 'Aqoxy5G00395' => 'aox', 'Aqoxy5G00396' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0C8NZA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5185HY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JZ1PRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MD3LS0' => 'arhy', 'AT3G22840' => 'ath', 'AT4G14690' => 'ath', 'ATR0665G054' => 'atr', 'Atru.chr4.2344' => 'acertr', 'Atru.chr4.2346' => 'acertr', 'Atru.chr4.2347' => 'acertr', 'Atru.chr4.2348' => 'acertr', 'Atru.chr4.2355' => 'acertr', 'Atru.chr4.2356' => 'acertr', 'Atru.chr4.2358' => 'acertr', 'Atru.chr4.2359' => 'acertr', 'Atru.chr4.2360' => 'acertr', 'Atru.chr4.2361' => 'acertr', 'AUR62030476' => 'cqu', 'AUR62030478' => 'cqu', 'AUR62030819' => 'cqu', 'AUR62030820' => 'cqu', 'BcaB03g14648' => 'bca', 'BcaB04g20492' => 'bca', 'BcaB06g26399' => 'bca', 'BcaC01g03416' => 'bca', 'BcaC01g03419' => 'bca', 'BcaC01g03421' => 'bca', 'BcaC01g03424' => 'bca', 'BcaC05g28012' => 'bca', 'BcaC09g49212' => 'bca', 'BcaC09g50140' => 'bca', 'BcaNung00346' => 'bca', 'BolC1t02785H' => 'bol', 'BolC1t04095H' => 'bol', 'BolC3t17545H' => 'bol', 'BolC5t32769H' => 'bol', 'BraA01t02211Z' => 'bra', 'BraA01t03359Z' => 'bra', 'BraA03t13441Z' => 'bra', 'BraA05t21476Z' => 'bra', 'C01p28420' => 'bna', 'C01p41350' => 'bna', 'C03p52750' => 'bna', 'C03p52780' => 'bna', 'C05p40270' => 'bna', 'CAN.G1437.9' => 'can', 'CANSAT78G0035' => 'cansat', 'CANSAT78G1036' => 'cansat', 'CANSAT78G2272' => 'cansat', 'CANSAT78G2478' => 'cansat', 'CARHR098700' => 'chi', 'CARHR221120' => 'chi', 'CARHR221150' => 'chi', 'Carub.0003s2297' => 'cru', 'Carub.0007s2749' => 'cru', 'Carub.0007s2750' => 'cru', 'Carub.0007s2751' => 'cru', 'Ca_10849_v3' => 'car', 'Cc03_g04300' => 'ccan', 'CDE02G3648' => 'cde', 'CDE05G0060' => 'cde', 'CDE05G0692' => 'cde', 'CDE05G2285' => 'cde', 'CDE05G2884' => 'cde', 'CDE05G3072' => 'cde', 'Cfa008439' => 'cfa', 'Cfa008441' => 'cfa', 'Cfa008443' => 'cfa', 'Cfa008448' => 'cfa', 'Ciclev10005974m.g' => 'ccl', 'Ciclev10006006m.g' => 'ccl', 'Ciclev10006775m.g' => 'ccl', 'CiPaw.02G120400' => 'cil', 'CiPaw.02G120500' => 'cil', 'CiPaw.02G120600' => 'cil', 'ClCG05G004850' => 'cla', 'COL.COLO4_21566' => 'col', 'Cpa.g.sc44.124' => 'cpa', 'Cre07.g320400' => 'cre', 'Cre07.g320450' => 'cre', 'Cre08.g384650' => 'cre', 'Cre09.g393173' => 'cre', 'Cre09.g394325' => 'cre', 'Cre14.g626750' => 'cre', 'Cre16.g679250' => 'cre', 'CsaV3_3G012890' => 'csa', 'CSS0010865' => 'camsi', 'CSS0044338' => 'camsi', 'DCAR_002366' => 'dca', 'DCAR_030687' => 'dca', 'DCAR_030688' => 'dca', 'Dinv14047' => 'din', 'Dinv14048' => 'din', 'Duzib151G0105' => 'dzi', 'Duzib151G0114' => 'dzi', 'Duzib212G1029' => 'dzi', 'ECA232G3536' => 'eca', 'ECA240G0786' => 'eca', 'ECA240G1802' => 'eca', 'ECA240G3760' => 'eca', 'ECA240G3920' => 'eca', 'EL10Ac5g12536' => 'bvu', 'EL10Ac5g12537' => 'bvu', 'EL10Ac5g12538' => 'bvu', 'Eucgr.B01004' => 'egr', 'Eucgr.B01006' => 'egr', 'Eucgr.B01007' => 'egr', 'Eucgr.B01008' => 'egr', 'Eucgr.B01895' => 'egr', 'Eucgr.B01896' => 'egr', 'FAN04G1456' => 'fan', 'FAN08G1769' => 'fan', 'FAN08G2160' => 'fan', 'FAN13G2403' => 'fan', 'FAN13G3303' => 'fan', 'FAN15G2435' => 'fan', 'FAN17G0672' => 'fan', 'FAN17G2441' => 'fan', 'FAN18G1024' => 'fan', 'FAN22G1458' => 'fan', 'FAN24G0037' => 'fan', 'FAN24G0429' => 'fan', 'FAN24G2387' => 'fan', 'FAN27G2746' => 'fan', 'FvH4_2g20400' => 'fve', 'FvH4_2g20420' => 'fve', 'FvH4_2g20430' => 'fve', 'FvH4_4g01270' => 'fve', 'FvH4_4g01290' => 'fve', 'FvH4_4g01300' => 'fve', 'FvH4_4g01310' => 'fve', 'FvH4_4g01330' => 'fve', 'FvH4_5g09070' => 'fve', 'Glyma.10G243800' => 'gma', 'Glyma.20G150600' => 'gma', 'Gohir.A09G219200' => 'ghi', 'Gohir.A09G219300' => 'ghi', 'Gohir.D09G221400' => 'ghi', 'Gohir.D09G221500' => 'ghi', 'Gorai.006G242600' => 'gra', 'Gorai.006G242700' => 'gra', 'GSVIVG01018044001' => 'vvi', 'HanXRQChr03g0083821' => 'han', 'HanXRQChr03g0083841' => 'han', 'HanXRQChr03g0083881' => 'han', 'HanXRQChr03g0083901' => 'han', 'HanXRQChr03g0083921' => 'han', 'HanXRQChr03g0085331' => 'han', 'HanXRQChr03g0085361' => 'han', 'HanXRQChr03g0085411' => 'han', 'HanXRQChr03g0085421' => 'han', 'HanXRQChr03g0085431' => 'han', 'HanXRQChr08g0221991' => 'han', 'HanXRQChr11g0336061' => 'han', 'HanXRQChr11g0336411' => 'han', 'Haze_11234' => 'cav', 'Hma1.2p1_0549F.1_g177010' => 'hma', 'Hma1.2p1_0602F.1_g187630' => 'hma', 'Hund14876' => 'sun', 'Hund14879' => 'sun', 'Lalb_Chr06g0160741' => 'lal', 'Lalb_Chr21g0304781' => 'lal', 'Lj3A726G19' => 'lonja', 'Lj3A726T23' => 'lonja', 'Lj3A726T24' => 'lonja', 'Lj3A726T25' => 'lonja', 'Lj3A727T17' => 'lonja', 'Lj3C726T0' => 'lonja', 'Lj3C726T2' => 'lonja', 'Lj3P725T35' => 'lonja', 'Lj3P727T10' => 'lonja', 'Lj3P727T12' => 'lonja', 'Lj3P727T14' => 'lonja', 'Lj5g0023109' => 'lja', 'Lj6P646T44' => 'lonja', 'Lsat_1_v5_gn_6_75760' => 'lsa', 'Lsat_1_v5_gn_6_75800' => 'lsa', 'Lsat_1_v5_gn_6_75900' => 'lsa', 'Lsat_1_v5_gn_6_76240' => 'lsa', 'Lsat_1_v5_gn_6_76441' => 'lsa', 'Lsat_1_v5_gn_6_76700' => 'lsa', 'Lsat_1_v5_gn_6_76760' => 'lsa', 'Manes.15G033100' => 'mes', 'Mapoly0004s0074' => 'mpo', 'Mapoly0004s0075' => 'mpo', 'Mapoly0004s0163' => 'mpo', 'Mapoly0004s0164' => 'mpo', 'Mapoly0021s0018' => 'mpo', 'Mapoly0041s0136' => 'mpo', 'Mapoly0041s0137' => 'mpo', 'Mapoly0041s0138' => 'mpo', 'Mapoly0041s0139' => 'mpo', 'Mapoly0041s0141' => 'mpo', 'Mapoly0041s0142' => 'mpo', 'Mapoly0041s0143' => 'mpo', 'Mapoly0041s0144' => 'mpo', 'Mapoly0041s0145' => 'mpo', 'Mapoly0047s0106' => 'mpo', 'Mapoly0047s0108' => 'mpo', 'Mapoly0050s0051' => 'mpo', 'Mapoly0050s0052' => 'mpo', 'Mapoly0050s0053' => 'mpo', 'Mapoly0058s0013' => 'mpo', 'Mapoly0091s0078' => 'mpo', 'Mapoly0091s0079' => 'mpo', 'Mapoly0091s0080' => 'mpo', 'Mapoly0091s0081' => 'mpo', 'Mapoly0278s0004' => 'mpo', 'Mapoly0278s0005' => 'mpo', 'Mapoly0278s0006' => 'mpo', 'MBI11_g30648_MAGBIO' => 'mbi', 'MCO03G194' => 'mco', 'MCO03G590' => 'mco', 'MCO07G312' => 'mco', 'MCO10G318' => 'mco', 'MCO12G244' => 'mco', 'MCO13G148' => 'mco', 'MCO13G194' => 'mco', 'MCO16G238' => 'mco', 'MD06G1134100' => 'mdo', 'MD13G1200100' => 'mdo', 'MD13G1200300' => 'mdo', 'MD13G1200600' => 'mdo', 'MD14G1150400' => 'mdo', 'MD16G1200000' => 'mdo', 'Medtr1g102570' => 'mtr', 'Medtr1g102780' => 'mtr', 'Medtr1g102800' => 'mtr', 'Medtr1g102810' => 'mtr', 'Medtr1g102830' => 'mtr', 'MELO3C006499.2' => 'cme', 'Migut.G00385' => 'egut', 'MSTRG.4063' => 'ama', 'Nitab4.5_0000090g0260' => 'nta', 'Nitab4.5_0000977g0030' => 'nta', 'Nitab4.5_0002541g0040' => 'nta', 'Nitab4.5_0007068g0040' => 'nta', 'Nn005s41408' => 'nnu', 'Nn005s41410' => 'nnu', 'Oeu010310.1' => 'oeu', 'Oeu010311.1' => 'oeu', 'Oeu043472.1' => 'oeu', 'Os01g0246400' => 'osa', 'Os04g0267950' => 'osa', 'Os07g0178700' => 'osa', 'Os07g0178800' => 'osa', 'Peaxi162Scf00316g00046' => 'pax', 'Peaxi162Scf00316g00049' => 'pax', 'Peaxi162Scf00316g00059' => 'pax', 'Peaxi162Scf00316g00328' => 'pax', 'Peaxi162Scf00316g00329' => 'pax', 'Peaxi162Scf00316g00411' => 'pax', 'Peaxi162Scf00316g00521' => 'pax', 'Peaxi162Scf00492g00068' => 'pax', 'Peaxi162Scf35631g00002' => 'pax', 'PGR142G3720' => 'pgr', 'PGSC0003DMG400006442' => 'stu', 'Phvul.007G062000' => 'pvu', 'Potri.008G157750' => 'ptr', 'Potri.008G157900' => 'ptr', 'Potri.008G158000' => 'ptr', 'Potri.008G158200' => 'ptr', 'Pp3c11_7280' => 'ppa', 'Pp3c11_7980' => 'ppa', 'Pp3c12_19450' => 'ppa', 'Pp3c14_1480' => 'ppa', 'Pp3c14_1501' => 'ppa', 'Pp3c16_4900' => 'ppa', 'Pp3c16_5010' => 'ppa', 'Pp3c16_5060' => 'ppa', 'Pp3c19_18250' => 'ppa', 'Pp3c23_8530' => 'ppa', 'Pp3c23_8550' => 'ppa', 'Pp3c24_9670' => 'ppa', 'Pp3c2_21390' => 'ppa', 'Pp3c2_31380' => 'ppa', 'Pp3c3_16620' => 'ppa', 'Pp3c3_8090' => 'ppa', 'Pp3c3_8110' => 'ppa', 'Pp3c3_8130' => 'ppa', 'Pp3c3_8150' => 'ppa', 'Pp3c4_14320' => 'ppa', 'Pp3c6_2560' => 'ppa', 'Pp3c9_16700' => 'ppa', 'PRCOL_00000234' => 'pco', 'PRCOL_00000235' => 'pco', 'PRCOL_00000777' => 'pco', 'PRCOL_00002344' => 'pco', 'PRCOL_00002372' => 'pco', 'PRCOL_00006120' => 'pco', 'Prupe.1G021400' => 'ppe', 'Prupe.1G021500' => 'ppe', 'Prupe.1G021600' => 'ppe', 'Prupe.1G021700' => 'ppe', 'Prupe.1G021800' => 'ppe', 'Prupe.5G145100' => 'ppe', 'Psat6g204040' => 'psa', 'Psat6g204800' => 'psa', 'Psat6g204920' => 'psa', 'Psat6g204960' => 'psa', 'Psat6g205080' => 'psa', 'PSO017G0271' => 'pso', 'PSO017G1276' => 'pso', 'PSO017G1429' => 'pso', 'PSO017G1861' => 'pso', 'PSO017G2787' => 'pso', 'PSO017G4466' => 'pso', 'PSO017G5118' => 'pso', 'PSO017G5420' => 'pso', 'PSO063G3678' => 'pso', 'PSO210G0546' => 'pso', 'PSO317G0001' => 'pso', 'PSO357G0512' => 'pso', 'PSO478G2682' => 'pso', 'PSO647G0001' => 'pso', 'PSO675G0001' => 'pso', 'PSO675G2699' => 'pso', 'PSO675G2849' => 'pso', 'PSO675G4991' => 'pso', 'PSO689G0001' => 'pso', 'QL06p000916' => 'qlo', 'QL06p000921' => 'qlo', 'QL06p001398' => 'qlo', 'QL06p001407' => 'qlo', 'QL06p002031' => 'qlo', 'RcHm_v2.0_Chr4g0387791' => 'rch', 'RcHm_v2.0_Chr4g0387801' => 'rch', 'RcHm_v2.0_Chr6g0286501' => 'rch', 'RcHm_v2.0_Chr6g0286511' => 'rch', 'RcHm_v2.0_Chr6g0286521' => 'rch', 'RcHm_v2.0_Chr6g0286531' => 'rch', 'RcHm_v2.0_Chr7g0189141' => 'rch', 'Rhsim02G0028700' => 'rsi', 'Rhsim02G0028800' => 'rsi', 'Rhsim02G0028900' => 'rsi', 'Rhsim02G0029000' => 'rsi', 'Rhsim02G0029100' => 'rsi', 'Rhsim02G0029200' => 'rsi', 'Rhsim02G0029300' => 'rsi', 'Rhsim02G0029400' => 'rsi', 'Rhsim02G0029500' => 'rsi', 'Rhsim02G0029600' => 'rsi', 'RhsimUnG0024000' => 'rsi', 'RhsimUnG0024100' => 'rsi', 'RhsimUnG0024200' => 'rsi', 'RhsimUnG0024300' => 'rsi', 'RhsimUnG0024400' => 'rsi', 'RhsimUnG0024500' => 'rsi', 'RhsimUnG0024700' => 'rsi', 'RhsimUnG0024800' => 'rsi', 'RhsimUnG0024900' => 'rsi', 'RhsimUnG0025100' => 'rsi', 'Sabra08G0120200' => 'sbr', 'Sabra08G0120300' => 'sbr', 'Sabra08G0120500' => 'sbr', 'Sabra08G0120600' => 'sbr', 'Sabra10G0158900' => 'sbr', 'SalBow2G3492' => 'sbo', 'Sc13g0004760' => 'sci', 'Sc13g0004770' => 'sci', 'Sed0003417' => 'sed', 'Sed0019750' => 'sed', 'SEGI_03419' => 'sgi', 'SEGI_05907' => 'sgi', 'SEGI_10682' => 'sgi', 'SEGI_13528' => 'sgi', 'SEGI_16081' => 'sgi', 'SEGI_19370' => 'sgi', 'SEGI_21015' => 'sgi', 'SEGI_21944' => 'sgi', 'SEGI_32906' => 'sgi', 'SEGI_33093' => 'sgi', 'SEGI_36110' => 'sgi', 'SEGI_40397' => 'sgi', 'SGA_v2.0_scaffold191G40426' => 'sas', 'SGA_v2.0_scaffold353G49717' => 'sas', 'SGA_v2.0_scaffold50G18550' => 'sas', 'SMO119G0173' => 'smo', 'SMO172G0002' => 'smo', 'Solyc09g082690.3' => 'sly', 'Solyc09g082700.2' => 'sly', 'Sopen09g031550' => 'spe', 'Sopen09g031560' => 'spe', 'Sp3g20540' => 'spa', 'Sp7g07580' => 'spa', 'TAR134G0002' => 'tar', 'TAR236G0001' => 'tar', 'TAR365G0892' => 'tar', 'TAR636G0166' => 'tar', 'TAR636G0646' => 'tar', 'TAR636G0869' => 'tar', 'TAR636G1317' => 'tar', 'TAR636G1744' => 'tar', 'TAR636G3358' => 'tar', 'TAR636G3436' => 'tar', 'THA.LOC104803047' => 'tha', 'Thecc.04G238900' => 'tca', 'Thhalv10021557m.g' => 'esa', 'Thhalv10026318m.g' => 'esa', 'Thhalv10026335m.g' => 'esa', 'TPR.G17433' => 'tpr', 'TPR.G18915' => 'tpr', 'TPR.G26125' => 'tpr', 'TWI09G0677' => 'twi', 'TWI73G0287' => 'twi', 'unitig_748.g8326' => 'ugi', 'vmacro15370' => 'vma', 'vmacro15371' => 'vma', 'vmacro15372' => 'vma', 'vmacro15373' => 'vma', 'vmacro15374' => 'vma', 'VMungo0720G2826' => 'vmu', 'Zm00001eb116960' => 'zma', 'Zm00001eb301260' => 'zma', 'Zm00001eb301270' => 'zma' ) $gf_id = 'HOM05D001460' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001460' ) $data_identifier = 'HOM05D001460' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 4, 'aag' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 2, 'aox' => (int) 2, 'arhy' => (int) 4, 'ath' => (int) 2, 'atr' => (int) 1, 'acertr' => (int) 10, 'cqu' => (int) 4, 'bca' => (int) 11, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 1, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 1, 'ccan' => (int) 1, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 1, 'col' => (int) 1, 'cpa' => (int) 1, 'cre' => (int) 7, 'csa' => (int) 1, 'camsi' => (int) 2, 'dca' => (int) 3, 'din' => (int) 2, 'dzi' => (int) 3, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 14, 'fve' => (int) 9, 'gma' => (int) 2, 'ghi' => (int) 4, 'gra' => (int) 2, 'vvi' => (int) 1, 'han' => (int) 13, 'cav' => (int) 1, 'hma' => (int) 2, 'sun' => (int) 2, 'lal' => (int) 2, 'lonja' => (int) 12, 'lja' => (int) 1, 'lsa' => (int) 7, 'mes' => (int) 1, 'mpo' => (int) 27, 'mbi' => (int) 1, 'mco' => (int) 8, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 1, 'egut' => (int) 1, 'ama' => (int) 1, 'nta' => (int) 4, 'nnu' => (int) 2, 'oeu' => (int) 3, 'osa' => (int) 4, 'pax' => (int) 9, 'pgr' => (int) 1, 'stu' => (int) 1, 'pvu' => (int) 1, 'ptr' => (int) 4, 'ppa' => (int) 22, 'pco' => (int) 6, 'ppe' => (int) 6, 'psa' => (int) 5, 'pso' => (int) 19, 'qlo' => (int) 5, 'rch' => (int) 7, 'rsi' => (int) 20, 'sbr' => (int) 5, 'sbo' => (int) 1, 'sci' => (int) 2, 'sed' => (int) 2, 'sgi' => (int) 12, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 2, 'tar' => (int) 10, 'tha' => (int) 1, 'tca' => (int) 1, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 2, 'ugi' => (int) 1, 'vma' => (int) 5, 'vmu' => (int) 1, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb301270' $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' => 'HOM05D001460', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '433', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p22980' => 'bna', 'A01p32340' => 'bna', 'A03p42970' => 'bna', 'A05p25880' => 'bna', 'Aa31LG8G9320' => 'aar', 'Aa31LG8G9330' => 'aar', 'Aa31LG8G9340' => 'aar', 'Aa31sc221G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1034' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1528' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.829' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2222' => 'aag', 'Ah.12g058830' => 'amhyb', 'Ah.12g058840' => 'amhyb', 'AL3G37160' => 'aly', 'AL7G41310' => 'aly', 'Aqoxy5G00395' => 'aox', 'Aqoxy5G00396' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0C8NZA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5185HY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JZ1PRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MD3LS0' => 'arhy', 'AT3G22840' => 'ath', 'AT4G14690' => 'ath', 'ATR0665G054' => 'atr', 'Atru.chr4.2344' => 'acertr', 'Atru.chr4.2346' => 'acertr', 'Atru.chr4.2347' => 'acertr', 'Atru.chr4.2348' => 'acertr', 'Atru.chr4.2355' => 'acertr', 'Atru.chr4.2356' => 'acertr', 'Atru.chr4.2358' => 'acertr', 'Atru.chr4.2359' => 'acertr', 'Atru.chr4.2360' => 'acertr', 'Atru.chr4.2361' => 'acertr', 'AUR62030476' => 'cqu', 'AUR62030478' => 'cqu', 'AUR62030819' => 'cqu', 'AUR62030820' => 'cqu', 'BcaB03g14648' => 'bca', 'BcaB04g20492' => 'bca', 'BcaB06g26399' => 'bca', 'BcaC01g03416' => 'bca', 'BcaC01g03419' => 'bca', 'BcaC01g03421' => 'bca', 'BcaC01g03424' => 'bca', 'BcaC05g28012' => 'bca', 'BcaC09g49212' => 'bca', 'BcaC09g50140' => 'bca', 'BcaNung00346' => 'bca', 'BolC1t02785H' => 'bol', 'BolC1t04095H' => 'bol', 'BolC3t17545H' => 'bol', 'BolC5t32769H' => 'bol', 'BraA01t02211Z' => 'bra', 'BraA01t03359Z' => 'bra', 'BraA03t13441Z' => 'bra', 'BraA05t21476Z' => 'bra', 'C01p28420' => 'bna', 'C01p41350' => 'bna', 'C03p52750' => 'bna', 'C03p52780' => 'bna', 'C05p40270' => 'bna', 'CAN.G1437.9' => 'can', 'CANSAT78G0035' => 'cansat', 'CANSAT78G1036' => 'cansat', 'CANSAT78G2272' => 'cansat', 'CANSAT78G2478' => 'cansat', 'CARHR098700' => 'chi', 'CARHR221120' => 'chi', 'CARHR221150' => 'chi', 'Carub.0003s2297' => 'cru', 'Carub.0007s2749' => 'cru', 'Carub.0007s2750' => 'cru', 'Carub.0007s2751' => 'cru', 'Ca_10849_v3' => 'car', 'Cc03_g04300' => 'ccan', 'CDE02G3648' => 'cde', 'CDE05G0060' => 'cde', 'CDE05G0692' => 'cde', 'CDE05G2285' => 'cde', 'CDE05G2884' => 'cde', 'CDE05G3072' => 'cde', 'Cfa008439' => 'cfa', 'Cfa008441' => 'cfa', 'Cfa008443' => 'cfa', 'Cfa008448' => 'cfa', 'Ciclev10005974m.g' => 'ccl', 'Ciclev10006006m.g' => 'ccl', 'Ciclev10006775m.g' => 'ccl', 'CiPaw.02G120400' => 'cil', 'CiPaw.02G120500' => 'cil', 'CiPaw.02G120600' => 'cil', 'ClCG05G004850' => 'cla', 'COL.COLO4_21566' => 'col', 'Cpa.g.sc44.124' => 'cpa', 'Cre07.g320400' => 'cre', 'Cre07.g320450' => 'cre', 'Cre08.g384650' => 'cre', 'Cre09.g393173' => 'cre', 'Cre09.g394325' => 'cre', 'Cre14.g626750' => 'cre', 'Cre16.g679250' => 'cre', 'CsaV3_3G012890' => 'csa', 'CSS0010865' => 'camsi', 'CSS0044338' => 'camsi', 'DCAR_002366' => 'dca', 'DCAR_030687' => 'dca', 'DCAR_030688' => 'dca', 'Dinv14047' => 'din', 'Dinv14048' => 'din', 'Duzib151G0105' => 'dzi', 'Duzib151G0114' => 'dzi', 'Duzib212G1029' => 'dzi', 'ECA232G3536' => 'eca', 'ECA240G0786' => 'eca', 'ECA240G1802' => 'eca', 'ECA240G3760' => 'eca', 'ECA240G3920' => 'eca', 'EL10Ac5g12536' => 'bvu', 'EL10Ac5g12537' => 'bvu', 'EL10Ac5g12538' => 'bvu', 'Eucgr.B01004' => 'egr', 'Eucgr.B01006' => 'egr', 'Eucgr.B01007' => 'egr', 'Eucgr.B01008' => 'egr', 'Eucgr.B01895' => 'egr', 'Eucgr.B01896' => 'egr', 'FAN04G1456' => 'fan', 'FAN08G1769' => 'fan', 'FAN08G2160' => 'fan', 'FAN13G2403' => 'fan', 'FAN13G3303' => 'fan', 'FAN15G2435' => 'fan', 'FAN17G0672' => 'fan', 'FAN17G2441' => 'fan', 'FAN18G1024' => 'fan', 'FAN22G1458' => 'fan', 'FAN24G0037' => 'fan', 'FAN24G0429' => 'fan', 'FAN24G2387' => 'fan', 'FAN27G2746' => 'fan', 'FvH4_2g20400' => 'fve', 'FvH4_2g20420' => 'fve', 'FvH4_2g20430' => 'fve', 'FvH4_4g01270' => 'fve', 'FvH4_4g01290' => 'fve', 'FvH4_4g01300' => 'fve', 'FvH4_4g01310' => 'fve', 'FvH4_4g01330' => 'fve', 'FvH4_5g09070' => 'fve', 'Glyma.10G243800' => 'gma', 'Glyma.20G150600' => 'gma', 'Gohir.A09G219200' => 'ghi', 'Gohir.A09G219300' => 'ghi', 'Gohir.D09G221400' => 'ghi', 'Gohir.D09G221500' => 'ghi', 'Gorai.006G242600' => 'gra', 'Gorai.006G242700' => 'gra', 'GSVIVG01018044001' => 'vvi', 'HanXRQChr03g0083821' => 'han', 'HanXRQChr03g0083841' => 'han', 'HanXRQChr03g0083881' => 'han', 'HanXRQChr03g0083901' => 'han', 'HanXRQChr03g0083921' => 'han', 'HanXRQChr03g0085331' => 'han', 'HanXRQChr03g0085361' => 'han', 'HanXRQChr03g0085411' => 'han', 'HanXRQChr03g0085421' => 'han', 'HanXRQChr03g0085431' => 'han', 'HanXRQChr08g0221991' => 'han', 'HanXRQChr11g0336061' => 'han', 'HanXRQChr11g0336411' => 'han', 'Haze_11234' => 'cav', 'Hma1.2p1_0549F.1_g177010' => 'hma', 'Hma1.2p1_0602F.1_g187630' => 'hma', 'Hund14876' => 'sun', 'Hund14879' => 'sun', 'Lalb_Chr06g0160741' => 'lal', 'Lalb_Chr21g0304781' => 'lal', 'Lj3A726G19' => 'lonja', 'Lj3A726T23' => 'lonja', 'Lj3A726T24' => 'lonja', 'Lj3A726T25' => 'lonja', 'Lj3A727T17' => 'lonja', 'Lj3C726T0' => 'lonja', 'Lj3C726T2' => 'lonja', 'Lj3P725T35' => 'lonja', 'Lj3P727T10' => 'lonja', 'Lj3P727T12' => 'lonja', 'Lj3P727T14' => 'lonja', 'Lj5g0023109' => 'lja', 'Lj6P646T44' => 'lonja', 'Lsat_1_v5_gn_6_75760' => 'lsa', 'Lsat_1_v5_gn_6_75800' => 'lsa', 'Lsat_1_v5_gn_6_75900' => 'lsa', 'Lsat_1_v5_gn_6_76240' => 'lsa', 'Lsat_1_v5_gn_6_76441' => 'lsa', 'Lsat_1_v5_gn_6_76700' => 'lsa', 'Lsat_1_v5_gn_6_76760' => 'lsa', 'Manes.15G033100' => 'mes', 'Mapoly0004s0074' => 'mpo', 'Mapoly0004s0075' => 'mpo', 'Mapoly0004s0163' => 'mpo', 'Mapoly0004s0164' => 'mpo', 'Mapoly0021s0018' => 'mpo', 'Mapoly0041s0136' => 'mpo', 'Mapoly0041s0137' => 'mpo', 'Mapoly0041s0138' => 'mpo', 'Mapoly0041s0139' => 'mpo', 'Mapoly0041s0141' => 'mpo', 'Mapoly0041s0142' => 'mpo', 'Mapoly0041s0143' => 'mpo', 'Mapoly0041s0144' => 'mpo', 'Mapoly0041s0145' => 'mpo', 'Mapoly0047s0106' => 'mpo', 'Mapoly0047s0108' => 'mpo', 'Mapoly0050s0051' => 'mpo', 'Mapoly0050s0052' => 'mpo', 'Mapoly0050s0053' => 'mpo', 'Mapoly0058s0013' => 'mpo', 'Mapoly0091s0078' => 'mpo', 'Mapoly0091s0079' => 'mpo', 'Mapoly0091s0080' => 'mpo', 'Mapoly0091s0081' => 'mpo', 'Mapoly0278s0004' => 'mpo', 'Mapoly0278s0005' => 'mpo', 'Mapoly0278s0006' => 'mpo', 'MBI11_g30648_MAGBIO' => 'mbi', 'MCO03G194' => 'mco', 'MCO03G590' => 'mco', 'MCO07G312' => 'mco', 'MCO10G318' => 'mco', 'MCO12G244' => 'mco', 'MCO13G148' => 'mco', 'MCO13G194' => 'mco', 'MCO16G238' => 'mco', 'MD06G1134100' => 'mdo', 'MD13G1200100' => 'mdo', 'MD13G1200300' => 'mdo', 'MD13G1200600' => 'mdo', 'MD14G1150400' => 'mdo', 'MD16G1200000' => 'mdo', 'Medtr1g102570' => 'mtr', 'Medtr1g102780' => 'mtr', 'Medtr1g102800' => 'mtr', 'Medtr1g102810' => 'mtr', 'Medtr1g102830' => 'mtr', 'MELO3C006499.2' => 'cme', 'Migut.G00385' => 'egut', 'MSTRG.4063' => 'ama', 'Nitab4.5_0000090g0260' => 'nta', 'Nitab4.5_0000977g0030' => 'nta', 'Nitab4.5_0002541g0040' => 'nta', 'Nitab4.5_0007068g0040' => 'nta', 'Nn005s41408' => 'nnu', 'Nn005s41410' => 'nnu', 'Oeu010310.1' => 'oeu', 'Oeu010311.1' => 'oeu', 'Oeu043472.1' => 'oeu', 'Os01g0246400' => 'osa', 'Os04g0267950' => 'osa', 'Os07g0178700' => 'osa', 'Os07g0178800' => 'osa', 'Peaxi162Scf00316g00046' => 'pax', 'Peaxi162Scf00316g00049' => 'pax', 'Peaxi162Scf00316g00059' => 'pax', 'Peaxi162Scf00316g00328' => 'pax', 'Peaxi162Scf00316g00329' => 'pax', 'Peaxi162Scf00316g00411' => 'pax', 'Peaxi162Scf00316g00521' => 'pax', 'Peaxi162Scf00492g00068' => 'pax', 'Peaxi162Scf35631g00002' => 'pax', 'PGR142G3720' => 'pgr', 'PGSC0003DMG400006442' => 'stu', 'Phvul.007G062000' => 'pvu', 'Potri.008G157750' => 'ptr', 'Potri.008G157900' => 'ptr', 'Potri.008G158000' => 'ptr', 'Potri.008G158200' => 'ptr', 'Pp3c11_7280' => 'ppa', 'Pp3c11_7980' => 'ppa', 'Pp3c12_19450' => 'ppa', 'Pp3c14_1480' => 'ppa', 'Pp3c14_1501' => 'ppa', 'Pp3c16_4900' => 'ppa', 'Pp3c16_5010' => 'ppa', 'Pp3c16_5060' => 'ppa', 'Pp3c19_18250' => 'ppa', 'Pp3c23_8530' => 'ppa', 'Pp3c23_8550' => 'ppa', 'Pp3c24_9670' => 'ppa', 'Pp3c2_21390' => 'ppa', 'Pp3c2_31380' => 'ppa', 'Pp3c3_16620' => 'ppa', 'Pp3c3_8090' => 'ppa', 'Pp3c3_8110' => 'ppa', 'Pp3c3_8130' => 'ppa', 'Pp3c3_8150' => 'ppa', 'Pp3c4_14320' => 'ppa', 'Pp3c6_2560' => 'ppa', 'Pp3c9_16700' => 'ppa', 'PRCOL_00000234' => 'pco', 'PRCOL_00000235' => 'pco', 'PRCOL_00000777' => 'pco', 'PRCOL_00002344' => 'pco', 'PRCOL_00002372' => 'pco', 'PRCOL_00006120' => 'pco', 'Prupe.1G021400' => 'ppe', 'Prupe.1G021500' => 'ppe', 'Prupe.1G021600' => 'ppe', 'Prupe.1G021700' => 'ppe', 'Prupe.1G021800' => 'ppe', 'Prupe.5G145100' => 'ppe', 'Psat6g204040' => 'psa', 'Psat6g204800' => 'psa', 'Psat6g204920' => 'psa', 'Psat6g204960' => 'psa', 'Psat6g205080' => 'psa', 'PSO017G0271' => 'pso', 'PSO017G1276' => 'pso', 'PSO017G1429' => 'pso', 'PSO017G1861' => 'pso', 'PSO017G2787' => 'pso', 'PSO017G4466' => 'pso', 'PSO017G5118' => 'pso', 'PSO017G5420' => 'pso', 'PSO063G3678' => 'pso', 'PSO210G0546' => 'pso', 'PSO317G0001' => 'pso', 'PSO357G0512' => 'pso', 'PSO478G2682' => 'pso', 'PSO647G0001' => 'pso', 'PSO675G0001' => 'pso', 'PSO675G2699' => 'pso', 'PSO675G2849' => 'pso', 'PSO675G4991' => 'pso', 'PSO689G0001' => 'pso', 'QL06p000916' => 'qlo', 'QL06p000921' => 'qlo', 'QL06p001398' => 'qlo', 'QL06p001407' => 'qlo', 'QL06p002031' => 'qlo', 'RcHm_v2.0_Chr4g0387791' => 'rch', 'RcHm_v2.0_Chr4g0387801' => 'rch', 'RcHm_v2.0_Chr6g0286501' => 'rch', 'RcHm_v2.0_Chr6g0286511' => 'rch', 'RcHm_v2.0_Chr6g0286521' => 'rch', 'RcHm_v2.0_Chr6g0286531' => 'rch', 'RcHm_v2.0_Chr7g0189141' => 'rch', 'Rhsim02G0028700' => 'rsi', 'Rhsim02G0028800' => 'rsi', 'Rhsim02G0028900' => 'rsi', 'Rhsim02G0029000' => 'rsi', 'Rhsim02G0029100' => 'rsi', 'Rhsim02G0029200' => 'rsi', 'Rhsim02G0029300' => 'rsi', 'Rhsim02G0029400' => 'rsi', 'Rhsim02G0029500' => 'rsi', 'Rhsim02G0029600' => 'rsi', 'RhsimUnG0024000' => 'rsi', 'RhsimUnG0024100' => 'rsi', 'RhsimUnG0024200' => 'rsi', 'RhsimUnG0024300' => 'rsi', 'RhsimUnG0024400' => 'rsi', 'RhsimUnG0024500' => 'rsi', 'RhsimUnG0024700' => 'rsi', 'RhsimUnG0024800' => 'rsi', 'RhsimUnG0024900' => 'rsi', 'RhsimUnG0025100' => 'rsi', 'Sabra08G0120200' => 'sbr', 'Sabra08G0120300' => 'sbr', 'Sabra08G0120500' => 'sbr', 'Sabra08G0120600' => 'sbr', 'Sabra10G0158900' => 'sbr', 'SalBow2G3492' => 'sbo', 'Sc13g0004760' => 'sci', 'Sc13g0004770' => 'sci', 'Sed0003417' => 'sed', 'Sed0019750' => 'sed', 'SEGI_03419' => 'sgi', 'SEGI_05907' => 'sgi', 'SEGI_10682' => 'sgi', 'SEGI_13528' => 'sgi', 'SEGI_16081' => 'sgi', 'SEGI_19370' => 'sgi', 'SEGI_21015' => 'sgi', 'SEGI_21944' => 'sgi', 'SEGI_32906' => 'sgi', 'SEGI_33093' => 'sgi', 'SEGI_36110' => 'sgi', 'SEGI_40397' => 'sgi', 'SGA_v2.0_scaffold191G40426' => 'sas', 'SGA_v2.0_scaffold353G49717' => 'sas', 'SGA_v2.0_scaffold50G18550' => 'sas', 'SMO119G0173' => 'smo', 'SMO172G0002' => 'smo', 'Solyc09g082690.3' => 'sly', 'Solyc09g082700.2' => 'sly', 'Sopen09g031550' => 'spe', 'Sopen09g031560' => 'spe', 'Sp3g20540' => 'spa', 'Sp7g07580' => 'spa', 'TAR134G0002' => 'tar', 'TAR236G0001' => 'tar', 'TAR365G0892' => 'tar', 'TAR636G0166' => 'tar', 'TAR636G0646' => 'tar', 'TAR636G0869' => 'tar', 'TAR636G1317' => 'tar', 'TAR636G1744' => 'tar', 'TAR636G3358' => 'tar', 'TAR636G3436' => 'tar', 'THA.LOC104803047' => 'tha', 'Thecc.04G238900' => 'tca', 'Thhalv10021557m.g' => 'esa', 'Thhalv10026318m.g' => 'esa', 'Thhalv10026335m.g' => 'esa', 'TPR.G17433' => 'tpr', 'TPR.G18915' => 'tpr', 'TPR.G26125' => 'tpr', 'TWI09G0677' => 'twi', 'TWI73G0287' => 'twi', 'unitig_748.g8326' => 'ugi', 'vmacro15370' => 'vma', 'vmacro15371' => 'vma', 'vmacro15372' => 'vma', 'vmacro15373' => 'vma', 'vmacro15374' => 'vma', 'VMungo0720G2826' => 'vmu', 'Zm00001eb116960' => 'zma', 'Zm00001eb301260' => 'zma', 'Zm00001eb301270' => 'zma' ), 'gf_id' => 'HOM05D001460', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001460' ), 'data_identifier' => 'HOM05D001460', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001460', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '433', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p22980' => 'bna', 'A01p32340' => 'bna', 'A03p42970' => 'bna', 'A05p25880' => 'bna', 'Aa31LG8G9320' => 'aar', 'Aa31LG8G9330' => 'aar', 'Aa31LG8G9340' => 'aar', 'Aa31sc221G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1034' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1528' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.829' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2222' => 'aag', 'Ah.12g058830' => 'amhyb', 'Ah.12g058840' => 'amhyb', 'AL3G37160' => 'aly', 'AL7G41310' => 'aly', 'Aqoxy5G00395' => 'aox', 'Aqoxy5G00396' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0C8NZA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5185HY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JZ1PRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MD3LS0' => 'arhy', 'AT3G22840' => 'ath', 'AT4G14690' => 'ath', 'ATR0665G054' => 'atr', 'Atru.chr4.2344' => 'acertr', 'Atru.chr4.2346' => 'acertr', 'Atru.chr4.2347' => 'acertr', 'Atru.chr4.2348' => 'acertr', 'Atru.chr4.2355' => 'acertr', 'Atru.chr4.2356' => 'acertr', 'Atru.chr4.2358' => 'acertr', 'Atru.chr4.2359' => 'acertr', 'Atru.chr4.2360' => 'acertr', 'Atru.chr4.2361' => 'acertr', 'AUR62030476' => 'cqu', 'AUR62030478' => 'cqu', 'AUR62030819' => 'cqu', 'AUR62030820' => 'cqu', 'BcaB03g14648' => 'bca', 'BcaB04g20492' => 'bca', 'BcaB06g26399' => 'bca', 'BcaC01g03416' => 'bca', 'BcaC01g03419' => 'bca', 'BcaC01g03421' => 'bca', 'BcaC01g03424' => 'bca', 'BcaC05g28012' => 'bca', 'BcaC09g49212' => 'bca', 'BcaC09g50140' => 'bca', 'BcaNung00346' => 'bca', 'BolC1t02785H' => 'bol', 'BolC1t04095H' => 'bol', 'BolC3t17545H' => 'bol', 'BolC5t32769H' => 'bol', 'BraA01t02211Z' => 'bra', 'BraA01t03359Z' => 'bra', 'BraA03t13441Z' => 'bra', 'BraA05t21476Z' => 'bra', 'C01p28420' => 'bna', 'C01p41350' => 'bna', 'C03p52750' => 'bna', 'C03p52780' => 'bna', 'C05p40270' => 'bna', 'CAN.G1437.9' => 'can', 'CANSAT78G0035' => 'cansat', 'CANSAT78G1036' => 'cansat', 'CANSAT78G2272' => 'cansat', 'CANSAT78G2478' => 'cansat', 'CARHR098700' => 'chi', 'CARHR221120' => 'chi', 'CARHR221150' => 'chi', 'Carub.0003s2297' => 'cru', 'Carub.0007s2749' => 'cru', 'Carub.0007s2750' => 'cru', 'Carub.0007s2751' => 'cru', 'Ca_10849_v3' => 'car', 'Cc03_g04300' => 'ccan', 'CDE02G3648' => 'cde', 'CDE05G0060' => 'cde', 'CDE05G0692' => 'cde', 'CDE05G2285' => 'cde', 'CDE05G2884' => 'cde', 'CDE05G3072' => 'cde', 'Cfa008439' => 'cfa', 'Cfa008441' => 'cfa', 'Cfa008443' => 'cfa', 'Cfa008448' => 'cfa', 'Ciclev10005974m.g' => 'ccl', 'Ciclev10006006m.g' => 'ccl', 'Ciclev10006775m.g' => 'ccl', 'CiPaw.02G120400' => 'cil', 'CiPaw.02G120500' => 'cil', 'CiPaw.02G120600' => 'cil', 'ClCG05G004850' => 'cla', 'COL.COLO4_21566' => 'col', 'Cpa.g.sc44.124' => 'cpa', 'Cre07.g320400' => 'cre', 'Cre07.g320450' => 'cre', 'Cre08.g384650' => 'cre', 'Cre09.g393173' => 'cre', 'Cre09.g394325' => 'cre', 'Cre14.g626750' => 'cre', 'Cre16.g679250' => 'cre', 'CsaV3_3G012890' => 'csa', 'CSS0010865' => 'camsi', 'CSS0044338' => 'camsi', 'DCAR_002366' => 'dca', 'DCAR_030687' => 'dca', 'DCAR_030688' => 'dca', 'Dinv14047' => 'din', 'Dinv14048' => 'din', 'Duzib151G0105' => 'dzi', 'Duzib151G0114' => 'dzi', 'Duzib212G1029' => 'dzi', 'ECA232G3536' => 'eca', 'ECA240G0786' => 'eca', 'ECA240G1802' => 'eca', 'ECA240G3760' => 'eca', 'ECA240G3920' => 'eca', 'EL10Ac5g12536' => 'bvu', 'EL10Ac5g12537' => 'bvu', 'EL10Ac5g12538' => 'bvu', 'Eucgr.B01004' => 'egr', 'Eucgr.B01006' => 'egr', 'Eucgr.B01007' => 'egr', 'Eucgr.B01008' => 'egr', 'Eucgr.B01895' => 'egr', 'Eucgr.B01896' => 'egr', 'FAN04G1456' => 'fan', 'FAN08G1769' => 'fan', 'FAN08G2160' => 'fan', 'FAN13G2403' => 'fan', 'FAN13G3303' => 'fan', 'FAN15G2435' => 'fan', 'FAN17G0672' => 'fan', 'FAN17G2441' => 'fan', 'FAN18G1024' => 'fan', 'FAN22G1458' => 'fan', 'FAN24G0037' => 'fan', 'FAN24G0429' => 'fan', 'FAN24G2387' => 'fan', 'FAN27G2746' => 'fan', 'FvH4_2g20400' => 'fve', 'FvH4_2g20420' => 'fve', 'FvH4_2g20430' => 'fve', 'FvH4_4g01270' => 'fve', 'FvH4_4g01290' => 'fve', 'FvH4_4g01300' => 'fve', 'FvH4_4g01310' => 'fve', 'FvH4_4g01330' => 'fve', 'FvH4_5g09070' => 'fve', 'Glyma.10G243800' => 'gma', 'Glyma.20G150600' => 'gma', 'Gohir.A09G219200' => 'ghi', 'Gohir.A09G219300' => 'ghi', 'Gohir.D09G221400' => 'ghi', 'Gohir.D09G221500' => 'ghi', 'Gorai.006G242600' => 'gra', 'Gorai.006G242700' => 'gra', 'GSVIVG01018044001' => 'vvi', 'HanXRQChr03g0083821' => 'han', 'HanXRQChr03g0083841' => 'han', 'HanXRQChr03g0083881' => 'han', 'HanXRQChr03g0083901' => 'han', 'HanXRQChr03g0083921' => 'han', 'HanXRQChr03g0085331' => 'han', 'HanXRQChr03g0085361' => 'han', 'HanXRQChr03g0085411' => 'han', 'HanXRQChr03g0085421' => 'han', 'HanXRQChr03g0085431' => 'han', 'HanXRQChr08g0221991' => 'han', 'HanXRQChr11g0336061' => 'han', 'HanXRQChr11g0336411' => 'han', 'Haze_11234' => 'cav', 'Hma1.2p1_0549F.1_g177010' => 'hma', 'Hma1.2p1_0602F.1_g187630' => 'hma', 'Hund14876' => 'sun', 'Hund14879' => 'sun', 'Lalb_Chr06g0160741' => 'lal', 'Lalb_Chr21g0304781' => 'lal', 'Lj3A726G19' => 'lonja', 'Lj3A726T23' => 'lonja', 'Lj3A726T24' => 'lonja', 'Lj3A726T25' => 'lonja', 'Lj3A727T17' => 'lonja', 'Lj3C726T0' => 'lonja', 'Lj3C726T2' => 'lonja', 'Lj3P725T35' => 'lonja', 'Lj3P727T10' => 'lonja', 'Lj3P727T12' => 'lonja', 'Lj3P727T14' => 'lonja', 'Lj5g0023109' => 'lja', 'Lj6P646T44' => 'lonja', 'Lsat_1_v5_gn_6_75760' => 'lsa', 'Lsat_1_v5_gn_6_75800' => 'lsa', 'Lsat_1_v5_gn_6_75900' => 'lsa', 'Lsat_1_v5_gn_6_76240' => 'lsa', 'Lsat_1_v5_gn_6_76441' => 'lsa', 'Lsat_1_v5_gn_6_76700' => 'lsa', 'Lsat_1_v5_gn_6_76760' => 'lsa', 'Manes.15G033100' => 'mes', 'Mapoly0004s0074' => 'mpo', 'Mapoly0004s0075' => 'mpo', 'Mapoly0004s0163' => 'mpo', 'Mapoly0004s0164' => 'mpo', 'Mapoly0021s0018' => 'mpo', 'Mapoly0041s0136' => 'mpo', 'Mapoly0041s0137' => 'mpo', 'Mapoly0041s0138' => 'mpo', 'Mapoly0041s0139' => 'mpo', 'Mapoly0041s0141' => 'mpo', 'Mapoly0041s0142' => 'mpo', 'Mapoly0041s0143' => 'mpo', 'Mapoly0041s0144' => 'mpo', 'Mapoly0041s0145' => 'mpo', 'Mapoly0047s0106' => 'mpo', 'Mapoly0047s0108' => 'mpo', 'Mapoly0050s0051' => 'mpo', 'Mapoly0050s0052' => 'mpo', 'Mapoly0050s0053' => 'mpo', 'Mapoly0058s0013' => 'mpo', 'Mapoly0091s0078' => 'mpo', 'Mapoly0091s0079' => 'mpo', 'Mapoly0091s0080' => 'mpo', 'Mapoly0091s0081' => 'mpo', 'Mapoly0278s0004' => 'mpo', 'Mapoly0278s0005' => 'mpo', 'Mapoly0278s0006' => 'mpo', 'MBI11_g30648_MAGBIO' => 'mbi', 'MCO03G194' => 'mco', 'MCO03G590' => 'mco', 'MCO07G312' => 'mco', 'MCO10G318' => 'mco', 'MCO12G244' => 'mco', 'MCO13G148' => 'mco', 'MCO13G194' => 'mco', 'MCO16G238' => 'mco', 'MD06G1134100' => 'mdo', 'MD13G1200100' => 'mdo', 'MD13G1200300' => 'mdo', 'MD13G1200600' => 'mdo', 'MD14G1150400' => 'mdo', 'MD16G1200000' => 'mdo', 'Medtr1g102570' => 'mtr', 'Medtr1g102780' => 'mtr', 'Medtr1g102800' => 'mtr', 'Medtr1g102810' => 'mtr', 'Medtr1g102830' => 'mtr', 'MELO3C006499.2' => 'cme', 'Migut.G00385' => 'egut', 'MSTRG.4063' => 'ama', 'Nitab4.5_0000090g0260' => 'nta', 'Nitab4.5_0000977g0030' => 'nta', 'Nitab4.5_0002541g0040' => 'nta', 'Nitab4.5_0007068g0040' => 'nta', 'Nn005s41408' => 'nnu', 'Nn005s41410' => 'nnu', 'Oeu010310.1' => 'oeu', 'Oeu010311.1' => 'oeu', 'Oeu043472.1' => 'oeu', 'Os01g0246400' => 'osa', 'Os04g0267950' => 'osa', 'Os07g0178700' => 'osa', 'Os07g0178800' => 'osa', 'Peaxi162Scf00316g00046' => 'pax', 'Peaxi162Scf00316g00049' => 'pax', 'Peaxi162Scf00316g00059' => 'pax', 'Peaxi162Scf00316g00328' => 'pax', 'Peaxi162Scf00316g00329' => 'pax', 'Peaxi162Scf00316g00411' => 'pax', 'Peaxi162Scf00316g00521' => 'pax', 'Peaxi162Scf00492g00068' => 'pax', 'Peaxi162Scf35631g00002' => 'pax', 'PGR142G3720' => 'pgr', 'PGSC0003DMG400006442' => 'stu', 'Phvul.007G062000' => 'pvu', 'Potri.008G157750' => 'ptr', 'Potri.008G157900' => 'ptr', 'Potri.008G158000' => 'ptr', 'Potri.008G158200' => 'ptr', 'Pp3c11_7280' => 'ppa', 'Pp3c11_7980' => 'ppa', 'Pp3c12_19450' => 'ppa', 'Pp3c14_1480' => 'ppa', 'Pp3c14_1501' => 'ppa', 'Pp3c16_4900' => 'ppa', 'Pp3c16_5010' => 'ppa', 'Pp3c16_5060' => 'ppa', 'Pp3c19_18250' => 'ppa', 'Pp3c23_8530' => 'ppa', 'Pp3c23_8550' => 'ppa', 'Pp3c24_9670' => 'ppa', 'Pp3c2_21390' => 'ppa', 'Pp3c2_31380' => 'ppa', 'Pp3c3_16620' => 'ppa', 'Pp3c3_8090' => 'ppa', 'Pp3c3_8110' => 'ppa', 'Pp3c3_8130' => 'ppa', 'Pp3c3_8150' => 'ppa', 'Pp3c4_14320' => 'ppa', 'Pp3c6_2560' => 'ppa', 'Pp3c9_16700' => 'ppa', 'PRCOL_00000234' => 'pco', 'PRCOL_00000235' => 'pco', 'PRCOL_00000777' => 'pco', 'PRCOL_00002344' => 'pco', 'PRCOL_00002372' => 'pco', 'PRCOL_00006120' => 'pco', 'Prupe.1G021400' => 'ppe', 'Prupe.1G021500' => 'ppe', 'Prupe.1G021600' => 'ppe', 'Prupe.1G021700' => 'ppe', 'Prupe.1G021800' => 'ppe', 'Prupe.5G145100' => 'ppe', 'Psat6g204040' => 'psa', 'Psat6g204800' => 'psa', 'Psat6g204920' => 'psa', 'Psat6g204960' => 'psa', 'Psat6g205080' => 'psa', 'PSO017G0271' => 'pso', 'PSO017G1276' => 'pso', 'PSO017G1429' => 'pso', 'PSO017G1861' => 'pso', 'PSO017G2787' => 'pso', 'PSO017G4466' => 'pso', 'PSO017G5118' => 'pso', 'PSO017G5420' => 'pso', 'PSO063G3678' => 'pso', 'PSO210G0546' => 'pso', 'PSO317G0001' => 'pso', 'PSO357G0512' => 'pso', 'PSO478G2682' => 'pso', 'PSO647G0001' => 'pso', 'PSO675G0001' => 'pso', 'PSO675G2699' => 'pso', 'PSO675G2849' => 'pso', 'PSO675G4991' => 'pso', 'PSO689G0001' => 'pso', 'QL06p000916' => 'qlo', 'QL06p000921' => 'qlo', 'QL06p001398' => 'qlo', 'QL06p001407' => 'qlo', 'QL06p002031' => 'qlo', 'RcHm_v2.0_Chr4g0387791' => 'rch', 'RcHm_v2.0_Chr4g0387801' => 'rch', 'RcHm_v2.0_Chr6g0286501' => 'rch', 'RcHm_v2.0_Chr6g0286511' => 'rch', 'RcHm_v2.0_Chr6g0286521' => 'rch', 'RcHm_v2.0_Chr6g0286531' => 'rch', 'RcHm_v2.0_Chr7g0189141' => 'rch', 'Rhsim02G0028700' => 'rsi', 'Rhsim02G0028800' => 'rsi', 'Rhsim02G0028900' => 'rsi', 'Rhsim02G0029000' => 'rsi', 'Rhsim02G0029100' => 'rsi', 'Rhsim02G0029200' => 'rsi', 'Rhsim02G0029300' => 'rsi', 'Rhsim02G0029400' => 'rsi', 'Rhsim02G0029500' => 'rsi', 'Rhsim02G0029600' => 'rsi', 'RhsimUnG0024000' => 'rsi', 'RhsimUnG0024100' => 'rsi', 'RhsimUnG0024200' => 'rsi', 'RhsimUnG0024300' => 'rsi', 'RhsimUnG0024400' => 'rsi', 'RhsimUnG0024500' => 'rsi', 'RhsimUnG0024700' => 'rsi', 'RhsimUnG0024800' => 'rsi', 'RhsimUnG0024900' => 'rsi', 'RhsimUnG0025100' => 'rsi', 'Sabra08G0120200' => 'sbr', 'Sabra08G0120300' => 'sbr', 'Sabra08G0120500' => 'sbr', 'Sabra08G0120600' => 'sbr', 'Sabra10G0158900' => 'sbr', 'SalBow2G3492' => 'sbo', 'Sc13g0004760' => 'sci', 'Sc13g0004770' => 'sci', 'Sed0003417' => 'sed', 'Sed0019750' => 'sed', 'SEGI_03419' => 'sgi', 'SEGI_05907' => 'sgi', 'SEGI_10682' => 'sgi', 'SEGI_13528' => 'sgi', 'SEGI_16081' => 'sgi', 'SEGI_19370' => 'sgi', 'SEGI_21015' => 'sgi', 'SEGI_21944' => 'sgi', 'SEGI_32906' => 'sgi', 'SEGI_33093' => 'sgi', 'SEGI_36110' => 'sgi', 'SEGI_40397' => 'sgi', 'SGA_v2.0_scaffold191G40426' => 'sas', 'SGA_v2.0_scaffold353G49717' => 'sas', 'SGA_v2.0_scaffold50G18550' => 'sas', 'SMO119G0173' => 'smo', 'SMO172G0002' => 'smo', 'Solyc09g082690.3' => 'sly', 'Solyc09g082700.2' => 'sly', 'Sopen09g031550' => 'spe', 'Sopen09g031560' => 'spe', 'Sp3g20540' => 'spa', 'Sp7g07580' => 'spa', 'TAR134G0002' => 'tar', 'TAR236G0001' => 'tar', 'TAR365G0892' => 'tar', 'TAR636G0166' => 'tar', 'TAR636G0646' => 'tar', 'TAR636G0869' => 'tar', 'TAR636G1317' => 'tar', 'TAR636G1744' => 'tar', 'TAR636G3358' => 'tar', 'TAR636G3436' => 'tar', 'THA.LOC104803047' => 'tha', 'Thecc.04G238900' => 'tca', 'Thhalv10021557m.g' => 'esa', 'Thhalv10026318m.g' => 'esa', 'Thhalv10026335m.g' => 'esa', 'TPR.G17433' => 'tpr', 'TPR.G18915' => 'tpr', 'TPR.G26125' => 'tpr', 'TWI09G0677' => 'twi', 'TWI73G0287' => 'twi', 'unitig_748.g8326' => 'ugi', 'vmacro15370' => 'vma', 'vmacro15371' => 'vma', 'vmacro15372' => 'vma', 'vmacro15373' => 'vma', 'vmacro15374' => 'vma', 'VMungo0720G2826' => 'vmu', 'Zm00001eb116960' => 'zma', 'Zm00001eb301260' => 'zma', 'Zm00001eb301270' => 'zma' ) $gf_id = 'HOM05D001460' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001460' ) $data_identifier = 'HOM05D001460' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 4, 'aag' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 2, 'aox' => (int) 2, 'arhy' => (int) 4, 'ath' => (int) 2, 'atr' => (int) 1, 'acertr' => (int) 10, 'cqu' => (int) 4, 'bca' => (int) 11, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 1, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 1, 'ccan' => (int) 1, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 1, 'col' => (int) 1, 'cpa' => (int) 1, 'cre' => (int) 7, 'csa' => (int) 1, 'camsi' => (int) 2, 'dca' => (int) 3, 'din' => (int) 2, 'dzi' => (int) 3, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 14, 'fve' => (int) 9, 'gma' => (int) 2, 'ghi' => (int) 4, 'gra' => (int) 2, 'vvi' => (int) 1, 'han' => (int) 13, 'cav' => (int) 1, 'hma' => (int) 2, 'sun' => (int) 2, 'lal' => (int) 2, 'lonja' => (int) 12, 'lja' => (int) 1, 'lsa' => (int) 7, 'mes' => (int) 1, 'mpo' => (int) 27, 'mbi' => (int) 1, 'mco' => (int) 8, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 1, 'egut' => (int) 1, 'ama' => (int) 1, 'nta' => (int) 4, 'nnu' => (int) 2, 'oeu' => (int) 3, 'osa' => (int) 4, 'pax' => (int) 9, 'pgr' => (int) 1, 'stu' => (int) 1, 'pvu' => (int) 1, 'ptr' => (int) 4, 'ppa' => (int) 22, 'pco' => (int) 6, 'ppe' => (int) 6, 'psa' => (int) 5, 'pso' => (int) 19, 'qlo' => (int) 5, 'rch' => (int) 7, 'rsi' => (int) 20, 'sbr' => (int) 5, 'sbo' => (int) 1, 'sci' => (int) 2, 'sed' => (int) 2, 'sgi' => (int) 12, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 2, 'tar' => (int) 10, 'tha' => (int) 1, 'tca' => (int) 1, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 2, 'ugi' => (int) 1, 'vma' => (int) 5, 'vmu' => (int) 1, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb301270' $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' => 'HOM05D001460', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '433', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p22980' => 'bna', 'A01p32340' => 'bna', 'A03p42970' => 'bna', 'A05p25880' => 'bna', 'Aa31LG8G9320' => 'aar', 'Aa31LG8G9330' => 'aar', 'Aa31LG8G9340' => 'aar', 'Aa31sc221G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1034' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1528' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.829' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2222' => 'aag', 'Ah.12g058830' => 'amhyb', 'Ah.12g058840' => 'amhyb', 'AL3G37160' => 'aly', 'AL7G41310' => 'aly', 'Aqoxy5G00395' => 'aox', 'Aqoxy5G00396' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0C8NZA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5185HY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JZ1PRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MD3LS0' => 'arhy', 'AT3G22840' => 'ath', 'AT4G14690' => 'ath', 'ATR0665G054' => 'atr', 'Atru.chr4.2344' => 'acertr', 'Atru.chr4.2346' => 'acertr', 'Atru.chr4.2347' => 'acertr', 'Atru.chr4.2348' => 'acertr', 'Atru.chr4.2355' => 'acertr', 'Atru.chr4.2356' => 'acertr', 'Atru.chr4.2358' => 'acertr', 'Atru.chr4.2359' => 'acertr', 'Atru.chr4.2360' => 'acertr', 'Atru.chr4.2361' => 'acertr', 'AUR62030476' => 'cqu', 'AUR62030478' => 'cqu', 'AUR62030819' => 'cqu', 'AUR62030820' => 'cqu', 'BcaB03g14648' => 'bca', 'BcaB04g20492' => 'bca', 'BcaB06g26399' => 'bca', 'BcaC01g03416' => 'bca', 'BcaC01g03419' => 'bca', 'BcaC01g03421' => 'bca', 'BcaC01g03424' => 'bca', 'BcaC05g28012' => 'bca', 'BcaC09g49212' => 'bca', 'BcaC09g50140' => 'bca', 'BcaNung00346' => 'bca', 'BolC1t02785H' => 'bol', 'BolC1t04095H' => 'bol', 'BolC3t17545H' => 'bol', 'BolC5t32769H' => 'bol', 'BraA01t02211Z' => 'bra', 'BraA01t03359Z' => 'bra', 'BraA03t13441Z' => 'bra', 'BraA05t21476Z' => 'bra', 'C01p28420' => 'bna', 'C01p41350' => 'bna', 'C03p52750' => 'bna', 'C03p52780' => 'bna', 'C05p40270' => 'bna', 'CAN.G1437.9' => 'can', 'CANSAT78G0035' => 'cansat', 'CANSAT78G1036' => 'cansat', 'CANSAT78G2272' => 'cansat', 'CANSAT78G2478' => 'cansat', 'CARHR098700' => 'chi', 'CARHR221120' => 'chi', 'CARHR221150' => 'chi', 'Carub.0003s2297' => 'cru', 'Carub.0007s2749' => 'cru', 'Carub.0007s2750' => 'cru', 'Carub.0007s2751' => 'cru', 'Ca_10849_v3' => 'car', 'Cc03_g04300' => 'ccan', 'CDE02G3648' => 'cde', 'CDE05G0060' => 'cde', 'CDE05G0692' => 'cde', 'CDE05G2285' => 'cde', 'CDE05G2884' => 'cde', 'CDE05G3072' => 'cde', 'Cfa008439' => 'cfa', 'Cfa008441' => 'cfa', 'Cfa008443' => 'cfa', 'Cfa008448' => 'cfa', 'Ciclev10005974m.g' => 'ccl', 'Ciclev10006006m.g' => 'ccl', 'Ciclev10006775m.g' => 'ccl', 'CiPaw.02G120400' => 'cil', 'CiPaw.02G120500' => 'cil', 'CiPaw.02G120600' => 'cil', 'ClCG05G004850' => 'cla', 'COL.COLO4_21566' => 'col', 'Cpa.g.sc44.124' => 'cpa', 'Cre07.g320400' => 'cre', 'Cre07.g320450' => 'cre', 'Cre08.g384650' => 'cre', 'Cre09.g393173' => 'cre', 'Cre09.g394325' => 'cre', 'Cre14.g626750' => 'cre', 'Cre16.g679250' => 'cre', 'CsaV3_3G012890' => 'csa', 'CSS0010865' => 'camsi', 'CSS0044338' => 'camsi', 'DCAR_002366' => 'dca', 'DCAR_030687' => 'dca', 'DCAR_030688' => 'dca', 'Dinv14047' => 'din', 'Dinv14048' => 'din', 'Duzib151G0105' => 'dzi', 'Duzib151G0114' => 'dzi', 'Duzib212G1029' => 'dzi', 'ECA232G3536' => 'eca', 'ECA240G0786' => 'eca', 'ECA240G1802' => 'eca', 'ECA240G3760' => 'eca', 'ECA240G3920' => 'eca', 'EL10Ac5g12536' => 'bvu', 'EL10Ac5g12537' => 'bvu', 'EL10Ac5g12538' => 'bvu', 'Eucgr.B01004' => 'egr', 'Eucgr.B01006' => 'egr', 'Eucgr.B01007' => 'egr', 'Eucgr.B01008' => 'egr', 'Eucgr.B01895' => 'egr', 'Eucgr.B01896' => 'egr', 'FAN04G1456' => 'fan', 'FAN08G1769' => 'fan', 'FAN08G2160' => 'fan', 'FAN13G2403' => 'fan', 'FAN13G3303' => 'fan', 'FAN15G2435' => 'fan', 'FAN17G0672' => 'fan', 'FAN17G2441' => 'fan', 'FAN18G1024' => 'fan', 'FAN22G1458' => 'fan', 'FAN24G0037' => 'fan', 'FAN24G0429' => 'fan', 'FAN24G2387' => 'fan', 'FAN27G2746' => 'fan', 'FvH4_2g20400' => 'fve', 'FvH4_2g20420' => 'fve', 'FvH4_2g20430' => 'fve', 'FvH4_4g01270' => 'fve', 'FvH4_4g01290' => 'fve', 'FvH4_4g01300' => 'fve', 'FvH4_4g01310' => 'fve', 'FvH4_4g01330' => 'fve', 'FvH4_5g09070' => 'fve', 'Glyma.10G243800' => 'gma', 'Glyma.20G150600' => 'gma', 'Gohir.A09G219200' => 'ghi', 'Gohir.A09G219300' => 'ghi', 'Gohir.D09G221400' => 'ghi', 'Gohir.D09G221500' => 'ghi', 'Gorai.006G242600' => 'gra', 'Gorai.006G242700' => 'gra', 'GSVIVG01018044001' => 'vvi', 'HanXRQChr03g0083821' => 'han', 'HanXRQChr03g0083841' => 'han', 'HanXRQChr03g0083881' => 'han', 'HanXRQChr03g0083901' => 'han', 'HanXRQChr03g0083921' => 'han', 'HanXRQChr03g0085331' => 'han', 'HanXRQChr03g0085361' => 'han', 'HanXRQChr03g0085411' => 'han', 'HanXRQChr03g0085421' => 'han', 'HanXRQChr03g0085431' => 'han', 'HanXRQChr08g0221991' => 'han', 'HanXRQChr11g0336061' => 'han', 'HanXRQChr11g0336411' => 'han', 'Haze_11234' => 'cav', 'Hma1.2p1_0549F.1_g177010' => 'hma', 'Hma1.2p1_0602F.1_g187630' => 'hma', 'Hund14876' => 'sun', 'Hund14879' => 'sun', 'Lalb_Chr06g0160741' => 'lal', 'Lalb_Chr21g0304781' => 'lal', 'Lj3A726G19' => 'lonja', 'Lj3A726T23' => 'lonja', 'Lj3A726T24' => 'lonja', 'Lj3A726T25' => 'lonja', 'Lj3A727T17' => 'lonja', 'Lj3C726T0' => 'lonja', 'Lj3C726T2' => 'lonja', 'Lj3P725T35' => 'lonja', 'Lj3P727T10' => 'lonja', 'Lj3P727T12' => 'lonja', 'Lj3P727T14' => 'lonja', 'Lj5g0023109' => 'lja', 'Lj6P646T44' => 'lonja', 'Lsat_1_v5_gn_6_75760' => 'lsa', 'Lsat_1_v5_gn_6_75800' => 'lsa', 'Lsat_1_v5_gn_6_75900' => 'lsa', 'Lsat_1_v5_gn_6_76240' => 'lsa', 'Lsat_1_v5_gn_6_76441' => 'lsa', 'Lsat_1_v5_gn_6_76700' => 'lsa', 'Lsat_1_v5_gn_6_76760' => 'lsa', 'Manes.15G033100' => 'mes', 'Mapoly0004s0074' => 'mpo', 'Mapoly0004s0075' => 'mpo', 'Mapoly0004s0163' => 'mpo', 'Mapoly0004s0164' => 'mpo', 'Mapoly0021s0018' => 'mpo', 'Mapoly0041s0136' => 'mpo', 'Mapoly0041s0137' => 'mpo', 'Mapoly0041s0138' => 'mpo', 'Mapoly0041s0139' => 'mpo', 'Mapoly0041s0141' => 'mpo', 'Mapoly0041s0142' => 'mpo', 'Mapoly0041s0143' => 'mpo', 'Mapoly0041s0144' => 'mpo', 'Mapoly0041s0145' => 'mpo', 'Mapoly0047s0106' => 'mpo', 'Mapoly0047s0108' => 'mpo', 'Mapoly0050s0051' => 'mpo', 'Mapoly0050s0052' => 'mpo', 'Mapoly0050s0053' => 'mpo', 'Mapoly0058s0013' => 'mpo', 'Mapoly0091s0078' => 'mpo', 'Mapoly0091s0079' => 'mpo', 'Mapoly0091s0080' => 'mpo', 'Mapoly0091s0081' => 'mpo', 'Mapoly0278s0004' => 'mpo', 'Mapoly0278s0005' => 'mpo', 'Mapoly0278s0006' => 'mpo', 'MBI11_g30648_MAGBIO' => 'mbi', 'MCO03G194' => 'mco', 'MCO03G590' => 'mco', 'MCO07G312' => 'mco', 'MCO10G318' => 'mco', 'MCO12G244' => 'mco', 'MCO13G148' => 'mco', 'MCO13G194' => 'mco', 'MCO16G238' => 'mco', 'MD06G1134100' => 'mdo', 'MD13G1200100' => 'mdo', 'MD13G1200300' => 'mdo', 'MD13G1200600' => 'mdo', 'MD14G1150400' => 'mdo', 'MD16G1200000' => 'mdo', 'Medtr1g102570' => 'mtr', 'Medtr1g102780' => 'mtr', 'Medtr1g102800' => 'mtr', 'Medtr1g102810' => 'mtr', 'Medtr1g102830' => 'mtr', 'MELO3C006499.2' => 'cme', 'Migut.G00385' => 'egut', 'MSTRG.4063' => 'ama', 'Nitab4.5_0000090g0260' => 'nta', 'Nitab4.5_0000977g0030' => 'nta', 'Nitab4.5_0002541g0040' => 'nta', 'Nitab4.5_0007068g0040' => 'nta', 'Nn005s41408' => 'nnu', 'Nn005s41410' => 'nnu', 'Oeu010310.1' => 'oeu', 'Oeu010311.1' => 'oeu', 'Oeu043472.1' => 'oeu', 'Os01g0246400' => 'osa', 'Os04g0267950' => 'osa', 'Os07g0178700' => 'osa', 'Os07g0178800' => 'osa', 'Peaxi162Scf00316g00046' => 'pax', 'Peaxi162Scf00316g00049' => 'pax', 'Peaxi162Scf00316g00059' => 'pax', 'Peaxi162Scf00316g00328' => 'pax', 'Peaxi162Scf00316g00329' => 'pax', 'Peaxi162Scf00316g00411' => 'pax', 'Peaxi162Scf00316g00521' => 'pax', 'Peaxi162Scf00492g00068' => 'pax', 'Peaxi162Scf35631g00002' => 'pax', 'PGR142G3720' => 'pgr', 'PGSC0003DMG400006442' => 'stu', 'Phvul.007G062000' => 'pvu', 'Potri.008G157750' => 'ptr', 'Potri.008G157900' => 'ptr', 'Potri.008G158000' => 'ptr', 'Potri.008G158200' => 'ptr', 'Pp3c11_7280' => 'ppa', 'Pp3c11_7980' => 'ppa', 'Pp3c12_19450' => 'ppa', 'Pp3c14_1480' => 'ppa', 'Pp3c14_1501' => 'ppa', 'Pp3c16_4900' => 'ppa', 'Pp3c16_5010' => 'ppa', 'Pp3c16_5060' => 'ppa', 'Pp3c19_18250' => 'ppa', 'Pp3c23_8530' => 'ppa', 'Pp3c23_8550' => 'ppa', 'Pp3c24_9670' => 'ppa', 'Pp3c2_21390' => 'ppa', 'Pp3c2_31380' => 'ppa', 'Pp3c3_16620' => 'ppa', 'Pp3c3_8090' => 'ppa', 'Pp3c3_8110' => 'ppa', 'Pp3c3_8130' => 'ppa', 'Pp3c3_8150' => 'ppa', 'Pp3c4_14320' => 'ppa', 'Pp3c6_2560' => 'ppa', 'Pp3c9_16700' => 'ppa', 'PRCOL_00000234' => 'pco', 'PRCOL_00000235' => 'pco', 'PRCOL_00000777' => 'pco', 'PRCOL_00002344' => 'pco', 'PRCOL_00002372' => 'pco', 'PRCOL_00006120' => 'pco', 'Prupe.1G021400' => 'ppe', 'Prupe.1G021500' => 'ppe', 'Prupe.1G021600' => 'ppe', 'Prupe.1G021700' => 'ppe', 'Prupe.1G021800' => 'ppe', 'Prupe.5G145100' => 'ppe', 'Psat6g204040' => 'psa', 'Psat6g204800' => 'psa', 'Psat6g204920' => 'psa', 'Psat6g204960' => 'psa', 'Psat6g205080' => 'psa', 'PSO017G0271' => 'pso', 'PSO017G1276' => 'pso', 'PSO017G1429' => 'pso', 'PSO017G1861' => 'pso', 'PSO017G2787' => 'pso', 'PSO017G4466' => 'pso', 'PSO017G5118' => 'pso', 'PSO017G5420' => 'pso', 'PSO063G3678' => 'pso', 'PSO210G0546' => 'pso', 'PSO317G0001' => 'pso', 'PSO357G0512' => 'pso', 'PSO478G2682' => 'pso', 'PSO647G0001' => 'pso', 'PSO675G0001' => 'pso', 'PSO675G2699' => 'pso', 'PSO675G2849' => 'pso', 'PSO675G4991' => 'pso', 'PSO689G0001' => 'pso', 'QL06p000916' => 'qlo', 'QL06p000921' => 'qlo', 'QL06p001398' => 'qlo', 'QL06p001407' => 'qlo', 'QL06p002031' => 'qlo', 'RcHm_v2.0_Chr4g0387791' => 'rch', 'RcHm_v2.0_Chr4g0387801' => 'rch', 'RcHm_v2.0_Chr6g0286501' => 'rch', 'RcHm_v2.0_Chr6g0286511' => 'rch', 'RcHm_v2.0_Chr6g0286521' => 'rch', 'RcHm_v2.0_Chr6g0286531' => 'rch', 'RcHm_v2.0_Chr7g0189141' => 'rch', 'Rhsim02G0028700' => 'rsi', 'Rhsim02G0028800' => 'rsi', 'Rhsim02G0028900' => 'rsi', 'Rhsim02G0029000' => 'rsi', 'Rhsim02G0029100' => 'rsi', 'Rhsim02G0029200' => 'rsi', 'Rhsim02G0029300' => 'rsi', 'Rhsim02G0029400' => 'rsi', 'Rhsim02G0029500' => 'rsi', 'Rhsim02G0029600' => 'rsi', 'RhsimUnG0024000' => 'rsi', 'RhsimUnG0024100' => 'rsi', 'RhsimUnG0024200' => 'rsi', 'RhsimUnG0024300' => 'rsi', 'RhsimUnG0024400' => 'rsi', 'RhsimUnG0024500' => 'rsi', 'RhsimUnG0024700' => 'rsi', 'RhsimUnG0024800' => 'rsi', 'RhsimUnG0024900' => 'rsi', 'RhsimUnG0025100' => 'rsi', 'Sabra08G0120200' => 'sbr', 'Sabra08G0120300' => 'sbr', 'Sabra08G0120500' => 'sbr', 'Sabra08G0120600' => 'sbr', 'Sabra10G0158900' => 'sbr', 'SalBow2G3492' => 'sbo', 'Sc13g0004760' => 'sci', 'Sc13g0004770' => 'sci', 'Sed0003417' => 'sed', 'Sed0019750' => 'sed', 'SEGI_03419' => 'sgi', 'SEGI_05907' => 'sgi', 'SEGI_10682' => 'sgi', 'SEGI_13528' => 'sgi', 'SEGI_16081' => 'sgi', 'SEGI_19370' => 'sgi', 'SEGI_21015' => 'sgi', 'SEGI_21944' => 'sgi', 'SEGI_32906' => 'sgi', 'SEGI_33093' => 'sgi', 'SEGI_36110' => 'sgi', 'SEGI_40397' => 'sgi', 'SGA_v2.0_scaffold191G40426' => 'sas', 'SGA_v2.0_scaffold353G49717' => 'sas', 'SGA_v2.0_scaffold50G18550' => 'sas', 'SMO119G0173' => 'smo', 'SMO172G0002' => 'smo', 'Solyc09g082690.3' => 'sly', 'Solyc09g082700.2' => 'sly', 'Sopen09g031550' => 'spe', 'Sopen09g031560' => 'spe', 'Sp3g20540' => 'spa', 'Sp7g07580' => 'spa', 'TAR134G0002' => 'tar', 'TAR236G0001' => 'tar', 'TAR365G0892' => 'tar', 'TAR636G0166' => 'tar', 'TAR636G0646' => 'tar', 'TAR636G0869' => 'tar', 'TAR636G1317' => 'tar', 'TAR636G1744' => 'tar', 'TAR636G3358' => 'tar', 'TAR636G3436' => 'tar', 'THA.LOC104803047' => 'tha', 'Thecc.04G238900' => 'tca', 'Thhalv10021557m.g' => 'esa', 'Thhalv10026318m.g' => 'esa', 'Thhalv10026335m.g' => 'esa', 'TPR.G17433' => 'tpr', 'TPR.G18915' => 'tpr', 'TPR.G26125' => 'tpr', 'TWI09G0677' => 'twi', 'TWI73G0287' => 'twi', 'unitig_748.g8326' => 'ugi', 'vmacro15370' => 'vma', 'vmacro15371' => 'vma', 'vmacro15372' => 'vma', 'vmacro15373' => 'vma', 'vmacro15374' => 'vma', 'VMungo0720G2826' => 'vmu', 'Zm00001eb116960' => 'zma', 'Zm00001eb301260' => 'zma', 'Zm00001eb301270' => 'zma' ), 'gf_id' => 'HOM05D001460', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001460' ), 'data_identifier' => 'HOM05D001460', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001460', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '433', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p22980' => 'bna', 'A01p32340' => 'bna', 'A03p42970' => 'bna', 'A05p25880' => 'bna', 'Aa31LG8G9320' => 'aar', 'Aa31LG8G9330' => 'aar', 'Aa31LG8G9340' => 'aar', 'Aa31sc221G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1034' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1528' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.829' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2222' => 'aag', 'Ah.12g058830' => 'amhyb', 'Ah.12g058840' => 'amhyb', 'AL3G37160' => 'aly', 'AL7G41310' => 'aly', 'Aqoxy5G00395' => 'aox', 'Aqoxy5G00396' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0C8NZA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5185HY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JZ1PRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MD3LS0' => 'arhy', 'AT3G22840' => 'ath', 'AT4G14690' => 'ath', 'ATR0665G054' => 'atr', 'Atru.chr4.2344' => 'acertr', 'Atru.chr4.2346' => 'acertr', 'Atru.chr4.2347' => 'acertr', 'Atru.chr4.2348' => 'acertr', 'Atru.chr4.2355' => 'acertr', 'Atru.chr4.2356' => 'acertr', 'Atru.chr4.2358' => 'acertr', 'Atru.chr4.2359' => 'acertr', 'Atru.chr4.2360' => 'acertr', 'Atru.chr4.2361' => 'acertr', 'AUR62030476' => 'cqu', 'AUR62030478' => 'cqu', 'AUR62030819' => 'cqu', 'AUR62030820' => 'cqu', 'BcaB03g14648' => 'bca', 'BcaB04g20492' => 'bca', 'BcaB06g26399' => 'bca', 'BcaC01g03416' => 'bca', 'BcaC01g03419' => 'bca', 'BcaC01g03421' => 'bca', 'BcaC01g03424' => 'bca', 'BcaC05g28012' => 'bca', 'BcaC09g49212' => 'bca', 'BcaC09g50140' => 'bca', 'BcaNung00346' => 'bca', 'BolC1t02785H' => 'bol', 'BolC1t04095H' => 'bol', 'BolC3t17545H' => 'bol', 'BolC5t32769H' => 'bol', 'BraA01t02211Z' => 'bra', 'BraA01t03359Z' => 'bra', 'BraA03t13441Z' => 'bra', 'BraA05t21476Z' => 'bra', 'C01p28420' => 'bna', 'C01p41350' => 'bna', 'C03p52750' => 'bna', 'C03p52780' => 'bna', 'C05p40270' => 'bna', 'CAN.G1437.9' => 'can', 'CANSAT78G0035' => 'cansat', 'CANSAT78G1036' => 'cansat', 'CANSAT78G2272' => 'cansat', 'CANSAT78G2478' => 'cansat', 'CARHR098700' => 'chi', 'CARHR221120' => 'chi', 'CARHR221150' => 'chi', 'Carub.0003s2297' => 'cru', 'Carub.0007s2749' => 'cru', 'Carub.0007s2750' => 'cru', 'Carub.0007s2751' => 'cru', 'Ca_10849_v3' => 'car', 'Cc03_g04300' => 'ccan', 'CDE02G3648' => 'cde', 'CDE05G0060' => 'cde', 'CDE05G0692' => 'cde', 'CDE05G2285' => 'cde', 'CDE05G2884' => 'cde', 'CDE05G3072' => 'cde', 'Cfa008439' => 'cfa', 'Cfa008441' => 'cfa', 'Cfa008443' => 'cfa', 'Cfa008448' => 'cfa', 'Ciclev10005974m.g' => 'ccl', 'Ciclev10006006m.g' => 'ccl', 'Ciclev10006775m.g' => 'ccl', 'CiPaw.02G120400' => 'cil', 'CiPaw.02G120500' => 'cil', 'CiPaw.02G120600' => 'cil', 'ClCG05G004850' => 'cla', 'COL.COLO4_21566' => 'col', 'Cpa.g.sc44.124' => 'cpa', 'Cre07.g320400' => 'cre', 'Cre07.g320450' => 'cre', 'Cre08.g384650' => 'cre', 'Cre09.g393173' => 'cre', 'Cre09.g394325' => 'cre', 'Cre14.g626750' => 'cre', 'Cre16.g679250' => 'cre', 'CsaV3_3G012890' => 'csa', 'CSS0010865' => 'camsi', 'CSS0044338' => 'camsi', 'DCAR_002366' => 'dca', 'DCAR_030687' => 'dca', 'DCAR_030688' => 'dca', 'Dinv14047' => 'din', 'Dinv14048' => 'din', 'Duzib151G0105' => 'dzi', 'Duzib151G0114' => 'dzi', 'Duzib212G1029' => 'dzi', 'ECA232G3536' => 'eca', 'ECA240G0786' => 'eca', 'ECA240G1802' => 'eca', 'ECA240G3760' => 'eca', 'ECA240G3920' => 'eca', 'EL10Ac5g12536' => 'bvu', 'EL10Ac5g12537' => 'bvu', 'EL10Ac5g12538' => 'bvu', 'Eucgr.B01004' => 'egr', 'Eucgr.B01006' => 'egr', 'Eucgr.B01007' => 'egr', 'Eucgr.B01008' => 'egr', 'Eucgr.B01895' => 'egr', 'Eucgr.B01896' => 'egr', 'FAN04G1456' => 'fan', 'FAN08G1769' => 'fan', 'FAN08G2160' => 'fan', 'FAN13G2403' => 'fan', 'FAN13G3303' => 'fan', 'FAN15G2435' => 'fan', 'FAN17G0672' => 'fan', 'FAN17G2441' => 'fan', 'FAN18G1024' => 'fan', 'FAN22G1458' => 'fan', 'FAN24G0037' => 'fan', 'FAN24G0429' => 'fan', 'FAN24G2387' => 'fan', 'FAN27G2746' => 'fan', 'FvH4_2g20400' => 'fve', 'FvH4_2g20420' => 'fve', 'FvH4_2g20430' => 'fve', 'FvH4_4g01270' => 'fve', 'FvH4_4g01290' => 'fve', 'FvH4_4g01300' => 'fve', 'FvH4_4g01310' => 'fve', 'FvH4_4g01330' => 'fve', 'FvH4_5g09070' => 'fve', 'Glyma.10G243800' => 'gma', 'Glyma.20G150600' => 'gma', 'Gohir.A09G219200' => 'ghi', 'Gohir.A09G219300' => 'ghi', 'Gohir.D09G221400' => 'ghi', 'Gohir.D09G221500' => 'ghi', 'Gorai.006G242600' => 'gra', 'Gorai.006G242700' => 'gra', 'GSVIVG01018044001' => 'vvi', 'HanXRQChr03g0083821' => 'han', 'HanXRQChr03g0083841' => 'han', 'HanXRQChr03g0083881' => 'han', 'HanXRQChr03g0083901' => 'han', 'HanXRQChr03g0083921' => 'han', 'HanXRQChr03g0085331' => 'han', 'HanXRQChr03g0085361' => 'han', 'HanXRQChr03g0085411' => 'han', 'HanXRQChr03g0085421' => 'han', 'HanXRQChr03g0085431' => 'han', 'HanXRQChr08g0221991' => 'han', 'HanXRQChr11g0336061' => 'han', 'HanXRQChr11g0336411' => 'han', 'Haze_11234' => 'cav', 'Hma1.2p1_0549F.1_g177010' => 'hma', 'Hma1.2p1_0602F.1_g187630' => 'hma', 'Hund14876' => 'sun', 'Hund14879' => 'sun', 'Lalb_Chr06g0160741' => 'lal', 'Lalb_Chr21g0304781' => 'lal', 'Lj3A726G19' => 'lonja', 'Lj3A726T23' => 'lonja', 'Lj3A726T24' => 'lonja', 'Lj3A726T25' => 'lonja', 'Lj3A727T17' => 'lonja', 'Lj3C726T0' => 'lonja', 'Lj3C726T2' => 'lonja', 'Lj3P725T35' => 'lonja', 'Lj3P727T10' => 'lonja', 'Lj3P727T12' => 'lonja', 'Lj3P727T14' => 'lonja', 'Lj5g0023109' => 'lja', 'Lj6P646T44' => 'lonja', 'Lsat_1_v5_gn_6_75760' => 'lsa', 'Lsat_1_v5_gn_6_75800' => 'lsa', 'Lsat_1_v5_gn_6_75900' => 'lsa', 'Lsat_1_v5_gn_6_76240' => 'lsa', 'Lsat_1_v5_gn_6_76441' => 'lsa', 'Lsat_1_v5_gn_6_76700' => 'lsa', 'Lsat_1_v5_gn_6_76760' => 'lsa', 'Manes.15G033100' => 'mes', 'Mapoly0004s0074' => 'mpo', 'Mapoly0004s0075' => 'mpo', 'Mapoly0004s0163' => 'mpo', 'Mapoly0004s0164' => 'mpo', 'Mapoly0021s0018' => 'mpo', 'Mapoly0041s0136' => 'mpo', 'Mapoly0041s0137' => 'mpo', 'Mapoly0041s0138' => 'mpo', 'Mapoly0041s0139' => 'mpo', 'Mapoly0041s0141' => 'mpo', 'Mapoly0041s0142' => 'mpo', 'Mapoly0041s0143' => 'mpo', 'Mapoly0041s0144' => 'mpo', 'Mapoly0041s0145' => 'mpo', 'Mapoly0047s0106' => 'mpo', 'Mapoly0047s0108' => 'mpo', 'Mapoly0050s0051' => 'mpo', 'Mapoly0050s0052' => 'mpo', 'Mapoly0050s0053' => 'mpo', 'Mapoly0058s0013' => 'mpo', 'Mapoly0091s0078' => 'mpo', 'Mapoly0091s0079' => 'mpo', 'Mapoly0091s0080' => 'mpo', 'Mapoly0091s0081' => 'mpo', 'Mapoly0278s0004' => 'mpo', 'Mapoly0278s0005' => 'mpo', 'Mapoly0278s0006' => 'mpo', 'MBI11_g30648_MAGBIO' => 'mbi', 'MCO03G194' => 'mco', 'MCO03G590' => 'mco', 'MCO07G312' => 'mco', 'MCO10G318' => 'mco', 'MCO12G244' => 'mco', 'MCO13G148' => 'mco', 'MCO13G194' => 'mco', 'MCO16G238' => 'mco', 'MD06G1134100' => 'mdo', 'MD13G1200100' => 'mdo', 'MD13G1200300' => 'mdo', 'MD13G1200600' => 'mdo', 'MD14G1150400' => 'mdo', 'MD16G1200000' => 'mdo', 'Medtr1g102570' => 'mtr', 'Medtr1g102780' => 'mtr', 'Medtr1g102800' => 'mtr', 'Medtr1g102810' => 'mtr', 'Medtr1g102830' => 'mtr', 'MELO3C006499.2' => 'cme', 'Migut.G00385' => 'egut', 'MSTRG.4063' => 'ama', 'Nitab4.5_0000090g0260' => 'nta', 'Nitab4.5_0000977g0030' => 'nta', 'Nitab4.5_0002541g0040' => 'nta', 'Nitab4.5_0007068g0040' => 'nta', 'Nn005s41408' => 'nnu', 'Nn005s41410' => 'nnu', 'Oeu010310.1' => 'oeu', 'Oeu010311.1' => 'oeu', 'Oeu043472.1' => 'oeu', 'Os01g0246400' => 'osa', 'Os04g0267950' => 'osa', 'Os07g0178700' => 'osa', 'Os07g0178800' => 'osa', 'Peaxi162Scf00316g00046' => 'pax', 'Peaxi162Scf00316g00049' => 'pax', 'Peaxi162Scf00316g00059' => 'pax', 'Peaxi162Scf00316g00328' => 'pax', 'Peaxi162Scf00316g00329' => 'pax', 'Peaxi162Scf00316g00411' => 'pax', 'Peaxi162Scf00316g00521' => 'pax', 'Peaxi162Scf00492g00068' => 'pax', 'Peaxi162Scf35631g00002' => 'pax', 'PGR142G3720' => 'pgr', 'PGSC0003DMG400006442' => 'stu', 'Phvul.007G062000' => 'pvu', 'Potri.008G157750' => 'ptr', 'Potri.008G157900' => 'ptr', 'Potri.008G158000' => 'ptr', 'Potri.008G158200' => 'ptr', 'Pp3c11_7280' => 'ppa', 'Pp3c11_7980' => 'ppa', 'Pp3c12_19450' => 'ppa', 'Pp3c14_1480' => 'ppa', 'Pp3c14_1501' => 'ppa', 'Pp3c16_4900' => 'ppa', 'Pp3c16_5010' => 'ppa', 'Pp3c16_5060' => 'ppa', 'Pp3c19_18250' => 'ppa', 'Pp3c23_8530' => 'ppa', 'Pp3c23_8550' => 'ppa', 'Pp3c24_9670' => 'ppa', 'Pp3c2_21390' => 'ppa', 'Pp3c2_31380' => 'ppa', 'Pp3c3_16620' => 'ppa', 'Pp3c3_8090' => 'ppa', 'Pp3c3_8110' => 'ppa', 'Pp3c3_8130' => 'ppa', 'Pp3c3_8150' => 'ppa', 'Pp3c4_14320' => 'ppa', 'Pp3c6_2560' => 'ppa', 'Pp3c9_16700' => 'ppa', 'PRCOL_00000234' => 'pco', 'PRCOL_00000235' => 'pco', 'PRCOL_00000777' => 'pco', 'PRCOL_00002344' => 'pco', 'PRCOL_00002372' => 'pco', 'PRCOL_00006120' => 'pco', 'Prupe.1G021400' => 'ppe', 'Prupe.1G021500' => 'ppe', 'Prupe.1G021600' => 'ppe', 'Prupe.1G021700' => 'ppe', 'Prupe.1G021800' => 'ppe', 'Prupe.5G145100' => 'ppe', 'Psat6g204040' => 'psa', 'Psat6g204800' => 'psa', 'Psat6g204920' => 'psa', 'Psat6g204960' => 'psa', 'Psat6g205080' => 'psa', 'PSO017G0271' => 'pso', 'PSO017G1276' => 'pso', 'PSO017G1429' => 'pso', 'PSO017G1861' => 'pso', 'PSO017G2787' => 'pso', 'PSO017G4466' => 'pso', 'PSO017G5118' => 'pso', 'PSO017G5420' => 'pso', 'PSO063G3678' => 'pso', 'PSO210G0546' => 'pso', 'PSO317G0001' => 'pso', 'PSO357G0512' => 'pso', 'PSO478G2682' => 'pso', 'PSO647G0001' => 'pso', 'PSO675G0001' => 'pso', 'PSO675G2699' => 'pso', 'PSO675G2849' => 'pso', 'PSO675G4991' => 'pso', 'PSO689G0001' => 'pso', 'QL06p000916' => 'qlo', 'QL06p000921' => 'qlo', 'QL06p001398' => 'qlo', 'QL06p001407' => 'qlo', 'QL06p002031' => 'qlo', 'RcHm_v2.0_Chr4g0387791' => 'rch', 'RcHm_v2.0_Chr4g0387801' => 'rch', 'RcHm_v2.0_Chr6g0286501' => 'rch', 'RcHm_v2.0_Chr6g0286511' => 'rch', 'RcHm_v2.0_Chr6g0286521' => 'rch', 'RcHm_v2.0_Chr6g0286531' => 'rch', 'RcHm_v2.0_Chr7g0189141' => 'rch', 'Rhsim02G0028700' => 'rsi', 'Rhsim02G0028800' => 'rsi', 'Rhsim02G0028900' => 'rsi', 'Rhsim02G0029000' => 'rsi', 'Rhsim02G0029100' => 'rsi', 'Rhsim02G0029200' => 'rsi', 'Rhsim02G0029300' => 'rsi', 'Rhsim02G0029400' => 'rsi', 'Rhsim02G0029500' => 'rsi', 'Rhsim02G0029600' => 'rsi', 'RhsimUnG0024000' => 'rsi', 'RhsimUnG0024100' => 'rsi', 'RhsimUnG0024200' => 'rsi', 'RhsimUnG0024300' => 'rsi', 'RhsimUnG0024400' => 'rsi', 'RhsimUnG0024500' => 'rsi', 'RhsimUnG0024700' => 'rsi', 'RhsimUnG0024800' => 'rsi', 'RhsimUnG0024900' => 'rsi', 'RhsimUnG0025100' => 'rsi', 'Sabra08G0120200' => 'sbr', 'Sabra08G0120300' => 'sbr', 'Sabra08G0120500' => 'sbr', 'Sabra08G0120600' => 'sbr', 'Sabra10G0158900' => 'sbr', 'SalBow2G3492' => 'sbo', 'Sc13g0004760' => 'sci', 'Sc13g0004770' => 'sci', 'Sed0003417' => 'sed', 'Sed0019750' => 'sed', 'SEGI_03419' => 'sgi', 'SEGI_05907' => 'sgi', 'SEGI_10682' => 'sgi', 'SEGI_13528' => 'sgi', 'SEGI_16081' => 'sgi', 'SEGI_19370' => 'sgi', 'SEGI_21015' => 'sgi', 'SEGI_21944' => 'sgi', 'SEGI_32906' => 'sgi', 'SEGI_33093' => 'sgi', 'SEGI_36110' => 'sgi', 'SEGI_40397' => 'sgi', 'SGA_v2.0_scaffold191G40426' => 'sas', 'SGA_v2.0_scaffold353G49717' => 'sas', 'SGA_v2.0_scaffold50G18550' => 'sas', 'SMO119G0173' => 'smo', 'SMO172G0002' => 'smo', 'Solyc09g082690.3' => 'sly', 'Solyc09g082700.2' => 'sly', 'Sopen09g031550' => 'spe', 'Sopen09g031560' => 'spe', 'Sp3g20540' => 'spa', 'Sp7g07580' => 'spa', 'TAR134G0002' => 'tar', 'TAR236G0001' => 'tar', 'TAR365G0892' => 'tar', 'TAR636G0166' => 'tar', 'TAR636G0646' => 'tar', 'TAR636G0869' => 'tar', 'TAR636G1317' => 'tar', 'TAR636G1744' => 'tar', 'TAR636G3358' => 'tar', 'TAR636G3436' => 'tar', 'THA.LOC104803047' => 'tha', 'Thecc.04G238900' => 'tca', 'Thhalv10021557m.g' => 'esa', 'Thhalv10026318m.g' => 'esa', 'Thhalv10026335m.g' => 'esa', 'TPR.G17433' => 'tpr', 'TPR.G18915' => 'tpr', 'TPR.G26125' => 'tpr', 'TWI09G0677' => 'twi', 'TWI73G0287' => 'twi', 'unitig_748.g8326' => 'ugi', 'vmacro15370' => 'vma', 'vmacro15371' => 'vma', 'vmacro15372' => 'vma', 'vmacro15373' => 'vma', 'vmacro15374' => 'vma', 'VMungo0720G2826' => 'vmu', 'Zm00001eb116960' => 'zma', 'Zm00001eb301260' => 'zma', 'Zm00001eb301270' => 'zma' ) $gf_id = 'HOM05D001460' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001460' ) $data_identifier = 'HOM05D001460' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 4, 'aag' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 2, 'aox' => (int) 2, 'arhy' => (int) 4, 'ath' => (int) 2, 'atr' => (int) 1, 'acertr' => (int) 10, 'cqu' => (int) 4, 'bca' => (int) 11, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 1, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 1, 'ccan' => (int) 1, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 1, 'col' => (int) 1, 'cpa' => (int) 1, 'cre' => (int) 7, 'csa' => (int) 1, 'camsi' => (int) 2, 'dca' => (int) 3, 'din' => (int) 2, 'dzi' => (int) 3, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 14, 'fve' => (int) 9, 'gma' => (int) 2, 'ghi' => (int) 4, 'gra' => (int) 2, 'vvi' => (int) 1, 'han' => (int) 13, 'cav' => (int) 1, 'hma' => (int) 2, 'sun' => (int) 2, 'lal' => (int) 2, 'lonja' => (int) 12, 'lja' => (int) 1, 'lsa' => (int) 7, 'mes' => (int) 1, 'mpo' => (int) 27, 'mbi' => (int) 1, 'mco' => (int) 8, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 1, 'egut' => (int) 1, 'ama' => (int) 1, 'nta' => (int) 4, 'nnu' => (int) 2, 'oeu' => (int) 3, 'osa' => (int) 4, 'pax' => (int) 9, 'pgr' => (int) 1, 'stu' => (int) 1, 'pvu' => (int) 1, 'ptr' => (int) 4, 'ppa' => (int) 22, 'pco' => (int) 6, 'ppe' => (int) 6, 'psa' => (int) 5, 'pso' => (int) 19, 'qlo' => (int) 5, 'rch' => (int) 7, 'rsi' => (int) 20, 'sbr' => (int) 5, 'sbo' => (int) 1, 'sci' => (int) 2, 'sed' => (int) 2, 'sgi' => (int) 12, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 2, 'tar' => (int) 10, 'tha' => (int) 1, 'tca' => (int) 1, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 2, 'ugi' => (int) 1, 'vma' => (int) 5, 'vmu' => (int) 1, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb301270' $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' => 'HOM05D001460', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '433', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p22980' => 'bna', 'A01p32340' => 'bna', 'A03p42970' => 'bna', 'A05p25880' => 'bna', 'Aa31LG8G9320' => 'aar', 'Aa31LG8G9330' => 'aar', 'Aa31LG8G9340' => 'aar', 'Aa31sc221G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1034' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1528' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.829' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2222' => 'aag', 'Ah.12g058830' => 'amhyb', 'Ah.12g058840' => 'amhyb', 'AL3G37160' => 'aly', 'AL7G41310' => 'aly', 'Aqoxy5G00395' => 'aox', 'Aqoxy5G00396' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0C8NZA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5185HY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JZ1PRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MD3LS0' => 'arhy', 'AT3G22840' => 'ath', 'AT4G14690' => 'ath', 'ATR0665G054' => 'atr', 'Atru.chr4.2344' => 'acertr', 'Atru.chr4.2346' => 'acertr', 'Atru.chr4.2347' => 'acertr', 'Atru.chr4.2348' => 'acertr', 'Atru.chr4.2355' => 'acertr', 'Atru.chr4.2356' => 'acertr', 'Atru.chr4.2358' => 'acertr', 'Atru.chr4.2359' => 'acertr', 'Atru.chr4.2360' => 'acertr', 'Atru.chr4.2361' => 'acertr', 'AUR62030476' => 'cqu', 'AUR62030478' => 'cqu', 'AUR62030819' => 'cqu', 'AUR62030820' => 'cqu', 'BcaB03g14648' => 'bca', 'BcaB04g20492' => 'bca', 'BcaB06g26399' => 'bca', 'BcaC01g03416' => 'bca', 'BcaC01g03419' => 'bca', 'BcaC01g03421' => 'bca', 'BcaC01g03424' => 'bca', 'BcaC05g28012' => 'bca', 'BcaC09g49212' => 'bca', 'BcaC09g50140' => 'bca', 'BcaNung00346' => 'bca', 'BolC1t02785H' => 'bol', 'BolC1t04095H' => 'bol', 'BolC3t17545H' => 'bol', 'BolC5t32769H' => 'bol', 'BraA01t02211Z' => 'bra', 'BraA01t03359Z' => 'bra', 'BraA03t13441Z' => 'bra', 'BraA05t21476Z' => 'bra', 'C01p28420' => 'bna', 'C01p41350' => 'bna', 'C03p52750' => 'bna', 'C03p52780' => 'bna', 'C05p40270' => 'bna', 'CAN.G1437.9' => 'can', 'CANSAT78G0035' => 'cansat', 'CANSAT78G1036' => 'cansat', 'CANSAT78G2272' => 'cansat', 'CANSAT78G2478' => 'cansat', 'CARHR098700' => 'chi', 'CARHR221120' => 'chi', 'CARHR221150' => 'chi', 'Carub.0003s2297' => 'cru', 'Carub.0007s2749' => 'cru', 'Carub.0007s2750' => 'cru', 'Carub.0007s2751' => 'cru', 'Ca_10849_v3' => 'car', 'Cc03_g04300' => 'ccan', 'CDE02G3648' => 'cde', 'CDE05G0060' => 'cde', 'CDE05G0692' => 'cde', 'CDE05G2285' => 'cde', 'CDE05G2884' => 'cde', 'CDE05G3072' => 'cde', 'Cfa008439' => 'cfa', 'Cfa008441' => 'cfa', 'Cfa008443' => 'cfa', 'Cfa008448' => 'cfa', 'Ciclev10005974m.g' => 'ccl', 'Ciclev10006006m.g' => 'ccl', 'Ciclev10006775m.g' => 'ccl', 'CiPaw.02G120400' => 'cil', 'CiPaw.02G120500' => 'cil', 'CiPaw.02G120600' => 'cil', 'ClCG05G004850' => 'cla', 'COL.COLO4_21566' => 'col', 'Cpa.g.sc44.124' => 'cpa', 'Cre07.g320400' => 'cre', 'Cre07.g320450' => 'cre', 'Cre08.g384650' => 'cre', 'Cre09.g393173' => 'cre', 'Cre09.g394325' => 'cre', 'Cre14.g626750' => 'cre', 'Cre16.g679250' => 'cre', 'CsaV3_3G012890' => 'csa', 'CSS0010865' => 'camsi', 'CSS0044338' => 'camsi', 'DCAR_002366' => 'dca', 'DCAR_030687' => 'dca', 'DCAR_030688' => 'dca', 'Dinv14047' => 'din', 'Dinv14048' => 'din', 'Duzib151G0105' => 'dzi', 'Duzib151G0114' => 'dzi', 'Duzib212G1029' => 'dzi', 'ECA232G3536' => 'eca', 'ECA240G0786' => 'eca', 'ECA240G1802' => 'eca', 'ECA240G3760' => 'eca', 'ECA240G3920' => 'eca', 'EL10Ac5g12536' => 'bvu', 'EL10Ac5g12537' => 'bvu', 'EL10Ac5g12538' => 'bvu', 'Eucgr.B01004' => 'egr', 'Eucgr.B01006' => 'egr', 'Eucgr.B01007' => 'egr', 'Eucgr.B01008' => 'egr', 'Eucgr.B01895' => 'egr', 'Eucgr.B01896' => 'egr', 'FAN04G1456' => 'fan', 'FAN08G1769' => 'fan', 'FAN08G2160' => 'fan', 'FAN13G2403' => 'fan', 'FAN13G3303' => 'fan', 'FAN15G2435' => 'fan', 'FAN17G0672' => 'fan', 'FAN17G2441' => 'fan', 'FAN18G1024' => 'fan', 'FAN22G1458' => 'fan', 'FAN24G0037' => 'fan', 'FAN24G0429' => 'fan', 'FAN24G2387' => 'fan', 'FAN27G2746' => 'fan', 'FvH4_2g20400' => 'fve', 'FvH4_2g20420' => 'fve', 'FvH4_2g20430' => 'fve', 'FvH4_4g01270' => 'fve', 'FvH4_4g01290' => 'fve', 'FvH4_4g01300' => 'fve', 'FvH4_4g01310' => 'fve', 'FvH4_4g01330' => 'fve', 'FvH4_5g09070' => 'fve', 'Glyma.10G243800' => 'gma', 'Glyma.20G150600' => 'gma', 'Gohir.A09G219200' => 'ghi', 'Gohir.A09G219300' => 'ghi', 'Gohir.D09G221400' => 'ghi', 'Gohir.D09G221500' => 'ghi', 'Gorai.006G242600' => 'gra', 'Gorai.006G242700' => 'gra', 'GSVIVG01018044001' => 'vvi', 'HanXRQChr03g0083821' => 'han', 'HanXRQChr03g0083841' => 'han', 'HanXRQChr03g0083881' => 'han', 'HanXRQChr03g0083901' => 'han', 'HanXRQChr03g0083921' => 'han', 'HanXRQChr03g0085331' => 'han', 'HanXRQChr03g0085361' => 'han', 'HanXRQChr03g0085411' => 'han', 'HanXRQChr03g0085421' => 'han', 'HanXRQChr03g0085431' => 'han', 'HanXRQChr08g0221991' => 'han', 'HanXRQChr11g0336061' => 'han', 'HanXRQChr11g0336411' => 'han', 'Haze_11234' => 'cav', 'Hma1.2p1_0549F.1_g177010' => 'hma', 'Hma1.2p1_0602F.1_g187630' => 'hma', 'Hund14876' => 'sun', 'Hund14879' => 'sun', 'Lalb_Chr06g0160741' => 'lal', 'Lalb_Chr21g0304781' => 'lal', 'Lj3A726G19' => 'lonja', 'Lj3A726T23' => 'lonja', 'Lj3A726T24' => 'lonja', 'Lj3A726T25' => 'lonja', 'Lj3A727T17' => 'lonja', 'Lj3C726T0' => 'lonja', 'Lj3C726T2' => 'lonja', 'Lj3P725T35' => 'lonja', 'Lj3P727T10' => 'lonja', 'Lj3P727T12' => 'lonja', 'Lj3P727T14' => 'lonja', 'Lj5g0023109' => 'lja', 'Lj6P646T44' => 'lonja', 'Lsat_1_v5_gn_6_75760' => 'lsa', 'Lsat_1_v5_gn_6_75800' => 'lsa', 'Lsat_1_v5_gn_6_75900' => 'lsa', 'Lsat_1_v5_gn_6_76240' => 'lsa', 'Lsat_1_v5_gn_6_76441' => 'lsa', 'Lsat_1_v5_gn_6_76700' => 'lsa', 'Lsat_1_v5_gn_6_76760' => 'lsa', 'Manes.15G033100' => 'mes', 'Mapoly0004s0074' => 'mpo', 'Mapoly0004s0075' => 'mpo', 'Mapoly0004s0163' => 'mpo', 'Mapoly0004s0164' => 'mpo', 'Mapoly0021s0018' => 'mpo', 'Mapoly0041s0136' => 'mpo', 'Mapoly0041s0137' => 'mpo', 'Mapoly0041s0138' => 'mpo', 'Mapoly0041s0139' => 'mpo', 'Mapoly0041s0141' => 'mpo', 'Mapoly0041s0142' => 'mpo', 'Mapoly0041s0143' => 'mpo', 'Mapoly0041s0144' => 'mpo', 'Mapoly0041s0145' => 'mpo', 'Mapoly0047s0106' => 'mpo', 'Mapoly0047s0108' => 'mpo', 'Mapoly0050s0051' => 'mpo', 'Mapoly0050s0052' => 'mpo', 'Mapoly0050s0053' => 'mpo', 'Mapoly0058s0013' => 'mpo', 'Mapoly0091s0078' => 'mpo', 'Mapoly0091s0079' => 'mpo', 'Mapoly0091s0080' => 'mpo', 'Mapoly0091s0081' => 'mpo', 'Mapoly0278s0004' => 'mpo', 'Mapoly0278s0005' => 'mpo', 'Mapoly0278s0006' => 'mpo', 'MBI11_g30648_MAGBIO' => 'mbi', 'MCO03G194' => 'mco', 'MCO03G590' => 'mco', 'MCO07G312' => 'mco', 'MCO10G318' => 'mco', 'MCO12G244' => 'mco', 'MCO13G148' => 'mco', 'MCO13G194' => 'mco', 'MCO16G238' => 'mco', 'MD06G1134100' => 'mdo', 'MD13G1200100' => 'mdo', 'MD13G1200300' => 'mdo', 'MD13G1200600' => 'mdo', 'MD14G1150400' => 'mdo', 'MD16G1200000' => 'mdo', 'Medtr1g102570' => 'mtr', 'Medtr1g102780' => 'mtr', 'Medtr1g102800' => 'mtr', 'Medtr1g102810' => 'mtr', 'Medtr1g102830' => 'mtr', 'MELO3C006499.2' => 'cme', 'Migut.G00385' => 'egut', 'MSTRG.4063' => 'ama', 'Nitab4.5_0000090g0260' => 'nta', 'Nitab4.5_0000977g0030' => 'nta', 'Nitab4.5_0002541g0040' => 'nta', 'Nitab4.5_0007068g0040' => 'nta', 'Nn005s41408' => 'nnu', 'Nn005s41410' => 'nnu', 'Oeu010310.1' => 'oeu', 'Oeu010311.1' => 'oeu', 'Oeu043472.1' => 'oeu', 'Os01g0246400' => 'osa', 'Os04g0267950' => 'osa', 'Os07g0178700' => 'osa', 'Os07g0178800' => 'osa', 'Peaxi162Scf00316g00046' => 'pax', 'Peaxi162Scf00316g00049' => 'pax', 'Peaxi162Scf00316g00059' => 'pax', 'Peaxi162Scf00316g00328' => 'pax', 'Peaxi162Scf00316g00329' => 'pax', 'Peaxi162Scf00316g00411' => 'pax', 'Peaxi162Scf00316g00521' => 'pax', 'Peaxi162Scf00492g00068' => 'pax', 'Peaxi162Scf35631g00002' => 'pax', 'PGR142G3720' => 'pgr', 'PGSC0003DMG400006442' => 'stu', 'Phvul.007G062000' => 'pvu', 'Potri.008G157750' => 'ptr', 'Potri.008G157900' => 'ptr', 'Potri.008G158000' => 'ptr', 'Potri.008G158200' => 'ptr', 'Pp3c11_7280' => 'ppa', 'Pp3c11_7980' => 'ppa', 'Pp3c12_19450' => 'ppa', 'Pp3c14_1480' => 'ppa', 'Pp3c14_1501' => 'ppa', 'Pp3c16_4900' => 'ppa', 'Pp3c16_5010' => 'ppa', 'Pp3c16_5060' => 'ppa', 'Pp3c19_18250' => 'ppa', 'Pp3c23_8530' => 'ppa', 'Pp3c23_8550' => 'ppa', 'Pp3c24_9670' => 'ppa', 'Pp3c2_21390' => 'ppa', 'Pp3c2_31380' => 'ppa', 'Pp3c3_16620' => 'ppa', 'Pp3c3_8090' => 'ppa', 'Pp3c3_8110' => 'ppa', 'Pp3c3_8130' => 'ppa', 'Pp3c3_8150' => 'ppa', 'Pp3c4_14320' => 'ppa', 'Pp3c6_2560' => 'ppa', 'Pp3c9_16700' => 'ppa', 'PRCOL_00000234' => 'pco', 'PRCOL_00000235' => 'pco', 'PRCOL_00000777' => 'pco', 'PRCOL_00002344' => 'pco', 'PRCOL_00002372' => 'pco', 'PRCOL_00006120' => 'pco', 'Prupe.1G021400' => 'ppe', 'Prupe.1G021500' => 'ppe', 'Prupe.1G021600' => 'ppe', 'Prupe.1G021700' => 'ppe', 'Prupe.1G021800' => 'ppe', 'Prupe.5G145100' => 'ppe', 'Psat6g204040' => 'psa', 'Psat6g204800' => 'psa', 'Psat6g204920' => 'psa', 'Psat6g204960' => 'psa', 'Psat6g205080' => 'psa', 'PSO017G0271' => 'pso', 'PSO017G1276' => 'pso', 'PSO017G1429' => 'pso', 'PSO017G1861' => 'pso', 'PSO017G2787' => 'pso', 'PSO017G4466' => 'pso', 'PSO017G5118' => 'pso', 'PSO017G5420' => 'pso', 'PSO063G3678' => 'pso', 'PSO210G0546' => 'pso', 'PSO317G0001' => 'pso', 'PSO357G0512' => 'pso', 'PSO478G2682' => 'pso', 'PSO647G0001' => 'pso', 'PSO675G0001' => 'pso', 'PSO675G2699' => 'pso', 'PSO675G2849' => 'pso', 'PSO675G4991' => 'pso', 'PSO689G0001' => 'pso', 'QL06p000916' => 'qlo', 'QL06p000921' => 'qlo', 'QL06p001398' => 'qlo', 'QL06p001407' => 'qlo', 'QL06p002031' => 'qlo', 'RcHm_v2.0_Chr4g0387791' => 'rch', 'RcHm_v2.0_Chr4g0387801' => 'rch', 'RcHm_v2.0_Chr6g0286501' => 'rch', 'RcHm_v2.0_Chr6g0286511' => 'rch', 'RcHm_v2.0_Chr6g0286521' => 'rch', 'RcHm_v2.0_Chr6g0286531' => 'rch', 'RcHm_v2.0_Chr7g0189141' => 'rch', 'Rhsim02G0028700' => 'rsi', 'Rhsim02G0028800' => 'rsi', 'Rhsim02G0028900' => 'rsi', 'Rhsim02G0029000' => 'rsi', 'Rhsim02G0029100' => 'rsi', 'Rhsim02G0029200' => 'rsi', 'Rhsim02G0029300' => 'rsi', 'Rhsim02G0029400' => 'rsi', 'Rhsim02G0029500' => 'rsi', 'Rhsim02G0029600' => 'rsi', 'RhsimUnG0024000' => 'rsi', 'RhsimUnG0024100' => 'rsi', 'RhsimUnG0024200' => 'rsi', 'RhsimUnG0024300' => 'rsi', 'RhsimUnG0024400' => 'rsi', 'RhsimUnG0024500' => 'rsi', 'RhsimUnG0024700' => 'rsi', 'RhsimUnG0024800' => 'rsi', 'RhsimUnG0024900' => 'rsi', 'RhsimUnG0025100' => 'rsi', 'Sabra08G0120200' => 'sbr', 'Sabra08G0120300' => 'sbr', 'Sabra08G0120500' => 'sbr', 'Sabra08G0120600' => 'sbr', 'Sabra10G0158900' => 'sbr', 'SalBow2G3492' => 'sbo', 'Sc13g0004760' => 'sci', 'Sc13g0004770' => 'sci', 'Sed0003417' => 'sed', 'Sed0019750' => 'sed', 'SEGI_03419' => 'sgi', 'SEGI_05907' => 'sgi', 'SEGI_10682' => 'sgi', 'SEGI_13528' => 'sgi', 'SEGI_16081' => 'sgi', 'SEGI_19370' => 'sgi', 'SEGI_21015' => 'sgi', 'SEGI_21944' => 'sgi', 'SEGI_32906' => 'sgi', 'SEGI_33093' => 'sgi', 'SEGI_36110' => 'sgi', 'SEGI_40397' => 'sgi', 'SGA_v2.0_scaffold191G40426' => 'sas', 'SGA_v2.0_scaffold353G49717' => 'sas', 'SGA_v2.0_scaffold50G18550' => 'sas', 'SMO119G0173' => 'smo', 'SMO172G0002' => 'smo', 'Solyc09g082690.3' => 'sly', 'Solyc09g082700.2' => 'sly', 'Sopen09g031550' => 'spe', 'Sopen09g031560' => 'spe', 'Sp3g20540' => 'spa', 'Sp7g07580' => 'spa', 'TAR134G0002' => 'tar', 'TAR236G0001' => 'tar', 'TAR365G0892' => 'tar', 'TAR636G0166' => 'tar', 'TAR636G0646' => 'tar', 'TAR636G0869' => 'tar', 'TAR636G1317' => 'tar', 'TAR636G1744' => 'tar', 'TAR636G3358' => 'tar', 'TAR636G3436' => 'tar', 'THA.LOC104803047' => 'tha', 'Thecc.04G238900' => 'tca', 'Thhalv10021557m.g' => 'esa', 'Thhalv10026318m.g' => 'esa', 'Thhalv10026335m.g' => 'esa', 'TPR.G17433' => 'tpr', 'TPR.G18915' => 'tpr', 'TPR.G26125' => 'tpr', 'TWI09G0677' => 'twi', 'TWI73G0287' => 'twi', 'unitig_748.g8326' => 'ugi', 'vmacro15370' => 'vma', 'vmacro15371' => 'vma', 'vmacro15372' => 'vma', 'vmacro15373' => 'vma', 'vmacro15374' => 'vma', 'VMungo0720G2826' => 'vmu', 'Zm00001eb116960' => 'zma', 'Zm00001eb301260' => 'zma', 'Zm00001eb301270' => 'zma' ), 'gf_id' => 'HOM05D001460', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001460' ), 'data_identifier' => 'HOM05D001460', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001460', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '433', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p22980' => 'bna', 'A01p32340' => 'bna', 'A03p42970' => 'bna', 'A05p25880' => 'bna', 'Aa31LG8G9320' => 'aar', 'Aa31LG8G9330' => 'aar', 'Aa31LG8G9340' => 'aar', 'Aa31sc221G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1034' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1528' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.829' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2222' => 'aag', 'Ah.12g058830' => 'amhyb', 'Ah.12g058840' => 'amhyb', 'AL3G37160' => 'aly', 'AL7G41310' => 'aly', 'Aqoxy5G00395' => 'aox', 'Aqoxy5G00396' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0C8NZA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5185HY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JZ1PRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MD3LS0' => 'arhy', 'AT3G22840' => 'ath', 'AT4G14690' => 'ath', 'ATR0665G054' => 'atr', 'Atru.chr4.2344' => 'acertr', 'Atru.chr4.2346' => 'acertr', 'Atru.chr4.2347' => 'acertr', 'Atru.chr4.2348' => 'acertr', 'Atru.chr4.2355' => 'acertr', 'Atru.chr4.2356' => 'acertr', 'Atru.chr4.2358' => 'acertr', 'Atru.chr4.2359' => 'acertr', 'Atru.chr4.2360' => 'acertr', 'Atru.chr4.2361' => 'acertr', 'AUR62030476' => 'cqu', 'AUR62030478' => 'cqu', 'AUR62030819' => 'cqu', 'AUR62030820' => 'cqu', 'BcaB03g14648' => 'bca', 'BcaB04g20492' => 'bca', 'BcaB06g26399' => 'bca', 'BcaC01g03416' => 'bca', 'BcaC01g03419' => 'bca', 'BcaC01g03421' => 'bca', 'BcaC01g03424' => 'bca', 'BcaC05g28012' => 'bca', 'BcaC09g49212' => 'bca', 'BcaC09g50140' => 'bca', 'BcaNung00346' => 'bca', 'BolC1t02785H' => 'bol', 'BolC1t04095H' => 'bol', 'BolC3t17545H' => 'bol', 'BolC5t32769H' => 'bol', 'BraA01t02211Z' => 'bra', 'BraA01t03359Z' => 'bra', 'BraA03t13441Z' => 'bra', 'BraA05t21476Z' => 'bra', 'C01p28420' => 'bna', 'C01p41350' => 'bna', 'C03p52750' => 'bna', 'C03p52780' => 'bna', 'C05p40270' => 'bna', 'CAN.G1437.9' => 'can', 'CANSAT78G0035' => 'cansat', 'CANSAT78G1036' => 'cansat', 'CANSAT78G2272' => 'cansat', 'CANSAT78G2478' => 'cansat', 'CARHR098700' => 'chi', 'CARHR221120' => 'chi', 'CARHR221150' => 'chi', 'Carub.0003s2297' => 'cru', 'Carub.0007s2749' => 'cru', 'Carub.0007s2750' => 'cru', 'Carub.0007s2751' => 'cru', 'Ca_10849_v3' => 'car', 'Cc03_g04300' => 'ccan', 'CDE02G3648' => 'cde', 'CDE05G0060' => 'cde', 'CDE05G0692' => 'cde', 'CDE05G2285' => 'cde', 'CDE05G2884' => 'cde', 'CDE05G3072' => 'cde', 'Cfa008439' => 'cfa', 'Cfa008441' => 'cfa', 'Cfa008443' => 'cfa', 'Cfa008448' => 'cfa', 'Ciclev10005974m.g' => 'ccl', 'Ciclev10006006m.g' => 'ccl', 'Ciclev10006775m.g' => 'ccl', 'CiPaw.02G120400' => 'cil', 'CiPaw.02G120500' => 'cil', 'CiPaw.02G120600' => 'cil', 'ClCG05G004850' => 'cla', 'COL.COLO4_21566' => 'col', 'Cpa.g.sc44.124' => 'cpa', 'Cre07.g320400' => 'cre', 'Cre07.g320450' => 'cre', 'Cre08.g384650' => 'cre', 'Cre09.g393173' => 'cre', 'Cre09.g394325' => 'cre', 'Cre14.g626750' => 'cre', 'Cre16.g679250' => 'cre', 'CsaV3_3G012890' => 'csa', 'CSS0010865' => 'camsi', 'CSS0044338' => 'camsi', 'DCAR_002366' => 'dca', 'DCAR_030687' => 'dca', 'DCAR_030688' => 'dca', 'Dinv14047' => 'din', 'Dinv14048' => 'din', 'Duzib151G0105' => 'dzi', 'Duzib151G0114' => 'dzi', 'Duzib212G1029' => 'dzi', 'ECA232G3536' => 'eca', 'ECA240G0786' => 'eca', 'ECA240G1802' => 'eca', 'ECA240G3760' => 'eca', 'ECA240G3920' => 'eca', 'EL10Ac5g12536' => 'bvu', 'EL10Ac5g12537' => 'bvu', 'EL10Ac5g12538' => 'bvu', 'Eucgr.B01004' => 'egr', 'Eucgr.B01006' => 'egr', 'Eucgr.B01007' => 'egr', 'Eucgr.B01008' => 'egr', 'Eucgr.B01895' => 'egr', 'Eucgr.B01896' => 'egr', 'FAN04G1456' => 'fan', 'FAN08G1769' => 'fan', 'FAN08G2160' => 'fan', 'FAN13G2403' => 'fan', 'FAN13G3303' => 'fan', 'FAN15G2435' => 'fan', 'FAN17G0672' => 'fan', 'FAN17G2441' => 'fan', 'FAN18G1024' => 'fan', 'FAN22G1458' => 'fan', 'FAN24G0037' => 'fan', 'FAN24G0429' => 'fan', 'FAN24G2387' => 'fan', 'FAN27G2746' => 'fan', 'FvH4_2g20400' => 'fve', 'FvH4_2g20420' => 'fve', 'FvH4_2g20430' => 'fve', 'FvH4_4g01270' => 'fve', 'FvH4_4g01290' => 'fve', 'FvH4_4g01300' => 'fve', 'FvH4_4g01310' => 'fve', 'FvH4_4g01330' => 'fve', 'FvH4_5g09070' => 'fve', 'Glyma.10G243800' => 'gma', 'Glyma.20G150600' => 'gma', 'Gohir.A09G219200' => 'ghi', 'Gohir.A09G219300' => 'ghi', 'Gohir.D09G221400' => 'ghi', 'Gohir.D09G221500' => 'ghi', 'Gorai.006G242600' => 'gra', 'Gorai.006G242700' => 'gra', 'GSVIVG01018044001' => 'vvi', 'HanXRQChr03g0083821' => 'han', 'HanXRQChr03g0083841' => 'han', 'HanXRQChr03g0083881' => 'han', 'HanXRQChr03g0083901' => 'han', 'HanXRQChr03g0083921' => 'han', 'HanXRQChr03g0085331' => 'han', 'HanXRQChr03g0085361' => 'han', 'HanXRQChr03g0085411' => 'han', 'HanXRQChr03g0085421' => 'han', 'HanXRQChr03g0085431' => 'han', 'HanXRQChr08g0221991' => 'han', 'HanXRQChr11g0336061' => 'han', 'HanXRQChr11g0336411' => 'han', 'Haze_11234' => 'cav', 'Hma1.2p1_0549F.1_g177010' => 'hma', 'Hma1.2p1_0602F.1_g187630' => 'hma', 'Hund14876' => 'sun', 'Hund14879' => 'sun', 'Lalb_Chr06g0160741' => 'lal', 'Lalb_Chr21g0304781' => 'lal', 'Lj3A726G19' => 'lonja', 'Lj3A726T23' => 'lonja', 'Lj3A726T24' => 'lonja', 'Lj3A726T25' => 'lonja', 'Lj3A727T17' => 'lonja', 'Lj3C726T0' => 'lonja', 'Lj3C726T2' => 'lonja', 'Lj3P725T35' => 'lonja', 'Lj3P727T10' => 'lonja', 'Lj3P727T12' => 'lonja', 'Lj3P727T14' => 'lonja', 'Lj5g0023109' => 'lja', 'Lj6P646T44' => 'lonja', 'Lsat_1_v5_gn_6_75760' => 'lsa', 'Lsat_1_v5_gn_6_75800' => 'lsa', 'Lsat_1_v5_gn_6_75900' => 'lsa', 'Lsat_1_v5_gn_6_76240' => 'lsa', 'Lsat_1_v5_gn_6_76441' => 'lsa', 'Lsat_1_v5_gn_6_76700' => 'lsa', 'Lsat_1_v5_gn_6_76760' => 'lsa', 'Manes.15G033100' => 'mes', 'Mapoly0004s0074' => 'mpo', 'Mapoly0004s0075' => 'mpo', 'Mapoly0004s0163' => 'mpo', 'Mapoly0004s0164' => 'mpo', 'Mapoly0021s0018' => 'mpo', 'Mapoly0041s0136' => 'mpo', 'Mapoly0041s0137' => 'mpo', 'Mapoly0041s0138' => 'mpo', 'Mapoly0041s0139' => 'mpo', 'Mapoly0041s0141' => 'mpo', 'Mapoly0041s0142' => 'mpo', 'Mapoly0041s0143' => 'mpo', 'Mapoly0041s0144' => 'mpo', 'Mapoly0041s0145' => 'mpo', 'Mapoly0047s0106' => 'mpo', 'Mapoly0047s0108' => 'mpo', 'Mapoly0050s0051' => 'mpo', 'Mapoly0050s0052' => 'mpo', 'Mapoly0050s0053' => 'mpo', 'Mapoly0058s0013' => 'mpo', 'Mapoly0091s0078' => 'mpo', 'Mapoly0091s0079' => 'mpo', 'Mapoly0091s0080' => 'mpo', 'Mapoly0091s0081' => 'mpo', 'Mapoly0278s0004' => 'mpo', 'Mapoly0278s0005' => 'mpo', 'Mapoly0278s0006' => 'mpo', 'MBI11_g30648_MAGBIO' => 'mbi', 'MCO03G194' => 'mco', 'MCO03G590' => 'mco', 'MCO07G312' => 'mco', 'MCO10G318' => 'mco', 'MCO12G244' => 'mco', 'MCO13G148' => 'mco', 'MCO13G194' => 'mco', 'MCO16G238' => 'mco', 'MD06G1134100' => 'mdo', 'MD13G1200100' => 'mdo', 'MD13G1200300' => 'mdo', 'MD13G1200600' => 'mdo', 'MD14G1150400' => 'mdo', 'MD16G1200000' => 'mdo', 'Medtr1g102570' => 'mtr', 'Medtr1g102780' => 'mtr', 'Medtr1g102800' => 'mtr', 'Medtr1g102810' => 'mtr', 'Medtr1g102830' => 'mtr', 'MELO3C006499.2' => 'cme', 'Migut.G00385' => 'egut', 'MSTRG.4063' => 'ama', 'Nitab4.5_0000090g0260' => 'nta', 'Nitab4.5_0000977g0030' => 'nta', 'Nitab4.5_0002541g0040' => 'nta', 'Nitab4.5_0007068g0040' => 'nta', 'Nn005s41408' => 'nnu', 'Nn005s41410' => 'nnu', 'Oeu010310.1' => 'oeu', 'Oeu010311.1' => 'oeu', 'Oeu043472.1' => 'oeu', 'Os01g0246400' => 'osa', 'Os04g0267950' => 'osa', 'Os07g0178700' => 'osa', 'Os07g0178800' => 'osa', 'Peaxi162Scf00316g00046' => 'pax', 'Peaxi162Scf00316g00049' => 'pax', 'Peaxi162Scf00316g00059' => 'pax', 'Peaxi162Scf00316g00328' => 'pax', 'Peaxi162Scf00316g00329' => 'pax', 'Peaxi162Scf00316g00411' => 'pax', 'Peaxi162Scf00316g00521' => 'pax', 'Peaxi162Scf00492g00068' => 'pax', 'Peaxi162Scf35631g00002' => 'pax', 'PGR142G3720' => 'pgr', 'PGSC0003DMG400006442' => 'stu', 'Phvul.007G062000' => 'pvu', 'Potri.008G157750' => 'ptr', 'Potri.008G157900' => 'ptr', 'Potri.008G158000' => 'ptr', 'Potri.008G158200' => 'ptr', 'Pp3c11_7280' => 'ppa', 'Pp3c11_7980' => 'ppa', 'Pp3c12_19450' => 'ppa', 'Pp3c14_1480' => 'ppa', 'Pp3c14_1501' => 'ppa', 'Pp3c16_4900' => 'ppa', 'Pp3c16_5010' => 'ppa', 'Pp3c16_5060' => 'ppa', 'Pp3c19_18250' => 'ppa', 'Pp3c23_8530' => 'ppa', 'Pp3c23_8550' => 'ppa', 'Pp3c24_9670' => 'ppa', 'Pp3c2_21390' => 'ppa', 'Pp3c2_31380' => 'ppa', 'Pp3c3_16620' => 'ppa', 'Pp3c3_8090' => 'ppa', 'Pp3c3_8110' => 'ppa', 'Pp3c3_8130' => 'ppa', 'Pp3c3_8150' => 'ppa', 'Pp3c4_14320' => 'ppa', 'Pp3c6_2560' => 'ppa', 'Pp3c9_16700' => 'ppa', 'PRCOL_00000234' => 'pco', 'PRCOL_00000235' => 'pco', 'PRCOL_00000777' => 'pco', 'PRCOL_00002344' => 'pco', 'PRCOL_00002372' => 'pco', 'PRCOL_00006120' => 'pco', 'Prupe.1G021400' => 'ppe', 'Prupe.1G021500' => 'ppe', 'Prupe.1G021600' => 'ppe', 'Prupe.1G021700' => 'ppe', 'Prupe.1G021800' => 'ppe', 'Prupe.5G145100' => 'ppe', 'Psat6g204040' => 'psa', 'Psat6g204800' => 'psa', 'Psat6g204920' => 'psa', 'Psat6g204960' => 'psa', 'Psat6g205080' => 'psa', 'PSO017G0271' => 'pso', 'PSO017G1276' => 'pso', 'PSO017G1429' => 'pso', 'PSO017G1861' => 'pso', 'PSO017G2787' => 'pso', 'PSO017G4466' => 'pso', 'PSO017G5118' => 'pso', 'PSO017G5420' => 'pso', 'PSO063G3678' => 'pso', 'PSO210G0546' => 'pso', 'PSO317G0001' => 'pso', 'PSO357G0512' => 'pso', 'PSO478G2682' => 'pso', 'PSO647G0001' => 'pso', 'PSO675G0001' => 'pso', 'PSO675G2699' => 'pso', 'PSO675G2849' => 'pso', 'PSO675G4991' => 'pso', 'PSO689G0001' => 'pso', 'QL06p000916' => 'qlo', 'QL06p000921' => 'qlo', 'QL06p001398' => 'qlo', 'QL06p001407' => 'qlo', 'QL06p002031' => 'qlo', 'RcHm_v2.0_Chr4g0387791' => 'rch', 'RcHm_v2.0_Chr4g0387801' => 'rch', 'RcHm_v2.0_Chr6g0286501' => 'rch', 'RcHm_v2.0_Chr6g0286511' => 'rch', 'RcHm_v2.0_Chr6g0286521' => 'rch', 'RcHm_v2.0_Chr6g0286531' => 'rch', 'RcHm_v2.0_Chr7g0189141' => 'rch', 'Rhsim02G0028700' => 'rsi', 'Rhsim02G0028800' => 'rsi', 'Rhsim02G0028900' => 'rsi', 'Rhsim02G0029000' => 'rsi', 'Rhsim02G0029100' => 'rsi', 'Rhsim02G0029200' => 'rsi', 'Rhsim02G0029300' => 'rsi', 'Rhsim02G0029400' => 'rsi', 'Rhsim02G0029500' => 'rsi', 'Rhsim02G0029600' => 'rsi', 'RhsimUnG0024000' => 'rsi', 'RhsimUnG0024100' => 'rsi', 'RhsimUnG0024200' => 'rsi', 'RhsimUnG0024300' => 'rsi', 'RhsimUnG0024400' => 'rsi', 'RhsimUnG0024500' => 'rsi', 'RhsimUnG0024700' => 'rsi', 'RhsimUnG0024800' => 'rsi', 'RhsimUnG0024900' => 'rsi', 'RhsimUnG0025100' => 'rsi', 'Sabra08G0120200' => 'sbr', 'Sabra08G0120300' => 'sbr', 'Sabra08G0120500' => 'sbr', 'Sabra08G0120600' => 'sbr', 'Sabra10G0158900' => 'sbr', 'SalBow2G3492' => 'sbo', 'Sc13g0004760' => 'sci', 'Sc13g0004770' => 'sci', 'Sed0003417' => 'sed', 'Sed0019750' => 'sed', 'SEGI_03419' => 'sgi', 'SEGI_05907' => 'sgi', 'SEGI_10682' => 'sgi', 'SEGI_13528' => 'sgi', 'SEGI_16081' => 'sgi', 'SEGI_19370' => 'sgi', 'SEGI_21015' => 'sgi', 'SEGI_21944' => 'sgi', 'SEGI_32906' => 'sgi', 'SEGI_33093' => 'sgi', 'SEGI_36110' => 'sgi', 'SEGI_40397' => 'sgi', 'SGA_v2.0_scaffold191G40426' => 'sas', 'SGA_v2.0_scaffold353G49717' => 'sas', 'SGA_v2.0_scaffold50G18550' => 'sas', 'SMO119G0173' => 'smo', 'SMO172G0002' => 'smo', 'Solyc09g082690.3' => 'sly', 'Solyc09g082700.2' => 'sly', 'Sopen09g031550' => 'spe', 'Sopen09g031560' => 'spe', 'Sp3g20540' => 'spa', 'Sp7g07580' => 'spa', 'TAR134G0002' => 'tar', 'TAR236G0001' => 'tar', 'TAR365G0892' => 'tar', 'TAR636G0166' => 'tar', 'TAR636G0646' => 'tar', 'TAR636G0869' => 'tar', 'TAR636G1317' => 'tar', 'TAR636G1744' => 'tar', 'TAR636G3358' => 'tar', 'TAR636G3436' => 'tar', 'THA.LOC104803047' => 'tha', 'Thecc.04G238900' => 'tca', 'Thhalv10021557m.g' => 'esa', 'Thhalv10026318m.g' => 'esa', 'Thhalv10026335m.g' => 'esa', 'TPR.G17433' => 'tpr', 'TPR.G18915' => 'tpr', 'TPR.G26125' => 'tpr', 'TWI09G0677' => 'twi', 'TWI73G0287' => 'twi', 'unitig_748.g8326' => 'ugi', 'vmacro15370' => 'vma', 'vmacro15371' => 'vma', 'vmacro15372' => 'vma', 'vmacro15373' => 'vma', 'vmacro15374' => 'vma', 'VMungo0720G2826' => 'vmu', 'Zm00001eb116960' => 'zma', 'Zm00001eb301260' => 'zma', 'Zm00001eb301270' => 'zma' ) $gf_id = 'HOM05D001460' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001460' ) $data_identifier = 'HOM05D001460' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 4, 'aag' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 2, 'aox' => (int) 2, 'arhy' => (int) 4, 'ath' => (int) 2, 'atr' => (int) 1, 'acertr' => (int) 10, 'cqu' => (int) 4, 'bca' => (int) 11, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 1, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 1, 'ccan' => (int) 1, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 1, 'col' => (int) 1, 'cpa' => (int) 1, 'cre' => (int) 7, 'csa' => (int) 1, 'camsi' => (int) 2, 'dca' => (int) 3, 'din' => (int) 2, 'dzi' => (int) 3, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 14, 'fve' => (int) 9, 'gma' => (int) 2, 'ghi' => (int) 4, 'gra' => (int) 2, 'vvi' => (int) 1, 'han' => (int) 13, 'cav' => (int) 1, 'hma' => (int) 2, 'sun' => (int) 2, 'lal' => (int) 2, 'lonja' => (int) 12, 'lja' => (int) 1, 'lsa' => (int) 7, 'mes' => (int) 1, 'mpo' => (int) 27, 'mbi' => (int) 1, 'mco' => (int) 8, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 1, 'egut' => (int) 1, 'ama' => (int) 1, 'nta' => (int) 4, 'nnu' => (int) 2, 'oeu' => (int) 3, 'osa' => (int) 4, 'pax' => (int) 9, 'pgr' => (int) 1, 'stu' => (int) 1, 'pvu' => (int) 1, 'ptr' => (int) 4, 'ppa' => (int) 22, 'pco' => (int) 6, 'ppe' => (int) 6, 'psa' => (int) 5, 'pso' => (int) 19, 'qlo' => (int) 5, 'rch' => (int) 7, 'rsi' => (int) 20, 'sbr' => (int) 5, 'sbo' => (int) 1, 'sci' => (int) 2, 'sed' => (int) 2, 'sgi' => (int) 12, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 2, 'tar' => (int) 10, 'tha' => (int) 1, 'tca' => (int) 1, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 2, 'ugi' => (int) 1, 'vma' => (int) 5, 'vmu' => (int) 1, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb301270' $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' => 'HOM05D001460', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '433', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p22980' => 'bna', 'A01p32340' => 'bna', 'A03p42970' => 'bna', 'A05p25880' => 'bna', 'Aa31LG8G9320' => 'aar', 'Aa31LG8G9330' => 'aar', 'Aa31LG8G9340' => 'aar', 'Aa31sc221G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1034' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1528' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.829' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2222' => 'aag', 'Ah.12g058830' => 'amhyb', 'Ah.12g058840' => 'amhyb', 'AL3G37160' => 'aly', 'AL7G41310' => 'aly', 'Aqoxy5G00395' => 'aox', 'Aqoxy5G00396' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0C8NZA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5185HY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JZ1PRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MD3LS0' => 'arhy', 'AT3G22840' => 'ath', 'AT4G14690' => 'ath', 'ATR0665G054' => 'atr', 'Atru.chr4.2344' => 'acertr', 'Atru.chr4.2346' => 'acertr', 'Atru.chr4.2347' => 'acertr', 'Atru.chr4.2348' => 'acertr', 'Atru.chr4.2355' => 'acertr', 'Atru.chr4.2356' => 'acertr', 'Atru.chr4.2358' => 'acertr', 'Atru.chr4.2359' => 'acertr', 'Atru.chr4.2360' => 'acertr', 'Atru.chr4.2361' => 'acertr', 'AUR62030476' => 'cqu', 'AUR62030478' => 'cqu', 'AUR62030819' => 'cqu', 'AUR62030820' => 'cqu', 'BcaB03g14648' => 'bca', 'BcaB04g20492' => 'bca', 'BcaB06g26399' => 'bca', 'BcaC01g03416' => 'bca', 'BcaC01g03419' => 'bca', 'BcaC01g03421' => 'bca', 'BcaC01g03424' => 'bca', 'BcaC05g28012' => 'bca', 'BcaC09g49212' => 'bca', 'BcaC09g50140' => 'bca', 'BcaNung00346' => 'bca', 'BolC1t02785H' => 'bol', 'BolC1t04095H' => 'bol', 'BolC3t17545H' => 'bol', 'BolC5t32769H' => 'bol', 'BraA01t02211Z' => 'bra', 'BraA01t03359Z' => 'bra', 'BraA03t13441Z' => 'bra', 'BraA05t21476Z' => 'bra', 'C01p28420' => 'bna', 'C01p41350' => 'bna', 'C03p52750' => 'bna', 'C03p52780' => 'bna', 'C05p40270' => 'bna', 'CAN.G1437.9' => 'can', 'CANSAT78G0035' => 'cansat', 'CANSAT78G1036' => 'cansat', 'CANSAT78G2272' => 'cansat', 'CANSAT78G2478' => 'cansat', 'CARHR098700' => 'chi', 'CARHR221120' => 'chi', 'CARHR221150' => 'chi', 'Carub.0003s2297' => 'cru', 'Carub.0007s2749' => 'cru', 'Carub.0007s2750' => 'cru', 'Carub.0007s2751' => 'cru', 'Ca_10849_v3' => 'car', 'Cc03_g04300' => 'ccan', 'CDE02G3648' => 'cde', 'CDE05G0060' => 'cde', 'CDE05G0692' => 'cde', 'CDE05G2285' => 'cde', 'CDE05G2884' => 'cde', 'CDE05G3072' => 'cde', 'Cfa008439' => 'cfa', 'Cfa008441' => 'cfa', 'Cfa008443' => 'cfa', 'Cfa008448' => 'cfa', 'Ciclev10005974m.g' => 'ccl', 'Ciclev10006006m.g' => 'ccl', 'Ciclev10006775m.g' => 'ccl', 'CiPaw.02G120400' => 'cil', 'CiPaw.02G120500' => 'cil', 'CiPaw.02G120600' => 'cil', 'ClCG05G004850' => 'cla', 'COL.COLO4_21566' => 'col', 'Cpa.g.sc44.124' => 'cpa', 'Cre07.g320400' => 'cre', 'Cre07.g320450' => 'cre', 'Cre08.g384650' => 'cre', 'Cre09.g393173' => 'cre', 'Cre09.g394325' => 'cre', 'Cre14.g626750' => 'cre', 'Cre16.g679250' => 'cre', 'CsaV3_3G012890' => 'csa', 'CSS0010865' => 'camsi', 'CSS0044338' => 'camsi', 'DCAR_002366' => 'dca', 'DCAR_030687' => 'dca', 'DCAR_030688' => 'dca', 'Dinv14047' => 'din', 'Dinv14048' => 'din', 'Duzib151G0105' => 'dzi', 'Duzib151G0114' => 'dzi', 'Duzib212G1029' => 'dzi', 'ECA232G3536' => 'eca', 'ECA240G0786' => 'eca', 'ECA240G1802' => 'eca', 'ECA240G3760' => 'eca', 'ECA240G3920' => 'eca', 'EL10Ac5g12536' => 'bvu', 'EL10Ac5g12537' => 'bvu', 'EL10Ac5g12538' => 'bvu', 'Eucgr.B01004' => 'egr', 'Eucgr.B01006' => 'egr', 'Eucgr.B01007' => 'egr', 'Eucgr.B01008' => 'egr', 'Eucgr.B01895' => 'egr', 'Eucgr.B01896' => 'egr', 'FAN04G1456' => 'fan', 'FAN08G1769' => 'fan', 'FAN08G2160' => 'fan', 'FAN13G2403' => 'fan', 'FAN13G3303' => 'fan', 'FAN15G2435' => 'fan', 'FAN17G0672' => 'fan', 'FAN17G2441' => 'fan', 'FAN18G1024' => 'fan', 'FAN22G1458' => 'fan', 'FAN24G0037' => 'fan', 'FAN24G0429' => 'fan', 'FAN24G2387' => 'fan', 'FAN27G2746' => 'fan', 'FvH4_2g20400' => 'fve', 'FvH4_2g20420' => 'fve', 'FvH4_2g20430' => 'fve', 'FvH4_4g01270' => 'fve', 'FvH4_4g01290' => 'fve', 'FvH4_4g01300' => 'fve', 'FvH4_4g01310' => 'fve', 'FvH4_4g01330' => 'fve', 'FvH4_5g09070' => 'fve', 'Glyma.10G243800' => 'gma', 'Glyma.20G150600' => 'gma', 'Gohir.A09G219200' => 'ghi', 'Gohir.A09G219300' => 'ghi', 'Gohir.D09G221400' => 'ghi', 'Gohir.D09G221500' => 'ghi', 'Gorai.006G242600' => 'gra', 'Gorai.006G242700' => 'gra', 'GSVIVG01018044001' => 'vvi', 'HanXRQChr03g0083821' => 'han', 'HanXRQChr03g0083841' => 'han', 'HanXRQChr03g0083881' => 'han', 'HanXRQChr03g0083901' => 'han', 'HanXRQChr03g0083921' => 'han', 'HanXRQChr03g0085331' => 'han', 'HanXRQChr03g0085361' => 'han', 'HanXRQChr03g0085411' => 'han', 'HanXRQChr03g0085421' => 'han', 'HanXRQChr03g0085431' => 'han', 'HanXRQChr08g0221991' => 'han', 'HanXRQChr11g0336061' => 'han', 'HanXRQChr11g0336411' => 'han', 'Haze_11234' => 'cav', 'Hma1.2p1_0549F.1_g177010' => 'hma', 'Hma1.2p1_0602F.1_g187630' => 'hma', 'Hund14876' => 'sun', 'Hund14879' => 'sun', 'Lalb_Chr06g0160741' => 'lal', 'Lalb_Chr21g0304781' => 'lal', 'Lj3A726G19' => 'lonja', 'Lj3A726T23' => 'lonja', 'Lj3A726T24' => 'lonja', 'Lj3A726T25' => 'lonja', 'Lj3A727T17' => 'lonja', 'Lj3C726T0' => 'lonja', 'Lj3C726T2' => 'lonja', 'Lj3P725T35' => 'lonja', 'Lj3P727T10' => 'lonja', 'Lj3P727T12' => 'lonja', 'Lj3P727T14' => 'lonja', 'Lj5g0023109' => 'lja', 'Lj6P646T44' => 'lonja', 'Lsat_1_v5_gn_6_75760' => 'lsa', 'Lsat_1_v5_gn_6_75800' => 'lsa', 'Lsat_1_v5_gn_6_75900' => 'lsa', 'Lsat_1_v5_gn_6_76240' => 'lsa', 'Lsat_1_v5_gn_6_76441' => 'lsa', 'Lsat_1_v5_gn_6_76700' => 'lsa', 'Lsat_1_v5_gn_6_76760' => 'lsa', 'Manes.15G033100' => 'mes', 'Mapoly0004s0074' => 'mpo', 'Mapoly0004s0075' => 'mpo', 'Mapoly0004s0163' => 'mpo', 'Mapoly0004s0164' => 'mpo', 'Mapoly0021s0018' => 'mpo', 'Mapoly0041s0136' => 'mpo', 'Mapoly0041s0137' => 'mpo', 'Mapoly0041s0138' => 'mpo', 'Mapoly0041s0139' => 'mpo', 'Mapoly0041s0141' => 'mpo', 'Mapoly0041s0142' => 'mpo', 'Mapoly0041s0143' => 'mpo', 'Mapoly0041s0144' => 'mpo', 'Mapoly0041s0145' => 'mpo', 'Mapoly0047s0106' => 'mpo', 'Mapoly0047s0108' => 'mpo', 'Mapoly0050s0051' => 'mpo', 'Mapoly0050s0052' => 'mpo', 'Mapoly0050s0053' => 'mpo', 'Mapoly0058s0013' => 'mpo', 'Mapoly0091s0078' => 'mpo', 'Mapoly0091s0079' => 'mpo', 'Mapoly0091s0080' => 'mpo', 'Mapoly0091s0081' => 'mpo', 'Mapoly0278s0004' => 'mpo', 'Mapoly0278s0005' => 'mpo', 'Mapoly0278s0006' => 'mpo', 'MBI11_g30648_MAGBIO' => 'mbi', 'MCO03G194' => 'mco', 'MCO03G590' => 'mco', 'MCO07G312' => 'mco', 'MCO10G318' => 'mco', 'MCO12G244' => 'mco', 'MCO13G148' => 'mco', 'MCO13G194' => 'mco', 'MCO16G238' => 'mco', 'MD06G1134100' => 'mdo', 'MD13G1200100' => 'mdo', 'MD13G1200300' => 'mdo', 'MD13G1200600' => 'mdo', 'MD14G1150400' => 'mdo', 'MD16G1200000' => 'mdo', 'Medtr1g102570' => 'mtr', 'Medtr1g102780' => 'mtr', 'Medtr1g102800' => 'mtr', 'Medtr1g102810' => 'mtr', 'Medtr1g102830' => 'mtr', 'MELO3C006499.2' => 'cme', 'Migut.G00385' => 'egut', 'MSTRG.4063' => 'ama', 'Nitab4.5_0000090g0260' => 'nta', 'Nitab4.5_0000977g0030' => 'nta', 'Nitab4.5_0002541g0040' => 'nta', 'Nitab4.5_0007068g0040' => 'nta', 'Nn005s41408' => 'nnu', 'Nn005s41410' => 'nnu', 'Oeu010310.1' => 'oeu', 'Oeu010311.1' => 'oeu', 'Oeu043472.1' => 'oeu', 'Os01g0246400' => 'osa', 'Os04g0267950' => 'osa', 'Os07g0178700' => 'osa', 'Os07g0178800' => 'osa', 'Peaxi162Scf00316g00046' => 'pax', 'Peaxi162Scf00316g00049' => 'pax', 'Peaxi162Scf00316g00059' => 'pax', 'Peaxi162Scf00316g00328' => 'pax', 'Peaxi162Scf00316g00329' => 'pax', 'Peaxi162Scf00316g00411' => 'pax', 'Peaxi162Scf00316g00521' => 'pax', 'Peaxi162Scf00492g00068' => 'pax', 'Peaxi162Scf35631g00002' => 'pax', 'PGR142G3720' => 'pgr', 'PGSC0003DMG400006442' => 'stu', 'Phvul.007G062000' => 'pvu', 'Potri.008G157750' => 'ptr', 'Potri.008G157900' => 'ptr', 'Potri.008G158000' => 'ptr', 'Potri.008G158200' => 'ptr', 'Pp3c11_7280' => 'ppa', 'Pp3c11_7980' => 'ppa', 'Pp3c12_19450' => 'ppa', 'Pp3c14_1480' => 'ppa', 'Pp3c14_1501' => 'ppa', 'Pp3c16_4900' => 'ppa', 'Pp3c16_5010' => 'ppa', 'Pp3c16_5060' => 'ppa', 'Pp3c19_18250' => 'ppa', 'Pp3c23_8530' => 'ppa', 'Pp3c23_8550' => 'ppa', 'Pp3c24_9670' => 'ppa', 'Pp3c2_21390' => 'ppa', 'Pp3c2_31380' => 'ppa', 'Pp3c3_16620' => 'ppa', 'Pp3c3_8090' => 'ppa', 'Pp3c3_8110' => 'ppa', 'Pp3c3_8130' => 'ppa', 'Pp3c3_8150' => 'ppa', 'Pp3c4_14320' => 'ppa', 'Pp3c6_2560' => 'ppa', 'Pp3c9_16700' => 'ppa', 'PRCOL_00000234' => 'pco', 'PRCOL_00000235' => 'pco', 'PRCOL_00000777' => 'pco', 'PRCOL_00002344' => 'pco', 'PRCOL_00002372' => 'pco', 'PRCOL_00006120' => 'pco', 'Prupe.1G021400' => 'ppe', 'Prupe.1G021500' => 'ppe', 'Prupe.1G021600' => 'ppe', 'Prupe.1G021700' => 'ppe', 'Prupe.1G021800' => 'ppe', 'Prupe.5G145100' => 'ppe', 'Psat6g204040' => 'psa', 'Psat6g204800' => 'psa', 'Psat6g204920' => 'psa', 'Psat6g204960' => 'psa', 'Psat6g205080' => 'psa', 'PSO017G0271' => 'pso', 'PSO017G1276' => 'pso', 'PSO017G1429' => 'pso', 'PSO017G1861' => 'pso', 'PSO017G2787' => 'pso', 'PSO017G4466' => 'pso', 'PSO017G5118' => 'pso', 'PSO017G5420' => 'pso', 'PSO063G3678' => 'pso', 'PSO210G0546' => 'pso', 'PSO317G0001' => 'pso', 'PSO357G0512' => 'pso', 'PSO478G2682' => 'pso', 'PSO647G0001' => 'pso', 'PSO675G0001' => 'pso', 'PSO675G2699' => 'pso', 'PSO675G2849' => 'pso', 'PSO675G4991' => 'pso', 'PSO689G0001' => 'pso', 'QL06p000916' => 'qlo', 'QL06p000921' => 'qlo', 'QL06p001398' => 'qlo', 'QL06p001407' => 'qlo', 'QL06p002031' => 'qlo', 'RcHm_v2.0_Chr4g0387791' => 'rch', 'RcHm_v2.0_Chr4g0387801' => 'rch', 'RcHm_v2.0_Chr6g0286501' => 'rch', 'RcHm_v2.0_Chr6g0286511' => 'rch', 'RcHm_v2.0_Chr6g0286521' => 'rch', 'RcHm_v2.0_Chr6g0286531' => 'rch', 'RcHm_v2.0_Chr7g0189141' => 'rch', 'Rhsim02G0028700' => 'rsi', 'Rhsim02G0028800' => 'rsi', 'Rhsim02G0028900' => 'rsi', 'Rhsim02G0029000' => 'rsi', 'Rhsim02G0029100' => 'rsi', 'Rhsim02G0029200' => 'rsi', 'Rhsim02G0029300' => 'rsi', 'Rhsim02G0029400' => 'rsi', 'Rhsim02G0029500' => 'rsi', 'Rhsim02G0029600' => 'rsi', 'RhsimUnG0024000' => 'rsi', 'RhsimUnG0024100' => 'rsi', 'RhsimUnG0024200' => 'rsi', 'RhsimUnG0024300' => 'rsi', 'RhsimUnG0024400' => 'rsi', 'RhsimUnG0024500' => 'rsi', 'RhsimUnG0024700' => 'rsi', 'RhsimUnG0024800' => 'rsi', 'RhsimUnG0024900' => 'rsi', 'RhsimUnG0025100' => 'rsi', 'Sabra08G0120200' => 'sbr', 'Sabra08G0120300' => 'sbr', 'Sabra08G0120500' => 'sbr', 'Sabra08G0120600' => 'sbr', 'Sabra10G0158900' => 'sbr', 'SalBow2G3492' => 'sbo', 'Sc13g0004760' => 'sci', 'Sc13g0004770' => 'sci', 'Sed0003417' => 'sed', 'Sed0019750' => 'sed', 'SEGI_03419' => 'sgi', 'SEGI_05907' => 'sgi', 'SEGI_10682' => 'sgi', 'SEGI_13528' => 'sgi', 'SEGI_16081' => 'sgi', 'SEGI_19370' => 'sgi', 'SEGI_21015' => 'sgi', 'SEGI_21944' => 'sgi', 'SEGI_32906' => 'sgi', 'SEGI_33093' => 'sgi', 'SEGI_36110' => 'sgi', 'SEGI_40397' => 'sgi', 'SGA_v2.0_scaffold191G40426' => 'sas', 'SGA_v2.0_scaffold353G49717' => 'sas', 'SGA_v2.0_scaffold50G18550' => 'sas', 'SMO119G0173' => 'smo', 'SMO172G0002' => 'smo', 'Solyc09g082690.3' => 'sly', 'Solyc09g082700.2' => 'sly', 'Sopen09g031550' => 'spe', 'Sopen09g031560' => 'spe', 'Sp3g20540' => 'spa', 'Sp7g07580' => 'spa', 'TAR134G0002' => 'tar', 'TAR236G0001' => 'tar', 'TAR365G0892' => 'tar', 'TAR636G0166' => 'tar', 'TAR636G0646' => 'tar', 'TAR636G0869' => 'tar', 'TAR636G1317' => 'tar', 'TAR636G1744' => 'tar', 'TAR636G3358' => 'tar', 'TAR636G3436' => 'tar', 'THA.LOC104803047' => 'tha', 'Thecc.04G238900' => 'tca', 'Thhalv10021557m.g' => 'esa', 'Thhalv10026318m.g' => 'esa', 'Thhalv10026335m.g' => 'esa', 'TPR.G17433' => 'tpr', 'TPR.G18915' => 'tpr', 'TPR.G26125' => 'tpr', 'TWI09G0677' => 'twi', 'TWI73G0287' => 'twi', 'unitig_748.g8326' => 'ugi', 'vmacro15370' => 'vma', 'vmacro15371' => 'vma', 'vmacro15372' => 'vma', 'vmacro15373' => 'vma', 'vmacro15374' => 'vma', 'VMungo0720G2826' => 'vmu', 'Zm00001eb116960' => 'zma', 'Zm00001eb301260' => 'zma', 'Zm00001eb301270' => 'zma' ), 'gf_id' => 'HOM05D001460', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001460' ), 'data_identifier' => 'HOM05D001460', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001460', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '433', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p22980' => 'bna', 'A01p32340' => 'bna', 'A03p42970' => 'bna', 'A05p25880' => 'bna', 'Aa31LG8G9320' => 'aar', 'Aa31LG8G9330' => 'aar', 'Aa31LG8G9340' => 'aar', 'Aa31sc221G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1034' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1528' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.829' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2222' => 'aag', 'Ah.12g058830' => 'amhyb', 'Ah.12g058840' => 'amhyb', 'AL3G37160' => 'aly', 'AL7G41310' => 'aly', 'Aqoxy5G00395' => 'aox', 'Aqoxy5G00396' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0C8NZA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5185HY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JZ1PRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MD3LS0' => 'arhy', 'AT3G22840' => 'ath', 'AT4G14690' => 'ath', 'ATR0665G054' => 'atr', 'Atru.chr4.2344' => 'acertr', 'Atru.chr4.2346' => 'acertr', 'Atru.chr4.2347' => 'acertr', 'Atru.chr4.2348' => 'acertr', 'Atru.chr4.2355' => 'acertr', 'Atru.chr4.2356' => 'acertr', 'Atru.chr4.2358' => 'acertr', 'Atru.chr4.2359' => 'acertr', 'Atru.chr4.2360' => 'acertr', 'Atru.chr4.2361' => 'acertr', 'AUR62030476' => 'cqu', 'AUR62030478' => 'cqu', 'AUR62030819' => 'cqu', 'AUR62030820' => 'cqu', 'BcaB03g14648' => 'bca', 'BcaB04g20492' => 'bca', 'BcaB06g26399' => 'bca', 'BcaC01g03416' => 'bca', 'BcaC01g03419' => 'bca', 'BcaC01g03421' => 'bca', 'BcaC01g03424' => 'bca', 'BcaC05g28012' => 'bca', 'BcaC09g49212' => 'bca', 'BcaC09g50140' => 'bca', 'BcaNung00346' => 'bca', 'BolC1t02785H' => 'bol', 'BolC1t04095H' => 'bol', 'BolC3t17545H' => 'bol', 'BolC5t32769H' => 'bol', 'BraA01t02211Z' => 'bra', 'BraA01t03359Z' => 'bra', 'BraA03t13441Z' => 'bra', 'BraA05t21476Z' => 'bra', 'C01p28420' => 'bna', 'C01p41350' => 'bna', 'C03p52750' => 'bna', 'C03p52780' => 'bna', 'C05p40270' => 'bna', 'CAN.G1437.9' => 'can', 'CANSAT78G0035' => 'cansat', 'CANSAT78G1036' => 'cansat', 'CANSAT78G2272' => 'cansat', 'CANSAT78G2478' => 'cansat', 'CARHR098700' => 'chi', 'CARHR221120' => 'chi', 'CARHR221150' => 'chi', 'Carub.0003s2297' => 'cru', 'Carub.0007s2749' => 'cru', 'Carub.0007s2750' => 'cru', 'Carub.0007s2751' => 'cru', 'Ca_10849_v3' => 'car', 'Cc03_g04300' => 'ccan', 'CDE02G3648' => 'cde', 'CDE05G0060' => 'cde', 'CDE05G0692' => 'cde', 'CDE05G2285' => 'cde', 'CDE05G2884' => 'cde', 'CDE05G3072' => 'cde', 'Cfa008439' => 'cfa', 'Cfa008441' => 'cfa', 'Cfa008443' => 'cfa', 'Cfa008448' => 'cfa', 'Ciclev10005974m.g' => 'ccl', 'Ciclev10006006m.g' => 'ccl', 'Ciclev10006775m.g' => 'ccl', 'CiPaw.02G120400' => 'cil', 'CiPaw.02G120500' => 'cil', 'CiPaw.02G120600' => 'cil', 'ClCG05G004850' => 'cla', 'COL.COLO4_21566' => 'col', 'Cpa.g.sc44.124' => 'cpa', 'Cre07.g320400' => 'cre', 'Cre07.g320450' => 'cre', 'Cre08.g384650' => 'cre', 'Cre09.g393173' => 'cre', 'Cre09.g394325' => 'cre', 'Cre14.g626750' => 'cre', 'Cre16.g679250' => 'cre', 'CsaV3_3G012890' => 'csa', 'CSS0010865' => 'camsi', 'CSS0044338' => 'camsi', 'DCAR_002366' => 'dca', 'DCAR_030687' => 'dca', 'DCAR_030688' => 'dca', 'Dinv14047' => 'din', 'Dinv14048' => 'din', 'Duzib151G0105' => 'dzi', 'Duzib151G0114' => 'dzi', 'Duzib212G1029' => 'dzi', 'ECA232G3536' => 'eca', 'ECA240G0786' => 'eca', 'ECA240G1802' => 'eca', 'ECA240G3760' => 'eca', 'ECA240G3920' => 'eca', 'EL10Ac5g12536' => 'bvu', 'EL10Ac5g12537' => 'bvu', 'EL10Ac5g12538' => 'bvu', 'Eucgr.B01004' => 'egr', 'Eucgr.B01006' => 'egr', 'Eucgr.B01007' => 'egr', 'Eucgr.B01008' => 'egr', 'Eucgr.B01895' => 'egr', 'Eucgr.B01896' => 'egr', 'FAN04G1456' => 'fan', 'FAN08G1769' => 'fan', 'FAN08G2160' => 'fan', 'FAN13G2403' => 'fan', 'FAN13G3303' => 'fan', 'FAN15G2435' => 'fan', 'FAN17G0672' => 'fan', 'FAN17G2441' => 'fan', 'FAN18G1024' => 'fan', 'FAN22G1458' => 'fan', 'FAN24G0037' => 'fan', 'FAN24G0429' => 'fan', 'FAN24G2387' => 'fan', 'FAN27G2746' => 'fan', 'FvH4_2g20400' => 'fve', 'FvH4_2g20420' => 'fve', 'FvH4_2g20430' => 'fve', 'FvH4_4g01270' => 'fve', 'FvH4_4g01290' => 'fve', 'FvH4_4g01300' => 'fve', 'FvH4_4g01310' => 'fve', 'FvH4_4g01330' => 'fve', 'FvH4_5g09070' => 'fve', 'Glyma.10G243800' => 'gma', 'Glyma.20G150600' => 'gma', 'Gohir.A09G219200' => 'ghi', 'Gohir.A09G219300' => 'ghi', 'Gohir.D09G221400' => 'ghi', 'Gohir.D09G221500' => 'ghi', 'Gorai.006G242600' => 'gra', 'Gorai.006G242700' => 'gra', 'GSVIVG01018044001' => 'vvi', 'HanXRQChr03g0083821' => 'han', 'HanXRQChr03g0083841' => 'han', 'HanXRQChr03g0083881' => 'han', 'HanXRQChr03g0083901' => 'han', 'HanXRQChr03g0083921' => 'han', 'HanXRQChr03g0085331' => 'han', 'HanXRQChr03g0085361' => 'han', 'HanXRQChr03g0085411' => 'han', 'HanXRQChr03g0085421' => 'han', 'HanXRQChr03g0085431' => 'han', 'HanXRQChr08g0221991' => 'han', 'HanXRQChr11g0336061' => 'han', 'HanXRQChr11g0336411' => 'han', 'Haze_11234' => 'cav', 'Hma1.2p1_0549F.1_g177010' => 'hma', 'Hma1.2p1_0602F.1_g187630' => 'hma', 'Hund14876' => 'sun', 'Hund14879' => 'sun', 'Lalb_Chr06g0160741' => 'lal', 'Lalb_Chr21g0304781' => 'lal', 'Lj3A726G19' => 'lonja', 'Lj3A726T23' => 'lonja', 'Lj3A726T24' => 'lonja', 'Lj3A726T25' => 'lonja', 'Lj3A727T17' => 'lonja', 'Lj3C726T0' => 'lonja', 'Lj3C726T2' => 'lonja', 'Lj3P725T35' => 'lonja', 'Lj3P727T10' => 'lonja', 'Lj3P727T12' => 'lonja', 'Lj3P727T14' => 'lonja', 'Lj5g0023109' => 'lja', 'Lj6P646T44' => 'lonja', 'Lsat_1_v5_gn_6_75760' => 'lsa', 'Lsat_1_v5_gn_6_75800' => 'lsa', 'Lsat_1_v5_gn_6_75900' => 'lsa', 'Lsat_1_v5_gn_6_76240' => 'lsa', 'Lsat_1_v5_gn_6_76441' => 'lsa', 'Lsat_1_v5_gn_6_76700' => 'lsa', 'Lsat_1_v5_gn_6_76760' => 'lsa', 'Manes.15G033100' => 'mes', 'Mapoly0004s0074' => 'mpo', 'Mapoly0004s0075' => 'mpo', 'Mapoly0004s0163' => 'mpo', 'Mapoly0004s0164' => 'mpo', 'Mapoly0021s0018' => 'mpo', 'Mapoly0041s0136' => 'mpo', 'Mapoly0041s0137' => 'mpo', 'Mapoly0041s0138' => 'mpo', 'Mapoly0041s0139' => 'mpo', 'Mapoly0041s0141' => 'mpo', 'Mapoly0041s0142' => 'mpo', 'Mapoly0041s0143' => 'mpo', 'Mapoly0041s0144' => 'mpo', 'Mapoly0041s0145' => 'mpo', 'Mapoly0047s0106' => 'mpo', 'Mapoly0047s0108' => 'mpo', 'Mapoly0050s0051' => 'mpo', 'Mapoly0050s0052' => 'mpo', 'Mapoly0050s0053' => 'mpo', 'Mapoly0058s0013' => 'mpo', 'Mapoly0091s0078' => 'mpo', 'Mapoly0091s0079' => 'mpo', 'Mapoly0091s0080' => 'mpo', 'Mapoly0091s0081' => 'mpo', 'Mapoly0278s0004' => 'mpo', 'Mapoly0278s0005' => 'mpo', 'Mapoly0278s0006' => 'mpo', 'MBI11_g30648_MAGBIO' => 'mbi', 'MCO03G194' => 'mco', 'MCO03G590' => 'mco', 'MCO07G312' => 'mco', 'MCO10G318' => 'mco', 'MCO12G244' => 'mco', 'MCO13G148' => 'mco', 'MCO13G194' => 'mco', 'MCO16G238' => 'mco', 'MD06G1134100' => 'mdo', 'MD13G1200100' => 'mdo', 'MD13G1200300' => 'mdo', 'MD13G1200600' => 'mdo', 'MD14G1150400' => 'mdo', 'MD16G1200000' => 'mdo', 'Medtr1g102570' => 'mtr', 'Medtr1g102780' => 'mtr', 'Medtr1g102800' => 'mtr', 'Medtr1g102810' => 'mtr', 'Medtr1g102830' => 'mtr', 'MELO3C006499.2' => 'cme', 'Migut.G00385' => 'egut', 'MSTRG.4063' => 'ama', 'Nitab4.5_0000090g0260' => 'nta', 'Nitab4.5_0000977g0030' => 'nta', 'Nitab4.5_0002541g0040' => 'nta', 'Nitab4.5_0007068g0040' => 'nta', 'Nn005s41408' => 'nnu', 'Nn005s41410' => 'nnu', 'Oeu010310.1' => 'oeu', 'Oeu010311.1' => 'oeu', 'Oeu043472.1' => 'oeu', 'Os01g0246400' => 'osa', 'Os04g0267950' => 'osa', 'Os07g0178700' => 'osa', 'Os07g0178800' => 'osa', 'Peaxi162Scf00316g00046' => 'pax', 'Peaxi162Scf00316g00049' => 'pax', 'Peaxi162Scf00316g00059' => 'pax', 'Peaxi162Scf00316g00328' => 'pax', 'Peaxi162Scf00316g00329' => 'pax', 'Peaxi162Scf00316g00411' => 'pax', 'Peaxi162Scf00316g00521' => 'pax', 'Peaxi162Scf00492g00068' => 'pax', 'Peaxi162Scf35631g00002' => 'pax', 'PGR142G3720' => 'pgr', 'PGSC0003DMG400006442' => 'stu', 'Phvul.007G062000' => 'pvu', 'Potri.008G157750' => 'ptr', 'Potri.008G157900' => 'ptr', 'Potri.008G158000' => 'ptr', 'Potri.008G158200' => 'ptr', 'Pp3c11_7280' => 'ppa', 'Pp3c11_7980' => 'ppa', 'Pp3c12_19450' => 'ppa', 'Pp3c14_1480' => 'ppa', 'Pp3c14_1501' => 'ppa', 'Pp3c16_4900' => 'ppa', 'Pp3c16_5010' => 'ppa', 'Pp3c16_5060' => 'ppa', 'Pp3c19_18250' => 'ppa', 'Pp3c23_8530' => 'ppa', 'Pp3c23_8550' => 'ppa', 'Pp3c24_9670' => 'ppa', 'Pp3c2_21390' => 'ppa', 'Pp3c2_31380' => 'ppa', 'Pp3c3_16620' => 'ppa', 'Pp3c3_8090' => 'ppa', 'Pp3c3_8110' => 'ppa', 'Pp3c3_8130' => 'ppa', 'Pp3c3_8150' => 'ppa', 'Pp3c4_14320' => 'ppa', 'Pp3c6_2560' => 'ppa', 'Pp3c9_16700' => 'ppa', 'PRCOL_00000234' => 'pco', 'PRCOL_00000235' => 'pco', 'PRCOL_00000777' => 'pco', 'PRCOL_00002344' => 'pco', 'PRCOL_00002372' => 'pco', 'PRCOL_00006120' => 'pco', 'Prupe.1G021400' => 'ppe', 'Prupe.1G021500' => 'ppe', 'Prupe.1G021600' => 'ppe', 'Prupe.1G021700' => 'ppe', 'Prupe.1G021800' => 'ppe', 'Prupe.5G145100' => 'ppe', 'Psat6g204040' => 'psa', 'Psat6g204800' => 'psa', 'Psat6g204920' => 'psa', 'Psat6g204960' => 'psa', 'Psat6g205080' => 'psa', 'PSO017G0271' => 'pso', 'PSO017G1276' => 'pso', 'PSO017G1429' => 'pso', 'PSO017G1861' => 'pso', 'PSO017G2787' => 'pso', 'PSO017G4466' => 'pso', 'PSO017G5118' => 'pso', 'PSO017G5420' => 'pso', 'PSO063G3678' => 'pso', 'PSO210G0546' => 'pso', 'PSO317G0001' => 'pso', 'PSO357G0512' => 'pso', 'PSO478G2682' => 'pso', 'PSO647G0001' => 'pso', 'PSO675G0001' => 'pso', 'PSO675G2699' => 'pso', 'PSO675G2849' => 'pso', 'PSO675G4991' => 'pso', 'PSO689G0001' => 'pso', 'QL06p000916' => 'qlo', 'QL06p000921' => 'qlo', 'QL06p001398' => 'qlo', 'QL06p001407' => 'qlo', 'QL06p002031' => 'qlo', 'RcHm_v2.0_Chr4g0387791' => 'rch', 'RcHm_v2.0_Chr4g0387801' => 'rch', 'RcHm_v2.0_Chr6g0286501' => 'rch', 'RcHm_v2.0_Chr6g0286511' => 'rch', 'RcHm_v2.0_Chr6g0286521' => 'rch', 'RcHm_v2.0_Chr6g0286531' => 'rch', 'RcHm_v2.0_Chr7g0189141' => 'rch', 'Rhsim02G0028700' => 'rsi', 'Rhsim02G0028800' => 'rsi', 'Rhsim02G0028900' => 'rsi', 'Rhsim02G0029000' => 'rsi', 'Rhsim02G0029100' => 'rsi', 'Rhsim02G0029200' => 'rsi', 'Rhsim02G0029300' => 'rsi', 'Rhsim02G0029400' => 'rsi', 'Rhsim02G0029500' => 'rsi', 'Rhsim02G0029600' => 'rsi', 'RhsimUnG0024000' => 'rsi', 'RhsimUnG0024100' => 'rsi', 'RhsimUnG0024200' => 'rsi', 'RhsimUnG0024300' => 'rsi', 'RhsimUnG0024400' => 'rsi', 'RhsimUnG0024500' => 'rsi', 'RhsimUnG0024700' => 'rsi', 'RhsimUnG0024800' => 'rsi', 'RhsimUnG0024900' => 'rsi', 'RhsimUnG0025100' => 'rsi', 'Sabra08G0120200' => 'sbr', 'Sabra08G0120300' => 'sbr', 'Sabra08G0120500' => 'sbr', 'Sabra08G0120600' => 'sbr', 'Sabra10G0158900' => 'sbr', 'SalBow2G3492' => 'sbo', 'Sc13g0004760' => 'sci', 'Sc13g0004770' => 'sci', 'Sed0003417' => 'sed', 'Sed0019750' => 'sed', 'SEGI_03419' => 'sgi', 'SEGI_05907' => 'sgi', 'SEGI_10682' => 'sgi', 'SEGI_13528' => 'sgi', 'SEGI_16081' => 'sgi', 'SEGI_19370' => 'sgi', 'SEGI_21015' => 'sgi', 'SEGI_21944' => 'sgi', 'SEGI_32906' => 'sgi', 'SEGI_33093' => 'sgi', 'SEGI_36110' => 'sgi', 'SEGI_40397' => 'sgi', 'SGA_v2.0_scaffold191G40426' => 'sas', 'SGA_v2.0_scaffold353G49717' => 'sas', 'SGA_v2.0_scaffold50G18550' => 'sas', 'SMO119G0173' => 'smo', 'SMO172G0002' => 'smo', 'Solyc09g082690.3' => 'sly', 'Solyc09g082700.2' => 'sly', 'Sopen09g031550' => 'spe', 'Sopen09g031560' => 'spe', 'Sp3g20540' => 'spa', 'Sp7g07580' => 'spa', 'TAR134G0002' => 'tar', 'TAR236G0001' => 'tar', 'TAR365G0892' => 'tar', 'TAR636G0166' => 'tar', 'TAR636G0646' => 'tar', 'TAR636G0869' => 'tar', 'TAR636G1317' => 'tar', 'TAR636G1744' => 'tar', 'TAR636G3358' => 'tar', 'TAR636G3436' => 'tar', 'THA.LOC104803047' => 'tha', 'Thecc.04G238900' => 'tca', 'Thhalv10021557m.g' => 'esa', 'Thhalv10026318m.g' => 'esa', 'Thhalv10026335m.g' => 'esa', 'TPR.G17433' => 'tpr', 'TPR.G18915' => 'tpr', 'TPR.G26125' => 'tpr', 'TWI09G0677' => 'twi', 'TWI73G0287' => 'twi', 'unitig_748.g8326' => 'ugi', 'vmacro15370' => 'vma', 'vmacro15371' => 'vma', 'vmacro15372' => 'vma', 'vmacro15373' => 'vma', 'vmacro15374' => 'vma', 'VMungo0720G2826' => 'vmu', 'Zm00001eb116960' => 'zma', 'Zm00001eb301260' => 'zma', 'Zm00001eb301270' => 'zma' ) $gf_id = 'HOM05D001460' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001460' ) $data_identifier = 'HOM05D001460' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 4, 'aag' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 2, 'aox' => (int) 2, 'arhy' => (int) 4, 'ath' => (int) 2, 'atr' => (int) 1, 'acertr' => (int) 10, 'cqu' => (int) 4, 'bca' => (int) 11, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 1, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 1, 'ccan' => (int) 1, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 1, 'col' => (int) 1, 'cpa' => (int) 1, 'cre' => (int) 7, 'csa' => (int) 1, 'camsi' => (int) 2, 'dca' => (int) 3, 'din' => (int) 2, 'dzi' => (int) 3, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 14, 'fve' => (int) 9, 'gma' => (int) 2, 'ghi' => (int) 4, 'gra' => (int) 2, 'vvi' => (int) 1, 'han' => (int) 13, 'cav' => (int) 1, 'hma' => (int) 2, 'sun' => (int) 2, 'lal' => (int) 2, 'lonja' => (int) 12, 'lja' => (int) 1, 'lsa' => (int) 7, 'mes' => (int) 1, 'mpo' => (int) 27, 'mbi' => (int) 1, 'mco' => (int) 8, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 1, 'egut' => (int) 1, 'ama' => (int) 1, 'nta' => (int) 4, 'nnu' => (int) 2, 'oeu' => (int) 3, 'osa' => (int) 4, 'pax' => (int) 9, 'pgr' => (int) 1, 'stu' => (int) 1, 'pvu' => (int) 1, 'ptr' => (int) 4, 'ppa' => (int) 22, 'pco' => (int) 6, 'ppe' => (int) 6, 'psa' => (int) 5, 'pso' => (int) 19, 'qlo' => (int) 5, 'rch' => (int) 7, 'rsi' => (int) 20, 'sbr' => (int) 5, 'sbo' => (int) 1, 'sci' => (int) 2, 'sed' => (int) 2, 'sgi' => (int) 12, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 2, 'tar' => (int) 10, 'tha' => (int) 1, 'tca' => (int) 1, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 2, 'ugi' => (int) 1, 'vma' => (int) 5, 'vmu' => (int) 1, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb301270' $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' => 'HOM05D001460', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '433', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p22980' => 'bna', 'A01p32340' => 'bna', 'A03p42970' => 'bna', 'A05p25880' => 'bna', 'Aa31LG8G9320' => 'aar', 'Aa31LG8G9330' => 'aar', 'Aa31LG8G9340' => 'aar', 'Aa31sc221G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1034' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1528' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.829' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2222' => 'aag', 'Ah.12g058830' => 'amhyb', 'Ah.12g058840' => 'amhyb', 'AL3G37160' => 'aly', 'AL7G41310' => 'aly', 'Aqoxy5G00395' => 'aox', 'Aqoxy5G00396' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0C8NZA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5185HY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JZ1PRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MD3LS0' => 'arhy', 'AT3G22840' => 'ath', 'AT4G14690' => 'ath', 'ATR0665G054' => 'atr', 'Atru.chr4.2344' => 'acertr', 'Atru.chr4.2346' => 'acertr', 'Atru.chr4.2347' => 'acertr', 'Atru.chr4.2348' => 'acertr', 'Atru.chr4.2355' => 'acertr', 'Atru.chr4.2356' => 'acertr', 'Atru.chr4.2358' => 'acertr', 'Atru.chr4.2359' => 'acertr', 'Atru.chr4.2360' => 'acertr', 'Atru.chr4.2361' => 'acertr', 'AUR62030476' => 'cqu', 'AUR62030478' => 'cqu', 'AUR62030819' => 'cqu', 'AUR62030820' => 'cqu', 'BcaB03g14648' => 'bca', 'BcaB04g20492' => 'bca', 'BcaB06g26399' => 'bca', 'BcaC01g03416' => 'bca', 'BcaC01g03419' => 'bca', 'BcaC01g03421' => 'bca', 'BcaC01g03424' => 'bca', 'BcaC05g28012' => 'bca', 'BcaC09g49212' => 'bca', 'BcaC09g50140' => 'bca', 'BcaNung00346' => 'bca', 'BolC1t02785H' => 'bol', 'BolC1t04095H' => 'bol', 'BolC3t17545H' => 'bol', 'BolC5t32769H' => 'bol', 'BraA01t02211Z' => 'bra', 'BraA01t03359Z' => 'bra', 'BraA03t13441Z' => 'bra', 'BraA05t21476Z' => 'bra', 'C01p28420' => 'bna', 'C01p41350' => 'bna', 'C03p52750' => 'bna', 'C03p52780' => 'bna', 'C05p40270' => 'bna', 'CAN.G1437.9' => 'can', 'CANSAT78G0035' => 'cansat', 'CANSAT78G1036' => 'cansat', 'CANSAT78G2272' => 'cansat', 'CANSAT78G2478' => 'cansat', 'CARHR098700' => 'chi', 'CARHR221120' => 'chi', 'CARHR221150' => 'chi', 'Carub.0003s2297' => 'cru', 'Carub.0007s2749' => 'cru', 'Carub.0007s2750' => 'cru', 'Carub.0007s2751' => 'cru', 'Ca_10849_v3' => 'car', 'Cc03_g04300' => 'ccan', 'CDE02G3648' => 'cde', 'CDE05G0060' => 'cde', 'CDE05G0692' => 'cde', 'CDE05G2285' => 'cde', 'CDE05G2884' => 'cde', 'CDE05G3072' => 'cde', 'Cfa008439' => 'cfa', 'Cfa008441' => 'cfa', 'Cfa008443' => 'cfa', 'Cfa008448' => 'cfa', 'Ciclev10005974m.g' => 'ccl', 'Ciclev10006006m.g' => 'ccl', 'Ciclev10006775m.g' => 'ccl', 'CiPaw.02G120400' => 'cil', 'CiPaw.02G120500' => 'cil', 'CiPaw.02G120600' => 'cil', 'ClCG05G004850' => 'cla', 'COL.COLO4_21566' => 'col', 'Cpa.g.sc44.124' => 'cpa', 'Cre07.g320400' => 'cre', 'Cre07.g320450' => 'cre', 'Cre08.g384650' => 'cre', 'Cre09.g393173' => 'cre', 'Cre09.g394325' => 'cre', 'Cre14.g626750' => 'cre', 'Cre16.g679250' => 'cre', 'CsaV3_3G012890' => 'csa', 'CSS0010865' => 'camsi', 'CSS0044338' => 'camsi', 'DCAR_002366' => 'dca', 'DCAR_030687' => 'dca', 'DCAR_030688' => 'dca', 'Dinv14047' => 'din', 'Dinv14048' => 'din', 'Duzib151G0105' => 'dzi', 'Duzib151G0114' => 'dzi', 'Duzib212G1029' => 'dzi', 'ECA232G3536' => 'eca', 'ECA240G0786' => 'eca', 'ECA240G1802' => 'eca', 'ECA240G3760' => 'eca', 'ECA240G3920' => 'eca', 'EL10Ac5g12536' => 'bvu', 'EL10Ac5g12537' => 'bvu', 'EL10Ac5g12538' => 'bvu', 'Eucgr.B01004' => 'egr', 'Eucgr.B01006' => 'egr', 'Eucgr.B01007' => 'egr', 'Eucgr.B01008' => 'egr', 'Eucgr.B01895' => 'egr', 'Eucgr.B01896' => 'egr', 'FAN04G1456' => 'fan', 'FAN08G1769' => 'fan', 'FAN08G2160' => 'fan', 'FAN13G2403' => 'fan', 'FAN13G3303' => 'fan', 'FAN15G2435' => 'fan', 'FAN17G0672' => 'fan', 'FAN17G2441' => 'fan', 'FAN18G1024' => 'fan', 'FAN22G1458' => 'fan', 'FAN24G0037' => 'fan', 'FAN24G0429' => 'fan', 'FAN24G2387' => 'fan', 'FAN27G2746' => 'fan', 'FvH4_2g20400' => 'fve', 'FvH4_2g20420' => 'fve', 'FvH4_2g20430' => 'fve', 'FvH4_4g01270' => 'fve', 'FvH4_4g01290' => 'fve', 'FvH4_4g01300' => 'fve', 'FvH4_4g01310' => 'fve', 'FvH4_4g01330' => 'fve', 'FvH4_5g09070' => 'fve', 'Glyma.10G243800' => 'gma', 'Glyma.20G150600' => 'gma', 'Gohir.A09G219200' => 'ghi', 'Gohir.A09G219300' => 'ghi', 'Gohir.D09G221400' => 'ghi', 'Gohir.D09G221500' => 'ghi', 'Gorai.006G242600' => 'gra', 'Gorai.006G242700' => 'gra', 'GSVIVG01018044001' => 'vvi', 'HanXRQChr03g0083821' => 'han', 'HanXRQChr03g0083841' => 'han', 'HanXRQChr03g0083881' => 'han', 'HanXRQChr03g0083901' => 'han', 'HanXRQChr03g0083921' => 'han', 'HanXRQChr03g0085331' => 'han', 'HanXRQChr03g0085361' => 'han', 'HanXRQChr03g0085411' => 'han', 'HanXRQChr03g0085421' => 'han', 'HanXRQChr03g0085431' => 'han', 'HanXRQChr08g0221991' => 'han', 'HanXRQChr11g0336061' => 'han', 'HanXRQChr11g0336411' => 'han', 'Haze_11234' => 'cav', 'Hma1.2p1_0549F.1_g177010' => 'hma', 'Hma1.2p1_0602F.1_g187630' => 'hma', 'Hund14876' => 'sun', 'Hund14879' => 'sun', 'Lalb_Chr06g0160741' => 'lal', 'Lalb_Chr21g0304781' => 'lal', 'Lj3A726G19' => 'lonja', 'Lj3A726T23' => 'lonja', 'Lj3A726T24' => 'lonja', 'Lj3A726T25' => 'lonja', 'Lj3A727T17' => 'lonja', 'Lj3C726T0' => 'lonja', 'Lj3C726T2' => 'lonja', 'Lj3P725T35' => 'lonja', 'Lj3P727T10' => 'lonja', 'Lj3P727T12' => 'lonja', 'Lj3P727T14' => 'lonja', 'Lj5g0023109' => 'lja', 'Lj6P646T44' => 'lonja', 'Lsat_1_v5_gn_6_75760' => 'lsa', 'Lsat_1_v5_gn_6_75800' => 'lsa', 'Lsat_1_v5_gn_6_75900' => 'lsa', 'Lsat_1_v5_gn_6_76240' => 'lsa', 'Lsat_1_v5_gn_6_76441' => 'lsa', 'Lsat_1_v5_gn_6_76700' => 'lsa', 'Lsat_1_v5_gn_6_76760' => 'lsa', 'Manes.15G033100' => 'mes', 'Mapoly0004s0074' => 'mpo', 'Mapoly0004s0075' => 'mpo', 'Mapoly0004s0163' => 'mpo', 'Mapoly0004s0164' => 'mpo', 'Mapoly0021s0018' => 'mpo', 'Mapoly0041s0136' => 'mpo', 'Mapoly0041s0137' => 'mpo', 'Mapoly0041s0138' => 'mpo', 'Mapoly0041s0139' => 'mpo', 'Mapoly0041s0141' => 'mpo', 'Mapoly0041s0142' => 'mpo', 'Mapoly0041s0143' => 'mpo', 'Mapoly0041s0144' => 'mpo', 'Mapoly0041s0145' => 'mpo', 'Mapoly0047s0106' => 'mpo', 'Mapoly0047s0108' => 'mpo', 'Mapoly0050s0051' => 'mpo', 'Mapoly0050s0052' => 'mpo', 'Mapoly0050s0053' => 'mpo', 'Mapoly0058s0013' => 'mpo', 'Mapoly0091s0078' => 'mpo', 'Mapoly0091s0079' => 'mpo', 'Mapoly0091s0080' => 'mpo', 'Mapoly0091s0081' => 'mpo', 'Mapoly0278s0004' => 'mpo', 'Mapoly0278s0005' => 'mpo', 'Mapoly0278s0006' => 'mpo', 'MBI11_g30648_MAGBIO' => 'mbi', 'MCO03G194' => 'mco', 'MCO03G590' => 'mco', 'MCO07G312' => 'mco', 'MCO10G318' => 'mco', 'MCO12G244' => 'mco', 'MCO13G148' => 'mco', 'MCO13G194' => 'mco', 'MCO16G238' => 'mco', 'MD06G1134100' => 'mdo', 'MD13G1200100' => 'mdo', 'MD13G1200300' => 'mdo', 'MD13G1200600' => 'mdo', 'MD14G1150400' => 'mdo', 'MD16G1200000' => 'mdo', 'Medtr1g102570' => 'mtr', 'Medtr1g102780' => 'mtr', 'Medtr1g102800' => 'mtr', 'Medtr1g102810' => 'mtr', 'Medtr1g102830' => 'mtr', 'MELO3C006499.2' => 'cme', 'Migut.G00385' => 'egut', 'MSTRG.4063' => 'ama', 'Nitab4.5_0000090g0260' => 'nta', 'Nitab4.5_0000977g0030' => 'nta', 'Nitab4.5_0002541g0040' => 'nta', 'Nitab4.5_0007068g0040' => 'nta', 'Nn005s41408' => 'nnu', 'Nn005s41410' => 'nnu', 'Oeu010310.1' => 'oeu', 'Oeu010311.1' => 'oeu', 'Oeu043472.1' => 'oeu', 'Os01g0246400' => 'osa', 'Os04g0267950' => 'osa', 'Os07g0178700' => 'osa', 'Os07g0178800' => 'osa', 'Peaxi162Scf00316g00046' => 'pax', 'Peaxi162Scf00316g00049' => 'pax', 'Peaxi162Scf00316g00059' => 'pax', 'Peaxi162Scf00316g00328' => 'pax', 'Peaxi162Scf00316g00329' => 'pax', 'Peaxi162Scf00316g00411' => 'pax', 'Peaxi162Scf00316g00521' => 'pax', 'Peaxi162Scf00492g00068' => 'pax', 'Peaxi162Scf35631g00002' => 'pax', 'PGR142G3720' => 'pgr', 'PGSC0003DMG400006442' => 'stu', 'Phvul.007G062000' => 'pvu', 'Potri.008G157750' => 'ptr', 'Potri.008G157900' => 'ptr', 'Potri.008G158000' => 'ptr', 'Potri.008G158200' => 'ptr', 'Pp3c11_7280' => 'ppa', 'Pp3c11_7980' => 'ppa', 'Pp3c12_19450' => 'ppa', 'Pp3c14_1480' => 'ppa', 'Pp3c14_1501' => 'ppa', 'Pp3c16_4900' => 'ppa', 'Pp3c16_5010' => 'ppa', 'Pp3c16_5060' => 'ppa', 'Pp3c19_18250' => 'ppa', 'Pp3c23_8530' => 'ppa', 'Pp3c23_8550' => 'ppa', 'Pp3c24_9670' => 'ppa', 'Pp3c2_21390' => 'ppa', 'Pp3c2_31380' => 'ppa', 'Pp3c3_16620' => 'ppa', 'Pp3c3_8090' => 'ppa', 'Pp3c3_8110' => 'ppa', 'Pp3c3_8130' => 'ppa', 'Pp3c3_8150' => 'ppa', 'Pp3c4_14320' => 'ppa', 'Pp3c6_2560' => 'ppa', 'Pp3c9_16700' => 'ppa', 'PRCOL_00000234' => 'pco', 'PRCOL_00000235' => 'pco', 'PRCOL_00000777' => 'pco', 'PRCOL_00002344' => 'pco', 'PRCOL_00002372' => 'pco', 'PRCOL_00006120' => 'pco', 'Prupe.1G021400' => 'ppe', 'Prupe.1G021500' => 'ppe', 'Prupe.1G021600' => 'ppe', 'Prupe.1G021700' => 'ppe', 'Prupe.1G021800' => 'ppe', 'Prupe.5G145100' => 'ppe', 'Psat6g204040' => 'psa', 'Psat6g204800' => 'psa', 'Psat6g204920' => 'psa', 'Psat6g204960' => 'psa', 'Psat6g205080' => 'psa', 'PSO017G0271' => 'pso', 'PSO017G1276' => 'pso', 'PSO017G1429' => 'pso', 'PSO017G1861' => 'pso', 'PSO017G2787' => 'pso', 'PSO017G4466' => 'pso', 'PSO017G5118' => 'pso', 'PSO017G5420' => 'pso', 'PSO063G3678' => 'pso', 'PSO210G0546' => 'pso', 'PSO317G0001' => 'pso', 'PSO357G0512' => 'pso', 'PSO478G2682' => 'pso', 'PSO647G0001' => 'pso', 'PSO675G0001' => 'pso', 'PSO675G2699' => 'pso', 'PSO675G2849' => 'pso', 'PSO675G4991' => 'pso', 'PSO689G0001' => 'pso', 'QL06p000916' => 'qlo', 'QL06p000921' => 'qlo', 'QL06p001398' => 'qlo', 'QL06p001407' => 'qlo', 'QL06p002031' => 'qlo', 'RcHm_v2.0_Chr4g0387791' => 'rch', 'RcHm_v2.0_Chr4g0387801' => 'rch', 'RcHm_v2.0_Chr6g0286501' => 'rch', 'RcHm_v2.0_Chr6g0286511' => 'rch', 'RcHm_v2.0_Chr6g0286521' => 'rch', 'RcHm_v2.0_Chr6g0286531' => 'rch', 'RcHm_v2.0_Chr7g0189141' => 'rch', 'Rhsim02G0028700' => 'rsi', 'Rhsim02G0028800' => 'rsi', 'Rhsim02G0028900' => 'rsi', 'Rhsim02G0029000' => 'rsi', 'Rhsim02G0029100' => 'rsi', 'Rhsim02G0029200' => 'rsi', 'Rhsim02G0029300' => 'rsi', 'Rhsim02G0029400' => 'rsi', 'Rhsim02G0029500' => 'rsi', 'Rhsim02G0029600' => 'rsi', 'RhsimUnG0024000' => 'rsi', 'RhsimUnG0024100' => 'rsi', 'RhsimUnG0024200' => 'rsi', 'RhsimUnG0024300' => 'rsi', 'RhsimUnG0024400' => 'rsi', 'RhsimUnG0024500' => 'rsi', 'RhsimUnG0024700' => 'rsi', 'RhsimUnG0024800' => 'rsi', 'RhsimUnG0024900' => 'rsi', 'RhsimUnG0025100' => 'rsi', 'Sabra08G0120200' => 'sbr', 'Sabra08G0120300' => 'sbr', 'Sabra08G0120500' => 'sbr', 'Sabra08G0120600' => 'sbr', 'Sabra10G0158900' => 'sbr', 'SalBow2G3492' => 'sbo', 'Sc13g0004760' => 'sci', 'Sc13g0004770' => 'sci', 'Sed0003417' => 'sed', 'Sed0019750' => 'sed', 'SEGI_03419' => 'sgi', 'SEGI_05907' => 'sgi', 'SEGI_10682' => 'sgi', 'SEGI_13528' => 'sgi', 'SEGI_16081' => 'sgi', 'SEGI_19370' => 'sgi', 'SEGI_21015' => 'sgi', 'SEGI_21944' => 'sgi', 'SEGI_32906' => 'sgi', 'SEGI_33093' => 'sgi', 'SEGI_36110' => 'sgi', 'SEGI_40397' => 'sgi', 'SGA_v2.0_scaffold191G40426' => 'sas', 'SGA_v2.0_scaffold353G49717' => 'sas', 'SGA_v2.0_scaffold50G18550' => 'sas', 'SMO119G0173' => 'smo', 'SMO172G0002' => 'smo', 'Solyc09g082690.3' => 'sly', 'Solyc09g082700.2' => 'sly', 'Sopen09g031550' => 'spe', 'Sopen09g031560' => 'spe', 'Sp3g20540' => 'spa', 'Sp7g07580' => 'spa', 'TAR134G0002' => 'tar', 'TAR236G0001' => 'tar', 'TAR365G0892' => 'tar', 'TAR636G0166' => 'tar', 'TAR636G0646' => 'tar', 'TAR636G0869' => 'tar', 'TAR636G1317' => 'tar', 'TAR636G1744' => 'tar', 'TAR636G3358' => 'tar', 'TAR636G3436' => 'tar', 'THA.LOC104803047' => 'tha', 'Thecc.04G238900' => 'tca', 'Thhalv10021557m.g' => 'esa', 'Thhalv10026318m.g' => 'esa', 'Thhalv10026335m.g' => 'esa', 'TPR.G17433' => 'tpr', 'TPR.G18915' => 'tpr', 'TPR.G26125' => 'tpr', 'TWI09G0677' => 'twi', 'TWI73G0287' => 'twi', 'unitig_748.g8326' => 'ugi', 'vmacro15370' => 'vma', 'vmacro15371' => 'vma', 'vmacro15372' => 'vma', 'vmacro15373' => 'vma', 'vmacro15374' => 'vma', 'VMungo0720G2826' => 'vmu', 'Zm00001eb116960' => 'zma', 'Zm00001eb301260' => 'zma', 'Zm00001eb301270' => 'zma' ), 'gf_id' => 'HOM05D001460', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001460' ), 'data_identifier' => 'HOM05D001460', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001460', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '433', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p22980' => 'bna', 'A01p32340' => 'bna', 'A03p42970' => 'bna', 'A05p25880' => 'bna', 'Aa31LG8G9320' => 'aar', 'Aa31LG8G9330' => 'aar', 'Aa31LG8G9340' => 'aar', 'Aa31sc221G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1034' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1528' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.829' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2222' => 'aag', 'Ah.12g058830' => 'amhyb', 'Ah.12g058840' => 'amhyb', 'AL3G37160' => 'aly', 'AL7G41310' => 'aly', 'Aqoxy5G00395' => 'aox', 'Aqoxy5G00396' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0C8NZA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5185HY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JZ1PRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MD3LS0' => 'arhy', 'AT3G22840' => 'ath', 'AT4G14690' => 'ath', 'ATR0665G054' => 'atr', 'Atru.chr4.2344' => 'acertr', 'Atru.chr4.2346' => 'acertr', 'Atru.chr4.2347' => 'acertr', 'Atru.chr4.2348' => 'acertr', 'Atru.chr4.2355' => 'acertr', 'Atru.chr4.2356' => 'acertr', 'Atru.chr4.2358' => 'acertr', 'Atru.chr4.2359' => 'acertr', 'Atru.chr4.2360' => 'acertr', 'Atru.chr4.2361' => 'acertr', 'AUR62030476' => 'cqu', 'AUR62030478' => 'cqu', 'AUR62030819' => 'cqu', 'AUR62030820' => 'cqu', 'BcaB03g14648' => 'bca', 'BcaB04g20492' => 'bca', 'BcaB06g26399' => 'bca', 'BcaC01g03416' => 'bca', 'BcaC01g03419' => 'bca', 'BcaC01g03421' => 'bca', 'BcaC01g03424' => 'bca', 'BcaC05g28012' => 'bca', 'BcaC09g49212' => 'bca', 'BcaC09g50140' => 'bca', 'BcaNung00346' => 'bca', 'BolC1t02785H' => 'bol', 'BolC1t04095H' => 'bol', 'BolC3t17545H' => 'bol', 'BolC5t32769H' => 'bol', 'BraA01t02211Z' => 'bra', 'BraA01t03359Z' => 'bra', 'BraA03t13441Z' => 'bra', 'BraA05t21476Z' => 'bra', 'C01p28420' => 'bna', 'C01p41350' => 'bna', 'C03p52750' => 'bna', 'C03p52780' => 'bna', 'C05p40270' => 'bna', 'CAN.G1437.9' => 'can', 'CANSAT78G0035' => 'cansat', 'CANSAT78G1036' => 'cansat', 'CANSAT78G2272' => 'cansat', 'CANSAT78G2478' => 'cansat', 'CARHR098700' => 'chi', 'CARHR221120' => 'chi', 'CARHR221150' => 'chi', 'Carub.0003s2297' => 'cru', 'Carub.0007s2749' => 'cru', 'Carub.0007s2750' => 'cru', 'Carub.0007s2751' => 'cru', 'Ca_10849_v3' => 'car', 'Cc03_g04300' => 'ccan', 'CDE02G3648' => 'cde', 'CDE05G0060' => 'cde', 'CDE05G0692' => 'cde', 'CDE05G2285' => 'cde', 'CDE05G2884' => 'cde', 'CDE05G3072' => 'cde', 'Cfa008439' => 'cfa', 'Cfa008441' => 'cfa', 'Cfa008443' => 'cfa', 'Cfa008448' => 'cfa', 'Ciclev10005974m.g' => 'ccl', 'Ciclev10006006m.g' => 'ccl', 'Ciclev10006775m.g' => 'ccl', 'CiPaw.02G120400' => 'cil', 'CiPaw.02G120500' => 'cil', 'CiPaw.02G120600' => 'cil', 'ClCG05G004850' => 'cla', 'COL.COLO4_21566' => 'col', 'Cpa.g.sc44.124' => 'cpa', 'Cre07.g320400' => 'cre', 'Cre07.g320450' => 'cre', 'Cre08.g384650' => 'cre', 'Cre09.g393173' => 'cre', 'Cre09.g394325' => 'cre', 'Cre14.g626750' => 'cre', 'Cre16.g679250' => 'cre', 'CsaV3_3G012890' => 'csa', 'CSS0010865' => 'camsi', 'CSS0044338' => 'camsi', 'DCAR_002366' => 'dca', 'DCAR_030687' => 'dca', 'DCAR_030688' => 'dca', 'Dinv14047' => 'din', 'Dinv14048' => 'din', 'Duzib151G0105' => 'dzi', 'Duzib151G0114' => 'dzi', 'Duzib212G1029' => 'dzi', 'ECA232G3536' => 'eca', 'ECA240G0786' => 'eca', 'ECA240G1802' => 'eca', 'ECA240G3760' => 'eca', 'ECA240G3920' => 'eca', 'EL10Ac5g12536' => 'bvu', 'EL10Ac5g12537' => 'bvu', 'EL10Ac5g12538' => 'bvu', 'Eucgr.B01004' => 'egr', 'Eucgr.B01006' => 'egr', 'Eucgr.B01007' => 'egr', 'Eucgr.B01008' => 'egr', 'Eucgr.B01895' => 'egr', 'Eucgr.B01896' => 'egr', 'FAN04G1456' => 'fan', 'FAN08G1769' => 'fan', 'FAN08G2160' => 'fan', 'FAN13G2403' => 'fan', 'FAN13G3303' => 'fan', 'FAN15G2435' => 'fan', 'FAN17G0672' => 'fan', 'FAN17G2441' => 'fan', 'FAN18G1024' => 'fan', 'FAN22G1458' => 'fan', 'FAN24G0037' => 'fan', 'FAN24G0429' => 'fan', 'FAN24G2387' => 'fan', 'FAN27G2746' => 'fan', 'FvH4_2g20400' => 'fve', 'FvH4_2g20420' => 'fve', 'FvH4_2g20430' => 'fve', 'FvH4_4g01270' => 'fve', 'FvH4_4g01290' => 'fve', 'FvH4_4g01300' => 'fve', 'FvH4_4g01310' => 'fve', 'FvH4_4g01330' => 'fve', 'FvH4_5g09070' => 'fve', 'Glyma.10G243800' => 'gma', 'Glyma.20G150600' => 'gma', 'Gohir.A09G219200' => 'ghi', 'Gohir.A09G219300' => 'ghi', 'Gohir.D09G221400' => 'ghi', 'Gohir.D09G221500' => 'ghi', 'Gorai.006G242600' => 'gra', 'Gorai.006G242700' => 'gra', 'GSVIVG01018044001' => 'vvi', 'HanXRQChr03g0083821' => 'han', 'HanXRQChr03g0083841' => 'han', 'HanXRQChr03g0083881' => 'han', 'HanXRQChr03g0083901' => 'han', 'HanXRQChr03g0083921' => 'han', 'HanXRQChr03g0085331' => 'han', 'HanXRQChr03g0085361' => 'han', 'HanXRQChr03g0085411' => 'han', 'HanXRQChr03g0085421' => 'han', 'HanXRQChr03g0085431' => 'han', 'HanXRQChr08g0221991' => 'han', 'HanXRQChr11g0336061' => 'han', 'HanXRQChr11g0336411' => 'han', 'Haze_11234' => 'cav', 'Hma1.2p1_0549F.1_g177010' => 'hma', 'Hma1.2p1_0602F.1_g187630' => 'hma', 'Hund14876' => 'sun', 'Hund14879' => 'sun', 'Lalb_Chr06g0160741' => 'lal', 'Lalb_Chr21g0304781' => 'lal', 'Lj3A726G19' => 'lonja', 'Lj3A726T23' => 'lonja', 'Lj3A726T24' => 'lonja', 'Lj3A726T25' => 'lonja', 'Lj3A727T17' => 'lonja', 'Lj3C726T0' => 'lonja', 'Lj3C726T2' => 'lonja', 'Lj3P725T35' => 'lonja', 'Lj3P727T10' => 'lonja', 'Lj3P727T12' => 'lonja', 'Lj3P727T14' => 'lonja', 'Lj5g0023109' => 'lja', 'Lj6P646T44' => 'lonja', 'Lsat_1_v5_gn_6_75760' => 'lsa', 'Lsat_1_v5_gn_6_75800' => 'lsa', 'Lsat_1_v5_gn_6_75900' => 'lsa', 'Lsat_1_v5_gn_6_76240' => 'lsa', 'Lsat_1_v5_gn_6_76441' => 'lsa', 'Lsat_1_v5_gn_6_76700' => 'lsa', 'Lsat_1_v5_gn_6_76760' => 'lsa', 'Manes.15G033100' => 'mes', 'Mapoly0004s0074' => 'mpo', 'Mapoly0004s0075' => 'mpo', 'Mapoly0004s0163' => 'mpo', 'Mapoly0004s0164' => 'mpo', 'Mapoly0021s0018' => 'mpo', 'Mapoly0041s0136' => 'mpo', 'Mapoly0041s0137' => 'mpo', 'Mapoly0041s0138' => 'mpo', 'Mapoly0041s0139' => 'mpo', 'Mapoly0041s0141' => 'mpo', 'Mapoly0041s0142' => 'mpo', 'Mapoly0041s0143' => 'mpo', 'Mapoly0041s0144' => 'mpo', 'Mapoly0041s0145' => 'mpo', 'Mapoly0047s0106' => 'mpo', 'Mapoly0047s0108' => 'mpo', 'Mapoly0050s0051' => 'mpo', 'Mapoly0050s0052' => 'mpo', 'Mapoly0050s0053' => 'mpo', 'Mapoly0058s0013' => 'mpo', 'Mapoly0091s0078' => 'mpo', 'Mapoly0091s0079' => 'mpo', 'Mapoly0091s0080' => 'mpo', 'Mapoly0091s0081' => 'mpo', 'Mapoly0278s0004' => 'mpo', 'Mapoly0278s0005' => 'mpo', 'Mapoly0278s0006' => 'mpo', 'MBI11_g30648_MAGBIO' => 'mbi', 'MCO03G194' => 'mco', 'MCO03G590' => 'mco', 'MCO07G312' => 'mco', 'MCO10G318' => 'mco', 'MCO12G244' => 'mco', 'MCO13G148' => 'mco', 'MCO13G194' => 'mco', 'MCO16G238' => 'mco', 'MD06G1134100' => 'mdo', 'MD13G1200100' => 'mdo', 'MD13G1200300' => 'mdo', 'MD13G1200600' => 'mdo', 'MD14G1150400' => 'mdo', 'MD16G1200000' => 'mdo', 'Medtr1g102570' => 'mtr', 'Medtr1g102780' => 'mtr', 'Medtr1g102800' => 'mtr', 'Medtr1g102810' => 'mtr', 'Medtr1g102830' => 'mtr', 'MELO3C006499.2' => 'cme', 'Migut.G00385' => 'egut', 'MSTRG.4063' => 'ama', 'Nitab4.5_0000090g0260' => 'nta', 'Nitab4.5_0000977g0030' => 'nta', 'Nitab4.5_0002541g0040' => 'nta', 'Nitab4.5_0007068g0040' => 'nta', 'Nn005s41408' => 'nnu', 'Nn005s41410' => 'nnu', 'Oeu010310.1' => 'oeu', 'Oeu010311.1' => 'oeu', 'Oeu043472.1' => 'oeu', 'Os01g0246400' => 'osa', 'Os04g0267950' => 'osa', 'Os07g0178700' => 'osa', 'Os07g0178800' => 'osa', 'Peaxi162Scf00316g00046' => 'pax', 'Peaxi162Scf00316g00049' => 'pax', 'Peaxi162Scf00316g00059' => 'pax', 'Peaxi162Scf00316g00328' => 'pax', 'Peaxi162Scf00316g00329' => 'pax', 'Peaxi162Scf00316g00411' => 'pax', 'Peaxi162Scf00316g00521' => 'pax', 'Peaxi162Scf00492g00068' => 'pax', 'Peaxi162Scf35631g00002' => 'pax', 'PGR142G3720' => 'pgr', 'PGSC0003DMG400006442' => 'stu', 'Phvul.007G062000' => 'pvu', 'Potri.008G157750' => 'ptr', 'Potri.008G157900' => 'ptr', 'Potri.008G158000' => 'ptr', 'Potri.008G158200' => 'ptr', 'Pp3c11_7280' => 'ppa', 'Pp3c11_7980' => 'ppa', 'Pp3c12_19450' => 'ppa', 'Pp3c14_1480' => 'ppa', 'Pp3c14_1501' => 'ppa', 'Pp3c16_4900' => 'ppa', 'Pp3c16_5010' => 'ppa', 'Pp3c16_5060' => 'ppa', 'Pp3c19_18250' => 'ppa', 'Pp3c23_8530' => 'ppa', 'Pp3c23_8550' => 'ppa', 'Pp3c24_9670' => 'ppa', 'Pp3c2_21390' => 'ppa', 'Pp3c2_31380' => 'ppa', 'Pp3c3_16620' => 'ppa', 'Pp3c3_8090' => 'ppa', 'Pp3c3_8110' => 'ppa', 'Pp3c3_8130' => 'ppa', 'Pp3c3_8150' => 'ppa', 'Pp3c4_14320' => 'ppa', 'Pp3c6_2560' => 'ppa', 'Pp3c9_16700' => 'ppa', 'PRCOL_00000234' => 'pco', 'PRCOL_00000235' => 'pco', 'PRCOL_00000777' => 'pco', 'PRCOL_00002344' => 'pco', 'PRCOL_00002372' => 'pco', 'PRCOL_00006120' => 'pco', 'Prupe.1G021400' => 'ppe', 'Prupe.1G021500' => 'ppe', 'Prupe.1G021600' => 'ppe', 'Prupe.1G021700' => 'ppe', 'Prupe.1G021800' => 'ppe', 'Prupe.5G145100' => 'ppe', 'Psat6g204040' => 'psa', 'Psat6g204800' => 'psa', 'Psat6g204920' => 'psa', 'Psat6g204960' => 'psa', 'Psat6g205080' => 'psa', 'PSO017G0271' => 'pso', 'PSO017G1276' => 'pso', 'PSO017G1429' => 'pso', 'PSO017G1861' => 'pso', 'PSO017G2787' => 'pso', 'PSO017G4466' => 'pso', 'PSO017G5118' => 'pso', 'PSO017G5420' => 'pso', 'PSO063G3678' => 'pso', 'PSO210G0546' => 'pso', 'PSO317G0001' => 'pso', 'PSO357G0512' => 'pso', 'PSO478G2682' => 'pso', 'PSO647G0001' => 'pso', 'PSO675G0001' => 'pso', 'PSO675G2699' => 'pso', 'PSO675G2849' => 'pso', 'PSO675G4991' => 'pso', 'PSO689G0001' => 'pso', 'QL06p000916' => 'qlo', 'QL06p000921' => 'qlo', 'QL06p001398' => 'qlo', 'QL06p001407' => 'qlo', 'QL06p002031' => 'qlo', 'RcHm_v2.0_Chr4g0387791' => 'rch', 'RcHm_v2.0_Chr4g0387801' => 'rch', 'RcHm_v2.0_Chr6g0286501' => 'rch', 'RcHm_v2.0_Chr6g0286511' => 'rch', 'RcHm_v2.0_Chr6g0286521' => 'rch', 'RcHm_v2.0_Chr6g0286531' => 'rch', 'RcHm_v2.0_Chr7g0189141' => 'rch', 'Rhsim02G0028700' => 'rsi', 'Rhsim02G0028800' => 'rsi', 'Rhsim02G0028900' => 'rsi', 'Rhsim02G0029000' => 'rsi', 'Rhsim02G0029100' => 'rsi', 'Rhsim02G0029200' => 'rsi', 'Rhsim02G0029300' => 'rsi', 'Rhsim02G0029400' => 'rsi', 'Rhsim02G0029500' => 'rsi', 'Rhsim02G0029600' => 'rsi', 'RhsimUnG0024000' => 'rsi', 'RhsimUnG0024100' => 'rsi', 'RhsimUnG0024200' => 'rsi', 'RhsimUnG0024300' => 'rsi', 'RhsimUnG0024400' => 'rsi', 'RhsimUnG0024500' => 'rsi', 'RhsimUnG0024700' => 'rsi', 'RhsimUnG0024800' => 'rsi', 'RhsimUnG0024900' => 'rsi', 'RhsimUnG0025100' => 'rsi', 'Sabra08G0120200' => 'sbr', 'Sabra08G0120300' => 'sbr', 'Sabra08G0120500' => 'sbr', 'Sabra08G0120600' => 'sbr', 'Sabra10G0158900' => 'sbr', 'SalBow2G3492' => 'sbo', 'Sc13g0004760' => 'sci', 'Sc13g0004770' => 'sci', 'Sed0003417' => 'sed', 'Sed0019750' => 'sed', 'SEGI_03419' => 'sgi', 'SEGI_05907' => 'sgi', 'SEGI_10682' => 'sgi', 'SEGI_13528' => 'sgi', 'SEGI_16081' => 'sgi', 'SEGI_19370' => 'sgi', 'SEGI_21015' => 'sgi', 'SEGI_21944' => 'sgi', 'SEGI_32906' => 'sgi', 'SEGI_33093' => 'sgi', 'SEGI_36110' => 'sgi', 'SEGI_40397' => 'sgi', 'SGA_v2.0_scaffold191G40426' => 'sas', 'SGA_v2.0_scaffold353G49717' => 'sas', 'SGA_v2.0_scaffold50G18550' => 'sas', 'SMO119G0173' => 'smo', 'SMO172G0002' => 'smo', 'Solyc09g082690.3' => 'sly', 'Solyc09g082700.2' => 'sly', 'Sopen09g031550' => 'spe', 'Sopen09g031560' => 'spe', 'Sp3g20540' => 'spa', 'Sp7g07580' => 'spa', 'TAR134G0002' => 'tar', 'TAR236G0001' => 'tar', 'TAR365G0892' => 'tar', 'TAR636G0166' => 'tar', 'TAR636G0646' => 'tar', 'TAR636G0869' => 'tar', 'TAR636G1317' => 'tar', 'TAR636G1744' => 'tar', 'TAR636G3358' => 'tar', 'TAR636G3436' => 'tar', 'THA.LOC104803047' => 'tha', 'Thecc.04G238900' => 'tca', 'Thhalv10021557m.g' => 'esa', 'Thhalv10026318m.g' => 'esa', 'Thhalv10026335m.g' => 'esa', 'TPR.G17433' => 'tpr', 'TPR.G18915' => 'tpr', 'TPR.G26125' => 'tpr', 'TWI09G0677' => 'twi', 'TWI73G0287' => 'twi', 'unitig_748.g8326' => 'ugi', 'vmacro15370' => 'vma', 'vmacro15371' => 'vma', 'vmacro15372' => 'vma', 'vmacro15373' => 'vma', 'vmacro15374' => 'vma', 'VMungo0720G2826' => 'vmu', 'Zm00001eb116960' => 'zma', 'Zm00001eb301260' => 'zma', 'Zm00001eb301270' => 'zma' ) $gf_id = 'HOM05D001460' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001460' ) $data_identifier = 'HOM05D001460' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 4, 'aag' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 2, 'aox' => (int) 2, 'arhy' => (int) 4, 'ath' => (int) 2, 'atr' => (int) 1, 'acertr' => (int) 10, 'cqu' => (int) 4, 'bca' => (int) 11, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 1, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 1, 'ccan' => (int) 1, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 1, 'col' => (int) 1, 'cpa' => (int) 1, 'cre' => (int) 7, 'csa' => (int) 1, 'camsi' => (int) 2, 'dca' => (int) 3, 'din' => (int) 2, 'dzi' => (int) 3, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 14, 'fve' => (int) 9, 'gma' => (int) 2, 'ghi' => (int) 4, 'gra' => (int) 2, 'vvi' => (int) 1, 'han' => (int) 13, 'cav' => (int) 1, 'hma' => (int) 2, 'sun' => (int) 2, 'lal' => (int) 2, 'lonja' => (int) 12, 'lja' => (int) 1, 'lsa' => (int) 7, 'mes' => (int) 1, 'mpo' => (int) 27, 'mbi' => (int) 1, 'mco' => (int) 8, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 1, 'egut' => (int) 1, 'ama' => (int) 1, 'nta' => (int) 4, 'nnu' => (int) 2, 'oeu' => (int) 3, 'osa' => (int) 4, 'pax' => (int) 9, 'pgr' => (int) 1, 'stu' => (int) 1, 'pvu' => (int) 1, 'ptr' => (int) 4, 'ppa' => (int) 22, 'pco' => (int) 6, 'ppe' => (int) 6, 'psa' => (int) 5, 'pso' => (int) 19, 'qlo' => (int) 5, 'rch' => (int) 7, 'rsi' => (int) 20, 'sbr' => (int) 5, 'sbo' => (int) 1, 'sci' => (int) 2, 'sed' => (int) 2, 'sgi' => (int) 12, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 2, 'tar' => (int) 10, 'tha' => (int) 1, 'tca' => (int) 1, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 2, 'ugi' => (int) 1, 'vma' => (int) 5, 'vmu' => (int) 1, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb301270' $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' => 'HOM05D001460', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '433', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p22980' => 'bna', 'A01p32340' => 'bna', 'A03p42970' => 'bna', 'A05p25880' => 'bna', 'Aa31LG8G9320' => 'aar', 'Aa31LG8G9330' => 'aar', 'Aa31LG8G9340' => 'aar', 'Aa31sc221G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1034' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1528' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.829' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2222' => 'aag', 'Ah.12g058830' => 'amhyb', 'Ah.12g058840' => 'amhyb', 'AL3G37160' => 'aly', 'AL7G41310' => 'aly', 'Aqoxy5G00395' => 'aox', 'Aqoxy5G00396' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0C8NZA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5185HY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JZ1PRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MD3LS0' => 'arhy', 'AT3G22840' => 'ath', 'AT4G14690' => 'ath', 'ATR0665G054' => 'atr', 'Atru.chr4.2344' => 'acertr', 'Atru.chr4.2346' => 'acertr', 'Atru.chr4.2347' => 'acertr', 'Atru.chr4.2348' => 'acertr', 'Atru.chr4.2355' => 'acertr', 'Atru.chr4.2356' => 'acertr', 'Atru.chr4.2358' => 'acertr', 'Atru.chr4.2359' => 'acertr', 'Atru.chr4.2360' => 'acertr', 'Atru.chr4.2361' => 'acertr', 'AUR62030476' => 'cqu', 'AUR62030478' => 'cqu', 'AUR62030819' => 'cqu', 'AUR62030820' => 'cqu', 'BcaB03g14648' => 'bca', 'BcaB04g20492' => 'bca', 'BcaB06g26399' => 'bca', 'BcaC01g03416' => 'bca', 'BcaC01g03419' => 'bca', 'BcaC01g03421' => 'bca', 'BcaC01g03424' => 'bca', 'BcaC05g28012' => 'bca', 'BcaC09g49212' => 'bca', 'BcaC09g50140' => 'bca', 'BcaNung00346' => 'bca', 'BolC1t02785H' => 'bol', 'BolC1t04095H' => 'bol', 'BolC3t17545H' => 'bol', 'BolC5t32769H' => 'bol', 'BraA01t02211Z' => 'bra', 'BraA01t03359Z' => 'bra', 'BraA03t13441Z' => 'bra', 'BraA05t21476Z' => 'bra', 'C01p28420' => 'bna', 'C01p41350' => 'bna', 'C03p52750' => 'bna', 'C03p52780' => 'bna', 'C05p40270' => 'bna', 'CAN.G1437.9' => 'can', 'CANSAT78G0035' => 'cansat', 'CANSAT78G1036' => 'cansat', 'CANSAT78G2272' => 'cansat', 'CANSAT78G2478' => 'cansat', 'CARHR098700' => 'chi', 'CARHR221120' => 'chi', 'CARHR221150' => 'chi', 'Carub.0003s2297' => 'cru', 'Carub.0007s2749' => 'cru', 'Carub.0007s2750' => 'cru', 'Carub.0007s2751' => 'cru', 'Ca_10849_v3' => 'car', 'Cc03_g04300' => 'ccan', 'CDE02G3648' => 'cde', 'CDE05G0060' => 'cde', 'CDE05G0692' => 'cde', 'CDE05G2285' => 'cde', 'CDE05G2884' => 'cde', 'CDE05G3072' => 'cde', 'Cfa008439' => 'cfa', 'Cfa008441' => 'cfa', 'Cfa008443' => 'cfa', 'Cfa008448' => 'cfa', 'Ciclev10005974m.g' => 'ccl', 'Ciclev10006006m.g' => 'ccl', 'Ciclev10006775m.g' => 'ccl', 'CiPaw.02G120400' => 'cil', 'CiPaw.02G120500' => 'cil', 'CiPaw.02G120600' => 'cil', 'ClCG05G004850' => 'cla', 'COL.COLO4_21566' => 'col', 'Cpa.g.sc44.124' => 'cpa', 'Cre07.g320400' => 'cre', 'Cre07.g320450' => 'cre', 'Cre08.g384650' => 'cre', 'Cre09.g393173' => 'cre', 'Cre09.g394325' => 'cre', 'Cre14.g626750' => 'cre', 'Cre16.g679250' => 'cre', 'CsaV3_3G012890' => 'csa', 'CSS0010865' => 'camsi', 'CSS0044338' => 'camsi', 'DCAR_002366' => 'dca', 'DCAR_030687' => 'dca', 'DCAR_030688' => 'dca', 'Dinv14047' => 'din', 'Dinv14048' => 'din', 'Duzib151G0105' => 'dzi', 'Duzib151G0114' => 'dzi', 'Duzib212G1029' => 'dzi', 'ECA232G3536' => 'eca', 'ECA240G0786' => 'eca', 'ECA240G1802' => 'eca', 'ECA240G3760' => 'eca', 'ECA240G3920' => 'eca', 'EL10Ac5g12536' => 'bvu', 'EL10Ac5g12537' => 'bvu', 'EL10Ac5g12538' => 'bvu', 'Eucgr.B01004' => 'egr', 'Eucgr.B01006' => 'egr', 'Eucgr.B01007' => 'egr', 'Eucgr.B01008' => 'egr', 'Eucgr.B01895' => 'egr', 'Eucgr.B01896' => 'egr', 'FAN04G1456' => 'fan', 'FAN08G1769' => 'fan', 'FAN08G2160' => 'fan', 'FAN13G2403' => 'fan', 'FAN13G3303' => 'fan', 'FAN15G2435' => 'fan', 'FAN17G0672' => 'fan', 'FAN17G2441' => 'fan', 'FAN18G1024' => 'fan', 'FAN22G1458' => 'fan', 'FAN24G0037' => 'fan', 'FAN24G0429' => 'fan', 'FAN24G2387' => 'fan', 'FAN27G2746' => 'fan', 'FvH4_2g20400' => 'fve', 'FvH4_2g20420' => 'fve', 'FvH4_2g20430' => 'fve', 'FvH4_4g01270' => 'fve', 'FvH4_4g01290' => 'fve', 'FvH4_4g01300' => 'fve', 'FvH4_4g01310' => 'fve', 'FvH4_4g01330' => 'fve', 'FvH4_5g09070' => 'fve', 'Glyma.10G243800' => 'gma', 'Glyma.20G150600' => 'gma', 'Gohir.A09G219200' => 'ghi', 'Gohir.A09G219300' => 'ghi', 'Gohir.D09G221400' => 'ghi', 'Gohir.D09G221500' => 'ghi', 'Gorai.006G242600' => 'gra', 'Gorai.006G242700' => 'gra', 'GSVIVG01018044001' => 'vvi', 'HanXRQChr03g0083821' => 'han', 'HanXRQChr03g0083841' => 'han', 'HanXRQChr03g0083881' => 'han', 'HanXRQChr03g0083901' => 'han', 'HanXRQChr03g0083921' => 'han', 'HanXRQChr03g0085331' => 'han', 'HanXRQChr03g0085361' => 'han', 'HanXRQChr03g0085411' => 'han', 'HanXRQChr03g0085421' => 'han', 'HanXRQChr03g0085431' => 'han', 'HanXRQChr08g0221991' => 'han', 'HanXRQChr11g0336061' => 'han', 'HanXRQChr11g0336411' => 'han', 'Haze_11234' => 'cav', 'Hma1.2p1_0549F.1_g177010' => 'hma', 'Hma1.2p1_0602F.1_g187630' => 'hma', 'Hund14876' => 'sun', 'Hund14879' => 'sun', 'Lalb_Chr06g0160741' => 'lal', 'Lalb_Chr21g0304781' => 'lal', 'Lj3A726G19' => 'lonja', 'Lj3A726T23' => 'lonja', 'Lj3A726T24' => 'lonja', 'Lj3A726T25' => 'lonja', 'Lj3A727T17' => 'lonja', 'Lj3C726T0' => 'lonja', 'Lj3C726T2' => 'lonja', 'Lj3P725T35' => 'lonja', 'Lj3P727T10' => 'lonja', 'Lj3P727T12' => 'lonja', 'Lj3P727T14' => 'lonja', 'Lj5g0023109' => 'lja', 'Lj6P646T44' => 'lonja', 'Lsat_1_v5_gn_6_75760' => 'lsa', 'Lsat_1_v5_gn_6_75800' => 'lsa', 'Lsat_1_v5_gn_6_75900' => 'lsa', 'Lsat_1_v5_gn_6_76240' => 'lsa', 'Lsat_1_v5_gn_6_76441' => 'lsa', 'Lsat_1_v5_gn_6_76700' => 'lsa', 'Lsat_1_v5_gn_6_76760' => 'lsa', 'Manes.15G033100' => 'mes', 'Mapoly0004s0074' => 'mpo', 'Mapoly0004s0075' => 'mpo', 'Mapoly0004s0163' => 'mpo', 'Mapoly0004s0164' => 'mpo', 'Mapoly0021s0018' => 'mpo', 'Mapoly0041s0136' => 'mpo', 'Mapoly0041s0137' => 'mpo', 'Mapoly0041s0138' => 'mpo', 'Mapoly0041s0139' => 'mpo', 'Mapoly0041s0141' => 'mpo', 'Mapoly0041s0142' => 'mpo', 'Mapoly0041s0143' => 'mpo', 'Mapoly0041s0144' => 'mpo', 'Mapoly0041s0145' => 'mpo', 'Mapoly0047s0106' => 'mpo', 'Mapoly0047s0108' => 'mpo', 'Mapoly0050s0051' => 'mpo', 'Mapoly0050s0052' => 'mpo', 'Mapoly0050s0053' => 'mpo', 'Mapoly0058s0013' => 'mpo', 'Mapoly0091s0078' => 'mpo', 'Mapoly0091s0079' => 'mpo', 'Mapoly0091s0080' => 'mpo', 'Mapoly0091s0081' => 'mpo', 'Mapoly0278s0004' => 'mpo', 'Mapoly0278s0005' => 'mpo', 'Mapoly0278s0006' => 'mpo', 'MBI11_g30648_MAGBIO' => 'mbi', 'MCO03G194' => 'mco', 'MCO03G590' => 'mco', 'MCO07G312' => 'mco', 'MCO10G318' => 'mco', 'MCO12G244' => 'mco', 'MCO13G148' => 'mco', 'MCO13G194' => 'mco', 'MCO16G238' => 'mco', 'MD06G1134100' => 'mdo', 'MD13G1200100' => 'mdo', 'MD13G1200300' => 'mdo', 'MD13G1200600' => 'mdo', 'MD14G1150400' => 'mdo', 'MD16G1200000' => 'mdo', 'Medtr1g102570' => 'mtr', 'Medtr1g102780' => 'mtr', 'Medtr1g102800' => 'mtr', 'Medtr1g102810' => 'mtr', 'Medtr1g102830' => 'mtr', 'MELO3C006499.2' => 'cme', 'Migut.G00385' => 'egut', 'MSTRG.4063' => 'ama', 'Nitab4.5_0000090g0260' => 'nta', 'Nitab4.5_0000977g0030' => 'nta', 'Nitab4.5_0002541g0040' => 'nta', 'Nitab4.5_0007068g0040' => 'nta', 'Nn005s41408' => 'nnu', 'Nn005s41410' => 'nnu', 'Oeu010310.1' => 'oeu', 'Oeu010311.1' => 'oeu', 'Oeu043472.1' => 'oeu', 'Os01g0246400' => 'osa', 'Os04g0267950' => 'osa', 'Os07g0178700' => 'osa', 'Os07g0178800' => 'osa', 'Peaxi162Scf00316g00046' => 'pax', 'Peaxi162Scf00316g00049' => 'pax', 'Peaxi162Scf00316g00059' => 'pax', 'Peaxi162Scf00316g00328' => 'pax', 'Peaxi162Scf00316g00329' => 'pax', 'Peaxi162Scf00316g00411' => 'pax', 'Peaxi162Scf00316g00521' => 'pax', 'Peaxi162Scf00492g00068' => 'pax', 'Peaxi162Scf35631g00002' => 'pax', 'PGR142G3720' => 'pgr', 'PGSC0003DMG400006442' => 'stu', 'Phvul.007G062000' => 'pvu', 'Potri.008G157750' => 'ptr', 'Potri.008G157900' => 'ptr', 'Potri.008G158000' => 'ptr', 'Potri.008G158200' => 'ptr', 'Pp3c11_7280' => 'ppa', 'Pp3c11_7980' => 'ppa', 'Pp3c12_19450' => 'ppa', 'Pp3c14_1480' => 'ppa', 'Pp3c14_1501' => 'ppa', 'Pp3c16_4900' => 'ppa', 'Pp3c16_5010' => 'ppa', 'Pp3c16_5060' => 'ppa', 'Pp3c19_18250' => 'ppa', 'Pp3c23_8530' => 'ppa', 'Pp3c23_8550' => 'ppa', 'Pp3c24_9670' => 'ppa', 'Pp3c2_21390' => 'ppa', 'Pp3c2_31380' => 'ppa', 'Pp3c3_16620' => 'ppa', 'Pp3c3_8090' => 'ppa', 'Pp3c3_8110' => 'ppa', 'Pp3c3_8130' => 'ppa', 'Pp3c3_8150' => 'ppa', 'Pp3c4_14320' => 'ppa', 'Pp3c6_2560' => 'ppa', 'Pp3c9_16700' => 'ppa', 'PRCOL_00000234' => 'pco', 'PRCOL_00000235' => 'pco', 'PRCOL_00000777' => 'pco', 'PRCOL_00002344' => 'pco', 'PRCOL_00002372' => 'pco', 'PRCOL_00006120' => 'pco', 'Prupe.1G021400' => 'ppe', 'Prupe.1G021500' => 'ppe', 'Prupe.1G021600' => 'ppe', 'Prupe.1G021700' => 'ppe', 'Prupe.1G021800' => 'ppe', 'Prupe.5G145100' => 'ppe', 'Psat6g204040' => 'psa', 'Psat6g204800' => 'psa', 'Psat6g204920' => 'psa', 'Psat6g204960' => 'psa', 'Psat6g205080' => 'psa', 'PSO017G0271' => 'pso', 'PSO017G1276' => 'pso', 'PSO017G1429' => 'pso', 'PSO017G1861' => 'pso', 'PSO017G2787' => 'pso', 'PSO017G4466' => 'pso', 'PSO017G5118' => 'pso', 'PSO017G5420' => 'pso', 'PSO063G3678' => 'pso', 'PSO210G0546' => 'pso', 'PSO317G0001' => 'pso', 'PSO357G0512' => 'pso', 'PSO478G2682' => 'pso', 'PSO647G0001' => 'pso', 'PSO675G0001' => 'pso', 'PSO675G2699' => 'pso', 'PSO675G2849' => 'pso', 'PSO675G4991' => 'pso', 'PSO689G0001' => 'pso', 'QL06p000916' => 'qlo', 'QL06p000921' => 'qlo', 'QL06p001398' => 'qlo', 'QL06p001407' => 'qlo', 'QL06p002031' => 'qlo', 'RcHm_v2.0_Chr4g0387791' => 'rch', 'RcHm_v2.0_Chr4g0387801' => 'rch', 'RcHm_v2.0_Chr6g0286501' => 'rch', 'RcHm_v2.0_Chr6g0286511' => 'rch', 'RcHm_v2.0_Chr6g0286521' => 'rch', 'RcHm_v2.0_Chr6g0286531' => 'rch', 'RcHm_v2.0_Chr7g0189141' => 'rch', 'Rhsim02G0028700' => 'rsi', 'Rhsim02G0028800' => 'rsi', 'Rhsim02G0028900' => 'rsi', 'Rhsim02G0029000' => 'rsi', 'Rhsim02G0029100' => 'rsi', 'Rhsim02G0029200' => 'rsi', 'Rhsim02G0029300' => 'rsi', 'Rhsim02G0029400' => 'rsi', 'Rhsim02G0029500' => 'rsi', 'Rhsim02G0029600' => 'rsi', 'RhsimUnG0024000' => 'rsi', 'RhsimUnG0024100' => 'rsi', 'RhsimUnG0024200' => 'rsi', 'RhsimUnG0024300' => 'rsi', 'RhsimUnG0024400' => 'rsi', 'RhsimUnG0024500' => 'rsi', 'RhsimUnG0024700' => 'rsi', 'RhsimUnG0024800' => 'rsi', 'RhsimUnG0024900' => 'rsi', 'RhsimUnG0025100' => 'rsi', 'Sabra08G0120200' => 'sbr', 'Sabra08G0120300' => 'sbr', 'Sabra08G0120500' => 'sbr', 'Sabra08G0120600' => 'sbr', 'Sabra10G0158900' => 'sbr', 'SalBow2G3492' => 'sbo', 'Sc13g0004760' => 'sci', 'Sc13g0004770' => 'sci', 'Sed0003417' => 'sed', 'Sed0019750' => 'sed', 'SEGI_03419' => 'sgi', 'SEGI_05907' => 'sgi', 'SEGI_10682' => 'sgi', 'SEGI_13528' => 'sgi', 'SEGI_16081' => 'sgi', 'SEGI_19370' => 'sgi', 'SEGI_21015' => 'sgi', 'SEGI_21944' => 'sgi', 'SEGI_32906' => 'sgi', 'SEGI_33093' => 'sgi', 'SEGI_36110' => 'sgi', 'SEGI_40397' => 'sgi', 'SGA_v2.0_scaffold191G40426' => 'sas', 'SGA_v2.0_scaffold353G49717' => 'sas', 'SGA_v2.0_scaffold50G18550' => 'sas', 'SMO119G0173' => 'smo', 'SMO172G0002' => 'smo', 'Solyc09g082690.3' => 'sly', 'Solyc09g082700.2' => 'sly', 'Sopen09g031550' => 'spe', 'Sopen09g031560' => 'spe', 'Sp3g20540' => 'spa', 'Sp7g07580' => 'spa', 'TAR134G0002' => 'tar', 'TAR236G0001' => 'tar', 'TAR365G0892' => 'tar', 'TAR636G0166' => 'tar', 'TAR636G0646' => 'tar', 'TAR636G0869' => 'tar', 'TAR636G1317' => 'tar', 'TAR636G1744' => 'tar', 'TAR636G3358' => 'tar', 'TAR636G3436' => 'tar', 'THA.LOC104803047' => 'tha', 'Thecc.04G238900' => 'tca', 'Thhalv10021557m.g' => 'esa', 'Thhalv10026318m.g' => 'esa', 'Thhalv10026335m.g' => 'esa', 'TPR.G17433' => 'tpr', 'TPR.G18915' => 'tpr', 'TPR.G26125' => 'tpr', 'TWI09G0677' => 'twi', 'TWI73G0287' => 'twi', 'unitig_748.g8326' => 'ugi', 'vmacro15370' => 'vma', 'vmacro15371' => 'vma', 'vmacro15372' => 'vma', 'vmacro15373' => 'vma', 'vmacro15374' => 'vma', 'VMungo0720G2826' => 'vmu', 'Zm00001eb116960' => 'zma', 'Zm00001eb301260' => 'zma', 'Zm00001eb301270' => 'zma' ), 'gf_id' => 'HOM05D001460', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001460' ), 'data_identifier' => 'HOM05D001460', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001460', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '433', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p22980' => 'bna', 'A01p32340' => 'bna', 'A03p42970' => 'bna', 'A05p25880' => 'bna', 'Aa31LG8G9320' => 'aar', 'Aa31LG8G9330' => 'aar', 'Aa31LG8G9340' => 'aar', 'Aa31sc221G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1034' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1528' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.829' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2222' => 'aag', 'Ah.12g058830' => 'amhyb', 'Ah.12g058840' => 'amhyb', 'AL3G37160' => 'aly', 'AL7G41310' => 'aly', 'Aqoxy5G00395' => 'aox', 'Aqoxy5G00396' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0C8NZA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5185HY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JZ1PRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MD3LS0' => 'arhy', 'AT3G22840' => 'ath', 'AT4G14690' => 'ath', 'ATR0665G054' => 'atr', 'Atru.chr4.2344' => 'acertr', 'Atru.chr4.2346' => 'acertr', 'Atru.chr4.2347' => 'acertr', 'Atru.chr4.2348' => 'acertr', 'Atru.chr4.2355' => 'acertr', 'Atru.chr4.2356' => 'acertr', 'Atru.chr4.2358' => 'acertr', 'Atru.chr4.2359' => 'acertr', 'Atru.chr4.2360' => 'acertr', 'Atru.chr4.2361' => 'acertr', 'AUR62030476' => 'cqu', 'AUR62030478' => 'cqu', 'AUR62030819' => 'cqu', 'AUR62030820' => 'cqu', 'BcaB03g14648' => 'bca', 'BcaB04g20492' => 'bca', 'BcaB06g26399' => 'bca', 'BcaC01g03416' => 'bca', 'BcaC01g03419' => 'bca', 'BcaC01g03421' => 'bca', 'BcaC01g03424' => 'bca', 'BcaC05g28012' => 'bca', 'BcaC09g49212' => 'bca', 'BcaC09g50140' => 'bca', 'BcaNung00346' => 'bca', 'BolC1t02785H' => 'bol', 'BolC1t04095H' => 'bol', 'BolC3t17545H' => 'bol', 'BolC5t32769H' => 'bol', 'BraA01t02211Z' => 'bra', 'BraA01t03359Z' => 'bra', 'BraA03t13441Z' => 'bra', 'BraA05t21476Z' => 'bra', 'C01p28420' => 'bna', 'C01p41350' => 'bna', 'C03p52750' => 'bna', 'C03p52780' => 'bna', 'C05p40270' => 'bna', 'CAN.G1437.9' => 'can', 'CANSAT78G0035' => 'cansat', 'CANSAT78G1036' => 'cansat', 'CANSAT78G2272' => 'cansat', 'CANSAT78G2478' => 'cansat', 'CARHR098700' => 'chi', 'CARHR221120' => 'chi', 'CARHR221150' => 'chi', 'Carub.0003s2297' => 'cru', 'Carub.0007s2749' => 'cru', 'Carub.0007s2750' => 'cru', 'Carub.0007s2751' => 'cru', 'Ca_10849_v3' => 'car', 'Cc03_g04300' => 'ccan', 'CDE02G3648' => 'cde', 'CDE05G0060' => 'cde', 'CDE05G0692' => 'cde', 'CDE05G2285' => 'cde', 'CDE05G2884' => 'cde', 'CDE05G3072' => 'cde', 'Cfa008439' => 'cfa', 'Cfa008441' => 'cfa', 'Cfa008443' => 'cfa', 'Cfa008448' => 'cfa', 'Ciclev10005974m.g' => 'ccl', 'Ciclev10006006m.g' => 'ccl', 'Ciclev10006775m.g' => 'ccl', 'CiPaw.02G120400' => 'cil', 'CiPaw.02G120500' => 'cil', 'CiPaw.02G120600' => 'cil', 'ClCG05G004850' => 'cla', 'COL.COLO4_21566' => 'col', 'Cpa.g.sc44.124' => 'cpa', 'Cre07.g320400' => 'cre', 'Cre07.g320450' => 'cre', 'Cre08.g384650' => 'cre', 'Cre09.g393173' => 'cre', 'Cre09.g394325' => 'cre', 'Cre14.g626750' => 'cre', 'Cre16.g679250' => 'cre', 'CsaV3_3G012890' => 'csa', 'CSS0010865' => 'camsi', 'CSS0044338' => 'camsi', 'DCAR_002366' => 'dca', 'DCAR_030687' => 'dca', 'DCAR_030688' => 'dca', 'Dinv14047' => 'din', 'Dinv14048' => 'din', 'Duzib151G0105' => 'dzi', 'Duzib151G0114' => 'dzi', 'Duzib212G1029' => 'dzi', 'ECA232G3536' => 'eca', 'ECA240G0786' => 'eca', 'ECA240G1802' => 'eca', 'ECA240G3760' => 'eca', 'ECA240G3920' => 'eca', 'EL10Ac5g12536' => 'bvu', 'EL10Ac5g12537' => 'bvu', 'EL10Ac5g12538' => 'bvu', 'Eucgr.B01004' => 'egr', 'Eucgr.B01006' => 'egr', 'Eucgr.B01007' => 'egr', 'Eucgr.B01008' => 'egr', 'Eucgr.B01895' => 'egr', 'Eucgr.B01896' => 'egr', 'FAN04G1456' => 'fan', 'FAN08G1769' => 'fan', 'FAN08G2160' => 'fan', 'FAN13G2403' => 'fan', 'FAN13G3303' => 'fan', 'FAN15G2435' => 'fan', 'FAN17G0672' => 'fan', 'FAN17G2441' => 'fan', 'FAN18G1024' => 'fan', 'FAN22G1458' => 'fan', 'FAN24G0037' => 'fan', 'FAN24G0429' => 'fan', 'FAN24G2387' => 'fan', 'FAN27G2746' => 'fan', 'FvH4_2g20400' => 'fve', 'FvH4_2g20420' => 'fve', 'FvH4_2g20430' => 'fve', 'FvH4_4g01270' => 'fve', 'FvH4_4g01290' => 'fve', 'FvH4_4g01300' => 'fve', 'FvH4_4g01310' => 'fve', 'FvH4_4g01330' => 'fve', 'FvH4_5g09070' => 'fve', 'Glyma.10G243800' => 'gma', 'Glyma.20G150600' => 'gma', 'Gohir.A09G219200' => 'ghi', 'Gohir.A09G219300' => 'ghi', 'Gohir.D09G221400' => 'ghi', 'Gohir.D09G221500' => 'ghi', 'Gorai.006G242600' => 'gra', 'Gorai.006G242700' => 'gra', 'GSVIVG01018044001' => 'vvi', 'HanXRQChr03g0083821' => 'han', 'HanXRQChr03g0083841' => 'han', 'HanXRQChr03g0083881' => 'han', 'HanXRQChr03g0083901' => 'han', 'HanXRQChr03g0083921' => 'han', 'HanXRQChr03g0085331' => 'han', 'HanXRQChr03g0085361' => 'han', 'HanXRQChr03g0085411' => 'han', 'HanXRQChr03g0085421' => 'han', 'HanXRQChr03g0085431' => 'han', 'HanXRQChr08g0221991' => 'han', 'HanXRQChr11g0336061' => 'han', 'HanXRQChr11g0336411' => 'han', 'Haze_11234' => 'cav', 'Hma1.2p1_0549F.1_g177010' => 'hma', 'Hma1.2p1_0602F.1_g187630' => 'hma', 'Hund14876' => 'sun', 'Hund14879' => 'sun', 'Lalb_Chr06g0160741' => 'lal', 'Lalb_Chr21g0304781' => 'lal', 'Lj3A726G19' => 'lonja', 'Lj3A726T23' => 'lonja', 'Lj3A726T24' => 'lonja', 'Lj3A726T25' => 'lonja', 'Lj3A727T17' => 'lonja', 'Lj3C726T0' => 'lonja', 'Lj3C726T2' => 'lonja', 'Lj3P725T35' => 'lonja', 'Lj3P727T10' => 'lonja', 'Lj3P727T12' => 'lonja', 'Lj3P727T14' => 'lonja', 'Lj5g0023109' => 'lja', 'Lj6P646T44' => 'lonja', 'Lsat_1_v5_gn_6_75760' => 'lsa', 'Lsat_1_v5_gn_6_75800' => 'lsa', 'Lsat_1_v5_gn_6_75900' => 'lsa', 'Lsat_1_v5_gn_6_76240' => 'lsa', 'Lsat_1_v5_gn_6_76441' => 'lsa', 'Lsat_1_v5_gn_6_76700' => 'lsa', 'Lsat_1_v5_gn_6_76760' => 'lsa', 'Manes.15G033100' => 'mes', 'Mapoly0004s0074' => 'mpo', 'Mapoly0004s0075' => 'mpo', 'Mapoly0004s0163' => 'mpo', 'Mapoly0004s0164' => 'mpo', 'Mapoly0021s0018' => 'mpo', 'Mapoly0041s0136' => 'mpo', 'Mapoly0041s0137' => 'mpo', 'Mapoly0041s0138' => 'mpo', 'Mapoly0041s0139' => 'mpo', 'Mapoly0041s0141' => 'mpo', 'Mapoly0041s0142' => 'mpo', 'Mapoly0041s0143' => 'mpo', 'Mapoly0041s0144' => 'mpo', 'Mapoly0041s0145' => 'mpo', 'Mapoly0047s0106' => 'mpo', 'Mapoly0047s0108' => 'mpo', 'Mapoly0050s0051' => 'mpo', 'Mapoly0050s0052' => 'mpo', 'Mapoly0050s0053' => 'mpo', 'Mapoly0058s0013' => 'mpo', 'Mapoly0091s0078' => 'mpo', 'Mapoly0091s0079' => 'mpo', 'Mapoly0091s0080' => 'mpo', 'Mapoly0091s0081' => 'mpo', 'Mapoly0278s0004' => 'mpo', 'Mapoly0278s0005' => 'mpo', 'Mapoly0278s0006' => 'mpo', 'MBI11_g30648_MAGBIO' => 'mbi', 'MCO03G194' => 'mco', 'MCO03G590' => 'mco', 'MCO07G312' => 'mco', 'MCO10G318' => 'mco', 'MCO12G244' => 'mco', 'MCO13G148' => 'mco', 'MCO13G194' => 'mco', 'MCO16G238' => 'mco', 'MD06G1134100' => 'mdo', 'MD13G1200100' => 'mdo', 'MD13G1200300' => 'mdo', 'MD13G1200600' => 'mdo', 'MD14G1150400' => 'mdo', 'MD16G1200000' => 'mdo', 'Medtr1g102570' => 'mtr', 'Medtr1g102780' => 'mtr', 'Medtr1g102800' => 'mtr', 'Medtr1g102810' => 'mtr', 'Medtr1g102830' => 'mtr', 'MELO3C006499.2' => 'cme', 'Migut.G00385' => 'egut', 'MSTRG.4063' => 'ama', 'Nitab4.5_0000090g0260' => 'nta', 'Nitab4.5_0000977g0030' => 'nta', 'Nitab4.5_0002541g0040' => 'nta', 'Nitab4.5_0007068g0040' => 'nta', 'Nn005s41408' => 'nnu', 'Nn005s41410' => 'nnu', 'Oeu010310.1' => 'oeu', 'Oeu010311.1' => 'oeu', 'Oeu043472.1' => 'oeu', 'Os01g0246400' => 'osa', 'Os04g0267950' => 'osa', 'Os07g0178700' => 'osa', 'Os07g0178800' => 'osa', 'Peaxi162Scf00316g00046' => 'pax', 'Peaxi162Scf00316g00049' => 'pax', 'Peaxi162Scf00316g00059' => 'pax', 'Peaxi162Scf00316g00328' => 'pax', 'Peaxi162Scf00316g00329' => 'pax', 'Peaxi162Scf00316g00411' => 'pax', 'Peaxi162Scf00316g00521' => 'pax', 'Peaxi162Scf00492g00068' => 'pax', 'Peaxi162Scf35631g00002' => 'pax', 'PGR142G3720' => 'pgr', 'PGSC0003DMG400006442' => 'stu', 'Phvul.007G062000' => 'pvu', 'Potri.008G157750' => 'ptr', 'Potri.008G157900' => 'ptr', 'Potri.008G158000' => 'ptr', 'Potri.008G158200' => 'ptr', 'Pp3c11_7280' => 'ppa', 'Pp3c11_7980' => 'ppa', 'Pp3c12_19450' => 'ppa', 'Pp3c14_1480' => 'ppa', 'Pp3c14_1501' => 'ppa', 'Pp3c16_4900' => 'ppa', 'Pp3c16_5010' => 'ppa', 'Pp3c16_5060' => 'ppa', 'Pp3c19_18250' => 'ppa', 'Pp3c23_8530' => 'ppa', 'Pp3c23_8550' => 'ppa', 'Pp3c24_9670' => 'ppa', 'Pp3c2_21390' => 'ppa', 'Pp3c2_31380' => 'ppa', 'Pp3c3_16620' => 'ppa', 'Pp3c3_8090' => 'ppa', 'Pp3c3_8110' => 'ppa', 'Pp3c3_8130' => 'ppa', 'Pp3c3_8150' => 'ppa', 'Pp3c4_14320' => 'ppa', 'Pp3c6_2560' => 'ppa', 'Pp3c9_16700' => 'ppa', 'PRCOL_00000234' => 'pco', 'PRCOL_00000235' => 'pco', 'PRCOL_00000777' => 'pco', 'PRCOL_00002344' => 'pco', 'PRCOL_00002372' => 'pco', 'PRCOL_00006120' => 'pco', 'Prupe.1G021400' => 'ppe', 'Prupe.1G021500' => 'ppe', 'Prupe.1G021600' => 'ppe', 'Prupe.1G021700' => 'ppe', 'Prupe.1G021800' => 'ppe', 'Prupe.5G145100' => 'ppe', 'Psat6g204040' => 'psa', 'Psat6g204800' => 'psa', 'Psat6g204920' => 'psa', 'Psat6g204960' => 'psa', 'Psat6g205080' => 'psa', 'PSO017G0271' => 'pso', 'PSO017G1276' => 'pso', 'PSO017G1429' => 'pso', 'PSO017G1861' => 'pso', 'PSO017G2787' => 'pso', 'PSO017G4466' => 'pso', 'PSO017G5118' => 'pso', 'PSO017G5420' => 'pso', 'PSO063G3678' => 'pso', 'PSO210G0546' => 'pso', 'PSO317G0001' => 'pso', 'PSO357G0512' => 'pso', 'PSO478G2682' => 'pso', 'PSO647G0001' => 'pso', 'PSO675G0001' => 'pso', 'PSO675G2699' => 'pso', 'PSO675G2849' => 'pso', 'PSO675G4991' => 'pso', 'PSO689G0001' => 'pso', 'QL06p000916' => 'qlo', 'QL06p000921' => 'qlo', 'QL06p001398' => 'qlo', 'QL06p001407' => 'qlo', 'QL06p002031' => 'qlo', 'RcHm_v2.0_Chr4g0387791' => 'rch', 'RcHm_v2.0_Chr4g0387801' => 'rch', 'RcHm_v2.0_Chr6g0286501' => 'rch', 'RcHm_v2.0_Chr6g0286511' => 'rch', 'RcHm_v2.0_Chr6g0286521' => 'rch', 'RcHm_v2.0_Chr6g0286531' => 'rch', 'RcHm_v2.0_Chr7g0189141' => 'rch', 'Rhsim02G0028700' => 'rsi', 'Rhsim02G0028800' => 'rsi', 'Rhsim02G0028900' => 'rsi', 'Rhsim02G0029000' => 'rsi', 'Rhsim02G0029100' => 'rsi', 'Rhsim02G0029200' => 'rsi', 'Rhsim02G0029300' => 'rsi', 'Rhsim02G0029400' => 'rsi', 'Rhsim02G0029500' => 'rsi', 'Rhsim02G0029600' => 'rsi', 'RhsimUnG0024000' => 'rsi', 'RhsimUnG0024100' => 'rsi', 'RhsimUnG0024200' => 'rsi', 'RhsimUnG0024300' => 'rsi', 'RhsimUnG0024400' => 'rsi', 'RhsimUnG0024500' => 'rsi', 'RhsimUnG0024700' => 'rsi', 'RhsimUnG0024800' => 'rsi', 'RhsimUnG0024900' => 'rsi', 'RhsimUnG0025100' => 'rsi', 'Sabra08G0120200' => 'sbr', 'Sabra08G0120300' => 'sbr', 'Sabra08G0120500' => 'sbr', 'Sabra08G0120600' => 'sbr', 'Sabra10G0158900' => 'sbr', 'SalBow2G3492' => 'sbo', 'Sc13g0004760' => 'sci', 'Sc13g0004770' => 'sci', 'Sed0003417' => 'sed', 'Sed0019750' => 'sed', 'SEGI_03419' => 'sgi', 'SEGI_05907' => 'sgi', 'SEGI_10682' => 'sgi', 'SEGI_13528' => 'sgi', 'SEGI_16081' => 'sgi', 'SEGI_19370' => 'sgi', 'SEGI_21015' => 'sgi', 'SEGI_21944' => 'sgi', 'SEGI_32906' => 'sgi', 'SEGI_33093' => 'sgi', 'SEGI_36110' => 'sgi', 'SEGI_40397' => 'sgi', 'SGA_v2.0_scaffold191G40426' => 'sas', 'SGA_v2.0_scaffold353G49717' => 'sas', 'SGA_v2.0_scaffold50G18550' => 'sas', 'SMO119G0173' => 'smo', 'SMO172G0002' => 'smo', 'Solyc09g082690.3' => 'sly', 'Solyc09g082700.2' => 'sly', 'Sopen09g031550' => 'spe', 'Sopen09g031560' => 'spe', 'Sp3g20540' => 'spa', 'Sp7g07580' => 'spa', 'TAR134G0002' => 'tar', 'TAR236G0001' => 'tar', 'TAR365G0892' => 'tar', 'TAR636G0166' => 'tar', 'TAR636G0646' => 'tar', 'TAR636G0869' => 'tar', 'TAR636G1317' => 'tar', 'TAR636G1744' => 'tar', 'TAR636G3358' => 'tar', 'TAR636G3436' => 'tar', 'THA.LOC104803047' => 'tha', 'Thecc.04G238900' => 'tca', 'Thhalv10021557m.g' => 'esa', 'Thhalv10026318m.g' => 'esa', 'Thhalv10026335m.g' => 'esa', 'TPR.G17433' => 'tpr', 'TPR.G18915' => 'tpr', 'TPR.G26125' => 'tpr', 'TWI09G0677' => 'twi', 'TWI73G0287' => 'twi', 'unitig_748.g8326' => 'ugi', 'vmacro15370' => 'vma', 'vmacro15371' => 'vma', 'vmacro15372' => 'vma', 'vmacro15373' => 'vma', 'vmacro15374' => 'vma', 'VMungo0720G2826' => 'vmu', 'Zm00001eb116960' => 'zma', 'Zm00001eb301260' => 'zma', 'Zm00001eb301270' => 'zma' ) $gf_id = 'HOM05D001460' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001460' ) $data_identifier = 'HOM05D001460' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 4, 'aag' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 2, 'aox' => (int) 2, 'arhy' => (int) 4, 'ath' => (int) 2, 'atr' => (int) 1, 'acertr' => (int) 10, 'cqu' => (int) 4, 'bca' => (int) 11, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 1, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 1, 'ccan' => (int) 1, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 1, 'col' => (int) 1, 'cpa' => (int) 1, 'cre' => (int) 7, 'csa' => (int) 1, 'camsi' => (int) 2, 'dca' => (int) 3, 'din' => (int) 2, 'dzi' => (int) 3, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 14, 'fve' => (int) 9, 'gma' => (int) 2, 'ghi' => (int) 4, 'gra' => (int) 2, 'vvi' => (int) 1, 'han' => (int) 13, 'cav' => (int) 1, 'hma' => (int) 2, 'sun' => (int) 2, 'lal' => (int) 2, 'lonja' => (int) 12, 'lja' => (int) 1, 'lsa' => (int) 7, 'mes' => (int) 1, 'mpo' => (int) 27, 'mbi' => (int) 1, 'mco' => (int) 8, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 1, 'egut' => (int) 1, 'ama' => (int) 1, 'nta' => (int) 4, 'nnu' => (int) 2, 'oeu' => (int) 3, 'osa' => (int) 4, 'pax' => (int) 9, 'pgr' => (int) 1, 'stu' => (int) 1, 'pvu' => (int) 1, 'ptr' => (int) 4, 'ppa' => (int) 22, 'pco' => (int) 6, 'ppe' => (int) 6, 'psa' => (int) 5, 'pso' => (int) 19, 'qlo' => (int) 5, 'rch' => (int) 7, 'rsi' => (int) 20, 'sbr' => (int) 5, 'sbo' => (int) 1, 'sci' => (int) 2, 'sed' => (int) 2, 'sgi' => (int) 12, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 2, 'tar' => (int) 10, 'tha' => (int) 1, 'tca' => (int) 1, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 2, 'ugi' => (int) 1, 'vma' => (int) 5, 'vmu' => (int) 1, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb301270' $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' => 'HOM05D001460', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '433', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p22980' => 'bna', 'A01p32340' => 'bna', 'A03p42970' => 'bna', 'A05p25880' => 'bna', 'Aa31LG8G9320' => 'aar', 'Aa31LG8G9330' => 'aar', 'Aa31LG8G9340' => 'aar', 'Aa31sc221G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1034' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1528' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.829' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2222' => 'aag', 'Ah.12g058830' => 'amhyb', 'Ah.12g058840' => 'amhyb', 'AL3G37160' => 'aly', 'AL7G41310' => 'aly', 'Aqoxy5G00395' => 'aox', 'Aqoxy5G00396' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0C8NZA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5185HY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JZ1PRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MD3LS0' => 'arhy', 'AT3G22840' => 'ath', 'AT4G14690' => 'ath', 'ATR0665G054' => 'atr', 'Atru.chr4.2344' => 'acertr', 'Atru.chr4.2346' => 'acertr', 'Atru.chr4.2347' => 'acertr', 'Atru.chr4.2348' => 'acertr', 'Atru.chr4.2355' => 'acertr', 'Atru.chr4.2356' => 'acertr', 'Atru.chr4.2358' => 'acertr', 'Atru.chr4.2359' => 'acertr', 'Atru.chr4.2360' => 'acertr', 'Atru.chr4.2361' => 'acertr', 'AUR62030476' => 'cqu', 'AUR62030478' => 'cqu', 'AUR62030819' => 'cqu', 'AUR62030820' => 'cqu', 'BcaB03g14648' => 'bca', 'BcaB04g20492' => 'bca', 'BcaB06g26399' => 'bca', 'BcaC01g03416' => 'bca', 'BcaC01g03419' => 'bca', 'BcaC01g03421' => 'bca', 'BcaC01g03424' => 'bca', 'BcaC05g28012' => 'bca', 'BcaC09g49212' => 'bca', 'BcaC09g50140' => 'bca', 'BcaNung00346' => 'bca', 'BolC1t02785H' => 'bol', 'BolC1t04095H' => 'bol', 'BolC3t17545H' => 'bol', 'BolC5t32769H' => 'bol', 'BraA01t02211Z' => 'bra', 'BraA01t03359Z' => 'bra', 'BraA03t13441Z' => 'bra', 'BraA05t21476Z' => 'bra', 'C01p28420' => 'bna', 'C01p41350' => 'bna', 'C03p52750' => 'bna', 'C03p52780' => 'bna', 'C05p40270' => 'bna', 'CAN.G1437.9' => 'can', 'CANSAT78G0035' => 'cansat', 'CANSAT78G1036' => 'cansat', 'CANSAT78G2272' => 'cansat', 'CANSAT78G2478' => 'cansat', 'CARHR098700' => 'chi', 'CARHR221120' => 'chi', 'CARHR221150' => 'chi', 'Carub.0003s2297' => 'cru', 'Carub.0007s2749' => 'cru', 'Carub.0007s2750' => 'cru', 'Carub.0007s2751' => 'cru', 'Ca_10849_v3' => 'car', 'Cc03_g04300' => 'ccan', 'CDE02G3648' => 'cde', 'CDE05G0060' => 'cde', 'CDE05G0692' => 'cde', 'CDE05G2285' => 'cde', 'CDE05G2884' => 'cde', 'CDE05G3072' => 'cde', 'Cfa008439' => 'cfa', 'Cfa008441' => 'cfa', 'Cfa008443' => 'cfa', 'Cfa008448' => 'cfa', 'Ciclev10005974m.g' => 'ccl', 'Ciclev10006006m.g' => 'ccl', 'Ciclev10006775m.g' => 'ccl', 'CiPaw.02G120400' => 'cil', 'CiPaw.02G120500' => 'cil', 'CiPaw.02G120600' => 'cil', 'ClCG05G004850' => 'cla', 'COL.COLO4_21566' => 'col', 'Cpa.g.sc44.124' => 'cpa', 'Cre07.g320400' => 'cre', 'Cre07.g320450' => 'cre', 'Cre08.g384650' => 'cre', 'Cre09.g393173' => 'cre', 'Cre09.g394325' => 'cre', 'Cre14.g626750' => 'cre', 'Cre16.g679250' => 'cre', 'CsaV3_3G012890' => 'csa', 'CSS0010865' => 'camsi', 'CSS0044338' => 'camsi', 'DCAR_002366' => 'dca', 'DCAR_030687' => 'dca', 'DCAR_030688' => 'dca', 'Dinv14047' => 'din', 'Dinv14048' => 'din', 'Duzib151G0105' => 'dzi', 'Duzib151G0114' => 'dzi', 'Duzib212G1029' => 'dzi', 'ECA232G3536' => 'eca', 'ECA240G0786' => 'eca', 'ECA240G1802' => 'eca', 'ECA240G3760' => 'eca', 'ECA240G3920' => 'eca', 'EL10Ac5g12536' => 'bvu', 'EL10Ac5g12537' => 'bvu', 'EL10Ac5g12538' => 'bvu', 'Eucgr.B01004' => 'egr', 'Eucgr.B01006' => 'egr', 'Eucgr.B01007' => 'egr', 'Eucgr.B01008' => 'egr', 'Eucgr.B01895' => 'egr', 'Eucgr.B01896' => 'egr', 'FAN04G1456' => 'fan', 'FAN08G1769' => 'fan', 'FAN08G2160' => 'fan', 'FAN13G2403' => 'fan', 'FAN13G3303' => 'fan', 'FAN15G2435' => 'fan', 'FAN17G0672' => 'fan', 'FAN17G2441' => 'fan', 'FAN18G1024' => 'fan', 'FAN22G1458' => 'fan', 'FAN24G0037' => 'fan', 'FAN24G0429' => 'fan', 'FAN24G2387' => 'fan', 'FAN27G2746' => 'fan', 'FvH4_2g20400' => 'fve', 'FvH4_2g20420' => 'fve', 'FvH4_2g20430' => 'fve', 'FvH4_4g01270' => 'fve', 'FvH4_4g01290' => 'fve', 'FvH4_4g01300' => 'fve', 'FvH4_4g01310' => 'fve', 'FvH4_4g01330' => 'fve', 'FvH4_5g09070' => 'fve', 'Glyma.10G243800' => 'gma', 'Glyma.20G150600' => 'gma', 'Gohir.A09G219200' => 'ghi', 'Gohir.A09G219300' => 'ghi', 'Gohir.D09G221400' => 'ghi', 'Gohir.D09G221500' => 'ghi', 'Gorai.006G242600' => 'gra', 'Gorai.006G242700' => 'gra', 'GSVIVG01018044001' => 'vvi', 'HanXRQChr03g0083821' => 'han', 'HanXRQChr03g0083841' => 'han', 'HanXRQChr03g0083881' => 'han', 'HanXRQChr03g0083901' => 'han', 'HanXRQChr03g0083921' => 'han', 'HanXRQChr03g0085331' => 'han', 'HanXRQChr03g0085361' => 'han', 'HanXRQChr03g0085411' => 'han', 'HanXRQChr03g0085421' => 'han', 'HanXRQChr03g0085431' => 'han', 'HanXRQChr08g0221991' => 'han', 'HanXRQChr11g0336061' => 'han', 'HanXRQChr11g0336411' => 'han', 'Haze_11234' => 'cav', 'Hma1.2p1_0549F.1_g177010' => 'hma', 'Hma1.2p1_0602F.1_g187630' => 'hma', 'Hund14876' => 'sun', 'Hund14879' => 'sun', 'Lalb_Chr06g0160741' => 'lal', 'Lalb_Chr21g0304781' => 'lal', 'Lj3A726G19' => 'lonja', 'Lj3A726T23' => 'lonja', 'Lj3A726T24' => 'lonja', 'Lj3A726T25' => 'lonja', 'Lj3A727T17' => 'lonja', 'Lj3C726T0' => 'lonja', 'Lj3C726T2' => 'lonja', 'Lj3P725T35' => 'lonja', 'Lj3P727T10' => 'lonja', 'Lj3P727T12' => 'lonja', 'Lj3P727T14' => 'lonja', 'Lj5g0023109' => 'lja', 'Lj6P646T44' => 'lonja', 'Lsat_1_v5_gn_6_75760' => 'lsa', 'Lsat_1_v5_gn_6_75800' => 'lsa', 'Lsat_1_v5_gn_6_75900' => 'lsa', 'Lsat_1_v5_gn_6_76240' => 'lsa', 'Lsat_1_v5_gn_6_76441' => 'lsa', 'Lsat_1_v5_gn_6_76700' => 'lsa', 'Lsat_1_v5_gn_6_76760' => 'lsa', 'Manes.15G033100' => 'mes', 'Mapoly0004s0074' => 'mpo', 'Mapoly0004s0075' => 'mpo', 'Mapoly0004s0163' => 'mpo', 'Mapoly0004s0164' => 'mpo', 'Mapoly0021s0018' => 'mpo', 'Mapoly0041s0136' => 'mpo', 'Mapoly0041s0137' => 'mpo', 'Mapoly0041s0138' => 'mpo', 'Mapoly0041s0139' => 'mpo', 'Mapoly0041s0141' => 'mpo', 'Mapoly0041s0142' => 'mpo', 'Mapoly0041s0143' => 'mpo', 'Mapoly0041s0144' => 'mpo', 'Mapoly0041s0145' => 'mpo', 'Mapoly0047s0106' => 'mpo', 'Mapoly0047s0108' => 'mpo', 'Mapoly0050s0051' => 'mpo', 'Mapoly0050s0052' => 'mpo', 'Mapoly0050s0053' => 'mpo', 'Mapoly0058s0013' => 'mpo', 'Mapoly0091s0078' => 'mpo', 'Mapoly0091s0079' => 'mpo', 'Mapoly0091s0080' => 'mpo', 'Mapoly0091s0081' => 'mpo', 'Mapoly0278s0004' => 'mpo', 'Mapoly0278s0005' => 'mpo', 'Mapoly0278s0006' => 'mpo', 'MBI11_g30648_MAGBIO' => 'mbi', 'MCO03G194' => 'mco', 'MCO03G590' => 'mco', 'MCO07G312' => 'mco', 'MCO10G318' => 'mco', 'MCO12G244' => 'mco', 'MCO13G148' => 'mco', 'MCO13G194' => 'mco', 'MCO16G238' => 'mco', 'MD06G1134100' => 'mdo', 'MD13G1200100' => 'mdo', 'MD13G1200300' => 'mdo', 'MD13G1200600' => 'mdo', 'MD14G1150400' => 'mdo', 'MD16G1200000' => 'mdo', 'Medtr1g102570' => 'mtr', 'Medtr1g102780' => 'mtr', 'Medtr1g102800' => 'mtr', 'Medtr1g102810' => 'mtr', 'Medtr1g102830' => 'mtr', 'MELO3C006499.2' => 'cme', 'Migut.G00385' => 'egut', 'MSTRG.4063' => 'ama', 'Nitab4.5_0000090g0260' => 'nta', 'Nitab4.5_0000977g0030' => 'nta', 'Nitab4.5_0002541g0040' => 'nta', 'Nitab4.5_0007068g0040' => 'nta', 'Nn005s41408' => 'nnu', 'Nn005s41410' => 'nnu', 'Oeu010310.1' => 'oeu', 'Oeu010311.1' => 'oeu', 'Oeu043472.1' => 'oeu', 'Os01g0246400' => 'osa', 'Os04g0267950' => 'osa', 'Os07g0178700' => 'osa', 'Os07g0178800' => 'osa', 'Peaxi162Scf00316g00046' => 'pax', 'Peaxi162Scf00316g00049' => 'pax', 'Peaxi162Scf00316g00059' => 'pax', 'Peaxi162Scf00316g00328' => 'pax', 'Peaxi162Scf00316g00329' => 'pax', 'Peaxi162Scf00316g00411' => 'pax', 'Peaxi162Scf00316g00521' => 'pax', 'Peaxi162Scf00492g00068' => 'pax', 'Peaxi162Scf35631g00002' => 'pax', 'PGR142G3720' => 'pgr', 'PGSC0003DMG400006442' => 'stu', 'Phvul.007G062000' => 'pvu', 'Potri.008G157750' => 'ptr', 'Potri.008G157900' => 'ptr', 'Potri.008G158000' => 'ptr', 'Potri.008G158200' => 'ptr', 'Pp3c11_7280' => 'ppa', 'Pp3c11_7980' => 'ppa', 'Pp3c12_19450' => 'ppa', 'Pp3c14_1480' => 'ppa', 'Pp3c14_1501' => 'ppa', 'Pp3c16_4900' => 'ppa', 'Pp3c16_5010' => 'ppa', 'Pp3c16_5060' => 'ppa', 'Pp3c19_18250' => 'ppa', 'Pp3c23_8530' => 'ppa', 'Pp3c23_8550' => 'ppa', 'Pp3c24_9670' => 'ppa', 'Pp3c2_21390' => 'ppa', 'Pp3c2_31380' => 'ppa', 'Pp3c3_16620' => 'ppa', 'Pp3c3_8090' => 'ppa', 'Pp3c3_8110' => 'ppa', 'Pp3c3_8130' => 'ppa', 'Pp3c3_8150' => 'ppa', 'Pp3c4_14320' => 'ppa', 'Pp3c6_2560' => 'ppa', 'Pp3c9_16700' => 'ppa', 'PRCOL_00000234' => 'pco', 'PRCOL_00000235' => 'pco', 'PRCOL_00000777' => 'pco', 'PRCOL_00002344' => 'pco', 'PRCOL_00002372' => 'pco', 'PRCOL_00006120' => 'pco', 'Prupe.1G021400' => 'ppe', 'Prupe.1G021500' => 'ppe', 'Prupe.1G021600' => 'ppe', 'Prupe.1G021700' => 'ppe', 'Prupe.1G021800' => 'ppe', 'Prupe.5G145100' => 'ppe', 'Psat6g204040' => 'psa', 'Psat6g204800' => 'psa', 'Psat6g204920' => 'psa', 'Psat6g204960' => 'psa', 'Psat6g205080' => 'psa', 'PSO017G0271' => 'pso', 'PSO017G1276' => 'pso', 'PSO017G1429' => 'pso', 'PSO017G1861' => 'pso', 'PSO017G2787' => 'pso', 'PSO017G4466' => 'pso', 'PSO017G5118' => 'pso', 'PSO017G5420' => 'pso', 'PSO063G3678' => 'pso', 'PSO210G0546' => 'pso', 'PSO317G0001' => 'pso', 'PSO357G0512' => 'pso', 'PSO478G2682' => 'pso', 'PSO647G0001' => 'pso', 'PSO675G0001' => 'pso', 'PSO675G2699' => 'pso', 'PSO675G2849' => 'pso', 'PSO675G4991' => 'pso', 'PSO689G0001' => 'pso', 'QL06p000916' => 'qlo', 'QL06p000921' => 'qlo', 'QL06p001398' => 'qlo', 'QL06p001407' => 'qlo', 'QL06p002031' => 'qlo', 'RcHm_v2.0_Chr4g0387791' => 'rch', 'RcHm_v2.0_Chr4g0387801' => 'rch', 'RcHm_v2.0_Chr6g0286501' => 'rch', 'RcHm_v2.0_Chr6g0286511' => 'rch', 'RcHm_v2.0_Chr6g0286521' => 'rch', 'RcHm_v2.0_Chr6g0286531' => 'rch', 'RcHm_v2.0_Chr7g0189141' => 'rch', 'Rhsim02G0028700' => 'rsi', 'Rhsim02G0028800' => 'rsi', 'Rhsim02G0028900' => 'rsi', 'Rhsim02G0029000' => 'rsi', 'Rhsim02G0029100' => 'rsi', 'Rhsim02G0029200' => 'rsi', 'Rhsim02G0029300' => 'rsi', 'Rhsim02G0029400' => 'rsi', 'Rhsim02G0029500' => 'rsi', 'Rhsim02G0029600' => 'rsi', 'RhsimUnG0024000' => 'rsi', 'RhsimUnG0024100' => 'rsi', 'RhsimUnG0024200' => 'rsi', 'RhsimUnG0024300' => 'rsi', 'RhsimUnG0024400' => 'rsi', 'RhsimUnG0024500' => 'rsi', 'RhsimUnG0024700' => 'rsi', 'RhsimUnG0024800' => 'rsi', 'RhsimUnG0024900' => 'rsi', 'RhsimUnG0025100' => 'rsi', 'Sabra08G0120200' => 'sbr', 'Sabra08G0120300' => 'sbr', 'Sabra08G0120500' => 'sbr', 'Sabra08G0120600' => 'sbr', 'Sabra10G0158900' => 'sbr', 'SalBow2G3492' => 'sbo', 'Sc13g0004760' => 'sci', 'Sc13g0004770' => 'sci', 'Sed0003417' => 'sed', 'Sed0019750' => 'sed', 'SEGI_03419' => 'sgi', 'SEGI_05907' => 'sgi', 'SEGI_10682' => 'sgi', 'SEGI_13528' => 'sgi', 'SEGI_16081' => 'sgi', 'SEGI_19370' => 'sgi', 'SEGI_21015' => 'sgi', 'SEGI_21944' => 'sgi', 'SEGI_32906' => 'sgi', 'SEGI_33093' => 'sgi', 'SEGI_36110' => 'sgi', 'SEGI_40397' => 'sgi', 'SGA_v2.0_scaffold191G40426' => 'sas', 'SGA_v2.0_scaffold353G49717' => 'sas', 'SGA_v2.0_scaffold50G18550' => 'sas', 'SMO119G0173' => 'smo', 'SMO172G0002' => 'smo', 'Solyc09g082690.3' => 'sly', 'Solyc09g082700.2' => 'sly', 'Sopen09g031550' => 'spe', 'Sopen09g031560' => 'spe', 'Sp3g20540' => 'spa', 'Sp7g07580' => 'spa', 'TAR134G0002' => 'tar', 'TAR236G0001' => 'tar', 'TAR365G0892' => 'tar', 'TAR636G0166' => 'tar', 'TAR636G0646' => 'tar', 'TAR636G0869' => 'tar', 'TAR636G1317' => 'tar', 'TAR636G1744' => 'tar', 'TAR636G3358' => 'tar', 'TAR636G3436' => 'tar', 'THA.LOC104803047' => 'tha', 'Thecc.04G238900' => 'tca', 'Thhalv10021557m.g' => 'esa', 'Thhalv10026318m.g' => 'esa', 'Thhalv10026335m.g' => 'esa', 'TPR.G17433' => 'tpr', 'TPR.G18915' => 'tpr', 'TPR.G26125' => 'tpr', 'TWI09G0677' => 'twi', 'TWI73G0287' => 'twi', 'unitig_748.g8326' => 'ugi', 'vmacro15370' => 'vma', 'vmacro15371' => 'vma', 'vmacro15372' => 'vma', 'vmacro15373' => 'vma', 'vmacro15374' => 'vma', 'VMungo0720G2826' => 'vmu', 'Zm00001eb116960' => 'zma', 'Zm00001eb301260' => 'zma', 'Zm00001eb301270' => 'zma' ), 'gf_id' => 'HOM05D001460', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001460' ), 'data_identifier' => 'HOM05D001460', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001460', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '433', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p22980' => 'bna', 'A01p32340' => 'bna', 'A03p42970' => 'bna', 'A05p25880' => 'bna', 'Aa31LG8G9320' => 'aar', 'Aa31LG8G9330' => 'aar', 'Aa31LG8G9340' => 'aar', 'Aa31sc221G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1034' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1528' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.829' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2222' => 'aag', 'Ah.12g058830' => 'amhyb', 'Ah.12g058840' => 'amhyb', 'AL3G37160' => 'aly', 'AL7G41310' => 'aly', 'Aqoxy5G00395' => 'aox', 'Aqoxy5G00396' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0C8NZA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5185HY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JZ1PRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MD3LS0' => 'arhy', 'AT3G22840' => 'ath', 'AT4G14690' => 'ath', 'ATR0665G054' => 'atr', 'Atru.chr4.2344' => 'acertr', 'Atru.chr4.2346' => 'acertr', 'Atru.chr4.2347' => 'acertr', 'Atru.chr4.2348' => 'acertr', 'Atru.chr4.2355' => 'acertr', 'Atru.chr4.2356' => 'acertr', 'Atru.chr4.2358' => 'acertr', 'Atru.chr4.2359' => 'acertr', 'Atru.chr4.2360' => 'acertr', 'Atru.chr4.2361' => 'acertr', 'AUR62030476' => 'cqu', 'AUR62030478' => 'cqu', 'AUR62030819' => 'cqu', 'AUR62030820' => 'cqu', 'BcaB03g14648' => 'bca', 'BcaB04g20492' => 'bca', 'BcaB06g26399' => 'bca', 'BcaC01g03416' => 'bca', 'BcaC01g03419' => 'bca', 'BcaC01g03421' => 'bca', 'BcaC01g03424' => 'bca', 'BcaC05g28012' => 'bca', 'BcaC09g49212' => 'bca', 'BcaC09g50140' => 'bca', 'BcaNung00346' => 'bca', 'BolC1t02785H' => 'bol', 'BolC1t04095H' => 'bol', 'BolC3t17545H' => 'bol', 'BolC5t32769H' => 'bol', 'BraA01t02211Z' => 'bra', 'BraA01t03359Z' => 'bra', 'BraA03t13441Z' => 'bra', 'BraA05t21476Z' => 'bra', 'C01p28420' => 'bna', 'C01p41350' => 'bna', 'C03p52750' => 'bna', 'C03p52780' => 'bna', 'C05p40270' => 'bna', 'CAN.G1437.9' => 'can', 'CANSAT78G0035' => 'cansat', 'CANSAT78G1036' => 'cansat', 'CANSAT78G2272' => 'cansat', 'CANSAT78G2478' => 'cansat', 'CARHR098700' => 'chi', 'CARHR221120' => 'chi', 'CARHR221150' => 'chi', 'Carub.0003s2297' => 'cru', 'Carub.0007s2749' => 'cru', 'Carub.0007s2750' => 'cru', 'Carub.0007s2751' => 'cru', 'Ca_10849_v3' => 'car', 'Cc03_g04300' => 'ccan', 'CDE02G3648' => 'cde', 'CDE05G0060' => 'cde', 'CDE05G0692' => 'cde', 'CDE05G2285' => 'cde', 'CDE05G2884' => 'cde', 'CDE05G3072' => 'cde', 'Cfa008439' => 'cfa', 'Cfa008441' => 'cfa', 'Cfa008443' => 'cfa', 'Cfa008448' => 'cfa', 'Ciclev10005974m.g' => 'ccl', 'Ciclev10006006m.g' => 'ccl', 'Ciclev10006775m.g' => 'ccl', 'CiPaw.02G120400' => 'cil', 'CiPaw.02G120500' => 'cil', 'CiPaw.02G120600' => 'cil', 'ClCG05G004850' => 'cla', 'COL.COLO4_21566' => 'col', 'Cpa.g.sc44.124' => 'cpa', 'Cre07.g320400' => 'cre', 'Cre07.g320450' => 'cre', 'Cre08.g384650' => 'cre', 'Cre09.g393173' => 'cre', 'Cre09.g394325' => 'cre', 'Cre14.g626750' => 'cre', 'Cre16.g679250' => 'cre', 'CsaV3_3G012890' => 'csa', 'CSS0010865' => 'camsi', 'CSS0044338' => 'camsi', 'DCAR_002366' => 'dca', 'DCAR_030687' => 'dca', 'DCAR_030688' => 'dca', 'Dinv14047' => 'din', 'Dinv14048' => 'din', 'Duzib151G0105' => 'dzi', 'Duzib151G0114' => 'dzi', 'Duzib212G1029' => 'dzi', 'ECA232G3536' => 'eca', 'ECA240G0786' => 'eca', 'ECA240G1802' => 'eca', 'ECA240G3760' => 'eca', 'ECA240G3920' => 'eca', 'EL10Ac5g12536' => 'bvu', 'EL10Ac5g12537' => 'bvu', 'EL10Ac5g12538' => 'bvu', 'Eucgr.B01004' => 'egr', 'Eucgr.B01006' => 'egr', 'Eucgr.B01007' => 'egr', 'Eucgr.B01008' => 'egr', 'Eucgr.B01895' => 'egr', 'Eucgr.B01896' => 'egr', 'FAN04G1456' => 'fan', 'FAN08G1769' => 'fan', 'FAN08G2160' => 'fan', 'FAN13G2403' => 'fan', 'FAN13G3303' => 'fan', 'FAN15G2435' => 'fan', 'FAN17G0672' => 'fan', 'FAN17G2441' => 'fan', 'FAN18G1024' => 'fan', 'FAN22G1458' => 'fan', 'FAN24G0037' => 'fan', 'FAN24G0429' => 'fan', 'FAN24G2387' => 'fan', 'FAN27G2746' => 'fan', 'FvH4_2g20400' => 'fve', 'FvH4_2g20420' => 'fve', 'FvH4_2g20430' => 'fve', 'FvH4_4g01270' => 'fve', 'FvH4_4g01290' => 'fve', 'FvH4_4g01300' => 'fve', 'FvH4_4g01310' => 'fve', 'FvH4_4g01330' => 'fve', 'FvH4_5g09070' => 'fve', 'Glyma.10G243800' => 'gma', 'Glyma.20G150600' => 'gma', 'Gohir.A09G219200' => 'ghi', 'Gohir.A09G219300' => 'ghi', 'Gohir.D09G221400' => 'ghi', 'Gohir.D09G221500' => 'ghi', 'Gorai.006G242600' => 'gra', 'Gorai.006G242700' => 'gra', 'GSVIVG01018044001' => 'vvi', 'HanXRQChr03g0083821' => 'han', 'HanXRQChr03g0083841' => 'han', 'HanXRQChr03g0083881' => 'han', 'HanXRQChr03g0083901' => 'han', 'HanXRQChr03g0083921' => 'han', 'HanXRQChr03g0085331' => 'han', 'HanXRQChr03g0085361' => 'han', 'HanXRQChr03g0085411' => 'han', 'HanXRQChr03g0085421' => 'han', 'HanXRQChr03g0085431' => 'han', 'HanXRQChr08g0221991' => 'han', 'HanXRQChr11g0336061' => 'han', 'HanXRQChr11g0336411' => 'han', 'Haze_11234' => 'cav', 'Hma1.2p1_0549F.1_g177010' => 'hma', 'Hma1.2p1_0602F.1_g187630' => 'hma', 'Hund14876' => 'sun', 'Hund14879' => 'sun', 'Lalb_Chr06g0160741' => 'lal', 'Lalb_Chr21g0304781' => 'lal', 'Lj3A726G19' => 'lonja', 'Lj3A726T23' => 'lonja', 'Lj3A726T24' => 'lonja', 'Lj3A726T25' => 'lonja', 'Lj3A727T17' => 'lonja', 'Lj3C726T0' => 'lonja', 'Lj3C726T2' => 'lonja', 'Lj3P725T35' => 'lonja', 'Lj3P727T10' => 'lonja', 'Lj3P727T12' => 'lonja', 'Lj3P727T14' => 'lonja', 'Lj5g0023109' => 'lja', 'Lj6P646T44' => 'lonja', 'Lsat_1_v5_gn_6_75760' => 'lsa', 'Lsat_1_v5_gn_6_75800' => 'lsa', 'Lsat_1_v5_gn_6_75900' => 'lsa', 'Lsat_1_v5_gn_6_76240' => 'lsa', 'Lsat_1_v5_gn_6_76441' => 'lsa', 'Lsat_1_v5_gn_6_76700' => 'lsa', 'Lsat_1_v5_gn_6_76760' => 'lsa', 'Manes.15G033100' => 'mes', 'Mapoly0004s0074' => 'mpo', 'Mapoly0004s0075' => 'mpo', 'Mapoly0004s0163' => 'mpo', 'Mapoly0004s0164' => 'mpo', 'Mapoly0021s0018' => 'mpo', 'Mapoly0041s0136' => 'mpo', 'Mapoly0041s0137' => 'mpo', 'Mapoly0041s0138' => 'mpo', 'Mapoly0041s0139' => 'mpo', 'Mapoly0041s0141' => 'mpo', 'Mapoly0041s0142' => 'mpo', 'Mapoly0041s0143' => 'mpo', 'Mapoly0041s0144' => 'mpo', 'Mapoly0041s0145' => 'mpo', 'Mapoly0047s0106' => 'mpo', 'Mapoly0047s0108' => 'mpo', 'Mapoly0050s0051' => 'mpo', 'Mapoly0050s0052' => 'mpo', 'Mapoly0050s0053' => 'mpo', 'Mapoly0058s0013' => 'mpo', 'Mapoly0091s0078' => 'mpo', 'Mapoly0091s0079' => 'mpo', 'Mapoly0091s0080' => 'mpo', 'Mapoly0091s0081' => 'mpo', 'Mapoly0278s0004' => 'mpo', 'Mapoly0278s0005' => 'mpo', 'Mapoly0278s0006' => 'mpo', 'MBI11_g30648_MAGBIO' => 'mbi', 'MCO03G194' => 'mco', 'MCO03G590' => 'mco', 'MCO07G312' => 'mco', 'MCO10G318' => 'mco', 'MCO12G244' => 'mco', 'MCO13G148' => 'mco', 'MCO13G194' => 'mco', 'MCO16G238' => 'mco', 'MD06G1134100' => 'mdo', 'MD13G1200100' => 'mdo', 'MD13G1200300' => 'mdo', 'MD13G1200600' => 'mdo', 'MD14G1150400' => 'mdo', 'MD16G1200000' => 'mdo', 'Medtr1g102570' => 'mtr', 'Medtr1g102780' => 'mtr', 'Medtr1g102800' => 'mtr', 'Medtr1g102810' => 'mtr', 'Medtr1g102830' => 'mtr', 'MELO3C006499.2' => 'cme', 'Migut.G00385' => 'egut', 'MSTRG.4063' => 'ama', 'Nitab4.5_0000090g0260' => 'nta', 'Nitab4.5_0000977g0030' => 'nta', 'Nitab4.5_0002541g0040' => 'nta', 'Nitab4.5_0007068g0040' => 'nta', 'Nn005s41408' => 'nnu', 'Nn005s41410' => 'nnu', 'Oeu010310.1' => 'oeu', 'Oeu010311.1' => 'oeu', 'Oeu043472.1' => 'oeu', 'Os01g0246400' => 'osa', 'Os04g0267950' => 'osa', 'Os07g0178700' => 'osa', 'Os07g0178800' => 'osa', 'Peaxi162Scf00316g00046' => 'pax', 'Peaxi162Scf00316g00049' => 'pax', 'Peaxi162Scf00316g00059' => 'pax', 'Peaxi162Scf00316g00328' => 'pax', 'Peaxi162Scf00316g00329' => 'pax', 'Peaxi162Scf00316g00411' => 'pax', 'Peaxi162Scf00316g00521' => 'pax', 'Peaxi162Scf00492g00068' => 'pax', 'Peaxi162Scf35631g00002' => 'pax', 'PGR142G3720' => 'pgr', 'PGSC0003DMG400006442' => 'stu', 'Phvul.007G062000' => 'pvu', 'Potri.008G157750' => 'ptr', 'Potri.008G157900' => 'ptr', 'Potri.008G158000' => 'ptr', 'Potri.008G158200' => 'ptr', 'Pp3c11_7280' => 'ppa', 'Pp3c11_7980' => 'ppa', 'Pp3c12_19450' => 'ppa', 'Pp3c14_1480' => 'ppa', 'Pp3c14_1501' => 'ppa', 'Pp3c16_4900' => 'ppa', 'Pp3c16_5010' => 'ppa', 'Pp3c16_5060' => 'ppa', 'Pp3c19_18250' => 'ppa', 'Pp3c23_8530' => 'ppa', 'Pp3c23_8550' => 'ppa', 'Pp3c24_9670' => 'ppa', 'Pp3c2_21390' => 'ppa', 'Pp3c2_31380' => 'ppa', 'Pp3c3_16620' => 'ppa', 'Pp3c3_8090' => 'ppa', 'Pp3c3_8110' => 'ppa', 'Pp3c3_8130' => 'ppa', 'Pp3c3_8150' => 'ppa', 'Pp3c4_14320' => 'ppa', 'Pp3c6_2560' => 'ppa', 'Pp3c9_16700' => 'ppa', 'PRCOL_00000234' => 'pco', 'PRCOL_00000235' => 'pco', 'PRCOL_00000777' => 'pco', 'PRCOL_00002344' => 'pco', 'PRCOL_00002372' => 'pco', 'PRCOL_00006120' => 'pco', 'Prupe.1G021400' => 'ppe', 'Prupe.1G021500' => 'ppe', 'Prupe.1G021600' => 'ppe', 'Prupe.1G021700' => 'ppe', 'Prupe.1G021800' => 'ppe', 'Prupe.5G145100' => 'ppe', 'Psat6g204040' => 'psa', 'Psat6g204800' => 'psa', 'Psat6g204920' => 'psa', 'Psat6g204960' => 'psa', 'Psat6g205080' => 'psa', 'PSO017G0271' => 'pso', 'PSO017G1276' => 'pso', 'PSO017G1429' => 'pso', 'PSO017G1861' => 'pso', 'PSO017G2787' => 'pso', 'PSO017G4466' => 'pso', 'PSO017G5118' => 'pso', 'PSO017G5420' => 'pso', 'PSO063G3678' => 'pso', 'PSO210G0546' => 'pso', 'PSO317G0001' => 'pso', 'PSO357G0512' => 'pso', 'PSO478G2682' => 'pso', 'PSO647G0001' => 'pso', 'PSO675G0001' => 'pso', 'PSO675G2699' => 'pso', 'PSO675G2849' => 'pso', 'PSO675G4991' => 'pso', 'PSO689G0001' => 'pso', 'QL06p000916' => 'qlo', 'QL06p000921' => 'qlo', 'QL06p001398' => 'qlo', 'QL06p001407' => 'qlo', 'QL06p002031' => 'qlo', 'RcHm_v2.0_Chr4g0387791' => 'rch', 'RcHm_v2.0_Chr4g0387801' => 'rch', 'RcHm_v2.0_Chr6g0286501' => 'rch', 'RcHm_v2.0_Chr6g0286511' => 'rch', 'RcHm_v2.0_Chr6g0286521' => 'rch', 'RcHm_v2.0_Chr6g0286531' => 'rch', 'RcHm_v2.0_Chr7g0189141' => 'rch', 'Rhsim02G0028700' => 'rsi', 'Rhsim02G0028800' => 'rsi', 'Rhsim02G0028900' => 'rsi', 'Rhsim02G0029000' => 'rsi', 'Rhsim02G0029100' => 'rsi', 'Rhsim02G0029200' => 'rsi', 'Rhsim02G0029300' => 'rsi', 'Rhsim02G0029400' => 'rsi', 'Rhsim02G0029500' => 'rsi', 'Rhsim02G0029600' => 'rsi', 'RhsimUnG0024000' => 'rsi', 'RhsimUnG0024100' => 'rsi', 'RhsimUnG0024200' => 'rsi', 'RhsimUnG0024300' => 'rsi', 'RhsimUnG0024400' => 'rsi', 'RhsimUnG0024500' => 'rsi', 'RhsimUnG0024700' => 'rsi', 'RhsimUnG0024800' => 'rsi', 'RhsimUnG0024900' => 'rsi', 'RhsimUnG0025100' => 'rsi', 'Sabra08G0120200' => 'sbr', 'Sabra08G0120300' => 'sbr', 'Sabra08G0120500' => 'sbr', 'Sabra08G0120600' => 'sbr', 'Sabra10G0158900' => 'sbr', 'SalBow2G3492' => 'sbo', 'Sc13g0004760' => 'sci', 'Sc13g0004770' => 'sci', 'Sed0003417' => 'sed', 'Sed0019750' => 'sed', 'SEGI_03419' => 'sgi', 'SEGI_05907' => 'sgi', 'SEGI_10682' => 'sgi', 'SEGI_13528' => 'sgi', 'SEGI_16081' => 'sgi', 'SEGI_19370' => 'sgi', 'SEGI_21015' => 'sgi', 'SEGI_21944' => 'sgi', 'SEGI_32906' => 'sgi', 'SEGI_33093' => 'sgi', 'SEGI_36110' => 'sgi', 'SEGI_40397' => 'sgi', 'SGA_v2.0_scaffold191G40426' => 'sas', 'SGA_v2.0_scaffold353G49717' => 'sas', 'SGA_v2.0_scaffold50G18550' => 'sas', 'SMO119G0173' => 'smo', 'SMO172G0002' => 'smo', 'Solyc09g082690.3' => 'sly', 'Solyc09g082700.2' => 'sly', 'Sopen09g031550' => 'spe', 'Sopen09g031560' => 'spe', 'Sp3g20540' => 'spa', 'Sp7g07580' => 'spa', 'TAR134G0002' => 'tar', 'TAR236G0001' => 'tar', 'TAR365G0892' => 'tar', 'TAR636G0166' => 'tar', 'TAR636G0646' => 'tar', 'TAR636G0869' => 'tar', 'TAR636G1317' => 'tar', 'TAR636G1744' => 'tar', 'TAR636G3358' => 'tar', 'TAR636G3436' => 'tar', 'THA.LOC104803047' => 'tha', 'Thecc.04G238900' => 'tca', 'Thhalv10021557m.g' => 'esa', 'Thhalv10026318m.g' => 'esa', 'Thhalv10026335m.g' => 'esa', 'TPR.G17433' => 'tpr', 'TPR.G18915' => 'tpr', 'TPR.G26125' => 'tpr', 'TWI09G0677' => 'twi', 'TWI73G0287' => 'twi', 'unitig_748.g8326' => 'ugi', 'vmacro15370' => 'vma', 'vmacro15371' => 'vma', 'vmacro15372' => 'vma', 'vmacro15373' => 'vma', 'vmacro15374' => 'vma', 'VMungo0720G2826' => 'vmu', 'Zm00001eb116960' => 'zma', 'Zm00001eb301260' => 'zma', 'Zm00001eb301270' => 'zma' ) $gf_id = 'HOM05D001460' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001460' ) $data_identifier = 'HOM05D001460' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 4, 'aag' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 2, 'aox' => (int) 2, 'arhy' => (int) 4, 'ath' => (int) 2, 'atr' => (int) 1, 'acertr' => (int) 10, 'cqu' => (int) 4, 'bca' => (int) 11, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 1, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 1, 'ccan' => (int) 1, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 1, 'col' => (int) 1, 'cpa' => (int) 1, 'cre' => (int) 7, 'csa' => (int) 1, 'camsi' => (int) 2, 'dca' => (int) 3, 'din' => (int) 2, 'dzi' => (int) 3, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 14, 'fve' => (int) 9, 'gma' => (int) 2, 'ghi' => (int) 4, 'gra' => (int) 2, 'vvi' => (int) 1, 'han' => (int) 13, 'cav' => (int) 1, 'hma' => (int) 2, 'sun' => (int) 2, 'lal' => (int) 2, 'lonja' => (int) 12, 'lja' => (int) 1, 'lsa' => (int) 7, 'mes' => (int) 1, 'mpo' => (int) 27, 'mbi' => (int) 1, 'mco' => (int) 8, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 1, 'egut' => (int) 1, 'ama' => (int) 1, 'nta' => (int) 4, 'nnu' => (int) 2, 'oeu' => (int) 3, 'osa' => (int) 4, 'pax' => (int) 9, 'pgr' => (int) 1, 'stu' => (int) 1, 'pvu' => (int) 1, 'ptr' => (int) 4, 'ppa' => (int) 22, 'pco' => (int) 6, 'ppe' => (int) 6, 'psa' => (int) 5, 'pso' => (int) 19, 'qlo' => (int) 5, 'rch' => (int) 7, 'rsi' => (int) 20, 'sbr' => (int) 5, 'sbo' => (int) 1, 'sci' => (int) 2, 'sed' => (int) 2, 'sgi' => (int) 12, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 2, 'tar' => (int) 10, 'tha' => (int) 1, 'tca' => (int) 1, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 2, 'ugi' => (int) 1, 'vma' => (int) 5, 'vmu' => (int) 1, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb301270' $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' => 'HOM05D001460', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '433', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p22980' => 'bna', 'A01p32340' => 'bna', 'A03p42970' => 'bna', 'A05p25880' => 'bna', 'Aa31LG8G9320' => 'aar', 'Aa31LG8G9330' => 'aar', 'Aa31LG8G9340' => 'aar', 'Aa31sc221G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1034' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1528' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.829' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2222' => 'aag', 'Ah.12g058830' => 'amhyb', 'Ah.12g058840' => 'amhyb', 'AL3G37160' => 'aly', 'AL7G41310' => 'aly', 'Aqoxy5G00395' => 'aox', 'Aqoxy5G00396' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0C8NZA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5185HY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JZ1PRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MD3LS0' => 'arhy', 'AT3G22840' => 'ath', 'AT4G14690' => 'ath', 'ATR0665G054' => 'atr', 'Atru.chr4.2344' => 'acertr', 'Atru.chr4.2346' => 'acertr', 'Atru.chr4.2347' => 'acertr', 'Atru.chr4.2348' => 'acertr', 'Atru.chr4.2355' => 'acertr', 'Atru.chr4.2356' => 'acertr', 'Atru.chr4.2358' => 'acertr', 'Atru.chr4.2359' => 'acertr', 'Atru.chr4.2360' => 'acertr', 'Atru.chr4.2361' => 'acertr', 'AUR62030476' => 'cqu', 'AUR62030478' => 'cqu', 'AUR62030819' => 'cqu', 'AUR62030820' => 'cqu', 'BcaB03g14648' => 'bca', 'BcaB04g20492' => 'bca', 'BcaB06g26399' => 'bca', 'BcaC01g03416' => 'bca', 'BcaC01g03419' => 'bca', 'BcaC01g03421' => 'bca', 'BcaC01g03424' => 'bca', 'BcaC05g28012' => 'bca', 'BcaC09g49212' => 'bca', 'BcaC09g50140' => 'bca', 'BcaNung00346' => 'bca', 'BolC1t02785H' => 'bol', 'BolC1t04095H' => 'bol', 'BolC3t17545H' => 'bol', 'BolC5t32769H' => 'bol', 'BraA01t02211Z' => 'bra', 'BraA01t03359Z' => 'bra', 'BraA03t13441Z' => 'bra', 'BraA05t21476Z' => 'bra', 'C01p28420' => 'bna', 'C01p41350' => 'bna', 'C03p52750' => 'bna', 'C03p52780' => 'bna', 'C05p40270' => 'bna', 'CAN.G1437.9' => 'can', 'CANSAT78G0035' => 'cansat', 'CANSAT78G1036' => 'cansat', 'CANSAT78G2272' => 'cansat', 'CANSAT78G2478' => 'cansat', 'CARHR098700' => 'chi', 'CARHR221120' => 'chi', 'CARHR221150' => 'chi', 'Carub.0003s2297' => 'cru', 'Carub.0007s2749' => 'cru', 'Carub.0007s2750' => 'cru', 'Carub.0007s2751' => 'cru', 'Ca_10849_v3' => 'car', 'Cc03_g04300' => 'ccan', 'CDE02G3648' => 'cde', 'CDE05G0060' => 'cde', 'CDE05G0692' => 'cde', 'CDE05G2285' => 'cde', 'CDE05G2884' => 'cde', 'CDE05G3072' => 'cde', 'Cfa008439' => 'cfa', 'Cfa008441' => 'cfa', 'Cfa008443' => 'cfa', 'Cfa008448' => 'cfa', 'Ciclev10005974m.g' => 'ccl', 'Ciclev10006006m.g' => 'ccl', 'Ciclev10006775m.g' => 'ccl', 'CiPaw.02G120400' => 'cil', 'CiPaw.02G120500' => 'cil', 'CiPaw.02G120600' => 'cil', 'ClCG05G004850' => 'cla', 'COL.COLO4_21566' => 'col', 'Cpa.g.sc44.124' => 'cpa', 'Cre07.g320400' => 'cre', 'Cre07.g320450' => 'cre', 'Cre08.g384650' => 'cre', 'Cre09.g393173' => 'cre', 'Cre09.g394325' => 'cre', 'Cre14.g626750' => 'cre', 'Cre16.g679250' => 'cre', 'CsaV3_3G012890' => 'csa', 'CSS0010865' => 'camsi', 'CSS0044338' => 'camsi', 'DCAR_002366' => 'dca', 'DCAR_030687' => 'dca', 'DCAR_030688' => 'dca', 'Dinv14047' => 'din', 'Dinv14048' => 'din', 'Duzib151G0105' => 'dzi', 'Duzib151G0114' => 'dzi', 'Duzib212G1029' => 'dzi', 'ECA232G3536' => 'eca', 'ECA240G0786' => 'eca', 'ECA240G1802' => 'eca', 'ECA240G3760' => 'eca', 'ECA240G3920' => 'eca', 'EL10Ac5g12536' => 'bvu', 'EL10Ac5g12537' => 'bvu', 'EL10Ac5g12538' => 'bvu', 'Eucgr.B01004' => 'egr', 'Eucgr.B01006' => 'egr', 'Eucgr.B01007' => 'egr', 'Eucgr.B01008' => 'egr', 'Eucgr.B01895' => 'egr', 'Eucgr.B01896' => 'egr', 'FAN04G1456' => 'fan', 'FAN08G1769' => 'fan', 'FAN08G2160' => 'fan', 'FAN13G2403' => 'fan', 'FAN13G3303' => 'fan', 'FAN15G2435' => 'fan', 'FAN17G0672' => 'fan', 'FAN17G2441' => 'fan', 'FAN18G1024' => 'fan', 'FAN22G1458' => 'fan', 'FAN24G0037' => 'fan', 'FAN24G0429' => 'fan', 'FAN24G2387' => 'fan', 'FAN27G2746' => 'fan', 'FvH4_2g20400' => 'fve', 'FvH4_2g20420' => 'fve', 'FvH4_2g20430' => 'fve', 'FvH4_4g01270' => 'fve', 'FvH4_4g01290' => 'fve', 'FvH4_4g01300' => 'fve', 'FvH4_4g01310' => 'fve', 'FvH4_4g01330' => 'fve', 'FvH4_5g09070' => 'fve', 'Glyma.10G243800' => 'gma', 'Glyma.20G150600' => 'gma', 'Gohir.A09G219200' => 'ghi', 'Gohir.A09G219300' => 'ghi', 'Gohir.D09G221400' => 'ghi', 'Gohir.D09G221500' => 'ghi', 'Gorai.006G242600' => 'gra', 'Gorai.006G242700' => 'gra', 'GSVIVG01018044001' => 'vvi', 'HanXRQChr03g0083821' => 'han', 'HanXRQChr03g0083841' => 'han', 'HanXRQChr03g0083881' => 'han', 'HanXRQChr03g0083901' => 'han', 'HanXRQChr03g0083921' => 'han', 'HanXRQChr03g0085331' => 'han', 'HanXRQChr03g0085361' => 'han', 'HanXRQChr03g0085411' => 'han', 'HanXRQChr03g0085421' => 'han', 'HanXRQChr03g0085431' => 'han', 'HanXRQChr08g0221991' => 'han', 'HanXRQChr11g0336061' => 'han', 'HanXRQChr11g0336411' => 'han', 'Haze_11234' => 'cav', 'Hma1.2p1_0549F.1_g177010' => 'hma', 'Hma1.2p1_0602F.1_g187630' => 'hma', 'Hund14876' => 'sun', 'Hund14879' => 'sun', 'Lalb_Chr06g0160741' => 'lal', 'Lalb_Chr21g0304781' => 'lal', 'Lj3A726G19' => 'lonja', 'Lj3A726T23' => 'lonja', 'Lj3A726T24' => 'lonja', 'Lj3A726T25' => 'lonja', 'Lj3A727T17' => 'lonja', 'Lj3C726T0' => 'lonja', 'Lj3C726T2' => 'lonja', 'Lj3P725T35' => 'lonja', 'Lj3P727T10' => 'lonja', 'Lj3P727T12' => 'lonja', 'Lj3P727T14' => 'lonja', 'Lj5g0023109' => 'lja', 'Lj6P646T44' => 'lonja', 'Lsat_1_v5_gn_6_75760' => 'lsa', 'Lsat_1_v5_gn_6_75800' => 'lsa', 'Lsat_1_v5_gn_6_75900' => 'lsa', 'Lsat_1_v5_gn_6_76240' => 'lsa', 'Lsat_1_v5_gn_6_76441' => 'lsa', 'Lsat_1_v5_gn_6_76700' => 'lsa', 'Lsat_1_v5_gn_6_76760' => 'lsa', 'Manes.15G033100' => 'mes', 'Mapoly0004s0074' => 'mpo', 'Mapoly0004s0075' => 'mpo', 'Mapoly0004s0163' => 'mpo', 'Mapoly0004s0164' => 'mpo', 'Mapoly0021s0018' => 'mpo', 'Mapoly0041s0136' => 'mpo', 'Mapoly0041s0137' => 'mpo', 'Mapoly0041s0138' => 'mpo', 'Mapoly0041s0139' => 'mpo', 'Mapoly0041s0141' => 'mpo', 'Mapoly0041s0142' => 'mpo', 'Mapoly0041s0143' => 'mpo', 'Mapoly0041s0144' => 'mpo', 'Mapoly0041s0145' => 'mpo', 'Mapoly0047s0106' => 'mpo', 'Mapoly0047s0108' => 'mpo', 'Mapoly0050s0051' => 'mpo', 'Mapoly0050s0052' => 'mpo', 'Mapoly0050s0053' => 'mpo', 'Mapoly0058s0013' => 'mpo', 'Mapoly0091s0078' => 'mpo', 'Mapoly0091s0079' => 'mpo', 'Mapoly0091s0080' => 'mpo', 'Mapoly0091s0081' => 'mpo', 'Mapoly0278s0004' => 'mpo', 'Mapoly0278s0005' => 'mpo', 'Mapoly0278s0006' => 'mpo', 'MBI11_g30648_MAGBIO' => 'mbi', 'MCO03G194' => 'mco', 'MCO03G590' => 'mco', 'MCO07G312' => 'mco', 'MCO10G318' => 'mco', 'MCO12G244' => 'mco', 'MCO13G148' => 'mco', 'MCO13G194' => 'mco', 'MCO16G238' => 'mco', 'MD06G1134100' => 'mdo', 'MD13G1200100' => 'mdo', 'MD13G1200300' => 'mdo', 'MD13G1200600' => 'mdo', 'MD14G1150400' => 'mdo', 'MD16G1200000' => 'mdo', 'Medtr1g102570' => 'mtr', 'Medtr1g102780' => 'mtr', 'Medtr1g102800' => 'mtr', 'Medtr1g102810' => 'mtr', 'Medtr1g102830' => 'mtr', 'MELO3C006499.2' => 'cme', 'Migut.G00385' => 'egut', 'MSTRG.4063' => 'ama', 'Nitab4.5_0000090g0260' => 'nta', 'Nitab4.5_0000977g0030' => 'nta', 'Nitab4.5_0002541g0040' => 'nta', 'Nitab4.5_0007068g0040' => 'nta', 'Nn005s41408' => 'nnu', 'Nn005s41410' => 'nnu', 'Oeu010310.1' => 'oeu', 'Oeu010311.1' => 'oeu', 'Oeu043472.1' => 'oeu', 'Os01g0246400' => 'osa', 'Os04g0267950' => 'osa', 'Os07g0178700' => 'osa', 'Os07g0178800' => 'osa', 'Peaxi162Scf00316g00046' => 'pax', 'Peaxi162Scf00316g00049' => 'pax', 'Peaxi162Scf00316g00059' => 'pax', 'Peaxi162Scf00316g00328' => 'pax', 'Peaxi162Scf00316g00329' => 'pax', 'Peaxi162Scf00316g00411' => 'pax', 'Peaxi162Scf00316g00521' => 'pax', 'Peaxi162Scf00492g00068' => 'pax', 'Peaxi162Scf35631g00002' => 'pax', 'PGR142G3720' => 'pgr', 'PGSC0003DMG400006442' => 'stu', 'Phvul.007G062000' => 'pvu', 'Potri.008G157750' => 'ptr', 'Potri.008G157900' => 'ptr', 'Potri.008G158000' => 'ptr', 'Potri.008G158200' => 'ptr', 'Pp3c11_7280' => 'ppa', 'Pp3c11_7980' => 'ppa', 'Pp3c12_19450' => 'ppa', 'Pp3c14_1480' => 'ppa', 'Pp3c14_1501' => 'ppa', 'Pp3c16_4900' => 'ppa', 'Pp3c16_5010' => 'ppa', 'Pp3c16_5060' => 'ppa', 'Pp3c19_18250' => 'ppa', 'Pp3c23_8530' => 'ppa', 'Pp3c23_8550' => 'ppa', 'Pp3c24_9670' => 'ppa', 'Pp3c2_21390' => 'ppa', 'Pp3c2_31380' => 'ppa', 'Pp3c3_16620' => 'ppa', 'Pp3c3_8090' => 'ppa', 'Pp3c3_8110' => 'ppa', 'Pp3c3_8130' => 'ppa', 'Pp3c3_8150' => 'ppa', 'Pp3c4_14320' => 'ppa', 'Pp3c6_2560' => 'ppa', 'Pp3c9_16700' => 'ppa', 'PRCOL_00000234' => 'pco', 'PRCOL_00000235' => 'pco', 'PRCOL_00000777' => 'pco', 'PRCOL_00002344' => 'pco', 'PRCOL_00002372' => 'pco', 'PRCOL_00006120' => 'pco', 'Prupe.1G021400' => 'ppe', 'Prupe.1G021500' => 'ppe', 'Prupe.1G021600' => 'ppe', 'Prupe.1G021700' => 'ppe', 'Prupe.1G021800' => 'ppe', 'Prupe.5G145100' => 'ppe', 'Psat6g204040' => 'psa', 'Psat6g204800' => 'psa', 'Psat6g204920' => 'psa', 'Psat6g204960' => 'psa', 'Psat6g205080' => 'psa', 'PSO017G0271' => 'pso', 'PSO017G1276' => 'pso', 'PSO017G1429' => 'pso', 'PSO017G1861' => 'pso', 'PSO017G2787' => 'pso', 'PSO017G4466' => 'pso', 'PSO017G5118' => 'pso', 'PSO017G5420' => 'pso', 'PSO063G3678' => 'pso', 'PSO210G0546' => 'pso', 'PSO317G0001' => 'pso', 'PSO357G0512' => 'pso', 'PSO478G2682' => 'pso', 'PSO647G0001' => 'pso', 'PSO675G0001' => 'pso', 'PSO675G2699' => 'pso', 'PSO675G2849' => 'pso', 'PSO675G4991' => 'pso', 'PSO689G0001' => 'pso', 'QL06p000916' => 'qlo', 'QL06p000921' => 'qlo', 'QL06p001398' => 'qlo', 'QL06p001407' => 'qlo', 'QL06p002031' => 'qlo', 'RcHm_v2.0_Chr4g0387791' => 'rch', 'RcHm_v2.0_Chr4g0387801' => 'rch', 'RcHm_v2.0_Chr6g0286501' => 'rch', 'RcHm_v2.0_Chr6g0286511' => 'rch', 'RcHm_v2.0_Chr6g0286521' => 'rch', 'RcHm_v2.0_Chr6g0286531' => 'rch', 'RcHm_v2.0_Chr7g0189141' => 'rch', 'Rhsim02G0028700' => 'rsi', 'Rhsim02G0028800' => 'rsi', 'Rhsim02G0028900' => 'rsi', 'Rhsim02G0029000' => 'rsi', 'Rhsim02G0029100' => 'rsi', 'Rhsim02G0029200' => 'rsi', 'Rhsim02G0029300' => 'rsi', 'Rhsim02G0029400' => 'rsi', 'Rhsim02G0029500' => 'rsi', 'Rhsim02G0029600' => 'rsi', 'RhsimUnG0024000' => 'rsi', 'RhsimUnG0024100' => 'rsi', 'RhsimUnG0024200' => 'rsi', 'RhsimUnG0024300' => 'rsi', 'RhsimUnG0024400' => 'rsi', 'RhsimUnG0024500' => 'rsi', 'RhsimUnG0024700' => 'rsi', 'RhsimUnG0024800' => 'rsi', 'RhsimUnG0024900' => 'rsi', 'RhsimUnG0025100' => 'rsi', 'Sabra08G0120200' => 'sbr', 'Sabra08G0120300' => 'sbr', 'Sabra08G0120500' => 'sbr', 'Sabra08G0120600' => 'sbr', 'Sabra10G0158900' => 'sbr', 'SalBow2G3492' => 'sbo', 'Sc13g0004760' => 'sci', 'Sc13g0004770' => 'sci', 'Sed0003417' => 'sed', 'Sed0019750' => 'sed', 'SEGI_03419' => 'sgi', 'SEGI_05907' => 'sgi', 'SEGI_10682' => 'sgi', 'SEGI_13528' => 'sgi', 'SEGI_16081' => 'sgi', 'SEGI_19370' => 'sgi', 'SEGI_21015' => 'sgi', 'SEGI_21944' => 'sgi', 'SEGI_32906' => 'sgi', 'SEGI_33093' => 'sgi', 'SEGI_36110' => 'sgi', 'SEGI_40397' => 'sgi', 'SGA_v2.0_scaffold191G40426' => 'sas', 'SGA_v2.0_scaffold353G49717' => 'sas', 'SGA_v2.0_scaffold50G18550' => 'sas', 'SMO119G0173' => 'smo', 'SMO172G0002' => 'smo', 'Solyc09g082690.3' => 'sly', 'Solyc09g082700.2' => 'sly', 'Sopen09g031550' => 'spe', 'Sopen09g031560' => 'spe', 'Sp3g20540' => 'spa', 'Sp7g07580' => 'spa', 'TAR134G0002' => 'tar', 'TAR236G0001' => 'tar', 'TAR365G0892' => 'tar', 'TAR636G0166' => 'tar', 'TAR636G0646' => 'tar', 'TAR636G0869' => 'tar', 'TAR636G1317' => 'tar', 'TAR636G1744' => 'tar', 'TAR636G3358' => 'tar', 'TAR636G3436' => 'tar', 'THA.LOC104803047' => 'tha', 'Thecc.04G238900' => 'tca', 'Thhalv10021557m.g' => 'esa', 'Thhalv10026318m.g' => 'esa', 'Thhalv10026335m.g' => 'esa', 'TPR.G17433' => 'tpr', 'TPR.G18915' => 'tpr', 'TPR.G26125' => 'tpr', 'TWI09G0677' => 'twi', 'TWI73G0287' => 'twi', 'unitig_748.g8326' => 'ugi', 'vmacro15370' => 'vma', 'vmacro15371' => 'vma', 'vmacro15372' => 'vma', 'vmacro15373' => 'vma', 'vmacro15374' => 'vma', 'VMungo0720G2826' => 'vmu', 'Zm00001eb116960' => 'zma', 'Zm00001eb301260' => 'zma', 'Zm00001eb301270' => 'zma' ), 'gf_id' => 'HOM05D001460', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001460' ), 'data_identifier' => 'HOM05D001460', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001460', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '433', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p22980' => 'bna', 'A01p32340' => 'bna', 'A03p42970' => 'bna', 'A05p25880' => 'bna', 'Aa31LG8G9320' => 'aar', 'Aa31LG8G9330' => 'aar', 'Aa31LG8G9340' => 'aar', 'Aa31sc221G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1034' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1528' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.829' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2222' => 'aag', 'Ah.12g058830' => 'amhyb', 'Ah.12g058840' => 'amhyb', 'AL3G37160' => 'aly', 'AL7G41310' => 'aly', 'Aqoxy5G00395' => 'aox', 'Aqoxy5G00396' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0C8NZA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5185HY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JZ1PRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MD3LS0' => 'arhy', 'AT3G22840' => 'ath', 'AT4G14690' => 'ath', 'ATR0665G054' => 'atr', 'Atru.chr4.2344' => 'acertr', 'Atru.chr4.2346' => 'acertr', 'Atru.chr4.2347' => 'acertr', 'Atru.chr4.2348' => 'acertr', 'Atru.chr4.2355' => 'acertr', 'Atru.chr4.2356' => 'acertr', 'Atru.chr4.2358' => 'acertr', 'Atru.chr4.2359' => 'acertr', 'Atru.chr4.2360' => 'acertr', 'Atru.chr4.2361' => 'acertr', 'AUR62030476' => 'cqu', 'AUR62030478' => 'cqu', 'AUR62030819' => 'cqu', 'AUR62030820' => 'cqu', 'BcaB03g14648' => 'bca', 'BcaB04g20492' => 'bca', 'BcaB06g26399' => 'bca', 'BcaC01g03416' => 'bca', 'BcaC01g03419' => 'bca', 'BcaC01g03421' => 'bca', 'BcaC01g03424' => 'bca', 'BcaC05g28012' => 'bca', 'BcaC09g49212' => 'bca', 'BcaC09g50140' => 'bca', 'BcaNung00346' => 'bca', 'BolC1t02785H' => 'bol', 'BolC1t04095H' => 'bol', 'BolC3t17545H' => 'bol', 'BolC5t32769H' => 'bol', 'BraA01t02211Z' => 'bra', 'BraA01t03359Z' => 'bra', 'BraA03t13441Z' => 'bra', 'BraA05t21476Z' => 'bra', 'C01p28420' => 'bna', 'C01p41350' => 'bna', 'C03p52750' => 'bna', 'C03p52780' => 'bna', 'C05p40270' => 'bna', 'CAN.G1437.9' => 'can', 'CANSAT78G0035' => 'cansat', 'CANSAT78G1036' => 'cansat', 'CANSAT78G2272' => 'cansat', 'CANSAT78G2478' => 'cansat', 'CARHR098700' => 'chi', 'CARHR221120' => 'chi', 'CARHR221150' => 'chi', 'Carub.0003s2297' => 'cru', 'Carub.0007s2749' => 'cru', 'Carub.0007s2750' => 'cru', 'Carub.0007s2751' => 'cru', 'Ca_10849_v3' => 'car', 'Cc03_g04300' => 'ccan', 'CDE02G3648' => 'cde', 'CDE05G0060' => 'cde', 'CDE05G0692' => 'cde', 'CDE05G2285' => 'cde', 'CDE05G2884' => 'cde', 'CDE05G3072' => 'cde', 'Cfa008439' => 'cfa', 'Cfa008441' => 'cfa', 'Cfa008443' => 'cfa', 'Cfa008448' => 'cfa', 'Ciclev10005974m.g' => 'ccl', 'Ciclev10006006m.g' => 'ccl', 'Ciclev10006775m.g' => 'ccl', 'CiPaw.02G120400' => 'cil', 'CiPaw.02G120500' => 'cil', 'CiPaw.02G120600' => 'cil', 'ClCG05G004850' => 'cla', 'COL.COLO4_21566' => 'col', 'Cpa.g.sc44.124' => 'cpa', 'Cre07.g320400' => 'cre', 'Cre07.g320450' => 'cre', 'Cre08.g384650' => 'cre', 'Cre09.g393173' => 'cre', 'Cre09.g394325' => 'cre', 'Cre14.g626750' => 'cre', 'Cre16.g679250' => 'cre', 'CsaV3_3G012890' => 'csa', 'CSS0010865' => 'camsi', 'CSS0044338' => 'camsi', 'DCAR_002366' => 'dca', 'DCAR_030687' => 'dca', 'DCAR_030688' => 'dca', 'Dinv14047' => 'din', 'Dinv14048' => 'din', 'Duzib151G0105' => 'dzi', 'Duzib151G0114' => 'dzi', 'Duzib212G1029' => 'dzi', 'ECA232G3536' => 'eca', 'ECA240G0786' => 'eca', 'ECA240G1802' => 'eca', 'ECA240G3760' => 'eca', 'ECA240G3920' => 'eca', 'EL10Ac5g12536' => 'bvu', 'EL10Ac5g12537' => 'bvu', 'EL10Ac5g12538' => 'bvu', 'Eucgr.B01004' => 'egr', 'Eucgr.B01006' => 'egr', 'Eucgr.B01007' => 'egr', 'Eucgr.B01008' => 'egr', 'Eucgr.B01895' => 'egr', 'Eucgr.B01896' => 'egr', 'FAN04G1456' => 'fan', 'FAN08G1769' => 'fan', 'FAN08G2160' => 'fan', 'FAN13G2403' => 'fan', 'FAN13G3303' => 'fan', 'FAN15G2435' => 'fan', 'FAN17G0672' => 'fan', 'FAN17G2441' => 'fan', 'FAN18G1024' => 'fan', 'FAN22G1458' => 'fan', 'FAN24G0037' => 'fan', 'FAN24G0429' => 'fan', 'FAN24G2387' => 'fan', 'FAN27G2746' => 'fan', 'FvH4_2g20400' => 'fve', 'FvH4_2g20420' => 'fve', 'FvH4_2g20430' => 'fve', 'FvH4_4g01270' => 'fve', 'FvH4_4g01290' => 'fve', 'FvH4_4g01300' => 'fve', 'FvH4_4g01310' => 'fve', 'FvH4_4g01330' => 'fve', 'FvH4_5g09070' => 'fve', 'Glyma.10G243800' => 'gma', 'Glyma.20G150600' => 'gma', 'Gohir.A09G219200' => 'ghi', 'Gohir.A09G219300' => 'ghi', 'Gohir.D09G221400' => 'ghi', 'Gohir.D09G221500' => 'ghi', 'Gorai.006G242600' => 'gra', 'Gorai.006G242700' => 'gra', 'GSVIVG01018044001' => 'vvi', 'HanXRQChr03g0083821' => 'han', 'HanXRQChr03g0083841' => 'han', 'HanXRQChr03g0083881' => 'han', 'HanXRQChr03g0083901' => 'han', 'HanXRQChr03g0083921' => 'han', 'HanXRQChr03g0085331' => 'han', 'HanXRQChr03g0085361' => 'han', 'HanXRQChr03g0085411' => 'han', 'HanXRQChr03g0085421' => 'han', 'HanXRQChr03g0085431' => 'han', 'HanXRQChr08g0221991' => 'han', 'HanXRQChr11g0336061' => 'han', 'HanXRQChr11g0336411' => 'han', 'Haze_11234' => 'cav', 'Hma1.2p1_0549F.1_g177010' => 'hma', 'Hma1.2p1_0602F.1_g187630' => 'hma', 'Hund14876' => 'sun', 'Hund14879' => 'sun', 'Lalb_Chr06g0160741' => 'lal', 'Lalb_Chr21g0304781' => 'lal', 'Lj3A726G19' => 'lonja', 'Lj3A726T23' => 'lonja', 'Lj3A726T24' => 'lonja', 'Lj3A726T25' => 'lonja', 'Lj3A727T17' => 'lonja', 'Lj3C726T0' => 'lonja', 'Lj3C726T2' => 'lonja', 'Lj3P725T35' => 'lonja', 'Lj3P727T10' => 'lonja', 'Lj3P727T12' => 'lonja', 'Lj3P727T14' => 'lonja', 'Lj5g0023109' => 'lja', 'Lj6P646T44' => 'lonja', 'Lsat_1_v5_gn_6_75760' => 'lsa', 'Lsat_1_v5_gn_6_75800' => 'lsa', 'Lsat_1_v5_gn_6_75900' => 'lsa', 'Lsat_1_v5_gn_6_76240' => 'lsa', 'Lsat_1_v5_gn_6_76441' => 'lsa', 'Lsat_1_v5_gn_6_76700' => 'lsa', 'Lsat_1_v5_gn_6_76760' => 'lsa', 'Manes.15G033100' => 'mes', 'Mapoly0004s0074' => 'mpo', 'Mapoly0004s0075' => 'mpo', 'Mapoly0004s0163' => 'mpo', 'Mapoly0004s0164' => 'mpo', 'Mapoly0021s0018' => 'mpo', 'Mapoly0041s0136' => 'mpo', 'Mapoly0041s0137' => 'mpo', 'Mapoly0041s0138' => 'mpo', 'Mapoly0041s0139' => 'mpo', 'Mapoly0041s0141' => 'mpo', 'Mapoly0041s0142' => 'mpo', 'Mapoly0041s0143' => 'mpo', 'Mapoly0041s0144' => 'mpo', 'Mapoly0041s0145' => 'mpo', 'Mapoly0047s0106' => 'mpo', 'Mapoly0047s0108' => 'mpo', 'Mapoly0050s0051' => 'mpo', 'Mapoly0050s0052' => 'mpo', 'Mapoly0050s0053' => 'mpo', 'Mapoly0058s0013' => 'mpo', 'Mapoly0091s0078' => 'mpo', 'Mapoly0091s0079' => 'mpo', 'Mapoly0091s0080' => 'mpo', 'Mapoly0091s0081' => 'mpo', 'Mapoly0278s0004' => 'mpo', 'Mapoly0278s0005' => 'mpo', 'Mapoly0278s0006' => 'mpo', 'MBI11_g30648_MAGBIO' => 'mbi', 'MCO03G194' => 'mco', 'MCO03G590' => 'mco', 'MCO07G312' => 'mco', 'MCO10G318' => 'mco', 'MCO12G244' => 'mco', 'MCO13G148' => 'mco', 'MCO13G194' => 'mco', 'MCO16G238' => 'mco', 'MD06G1134100' => 'mdo', 'MD13G1200100' => 'mdo', 'MD13G1200300' => 'mdo', 'MD13G1200600' => 'mdo', 'MD14G1150400' => 'mdo', 'MD16G1200000' => 'mdo', 'Medtr1g102570' => 'mtr', 'Medtr1g102780' => 'mtr', 'Medtr1g102800' => 'mtr', 'Medtr1g102810' => 'mtr', 'Medtr1g102830' => 'mtr', 'MELO3C006499.2' => 'cme', 'Migut.G00385' => 'egut', 'MSTRG.4063' => 'ama', 'Nitab4.5_0000090g0260' => 'nta', 'Nitab4.5_0000977g0030' => 'nta', 'Nitab4.5_0002541g0040' => 'nta', 'Nitab4.5_0007068g0040' => 'nta', 'Nn005s41408' => 'nnu', 'Nn005s41410' => 'nnu', 'Oeu010310.1' => 'oeu', 'Oeu010311.1' => 'oeu', 'Oeu043472.1' => 'oeu', 'Os01g0246400' => 'osa', 'Os04g0267950' => 'osa', 'Os07g0178700' => 'osa', 'Os07g0178800' => 'osa', 'Peaxi162Scf00316g00046' => 'pax', 'Peaxi162Scf00316g00049' => 'pax', 'Peaxi162Scf00316g00059' => 'pax', 'Peaxi162Scf00316g00328' => 'pax', 'Peaxi162Scf00316g00329' => 'pax', 'Peaxi162Scf00316g00411' => 'pax', 'Peaxi162Scf00316g00521' => 'pax', 'Peaxi162Scf00492g00068' => 'pax', 'Peaxi162Scf35631g00002' => 'pax', 'PGR142G3720' => 'pgr', 'PGSC0003DMG400006442' => 'stu', 'Phvul.007G062000' => 'pvu', 'Potri.008G157750' => 'ptr', 'Potri.008G157900' => 'ptr', 'Potri.008G158000' => 'ptr', 'Potri.008G158200' => 'ptr', 'Pp3c11_7280' => 'ppa', 'Pp3c11_7980' => 'ppa', 'Pp3c12_19450' => 'ppa', 'Pp3c14_1480' => 'ppa', 'Pp3c14_1501' => 'ppa', 'Pp3c16_4900' => 'ppa', 'Pp3c16_5010' => 'ppa', 'Pp3c16_5060' => 'ppa', 'Pp3c19_18250' => 'ppa', 'Pp3c23_8530' => 'ppa', 'Pp3c23_8550' => 'ppa', 'Pp3c24_9670' => 'ppa', 'Pp3c2_21390' => 'ppa', 'Pp3c2_31380' => 'ppa', 'Pp3c3_16620' => 'ppa', 'Pp3c3_8090' => 'ppa', 'Pp3c3_8110' => 'ppa', 'Pp3c3_8130' => 'ppa', 'Pp3c3_8150' => 'ppa', 'Pp3c4_14320' => 'ppa', 'Pp3c6_2560' => 'ppa', 'Pp3c9_16700' => 'ppa', 'PRCOL_00000234' => 'pco', 'PRCOL_00000235' => 'pco', 'PRCOL_00000777' => 'pco', 'PRCOL_00002344' => 'pco', 'PRCOL_00002372' => 'pco', 'PRCOL_00006120' => 'pco', 'Prupe.1G021400' => 'ppe', 'Prupe.1G021500' => 'ppe', 'Prupe.1G021600' => 'ppe', 'Prupe.1G021700' => 'ppe', 'Prupe.1G021800' => 'ppe', 'Prupe.5G145100' => 'ppe', 'Psat6g204040' => 'psa', 'Psat6g204800' => 'psa', 'Psat6g204920' => 'psa', 'Psat6g204960' => 'psa', 'Psat6g205080' => 'psa', 'PSO017G0271' => 'pso', 'PSO017G1276' => 'pso', 'PSO017G1429' => 'pso', 'PSO017G1861' => 'pso', 'PSO017G2787' => 'pso', 'PSO017G4466' => 'pso', 'PSO017G5118' => 'pso', 'PSO017G5420' => 'pso', 'PSO063G3678' => 'pso', 'PSO210G0546' => 'pso', 'PSO317G0001' => 'pso', 'PSO357G0512' => 'pso', 'PSO478G2682' => 'pso', 'PSO647G0001' => 'pso', 'PSO675G0001' => 'pso', 'PSO675G2699' => 'pso', 'PSO675G2849' => 'pso', 'PSO675G4991' => 'pso', 'PSO689G0001' => 'pso', 'QL06p000916' => 'qlo', 'QL06p000921' => 'qlo', 'QL06p001398' => 'qlo', 'QL06p001407' => 'qlo', 'QL06p002031' => 'qlo', 'RcHm_v2.0_Chr4g0387791' => 'rch', 'RcHm_v2.0_Chr4g0387801' => 'rch', 'RcHm_v2.0_Chr6g0286501' => 'rch', 'RcHm_v2.0_Chr6g0286511' => 'rch', 'RcHm_v2.0_Chr6g0286521' => 'rch', 'RcHm_v2.0_Chr6g0286531' => 'rch', 'RcHm_v2.0_Chr7g0189141' => 'rch', 'Rhsim02G0028700' => 'rsi', 'Rhsim02G0028800' => 'rsi', 'Rhsim02G0028900' => 'rsi', 'Rhsim02G0029000' => 'rsi', 'Rhsim02G0029100' => 'rsi', 'Rhsim02G0029200' => 'rsi', 'Rhsim02G0029300' => 'rsi', 'Rhsim02G0029400' => 'rsi', 'Rhsim02G0029500' => 'rsi', 'Rhsim02G0029600' => 'rsi', 'RhsimUnG0024000' => 'rsi', 'RhsimUnG0024100' => 'rsi', 'RhsimUnG0024200' => 'rsi', 'RhsimUnG0024300' => 'rsi', 'RhsimUnG0024400' => 'rsi', 'RhsimUnG0024500' => 'rsi', 'RhsimUnG0024700' => 'rsi', 'RhsimUnG0024800' => 'rsi', 'RhsimUnG0024900' => 'rsi', 'RhsimUnG0025100' => 'rsi', 'Sabra08G0120200' => 'sbr', 'Sabra08G0120300' => 'sbr', 'Sabra08G0120500' => 'sbr', 'Sabra08G0120600' => 'sbr', 'Sabra10G0158900' => 'sbr', 'SalBow2G3492' => 'sbo', 'Sc13g0004760' => 'sci', 'Sc13g0004770' => 'sci', 'Sed0003417' => 'sed', 'Sed0019750' => 'sed', 'SEGI_03419' => 'sgi', 'SEGI_05907' => 'sgi', 'SEGI_10682' => 'sgi', 'SEGI_13528' => 'sgi', 'SEGI_16081' => 'sgi', 'SEGI_19370' => 'sgi', 'SEGI_21015' => 'sgi', 'SEGI_21944' => 'sgi', 'SEGI_32906' => 'sgi', 'SEGI_33093' => 'sgi', 'SEGI_36110' => 'sgi', 'SEGI_40397' => 'sgi', 'SGA_v2.0_scaffold191G40426' => 'sas', 'SGA_v2.0_scaffold353G49717' => 'sas', 'SGA_v2.0_scaffold50G18550' => 'sas', 'SMO119G0173' => 'smo', 'SMO172G0002' => 'smo', 'Solyc09g082690.3' => 'sly', 'Solyc09g082700.2' => 'sly', 'Sopen09g031550' => 'spe', 'Sopen09g031560' => 'spe', 'Sp3g20540' => 'spa', 'Sp7g07580' => 'spa', 'TAR134G0002' => 'tar', 'TAR236G0001' => 'tar', 'TAR365G0892' => 'tar', 'TAR636G0166' => 'tar', 'TAR636G0646' => 'tar', 'TAR636G0869' => 'tar', 'TAR636G1317' => 'tar', 'TAR636G1744' => 'tar', 'TAR636G3358' => 'tar', 'TAR636G3436' => 'tar', 'THA.LOC104803047' => 'tha', 'Thecc.04G238900' => 'tca', 'Thhalv10021557m.g' => 'esa', 'Thhalv10026318m.g' => 'esa', 'Thhalv10026335m.g' => 'esa', 'TPR.G17433' => 'tpr', 'TPR.G18915' => 'tpr', 'TPR.G26125' => 'tpr', 'TWI09G0677' => 'twi', 'TWI73G0287' => 'twi', 'unitig_748.g8326' => 'ugi', 'vmacro15370' => 'vma', 'vmacro15371' => 'vma', 'vmacro15372' => 'vma', 'vmacro15373' => 'vma', 'vmacro15374' => 'vma', 'VMungo0720G2826' => 'vmu', 'Zm00001eb116960' => 'zma', 'Zm00001eb301260' => 'zma', 'Zm00001eb301270' => 'zma' ) $gf_id = 'HOM05D001460' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001460' ) $data_identifier = 'HOM05D001460' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 4, 'aag' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 2, 'aox' => (int) 2, 'arhy' => (int) 4, 'ath' => (int) 2, 'atr' => (int) 1, 'acertr' => (int) 10, 'cqu' => (int) 4, 'bca' => (int) 11, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 1, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 1, 'ccan' => (int) 1, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 1, 'col' => (int) 1, 'cpa' => (int) 1, 'cre' => (int) 7, 'csa' => (int) 1, 'camsi' => (int) 2, 'dca' => (int) 3, 'din' => (int) 2, 'dzi' => (int) 3, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 14, 'fve' => (int) 9, 'gma' => (int) 2, 'ghi' => (int) 4, 'gra' => (int) 2, 'vvi' => (int) 1, 'han' => (int) 13, 'cav' => (int) 1, 'hma' => (int) 2, 'sun' => (int) 2, 'lal' => (int) 2, 'lonja' => (int) 12, 'lja' => (int) 1, 'lsa' => (int) 7, 'mes' => (int) 1, 'mpo' => (int) 27, 'mbi' => (int) 1, 'mco' => (int) 8, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 1, 'egut' => (int) 1, 'ama' => (int) 1, 'nta' => (int) 4, 'nnu' => (int) 2, 'oeu' => (int) 3, 'osa' => (int) 4, 'pax' => (int) 9, 'pgr' => (int) 1, 'stu' => (int) 1, 'pvu' => (int) 1, 'ptr' => (int) 4, 'ppa' => (int) 22, 'pco' => (int) 6, 'ppe' => (int) 6, 'psa' => (int) 5, 'pso' => (int) 19, 'qlo' => (int) 5, 'rch' => (int) 7, 'rsi' => (int) 20, 'sbr' => (int) 5, 'sbo' => (int) 1, 'sci' => (int) 2, 'sed' => (int) 2, 'sgi' => (int) 12, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 2, 'tar' => (int) 10, 'tha' => (int) 1, 'tca' => (int) 1, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 2, 'ugi' => (int) 1, 'vma' => (int) 5, 'vmu' => (int) 1, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb301270' $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' => 'HOM05D001460', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '433', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p22980' => 'bna', 'A01p32340' => 'bna', 'A03p42970' => 'bna', 'A05p25880' => 'bna', 'Aa31LG8G9320' => 'aar', 'Aa31LG8G9330' => 'aar', 'Aa31LG8G9340' => 'aar', 'Aa31sc221G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1034' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1528' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.829' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2222' => 'aag', 'Ah.12g058830' => 'amhyb', 'Ah.12g058840' => 'amhyb', 'AL3G37160' => 'aly', 'AL7G41310' => 'aly', 'Aqoxy5G00395' => 'aox', 'Aqoxy5G00396' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0C8NZA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5185HY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JZ1PRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MD3LS0' => 'arhy', 'AT3G22840' => 'ath', 'AT4G14690' => 'ath', 'ATR0665G054' => 'atr', 'Atru.chr4.2344' => 'acertr', 'Atru.chr4.2346' => 'acertr', 'Atru.chr4.2347' => 'acertr', 'Atru.chr4.2348' => 'acertr', 'Atru.chr4.2355' => 'acertr', 'Atru.chr4.2356' => 'acertr', 'Atru.chr4.2358' => 'acertr', 'Atru.chr4.2359' => 'acertr', 'Atru.chr4.2360' => 'acertr', 'Atru.chr4.2361' => 'acertr', 'AUR62030476' => 'cqu', 'AUR62030478' => 'cqu', 'AUR62030819' => 'cqu', 'AUR62030820' => 'cqu', 'BcaB03g14648' => 'bca', 'BcaB04g20492' => 'bca', 'BcaB06g26399' => 'bca', 'BcaC01g03416' => 'bca', 'BcaC01g03419' => 'bca', 'BcaC01g03421' => 'bca', 'BcaC01g03424' => 'bca', 'BcaC05g28012' => 'bca', 'BcaC09g49212' => 'bca', 'BcaC09g50140' => 'bca', 'BcaNung00346' => 'bca', 'BolC1t02785H' => 'bol', 'BolC1t04095H' => 'bol', 'BolC3t17545H' => 'bol', 'BolC5t32769H' => 'bol', 'BraA01t02211Z' => 'bra', 'BraA01t03359Z' => 'bra', 'BraA03t13441Z' => 'bra', 'BraA05t21476Z' => 'bra', 'C01p28420' => 'bna', 'C01p41350' => 'bna', 'C03p52750' => 'bna', 'C03p52780' => 'bna', 'C05p40270' => 'bna', 'CAN.G1437.9' => 'can', 'CANSAT78G0035' => 'cansat', 'CANSAT78G1036' => 'cansat', 'CANSAT78G2272' => 'cansat', 'CANSAT78G2478' => 'cansat', 'CARHR098700' => 'chi', 'CARHR221120' => 'chi', 'CARHR221150' => 'chi', 'Carub.0003s2297' => 'cru', 'Carub.0007s2749' => 'cru', 'Carub.0007s2750' => 'cru', 'Carub.0007s2751' => 'cru', 'Ca_10849_v3' => 'car', 'Cc03_g04300' => 'ccan', 'CDE02G3648' => 'cde', 'CDE05G0060' => 'cde', 'CDE05G0692' => 'cde', 'CDE05G2285' => 'cde', 'CDE05G2884' => 'cde', 'CDE05G3072' => 'cde', 'Cfa008439' => 'cfa', 'Cfa008441' => 'cfa', 'Cfa008443' => 'cfa', 'Cfa008448' => 'cfa', 'Ciclev10005974m.g' => 'ccl', 'Ciclev10006006m.g' => 'ccl', 'Ciclev10006775m.g' => 'ccl', 'CiPaw.02G120400' => 'cil', 'CiPaw.02G120500' => 'cil', 'CiPaw.02G120600' => 'cil', 'ClCG05G004850' => 'cla', 'COL.COLO4_21566' => 'col', 'Cpa.g.sc44.124' => 'cpa', 'Cre07.g320400' => 'cre', 'Cre07.g320450' => 'cre', 'Cre08.g384650' => 'cre', 'Cre09.g393173' => 'cre', 'Cre09.g394325' => 'cre', 'Cre14.g626750' => 'cre', 'Cre16.g679250' => 'cre', 'CsaV3_3G012890' => 'csa', 'CSS0010865' => 'camsi', 'CSS0044338' => 'camsi', 'DCAR_002366' => 'dca', 'DCAR_030687' => 'dca', 'DCAR_030688' => 'dca', 'Dinv14047' => 'din', 'Dinv14048' => 'din', 'Duzib151G0105' => 'dzi', 'Duzib151G0114' => 'dzi', 'Duzib212G1029' => 'dzi', 'ECA232G3536' => 'eca', 'ECA240G0786' => 'eca', 'ECA240G1802' => 'eca', 'ECA240G3760' => 'eca', 'ECA240G3920' => 'eca', 'EL10Ac5g12536' => 'bvu', 'EL10Ac5g12537' => 'bvu', 'EL10Ac5g12538' => 'bvu', 'Eucgr.B01004' => 'egr', 'Eucgr.B01006' => 'egr', 'Eucgr.B01007' => 'egr', 'Eucgr.B01008' => 'egr', 'Eucgr.B01895' => 'egr', 'Eucgr.B01896' => 'egr', 'FAN04G1456' => 'fan', 'FAN08G1769' => 'fan', 'FAN08G2160' => 'fan', 'FAN13G2403' => 'fan', 'FAN13G3303' => 'fan', 'FAN15G2435' => 'fan', 'FAN17G0672' => 'fan', 'FAN17G2441' => 'fan', 'FAN18G1024' => 'fan', 'FAN22G1458' => 'fan', 'FAN24G0037' => 'fan', 'FAN24G0429' => 'fan', 'FAN24G2387' => 'fan', 'FAN27G2746' => 'fan', 'FvH4_2g20400' => 'fve', 'FvH4_2g20420' => 'fve', 'FvH4_2g20430' => 'fve', 'FvH4_4g01270' => 'fve', 'FvH4_4g01290' => 'fve', 'FvH4_4g01300' => 'fve', 'FvH4_4g01310' => 'fve', 'FvH4_4g01330' => 'fve', 'FvH4_5g09070' => 'fve', 'Glyma.10G243800' => 'gma', 'Glyma.20G150600' => 'gma', 'Gohir.A09G219200' => 'ghi', 'Gohir.A09G219300' => 'ghi', 'Gohir.D09G221400' => 'ghi', 'Gohir.D09G221500' => 'ghi', 'Gorai.006G242600' => 'gra', 'Gorai.006G242700' => 'gra', 'GSVIVG01018044001' => 'vvi', 'HanXRQChr03g0083821' => 'han', 'HanXRQChr03g0083841' => 'han', 'HanXRQChr03g0083881' => 'han', 'HanXRQChr03g0083901' => 'han', 'HanXRQChr03g0083921' => 'han', 'HanXRQChr03g0085331' => 'han', 'HanXRQChr03g0085361' => 'han', 'HanXRQChr03g0085411' => 'han', 'HanXRQChr03g0085421' => 'han', 'HanXRQChr03g0085431' => 'han', 'HanXRQChr08g0221991' => 'han', 'HanXRQChr11g0336061' => 'han', 'HanXRQChr11g0336411' => 'han', 'Haze_11234' => 'cav', 'Hma1.2p1_0549F.1_g177010' => 'hma', 'Hma1.2p1_0602F.1_g187630' => 'hma', 'Hund14876' => 'sun', 'Hund14879' => 'sun', 'Lalb_Chr06g0160741' => 'lal', 'Lalb_Chr21g0304781' => 'lal', 'Lj3A726G19' => 'lonja', 'Lj3A726T23' => 'lonja', 'Lj3A726T24' => 'lonja', 'Lj3A726T25' => 'lonja', 'Lj3A727T17' => 'lonja', 'Lj3C726T0' => 'lonja', 'Lj3C726T2' => 'lonja', 'Lj3P725T35' => 'lonja', 'Lj3P727T10' => 'lonja', 'Lj3P727T12' => 'lonja', 'Lj3P727T14' => 'lonja', 'Lj5g0023109' => 'lja', 'Lj6P646T44' => 'lonja', 'Lsat_1_v5_gn_6_75760' => 'lsa', 'Lsat_1_v5_gn_6_75800' => 'lsa', 'Lsat_1_v5_gn_6_75900' => 'lsa', 'Lsat_1_v5_gn_6_76240' => 'lsa', 'Lsat_1_v5_gn_6_76441' => 'lsa', 'Lsat_1_v5_gn_6_76700' => 'lsa', 'Lsat_1_v5_gn_6_76760' => 'lsa', 'Manes.15G033100' => 'mes', 'Mapoly0004s0074' => 'mpo', 'Mapoly0004s0075' => 'mpo', 'Mapoly0004s0163' => 'mpo', 'Mapoly0004s0164' => 'mpo', 'Mapoly0021s0018' => 'mpo', 'Mapoly0041s0136' => 'mpo', 'Mapoly0041s0137' => 'mpo', 'Mapoly0041s0138' => 'mpo', 'Mapoly0041s0139' => 'mpo', 'Mapoly0041s0141' => 'mpo', 'Mapoly0041s0142' => 'mpo', 'Mapoly0041s0143' => 'mpo', 'Mapoly0041s0144' => 'mpo', 'Mapoly0041s0145' => 'mpo', 'Mapoly0047s0106' => 'mpo', 'Mapoly0047s0108' => 'mpo', 'Mapoly0050s0051' => 'mpo', 'Mapoly0050s0052' => 'mpo', 'Mapoly0050s0053' => 'mpo', 'Mapoly0058s0013' => 'mpo', 'Mapoly0091s0078' => 'mpo', 'Mapoly0091s0079' => 'mpo', 'Mapoly0091s0080' => 'mpo', 'Mapoly0091s0081' => 'mpo', 'Mapoly0278s0004' => 'mpo', 'Mapoly0278s0005' => 'mpo', 'Mapoly0278s0006' => 'mpo', 'MBI11_g30648_MAGBIO' => 'mbi', 'MCO03G194' => 'mco', 'MCO03G590' => 'mco', 'MCO07G312' => 'mco', 'MCO10G318' => 'mco', 'MCO12G244' => 'mco', 'MCO13G148' => 'mco', 'MCO13G194' => 'mco', 'MCO16G238' => 'mco', 'MD06G1134100' => 'mdo', 'MD13G1200100' => 'mdo', 'MD13G1200300' => 'mdo', 'MD13G1200600' => 'mdo', 'MD14G1150400' => 'mdo', 'MD16G1200000' => 'mdo', 'Medtr1g102570' => 'mtr', 'Medtr1g102780' => 'mtr', 'Medtr1g102800' => 'mtr', 'Medtr1g102810' => 'mtr', 'Medtr1g102830' => 'mtr', 'MELO3C006499.2' => 'cme', 'Migut.G00385' => 'egut', 'MSTRG.4063' => 'ama', 'Nitab4.5_0000090g0260' => 'nta', 'Nitab4.5_0000977g0030' => 'nta', 'Nitab4.5_0002541g0040' => 'nta', 'Nitab4.5_0007068g0040' => 'nta', 'Nn005s41408' => 'nnu', 'Nn005s41410' => 'nnu', 'Oeu010310.1' => 'oeu', 'Oeu010311.1' => 'oeu', 'Oeu043472.1' => 'oeu', 'Os01g0246400' => 'osa', 'Os04g0267950' => 'osa', 'Os07g0178700' => 'osa', 'Os07g0178800' => 'osa', 'Peaxi162Scf00316g00046' => 'pax', 'Peaxi162Scf00316g00049' => 'pax', 'Peaxi162Scf00316g00059' => 'pax', 'Peaxi162Scf00316g00328' => 'pax', 'Peaxi162Scf00316g00329' => 'pax', 'Peaxi162Scf00316g00411' => 'pax', 'Peaxi162Scf00316g00521' => 'pax', 'Peaxi162Scf00492g00068' => 'pax', 'Peaxi162Scf35631g00002' => 'pax', 'PGR142G3720' => 'pgr', 'PGSC0003DMG400006442' => 'stu', 'Phvul.007G062000' => 'pvu', 'Potri.008G157750' => 'ptr', 'Potri.008G157900' => 'ptr', 'Potri.008G158000' => 'ptr', 'Potri.008G158200' => 'ptr', 'Pp3c11_7280' => 'ppa', 'Pp3c11_7980' => 'ppa', 'Pp3c12_19450' => 'ppa', 'Pp3c14_1480' => 'ppa', 'Pp3c14_1501' => 'ppa', 'Pp3c16_4900' => 'ppa', 'Pp3c16_5010' => 'ppa', 'Pp3c16_5060' => 'ppa', 'Pp3c19_18250' => 'ppa', 'Pp3c23_8530' => 'ppa', 'Pp3c23_8550' => 'ppa', 'Pp3c24_9670' => 'ppa', 'Pp3c2_21390' => 'ppa', 'Pp3c2_31380' => 'ppa', 'Pp3c3_16620' => 'ppa', 'Pp3c3_8090' => 'ppa', 'Pp3c3_8110' => 'ppa', 'Pp3c3_8130' => 'ppa', 'Pp3c3_8150' => 'ppa', 'Pp3c4_14320' => 'ppa', 'Pp3c6_2560' => 'ppa', 'Pp3c9_16700' => 'ppa', 'PRCOL_00000234' => 'pco', 'PRCOL_00000235' => 'pco', 'PRCOL_00000777' => 'pco', 'PRCOL_00002344' => 'pco', 'PRCOL_00002372' => 'pco', 'PRCOL_00006120' => 'pco', 'Prupe.1G021400' => 'ppe', 'Prupe.1G021500' => 'ppe', 'Prupe.1G021600' => 'ppe', 'Prupe.1G021700' => 'ppe', 'Prupe.1G021800' => 'ppe', 'Prupe.5G145100' => 'ppe', 'Psat6g204040' => 'psa', 'Psat6g204800' => 'psa', 'Psat6g204920' => 'psa', 'Psat6g204960' => 'psa', 'Psat6g205080' => 'psa', 'PSO017G0271' => 'pso', 'PSO017G1276' => 'pso', 'PSO017G1429' => 'pso', 'PSO017G1861' => 'pso', 'PSO017G2787' => 'pso', 'PSO017G4466' => 'pso', 'PSO017G5118' => 'pso', 'PSO017G5420' => 'pso', 'PSO063G3678' => 'pso', 'PSO210G0546' => 'pso', 'PSO317G0001' => 'pso', 'PSO357G0512' => 'pso', 'PSO478G2682' => 'pso', 'PSO647G0001' => 'pso', 'PSO675G0001' => 'pso', 'PSO675G2699' => 'pso', 'PSO675G2849' => 'pso', 'PSO675G4991' => 'pso', 'PSO689G0001' => 'pso', 'QL06p000916' => 'qlo', 'QL06p000921' => 'qlo', 'QL06p001398' => 'qlo', 'QL06p001407' => 'qlo', 'QL06p002031' => 'qlo', 'RcHm_v2.0_Chr4g0387791' => 'rch', 'RcHm_v2.0_Chr4g0387801' => 'rch', 'RcHm_v2.0_Chr6g0286501' => 'rch', 'RcHm_v2.0_Chr6g0286511' => 'rch', 'RcHm_v2.0_Chr6g0286521' => 'rch', 'RcHm_v2.0_Chr6g0286531' => 'rch', 'RcHm_v2.0_Chr7g0189141' => 'rch', 'Rhsim02G0028700' => 'rsi', 'Rhsim02G0028800' => 'rsi', 'Rhsim02G0028900' => 'rsi', 'Rhsim02G0029000' => 'rsi', 'Rhsim02G0029100' => 'rsi', 'Rhsim02G0029200' => 'rsi', 'Rhsim02G0029300' => 'rsi', 'Rhsim02G0029400' => 'rsi', 'Rhsim02G0029500' => 'rsi', 'Rhsim02G0029600' => 'rsi', 'RhsimUnG0024000' => 'rsi', 'RhsimUnG0024100' => 'rsi', 'RhsimUnG0024200' => 'rsi', 'RhsimUnG0024300' => 'rsi', 'RhsimUnG0024400' => 'rsi', 'RhsimUnG0024500' => 'rsi', 'RhsimUnG0024700' => 'rsi', 'RhsimUnG0024800' => 'rsi', 'RhsimUnG0024900' => 'rsi', 'RhsimUnG0025100' => 'rsi', 'Sabra08G0120200' => 'sbr', 'Sabra08G0120300' => 'sbr', 'Sabra08G0120500' => 'sbr', 'Sabra08G0120600' => 'sbr', 'Sabra10G0158900' => 'sbr', 'SalBow2G3492' => 'sbo', 'Sc13g0004760' => 'sci', 'Sc13g0004770' => 'sci', 'Sed0003417' => 'sed', 'Sed0019750' => 'sed', 'SEGI_03419' => 'sgi', 'SEGI_05907' => 'sgi', 'SEGI_10682' => 'sgi', 'SEGI_13528' => 'sgi', 'SEGI_16081' => 'sgi', 'SEGI_19370' => 'sgi', 'SEGI_21015' => 'sgi', 'SEGI_21944' => 'sgi', 'SEGI_32906' => 'sgi', 'SEGI_33093' => 'sgi', 'SEGI_36110' => 'sgi', 'SEGI_40397' => 'sgi', 'SGA_v2.0_scaffold191G40426' => 'sas', 'SGA_v2.0_scaffold353G49717' => 'sas', 'SGA_v2.0_scaffold50G18550' => 'sas', 'SMO119G0173' => 'smo', 'SMO172G0002' => 'smo', 'Solyc09g082690.3' => 'sly', 'Solyc09g082700.2' => 'sly', 'Sopen09g031550' => 'spe', 'Sopen09g031560' => 'spe', 'Sp3g20540' => 'spa', 'Sp7g07580' => 'spa', 'TAR134G0002' => 'tar', 'TAR236G0001' => 'tar', 'TAR365G0892' => 'tar', 'TAR636G0166' => 'tar', 'TAR636G0646' => 'tar', 'TAR636G0869' => 'tar', 'TAR636G1317' => 'tar', 'TAR636G1744' => 'tar', 'TAR636G3358' => 'tar', 'TAR636G3436' => 'tar', 'THA.LOC104803047' => 'tha', 'Thecc.04G238900' => 'tca', 'Thhalv10021557m.g' => 'esa', 'Thhalv10026318m.g' => 'esa', 'Thhalv10026335m.g' => 'esa', 'TPR.G17433' => 'tpr', 'TPR.G18915' => 'tpr', 'TPR.G26125' => 'tpr', 'TWI09G0677' => 'twi', 'TWI73G0287' => 'twi', 'unitig_748.g8326' => 'ugi', 'vmacro15370' => 'vma', 'vmacro15371' => 'vma', 'vmacro15372' => 'vma', 'vmacro15373' => 'vma', 'vmacro15374' => 'vma', 'VMungo0720G2826' => 'vmu', 'Zm00001eb116960' => 'zma', 'Zm00001eb301260' => 'zma', 'Zm00001eb301270' => 'zma' ), 'gf_id' => 'HOM05D001460', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001460' ), 'data_identifier' => 'HOM05D001460', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001460', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '433', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p22980' => 'bna', 'A01p32340' => 'bna', 'A03p42970' => 'bna', 'A05p25880' => 'bna', 'Aa31LG8G9320' => 'aar', 'Aa31LG8G9330' => 'aar', 'Aa31LG8G9340' => 'aar', 'Aa31sc221G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1034' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1528' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.829' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2222' => 'aag', 'Ah.12g058830' => 'amhyb', 'Ah.12g058840' => 'amhyb', 'AL3G37160' => 'aly', 'AL7G41310' => 'aly', 'Aqoxy5G00395' => 'aox', 'Aqoxy5G00396' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0C8NZA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5185HY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JZ1PRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MD3LS0' => 'arhy', 'AT3G22840' => 'ath', 'AT4G14690' => 'ath', 'ATR0665G054' => 'atr', 'Atru.chr4.2344' => 'acertr', 'Atru.chr4.2346' => 'acertr', 'Atru.chr4.2347' => 'acertr', 'Atru.chr4.2348' => 'acertr', 'Atru.chr4.2355' => 'acertr', 'Atru.chr4.2356' => 'acertr', 'Atru.chr4.2358' => 'acertr', 'Atru.chr4.2359' => 'acertr', 'Atru.chr4.2360' => 'acertr', 'Atru.chr4.2361' => 'acertr', 'AUR62030476' => 'cqu', 'AUR62030478' => 'cqu', 'AUR62030819' => 'cqu', 'AUR62030820' => 'cqu', 'BcaB03g14648' => 'bca', 'BcaB04g20492' => 'bca', 'BcaB06g26399' => 'bca', 'BcaC01g03416' => 'bca', 'BcaC01g03419' => 'bca', 'BcaC01g03421' => 'bca', 'BcaC01g03424' => 'bca', 'BcaC05g28012' => 'bca', 'BcaC09g49212' => 'bca', 'BcaC09g50140' => 'bca', 'BcaNung00346' => 'bca', 'BolC1t02785H' => 'bol', 'BolC1t04095H' => 'bol', 'BolC3t17545H' => 'bol', 'BolC5t32769H' => 'bol', 'BraA01t02211Z' => 'bra', 'BraA01t03359Z' => 'bra', 'BraA03t13441Z' => 'bra', 'BraA05t21476Z' => 'bra', 'C01p28420' => 'bna', 'C01p41350' => 'bna', 'C03p52750' => 'bna', 'C03p52780' => 'bna', 'C05p40270' => 'bna', 'CAN.G1437.9' => 'can', 'CANSAT78G0035' => 'cansat', 'CANSAT78G1036' => 'cansat', 'CANSAT78G2272' => 'cansat', 'CANSAT78G2478' => 'cansat', 'CARHR098700' => 'chi', 'CARHR221120' => 'chi', 'CARHR221150' => 'chi', 'Carub.0003s2297' => 'cru', 'Carub.0007s2749' => 'cru', 'Carub.0007s2750' => 'cru', 'Carub.0007s2751' => 'cru', 'Ca_10849_v3' => 'car', 'Cc03_g04300' => 'ccan', 'CDE02G3648' => 'cde', 'CDE05G0060' => 'cde', 'CDE05G0692' => 'cde', 'CDE05G2285' => 'cde', 'CDE05G2884' => 'cde', 'CDE05G3072' => 'cde', 'Cfa008439' => 'cfa', 'Cfa008441' => 'cfa', 'Cfa008443' => 'cfa', 'Cfa008448' => 'cfa', 'Ciclev10005974m.g' => 'ccl', 'Ciclev10006006m.g' => 'ccl', 'Ciclev10006775m.g' => 'ccl', 'CiPaw.02G120400' => 'cil', 'CiPaw.02G120500' => 'cil', 'CiPaw.02G120600' => 'cil', 'ClCG05G004850' => 'cla', 'COL.COLO4_21566' => 'col', 'Cpa.g.sc44.124' => 'cpa', 'Cre07.g320400' => 'cre', 'Cre07.g320450' => 'cre', 'Cre08.g384650' => 'cre', 'Cre09.g393173' => 'cre', 'Cre09.g394325' => 'cre', 'Cre14.g626750' => 'cre', 'Cre16.g679250' => 'cre', 'CsaV3_3G012890' => 'csa', 'CSS0010865' => 'camsi', 'CSS0044338' => 'camsi', 'DCAR_002366' => 'dca', 'DCAR_030687' => 'dca', 'DCAR_030688' => 'dca', 'Dinv14047' => 'din', 'Dinv14048' => 'din', 'Duzib151G0105' => 'dzi', 'Duzib151G0114' => 'dzi', 'Duzib212G1029' => 'dzi', 'ECA232G3536' => 'eca', 'ECA240G0786' => 'eca', 'ECA240G1802' => 'eca', 'ECA240G3760' => 'eca', 'ECA240G3920' => 'eca', 'EL10Ac5g12536' => 'bvu', 'EL10Ac5g12537' => 'bvu', 'EL10Ac5g12538' => 'bvu', 'Eucgr.B01004' => 'egr', 'Eucgr.B01006' => 'egr', 'Eucgr.B01007' => 'egr', 'Eucgr.B01008' => 'egr', 'Eucgr.B01895' => 'egr', 'Eucgr.B01896' => 'egr', 'FAN04G1456' => 'fan', 'FAN08G1769' => 'fan', 'FAN08G2160' => 'fan', 'FAN13G2403' => 'fan', 'FAN13G3303' => 'fan', 'FAN15G2435' => 'fan', 'FAN17G0672' => 'fan', 'FAN17G2441' => 'fan', 'FAN18G1024' => 'fan', 'FAN22G1458' => 'fan', 'FAN24G0037' => 'fan', 'FAN24G0429' => 'fan', 'FAN24G2387' => 'fan', 'FAN27G2746' => 'fan', 'FvH4_2g20400' => 'fve', 'FvH4_2g20420' => 'fve', 'FvH4_2g20430' => 'fve', 'FvH4_4g01270' => 'fve', 'FvH4_4g01290' => 'fve', 'FvH4_4g01300' => 'fve', 'FvH4_4g01310' => 'fve', 'FvH4_4g01330' => 'fve', 'FvH4_5g09070' => 'fve', 'Glyma.10G243800' => 'gma', 'Glyma.20G150600' => 'gma', 'Gohir.A09G219200' => 'ghi', 'Gohir.A09G219300' => 'ghi', 'Gohir.D09G221400' => 'ghi', 'Gohir.D09G221500' => 'ghi', 'Gorai.006G242600' => 'gra', 'Gorai.006G242700' => 'gra', 'GSVIVG01018044001' => 'vvi', 'HanXRQChr03g0083821' => 'han', 'HanXRQChr03g0083841' => 'han', 'HanXRQChr03g0083881' => 'han', 'HanXRQChr03g0083901' => 'han', 'HanXRQChr03g0083921' => 'han', 'HanXRQChr03g0085331' => 'han', 'HanXRQChr03g0085361' => 'han', 'HanXRQChr03g0085411' => 'han', 'HanXRQChr03g0085421' => 'han', 'HanXRQChr03g0085431' => 'han', 'HanXRQChr08g0221991' => 'han', 'HanXRQChr11g0336061' => 'han', 'HanXRQChr11g0336411' => 'han', 'Haze_11234' => 'cav', 'Hma1.2p1_0549F.1_g177010' => 'hma', 'Hma1.2p1_0602F.1_g187630' => 'hma', 'Hund14876' => 'sun', 'Hund14879' => 'sun', 'Lalb_Chr06g0160741' => 'lal', 'Lalb_Chr21g0304781' => 'lal', 'Lj3A726G19' => 'lonja', 'Lj3A726T23' => 'lonja', 'Lj3A726T24' => 'lonja', 'Lj3A726T25' => 'lonja', 'Lj3A727T17' => 'lonja', 'Lj3C726T0' => 'lonja', 'Lj3C726T2' => 'lonja', 'Lj3P725T35' => 'lonja', 'Lj3P727T10' => 'lonja', 'Lj3P727T12' => 'lonja', 'Lj3P727T14' => 'lonja', 'Lj5g0023109' => 'lja', 'Lj6P646T44' => 'lonja', 'Lsat_1_v5_gn_6_75760' => 'lsa', 'Lsat_1_v5_gn_6_75800' => 'lsa', 'Lsat_1_v5_gn_6_75900' => 'lsa', 'Lsat_1_v5_gn_6_76240' => 'lsa', 'Lsat_1_v5_gn_6_76441' => 'lsa', 'Lsat_1_v5_gn_6_76700' => 'lsa', 'Lsat_1_v5_gn_6_76760' => 'lsa', 'Manes.15G033100' => 'mes', 'Mapoly0004s0074' => 'mpo', 'Mapoly0004s0075' => 'mpo', 'Mapoly0004s0163' => 'mpo', 'Mapoly0004s0164' => 'mpo', 'Mapoly0021s0018' => 'mpo', 'Mapoly0041s0136' => 'mpo', 'Mapoly0041s0137' => 'mpo', 'Mapoly0041s0138' => 'mpo', 'Mapoly0041s0139' => 'mpo', 'Mapoly0041s0141' => 'mpo', 'Mapoly0041s0142' => 'mpo', 'Mapoly0041s0143' => 'mpo', 'Mapoly0041s0144' => 'mpo', 'Mapoly0041s0145' => 'mpo', 'Mapoly0047s0106' => 'mpo', 'Mapoly0047s0108' => 'mpo', 'Mapoly0050s0051' => 'mpo', 'Mapoly0050s0052' => 'mpo', 'Mapoly0050s0053' => 'mpo', 'Mapoly0058s0013' => 'mpo', 'Mapoly0091s0078' => 'mpo', 'Mapoly0091s0079' => 'mpo', 'Mapoly0091s0080' => 'mpo', 'Mapoly0091s0081' => 'mpo', 'Mapoly0278s0004' => 'mpo', 'Mapoly0278s0005' => 'mpo', 'Mapoly0278s0006' => 'mpo', 'MBI11_g30648_MAGBIO' => 'mbi', 'MCO03G194' => 'mco', 'MCO03G590' => 'mco', 'MCO07G312' => 'mco', 'MCO10G318' => 'mco', 'MCO12G244' => 'mco', 'MCO13G148' => 'mco', 'MCO13G194' => 'mco', 'MCO16G238' => 'mco', 'MD06G1134100' => 'mdo', 'MD13G1200100' => 'mdo', 'MD13G1200300' => 'mdo', 'MD13G1200600' => 'mdo', 'MD14G1150400' => 'mdo', 'MD16G1200000' => 'mdo', 'Medtr1g102570' => 'mtr', 'Medtr1g102780' => 'mtr', 'Medtr1g102800' => 'mtr', 'Medtr1g102810' => 'mtr', 'Medtr1g102830' => 'mtr', 'MELO3C006499.2' => 'cme', 'Migut.G00385' => 'egut', 'MSTRG.4063' => 'ama', 'Nitab4.5_0000090g0260' => 'nta', 'Nitab4.5_0000977g0030' => 'nta', 'Nitab4.5_0002541g0040' => 'nta', 'Nitab4.5_0007068g0040' => 'nta', 'Nn005s41408' => 'nnu', 'Nn005s41410' => 'nnu', 'Oeu010310.1' => 'oeu', 'Oeu010311.1' => 'oeu', 'Oeu043472.1' => 'oeu', 'Os01g0246400' => 'osa', 'Os04g0267950' => 'osa', 'Os07g0178700' => 'osa', 'Os07g0178800' => 'osa', 'Peaxi162Scf00316g00046' => 'pax', 'Peaxi162Scf00316g00049' => 'pax', 'Peaxi162Scf00316g00059' => 'pax', 'Peaxi162Scf00316g00328' => 'pax', 'Peaxi162Scf00316g00329' => 'pax', 'Peaxi162Scf00316g00411' => 'pax', 'Peaxi162Scf00316g00521' => 'pax', 'Peaxi162Scf00492g00068' => 'pax', 'Peaxi162Scf35631g00002' => 'pax', 'PGR142G3720' => 'pgr', 'PGSC0003DMG400006442' => 'stu', 'Phvul.007G062000' => 'pvu', 'Potri.008G157750' => 'ptr', 'Potri.008G157900' => 'ptr', 'Potri.008G158000' => 'ptr', 'Potri.008G158200' => 'ptr', 'Pp3c11_7280' => 'ppa', 'Pp3c11_7980' => 'ppa', 'Pp3c12_19450' => 'ppa', 'Pp3c14_1480' => 'ppa', 'Pp3c14_1501' => 'ppa', 'Pp3c16_4900' => 'ppa', 'Pp3c16_5010' => 'ppa', 'Pp3c16_5060' => 'ppa', 'Pp3c19_18250' => 'ppa', 'Pp3c23_8530' => 'ppa', 'Pp3c23_8550' => 'ppa', 'Pp3c24_9670' => 'ppa', 'Pp3c2_21390' => 'ppa', 'Pp3c2_31380' => 'ppa', 'Pp3c3_16620' => 'ppa', 'Pp3c3_8090' => 'ppa', 'Pp3c3_8110' => 'ppa', 'Pp3c3_8130' => 'ppa', 'Pp3c3_8150' => 'ppa', 'Pp3c4_14320' => 'ppa', 'Pp3c6_2560' => 'ppa', 'Pp3c9_16700' => 'ppa', 'PRCOL_00000234' => 'pco', 'PRCOL_00000235' => 'pco', 'PRCOL_00000777' => 'pco', 'PRCOL_00002344' => 'pco', 'PRCOL_00002372' => 'pco', 'PRCOL_00006120' => 'pco', 'Prupe.1G021400' => 'ppe', 'Prupe.1G021500' => 'ppe', 'Prupe.1G021600' => 'ppe', 'Prupe.1G021700' => 'ppe', 'Prupe.1G021800' => 'ppe', 'Prupe.5G145100' => 'ppe', 'Psat6g204040' => 'psa', 'Psat6g204800' => 'psa', 'Psat6g204920' => 'psa', 'Psat6g204960' => 'psa', 'Psat6g205080' => 'psa', 'PSO017G0271' => 'pso', 'PSO017G1276' => 'pso', 'PSO017G1429' => 'pso', 'PSO017G1861' => 'pso', 'PSO017G2787' => 'pso', 'PSO017G4466' => 'pso', 'PSO017G5118' => 'pso', 'PSO017G5420' => 'pso', 'PSO063G3678' => 'pso', 'PSO210G0546' => 'pso', 'PSO317G0001' => 'pso', 'PSO357G0512' => 'pso', 'PSO478G2682' => 'pso', 'PSO647G0001' => 'pso', 'PSO675G0001' => 'pso', 'PSO675G2699' => 'pso', 'PSO675G2849' => 'pso', 'PSO675G4991' => 'pso', 'PSO689G0001' => 'pso', 'QL06p000916' => 'qlo', 'QL06p000921' => 'qlo', 'QL06p001398' => 'qlo', 'QL06p001407' => 'qlo', 'QL06p002031' => 'qlo', 'RcHm_v2.0_Chr4g0387791' => 'rch', 'RcHm_v2.0_Chr4g0387801' => 'rch', 'RcHm_v2.0_Chr6g0286501' => 'rch', 'RcHm_v2.0_Chr6g0286511' => 'rch', 'RcHm_v2.0_Chr6g0286521' => 'rch', 'RcHm_v2.0_Chr6g0286531' => 'rch', 'RcHm_v2.0_Chr7g0189141' => 'rch', 'Rhsim02G0028700' => 'rsi', 'Rhsim02G0028800' => 'rsi', 'Rhsim02G0028900' => 'rsi', 'Rhsim02G0029000' => 'rsi', 'Rhsim02G0029100' => 'rsi', 'Rhsim02G0029200' => 'rsi', 'Rhsim02G0029300' => 'rsi', 'Rhsim02G0029400' => 'rsi', 'Rhsim02G0029500' => 'rsi', 'Rhsim02G0029600' => 'rsi', 'RhsimUnG0024000' => 'rsi', 'RhsimUnG0024100' => 'rsi', 'RhsimUnG0024200' => 'rsi', 'RhsimUnG0024300' => 'rsi', 'RhsimUnG0024400' => 'rsi', 'RhsimUnG0024500' => 'rsi', 'RhsimUnG0024700' => 'rsi', 'RhsimUnG0024800' => 'rsi', 'RhsimUnG0024900' => 'rsi', 'RhsimUnG0025100' => 'rsi', 'Sabra08G0120200' => 'sbr', 'Sabra08G0120300' => 'sbr', 'Sabra08G0120500' => 'sbr', 'Sabra08G0120600' => 'sbr', 'Sabra10G0158900' => 'sbr', 'SalBow2G3492' => 'sbo', 'Sc13g0004760' => 'sci', 'Sc13g0004770' => 'sci', 'Sed0003417' => 'sed', 'Sed0019750' => 'sed', 'SEGI_03419' => 'sgi', 'SEGI_05907' => 'sgi', 'SEGI_10682' => 'sgi', 'SEGI_13528' => 'sgi', 'SEGI_16081' => 'sgi', 'SEGI_19370' => 'sgi', 'SEGI_21015' => 'sgi', 'SEGI_21944' => 'sgi', 'SEGI_32906' => 'sgi', 'SEGI_33093' => 'sgi', 'SEGI_36110' => 'sgi', 'SEGI_40397' => 'sgi', 'SGA_v2.0_scaffold191G40426' => 'sas', 'SGA_v2.0_scaffold353G49717' => 'sas', 'SGA_v2.0_scaffold50G18550' => 'sas', 'SMO119G0173' => 'smo', 'SMO172G0002' => 'smo', 'Solyc09g082690.3' => 'sly', 'Solyc09g082700.2' => 'sly', 'Sopen09g031550' => 'spe', 'Sopen09g031560' => 'spe', 'Sp3g20540' => 'spa', 'Sp7g07580' => 'spa', 'TAR134G0002' => 'tar', 'TAR236G0001' => 'tar', 'TAR365G0892' => 'tar', 'TAR636G0166' => 'tar', 'TAR636G0646' => 'tar', 'TAR636G0869' => 'tar', 'TAR636G1317' => 'tar', 'TAR636G1744' => 'tar', 'TAR636G3358' => 'tar', 'TAR636G3436' => 'tar', 'THA.LOC104803047' => 'tha', 'Thecc.04G238900' => 'tca', 'Thhalv10021557m.g' => 'esa', 'Thhalv10026318m.g' => 'esa', 'Thhalv10026335m.g' => 'esa', 'TPR.G17433' => 'tpr', 'TPR.G18915' => 'tpr', 'TPR.G26125' => 'tpr', 'TWI09G0677' => 'twi', 'TWI73G0287' => 'twi', 'unitig_748.g8326' => 'ugi', 'vmacro15370' => 'vma', 'vmacro15371' => 'vma', 'vmacro15372' => 'vma', 'vmacro15373' => 'vma', 'vmacro15374' => 'vma', 'VMungo0720G2826' => 'vmu', 'Zm00001eb116960' => 'zma', 'Zm00001eb301260' => 'zma', 'Zm00001eb301270' => 'zma' ) $gf_id = 'HOM05D001460' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001460' ) $data_identifier = 'HOM05D001460' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 4, 'aag' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 2, 'aox' => (int) 2, 'arhy' => (int) 4, 'ath' => (int) 2, 'atr' => (int) 1, 'acertr' => (int) 10, 'cqu' => (int) 4, 'bca' => (int) 11, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 1, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 1, 'ccan' => (int) 1, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 1, 'col' => (int) 1, 'cpa' => (int) 1, 'cre' => (int) 7, 'csa' => (int) 1, 'camsi' => (int) 2, 'dca' => (int) 3, 'din' => (int) 2, 'dzi' => (int) 3, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 14, 'fve' => (int) 9, 'gma' => (int) 2, 'ghi' => (int) 4, 'gra' => (int) 2, 'vvi' => (int) 1, 'han' => (int) 13, 'cav' => (int) 1, 'hma' => (int) 2, 'sun' => (int) 2, 'lal' => (int) 2, 'lonja' => (int) 12, 'lja' => (int) 1, 'lsa' => (int) 7, 'mes' => (int) 1, 'mpo' => (int) 27, 'mbi' => (int) 1, 'mco' => (int) 8, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 1, 'egut' => (int) 1, 'ama' => (int) 1, 'nta' => (int) 4, 'nnu' => (int) 2, 'oeu' => (int) 3, 'osa' => (int) 4, 'pax' => (int) 9, 'pgr' => (int) 1, 'stu' => (int) 1, 'pvu' => (int) 1, 'ptr' => (int) 4, 'ppa' => (int) 22, 'pco' => (int) 6, 'ppe' => (int) 6, 'psa' => (int) 5, 'pso' => (int) 19, 'qlo' => (int) 5, 'rch' => (int) 7, 'rsi' => (int) 20, 'sbr' => (int) 5, 'sbo' => (int) 1, 'sci' => (int) 2, 'sed' => (int) 2, 'sgi' => (int) 12, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 2, 'tar' => (int) 10, 'tha' => (int) 1, 'tca' => (int) 1, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 2, 'ugi' => (int) 1, 'vma' => (int) 5, 'vmu' => (int) 1, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb301270' $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' => 'HOM05D001460', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '433', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p22980' => 'bna', 'A01p32340' => 'bna', 'A03p42970' => 'bna', 'A05p25880' => 'bna', 'Aa31LG8G9320' => 'aar', 'Aa31LG8G9330' => 'aar', 'Aa31LG8G9340' => 'aar', 'Aa31sc221G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1034' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1528' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.829' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2222' => 'aag', 'Ah.12g058830' => 'amhyb', 'Ah.12g058840' => 'amhyb', 'AL3G37160' => 'aly', 'AL7G41310' => 'aly', 'Aqoxy5G00395' => 'aox', 'Aqoxy5G00396' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0C8NZA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5185HY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JZ1PRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MD3LS0' => 'arhy', 'AT3G22840' => 'ath', 'AT4G14690' => 'ath', 'ATR0665G054' => 'atr', 'Atru.chr4.2344' => 'acertr', 'Atru.chr4.2346' => 'acertr', 'Atru.chr4.2347' => 'acertr', 'Atru.chr4.2348' => 'acertr', 'Atru.chr4.2355' => 'acertr', 'Atru.chr4.2356' => 'acertr', 'Atru.chr4.2358' => 'acertr', 'Atru.chr4.2359' => 'acertr', 'Atru.chr4.2360' => 'acertr', 'Atru.chr4.2361' => 'acertr', 'AUR62030476' => 'cqu', 'AUR62030478' => 'cqu', 'AUR62030819' => 'cqu', 'AUR62030820' => 'cqu', 'BcaB03g14648' => 'bca', 'BcaB04g20492' => 'bca', 'BcaB06g26399' => 'bca', 'BcaC01g03416' => 'bca', 'BcaC01g03419' => 'bca', 'BcaC01g03421' => 'bca', 'BcaC01g03424' => 'bca', 'BcaC05g28012' => 'bca', 'BcaC09g49212' => 'bca', 'BcaC09g50140' => 'bca', 'BcaNung00346' => 'bca', 'BolC1t02785H' => 'bol', 'BolC1t04095H' => 'bol', 'BolC3t17545H' => 'bol', 'BolC5t32769H' => 'bol', 'BraA01t02211Z' => 'bra', 'BraA01t03359Z' => 'bra', 'BraA03t13441Z' => 'bra', 'BraA05t21476Z' => 'bra', 'C01p28420' => 'bna', 'C01p41350' => 'bna', 'C03p52750' => 'bna', 'C03p52780' => 'bna', 'C05p40270' => 'bna', 'CAN.G1437.9' => 'can', 'CANSAT78G0035' => 'cansat', 'CANSAT78G1036' => 'cansat', 'CANSAT78G2272' => 'cansat', 'CANSAT78G2478' => 'cansat', 'CARHR098700' => 'chi', 'CARHR221120' => 'chi', 'CARHR221150' => 'chi', 'Carub.0003s2297' => 'cru', 'Carub.0007s2749' => 'cru', 'Carub.0007s2750' => 'cru', 'Carub.0007s2751' => 'cru', 'Ca_10849_v3' => 'car', 'Cc03_g04300' => 'ccan', 'CDE02G3648' => 'cde', 'CDE05G0060' => 'cde', 'CDE05G0692' => 'cde', 'CDE05G2285' => 'cde', 'CDE05G2884' => 'cde', 'CDE05G3072' => 'cde', 'Cfa008439' => 'cfa', 'Cfa008441' => 'cfa', 'Cfa008443' => 'cfa', 'Cfa008448' => 'cfa', 'Ciclev10005974m.g' => 'ccl', 'Ciclev10006006m.g' => 'ccl', 'Ciclev10006775m.g' => 'ccl', 'CiPaw.02G120400' => 'cil', 'CiPaw.02G120500' => 'cil', 'CiPaw.02G120600' => 'cil', 'ClCG05G004850' => 'cla', 'COL.COLO4_21566' => 'col', 'Cpa.g.sc44.124' => 'cpa', 'Cre07.g320400' => 'cre', 'Cre07.g320450' => 'cre', 'Cre08.g384650' => 'cre', 'Cre09.g393173' => 'cre', 'Cre09.g394325' => 'cre', 'Cre14.g626750' => 'cre', 'Cre16.g679250' => 'cre', 'CsaV3_3G012890' => 'csa', 'CSS0010865' => 'camsi', 'CSS0044338' => 'camsi', 'DCAR_002366' => 'dca', 'DCAR_030687' => 'dca', 'DCAR_030688' => 'dca', 'Dinv14047' => 'din', 'Dinv14048' => 'din', 'Duzib151G0105' => 'dzi', 'Duzib151G0114' => 'dzi', 'Duzib212G1029' => 'dzi', 'ECA232G3536' => 'eca', 'ECA240G0786' => 'eca', 'ECA240G1802' => 'eca', 'ECA240G3760' => 'eca', 'ECA240G3920' => 'eca', 'EL10Ac5g12536' => 'bvu', 'EL10Ac5g12537' => 'bvu', 'EL10Ac5g12538' => 'bvu', 'Eucgr.B01004' => 'egr', 'Eucgr.B01006' => 'egr', 'Eucgr.B01007' => 'egr', 'Eucgr.B01008' => 'egr', 'Eucgr.B01895' => 'egr', 'Eucgr.B01896' => 'egr', 'FAN04G1456' => 'fan', 'FAN08G1769' => 'fan', 'FAN08G2160' => 'fan', 'FAN13G2403' => 'fan', 'FAN13G3303' => 'fan', 'FAN15G2435' => 'fan', 'FAN17G0672' => 'fan', 'FAN17G2441' => 'fan', 'FAN18G1024' => 'fan', 'FAN22G1458' => 'fan', 'FAN24G0037' => 'fan', 'FAN24G0429' => 'fan', 'FAN24G2387' => 'fan', 'FAN27G2746' => 'fan', 'FvH4_2g20400' => 'fve', 'FvH4_2g20420' => 'fve', 'FvH4_2g20430' => 'fve', 'FvH4_4g01270' => 'fve', 'FvH4_4g01290' => 'fve', 'FvH4_4g01300' => 'fve', 'FvH4_4g01310' => 'fve', 'FvH4_4g01330' => 'fve', 'FvH4_5g09070' => 'fve', 'Glyma.10G243800' => 'gma', 'Glyma.20G150600' => 'gma', 'Gohir.A09G219200' => 'ghi', 'Gohir.A09G219300' => 'ghi', 'Gohir.D09G221400' => 'ghi', 'Gohir.D09G221500' => 'ghi', 'Gorai.006G242600' => 'gra', 'Gorai.006G242700' => 'gra', 'GSVIVG01018044001' => 'vvi', 'HanXRQChr03g0083821' => 'han', 'HanXRQChr03g0083841' => 'han', 'HanXRQChr03g0083881' => 'han', 'HanXRQChr03g0083901' => 'han', 'HanXRQChr03g0083921' => 'han', 'HanXRQChr03g0085331' => 'han', 'HanXRQChr03g0085361' => 'han', 'HanXRQChr03g0085411' => 'han', 'HanXRQChr03g0085421' => 'han', 'HanXRQChr03g0085431' => 'han', 'HanXRQChr08g0221991' => 'han', 'HanXRQChr11g0336061' => 'han', 'HanXRQChr11g0336411' => 'han', 'Haze_11234' => 'cav', 'Hma1.2p1_0549F.1_g177010' => 'hma', 'Hma1.2p1_0602F.1_g187630' => 'hma', 'Hund14876' => 'sun', 'Hund14879' => 'sun', 'Lalb_Chr06g0160741' => 'lal', 'Lalb_Chr21g0304781' => 'lal', 'Lj3A726G19' => 'lonja', 'Lj3A726T23' => 'lonja', 'Lj3A726T24' => 'lonja', 'Lj3A726T25' => 'lonja', 'Lj3A727T17' => 'lonja', 'Lj3C726T0' => 'lonja', 'Lj3C726T2' => 'lonja', 'Lj3P725T35' => 'lonja', 'Lj3P727T10' => 'lonja', 'Lj3P727T12' => 'lonja', 'Lj3P727T14' => 'lonja', 'Lj5g0023109' => 'lja', 'Lj6P646T44' => 'lonja', 'Lsat_1_v5_gn_6_75760' => 'lsa', 'Lsat_1_v5_gn_6_75800' => 'lsa', 'Lsat_1_v5_gn_6_75900' => 'lsa', 'Lsat_1_v5_gn_6_76240' => 'lsa', 'Lsat_1_v5_gn_6_76441' => 'lsa', 'Lsat_1_v5_gn_6_76700' => 'lsa', 'Lsat_1_v5_gn_6_76760' => 'lsa', 'Manes.15G033100' => 'mes', 'Mapoly0004s0074' => 'mpo', 'Mapoly0004s0075' => 'mpo', 'Mapoly0004s0163' => 'mpo', 'Mapoly0004s0164' => 'mpo', 'Mapoly0021s0018' => 'mpo', 'Mapoly0041s0136' => 'mpo', 'Mapoly0041s0137' => 'mpo', 'Mapoly0041s0138' => 'mpo', 'Mapoly0041s0139' => 'mpo', 'Mapoly0041s0141' => 'mpo', 'Mapoly0041s0142' => 'mpo', 'Mapoly0041s0143' => 'mpo', 'Mapoly0041s0144' => 'mpo', 'Mapoly0041s0145' => 'mpo', 'Mapoly0047s0106' => 'mpo', 'Mapoly0047s0108' => 'mpo', 'Mapoly0050s0051' => 'mpo', 'Mapoly0050s0052' => 'mpo', 'Mapoly0050s0053' => 'mpo', 'Mapoly0058s0013' => 'mpo', 'Mapoly0091s0078' => 'mpo', 'Mapoly0091s0079' => 'mpo', 'Mapoly0091s0080' => 'mpo', 'Mapoly0091s0081' => 'mpo', 'Mapoly0278s0004' => 'mpo', 'Mapoly0278s0005' => 'mpo', 'Mapoly0278s0006' => 'mpo', 'MBI11_g30648_MAGBIO' => 'mbi', 'MCO03G194' => 'mco', 'MCO03G590' => 'mco', 'MCO07G312' => 'mco', 'MCO10G318' => 'mco', 'MCO12G244' => 'mco', 'MCO13G148' => 'mco', 'MCO13G194' => 'mco', 'MCO16G238' => 'mco', 'MD06G1134100' => 'mdo', 'MD13G1200100' => 'mdo', 'MD13G1200300' => 'mdo', 'MD13G1200600' => 'mdo', 'MD14G1150400' => 'mdo', 'MD16G1200000' => 'mdo', 'Medtr1g102570' => 'mtr', 'Medtr1g102780' => 'mtr', 'Medtr1g102800' => 'mtr', 'Medtr1g102810' => 'mtr', 'Medtr1g102830' => 'mtr', 'MELO3C006499.2' => 'cme', 'Migut.G00385' => 'egut', 'MSTRG.4063' => 'ama', 'Nitab4.5_0000090g0260' => 'nta', 'Nitab4.5_0000977g0030' => 'nta', 'Nitab4.5_0002541g0040' => 'nta', 'Nitab4.5_0007068g0040' => 'nta', 'Nn005s41408' => 'nnu', 'Nn005s41410' => 'nnu', 'Oeu010310.1' => 'oeu', 'Oeu010311.1' => 'oeu', 'Oeu043472.1' => 'oeu', 'Os01g0246400' => 'osa', 'Os04g0267950' => 'osa', 'Os07g0178700' => 'osa', 'Os07g0178800' => 'osa', 'Peaxi162Scf00316g00046' => 'pax', 'Peaxi162Scf00316g00049' => 'pax', 'Peaxi162Scf00316g00059' => 'pax', 'Peaxi162Scf00316g00328' => 'pax', 'Peaxi162Scf00316g00329' => 'pax', 'Peaxi162Scf00316g00411' => 'pax', 'Peaxi162Scf00316g00521' => 'pax', 'Peaxi162Scf00492g00068' => 'pax', 'Peaxi162Scf35631g00002' => 'pax', 'PGR142G3720' => 'pgr', 'PGSC0003DMG400006442' => 'stu', 'Phvul.007G062000' => 'pvu', 'Potri.008G157750' => 'ptr', 'Potri.008G157900' => 'ptr', 'Potri.008G158000' => 'ptr', 'Potri.008G158200' => 'ptr', 'Pp3c11_7280' => 'ppa', 'Pp3c11_7980' => 'ppa', 'Pp3c12_19450' => 'ppa', 'Pp3c14_1480' => 'ppa', 'Pp3c14_1501' => 'ppa', 'Pp3c16_4900' => 'ppa', 'Pp3c16_5010' => 'ppa', 'Pp3c16_5060' => 'ppa', 'Pp3c19_18250' => 'ppa', 'Pp3c23_8530' => 'ppa', 'Pp3c23_8550' => 'ppa', 'Pp3c24_9670' => 'ppa', 'Pp3c2_21390' => 'ppa', 'Pp3c2_31380' => 'ppa', 'Pp3c3_16620' => 'ppa', 'Pp3c3_8090' => 'ppa', 'Pp3c3_8110' => 'ppa', 'Pp3c3_8130' => 'ppa', 'Pp3c3_8150' => 'ppa', 'Pp3c4_14320' => 'ppa', 'Pp3c6_2560' => 'ppa', 'Pp3c9_16700' => 'ppa', 'PRCOL_00000234' => 'pco', 'PRCOL_00000235' => 'pco', 'PRCOL_00000777' => 'pco', 'PRCOL_00002344' => 'pco', 'PRCOL_00002372' => 'pco', 'PRCOL_00006120' => 'pco', 'Prupe.1G021400' => 'ppe', 'Prupe.1G021500' => 'ppe', 'Prupe.1G021600' => 'ppe', 'Prupe.1G021700' => 'ppe', 'Prupe.1G021800' => 'ppe', 'Prupe.5G145100' => 'ppe', 'Psat6g204040' => 'psa', 'Psat6g204800' => 'psa', 'Psat6g204920' => 'psa', 'Psat6g204960' => 'psa', 'Psat6g205080' => 'psa', 'PSO017G0271' => 'pso', 'PSO017G1276' => 'pso', 'PSO017G1429' => 'pso', 'PSO017G1861' => 'pso', 'PSO017G2787' => 'pso', 'PSO017G4466' => 'pso', 'PSO017G5118' => 'pso', 'PSO017G5420' => 'pso', 'PSO063G3678' => 'pso', 'PSO210G0546' => 'pso', 'PSO317G0001' => 'pso', 'PSO357G0512' => 'pso', 'PSO478G2682' => 'pso', 'PSO647G0001' => 'pso', 'PSO675G0001' => 'pso', 'PSO675G2699' => 'pso', 'PSO675G2849' => 'pso', 'PSO675G4991' => 'pso', 'PSO689G0001' => 'pso', 'QL06p000916' => 'qlo', 'QL06p000921' => 'qlo', 'QL06p001398' => 'qlo', 'QL06p001407' => 'qlo', 'QL06p002031' => 'qlo', 'RcHm_v2.0_Chr4g0387791' => 'rch', 'RcHm_v2.0_Chr4g0387801' => 'rch', 'RcHm_v2.0_Chr6g0286501' => 'rch', 'RcHm_v2.0_Chr6g0286511' => 'rch', 'RcHm_v2.0_Chr6g0286521' => 'rch', 'RcHm_v2.0_Chr6g0286531' => 'rch', 'RcHm_v2.0_Chr7g0189141' => 'rch', 'Rhsim02G0028700' => 'rsi', 'Rhsim02G0028800' => 'rsi', 'Rhsim02G0028900' => 'rsi', 'Rhsim02G0029000' => 'rsi', 'Rhsim02G0029100' => 'rsi', 'Rhsim02G0029200' => 'rsi', 'Rhsim02G0029300' => 'rsi', 'Rhsim02G0029400' => 'rsi', 'Rhsim02G0029500' => 'rsi', 'Rhsim02G0029600' => 'rsi', 'RhsimUnG0024000' => 'rsi', 'RhsimUnG0024100' => 'rsi', 'RhsimUnG0024200' => 'rsi', 'RhsimUnG0024300' => 'rsi', 'RhsimUnG0024400' => 'rsi', 'RhsimUnG0024500' => 'rsi', 'RhsimUnG0024700' => 'rsi', 'RhsimUnG0024800' => 'rsi', 'RhsimUnG0024900' => 'rsi', 'RhsimUnG0025100' => 'rsi', 'Sabra08G0120200' => 'sbr', 'Sabra08G0120300' => 'sbr', 'Sabra08G0120500' => 'sbr', 'Sabra08G0120600' => 'sbr', 'Sabra10G0158900' => 'sbr', 'SalBow2G3492' => 'sbo', 'Sc13g0004760' => 'sci', 'Sc13g0004770' => 'sci', 'Sed0003417' => 'sed', 'Sed0019750' => 'sed', 'SEGI_03419' => 'sgi', 'SEGI_05907' => 'sgi', 'SEGI_10682' => 'sgi', 'SEGI_13528' => 'sgi', 'SEGI_16081' => 'sgi', 'SEGI_19370' => 'sgi', 'SEGI_21015' => 'sgi', 'SEGI_21944' => 'sgi', 'SEGI_32906' => 'sgi', 'SEGI_33093' => 'sgi', 'SEGI_36110' => 'sgi', 'SEGI_40397' => 'sgi', 'SGA_v2.0_scaffold191G40426' => 'sas', 'SGA_v2.0_scaffold353G49717' => 'sas', 'SGA_v2.0_scaffold50G18550' => 'sas', 'SMO119G0173' => 'smo', 'SMO172G0002' => 'smo', 'Solyc09g082690.3' => 'sly', 'Solyc09g082700.2' => 'sly', 'Sopen09g031550' => 'spe', 'Sopen09g031560' => 'spe', 'Sp3g20540' => 'spa', 'Sp7g07580' => 'spa', 'TAR134G0002' => 'tar', 'TAR236G0001' => 'tar', 'TAR365G0892' => 'tar', 'TAR636G0166' => 'tar', 'TAR636G0646' => 'tar', 'TAR636G0869' => 'tar', 'TAR636G1317' => 'tar', 'TAR636G1744' => 'tar', 'TAR636G3358' => 'tar', 'TAR636G3436' => 'tar', 'THA.LOC104803047' => 'tha', 'Thecc.04G238900' => 'tca', 'Thhalv10021557m.g' => 'esa', 'Thhalv10026318m.g' => 'esa', 'Thhalv10026335m.g' => 'esa', 'TPR.G17433' => 'tpr', 'TPR.G18915' => 'tpr', 'TPR.G26125' => 'tpr', 'TWI09G0677' => 'twi', 'TWI73G0287' => 'twi', 'unitig_748.g8326' => 'ugi', 'vmacro15370' => 'vma', 'vmacro15371' => 'vma', 'vmacro15372' => 'vma', 'vmacro15373' => 'vma', 'vmacro15374' => 'vma', 'VMungo0720G2826' => 'vmu', 'Zm00001eb116960' => 'zma', 'Zm00001eb301260' => 'zma', 'Zm00001eb301270' => 'zma' ), 'gf_id' => 'HOM05D001460', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001460' ), 'data_identifier' => 'HOM05D001460', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001460', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '433', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p22980' => 'bna', 'A01p32340' => 'bna', 'A03p42970' => 'bna', 'A05p25880' => 'bna', 'Aa31LG8G9320' => 'aar', 'Aa31LG8G9330' => 'aar', 'Aa31LG8G9340' => 'aar', 'Aa31sc221G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1034' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1528' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.829' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2222' => 'aag', 'Ah.12g058830' => 'amhyb', 'Ah.12g058840' => 'amhyb', 'AL3G37160' => 'aly', 'AL7G41310' => 'aly', 'Aqoxy5G00395' => 'aox', 'Aqoxy5G00396' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0C8NZA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5185HY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JZ1PRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MD3LS0' => 'arhy', 'AT3G22840' => 'ath', 'AT4G14690' => 'ath', 'ATR0665G054' => 'atr', 'Atru.chr4.2344' => 'acertr', 'Atru.chr4.2346' => 'acertr', 'Atru.chr4.2347' => 'acertr', 'Atru.chr4.2348' => 'acertr', 'Atru.chr4.2355' => 'acertr', 'Atru.chr4.2356' => 'acertr', 'Atru.chr4.2358' => 'acertr', 'Atru.chr4.2359' => 'acertr', 'Atru.chr4.2360' => 'acertr', 'Atru.chr4.2361' => 'acertr', 'AUR62030476' => 'cqu', 'AUR62030478' => 'cqu', 'AUR62030819' => 'cqu', 'AUR62030820' => 'cqu', 'BcaB03g14648' => 'bca', 'BcaB04g20492' => 'bca', 'BcaB06g26399' => 'bca', 'BcaC01g03416' => 'bca', 'BcaC01g03419' => 'bca', 'BcaC01g03421' => 'bca', 'BcaC01g03424' => 'bca', 'BcaC05g28012' => 'bca', 'BcaC09g49212' => 'bca', 'BcaC09g50140' => 'bca', 'BcaNung00346' => 'bca', 'BolC1t02785H' => 'bol', 'BolC1t04095H' => 'bol', 'BolC3t17545H' => 'bol', 'BolC5t32769H' => 'bol', 'BraA01t02211Z' => 'bra', 'BraA01t03359Z' => 'bra', 'BraA03t13441Z' => 'bra', 'BraA05t21476Z' => 'bra', 'C01p28420' => 'bna', 'C01p41350' => 'bna', 'C03p52750' => 'bna', 'C03p52780' => 'bna', 'C05p40270' => 'bna', 'CAN.G1437.9' => 'can', 'CANSAT78G0035' => 'cansat', 'CANSAT78G1036' => 'cansat', 'CANSAT78G2272' => 'cansat', 'CANSAT78G2478' => 'cansat', 'CARHR098700' => 'chi', 'CARHR221120' => 'chi', 'CARHR221150' => 'chi', 'Carub.0003s2297' => 'cru', 'Carub.0007s2749' => 'cru', 'Carub.0007s2750' => 'cru', 'Carub.0007s2751' => 'cru', 'Ca_10849_v3' => 'car', 'Cc03_g04300' => 'ccan', 'CDE02G3648' => 'cde', 'CDE05G0060' => 'cde', 'CDE05G0692' => 'cde', 'CDE05G2285' => 'cde', 'CDE05G2884' => 'cde', 'CDE05G3072' => 'cde', 'Cfa008439' => 'cfa', 'Cfa008441' => 'cfa', 'Cfa008443' => 'cfa', 'Cfa008448' => 'cfa', 'Ciclev10005974m.g' => 'ccl', 'Ciclev10006006m.g' => 'ccl', 'Ciclev10006775m.g' => 'ccl', 'CiPaw.02G120400' => 'cil', 'CiPaw.02G120500' => 'cil', 'CiPaw.02G120600' => 'cil', 'ClCG05G004850' => 'cla', 'COL.COLO4_21566' => 'col', 'Cpa.g.sc44.124' => 'cpa', 'Cre07.g320400' => 'cre', 'Cre07.g320450' => 'cre', 'Cre08.g384650' => 'cre', 'Cre09.g393173' => 'cre', 'Cre09.g394325' => 'cre', 'Cre14.g626750' => 'cre', 'Cre16.g679250' => 'cre', 'CsaV3_3G012890' => 'csa', 'CSS0010865' => 'camsi', 'CSS0044338' => 'camsi', 'DCAR_002366' => 'dca', 'DCAR_030687' => 'dca', 'DCAR_030688' => 'dca', 'Dinv14047' => 'din', 'Dinv14048' => 'din', 'Duzib151G0105' => 'dzi', 'Duzib151G0114' => 'dzi', 'Duzib212G1029' => 'dzi', 'ECA232G3536' => 'eca', 'ECA240G0786' => 'eca', 'ECA240G1802' => 'eca', 'ECA240G3760' => 'eca', 'ECA240G3920' => 'eca', 'EL10Ac5g12536' => 'bvu', 'EL10Ac5g12537' => 'bvu', 'EL10Ac5g12538' => 'bvu', 'Eucgr.B01004' => 'egr', 'Eucgr.B01006' => 'egr', 'Eucgr.B01007' => 'egr', 'Eucgr.B01008' => 'egr', 'Eucgr.B01895' => 'egr', 'Eucgr.B01896' => 'egr', 'FAN04G1456' => 'fan', 'FAN08G1769' => 'fan', 'FAN08G2160' => 'fan', 'FAN13G2403' => 'fan', 'FAN13G3303' => 'fan', 'FAN15G2435' => 'fan', 'FAN17G0672' => 'fan', 'FAN17G2441' => 'fan', 'FAN18G1024' => 'fan', 'FAN22G1458' => 'fan', 'FAN24G0037' => 'fan', 'FAN24G0429' => 'fan', 'FAN24G2387' => 'fan', 'FAN27G2746' => 'fan', 'FvH4_2g20400' => 'fve', 'FvH4_2g20420' => 'fve', 'FvH4_2g20430' => 'fve', 'FvH4_4g01270' => 'fve', 'FvH4_4g01290' => 'fve', 'FvH4_4g01300' => 'fve', 'FvH4_4g01310' => 'fve', 'FvH4_4g01330' => 'fve', 'FvH4_5g09070' => 'fve', 'Glyma.10G243800' => 'gma', 'Glyma.20G150600' => 'gma', 'Gohir.A09G219200' => 'ghi', 'Gohir.A09G219300' => 'ghi', 'Gohir.D09G221400' => 'ghi', 'Gohir.D09G221500' => 'ghi', 'Gorai.006G242600' => 'gra', 'Gorai.006G242700' => 'gra', 'GSVIVG01018044001' => 'vvi', 'HanXRQChr03g0083821' => 'han', 'HanXRQChr03g0083841' => 'han', 'HanXRQChr03g0083881' => 'han', 'HanXRQChr03g0083901' => 'han', 'HanXRQChr03g0083921' => 'han', 'HanXRQChr03g0085331' => 'han', 'HanXRQChr03g0085361' => 'han', 'HanXRQChr03g0085411' => 'han', 'HanXRQChr03g0085421' => 'han', 'HanXRQChr03g0085431' => 'han', 'HanXRQChr08g0221991' => 'han', 'HanXRQChr11g0336061' => 'han', 'HanXRQChr11g0336411' => 'han', 'Haze_11234' => 'cav', 'Hma1.2p1_0549F.1_g177010' => 'hma', 'Hma1.2p1_0602F.1_g187630' => 'hma', 'Hund14876' => 'sun', 'Hund14879' => 'sun', 'Lalb_Chr06g0160741' => 'lal', 'Lalb_Chr21g0304781' => 'lal', 'Lj3A726G19' => 'lonja', 'Lj3A726T23' => 'lonja', 'Lj3A726T24' => 'lonja', 'Lj3A726T25' => 'lonja', 'Lj3A727T17' => 'lonja', 'Lj3C726T0' => 'lonja', 'Lj3C726T2' => 'lonja', 'Lj3P725T35' => 'lonja', 'Lj3P727T10' => 'lonja', 'Lj3P727T12' => 'lonja', 'Lj3P727T14' => 'lonja', 'Lj5g0023109' => 'lja', 'Lj6P646T44' => 'lonja', 'Lsat_1_v5_gn_6_75760' => 'lsa', 'Lsat_1_v5_gn_6_75800' => 'lsa', 'Lsat_1_v5_gn_6_75900' => 'lsa', 'Lsat_1_v5_gn_6_76240' => 'lsa', 'Lsat_1_v5_gn_6_76441' => 'lsa', 'Lsat_1_v5_gn_6_76700' => 'lsa', 'Lsat_1_v5_gn_6_76760' => 'lsa', 'Manes.15G033100' => 'mes', 'Mapoly0004s0074' => 'mpo', 'Mapoly0004s0075' => 'mpo', 'Mapoly0004s0163' => 'mpo', 'Mapoly0004s0164' => 'mpo', 'Mapoly0021s0018' => 'mpo', 'Mapoly0041s0136' => 'mpo', 'Mapoly0041s0137' => 'mpo', 'Mapoly0041s0138' => 'mpo', 'Mapoly0041s0139' => 'mpo', 'Mapoly0041s0141' => 'mpo', 'Mapoly0041s0142' => 'mpo', 'Mapoly0041s0143' => 'mpo', 'Mapoly0041s0144' => 'mpo', 'Mapoly0041s0145' => 'mpo', 'Mapoly0047s0106' => 'mpo', 'Mapoly0047s0108' => 'mpo', 'Mapoly0050s0051' => 'mpo', 'Mapoly0050s0052' => 'mpo', 'Mapoly0050s0053' => 'mpo', 'Mapoly0058s0013' => 'mpo', 'Mapoly0091s0078' => 'mpo', 'Mapoly0091s0079' => 'mpo', 'Mapoly0091s0080' => 'mpo', 'Mapoly0091s0081' => 'mpo', 'Mapoly0278s0004' => 'mpo', 'Mapoly0278s0005' => 'mpo', 'Mapoly0278s0006' => 'mpo', 'MBI11_g30648_MAGBIO' => 'mbi', 'MCO03G194' => 'mco', 'MCO03G590' => 'mco', 'MCO07G312' => 'mco', 'MCO10G318' => 'mco', 'MCO12G244' => 'mco', 'MCO13G148' => 'mco', 'MCO13G194' => 'mco', 'MCO16G238' => 'mco', 'MD06G1134100' => 'mdo', 'MD13G1200100' => 'mdo', 'MD13G1200300' => 'mdo', 'MD13G1200600' => 'mdo', 'MD14G1150400' => 'mdo', 'MD16G1200000' => 'mdo', 'Medtr1g102570' => 'mtr', 'Medtr1g102780' => 'mtr', 'Medtr1g102800' => 'mtr', 'Medtr1g102810' => 'mtr', 'Medtr1g102830' => 'mtr', 'MELO3C006499.2' => 'cme', 'Migut.G00385' => 'egut', 'MSTRG.4063' => 'ama', 'Nitab4.5_0000090g0260' => 'nta', 'Nitab4.5_0000977g0030' => 'nta', 'Nitab4.5_0002541g0040' => 'nta', 'Nitab4.5_0007068g0040' => 'nta', 'Nn005s41408' => 'nnu', 'Nn005s41410' => 'nnu', 'Oeu010310.1' => 'oeu', 'Oeu010311.1' => 'oeu', 'Oeu043472.1' => 'oeu', 'Os01g0246400' => 'osa', 'Os04g0267950' => 'osa', 'Os07g0178700' => 'osa', 'Os07g0178800' => 'osa', 'Peaxi162Scf00316g00046' => 'pax', 'Peaxi162Scf00316g00049' => 'pax', 'Peaxi162Scf00316g00059' => 'pax', 'Peaxi162Scf00316g00328' => 'pax', 'Peaxi162Scf00316g00329' => 'pax', 'Peaxi162Scf00316g00411' => 'pax', 'Peaxi162Scf00316g00521' => 'pax', 'Peaxi162Scf00492g00068' => 'pax', 'Peaxi162Scf35631g00002' => 'pax', 'PGR142G3720' => 'pgr', 'PGSC0003DMG400006442' => 'stu', 'Phvul.007G062000' => 'pvu', 'Potri.008G157750' => 'ptr', 'Potri.008G157900' => 'ptr', 'Potri.008G158000' => 'ptr', 'Potri.008G158200' => 'ptr', 'Pp3c11_7280' => 'ppa', 'Pp3c11_7980' => 'ppa', 'Pp3c12_19450' => 'ppa', 'Pp3c14_1480' => 'ppa', 'Pp3c14_1501' => 'ppa', 'Pp3c16_4900' => 'ppa', 'Pp3c16_5010' => 'ppa', 'Pp3c16_5060' => 'ppa', 'Pp3c19_18250' => 'ppa', 'Pp3c23_8530' => 'ppa', 'Pp3c23_8550' => 'ppa', 'Pp3c24_9670' => 'ppa', 'Pp3c2_21390' => 'ppa', 'Pp3c2_31380' => 'ppa', 'Pp3c3_16620' => 'ppa', 'Pp3c3_8090' => 'ppa', 'Pp3c3_8110' => 'ppa', 'Pp3c3_8130' => 'ppa', 'Pp3c3_8150' => 'ppa', 'Pp3c4_14320' => 'ppa', 'Pp3c6_2560' => 'ppa', 'Pp3c9_16700' => 'ppa', 'PRCOL_00000234' => 'pco', 'PRCOL_00000235' => 'pco', 'PRCOL_00000777' => 'pco', 'PRCOL_00002344' => 'pco', 'PRCOL_00002372' => 'pco', 'PRCOL_00006120' => 'pco', 'Prupe.1G021400' => 'ppe', 'Prupe.1G021500' => 'ppe', 'Prupe.1G021600' => 'ppe', 'Prupe.1G021700' => 'ppe', 'Prupe.1G021800' => 'ppe', 'Prupe.5G145100' => 'ppe', 'Psat6g204040' => 'psa', 'Psat6g204800' => 'psa', 'Psat6g204920' => 'psa', 'Psat6g204960' => 'psa', 'Psat6g205080' => 'psa', 'PSO017G0271' => 'pso', 'PSO017G1276' => 'pso', 'PSO017G1429' => 'pso', 'PSO017G1861' => 'pso', 'PSO017G2787' => 'pso', 'PSO017G4466' => 'pso', 'PSO017G5118' => 'pso', 'PSO017G5420' => 'pso', 'PSO063G3678' => 'pso', 'PSO210G0546' => 'pso', 'PSO317G0001' => 'pso', 'PSO357G0512' => 'pso', 'PSO478G2682' => 'pso', 'PSO647G0001' => 'pso', 'PSO675G0001' => 'pso', 'PSO675G2699' => 'pso', 'PSO675G2849' => 'pso', 'PSO675G4991' => 'pso', 'PSO689G0001' => 'pso', 'QL06p000916' => 'qlo', 'QL06p000921' => 'qlo', 'QL06p001398' => 'qlo', 'QL06p001407' => 'qlo', 'QL06p002031' => 'qlo', 'RcHm_v2.0_Chr4g0387791' => 'rch', 'RcHm_v2.0_Chr4g0387801' => 'rch', 'RcHm_v2.0_Chr6g0286501' => 'rch', 'RcHm_v2.0_Chr6g0286511' => 'rch', 'RcHm_v2.0_Chr6g0286521' => 'rch', 'RcHm_v2.0_Chr6g0286531' => 'rch', 'RcHm_v2.0_Chr7g0189141' => 'rch', 'Rhsim02G0028700' => 'rsi', 'Rhsim02G0028800' => 'rsi', 'Rhsim02G0028900' => 'rsi', 'Rhsim02G0029000' => 'rsi', 'Rhsim02G0029100' => 'rsi', 'Rhsim02G0029200' => 'rsi', 'Rhsim02G0029300' => 'rsi', 'Rhsim02G0029400' => 'rsi', 'Rhsim02G0029500' => 'rsi', 'Rhsim02G0029600' => 'rsi', 'RhsimUnG0024000' => 'rsi', 'RhsimUnG0024100' => 'rsi', 'RhsimUnG0024200' => 'rsi', 'RhsimUnG0024300' => 'rsi', 'RhsimUnG0024400' => 'rsi', 'RhsimUnG0024500' => 'rsi', 'RhsimUnG0024700' => 'rsi', 'RhsimUnG0024800' => 'rsi', 'RhsimUnG0024900' => 'rsi', 'RhsimUnG0025100' => 'rsi', 'Sabra08G0120200' => 'sbr', 'Sabra08G0120300' => 'sbr', 'Sabra08G0120500' => 'sbr', 'Sabra08G0120600' => 'sbr', 'Sabra10G0158900' => 'sbr', 'SalBow2G3492' => 'sbo', 'Sc13g0004760' => 'sci', 'Sc13g0004770' => 'sci', 'Sed0003417' => 'sed', 'Sed0019750' => 'sed', 'SEGI_03419' => 'sgi', 'SEGI_05907' => 'sgi', 'SEGI_10682' => 'sgi', 'SEGI_13528' => 'sgi', 'SEGI_16081' => 'sgi', 'SEGI_19370' => 'sgi', 'SEGI_21015' => 'sgi', 'SEGI_21944' => 'sgi', 'SEGI_32906' => 'sgi', 'SEGI_33093' => 'sgi', 'SEGI_36110' => 'sgi', 'SEGI_40397' => 'sgi', 'SGA_v2.0_scaffold191G40426' => 'sas', 'SGA_v2.0_scaffold353G49717' => 'sas', 'SGA_v2.0_scaffold50G18550' => 'sas', 'SMO119G0173' => 'smo', 'SMO172G0002' => 'smo', 'Solyc09g082690.3' => 'sly', 'Solyc09g082700.2' => 'sly', 'Sopen09g031550' => 'spe', 'Sopen09g031560' => 'spe', 'Sp3g20540' => 'spa', 'Sp7g07580' => 'spa', 'TAR134G0002' => 'tar', 'TAR236G0001' => 'tar', 'TAR365G0892' => 'tar', 'TAR636G0166' => 'tar', 'TAR636G0646' => 'tar', 'TAR636G0869' => 'tar', 'TAR636G1317' => 'tar', 'TAR636G1744' => 'tar', 'TAR636G3358' => 'tar', 'TAR636G3436' => 'tar', 'THA.LOC104803047' => 'tha', 'Thecc.04G238900' => 'tca', 'Thhalv10021557m.g' => 'esa', 'Thhalv10026318m.g' => 'esa', 'Thhalv10026335m.g' => 'esa', 'TPR.G17433' => 'tpr', 'TPR.G18915' => 'tpr', 'TPR.G26125' => 'tpr', 'TWI09G0677' => 'twi', 'TWI73G0287' => 'twi', 'unitig_748.g8326' => 'ugi', 'vmacro15370' => 'vma', 'vmacro15371' => 'vma', 'vmacro15372' => 'vma', 'vmacro15373' => 'vma', 'vmacro15374' => 'vma', 'VMungo0720G2826' => 'vmu', 'Zm00001eb116960' => 'zma', 'Zm00001eb301260' => 'zma', 'Zm00001eb301270' => 'zma' ) $gf_id = 'HOM05D001460' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001460' ) $data_identifier = 'HOM05D001460' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 4, 'aag' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 2, 'aox' => (int) 2, 'arhy' => (int) 4, 'ath' => (int) 2, 'atr' => (int) 1, 'acertr' => (int) 10, 'cqu' => (int) 4, 'bca' => (int) 11, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 1, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 1, 'ccan' => (int) 1, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 1, 'col' => (int) 1, 'cpa' => (int) 1, 'cre' => (int) 7, 'csa' => (int) 1, 'camsi' => (int) 2, 'dca' => (int) 3, 'din' => (int) 2, 'dzi' => (int) 3, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 14, 'fve' => (int) 9, 'gma' => (int) 2, 'ghi' => (int) 4, 'gra' => (int) 2, 'vvi' => (int) 1, 'han' => (int) 13, 'cav' => (int) 1, 'hma' => (int) 2, 'sun' => (int) 2, 'lal' => (int) 2, 'lonja' => (int) 12, 'lja' => (int) 1, 'lsa' => (int) 7, 'mes' => (int) 1, 'mpo' => (int) 27, 'mbi' => (int) 1, 'mco' => (int) 8, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 1, 'egut' => (int) 1, 'ama' => (int) 1, 'nta' => (int) 4, 'nnu' => (int) 2, 'oeu' => (int) 3, 'osa' => (int) 4, 'pax' => (int) 9, 'pgr' => (int) 1, 'stu' => (int) 1, 'pvu' => (int) 1, 'ptr' => (int) 4, 'ppa' => (int) 22, 'pco' => (int) 6, 'ppe' => (int) 6, 'psa' => (int) 5, 'pso' => (int) 19, 'qlo' => (int) 5, 'rch' => (int) 7, 'rsi' => (int) 20, 'sbr' => (int) 5, 'sbo' => (int) 1, 'sci' => (int) 2, 'sed' => (int) 2, 'sgi' => (int) 12, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 2, 'tar' => (int) 10, 'tha' => (int) 1, 'tca' => (int) 1, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 2, 'ugi' => (int) 1, 'vma' => (int) 5, 'vmu' => (int) 1, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb301270' $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' => 'HOM05D001460', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '433', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p22980' => 'bna', 'A01p32340' => 'bna', 'A03p42970' => 'bna', 'A05p25880' => 'bna', 'Aa31LG8G9320' => 'aar', 'Aa31LG8G9330' => 'aar', 'Aa31LG8G9340' => 'aar', 'Aa31sc221G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1034' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1528' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.829' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2222' => 'aag', 'Ah.12g058830' => 'amhyb', 'Ah.12g058840' => 'amhyb', 'AL3G37160' => 'aly', 'AL7G41310' => 'aly', 'Aqoxy5G00395' => 'aox', 'Aqoxy5G00396' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0C8NZA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5185HY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JZ1PRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MD3LS0' => 'arhy', 'AT3G22840' => 'ath', 'AT4G14690' => 'ath', 'ATR0665G054' => 'atr', 'Atru.chr4.2344' => 'acertr', 'Atru.chr4.2346' => 'acertr', 'Atru.chr4.2347' => 'acertr', 'Atru.chr4.2348' => 'acertr', 'Atru.chr4.2355' => 'acertr', 'Atru.chr4.2356' => 'acertr', 'Atru.chr4.2358' => 'acertr', 'Atru.chr4.2359' => 'acertr', 'Atru.chr4.2360' => 'acertr', 'Atru.chr4.2361' => 'acertr', 'AUR62030476' => 'cqu', 'AUR62030478' => 'cqu', 'AUR62030819' => 'cqu', 'AUR62030820' => 'cqu', 'BcaB03g14648' => 'bca', 'BcaB04g20492' => 'bca', 'BcaB06g26399' => 'bca', 'BcaC01g03416' => 'bca', 'BcaC01g03419' => 'bca', 'BcaC01g03421' => 'bca', 'BcaC01g03424' => 'bca', 'BcaC05g28012' => 'bca', 'BcaC09g49212' => 'bca', 'BcaC09g50140' => 'bca', 'BcaNung00346' => 'bca', 'BolC1t02785H' => 'bol', 'BolC1t04095H' => 'bol', 'BolC3t17545H' => 'bol', 'BolC5t32769H' => 'bol', 'BraA01t02211Z' => 'bra', 'BraA01t03359Z' => 'bra', 'BraA03t13441Z' => 'bra', 'BraA05t21476Z' => 'bra', 'C01p28420' => 'bna', 'C01p41350' => 'bna', 'C03p52750' => 'bna', 'C03p52780' => 'bna', 'C05p40270' => 'bna', 'CAN.G1437.9' => 'can', 'CANSAT78G0035' => 'cansat', 'CANSAT78G1036' => 'cansat', 'CANSAT78G2272' => 'cansat', 'CANSAT78G2478' => 'cansat', 'CARHR098700' => 'chi', 'CARHR221120' => 'chi', 'CARHR221150' => 'chi', 'Carub.0003s2297' => 'cru', 'Carub.0007s2749' => 'cru', 'Carub.0007s2750' => 'cru', 'Carub.0007s2751' => 'cru', 'Ca_10849_v3' => 'car', 'Cc03_g04300' => 'ccan', 'CDE02G3648' => 'cde', 'CDE05G0060' => 'cde', 'CDE05G0692' => 'cde', 'CDE05G2285' => 'cde', 'CDE05G2884' => 'cde', 'CDE05G3072' => 'cde', 'Cfa008439' => 'cfa', 'Cfa008441' => 'cfa', 'Cfa008443' => 'cfa', 'Cfa008448' => 'cfa', 'Ciclev10005974m.g' => 'ccl', 'Ciclev10006006m.g' => 'ccl', 'Ciclev10006775m.g' => 'ccl', 'CiPaw.02G120400' => 'cil', 'CiPaw.02G120500' => 'cil', 'CiPaw.02G120600' => 'cil', 'ClCG05G004850' => 'cla', 'COL.COLO4_21566' => 'col', 'Cpa.g.sc44.124' => 'cpa', 'Cre07.g320400' => 'cre', 'Cre07.g320450' => 'cre', 'Cre08.g384650' => 'cre', 'Cre09.g393173' => 'cre', 'Cre09.g394325' => 'cre', 'Cre14.g626750' => 'cre', 'Cre16.g679250' => 'cre', 'CsaV3_3G012890' => 'csa', 'CSS0010865' => 'camsi', 'CSS0044338' => 'camsi', 'DCAR_002366' => 'dca', 'DCAR_030687' => 'dca', 'DCAR_030688' => 'dca', 'Dinv14047' => 'din', 'Dinv14048' => 'din', 'Duzib151G0105' => 'dzi', 'Duzib151G0114' => 'dzi', 'Duzib212G1029' => 'dzi', 'ECA232G3536' => 'eca', 'ECA240G0786' => 'eca', 'ECA240G1802' => 'eca', 'ECA240G3760' => 'eca', 'ECA240G3920' => 'eca', 'EL10Ac5g12536' => 'bvu', 'EL10Ac5g12537' => 'bvu', 'EL10Ac5g12538' => 'bvu', 'Eucgr.B01004' => 'egr', 'Eucgr.B01006' => 'egr', 'Eucgr.B01007' => 'egr', 'Eucgr.B01008' => 'egr', 'Eucgr.B01895' => 'egr', 'Eucgr.B01896' => 'egr', 'FAN04G1456' => 'fan', 'FAN08G1769' => 'fan', 'FAN08G2160' => 'fan', 'FAN13G2403' => 'fan', 'FAN13G3303' => 'fan', 'FAN15G2435' => 'fan', 'FAN17G0672' => 'fan', 'FAN17G2441' => 'fan', 'FAN18G1024' => 'fan', 'FAN22G1458' => 'fan', 'FAN24G0037' => 'fan', 'FAN24G0429' => 'fan', 'FAN24G2387' => 'fan', 'FAN27G2746' => 'fan', 'FvH4_2g20400' => 'fve', 'FvH4_2g20420' => 'fve', 'FvH4_2g20430' => 'fve', 'FvH4_4g01270' => 'fve', 'FvH4_4g01290' => 'fve', 'FvH4_4g01300' => 'fve', 'FvH4_4g01310' => 'fve', 'FvH4_4g01330' => 'fve', 'FvH4_5g09070' => 'fve', 'Glyma.10G243800' => 'gma', 'Glyma.20G150600' => 'gma', 'Gohir.A09G219200' => 'ghi', 'Gohir.A09G219300' => 'ghi', 'Gohir.D09G221400' => 'ghi', 'Gohir.D09G221500' => 'ghi', 'Gorai.006G242600' => 'gra', 'Gorai.006G242700' => 'gra', 'GSVIVG01018044001' => 'vvi', 'HanXRQChr03g0083821' => 'han', 'HanXRQChr03g0083841' => 'han', 'HanXRQChr03g0083881' => 'han', 'HanXRQChr03g0083901' => 'han', 'HanXRQChr03g0083921' => 'han', 'HanXRQChr03g0085331' => 'han', 'HanXRQChr03g0085361' => 'han', 'HanXRQChr03g0085411' => 'han', 'HanXRQChr03g0085421' => 'han', 'HanXRQChr03g0085431' => 'han', 'HanXRQChr08g0221991' => 'han', 'HanXRQChr11g0336061' => 'han', 'HanXRQChr11g0336411' => 'han', 'Haze_11234' => 'cav', 'Hma1.2p1_0549F.1_g177010' => 'hma', 'Hma1.2p1_0602F.1_g187630' => 'hma', 'Hund14876' => 'sun', 'Hund14879' => 'sun', 'Lalb_Chr06g0160741' => 'lal', 'Lalb_Chr21g0304781' => 'lal', 'Lj3A726G19' => 'lonja', 'Lj3A726T23' => 'lonja', 'Lj3A726T24' => 'lonja', 'Lj3A726T25' => 'lonja', 'Lj3A727T17' => 'lonja', 'Lj3C726T0' => 'lonja', 'Lj3C726T2' => 'lonja', 'Lj3P725T35' => 'lonja', 'Lj3P727T10' => 'lonja', 'Lj3P727T12' => 'lonja', 'Lj3P727T14' => 'lonja', 'Lj5g0023109' => 'lja', 'Lj6P646T44' => 'lonja', 'Lsat_1_v5_gn_6_75760' => 'lsa', 'Lsat_1_v5_gn_6_75800' => 'lsa', 'Lsat_1_v5_gn_6_75900' => 'lsa', 'Lsat_1_v5_gn_6_76240' => 'lsa', 'Lsat_1_v5_gn_6_76441' => 'lsa', 'Lsat_1_v5_gn_6_76700' => 'lsa', 'Lsat_1_v5_gn_6_76760' => 'lsa', 'Manes.15G033100' => 'mes', 'Mapoly0004s0074' => 'mpo', 'Mapoly0004s0075' => 'mpo', 'Mapoly0004s0163' => 'mpo', 'Mapoly0004s0164' => 'mpo', 'Mapoly0021s0018' => 'mpo', 'Mapoly0041s0136' => 'mpo', 'Mapoly0041s0137' => 'mpo', 'Mapoly0041s0138' => 'mpo', 'Mapoly0041s0139' => 'mpo', 'Mapoly0041s0141' => 'mpo', 'Mapoly0041s0142' => 'mpo', 'Mapoly0041s0143' => 'mpo', 'Mapoly0041s0144' => 'mpo', 'Mapoly0041s0145' => 'mpo', 'Mapoly0047s0106' => 'mpo', 'Mapoly0047s0108' => 'mpo', 'Mapoly0050s0051' => 'mpo', 'Mapoly0050s0052' => 'mpo', 'Mapoly0050s0053' => 'mpo', 'Mapoly0058s0013' => 'mpo', 'Mapoly0091s0078' => 'mpo', 'Mapoly0091s0079' => 'mpo', 'Mapoly0091s0080' => 'mpo', 'Mapoly0091s0081' => 'mpo', 'Mapoly0278s0004' => 'mpo', 'Mapoly0278s0005' => 'mpo', 'Mapoly0278s0006' => 'mpo', 'MBI11_g30648_MAGBIO' => 'mbi', 'MCO03G194' => 'mco', 'MCO03G590' => 'mco', 'MCO07G312' => 'mco', 'MCO10G318' => 'mco', 'MCO12G244' => 'mco', 'MCO13G148' => 'mco', 'MCO13G194' => 'mco', 'MCO16G238' => 'mco', 'MD06G1134100' => 'mdo', 'MD13G1200100' => 'mdo', 'MD13G1200300' => 'mdo', 'MD13G1200600' => 'mdo', 'MD14G1150400' => 'mdo', 'MD16G1200000' => 'mdo', 'Medtr1g102570' => 'mtr', 'Medtr1g102780' => 'mtr', 'Medtr1g102800' => 'mtr', 'Medtr1g102810' => 'mtr', 'Medtr1g102830' => 'mtr', 'MELO3C006499.2' => 'cme', 'Migut.G00385' => 'egut', 'MSTRG.4063' => 'ama', 'Nitab4.5_0000090g0260' => 'nta', 'Nitab4.5_0000977g0030' => 'nta', 'Nitab4.5_0002541g0040' => 'nta', 'Nitab4.5_0007068g0040' => 'nta', 'Nn005s41408' => 'nnu', 'Nn005s41410' => 'nnu', 'Oeu010310.1' => 'oeu', 'Oeu010311.1' => 'oeu', 'Oeu043472.1' => 'oeu', 'Os01g0246400' => 'osa', 'Os04g0267950' => 'osa', 'Os07g0178700' => 'osa', 'Os07g0178800' => 'osa', 'Peaxi162Scf00316g00046' => 'pax', 'Peaxi162Scf00316g00049' => 'pax', 'Peaxi162Scf00316g00059' => 'pax', 'Peaxi162Scf00316g00328' => 'pax', 'Peaxi162Scf00316g00329' => 'pax', 'Peaxi162Scf00316g00411' => 'pax', 'Peaxi162Scf00316g00521' => 'pax', 'Peaxi162Scf00492g00068' => 'pax', 'Peaxi162Scf35631g00002' => 'pax', 'PGR142G3720' => 'pgr', 'PGSC0003DMG400006442' => 'stu', 'Phvul.007G062000' => 'pvu', 'Potri.008G157750' => 'ptr', 'Potri.008G157900' => 'ptr', 'Potri.008G158000' => 'ptr', 'Potri.008G158200' => 'ptr', 'Pp3c11_7280' => 'ppa', 'Pp3c11_7980' => 'ppa', 'Pp3c12_19450' => 'ppa', 'Pp3c14_1480' => 'ppa', 'Pp3c14_1501' => 'ppa', 'Pp3c16_4900' => 'ppa', 'Pp3c16_5010' => 'ppa', 'Pp3c16_5060' => 'ppa', 'Pp3c19_18250' => 'ppa', 'Pp3c23_8530' => 'ppa', 'Pp3c23_8550' => 'ppa', 'Pp3c24_9670' => 'ppa', 'Pp3c2_21390' => 'ppa', 'Pp3c2_31380' => 'ppa', 'Pp3c3_16620' => 'ppa', 'Pp3c3_8090' => 'ppa', 'Pp3c3_8110' => 'ppa', 'Pp3c3_8130' => 'ppa', 'Pp3c3_8150' => 'ppa', 'Pp3c4_14320' => 'ppa', 'Pp3c6_2560' => 'ppa', 'Pp3c9_16700' => 'ppa', 'PRCOL_00000234' => 'pco', 'PRCOL_00000235' => 'pco', 'PRCOL_00000777' => 'pco', 'PRCOL_00002344' => 'pco', 'PRCOL_00002372' => 'pco', 'PRCOL_00006120' => 'pco', 'Prupe.1G021400' => 'ppe', 'Prupe.1G021500' => 'ppe', 'Prupe.1G021600' => 'ppe', 'Prupe.1G021700' => 'ppe', 'Prupe.1G021800' => 'ppe', 'Prupe.5G145100' => 'ppe', 'Psat6g204040' => 'psa', 'Psat6g204800' => 'psa', 'Psat6g204920' => 'psa', 'Psat6g204960' => 'psa', 'Psat6g205080' => 'psa', 'PSO017G0271' => 'pso', 'PSO017G1276' => 'pso', 'PSO017G1429' => 'pso', 'PSO017G1861' => 'pso', 'PSO017G2787' => 'pso', 'PSO017G4466' => 'pso', 'PSO017G5118' => 'pso', 'PSO017G5420' => 'pso', 'PSO063G3678' => 'pso', 'PSO210G0546' => 'pso', 'PSO317G0001' => 'pso', 'PSO357G0512' => 'pso', 'PSO478G2682' => 'pso', 'PSO647G0001' => 'pso', 'PSO675G0001' => 'pso', 'PSO675G2699' => 'pso', 'PSO675G2849' => 'pso', 'PSO675G4991' => 'pso', 'PSO689G0001' => 'pso', 'QL06p000916' => 'qlo', 'QL06p000921' => 'qlo', 'QL06p001398' => 'qlo', 'QL06p001407' => 'qlo', 'QL06p002031' => 'qlo', 'RcHm_v2.0_Chr4g0387791' => 'rch', 'RcHm_v2.0_Chr4g0387801' => 'rch', 'RcHm_v2.0_Chr6g0286501' => 'rch', 'RcHm_v2.0_Chr6g0286511' => 'rch', 'RcHm_v2.0_Chr6g0286521' => 'rch', 'RcHm_v2.0_Chr6g0286531' => 'rch', 'RcHm_v2.0_Chr7g0189141' => 'rch', 'Rhsim02G0028700' => 'rsi', 'Rhsim02G0028800' => 'rsi', 'Rhsim02G0028900' => 'rsi', 'Rhsim02G0029000' => 'rsi', 'Rhsim02G0029100' => 'rsi', 'Rhsim02G0029200' => 'rsi', 'Rhsim02G0029300' => 'rsi', 'Rhsim02G0029400' => 'rsi', 'Rhsim02G0029500' => 'rsi', 'Rhsim02G0029600' => 'rsi', 'RhsimUnG0024000' => 'rsi', 'RhsimUnG0024100' => 'rsi', 'RhsimUnG0024200' => 'rsi', 'RhsimUnG0024300' => 'rsi', 'RhsimUnG0024400' => 'rsi', 'RhsimUnG0024500' => 'rsi', 'RhsimUnG0024700' => 'rsi', 'RhsimUnG0024800' => 'rsi', 'RhsimUnG0024900' => 'rsi', 'RhsimUnG0025100' => 'rsi', 'Sabra08G0120200' => 'sbr', 'Sabra08G0120300' => 'sbr', 'Sabra08G0120500' => 'sbr', 'Sabra08G0120600' => 'sbr', 'Sabra10G0158900' => 'sbr', 'SalBow2G3492' => 'sbo', 'Sc13g0004760' => 'sci', 'Sc13g0004770' => 'sci', 'Sed0003417' => 'sed', 'Sed0019750' => 'sed', 'SEGI_03419' => 'sgi', 'SEGI_05907' => 'sgi', 'SEGI_10682' => 'sgi', 'SEGI_13528' => 'sgi', 'SEGI_16081' => 'sgi', 'SEGI_19370' => 'sgi', 'SEGI_21015' => 'sgi', 'SEGI_21944' => 'sgi', 'SEGI_32906' => 'sgi', 'SEGI_33093' => 'sgi', 'SEGI_36110' => 'sgi', 'SEGI_40397' => 'sgi', 'SGA_v2.0_scaffold191G40426' => 'sas', 'SGA_v2.0_scaffold353G49717' => 'sas', 'SGA_v2.0_scaffold50G18550' => 'sas', 'SMO119G0173' => 'smo', 'SMO172G0002' => 'smo', 'Solyc09g082690.3' => 'sly', 'Solyc09g082700.2' => 'sly', 'Sopen09g031550' => 'spe', 'Sopen09g031560' => 'spe', 'Sp3g20540' => 'spa', 'Sp7g07580' => 'spa', 'TAR134G0002' => 'tar', 'TAR236G0001' => 'tar', 'TAR365G0892' => 'tar', 'TAR636G0166' => 'tar', 'TAR636G0646' => 'tar', 'TAR636G0869' => 'tar', 'TAR636G1317' => 'tar', 'TAR636G1744' => 'tar', 'TAR636G3358' => 'tar', 'TAR636G3436' => 'tar', 'THA.LOC104803047' => 'tha', 'Thecc.04G238900' => 'tca', 'Thhalv10021557m.g' => 'esa', 'Thhalv10026318m.g' => 'esa', 'Thhalv10026335m.g' => 'esa', 'TPR.G17433' => 'tpr', 'TPR.G18915' => 'tpr', 'TPR.G26125' => 'tpr', 'TWI09G0677' => 'twi', 'TWI73G0287' => 'twi', 'unitig_748.g8326' => 'ugi', 'vmacro15370' => 'vma', 'vmacro15371' => 'vma', 'vmacro15372' => 'vma', 'vmacro15373' => 'vma', 'vmacro15374' => 'vma', 'VMungo0720G2826' => 'vmu', 'Zm00001eb116960' => 'zma', 'Zm00001eb301260' => 'zma', 'Zm00001eb301270' => 'zma' ), 'gf_id' => 'HOM05D001460', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001460' ), 'data_identifier' => 'HOM05D001460', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001460', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '433', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p22980' => 'bna', 'A01p32340' => 'bna', 'A03p42970' => 'bna', 'A05p25880' => 'bna', 'Aa31LG8G9320' => 'aar', 'Aa31LG8G9330' => 'aar', 'Aa31LG8G9340' => 'aar', 'Aa31sc221G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1034' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1528' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.829' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2222' => 'aag', 'Ah.12g058830' => 'amhyb', 'Ah.12g058840' => 'amhyb', 'AL3G37160' => 'aly', 'AL7G41310' => 'aly', 'Aqoxy5G00395' => 'aox', 'Aqoxy5G00396' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0C8NZA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5185HY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JZ1PRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MD3LS0' => 'arhy', 'AT3G22840' => 'ath', 'AT4G14690' => 'ath', 'ATR0665G054' => 'atr', 'Atru.chr4.2344' => 'acertr', 'Atru.chr4.2346' => 'acertr', 'Atru.chr4.2347' => 'acertr', 'Atru.chr4.2348' => 'acertr', 'Atru.chr4.2355' => 'acertr', 'Atru.chr4.2356' => 'acertr', 'Atru.chr4.2358' => 'acertr', 'Atru.chr4.2359' => 'acertr', 'Atru.chr4.2360' => 'acertr', 'Atru.chr4.2361' => 'acertr', 'AUR62030476' => 'cqu', 'AUR62030478' => 'cqu', 'AUR62030819' => 'cqu', 'AUR62030820' => 'cqu', 'BcaB03g14648' => 'bca', 'BcaB04g20492' => 'bca', 'BcaB06g26399' => 'bca', 'BcaC01g03416' => 'bca', 'BcaC01g03419' => 'bca', 'BcaC01g03421' => 'bca', 'BcaC01g03424' => 'bca', 'BcaC05g28012' => 'bca', 'BcaC09g49212' => 'bca', 'BcaC09g50140' => 'bca', 'BcaNung00346' => 'bca', 'BolC1t02785H' => 'bol', 'BolC1t04095H' => 'bol', 'BolC3t17545H' => 'bol', 'BolC5t32769H' => 'bol', 'BraA01t02211Z' => 'bra', 'BraA01t03359Z' => 'bra', 'BraA03t13441Z' => 'bra', 'BraA05t21476Z' => 'bra', 'C01p28420' => 'bna', 'C01p41350' => 'bna', 'C03p52750' => 'bna', 'C03p52780' => 'bna', 'C05p40270' => 'bna', 'CAN.G1437.9' => 'can', 'CANSAT78G0035' => 'cansat', 'CANSAT78G1036' => 'cansat', 'CANSAT78G2272' => 'cansat', 'CANSAT78G2478' => 'cansat', 'CARHR098700' => 'chi', 'CARHR221120' => 'chi', 'CARHR221150' => 'chi', 'Carub.0003s2297' => 'cru', 'Carub.0007s2749' => 'cru', 'Carub.0007s2750' => 'cru', 'Carub.0007s2751' => 'cru', 'Ca_10849_v3' => 'car', 'Cc03_g04300' => 'ccan', 'CDE02G3648' => 'cde', 'CDE05G0060' => 'cde', 'CDE05G0692' => 'cde', 'CDE05G2285' => 'cde', 'CDE05G2884' => 'cde', 'CDE05G3072' => 'cde', 'Cfa008439' => 'cfa', 'Cfa008441' => 'cfa', 'Cfa008443' => 'cfa', 'Cfa008448' => 'cfa', 'Ciclev10005974m.g' => 'ccl', 'Ciclev10006006m.g' => 'ccl', 'Ciclev10006775m.g' => 'ccl', 'CiPaw.02G120400' => 'cil', 'CiPaw.02G120500' => 'cil', 'CiPaw.02G120600' => 'cil', 'ClCG05G004850' => 'cla', 'COL.COLO4_21566' => 'col', 'Cpa.g.sc44.124' => 'cpa', 'Cre07.g320400' => 'cre', 'Cre07.g320450' => 'cre', 'Cre08.g384650' => 'cre', 'Cre09.g393173' => 'cre', 'Cre09.g394325' => 'cre', 'Cre14.g626750' => 'cre', 'Cre16.g679250' => 'cre', 'CsaV3_3G012890' => 'csa', 'CSS0010865' => 'camsi', 'CSS0044338' => 'camsi', 'DCAR_002366' => 'dca', 'DCAR_030687' => 'dca', 'DCAR_030688' => 'dca', 'Dinv14047' => 'din', 'Dinv14048' => 'din', 'Duzib151G0105' => 'dzi', 'Duzib151G0114' => 'dzi', 'Duzib212G1029' => 'dzi', 'ECA232G3536' => 'eca', 'ECA240G0786' => 'eca', 'ECA240G1802' => 'eca', 'ECA240G3760' => 'eca', 'ECA240G3920' => 'eca', 'EL10Ac5g12536' => 'bvu', 'EL10Ac5g12537' => 'bvu', 'EL10Ac5g12538' => 'bvu', 'Eucgr.B01004' => 'egr', 'Eucgr.B01006' => 'egr', 'Eucgr.B01007' => 'egr', 'Eucgr.B01008' => 'egr', 'Eucgr.B01895' => 'egr', 'Eucgr.B01896' => 'egr', 'FAN04G1456' => 'fan', 'FAN08G1769' => 'fan', 'FAN08G2160' => 'fan', 'FAN13G2403' => 'fan', 'FAN13G3303' => 'fan', 'FAN15G2435' => 'fan', 'FAN17G0672' => 'fan', 'FAN17G2441' => 'fan', 'FAN18G1024' => 'fan', 'FAN22G1458' => 'fan', 'FAN24G0037' => 'fan', 'FAN24G0429' => 'fan', 'FAN24G2387' => 'fan', 'FAN27G2746' => 'fan', 'FvH4_2g20400' => 'fve', 'FvH4_2g20420' => 'fve', 'FvH4_2g20430' => 'fve', 'FvH4_4g01270' => 'fve', 'FvH4_4g01290' => 'fve', 'FvH4_4g01300' => 'fve', 'FvH4_4g01310' => 'fve', 'FvH4_4g01330' => 'fve', 'FvH4_5g09070' => 'fve', 'Glyma.10G243800' => 'gma', 'Glyma.20G150600' => 'gma', 'Gohir.A09G219200' => 'ghi', 'Gohir.A09G219300' => 'ghi', 'Gohir.D09G221400' => 'ghi', 'Gohir.D09G221500' => 'ghi', 'Gorai.006G242600' => 'gra', 'Gorai.006G242700' => 'gra', 'GSVIVG01018044001' => 'vvi', 'HanXRQChr03g0083821' => 'han', 'HanXRQChr03g0083841' => 'han', 'HanXRQChr03g0083881' => 'han', 'HanXRQChr03g0083901' => 'han', 'HanXRQChr03g0083921' => 'han', 'HanXRQChr03g0085331' => 'han', 'HanXRQChr03g0085361' => 'han', 'HanXRQChr03g0085411' => 'han', 'HanXRQChr03g0085421' => 'han', 'HanXRQChr03g0085431' => 'han', 'HanXRQChr08g0221991' => 'han', 'HanXRQChr11g0336061' => 'han', 'HanXRQChr11g0336411' => 'han', 'Haze_11234' => 'cav', 'Hma1.2p1_0549F.1_g177010' => 'hma', 'Hma1.2p1_0602F.1_g187630' => 'hma', 'Hund14876' => 'sun', 'Hund14879' => 'sun', 'Lalb_Chr06g0160741' => 'lal', 'Lalb_Chr21g0304781' => 'lal', 'Lj3A726G19' => 'lonja', 'Lj3A726T23' => 'lonja', 'Lj3A726T24' => 'lonja', 'Lj3A726T25' => 'lonja', 'Lj3A727T17' => 'lonja', 'Lj3C726T0' => 'lonja', 'Lj3C726T2' => 'lonja', 'Lj3P725T35' => 'lonja', 'Lj3P727T10' => 'lonja', 'Lj3P727T12' => 'lonja', 'Lj3P727T14' => 'lonja', 'Lj5g0023109' => 'lja', 'Lj6P646T44' => 'lonja', 'Lsat_1_v5_gn_6_75760' => 'lsa', 'Lsat_1_v5_gn_6_75800' => 'lsa', 'Lsat_1_v5_gn_6_75900' => 'lsa', 'Lsat_1_v5_gn_6_76240' => 'lsa', 'Lsat_1_v5_gn_6_76441' => 'lsa', 'Lsat_1_v5_gn_6_76700' => 'lsa', 'Lsat_1_v5_gn_6_76760' => 'lsa', 'Manes.15G033100' => 'mes', 'Mapoly0004s0074' => 'mpo', 'Mapoly0004s0075' => 'mpo', 'Mapoly0004s0163' => 'mpo', 'Mapoly0004s0164' => 'mpo', 'Mapoly0021s0018' => 'mpo', 'Mapoly0041s0136' => 'mpo', 'Mapoly0041s0137' => 'mpo', 'Mapoly0041s0138' => 'mpo', 'Mapoly0041s0139' => 'mpo', 'Mapoly0041s0141' => 'mpo', 'Mapoly0041s0142' => 'mpo', 'Mapoly0041s0143' => 'mpo', 'Mapoly0041s0144' => 'mpo', 'Mapoly0041s0145' => 'mpo', 'Mapoly0047s0106' => 'mpo', 'Mapoly0047s0108' => 'mpo', 'Mapoly0050s0051' => 'mpo', 'Mapoly0050s0052' => 'mpo', 'Mapoly0050s0053' => 'mpo', 'Mapoly0058s0013' => 'mpo', 'Mapoly0091s0078' => 'mpo', 'Mapoly0091s0079' => 'mpo', 'Mapoly0091s0080' => 'mpo', 'Mapoly0091s0081' => 'mpo', 'Mapoly0278s0004' => 'mpo', 'Mapoly0278s0005' => 'mpo', 'Mapoly0278s0006' => 'mpo', 'MBI11_g30648_MAGBIO' => 'mbi', 'MCO03G194' => 'mco', 'MCO03G590' => 'mco', 'MCO07G312' => 'mco', 'MCO10G318' => 'mco', 'MCO12G244' => 'mco', 'MCO13G148' => 'mco', 'MCO13G194' => 'mco', 'MCO16G238' => 'mco', 'MD06G1134100' => 'mdo', 'MD13G1200100' => 'mdo', 'MD13G1200300' => 'mdo', 'MD13G1200600' => 'mdo', 'MD14G1150400' => 'mdo', 'MD16G1200000' => 'mdo', 'Medtr1g102570' => 'mtr', 'Medtr1g102780' => 'mtr', 'Medtr1g102800' => 'mtr', 'Medtr1g102810' => 'mtr', 'Medtr1g102830' => 'mtr', 'MELO3C006499.2' => 'cme', 'Migut.G00385' => 'egut', 'MSTRG.4063' => 'ama', 'Nitab4.5_0000090g0260' => 'nta', 'Nitab4.5_0000977g0030' => 'nta', 'Nitab4.5_0002541g0040' => 'nta', 'Nitab4.5_0007068g0040' => 'nta', 'Nn005s41408' => 'nnu', 'Nn005s41410' => 'nnu', 'Oeu010310.1' => 'oeu', 'Oeu010311.1' => 'oeu', 'Oeu043472.1' => 'oeu', 'Os01g0246400' => 'osa', 'Os04g0267950' => 'osa', 'Os07g0178700' => 'osa', 'Os07g0178800' => 'osa', 'Peaxi162Scf00316g00046' => 'pax', 'Peaxi162Scf00316g00049' => 'pax', 'Peaxi162Scf00316g00059' => 'pax', 'Peaxi162Scf00316g00328' => 'pax', 'Peaxi162Scf00316g00329' => 'pax', 'Peaxi162Scf00316g00411' => 'pax', 'Peaxi162Scf00316g00521' => 'pax', 'Peaxi162Scf00492g00068' => 'pax', 'Peaxi162Scf35631g00002' => 'pax', 'PGR142G3720' => 'pgr', 'PGSC0003DMG400006442' => 'stu', 'Phvul.007G062000' => 'pvu', 'Potri.008G157750' => 'ptr', 'Potri.008G157900' => 'ptr', 'Potri.008G158000' => 'ptr', 'Potri.008G158200' => 'ptr', 'Pp3c11_7280' => 'ppa', 'Pp3c11_7980' => 'ppa', 'Pp3c12_19450' => 'ppa', 'Pp3c14_1480' => 'ppa', 'Pp3c14_1501' => 'ppa', 'Pp3c16_4900' => 'ppa', 'Pp3c16_5010' => 'ppa', 'Pp3c16_5060' => 'ppa', 'Pp3c19_18250' => 'ppa', 'Pp3c23_8530' => 'ppa', 'Pp3c23_8550' => 'ppa', 'Pp3c24_9670' => 'ppa', 'Pp3c2_21390' => 'ppa', 'Pp3c2_31380' => 'ppa', 'Pp3c3_16620' => 'ppa', 'Pp3c3_8090' => 'ppa', 'Pp3c3_8110' => 'ppa', 'Pp3c3_8130' => 'ppa', 'Pp3c3_8150' => 'ppa', 'Pp3c4_14320' => 'ppa', 'Pp3c6_2560' => 'ppa', 'Pp3c9_16700' => 'ppa', 'PRCOL_00000234' => 'pco', 'PRCOL_00000235' => 'pco', 'PRCOL_00000777' => 'pco', 'PRCOL_00002344' => 'pco', 'PRCOL_00002372' => 'pco', 'PRCOL_00006120' => 'pco', 'Prupe.1G021400' => 'ppe', 'Prupe.1G021500' => 'ppe', 'Prupe.1G021600' => 'ppe', 'Prupe.1G021700' => 'ppe', 'Prupe.1G021800' => 'ppe', 'Prupe.5G145100' => 'ppe', 'Psat6g204040' => 'psa', 'Psat6g204800' => 'psa', 'Psat6g204920' => 'psa', 'Psat6g204960' => 'psa', 'Psat6g205080' => 'psa', 'PSO017G0271' => 'pso', 'PSO017G1276' => 'pso', 'PSO017G1429' => 'pso', 'PSO017G1861' => 'pso', 'PSO017G2787' => 'pso', 'PSO017G4466' => 'pso', 'PSO017G5118' => 'pso', 'PSO017G5420' => 'pso', 'PSO063G3678' => 'pso', 'PSO210G0546' => 'pso', 'PSO317G0001' => 'pso', 'PSO357G0512' => 'pso', 'PSO478G2682' => 'pso', 'PSO647G0001' => 'pso', 'PSO675G0001' => 'pso', 'PSO675G2699' => 'pso', 'PSO675G2849' => 'pso', 'PSO675G4991' => 'pso', 'PSO689G0001' => 'pso', 'QL06p000916' => 'qlo', 'QL06p000921' => 'qlo', 'QL06p001398' => 'qlo', 'QL06p001407' => 'qlo', 'QL06p002031' => 'qlo', 'RcHm_v2.0_Chr4g0387791' => 'rch', 'RcHm_v2.0_Chr4g0387801' => 'rch', 'RcHm_v2.0_Chr6g0286501' => 'rch', 'RcHm_v2.0_Chr6g0286511' => 'rch', 'RcHm_v2.0_Chr6g0286521' => 'rch', 'RcHm_v2.0_Chr6g0286531' => 'rch', 'RcHm_v2.0_Chr7g0189141' => 'rch', 'Rhsim02G0028700' => 'rsi', 'Rhsim02G0028800' => 'rsi', 'Rhsim02G0028900' => 'rsi', 'Rhsim02G0029000' => 'rsi', 'Rhsim02G0029100' => 'rsi', 'Rhsim02G0029200' => 'rsi', 'Rhsim02G0029300' => 'rsi', 'Rhsim02G0029400' => 'rsi', 'Rhsim02G0029500' => 'rsi', 'Rhsim02G0029600' => 'rsi', 'RhsimUnG0024000' => 'rsi', 'RhsimUnG0024100' => 'rsi', 'RhsimUnG0024200' => 'rsi', 'RhsimUnG0024300' => 'rsi', 'RhsimUnG0024400' => 'rsi', 'RhsimUnG0024500' => 'rsi', 'RhsimUnG0024700' => 'rsi', 'RhsimUnG0024800' => 'rsi', 'RhsimUnG0024900' => 'rsi', 'RhsimUnG0025100' => 'rsi', 'Sabra08G0120200' => 'sbr', 'Sabra08G0120300' => 'sbr', 'Sabra08G0120500' => 'sbr', 'Sabra08G0120600' => 'sbr', 'Sabra10G0158900' => 'sbr', 'SalBow2G3492' => 'sbo', 'Sc13g0004760' => 'sci', 'Sc13g0004770' => 'sci', 'Sed0003417' => 'sed', 'Sed0019750' => 'sed', 'SEGI_03419' => 'sgi', 'SEGI_05907' => 'sgi', 'SEGI_10682' => 'sgi', 'SEGI_13528' => 'sgi', 'SEGI_16081' => 'sgi', 'SEGI_19370' => 'sgi', 'SEGI_21015' => 'sgi', 'SEGI_21944' => 'sgi', 'SEGI_32906' => 'sgi', 'SEGI_33093' => 'sgi', 'SEGI_36110' => 'sgi', 'SEGI_40397' => 'sgi', 'SGA_v2.0_scaffold191G40426' => 'sas', 'SGA_v2.0_scaffold353G49717' => 'sas', 'SGA_v2.0_scaffold50G18550' => 'sas', 'SMO119G0173' => 'smo', 'SMO172G0002' => 'smo', 'Solyc09g082690.3' => 'sly', 'Solyc09g082700.2' => 'sly', 'Sopen09g031550' => 'spe', 'Sopen09g031560' => 'spe', 'Sp3g20540' => 'spa', 'Sp7g07580' => 'spa', 'TAR134G0002' => 'tar', 'TAR236G0001' => 'tar', 'TAR365G0892' => 'tar', 'TAR636G0166' => 'tar', 'TAR636G0646' => 'tar', 'TAR636G0869' => 'tar', 'TAR636G1317' => 'tar', 'TAR636G1744' => 'tar', 'TAR636G3358' => 'tar', 'TAR636G3436' => 'tar', 'THA.LOC104803047' => 'tha', 'Thecc.04G238900' => 'tca', 'Thhalv10021557m.g' => 'esa', 'Thhalv10026318m.g' => 'esa', 'Thhalv10026335m.g' => 'esa', 'TPR.G17433' => 'tpr', 'TPR.G18915' => 'tpr', 'TPR.G26125' => 'tpr', 'TWI09G0677' => 'twi', 'TWI73G0287' => 'twi', 'unitig_748.g8326' => 'ugi', 'vmacro15370' => 'vma', 'vmacro15371' => 'vma', 'vmacro15372' => 'vma', 'vmacro15373' => 'vma', 'vmacro15374' => 'vma', 'VMungo0720G2826' => 'vmu', 'Zm00001eb116960' => 'zma', 'Zm00001eb301260' => 'zma', 'Zm00001eb301270' => 'zma' ) $gf_id = 'HOM05D001460' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001460' ) $data_identifier = 'HOM05D001460' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 4, 'aag' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 2, 'aox' => (int) 2, 'arhy' => (int) 4, 'ath' => (int) 2, 'atr' => (int) 1, 'acertr' => (int) 10, 'cqu' => (int) 4, 'bca' => (int) 11, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 1, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 1, 'ccan' => (int) 1, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 1, 'col' => (int) 1, 'cpa' => (int) 1, 'cre' => (int) 7, 'csa' => (int) 1, 'camsi' => (int) 2, 'dca' => (int) 3, 'din' => (int) 2, 'dzi' => (int) 3, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 14, 'fve' => (int) 9, 'gma' => (int) 2, 'ghi' => (int) 4, 'gra' => (int) 2, 'vvi' => (int) 1, 'han' => (int) 13, 'cav' => (int) 1, 'hma' => (int) 2, 'sun' => (int) 2, 'lal' => (int) 2, 'lonja' => (int) 12, 'lja' => (int) 1, 'lsa' => (int) 7, 'mes' => (int) 1, 'mpo' => (int) 27, 'mbi' => (int) 1, 'mco' => (int) 8, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 1, 'egut' => (int) 1, 'ama' => (int) 1, 'nta' => (int) 4, 'nnu' => (int) 2, 'oeu' => (int) 3, 'osa' => (int) 4, 'pax' => (int) 9, 'pgr' => (int) 1, 'stu' => (int) 1, 'pvu' => (int) 1, 'ptr' => (int) 4, 'ppa' => (int) 22, 'pco' => (int) 6, 'ppe' => (int) 6, 'psa' => (int) 5, 'pso' => (int) 19, 'qlo' => (int) 5, 'rch' => (int) 7, 'rsi' => (int) 20, 'sbr' => (int) 5, 'sbo' => (int) 1, 'sci' => (int) 2, 'sed' => (int) 2, 'sgi' => (int) 12, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 2, 'tar' => (int) 10, 'tha' => (int) 1, 'tca' => (int) 1, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 2, 'ugi' => (int) 1, 'vma' => (int) 5, 'vmu' => (int) 1, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb301270' $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' => 'HOM05D001460', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '433', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p22980' => 'bna', 'A01p32340' => 'bna', 'A03p42970' => 'bna', 'A05p25880' => 'bna', 'Aa31LG8G9320' => 'aar', 'Aa31LG8G9330' => 'aar', 'Aa31LG8G9340' => 'aar', 'Aa31sc221G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1034' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1528' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.829' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2222' => 'aag', 'Ah.12g058830' => 'amhyb', 'Ah.12g058840' => 'amhyb', 'AL3G37160' => 'aly', 'AL7G41310' => 'aly', 'Aqoxy5G00395' => 'aox', 'Aqoxy5G00396' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0C8NZA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5185HY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JZ1PRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MD3LS0' => 'arhy', 'AT3G22840' => 'ath', 'AT4G14690' => 'ath', 'ATR0665G054' => 'atr', 'Atru.chr4.2344' => 'acertr', 'Atru.chr4.2346' => 'acertr', 'Atru.chr4.2347' => 'acertr', 'Atru.chr4.2348' => 'acertr', 'Atru.chr4.2355' => 'acertr', 'Atru.chr4.2356' => 'acertr', 'Atru.chr4.2358' => 'acertr', 'Atru.chr4.2359' => 'acertr', 'Atru.chr4.2360' => 'acertr', 'Atru.chr4.2361' => 'acertr', 'AUR62030476' => 'cqu', 'AUR62030478' => 'cqu', 'AUR62030819' => 'cqu', 'AUR62030820' => 'cqu', 'BcaB03g14648' => 'bca', 'BcaB04g20492' => 'bca', 'BcaB06g26399' => 'bca', 'BcaC01g03416' => 'bca', 'BcaC01g03419' => 'bca', 'BcaC01g03421' => 'bca', 'BcaC01g03424' => 'bca', 'BcaC05g28012' => 'bca', 'BcaC09g49212' => 'bca', 'BcaC09g50140' => 'bca', 'BcaNung00346' => 'bca', 'BolC1t02785H' => 'bol', 'BolC1t04095H' => 'bol', 'BolC3t17545H' => 'bol', 'BolC5t32769H' => 'bol', 'BraA01t02211Z' => 'bra', 'BraA01t03359Z' => 'bra', 'BraA03t13441Z' => 'bra', 'BraA05t21476Z' => 'bra', 'C01p28420' => 'bna', 'C01p41350' => 'bna', 'C03p52750' => 'bna', 'C03p52780' => 'bna', 'C05p40270' => 'bna', 'CAN.G1437.9' => 'can', 'CANSAT78G0035' => 'cansat', 'CANSAT78G1036' => 'cansat', 'CANSAT78G2272' => 'cansat', 'CANSAT78G2478' => 'cansat', 'CARHR098700' => 'chi', 'CARHR221120' => 'chi', 'CARHR221150' => 'chi', 'Carub.0003s2297' => 'cru', 'Carub.0007s2749' => 'cru', 'Carub.0007s2750' => 'cru', 'Carub.0007s2751' => 'cru', 'Ca_10849_v3' => 'car', 'Cc03_g04300' => 'ccan', 'CDE02G3648' => 'cde', 'CDE05G0060' => 'cde', 'CDE05G0692' => 'cde', 'CDE05G2285' => 'cde', 'CDE05G2884' => 'cde', 'CDE05G3072' => 'cde', 'Cfa008439' => 'cfa', 'Cfa008441' => 'cfa', 'Cfa008443' => 'cfa', 'Cfa008448' => 'cfa', 'Ciclev10005974m.g' => 'ccl', 'Ciclev10006006m.g' => 'ccl', 'Ciclev10006775m.g' => 'ccl', 'CiPaw.02G120400' => 'cil', 'CiPaw.02G120500' => 'cil', 'CiPaw.02G120600' => 'cil', 'ClCG05G004850' => 'cla', 'COL.COLO4_21566' => 'col', 'Cpa.g.sc44.124' => 'cpa', 'Cre07.g320400' => 'cre', 'Cre07.g320450' => 'cre', 'Cre08.g384650' => 'cre', 'Cre09.g393173' => 'cre', 'Cre09.g394325' => 'cre', 'Cre14.g626750' => 'cre', 'Cre16.g679250' => 'cre', 'CsaV3_3G012890' => 'csa', 'CSS0010865' => 'camsi', 'CSS0044338' => 'camsi', 'DCAR_002366' => 'dca', 'DCAR_030687' => 'dca', 'DCAR_030688' => 'dca', 'Dinv14047' => 'din', 'Dinv14048' => 'din', 'Duzib151G0105' => 'dzi', 'Duzib151G0114' => 'dzi', 'Duzib212G1029' => 'dzi', 'ECA232G3536' => 'eca', 'ECA240G0786' => 'eca', 'ECA240G1802' => 'eca', 'ECA240G3760' => 'eca', 'ECA240G3920' => 'eca', 'EL10Ac5g12536' => 'bvu', 'EL10Ac5g12537' => 'bvu', 'EL10Ac5g12538' => 'bvu', 'Eucgr.B01004' => 'egr', 'Eucgr.B01006' => 'egr', 'Eucgr.B01007' => 'egr', 'Eucgr.B01008' => 'egr', 'Eucgr.B01895' => 'egr', 'Eucgr.B01896' => 'egr', 'FAN04G1456' => 'fan', 'FAN08G1769' => 'fan', 'FAN08G2160' => 'fan', 'FAN13G2403' => 'fan', 'FAN13G3303' => 'fan', 'FAN15G2435' => 'fan', 'FAN17G0672' => 'fan', 'FAN17G2441' => 'fan', 'FAN18G1024' => 'fan', 'FAN22G1458' => 'fan', 'FAN24G0037' => 'fan', 'FAN24G0429' => 'fan', 'FAN24G2387' => 'fan', 'FAN27G2746' => 'fan', 'FvH4_2g20400' => 'fve', 'FvH4_2g20420' => 'fve', 'FvH4_2g20430' => 'fve', 'FvH4_4g01270' => 'fve', 'FvH4_4g01290' => 'fve', 'FvH4_4g01300' => 'fve', 'FvH4_4g01310' => 'fve', 'FvH4_4g01330' => 'fve', 'FvH4_5g09070' => 'fve', 'Glyma.10G243800' => 'gma', 'Glyma.20G150600' => 'gma', 'Gohir.A09G219200' => 'ghi', 'Gohir.A09G219300' => 'ghi', 'Gohir.D09G221400' => 'ghi', 'Gohir.D09G221500' => 'ghi', 'Gorai.006G242600' => 'gra', 'Gorai.006G242700' => 'gra', 'GSVIVG01018044001' => 'vvi', 'HanXRQChr03g0083821' => 'han', 'HanXRQChr03g0083841' => 'han', 'HanXRQChr03g0083881' => 'han', 'HanXRQChr03g0083901' => 'han', 'HanXRQChr03g0083921' => 'han', 'HanXRQChr03g0085331' => 'han', 'HanXRQChr03g0085361' => 'han', 'HanXRQChr03g0085411' => 'han', 'HanXRQChr03g0085421' => 'han', 'HanXRQChr03g0085431' => 'han', 'HanXRQChr08g0221991' => 'han', 'HanXRQChr11g0336061' => 'han', 'HanXRQChr11g0336411' => 'han', 'Haze_11234' => 'cav', 'Hma1.2p1_0549F.1_g177010' => 'hma', 'Hma1.2p1_0602F.1_g187630' => 'hma', 'Hund14876' => 'sun', 'Hund14879' => 'sun', 'Lalb_Chr06g0160741' => 'lal', 'Lalb_Chr21g0304781' => 'lal', 'Lj3A726G19' => 'lonja', 'Lj3A726T23' => 'lonja', 'Lj3A726T24' => 'lonja', 'Lj3A726T25' => 'lonja', 'Lj3A727T17' => 'lonja', 'Lj3C726T0' => 'lonja', 'Lj3C726T2' => 'lonja', 'Lj3P725T35' => 'lonja', 'Lj3P727T10' => 'lonja', 'Lj3P727T12' => 'lonja', 'Lj3P727T14' => 'lonja', 'Lj5g0023109' => 'lja', 'Lj6P646T44' => 'lonja', 'Lsat_1_v5_gn_6_75760' => 'lsa', 'Lsat_1_v5_gn_6_75800' => 'lsa', 'Lsat_1_v5_gn_6_75900' => 'lsa', 'Lsat_1_v5_gn_6_76240' => 'lsa', 'Lsat_1_v5_gn_6_76441' => 'lsa', 'Lsat_1_v5_gn_6_76700' => 'lsa', 'Lsat_1_v5_gn_6_76760' => 'lsa', 'Manes.15G033100' => 'mes', 'Mapoly0004s0074' => 'mpo', 'Mapoly0004s0075' => 'mpo', 'Mapoly0004s0163' => 'mpo', 'Mapoly0004s0164' => 'mpo', 'Mapoly0021s0018' => 'mpo', 'Mapoly0041s0136' => 'mpo', 'Mapoly0041s0137' => 'mpo', 'Mapoly0041s0138' => 'mpo', 'Mapoly0041s0139' => 'mpo', 'Mapoly0041s0141' => 'mpo', 'Mapoly0041s0142' => 'mpo', 'Mapoly0041s0143' => 'mpo', 'Mapoly0041s0144' => 'mpo', 'Mapoly0041s0145' => 'mpo', 'Mapoly0047s0106' => 'mpo', 'Mapoly0047s0108' => 'mpo', 'Mapoly0050s0051' => 'mpo', 'Mapoly0050s0052' => 'mpo', 'Mapoly0050s0053' => 'mpo', 'Mapoly0058s0013' => 'mpo', 'Mapoly0091s0078' => 'mpo', 'Mapoly0091s0079' => 'mpo', 'Mapoly0091s0080' => 'mpo', 'Mapoly0091s0081' => 'mpo', 'Mapoly0278s0004' => 'mpo', 'Mapoly0278s0005' => 'mpo', 'Mapoly0278s0006' => 'mpo', 'MBI11_g30648_MAGBIO' => 'mbi', 'MCO03G194' => 'mco', 'MCO03G590' => 'mco', 'MCO07G312' => 'mco', 'MCO10G318' => 'mco', 'MCO12G244' => 'mco', 'MCO13G148' => 'mco', 'MCO13G194' => 'mco', 'MCO16G238' => 'mco', 'MD06G1134100' => 'mdo', 'MD13G1200100' => 'mdo', 'MD13G1200300' => 'mdo', 'MD13G1200600' => 'mdo', 'MD14G1150400' => 'mdo', 'MD16G1200000' => 'mdo', 'Medtr1g102570' => 'mtr', 'Medtr1g102780' => 'mtr', 'Medtr1g102800' => 'mtr', 'Medtr1g102810' => 'mtr', 'Medtr1g102830' => 'mtr', 'MELO3C006499.2' => 'cme', 'Migut.G00385' => 'egut', 'MSTRG.4063' => 'ama', 'Nitab4.5_0000090g0260' => 'nta', 'Nitab4.5_0000977g0030' => 'nta', 'Nitab4.5_0002541g0040' => 'nta', 'Nitab4.5_0007068g0040' => 'nta', 'Nn005s41408' => 'nnu', 'Nn005s41410' => 'nnu', 'Oeu010310.1' => 'oeu', 'Oeu010311.1' => 'oeu', 'Oeu043472.1' => 'oeu', 'Os01g0246400' => 'osa', 'Os04g0267950' => 'osa', 'Os07g0178700' => 'osa', 'Os07g0178800' => 'osa', 'Peaxi162Scf00316g00046' => 'pax', 'Peaxi162Scf00316g00049' => 'pax', 'Peaxi162Scf00316g00059' => 'pax', 'Peaxi162Scf00316g00328' => 'pax', 'Peaxi162Scf00316g00329' => 'pax', 'Peaxi162Scf00316g00411' => 'pax', 'Peaxi162Scf00316g00521' => 'pax', 'Peaxi162Scf00492g00068' => 'pax', 'Peaxi162Scf35631g00002' => 'pax', 'PGR142G3720' => 'pgr', 'PGSC0003DMG400006442' => 'stu', 'Phvul.007G062000' => 'pvu', 'Potri.008G157750' => 'ptr', 'Potri.008G157900' => 'ptr', 'Potri.008G158000' => 'ptr', 'Potri.008G158200' => 'ptr', 'Pp3c11_7280' => 'ppa', 'Pp3c11_7980' => 'ppa', 'Pp3c12_19450' => 'ppa', 'Pp3c14_1480' => 'ppa', 'Pp3c14_1501' => 'ppa', 'Pp3c16_4900' => 'ppa', 'Pp3c16_5010' => 'ppa', 'Pp3c16_5060' => 'ppa', 'Pp3c19_18250' => 'ppa', 'Pp3c23_8530' => 'ppa', 'Pp3c23_8550' => 'ppa', 'Pp3c24_9670' => 'ppa', 'Pp3c2_21390' => 'ppa', 'Pp3c2_31380' => 'ppa', 'Pp3c3_16620' => 'ppa', 'Pp3c3_8090' => 'ppa', 'Pp3c3_8110' => 'ppa', 'Pp3c3_8130' => 'ppa', 'Pp3c3_8150' => 'ppa', 'Pp3c4_14320' => 'ppa', 'Pp3c6_2560' => 'ppa', 'Pp3c9_16700' => 'ppa', 'PRCOL_00000234' => 'pco', 'PRCOL_00000235' => 'pco', 'PRCOL_00000777' => 'pco', 'PRCOL_00002344' => 'pco', 'PRCOL_00002372' => 'pco', 'PRCOL_00006120' => 'pco', 'Prupe.1G021400' => 'ppe', 'Prupe.1G021500' => 'ppe', 'Prupe.1G021600' => 'ppe', 'Prupe.1G021700' => 'ppe', 'Prupe.1G021800' => 'ppe', 'Prupe.5G145100' => 'ppe', 'Psat6g204040' => 'psa', 'Psat6g204800' => 'psa', 'Psat6g204920' => 'psa', 'Psat6g204960' => 'psa', 'Psat6g205080' => 'psa', 'PSO017G0271' => 'pso', 'PSO017G1276' => 'pso', 'PSO017G1429' => 'pso', 'PSO017G1861' => 'pso', 'PSO017G2787' => 'pso', 'PSO017G4466' => 'pso', 'PSO017G5118' => 'pso', 'PSO017G5420' => 'pso', 'PSO063G3678' => 'pso', 'PSO210G0546' => 'pso', 'PSO317G0001' => 'pso', 'PSO357G0512' => 'pso', 'PSO478G2682' => 'pso', 'PSO647G0001' => 'pso', 'PSO675G0001' => 'pso', 'PSO675G2699' => 'pso', 'PSO675G2849' => 'pso', 'PSO675G4991' => 'pso', 'PSO689G0001' => 'pso', 'QL06p000916' => 'qlo', 'QL06p000921' => 'qlo', 'QL06p001398' => 'qlo', 'QL06p001407' => 'qlo', 'QL06p002031' => 'qlo', 'RcHm_v2.0_Chr4g0387791' => 'rch', 'RcHm_v2.0_Chr4g0387801' => 'rch', 'RcHm_v2.0_Chr6g0286501' => 'rch', 'RcHm_v2.0_Chr6g0286511' => 'rch', 'RcHm_v2.0_Chr6g0286521' => 'rch', 'RcHm_v2.0_Chr6g0286531' => 'rch', 'RcHm_v2.0_Chr7g0189141' => 'rch', 'Rhsim02G0028700' => 'rsi', 'Rhsim02G0028800' => 'rsi', 'Rhsim02G0028900' => 'rsi', 'Rhsim02G0029000' => 'rsi', 'Rhsim02G0029100' => 'rsi', 'Rhsim02G0029200' => 'rsi', 'Rhsim02G0029300' => 'rsi', 'Rhsim02G0029400' => 'rsi', 'Rhsim02G0029500' => 'rsi', 'Rhsim02G0029600' => 'rsi', 'RhsimUnG0024000' => 'rsi', 'RhsimUnG0024100' => 'rsi', 'RhsimUnG0024200' => 'rsi', 'RhsimUnG0024300' => 'rsi', 'RhsimUnG0024400' => 'rsi', 'RhsimUnG0024500' => 'rsi', 'RhsimUnG0024700' => 'rsi', 'RhsimUnG0024800' => 'rsi', 'RhsimUnG0024900' => 'rsi', 'RhsimUnG0025100' => 'rsi', 'Sabra08G0120200' => 'sbr', 'Sabra08G0120300' => 'sbr', 'Sabra08G0120500' => 'sbr', 'Sabra08G0120600' => 'sbr', 'Sabra10G0158900' => 'sbr', 'SalBow2G3492' => 'sbo', 'Sc13g0004760' => 'sci', 'Sc13g0004770' => 'sci', 'Sed0003417' => 'sed', 'Sed0019750' => 'sed', 'SEGI_03419' => 'sgi', 'SEGI_05907' => 'sgi', 'SEGI_10682' => 'sgi', 'SEGI_13528' => 'sgi', 'SEGI_16081' => 'sgi', 'SEGI_19370' => 'sgi', 'SEGI_21015' => 'sgi', 'SEGI_21944' => 'sgi', 'SEGI_32906' => 'sgi', 'SEGI_33093' => 'sgi', 'SEGI_36110' => 'sgi', 'SEGI_40397' => 'sgi', 'SGA_v2.0_scaffold191G40426' => 'sas', 'SGA_v2.0_scaffold353G49717' => 'sas', 'SGA_v2.0_scaffold50G18550' => 'sas', 'SMO119G0173' => 'smo', 'SMO172G0002' => 'smo', 'Solyc09g082690.3' => 'sly', 'Solyc09g082700.2' => 'sly', 'Sopen09g031550' => 'spe', 'Sopen09g031560' => 'spe', 'Sp3g20540' => 'spa', 'Sp7g07580' => 'spa', 'TAR134G0002' => 'tar', 'TAR236G0001' => 'tar', 'TAR365G0892' => 'tar', 'TAR636G0166' => 'tar', 'TAR636G0646' => 'tar', 'TAR636G0869' => 'tar', 'TAR636G1317' => 'tar', 'TAR636G1744' => 'tar', 'TAR636G3358' => 'tar', 'TAR636G3436' => 'tar', 'THA.LOC104803047' => 'tha', 'Thecc.04G238900' => 'tca', 'Thhalv10021557m.g' => 'esa', 'Thhalv10026318m.g' => 'esa', 'Thhalv10026335m.g' => 'esa', 'TPR.G17433' => 'tpr', 'TPR.G18915' => 'tpr', 'TPR.G26125' => 'tpr', 'TWI09G0677' => 'twi', 'TWI73G0287' => 'twi', 'unitig_748.g8326' => 'ugi', 'vmacro15370' => 'vma', 'vmacro15371' => 'vma', 'vmacro15372' => 'vma', 'vmacro15373' => 'vma', 'vmacro15374' => 'vma', 'VMungo0720G2826' => 'vmu', 'Zm00001eb116960' => 'zma', 'Zm00001eb301260' => 'zma', 'Zm00001eb301270' => 'zma' ), 'gf_id' => 'HOM05D001460', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001460' ), 'data_identifier' => 'HOM05D001460', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001460', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '433', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p22980' => 'bna', 'A01p32340' => 'bna', 'A03p42970' => 'bna', 'A05p25880' => 'bna', 'Aa31LG8G9320' => 'aar', 'Aa31LG8G9330' => 'aar', 'Aa31LG8G9340' => 'aar', 'Aa31sc221G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1034' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1528' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.829' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2222' => 'aag', 'Ah.12g058830' => 'amhyb', 'Ah.12g058840' => 'amhyb', 'AL3G37160' => 'aly', 'AL7G41310' => 'aly', 'Aqoxy5G00395' => 'aox', 'Aqoxy5G00396' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0C8NZA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5185HY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JZ1PRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MD3LS0' => 'arhy', 'AT3G22840' => 'ath', 'AT4G14690' => 'ath', 'ATR0665G054' => 'atr', 'Atru.chr4.2344' => 'acertr', 'Atru.chr4.2346' => 'acertr', 'Atru.chr4.2347' => 'acertr', 'Atru.chr4.2348' => 'acertr', 'Atru.chr4.2355' => 'acertr', 'Atru.chr4.2356' => 'acertr', 'Atru.chr4.2358' => 'acertr', 'Atru.chr4.2359' => 'acertr', 'Atru.chr4.2360' => 'acertr', 'Atru.chr4.2361' => 'acertr', 'AUR62030476' => 'cqu', 'AUR62030478' => 'cqu', 'AUR62030819' => 'cqu', 'AUR62030820' => 'cqu', 'BcaB03g14648' => 'bca', 'BcaB04g20492' => 'bca', 'BcaB06g26399' => 'bca', 'BcaC01g03416' => 'bca', 'BcaC01g03419' => 'bca', 'BcaC01g03421' => 'bca', 'BcaC01g03424' => 'bca', 'BcaC05g28012' => 'bca', 'BcaC09g49212' => 'bca', 'BcaC09g50140' => 'bca', 'BcaNung00346' => 'bca', 'BolC1t02785H' => 'bol', 'BolC1t04095H' => 'bol', 'BolC3t17545H' => 'bol', 'BolC5t32769H' => 'bol', 'BraA01t02211Z' => 'bra', 'BraA01t03359Z' => 'bra', 'BraA03t13441Z' => 'bra', 'BraA05t21476Z' => 'bra', 'C01p28420' => 'bna', 'C01p41350' => 'bna', 'C03p52750' => 'bna', 'C03p52780' => 'bna', 'C05p40270' => 'bna', 'CAN.G1437.9' => 'can', 'CANSAT78G0035' => 'cansat', 'CANSAT78G1036' => 'cansat', 'CANSAT78G2272' => 'cansat', 'CANSAT78G2478' => 'cansat', 'CARHR098700' => 'chi', 'CARHR221120' => 'chi', 'CARHR221150' => 'chi', 'Carub.0003s2297' => 'cru', 'Carub.0007s2749' => 'cru', 'Carub.0007s2750' => 'cru', 'Carub.0007s2751' => 'cru', 'Ca_10849_v3' => 'car', 'Cc03_g04300' => 'ccan', 'CDE02G3648' => 'cde', 'CDE05G0060' => 'cde', 'CDE05G0692' => 'cde', 'CDE05G2285' => 'cde', 'CDE05G2884' => 'cde', 'CDE05G3072' => 'cde', 'Cfa008439' => 'cfa', 'Cfa008441' => 'cfa', 'Cfa008443' => 'cfa', 'Cfa008448' => 'cfa', 'Ciclev10005974m.g' => 'ccl', 'Ciclev10006006m.g' => 'ccl', 'Ciclev10006775m.g' => 'ccl', 'CiPaw.02G120400' => 'cil', 'CiPaw.02G120500' => 'cil', 'CiPaw.02G120600' => 'cil', 'ClCG05G004850' => 'cla', 'COL.COLO4_21566' => 'col', 'Cpa.g.sc44.124' => 'cpa', 'Cre07.g320400' => 'cre', 'Cre07.g320450' => 'cre', 'Cre08.g384650' => 'cre', 'Cre09.g393173' => 'cre', 'Cre09.g394325' => 'cre', 'Cre14.g626750' => 'cre', 'Cre16.g679250' => 'cre', 'CsaV3_3G012890' => 'csa', 'CSS0010865' => 'camsi', 'CSS0044338' => 'camsi', 'DCAR_002366' => 'dca', 'DCAR_030687' => 'dca', 'DCAR_030688' => 'dca', 'Dinv14047' => 'din', 'Dinv14048' => 'din', 'Duzib151G0105' => 'dzi', 'Duzib151G0114' => 'dzi', 'Duzib212G1029' => 'dzi', 'ECA232G3536' => 'eca', 'ECA240G0786' => 'eca', 'ECA240G1802' => 'eca', 'ECA240G3760' => 'eca', 'ECA240G3920' => 'eca', 'EL10Ac5g12536' => 'bvu', 'EL10Ac5g12537' => 'bvu', 'EL10Ac5g12538' => 'bvu', 'Eucgr.B01004' => 'egr', 'Eucgr.B01006' => 'egr', 'Eucgr.B01007' => 'egr', 'Eucgr.B01008' => 'egr', 'Eucgr.B01895' => 'egr', 'Eucgr.B01896' => 'egr', 'FAN04G1456' => 'fan', 'FAN08G1769' => 'fan', 'FAN08G2160' => 'fan', 'FAN13G2403' => 'fan', 'FAN13G3303' => 'fan', 'FAN15G2435' => 'fan', 'FAN17G0672' => 'fan', 'FAN17G2441' => 'fan', 'FAN18G1024' => 'fan', 'FAN22G1458' => 'fan', 'FAN24G0037' => 'fan', 'FAN24G0429' => 'fan', 'FAN24G2387' => 'fan', 'FAN27G2746' => 'fan', 'FvH4_2g20400' => 'fve', 'FvH4_2g20420' => 'fve', 'FvH4_2g20430' => 'fve', 'FvH4_4g01270' => 'fve', 'FvH4_4g01290' => 'fve', 'FvH4_4g01300' => 'fve', 'FvH4_4g01310' => 'fve', 'FvH4_4g01330' => 'fve', 'FvH4_5g09070' => 'fve', 'Glyma.10G243800' => 'gma', 'Glyma.20G150600' => 'gma', 'Gohir.A09G219200' => 'ghi', 'Gohir.A09G219300' => 'ghi', 'Gohir.D09G221400' => 'ghi', 'Gohir.D09G221500' => 'ghi', 'Gorai.006G242600' => 'gra', 'Gorai.006G242700' => 'gra', 'GSVIVG01018044001' => 'vvi', 'HanXRQChr03g0083821' => 'han', 'HanXRQChr03g0083841' => 'han', 'HanXRQChr03g0083881' => 'han', 'HanXRQChr03g0083901' => 'han', 'HanXRQChr03g0083921' => 'han', 'HanXRQChr03g0085331' => 'han', 'HanXRQChr03g0085361' => 'han', 'HanXRQChr03g0085411' => 'han', 'HanXRQChr03g0085421' => 'han', 'HanXRQChr03g0085431' => 'han', 'HanXRQChr08g0221991' => 'han', 'HanXRQChr11g0336061' => 'han', 'HanXRQChr11g0336411' => 'han', 'Haze_11234' => 'cav', 'Hma1.2p1_0549F.1_g177010' => 'hma', 'Hma1.2p1_0602F.1_g187630' => 'hma', 'Hund14876' => 'sun', 'Hund14879' => 'sun', 'Lalb_Chr06g0160741' => 'lal', 'Lalb_Chr21g0304781' => 'lal', 'Lj3A726G19' => 'lonja', 'Lj3A726T23' => 'lonja', 'Lj3A726T24' => 'lonja', 'Lj3A726T25' => 'lonja', 'Lj3A727T17' => 'lonja', 'Lj3C726T0' => 'lonja', 'Lj3C726T2' => 'lonja', 'Lj3P725T35' => 'lonja', 'Lj3P727T10' => 'lonja', 'Lj3P727T12' => 'lonja', 'Lj3P727T14' => 'lonja', 'Lj5g0023109' => 'lja', 'Lj6P646T44' => 'lonja', 'Lsat_1_v5_gn_6_75760' => 'lsa', 'Lsat_1_v5_gn_6_75800' => 'lsa', 'Lsat_1_v5_gn_6_75900' => 'lsa', 'Lsat_1_v5_gn_6_76240' => 'lsa', 'Lsat_1_v5_gn_6_76441' => 'lsa', 'Lsat_1_v5_gn_6_76700' => 'lsa', 'Lsat_1_v5_gn_6_76760' => 'lsa', 'Manes.15G033100' => 'mes', 'Mapoly0004s0074' => 'mpo', 'Mapoly0004s0075' => 'mpo', 'Mapoly0004s0163' => 'mpo', 'Mapoly0004s0164' => 'mpo', 'Mapoly0021s0018' => 'mpo', 'Mapoly0041s0136' => 'mpo', 'Mapoly0041s0137' => 'mpo', 'Mapoly0041s0138' => 'mpo', 'Mapoly0041s0139' => 'mpo', 'Mapoly0041s0141' => 'mpo', 'Mapoly0041s0142' => 'mpo', 'Mapoly0041s0143' => 'mpo', 'Mapoly0041s0144' => 'mpo', 'Mapoly0041s0145' => 'mpo', 'Mapoly0047s0106' => 'mpo', 'Mapoly0047s0108' => 'mpo', 'Mapoly0050s0051' => 'mpo', 'Mapoly0050s0052' => 'mpo', 'Mapoly0050s0053' => 'mpo', 'Mapoly0058s0013' => 'mpo', 'Mapoly0091s0078' => 'mpo', 'Mapoly0091s0079' => 'mpo', 'Mapoly0091s0080' => 'mpo', 'Mapoly0091s0081' => 'mpo', 'Mapoly0278s0004' => 'mpo', 'Mapoly0278s0005' => 'mpo', 'Mapoly0278s0006' => 'mpo', 'MBI11_g30648_MAGBIO' => 'mbi', 'MCO03G194' => 'mco', 'MCO03G590' => 'mco', 'MCO07G312' => 'mco', 'MCO10G318' => 'mco', 'MCO12G244' => 'mco', 'MCO13G148' => 'mco', 'MCO13G194' => 'mco', 'MCO16G238' => 'mco', 'MD06G1134100' => 'mdo', 'MD13G1200100' => 'mdo', 'MD13G1200300' => 'mdo', 'MD13G1200600' => 'mdo', 'MD14G1150400' => 'mdo', 'MD16G1200000' => 'mdo', 'Medtr1g102570' => 'mtr', 'Medtr1g102780' => 'mtr', 'Medtr1g102800' => 'mtr', 'Medtr1g102810' => 'mtr', 'Medtr1g102830' => 'mtr', 'MELO3C006499.2' => 'cme', 'Migut.G00385' => 'egut', 'MSTRG.4063' => 'ama', 'Nitab4.5_0000090g0260' => 'nta', 'Nitab4.5_0000977g0030' => 'nta', 'Nitab4.5_0002541g0040' => 'nta', 'Nitab4.5_0007068g0040' => 'nta', 'Nn005s41408' => 'nnu', 'Nn005s41410' => 'nnu', 'Oeu010310.1' => 'oeu', 'Oeu010311.1' => 'oeu', 'Oeu043472.1' => 'oeu', 'Os01g0246400' => 'osa', 'Os04g0267950' => 'osa', 'Os07g0178700' => 'osa', 'Os07g0178800' => 'osa', 'Peaxi162Scf00316g00046' => 'pax', 'Peaxi162Scf00316g00049' => 'pax', 'Peaxi162Scf00316g00059' => 'pax', 'Peaxi162Scf00316g00328' => 'pax', 'Peaxi162Scf00316g00329' => 'pax', 'Peaxi162Scf00316g00411' => 'pax', 'Peaxi162Scf00316g00521' => 'pax', 'Peaxi162Scf00492g00068' => 'pax', 'Peaxi162Scf35631g00002' => 'pax', 'PGR142G3720' => 'pgr', 'PGSC0003DMG400006442' => 'stu', 'Phvul.007G062000' => 'pvu', 'Potri.008G157750' => 'ptr', 'Potri.008G157900' => 'ptr', 'Potri.008G158000' => 'ptr', 'Potri.008G158200' => 'ptr', 'Pp3c11_7280' => 'ppa', 'Pp3c11_7980' => 'ppa', 'Pp3c12_19450' => 'ppa', 'Pp3c14_1480' => 'ppa', 'Pp3c14_1501' => 'ppa', 'Pp3c16_4900' => 'ppa', 'Pp3c16_5010' => 'ppa', 'Pp3c16_5060' => 'ppa', 'Pp3c19_18250' => 'ppa', 'Pp3c23_8530' => 'ppa', 'Pp3c23_8550' => 'ppa', 'Pp3c24_9670' => 'ppa', 'Pp3c2_21390' => 'ppa', 'Pp3c2_31380' => 'ppa', 'Pp3c3_16620' => 'ppa', 'Pp3c3_8090' => 'ppa', 'Pp3c3_8110' => 'ppa', 'Pp3c3_8130' => 'ppa', 'Pp3c3_8150' => 'ppa', 'Pp3c4_14320' => 'ppa', 'Pp3c6_2560' => 'ppa', 'Pp3c9_16700' => 'ppa', 'PRCOL_00000234' => 'pco', 'PRCOL_00000235' => 'pco', 'PRCOL_00000777' => 'pco', 'PRCOL_00002344' => 'pco', 'PRCOL_00002372' => 'pco', 'PRCOL_00006120' => 'pco', 'Prupe.1G021400' => 'ppe', 'Prupe.1G021500' => 'ppe', 'Prupe.1G021600' => 'ppe', 'Prupe.1G021700' => 'ppe', 'Prupe.1G021800' => 'ppe', 'Prupe.5G145100' => 'ppe', 'Psat6g204040' => 'psa', 'Psat6g204800' => 'psa', 'Psat6g204920' => 'psa', 'Psat6g204960' => 'psa', 'Psat6g205080' => 'psa', 'PSO017G0271' => 'pso', 'PSO017G1276' => 'pso', 'PSO017G1429' => 'pso', 'PSO017G1861' => 'pso', 'PSO017G2787' => 'pso', 'PSO017G4466' => 'pso', 'PSO017G5118' => 'pso', 'PSO017G5420' => 'pso', 'PSO063G3678' => 'pso', 'PSO210G0546' => 'pso', 'PSO317G0001' => 'pso', 'PSO357G0512' => 'pso', 'PSO478G2682' => 'pso', 'PSO647G0001' => 'pso', 'PSO675G0001' => 'pso', 'PSO675G2699' => 'pso', 'PSO675G2849' => 'pso', 'PSO675G4991' => 'pso', 'PSO689G0001' => 'pso', 'QL06p000916' => 'qlo', 'QL06p000921' => 'qlo', 'QL06p001398' => 'qlo', 'QL06p001407' => 'qlo', 'QL06p002031' => 'qlo', 'RcHm_v2.0_Chr4g0387791' => 'rch', 'RcHm_v2.0_Chr4g0387801' => 'rch', 'RcHm_v2.0_Chr6g0286501' => 'rch', 'RcHm_v2.0_Chr6g0286511' => 'rch', 'RcHm_v2.0_Chr6g0286521' => 'rch', 'RcHm_v2.0_Chr6g0286531' => 'rch', 'RcHm_v2.0_Chr7g0189141' => 'rch', 'Rhsim02G0028700' => 'rsi', 'Rhsim02G0028800' => 'rsi', 'Rhsim02G0028900' => 'rsi', 'Rhsim02G0029000' => 'rsi', 'Rhsim02G0029100' => 'rsi', 'Rhsim02G0029200' => 'rsi', 'Rhsim02G0029300' => 'rsi', 'Rhsim02G0029400' => 'rsi', 'Rhsim02G0029500' => 'rsi', 'Rhsim02G0029600' => 'rsi', 'RhsimUnG0024000' => 'rsi', 'RhsimUnG0024100' => 'rsi', 'RhsimUnG0024200' => 'rsi', 'RhsimUnG0024300' => 'rsi', 'RhsimUnG0024400' => 'rsi', 'RhsimUnG0024500' => 'rsi', 'RhsimUnG0024700' => 'rsi', 'RhsimUnG0024800' => 'rsi', 'RhsimUnG0024900' => 'rsi', 'RhsimUnG0025100' => 'rsi', 'Sabra08G0120200' => 'sbr', 'Sabra08G0120300' => 'sbr', 'Sabra08G0120500' => 'sbr', 'Sabra08G0120600' => 'sbr', 'Sabra10G0158900' => 'sbr', 'SalBow2G3492' => 'sbo', 'Sc13g0004760' => 'sci', 'Sc13g0004770' => 'sci', 'Sed0003417' => 'sed', 'Sed0019750' => 'sed', 'SEGI_03419' => 'sgi', 'SEGI_05907' => 'sgi', 'SEGI_10682' => 'sgi', 'SEGI_13528' => 'sgi', 'SEGI_16081' => 'sgi', 'SEGI_19370' => 'sgi', 'SEGI_21015' => 'sgi', 'SEGI_21944' => 'sgi', 'SEGI_32906' => 'sgi', 'SEGI_33093' => 'sgi', 'SEGI_36110' => 'sgi', 'SEGI_40397' => 'sgi', 'SGA_v2.0_scaffold191G40426' => 'sas', 'SGA_v2.0_scaffold353G49717' => 'sas', 'SGA_v2.0_scaffold50G18550' => 'sas', 'SMO119G0173' => 'smo', 'SMO172G0002' => 'smo', 'Solyc09g082690.3' => 'sly', 'Solyc09g082700.2' => 'sly', 'Sopen09g031550' => 'spe', 'Sopen09g031560' => 'spe', 'Sp3g20540' => 'spa', 'Sp7g07580' => 'spa', 'TAR134G0002' => 'tar', 'TAR236G0001' => 'tar', 'TAR365G0892' => 'tar', 'TAR636G0166' => 'tar', 'TAR636G0646' => 'tar', 'TAR636G0869' => 'tar', 'TAR636G1317' => 'tar', 'TAR636G1744' => 'tar', 'TAR636G3358' => 'tar', 'TAR636G3436' => 'tar', 'THA.LOC104803047' => 'tha', 'Thecc.04G238900' => 'tca', 'Thhalv10021557m.g' => 'esa', 'Thhalv10026318m.g' => 'esa', 'Thhalv10026335m.g' => 'esa', 'TPR.G17433' => 'tpr', 'TPR.G18915' => 'tpr', 'TPR.G26125' => 'tpr', 'TWI09G0677' => 'twi', 'TWI73G0287' => 'twi', 'unitig_748.g8326' => 'ugi', 'vmacro15370' => 'vma', 'vmacro15371' => 'vma', 'vmacro15372' => 'vma', 'vmacro15373' => 'vma', 'vmacro15374' => 'vma', 'VMungo0720G2826' => 'vmu', 'Zm00001eb116960' => 'zma', 'Zm00001eb301260' => 'zma', 'Zm00001eb301270' => 'zma' ) $gf_id = 'HOM05D001460' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001460' ) $data_identifier = 'HOM05D001460' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 4, 'aag' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 2, 'aox' => (int) 2, 'arhy' => (int) 4, 'ath' => (int) 2, 'atr' => (int) 1, 'acertr' => (int) 10, 'cqu' => (int) 4, 'bca' => (int) 11, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 1, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 1, 'ccan' => (int) 1, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 1, 'col' => (int) 1, 'cpa' => (int) 1, 'cre' => (int) 7, 'csa' => (int) 1, 'camsi' => (int) 2, 'dca' => (int) 3, 'din' => (int) 2, 'dzi' => (int) 3, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 14, 'fve' => (int) 9, 'gma' => (int) 2, 'ghi' => (int) 4, 'gra' => (int) 2, 'vvi' => (int) 1, 'han' => (int) 13, 'cav' => (int) 1, 'hma' => (int) 2, 'sun' => (int) 2, 'lal' => (int) 2, 'lonja' => (int) 12, 'lja' => (int) 1, 'lsa' => (int) 7, 'mes' => (int) 1, 'mpo' => (int) 27, 'mbi' => (int) 1, 'mco' => (int) 8, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 1, 'egut' => (int) 1, 'ama' => (int) 1, 'nta' => (int) 4, 'nnu' => (int) 2, 'oeu' => (int) 3, 'osa' => (int) 4, 'pax' => (int) 9, 'pgr' => (int) 1, 'stu' => (int) 1, 'pvu' => (int) 1, 'ptr' => (int) 4, 'ppa' => (int) 22, 'pco' => (int) 6, 'ppe' => (int) 6, 'psa' => (int) 5, 'pso' => (int) 19, 'qlo' => (int) 5, 'rch' => (int) 7, 'rsi' => (int) 20, 'sbr' => (int) 5, 'sbo' => (int) 1, 'sci' => (int) 2, 'sed' => (int) 2, 'sgi' => (int) 12, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 2, 'tar' => (int) 10, 'tha' => (int) 1, 'tca' => (int) 1, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 2, 'ugi' => (int) 1, 'vma' => (int) 5, 'vmu' => (int) 1, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb301270' $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' => 'HOM05D001460', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '433', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p22980' => 'bna', 'A01p32340' => 'bna', 'A03p42970' => 'bna', 'A05p25880' => 'bna', 'Aa31LG8G9320' => 'aar', 'Aa31LG8G9330' => 'aar', 'Aa31LG8G9340' => 'aar', 'Aa31sc221G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1034' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1528' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.829' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2222' => 'aag', 'Ah.12g058830' => 'amhyb', 'Ah.12g058840' => 'amhyb', 'AL3G37160' => 'aly', 'AL7G41310' => 'aly', 'Aqoxy5G00395' => 'aox', 'Aqoxy5G00396' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0C8NZA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5185HY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JZ1PRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MD3LS0' => 'arhy', 'AT3G22840' => 'ath', 'AT4G14690' => 'ath', 'ATR0665G054' => 'atr', 'Atru.chr4.2344' => 'acertr', 'Atru.chr4.2346' => 'acertr', 'Atru.chr4.2347' => 'acertr', 'Atru.chr4.2348' => 'acertr', 'Atru.chr4.2355' => 'acertr', 'Atru.chr4.2356' => 'acertr', 'Atru.chr4.2358' => 'acertr', 'Atru.chr4.2359' => 'acertr', 'Atru.chr4.2360' => 'acertr', 'Atru.chr4.2361' => 'acertr', 'AUR62030476' => 'cqu', 'AUR62030478' => 'cqu', 'AUR62030819' => 'cqu', 'AUR62030820' => 'cqu', 'BcaB03g14648' => 'bca', 'BcaB04g20492' => 'bca', 'BcaB06g26399' => 'bca', 'BcaC01g03416' => 'bca', 'BcaC01g03419' => 'bca', 'BcaC01g03421' => 'bca', 'BcaC01g03424' => 'bca', 'BcaC05g28012' => 'bca', 'BcaC09g49212' => 'bca', 'BcaC09g50140' => 'bca', 'BcaNung00346' => 'bca', 'BolC1t02785H' => 'bol', 'BolC1t04095H' => 'bol', 'BolC3t17545H' => 'bol', 'BolC5t32769H' => 'bol', 'BraA01t02211Z' => 'bra', 'BraA01t03359Z' => 'bra', 'BraA03t13441Z' => 'bra', 'BraA05t21476Z' => 'bra', 'C01p28420' => 'bna', 'C01p41350' => 'bna', 'C03p52750' => 'bna', 'C03p52780' => 'bna', 'C05p40270' => 'bna', 'CAN.G1437.9' => 'can', 'CANSAT78G0035' => 'cansat', 'CANSAT78G1036' => 'cansat', 'CANSAT78G2272' => 'cansat', 'CANSAT78G2478' => 'cansat', 'CARHR098700' => 'chi', 'CARHR221120' => 'chi', 'CARHR221150' => 'chi', 'Carub.0003s2297' => 'cru', 'Carub.0007s2749' => 'cru', 'Carub.0007s2750' => 'cru', 'Carub.0007s2751' => 'cru', 'Ca_10849_v3' => 'car', 'Cc03_g04300' => 'ccan', 'CDE02G3648' => 'cde', 'CDE05G0060' => 'cde', 'CDE05G0692' => 'cde', 'CDE05G2285' => 'cde', 'CDE05G2884' => 'cde', 'CDE05G3072' => 'cde', 'Cfa008439' => 'cfa', 'Cfa008441' => 'cfa', 'Cfa008443' => 'cfa', 'Cfa008448' => 'cfa', 'Ciclev10005974m.g' => 'ccl', 'Ciclev10006006m.g' => 'ccl', 'Ciclev10006775m.g' => 'ccl', 'CiPaw.02G120400' => 'cil', 'CiPaw.02G120500' => 'cil', 'CiPaw.02G120600' => 'cil', 'ClCG05G004850' => 'cla', 'COL.COLO4_21566' => 'col', 'Cpa.g.sc44.124' => 'cpa', 'Cre07.g320400' => 'cre', 'Cre07.g320450' => 'cre', 'Cre08.g384650' => 'cre', 'Cre09.g393173' => 'cre', 'Cre09.g394325' => 'cre', 'Cre14.g626750' => 'cre', 'Cre16.g679250' => 'cre', 'CsaV3_3G012890' => 'csa', 'CSS0010865' => 'camsi', 'CSS0044338' => 'camsi', 'DCAR_002366' => 'dca', 'DCAR_030687' => 'dca', 'DCAR_030688' => 'dca', 'Dinv14047' => 'din', 'Dinv14048' => 'din', 'Duzib151G0105' => 'dzi', 'Duzib151G0114' => 'dzi', 'Duzib212G1029' => 'dzi', 'ECA232G3536' => 'eca', 'ECA240G0786' => 'eca', 'ECA240G1802' => 'eca', 'ECA240G3760' => 'eca', 'ECA240G3920' => 'eca', 'EL10Ac5g12536' => 'bvu', 'EL10Ac5g12537' => 'bvu', 'EL10Ac5g12538' => 'bvu', 'Eucgr.B01004' => 'egr', 'Eucgr.B01006' => 'egr', 'Eucgr.B01007' => 'egr', 'Eucgr.B01008' => 'egr', 'Eucgr.B01895' => 'egr', 'Eucgr.B01896' => 'egr', 'FAN04G1456' => 'fan', 'FAN08G1769' => 'fan', 'FAN08G2160' => 'fan', 'FAN13G2403' => 'fan', 'FAN13G3303' => 'fan', 'FAN15G2435' => 'fan', 'FAN17G0672' => 'fan', 'FAN17G2441' => 'fan', 'FAN18G1024' => 'fan', 'FAN22G1458' => 'fan', 'FAN24G0037' => 'fan', 'FAN24G0429' => 'fan', 'FAN24G2387' => 'fan', 'FAN27G2746' => 'fan', 'FvH4_2g20400' => 'fve', 'FvH4_2g20420' => 'fve', 'FvH4_2g20430' => 'fve', 'FvH4_4g01270' => 'fve', 'FvH4_4g01290' => 'fve', 'FvH4_4g01300' => 'fve', 'FvH4_4g01310' => 'fve', 'FvH4_4g01330' => 'fve', 'FvH4_5g09070' => 'fve', 'Glyma.10G243800' => 'gma', 'Glyma.20G150600' => 'gma', 'Gohir.A09G219200' => 'ghi', 'Gohir.A09G219300' => 'ghi', 'Gohir.D09G221400' => 'ghi', 'Gohir.D09G221500' => 'ghi', 'Gorai.006G242600' => 'gra', 'Gorai.006G242700' => 'gra', 'GSVIVG01018044001' => 'vvi', 'HanXRQChr03g0083821' => 'han', 'HanXRQChr03g0083841' => 'han', 'HanXRQChr03g0083881' => 'han', 'HanXRQChr03g0083901' => 'han', 'HanXRQChr03g0083921' => 'han', 'HanXRQChr03g0085331' => 'han', 'HanXRQChr03g0085361' => 'han', 'HanXRQChr03g0085411' => 'han', 'HanXRQChr03g0085421' => 'han', 'HanXRQChr03g0085431' => 'han', 'HanXRQChr08g0221991' => 'han', 'HanXRQChr11g0336061' => 'han', 'HanXRQChr11g0336411' => 'han', 'Haze_11234' => 'cav', 'Hma1.2p1_0549F.1_g177010' => 'hma', 'Hma1.2p1_0602F.1_g187630' => 'hma', 'Hund14876' => 'sun', 'Hund14879' => 'sun', 'Lalb_Chr06g0160741' => 'lal', 'Lalb_Chr21g0304781' => 'lal', 'Lj3A726G19' => 'lonja', 'Lj3A726T23' => 'lonja', 'Lj3A726T24' => 'lonja', 'Lj3A726T25' => 'lonja', 'Lj3A727T17' => 'lonja', 'Lj3C726T0' => 'lonja', 'Lj3C726T2' => 'lonja', 'Lj3P725T35' => 'lonja', 'Lj3P727T10' => 'lonja', 'Lj3P727T12' => 'lonja', 'Lj3P727T14' => 'lonja', 'Lj5g0023109' => 'lja', 'Lj6P646T44' => 'lonja', 'Lsat_1_v5_gn_6_75760' => 'lsa', 'Lsat_1_v5_gn_6_75800' => 'lsa', 'Lsat_1_v5_gn_6_75900' => 'lsa', 'Lsat_1_v5_gn_6_76240' => 'lsa', 'Lsat_1_v5_gn_6_76441' => 'lsa', 'Lsat_1_v5_gn_6_76700' => 'lsa', 'Lsat_1_v5_gn_6_76760' => 'lsa', 'Manes.15G033100' => 'mes', 'Mapoly0004s0074' => 'mpo', 'Mapoly0004s0075' => 'mpo', 'Mapoly0004s0163' => 'mpo', 'Mapoly0004s0164' => 'mpo', 'Mapoly0021s0018' => 'mpo', 'Mapoly0041s0136' => 'mpo', 'Mapoly0041s0137' => 'mpo', 'Mapoly0041s0138' => 'mpo', 'Mapoly0041s0139' => 'mpo', 'Mapoly0041s0141' => 'mpo', 'Mapoly0041s0142' => 'mpo', 'Mapoly0041s0143' => 'mpo', 'Mapoly0041s0144' => 'mpo', 'Mapoly0041s0145' => 'mpo', 'Mapoly0047s0106' => 'mpo', 'Mapoly0047s0108' => 'mpo', 'Mapoly0050s0051' => 'mpo', 'Mapoly0050s0052' => 'mpo', 'Mapoly0050s0053' => 'mpo', 'Mapoly0058s0013' => 'mpo', 'Mapoly0091s0078' => 'mpo', 'Mapoly0091s0079' => 'mpo', 'Mapoly0091s0080' => 'mpo', 'Mapoly0091s0081' => 'mpo', 'Mapoly0278s0004' => 'mpo', 'Mapoly0278s0005' => 'mpo', 'Mapoly0278s0006' => 'mpo', 'MBI11_g30648_MAGBIO' => 'mbi', 'MCO03G194' => 'mco', 'MCO03G590' => 'mco', 'MCO07G312' => 'mco', 'MCO10G318' => 'mco', 'MCO12G244' => 'mco', 'MCO13G148' => 'mco', 'MCO13G194' => 'mco', 'MCO16G238' => 'mco', 'MD06G1134100' => 'mdo', 'MD13G1200100' => 'mdo', 'MD13G1200300' => 'mdo', 'MD13G1200600' => 'mdo', 'MD14G1150400' => 'mdo', 'MD16G1200000' => 'mdo', 'Medtr1g102570' => 'mtr', 'Medtr1g102780' => 'mtr', 'Medtr1g102800' => 'mtr', 'Medtr1g102810' => 'mtr', 'Medtr1g102830' => 'mtr', 'MELO3C006499.2' => 'cme', 'Migut.G00385' => 'egut', 'MSTRG.4063' => 'ama', 'Nitab4.5_0000090g0260' => 'nta', 'Nitab4.5_0000977g0030' => 'nta', 'Nitab4.5_0002541g0040' => 'nta', 'Nitab4.5_0007068g0040' => 'nta', 'Nn005s41408' => 'nnu', 'Nn005s41410' => 'nnu', 'Oeu010310.1' => 'oeu', 'Oeu010311.1' => 'oeu', 'Oeu043472.1' => 'oeu', 'Os01g0246400' => 'osa', 'Os04g0267950' => 'osa', 'Os07g0178700' => 'osa', 'Os07g0178800' => 'osa', 'Peaxi162Scf00316g00046' => 'pax', 'Peaxi162Scf00316g00049' => 'pax', 'Peaxi162Scf00316g00059' => 'pax', 'Peaxi162Scf00316g00328' => 'pax', 'Peaxi162Scf00316g00329' => 'pax', 'Peaxi162Scf00316g00411' => 'pax', 'Peaxi162Scf00316g00521' => 'pax', 'Peaxi162Scf00492g00068' => 'pax', 'Peaxi162Scf35631g00002' => 'pax', 'PGR142G3720' => 'pgr', 'PGSC0003DMG400006442' => 'stu', 'Phvul.007G062000' => 'pvu', 'Potri.008G157750' => 'ptr', 'Potri.008G157900' => 'ptr', 'Potri.008G158000' => 'ptr', 'Potri.008G158200' => 'ptr', 'Pp3c11_7280' => 'ppa', 'Pp3c11_7980' => 'ppa', 'Pp3c12_19450' => 'ppa', 'Pp3c14_1480' => 'ppa', 'Pp3c14_1501' => 'ppa', 'Pp3c16_4900' => 'ppa', 'Pp3c16_5010' => 'ppa', 'Pp3c16_5060' => 'ppa', 'Pp3c19_18250' => 'ppa', 'Pp3c23_8530' => 'ppa', 'Pp3c23_8550' => 'ppa', 'Pp3c24_9670' => 'ppa', 'Pp3c2_21390' => 'ppa', 'Pp3c2_31380' => 'ppa', 'Pp3c3_16620' => 'ppa', 'Pp3c3_8090' => 'ppa', 'Pp3c3_8110' => 'ppa', 'Pp3c3_8130' => 'ppa', 'Pp3c3_8150' => 'ppa', 'Pp3c4_14320' => 'ppa', 'Pp3c6_2560' => 'ppa', 'Pp3c9_16700' => 'ppa', 'PRCOL_00000234' => 'pco', 'PRCOL_00000235' => 'pco', 'PRCOL_00000777' => 'pco', 'PRCOL_00002344' => 'pco', 'PRCOL_00002372' => 'pco', 'PRCOL_00006120' => 'pco', 'Prupe.1G021400' => 'ppe', 'Prupe.1G021500' => 'ppe', 'Prupe.1G021600' => 'ppe', 'Prupe.1G021700' => 'ppe', 'Prupe.1G021800' => 'ppe', 'Prupe.5G145100' => 'ppe', 'Psat6g204040' => 'psa', 'Psat6g204800' => 'psa', 'Psat6g204920' => 'psa', 'Psat6g204960' => 'psa', 'Psat6g205080' => 'psa', 'PSO017G0271' => 'pso', 'PSO017G1276' => 'pso', 'PSO017G1429' => 'pso', 'PSO017G1861' => 'pso', 'PSO017G2787' => 'pso', 'PSO017G4466' => 'pso', 'PSO017G5118' => 'pso', 'PSO017G5420' => 'pso', 'PSO063G3678' => 'pso', 'PSO210G0546' => 'pso', 'PSO317G0001' => 'pso', 'PSO357G0512' => 'pso', 'PSO478G2682' => 'pso', 'PSO647G0001' => 'pso', 'PSO675G0001' => 'pso', 'PSO675G2699' => 'pso', 'PSO675G2849' => 'pso', 'PSO675G4991' => 'pso', 'PSO689G0001' => 'pso', 'QL06p000916' => 'qlo', 'QL06p000921' => 'qlo', 'QL06p001398' => 'qlo', 'QL06p001407' => 'qlo', 'QL06p002031' => 'qlo', 'RcHm_v2.0_Chr4g0387791' => 'rch', 'RcHm_v2.0_Chr4g0387801' => 'rch', 'RcHm_v2.0_Chr6g0286501' => 'rch', 'RcHm_v2.0_Chr6g0286511' => 'rch', 'RcHm_v2.0_Chr6g0286521' => 'rch', 'RcHm_v2.0_Chr6g0286531' => 'rch', 'RcHm_v2.0_Chr7g0189141' => 'rch', 'Rhsim02G0028700' => 'rsi', 'Rhsim02G0028800' => 'rsi', 'Rhsim02G0028900' => 'rsi', 'Rhsim02G0029000' => 'rsi', 'Rhsim02G0029100' => 'rsi', 'Rhsim02G0029200' => 'rsi', 'Rhsim02G0029300' => 'rsi', 'Rhsim02G0029400' => 'rsi', 'Rhsim02G0029500' => 'rsi', 'Rhsim02G0029600' => 'rsi', 'RhsimUnG0024000' => 'rsi', 'RhsimUnG0024100' => 'rsi', 'RhsimUnG0024200' => 'rsi', 'RhsimUnG0024300' => 'rsi', 'RhsimUnG0024400' => 'rsi', 'RhsimUnG0024500' => 'rsi', 'RhsimUnG0024700' => 'rsi', 'RhsimUnG0024800' => 'rsi', 'RhsimUnG0024900' => 'rsi', 'RhsimUnG0025100' => 'rsi', 'Sabra08G0120200' => 'sbr', 'Sabra08G0120300' => 'sbr', 'Sabra08G0120500' => 'sbr', 'Sabra08G0120600' => 'sbr', 'Sabra10G0158900' => 'sbr', 'SalBow2G3492' => 'sbo', 'Sc13g0004760' => 'sci', 'Sc13g0004770' => 'sci', 'Sed0003417' => 'sed', 'Sed0019750' => 'sed', 'SEGI_03419' => 'sgi', 'SEGI_05907' => 'sgi', 'SEGI_10682' => 'sgi', 'SEGI_13528' => 'sgi', 'SEGI_16081' => 'sgi', 'SEGI_19370' => 'sgi', 'SEGI_21015' => 'sgi', 'SEGI_21944' => 'sgi', 'SEGI_32906' => 'sgi', 'SEGI_33093' => 'sgi', 'SEGI_36110' => 'sgi', 'SEGI_40397' => 'sgi', 'SGA_v2.0_scaffold191G40426' => 'sas', 'SGA_v2.0_scaffold353G49717' => 'sas', 'SGA_v2.0_scaffold50G18550' => 'sas', 'SMO119G0173' => 'smo', 'SMO172G0002' => 'smo', 'Solyc09g082690.3' => 'sly', 'Solyc09g082700.2' => 'sly', 'Sopen09g031550' => 'spe', 'Sopen09g031560' => 'spe', 'Sp3g20540' => 'spa', 'Sp7g07580' => 'spa', 'TAR134G0002' => 'tar', 'TAR236G0001' => 'tar', 'TAR365G0892' => 'tar', 'TAR636G0166' => 'tar', 'TAR636G0646' => 'tar', 'TAR636G0869' => 'tar', 'TAR636G1317' => 'tar', 'TAR636G1744' => 'tar', 'TAR636G3358' => 'tar', 'TAR636G3436' => 'tar', 'THA.LOC104803047' => 'tha', 'Thecc.04G238900' => 'tca', 'Thhalv10021557m.g' => 'esa', 'Thhalv10026318m.g' => 'esa', 'Thhalv10026335m.g' => 'esa', 'TPR.G17433' => 'tpr', 'TPR.G18915' => 'tpr', 'TPR.G26125' => 'tpr', 'TWI09G0677' => 'twi', 'TWI73G0287' => 'twi', 'unitig_748.g8326' => 'ugi', 'vmacro15370' => 'vma', 'vmacro15371' => 'vma', 'vmacro15372' => 'vma', 'vmacro15373' => 'vma', 'vmacro15374' => 'vma', 'VMungo0720G2826' => 'vmu', 'Zm00001eb116960' => 'zma', 'Zm00001eb301260' => 'zma', 'Zm00001eb301270' => 'zma' ), 'gf_id' => 'HOM05D001460', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001460' ), 'data_identifier' => 'HOM05D001460', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001460', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '433', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p22980' => 'bna', 'A01p32340' => 'bna', 'A03p42970' => 'bna', 'A05p25880' => 'bna', 'Aa31LG8G9320' => 'aar', 'Aa31LG8G9330' => 'aar', 'Aa31LG8G9340' => 'aar', 'Aa31sc221G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1034' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1528' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.829' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2222' => 'aag', 'Ah.12g058830' => 'amhyb', 'Ah.12g058840' => 'amhyb', 'AL3G37160' => 'aly', 'AL7G41310' => 'aly', 'Aqoxy5G00395' => 'aox', 'Aqoxy5G00396' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0C8NZA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5185HY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JZ1PRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MD3LS0' => 'arhy', 'AT3G22840' => 'ath', 'AT4G14690' => 'ath', 'ATR0665G054' => 'atr', 'Atru.chr4.2344' => 'acertr', 'Atru.chr4.2346' => 'acertr', 'Atru.chr4.2347' => 'acertr', 'Atru.chr4.2348' => 'acertr', 'Atru.chr4.2355' => 'acertr', 'Atru.chr4.2356' => 'acertr', 'Atru.chr4.2358' => 'acertr', 'Atru.chr4.2359' => 'acertr', 'Atru.chr4.2360' => 'acertr', 'Atru.chr4.2361' => 'acertr', 'AUR62030476' => 'cqu', 'AUR62030478' => 'cqu', 'AUR62030819' => 'cqu', 'AUR62030820' => 'cqu', 'BcaB03g14648' => 'bca', 'BcaB04g20492' => 'bca', 'BcaB06g26399' => 'bca', 'BcaC01g03416' => 'bca', 'BcaC01g03419' => 'bca', 'BcaC01g03421' => 'bca', 'BcaC01g03424' => 'bca', 'BcaC05g28012' => 'bca', 'BcaC09g49212' => 'bca', 'BcaC09g50140' => 'bca', 'BcaNung00346' => 'bca', 'BolC1t02785H' => 'bol', 'BolC1t04095H' => 'bol', 'BolC3t17545H' => 'bol', 'BolC5t32769H' => 'bol', 'BraA01t02211Z' => 'bra', 'BraA01t03359Z' => 'bra', 'BraA03t13441Z' => 'bra', 'BraA05t21476Z' => 'bra', 'C01p28420' => 'bna', 'C01p41350' => 'bna', 'C03p52750' => 'bna', 'C03p52780' => 'bna', 'C05p40270' => 'bna', 'CAN.G1437.9' => 'can', 'CANSAT78G0035' => 'cansat', 'CANSAT78G1036' => 'cansat', 'CANSAT78G2272' => 'cansat', 'CANSAT78G2478' => 'cansat', 'CARHR098700' => 'chi', 'CARHR221120' => 'chi', 'CARHR221150' => 'chi', 'Carub.0003s2297' => 'cru', 'Carub.0007s2749' => 'cru', 'Carub.0007s2750' => 'cru', 'Carub.0007s2751' => 'cru', 'Ca_10849_v3' => 'car', 'Cc03_g04300' => 'ccan', 'CDE02G3648' => 'cde', 'CDE05G0060' => 'cde', 'CDE05G0692' => 'cde', 'CDE05G2285' => 'cde', 'CDE05G2884' => 'cde', 'CDE05G3072' => 'cde', 'Cfa008439' => 'cfa', 'Cfa008441' => 'cfa', 'Cfa008443' => 'cfa', 'Cfa008448' => 'cfa', 'Ciclev10005974m.g' => 'ccl', 'Ciclev10006006m.g' => 'ccl', 'Ciclev10006775m.g' => 'ccl', 'CiPaw.02G120400' => 'cil', 'CiPaw.02G120500' => 'cil', 'CiPaw.02G120600' => 'cil', 'ClCG05G004850' => 'cla', 'COL.COLO4_21566' => 'col', 'Cpa.g.sc44.124' => 'cpa', 'Cre07.g320400' => 'cre', 'Cre07.g320450' => 'cre', 'Cre08.g384650' => 'cre', 'Cre09.g393173' => 'cre', 'Cre09.g394325' => 'cre', 'Cre14.g626750' => 'cre', 'Cre16.g679250' => 'cre', 'CsaV3_3G012890' => 'csa', 'CSS0010865' => 'camsi', 'CSS0044338' => 'camsi', 'DCAR_002366' => 'dca', 'DCAR_030687' => 'dca', 'DCAR_030688' => 'dca', 'Dinv14047' => 'din', 'Dinv14048' => 'din', 'Duzib151G0105' => 'dzi', 'Duzib151G0114' => 'dzi', 'Duzib212G1029' => 'dzi', 'ECA232G3536' => 'eca', 'ECA240G0786' => 'eca', 'ECA240G1802' => 'eca', 'ECA240G3760' => 'eca', 'ECA240G3920' => 'eca', 'EL10Ac5g12536' => 'bvu', 'EL10Ac5g12537' => 'bvu', 'EL10Ac5g12538' => 'bvu', 'Eucgr.B01004' => 'egr', 'Eucgr.B01006' => 'egr', 'Eucgr.B01007' => 'egr', 'Eucgr.B01008' => 'egr', 'Eucgr.B01895' => 'egr', 'Eucgr.B01896' => 'egr', 'FAN04G1456' => 'fan', 'FAN08G1769' => 'fan', 'FAN08G2160' => 'fan', 'FAN13G2403' => 'fan', 'FAN13G3303' => 'fan', 'FAN15G2435' => 'fan', 'FAN17G0672' => 'fan', 'FAN17G2441' => 'fan', 'FAN18G1024' => 'fan', 'FAN22G1458' => 'fan', 'FAN24G0037' => 'fan', 'FAN24G0429' => 'fan', 'FAN24G2387' => 'fan', 'FAN27G2746' => 'fan', 'FvH4_2g20400' => 'fve', 'FvH4_2g20420' => 'fve', 'FvH4_2g20430' => 'fve', 'FvH4_4g01270' => 'fve', 'FvH4_4g01290' => 'fve', 'FvH4_4g01300' => 'fve', 'FvH4_4g01310' => 'fve', 'FvH4_4g01330' => 'fve', 'FvH4_5g09070' => 'fve', 'Glyma.10G243800' => 'gma', 'Glyma.20G150600' => 'gma', 'Gohir.A09G219200' => 'ghi', 'Gohir.A09G219300' => 'ghi', 'Gohir.D09G221400' => 'ghi', 'Gohir.D09G221500' => 'ghi', 'Gorai.006G242600' => 'gra', 'Gorai.006G242700' => 'gra', 'GSVIVG01018044001' => 'vvi', 'HanXRQChr03g0083821' => 'han', 'HanXRQChr03g0083841' => 'han', 'HanXRQChr03g0083881' => 'han', 'HanXRQChr03g0083901' => 'han', 'HanXRQChr03g0083921' => 'han', 'HanXRQChr03g0085331' => 'han', 'HanXRQChr03g0085361' => 'han', 'HanXRQChr03g0085411' => 'han', 'HanXRQChr03g0085421' => 'han', 'HanXRQChr03g0085431' => 'han', 'HanXRQChr08g0221991' => 'han', 'HanXRQChr11g0336061' => 'han', 'HanXRQChr11g0336411' => 'han', 'Haze_11234' => 'cav', 'Hma1.2p1_0549F.1_g177010' => 'hma', 'Hma1.2p1_0602F.1_g187630' => 'hma', 'Hund14876' => 'sun', 'Hund14879' => 'sun', 'Lalb_Chr06g0160741' => 'lal', 'Lalb_Chr21g0304781' => 'lal', 'Lj3A726G19' => 'lonja', 'Lj3A726T23' => 'lonja', 'Lj3A726T24' => 'lonja', 'Lj3A726T25' => 'lonja', 'Lj3A727T17' => 'lonja', 'Lj3C726T0' => 'lonja', 'Lj3C726T2' => 'lonja', 'Lj3P725T35' => 'lonja', 'Lj3P727T10' => 'lonja', 'Lj3P727T12' => 'lonja', 'Lj3P727T14' => 'lonja', 'Lj5g0023109' => 'lja', 'Lj6P646T44' => 'lonja', 'Lsat_1_v5_gn_6_75760' => 'lsa', 'Lsat_1_v5_gn_6_75800' => 'lsa', 'Lsat_1_v5_gn_6_75900' => 'lsa', 'Lsat_1_v5_gn_6_76240' => 'lsa', 'Lsat_1_v5_gn_6_76441' => 'lsa', 'Lsat_1_v5_gn_6_76700' => 'lsa', 'Lsat_1_v5_gn_6_76760' => 'lsa', 'Manes.15G033100' => 'mes', 'Mapoly0004s0074' => 'mpo', 'Mapoly0004s0075' => 'mpo', 'Mapoly0004s0163' => 'mpo', 'Mapoly0004s0164' => 'mpo', 'Mapoly0021s0018' => 'mpo', 'Mapoly0041s0136' => 'mpo', 'Mapoly0041s0137' => 'mpo', 'Mapoly0041s0138' => 'mpo', 'Mapoly0041s0139' => 'mpo', 'Mapoly0041s0141' => 'mpo', 'Mapoly0041s0142' => 'mpo', 'Mapoly0041s0143' => 'mpo', 'Mapoly0041s0144' => 'mpo', 'Mapoly0041s0145' => 'mpo', 'Mapoly0047s0106' => 'mpo', 'Mapoly0047s0108' => 'mpo', 'Mapoly0050s0051' => 'mpo', 'Mapoly0050s0052' => 'mpo', 'Mapoly0050s0053' => 'mpo', 'Mapoly0058s0013' => 'mpo', 'Mapoly0091s0078' => 'mpo', 'Mapoly0091s0079' => 'mpo', 'Mapoly0091s0080' => 'mpo', 'Mapoly0091s0081' => 'mpo', 'Mapoly0278s0004' => 'mpo', 'Mapoly0278s0005' => 'mpo', 'Mapoly0278s0006' => 'mpo', 'MBI11_g30648_MAGBIO' => 'mbi', 'MCO03G194' => 'mco', 'MCO03G590' => 'mco', 'MCO07G312' => 'mco', 'MCO10G318' => 'mco', 'MCO12G244' => 'mco', 'MCO13G148' => 'mco', 'MCO13G194' => 'mco', 'MCO16G238' => 'mco', 'MD06G1134100' => 'mdo', 'MD13G1200100' => 'mdo', 'MD13G1200300' => 'mdo', 'MD13G1200600' => 'mdo', 'MD14G1150400' => 'mdo', 'MD16G1200000' => 'mdo', 'Medtr1g102570' => 'mtr', 'Medtr1g102780' => 'mtr', 'Medtr1g102800' => 'mtr', 'Medtr1g102810' => 'mtr', 'Medtr1g102830' => 'mtr', 'MELO3C006499.2' => 'cme', 'Migut.G00385' => 'egut', 'MSTRG.4063' => 'ama', 'Nitab4.5_0000090g0260' => 'nta', 'Nitab4.5_0000977g0030' => 'nta', 'Nitab4.5_0002541g0040' => 'nta', 'Nitab4.5_0007068g0040' => 'nta', 'Nn005s41408' => 'nnu', 'Nn005s41410' => 'nnu', 'Oeu010310.1' => 'oeu', 'Oeu010311.1' => 'oeu', 'Oeu043472.1' => 'oeu', 'Os01g0246400' => 'osa', 'Os04g0267950' => 'osa', 'Os07g0178700' => 'osa', 'Os07g0178800' => 'osa', 'Peaxi162Scf00316g00046' => 'pax', 'Peaxi162Scf00316g00049' => 'pax', 'Peaxi162Scf00316g00059' => 'pax', 'Peaxi162Scf00316g00328' => 'pax', 'Peaxi162Scf00316g00329' => 'pax', 'Peaxi162Scf00316g00411' => 'pax', 'Peaxi162Scf00316g00521' => 'pax', 'Peaxi162Scf00492g00068' => 'pax', 'Peaxi162Scf35631g00002' => 'pax', 'PGR142G3720' => 'pgr', 'PGSC0003DMG400006442' => 'stu', 'Phvul.007G062000' => 'pvu', 'Potri.008G157750' => 'ptr', 'Potri.008G157900' => 'ptr', 'Potri.008G158000' => 'ptr', 'Potri.008G158200' => 'ptr', 'Pp3c11_7280' => 'ppa', 'Pp3c11_7980' => 'ppa', 'Pp3c12_19450' => 'ppa', 'Pp3c14_1480' => 'ppa', 'Pp3c14_1501' => 'ppa', 'Pp3c16_4900' => 'ppa', 'Pp3c16_5010' => 'ppa', 'Pp3c16_5060' => 'ppa', 'Pp3c19_18250' => 'ppa', 'Pp3c23_8530' => 'ppa', 'Pp3c23_8550' => 'ppa', 'Pp3c24_9670' => 'ppa', 'Pp3c2_21390' => 'ppa', 'Pp3c2_31380' => 'ppa', 'Pp3c3_16620' => 'ppa', 'Pp3c3_8090' => 'ppa', 'Pp3c3_8110' => 'ppa', 'Pp3c3_8130' => 'ppa', 'Pp3c3_8150' => 'ppa', 'Pp3c4_14320' => 'ppa', 'Pp3c6_2560' => 'ppa', 'Pp3c9_16700' => 'ppa', 'PRCOL_00000234' => 'pco', 'PRCOL_00000235' => 'pco', 'PRCOL_00000777' => 'pco', 'PRCOL_00002344' => 'pco', 'PRCOL_00002372' => 'pco', 'PRCOL_00006120' => 'pco', 'Prupe.1G021400' => 'ppe', 'Prupe.1G021500' => 'ppe', 'Prupe.1G021600' => 'ppe', 'Prupe.1G021700' => 'ppe', 'Prupe.1G021800' => 'ppe', 'Prupe.5G145100' => 'ppe', 'Psat6g204040' => 'psa', 'Psat6g204800' => 'psa', 'Psat6g204920' => 'psa', 'Psat6g204960' => 'psa', 'Psat6g205080' => 'psa', 'PSO017G0271' => 'pso', 'PSO017G1276' => 'pso', 'PSO017G1429' => 'pso', 'PSO017G1861' => 'pso', 'PSO017G2787' => 'pso', 'PSO017G4466' => 'pso', 'PSO017G5118' => 'pso', 'PSO017G5420' => 'pso', 'PSO063G3678' => 'pso', 'PSO210G0546' => 'pso', 'PSO317G0001' => 'pso', 'PSO357G0512' => 'pso', 'PSO478G2682' => 'pso', 'PSO647G0001' => 'pso', 'PSO675G0001' => 'pso', 'PSO675G2699' => 'pso', 'PSO675G2849' => 'pso', 'PSO675G4991' => 'pso', 'PSO689G0001' => 'pso', 'QL06p000916' => 'qlo', 'QL06p000921' => 'qlo', 'QL06p001398' => 'qlo', 'QL06p001407' => 'qlo', 'QL06p002031' => 'qlo', 'RcHm_v2.0_Chr4g0387791' => 'rch', 'RcHm_v2.0_Chr4g0387801' => 'rch', 'RcHm_v2.0_Chr6g0286501' => 'rch', 'RcHm_v2.0_Chr6g0286511' => 'rch', 'RcHm_v2.0_Chr6g0286521' => 'rch', 'RcHm_v2.0_Chr6g0286531' => 'rch', 'RcHm_v2.0_Chr7g0189141' => 'rch', 'Rhsim02G0028700' => 'rsi', 'Rhsim02G0028800' => 'rsi', 'Rhsim02G0028900' => 'rsi', 'Rhsim02G0029000' => 'rsi', 'Rhsim02G0029100' => 'rsi', 'Rhsim02G0029200' => 'rsi', 'Rhsim02G0029300' => 'rsi', 'Rhsim02G0029400' => 'rsi', 'Rhsim02G0029500' => 'rsi', 'Rhsim02G0029600' => 'rsi', 'RhsimUnG0024000' => 'rsi', 'RhsimUnG0024100' => 'rsi', 'RhsimUnG0024200' => 'rsi', 'RhsimUnG0024300' => 'rsi', 'RhsimUnG0024400' => 'rsi', 'RhsimUnG0024500' => 'rsi', 'RhsimUnG0024700' => 'rsi', 'RhsimUnG0024800' => 'rsi', 'RhsimUnG0024900' => 'rsi', 'RhsimUnG0025100' => 'rsi', 'Sabra08G0120200' => 'sbr', 'Sabra08G0120300' => 'sbr', 'Sabra08G0120500' => 'sbr', 'Sabra08G0120600' => 'sbr', 'Sabra10G0158900' => 'sbr', 'SalBow2G3492' => 'sbo', 'Sc13g0004760' => 'sci', 'Sc13g0004770' => 'sci', 'Sed0003417' => 'sed', 'Sed0019750' => 'sed', 'SEGI_03419' => 'sgi', 'SEGI_05907' => 'sgi', 'SEGI_10682' => 'sgi', 'SEGI_13528' => 'sgi', 'SEGI_16081' => 'sgi', 'SEGI_19370' => 'sgi', 'SEGI_21015' => 'sgi', 'SEGI_21944' => 'sgi', 'SEGI_32906' => 'sgi', 'SEGI_33093' => 'sgi', 'SEGI_36110' => 'sgi', 'SEGI_40397' => 'sgi', 'SGA_v2.0_scaffold191G40426' => 'sas', 'SGA_v2.0_scaffold353G49717' => 'sas', 'SGA_v2.0_scaffold50G18550' => 'sas', 'SMO119G0173' => 'smo', 'SMO172G0002' => 'smo', 'Solyc09g082690.3' => 'sly', 'Solyc09g082700.2' => 'sly', 'Sopen09g031550' => 'spe', 'Sopen09g031560' => 'spe', 'Sp3g20540' => 'spa', 'Sp7g07580' => 'spa', 'TAR134G0002' => 'tar', 'TAR236G0001' => 'tar', 'TAR365G0892' => 'tar', 'TAR636G0166' => 'tar', 'TAR636G0646' => 'tar', 'TAR636G0869' => 'tar', 'TAR636G1317' => 'tar', 'TAR636G1744' => 'tar', 'TAR636G3358' => 'tar', 'TAR636G3436' => 'tar', 'THA.LOC104803047' => 'tha', 'Thecc.04G238900' => 'tca', 'Thhalv10021557m.g' => 'esa', 'Thhalv10026318m.g' => 'esa', 'Thhalv10026335m.g' => 'esa', 'TPR.G17433' => 'tpr', 'TPR.G18915' => 'tpr', 'TPR.G26125' => 'tpr', 'TWI09G0677' => 'twi', 'TWI73G0287' => 'twi', 'unitig_748.g8326' => 'ugi', 'vmacro15370' => 'vma', 'vmacro15371' => 'vma', 'vmacro15372' => 'vma', 'vmacro15373' => 'vma', 'vmacro15374' => 'vma', 'VMungo0720G2826' => 'vmu', 'Zm00001eb116960' => 'zma', 'Zm00001eb301260' => 'zma', 'Zm00001eb301270' => 'zma' ) $gf_id = 'HOM05D001460' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001460' ) $data_identifier = 'HOM05D001460' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 4, 'aag' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 2, 'aox' => (int) 2, 'arhy' => (int) 4, 'ath' => (int) 2, 'atr' => (int) 1, 'acertr' => (int) 10, 'cqu' => (int) 4, 'bca' => (int) 11, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 1, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 1, 'ccan' => (int) 1, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 1, 'col' => (int) 1, 'cpa' => (int) 1, 'cre' => (int) 7, 'csa' => (int) 1, 'camsi' => (int) 2, 'dca' => (int) 3, 'din' => (int) 2, 'dzi' => (int) 3, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 14, 'fve' => (int) 9, 'gma' => (int) 2, 'ghi' => (int) 4, 'gra' => (int) 2, 'vvi' => (int) 1, 'han' => (int) 13, 'cav' => (int) 1, 'hma' => (int) 2, 'sun' => (int) 2, 'lal' => (int) 2, 'lonja' => (int) 12, 'lja' => (int) 1, 'lsa' => (int) 7, 'mes' => (int) 1, 'mpo' => (int) 27, 'mbi' => (int) 1, 'mco' => (int) 8, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 1, 'egut' => (int) 1, 'ama' => (int) 1, 'nta' => (int) 4, 'nnu' => (int) 2, 'oeu' => (int) 3, 'osa' => (int) 4, 'pax' => (int) 9, 'pgr' => (int) 1, 'stu' => (int) 1, 'pvu' => (int) 1, 'ptr' => (int) 4, 'ppa' => (int) 22, 'pco' => (int) 6, 'ppe' => (int) 6, 'psa' => (int) 5, 'pso' => (int) 19, 'qlo' => (int) 5, 'rch' => (int) 7, 'rsi' => (int) 20, 'sbr' => (int) 5, 'sbo' => (int) 1, 'sci' => (int) 2, 'sed' => (int) 2, 'sgi' => (int) 12, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 2, 'tar' => (int) 10, 'tha' => (int) 1, 'tca' => (int) 1, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 2, 'ugi' => (int) 1, 'vma' => (int) 5, 'vmu' => (int) 1, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb301270' $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' => 'HOM05D001460', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '433', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p22980' => 'bna', 'A01p32340' => 'bna', 'A03p42970' => 'bna', 'A05p25880' => 'bna', 'Aa31LG8G9320' => 'aar', 'Aa31LG8G9330' => 'aar', 'Aa31LG8G9340' => 'aar', 'Aa31sc221G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1034' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1528' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.829' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2222' => 'aag', 'Ah.12g058830' => 'amhyb', 'Ah.12g058840' => 'amhyb', 'AL3G37160' => 'aly', 'AL7G41310' => 'aly', 'Aqoxy5G00395' => 'aox', 'Aqoxy5G00396' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0C8NZA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5185HY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JZ1PRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MD3LS0' => 'arhy', 'AT3G22840' => 'ath', 'AT4G14690' => 'ath', 'ATR0665G054' => 'atr', 'Atru.chr4.2344' => 'acertr', 'Atru.chr4.2346' => 'acertr', 'Atru.chr4.2347' => 'acertr', 'Atru.chr4.2348' => 'acertr', 'Atru.chr4.2355' => 'acertr', 'Atru.chr4.2356' => 'acertr', 'Atru.chr4.2358' => 'acertr', 'Atru.chr4.2359' => 'acertr', 'Atru.chr4.2360' => 'acertr', 'Atru.chr4.2361' => 'acertr', 'AUR62030476' => 'cqu', 'AUR62030478' => 'cqu', 'AUR62030819' => 'cqu', 'AUR62030820' => 'cqu', 'BcaB03g14648' => 'bca', 'BcaB04g20492' => 'bca', 'BcaB06g26399' => 'bca', 'BcaC01g03416' => 'bca', 'BcaC01g03419' => 'bca', 'BcaC01g03421' => 'bca', 'BcaC01g03424' => 'bca', 'BcaC05g28012' => 'bca', 'BcaC09g49212' => 'bca', 'BcaC09g50140' => 'bca', 'BcaNung00346' => 'bca', 'BolC1t02785H' => 'bol', 'BolC1t04095H' => 'bol', 'BolC3t17545H' => 'bol', 'BolC5t32769H' => 'bol', 'BraA01t02211Z' => 'bra', 'BraA01t03359Z' => 'bra', 'BraA03t13441Z' => 'bra', 'BraA05t21476Z' => 'bra', 'C01p28420' => 'bna', 'C01p41350' => 'bna', 'C03p52750' => 'bna', 'C03p52780' => 'bna', 'C05p40270' => 'bna', 'CAN.G1437.9' => 'can', 'CANSAT78G0035' => 'cansat', 'CANSAT78G1036' => 'cansat', 'CANSAT78G2272' => 'cansat', 'CANSAT78G2478' => 'cansat', 'CARHR098700' => 'chi', 'CARHR221120' => 'chi', 'CARHR221150' => 'chi', 'Carub.0003s2297' => 'cru', 'Carub.0007s2749' => 'cru', 'Carub.0007s2750' => 'cru', 'Carub.0007s2751' => 'cru', 'Ca_10849_v3' => 'car', 'Cc03_g04300' => 'ccan', 'CDE02G3648' => 'cde', 'CDE05G0060' => 'cde', 'CDE05G0692' => 'cde', 'CDE05G2285' => 'cde', 'CDE05G2884' => 'cde', 'CDE05G3072' => 'cde', 'Cfa008439' => 'cfa', 'Cfa008441' => 'cfa', 'Cfa008443' => 'cfa', 'Cfa008448' => 'cfa', 'Ciclev10005974m.g' => 'ccl', 'Ciclev10006006m.g' => 'ccl', 'Ciclev10006775m.g' => 'ccl', 'CiPaw.02G120400' => 'cil', 'CiPaw.02G120500' => 'cil', 'CiPaw.02G120600' => 'cil', 'ClCG05G004850' => 'cla', 'COL.COLO4_21566' => 'col', 'Cpa.g.sc44.124' => 'cpa', 'Cre07.g320400' => 'cre', 'Cre07.g320450' => 'cre', 'Cre08.g384650' => 'cre', 'Cre09.g393173' => 'cre', 'Cre09.g394325' => 'cre', 'Cre14.g626750' => 'cre', 'Cre16.g679250' => 'cre', 'CsaV3_3G012890' => 'csa', 'CSS0010865' => 'camsi', 'CSS0044338' => 'camsi', 'DCAR_002366' => 'dca', 'DCAR_030687' => 'dca', 'DCAR_030688' => 'dca', 'Dinv14047' => 'din', 'Dinv14048' => 'din', 'Duzib151G0105' => 'dzi', 'Duzib151G0114' => 'dzi', 'Duzib212G1029' => 'dzi', 'ECA232G3536' => 'eca', 'ECA240G0786' => 'eca', 'ECA240G1802' => 'eca', 'ECA240G3760' => 'eca', 'ECA240G3920' => 'eca', 'EL10Ac5g12536' => 'bvu', 'EL10Ac5g12537' => 'bvu', 'EL10Ac5g12538' => 'bvu', 'Eucgr.B01004' => 'egr', 'Eucgr.B01006' => 'egr', 'Eucgr.B01007' => 'egr', 'Eucgr.B01008' => 'egr', 'Eucgr.B01895' => 'egr', 'Eucgr.B01896' => 'egr', 'FAN04G1456' => 'fan', 'FAN08G1769' => 'fan', 'FAN08G2160' => 'fan', 'FAN13G2403' => 'fan', 'FAN13G3303' => 'fan', 'FAN15G2435' => 'fan', 'FAN17G0672' => 'fan', 'FAN17G2441' => 'fan', 'FAN18G1024' => 'fan', 'FAN22G1458' => 'fan', 'FAN24G0037' => 'fan', 'FAN24G0429' => 'fan', 'FAN24G2387' => 'fan', 'FAN27G2746' => 'fan', 'FvH4_2g20400' => 'fve', 'FvH4_2g20420' => 'fve', 'FvH4_2g20430' => 'fve', 'FvH4_4g01270' => 'fve', 'FvH4_4g01290' => 'fve', 'FvH4_4g01300' => 'fve', 'FvH4_4g01310' => 'fve', 'FvH4_4g01330' => 'fve', 'FvH4_5g09070' => 'fve', 'Glyma.10G243800' => 'gma', 'Glyma.20G150600' => 'gma', 'Gohir.A09G219200' => 'ghi', 'Gohir.A09G219300' => 'ghi', 'Gohir.D09G221400' => 'ghi', 'Gohir.D09G221500' => 'ghi', 'Gorai.006G242600' => 'gra', 'Gorai.006G242700' => 'gra', 'GSVIVG01018044001' => 'vvi', 'HanXRQChr03g0083821' => 'han', 'HanXRQChr03g0083841' => 'han', 'HanXRQChr03g0083881' => 'han', 'HanXRQChr03g0083901' => 'han', 'HanXRQChr03g0083921' => 'han', 'HanXRQChr03g0085331' => 'han', 'HanXRQChr03g0085361' => 'han', 'HanXRQChr03g0085411' => 'han', 'HanXRQChr03g0085421' => 'han', 'HanXRQChr03g0085431' => 'han', 'HanXRQChr08g0221991' => 'han', 'HanXRQChr11g0336061' => 'han', 'HanXRQChr11g0336411' => 'han', 'Haze_11234' => 'cav', 'Hma1.2p1_0549F.1_g177010' => 'hma', 'Hma1.2p1_0602F.1_g187630' => 'hma', 'Hund14876' => 'sun', 'Hund14879' => 'sun', 'Lalb_Chr06g0160741' => 'lal', 'Lalb_Chr21g0304781' => 'lal', 'Lj3A726G19' => 'lonja', 'Lj3A726T23' => 'lonja', 'Lj3A726T24' => 'lonja', 'Lj3A726T25' => 'lonja', 'Lj3A727T17' => 'lonja', 'Lj3C726T0' => 'lonja', 'Lj3C726T2' => 'lonja', 'Lj3P725T35' => 'lonja', 'Lj3P727T10' => 'lonja', 'Lj3P727T12' => 'lonja', 'Lj3P727T14' => 'lonja', 'Lj5g0023109' => 'lja', 'Lj6P646T44' => 'lonja', 'Lsat_1_v5_gn_6_75760' => 'lsa', 'Lsat_1_v5_gn_6_75800' => 'lsa', 'Lsat_1_v5_gn_6_75900' => 'lsa', 'Lsat_1_v5_gn_6_76240' => 'lsa', 'Lsat_1_v5_gn_6_76441' => 'lsa', 'Lsat_1_v5_gn_6_76700' => 'lsa', 'Lsat_1_v5_gn_6_76760' => 'lsa', 'Manes.15G033100' => 'mes', 'Mapoly0004s0074' => 'mpo', 'Mapoly0004s0075' => 'mpo', 'Mapoly0004s0163' => 'mpo', 'Mapoly0004s0164' => 'mpo', 'Mapoly0021s0018' => 'mpo', 'Mapoly0041s0136' => 'mpo', 'Mapoly0041s0137' => 'mpo', 'Mapoly0041s0138' => 'mpo', 'Mapoly0041s0139' => 'mpo', 'Mapoly0041s0141' => 'mpo', 'Mapoly0041s0142' => 'mpo', 'Mapoly0041s0143' => 'mpo', 'Mapoly0041s0144' => 'mpo', 'Mapoly0041s0145' => 'mpo', 'Mapoly0047s0106' => 'mpo', 'Mapoly0047s0108' => 'mpo', 'Mapoly0050s0051' => 'mpo', 'Mapoly0050s0052' => 'mpo', 'Mapoly0050s0053' => 'mpo', 'Mapoly0058s0013' => 'mpo', 'Mapoly0091s0078' => 'mpo', 'Mapoly0091s0079' => 'mpo', 'Mapoly0091s0080' => 'mpo', 'Mapoly0091s0081' => 'mpo', 'Mapoly0278s0004' => 'mpo', 'Mapoly0278s0005' => 'mpo', 'Mapoly0278s0006' => 'mpo', 'MBI11_g30648_MAGBIO' => 'mbi', 'MCO03G194' => 'mco', 'MCO03G590' => 'mco', 'MCO07G312' => 'mco', 'MCO10G318' => 'mco', 'MCO12G244' => 'mco', 'MCO13G148' => 'mco', 'MCO13G194' => 'mco', 'MCO16G238' => 'mco', 'MD06G1134100' => 'mdo', 'MD13G1200100' => 'mdo', 'MD13G1200300' => 'mdo', 'MD13G1200600' => 'mdo', 'MD14G1150400' => 'mdo', 'MD16G1200000' => 'mdo', 'Medtr1g102570' => 'mtr', 'Medtr1g102780' => 'mtr', 'Medtr1g102800' => 'mtr', 'Medtr1g102810' => 'mtr', 'Medtr1g102830' => 'mtr', 'MELO3C006499.2' => 'cme', 'Migut.G00385' => 'egut', 'MSTRG.4063' => 'ama', 'Nitab4.5_0000090g0260' => 'nta', 'Nitab4.5_0000977g0030' => 'nta', 'Nitab4.5_0002541g0040' => 'nta', 'Nitab4.5_0007068g0040' => 'nta', 'Nn005s41408' => 'nnu', 'Nn005s41410' => 'nnu', 'Oeu010310.1' => 'oeu', 'Oeu010311.1' => 'oeu', 'Oeu043472.1' => 'oeu', 'Os01g0246400' => 'osa', 'Os04g0267950' => 'osa', 'Os07g0178700' => 'osa', 'Os07g0178800' => 'osa', 'Peaxi162Scf00316g00046' => 'pax', 'Peaxi162Scf00316g00049' => 'pax', 'Peaxi162Scf00316g00059' => 'pax', 'Peaxi162Scf00316g00328' => 'pax', 'Peaxi162Scf00316g00329' => 'pax', 'Peaxi162Scf00316g00411' => 'pax', 'Peaxi162Scf00316g00521' => 'pax', 'Peaxi162Scf00492g00068' => 'pax', 'Peaxi162Scf35631g00002' => 'pax', 'PGR142G3720' => 'pgr', 'PGSC0003DMG400006442' => 'stu', 'Phvul.007G062000' => 'pvu', 'Potri.008G157750' => 'ptr', 'Potri.008G157900' => 'ptr', 'Potri.008G158000' => 'ptr', 'Potri.008G158200' => 'ptr', 'Pp3c11_7280' => 'ppa', 'Pp3c11_7980' => 'ppa', 'Pp3c12_19450' => 'ppa', 'Pp3c14_1480' => 'ppa', 'Pp3c14_1501' => 'ppa', 'Pp3c16_4900' => 'ppa', 'Pp3c16_5010' => 'ppa', 'Pp3c16_5060' => 'ppa', 'Pp3c19_18250' => 'ppa', 'Pp3c23_8530' => 'ppa', 'Pp3c23_8550' => 'ppa', 'Pp3c24_9670' => 'ppa', 'Pp3c2_21390' => 'ppa', 'Pp3c2_31380' => 'ppa', 'Pp3c3_16620' => 'ppa', 'Pp3c3_8090' => 'ppa', 'Pp3c3_8110' => 'ppa', 'Pp3c3_8130' => 'ppa', 'Pp3c3_8150' => 'ppa', 'Pp3c4_14320' => 'ppa', 'Pp3c6_2560' => 'ppa', 'Pp3c9_16700' => 'ppa', 'PRCOL_00000234' => 'pco', 'PRCOL_00000235' => 'pco', 'PRCOL_00000777' => 'pco', 'PRCOL_00002344' => 'pco', 'PRCOL_00002372' => 'pco', 'PRCOL_00006120' => 'pco', 'Prupe.1G021400' => 'ppe', 'Prupe.1G021500' => 'ppe', 'Prupe.1G021600' => 'ppe', 'Prupe.1G021700' => 'ppe', 'Prupe.1G021800' => 'ppe', 'Prupe.5G145100' => 'ppe', 'Psat6g204040' => 'psa', 'Psat6g204800' => 'psa', 'Psat6g204920' => 'psa', 'Psat6g204960' => 'psa', 'Psat6g205080' => 'psa', 'PSO017G0271' => 'pso', 'PSO017G1276' => 'pso', 'PSO017G1429' => 'pso', 'PSO017G1861' => 'pso', 'PSO017G2787' => 'pso', 'PSO017G4466' => 'pso', 'PSO017G5118' => 'pso', 'PSO017G5420' => 'pso', 'PSO063G3678' => 'pso', 'PSO210G0546' => 'pso', 'PSO317G0001' => 'pso', 'PSO357G0512' => 'pso', 'PSO478G2682' => 'pso', 'PSO647G0001' => 'pso', 'PSO675G0001' => 'pso', 'PSO675G2699' => 'pso', 'PSO675G2849' => 'pso', 'PSO675G4991' => 'pso', 'PSO689G0001' => 'pso', 'QL06p000916' => 'qlo', 'QL06p000921' => 'qlo', 'QL06p001398' => 'qlo', 'QL06p001407' => 'qlo', 'QL06p002031' => 'qlo', 'RcHm_v2.0_Chr4g0387791' => 'rch', 'RcHm_v2.0_Chr4g0387801' => 'rch', 'RcHm_v2.0_Chr6g0286501' => 'rch', 'RcHm_v2.0_Chr6g0286511' => 'rch', 'RcHm_v2.0_Chr6g0286521' => 'rch', 'RcHm_v2.0_Chr6g0286531' => 'rch', 'RcHm_v2.0_Chr7g0189141' => 'rch', 'Rhsim02G0028700' => 'rsi', 'Rhsim02G0028800' => 'rsi', 'Rhsim02G0028900' => 'rsi', 'Rhsim02G0029000' => 'rsi', 'Rhsim02G0029100' => 'rsi', 'Rhsim02G0029200' => 'rsi', 'Rhsim02G0029300' => 'rsi', 'Rhsim02G0029400' => 'rsi', 'Rhsim02G0029500' => 'rsi', 'Rhsim02G0029600' => 'rsi', 'RhsimUnG0024000' => 'rsi', 'RhsimUnG0024100' => 'rsi', 'RhsimUnG0024200' => 'rsi', 'RhsimUnG0024300' => 'rsi', 'RhsimUnG0024400' => 'rsi', 'RhsimUnG0024500' => 'rsi', 'RhsimUnG0024700' => 'rsi', 'RhsimUnG0024800' => 'rsi', 'RhsimUnG0024900' => 'rsi', 'RhsimUnG0025100' => 'rsi', 'Sabra08G0120200' => 'sbr', 'Sabra08G0120300' => 'sbr', 'Sabra08G0120500' => 'sbr', 'Sabra08G0120600' => 'sbr', 'Sabra10G0158900' => 'sbr', 'SalBow2G3492' => 'sbo', 'Sc13g0004760' => 'sci', 'Sc13g0004770' => 'sci', 'Sed0003417' => 'sed', 'Sed0019750' => 'sed', 'SEGI_03419' => 'sgi', 'SEGI_05907' => 'sgi', 'SEGI_10682' => 'sgi', 'SEGI_13528' => 'sgi', 'SEGI_16081' => 'sgi', 'SEGI_19370' => 'sgi', 'SEGI_21015' => 'sgi', 'SEGI_21944' => 'sgi', 'SEGI_32906' => 'sgi', 'SEGI_33093' => 'sgi', 'SEGI_36110' => 'sgi', 'SEGI_40397' => 'sgi', 'SGA_v2.0_scaffold191G40426' => 'sas', 'SGA_v2.0_scaffold353G49717' => 'sas', 'SGA_v2.0_scaffold50G18550' => 'sas', 'SMO119G0173' => 'smo', 'SMO172G0002' => 'smo', 'Solyc09g082690.3' => 'sly', 'Solyc09g082700.2' => 'sly', 'Sopen09g031550' => 'spe', 'Sopen09g031560' => 'spe', 'Sp3g20540' => 'spa', 'Sp7g07580' => 'spa', 'TAR134G0002' => 'tar', 'TAR236G0001' => 'tar', 'TAR365G0892' => 'tar', 'TAR636G0166' => 'tar', 'TAR636G0646' => 'tar', 'TAR636G0869' => 'tar', 'TAR636G1317' => 'tar', 'TAR636G1744' => 'tar', 'TAR636G3358' => 'tar', 'TAR636G3436' => 'tar', 'THA.LOC104803047' => 'tha', 'Thecc.04G238900' => 'tca', 'Thhalv10021557m.g' => 'esa', 'Thhalv10026318m.g' => 'esa', 'Thhalv10026335m.g' => 'esa', 'TPR.G17433' => 'tpr', 'TPR.G18915' => 'tpr', 'TPR.G26125' => 'tpr', 'TWI09G0677' => 'twi', 'TWI73G0287' => 'twi', 'unitig_748.g8326' => 'ugi', 'vmacro15370' => 'vma', 'vmacro15371' => 'vma', 'vmacro15372' => 'vma', 'vmacro15373' => 'vma', 'vmacro15374' => 'vma', 'VMungo0720G2826' => 'vmu', 'Zm00001eb116960' => 'zma', 'Zm00001eb301260' => 'zma', 'Zm00001eb301270' => 'zma' ), 'gf_id' => 'HOM05D001460', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001460' ), 'data_identifier' => 'HOM05D001460', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001460', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '433', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p22980' => 'bna', 'A01p32340' => 'bna', 'A03p42970' => 'bna', 'A05p25880' => 'bna', 'Aa31LG8G9320' => 'aar', 'Aa31LG8G9330' => 'aar', 'Aa31LG8G9340' => 'aar', 'Aa31sc221G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1034' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1528' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.829' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2222' => 'aag', 'Ah.12g058830' => 'amhyb', 'Ah.12g058840' => 'amhyb', 'AL3G37160' => 'aly', 'AL7G41310' => 'aly', 'Aqoxy5G00395' => 'aox', 'Aqoxy5G00396' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0C8NZA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5185HY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JZ1PRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MD3LS0' => 'arhy', 'AT3G22840' => 'ath', 'AT4G14690' => 'ath', 'ATR0665G054' => 'atr', 'Atru.chr4.2344' => 'acertr', 'Atru.chr4.2346' => 'acertr', 'Atru.chr4.2347' => 'acertr', 'Atru.chr4.2348' => 'acertr', 'Atru.chr4.2355' => 'acertr', 'Atru.chr4.2356' => 'acertr', 'Atru.chr4.2358' => 'acertr', 'Atru.chr4.2359' => 'acertr', 'Atru.chr4.2360' => 'acertr', 'Atru.chr4.2361' => 'acertr', 'AUR62030476' => 'cqu', 'AUR62030478' => 'cqu', 'AUR62030819' => 'cqu', 'AUR62030820' => 'cqu', 'BcaB03g14648' => 'bca', 'BcaB04g20492' => 'bca', 'BcaB06g26399' => 'bca', 'BcaC01g03416' => 'bca', 'BcaC01g03419' => 'bca', 'BcaC01g03421' => 'bca', 'BcaC01g03424' => 'bca', 'BcaC05g28012' => 'bca', 'BcaC09g49212' => 'bca', 'BcaC09g50140' => 'bca', 'BcaNung00346' => 'bca', 'BolC1t02785H' => 'bol', 'BolC1t04095H' => 'bol', 'BolC3t17545H' => 'bol', 'BolC5t32769H' => 'bol', 'BraA01t02211Z' => 'bra', 'BraA01t03359Z' => 'bra', 'BraA03t13441Z' => 'bra', 'BraA05t21476Z' => 'bra', 'C01p28420' => 'bna', 'C01p41350' => 'bna', 'C03p52750' => 'bna', 'C03p52780' => 'bna', 'C05p40270' => 'bna', 'CAN.G1437.9' => 'can', 'CANSAT78G0035' => 'cansat', 'CANSAT78G1036' => 'cansat', 'CANSAT78G2272' => 'cansat', 'CANSAT78G2478' => 'cansat', 'CARHR098700' => 'chi', 'CARHR221120' => 'chi', 'CARHR221150' => 'chi', 'Carub.0003s2297' => 'cru', 'Carub.0007s2749' => 'cru', 'Carub.0007s2750' => 'cru', 'Carub.0007s2751' => 'cru', 'Ca_10849_v3' => 'car', 'Cc03_g04300' => 'ccan', 'CDE02G3648' => 'cde', 'CDE05G0060' => 'cde', 'CDE05G0692' => 'cde', 'CDE05G2285' => 'cde', 'CDE05G2884' => 'cde', 'CDE05G3072' => 'cde', 'Cfa008439' => 'cfa', 'Cfa008441' => 'cfa', 'Cfa008443' => 'cfa', 'Cfa008448' => 'cfa', 'Ciclev10005974m.g' => 'ccl', 'Ciclev10006006m.g' => 'ccl', 'Ciclev10006775m.g' => 'ccl', 'CiPaw.02G120400' => 'cil', 'CiPaw.02G120500' => 'cil', 'CiPaw.02G120600' => 'cil', 'ClCG05G004850' => 'cla', 'COL.COLO4_21566' => 'col', 'Cpa.g.sc44.124' => 'cpa', 'Cre07.g320400' => 'cre', 'Cre07.g320450' => 'cre', 'Cre08.g384650' => 'cre', 'Cre09.g393173' => 'cre', 'Cre09.g394325' => 'cre', 'Cre14.g626750' => 'cre', 'Cre16.g679250' => 'cre', 'CsaV3_3G012890' => 'csa', 'CSS0010865' => 'camsi', 'CSS0044338' => 'camsi', 'DCAR_002366' => 'dca', 'DCAR_030687' => 'dca', 'DCAR_030688' => 'dca', 'Dinv14047' => 'din', 'Dinv14048' => 'din', 'Duzib151G0105' => 'dzi', 'Duzib151G0114' => 'dzi', 'Duzib212G1029' => 'dzi', 'ECA232G3536' => 'eca', 'ECA240G0786' => 'eca', 'ECA240G1802' => 'eca', 'ECA240G3760' => 'eca', 'ECA240G3920' => 'eca', 'EL10Ac5g12536' => 'bvu', 'EL10Ac5g12537' => 'bvu', 'EL10Ac5g12538' => 'bvu', 'Eucgr.B01004' => 'egr', 'Eucgr.B01006' => 'egr', 'Eucgr.B01007' => 'egr', 'Eucgr.B01008' => 'egr', 'Eucgr.B01895' => 'egr', 'Eucgr.B01896' => 'egr', 'FAN04G1456' => 'fan', 'FAN08G1769' => 'fan', 'FAN08G2160' => 'fan', 'FAN13G2403' => 'fan', 'FAN13G3303' => 'fan', 'FAN15G2435' => 'fan', 'FAN17G0672' => 'fan', 'FAN17G2441' => 'fan', 'FAN18G1024' => 'fan', 'FAN22G1458' => 'fan', 'FAN24G0037' => 'fan', 'FAN24G0429' => 'fan', 'FAN24G2387' => 'fan', 'FAN27G2746' => 'fan', 'FvH4_2g20400' => 'fve', 'FvH4_2g20420' => 'fve', 'FvH4_2g20430' => 'fve', 'FvH4_4g01270' => 'fve', 'FvH4_4g01290' => 'fve', 'FvH4_4g01300' => 'fve', 'FvH4_4g01310' => 'fve', 'FvH4_4g01330' => 'fve', 'FvH4_5g09070' => 'fve', 'Glyma.10G243800' => 'gma', 'Glyma.20G150600' => 'gma', 'Gohir.A09G219200' => 'ghi', 'Gohir.A09G219300' => 'ghi', 'Gohir.D09G221400' => 'ghi', 'Gohir.D09G221500' => 'ghi', 'Gorai.006G242600' => 'gra', 'Gorai.006G242700' => 'gra', 'GSVIVG01018044001' => 'vvi', 'HanXRQChr03g0083821' => 'han', 'HanXRQChr03g0083841' => 'han', 'HanXRQChr03g0083881' => 'han', 'HanXRQChr03g0083901' => 'han', 'HanXRQChr03g0083921' => 'han', 'HanXRQChr03g0085331' => 'han', 'HanXRQChr03g0085361' => 'han', 'HanXRQChr03g0085411' => 'han', 'HanXRQChr03g0085421' => 'han', 'HanXRQChr03g0085431' => 'han', 'HanXRQChr08g0221991' => 'han', 'HanXRQChr11g0336061' => 'han', 'HanXRQChr11g0336411' => 'han', 'Haze_11234' => 'cav', 'Hma1.2p1_0549F.1_g177010' => 'hma', 'Hma1.2p1_0602F.1_g187630' => 'hma', 'Hund14876' => 'sun', 'Hund14879' => 'sun', 'Lalb_Chr06g0160741' => 'lal', 'Lalb_Chr21g0304781' => 'lal', 'Lj3A726G19' => 'lonja', 'Lj3A726T23' => 'lonja', 'Lj3A726T24' => 'lonja', 'Lj3A726T25' => 'lonja', 'Lj3A727T17' => 'lonja', 'Lj3C726T0' => 'lonja', 'Lj3C726T2' => 'lonja', 'Lj3P725T35' => 'lonja', 'Lj3P727T10' => 'lonja', 'Lj3P727T12' => 'lonja', 'Lj3P727T14' => 'lonja', 'Lj5g0023109' => 'lja', 'Lj6P646T44' => 'lonja', 'Lsat_1_v5_gn_6_75760' => 'lsa', 'Lsat_1_v5_gn_6_75800' => 'lsa', 'Lsat_1_v5_gn_6_75900' => 'lsa', 'Lsat_1_v5_gn_6_76240' => 'lsa', 'Lsat_1_v5_gn_6_76441' => 'lsa', 'Lsat_1_v5_gn_6_76700' => 'lsa', 'Lsat_1_v5_gn_6_76760' => 'lsa', 'Manes.15G033100' => 'mes', 'Mapoly0004s0074' => 'mpo', 'Mapoly0004s0075' => 'mpo', 'Mapoly0004s0163' => 'mpo', 'Mapoly0004s0164' => 'mpo', 'Mapoly0021s0018' => 'mpo', 'Mapoly0041s0136' => 'mpo', 'Mapoly0041s0137' => 'mpo', 'Mapoly0041s0138' => 'mpo', 'Mapoly0041s0139' => 'mpo', 'Mapoly0041s0141' => 'mpo', 'Mapoly0041s0142' => 'mpo', 'Mapoly0041s0143' => 'mpo', 'Mapoly0041s0144' => 'mpo', 'Mapoly0041s0145' => 'mpo', 'Mapoly0047s0106' => 'mpo', 'Mapoly0047s0108' => 'mpo', 'Mapoly0050s0051' => 'mpo', 'Mapoly0050s0052' => 'mpo', 'Mapoly0050s0053' => 'mpo', 'Mapoly0058s0013' => 'mpo', 'Mapoly0091s0078' => 'mpo', 'Mapoly0091s0079' => 'mpo', 'Mapoly0091s0080' => 'mpo', 'Mapoly0091s0081' => 'mpo', 'Mapoly0278s0004' => 'mpo', 'Mapoly0278s0005' => 'mpo', 'Mapoly0278s0006' => 'mpo', 'MBI11_g30648_MAGBIO' => 'mbi', 'MCO03G194' => 'mco', 'MCO03G590' => 'mco', 'MCO07G312' => 'mco', 'MCO10G318' => 'mco', 'MCO12G244' => 'mco', 'MCO13G148' => 'mco', 'MCO13G194' => 'mco', 'MCO16G238' => 'mco', 'MD06G1134100' => 'mdo', 'MD13G1200100' => 'mdo', 'MD13G1200300' => 'mdo', 'MD13G1200600' => 'mdo', 'MD14G1150400' => 'mdo', 'MD16G1200000' => 'mdo', 'Medtr1g102570' => 'mtr', 'Medtr1g102780' => 'mtr', 'Medtr1g102800' => 'mtr', 'Medtr1g102810' => 'mtr', 'Medtr1g102830' => 'mtr', 'MELO3C006499.2' => 'cme', 'Migut.G00385' => 'egut', 'MSTRG.4063' => 'ama', 'Nitab4.5_0000090g0260' => 'nta', 'Nitab4.5_0000977g0030' => 'nta', 'Nitab4.5_0002541g0040' => 'nta', 'Nitab4.5_0007068g0040' => 'nta', 'Nn005s41408' => 'nnu', 'Nn005s41410' => 'nnu', 'Oeu010310.1' => 'oeu', 'Oeu010311.1' => 'oeu', 'Oeu043472.1' => 'oeu', 'Os01g0246400' => 'osa', 'Os04g0267950' => 'osa', 'Os07g0178700' => 'osa', 'Os07g0178800' => 'osa', 'Peaxi162Scf00316g00046' => 'pax', 'Peaxi162Scf00316g00049' => 'pax', 'Peaxi162Scf00316g00059' => 'pax', 'Peaxi162Scf00316g00328' => 'pax', 'Peaxi162Scf00316g00329' => 'pax', 'Peaxi162Scf00316g00411' => 'pax', 'Peaxi162Scf00316g00521' => 'pax', 'Peaxi162Scf00492g00068' => 'pax', 'Peaxi162Scf35631g00002' => 'pax', 'PGR142G3720' => 'pgr', 'PGSC0003DMG400006442' => 'stu', 'Phvul.007G062000' => 'pvu', 'Potri.008G157750' => 'ptr', 'Potri.008G157900' => 'ptr', 'Potri.008G158000' => 'ptr', 'Potri.008G158200' => 'ptr', 'Pp3c11_7280' => 'ppa', 'Pp3c11_7980' => 'ppa', 'Pp3c12_19450' => 'ppa', 'Pp3c14_1480' => 'ppa', 'Pp3c14_1501' => 'ppa', 'Pp3c16_4900' => 'ppa', 'Pp3c16_5010' => 'ppa', 'Pp3c16_5060' => 'ppa', 'Pp3c19_18250' => 'ppa', 'Pp3c23_8530' => 'ppa', 'Pp3c23_8550' => 'ppa', 'Pp3c24_9670' => 'ppa', 'Pp3c2_21390' => 'ppa', 'Pp3c2_31380' => 'ppa', 'Pp3c3_16620' => 'ppa', 'Pp3c3_8090' => 'ppa', 'Pp3c3_8110' => 'ppa', 'Pp3c3_8130' => 'ppa', 'Pp3c3_8150' => 'ppa', 'Pp3c4_14320' => 'ppa', 'Pp3c6_2560' => 'ppa', 'Pp3c9_16700' => 'ppa', 'PRCOL_00000234' => 'pco', 'PRCOL_00000235' => 'pco', 'PRCOL_00000777' => 'pco', 'PRCOL_00002344' => 'pco', 'PRCOL_00002372' => 'pco', 'PRCOL_00006120' => 'pco', 'Prupe.1G021400' => 'ppe', 'Prupe.1G021500' => 'ppe', 'Prupe.1G021600' => 'ppe', 'Prupe.1G021700' => 'ppe', 'Prupe.1G021800' => 'ppe', 'Prupe.5G145100' => 'ppe', 'Psat6g204040' => 'psa', 'Psat6g204800' => 'psa', 'Psat6g204920' => 'psa', 'Psat6g204960' => 'psa', 'Psat6g205080' => 'psa', 'PSO017G0271' => 'pso', 'PSO017G1276' => 'pso', 'PSO017G1429' => 'pso', 'PSO017G1861' => 'pso', 'PSO017G2787' => 'pso', 'PSO017G4466' => 'pso', 'PSO017G5118' => 'pso', 'PSO017G5420' => 'pso', 'PSO063G3678' => 'pso', 'PSO210G0546' => 'pso', 'PSO317G0001' => 'pso', 'PSO357G0512' => 'pso', 'PSO478G2682' => 'pso', 'PSO647G0001' => 'pso', 'PSO675G0001' => 'pso', 'PSO675G2699' => 'pso', 'PSO675G2849' => 'pso', 'PSO675G4991' => 'pso', 'PSO689G0001' => 'pso', 'QL06p000916' => 'qlo', 'QL06p000921' => 'qlo', 'QL06p001398' => 'qlo', 'QL06p001407' => 'qlo', 'QL06p002031' => 'qlo', 'RcHm_v2.0_Chr4g0387791' => 'rch', 'RcHm_v2.0_Chr4g0387801' => 'rch', 'RcHm_v2.0_Chr6g0286501' => 'rch', 'RcHm_v2.0_Chr6g0286511' => 'rch', 'RcHm_v2.0_Chr6g0286521' => 'rch', 'RcHm_v2.0_Chr6g0286531' => 'rch', 'RcHm_v2.0_Chr7g0189141' => 'rch', 'Rhsim02G0028700' => 'rsi', 'Rhsim02G0028800' => 'rsi', 'Rhsim02G0028900' => 'rsi', 'Rhsim02G0029000' => 'rsi', 'Rhsim02G0029100' => 'rsi', 'Rhsim02G0029200' => 'rsi', 'Rhsim02G0029300' => 'rsi', 'Rhsim02G0029400' => 'rsi', 'Rhsim02G0029500' => 'rsi', 'Rhsim02G0029600' => 'rsi', 'RhsimUnG0024000' => 'rsi', 'RhsimUnG0024100' => 'rsi', 'RhsimUnG0024200' => 'rsi', 'RhsimUnG0024300' => 'rsi', 'RhsimUnG0024400' => 'rsi', 'RhsimUnG0024500' => 'rsi', 'RhsimUnG0024700' => 'rsi', 'RhsimUnG0024800' => 'rsi', 'RhsimUnG0024900' => 'rsi', 'RhsimUnG0025100' => 'rsi', 'Sabra08G0120200' => 'sbr', 'Sabra08G0120300' => 'sbr', 'Sabra08G0120500' => 'sbr', 'Sabra08G0120600' => 'sbr', 'Sabra10G0158900' => 'sbr', 'SalBow2G3492' => 'sbo', 'Sc13g0004760' => 'sci', 'Sc13g0004770' => 'sci', 'Sed0003417' => 'sed', 'Sed0019750' => 'sed', 'SEGI_03419' => 'sgi', 'SEGI_05907' => 'sgi', 'SEGI_10682' => 'sgi', 'SEGI_13528' => 'sgi', 'SEGI_16081' => 'sgi', 'SEGI_19370' => 'sgi', 'SEGI_21015' => 'sgi', 'SEGI_21944' => 'sgi', 'SEGI_32906' => 'sgi', 'SEGI_33093' => 'sgi', 'SEGI_36110' => 'sgi', 'SEGI_40397' => 'sgi', 'SGA_v2.0_scaffold191G40426' => 'sas', 'SGA_v2.0_scaffold353G49717' => 'sas', 'SGA_v2.0_scaffold50G18550' => 'sas', 'SMO119G0173' => 'smo', 'SMO172G0002' => 'smo', 'Solyc09g082690.3' => 'sly', 'Solyc09g082700.2' => 'sly', 'Sopen09g031550' => 'spe', 'Sopen09g031560' => 'spe', 'Sp3g20540' => 'spa', 'Sp7g07580' => 'spa', 'TAR134G0002' => 'tar', 'TAR236G0001' => 'tar', 'TAR365G0892' => 'tar', 'TAR636G0166' => 'tar', 'TAR636G0646' => 'tar', 'TAR636G0869' => 'tar', 'TAR636G1317' => 'tar', 'TAR636G1744' => 'tar', 'TAR636G3358' => 'tar', 'TAR636G3436' => 'tar', 'THA.LOC104803047' => 'tha', 'Thecc.04G238900' => 'tca', 'Thhalv10021557m.g' => 'esa', 'Thhalv10026318m.g' => 'esa', 'Thhalv10026335m.g' => 'esa', 'TPR.G17433' => 'tpr', 'TPR.G18915' => 'tpr', 'TPR.G26125' => 'tpr', 'TWI09G0677' => 'twi', 'TWI73G0287' => 'twi', 'unitig_748.g8326' => 'ugi', 'vmacro15370' => 'vma', 'vmacro15371' => 'vma', 'vmacro15372' => 'vma', 'vmacro15373' => 'vma', 'vmacro15374' => 'vma', 'VMungo0720G2826' => 'vmu', 'Zm00001eb116960' => 'zma', 'Zm00001eb301260' => 'zma', 'Zm00001eb301270' => 'zma' ) $gf_id = 'HOM05D001460' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001460' ) $data_identifier = 'HOM05D001460' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 4, 'aag' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 2, 'aox' => (int) 2, 'arhy' => (int) 4, 'ath' => (int) 2, 'atr' => (int) 1, 'acertr' => (int) 10, 'cqu' => (int) 4, 'bca' => (int) 11, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 1, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 1, 'ccan' => (int) 1, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 1, 'col' => (int) 1, 'cpa' => (int) 1, 'cre' => (int) 7, 'csa' => (int) 1, 'camsi' => (int) 2, 'dca' => (int) 3, 'din' => (int) 2, 'dzi' => (int) 3, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 14, 'fve' => (int) 9, 'gma' => (int) 2, 'ghi' => (int) 4, 'gra' => (int) 2, 'vvi' => (int) 1, 'han' => (int) 13, 'cav' => (int) 1, 'hma' => (int) 2, 'sun' => (int) 2, 'lal' => (int) 2, 'lonja' => (int) 12, 'lja' => (int) 1, 'lsa' => (int) 7, 'mes' => (int) 1, 'mpo' => (int) 27, 'mbi' => (int) 1, 'mco' => (int) 8, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 1, 'egut' => (int) 1, 'ama' => (int) 1, 'nta' => (int) 4, 'nnu' => (int) 2, 'oeu' => (int) 3, 'osa' => (int) 4, 'pax' => (int) 9, 'pgr' => (int) 1, 'stu' => (int) 1, 'pvu' => (int) 1, 'ptr' => (int) 4, 'ppa' => (int) 22, 'pco' => (int) 6, 'ppe' => (int) 6, 'psa' => (int) 5, 'pso' => (int) 19, 'qlo' => (int) 5, 'rch' => (int) 7, 'rsi' => (int) 20, 'sbr' => (int) 5, 'sbo' => (int) 1, 'sci' => (int) 2, 'sed' => (int) 2, 'sgi' => (int) 12, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 2, 'tar' => (int) 10, 'tha' => (int) 1, 'tca' => (int) 1, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 2, 'ugi' => (int) 1, 'vma' => (int) 5, 'vmu' => (int) 1, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb301270' $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' => 'HOM05D001460', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '433', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p22980' => 'bna', 'A01p32340' => 'bna', 'A03p42970' => 'bna', 'A05p25880' => 'bna', 'Aa31LG8G9320' => 'aar', 'Aa31LG8G9330' => 'aar', 'Aa31LG8G9340' => 'aar', 'Aa31sc221G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1034' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1528' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.829' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2222' => 'aag', 'Ah.12g058830' => 'amhyb', 'Ah.12g058840' => 'amhyb', 'AL3G37160' => 'aly', 'AL7G41310' => 'aly', 'Aqoxy5G00395' => 'aox', 'Aqoxy5G00396' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0C8NZA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5185HY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JZ1PRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MD3LS0' => 'arhy', 'AT3G22840' => 'ath', 'AT4G14690' => 'ath', 'ATR0665G054' => 'atr', 'Atru.chr4.2344' => 'acertr', 'Atru.chr4.2346' => 'acertr', 'Atru.chr4.2347' => 'acertr', 'Atru.chr4.2348' => 'acertr', 'Atru.chr4.2355' => 'acertr', 'Atru.chr4.2356' => 'acertr', 'Atru.chr4.2358' => 'acertr', 'Atru.chr4.2359' => 'acertr', 'Atru.chr4.2360' => 'acertr', 'Atru.chr4.2361' => 'acertr', 'AUR62030476' => 'cqu', 'AUR62030478' => 'cqu', 'AUR62030819' => 'cqu', 'AUR62030820' => 'cqu', 'BcaB03g14648' => 'bca', 'BcaB04g20492' => 'bca', 'BcaB06g26399' => 'bca', 'BcaC01g03416' => 'bca', 'BcaC01g03419' => 'bca', 'BcaC01g03421' => 'bca', 'BcaC01g03424' => 'bca', 'BcaC05g28012' => 'bca', 'BcaC09g49212' => 'bca', 'BcaC09g50140' => 'bca', 'BcaNung00346' => 'bca', 'BolC1t02785H' => 'bol', 'BolC1t04095H' => 'bol', 'BolC3t17545H' => 'bol', 'BolC5t32769H' => 'bol', 'BraA01t02211Z' => 'bra', 'BraA01t03359Z' => 'bra', 'BraA03t13441Z' => 'bra', 'BraA05t21476Z' => 'bra', 'C01p28420' => 'bna', 'C01p41350' => 'bna', 'C03p52750' => 'bna', 'C03p52780' => 'bna', 'C05p40270' => 'bna', 'CAN.G1437.9' => 'can', 'CANSAT78G0035' => 'cansat', 'CANSAT78G1036' => 'cansat', 'CANSAT78G2272' => 'cansat', 'CANSAT78G2478' => 'cansat', 'CARHR098700' => 'chi', 'CARHR221120' => 'chi', 'CARHR221150' => 'chi', 'Carub.0003s2297' => 'cru', 'Carub.0007s2749' => 'cru', 'Carub.0007s2750' => 'cru', 'Carub.0007s2751' => 'cru', 'Ca_10849_v3' => 'car', 'Cc03_g04300' => 'ccan', 'CDE02G3648' => 'cde', 'CDE05G0060' => 'cde', 'CDE05G0692' => 'cde', 'CDE05G2285' => 'cde', 'CDE05G2884' => 'cde', 'CDE05G3072' => 'cde', 'Cfa008439' => 'cfa', 'Cfa008441' => 'cfa', 'Cfa008443' => 'cfa', 'Cfa008448' => 'cfa', 'Ciclev10005974m.g' => 'ccl', 'Ciclev10006006m.g' => 'ccl', 'Ciclev10006775m.g' => 'ccl', 'CiPaw.02G120400' => 'cil', 'CiPaw.02G120500' => 'cil', 'CiPaw.02G120600' => 'cil', 'ClCG05G004850' => 'cla', 'COL.COLO4_21566' => 'col', 'Cpa.g.sc44.124' => 'cpa', 'Cre07.g320400' => 'cre', 'Cre07.g320450' => 'cre', 'Cre08.g384650' => 'cre', 'Cre09.g393173' => 'cre', 'Cre09.g394325' => 'cre', 'Cre14.g626750' => 'cre', 'Cre16.g679250' => 'cre', 'CsaV3_3G012890' => 'csa', 'CSS0010865' => 'camsi', 'CSS0044338' => 'camsi', 'DCAR_002366' => 'dca', 'DCAR_030687' => 'dca', 'DCAR_030688' => 'dca', 'Dinv14047' => 'din', 'Dinv14048' => 'din', 'Duzib151G0105' => 'dzi', 'Duzib151G0114' => 'dzi', 'Duzib212G1029' => 'dzi', 'ECA232G3536' => 'eca', 'ECA240G0786' => 'eca', 'ECA240G1802' => 'eca', 'ECA240G3760' => 'eca', 'ECA240G3920' => 'eca', 'EL10Ac5g12536' => 'bvu', 'EL10Ac5g12537' => 'bvu', 'EL10Ac5g12538' => 'bvu', 'Eucgr.B01004' => 'egr', 'Eucgr.B01006' => 'egr', 'Eucgr.B01007' => 'egr', 'Eucgr.B01008' => 'egr', 'Eucgr.B01895' => 'egr', 'Eucgr.B01896' => 'egr', 'FAN04G1456' => 'fan', 'FAN08G1769' => 'fan', 'FAN08G2160' => 'fan', 'FAN13G2403' => 'fan', 'FAN13G3303' => 'fan', 'FAN15G2435' => 'fan', 'FAN17G0672' => 'fan', 'FAN17G2441' => 'fan', 'FAN18G1024' => 'fan', 'FAN22G1458' => 'fan', 'FAN24G0037' => 'fan', 'FAN24G0429' => 'fan', 'FAN24G2387' => 'fan', 'FAN27G2746' => 'fan', 'FvH4_2g20400' => 'fve', 'FvH4_2g20420' => 'fve', 'FvH4_2g20430' => 'fve', 'FvH4_4g01270' => 'fve', 'FvH4_4g01290' => 'fve', 'FvH4_4g01300' => 'fve', 'FvH4_4g01310' => 'fve', 'FvH4_4g01330' => 'fve', 'FvH4_5g09070' => 'fve', 'Glyma.10G243800' => 'gma', 'Glyma.20G150600' => 'gma', 'Gohir.A09G219200' => 'ghi', 'Gohir.A09G219300' => 'ghi', 'Gohir.D09G221400' => 'ghi', 'Gohir.D09G221500' => 'ghi', 'Gorai.006G242600' => 'gra', 'Gorai.006G242700' => 'gra', 'GSVIVG01018044001' => 'vvi', 'HanXRQChr03g0083821' => 'han', 'HanXRQChr03g0083841' => 'han', 'HanXRQChr03g0083881' => 'han', 'HanXRQChr03g0083901' => 'han', 'HanXRQChr03g0083921' => 'han', 'HanXRQChr03g0085331' => 'han', 'HanXRQChr03g0085361' => 'han', 'HanXRQChr03g0085411' => 'han', 'HanXRQChr03g0085421' => 'han', 'HanXRQChr03g0085431' => 'han', 'HanXRQChr08g0221991' => 'han', 'HanXRQChr11g0336061' => 'han', 'HanXRQChr11g0336411' => 'han', 'Haze_11234' => 'cav', 'Hma1.2p1_0549F.1_g177010' => 'hma', 'Hma1.2p1_0602F.1_g187630' => 'hma', 'Hund14876' => 'sun', 'Hund14879' => 'sun', 'Lalb_Chr06g0160741' => 'lal', 'Lalb_Chr21g0304781' => 'lal', 'Lj3A726G19' => 'lonja', 'Lj3A726T23' => 'lonja', 'Lj3A726T24' => 'lonja', 'Lj3A726T25' => 'lonja', 'Lj3A727T17' => 'lonja', 'Lj3C726T0' => 'lonja', 'Lj3C726T2' => 'lonja', 'Lj3P725T35' => 'lonja', 'Lj3P727T10' => 'lonja', 'Lj3P727T12' => 'lonja', 'Lj3P727T14' => 'lonja', 'Lj5g0023109' => 'lja', 'Lj6P646T44' => 'lonja', 'Lsat_1_v5_gn_6_75760' => 'lsa', 'Lsat_1_v5_gn_6_75800' => 'lsa', 'Lsat_1_v5_gn_6_75900' => 'lsa', 'Lsat_1_v5_gn_6_76240' => 'lsa', 'Lsat_1_v5_gn_6_76441' => 'lsa', 'Lsat_1_v5_gn_6_76700' => 'lsa', 'Lsat_1_v5_gn_6_76760' => 'lsa', 'Manes.15G033100' => 'mes', 'Mapoly0004s0074' => 'mpo', 'Mapoly0004s0075' => 'mpo', 'Mapoly0004s0163' => 'mpo', 'Mapoly0004s0164' => 'mpo', 'Mapoly0021s0018' => 'mpo', 'Mapoly0041s0136' => 'mpo', 'Mapoly0041s0137' => 'mpo', 'Mapoly0041s0138' => 'mpo', 'Mapoly0041s0139' => 'mpo', 'Mapoly0041s0141' => 'mpo', 'Mapoly0041s0142' => 'mpo', 'Mapoly0041s0143' => 'mpo', 'Mapoly0041s0144' => 'mpo', 'Mapoly0041s0145' => 'mpo', 'Mapoly0047s0106' => 'mpo', 'Mapoly0047s0108' => 'mpo', 'Mapoly0050s0051' => 'mpo', 'Mapoly0050s0052' => 'mpo', 'Mapoly0050s0053' => 'mpo', 'Mapoly0058s0013' => 'mpo', 'Mapoly0091s0078' => 'mpo', 'Mapoly0091s0079' => 'mpo', 'Mapoly0091s0080' => 'mpo', 'Mapoly0091s0081' => 'mpo', 'Mapoly0278s0004' => 'mpo', 'Mapoly0278s0005' => 'mpo', 'Mapoly0278s0006' => 'mpo', 'MBI11_g30648_MAGBIO' => 'mbi', 'MCO03G194' => 'mco', 'MCO03G590' => 'mco', 'MCO07G312' => 'mco', 'MCO10G318' => 'mco', 'MCO12G244' => 'mco', 'MCO13G148' => 'mco', 'MCO13G194' => 'mco', 'MCO16G238' => 'mco', 'MD06G1134100' => 'mdo', 'MD13G1200100' => 'mdo', 'MD13G1200300' => 'mdo', 'MD13G1200600' => 'mdo', 'MD14G1150400' => 'mdo', 'MD16G1200000' => 'mdo', 'Medtr1g102570' => 'mtr', 'Medtr1g102780' => 'mtr', 'Medtr1g102800' => 'mtr', 'Medtr1g102810' => 'mtr', 'Medtr1g102830' => 'mtr', 'MELO3C006499.2' => 'cme', 'Migut.G00385' => 'egut', 'MSTRG.4063' => 'ama', 'Nitab4.5_0000090g0260' => 'nta', 'Nitab4.5_0000977g0030' => 'nta', 'Nitab4.5_0002541g0040' => 'nta', 'Nitab4.5_0007068g0040' => 'nta', 'Nn005s41408' => 'nnu', 'Nn005s41410' => 'nnu', 'Oeu010310.1' => 'oeu', 'Oeu010311.1' => 'oeu', 'Oeu043472.1' => 'oeu', 'Os01g0246400' => 'osa', 'Os04g0267950' => 'osa', 'Os07g0178700' => 'osa', 'Os07g0178800' => 'osa', 'Peaxi162Scf00316g00046' => 'pax', 'Peaxi162Scf00316g00049' => 'pax', 'Peaxi162Scf00316g00059' => 'pax', 'Peaxi162Scf00316g00328' => 'pax', 'Peaxi162Scf00316g00329' => 'pax', 'Peaxi162Scf00316g00411' => 'pax', 'Peaxi162Scf00316g00521' => 'pax', 'Peaxi162Scf00492g00068' => 'pax', 'Peaxi162Scf35631g00002' => 'pax', 'PGR142G3720' => 'pgr', 'PGSC0003DMG400006442' => 'stu', 'Phvul.007G062000' => 'pvu', 'Potri.008G157750' => 'ptr', 'Potri.008G157900' => 'ptr', 'Potri.008G158000' => 'ptr', 'Potri.008G158200' => 'ptr', 'Pp3c11_7280' => 'ppa', 'Pp3c11_7980' => 'ppa', 'Pp3c12_19450' => 'ppa', 'Pp3c14_1480' => 'ppa', 'Pp3c14_1501' => 'ppa', 'Pp3c16_4900' => 'ppa', 'Pp3c16_5010' => 'ppa', 'Pp3c16_5060' => 'ppa', 'Pp3c19_18250' => 'ppa', 'Pp3c23_8530' => 'ppa', 'Pp3c23_8550' => 'ppa', 'Pp3c24_9670' => 'ppa', 'Pp3c2_21390' => 'ppa', 'Pp3c2_31380' => 'ppa', 'Pp3c3_16620' => 'ppa', 'Pp3c3_8090' => 'ppa', 'Pp3c3_8110' => 'ppa', 'Pp3c3_8130' => 'ppa', 'Pp3c3_8150' => 'ppa', 'Pp3c4_14320' => 'ppa', 'Pp3c6_2560' => 'ppa', 'Pp3c9_16700' => 'ppa', 'PRCOL_00000234' => 'pco', 'PRCOL_00000235' => 'pco', 'PRCOL_00000777' => 'pco', 'PRCOL_00002344' => 'pco', 'PRCOL_00002372' => 'pco', 'PRCOL_00006120' => 'pco', 'Prupe.1G021400' => 'ppe', 'Prupe.1G021500' => 'ppe', 'Prupe.1G021600' => 'ppe', 'Prupe.1G021700' => 'ppe', 'Prupe.1G021800' => 'ppe', 'Prupe.5G145100' => 'ppe', 'Psat6g204040' => 'psa', 'Psat6g204800' => 'psa', 'Psat6g204920' => 'psa', 'Psat6g204960' => 'psa', 'Psat6g205080' => 'psa', 'PSO017G0271' => 'pso', 'PSO017G1276' => 'pso', 'PSO017G1429' => 'pso', 'PSO017G1861' => 'pso', 'PSO017G2787' => 'pso', 'PSO017G4466' => 'pso', 'PSO017G5118' => 'pso', 'PSO017G5420' => 'pso', 'PSO063G3678' => 'pso', 'PSO210G0546' => 'pso', 'PSO317G0001' => 'pso', 'PSO357G0512' => 'pso', 'PSO478G2682' => 'pso', 'PSO647G0001' => 'pso', 'PSO675G0001' => 'pso', 'PSO675G2699' => 'pso', 'PSO675G2849' => 'pso', 'PSO675G4991' => 'pso', 'PSO689G0001' => 'pso', 'QL06p000916' => 'qlo', 'QL06p000921' => 'qlo', 'QL06p001398' => 'qlo', 'QL06p001407' => 'qlo', 'QL06p002031' => 'qlo', 'RcHm_v2.0_Chr4g0387791' => 'rch', 'RcHm_v2.0_Chr4g0387801' => 'rch', 'RcHm_v2.0_Chr6g0286501' => 'rch', 'RcHm_v2.0_Chr6g0286511' => 'rch', 'RcHm_v2.0_Chr6g0286521' => 'rch', 'RcHm_v2.0_Chr6g0286531' => 'rch', 'RcHm_v2.0_Chr7g0189141' => 'rch', 'Rhsim02G0028700' => 'rsi', 'Rhsim02G0028800' => 'rsi', 'Rhsim02G0028900' => 'rsi', 'Rhsim02G0029000' => 'rsi', 'Rhsim02G0029100' => 'rsi', 'Rhsim02G0029200' => 'rsi', 'Rhsim02G0029300' => 'rsi', 'Rhsim02G0029400' => 'rsi', 'Rhsim02G0029500' => 'rsi', 'Rhsim02G0029600' => 'rsi', 'RhsimUnG0024000' => 'rsi', 'RhsimUnG0024100' => 'rsi', 'RhsimUnG0024200' => 'rsi', 'RhsimUnG0024300' => 'rsi', 'RhsimUnG0024400' => 'rsi', 'RhsimUnG0024500' => 'rsi', 'RhsimUnG0024700' => 'rsi', 'RhsimUnG0024800' => 'rsi', 'RhsimUnG0024900' => 'rsi', 'RhsimUnG0025100' => 'rsi', 'Sabra08G0120200' => 'sbr', 'Sabra08G0120300' => 'sbr', 'Sabra08G0120500' => 'sbr', 'Sabra08G0120600' => 'sbr', 'Sabra10G0158900' => 'sbr', 'SalBow2G3492' => 'sbo', 'Sc13g0004760' => 'sci', 'Sc13g0004770' => 'sci', 'Sed0003417' => 'sed', 'Sed0019750' => 'sed', 'SEGI_03419' => 'sgi', 'SEGI_05907' => 'sgi', 'SEGI_10682' => 'sgi', 'SEGI_13528' => 'sgi', 'SEGI_16081' => 'sgi', 'SEGI_19370' => 'sgi', 'SEGI_21015' => 'sgi', 'SEGI_21944' => 'sgi', 'SEGI_32906' => 'sgi', 'SEGI_33093' => 'sgi', 'SEGI_36110' => 'sgi', 'SEGI_40397' => 'sgi', 'SGA_v2.0_scaffold191G40426' => 'sas', 'SGA_v2.0_scaffold353G49717' => 'sas', 'SGA_v2.0_scaffold50G18550' => 'sas', 'SMO119G0173' => 'smo', 'SMO172G0002' => 'smo', 'Solyc09g082690.3' => 'sly', 'Solyc09g082700.2' => 'sly', 'Sopen09g031550' => 'spe', 'Sopen09g031560' => 'spe', 'Sp3g20540' => 'spa', 'Sp7g07580' => 'spa', 'TAR134G0002' => 'tar', 'TAR236G0001' => 'tar', 'TAR365G0892' => 'tar', 'TAR636G0166' => 'tar', 'TAR636G0646' => 'tar', 'TAR636G0869' => 'tar', 'TAR636G1317' => 'tar', 'TAR636G1744' => 'tar', 'TAR636G3358' => 'tar', 'TAR636G3436' => 'tar', 'THA.LOC104803047' => 'tha', 'Thecc.04G238900' => 'tca', 'Thhalv10021557m.g' => 'esa', 'Thhalv10026318m.g' => 'esa', 'Thhalv10026335m.g' => 'esa', 'TPR.G17433' => 'tpr', 'TPR.G18915' => 'tpr', 'TPR.G26125' => 'tpr', 'TWI09G0677' => 'twi', 'TWI73G0287' => 'twi', 'unitig_748.g8326' => 'ugi', 'vmacro15370' => 'vma', 'vmacro15371' => 'vma', 'vmacro15372' => 'vma', 'vmacro15373' => 'vma', 'vmacro15374' => 'vma', 'VMungo0720G2826' => 'vmu', 'Zm00001eb116960' => 'zma', 'Zm00001eb301260' => 'zma', 'Zm00001eb301270' => 'zma' ), 'gf_id' => 'HOM05D001460', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001460' ), 'data_identifier' => 'HOM05D001460', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001460', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '433', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p22980' => 'bna', 'A01p32340' => 'bna', 'A03p42970' => 'bna', 'A05p25880' => 'bna', 'Aa31LG8G9320' => 'aar', 'Aa31LG8G9330' => 'aar', 'Aa31LG8G9340' => 'aar', 'Aa31sc221G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1034' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1528' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.829' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2222' => 'aag', 'Ah.12g058830' => 'amhyb', 'Ah.12g058840' => 'amhyb', 'AL3G37160' => 'aly', 'AL7G41310' => 'aly', 'Aqoxy5G00395' => 'aox', 'Aqoxy5G00396' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0C8NZA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5185HY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JZ1PRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MD3LS0' => 'arhy', 'AT3G22840' => 'ath', 'AT4G14690' => 'ath', 'ATR0665G054' => 'atr', 'Atru.chr4.2344' => 'acertr', 'Atru.chr4.2346' => 'acertr', 'Atru.chr4.2347' => 'acertr', 'Atru.chr4.2348' => 'acertr', 'Atru.chr4.2355' => 'acertr', 'Atru.chr4.2356' => 'acertr', 'Atru.chr4.2358' => 'acertr', 'Atru.chr4.2359' => 'acertr', 'Atru.chr4.2360' => 'acertr', 'Atru.chr4.2361' => 'acertr', 'AUR62030476' => 'cqu', 'AUR62030478' => 'cqu', 'AUR62030819' => 'cqu', 'AUR62030820' => 'cqu', 'BcaB03g14648' => 'bca', 'BcaB04g20492' => 'bca', 'BcaB06g26399' => 'bca', 'BcaC01g03416' => 'bca', 'BcaC01g03419' => 'bca', 'BcaC01g03421' => 'bca', 'BcaC01g03424' => 'bca', 'BcaC05g28012' => 'bca', 'BcaC09g49212' => 'bca', 'BcaC09g50140' => 'bca', 'BcaNung00346' => 'bca', 'BolC1t02785H' => 'bol', 'BolC1t04095H' => 'bol', 'BolC3t17545H' => 'bol', 'BolC5t32769H' => 'bol', 'BraA01t02211Z' => 'bra', 'BraA01t03359Z' => 'bra', 'BraA03t13441Z' => 'bra', 'BraA05t21476Z' => 'bra', 'C01p28420' => 'bna', 'C01p41350' => 'bna', 'C03p52750' => 'bna', 'C03p52780' => 'bna', 'C05p40270' => 'bna', 'CAN.G1437.9' => 'can', 'CANSAT78G0035' => 'cansat', 'CANSAT78G1036' => 'cansat', 'CANSAT78G2272' => 'cansat', 'CANSAT78G2478' => 'cansat', 'CARHR098700' => 'chi', 'CARHR221120' => 'chi', 'CARHR221150' => 'chi', 'Carub.0003s2297' => 'cru', 'Carub.0007s2749' => 'cru', 'Carub.0007s2750' => 'cru', 'Carub.0007s2751' => 'cru', 'Ca_10849_v3' => 'car', 'Cc03_g04300' => 'ccan', 'CDE02G3648' => 'cde', 'CDE05G0060' => 'cde', 'CDE05G0692' => 'cde', 'CDE05G2285' => 'cde', 'CDE05G2884' => 'cde', 'CDE05G3072' => 'cde', 'Cfa008439' => 'cfa', 'Cfa008441' => 'cfa', 'Cfa008443' => 'cfa', 'Cfa008448' => 'cfa', 'Ciclev10005974m.g' => 'ccl', 'Ciclev10006006m.g' => 'ccl', 'Ciclev10006775m.g' => 'ccl', 'CiPaw.02G120400' => 'cil', 'CiPaw.02G120500' => 'cil', 'CiPaw.02G120600' => 'cil', 'ClCG05G004850' => 'cla', 'COL.COLO4_21566' => 'col', 'Cpa.g.sc44.124' => 'cpa', 'Cre07.g320400' => 'cre', 'Cre07.g320450' => 'cre', 'Cre08.g384650' => 'cre', 'Cre09.g393173' => 'cre', 'Cre09.g394325' => 'cre', 'Cre14.g626750' => 'cre', 'Cre16.g679250' => 'cre', 'CsaV3_3G012890' => 'csa', 'CSS0010865' => 'camsi', 'CSS0044338' => 'camsi', 'DCAR_002366' => 'dca', 'DCAR_030687' => 'dca', 'DCAR_030688' => 'dca', 'Dinv14047' => 'din', 'Dinv14048' => 'din', 'Duzib151G0105' => 'dzi', 'Duzib151G0114' => 'dzi', 'Duzib212G1029' => 'dzi', 'ECA232G3536' => 'eca', 'ECA240G0786' => 'eca', 'ECA240G1802' => 'eca', 'ECA240G3760' => 'eca', 'ECA240G3920' => 'eca', 'EL10Ac5g12536' => 'bvu', 'EL10Ac5g12537' => 'bvu', 'EL10Ac5g12538' => 'bvu', 'Eucgr.B01004' => 'egr', 'Eucgr.B01006' => 'egr', 'Eucgr.B01007' => 'egr', 'Eucgr.B01008' => 'egr', 'Eucgr.B01895' => 'egr', 'Eucgr.B01896' => 'egr', 'FAN04G1456' => 'fan', 'FAN08G1769' => 'fan', 'FAN08G2160' => 'fan', 'FAN13G2403' => 'fan', 'FAN13G3303' => 'fan', 'FAN15G2435' => 'fan', 'FAN17G0672' => 'fan', 'FAN17G2441' => 'fan', 'FAN18G1024' => 'fan', 'FAN22G1458' => 'fan', 'FAN24G0037' => 'fan', 'FAN24G0429' => 'fan', 'FAN24G2387' => 'fan', 'FAN27G2746' => 'fan', 'FvH4_2g20400' => 'fve', 'FvH4_2g20420' => 'fve', 'FvH4_2g20430' => 'fve', 'FvH4_4g01270' => 'fve', 'FvH4_4g01290' => 'fve', 'FvH4_4g01300' => 'fve', 'FvH4_4g01310' => 'fve', 'FvH4_4g01330' => 'fve', 'FvH4_5g09070' => 'fve', 'Glyma.10G243800' => 'gma', 'Glyma.20G150600' => 'gma', 'Gohir.A09G219200' => 'ghi', 'Gohir.A09G219300' => 'ghi', 'Gohir.D09G221400' => 'ghi', 'Gohir.D09G221500' => 'ghi', 'Gorai.006G242600' => 'gra', 'Gorai.006G242700' => 'gra', 'GSVIVG01018044001' => 'vvi', 'HanXRQChr03g0083821' => 'han', 'HanXRQChr03g0083841' => 'han', 'HanXRQChr03g0083881' => 'han', 'HanXRQChr03g0083901' => 'han', 'HanXRQChr03g0083921' => 'han', 'HanXRQChr03g0085331' => 'han', 'HanXRQChr03g0085361' => 'han', 'HanXRQChr03g0085411' => 'han', 'HanXRQChr03g0085421' => 'han', 'HanXRQChr03g0085431' => 'han', 'HanXRQChr08g0221991' => 'han', 'HanXRQChr11g0336061' => 'han', 'HanXRQChr11g0336411' => 'han', 'Haze_11234' => 'cav', 'Hma1.2p1_0549F.1_g177010' => 'hma', 'Hma1.2p1_0602F.1_g187630' => 'hma', 'Hund14876' => 'sun', 'Hund14879' => 'sun', 'Lalb_Chr06g0160741' => 'lal', 'Lalb_Chr21g0304781' => 'lal', 'Lj3A726G19' => 'lonja', 'Lj3A726T23' => 'lonja', 'Lj3A726T24' => 'lonja', 'Lj3A726T25' => 'lonja', 'Lj3A727T17' => 'lonja', 'Lj3C726T0' => 'lonja', 'Lj3C726T2' => 'lonja', 'Lj3P725T35' => 'lonja', 'Lj3P727T10' => 'lonja', 'Lj3P727T12' => 'lonja', 'Lj3P727T14' => 'lonja', 'Lj5g0023109' => 'lja', 'Lj6P646T44' => 'lonja', 'Lsat_1_v5_gn_6_75760' => 'lsa', 'Lsat_1_v5_gn_6_75800' => 'lsa', 'Lsat_1_v5_gn_6_75900' => 'lsa', 'Lsat_1_v5_gn_6_76240' => 'lsa', 'Lsat_1_v5_gn_6_76441' => 'lsa', 'Lsat_1_v5_gn_6_76700' => 'lsa', 'Lsat_1_v5_gn_6_76760' => 'lsa', 'Manes.15G033100' => 'mes', 'Mapoly0004s0074' => 'mpo', 'Mapoly0004s0075' => 'mpo', 'Mapoly0004s0163' => 'mpo', 'Mapoly0004s0164' => 'mpo', 'Mapoly0021s0018' => 'mpo', 'Mapoly0041s0136' => 'mpo', 'Mapoly0041s0137' => 'mpo', 'Mapoly0041s0138' => 'mpo', 'Mapoly0041s0139' => 'mpo', 'Mapoly0041s0141' => 'mpo', 'Mapoly0041s0142' => 'mpo', 'Mapoly0041s0143' => 'mpo', 'Mapoly0041s0144' => 'mpo', 'Mapoly0041s0145' => 'mpo', 'Mapoly0047s0106' => 'mpo', 'Mapoly0047s0108' => 'mpo', 'Mapoly0050s0051' => 'mpo', 'Mapoly0050s0052' => 'mpo', 'Mapoly0050s0053' => 'mpo', 'Mapoly0058s0013' => 'mpo', 'Mapoly0091s0078' => 'mpo', 'Mapoly0091s0079' => 'mpo', 'Mapoly0091s0080' => 'mpo', 'Mapoly0091s0081' => 'mpo', 'Mapoly0278s0004' => 'mpo', 'Mapoly0278s0005' => 'mpo', 'Mapoly0278s0006' => 'mpo', 'MBI11_g30648_MAGBIO' => 'mbi', 'MCO03G194' => 'mco', 'MCO03G590' => 'mco', 'MCO07G312' => 'mco', 'MCO10G318' => 'mco', 'MCO12G244' => 'mco', 'MCO13G148' => 'mco', 'MCO13G194' => 'mco', 'MCO16G238' => 'mco', 'MD06G1134100' => 'mdo', 'MD13G1200100' => 'mdo', 'MD13G1200300' => 'mdo', 'MD13G1200600' => 'mdo', 'MD14G1150400' => 'mdo', 'MD16G1200000' => 'mdo', 'Medtr1g102570' => 'mtr', 'Medtr1g102780' => 'mtr', 'Medtr1g102800' => 'mtr', 'Medtr1g102810' => 'mtr', 'Medtr1g102830' => 'mtr', 'MELO3C006499.2' => 'cme', 'Migut.G00385' => 'egut', 'MSTRG.4063' => 'ama', 'Nitab4.5_0000090g0260' => 'nta', 'Nitab4.5_0000977g0030' => 'nta', 'Nitab4.5_0002541g0040' => 'nta', 'Nitab4.5_0007068g0040' => 'nta', 'Nn005s41408' => 'nnu', 'Nn005s41410' => 'nnu', 'Oeu010310.1' => 'oeu', 'Oeu010311.1' => 'oeu', 'Oeu043472.1' => 'oeu', 'Os01g0246400' => 'osa', 'Os04g0267950' => 'osa', 'Os07g0178700' => 'osa', 'Os07g0178800' => 'osa', 'Peaxi162Scf00316g00046' => 'pax', 'Peaxi162Scf00316g00049' => 'pax', 'Peaxi162Scf00316g00059' => 'pax', 'Peaxi162Scf00316g00328' => 'pax', 'Peaxi162Scf00316g00329' => 'pax', 'Peaxi162Scf00316g00411' => 'pax', 'Peaxi162Scf00316g00521' => 'pax', 'Peaxi162Scf00492g00068' => 'pax', 'Peaxi162Scf35631g00002' => 'pax', 'PGR142G3720' => 'pgr', 'PGSC0003DMG400006442' => 'stu', 'Phvul.007G062000' => 'pvu', 'Potri.008G157750' => 'ptr', 'Potri.008G157900' => 'ptr', 'Potri.008G158000' => 'ptr', 'Potri.008G158200' => 'ptr', 'Pp3c11_7280' => 'ppa', 'Pp3c11_7980' => 'ppa', 'Pp3c12_19450' => 'ppa', 'Pp3c14_1480' => 'ppa', 'Pp3c14_1501' => 'ppa', 'Pp3c16_4900' => 'ppa', 'Pp3c16_5010' => 'ppa', 'Pp3c16_5060' => 'ppa', 'Pp3c19_18250' => 'ppa', 'Pp3c23_8530' => 'ppa', 'Pp3c23_8550' => 'ppa', 'Pp3c24_9670' => 'ppa', 'Pp3c2_21390' => 'ppa', 'Pp3c2_31380' => 'ppa', 'Pp3c3_16620' => 'ppa', 'Pp3c3_8090' => 'ppa', 'Pp3c3_8110' => 'ppa', 'Pp3c3_8130' => 'ppa', 'Pp3c3_8150' => 'ppa', 'Pp3c4_14320' => 'ppa', 'Pp3c6_2560' => 'ppa', 'Pp3c9_16700' => 'ppa', 'PRCOL_00000234' => 'pco', 'PRCOL_00000235' => 'pco', 'PRCOL_00000777' => 'pco', 'PRCOL_00002344' => 'pco', 'PRCOL_00002372' => 'pco', 'PRCOL_00006120' => 'pco', 'Prupe.1G021400' => 'ppe', 'Prupe.1G021500' => 'ppe', 'Prupe.1G021600' => 'ppe', 'Prupe.1G021700' => 'ppe', 'Prupe.1G021800' => 'ppe', 'Prupe.5G145100' => 'ppe', 'Psat6g204040' => 'psa', 'Psat6g204800' => 'psa', 'Psat6g204920' => 'psa', 'Psat6g204960' => 'psa', 'Psat6g205080' => 'psa', 'PSO017G0271' => 'pso', 'PSO017G1276' => 'pso', 'PSO017G1429' => 'pso', 'PSO017G1861' => 'pso', 'PSO017G2787' => 'pso', 'PSO017G4466' => 'pso', 'PSO017G5118' => 'pso', 'PSO017G5420' => 'pso', 'PSO063G3678' => 'pso', 'PSO210G0546' => 'pso', 'PSO317G0001' => 'pso', 'PSO357G0512' => 'pso', 'PSO478G2682' => 'pso', 'PSO647G0001' => 'pso', 'PSO675G0001' => 'pso', 'PSO675G2699' => 'pso', 'PSO675G2849' => 'pso', 'PSO675G4991' => 'pso', 'PSO689G0001' => 'pso', 'QL06p000916' => 'qlo', 'QL06p000921' => 'qlo', 'QL06p001398' => 'qlo', 'QL06p001407' => 'qlo', 'QL06p002031' => 'qlo', 'RcHm_v2.0_Chr4g0387791' => 'rch', 'RcHm_v2.0_Chr4g0387801' => 'rch', 'RcHm_v2.0_Chr6g0286501' => 'rch', 'RcHm_v2.0_Chr6g0286511' => 'rch', 'RcHm_v2.0_Chr6g0286521' => 'rch', 'RcHm_v2.0_Chr6g0286531' => 'rch', 'RcHm_v2.0_Chr7g0189141' => 'rch', 'Rhsim02G0028700' => 'rsi', 'Rhsim02G0028800' => 'rsi', 'Rhsim02G0028900' => 'rsi', 'Rhsim02G0029000' => 'rsi', 'Rhsim02G0029100' => 'rsi', 'Rhsim02G0029200' => 'rsi', 'Rhsim02G0029300' => 'rsi', 'Rhsim02G0029400' => 'rsi', 'Rhsim02G0029500' => 'rsi', 'Rhsim02G0029600' => 'rsi', 'RhsimUnG0024000' => 'rsi', 'RhsimUnG0024100' => 'rsi', 'RhsimUnG0024200' => 'rsi', 'RhsimUnG0024300' => 'rsi', 'RhsimUnG0024400' => 'rsi', 'RhsimUnG0024500' => 'rsi', 'RhsimUnG0024700' => 'rsi', 'RhsimUnG0024800' => 'rsi', 'RhsimUnG0024900' => 'rsi', 'RhsimUnG0025100' => 'rsi', 'Sabra08G0120200' => 'sbr', 'Sabra08G0120300' => 'sbr', 'Sabra08G0120500' => 'sbr', 'Sabra08G0120600' => 'sbr', 'Sabra10G0158900' => 'sbr', 'SalBow2G3492' => 'sbo', 'Sc13g0004760' => 'sci', 'Sc13g0004770' => 'sci', 'Sed0003417' => 'sed', 'Sed0019750' => 'sed', 'SEGI_03419' => 'sgi', 'SEGI_05907' => 'sgi', 'SEGI_10682' => 'sgi', 'SEGI_13528' => 'sgi', 'SEGI_16081' => 'sgi', 'SEGI_19370' => 'sgi', 'SEGI_21015' => 'sgi', 'SEGI_21944' => 'sgi', 'SEGI_32906' => 'sgi', 'SEGI_33093' => 'sgi', 'SEGI_36110' => 'sgi', 'SEGI_40397' => 'sgi', 'SGA_v2.0_scaffold191G40426' => 'sas', 'SGA_v2.0_scaffold353G49717' => 'sas', 'SGA_v2.0_scaffold50G18550' => 'sas', 'SMO119G0173' => 'smo', 'SMO172G0002' => 'smo', 'Solyc09g082690.3' => 'sly', 'Solyc09g082700.2' => 'sly', 'Sopen09g031550' => 'spe', 'Sopen09g031560' => 'spe', 'Sp3g20540' => 'spa', 'Sp7g07580' => 'spa', 'TAR134G0002' => 'tar', 'TAR236G0001' => 'tar', 'TAR365G0892' => 'tar', 'TAR636G0166' => 'tar', 'TAR636G0646' => 'tar', 'TAR636G0869' => 'tar', 'TAR636G1317' => 'tar', 'TAR636G1744' => 'tar', 'TAR636G3358' => 'tar', 'TAR636G3436' => 'tar', 'THA.LOC104803047' => 'tha', 'Thecc.04G238900' => 'tca', 'Thhalv10021557m.g' => 'esa', 'Thhalv10026318m.g' => 'esa', 'Thhalv10026335m.g' => 'esa', 'TPR.G17433' => 'tpr', 'TPR.G18915' => 'tpr', 'TPR.G26125' => 'tpr', 'TWI09G0677' => 'twi', 'TWI73G0287' => 'twi', 'unitig_748.g8326' => 'ugi', 'vmacro15370' => 'vma', 'vmacro15371' => 'vma', 'vmacro15372' => 'vma', 'vmacro15373' => 'vma', 'vmacro15374' => 'vma', 'VMungo0720G2826' => 'vmu', 'Zm00001eb116960' => 'zma', 'Zm00001eb301260' => 'zma', 'Zm00001eb301270' => 'zma' ) $gf_id = 'HOM05D001460' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001460' ) $data_identifier = 'HOM05D001460' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 4, 'aag' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 2, 'aox' => (int) 2, 'arhy' => (int) 4, 'ath' => (int) 2, 'atr' => (int) 1, 'acertr' => (int) 10, 'cqu' => (int) 4, 'bca' => (int) 11, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 1, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 1, 'ccan' => (int) 1, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 1, 'col' => (int) 1, 'cpa' => (int) 1, 'cre' => (int) 7, 'csa' => (int) 1, 'camsi' => (int) 2, 'dca' => (int) 3, 'din' => (int) 2, 'dzi' => (int) 3, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 14, 'fve' => (int) 9, 'gma' => (int) 2, 'ghi' => (int) 4, 'gra' => (int) 2, 'vvi' => (int) 1, 'han' => (int) 13, 'cav' => (int) 1, 'hma' => (int) 2, 'sun' => (int) 2, 'lal' => (int) 2, 'lonja' => (int) 12, 'lja' => (int) 1, 'lsa' => (int) 7, 'mes' => (int) 1, 'mpo' => (int) 27, 'mbi' => (int) 1, 'mco' => (int) 8, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 1, 'egut' => (int) 1, 'ama' => (int) 1, 'nta' => (int) 4, 'nnu' => (int) 2, 'oeu' => (int) 3, 'osa' => (int) 4, 'pax' => (int) 9, 'pgr' => (int) 1, 'stu' => (int) 1, 'pvu' => (int) 1, 'ptr' => (int) 4, 'ppa' => (int) 22, 'pco' => (int) 6, 'ppe' => (int) 6, 'psa' => (int) 5, 'pso' => (int) 19, 'qlo' => (int) 5, 'rch' => (int) 7, 'rsi' => (int) 20, 'sbr' => (int) 5, 'sbo' => (int) 1, 'sci' => (int) 2, 'sed' => (int) 2, 'sgi' => (int) 12, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 2, 'tar' => (int) 10, 'tha' => (int) 1, 'tca' => (int) 1, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 2, 'ugi' => (int) 1, 'vma' => (int) 5, 'vmu' => (int) 1, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb301270' $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' => 'HOM05D001460', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '433', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p22980' => 'bna', 'A01p32340' => 'bna', 'A03p42970' => 'bna', 'A05p25880' => 'bna', 'Aa31LG8G9320' => 'aar', 'Aa31LG8G9330' => 'aar', 'Aa31LG8G9340' => 'aar', 'Aa31sc221G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1034' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1528' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.829' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2222' => 'aag', 'Ah.12g058830' => 'amhyb', 'Ah.12g058840' => 'amhyb', 'AL3G37160' => 'aly', 'AL7G41310' => 'aly', 'Aqoxy5G00395' => 'aox', 'Aqoxy5G00396' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0C8NZA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5185HY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JZ1PRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MD3LS0' => 'arhy', 'AT3G22840' => 'ath', 'AT4G14690' => 'ath', 'ATR0665G054' => 'atr', 'Atru.chr4.2344' => 'acertr', 'Atru.chr4.2346' => 'acertr', 'Atru.chr4.2347' => 'acertr', 'Atru.chr4.2348' => 'acertr', 'Atru.chr4.2355' => 'acertr', 'Atru.chr4.2356' => 'acertr', 'Atru.chr4.2358' => 'acertr', 'Atru.chr4.2359' => 'acertr', 'Atru.chr4.2360' => 'acertr', 'Atru.chr4.2361' => 'acertr', 'AUR62030476' => 'cqu', 'AUR62030478' => 'cqu', 'AUR62030819' => 'cqu', 'AUR62030820' => 'cqu', 'BcaB03g14648' => 'bca', 'BcaB04g20492' => 'bca', 'BcaB06g26399' => 'bca', 'BcaC01g03416' => 'bca', 'BcaC01g03419' => 'bca', 'BcaC01g03421' => 'bca', 'BcaC01g03424' => 'bca', 'BcaC05g28012' => 'bca', 'BcaC09g49212' => 'bca', 'BcaC09g50140' => 'bca', 'BcaNung00346' => 'bca', 'BolC1t02785H' => 'bol', 'BolC1t04095H' => 'bol', 'BolC3t17545H' => 'bol', 'BolC5t32769H' => 'bol', 'BraA01t02211Z' => 'bra', 'BraA01t03359Z' => 'bra', 'BraA03t13441Z' => 'bra', 'BraA05t21476Z' => 'bra', 'C01p28420' => 'bna', 'C01p41350' => 'bna', 'C03p52750' => 'bna', 'C03p52780' => 'bna', 'C05p40270' => 'bna', 'CAN.G1437.9' => 'can', 'CANSAT78G0035' => 'cansat', 'CANSAT78G1036' => 'cansat', 'CANSAT78G2272' => 'cansat', 'CANSAT78G2478' => 'cansat', 'CARHR098700' => 'chi', 'CARHR221120' => 'chi', 'CARHR221150' => 'chi', 'Carub.0003s2297' => 'cru', 'Carub.0007s2749' => 'cru', 'Carub.0007s2750' => 'cru', 'Carub.0007s2751' => 'cru', 'Ca_10849_v3' => 'car', 'Cc03_g04300' => 'ccan', 'CDE02G3648' => 'cde', 'CDE05G0060' => 'cde', 'CDE05G0692' => 'cde', 'CDE05G2285' => 'cde', 'CDE05G2884' => 'cde', 'CDE05G3072' => 'cde', 'Cfa008439' => 'cfa', 'Cfa008441' => 'cfa', 'Cfa008443' => 'cfa', 'Cfa008448' => 'cfa', 'Ciclev10005974m.g' => 'ccl', 'Ciclev10006006m.g' => 'ccl', 'Ciclev10006775m.g' => 'ccl', 'CiPaw.02G120400' => 'cil', 'CiPaw.02G120500' => 'cil', 'CiPaw.02G120600' => 'cil', 'ClCG05G004850' => 'cla', 'COL.COLO4_21566' => 'col', 'Cpa.g.sc44.124' => 'cpa', 'Cre07.g320400' => 'cre', 'Cre07.g320450' => 'cre', 'Cre08.g384650' => 'cre', 'Cre09.g393173' => 'cre', 'Cre09.g394325' => 'cre', 'Cre14.g626750' => 'cre', 'Cre16.g679250' => 'cre', 'CsaV3_3G012890' => 'csa', 'CSS0010865' => 'camsi', 'CSS0044338' => 'camsi', 'DCAR_002366' => 'dca', 'DCAR_030687' => 'dca', 'DCAR_030688' => 'dca', 'Dinv14047' => 'din', 'Dinv14048' => 'din', 'Duzib151G0105' => 'dzi', 'Duzib151G0114' => 'dzi', 'Duzib212G1029' => 'dzi', 'ECA232G3536' => 'eca', 'ECA240G0786' => 'eca', 'ECA240G1802' => 'eca', 'ECA240G3760' => 'eca', 'ECA240G3920' => 'eca', 'EL10Ac5g12536' => 'bvu', 'EL10Ac5g12537' => 'bvu', 'EL10Ac5g12538' => 'bvu', 'Eucgr.B01004' => 'egr', 'Eucgr.B01006' => 'egr', 'Eucgr.B01007' => 'egr', 'Eucgr.B01008' => 'egr', 'Eucgr.B01895' => 'egr', 'Eucgr.B01896' => 'egr', 'FAN04G1456' => 'fan', 'FAN08G1769' => 'fan', 'FAN08G2160' => 'fan', 'FAN13G2403' => 'fan', 'FAN13G3303' => 'fan', 'FAN15G2435' => 'fan', 'FAN17G0672' => 'fan', 'FAN17G2441' => 'fan', 'FAN18G1024' => 'fan', 'FAN22G1458' => 'fan', 'FAN24G0037' => 'fan', 'FAN24G0429' => 'fan', 'FAN24G2387' => 'fan', 'FAN27G2746' => 'fan', 'FvH4_2g20400' => 'fve', 'FvH4_2g20420' => 'fve', 'FvH4_2g20430' => 'fve', 'FvH4_4g01270' => 'fve', 'FvH4_4g01290' => 'fve', 'FvH4_4g01300' => 'fve', 'FvH4_4g01310' => 'fve', 'FvH4_4g01330' => 'fve', 'FvH4_5g09070' => 'fve', 'Glyma.10G243800' => 'gma', 'Glyma.20G150600' => 'gma', 'Gohir.A09G219200' => 'ghi', 'Gohir.A09G219300' => 'ghi', 'Gohir.D09G221400' => 'ghi', 'Gohir.D09G221500' => 'ghi', 'Gorai.006G242600' => 'gra', 'Gorai.006G242700' => 'gra', 'GSVIVG01018044001' => 'vvi', 'HanXRQChr03g0083821' => 'han', 'HanXRQChr03g0083841' => 'han', 'HanXRQChr03g0083881' => 'han', 'HanXRQChr03g0083901' => 'han', 'HanXRQChr03g0083921' => 'han', 'HanXRQChr03g0085331' => 'han', 'HanXRQChr03g0085361' => 'han', 'HanXRQChr03g0085411' => 'han', 'HanXRQChr03g0085421' => 'han', 'HanXRQChr03g0085431' => 'han', 'HanXRQChr08g0221991' => 'han', 'HanXRQChr11g0336061' => 'han', 'HanXRQChr11g0336411' => 'han', 'Haze_11234' => 'cav', 'Hma1.2p1_0549F.1_g177010' => 'hma', 'Hma1.2p1_0602F.1_g187630' => 'hma', 'Hund14876' => 'sun', 'Hund14879' => 'sun', 'Lalb_Chr06g0160741' => 'lal', 'Lalb_Chr21g0304781' => 'lal', 'Lj3A726G19' => 'lonja', 'Lj3A726T23' => 'lonja', 'Lj3A726T24' => 'lonja', 'Lj3A726T25' => 'lonja', 'Lj3A727T17' => 'lonja', 'Lj3C726T0' => 'lonja', 'Lj3C726T2' => 'lonja', 'Lj3P725T35' => 'lonja', 'Lj3P727T10' => 'lonja', 'Lj3P727T12' => 'lonja', 'Lj3P727T14' => 'lonja', 'Lj5g0023109' => 'lja', 'Lj6P646T44' => 'lonja', 'Lsat_1_v5_gn_6_75760' => 'lsa', 'Lsat_1_v5_gn_6_75800' => 'lsa', 'Lsat_1_v5_gn_6_75900' => 'lsa', 'Lsat_1_v5_gn_6_76240' => 'lsa', 'Lsat_1_v5_gn_6_76441' => 'lsa', 'Lsat_1_v5_gn_6_76700' => 'lsa', 'Lsat_1_v5_gn_6_76760' => 'lsa', 'Manes.15G033100' => 'mes', 'Mapoly0004s0074' => 'mpo', 'Mapoly0004s0075' => 'mpo', 'Mapoly0004s0163' => 'mpo', 'Mapoly0004s0164' => 'mpo', 'Mapoly0021s0018' => 'mpo', 'Mapoly0041s0136' => 'mpo', 'Mapoly0041s0137' => 'mpo', 'Mapoly0041s0138' => 'mpo', 'Mapoly0041s0139' => 'mpo', 'Mapoly0041s0141' => 'mpo', 'Mapoly0041s0142' => 'mpo', 'Mapoly0041s0143' => 'mpo', 'Mapoly0041s0144' => 'mpo', 'Mapoly0041s0145' => 'mpo', 'Mapoly0047s0106' => 'mpo', 'Mapoly0047s0108' => 'mpo', 'Mapoly0050s0051' => 'mpo', 'Mapoly0050s0052' => 'mpo', 'Mapoly0050s0053' => 'mpo', 'Mapoly0058s0013' => 'mpo', 'Mapoly0091s0078' => 'mpo', 'Mapoly0091s0079' => 'mpo', 'Mapoly0091s0080' => 'mpo', 'Mapoly0091s0081' => 'mpo', 'Mapoly0278s0004' => 'mpo', 'Mapoly0278s0005' => 'mpo', 'Mapoly0278s0006' => 'mpo', 'MBI11_g30648_MAGBIO' => 'mbi', 'MCO03G194' => 'mco', 'MCO03G590' => 'mco', 'MCO07G312' => 'mco', 'MCO10G318' => 'mco', 'MCO12G244' => 'mco', 'MCO13G148' => 'mco', 'MCO13G194' => 'mco', 'MCO16G238' => 'mco', 'MD06G1134100' => 'mdo', 'MD13G1200100' => 'mdo', 'MD13G1200300' => 'mdo', 'MD13G1200600' => 'mdo', 'MD14G1150400' => 'mdo', 'MD16G1200000' => 'mdo', 'Medtr1g102570' => 'mtr', 'Medtr1g102780' => 'mtr', 'Medtr1g102800' => 'mtr', 'Medtr1g102810' => 'mtr', 'Medtr1g102830' => 'mtr', 'MELO3C006499.2' => 'cme', 'Migut.G00385' => 'egut', 'MSTRG.4063' => 'ama', 'Nitab4.5_0000090g0260' => 'nta', 'Nitab4.5_0000977g0030' => 'nta', 'Nitab4.5_0002541g0040' => 'nta', 'Nitab4.5_0007068g0040' => 'nta', 'Nn005s41408' => 'nnu', 'Nn005s41410' => 'nnu', 'Oeu010310.1' => 'oeu', 'Oeu010311.1' => 'oeu', 'Oeu043472.1' => 'oeu', 'Os01g0246400' => 'osa', 'Os04g0267950' => 'osa', 'Os07g0178700' => 'osa', 'Os07g0178800' => 'osa', 'Peaxi162Scf00316g00046' => 'pax', 'Peaxi162Scf00316g00049' => 'pax', 'Peaxi162Scf00316g00059' => 'pax', 'Peaxi162Scf00316g00328' => 'pax', 'Peaxi162Scf00316g00329' => 'pax', 'Peaxi162Scf00316g00411' => 'pax', 'Peaxi162Scf00316g00521' => 'pax', 'Peaxi162Scf00492g00068' => 'pax', 'Peaxi162Scf35631g00002' => 'pax', 'PGR142G3720' => 'pgr', 'PGSC0003DMG400006442' => 'stu', 'Phvul.007G062000' => 'pvu', 'Potri.008G157750' => 'ptr', 'Potri.008G157900' => 'ptr', 'Potri.008G158000' => 'ptr', 'Potri.008G158200' => 'ptr', 'Pp3c11_7280' => 'ppa', 'Pp3c11_7980' => 'ppa', 'Pp3c12_19450' => 'ppa', 'Pp3c14_1480' => 'ppa', 'Pp3c14_1501' => 'ppa', 'Pp3c16_4900' => 'ppa', 'Pp3c16_5010' => 'ppa', 'Pp3c16_5060' => 'ppa', 'Pp3c19_18250' => 'ppa', 'Pp3c23_8530' => 'ppa', 'Pp3c23_8550' => 'ppa', 'Pp3c24_9670' => 'ppa', 'Pp3c2_21390' => 'ppa', 'Pp3c2_31380' => 'ppa', 'Pp3c3_16620' => 'ppa', 'Pp3c3_8090' => 'ppa', 'Pp3c3_8110' => 'ppa', 'Pp3c3_8130' => 'ppa', 'Pp3c3_8150' => 'ppa', 'Pp3c4_14320' => 'ppa', 'Pp3c6_2560' => 'ppa', 'Pp3c9_16700' => 'ppa', 'PRCOL_00000234' => 'pco', 'PRCOL_00000235' => 'pco', 'PRCOL_00000777' => 'pco', 'PRCOL_00002344' => 'pco', 'PRCOL_00002372' => 'pco', 'PRCOL_00006120' => 'pco', 'Prupe.1G021400' => 'ppe', 'Prupe.1G021500' => 'ppe', 'Prupe.1G021600' => 'ppe', 'Prupe.1G021700' => 'ppe', 'Prupe.1G021800' => 'ppe', 'Prupe.5G145100' => 'ppe', 'Psat6g204040' => 'psa', 'Psat6g204800' => 'psa', 'Psat6g204920' => 'psa', 'Psat6g204960' => 'psa', 'Psat6g205080' => 'psa', 'PSO017G0271' => 'pso', 'PSO017G1276' => 'pso', 'PSO017G1429' => 'pso', 'PSO017G1861' => 'pso', 'PSO017G2787' => 'pso', 'PSO017G4466' => 'pso', 'PSO017G5118' => 'pso', 'PSO017G5420' => 'pso', 'PSO063G3678' => 'pso', 'PSO210G0546' => 'pso', 'PSO317G0001' => 'pso', 'PSO357G0512' => 'pso', 'PSO478G2682' => 'pso', 'PSO647G0001' => 'pso', 'PSO675G0001' => 'pso', 'PSO675G2699' => 'pso', 'PSO675G2849' => 'pso', 'PSO675G4991' => 'pso', 'PSO689G0001' => 'pso', 'QL06p000916' => 'qlo', 'QL06p000921' => 'qlo', 'QL06p001398' => 'qlo', 'QL06p001407' => 'qlo', 'QL06p002031' => 'qlo', 'RcHm_v2.0_Chr4g0387791' => 'rch', 'RcHm_v2.0_Chr4g0387801' => 'rch', 'RcHm_v2.0_Chr6g0286501' => 'rch', 'RcHm_v2.0_Chr6g0286511' => 'rch', 'RcHm_v2.0_Chr6g0286521' => 'rch', 'RcHm_v2.0_Chr6g0286531' => 'rch', 'RcHm_v2.0_Chr7g0189141' => 'rch', 'Rhsim02G0028700' => 'rsi', 'Rhsim02G0028800' => 'rsi', 'Rhsim02G0028900' => 'rsi', 'Rhsim02G0029000' => 'rsi', 'Rhsim02G0029100' => 'rsi', 'Rhsim02G0029200' => 'rsi', 'Rhsim02G0029300' => 'rsi', 'Rhsim02G0029400' => 'rsi', 'Rhsim02G0029500' => 'rsi', 'Rhsim02G0029600' => 'rsi', 'RhsimUnG0024000' => 'rsi', 'RhsimUnG0024100' => 'rsi', 'RhsimUnG0024200' => 'rsi', 'RhsimUnG0024300' => 'rsi', 'RhsimUnG0024400' => 'rsi', 'RhsimUnG0024500' => 'rsi', 'RhsimUnG0024700' => 'rsi', 'RhsimUnG0024800' => 'rsi', 'RhsimUnG0024900' => 'rsi', 'RhsimUnG0025100' => 'rsi', 'Sabra08G0120200' => 'sbr', 'Sabra08G0120300' => 'sbr', 'Sabra08G0120500' => 'sbr', 'Sabra08G0120600' => 'sbr', 'Sabra10G0158900' => 'sbr', 'SalBow2G3492' => 'sbo', 'Sc13g0004760' => 'sci', 'Sc13g0004770' => 'sci', 'Sed0003417' => 'sed', 'Sed0019750' => 'sed', 'SEGI_03419' => 'sgi', 'SEGI_05907' => 'sgi', 'SEGI_10682' => 'sgi', 'SEGI_13528' => 'sgi', 'SEGI_16081' => 'sgi', 'SEGI_19370' => 'sgi', 'SEGI_21015' => 'sgi', 'SEGI_21944' => 'sgi', 'SEGI_32906' => 'sgi', 'SEGI_33093' => 'sgi', 'SEGI_36110' => 'sgi', 'SEGI_40397' => 'sgi', 'SGA_v2.0_scaffold191G40426' => 'sas', 'SGA_v2.0_scaffold353G49717' => 'sas', 'SGA_v2.0_scaffold50G18550' => 'sas', 'SMO119G0173' => 'smo', 'SMO172G0002' => 'smo', 'Solyc09g082690.3' => 'sly', 'Solyc09g082700.2' => 'sly', 'Sopen09g031550' => 'spe', 'Sopen09g031560' => 'spe', 'Sp3g20540' => 'spa', 'Sp7g07580' => 'spa', 'TAR134G0002' => 'tar', 'TAR236G0001' => 'tar', 'TAR365G0892' => 'tar', 'TAR636G0166' => 'tar', 'TAR636G0646' => 'tar', 'TAR636G0869' => 'tar', 'TAR636G1317' => 'tar', 'TAR636G1744' => 'tar', 'TAR636G3358' => 'tar', 'TAR636G3436' => 'tar', 'THA.LOC104803047' => 'tha', 'Thecc.04G238900' => 'tca', 'Thhalv10021557m.g' => 'esa', 'Thhalv10026318m.g' => 'esa', 'Thhalv10026335m.g' => 'esa', 'TPR.G17433' => 'tpr', 'TPR.G18915' => 'tpr', 'TPR.G26125' => 'tpr', 'TWI09G0677' => 'twi', 'TWI73G0287' => 'twi', 'unitig_748.g8326' => 'ugi', 'vmacro15370' => 'vma', 'vmacro15371' => 'vma', 'vmacro15372' => 'vma', 'vmacro15373' => 'vma', 'vmacro15374' => 'vma', 'VMungo0720G2826' => 'vmu', 'Zm00001eb116960' => 'zma', 'Zm00001eb301260' => 'zma', 'Zm00001eb301270' => 'zma' ), 'gf_id' => 'HOM05D001460', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001460' ), 'data_identifier' => 'HOM05D001460', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001460', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '433', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p22980' => 'bna', 'A01p32340' => 'bna', 'A03p42970' => 'bna', 'A05p25880' => 'bna', 'Aa31LG8G9320' => 'aar', 'Aa31LG8G9330' => 'aar', 'Aa31LG8G9340' => 'aar', 'Aa31sc221G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1034' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1528' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.829' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2222' => 'aag', 'Ah.12g058830' => 'amhyb', 'Ah.12g058840' => 'amhyb', 'AL3G37160' => 'aly', 'AL7G41310' => 'aly', 'Aqoxy5G00395' => 'aox', 'Aqoxy5G00396' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0C8NZA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5185HY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JZ1PRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MD3LS0' => 'arhy', 'AT3G22840' => 'ath', 'AT4G14690' => 'ath', 'ATR0665G054' => 'atr', 'Atru.chr4.2344' => 'acertr', 'Atru.chr4.2346' => 'acertr', 'Atru.chr4.2347' => 'acertr', 'Atru.chr4.2348' => 'acertr', 'Atru.chr4.2355' => 'acertr', 'Atru.chr4.2356' => 'acertr', 'Atru.chr4.2358' => 'acertr', 'Atru.chr4.2359' => 'acertr', 'Atru.chr4.2360' => 'acertr', 'Atru.chr4.2361' => 'acertr', 'AUR62030476' => 'cqu', 'AUR62030478' => 'cqu', 'AUR62030819' => 'cqu', 'AUR62030820' => 'cqu', 'BcaB03g14648' => 'bca', 'BcaB04g20492' => 'bca', 'BcaB06g26399' => 'bca', 'BcaC01g03416' => 'bca', 'BcaC01g03419' => 'bca', 'BcaC01g03421' => 'bca', 'BcaC01g03424' => 'bca', 'BcaC05g28012' => 'bca', 'BcaC09g49212' => 'bca', 'BcaC09g50140' => 'bca', 'BcaNung00346' => 'bca', 'BolC1t02785H' => 'bol', 'BolC1t04095H' => 'bol', 'BolC3t17545H' => 'bol', 'BolC5t32769H' => 'bol', 'BraA01t02211Z' => 'bra', 'BraA01t03359Z' => 'bra', 'BraA03t13441Z' => 'bra', 'BraA05t21476Z' => 'bra', 'C01p28420' => 'bna', 'C01p41350' => 'bna', 'C03p52750' => 'bna', 'C03p52780' => 'bna', 'C05p40270' => 'bna', 'CAN.G1437.9' => 'can', 'CANSAT78G0035' => 'cansat', 'CANSAT78G1036' => 'cansat', 'CANSAT78G2272' => 'cansat', 'CANSAT78G2478' => 'cansat', 'CARHR098700' => 'chi', 'CARHR221120' => 'chi', 'CARHR221150' => 'chi', 'Carub.0003s2297' => 'cru', 'Carub.0007s2749' => 'cru', 'Carub.0007s2750' => 'cru', 'Carub.0007s2751' => 'cru', 'Ca_10849_v3' => 'car', 'Cc03_g04300' => 'ccan', 'CDE02G3648' => 'cde', 'CDE05G0060' => 'cde', 'CDE05G0692' => 'cde', 'CDE05G2285' => 'cde', 'CDE05G2884' => 'cde', 'CDE05G3072' => 'cde', 'Cfa008439' => 'cfa', 'Cfa008441' => 'cfa', 'Cfa008443' => 'cfa', 'Cfa008448' => 'cfa', 'Ciclev10005974m.g' => 'ccl', 'Ciclev10006006m.g' => 'ccl', 'Ciclev10006775m.g' => 'ccl', 'CiPaw.02G120400' => 'cil', 'CiPaw.02G120500' => 'cil', 'CiPaw.02G120600' => 'cil', 'ClCG05G004850' => 'cla', 'COL.COLO4_21566' => 'col', 'Cpa.g.sc44.124' => 'cpa', 'Cre07.g320400' => 'cre', 'Cre07.g320450' => 'cre', 'Cre08.g384650' => 'cre', 'Cre09.g393173' => 'cre', 'Cre09.g394325' => 'cre', 'Cre14.g626750' => 'cre', 'Cre16.g679250' => 'cre', 'CsaV3_3G012890' => 'csa', 'CSS0010865' => 'camsi', 'CSS0044338' => 'camsi', 'DCAR_002366' => 'dca', 'DCAR_030687' => 'dca', 'DCAR_030688' => 'dca', 'Dinv14047' => 'din', 'Dinv14048' => 'din', 'Duzib151G0105' => 'dzi', 'Duzib151G0114' => 'dzi', 'Duzib212G1029' => 'dzi', 'ECA232G3536' => 'eca', 'ECA240G0786' => 'eca', 'ECA240G1802' => 'eca', 'ECA240G3760' => 'eca', 'ECA240G3920' => 'eca', 'EL10Ac5g12536' => 'bvu', 'EL10Ac5g12537' => 'bvu', 'EL10Ac5g12538' => 'bvu', 'Eucgr.B01004' => 'egr', 'Eucgr.B01006' => 'egr', 'Eucgr.B01007' => 'egr', 'Eucgr.B01008' => 'egr', 'Eucgr.B01895' => 'egr', 'Eucgr.B01896' => 'egr', 'FAN04G1456' => 'fan', 'FAN08G1769' => 'fan', 'FAN08G2160' => 'fan', 'FAN13G2403' => 'fan', 'FAN13G3303' => 'fan', 'FAN15G2435' => 'fan', 'FAN17G0672' => 'fan', 'FAN17G2441' => 'fan', 'FAN18G1024' => 'fan', 'FAN22G1458' => 'fan', 'FAN24G0037' => 'fan', 'FAN24G0429' => 'fan', 'FAN24G2387' => 'fan', 'FAN27G2746' => 'fan', 'FvH4_2g20400' => 'fve', 'FvH4_2g20420' => 'fve', 'FvH4_2g20430' => 'fve', 'FvH4_4g01270' => 'fve', 'FvH4_4g01290' => 'fve', 'FvH4_4g01300' => 'fve', 'FvH4_4g01310' => 'fve', 'FvH4_4g01330' => 'fve', 'FvH4_5g09070' => 'fve', 'Glyma.10G243800' => 'gma', 'Glyma.20G150600' => 'gma', 'Gohir.A09G219200' => 'ghi', 'Gohir.A09G219300' => 'ghi', 'Gohir.D09G221400' => 'ghi', 'Gohir.D09G221500' => 'ghi', 'Gorai.006G242600' => 'gra', 'Gorai.006G242700' => 'gra', 'GSVIVG01018044001' => 'vvi', 'HanXRQChr03g0083821' => 'han', 'HanXRQChr03g0083841' => 'han', 'HanXRQChr03g0083881' => 'han', 'HanXRQChr03g0083901' => 'han', 'HanXRQChr03g0083921' => 'han', 'HanXRQChr03g0085331' => 'han', 'HanXRQChr03g0085361' => 'han', 'HanXRQChr03g0085411' => 'han', 'HanXRQChr03g0085421' => 'han', 'HanXRQChr03g0085431' => 'han', 'HanXRQChr08g0221991' => 'han', 'HanXRQChr11g0336061' => 'han', 'HanXRQChr11g0336411' => 'han', 'Haze_11234' => 'cav', 'Hma1.2p1_0549F.1_g177010' => 'hma', 'Hma1.2p1_0602F.1_g187630' => 'hma', 'Hund14876' => 'sun', 'Hund14879' => 'sun', 'Lalb_Chr06g0160741' => 'lal', 'Lalb_Chr21g0304781' => 'lal', 'Lj3A726G19' => 'lonja', 'Lj3A726T23' => 'lonja', 'Lj3A726T24' => 'lonja', 'Lj3A726T25' => 'lonja', 'Lj3A727T17' => 'lonja', 'Lj3C726T0' => 'lonja', 'Lj3C726T2' => 'lonja', 'Lj3P725T35' => 'lonja', 'Lj3P727T10' => 'lonja', 'Lj3P727T12' => 'lonja', 'Lj3P727T14' => 'lonja', 'Lj5g0023109' => 'lja', 'Lj6P646T44' => 'lonja', 'Lsat_1_v5_gn_6_75760' => 'lsa', 'Lsat_1_v5_gn_6_75800' => 'lsa', 'Lsat_1_v5_gn_6_75900' => 'lsa', 'Lsat_1_v5_gn_6_76240' => 'lsa', 'Lsat_1_v5_gn_6_76441' => 'lsa', 'Lsat_1_v5_gn_6_76700' => 'lsa', 'Lsat_1_v5_gn_6_76760' => 'lsa', 'Manes.15G033100' => 'mes', 'Mapoly0004s0074' => 'mpo', 'Mapoly0004s0075' => 'mpo', 'Mapoly0004s0163' => 'mpo', 'Mapoly0004s0164' => 'mpo', 'Mapoly0021s0018' => 'mpo', 'Mapoly0041s0136' => 'mpo', 'Mapoly0041s0137' => 'mpo', 'Mapoly0041s0138' => 'mpo', 'Mapoly0041s0139' => 'mpo', 'Mapoly0041s0141' => 'mpo', 'Mapoly0041s0142' => 'mpo', 'Mapoly0041s0143' => 'mpo', 'Mapoly0041s0144' => 'mpo', 'Mapoly0041s0145' => 'mpo', 'Mapoly0047s0106' => 'mpo', 'Mapoly0047s0108' => 'mpo', 'Mapoly0050s0051' => 'mpo', 'Mapoly0050s0052' => 'mpo', 'Mapoly0050s0053' => 'mpo', 'Mapoly0058s0013' => 'mpo', 'Mapoly0091s0078' => 'mpo', 'Mapoly0091s0079' => 'mpo', 'Mapoly0091s0080' => 'mpo', 'Mapoly0091s0081' => 'mpo', 'Mapoly0278s0004' => 'mpo', 'Mapoly0278s0005' => 'mpo', 'Mapoly0278s0006' => 'mpo', 'MBI11_g30648_MAGBIO' => 'mbi', 'MCO03G194' => 'mco', 'MCO03G590' => 'mco', 'MCO07G312' => 'mco', 'MCO10G318' => 'mco', 'MCO12G244' => 'mco', 'MCO13G148' => 'mco', 'MCO13G194' => 'mco', 'MCO16G238' => 'mco', 'MD06G1134100' => 'mdo', 'MD13G1200100' => 'mdo', 'MD13G1200300' => 'mdo', 'MD13G1200600' => 'mdo', 'MD14G1150400' => 'mdo', 'MD16G1200000' => 'mdo', 'Medtr1g102570' => 'mtr', 'Medtr1g102780' => 'mtr', 'Medtr1g102800' => 'mtr', 'Medtr1g102810' => 'mtr', 'Medtr1g102830' => 'mtr', 'MELO3C006499.2' => 'cme', 'Migut.G00385' => 'egut', 'MSTRG.4063' => 'ama', 'Nitab4.5_0000090g0260' => 'nta', 'Nitab4.5_0000977g0030' => 'nta', 'Nitab4.5_0002541g0040' => 'nta', 'Nitab4.5_0007068g0040' => 'nta', 'Nn005s41408' => 'nnu', 'Nn005s41410' => 'nnu', 'Oeu010310.1' => 'oeu', 'Oeu010311.1' => 'oeu', 'Oeu043472.1' => 'oeu', 'Os01g0246400' => 'osa', 'Os04g0267950' => 'osa', 'Os07g0178700' => 'osa', 'Os07g0178800' => 'osa', 'Peaxi162Scf00316g00046' => 'pax', 'Peaxi162Scf00316g00049' => 'pax', 'Peaxi162Scf00316g00059' => 'pax', 'Peaxi162Scf00316g00328' => 'pax', 'Peaxi162Scf00316g00329' => 'pax', 'Peaxi162Scf00316g00411' => 'pax', 'Peaxi162Scf00316g00521' => 'pax', 'Peaxi162Scf00492g00068' => 'pax', 'Peaxi162Scf35631g00002' => 'pax', 'PGR142G3720' => 'pgr', 'PGSC0003DMG400006442' => 'stu', 'Phvul.007G062000' => 'pvu', 'Potri.008G157750' => 'ptr', 'Potri.008G157900' => 'ptr', 'Potri.008G158000' => 'ptr', 'Potri.008G158200' => 'ptr', 'Pp3c11_7280' => 'ppa', 'Pp3c11_7980' => 'ppa', 'Pp3c12_19450' => 'ppa', 'Pp3c14_1480' => 'ppa', 'Pp3c14_1501' => 'ppa', 'Pp3c16_4900' => 'ppa', 'Pp3c16_5010' => 'ppa', 'Pp3c16_5060' => 'ppa', 'Pp3c19_18250' => 'ppa', 'Pp3c23_8530' => 'ppa', 'Pp3c23_8550' => 'ppa', 'Pp3c24_9670' => 'ppa', 'Pp3c2_21390' => 'ppa', 'Pp3c2_31380' => 'ppa', 'Pp3c3_16620' => 'ppa', 'Pp3c3_8090' => 'ppa', 'Pp3c3_8110' => 'ppa', 'Pp3c3_8130' => 'ppa', 'Pp3c3_8150' => 'ppa', 'Pp3c4_14320' => 'ppa', 'Pp3c6_2560' => 'ppa', 'Pp3c9_16700' => 'ppa', 'PRCOL_00000234' => 'pco', 'PRCOL_00000235' => 'pco', 'PRCOL_00000777' => 'pco', 'PRCOL_00002344' => 'pco', 'PRCOL_00002372' => 'pco', 'PRCOL_00006120' => 'pco', 'Prupe.1G021400' => 'ppe', 'Prupe.1G021500' => 'ppe', 'Prupe.1G021600' => 'ppe', 'Prupe.1G021700' => 'ppe', 'Prupe.1G021800' => 'ppe', 'Prupe.5G145100' => 'ppe', 'Psat6g204040' => 'psa', 'Psat6g204800' => 'psa', 'Psat6g204920' => 'psa', 'Psat6g204960' => 'psa', 'Psat6g205080' => 'psa', 'PSO017G0271' => 'pso', 'PSO017G1276' => 'pso', 'PSO017G1429' => 'pso', 'PSO017G1861' => 'pso', 'PSO017G2787' => 'pso', 'PSO017G4466' => 'pso', 'PSO017G5118' => 'pso', 'PSO017G5420' => 'pso', 'PSO063G3678' => 'pso', 'PSO210G0546' => 'pso', 'PSO317G0001' => 'pso', 'PSO357G0512' => 'pso', 'PSO478G2682' => 'pso', 'PSO647G0001' => 'pso', 'PSO675G0001' => 'pso', 'PSO675G2699' => 'pso', 'PSO675G2849' => 'pso', 'PSO675G4991' => 'pso', 'PSO689G0001' => 'pso', 'QL06p000916' => 'qlo', 'QL06p000921' => 'qlo', 'QL06p001398' => 'qlo', 'QL06p001407' => 'qlo', 'QL06p002031' => 'qlo', 'RcHm_v2.0_Chr4g0387791' => 'rch', 'RcHm_v2.0_Chr4g0387801' => 'rch', 'RcHm_v2.0_Chr6g0286501' => 'rch', 'RcHm_v2.0_Chr6g0286511' => 'rch', 'RcHm_v2.0_Chr6g0286521' => 'rch', 'RcHm_v2.0_Chr6g0286531' => 'rch', 'RcHm_v2.0_Chr7g0189141' => 'rch', 'Rhsim02G0028700' => 'rsi', 'Rhsim02G0028800' => 'rsi', 'Rhsim02G0028900' => 'rsi', 'Rhsim02G0029000' => 'rsi', 'Rhsim02G0029100' => 'rsi', 'Rhsim02G0029200' => 'rsi', 'Rhsim02G0029300' => 'rsi', 'Rhsim02G0029400' => 'rsi', 'Rhsim02G0029500' => 'rsi', 'Rhsim02G0029600' => 'rsi', 'RhsimUnG0024000' => 'rsi', 'RhsimUnG0024100' => 'rsi', 'RhsimUnG0024200' => 'rsi', 'RhsimUnG0024300' => 'rsi', 'RhsimUnG0024400' => 'rsi', 'RhsimUnG0024500' => 'rsi', 'RhsimUnG0024700' => 'rsi', 'RhsimUnG0024800' => 'rsi', 'RhsimUnG0024900' => 'rsi', 'RhsimUnG0025100' => 'rsi', 'Sabra08G0120200' => 'sbr', 'Sabra08G0120300' => 'sbr', 'Sabra08G0120500' => 'sbr', 'Sabra08G0120600' => 'sbr', 'Sabra10G0158900' => 'sbr', 'SalBow2G3492' => 'sbo', 'Sc13g0004760' => 'sci', 'Sc13g0004770' => 'sci', 'Sed0003417' => 'sed', 'Sed0019750' => 'sed', 'SEGI_03419' => 'sgi', 'SEGI_05907' => 'sgi', 'SEGI_10682' => 'sgi', 'SEGI_13528' => 'sgi', 'SEGI_16081' => 'sgi', 'SEGI_19370' => 'sgi', 'SEGI_21015' => 'sgi', 'SEGI_21944' => 'sgi', 'SEGI_32906' => 'sgi', 'SEGI_33093' => 'sgi', 'SEGI_36110' => 'sgi', 'SEGI_40397' => 'sgi', 'SGA_v2.0_scaffold191G40426' => 'sas', 'SGA_v2.0_scaffold353G49717' => 'sas', 'SGA_v2.0_scaffold50G18550' => 'sas', 'SMO119G0173' => 'smo', 'SMO172G0002' => 'smo', 'Solyc09g082690.3' => 'sly', 'Solyc09g082700.2' => 'sly', 'Sopen09g031550' => 'spe', 'Sopen09g031560' => 'spe', 'Sp3g20540' => 'spa', 'Sp7g07580' => 'spa', 'TAR134G0002' => 'tar', 'TAR236G0001' => 'tar', 'TAR365G0892' => 'tar', 'TAR636G0166' => 'tar', 'TAR636G0646' => 'tar', 'TAR636G0869' => 'tar', 'TAR636G1317' => 'tar', 'TAR636G1744' => 'tar', 'TAR636G3358' => 'tar', 'TAR636G3436' => 'tar', 'THA.LOC104803047' => 'tha', 'Thecc.04G238900' => 'tca', 'Thhalv10021557m.g' => 'esa', 'Thhalv10026318m.g' => 'esa', 'Thhalv10026335m.g' => 'esa', 'TPR.G17433' => 'tpr', 'TPR.G18915' => 'tpr', 'TPR.G26125' => 'tpr', 'TWI09G0677' => 'twi', 'TWI73G0287' => 'twi', 'unitig_748.g8326' => 'ugi', 'vmacro15370' => 'vma', 'vmacro15371' => 'vma', 'vmacro15372' => 'vma', 'vmacro15373' => 'vma', 'vmacro15374' => 'vma', 'VMungo0720G2826' => 'vmu', 'Zm00001eb116960' => 'zma', 'Zm00001eb301260' => 'zma', 'Zm00001eb301270' => 'zma' ) $gf_id = 'HOM05D001460' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001460' ) $data_identifier = 'HOM05D001460' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 4, 'aag' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 2, 'aox' => (int) 2, 'arhy' => (int) 4, 'ath' => (int) 2, 'atr' => (int) 1, 'acertr' => (int) 10, 'cqu' => (int) 4, 'bca' => (int) 11, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 1, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 1, 'ccan' => (int) 1, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 1, 'col' => (int) 1, 'cpa' => (int) 1, 'cre' => (int) 7, 'csa' => (int) 1, 'camsi' => (int) 2, 'dca' => (int) 3, 'din' => (int) 2, 'dzi' => (int) 3, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 14, 'fve' => (int) 9, 'gma' => (int) 2, 'ghi' => (int) 4, 'gra' => (int) 2, 'vvi' => (int) 1, 'han' => (int) 13, 'cav' => (int) 1, 'hma' => (int) 2, 'sun' => (int) 2, 'lal' => (int) 2, 'lonja' => (int) 12, 'lja' => (int) 1, 'lsa' => (int) 7, 'mes' => (int) 1, 'mpo' => (int) 27, 'mbi' => (int) 1, 'mco' => (int) 8, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 1, 'egut' => (int) 1, 'ama' => (int) 1, 'nta' => (int) 4, 'nnu' => (int) 2, 'oeu' => (int) 3, 'osa' => (int) 4, 'pax' => (int) 9, 'pgr' => (int) 1, 'stu' => (int) 1, 'pvu' => (int) 1, 'ptr' => (int) 4, 'ppa' => (int) 22, 'pco' => (int) 6, 'ppe' => (int) 6, 'psa' => (int) 5, 'pso' => (int) 19, 'qlo' => (int) 5, 'rch' => (int) 7, 'rsi' => (int) 20, 'sbr' => (int) 5, 'sbo' => (int) 1, 'sci' => (int) 2, 'sed' => (int) 2, 'sgi' => (int) 12, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 2, 'tar' => (int) 10, 'tha' => (int) 1, 'tca' => (int) 1, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 2, 'ugi' => (int) 1, 'vma' => (int) 5, 'vmu' => (int) 1, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb301270' $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' => 'HOM05D001460', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '433', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p22980' => 'bna', 'A01p32340' => 'bna', 'A03p42970' => 'bna', 'A05p25880' => 'bna', 'Aa31LG8G9320' => 'aar', 'Aa31LG8G9330' => 'aar', 'Aa31LG8G9340' => 'aar', 'Aa31sc221G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1034' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1528' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.829' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2222' => 'aag', 'Ah.12g058830' => 'amhyb', 'Ah.12g058840' => 'amhyb', 'AL3G37160' => 'aly', 'AL7G41310' => 'aly', 'Aqoxy5G00395' => 'aox', 'Aqoxy5G00396' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0C8NZA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5185HY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JZ1PRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MD3LS0' => 'arhy', 'AT3G22840' => 'ath', 'AT4G14690' => 'ath', 'ATR0665G054' => 'atr', 'Atru.chr4.2344' => 'acertr', 'Atru.chr4.2346' => 'acertr', 'Atru.chr4.2347' => 'acertr', 'Atru.chr4.2348' => 'acertr', 'Atru.chr4.2355' => 'acertr', 'Atru.chr4.2356' => 'acertr', 'Atru.chr4.2358' => 'acertr', 'Atru.chr4.2359' => 'acertr', 'Atru.chr4.2360' => 'acertr', 'Atru.chr4.2361' => 'acertr', 'AUR62030476' => 'cqu', 'AUR62030478' => 'cqu', 'AUR62030819' => 'cqu', 'AUR62030820' => 'cqu', 'BcaB03g14648' => 'bca', 'BcaB04g20492' => 'bca', 'BcaB06g26399' => 'bca', 'BcaC01g03416' => 'bca', 'BcaC01g03419' => 'bca', 'BcaC01g03421' => 'bca', 'BcaC01g03424' => 'bca', 'BcaC05g28012' => 'bca', 'BcaC09g49212' => 'bca', 'BcaC09g50140' => 'bca', 'BcaNung00346' => 'bca', 'BolC1t02785H' => 'bol', 'BolC1t04095H' => 'bol', 'BolC3t17545H' => 'bol', 'BolC5t32769H' => 'bol', 'BraA01t02211Z' => 'bra', 'BraA01t03359Z' => 'bra', 'BraA03t13441Z' => 'bra', 'BraA05t21476Z' => 'bra', 'C01p28420' => 'bna', 'C01p41350' => 'bna', 'C03p52750' => 'bna', 'C03p52780' => 'bna', 'C05p40270' => 'bna', 'CAN.G1437.9' => 'can', 'CANSAT78G0035' => 'cansat', 'CANSAT78G1036' => 'cansat', 'CANSAT78G2272' => 'cansat', 'CANSAT78G2478' => 'cansat', 'CARHR098700' => 'chi', 'CARHR221120' => 'chi', 'CARHR221150' => 'chi', 'Carub.0003s2297' => 'cru', 'Carub.0007s2749' => 'cru', 'Carub.0007s2750' => 'cru', 'Carub.0007s2751' => 'cru', 'Ca_10849_v3' => 'car', 'Cc03_g04300' => 'ccan', 'CDE02G3648' => 'cde', 'CDE05G0060' => 'cde', 'CDE05G0692' => 'cde', 'CDE05G2285' => 'cde', 'CDE05G2884' => 'cde', 'CDE05G3072' => 'cde', 'Cfa008439' => 'cfa', 'Cfa008441' => 'cfa', 'Cfa008443' => 'cfa', 'Cfa008448' => 'cfa', 'Ciclev10005974m.g' => 'ccl', 'Ciclev10006006m.g' => 'ccl', 'Ciclev10006775m.g' => 'ccl', 'CiPaw.02G120400' => 'cil', 'CiPaw.02G120500' => 'cil', 'CiPaw.02G120600' => 'cil', 'ClCG05G004850' => 'cla', 'COL.COLO4_21566' => 'col', 'Cpa.g.sc44.124' => 'cpa', 'Cre07.g320400' => 'cre', 'Cre07.g320450' => 'cre', 'Cre08.g384650' => 'cre', 'Cre09.g393173' => 'cre', 'Cre09.g394325' => 'cre', 'Cre14.g626750' => 'cre', 'Cre16.g679250' => 'cre', 'CsaV3_3G012890' => 'csa', 'CSS0010865' => 'camsi', 'CSS0044338' => 'camsi', 'DCAR_002366' => 'dca', 'DCAR_030687' => 'dca', 'DCAR_030688' => 'dca', 'Dinv14047' => 'din', 'Dinv14048' => 'din', 'Duzib151G0105' => 'dzi', 'Duzib151G0114' => 'dzi', 'Duzib212G1029' => 'dzi', 'ECA232G3536' => 'eca', 'ECA240G0786' => 'eca', 'ECA240G1802' => 'eca', 'ECA240G3760' => 'eca', 'ECA240G3920' => 'eca', 'EL10Ac5g12536' => 'bvu', 'EL10Ac5g12537' => 'bvu', 'EL10Ac5g12538' => 'bvu', 'Eucgr.B01004' => 'egr', 'Eucgr.B01006' => 'egr', 'Eucgr.B01007' => 'egr', 'Eucgr.B01008' => 'egr', 'Eucgr.B01895' => 'egr', 'Eucgr.B01896' => 'egr', 'FAN04G1456' => 'fan', 'FAN08G1769' => 'fan', 'FAN08G2160' => 'fan', 'FAN13G2403' => 'fan', 'FAN13G3303' => 'fan', 'FAN15G2435' => 'fan', 'FAN17G0672' => 'fan', 'FAN17G2441' => 'fan', 'FAN18G1024' => 'fan', 'FAN22G1458' => 'fan', 'FAN24G0037' => 'fan', 'FAN24G0429' => 'fan', 'FAN24G2387' => 'fan', 'FAN27G2746' => 'fan', 'FvH4_2g20400' => 'fve', 'FvH4_2g20420' => 'fve', 'FvH4_2g20430' => 'fve', 'FvH4_4g01270' => 'fve', 'FvH4_4g01290' => 'fve', 'FvH4_4g01300' => 'fve', 'FvH4_4g01310' => 'fve', 'FvH4_4g01330' => 'fve', 'FvH4_5g09070' => 'fve', 'Glyma.10G243800' => 'gma', 'Glyma.20G150600' => 'gma', 'Gohir.A09G219200' => 'ghi', 'Gohir.A09G219300' => 'ghi', 'Gohir.D09G221400' => 'ghi', 'Gohir.D09G221500' => 'ghi', 'Gorai.006G242600' => 'gra', 'Gorai.006G242700' => 'gra', 'GSVIVG01018044001' => 'vvi', 'HanXRQChr03g0083821' => 'han', 'HanXRQChr03g0083841' => 'han', 'HanXRQChr03g0083881' => 'han', 'HanXRQChr03g0083901' => 'han', 'HanXRQChr03g0083921' => 'han', 'HanXRQChr03g0085331' => 'han', 'HanXRQChr03g0085361' => 'han', 'HanXRQChr03g0085411' => 'han', 'HanXRQChr03g0085421' => 'han', 'HanXRQChr03g0085431' => 'han', 'HanXRQChr08g0221991' => 'han', 'HanXRQChr11g0336061' => 'han', 'HanXRQChr11g0336411' => 'han', 'Haze_11234' => 'cav', 'Hma1.2p1_0549F.1_g177010' => 'hma', 'Hma1.2p1_0602F.1_g187630' => 'hma', 'Hund14876' => 'sun', 'Hund14879' => 'sun', 'Lalb_Chr06g0160741' => 'lal', 'Lalb_Chr21g0304781' => 'lal', 'Lj3A726G19' => 'lonja', 'Lj3A726T23' => 'lonja', 'Lj3A726T24' => 'lonja', 'Lj3A726T25' => 'lonja', 'Lj3A727T17' => 'lonja', 'Lj3C726T0' => 'lonja', 'Lj3C726T2' => 'lonja', 'Lj3P725T35' => 'lonja', 'Lj3P727T10' => 'lonja', 'Lj3P727T12' => 'lonja', 'Lj3P727T14' => 'lonja', 'Lj5g0023109' => 'lja', 'Lj6P646T44' => 'lonja', 'Lsat_1_v5_gn_6_75760' => 'lsa', 'Lsat_1_v5_gn_6_75800' => 'lsa', 'Lsat_1_v5_gn_6_75900' => 'lsa', 'Lsat_1_v5_gn_6_76240' => 'lsa', 'Lsat_1_v5_gn_6_76441' => 'lsa', 'Lsat_1_v5_gn_6_76700' => 'lsa', 'Lsat_1_v5_gn_6_76760' => 'lsa', 'Manes.15G033100' => 'mes', 'Mapoly0004s0074' => 'mpo', 'Mapoly0004s0075' => 'mpo', 'Mapoly0004s0163' => 'mpo', 'Mapoly0004s0164' => 'mpo', 'Mapoly0021s0018' => 'mpo', 'Mapoly0041s0136' => 'mpo', 'Mapoly0041s0137' => 'mpo', 'Mapoly0041s0138' => 'mpo', 'Mapoly0041s0139' => 'mpo', 'Mapoly0041s0141' => 'mpo', 'Mapoly0041s0142' => 'mpo', 'Mapoly0041s0143' => 'mpo', 'Mapoly0041s0144' => 'mpo', 'Mapoly0041s0145' => 'mpo', 'Mapoly0047s0106' => 'mpo', 'Mapoly0047s0108' => 'mpo', 'Mapoly0050s0051' => 'mpo', 'Mapoly0050s0052' => 'mpo', 'Mapoly0050s0053' => 'mpo', 'Mapoly0058s0013' => 'mpo', 'Mapoly0091s0078' => 'mpo', 'Mapoly0091s0079' => 'mpo', 'Mapoly0091s0080' => 'mpo', 'Mapoly0091s0081' => 'mpo', 'Mapoly0278s0004' => 'mpo', 'Mapoly0278s0005' => 'mpo', 'Mapoly0278s0006' => 'mpo', 'MBI11_g30648_MAGBIO' => 'mbi', 'MCO03G194' => 'mco', 'MCO03G590' => 'mco', 'MCO07G312' => 'mco', 'MCO10G318' => 'mco', 'MCO12G244' => 'mco', 'MCO13G148' => 'mco', 'MCO13G194' => 'mco', 'MCO16G238' => 'mco', 'MD06G1134100' => 'mdo', 'MD13G1200100' => 'mdo', 'MD13G1200300' => 'mdo', 'MD13G1200600' => 'mdo', 'MD14G1150400' => 'mdo', 'MD16G1200000' => 'mdo', 'Medtr1g102570' => 'mtr', 'Medtr1g102780' => 'mtr', 'Medtr1g102800' => 'mtr', 'Medtr1g102810' => 'mtr', 'Medtr1g102830' => 'mtr', 'MELO3C006499.2' => 'cme', 'Migut.G00385' => 'egut', 'MSTRG.4063' => 'ama', 'Nitab4.5_0000090g0260' => 'nta', 'Nitab4.5_0000977g0030' => 'nta', 'Nitab4.5_0002541g0040' => 'nta', 'Nitab4.5_0007068g0040' => 'nta', 'Nn005s41408' => 'nnu', 'Nn005s41410' => 'nnu', 'Oeu010310.1' => 'oeu', 'Oeu010311.1' => 'oeu', 'Oeu043472.1' => 'oeu', 'Os01g0246400' => 'osa', 'Os04g0267950' => 'osa', 'Os07g0178700' => 'osa', 'Os07g0178800' => 'osa', 'Peaxi162Scf00316g00046' => 'pax', 'Peaxi162Scf00316g00049' => 'pax', 'Peaxi162Scf00316g00059' => 'pax', 'Peaxi162Scf00316g00328' => 'pax', 'Peaxi162Scf00316g00329' => 'pax', 'Peaxi162Scf00316g00411' => 'pax', 'Peaxi162Scf00316g00521' => 'pax', 'Peaxi162Scf00492g00068' => 'pax', 'Peaxi162Scf35631g00002' => 'pax', 'PGR142G3720' => 'pgr', 'PGSC0003DMG400006442' => 'stu', 'Phvul.007G062000' => 'pvu', 'Potri.008G157750' => 'ptr', 'Potri.008G157900' => 'ptr', 'Potri.008G158000' => 'ptr', 'Potri.008G158200' => 'ptr', 'Pp3c11_7280' => 'ppa', 'Pp3c11_7980' => 'ppa', 'Pp3c12_19450' => 'ppa', 'Pp3c14_1480' => 'ppa', 'Pp3c14_1501' => 'ppa', 'Pp3c16_4900' => 'ppa', 'Pp3c16_5010' => 'ppa', 'Pp3c16_5060' => 'ppa', 'Pp3c19_18250' => 'ppa', 'Pp3c23_8530' => 'ppa', 'Pp3c23_8550' => 'ppa', 'Pp3c24_9670' => 'ppa', 'Pp3c2_21390' => 'ppa', 'Pp3c2_31380' => 'ppa', 'Pp3c3_16620' => 'ppa', 'Pp3c3_8090' => 'ppa', 'Pp3c3_8110' => 'ppa', 'Pp3c3_8130' => 'ppa', 'Pp3c3_8150' => 'ppa', 'Pp3c4_14320' => 'ppa', 'Pp3c6_2560' => 'ppa', 'Pp3c9_16700' => 'ppa', 'PRCOL_00000234' => 'pco', 'PRCOL_00000235' => 'pco', 'PRCOL_00000777' => 'pco', 'PRCOL_00002344' => 'pco', 'PRCOL_00002372' => 'pco', 'PRCOL_00006120' => 'pco', 'Prupe.1G021400' => 'ppe', 'Prupe.1G021500' => 'ppe', 'Prupe.1G021600' => 'ppe', 'Prupe.1G021700' => 'ppe', 'Prupe.1G021800' => 'ppe', 'Prupe.5G145100' => 'ppe', 'Psat6g204040' => 'psa', 'Psat6g204800' => 'psa', 'Psat6g204920' => 'psa', 'Psat6g204960' => 'psa', 'Psat6g205080' => 'psa', 'PSO017G0271' => 'pso', 'PSO017G1276' => 'pso', 'PSO017G1429' => 'pso', 'PSO017G1861' => 'pso', 'PSO017G2787' => 'pso', 'PSO017G4466' => 'pso', 'PSO017G5118' => 'pso', 'PSO017G5420' => 'pso', 'PSO063G3678' => 'pso', 'PSO210G0546' => 'pso', 'PSO317G0001' => 'pso', 'PSO357G0512' => 'pso', 'PSO478G2682' => 'pso', 'PSO647G0001' => 'pso', 'PSO675G0001' => 'pso', 'PSO675G2699' => 'pso', 'PSO675G2849' => 'pso', 'PSO675G4991' => 'pso', 'PSO689G0001' => 'pso', 'QL06p000916' => 'qlo', 'QL06p000921' => 'qlo', 'QL06p001398' => 'qlo', 'QL06p001407' => 'qlo', 'QL06p002031' => 'qlo', 'RcHm_v2.0_Chr4g0387791' => 'rch', 'RcHm_v2.0_Chr4g0387801' => 'rch', 'RcHm_v2.0_Chr6g0286501' => 'rch', 'RcHm_v2.0_Chr6g0286511' => 'rch', 'RcHm_v2.0_Chr6g0286521' => 'rch', 'RcHm_v2.0_Chr6g0286531' => 'rch', 'RcHm_v2.0_Chr7g0189141' => 'rch', 'Rhsim02G0028700' => 'rsi', 'Rhsim02G0028800' => 'rsi', 'Rhsim02G0028900' => 'rsi', 'Rhsim02G0029000' => 'rsi', 'Rhsim02G0029100' => 'rsi', 'Rhsim02G0029200' => 'rsi', 'Rhsim02G0029300' => 'rsi', 'Rhsim02G0029400' => 'rsi', 'Rhsim02G0029500' => 'rsi', 'Rhsim02G0029600' => 'rsi', 'RhsimUnG0024000' => 'rsi', 'RhsimUnG0024100' => 'rsi', 'RhsimUnG0024200' => 'rsi', 'RhsimUnG0024300' => 'rsi', 'RhsimUnG0024400' => 'rsi', 'RhsimUnG0024500' => 'rsi', 'RhsimUnG0024700' => 'rsi', 'RhsimUnG0024800' => 'rsi', 'RhsimUnG0024900' => 'rsi', 'RhsimUnG0025100' => 'rsi', 'Sabra08G0120200' => 'sbr', 'Sabra08G0120300' => 'sbr', 'Sabra08G0120500' => 'sbr', 'Sabra08G0120600' => 'sbr', 'Sabra10G0158900' => 'sbr', 'SalBow2G3492' => 'sbo', 'Sc13g0004760' => 'sci', 'Sc13g0004770' => 'sci', 'Sed0003417' => 'sed', 'Sed0019750' => 'sed', 'SEGI_03419' => 'sgi', 'SEGI_05907' => 'sgi', 'SEGI_10682' => 'sgi', 'SEGI_13528' => 'sgi', 'SEGI_16081' => 'sgi', 'SEGI_19370' => 'sgi', 'SEGI_21015' => 'sgi', 'SEGI_21944' => 'sgi', 'SEGI_32906' => 'sgi', 'SEGI_33093' => 'sgi', 'SEGI_36110' => 'sgi', 'SEGI_40397' => 'sgi', 'SGA_v2.0_scaffold191G40426' => 'sas', 'SGA_v2.0_scaffold353G49717' => 'sas', 'SGA_v2.0_scaffold50G18550' => 'sas', 'SMO119G0173' => 'smo', 'SMO172G0002' => 'smo', 'Solyc09g082690.3' => 'sly', 'Solyc09g082700.2' => 'sly', 'Sopen09g031550' => 'spe', 'Sopen09g031560' => 'spe', 'Sp3g20540' => 'spa', 'Sp7g07580' => 'spa', 'TAR134G0002' => 'tar', 'TAR236G0001' => 'tar', 'TAR365G0892' => 'tar', 'TAR636G0166' => 'tar', 'TAR636G0646' => 'tar', 'TAR636G0869' => 'tar', 'TAR636G1317' => 'tar', 'TAR636G1744' => 'tar', 'TAR636G3358' => 'tar', 'TAR636G3436' => 'tar', 'THA.LOC104803047' => 'tha', 'Thecc.04G238900' => 'tca', 'Thhalv10021557m.g' => 'esa', 'Thhalv10026318m.g' => 'esa', 'Thhalv10026335m.g' => 'esa', 'TPR.G17433' => 'tpr', 'TPR.G18915' => 'tpr', 'TPR.G26125' => 'tpr', 'TWI09G0677' => 'twi', 'TWI73G0287' => 'twi', 'unitig_748.g8326' => 'ugi', 'vmacro15370' => 'vma', 'vmacro15371' => 'vma', 'vmacro15372' => 'vma', 'vmacro15373' => 'vma', 'vmacro15374' => 'vma', 'VMungo0720G2826' => 'vmu', 'Zm00001eb116960' => 'zma', 'Zm00001eb301260' => 'zma', 'Zm00001eb301270' => 'zma' ), 'gf_id' => 'HOM05D001460', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001460' ), 'data_identifier' => 'HOM05D001460', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001460', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '433', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p22980' => 'bna', 'A01p32340' => 'bna', 'A03p42970' => 'bna', 'A05p25880' => 'bna', 'Aa31LG8G9320' => 'aar', 'Aa31LG8G9330' => 'aar', 'Aa31LG8G9340' => 'aar', 'Aa31sc221G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1034' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1528' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.829' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2222' => 'aag', 'Ah.12g058830' => 'amhyb', 'Ah.12g058840' => 'amhyb', 'AL3G37160' => 'aly', 'AL7G41310' => 'aly', 'Aqoxy5G00395' => 'aox', 'Aqoxy5G00396' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0C8NZA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5185HY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JZ1PRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MD3LS0' => 'arhy', 'AT3G22840' => 'ath', 'AT4G14690' => 'ath', 'ATR0665G054' => 'atr', 'Atru.chr4.2344' => 'acertr', 'Atru.chr4.2346' => 'acertr', 'Atru.chr4.2347' => 'acertr', 'Atru.chr4.2348' => 'acertr', 'Atru.chr4.2355' => 'acertr', 'Atru.chr4.2356' => 'acertr', 'Atru.chr4.2358' => 'acertr', 'Atru.chr4.2359' => 'acertr', 'Atru.chr4.2360' => 'acertr', 'Atru.chr4.2361' => 'acertr', 'AUR62030476' => 'cqu', 'AUR62030478' => 'cqu', 'AUR62030819' => 'cqu', 'AUR62030820' => 'cqu', 'BcaB03g14648' => 'bca', 'BcaB04g20492' => 'bca', 'BcaB06g26399' => 'bca', 'BcaC01g03416' => 'bca', 'BcaC01g03419' => 'bca', 'BcaC01g03421' => 'bca', 'BcaC01g03424' => 'bca', 'BcaC05g28012' => 'bca', 'BcaC09g49212' => 'bca', 'BcaC09g50140' => 'bca', 'BcaNung00346' => 'bca', 'BolC1t02785H' => 'bol', 'BolC1t04095H' => 'bol', 'BolC3t17545H' => 'bol', 'BolC5t32769H' => 'bol', 'BraA01t02211Z' => 'bra', 'BraA01t03359Z' => 'bra', 'BraA03t13441Z' => 'bra', 'BraA05t21476Z' => 'bra', 'C01p28420' => 'bna', 'C01p41350' => 'bna', 'C03p52750' => 'bna', 'C03p52780' => 'bna', 'C05p40270' => 'bna', 'CAN.G1437.9' => 'can', 'CANSAT78G0035' => 'cansat', 'CANSAT78G1036' => 'cansat', 'CANSAT78G2272' => 'cansat', 'CANSAT78G2478' => 'cansat', 'CARHR098700' => 'chi', 'CARHR221120' => 'chi', 'CARHR221150' => 'chi', 'Carub.0003s2297' => 'cru', 'Carub.0007s2749' => 'cru', 'Carub.0007s2750' => 'cru', 'Carub.0007s2751' => 'cru', 'Ca_10849_v3' => 'car', 'Cc03_g04300' => 'ccan', 'CDE02G3648' => 'cde', 'CDE05G0060' => 'cde', 'CDE05G0692' => 'cde', 'CDE05G2285' => 'cde', 'CDE05G2884' => 'cde', 'CDE05G3072' => 'cde', 'Cfa008439' => 'cfa', 'Cfa008441' => 'cfa', 'Cfa008443' => 'cfa', 'Cfa008448' => 'cfa', 'Ciclev10005974m.g' => 'ccl', 'Ciclev10006006m.g' => 'ccl', 'Ciclev10006775m.g' => 'ccl', 'CiPaw.02G120400' => 'cil', 'CiPaw.02G120500' => 'cil', 'CiPaw.02G120600' => 'cil', 'ClCG05G004850' => 'cla', 'COL.COLO4_21566' => 'col', 'Cpa.g.sc44.124' => 'cpa', 'Cre07.g320400' => 'cre', 'Cre07.g320450' => 'cre', 'Cre08.g384650' => 'cre', 'Cre09.g393173' => 'cre', 'Cre09.g394325' => 'cre', 'Cre14.g626750' => 'cre', 'Cre16.g679250' => 'cre', 'CsaV3_3G012890' => 'csa', 'CSS0010865' => 'camsi', 'CSS0044338' => 'camsi', 'DCAR_002366' => 'dca', 'DCAR_030687' => 'dca', 'DCAR_030688' => 'dca', 'Dinv14047' => 'din', 'Dinv14048' => 'din', 'Duzib151G0105' => 'dzi', 'Duzib151G0114' => 'dzi', 'Duzib212G1029' => 'dzi', 'ECA232G3536' => 'eca', 'ECA240G0786' => 'eca', 'ECA240G1802' => 'eca', 'ECA240G3760' => 'eca', 'ECA240G3920' => 'eca', 'EL10Ac5g12536' => 'bvu', 'EL10Ac5g12537' => 'bvu', 'EL10Ac5g12538' => 'bvu', 'Eucgr.B01004' => 'egr', 'Eucgr.B01006' => 'egr', 'Eucgr.B01007' => 'egr', 'Eucgr.B01008' => 'egr', 'Eucgr.B01895' => 'egr', 'Eucgr.B01896' => 'egr', 'FAN04G1456' => 'fan', 'FAN08G1769' => 'fan', 'FAN08G2160' => 'fan', 'FAN13G2403' => 'fan', 'FAN13G3303' => 'fan', 'FAN15G2435' => 'fan', 'FAN17G0672' => 'fan', 'FAN17G2441' => 'fan', 'FAN18G1024' => 'fan', 'FAN22G1458' => 'fan', 'FAN24G0037' => 'fan', 'FAN24G0429' => 'fan', 'FAN24G2387' => 'fan', 'FAN27G2746' => 'fan', 'FvH4_2g20400' => 'fve', 'FvH4_2g20420' => 'fve', 'FvH4_2g20430' => 'fve', 'FvH4_4g01270' => 'fve', 'FvH4_4g01290' => 'fve', 'FvH4_4g01300' => 'fve', 'FvH4_4g01310' => 'fve', 'FvH4_4g01330' => 'fve', 'FvH4_5g09070' => 'fve', 'Glyma.10G243800' => 'gma', 'Glyma.20G150600' => 'gma', 'Gohir.A09G219200' => 'ghi', 'Gohir.A09G219300' => 'ghi', 'Gohir.D09G221400' => 'ghi', 'Gohir.D09G221500' => 'ghi', 'Gorai.006G242600' => 'gra', 'Gorai.006G242700' => 'gra', 'GSVIVG01018044001' => 'vvi', 'HanXRQChr03g0083821' => 'han', 'HanXRQChr03g0083841' => 'han', 'HanXRQChr03g0083881' => 'han', 'HanXRQChr03g0083901' => 'han', 'HanXRQChr03g0083921' => 'han', 'HanXRQChr03g0085331' => 'han', 'HanXRQChr03g0085361' => 'han', 'HanXRQChr03g0085411' => 'han', 'HanXRQChr03g0085421' => 'han', 'HanXRQChr03g0085431' => 'han', 'HanXRQChr08g0221991' => 'han', 'HanXRQChr11g0336061' => 'han', 'HanXRQChr11g0336411' => 'han', 'Haze_11234' => 'cav', 'Hma1.2p1_0549F.1_g177010' => 'hma', 'Hma1.2p1_0602F.1_g187630' => 'hma', 'Hund14876' => 'sun', 'Hund14879' => 'sun', 'Lalb_Chr06g0160741' => 'lal', 'Lalb_Chr21g0304781' => 'lal', 'Lj3A726G19' => 'lonja', 'Lj3A726T23' => 'lonja', 'Lj3A726T24' => 'lonja', 'Lj3A726T25' => 'lonja', 'Lj3A727T17' => 'lonja', 'Lj3C726T0' => 'lonja', 'Lj3C726T2' => 'lonja', 'Lj3P725T35' => 'lonja', 'Lj3P727T10' => 'lonja', 'Lj3P727T12' => 'lonja', 'Lj3P727T14' => 'lonja', 'Lj5g0023109' => 'lja', 'Lj6P646T44' => 'lonja', 'Lsat_1_v5_gn_6_75760' => 'lsa', 'Lsat_1_v5_gn_6_75800' => 'lsa', 'Lsat_1_v5_gn_6_75900' => 'lsa', 'Lsat_1_v5_gn_6_76240' => 'lsa', 'Lsat_1_v5_gn_6_76441' => 'lsa', 'Lsat_1_v5_gn_6_76700' => 'lsa', 'Lsat_1_v5_gn_6_76760' => 'lsa', 'Manes.15G033100' => 'mes', 'Mapoly0004s0074' => 'mpo', 'Mapoly0004s0075' => 'mpo', 'Mapoly0004s0163' => 'mpo', 'Mapoly0004s0164' => 'mpo', 'Mapoly0021s0018' => 'mpo', 'Mapoly0041s0136' => 'mpo', 'Mapoly0041s0137' => 'mpo', 'Mapoly0041s0138' => 'mpo', 'Mapoly0041s0139' => 'mpo', 'Mapoly0041s0141' => 'mpo', 'Mapoly0041s0142' => 'mpo', 'Mapoly0041s0143' => 'mpo', 'Mapoly0041s0144' => 'mpo', 'Mapoly0041s0145' => 'mpo', 'Mapoly0047s0106' => 'mpo', 'Mapoly0047s0108' => 'mpo', 'Mapoly0050s0051' => 'mpo', 'Mapoly0050s0052' => 'mpo', 'Mapoly0050s0053' => 'mpo', 'Mapoly0058s0013' => 'mpo', 'Mapoly0091s0078' => 'mpo', 'Mapoly0091s0079' => 'mpo', 'Mapoly0091s0080' => 'mpo', 'Mapoly0091s0081' => 'mpo', 'Mapoly0278s0004' => 'mpo', 'Mapoly0278s0005' => 'mpo', 'Mapoly0278s0006' => 'mpo', 'MBI11_g30648_MAGBIO' => 'mbi', 'MCO03G194' => 'mco', 'MCO03G590' => 'mco', 'MCO07G312' => 'mco', 'MCO10G318' => 'mco', 'MCO12G244' => 'mco', 'MCO13G148' => 'mco', 'MCO13G194' => 'mco', 'MCO16G238' => 'mco', 'MD06G1134100' => 'mdo', 'MD13G1200100' => 'mdo', 'MD13G1200300' => 'mdo', 'MD13G1200600' => 'mdo', 'MD14G1150400' => 'mdo', 'MD16G1200000' => 'mdo', 'Medtr1g102570' => 'mtr', 'Medtr1g102780' => 'mtr', 'Medtr1g102800' => 'mtr', 'Medtr1g102810' => 'mtr', 'Medtr1g102830' => 'mtr', 'MELO3C006499.2' => 'cme', 'Migut.G00385' => 'egut', 'MSTRG.4063' => 'ama', 'Nitab4.5_0000090g0260' => 'nta', 'Nitab4.5_0000977g0030' => 'nta', 'Nitab4.5_0002541g0040' => 'nta', 'Nitab4.5_0007068g0040' => 'nta', 'Nn005s41408' => 'nnu', 'Nn005s41410' => 'nnu', 'Oeu010310.1' => 'oeu', 'Oeu010311.1' => 'oeu', 'Oeu043472.1' => 'oeu', 'Os01g0246400' => 'osa', 'Os04g0267950' => 'osa', 'Os07g0178700' => 'osa', 'Os07g0178800' => 'osa', 'Peaxi162Scf00316g00046' => 'pax', 'Peaxi162Scf00316g00049' => 'pax', 'Peaxi162Scf00316g00059' => 'pax', 'Peaxi162Scf00316g00328' => 'pax', 'Peaxi162Scf00316g00329' => 'pax', 'Peaxi162Scf00316g00411' => 'pax', 'Peaxi162Scf00316g00521' => 'pax', 'Peaxi162Scf00492g00068' => 'pax', 'Peaxi162Scf35631g00002' => 'pax', 'PGR142G3720' => 'pgr', 'PGSC0003DMG400006442' => 'stu', 'Phvul.007G062000' => 'pvu', 'Potri.008G157750' => 'ptr', 'Potri.008G157900' => 'ptr', 'Potri.008G158000' => 'ptr', 'Potri.008G158200' => 'ptr', 'Pp3c11_7280' => 'ppa', 'Pp3c11_7980' => 'ppa', 'Pp3c12_19450' => 'ppa', 'Pp3c14_1480' => 'ppa', 'Pp3c14_1501' => 'ppa', 'Pp3c16_4900' => 'ppa', 'Pp3c16_5010' => 'ppa', 'Pp3c16_5060' => 'ppa', 'Pp3c19_18250' => 'ppa', 'Pp3c23_8530' => 'ppa', 'Pp3c23_8550' => 'ppa', 'Pp3c24_9670' => 'ppa', 'Pp3c2_21390' => 'ppa', 'Pp3c2_31380' => 'ppa', 'Pp3c3_16620' => 'ppa', 'Pp3c3_8090' => 'ppa', 'Pp3c3_8110' => 'ppa', 'Pp3c3_8130' => 'ppa', 'Pp3c3_8150' => 'ppa', 'Pp3c4_14320' => 'ppa', 'Pp3c6_2560' => 'ppa', 'Pp3c9_16700' => 'ppa', 'PRCOL_00000234' => 'pco', 'PRCOL_00000235' => 'pco', 'PRCOL_00000777' => 'pco', 'PRCOL_00002344' => 'pco', 'PRCOL_00002372' => 'pco', 'PRCOL_00006120' => 'pco', 'Prupe.1G021400' => 'ppe', 'Prupe.1G021500' => 'ppe', 'Prupe.1G021600' => 'ppe', 'Prupe.1G021700' => 'ppe', 'Prupe.1G021800' => 'ppe', 'Prupe.5G145100' => 'ppe', 'Psat6g204040' => 'psa', 'Psat6g204800' => 'psa', 'Psat6g204920' => 'psa', 'Psat6g204960' => 'psa', 'Psat6g205080' => 'psa', 'PSO017G0271' => 'pso', 'PSO017G1276' => 'pso', 'PSO017G1429' => 'pso', 'PSO017G1861' => 'pso', 'PSO017G2787' => 'pso', 'PSO017G4466' => 'pso', 'PSO017G5118' => 'pso', 'PSO017G5420' => 'pso', 'PSO063G3678' => 'pso', 'PSO210G0546' => 'pso', 'PSO317G0001' => 'pso', 'PSO357G0512' => 'pso', 'PSO478G2682' => 'pso', 'PSO647G0001' => 'pso', 'PSO675G0001' => 'pso', 'PSO675G2699' => 'pso', 'PSO675G2849' => 'pso', 'PSO675G4991' => 'pso', 'PSO689G0001' => 'pso', 'QL06p000916' => 'qlo', 'QL06p000921' => 'qlo', 'QL06p001398' => 'qlo', 'QL06p001407' => 'qlo', 'QL06p002031' => 'qlo', 'RcHm_v2.0_Chr4g0387791' => 'rch', 'RcHm_v2.0_Chr4g0387801' => 'rch', 'RcHm_v2.0_Chr6g0286501' => 'rch', 'RcHm_v2.0_Chr6g0286511' => 'rch', 'RcHm_v2.0_Chr6g0286521' => 'rch', 'RcHm_v2.0_Chr6g0286531' => 'rch', 'RcHm_v2.0_Chr7g0189141' => 'rch', 'Rhsim02G0028700' => 'rsi', 'Rhsim02G0028800' => 'rsi', 'Rhsim02G0028900' => 'rsi', 'Rhsim02G0029000' => 'rsi', 'Rhsim02G0029100' => 'rsi', 'Rhsim02G0029200' => 'rsi', 'Rhsim02G0029300' => 'rsi', 'Rhsim02G0029400' => 'rsi', 'Rhsim02G0029500' => 'rsi', 'Rhsim02G0029600' => 'rsi', 'RhsimUnG0024000' => 'rsi', 'RhsimUnG0024100' => 'rsi', 'RhsimUnG0024200' => 'rsi', 'RhsimUnG0024300' => 'rsi', 'RhsimUnG0024400' => 'rsi', 'RhsimUnG0024500' => 'rsi', 'RhsimUnG0024700' => 'rsi', 'RhsimUnG0024800' => 'rsi', 'RhsimUnG0024900' => 'rsi', 'RhsimUnG0025100' => 'rsi', 'Sabra08G0120200' => 'sbr', 'Sabra08G0120300' => 'sbr', 'Sabra08G0120500' => 'sbr', 'Sabra08G0120600' => 'sbr', 'Sabra10G0158900' => 'sbr', 'SalBow2G3492' => 'sbo', 'Sc13g0004760' => 'sci', 'Sc13g0004770' => 'sci', 'Sed0003417' => 'sed', 'Sed0019750' => 'sed', 'SEGI_03419' => 'sgi', 'SEGI_05907' => 'sgi', 'SEGI_10682' => 'sgi', 'SEGI_13528' => 'sgi', 'SEGI_16081' => 'sgi', 'SEGI_19370' => 'sgi', 'SEGI_21015' => 'sgi', 'SEGI_21944' => 'sgi', 'SEGI_32906' => 'sgi', 'SEGI_33093' => 'sgi', 'SEGI_36110' => 'sgi', 'SEGI_40397' => 'sgi', 'SGA_v2.0_scaffold191G40426' => 'sas', 'SGA_v2.0_scaffold353G49717' => 'sas', 'SGA_v2.0_scaffold50G18550' => 'sas', 'SMO119G0173' => 'smo', 'SMO172G0002' => 'smo', 'Solyc09g082690.3' => 'sly', 'Solyc09g082700.2' => 'sly', 'Sopen09g031550' => 'spe', 'Sopen09g031560' => 'spe', 'Sp3g20540' => 'spa', 'Sp7g07580' => 'spa', 'TAR134G0002' => 'tar', 'TAR236G0001' => 'tar', 'TAR365G0892' => 'tar', 'TAR636G0166' => 'tar', 'TAR636G0646' => 'tar', 'TAR636G0869' => 'tar', 'TAR636G1317' => 'tar', 'TAR636G1744' => 'tar', 'TAR636G3358' => 'tar', 'TAR636G3436' => 'tar', 'THA.LOC104803047' => 'tha', 'Thecc.04G238900' => 'tca', 'Thhalv10021557m.g' => 'esa', 'Thhalv10026318m.g' => 'esa', 'Thhalv10026335m.g' => 'esa', 'TPR.G17433' => 'tpr', 'TPR.G18915' => 'tpr', 'TPR.G26125' => 'tpr', 'TWI09G0677' => 'twi', 'TWI73G0287' => 'twi', 'unitig_748.g8326' => 'ugi', 'vmacro15370' => 'vma', 'vmacro15371' => 'vma', 'vmacro15372' => 'vma', 'vmacro15373' => 'vma', 'vmacro15374' => 'vma', 'VMungo0720G2826' => 'vmu', 'Zm00001eb116960' => 'zma', 'Zm00001eb301260' => 'zma', 'Zm00001eb301270' => 'zma' ) $gf_id = 'HOM05D001460' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001460' ) $data_identifier = 'HOM05D001460' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 4, 'aag' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 2, 'aox' => (int) 2, 'arhy' => (int) 4, 'ath' => (int) 2, 'atr' => (int) 1, 'acertr' => (int) 10, 'cqu' => (int) 4, 'bca' => (int) 11, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 1, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 1, 'ccan' => (int) 1, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 1, 'col' => (int) 1, 'cpa' => (int) 1, 'cre' => (int) 7, 'csa' => (int) 1, 'camsi' => (int) 2, 'dca' => (int) 3, 'din' => (int) 2, 'dzi' => (int) 3, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 14, 'fve' => (int) 9, 'gma' => (int) 2, 'ghi' => (int) 4, 'gra' => (int) 2, 'vvi' => (int) 1, 'han' => (int) 13, 'cav' => (int) 1, 'hma' => (int) 2, 'sun' => (int) 2, 'lal' => (int) 2, 'lonja' => (int) 12, 'lja' => (int) 1, 'lsa' => (int) 7, 'mes' => (int) 1, 'mpo' => (int) 27, 'mbi' => (int) 1, 'mco' => (int) 8, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 1, 'egut' => (int) 1, 'ama' => (int) 1, 'nta' => (int) 4, 'nnu' => (int) 2, 'oeu' => (int) 3, 'osa' => (int) 4, 'pax' => (int) 9, 'pgr' => (int) 1, 'stu' => (int) 1, 'pvu' => (int) 1, 'ptr' => (int) 4, 'ppa' => (int) 22, 'pco' => (int) 6, 'ppe' => (int) 6, 'psa' => (int) 5, 'pso' => (int) 19, 'qlo' => (int) 5, 'rch' => (int) 7, 'rsi' => (int) 20, 'sbr' => (int) 5, 'sbo' => (int) 1, 'sci' => (int) 2, 'sed' => (int) 2, 'sgi' => (int) 12, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 2, 'tar' => (int) 10, 'tha' => (int) 1, 'tca' => (int) 1, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 2, 'ugi' => (int) 1, 'vma' => (int) 5, 'vmu' => (int) 1, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb301270' $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' => 'HOM05D001460', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '433', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p22980' => 'bna', 'A01p32340' => 'bna', 'A03p42970' => 'bna', 'A05p25880' => 'bna', 'Aa31LG8G9320' => 'aar', 'Aa31LG8G9330' => 'aar', 'Aa31LG8G9340' => 'aar', 'Aa31sc221G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1034' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1528' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.829' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2222' => 'aag', 'Ah.12g058830' => 'amhyb', 'Ah.12g058840' => 'amhyb', 'AL3G37160' => 'aly', 'AL7G41310' => 'aly', 'Aqoxy5G00395' => 'aox', 'Aqoxy5G00396' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0C8NZA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5185HY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JZ1PRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MD3LS0' => 'arhy', 'AT3G22840' => 'ath', 'AT4G14690' => 'ath', 'ATR0665G054' => 'atr', 'Atru.chr4.2344' => 'acertr', 'Atru.chr4.2346' => 'acertr', 'Atru.chr4.2347' => 'acertr', 'Atru.chr4.2348' => 'acertr', 'Atru.chr4.2355' => 'acertr', 'Atru.chr4.2356' => 'acertr', 'Atru.chr4.2358' => 'acertr', 'Atru.chr4.2359' => 'acertr', 'Atru.chr4.2360' => 'acertr', 'Atru.chr4.2361' => 'acertr', 'AUR62030476' => 'cqu', 'AUR62030478' => 'cqu', 'AUR62030819' => 'cqu', 'AUR62030820' => 'cqu', 'BcaB03g14648' => 'bca', 'BcaB04g20492' => 'bca', 'BcaB06g26399' => 'bca', 'BcaC01g03416' => 'bca', 'BcaC01g03419' => 'bca', 'BcaC01g03421' => 'bca', 'BcaC01g03424' => 'bca', 'BcaC05g28012' => 'bca', 'BcaC09g49212' => 'bca', 'BcaC09g50140' => 'bca', 'BcaNung00346' => 'bca', 'BolC1t02785H' => 'bol', 'BolC1t04095H' => 'bol', 'BolC3t17545H' => 'bol', 'BolC5t32769H' => 'bol', 'BraA01t02211Z' => 'bra', 'BraA01t03359Z' => 'bra', 'BraA03t13441Z' => 'bra', 'BraA05t21476Z' => 'bra', 'C01p28420' => 'bna', 'C01p41350' => 'bna', 'C03p52750' => 'bna', 'C03p52780' => 'bna', 'C05p40270' => 'bna', 'CAN.G1437.9' => 'can', 'CANSAT78G0035' => 'cansat', 'CANSAT78G1036' => 'cansat', 'CANSAT78G2272' => 'cansat', 'CANSAT78G2478' => 'cansat', 'CARHR098700' => 'chi', 'CARHR221120' => 'chi', 'CARHR221150' => 'chi', 'Carub.0003s2297' => 'cru', 'Carub.0007s2749' => 'cru', 'Carub.0007s2750' => 'cru', 'Carub.0007s2751' => 'cru', 'Ca_10849_v3' => 'car', 'Cc03_g04300' => 'ccan', 'CDE02G3648' => 'cde', 'CDE05G0060' => 'cde', 'CDE05G0692' => 'cde', 'CDE05G2285' => 'cde', 'CDE05G2884' => 'cde', 'CDE05G3072' => 'cde', 'Cfa008439' => 'cfa', 'Cfa008441' => 'cfa', 'Cfa008443' => 'cfa', 'Cfa008448' => 'cfa', 'Ciclev10005974m.g' => 'ccl', 'Ciclev10006006m.g' => 'ccl', 'Ciclev10006775m.g' => 'ccl', 'CiPaw.02G120400' => 'cil', 'CiPaw.02G120500' => 'cil', 'CiPaw.02G120600' => 'cil', 'ClCG05G004850' => 'cla', 'COL.COLO4_21566' => 'col', 'Cpa.g.sc44.124' => 'cpa', 'Cre07.g320400' => 'cre', 'Cre07.g320450' => 'cre', 'Cre08.g384650' => 'cre', 'Cre09.g393173' => 'cre', 'Cre09.g394325' => 'cre', 'Cre14.g626750' => 'cre', 'Cre16.g679250' => 'cre', 'CsaV3_3G012890' => 'csa', 'CSS0010865' => 'camsi', 'CSS0044338' => 'camsi', 'DCAR_002366' => 'dca', 'DCAR_030687' => 'dca', 'DCAR_030688' => 'dca', 'Dinv14047' => 'din', 'Dinv14048' => 'din', 'Duzib151G0105' => 'dzi', 'Duzib151G0114' => 'dzi', 'Duzib212G1029' => 'dzi', 'ECA232G3536' => 'eca', 'ECA240G0786' => 'eca', 'ECA240G1802' => 'eca', 'ECA240G3760' => 'eca', 'ECA240G3920' => 'eca', 'EL10Ac5g12536' => 'bvu', 'EL10Ac5g12537' => 'bvu', 'EL10Ac5g12538' => 'bvu', 'Eucgr.B01004' => 'egr', 'Eucgr.B01006' => 'egr', 'Eucgr.B01007' => 'egr', 'Eucgr.B01008' => 'egr', 'Eucgr.B01895' => 'egr', 'Eucgr.B01896' => 'egr', 'FAN04G1456' => 'fan', 'FAN08G1769' => 'fan', 'FAN08G2160' => 'fan', 'FAN13G2403' => 'fan', 'FAN13G3303' => 'fan', 'FAN15G2435' => 'fan', 'FAN17G0672' => 'fan', 'FAN17G2441' => 'fan', 'FAN18G1024' => 'fan', 'FAN22G1458' => 'fan', 'FAN24G0037' => 'fan', 'FAN24G0429' => 'fan', 'FAN24G2387' => 'fan', 'FAN27G2746' => 'fan', 'FvH4_2g20400' => 'fve', 'FvH4_2g20420' => 'fve', 'FvH4_2g20430' => 'fve', 'FvH4_4g01270' => 'fve', 'FvH4_4g01290' => 'fve', 'FvH4_4g01300' => 'fve', 'FvH4_4g01310' => 'fve', 'FvH4_4g01330' => 'fve', 'FvH4_5g09070' => 'fve', 'Glyma.10G243800' => 'gma', 'Glyma.20G150600' => 'gma', 'Gohir.A09G219200' => 'ghi', 'Gohir.A09G219300' => 'ghi', 'Gohir.D09G221400' => 'ghi', 'Gohir.D09G221500' => 'ghi', 'Gorai.006G242600' => 'gra', 'Gorai.006G242700' => 'gra', 'GSVIVG01018044001' => 'vvi', 'HanXRQChr03g0083821' => 'han', 'HanXRQChr03g0083841' => 'han', 'HanXRQChr03g0083881' => 'han', 'HanXRQChr03g0083901' => 'han', 'HanXRQChr03g0083921' => 'han', 'HanXRQChr03g0085331' => 'han', 'HanXRQChr03g0085361' => 'han', 'HanXRQChr03g0085411' => 'han', 'HanXRQChr03g0085421' => 'han', 'HanXRQChr03g0085431' => 'han', 'HanXRQChr08g0221991' => 'han', 'HanXRQChr11g0336061' => 'han', 'HanXRQChr11g0336411' => 'han', 'Haze_11234' => 'cav', 'Hma1.2p1_0549F.1_g177010' => 'hma', 'Hma1.2p1_0602F.1_g187630' => 'hma', 'Hund14876' => 'sun', 'Hund14879' => 'sun', 'Lalb_Chr06g0160741' => 'lal', 'Lalb_Chr21g0304781' => 'lal', 'Lj3A726G19' => 'lonja', 'Lj3A726T23' => 'lonja', 'Lj3A726T24' => 'lonja', 'Lj3A726T25' => 'lonja', 'Lj3A727T17' => 'lonja', 'Lj3C726T0' => 'lonja', 'Lj3C726T2' => 'lonja', 'Lj3P725T35' => 'lonja', 'Lj3P727T10' => 'lonja', 'Lj3P727T12' => 'lonja', 'Lj3P727T14' => 'lonja', 'Lj5g0023109' => 'lja', 'Lj6P646T44' => 'lonja', 'Lsat_1_v5_gn_6_75760' => 'lsa', 'Lsat_1_v5_gn_6_75800' => 'lsa', 'Lsat_1_v5_gn_6_75900' => 'lsa', 'Lsat_1_v5_gn_6_76240' => 'lsa', 'Lsat_1_v5_gn_6_76441' => 'lsa', 'Lsat_1_v5_gn_6_76700' => 'lsa', 'Lsat_1_v5_gn_6_76760' => 'lsa', 'Manes.15G033100' => 'mes', 'Mapoly0004s0074' => 'mpo', 'Mapoly0004s0075' => 'mpo', 'Mapoly0004s0163' => 'mpo', 'Mapoly0004s0164' => 'mpo', 'Mapoly0021s0018' => 'mpo', 'Mapoly0041s0136' => 'mpo', 'Mapoly0041s0137' => 'mpo', 'Mapoly0041s0138' => 'mpo', 'Mapoly0041s0139' => 'mpo', 'Mapoly0041s0141' => 'mpo', 'Mapoly0041s0142' => 'mpo', 'Mapoly0041s0143' => 'mpo', 'Mapoly0041s0144' => 'mpo', 'Mapoly0041s0145' => 'mpo', 'Mapoly0047s0106' => 'mpo', 'Mapoly0047s0108' => 'mpo', 'Mapoly0050s0051' => 'mpo', 'Mapoly0050s0052' => 'mpo', 'Mapoly0050s0053' => 'mpo', 'Mapoly0058s0013' => 'mpo', 'Mapoly0091s0078' => 'mpo', 'Mapoly0091s0079' => 'mpo', 'Mapoly0091s0080' => 'mpo', 'Mapoly0091s0081' => 'mpo', 'Mapoly0278s0004' => 'mpo', 'Mapoly0278s0005' => 'mpo', 'Mapoly0278s0006' => 'mpo', 'MBI11_g30648_MAGBIO' => 'mbi', 'MCO03G194' => 'mco', 'MCO03G590' => 'mco', 'MCO07G312' => 'mco', 'MCO10G318' => 'mco', 'MCO12G244' => 'mco', 'MCO13G148' => 'mco', 'MCO13G194' => 'mco', 'MCO16G238' => 'mco', 'MD06G1134100' => 'mdo', 'MD13G1200100' => 'mdo', 'MD13G1200300' => 'mdo', 'MD13G1200600' => 'mdo', 'MD14G1150400' => 'mdo', 'MD16G1200000' => 'mdo', 'Medtr1g102570' => 'mtr', 'Medtr1g102780' => 'mtr', 'Medtr1g102800' => 'mtr', 'Medtr1g102810' => 'mtr', 'Medtr1g102830' => 'mtr', 'MELO3C006499.2' => 'cme', 'Migut.G00385' => 'egut', 'MSTRG.4063' => 'ama', 'Nitab4.5_0000090g0260' => 'nta', 'Nitab4.5_0000977g0030' => 'nta', 'Nitab4.5_0002541g0040' => 'nta', 'Nitab4.5_0007068g0040' => 'nta', 'Nn005s41408' => 'nnu', 'Nn005s41410' => 'nnu', 'Oeu010310.1' => 'oeu', 'Oeu010311.1' => 'oeu', 'Oeu043472.1' => 'oeu', 'Os01g0246400' => 'osa', 'Os04g0267950' => 'osa', 'Os07g0178700' => 'osa', 'Os07g0178800' => 'osa', 'Peaxi162Scf00316g00046' => 'pax', 'Peaxi162Scf00316g00049' => 'pax', 'Peaxi162Scf00316g00059' => 'pax', 'Peaxi162Scf00316g00328' => 'pax', 'Peaxi162Scf00316g00329' => 'pax', 'Peaxi162Scf00316g00411' => 'pax', 'Peaxi162Scf00316g00521' => 'pax', 'Peaxi162Scf00492g00068' => 'pax', 'Peaxi162Scf35631g00002' => 'pax', 'PGR142G3720' => 'pgr', 'PGSC0003DMG400006442' => 'stu', 'Phvul.007G062000' => 'pvu', 'Potri.008G157750' => 'ptr', 'Potri.008G157900' => 'ptr', 'Potri.008G158000' => 'ptr', 'Potri.008G158200' => 'ptr', 'Pp3c11_7280' => 'ppa', 'Pp3c11_7980' => 'ppa', 'Pp3c12_19450' => 'ppa', 'Pp3c14_1480' => 'ppa', 'Pp3c14_1501' => 'ppa', 'Pp3c16_4900' => 'ppa', 'Pp3c16_5010' => 'ppa', 'Pp3c16_5060' => 'ppa', 'Pp3c19_18250' => 'ppa', 'Pp3c23_8530' => 'ppa', 'Pp3c23_8550' => 'ppa', 'Pp3c24_9670' => 'ppa', 'Pp3c2_21390' => 'ppa', 'Pp3c2_31380' => 'ppa', 'Pp3c3_16620' => 'ppa', 'Pp3c3_8090' => 'ppa', 'Pp3c3_8110' => 'ppa', 'Pp3c3_8130' => 'ppa', 'Pp3c3_8150' => 'ppa', 'Pp3c4_14320' => 'ppa', 'Pp3c6_2560' => 'ppa', 'Pp3c9_16700' => 'ppa', 'PRCOL_00000234' => 'pco', 'PRCOL_00000235' => 'pco', 'PRCOL_00000777' => 'pco', 'PRCOL_00002344' => 'pco', 'PRCOL_00002372' => 'pco', 'PRCOL_00006120' => 'pco', 'Prupe.1G021400' => 'ppe', 'Prupe.1G021500' => 'ppe', 'Prupe.1G021600' => 'ppe', 'Prupe.1G021700' => 'ppe', 'Prupe.1G021800' => 'ppe', 'Prupe.5G145100' => 'ppe', 'Psat6g204040' => 'psa', 'Psat6g204800' => 'psa', 'Psat6g204920' => 'psa', 'Psat6g204960' => 'psa', 'Psat6g205080' => 'psa', 'PSO017G0271' => 'pso', 'PSO017G1276' => 'pso', 'PSO017G1429' => 'pso', 'PSO017G1861' => 'pso', 'PSO017G2787' => 'pso', 'PSO017G4466' => 'pso', 'PSO017G5118' => 'pso', 'PSO017G5420' => 'pso', 'PSO063G3678' => 'pso', 'PSO210G0546' => 'pso', 'PSO317G0001' => 'pso', 'PSO357G0512' => 'pso', 'PSO478G2682' => 'pso', 'PSO647G0001' => 'pso', 'PSO675G0001' => 'pso', 'PSO675G2699' => 'pso', 'PSO675G2849' => 'pso', 'PSO675G4991' => 'pso', 'PSO689G0001' => 'pso', 'QL06p000916' => 'qlo', 'QL06p000921' => 'qlo', 'QL06p001398' => 'qlo', 'QL06p001407' => 'qlo', 'QL06p002031' => 'qlo', 'RcHm_v2.0_Chr4g0387791' => 'rch', 'RcHm_v2.0_Chr4g0387801' => 'rch', 'RcHm_v2.0_Chr6g0286501' => 'rch', 'RcHm_v2.0_Chr6g0286511' => 'rch', 'RcHm_v2.0_Chr6g0286521' => 'rch', 'RcHm_v2.0_Chr6g0286531' => 'rch', 'RcHm_v2.0_Chr7g0189141' => 'rch', 'Rhsim02G0028700' => 'rsi', 'Rhsim02G0028800' => 'rsi', 'Rhsim02G0028900' => 'rsi', 'Rhsim02G0029000' => 'rsi', 'Rhsim02G0029100' => 'rsi', 'Rhsim02G0029200' => 'rsi', 'Rhsim02G0029300' => 'rsi', 'Rhsim02G0029400' => 'rsi', 'Rhsim02G0029500' => 'rsi', 'Rhsim02G0029600' => 'rsi', 'RhsimUnG0024000' => 'rsi', 'RhsimUnG0024100' => 'rsi', 'RhsimUnG0024200' => 'rsi', 'RhsimUnG0024300' => 'rsi', 'RhsimUnG0024400' => 'rsi', 'RhsimUnG0024500' => 'rsi', 'RhsimUnG0024700' => 'rsi', 'RhsimUnG0024800' => 'rsi', 'RhsimUnG0024900' => 'rsi', 'RhsimUnG0025100' => 'rsi', 'Sabra08G0120200' => 'sbr', 'Sabra08G0120300' => 'sbr', 'Sabra08G0120500' => 'sbr', 'Sabra08G0120600' => 'sbr', 'Sabra10G0158900' => 'sbr', 'SalBow2G3492' => 'sbo', 'Sc13g0004760' => 'sci', 'Sc13g0004770' => 'sci', 'Sed0003417' => 'sed', 'Sed0019750' => 'sed', 'SEGI_03419' => 'sgi', 'SEGI_05907' => 'sgi', 'SEGI_10682' => 'sgi', 'SEGI_13528' => 'sgi', 'SEGI_16081' => 'sgi', 'SEGI_19370' => 'sgi', 'SEGI_21015' => 'sgi', 'SEGI_21944' => 'sgi', 'SEGI_32906' => 'sgi', 'SEGI_33093' => 'sgi', 'SEGI_36110' => 'sgi', 'SEGI_40397' => 'sgi', 'SGA_v2.0_scaffold191G40426' => 'sas', 'SGA_v2.0_scaffold353G49717' => 'sas', 'SGA_v2.0_scaffold50G18550' => 'sas', 'SMO119G0173' => 'smo', 'SMO172G0002' => 'smo', 'Solyc09g082690.3' => 'sly', 'Solyc09g082700.2' => 'sly', 'Sopen09g031550' => 'spe', 'Sopen09g031560' => 'spe', 'Sp3g20540' => 'spa', 'Sp7g07580' => 'spa', 'TAR134G0002' => 'tar', 'TAR236G0001' => 'tar', 'TAR365G0892' => 'tar', 'TAR636G0166' => 'tar', 'TAR636G0646' => 'tar', 'TAR636G0869' => 'tar', 'TAR636G1317' => 'tar', 'TAR636G1744' => 'tar', 'TAR636G3358' => 'tar', 'TAR636G3436' => 'tar', 'THA.LOC104803047' => 'tha', 'Thecc.04G238900' => 'tca', 'Thhalv10021557m.g' => 'esa', 'Thhalv10026318m.g' => 'esa', 'Thhalv10026335m.g' => 'esa', 'TPR.G17433' => 'tpr', 'TPR.G18915' => 'tpr', 'TPR.G26125' => 'tpr', 'TWI09G0677' => 'twi', 'TWI73G0287' => 'twi', 'unitig_748.g8326' => 'ugi', 'vmacro15370' => 'vma', 'vmacro15371' => 'vma', 'vmacro15372' => 'vma', 'vmacro15373' => 'vma', 'vmacro15374' => 'vma', 'VMungo0720G2826' => 'vmu', 'Zm00001eb116960' => 'zma', 'Zm00001eb301260' => 'zma', 'Zm00001eb301270' => 'zma' ), 'gf_id' => 'HOM05D001460', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001460' ), 'data_identifier' => 'HOM05D001460', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001460', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '433', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p22980' => 'bna', 'A01p32340' => 'bna', 'A03p42970' => 'bna', 'A05p25880' => 'bna', 'Aa31LG8G9320' => 'aar', 'Aa31LG8G9330' => 'aar', 'Aa31LG8G9340' => 'aar', 'Aa31sc221G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1034' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1528' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.829' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2222' => 'aag', 'Ah.12g058830' => 'amhyb', 'Ah.12g058840' => 'amhyb', 'AL3G37160' => 'aly', 'AL7G41310' => 'aly', 'Aqoxy5G00395' => 'aox', 'Aqoxy5G00396' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0C8NZA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5185HY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JZ1PRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MD3LS0' => 'arhy', 'AT3G22840' => 'ath', 'AT4G14690' => 'ath', 'ATR0665G054' => 'atr', 'Atru.chr4.2344' => 'acertr', 'Atru.chr4.2346' => 'acertr', 'Atru.chr4.2347' => 'acertr', 'Atru.chr4.2348' => 'acertr', 'Atru.chr4.2355' => 'acertr', 'Atru.chr4.2356' => 'acertr', 'Atru.chr4.2358' => 'acertr', 'Atru.chr4.2359' => 'acertr', 'Atru.chr4.2360' => 'acertr', 'Atru.chr4.2361' => 'acertr', 'AUR62030476' => 'cqu', 'AUR62030478' => 'cqu', 'AUR62030819' => 'cqu', 'AUR62030820' => 'cqu', 'BcaB03g14648' => 'bca', 'BcaB04g20492' => 'bca', 'BcaB06g26399' => 'bca', 'BcaC01g03416' => 'bca', 'BcaC01g03419' => 'bca', 'BcaC01g03421' => 'bca', 'BcaC01g03424' => 'bca', 'BcaC05g28012' => 'bca', 'BcaC09g49212' => 'bca', 'BcaC09g50140' => 'bca', 'BcaNung00346' => 'bca', 'BolC1t02785H' => 'bol', 'BolC1t04095H' => 'bol', 'BolC3t17545H' => 'bol', 'BolC5t32769H' => 'bol', 'BraA01t02211Z' => 'bra', 'BraA01t03359Z' => 'bra', 'BraA03t13441Z' => 'bra', 'BraA05t21476Z' => 'bra', 'C01p28420' => 'bna', 'C01p41350' => 'bna', 'C03p52750' => 'bna', 'C03p52780' => 'bna', 'C05p40270' => 'bna', 'CAN.G1437.9' => 'can', 'CANSAT78G0035' => 'cansat', 'CANSAT78G1036' => 'cansat', 'CANSAT78G2272' => 'cansat', 'CANSAT78G2478' => 'cansat', 'CARHR098700' => 'chi', 'CARHR221120' => 'chi', 'CARHR221150' => 'chi', 'Carub.0003s2297' => 'cru', 'Carub.0007s2749' => 'cru', 'Carub.0007s2750' => 'cru', 'Carub.0007s2751' => 'cru', 'Ca_10849_v3' => 'car', 'Cc03_g04300' => 'ccan', 'CDE02G3648' => 'cde', 'CDE05G0060' => 'cde', 'CDE05G0692' => 'cde', 'CDE05G2285' => 'cde', 'CDE05G2884' => 'cde', 'CDE05G3072' => 'cde', 'Cfa008439' => 'cfa', 'Cfa008441' => 'cfa', 'Cfa008443' => 'cfa', 'Cfa008448' => 'cfa', 'Ciclev10005974m.g' => 'ccl', 'Ciclev10006006m.g' => 'ccl', 'Ciclev10006775m.g' => 'ccl', 'CiPaw.02G120400' => 'cil', 'CiPaw.02G120500' => 'cil', 'CiPaw.02G120600' => 'cil', 'ClCG05G004850' => 'cla', 'COL.COLO4_21566' => 'col', 'Cpa.g.sc44.124' => 'cpa', 'Cre07.g320400' => 'cre', 'Cre07.g320450' => 'cre', 'Cre08.g384650' => 'cre', 'Cre09.g393173' => 'cre', 'Cre09.g394325' => 'cre', 'Cre14.g626750' => 'cre', 'Cre16.g679250' => 'cre', 'CsaV3_3G012890' => 'csa', 'CSS0010865' => 'camsi', 'CSS0044338' => 'camsi', 'DCAR_002366' => 'dca', 'DCAR_030687' => 'dca', 'DCAR_030688' => 'dca', 'Dinv14047' => 'din', 'Dinv14048' => 'din', 'Duzib151G0105' => 'dzi', 'Duzib151G0114' => 'dzi', 'Duzib212G1029' => 'dzi', 'ECA232G3536' => 'eca', 'ECA240G0786' => 'eca', 'ECA240G1802' => 'eca', 'ECA240G3760' => 'eca', 'ECA240G3920' => 'eca', 'EL10Ac5g12536' => 'bvu', 'EL10Ac5g12537' => 'bvu', 'EL10Ac5g12538' => 'bvu', 'Eucgr.B01004' => 'egr', 'Eucgr.B01006' => 'egr', 'Eucgr.B01007' => 'egr', 'Eucgr.B01008' => 'egr', 'Eucgr.B01895' => 'egr', 'Eucgr.B01896' => 'egr', 'FAN04G1456' => 'fan', 'FAN08G1769' => 'fan', 'FAN08G2160' => 'fan', 'FAN13G2403' => 'fan', 'FAN13G3303' => 'fan', 'FAN15G2435' => 'fan', 'FAN17G0672' => 'fan', 'FAN17G2441' => 'fan', 'FAN18G1024' => 'fan', 'FAN22G1458' => 'fan', 'FAN24G0037' => 'fan', 'FAN24G0429' => 'fan', 'FAN24G2387' => 'fan', 'FAN27G2746' => 'fan', 'FvH4_2g20400' => 'fve', 'FvH4_2g20420' => 'fve', 'FvH4_2g20430' => 'fve', 'FvH4_4g01270' => 'fve', 'FvH4_4g01290' => 'fve', 'FvH4_4g01300' => 'fve', 'FvH4_4g01310' => 'fve', 'FvH4_4g01330' => 'fve', 'FvH4_5g09070' => 'fve', 'Glyma.10G243800' => 'gma', 'Glyma.20G150600' => 'gma', 'Gohir.A09G219200' => 'ghi', 'Gohir.A09G219300' => 'ghi', 'Gohir.D09G221400' => 'ghi', 'Gohir.D09G221500' => 'ghi', 'Gorai.006G242600' => 'gra', 'Gorai.006G242700' => 'gra', 'GSVIVG01018044001' => 'vvi', 'HanXRQChr03g0083821' => 'han', 'HanXRQChr03g0083841' => 'han', 'HanXRQChr03g0083881' => 'han', 'HanXRQChr03g0083901' => 'han', 'HanXRQChr03g0083921' => 'han', 'HanXRQChr03g0085331' => 'han', 'HanXRQChr03g0085361' => 'han', 'HanXRQChr03g0085411' => 'han', 'HanXRQChr03g0085421' => 'han', 'HanXRQChr03g0085431' => 'han', 'HanXRQChr08g0221991' => 'han', 'HanXRQChr11g0336061' => 'han', 'HanXRQChr11g0336411' => 'han', 'Haze_11234' => 'cav', 'Hma1.2p1_0549F.1_g177010' => 'hma', 'Hma1.2p1_0602F.1_g187630' => 'hma', 'Hund14876' => 'sun', 'Hund14879' => 'sun', 'Lalb_Chr06g0160741' => 'lal', 'Lalb_Chr21g0304781' => 'lal', 'Lj3A726G19' => 'lonja', 'Lj3A726T23' => 'lonja', 'Lj3A726T24' => 'lonja', 'Lj3A726T25' => 'lonja', 'Lj3A727T17' => 'lonja', 'Lj3C726T0' => 'lonja', 'Lj3C726T2' => 'lonja', 'Lj3P725T35' => 'lonja', 'Lj3P727T10' => 'lonja', 'Lj3P727T12' => 'lonja', 'Lj3P727T14' => 'lonja', 'Lj5g0023109' => 'lja', 'Lj6P646T44' => 'lonja', 'Lsat_1_v5_gn_6_75760' => 'lsa', 'Lsat_1_v5_gn_6_75800' => 'lsa', 'Lsat_1_v5_gn_6_75900' => 'lsa', 'Lsat_1_v5_gn_6_76240' => 'lsa', 'Lsat_1_v5_gn_6_76441' => 'lsa', 'Lsat_1_v5_gn_6_76700' => 'lsa', 'Lsat_1_v5_gn_6_76760' => 'lsa', 'Manes.15G033100' => 'mes', 'Mapoly0004s0074' => 'mpo', 'Mapoly0004s0075' => 'mpo', 'Mapoly0004s0163' => 'mpo', 'Mapoly0004s0164' => 'mpo', 'Mapoly0021s0018' => 'mpo', 'Mapoly0041s0136' => 'mpo', 'Mapoly0041s0137' => 'mpo', 'Mapoly0041s0138' => 'mpo', 'Mapoly0041s0139' => 'mpo', 'Mapoly0041s0141' => 'mpo', 'Mapoly0041s0142' => 'mpo', 'Mapoly0041s0143' => 'mpo', 'Mapoly0041s0144' => 'mpo', 'Mapoly0041s0145' => 'mpo', 'Mapoly0047s0106' => 'mpo', 'Mapoly0047s0108' => 'mpo', 'Mapoly0050s0051' => 'mpo', 'Mapoly0050s0052' => 'mpo', 'Mapoly0050s0053' => 'mpo', 'Mapoly0058s0013' => 'mpo', 'Mapoly0091s0078' => 'mpo', 'Mapoly0091s0079' => 'mpo', 'Mapoly0091s0080' => 'mpo', 'Mapoly0091s0081' => 'mpo', 'Mapoly0278s0004' => 'mpo', 'Mapoly0278s0005' => 'mpo', 'Mapoly0278s0006' => 'mpo', 'MBI11_g30648_MAGBIO' => 'mbi', 'MCO03G194' => 'mco', 'MCO03G590' => 'mco', 'MCO07G312' => 'mco', 'MCO10G318' => 'mco', 'MCO12G244' => 'mco', 'MCO13G148' => 'mco', 'MCO13G194' => 'mco', 'MCO16G238' => 'mco', 'MD06G1134100' => 'mdo', 'MD13G1200100' => 'mdo', 'MD13G1200300' => 'mdo', 'MD13G1200600' => 'mdo', 'MD14G1150400' => 'mdo', 'MD16G1200000' => 'mdo', 'Medtr1g102570' => 'mtr', 'Medtr1g102780' => 'mtr', 'Medtr1g102800' => 'mtr', 'Medtr1g102810' => 'mtr', 'Medtr1g102830' => 'mtr', 'MELO3C006499.2' => 'cme', 'Migut.G00385' => 'egut', 'MSTRG.4063' => 'ama', 'Nitab4.5_0000090g0260' => 'nta', 'Nitab4.5_0000977g0030' => 'nta', 'Nitab4.5_0002541g0040' => 'nta', 'Nitab4.5_0007068g0040' => 'nta', 'Nn005s41408' => 'nnu', 'Nn005s41410' => 'nnu', 'Oeu010310.1' => 'oeu', 'Oeu010311.1' => 'oeu', 'Oeu043472.1' => 'oeu', 'Os01g0246400' => 'osa', 'Os04g0267950' => 'osa', 'Os07g0178700' => 'osa', 'Os07g0178800' => 'osa', 'Peaxi162Scf00316g00046' => 'pax', 'Peaxi162Scf00316g00049' => 'pax', 'Peaxi162Scf00316g00059' => 'pax', 'Peaxi162Scf00316g00328' => 'pax', 'Peaxi162Scf00316g00329' => 'pax', 'Peaxi162Scf00316g00411' => 'pax', 'Peaxi162Scf00316g00521' => 'pax', 'Peaxi162Scf00492g00068' => 'pax', 'Peaxi162Scf35631g00002' => 'pax', 'PGR142G3720' => 'pgr', 'PGSC0003DMG400006442' => 'stu', 'Phvul.007G062000' => 'pvu', 'Potri.008G157750' => 'ptr', 'Potri.008G157900' => 'ptr', 'Potri.008G158000' => 'ptr', 'Potri.008G158200' => 'ptr', 'Pp3c11_7280' => 'ppa', 'Pp3c11_7980' => 'ppa', 'Pp3c12_19450' => 'ppa', 'Pp3c14_1480' => 'ppa', 'Pp3c14_1501' => 'ppa', 'Pp3c16_4900' => 'ppa', 'Pp3c16_5010' => 'ppa', 'Pp3c16_5060' => 'ppa', 'Pp3c19_18250' => 'ppa', 'Pp3c23_8530' => 'ppa', 'Pp3c23_8550' => 'ppa', 'Pp3c24_9670' => 'ppa', 'Pp3c2_21390' => 'ppa', 'Pp3c2_31380' => 'ppa', 'Pp3c3_16620' => 'ppa', 'Pp3c3_8090' => 'ppa', 'Pp3c3_8110' => 'ppa', 'Pp3c3_8130' => 'ppa', 'Pp3c3_8150' => 'ppa', 'Pp3c4_14320' => 'ppa', 'Pp3c6_2560' => 'ppa', 'Pp3c9_16700' => 'ppa', 'PRCOL_00000234' => 'pco', 'PRCOL_00000235' => 'pco', 'PRCOL_00000777' => 'pco', 'PRCOL_00002344' => 'pco', 'PRCOL_00002372' => 'pco', 'PRCOL_00006120' => 'pco', 'Prupe.1G021400' => 'ppe', 'Prupe.1G021500' => 'ppe', 'Prupe.1G021600' => 'ppe', 'Prupe.1G021700' => 'ppe', 'Prupe.1G021800' => 'ppe', 'Prupe.5G145100' => 'ppe', 'Psat6g204040' => 'psa', 'Psat6g204800' => 'psa', 'Psat6g204920' => 'psa', 'Psat6g204960' => 'psa', 'Psat6g205080' => 'psa', 'PSO017G0271' => 'pso', 'PSO017G1276' => 'pso', 'PSO017G1429' => 'pso', 'PSO017G1861' => 'pso', 'PSO017G2787' => 'pso', 'PSO017G4466' => 'pso', 'PSO017G5118' => 'pso', 'PSO017G5420' => 'pso', 'PSO063G3678' => 'pso', 'PSO210G0546' => 'pso', 'PSO317G0001' => 'pso', 'PSO357G0512' => 'pso', 'PSO478G2682' => 'pso', 'PSO647G0001' => 'pso', 'PSO675G0001' => 'pso', 'PSO675G2699' => 'pso', 'PSO675G2849' => 'pso', 'PSO675G4991' => 'pso', 'PSO689G0001' => 'pso', 'QL06p000916' => 'qlo', 'QL06p000921' => 'qlo', 'QL06p001398' => 'qlo', 'QL06p001407' => 'qlo', 'QL06p002031' => 'qlo', 'RcHm_v2.0_Chr4g0387791' => 'rch', 'RcHm_v2.0_Chr4g0387801' => 'rch', 'RcHm_v2.0_Chr6g0286501' => 'rch', 'RcHm_v2.0_Chr6g0286511' => 'rch', 'RcHm_v2.0_Chr6g0286521' => 'rch', 'RcHm_v2.0_Chr6g0286531' => 'rch', 'RcHm_v2.0_Chr7g0189141' => 'rch', 'Rhsim02G0028700' => 'rsi', 'Rhsim02G0028800' => 'rsi', 'Rhsim02G0028900' => 'rsi', 'Rhsim02G0029000' => 'rsi', 'Rhsim02G0029100' => 'rsi', 'Rhsim02G0029200' => 'rsi', 'Rhsim02G0029300' => 'rsi', 'Rhsim02G0029400' => 'rsi', 'Rhsim02G0029500' => 'rsi', 'Rhsim02G0029600' => 'rsi', 'RhsimUnG0024000' => 'rsi', 'RhsimUnG0024100' => 'rsi', 'RhsimUnG0024200' => 'rsi', 'RhsimUnG0024300' => 'rsi', 'RhsimUnG0024400' => 'rsi', 'RhsimUnG0024500' => 'rsi', 'RhsimUnG0024700' => 'rsi', 'RhsimUnG0024800' => 'rsi', 'RhsimUnG0024900' => 'rsi', 'RhsimUnG0025100' => 'rsi', 'Sabra08G0120200' => 'sbr', 'Sabra08G0120300' => 'sbr', 'Sabra08G0120500' => 'sbr', 'Sabra08G0120600' => 'sbr', 'Sabra10G0158900' => 'sbr', 'SalBow2G3492' => 'sbo', 'Sc13g0004760' => 'sci', 'Sc13g0004770' => 'sci', 'Sed0003417' => 'sed', 'Sed0019750' => 'sed', 'SEGI_03419' => 'sgi', 'SEGI_05907' => 'sgi', 'SEGI_10682' => 'sgi', 'SEGI_13528' => 'sgi', 'SEGI_16081' => 'sgi', 'SEGI_19370' => 'sgi', 'SEGI_21015' => 'sgi', 'SEGI_21944' => 'sgi', 'SEGI_32906' => 'sgi', 'SEGI_33093' => 'sgi', 'SEGI_36110' => 'sgi', 'SEGI_40397' => 'sgi', 'SGA_v2.0_scaffold191G40426' => 'sas', 'SGA_v2.0_scaffold353G49717' => 'sas', 'SGA_v2.0_scaffold50G18550' => 'sas', 'SMO119G0173' => 'smo', 'SMO172G0002' => 'smo', 'Solyc09g082690.3' => 'sly', 'Solyc09g082700.2' => 'sly', 'Sopen09g031550' => 'spe', 'Sopen09g031560' => 'spe', 'Sp3g20540' => 'spa', 'Sp7g07580' => 'spa', 'TAR134G0002' => 'tar', 'TAR236G0001' => 'tar', 'TAR365G0892' => 'tar', 'TAR636G0166' => 'tar', 'TAR636G0646' => 'tar', 'TAR636G0869' => 'tar', 'TAR636G1317' => 'tar', 'TAR636G1744' => 'tar', 'TAR636G3358' => 'tar', 'TAR636G3436' => 'tar', 'THA.LOC104803047' => 'tha', 'Thecc.04G238900' => 'tca', 'Thhalv10021557m.g' => 'esa', 'Thhalv10026318m.g' => 'esa', 'Thhalv10026335m.g' => 'esa', 'TPR.G17433' => 'tpr', 'TPR.G18915' => 'tpr', 'TPR.G26125' => 'tpr', 'TWI09G0677' => 'twi', 'TWI73G0287' => 'twi', 'unitig_748.g8326' => 'ugi', 'vmacro15370' => 'vma', 'vmacro15371' => 'vma', 'vmacro15372' => 'vma', 'vmacro15373' => 'vma', 'vmacro15374' => 'vma', 'VMungo0720G2826' => 'vmu', 'Zm00001eb116960' => 'zma', 'Zm00001eb301260' => 'zma', 'Zm00001eb301270' => 'zma' ) $gf_id = 'HOM05D001460' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001460' ) $data_identifier = 'HOM05D001460' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 4, 'aag' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 2, 'aox' => (int) 2, 'arhy' => (int) 4, 'ath' => (int) 2, 'atr' => (int) 1, 'acertr' => (int) 10, 'cqu' => (int) 4, 'bca' => (int) 11, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 1, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 1, 'ccan' => (int) 1, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 1, 'col' => (int) 1, 'cpa' => (int) 1, 'cre' => (int) 7, 'csa' => (int) 1, 'camsi' => (int) 2, 'dca' => (int) 3, 'din' => (int) 2, 'dzi' => (int) 3, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 14, 'fve' => (int) 9, 'gma' => (int) 2, 'ghi' => (int) 4, 'gra' => (int) 2, 'vvi' => (int) 1, 'han' => (int) 13, 'cav' => (int) 1, 'hma' => (int) 2, 'sun' => (int) 2, 'lal' => (int) 2, 'lonja' => (int) 12, 'lja' => (int) 1, 'lsa' => (int) 7, 'mes' => (int) 1, 'mpo' => (int) 27, 'mbi' => (int) 1, 'mco' => (int) 8, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 1, 'egut' => (int) 1, 'ama' => (int) 1, 'nta' => (int) 4, 'nnu' => (int) 2, 'oeu' => (int) 3, 'osa' => (int) 4, 'pax' => (int) 9, 'pgr' => (int) 1, 'stu' => (int) 1, 'pvu' => (int) 1, 'ptr' => (int) 4, 'ppa' => (int) 22, 'pco' => (int) 6, 'ppe' => (int) 6, 'psa' => (int) 5, 'pso' => (int) 19, 'qlo' => (int) 5, 'rch' => (int) 7, 'rsi' => (int) 20, 'sbr' => (int) 5, 'sbo' => (int) 1, 'sci' => (int) 2, 'sed' => (int) 2, 'sgi' => (int) 12, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 2, 'tar' => (int) 10, 'tha' => (int) 1, 'tca' => (int) 1, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 2, 'ugi' => (int) 1, 'vma' => (int) 5, 'vmu' => (int) 1, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb301270' $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' => 'HOM05D001460', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '433', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p22980' => 'bna', 'A01p32340' => 'bna', 'A03p42970' => 'bna', 'A05p25880' => 'bna', 'Aa31LG8G9320' => 'aar', 'Aa31LG8G9330' => 'aar', 'Aa31LG8G9340' => 'aar', 'Aa31sc221G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1034' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1528' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.829' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2222' => 'aag', 'Ah.12g058830' => 'amhyb', 'Ah.12g058840' => 'amhyb', 'AL3G37160' => 'aly', 'AL7G41310' => 'aly', 'Aqoxy5G00395' => 'aox', 'Aqoxy5G00396' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0C8NZA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5185HY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JZ1PRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MD3LS0' => 'arhy', 'AT3G22840' => 'ath', 'AT4G14690' => 'ath', 'ATR0665G054' => 'atr', 'Atru.chr4.2344' => 'acertr', 'Atru.chr4.2346' => 'acertr', 'Atru.chr4.2347' => 'acertr', 'Atru.chr4.2348' => 'acertr', 'Atru.chr4.2355' => 'acertr', 'Atru.chr4.2356' => 'acertr', 'Atru.chr4.2358' => 'acertr', 'Atru.chr4.2359' => 'acertr', 'Atru.chr4.2360' => 'acertr', 'Atru.chr4.2361' => 'acertr', 'AUR62030476' => 'cqu', 'AUR62030478' => 'cqu', 'AUR62030819' => 'cqu', 'AUR62030820' => 'cqu', 'BcaB03g14648' => 'bca', 'BcaB04g20492' => 'bca', 'BcaB06g26399' => 'bca', 'BcaC01g03416' => 'bca', 'BcaC01g03419' => 'bca', 'BcaC01g03421' => 'bca', 'BcaC01g03424' => 'bca', 'BcaC05g28012' => 'bca', 'BcaC09g49212' => 'bca', 'BcaC09g50140' => 'bca', 'BcaNung00346' => 'bca', 'BolC1t02785H' => 'bol', 'BolC1t04095H' => 'bol', 'BolC3t17545H' => 'bol', 'BolC5t32769H' => 'bol', 'BraA01t02211Z' => 'bra', 'BraA01t03359Z' => 'bra', 'BraA03t13441Z' => 'bra', 'BraA05t21476Z' => 'bra', 'C01p28420' => 'bna', 'C01p41350' => 'bna', 'C03p52750' => 'bna', 'C03p52780' => 'bna', 'C05p40270' => 'bna', 'CAN.G1437.9' => 'can', 'CANSAT78G0035' => 'cansat', 'CANSAT78G1036' => 'cansat', 'CANSAT78G2272' => 'cansat', 'CANSAT78G2478' => 'cansat', 'CARHR098700' => 'chi', 'CARHR221120' => 'chi', 'CARHR221150' => 'chi', 'Carub.0003s2297' => 'cru', 'Carub.0007s2749' => 'cru', 'Carub.0007s2750' => 'cru', 'Carub.0007s2751' => 'cru', 'Ca_10849_v3' => 'car', 'Cc03_g04300' => 'ccan', 'CDE02G3648' => 'cde', 'CDE05G0060' => 'cde', 'CDE05G0692' => 'cde', 'CDE05G2285' => 'cde', 'CDE05G2884' => 'cde', 'CDE05G3072' => 'cde', 'Cfa008439' => 'cfa', 'Cfa008441' => 'cfa', 'Cfa008443' => 'cfa', 'Cfa008448' => 'cfa', 'Ciclev10005974m.g' => 'ccl', 'Ciclev10006006m.g' => 'ccl', 'Ciclev10006775m.g' => 'ccl', 'CiPaw.02G120400' => 'cil', 'CiPaw.02G120500' => 'cil', 'CiPaw.02G120600' => 'cil', 'ClCG05G004850' => 'cla', 'COL.COLO4_21566' => 'col', 'Cpa.g.sc44.124' => 'cpa', 'Cre07.g320400' => 'cre', 'Cre07.g320450' => 'cre', 'Cre08.g384650' => 'cre', 'Cre09.g393173' => 'cre', 'Cre09.g394325' => 'cre', 'Cre14.g626750' => 'cre', 'Cre16.g679250' => 'cre', 'CsaV3_3G012890' => 'csa', 'CSS0010865' => 'camsi', 'CSS0044338' => 'camsi', 'DCAR_002366' => 'dca', 'DCAR_030687' => 'dca', 'DCAR_030688' => 'dca', 'Dinv14047' => 'din', 'Dinv14048' => 'din', 'Duzib151G0105' => 'dzi', 'Duzib151G0114' => 'dzi', 'Duzib212G1029' => 'dzi', 'ECA232G3536' => 'eca', 'ECA240G0786' => 'eca', 'ECA240G1802' => 'eca', 'ECA240G3760' => 'eca', 'ECA240G3920' => 'eca', 'EL10Ac5g12536' => 'bvu', 'EL10Ac5g12537' => 'bvu', 'EL10Ac5g12538' => 'bvu', 'Eucgr.B01004' => 'egr', 'Eucgr.B01006' => 'egr', 'Eucgr.B01007' => 'egr', 'Eucgr.B01008' => 'egr', 'Eucgr.B01895' => 'egr', 'Eucgr.B01896' => 'egr', 'FAN04G1456' => 'fan', 'FAN08G1769' => 'fan', 'FAN08G2160' => 'fan', 'FAN13G2403' => 'fan', 'FAN13G3303' => 'fan', 'FAN15G2435' => 'fan', 'FAN17G0672' => 'fan', 'FAN17G2441' => 'fan', 'FAN18G1024' => 'fan', 'FAN22G1458' => 'fan', 'FAN24G0037' => 'fan', 'FAN24G0429' => 'fan', 'FAN24G2387' => 'fan', 'FAN27G2746' => 'fan', 'FvH4_2g20400' => 'fve', 'FvH4_2g20420' => 'fve', 'FvH4_2g20430' => 'fve', 'FvH4_4g01270' => 'fve', 'FvH4_4g01290' => 'fve', 'FvH4_4g01300' => 'fve', 'FvH4_4g01310' => 'fve', 'FvH4_4g01330' => 'fve', 'FvH4_5g09070' => 'fve', 'Glyma.10G243800' => 'gma', 'Glyma.20G150600' => 'gma', 'Gohir.A09G219200' => 'ghi', 'Gohir.A09G219300' => 'ghi', 'Gohir.D09G221400' => 'ghi', 'Gohir.D09G221500' => 'ghi', 'Gorai.006G242600' => 'gra', 'Gorai.006G242700' => 'gra', 'GSVIVG01018044001' => 'vvi', 'HanXRQChr03g0083821' => 'han', 'HanXRQChr03g0083841' => 'han', 'HanXRQChr03g0083881' => 'han', 'HanXRQChr03g0083901' => 'han', 'HanXRQChr03g0083921' => 'han', 'HanXRQChr03g0085331' => 'han', 'HanXRQChr03g0085361' => 'han', 'HanXRQChr03g0085411' => 'han', 'HanXRQChr03g0085421' => 'han', 'HanXRQChr03g0085431' => 'han', 'HanXRQChr08g0221991' => 'han', 'HanXRQChr11g0336061' => 'han', 'HanXRQChr11g0336411' => 'han', 'Haze_11234' => 'cav', 'Hma1.2p1_0549F.1_g177010' => 'hma', 'Hma1.2p1_0602F.1_g187630' => 'hma', 'Hund14876' => 'sun', 'Hund14879' => 'sun', 'Lalb_Chr06g0160741' => 'lal', 'Lalb_Chr21g0304781' => 'lal', 'Lj3A726G19' => 'lonja', 'Lj3A726T23' => 'lonja', 'Lj3A726T24' => 'lonja', 'Lj3A726T25' => 'lonja', 'Lj3A727T17' => 'lonja', 'Lj3C726T0' => 'lonja', 'Lj3C726T2' => 'lonja', 'Lj3P725T35' => 'lonja', 'Lj3P727T10' => 'lonja', 'Lj3P727T12' => 'lonja', 'Lj3P727T14' => 'lonja', 'Lj5g0023109' => 'lja', 'Lj6P646T44' => 'lonja', 'Lsat_1_v5_gn_6_75760' => 'lsa', 'Lsat_1_v5_gn_6_75800' => 'lsa', 'Lsat_1_v5_gn_6_75900' => 'lsa', 'Lsat_1_v5_gn_6_76240' => 'lsa', 'Lsat_1_v5_gn_6_76441' => 'lsa', 'Lsat_1_v5_gn_6_76700' => 'lsa', 'Lsat_1_v5_gn_6_76760' => 'lsa', 'Manes.15G033100' => 'mes', 'Mapoly0004s0074' => 'mpo', 'Mapoly0004s0075' => 'mpo', 'Mapoly0004s0163' => 'mpo', 'Mapoly0004s0164' => 'mpo', 'Mapoly0021s0018' => 'mpo', 'Mapoly0041s0136' => 'mpo', 'Mapoly0041s0137' => 'mpo', 'Mapoly0041s0138' => 'mpo', 'Mapoly0041s0139' => 'mpo', 'Mapoly0041s0141' => 'mpo', 'Mapoly0041s0142' => 'mpo', 'Mapoly0041s0143' => 'mpo', 'Mapoly0041s0144' => 'mpo', 'Mapoly0041s0145' => 'mpo', 'Mapoly0047s0106' => 'mpo', 'Mapoly0047s0108' => 'mpo', 'Mapoly0050s0051' => 'mpo', 'Mapoly0050s0052' => 'mpo', 'Mapoly0050s0053' => 'mpo', 'Mapoly0058s0013' => 'mpo', 'Mapoly0091s0078' => 'mpo', 'Mapoly0091s0079' => 'mpo', 'Mapoly0091s0080' => 'mpo', 'Mapoly0091s0081' => 'mpo', 'Mapoly0278s0004' => 'mpo', 'Mapoly0278s0005' => 'mpo', 'Mapoly0278s0006' => 'mpo', 'MBI11_g30648_MAGBIO' => 'mbi', 'MCO03G194' => 'mco', 'MCO03G590' => 'mco', 'MCO07G312' => 'mco', 'MCO10G318' => 'mco', 'MCO12G244' => 'mco', 'MCO13G148' => 'mco', 'MCO13G194' => 'mco', 'MCO16G238' => 'mco', 'MD06G1134100' => 'mdo', 'MD13G1200100' => 'mdo', 'MD13G1200300' => 'mdo', 'MD13G1200600' => 'mdo', 'MD14G1150400' => 'mdo', 'MD16G1200000' => 'mdo', 'Medtr1g102570' => 'mtr', 'Medtr1g102780' => 'mtr', 'Medtr1g102800' => 'mtr', 'Medtr1g102810' => 'mtr', 'Medtr1g102830' => 'mtr', 'MELO3C006499.2' => 'cme', 'Migut.G00385' => 'egut', 'MSTRG.4063' => 'ama', 'Nitab4.5_0000090g0260' => 'nta', 'Nitab4.5_0000977g0030' => 'nta', 'Nitab4.5_0002541g0040' => 'nta', 'Nitab4.5_0007068g0040' => 'nta', 'Nn005s41408' => 'nnu', 'Nn005s41410' => 'nnu', 'Oeu010310.1' => 'oeu', 'Oeu010311.1' => 'oeu', 'Oeu043472.1' => 'oeu', 'Os01g0246400' => 'osa', 'Os04g0267950' => 'osa', 'Os07g0178700' => 'osa', 'Os07g0178800' => 'osa', 'Peaxi162Scf00316g00046' => 'pax', 'Peaxi162Scf00316g00049' => 'pax', 'Peaxi162Scf00316g00059' => 'pax', 'Peaxi162Scf00316g00328' => 'pax', 'Peaxi162Scf00316g00329' => 'pax', 'Peaxi162Scf00316g00411' => 'pax', 'Peaxi162Scf00316g00521' => 'pax', 'Peaxi162Scf00492g00068' => 'pax', 'Peaxi162Scf35631g00002' => 'pax', 'PGR142G3720' => 'pgr', 'PGSC0003DMG400006442' => 'stu', 'Phvul.007G062000' => 'pvu', 'Potri.008G157750' => 'ptr', 'Potri.008G157900' => 'ptr', 'Potri.008G158000' => 'ptr', 'Potri.008G158200' => 'ptr', 'Pp3c11_7280' => 'ppa', 'Pp3c11_7980' => 'ppa', 'Pp3c12_19450' => 'ppa', 'Pp3c14_1480' => 'ppa', 'Pp3c14_1501' => 'ppa', 'Pp3c16_4900' => 'ppa', 'Pp3c16_5010' => 'ppa', 'Pp3c16_5060' => 'ppa', 'Pp3c19_18250' => 'ppa', 'Pp3c23_8530' => 'ppa', 'Pp3c23_8550' => 'ppa', 'Pp3c24_9670' => 'ppa', 'Pp3c2_21390' => 'ppa', 'Pp3c2_31380' => 'ppa', 'Pp3c3_16620' => 'ppa', 'Pp3c3_8090' => 'ppa', 'Pp3c3_8110' => 'ppa', 'Pp3c3_8130' => 'ppa', 'Pp3c3_8150' => 'ppa', 'Pp3c4_14320' => 'ppa', 'Pp3c6_2560' => 'ppa', 'Pp3c9_16700' => 'ppa', 'PRCOL_00000234' => 'pco', 'PRCOL_00000235' => 'pco', 'PRCOL_00000777' => 'pco', 'PRCOL_00002344' => 'pco', 'PRCOL_00002372' => 'pco', 'PRCOL_00006120' => 'pco', 'Prupe.1G021400' => 'ppe', 'Prupe.1G021500' => 'ppe', 'Prupe.1G021600' => 'ppe', 'Prupe.1G021700' => 'ppe', 'Prupe.1G021800' => 'ppe', 'Prupe.5G145100' => 'ppe', 'Psat6g204040' => 'psa', 'Psat6g204800' => 'psa', 'Psat6g204920' => 'psa', 'Psat6g204960' => 'psa', 'Psat6g205080' => 'psa', 'PSO017G0271' => 'pso', 'PSO017G1276' => 'pso', 'PSO017G1429' => 'pso', 'PSO017G1861' => 'pso', 'PSO017G2787' => 'pso', 'PSO017G4466' => 'pso', 'PSO017G5118' => 'pso', 'PSO017G5420' => 'pso', 'PSO063G3678' => 'pso', 'PSO210G0546' => 'pso', 'PSO317G0001' => 'pso', 'PSO357G0512' => 'pso', 'PSO478G2682' => 'pso', 'PSO647G0001' => 'pso', 'PSO675G0001' => 'pso', 'PSO675G2699' => 'pso', 'PSO675G2849' => 'pso', 'PSO675G4991' => 'pso', 'PSO689G0001' => 'pso', 'QL06p000916' => 'qlo', 'QL06p000921' => 'qlo', 'QL06p001398' => 'qlo', 'QL06p001407' => 'qlo', 'QL06p002031' => 'qlo', 'RcHm_v2.0_Chr4g0387791' => 'rch', 'RcHm_v2.0_Chr4g0387801' => 'rch', 'RcHm_v2.0_Chr6g0286501' => 'rch', 'RcHm_v2.0_Chr6g0286511' => 'rch', 'RcHm_v2.0_Chr6g0286521' => 'rch', 'RcHm_v2.0_Chr6g0286531' => 'rch', 'RcHm_v2.0_Chr7g0189141' => 'rch', 'Rhsim02G0028700' => 'rsi', 'Rhsim02G0028800' => 'rsi', 'Rhsim02G0028900' => 'rsi', 'Rhsim02G0029000' => 'rsi', 'Rhsim02G0029100' => 'rsi', 'Rhsim02G0029200' => 'rsi', 'Rhsim02G0029300' => 'rsi', 'Rhsim02G0029400' => 'rsi', 'Rhsim02G0029500' => 'rsi', 'Rhsim02G0029600' => 'rsi', 'RhsimUnG0024000' => 'rsi', 'RhsimUnG0024100' => 'rsi', 'RhsimUnG0024200' => 'rsi', 'RhsimUnG0024300' => 'rsi', 'RhsimUnG0024400' => 'rsi', 'RhsimUnG0024500' => 'rsi', 'RhsimUnG0024700' => 'rsi', 'RhsimUnG0024800' => 'rsi', 'RhsimUnG0024900' => 'rsi', 'RhsimUnG0025100' => 'rsi', 'Sabra08G0120200' => 'sbr', 'Sabra08G0120300' => 'sbr', 'Sabra08G0120500' => 'sbr', 'Sabra08G0120600' => 'sbr', 'Sabra10G0158900' => 'sbr', 'SalBow2G3492' => 'sbo', 'Sc13g0004760' => 'sci', 'Sc13g0004770' => 'sci', 'Sed0003417' => 'sed', 'Sed0019750' => 'sed', 'SEGI_03419' => 'sgi', 'SEGI_05907' => 'sgi', 'SEGI_10682' => 'sgi', 'SEGI_13528' => 'sgi', 'SEGI_16081' => 'sgi', 'SEGI_19370' => 'sgi', 'SEGI_21015' => 'sgi', 'SEGI_21944' => 'sgi', 'SEGI_32906' => 'sgi', 'SEGI_33093' => 'sgi', 'SEGI_36110' => 'sgi', 'SEGI_40397' => 'sgi', 'SGA_v2.0_scaffold191G40426' => 'sas', 'SGA_v2.0_scaffold353G49717' => 'sas', 'SGA_v2.0_scaffold50G18550' => 'sas', 'SMO119G0173' => 'smo', 'SMO172G0002' => 'smo', 'Solyc09g082690.3' => 'sly', 'Solyc09g082700.2' => 'sly', 'Sopen09g031550' => 'spe', 'Sopen09g031560' => 'spe', 'Sp3g20540' => 'spa', 'Sp7g07580' => 'spa', 'TAR134G0002' => 'tar', 'TAR236G0001' => 'tar', 'TAR365G0892' => 'tar', 'TAR636G0166' => 'tar', 'TAR636G0646' => 'tar', 'TAR636G0869' => 'tar', 'TAR636G1317' => 'tar', 'TAR636G1744' => 'tar', 'TAR636G3358' => 'tar', 'TAR636G3436' => 'tar', 'THA.LOC104803047' => 'tha', 'Thecc.04G238900' => 'tca', 'Thhalv10021557m.g' => 'esa', 'Thhalv10026318m.g' => 'esa', 'Thhalv10026335m.g' => 'esa', 'TPR.G17433' => 'tpr', 'TPR.G18915' => 'tpr', 'TPR.G26125' => 'tpr', 'TWI09G0677' => 'twi', 'TWI73G0287' => 'twi', 'unitig_748.g8326' => 'ugi', 'vmacro15370' => 'vma', 'vmacro15371' => 'vma', 'vmacro15372' => 'vma', 'vmacro15373' => 'vma', 'vmacro15374' => 'vma', 'VMungo0720G2826' => 'vmu', 'Zm00001eb116960' => 'zma', 'Zm00001eb301260' => 'zma', 'Zm00001eb301270' => 'zma' ), 'gf_id' => 'HOM05D001460', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001460' ), 'data_identifier' => 'HOM05D001460', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001460', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '433', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p22980' => 'bna', 'A01p32340' => 'bna', 'A03p42970' => 'bna', 'A05p25880' => 'bna', 'Aa31LG8G9320' => 'aar', 'Aa31LG8G9330' => 'aar', 'Aa31LG8G9340' => 'aar', 'Aa31sc221G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1034' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1528' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.829' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2222' => 'aag', 'Ah.12g058830' => 'amhyb', 'Ah.12g058840' => 'amhyb', 'AL3G37160' => 'aly', 'AL7G41310' => 'aly', 'Aqoxy5G00395' => 'aox', 'Aqoxy5G00396' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0C8NZA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5185HY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JZ1PRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MD3LS0' => 'arhy', 'AT3G22840' => 'ath', 'AT4G14690' => 'ath', 'ATR0665G054' => 'atr', 'Atru.chr4.2344' => 'acertr', 'Atru.chr4.2346' => 'acertr', 'Atru.chr4.2347' => 'acertr', 'Atru.chr4.2348' => 'acertr', 'Atru.chr4.2355' => 'acertr', 'Atru.chr4.2356' => 'acertr', 'Atru.chr4.2358' => 'acertr', 'Atru.chr4.2359' => 'acertr', 'Atru.chr4.2360' => 'acertr', 'Atru.chr4.2361' => 'acertr', 'AUR62030476' => 'cqu', 'AUR62030478' => 'cqu', 'AUR62030819' => 'cqu', 'AUR62030820' => 'cqu', 'BcaB03g14648' => 'bca', 'BcaB04g20492' => 'bca', 'BcaB06g26399' => 'bca', 'BcaC01g03416' => 'bca', 'BcaC01g03419' => 'bca', 'BcaC01g03421' => 'bca', 'BcaC01g03424' => 'bca', 'BcaC05g28012' => 'bca', 'BcaC09g49212' => 'bca', 'BcaC09g50140' => 'bca', 'BcaNung00346' => 'bca', 'BolC1t02785H' => 'bol', 'BolC1t04095H' => 'bol', 'BolC3t17545H' => 'bol', 'BolC5t32769H' => 'bol', 'BraA01t02211Z' => 'bra', 'BraA01t03359Z' => 'bra', 'BraA03t13441Z' => 'bra', 'BraA05t21476Z' => 'bra', 'C01p28420' => 'bna', 'C01p41350' => 'bna', 'C03p52750' => 'bna', 'C03p52780' => 'bna', 'C05p40270' => 'bna', 'CAN.G1437.9' => 'can', 'CANSAT78G0035' => 'cansat', 'CANSAT78G1036' => 'cansat', 'CANSAT78G2272' => 'cansat', 'CANSAT78G2478' => 'cansat', 'CARHR098700' => 'chi', 'CARHR221120' => 'chi', 'CARHR221150' => 'chi', 'Carub.0003s2297' => 'cru', 'Carub.0007s2749' => 'cru', 'Carub.0007s2750' => 'cru', 'Carub.0007s2751' => 'cru', 'Ca_10849_v3' => 'car', 'Cc03_g04300' => 'ccan', 'CDE02G3648' => 'cde', 'CDE05G0060' => 'cde', 'CDE05G0692' => 'cde', 'CDE05G2285' => 'cde', 'CDE05G2884' => 'cde', 'CDE05G3072' => 'cde', 'Cfa008439' => 'cfa', 'Cfa008441' => 'cfa', 'Cfa008443' => 'cfa', 'Cfa008448' => 'cfa', 'Ciclev10005974m.g' => 'ccl', 'Ciclev10006006m.g' => 'ccl', 'Ciclev10006775m.g' => 'ccl', 'CiPaw.02G120400' => 'cil', 'CiPaw.02G120500' => 'cil', 'CiPaw.02G120600' => 'cil', 'ClCG05G004850' => 'cla', 'COL.COLO4_21566' => 'col', 'Cpa.g.sc44.124' => 'cpa', 'Cre07.g320400' => 'cre', 'Cre07.g320450' => 'cre', 'Cre08.g384650' => 'cre', 'Cre09.g393173' => 'cre', 'Cre09.g394325' => 'cre', 'Cre14.g626750' => 'cre', 'Cre16.g679250' => 'cre', 'CsaV3_3G012890' => 'csa', 'CSS0010865' => 'camsi', 'CSS0044338' => 'camsi', 'DCAR_002366' => 'dca', 'DCAR_030687' => 'dca', 'DCAR_030688' => 'dca', 'Dinv14047' => 'din', 'Dinv14048' => 'din', 'Duzib151G0105' => 'dzi', 'Duzib151G0114' => 'dzi', 'Duzib212G1029' => 'dzi', 'ECA232G3536' => 'eca', 'ECA240G0786' => 'eca', 'ECA240G1802' => 'eca', 'ECA240G3760' => 'eca', 'ECA240G3920' => 'eca', 'EL10Ac5g12536' => 'bvu', 'EL10Ac5g12537' => 'bvu', 'EL10Ac5g12538' => 'bvu', 'Eucgr.B01004' => 'egr', 'Eucgr.B01006' => 'egr', 'Eucgr.B01007' => 'egr', 'Eucgr.B01008' => 'egr', 'Eucgr.B01895' => 'egr', 'Eucgr.B01896' => 'egr', 'FAN04G1456' => 'fan', 'FAN08G1769' => 'fan', 'FAN08G2160' => 'fan', 'FAN13G2403' => 'fan', 'FAN13G3303' => 'fan', 'FAN15G2435' => 'fan', 'FAN17G0672' => 'fan', 'FAN17G2441' => 'fan', 'FAN18G1024' => 'fan', 'FAN22G1458' => 'fan', 'FAN24G0037' => 'fan', 'FAN24G0429' => 'fan', 'FAN24G2387' => 'fan', 'FAN27G2746' => 'fan', 'FvH4_2g20400' => 'fve', 'FvH4_2g20420' => 'fve', 'FvH4_2g20430' => 'fve', 'FvH4_4g01270' => 'fve', 'FvH4_4g01290' => 'fve', 'FvH4_4g01300' => 'fve', 'FvH4_4g01310' => 'fve', 'FvH4_4g01330' => 'fve', 'FvH4_5g09070' => 'fve', 'Glyma.10G243800' => 'gma', 'Glyma.20G150600' => 'gma', 'Gohir.A09G219200' => 'ghi', 'Gohir.A09G219300' => 'ghi', 'Gohir.D09G221400' => 'ghi', 'Gohir.D09G221500' => 'ghi', 'Gorai.006G242600' => 'gra', 'Gorai.006G242700' => 'gra', 'GSVIVG01018044001' => 'vvi', 'HanXRQChr03g0083821' => 'han', 'HanXRQChr03g0083841' => 'han', 'HanXRQChr03g0083881' => 'han', 'HanXRQChr03g0083901' => 'han', 'HanXRQChr03g0083921' => 'han', 'HanXRQChr03g0085331' => 'han', 'HanXRQChr03g0085361' => 'han', 'HanXRQChr03g0085411' => 'han', 'HanXRQChr03g0085421' => 'han', 'HanXRQChr03g0085431' => 'han', 'HanXRQChr08g0221991' => 'han', 'HanXRQChr11g0336061' => 'han', 'HanXRQChr11g0336411' => 'han', 'Haze_11234' => 'cav', 'Hma1.2p1_0549F.1_g177010' => 'hma', 'Hma1.2p1_0602F.1_g187630' => 'hma', 'Hund14876' => 'sun', 'Hund14879' => 'sun', 'Lalb_Chr06g0160741' => 'lal', 'Lalb_Chr21g0304781' => 'lal', 'Lj3A726G19' => 'lonja', 'Lj3A726T23' => 'lonja', 'Lj3A726T24' => 'lonja', 'Lj3A726T25' => 'lonja', 'Lj3A727T17' => 'lonja', 'Lj3C726T0' => 'lonja', 'Lj3C726T2' => 'lonja', 'Lj3P725T35' => 'lonja', 'Lj3P727T10' => 'lonja', 'Lj3P727T12' => 'lonja', 'Lj3P727T14' => 'lonja', 'Lj5g0023109' => 'lja', 'Lj6P646T44' => 'lonja', 'Lsat_1_v5_gn_6_75760' => 'lsa', 'Lsat_1_v5_gn_6_75800' => 'lsa', 'Lsat_1_v5_gn_6_75900' => 'lsa', 'Lsat_1_v5_gn_6_76240' => 'lsa', 'Lsat_1_v5_gn_6_76441' => 'lsa', 'Lsat_1_v5_gn_6_76700' => 'lsa', 'Lsat_1_v5_gn_6_76760' => 'lsa', 'Manes.15G033100' => 'mes', 'Mapoly0004s0074' => 'mpo', 'Mapoly0004s0075' => 'mpo', 'Mapoly0004s0163' => 'mpo', 'Mapoly0004s0164' => 'mpo', 'Mapoly0021s0018' => 'mpo', 'Mapoly0041s0136' => 'mpo', 'Mapoly0041s0137' => 'mpo', 'Mapoly0041s0138' => 'mpo', 'Mapoly0041s0139' => 'mpo', 'Mapoly0041s0141' => 'mpo', 'Mapoly0041s0142' => 'mpo', 'Mapoly0041s0143' => 'mpo', 'Mapoly0041s0144' => 'mpo', 'Mapoly0041s0145' => 'mpo', 'Mapoly0047s0106' => 'mpo', 'Mapoly0047s0108' => 'mpo', 'Mapoly0050s0051' => 'mpo', 'Mapoly0050s0052' => 'mpo', 'Mapoly0050s0053' => 'mpo', 'Mapoly0058s0013' => 'mpo', 'Mapoly0091s0078' => 'mpo', 'Mapoly0091s0079' => 'mpo', 'Mapoly0091s0080' => 'mpo', 'Mapoly0091s0081' => 'mpo', 'Mapoly0278s0004' => 'mpo', 'Mapoly0278s0005' => 'mpo', 'Mapoly0278s0006' => 'mpo', 'MBI11_g30648_MAGBIO' => 'mbi', 'MCO03G194' => 'mco', 'MCO03G590' => 'mco', 'MCO07G312' => 'mco', 'MCO10G318' => 'mco', 'MCO12G244' => 'mco', 'MCO13G148' => 'mco', 'MCO13G194' => 'mco', 'MCO16G238' => 'mco', 'MD06G1134100' => 'mdo', 'MD13G1200100' => 'mdo', 'MD13G1200300' => 'mdo', 'MD13G1200600' => 'mdo', 'MD14G1150400' => 'mdo', 'MD16G1200000' => 'mdo', 'Medtr1g102570' => 'mtr', 'Medtr1g102780' => 'mtr', 'Medtr1g102800' => 'mtr', 'Medtr1g102810' => 'mtr', 'Medtr1g102830' => 'mtr', 'MELO3C006499.2' => 'cme', 'Migut.G00385' => 'egut', 'MSTRG.4063' => 'ama', 'Nitab4.5_0000090g0260' => 'nta', 'Nitab4.5_0000977g0030' => 'nta', 'Nitab4.5_0002541g0040' => 'nta', 'Nitab4.5_0007068g0040' => 'nta', 'Nn005s41408' => 'nnu', 'Nn005s41410' => 'nnu', 'Oeu010310.1' => 'oeu', 'Oeu010311.1' => 'oeu', 'Oeu043472.1' => 'oeu', 'Os01g0246400' => 'osa', 'Os04g0267950' => 'osa', 'Os07g0178700' => 'osa', 'Os07g0178800' => 'osa', 'Peaxi162Scf00316g00046' => 'pax', 'Peaxi162Scf00316g00049' => 'pax', 'Peaxi162Scf00316g00059' => 'pax', 'Peaxi162Scf00316g00328' => 'pax', 'Peaxi162Scf00316g00329' => 'pax', 'Peaxi162Scf00316g00411' => 'pax', 'Peaxi162Scf00316g00521' => 'pax', 'Peaxi162Scf00492g00068' => 'pax', 'Peaxi162Scf35631g00002' => 'pax', 'PGR142G3720' => 'pgr', 'PGSC0003DMG400006442' => 'stu', 'Phvul.007G062000' => 'pvu', 'Potri.008G157750' => 'ptr', 'Potri.008G157900' => 'ptr', 'Potri.008G158000' => 'ptr', 'Potri.008G158200' => 'ptr', 'Pp3c11_7280' => 'ppa', 'Pp3c11_7980' => 'ppa', 'Pp3c12_19450' => 'ppa', 'Pp3c14_1480' => 'ppa', 'Pp3c14_1501' => 'ppa', 'Pp3c16_4900' => 'ppa', 'Pp3c16_5010' => 'ppa', 'Pp3c16_5060' => 'ppa', 'Pp3c19_18250' => 'ppa', 'Pp3c23_8530' => 'ppa', 'Pp3c23_8550' => 'ppa', 'Pp3c24_9670' => 'ppa', 'Pp3c2_21390' => 'ppa', 'Pp3c2_31380' => 'ppa', 'Pp3c3_16620' => 'ppa', 'Pp3c3_8090' => 'ppa', 'Pp3c3_8110' => 'ppa', 'Pp3c3_8130' => 'ppa', 'Pp3c3_8150' => 'ppa', 'Pp3c4_14320' => 'ppa', 'Pp3c6_2560' => 'ppa', 'Pp3c9_16700' => 'ppa', 'PRCOL_00000234' => 'pco', 'PRCOL_00000235' => 'pco', 'PRCOL_00000777' => 'pco', 'PRCOL_00002344' => 'pco', 'PRCOL_00002372' => 'pco', 'PRCOL_00006120' => 'pco', 'Prupe.1G021400' => 'ppe', 'Prupe.1G021500' => 'ppe', 'Prupe.1G021600' => 'ppe', 'Prupe.1G021700' => 'ppe', 'Prupe.1G021800' => 'ppe', 'Prupe.5G145100' => 'ppe', 'Psat6g204040' => 'psa', 'Psat6g204800' => 'psa', 'Psat6g204920' => 'psa', 'Psat6g204960' => 'psa', 'Psat6g205080' => 'psa', 'PSO017G0271' => 'pso', 'PSO017G1276' => 'pso', 'PSO017G1429' => 'pso', 'PSO017G1861' => 'pso', 'PSO017G2787' => 'pso', 'PSO017G4466' => 'pso', 'PSO017G5118' => 'pso', 'PSO017G5420' => 'pso', 'PSO063G3678' => 'pso', 'PSO210G0546' => 'pso', 'PSO317G0001' => 'pso', 'PSO357G0512' => 'pso', 'PSO478G2682' => 'pso', 'PSO647G0001' => 'pso', 'PSO675G0001' => 'pso', 'PSO675G2699' => 'pso', 'PSO675G2849' => 'pso', 'PSO675G4991' => 'pso', 'PSO689G0001' => 'pso', 'QL06p000916' => 'qlo', 'QL06p000921' => 'qlo', 'QL06p001398' => 'qlo', 'QL06p001407' => 'qlo', 'QL06p002031' => 'qlo', 'RcHm_v2.0_Chr4g0387791' => 'rch', 'RcHm_v2.0_Chr4g0387801' => 'rch', 'RcHm_v2.0_Chr6g0286501' => 'rch', 'RcHm_v2.0_Chr6g0286511' => 'rch', 'RcHm_v2.0_Chr6g0286521' => 'rch', 'RcHm_v2.0_Chr6g0286531' => 'rch', 'RcHm_v2.0_Chr7g0189141' => 'rch', 'Rhsim02G0028700' => 'rsi', 'Rhsim02G0028800' => 'rsi', 'Rhsim02G0028900' => 'rsi', 'Rhsim02G0029000' => 'rsi', 'Rhsim02G0029100' => 'rsi', 'Rhsim02G0029200' => 'rsi', 'Rhsim02G0029300' => 'rsi', 'Rhsim02G0029400' => 'rsi', 'Rhsim02G0029500' => 'rsi', 'Rhsim02G0029600' => 'rsi', 'RhsimUnG0024000' => 'rsi', 'RhsimUnG0024100' => 'rsi', 'RhsimUnG0024200' => 'rsi', 'RhsimUnG0024300' => 'rsi', 'RhsimUnG0024400' => 'rsi', 'RhsimUnG0024500' => 'rsi', 'RhsimUnG0024700' => 'rsi', 'RhsimUnG0024800' => 'rsi', 'RhsimUnG0024900' => 'rsi', 'RhsimUnG0025100' => 'rsi', 'Sabra08G0120200' => 'sbr', 'Sabra08G0120300' => 'sbr', 'Sabra08G0120500' => 'sbr', 'Sabra08G0120600' => 'sbr', 'Sabra10G0158900' => 'sbr', 'SalBow2G3492' => 'sbo', 'Sc13g0004760' => 'sci', 'Sc13g0004770' => 'sci', 'Sed0003417' => 'sed', 'Sed0019750' => 'sed', 'SEGI_03419' => 'sgi', 'SEGI_05907' => 'sgi', 'SEGI_10682' => 'sgi', 'SEGI_13528' => 'sgi', 'SEGI_16081' => 'sgi', 'SEGI_19370' => 'sgi', 'SEGI_21015' => 'sgi', 'SEGI_21944' => 'sgi', 'SEGI_32906' => 'sgi', 'SEGI_33093' => 'sgi', 'SEGI_36110' => 'sgi', 'SEGI_40397' => 'sgi', 'SGA_v2.0_scaffold191G40426' => 'sas', 'SGA_v2.0_scaffold353G49717' => 'sas', 'SGA_v2.0_scaffold50G18550' => 'sas', 'SMO119G0173' => 'smo', 'SMO172G0002' => 'smo', 'Solyc09g082690.3' => 'sly', 'Solyc09g082700.2' => 'sly', 'Sopen09g031550' => 'spe', 'Sopen09g031560' => 'spe', 'Sp3g20540' => 'spa', 'Sp7g07580' => 'spa', 'TAR134G0002' => 'tar', 'TAR236G0001' => 'tar', 'TAR365G0892' => 'tar', 'TAR636G0166' => 'tar', 'TAR636G0646' => 'tar', 'TAR636G0869' => 'tar', 'TAR636G1317' => 'tar', 'TAR636G1744' => 'tar', 'TAR636G3358' => 'tar', 'TAR636G3436' => 'tar', 'THA.LOC104803047' => 'tha', 'Thecc.04G238900' => 'tca', 'Thhalv10021557m.g' => 'esa', 'Thhalv10026318m.g' => 'esa', 'Thhalv10026335m.g' => 'esa', 'TPR.G17433' => 'tpr', 'TPR.G18915' => 'tpr', 'TPR.G26125' => 'tpr', 'TWI09G0677' => 'twi', 'TWI73G0287' => 'twi', 'unitig_748.g8326' => 'ugi', 'vmacro15370' => 'vma', 'vmacro15371' => 'vma', 'vmacro15372' => 'vma', 'vmacro15373' => 'vma', 'vmacro15374' => 'vma', 'VMungo0720G2826' => 'vmu', 'Zm00001eb116960' => 'zma', 'Zm00001eb301260' => 'zma', 'Zm00001eb301270' => 'zma' ) $gf_id = 'HOM05D001460' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001460' ) $data_identifier = 'HOM05D001460' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 4, 'aag' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 2, 'aox' => (int) 2, 'arhy' => (int) 4, 'ath' => (int) 2, 'atr' => (int) 1, 'acertr' => (int) 10, 'cqu' => (int) 4, 'bca' => (int) 11, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 1, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 1, 'ccan' => (int) 1, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 1, 'col' => (int) 1, 'cpa' => (int) 1, 'cre' => (int) 7, 'csa' => (int) 1, 'camsi' => (int) 2, 'dca' => (int) 3, 'din' => (int) 2, 'dzi' => (int) 3, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 14, 'fve' => (int) 9, 'gma' => (int) 2, 'ghi' => (int) 4, 'gra' => (int) 2, 'vvi' => (int) 1, 'han' => (int) 13, 'cav' => (int) 1, 'hma' => (int) 2, 'sun' => (int) 2, 'lal' => (int) 2, 'lonja' => (int) 12, 'lja' => (int) 1, 'lsa' => (int) 7, 'mes' => (int) 1, 'mpo' => (int) 27, 'mbi' => (int) 1, 'mco' => (int) 8, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 1, 'egut' => (int) 1, 'ama' => (int) 1, 'nta' => (int) 4, 'nnu' => (int) 2, 'oeu' => (int) 3, 'osa' => (int) 4, 'pax' => (int) 9, 'pgr' => (int) 1, 'stu' => (int) 1, 'pvu' => (int) 1, 'ptr' => (int) 4, 'ppa' => (int) 22, 'pco' => (int) 6, 'ppe' => (int) 6, 'psa' => (int) 5, 'pso' => (int) 19, 'qlo' => (int) 5, 'rch' => (int) 7, 'rsi' => (int) 20, 'sbr' => (int) 5, 'sbo' => (int) 1, 'sci' => (int) 2, 'sed' => (int) 2, 'sgi' => (int) 12, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 2, 'tar' => (int) 10, 'tha' => (int) 1, 'tca' => (int) 1, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 2, 'ugi' => (int) 1, 'vma' => (int) 5, 'vmu' => (int) 1, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb301270' $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' => 'HOM05D001460', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '433', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p22980' => 'bna', 'A01p32340' => 'bna', 'A03p42970' => 'bna', 'A05p25880' => 'bna', 'Aa31LG8G9320' => 'aar', 'Aa31LG8G9330' => 'aar', 'Aa31LG8G9340' => 'aar', 'Aa31sc221G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1034' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1528' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.829' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2222' => 'aag', 'Ah.12g058830' => 'amhyb', 'Ah.12g058840' => 'amhyb', 'AL3G37160' => 'aly', 'AL7G41310' => 'aly', 'Aqoxy5G00395' => 'aox', 'Aqoxy5G00396' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0C8NZA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5185HY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JZ1PRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MD3LS0' => 'arhy', 'AT3G22840' => 'ath', 'AT4G14690' => 'ath', 'ATR0665G054' => 'atr', 'Atru.chr4.2344' => 'acertr', 'Atru.chr4.2346' => 'acertr', 'Atru.chr4.2347' => 'acertr', 'Atru.chr4.2348' => 'acertr', 'Atru.chr4.2355' => 'acertr', 'Atru.chr4.2356' => 'acertr', 'Atru.chr4.2358' => 'acertr', 'Atru.chr4.2359' => 'acertr', 'Atru.chr4.2360' => 'acertr', 'Atru.chr4.2361' => 'acertr', 'AUR62030476' => 'cqu', 'AUR62030478' => 'cqu', 'AUR62030819' => 'cqu', 'AUR62030820' => 'cqu', 'BcaB03g14648' => 'bca', 'BcaB04g20492' => 'bca', 'BcaB06g26399' => 'bca', 'BcaC01g03416' => 'bca', 'BcaC01g03419' => 'bca', 'BcaC01g03421' => 'bca', 'BcaC01g03424' => 'bca', 'BcaC05g28012' => 'bca', 'BcaC09g49212' => 'bca', 'BcaC09g50140' => 'bca', 'BcaNung00346' => 'bca', 'BolC1t02785H' => 'bol', 'BolC1t04095H' => 'bol', 'BolC3t17545H' => 'bol', 'BolC5t32769H' => 'bol', 'BraA01t02211Z' => 'bra', 'BraA01t03359Z' => 'bra', 'BraA03t13441Z' => 'bra', 'BraA05t21476Z' => 'bra', 'C01p28420' => 'bna', 'C01p41350' => 'bna', 'C03p52750' => 'bna', 'C03p52780' => 'bna', 'C05p40270' => 'bna', 'CAN.G1437.9' => 'can', 'CANSAT78G0035' => 'cansat', 'CANSAT78G1036' => 'cansat', 'CANSAT78G2272' => 'cansat', 'CANSAT78G2478' => 'cansat', 'CARHR098700' => 'chi', 'CARHR221120' => 'chi', 'CARHR221150' => 'chi', 'Carub.0003s2297' => 'cru', 'Carub.0007s2749' => 'cru', 'Carub.0007s2750' => 'cru', 'Carub.0007s2751' => 'cru', 'Ca_10849_v3' => 'car', 'Cc03_g04300' => 'ccan', 'CDE02G3648' => 'cde', 'CDE05G0060' => 'cde', 'CDE05G0692' => 'cde', 'CDE05G2285' => 'cde', 'CDE05G2884' => 'cde', 'CDE05G3072' => 'cde', 'Cfa008439' => 'cfa', 'Cfa008441' => 'cfa', 'Cfa008443' => 'cfa', 'Cfa008448' => 'cfa', 'Ciclev10005974m.g' => 'ccl', 'Ciclev10006006m.g' => 'ccl', 'Ciclev10006775m.g' => 'ccl', 'CiPaw.02G120400' => 'cil', 'CiPaw.02G120500' => 'cil', 'CiPaw.02G120600' => 'cil', 'ClCG05G004850' => 'cla', 'COL.COLO4_21566' => 'col', 'Cpa.g.sc44.124' => 'cpa', 'Cre07.g320400' => 'cre', 'Cre07.g320450' => 'cre', 'Cre08.g384650' => 'cre', 'Cre09.g393173' => 'cre', 'Cre09.g394325' => 'cre', 'Cre14.g626750' => 'cre', 'Cre16.g679250' => 'cre', 'CsaV3_3G012890' => 'csa', 'CSS0010865' => 'camsi', 'CSS0044338' => 'camsi', 'DCAR_002366' => 'dca', 'DCAR_030687' => 'dca', 'DCAR_030688' => 'dca', 'Dinv14047' => 'din', 'Dinv14048' => 'din', 'Duzib151G0105' => 'dzi', 'Duzib151G0114' => 'dzi', 'Duzib212G1029' => 'dzi', 'ECA232G3536' => 'eca', 'ECA240G0786' => 'eca', 'ECA240G1802' => 'eca', 'ECA240G3760' => 'eca', 'ECA240G3920' => 'eca', 'EL10Ac5g12536' => 'bvu', 'EL10Ac5g12537' => 'bvu', 'EL10Ac5g12538' => 'bvu', 'Eucgr.B01004' => 'egr', 'Eucgr.B01006' => 'egr', 'Eucgr.B01007' => 'egr', 'Eucgr.B01008' => 'egr', 'Eucgr.B01895' => 'egr', 'Eucgr.B01896' => 'egr', 'FAN04G1456' => 'fan', 'FAN08G1769' => 'fan', 'FAN08G2160' => 'fan', 'FAN13G2403' => 'fan', 'FAN13G3303' => 'fan', 'FAN15G2435' => 'fan', 'FAN17G0672' => 'fan', 'FAN17G2441' => 'fan', 'FAN18G1024' => 'fan', 'FAN22G1458' => 'fan', 'FAN24G0037' => 'fan', 'FAN24G0429' => 'fan', 'FAN24G2387' => 'fan', 'FAN27G2746' => 'fan', 'FvH4_2g20400' => 'fve', 'FvH4_2g20420' => 'fve', 'FvH4_2g20430' => 'fve', 'FvH4_4g01270' => 'fve', 'FvH4_4g01290' => 'fve', 'FvH4_4g01300' => 'fve', 'FvH4_4g01310' => 'fve', 'FvH4_4g01330' => 'fve', 'FvH4_5g09070' => 'fve', 'Glyma.10G243800' => 'gma', 'Glyma.20G150600' => 'gma', 'Gohir.A09G219200' => 'ghi', 'Gohir.A09G219300' => 'ghi', 'Gohir.D09G221400' => 'ghi', 'Gohir.D09G221500' => 'ghi', 'Gorai.006G242600' => 'gra', 'Gorai.006G242700' => 'gra', 'GSVIVG01018044001' => 'vvi', 'HanXRQChr03g0083821' => 'han', 'HanXRQChr03g0083841' => 'han', 'HanXRQChr03g0083881' => 'han', 'HanXRQChr03g0083901' => 'han', 'HanXRQChr03g0083921' => 'han', 'HanXRQChr03g0085331' => 'han', 'HanXRQChr03g0085361' => 'han', 'HanXRQChr03g0085411' => 'han', 'HanXRQChr03g0085421' => 'han', 'HanXRQChr03g0085431' => 'han', 'HanXRQChr08g0221991' => 'han', 'HanXRQChr11g0336061' => 'han', 'HanXRQChr11g0336411' => 'han', 'Haze_11234' => 'cav', 'Hma1.2p1_0549F.1_g177010' => 'hma', 'Hma1.2p1_0602F.1_g187630' => 'hma', 'Hund14876' => 'sun', 'Hund14879' => 'sun', 'Lalb_Chr06g0160741' => 'lal', 'Lalb_Chr21g0304781' => 'lal', 'Lj3A726G19' => 'lonja', 'Lj3A726T23' => 'lonja', 'Lj3A726T24' => 'lonja', 'Lj3A726T25' => 'lonja', 'Lj3A727T17' => 'lonja', 'Lj3C726T0' => 'lonja', 'Lj3C726T2' => 'lonja', 'Lj3P725T35' => 'lonja', 'Lj3P727T10' => 'lonja', 'Lj3P727T12' => 'lonja', 'Lj3P727T14' => 'lonja', 'Lj5g0023109' => 'lja', 'Lj6P646T44' => 'lonja', 'Lsat_1_v5_gn_6_75760' => 'lsa', 'Lsat_1_v5_gn_6_75800' => 'lsa', 'Lsat_1_v5_gn_6_75900' => 'lsa', 'Lsat_1_v5_gn_6_76240' => 'lsa', 'Lsat_1_v5_gn_6_76441' => 'lsa', 'Lsat_1_v5_gn_6_76700' => 'lsa', 'Lsat_1_v5_gn_6_76760' => 'lsa', 'Manes.15G033100' => 'mes', 'Mapoly0004s0074' => 'mpo', 'Mapoly0004s0075' => 'mpo', 'Mapoly0004s0163' => 'mpo', 'Mapoly0004s0164' => 'mpo', 'Mapoly0021s0018' => 'mpo', 'Mapoly0041s0136' => 'mpo', 'Mapoly0041s0137' => 'mpo', 'Mapoly0041s0138' => 'mpo', 'Mapoly0041s0139' => 'mpo', 'Mapoly0041s0141' => 'mpo', 'Mapoly0041s0142' => 'mpo', 'Mapoly0041s0143' => 'mpo', 'Mapoly0041s0144' => 'mpo', 'Mapoly0041s0145' => 'mpo', 'Mapoly0047s0106' => 'mpo', 'Mapoly0047s0108' => 'mpo', 'Mapoly0050s0051' => 'mpo', 'Mapoly0050s0052' => 'mpo', 'Mapoly0050s0053' => 'mpo', 'Mapoly0058s0013' => 'mpo', 'Mapoly0091s0078' => 'mpo', 'Mapoly0091s0079' => 'mpo', 'Mapoly0091s0080' => 'mpo', 'Mapoly0091s0081' => 'mpo', 'Mapoly0278s0004' => 'mpo', 'Mapoly0278s0005' => 'mpo', 'Mapoly0278s0006' => 'mpo', 'MBI11_g30648_MAGBIO' => 'mbi', 'MCO03G194' => 'mco', 'MCO03G590' => 'mco', 'MCO07G312' => 'mco', 'MCO10G318' => 'mco', 'MCO12G244' => 'mco', 'MCO13G148' => 'mco', 'MCO13G194' => 'mco', 'MCO16G238' => 'mco', 'MD06G1134100' => 'mdo', 'MD13G1200100' => 'mdo', 'MD13G1200300' => 'mdo', 'MD13G1200600' => 'mdo', 'MD14G1150400' => 'mdo', 'MD16G1200000' => 'mdo', 'Medtr1g102570' => 'mtr', 'Medtr1g102780' => 'mtr', 'Medtr1g102800' => 'mtr', 'Medtr1g102810' => 'mtr', 'Medtr1g102830' => 'mtr', 'MELO3C006499.2' => 'cme', 'Migut.G00385' => 'egut', 'MSTRG.4063' => 'ama', 'Nitab4.5_0000090g0260' => 'nta', 'Nitab4.5_0000977g0030' => 'nta', 'Nitab4.5_0002541g0040' => 'nta', 'Nitab4.5_0007068g0040' => 'nta', 'Nn005s41408' => 'nnu', 'Nn005s41410' => 'nnu', 'Oeu010310.1' => 'oeu', 'Oeu010311.1' => 'oeu', 'Oeu043472.1' => 'oeu', 'Os01g0246400' => 'osa', 'Os04g0267950' => 'osa', 'Os07g0178700' => 'osa', 'Os07g0178800' => 'osa', 'Peaxi162Scf00316g00046' => 'pax', 'Peaxi162Scf00316g00049' => 'pax', 'Peaxi162Scf00316g00059' => 'pax', 'Peaxi162Scf00316g00328' => 'pax', 'Peaxi162Scf00316g00329' => 'pax', 'Peaxi162Scf00316g00411' => 'pax', 'Peaxi162Scf00316g00521' => 'pax', 'Peaxi162Scf00492g00068' => 'pax', 'Peaxi162Scf35631g00002' => 'pax', 'PGR142G3720' => 'pgr', 'PGSC0003DMG400006442' => 'stu', 'Phvul.007G062000' => 'pvu', 'Potri.008G157750' => 'ptr', 'Potri.008G157900' => 'ptr', 'Potri.008G158000' => 'ptr', 'Potri.008G158200' => 'ptr', 'Pp3c11_7280' => 'ppa', 'Pp3c11_7980' => 'ppa', 'Pp3c12_19450' => 'ppa', 'Pp3c14_1480' => 'ppa', 'Pp3c14_1501' => 'ppa', 'Pp3c16_4900' => 'ppa', 'Pp3c16_5010' => 'ppa', 'Pp3c16_5060' => 'ppa', 'Pp3c19_18250' => 'ppa', 'Pp3c23_8530' => 'ppa', 'Pp3c23_8550' => 'ppa', 'Pp3c24_9670' => 'ppa', 'Pp3c2_21390' => 'ppa', 'Pp3c2_31380' => 'ppa', 'Pp3c3_16620' => 'ppa', 'Pp3c3_8090' => 'ppa', 'Pp3c3_8110' => 'ppa', 'Pp3c3_8130' => 'ppa', 'Pp3c3_8150' => 'ppa', 'Pp3c4_14320' => 'ppa', 'Pp3c6_2560' => 'ppa', 'Pp3c9_16700' => 'ppa', 'PRCOL_00000234' => 'pco', 'PRCOL_00000235' => 'pco', 'PRCOL_00000777' => 'pco', 'PRCOL_00002344' => 'pco', 'PRCOL_00002372' => 'pco', 'PRCOL_00006120' => 'pco', 'Prupe.1G021400' => 'ppe', 'Prupe.1G021500' => 'ppe', 'Prupe.1G021600' => 'ppe', 'Prupe.1G021700' => 'ppe', 'Prupe.1G021800' => 'ppe', 'Prupe.5G145100' => 'ppe', 'Psat6g204040' => 'psa', 'Psat6g204800' => 'psa', 'Psat6g204920' => 'psa', 'Psat6g204960' => 'psa', 'Psat6g205080' => 'psa', 'PSO017G0271' => 'pso', 'PSO017G1276' => 'pso', 'PSO017G1429' => 'pso', 'PSO017G1861' => 'pso', 'PSO017G2787' => 'pso', 'PSO017G4466' => 'pso', 'PSO017G5118' => 'pso', 'PSO017G5420' => 'pso', 'PSO063G3678' => 'pso', 'PSO210G0546' => 'pso', 'PSO317G0001' => 'pso', 'PSO357G0512' => 'pso', 'PSO478G2682' => 'pso', 'PSO647G0001' => 'pso', 'PSO675G0001' => 'pso', 'PSO675G2699' => 'pso', 'PSO675G2849' => 'pso', 'PSO675G4991' => 'pso', 'PSO689G0001' => 'pso', 'QL06p000916' => 'qlo', 'QL06p000921' => 'qlo', 'QL06p001398' => 'qlo', 'QL06p001407' => 'qlo', 'QL06p002031' => 'qlo', 'RcHm_v2.0_Chr4g0387791' => 'rch', 'RcHm_v2.0_Chr4g0387801' => 'rch', 'RcHm_v2.0_Chr6g0286501' => 'rch', 'RcHm_v2.0_Chr6g0286511' => 'rch', 'RcHm_v2.0_Chr6g0286521' => 'rch', 'RcHm_v2.0_Chr6g0286531' => 'rch', 'RcHm_v2.0_Chr7g0189141' => 'rch', 'Rhsim02G0028700' => 'rsi', 'Rhsim02G0028800' => 'rsi', 'Rhsim02G0028900' => 'rsi', 'Rhsim02G0029000' => 'rsi', 'Rhsim02G0029100' => 'rsi', 'Rhsim02G0029200' => 'rsi', 'Rhsim02G0029300' => 'rsi', 'Rhsim02G0029400' => 'rsi', 'Rhsim02G0029500' => 'rsi', 'Rhsim02G0029600' => 'rsi', 'RhsimUnG0024000' => 'rsi', 'RhsimUnG0024100' => 'rsi', 'RhsimUnG0024200' => 'rsi', 'RhsimUnG0024300' => 'rsi', 'RhsimUnG0024400' => 'rsi', 'RhsimUnG0024500' => 'rsi', 'RhsimUnG0024700' => 'rsi', 'RhsimUnG0024800' => 'rsi', 'RhsimUnG0024900' => 'rsi', 'RhsimUnG0025100' => 'rsi', 'Sabra08G0120200' => 'sbr', 'Sabra08G0120300' => 'sbr', 'Sabra08G0120500' => 'sbr', 'Sabra08G0120600' => 'sbr', 'Sabra10G0158900' => 'sbr', 'SalBow2G3492' => 'sbo', 'Sc13g0004760' => 'sci', 'Sc13g0004770' => 'sci', 'Sed0003417' => 'sed', 'Sed0019750' => 'sed', 'SEGI_03419' => 'sgi', 'SEGI_05907' => 'sgi', 'SEGI_10682' => 'sgi', 'SEGI_13528' => 'sgi', 'SEGI_16081' => 'sgi', 'SEGI_19370' => 'sgi', 'SEGI_21015' => 'sgi', 'SEGI_21944' => 'sgi', 'SEGI_32906' => 'sgi', 'SEGI_33093' => 'sgi', 'SEGI_36110' => 'sgi', 'SEGI_40397' => 'sgi', 'SGA_v2.0_scaffold191G40426' => 'sas', 'SGA_v2.0_scaffold353G49717' => 'sas', 'SGA_v2.0_scaffold50G18550' => 'sas', 'SMO119G0173' => 'smo', 'SMO172G0002' => 'smo', 'Solyc09g082690.3' => 'sly', 'Solyc09g082700.2' => 'sly', 'Sopen09g031550' => 'spe', 'Sopen09g031560' => 'spe', 'Sp3g20540' => 'spa', 'Sp7g07580' => 'spa', 'TAR134G0002' => 'tar', 'TAR236G0001' => 'tar', 'TAR365G0892' => 'tar', 'TAR636G0166' => 'tar', 'TAR636G0646' => 'tar', 'TAR636G0869' => 'tar', 'TAR636G1317' => 'tar', 'TAR636G1744' => 'tar', 'TAR636G3358' => 'tar', 'TAR636G3436' => 'tar', 'THA.LOC104803047' => 'tha', 'Thecc.04G238900' => 'tca', 'Thhalv10021557m.g' => 'esa', 'Thhalv10026318m.g' => 'esa', 'Thhalv10026335m.g' => 'esa', 'TPR.G17433' => 'tpr', 'TPR.G18915' => 'tpr', 'TPR.G26125' => 'tpr', 'TWI09G0677' => 'twi', 'TWI73G0287' => 'twi', 'unitig_748.g8326' => 'ugi', 'vmacro15370' => 'vma', 'vmacro15371' => 'vma', 'vmacro15372' => 'vma', 'vmacro15373' => 'vma', 'vmacro15374' => 'vma', 'VMungo0720G2826' => 'vmu', 'Zm00001eb116960' => 'zma', 'Zm00001eb301260' => 'zma', 'Zm00001eb301270' => 'zma' ), 'gf_id' => 'HOM05D001460', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001460' ), 'data_identifier' => 'HOM05D001460', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001460', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '433', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p22980' => 'bna', 'A01p32340' => 'bna', 'A03p42970' => 'bna', 'A05p25880' => 'bna', 'Aa31LG8G9320' => 'aar', 'Aa31LG8G9330' => 'aar', 'Aa31LG8G9340' => 'aar', 'Aa31sc221G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1034' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1528' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.829' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2222' => 'aag', 'Ah.12g058830' => 'amhyb', 'Ah.12g058840' => 'amhyb', 'AL3G37160' => 'aly', 'AL7G41310' => 'aly', 'Aqoxy5G00395' => 'aox', 'Aqoxy5G00396' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0C8NZA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5185HY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JZ1PRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MD3LS0' => 'arhy', 'AT3G22840' => 'ath', 'AT4G14690' => 'ath', 'ATR0665G054' => 'atr', 'Atru.chr4.2344' => 'acertr', 'Atru.chr4.2346' => 'acertr', 'Atru.chr4.2347' => 'acertr', 'Atru.chr4.2348' => 'acertr', 'Atru.chr4.2355' => 'acertr', 'Atru.chr4.2356' => 'acertr', 'Atru.chr4.2358' => 'acertr', 'Atru.chr4.2359' => 'acertr', 'Atru.chr4.2360' => 'acertr', 'Atru.chr4.2361' => 'acertr', 'AUR62030476' => 'cqu', 'AUR62030478' => 'cqu', 'AUR62030819' => 'cqu', 'AUR62030820' => 'cqu', 'BcaB03g14648' => 'bca', 'BcaB04g20492' => 'bca', 'BcaB06g26399' => 'bca', 'BcaC01g03416' => 'bca', 'BcaC01g03419' => 'bca', 'BcaC01g03421' => 'bca', 'BcaC01g03424' => 'bca', 'BcaC05g28012' => 'bca', 'BcaC09g49212' => 'bca', 'BcaC09g50140' => 'bca', 'BcaNung00346' => 'bca', 'BolC1t02785H' => 'bol', 'BolC1t04095H' => 'bol', 'BolC3t17545H' => 'bol', 'BolC5t32769H' => 'bol', 'BraA01t02211Z' => 'bra', 'BraA01t03359Z' => 'bra', 'BraA03t13441Z' => 'bra', 'BraA05t21476Z' => 'bra', 'C01p28420' => 'bna', 'C01p41350' => 'bna', 'C03p52750' => 'bna', 'C03p52780' => 'bna', 'C05p40270' => 'bna', 'CAN.G1437.9' => 'can', 'CANSAT78G0035' => 'cansat', 'CANSAT78G1036' => 'cansat', 'CANSAT78G2272' => 'cansat', 'CANSAT78G2478' => 'cansat', 'CARHR098700' => 'chi', 'CARHR221120' => 'chi', 'CARHR221150' => 'chi', 'Carub.0003s2297' => 'cru', 'Carub.0007s2749' => 'cru', 'Carub.0007s2750' => 'cru', 'Carub.0007s2751' => 'cru', 'Ca_10849_v3' => 'car', 'Cc03_g04300' => 'ccan', 'CDE02G3648' => 'cde', 'CDE05G0060' => 'cde', 'CDE05G0692' => 'cde', 'CDE05G2285' => 'cde', 'CDE05G2884' => 'cde', 'CDE05G3072' => 'cde', 'Cfa008439' => 'cfa', 'Cfa008441' => 'cfa', 'Cfa008443' => 'cfa', 'Cfa008448' => 'cfa', 'Ciclev10005974m.g' => 'ccl', 'Ciclev10006006m.g' => 'ccl', 'Ciclev10006775m.g' => 'ccl', 'CiPaw.02G120400' => 'cil', 'CiPaw.02G120500' => 'cil', 'CiPaw.02G120600' => 'cil', 'ClCG05G004850' => 'cla', 'COL.COLO4_21566' => 'col', 'Cpa.g.sc44.124' => 'cpa', 'Cre07.g320400' => 'cre', 'Cre07.g320450' => 'cre', 'Cre08.g384650' => 'cre', 'Cre09.g393173' => 'cre', 'Cre09.g394325' => 'cre', 'Cre14.g626750' => 'cre', 'Cre16.g679250' => 'cre', 'CsaV3_3G012890' => 'csa', 'CSS0010865' => 'camsi', 'CSS0044338' => 'camsi', 'DCAR_002366' => 'dca', 'DCAR_030687' => 'dca', 'DCAR_030688' => 'dca', 'Dinv14047' => 'din', 'Dinv14048' => 'din', 'Duzib151G0105' => 'dzi', 'Duzib151G0114' => 'dzi', 'Duzib212G1029' => 'dzi', 'ECA232G3536' => 'eca', 'ECA240G0786' => 'eca', 'ECA240G1802' => 'eca', 'ECA240G3760' => 'eca', 'ECA240G3920' => 'eca', 'EL10Ac5g12536' => 'bvu', 'EL10Ac5g12537' => 'bvu', 'EL10Ac5g12538' => 'bvu', 'Eucgr.B01004' => 'egr', 'Eucgr.B01006' => 'egr', 'Eucgr.B01007' => 'egr', 'Eucgr.B01008' => 'egr', 'Eucgr.B01895' => 'egr', 'Eucgr.B01896' => 'egr', 'FAN04G1456' => 'fan', 'FAN08G1769' => 'fan', 'FAN08G2160' => 'fan', 'FAN13G2403' => 'fan', 'FAN13G3303' => 'fan', 'FAN15G2435' => 'fan', 'FAN17G0672' => 'fan', 'FAN17G2441' => 'fan', 'FAN18G1024' => 'fan', 'FAN22G1458' => 'fan', 'FAN24G0037' => 'fan', 'FAN24G0429' => 'fan', 'FAN24G2387' => 'fan', 'FAN27G2746' => 'fan', 'FvH4_2g20400' => 'fve', 'FvH4_2g20420' => 'fve', 'FvH4_2g20430' => 'fve', 'FvH4_4g01270' => 'fve', 'FvH4_4g01290' => 'fve', 'FvH4_4g01300' => 'fve', 'FvH4_4g01310' => 'fve', 'FvH4_4g01330' => 'fve', 'FvH4_5g09070' => 'fve', 'Glyma.10G243800' => 'gma', 'Glyma.20G150600' => 'gma', 'Gohir.A09G219200' => 'ghi', 'Gohir.A09G219300' => 'ghi', 'Gohir.D09G221400' => 'ghi', 'Gohir.D09G221500' => 'ghi', 'Gorai.006G242600' => 'gra', 'Gorai.006G242700' => 'gra', 'GSVIVG01018044001' => 'vvi', 'HanXRQChr03g0083821' => 'han', 'HanXRQChr03g0083841' => 'han', 'HanXRQChr03g0083881' => 'han', 'HanXRQChr03g0083901' => 'han', 'HanXRQChr03g0083921' => 'han', 'HanXRQChr03g0085331' => 'han', 'HanXRQChr03g0085361' => 'han', 'HanXRQChr03g0085411' => 'han', 'HanXRQChr03g0085421' => 'han', 'HanXRQChr03g0085431' => 'han', 'HanXRQChr08g0221991' => 'han', 'HanXRQChr11g0336061' => 'han', 'HanXRQChr11g0336411' => 'han', 'Haze_11234' => 'cav', 'Hma1.2p1_0549F.1_g177010' => 'hma', 'Hma1.2p1_0602F.1_g187630' => 'hma', 'Hund14876' => 'sun', 'Hund14879' => 'sun', 'Lalb_Chr06g0160741' => 'lal', 'Lalb_Chr21g0304781' => 'lal', 'Lj3A726G19' => 'lonja', 'Lj3A726T23' => 'lonja', 'Lj3A726T24' => 'lonja', 'Lj3A726T25' => 'lonja', 'Lj3A727T17' => 'lonja', 'Lj3C726T0' => 'lonja', 'Lj3C726T2' => 'lonja', 'Lj3P725T35' => 'lonja', 'Lj3P727T10' => 'lonja', 'Lj3P727T12' => 'lonja', 'Lj3P727T14' => 'lonja', 'Lj5g0023109' => 'lja', 'Lj6P646T44' => 'lonja', 'Lsat_1_v5_gn_6_75760' => 'lsa', 'Lsat_1_v5_gn_6_75800' => 'lsa', 'Lsat_1_v5_gn_6_75900' => 'lsa', 'Lsat_1_v5_gn_6_76240' => 'lsa', 'Lsat_1_v5_gn_6_76441' => 'lsa', 'Lsat_1_v5_gn_6_76700' => 'lsa', 'Lsat_1_v5_gn_6_76760' => 'lsa', 'Manes.15G033100' => 'mes', 'Mapoly0004s0074' => 'mpo', 'Mapoly0004s0075' => 'mpo', 'Mapoly0004s0163' => 'mpo', 'Mapoly0004s0164' => 'mpo', 'Mapoly0021s0018' => 'mpo', 'Mapoly0041s0136' => 'mpo', 'Mapoly0041s0137' => 'mpo', 'Mapoly0041s0138' => 'mpo', 'Mapoly0041s0139' => 'mpo', 'Mapoly0041s0141' => 'mpo', 'Mapoly0041s0142' => 'mpo', 'Mapoly0041s0143' => 'mpo', 'Mapoly0041s0144' => 'mpo', 'Mapoly0041s0145' => 'mpo', 'Mapoly0047s0106' => 'mpo', 'Mapoly0047s0108' => 'mpo', 'Mapoly0050s0051' => 'mpo', 'Mapoly0050s0052' => 'mpo', 'Mapoly0050s0053' => 'mpo', 'Mapoly0058s0013' => 'mpo', 'Mapoly0091s0078' => 'mpo', 'Mapoly0091s0079' => 'mpo', 'Mapoly0091s0080' => 'mpo', 'Mapoly0091s0081' => 'mpo', 'Mapoly0278s0004' => 'mpo', 'Mapoly0278s0005' => 'mpo', 'Mapoly0278s0006' => 'mpo', 'MBI11_g30648_MAGBIO' => 'mbi', 'MCO03G194' => 'mco', 'MCO03G590' => 'mco', 'MCO07G312' => 'mco', 'MCO10G318' => 'mco', 'MCO12G244' => 'mco', 'MCO13G148' => 'mco', 'MCO13G194' => 'mco', 'MCO16G238' => 'mco', 'MD06G1134100' => 'mdo', 'MD13G1200100' => 'mdo', 'MD13G1200300' => 'mdo', 'MD13G1200600' => 'mdo', 'MD14G1150400' => 'mdo', 'MD16G1200000' => 'mdo', 'Medtr1g102570' => 'mtr', 'Medtr1g102780' => 'mtr', 'Medtr1g102800' => 'mtr', 'Medtr1g102810' => 'mtr', 'Medtr1g102830' => 'mtr', 'MELO3C006499.2' => 'cme', 'Migut.G00385' => 'egut', 'MSTRG.4063' => 'ama', 'Nitab4.5_0000090g0260' => 'nta', 'Nitab4.5_0000977g0030' => 'nta', 'Nitab4.5_0002541g0040' => 'nta', 'Nitab4.5_0007068g0040' => 'nta', 'Nn005s41408' => 'nnu', 'Nn005s41410' => 'nnu', 'Oeu010310.1' => 'oeu', 'Oeu010311.1' => 'oeu', 'Oeu043472.1' => 'oeu', 'Os01g0246400' => 'osa', 'Os04g0267950' => 'osa', 'Os07g0178700' => 'osa', 'Os07g0178800' => 'osa', 'Peaxi162Scf00316g00046' => 'pax', 'Peaxi162Scf00316g00049' => 'pax', 'Peaxi162Scf00316g00059' => 'pax', 'Peaxi162Scf00316g00328' => 'pax', 'Peaxi162Scf00316g00329' => 'pax', 'Peaxi162Scf00316g00411' => 'pax', 'Peaxi162Scf00316g00521' => 'pax', 'Peaxi162Scf00492g00068' => 'pax', 'Peaxi162Scf35631g00002' => 'pax', 'PGR142G3720' => 'pgr', 'PGSC0003DMG400006442' => 'stu', 'Phvul.007G062000' => 'pvu', 'Potri.008G157750' => 'ptr', 'Potri.008G157900' => 'ptr', 'Potri.008G158000' => 'ptr', 'Potri.008G158200' => 'ptr', 'Pp3c11_7280' => 'ppa', 'Pp3c11_7980' => 'ppa', 'Pp3c12_19450' => 'ppa', 'Pp3c14_1480' => 'ppa', 'Pp3c14_1501' => 'ppa', 'Pp3c16_4900' => 'ppa', 'Pp3c16_5010' => 'ppa', 'Pp3c16_5060' => 'ppa', 'Pp3c19_18250' => 'ppa', 'Pp3c23_8530' => 'ppa', 'Pp3c23_8550' => 'ppa', 'Pp3c24_9670' => 'ppa', 'Pp3c2_21390' => 'ppa', 'Pp3c2_31380' => 'ppa', 'Pp3c3_16620' => 'ppa', 'Pp3c3_8090' => 'ppa', 'Pp3c3_8110' => 'ppa', 'Pp3c3_8130' => 'ppa', 'Pp3c3_8150' => 'ppa', 'Pp3c4_14320' => 'ppa', 'Pp3c6_2560' => 'ppa', 'Pp3c9_16700' => 'ppa', 'PRCOL_00000234' => 'pco', 'PRCOL_00000235' => 'pco', 'PRCOL_00000777' => 'pco', 'PRCOL_00002344' => 'pco', 'PRCOL_00002372' => 'pco', 'PRCOL_00006120' => 'pco', 'Prupe.1G021400' => 'ppe', 'Prupe.1G021500' => 'ppe', 'Prupe.1G021600' => 'ppe', 'Prupe.1G021700' => 'ppe', 'Prupe.1G021800' => 'ppe', 'Prupe.5G145100' => 'ppe', 'Psat6g204040' => 'psa', 'Psat6g204800' => 'psa', 'Psat6g204920' => 'psa', 'Psat6g204960' => 'psa', 'Psat6g205080' => 'psa', 'PSO017G0271' => 'pso', 'PSO017G1276' => 'pso', 'PSO017G1429' => 'pso', 'PSO017G1861' => 'pso', 'PSO017G2787' => 'pso', 'PSO017G4466' => 'pso', 'PSO017G5118' => 'pso', 'PSO017G5420' => 'pso', 'PSO063G3678' => 'pso', 'PSO210G0546' => 'pso', 'PSO317G0001' => 'pso', 'PSO357G0512' => 'pso', 'PSO478G2682' => 'pso', 'PSO647G0001' => 'pso', 'PSO675G0001' => 'pso', 'PSO675G2699' => 'pso', 'PSO675G2849' => 'pso', 'PSO675G4991' => 'pso', 'PSO689G0001' => 'pso', 'QL06p000916' => 'qlo', 'QL06p000921' => 'qlo', 'QL06p001398' => 'qlo', 'QL06p001407' => 'qlo', 'QL06p002031' => 'qlo', 'RcHm_v2.0_Chr4g0387791' => 'rch', 'RcHm_v2.0_Chr4g0387801' => 'rch', 'RcHm_v2.0_Chr6g0286501' => 'rch', 'RcHm_v2.0_Chr6g0286511' => 'rch', 'RcHm_v2.0_Chr6g0286521' => 'rch', 'RcHm_v2.0_Chr6g0286531' => 'rch', 'RcHm_v2.0_Chr7g0189141' => 'rch', 'Rhsim02G0028700' => 'rsi', 'Rhsim02G0028800' => 'rsi', 'Rhsim02G0028900' => 'rsi', 'Rhsim02G0029000' => 'rsi', 'Rhsim02G0029100' => 'rsi', 'Rhsim02G0029200' => 'rsi', 'Rhsim02G0029300' => 'rsi', 'Rhsim02G0029400' => 'rsi', 'Rhsim02G0029500' => 'rsi', 'Rhsim02G0029600' => 'rsi', 'RhsimUnG0024000' => 'rsi', 'RhsimUnG0024100' => 'rsi', 'RhsimUnG0024200' => 'rsi', 'RhsimUnG0024300' => 'rsi', 'RhsimUnG0024400' => 'rsi', 'RhsimUnG0024500' => 'rsi', 'RhsimUnG0024700' => 'rsi', 'RhsimUnG0024800' => 'rsi', 'RhsimUnG0024900' => 'rsi', 'RhsimUnG0025100' => 'rsi', 'Sabra08G0120200' => 'sbr', 'Sabra08G0120300' => 'sbr', 'Sabra08G0120500' => 'sbr', 'Sabra08G0120600' => 'sbr', 'Sabra10G0158900' => 'sbr', 'SalBow2G3492' => 'sbo', 'Sc13g0004760' => 'sci', 'Sc13g0004770' => 'sci', 'Sed0003417' => 'sed', 'Sed0019750' => 'sed', 'SEGI_03419' => 'sgi', 'SEGI_05907' => 'sgi', 'SEGI_10682' => 'sgi', 'SEGI_13528' => 'sgi', 'SEGI_16081' => 'sgi', 'SEGI_19370' => 'sgi', 'SEGI_21015' => 'sgi', 'SEGI_21944' => 'sgi', 'SEGI_32906' => 'sgi', 'SEGI_33093' => 'sgi', 'SEGI_36110' => 'sgi', 'SEGI_40397' => 'sgi', 'SGA_v2.0_scaffold191G40426' => 'sas', 'SGA_v2.0_scaffold353G49717' => 'sas', 'SGA_v2.0_scaffold50G18550' => 'sas', 'SMO119G0173' => 'smo', 'SMO172G0002' => 'smo', 'Solyc09g082690.3' => 'sly', 'Solyc09g082700.2' => 'sly', 'Sopen09g031550' => 'spe', 'Sopen09g031560' => 'spe', 'Sp3g20540' => 'spa', 'Sp7g07580' => 'spa', 'TAR134G0002' => 'tar', 'TAR236G0001' => 'tar', 'TAR365G0892' => 'tar', 'TAR636G0166' => 'tar', 'TAR636G0646' => 'tar', 'TAR636G0869' => 'tar', 'TAR636G1317' => 'tar', 'TAR636G1744' => 'tar', 'TAR636G3358' => 'tar', 'TAR636G3436' => 'tar', 'THA.LOC104803047' => 'tha', 'Thecc.04G238900' => 'tca', 'Thhalv10021557m.g' => 'esa', 'Thhalv10026318m.g' => 'esa', 'Thhalv10026335m.g' => 'esa', 'TPR.G17433' => 'tpr', 'TPR.G18915' => 'tpr', 'TPR.G26125' => 'tpr', 'TWI09G0677' => 'twi', 'TWI73G0287' => 'twi', 'unitig_748.g8326' => 'ugi', 'vmacro15370' => 'vma', 'vmacro15371' => 'vma', 'vmacro15372' => 'vma', 'vmacro15373' => 'vma', 'vmacro15374' => 'vma', 'VMungo0720G2826' => 'vmu', 'Zm00001eb116960' => 'zma', 'Zm00001eb301260' => 'zma', 'Zm00001eb301270' => 'zma' ) $gf_id = 'HOM05D001460' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001460' ) $data_identifier = 'HOM05D001460' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 4, 'aag' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 2, 'aox' => (int) 2, 'arhy' => (int) 4, 'ath' => (int) 2, 'atr' => (int) 1, 'acertr' => (int) 10, 'cqu' => (int) 4, 'bca' => (int) 11, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 1, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 1, 'ccan' => (int) 1, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 1, 'col' => (int) 1, 'cpa' => (int) 1, 'cre' => (int) 7, 'csa' => (int) 1, 'camsi' => (int) 2, 'dca' => (int) 3, 'din' => (int) 2, 'dzi' => (int) 3, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 14, 'fve' => (int) 9, 'gma' => (int) 2, 'ghi' => (int) 4, 'gra' => (int) 2, 'vvi' => (int) 1, 'han' => (int) 13, 'cav' => (int) 1, 'hma' => (int) 2, 'sun' => (int) 2, 'lal' => (int) 2, 'lonja' => (int) 12, 'lja' => (int) 1, 'lsa' => (int) 7, 'mes' => (int) 1, 'mpo' => (int) 27, 'mbi' => (int) 1, 'mco' => (int) 8, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 1, 'egut' => (int) 1, 'ama' => (int) 1, 'nta' => (int) 4, 'nnu' => (int) 2, 'oeu' => (int) 3, 'osa' => (int) 4, 'pax' => (int) 9, 'pgr' => (int) 1, 'stu' => (int) 1, 'pvu' => (int) 1, 'ptr' => (int) 4, 'ppa' => (int) 22, 'pco' => (int) 6, 'ppe' => (int) 6, 'psa' => (int) 5, 'pso' => (int) 19, 'qlo' => (int) 5, 'rch' => (int) 7, 'rsi' => (int) 20, 'sbr' => (int) 5, 'sbo' => (int) 1, 'sci' => (int) 2, 'sed' => (int) 2, 'sgi' => (int) 12, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 2, 'tar' => (int) 10, 'tha' => (int) 1, 'tca' => (int) 1, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 2, 'ugi' => (int) 1, 'vma' => (int) 5, 'vmu' => (int) 1, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb301270' $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' => 'HOM05D001460', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '433', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p22980' => 'bna', 'A01p32340' => 'bna', 'A03p42970' => 'bna', 'A05p25880' => 'bna', 'Aa31LG8G9320' => 'aar', 'Aa31LG8G9330' => 'aar', 'Aa31LG8G9340' => 'aar', 'Aa31sc221G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1034' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1528' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.829' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2222' => 'aag', 'Ah.12g058830' => 'amhyb', 'Ah.12g058840' => 'amhyb', 'AL3G37160' => 'aly', 'AL7G41310' => 'aly', 'Aqoxy5G00395' => 'aox', 'Aqoxy5G00396' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0C8NZA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5185HY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JZ1PRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MD3LS0' => 'arhy', 'AT3G22840' => 'ath', 'AT4G14690' => 'ath', 'ATR0665G054' => 'atr', 'Atru.chr4.2344' => 'acertr', 'Atru.chr4.2346' => 'acertr', 'Atru.chr4.2347' => 'acertr', 'Atru.chr4.2348' => 'acertr', 'Atru.chr4.2355' => 'acertr', 'Atru.chr4.2356' => 'acertr', 'Atru.chr4.2358' => 'acertr', 'Atru.chr4.2359' => 'acertr', 'Atru.chr4.2360' => 'acertr', 'Atru.chr4.2361' => 'acertr', 'AUR62030476' => 'cqu', 'AUR62030478' => 'cqu', 'AUR62030819' => 'cqu', 'AUR62030820' => 'cqu', 'BcaB03g14648' => 'bca', 'BcaB04g20492' => 'bca', 'BcaB06g26399' => 'bca', 'BcaC01g03416' => 'bca', 'BcaC01g03419' => 'bca', 'BcaC01g03421' => 'bca', 'BcaC01g03424' => 'bca', 'BcaC05g28012' => 'bca', 'BcaC09g49212' => 'bca', 'BcaC09g50140' => 'bca', 'BcaNung00346' => 'bca', 'BolC1t02785H' => 'bol', 'BolC1t04095H' => 'bol', 'BolC3t17545H' => 'bol', 'BolC5t32769H' => 'bol', 'BraA01t02211Z' => 'bra', 'BraA01t03359Z' => 'bra', 'BraA03t13441Z' => 'bra', 'BraA05t21476Z' => 'bra', 'C01p28420' => 'bna', 'C01p41350' => 'bna', 'C03p52750' => 'bna', 'C03p52780' => 'bna', 'C05p40270' => 'bna', 'CAN.G1437.9' => 'can', 'CANSAT78G0035' => 'cansat', 'CANSAT78G1036' => 'cansat', 'CANSAT78G2272' => 'cansat', 'CANSAT78G2478' => 'cansat', 'CARHR098700' => 'chi', 'CARHR221120' => 'chi', 'CARHR221150' => 'chi', 'Carub.0003s2297' => 'cru', 'Carub.0007s2749' => 'cru', 'Carub.0007s2750' => 'cru', 'Carub.0007s2751' => 'cru', 'Ca_10849_v3' => 'car', 'Cc03_g04300' => 'ccan', 'CDE02G3648' => 'cde', 'CDE05G0060' => 'cde', 'CDE05G0692' => 'cde', 'CDE05G2285' => 'cde', 'CDE05G2884' => 'cde', 'CDE05G3072' => 'cde', 'Cfa008439' => 'cfa', 'Cfa008441' => 'cfa', 'Cfa008443' => 'cfa', 'Cfa008448' => 'cfa', 'Ciclev10005974m.g' => 'ccl', 'Ciclev10006006m.g' => 'ccl', 'Ciclev10006775m.g' => 'ccl', 'CiPaw.02G120400' => 'cil', 'CiPaw.02G120500' => 'cil', 'CiPaw.02G120600' => 'cil', 'ClCG05G004850' => 'cla', 'COL.COLO4_21566' => 'col', 'Cpa.g.sc44.124' => 'cpa', 'Cre07.g320400' => 'cre', 'Cre07.g320450' => 'cre', 'Cre08.g384650' => 'cre', 'Cre09.g393173' => 'cre', 'Cre09.g394325' => 'cre', 'Cre14.g626750' => 'cre', 'Cre16.g679250' => 'cre', 'CsaV3_3G012890' => 'csa', 'CSS0010865' => 'camsi', 'CSS0044338' => 'camsi', 'DCAR_002366' => 'dca', 'DCAR_030687' => 'dca', 'DCAR_030688' => 'dca', 'Dinv14047' => 'din', 'Dinv14048' => 'din', 'Duzib151G0105' => 'dzi', 'Duzib151G0114' => 'dzi', 'Duzib212G1029' => 'dzi', 'ECA232G3536' => 'eca', 'ECA240G0786' => 'eca', 'ECA240G1802' => 'eca', 'ECA240G3760' => 'eca', 'ECA240G3920' => 'eca', 'EL10Ac5g12536' => 'bvu', 'EL10Ac5g12537' => 'bvu', 'EL10Ac5g12538' => 'bvu', 'Eucgr.B01004' => 'egr', 'Eucgr.B01006' => 'egr', 'Eucgr.B01007' => 'egr', 'Eucgr.B01008' => 'egr', 'Eucgr.B01895' => 'egr', 'Eucgr.B01896' => 'egr', 'FAN04G1456' => 'fan', 'FAN08G1769' => 'fan', 'FAN08G2160' => 'fan', 'FAN13G2403' => 'fan', 'FAN13G3303' => 'fan', 'FAN15G2435' => 'fan', 'FAN17G0672' => 'fan', 'FAN17G2441' => 'fan', 'FAN18G1024' => 'fan', 'FAN22G1458' => 'fan', 'FAN24G0037' => 'fan', 'FAN24G0429' => 'fan', 'FAN24G2387' => 'fan', 'FAN27G2746' => 'fan', 'FvH4_2g20400' => 'fve', 'FvH4_2g20420' => 'fve', 'FvH4_2g20430' => 'fve', 'FvH4_4g01270' => 'fve', 'FvH4_4g01290' => 'fve', 'FvH4_4g01300' => 'fve', 'FvH4_4g01310' => 'fve', 'FvH4_4g01330' => 'fve', 'FvH4_5g09070' => 'fve', 'Glyma.10G243800' => 'gma', 'Glyma.20G150600' => 'gma', 'Gohir.A09G219200' => 'ghi', 'Gohir.A09G219300' => 'ghi', 'Gohir.D09G221400' => 'ghi', 'Gohir.D09G221500' => 'ghi', 'Gorai.006G242600' => 'gra', 'Gorai.006G242700' => 'gra', 'GSVIVG01018044001' => 'vvi', 'HanXRQChr03g0083821' => 'han', 'HanXRQChr03g0083841' => 'han', 'HanXRQChr03g0083881' => 'han', 'HanXRQChr03g0083901' => 'han', 'HanXRQChr03g0083921' => 'han', 'HanXRQChr03g0085331' => 'han', 'HanXRQChr03g0085361' => 'han', 'HanXRQChr03g0085411' => 'han', 'HanXRQChr03g0085421' => 'han', 'HanXRQChr03g0085431' => 'han', 'HanXRQChr08g0221991' => 'han', 'HanXRQChr11g0336061' => 'han', 'HanXRQChr11g0336411' => 'han', 'Haze_11234' => 'cav', 'Hma1.2p1_0549F.1_g177010' => 'hma', 'Hma1.2p1_0602F.1_g187630' => 'hma', 'Hund14876' => 'sun', 'Hund14879' => 'sun', 'Lalb_Chr06g0160741' => 'lal', 'Lalb_Chr21g0304781' => 'lal', 'Lj3A726G19' => 'lonja', 'Lj3A726T23' => 'lonja', 'Lj3A726T24' => 'lonja', 'Lj3A726T25' => 'lonja', 'Lj3A727T17' => 'lonja', 'Lj3C726T0' => 'lonja', 'Lj3C726T2' => 'lonja', 'Lj3P725T35' => 'lonja', 'Lj3P727T10' => 'lonja', 'Lj3P727T12' => 'lonja', 'Lj3P727T14' => 'lonja', 'Lj5g0023109' => 'lja', 'Lj6P646T44' => 'lonja', 'Lsat_1_v5_gn_6_75760' => 'lsa', 'Lsat_1_v5_gn_6_75800' => 'lsa', 'Lsat_1_v5_gn_6_75900' => 'lsa', 'Lsat_1_v5_gn_6_76240' => 'lsa', 'Lsat_1_v5_gn_6_76441' => 'lsa', 'Lsat_1_v5_gn_6_76700' => 'lsa', 'Lsat_1_v5_gn_6_76760' => 'lsa', 'Manes.15G033100' => 'mes', 'Mapoly0004s0074' => 'mpo', 'Mapoly0004s0075' => 'mpo', 'Mapoly0004s0163' => 'mpo', 'Mapoly0004s0164' => 'mpo', 'Mapoly0021s0018' => 'mpo', 'Mapoly0041s0136' => 'mpo', 'Mapoly0041s0137' => 'mpo', 'Mapoly0041s0138' => 'mpo', 'Mapoly0041s0139' => 'mpo', 'Mapoly0041s0141' => 'mpo', 'Mapoly0041s0142' => 'mpo', 'Mapoly0041s0143' => 'mpo', 'Mapoly0041s0144' => 'mpo', 'Mapoly0041s0145' => 'mpo', 'Mapoly0047s0106' => 'mpo', 'Mapoly0047s0108' => 'mpo', 'Mapoly0050s0051' => 'mpo', 'Mapoly0050s0052' => 'mpo', 'Mapoly0050s0053' => 'mpo', 'Mapoly0058s0013' => 'mpo', 'Mapoly0091s0078' => 'mpo', 'Mapoly0091s0079' => 'mpo', 'Mapoly0091s0080' => 'mpo', 'Mapoly0091s0081' => 'mpo', 'Mapoly0278s0004' => 'mpo', 'Mapoly0278s0005' => 'mpo', 'Mapoly0278s0006' => 'mpo', 'MBI11_g30648_MAGBIO' => 'mbi', 'MCO03G194' => 'mco', 'MCO03G590' => 'mco', 'MCO07G312' => 'mco', 'MCO10G318' => 'mco', 'MCO12G244' => 'mco', 'MCO13G148' => 'mco', 'MCO13G194' => 'mco', 'MCO16G238' => 'mco', 'MD06G1134100' => 'mdo', 'MD13G1200100' => 'mdo', 'MD13G1200300' => 'mdo', 'MD13G1200600' => 'mdo', 'MD14G1150400' => 'mdo', 'MD16G1200000' => 'mdo', 'Medtr1g102570' => 'mtr', 'Medtr1g102780' => 'mtr', 'Medtr1g102800' => 'mtr', 'Medtr1g102810' => 'mtr', 'Medtr1g102830' => 'mtr', 'MELO3C006499.2' => 'cme', 'Migut.G00385' => 'egut', 'MSTRG.4063' => 'ama', 'Nitab4.5_0000090g0260' => 'nta', 'Nitab4.5_0000977g0030' => 'nta', 'Nitab4.5_0002541g0040' => 'nta', 'Nitab4.5_0007068g0040' => 'nta', 'Nn005s41408' => 'nnu', 'Nn005s41410' => 'nnu', 'Oeu010310.1' => 'oeu', 'Oeu010311.1' => 'oeu', 'Oeu043472.1' => 'oeu', 'Os01g0246400' => 'osa', 'Os04g0267950' => 'osa', 'Os07g0178700' => 'osa', 'Os07g0178800' => 'osa', 'Peaxi162Scf00316g00046' => 'pax', 'Peaxi162Scf00316g00049' => 'pax', 'Peaxi162Scf00316g00059' => 'pax', 'Peaxi162Scf00316g00328' => 'pax', 'Peaxi162Scf00316g00329' => 'pax', 'Peaxi162Scf00316g00411' => 'pax', 'Peaxi162Scf00316g00521' => 'pax', 'Peaxi162Scf00492g00068' => 'pax', 'Peaxi162Scf35631g00002' => 'pax', 'PGR142G3720' => 'pgr', 'PGSC0003DMG400006442' => 'stu', 'Phvul.007G062000' => 'pvu', 'Potri.008G157750' => 'ptr', 'Potri.008G157900' => 'ptr', 'Potri.008G158000' => 'ptr', 'Potri.008G158200' => 'ptr', 'Pp3c11_7280' => 'ppa', 'Pp3c11_7980' => 'ppa', 'Pp3c12_19450' => 'ppa', 'Pp3c14_1480' => 'ppa', 'Pp3c14_1501' => 'ppa', 'Pp3c16_4900' => 'ppa', 'Pp3c16_5010' => 'ppa', 'Pp3c16_5060' => 'ppa', 'Pp3c19_18250' => 'ppa', 'Pp3c23_8530' => 'ppa', 'Pp3c23_8550' => 'ppa', 'Pp3c24_9670' => 'ppa', 'Pp3c2_21390' => 'ppa', 'Pp3c2_31380' => 'ppa', 'Pp3c3_16620' => 'ppa', 'Pp3c3_8090' => 'ppa', 'Pp3c3_8110' => 'ppa', 'Pp3c3_8130' => 'ppa', 'Pp3c3_8150' => 'ppa', 'Pp3c4_14320' => 'ppa', 'Pp3c6_2560' => 'ppa', 'Pp3c9_16700' => 'ppa', 'PRCOL_00000234' => 'pco', 'PRCOL_00000235' => 'pco', 'PRCOL_00000777' => 'pco', 'PRCOL_00002344' => 'pco', 'PRCOL_00002372' => 'pco', 'PRCOL_00006120' => 'pco', 'Prupe.1G021400' => 'ppe', 'Prupe.1G021500' => 'ppe', 'Prupe.1G021600' => 'ppe', 'Prupe.1G021700' => 'ppe', 'Prupe.1G021800' => 'ppe', 'Prupe.5G145100' => 'ppe', 'Psat6g204040' => 'psa', 'Psat6g204800' => 'psa', 'Psat6g204920' => 'psa', 'Psat6g204960' => 'psa', 'Psat6g205080' => 'psa', 'PSO017G0271' => 'pso', 'PSO017G1276' => 'pso', 'PSO017G1429' => 'pso', 'PSO017G1861' => 'pso', 'PSO017G2787' => 'pso', 'PSO017G4466' => 'pso', 'PSO017G5118' => 'pso', 'PSO017G5420' => 'pso', 'PSO063G3678' => 'pso', 'PSO210G0546' => 'pso', 'PSO317G0001' => 'pso', 'PSO357G0512' => 'pso', 'PSO478G2682' => 'pso', 'PSO647G0001' => 'pso', 'PSO675G0001' => 'pso', 'PSO675G2699' => 'pso', 'PSO675G2849' => 'pso', 'PSO675G4991' => 'pso', 'PSO689G0001' => 'pso', 'QL06p000916' => 'qlo', 'QL06p000921' => 'qlo', 'QL06p001398' => 'qlo', 'QL06p001407' => 'qlo', 'QL06p002031' => 'qlo', 'RcHm_v2.0_Chr4g0387791' => 'rch', 'RcHm_v2.0_Chr4g0387801' => 'rch', 'RcHm_v2.0_Chr6g0286501' => 'rch', 'RcHm_v2.0_Chr6g0286511' => 'rch', 'RcHm_v2.0_Chr6g0286521' => 'rch', 'RcHm_v2.0_Chr6g0286531' => 'rch', 'RcHm_v2.0_Chr7g0189141' => 'rch', 'Rhsim02G0028700' => 'rsi', 'Rhsim02G0028800' => 'rsi', 'Rhsim02G0028900' => 'rsi', 'Rhsim02G0029000' => 'rsi', 'Rhsim02G0029100' => 'rsi', 'Rhsim02G0029200' => 'rsi', 'Rhsim02G0029300' => 'rsi', 'Rhsim02G0029400' => 'rsi', 'Rhsim02G0029500' => 'rsi', 'Rhsim02G0029600' => 'rsi', 'RhsimUnG0024000' => 'rsi', 'RhsimUnG0024100' => 'rsi', 'RhsimUnG0024200' => 'rsi', 'RhsimUnG0024300' => 'rsi', 'RhsimUnG0024400' => 'rsi', 'RhsimUnG0024500' => 'rsi', 'RhsimUnG0024700' => 'rsi', 'RhsimUnG0024800' => 'rsi', 'RhsimUnG0024900' => 'rsi', 'RhsimUnG0025100' => 'rsi', 'Sabra08G0120200' => 'sbr', 'Sabra08G0120300' => 'sbr', 'Sabra08G0120500' => 'sbr', 'Sabra08G0120600' => 'sbr', 'Sabra10G0158900' => 'sbr', 'SalBow2G3492' => 'sbo', 'Sc13g0004760' => 'sci', 'Sc13g0004770' => 'sci', 'Sed0003417' => 'sed', 'Sed0019750' => 'sed', 'SEGI_03419' => 'sgi', 'SEGI_05907' => 'sgi', 'SEGI_10682' => 'sgi', 'SEGI_13528' => 'sgi', 'SEGI_16081' => 'sgi', 'SEGI_19370' => 'sgi', 'SEGI_21015' => 'sgi', 'SEGI_21944' => 'sgi', 'SEGI_32906' => 'sgi', 'SEGI_33093' => 'sgi', 'SEGI_36110' => 'sgi', 'SEGI_40397' => 'sgi', 'SGA_v2.0_scaffold191G40426' => 'sas', 'SGA_v2.0_scaffold353G49717' => 'sas', 'SGA_v2.0_scaffold50G18550' => 'sas', 'SMO119G0173' => 'smo', 'SMO172G0002' => 'smo', 'Solyc09g082690.3' => 'sly', 'Solyc09g082700.2' => 'sly', 'Sopen09g031550' => 'spe', 'Sopen09g031560' => 'spe', 'Sp3g20540' => 'spa', 'Sp7g07580' => 'spa', 'TAR134G0002' => 'tar', 'TAR236G0001' => 'tar', 'TAR365G0892' => 'tar', 'TAR636G0166' => 'tar', 'TAR636G0646' => 'tar', 'TAR636G0869' => 'tar', 'TAR636G1317' => 'tar', 'TAR636G1744' => 'tar', 'TAR636G3358' => 'tar', 'TAR636G3436' => 'tar', 'THA.LOC104803047' => 'tha', 'Thecc.04G238900' => 'tca', 'Thhalv10021557m.g' => 'esa', 'Thhalv10026318m.g' => 'esa', 'Thhalv10026335m.g' => 'esa', 'TPR.G17433' => 'tpr', 'TPR.G18915' => 'tpr', 'TPR.G26125' => 'tpr', 'TWI09G0677' => 'twi', 'TWI73G0287' => 'twi', 'unitig_748.g8326' => 'ugi', 'vmacro15370' => 'vma', 'vmacro15371' => 'vma', 'vmacro15372' => 'vma', 'vmacro15373' => 'vma', 'vmacro15374' => 'vma', 'VMungo0720G2826' => 'vmu', 'Zm00001eb116960' => 'zma', 'Zm00001eb301260' => 'zma', 'Zm00001eb301270' => 'zma' ), 'gf_id' => 'HOM05D001460', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001460' ), 'data_identifier' => 'HOM05D001460', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001460', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '433', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p22980' => 'bna', 'A01p32340' => 'bna', 'A03p42970' => 'bna', 'A05p25880' => 'bna', 'Aa31LG8G9320' => 'aar', 'Aa31LG8G9330' => 'aar', 'Aa31LG8G9340' => 'aar', 'Aa31sc221G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1034' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1528' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.829' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2222' => 'aag', 'Ah.12g058830' => 'amhyb', 'Ah.12g058840' => 'amhyb', 'AL3G37160' => 'aly', 'AL7G41310' => 'aly', 'Aqoxy5G00395' => 'aox', 'Aqoxy5G00396' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0C8NZA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5185HY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JZ1PRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MD3LS0' => 'arhy', 'AT3G22840' => 'ath', 'AT4G14690' => 'ath', 'ATR0665G054' => 'atr', 'Atru.chr4.2344' => 'acertr', 'Atru.chr4.2346' => 'acertr', 'Atru.chr4.2347' => 'acertr', 'Atru.chr4.2348' => 'acertr', 'Atru.chr4.2355' => 'acertr', 'Atru.chr4.2356' => 'acertr', 'Atru.chr4.2358' => 'acertr', 'Atru.chr4.2359' => 'acertr', 'Atru.chr4.2360' => 'acertr', 'Atru.chr4.2361' => 'acertr', 'AUR62030476' => 'cqu', 'AUR62030478' => 'cqu', 'AUR62030819' => 'cqu', 'AUR62030820' => 'cqu', 'BcaB03g14648' => 'bca', 'BcaB04g20492' => 'bca', 'BcaB06g26399' => 'bca', 'BcaC01g03416' => 'bca', 'BcaC01g03419' => 'bca', 'BcaC01g03421' => 'bca', 'BcaC01g03424' => 'bca', 'BcaC05g28012' => 'bca', 'BcaC09g49212' => 'bca', 'BcaC09g50140' => 'bca', 'BcaNung00346' => 'bca', 'BolC1t02785H' => 'bol', 'BolC1t04095H' => 'bol', 'BolC3t17545H' => 'bol', 'BolC5t32769H' => 'bol', 'BraA01t02211Z' => 'bra', 'BraA01t03359Z' => 'bra', 'BraA03t13441Z' => 'bra', 'BraA05t21476Z' => 'bra', 'C01p28420' => 'bna', 'C01p41350' => 'bna', 'C03p52750' => 'bna', 'C03p52780' => 'bna', 'C05p40270' => 'bna', 'CAN.G1437.9' => 'can', 'CANSAT78G0035' => 'cansat', 'CANSAT78G1036' => 'cansat', 'CANSAT78G2272' => 'cansat', 'CANSAT78G2478' => 'cansat', 'CARHR098700' => 'chi', 'CARHR221120' => 'chi', 'CARHR221150' => 'chi', 'Carub.0003s2297' => 'cru', 'Carub.0007s2749' => 'cru', 'Carub.0007s2750' => 'cru', 'Carub.0007s2751' => 'cru', 'Ca_10849_v3' => 'car', 'Cc03_g04300' => 'ccan', 'CDE02G3648' => 'cde', 'CDE05G0060' => 'cde', 'CDE05G0692' => 'cde', 'CDE05G2285' => 'cde', 'CDE05G2884' => 'cde', 'CDE05G3072' => 'cde', 'Cfa008439' => 'cfa', 'Cfa008441' => 'cfa', 'Cfa008443' => 'cfa', 'Cfa008448' => 'cfa', 'Ciclev10005974m.g' => 'ccl', 'Ciclev10006006m.g' => 'ccl', 'Ciclev10006775m.g' => 'ccl', 'CiPaw.02G120400' => 'cil', 'CiPaw.02G120500' => 'cil', 'CiPaw.02G120600' => 'cil', 'ClCG05G004850' => 'cla', 'COL.COLO4_21566' => 'col', 'Cpa.g.sc44.124' => 'cpa', 'Cre07.g320400' => 'cre', 'Cre07.g320450' => 'cre', 'Cre08.g384650' => 'cre', 'Cre09.g393173' => 'cre', 'Cre09.g394325' => 'cre', 'Cre14.g626750' => 'cre', 'Cre16.g679250' => 'cre', 'CsaV3_3G012890' => 'csa', 'CSS0010865' => 'camsi', 'CSS0044338' => 'camsi', 'DCAR_002366' => 'dca', 'DCAR_030687' => 'dca', 'DCAR_030688' => 'dca', 'Dinv14047' => 'din', 'Dinv14048' => 'din', 'Duzib151G0105' => 'dzi', 'Duzib151G0114' => 'dzi', 'Duzib212G1029' => 'dzi', 'ECA232G3536' => 'eca', 'ECA240G0786' => 'eca', 'ECA240G1802' => 'eca', 'ECA240G3760' => 'eca', 'ECA240G3920' => 'eca', 'EL10Ac5g12536' => 'bvu', 'EL10Ac5g12537' => 'bvu', 'EL10Ac5g12538' => 'bvu', 'Eucgr.B01004' => 'egr', 'Eucgr.B01006' => 'egr', 'Eucgr.B01007' => 'egr', 'Eucgr.B01008' => 'egr', 'Eucgr.B01895' => 'egr', 'Eucgr.B01896' => 'egr', 'FAN04G1456' => 'fan', 'FAN08G1769' => 'fan', 'FAN08G2160' => 'fan', 'FAN13G2403' => 'fan', 'FAN13G3303' => 'fan', 'FAN15G2435' => 'fan', 'FAN17G0672' => 'fan', 'FAN17G2441' => 'fan', 'FAN18G1024' => 'fan', 'FAN22G1458' => 'fan', 'FAN24G0037' => 'fan', 'FAN24G0429' => 'fan', 'FAN24G2387' => 'fan', 'FAN27G2746' => 'fan', 'FvH4_2g20400' => 'fve', 'FvH4_2g20420' => 'fve', 'FvH4_2g20430' => 'fve', 'FvH4_4g01270' => 'fve', 'FvH4_4g01290' => 'fve', 'FvH4_4g01300' => 'fve', 'FvH4_4g01310' => 'fve', 'FvH4_4g01330' => 'fve', 'FvH4_5g09070' => 'fve', 'Glyma.10G243800' => 'gma', 'Glyma.20G150600' => 'gma', 'Gohir.A09G219200' => 'ghi', 'Gohir.A09G219300' => 'ghi', 'Gohir.D09G221400' => 'ghi', 'Gohir.D09G221500' => 'ghi', 'Gorai.006G242600' => 'gra', 'Gorai.006G242700' => 'gra', 'GSVIVG01018044001' => 'vvi', 'HanXRQChr03g0083821' => 'han', 'HanXRQChr03g0083841' => 'han', 'HanXRQChr03g0083881' => 'han', 'HanXRQChr03g0083901' => 'han', 'HanXRQChr03g0083921' => 'han', 'HanXRQChr03g0085331' => 'han', 'HanXRQChr03g0085361' => 'han', 'HanXRQChr03g0085411' => 'han', 'HanXRQChr03g0085421' => 'han', 'HanXRQChr03g0085431' => 'han', 'HanXRQChr08g0221991' => 'han', 'HanXRQChr11g0336061' => 'han', 'HanXRQChr11g0336411' => 'han', 'Haze_11234' => 'cav', 'Hma1.2p1_0549F.1_g177010' => 'hma', 'Hma1.2p1_0602F.1_g187630' => 'hma', 'Hund14876' => 'sun', 'Hund14879' => 'sun', 'Lalb_Chr06g0160741' => 'lal', 'Lalb_Chr21g0304781' => 'lal', 'Lj3A726G19' => 'lonja', 'Lj3A726T23' => 'lonja', 'Lj3A726T24' => 'lonja', 'Lj3A726T25' => 'lonja', 'Lj3A727T17' => 'lonja', 'Lj3C726T0' => 'lonja', 'Lj3C726T2' => 'lonja', 'Lj3P725T35' => 'lonja', 'Lj3P727T10' => 'lonja', 'Lj3P727T12' => 'lonja', 'Lj3P727T14' => 'lonja', 'Lj5g0023109' => 'lja', 'Lj6P646T44' => 'lonja', 'Lsat_1_v5_gn_6_75760' => 'lsa', 'Lsat_1_v5_gn_6_75800' => 'lsa', 'Lsat_1_v5_gn_6_75900' => 'lsa', 'Lsat_1_v5_gn_6_76240' => 'lsa', 'Lsat_1_v5_gn_6_76441' => 'lsa', 'Lsat_1_v5_gn_6_76700' => 'lsa', 'Lsat_1_v5_gn_6_76760' => 'lsa', 'Manes.15G033100' => 'mes', 'Mapoly0004s0074' => 'mpo', 'Mapoly0004s0075' => 'mpo', 'Mapoly0004s0163' => 'mpo', 'Mapoly0004s0164' => 'mpo', 'Mapoly0021s0018' => 'mpo', 'Mapoly0041s0136' => 'mpo', 'Mapoly0041s0137' => 'mpo', 'Mapoly0041s0138' => 'mpo', 'Mapoly0041s0139' => 'mpo', 'Mapoly0041s0141' => 'mpo', 'Mapoly0041s0142' => 'mpo', 'Mapoly0041s0143' => 'mpo', 'Mapoly0041s0144' => 'mpo', 'Mapoly0041s0145' => 'mpo', 'Mapoly0047s0106' => 'mpo', 'Mapoly0047s0108' => 'mpo', 'Mapoly0050s0051' => 'mpo', 'Mapoly0050s0052' => 'mpo', 'Mapoly0050s0053' => 'mpo', 'Mapoly0058s0013' => 'mpo', 'Mapoly0091s0078' => 'mpo', 'Mapoly0091s0079' => 'mpo', 'Mapoly0091s0080' => 'mpo', 'Mapoly0091s0081' => 'mpo', 'Mapoly0278s0004' => 'mpo', 'Mapoly0278s0005' => 'mpo', 'Mapoly0278s0006' => 'mpo', 'MBI11_g30648_MAGBIO' => 'mbi', 'MCO03G194' => 'mco', 'MCO03G590' => 'mco', 'MCO07G312' => 'mco', 'MCO10G318' => 'mco', 'MCO12G244' => 'mco', 'MCO13G148' => 'mco', 'MCO13G194' => 'mco', 'MCO16G238' => 'mco', 'MD06G1134100' => 'mdo', 'MD13G1200100' => 'mdo', 'MD13G1200300' => 'mdo', 'MD13G1200600' => 'mdo', 'MD14G1150400' => 'mdo', 'MD16G1200000' => 'mdo', 'Medtr1g102570' => 'mtr', 'Medtr1g102780' => 'mtr', 'Medtr1g102800' => 'mtr', 'Medtr1g102810' => 'mtr', 'Medtr1g102830' => 'mtr', 'MELO3C006499.2' => 'cme', 'Migut.G00385' => 'egut', 'MSTRG.4063' => 'ama', 'Nitab4.5_0000090g0260' => 'nta', 'Nitab4.5_0000977g0030' => 'nta', 'Nitab4.5_0002541g0040' => 'nta', 'Nitab4.5_0007068g0040' => 'nta', 'Nn005s41408' => 'nnu', 'Nn005s41410' => 'nnu', 'Oeu010310.1' => 'oeu', 'Oeu010311.1' => 'oeu', 'Oeu043472.1' => 'oeu', 'Os01g0246400' => 'osa', 'Os04g0267950' => 'osa', 'Os07g0178700' => 'osa', 'Os07g0178800' => 'osa', 'Peaxi162Scf00316g00046' => 'pax', 'Peaxi162Scf00316g00049' => 'pax', 'Peaxi162Scf00316g00059' => 'pax', 'Peaxi162Scf00316g00328' => 'pax', 'Peaxi162Scf00316g00329' => 'pax', 'Peaxi162Scf00316g00411' => 'pax', 'Peaxi162Scf00316g00521' => 'pax', 'Peaxi162Scf00492g00068' => 'pax', 'Peaxi162Scf35631g00002' => 'pax', 'PGR142G3720' => 'pgr', 'PGSC0003DMG400006442' => 'stu', 'Phvul.007G062000' => 'pvu', 'Potri.008G157750' => 'ptr', 'Potri.008G157900' => 'ptr', 'Potri.008G158000' => 'ptr', 'Potri.008G158200' => 'ptr', 'Pp3c11_7280' => 'ppa', 'Pp3c11_7980' => 'ppa', 'Pp3c12_19450' => 'ppa', 'Pp3c14_1480' => 'ppa', 'Pp3c14_1501' => 'ppa', 'Pp3c16_4900' => 'ppa', 'Pp3c16_5010' => 'ppa', 'Pp3c16_5060' => 'ppa', 'Pp3c19_18250' => 'ppa', 'Pp3c23_8530' => 'ppa', 'Pp3c23_8550' => 'ppa', 'Pp3c24_9670' => 'ppa', 'Pp3c2_21390' => 'ppa', 'Pp3c2_31380' => 'ppa', 'Pp3c3_16620' => 'ppa', 'Pp3c3_8090' => 'ppa', 'Pp3c3_8110' => 'ppa', 'Pp3c3_8130' => 'ppa', 'Pp3c3_8150' => 'ppa', 'Pp3c4_14320' => 'ppa', 'Pp3c6_2560' => 'ppa', 'Pp3c9_16700' => 'ppa', 'PRCOL_00000234' => 'pco', 'PRCOL_00000235' => 'pco', 'PRCOL_00000777' => 'pco', 'PRCOL_00002344' => 'pco', 'PRCOL_00002372' => 'pco', 'PRCOL_00006120' => 'pco', 'Prupe.1G021400' => 'ppe', 'Prupe.1G021500' => 'ppe', 'Prupe.1G021600' => 'ppe', 'Prupe.1G021700' => 'ppe', 'Prupe.1G021800' => 'ppe', 'Prupe.5G145100' => 'ppe', 'Psat6g204040' => 'psa', 'Psat6g204800' => 'psa', 'Psat6g204920' => 'psa', 'Psat6g204960' => 'psa', 'Psat6g205080' => 'psa', 'PSO017G0271' => 'pso', 'PSO017G1276' => 'pso', 'PSO017G1429' => 'pso', 'PSO017G1861' => 'pso', 'PSO017G2787' => 'pso', 'PSO017G4466' => 'pso', 'PSO017G5118' => 'pso', 'PSO017G5420' => 'pso', 'PSO063G3678' => 'pso', 'PSO210G0546' => 'pso', 'PSO317G0001' => 'pso', 'PSO357G0512' => 'pso', 'PSO478G2682' => 'pso', 'PSO647G0001' => 'pso', 'PSO675G0001' => 'pso', 'PSO675G2699' => 'pso', 'PSO675G2849' => 'pso', 'PSO675G4991' => 'pso', 'PSO689G0001' => 'pso', 'QL06p000916' => 'qlo', 'QL06p000921' => 'qlo', 'QL06p001398' => 'qlo', 'QL06p001407' => 'qlo', 'QL06p002031' => 'qlo', 'RcHm_v2.0_Chr4g0387791' => 'rch', 'RcHm_v2.0_Chr4g0387801' => 'rch', 'RcHm_v2.0_Chr6g0286501' => 'rch', 'RcHm_v2.0_Chr6g0286511' => 'rch', 'RcHm_v2.0_Chr6g0286521' => 'rch', 'RcHm_v2.0_Chr6g0286531' => 'rch', 'RcHm_v2.0_Chr7g0189141' => 'rch', 'Rhsim02G0028700' => 'rsi', 'Rhsim02G0028800' => 'rsi', 'Rhsim02G0028900' => 'rsi', 'Rhsim02G0029000' => 'rsi', 'Rhsim02G0029100' => 'rsi', 'Rhsim02G0029200' => 'rsi', 'Rhsim02G0029300' => 'rsi', 'Rhsim02G0029400' => 'rsi', 'Rhsim02G0029500' => 'rsi', 'Rhsim02G0029600' => 'rsi', 'RhsimUnG0024000' => 'rsi', 'RhsimUnG0024100' => 'rsi', 'RhsimUnG0024200' => 'rsi', 'RhsimUnG0024300' => 'rsi', 'RhsimUnG0024400' => 'rsi', 'RhsimUnG0024500' => 'rsi', 'RhsimUnG0024700' => 'rsi', 'RhsimUnG0024800' => 'rsi', 'RhsimUnG0024900' => 'rsi', 'RhsimUnG0025100' => 'rsi', 'Sabra08G0120200' => 'sbr', 'Sabra08G0120300' => 'sbr', 'Sabra08G0120500' => 'sbr', 'Sabra08G0120600' => 'sbr', 'Sabra10G0158900' => 'sbr', 'SalBow2G3492' => 'sbo', 'Sc13g0004760' => 'sci', 'Sc13g0004770' => 'sci', 'Sed0003417' => 'sed', 'Sed0019750' => 'sed', 'SEGI_03419' => 'sgi', 'SEGI_05907' => 'sgi', 'SEGI_10682' => 'sgi', 'SEGI_13528' => 'sgi', 'SEGI_16081' => 'sgi', 'SEGI_19370' => 'sgi', 'SEGI_21015' => 'sgi', 'SEGI_21944' => 'sgi', 'SEGI_32906' => 'sgi', 'SEGI_33093' => 'sgi', 'SEGI_36110' => 'sgi', 'SEGI_40397' => 'sgi', 'SGA_v2.0_scaffold191G40426' => 'sas', 'SGA_v2.0_scaffold353G49717' => 'sas', 'SGA_v2.0_scaffold50G18550' => 'sas', 'SMO119G0173' => 'smo', 'SMO172G0002' => 'smo', 'Solyc09g082690.3' => 'sly', 'Solyc09g082700.2' => 'sly', 'Sopen09g031550' => 'spe', 'Sopen09g031560' => 'spe', 'Sp3g20540' => 'spa', 'Sp7g07580' => 'spa', 'TAR134G0002' => 'tar', 'TAR236G0001' => 'tar', 'TAR365G0892' => 'tar', 'TAR636G0166' => 'tar', 'TAR636G0646' => 'tar', 'TAR636G0869' => 'tar', 'TAR636G1317' => 'tar', 'TAR636G1744' => 'tar', 'TAR636G3358' => 'tar', 'TAR636G3436' => 'tar', 'THA.LOC104803047' => 'tha', 'Thecc.04G238900' => 'tca', 'Thhalv10021557m.g' => 'esa', 'Thhalv10026318m.g' => 'esa', 'Thhalv10026335m.g' => 'esa', 'TPR.G17433' => 'tpr', 'TPR.G18915' => 'tpr', 'TPR.G26125' => 'tpr', 'TWI09G0677' => 'twi', 'TWI73G0287' => 'twi', 'unitig_748.g8326' => 'ugi', 'vmacro15370' => 'vma', 'vmacro15371' => 'vma', 'vmacro15372' => 'vma', 'vmacro15373' => 'vma', 'vmacro15374' => 'vma', 'VMungo0720G2826' => 'vmu', 'Zm00001eb116960' => 'zma', 'Zm00001eb301260' => 'zma', 'Zm00001eb301270' => 'zma' ) $gf_id = 'HOM05D001460' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001460' ) $data_identifier = 'HOM05D001460' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 4, 'aag' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 2, 'aox' => (int) 2, 'arhy' => (int) 4, 'ath' => (int) 2, 'atr' => (int) 1, 'acertr' => (int) 10, 'cqu' => (int) 4, 'bca' => (int) 11, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 1, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 1, 'ccan' => (int) 1, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 1, 'col' => (int) 1, 'cpa' => (int) 1, 'cre' => (int) 7, 'csa' => (int) 1, 'camsi' => (int) 2, 'dca' => (int) 3, 'din' => (int) 2, 'dzi' => (int) 3, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 14, 'fve' => (int) 9, 'gma' => (int) 2, 'ghi' => (int) 4, 'gra' => (int) 2, 'vvi' => (int) 1, 'han' => (int) 13, 'cav' => (int) 1, 'hma' => (int) 2, 'sun' => (int) 2, 'lal' => (int) 2, 'lonja' => (int) 12, 'lja' => (int) 1, 'lsa' => (int) 7, 'mes' => (int) 1, 'mpo' => (int) 27, 'mbi' => (int) 1, 'mco' => (int) 8, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 1, 'egut' => (int) 1, 'ama' => (int) 1, 'nta' => (int) 4, 'nnu' => (int) 2, 'oeu' => (int) 3, 'osa' => (int) 4, 'pax' => (int) 9, 'pgr' => (int) 1, 'stu' => (int) 1, 'pvu' => (int) 1, 'ptr' => (int) 4, 'ppa' => (int) 22, 'pco' => (int) 6, 'ppe' => (int) 6, 'psa' => (int) 5, 'pso' => (int) 19, 'qlo' => (int) 5, 'rch' => (int) 7, 'rsi' => (int) 20, 'sbr' => (int) 5, 'sbo' => (int) 1, 'sci' => (int) 2, 'sed' => (int) 2, 'sgi' => (int) 12, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 2, 'tar' => (int) 10, 'tha' => (int) 1, 'tca' => (int) 1, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 2, 'ugi' => (int) 1, 'vma' => (int) 5, 'vmu' => (int) 1, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb301270' $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' => 'HOM05D001460', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '433', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p22980' => 'bna', 'A01p32340' => 'bna', 'A03p42970' => 'bna', 'A05p25880' => 'bna', 'Aa31LG8G9320' => 'aar', 'Aa31LG8G9330' => 'aar', 'Aa31LG8G9340' => 'aar', 'Aa31sc221G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1034' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1528' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.829' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2222' => 'aag', 'Ah.12g058830' => 'amhyb', 'Ah.12g058840' => 'amhyb', 'AL3G37160' => 'aly', 'AL7G41310' => 'aly', 'Aqoxy5G00395' => 'aox', 'Aqoxy5G00396' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0C8NZA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5185HY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JZ1PRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MD3LS0' => 'arhy', 'AT3G22840' => 'ath', 'AT4G14690' => 'ath', 'ATR0665G054' => 'atr', 'Atru.chr4.2344' => 'acertr', 'Atru.chr4.2346' => 'acertr', 'Atru.chr4.2347' => 'acertr', 'Atru.chr4.2348' => 'acertr', 'Atru.chr4.2355' => 'acertr', 'Atru.chr4.2356' => 'acertr', 'Atru.chr4.2358' => 'acertr', 'Atru.chr4.2359' => 'acertr', 'Atru.chr4.2360' => 'acertr', 'Atru.chr4.2361' => 'acertr', 'AUR62030476' => 'cqu', 'AUR62030478' => 'cqu', 'AUR62030819' => 'cqu', 'AUR62030820' => 'cqu', 'BcaB03g14648' => 'bca', 'BcaB04g20492' => 'bca', 'BcaB06g26399' => 'bca', 'BcaC01g03416' => 'bca', 'BcaC01g03419' => 'bca', 'BcaC01g03421' => 'bca', 'BcaC01g03424' => 'bca', 'BcaC05g28012' => 'bca', 'BcaC09g49212' => 'bca', 'BcaC09g50140' => 'bca', 'BcaNung00346' => 'bca', 'BolC1t02785H' => 'bol', 'BolC1t04095H' => 'bol', 'BolC3t17545H' => 'bol', 'BolC5t32769H' => 'bol', 'BraA01t02211Z' => 'bra', 'BraA01t03359Z' => 'bra', 'BraA03t13441Z' => 'bra', 'BraA05t21476Z' => 'bra', 'C01p28420' => 'bna', 'C01p41350' => 'bna', 'C03p52750' => 'bna', 'C03p52780' => 'bna', 'C05p40270' => 'bna', 'CAN.G1437.9' => 'can', 'CANSAT78G0035' => 'cansat', 'CANSAT78G1036' => 'cansat', 'CANSAT78G2272' => 'cansat', 'CANSAT78G2478' => 'cansat', 'CARHR098700' => 'chi', 'CARHR221120' => 'chi', 'CARHR221150' => 'chi', 'Carub.0003s2297' => 'cru', 'Carub.0007s2749' => 'cru', 'Carub.0007s2750' => 'cru', 'Carub.0007s2751' => 'cru', 'Ca_10849_v3' => 'car', 'Cc03_g04300' => 'ccan', 'CDE02G3648' => 'cde', 'CDE05G0060' => 'cde', 'CDE05G0692' => 'cde', 'CDE05G2285' => 'cde', 'CDE05G2884' => 'cde', 'CDE05G3072' => 'cde', 'Cfa008439' => 'cfa', 'Cfa008441' => 'cfa', 'Cfa008443' => 'cfa', 'Cfa008448' => 'cfa', 'Ciclev10005974m.g' => 'ccl', 'Ciclev10006006m.g' => 'ccl', 'Ciclev10006775m.g' => 'ccl', 'CiPaw.02G120400' => 'cil', 'CiPaw.02G120500' => 'cil', 'CiPaw.02G120600' => 'cil', 'ClCG05G004850' => 'cla', 'COL.COLO4_21566' => 'col', 'Cpa.g.sc44.124' => 'cpa', 'Cre07.g320400' => 'cre', 'Cre07.g320450' => 'cre', 'Cre08.g384650' => 'cre', 'Cre09.g393173' => 'cre', 'Cre09.g394325' => 'cre', 'Cre14.g626750' => 'cre', 'Cre16.g679250' => 'cre', 'CsaV3_3G012890' => 'csa', 'CSS0010865' => 'camsi', 'CSS0044338' => 'camsi', 'DCAR_002366' => 'dca', 'DCAR_030687' => 'dca', 'DCAR_030688' => 'dca', 'Dinv14047' => 'din', 'Dinv14048' => 'din', 'Duzib151G0105' => 'dzi', 'Duzib151G0114' => 'dzi', 'Duzib212G1029' => 'dzi', 'ECA232G3536' => 'eca', 'ECA240G0786' => 'eca', 'ECA240G1802' => 'eca', 'ECA240G3760' => 'eca', 'ECA240G3920' => 'eca', 'EL10Ac5g12536' => 'bvu', 'EL10Ac5g12537' => 'bvu', 'EL10Ac5g12538' => 'bvu', 'Eucgr.B01004' => 'egr', 'Eucgr.B01006' => 'egr', 'Eucgr.B01007' => 'egr', 'Eucgr.B01008' => 'egr', 'Eucgr.B01895' => 'egr', 'Eucgr.B01896' => 'egr', 'FAN04G1456' => 'fan', 'FAN08G1769' => 'fan', 'FAN08G2160' => 'fan', 'FAN13G2403' => 'fan', 'FAN13G3303' => 'fan', 'FAN15G2435' => 'fan', 'FAN17G0672' => 'fan', 'FAN17G2441' => 'fan', 'FAN18G1024' => 'fan', 'FAN22G1458' => 'fan', 'FAN24G0037' => 'fan', 'FAN24G0429' => 'fan', 'FAN24G2387' => 'fan', 'FAN27G2746' => 'fan', 'FvH4_2g20400' => 'fve', 'FvH4_2g20420' => 'fve', 'FvH4_2g20430' => 'fve', 'FvH4_4g01270' => 'fve', 'FvH4_4g01290' => 'fve', 'FvH4_4g01300' => 'fve', 'FvH4_4g01310' => 'fve', 'FvH4_4g01330' => 'fve', 'FvH4_5g09070' => 'fve', 'Glyma.10G243800' => 'gma', 'Glyma.20G150600' => 'gma', 'Gohir.A09G219200' => 'ghi', 'Gohir.A09G219300' => 'ghi', 'Gohir.D09G221400' => 'ghi', 'Gohir.D09G221500' => 'ghi', 'Gorai.006G242600' => 'gra', 'Gorai.006G242700' => 'gra', 'GSVIVG01018044001' => 'vvi', 'HanXRQChr03g0083821' => 'han', 'HanXRQChr03g0083841' => 'han', 'HanXRQChr03g0083881' => 'han', 'HanXRQChr03g0083901' => 'han', 'HanXRQChr03g0083921' => 'han', 'HanXRQChr03g0085331' => 'han', 'HanXRQChr03g0085361' => 'han', 'HanXRQChr03g0085411' => 'han', 'HanXRQChr03g0085421' => 'han', 'HanXRQChr03g0085431' => 'han', 'HanXRQChr08g0221991' => 'han', 'HanXRQChr11g0336061' => 'han', 'HanXRQChr11g0336411' => 'han', 'Haze_11234' => 'cav', 'Hma1.2p1_0549F.1_g177010' => 'hma', 'Hma1.2p1_0602F.1_g187630' => 'hma', 'Hund14876' => 'sun', 'Hund14879' => 'sun', 'Lalb_Chr06g0160741' => 'lal', 'Lalb_Chr21g0304781' => 'lal', 'Lj3A726G19' => 'lonja', 'Lj3A726T23' => 'lonja', 'Lj3A726T24' => 'lonja', 'Lj3A726T25' => 'lonja', 'Lj3A727T17' => 'lonja', 'Lj3C726T0' => 'lonja', 'Lj3C726T2' => 'lonja', 'Lj3P725T35' => 'lonja', 'Lj3P727T10' => 'lonja', 'Lj3P727T12' => 'lonja', 'Lj3P727T14' => 'lonja', 'Lj5g0023109' => 'lja', 'Lj6P646T44' => 'lonja', 'Lsat_1_v5_gn_6_75760' => 'lsa', 'Lsat_1_v5_gn_6_75800' => 'lsa', 'Lsat_1_v5_gn_6_75900' => 'lsa', 'Lsat_1_v5_gn_6_76240' => 'lsa', 'Lsat_1_v5_gn_6_76441' => 'lsa', 'Lsat_1_v5_gn_6_76700' => 'lsa', 'Lsat_1_v5_gn_6_76760' => 'lsa', 'Manes.15G033100' => 'mes', 'Mapoly0004s0074' => 'mpo', 'Mapoly0004s0075' => 'mpo', 'Mapoly0004s0163' => 'mpo', 'Mapoly0004s0164' => 'mpo', 'Mapoly0021s0018' => 'mpo', 'Mapoly0041s0136' => 'mpo', 'Mapoly0041s0137' => 'mpo', 'Mapoly0041s0138' => 'mpo', 'Mapoly0041s0139' => 'mpo', 'Mapoly0041s0141' => 'mpo', 'Mapoly0041s0142' => 'mpo', 'Mapoly0041s0143' => 'mpo', 'Mapoly0041s0144' => 'mpo', 'Mapoly0041s0145' => 'mpo', 'Mapoly0047s0106' => 'mpo', 'Mapoly0047s0108' => 'mpo', 'Mapoly0050s0051' => 'mpo', 'Mapoly0050s0052' => 'mpo', 'Mapoly0050s0053' => 'mpo', 'Mapoly0058s0013' => 'mpo', 'Mapoly0091s0078' => 'mpo', 'Mapoly0091s0079' => 'mpo', 'Mapoly0091s0080' => 'mpo', 'Mapoly0091s0081' => 'mpo', 'Mapoly0278s0004' => 'mpo', 'Mapoly0278s0005' => 'mpo', 'Mapoly0278s0006' => 'mpo', 'MBI11_g30648_MAGBIO' => 'mbi', 'MCO03G194' => 'mco', 'MCO03G590' => 'mco', 'MCO07G312' => 'mco', 'MCO10G318' => 'mco', 'MCO12G244' => 'mco', 'MCO13G148' => 'mco', 'MCO13G194' => 'mco', 'MCO16G238' => 'mco', 'MD06G1134100' => 'mdo', 'MD13G1200100' => 'mdo', 'MD13G1200300' => 'mdo', 'MD13G1200600' => 'mdo', 'MD14G1150400' => 'mdo', 'MD16G1200000' => 'mdo', 'Medtr1g102570' => 'mtr', 'Medtr1g102780' => 'mtr', 'Medtr1g102800' => 'mtr', 'Medtr1g102810' => 'mtr', 'Medtr1g102830' => 'mtr', 'MELO3C006499.2' => 'cme', 'Migut.G00385' => 'egut', 'MSTRG.4063' => 'ama', 'Nitab4.5_0000090g0260' => 'nta', 'Nitab4.5_0000977g0030' => 'nta', 'Nitab4.5_0002541g0040' => 'nta', 'Nitab4.5_0007068g0040' => 'nta', 'Nn005s41408' => 'nnu', 'Nn005s41410' => 'nnu', 'Oeu010310.1' => 'oeu', 'Oeu010311.1' => 'oeu', 'Oeu043472.1' => 'oeu', 'Os01g0246400' => 'osa', 'Os04g0267950' => 'osa', 'Os07g0178700' => 'osa', 'Os07g0178800' => 'osa', 'Peaxi162Scf00316g00046' => 'pax', 'Peaxi162Scf00316g00049' => 'pax', 'Peaxi162Scf00316g00059' => 'pax', 'Peaxi162Scf00316g00328' => 'pax', 'Peaxi162Scf00316g00329' => 'pax', 'Peaxi162Scf00316g00411' => 'pax', 'Peaxi162Scf00316g00521' => 'pax', 'Peaxi162Scf00492g00068' => 'pax', 'Peaxi162Scf35631g00002' => 'pax', 'PGR142G3720' => 'pgr', 'PGSC0003DMG400006442' => 'stu', 'Phvul.007G062000' => 'pvu', 'Potri.008G157750' => 'ptr', 'Potri.008G157900' => 'ptr', 'Potri.008G158000' => 'ptr', 'Potri.008G158200' => 'ptr', 'Pp3c11_7280' => 'ppa', 'Pp3c11_7980' => 'ppa', 'Pp3c12_19450' => 'ppa', 'Pp3c14_1480' => 'ppa', 'Pp3c14_1501' => 'ppa', 'Pp3c16_4900' => 'ppa', 'Pp3c16_5010' => 'ppa', 'Pp3c16_5060' => 'ppa', 'Pp3c19_18250' => 'ppa', 'Pp3c23_8530' => 'ppa', 'Pp3c23_8550' => 'ppa', 'Pp3c24_9670' => 'ppa', 'Pp3c2_21390' => 'ppa', 'Pp3c2_31380' => 'ppa', 'Pp3c3_16620' => 'ppa', 'Pp3c3_8090' => 'ppa', 'Pp3c3_8110' => 'ppa', 'Pp3c3_8130' => 'ppa', 'Pp3c3_8150' => 'ppa', 'Pp3c4_14320' => 'ppa', 'Pp3c6_2560' => 'ppa', 'Pp3c9_16700' => 'ppa', 'PRCOL_00000234' => 'pco', 'PRCOL_00000235' => 'pco', 'PRCOL_00000777' => 'pco', 'PRCOL_00002344' => 'pco', 'PRCOL_00002372' => 'pco', 'PRCOL_00006120' => 'pco', 'Prupe.1G021400' => 'ppe', 'Prupe.1G021500' => 'ppe', 'Prupe.1G021600' => 'ppe', 'Prupe.1G021700' => 'ppe', 'Prupe.1G021800' => 'ppe', 'Prupe.5G145100' => 'ppe', 'Psat6g204040' => 'psa', 'Psat6g204800' => 'psa', 'Psat6g204920' => 'psa', 'Psat6g204960' => 'psa', 'Psat6g205080' => 'psa', 'PSO017G0271' => 'pso', 'PSO017G1276' => 'pso', 'PSO017G1429' => 'pso', 'PSO017G1861' => 'pso', 'PSO017G2787' => 'pso', 'PSO017G4466' => 'pso', 'PSO017G5118' => 'pso', 'PSO017G5420' => 'pso', 'PSO063G3678' => 'pso', 'PSO210G0546' => 'pso', 'PSO317G0001' => 'pso', 'PSO357G0512' => 'pso', 'PSO478G2682' => 'pso', 'PSO647G0001' => 'pso', 'PSO675G0001' => 'pso', 'PSO675G2699' => 'pso', 'PSO675G2849' => 'pso', 'PSO675G4991' => 'pso', 'PSO689G0001' => 'pso', 'QL06p000916' => 'qlo', 'QL06p000921' => 'qlo', 'QL06p001398' => 'qlo', 'QL06p001407' => 'qlo', 'QL06p002031' => 'qlo', 'RcHm_v2.0_Chr4g0387791' => 'rch', 'RcHm_v2.0_Chr4g0387801' => 'rch', 'RcHm_v2.0_Chr6g0286501' => 'rch', 'RcHm_v2.0_Chr6g0286511' => 'rch', 'RcHm_v2.0_Chr6g0286521' => 'rch', 'RcHm_v2.0_Chr6g0286531' => 'rch', 'RcHm_v2.0_Chr7g0189141' => 'rch', 'Rhsim02G0028700' => 'rsi', 'Rhsim02G0028800' => 'rsi', 'Rhsim02G0028900' => 'rsi', 'Rhsim02G0029000' => 'rsi', 'Rhsim02G0029100' => 'rsi', 'Rhsim02G0029200' => 'rsi', 'Rhsim02G0029300' => 'rsi', 'Rhsim02G0029400' => 'rsi', 'Rhsim02G0029500' => 'rsi', 'Rhsim02G0029600' => 'rsi', 'RhsimUnG0024000' => 'rsi', 'RhsimUnG0024100' => 'rsi', 'RhsimUnG0024200' => 'rsi', 'RhsimUnG0024300' => 'rsi', 'RhsimUnG0024400' => 'rsi', 'RhsimUnG0024500' => 'rsi', 'RhsimUnG0024700' => 'rsi', 'RhsimUnG0024800' => 'rsi', 'RhsimUnG0024900' => 'rsi', 'RhsimUnG0025100' => 'rsi', 'Sabra08G0120200' => 'sbr', 'Sabra08G0120300' => 'sbr', 'Sabra08G0120500' => 'sbr', 'Sabra08G0120600' => 'sbr', 'Sabra10G0158900' => 'sbr', 'SalBow2G3492' => 'sbo', 'Sc13g0004760' => 'sci', 'Sc13g0004770' => 'sci', 'Sed0003417' => 'sed', 'Sed0019750' => 'sed', 'SEGI_03419' => 'sgi', 'SEGI_05907' => 'sgi', 'SEGI_10682' => 'sgi', 'SEGI_13528' => 'sgi', 'SEGI_16081' => 'sgi', 'SEGI_19370' => 'sgi', 'SEGI_21015' => 'sgi', 'SEGI_21944' => 'sgi', 'SEGI_32906' => 'sgi', 'SEGI_33093' => 'sgi', 'SEGI_36110' => 'sgi', 'SEGI_40397' => 'sgi', 'SGA_v2.0_scaffold191G40426' => 'sas', 'SGA_v2.0_scaffold353G49717' => 'sas', 'SGA_v2.0_scaffold50G18550' => 'sas', 'SMO119G0173' => 'smo', 'SMO172G0002' => 'smo', 'Solyc09g082690.3' => 'sly', 'Solyc09g082700.2' => 'sly', 'Sopen09g031550' => 'spe', 'Sopen09g031560' => 'spe', 'Sp3g20540' => 'spa', 'Sp7g07580' => 'spa', 'TAR134G0002' => 'tar', 'TAR236G0001' => 'tar', 'TAR365G0892' => 'tar', 'TAR636G0166' => 'tar', 'TAR636G0646' => 'tar', 'TAR636G0869' => 'tar', 'TAR636G1317' => 'tar', 'TAR636G1744' => 'tar', 'TAR636G3358' => 'tar', 'TAR636G3436' => 'tar', 'THA.LOC104803047' => 'tha', 'Thecc.04G238900' => 'tca', 'Thhalv10021557m.g' => 'esa', 'Thhalv10026318m.g' => 'esa', 'Thhalv10026335m.g' => 'esa', 'TPR.G17433' => 'tpr', 'TPR.G18915' => 'tpr', 'TPR.G26125' => 'tpr', 'TWI09G0677' => 'twi', 'TWI73G0287' => 'twi', 'unitig_748.g8326' => 'ugi', 'vmacro15370' => 'vma', 'vmacro15371' => 'vma', 'vmacro15372' => 'vma', 'vmacro15373' => 'vma', 'vmacro15374' => 'vma', 'VMungo0720G2826' => 'vmu', 'Zm00001eb116960' => 'zma', 'Zm00001eb301260' => 'zma', 'Zm00001eb301270' => 'zma' ), 'gf_id' => 'HOM05D001460', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001460' ), 'data_identifier' => 'HOM05D001460', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001460', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '433', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p22980' => 'bna', 'A01p32340' => 'bna', 'A03p42970' => 'bna', 'A05p25880' => 'bna', 'Aa31LG8G9320' => 'aar', 'Aa31LG8G9330' => 'aar', 'Aa31LG8G9340' => 'aar', 'Aa31sc221G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1034' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1528' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.829' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2222' => 'aag', 'Ah.12g058830' => 'amhyb', 'Ah.12g058840' => 'amhyb', 'AL3G37160' => 'aly', 'AL7G41310' => 'aly', 'Aqoxy5G00395' => 'aox', 'Aqoxy5G00396' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0C8NZA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5185HY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JZ1PRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MD3LS0' => 'arhy', 'AT3G22840' => 'ath', 'AT4G14690' => 'ath', 'ATR0665G054' => 'atr', 'Atru.chr4.2344' => 'acertr', 'Atru.chr4.2346' => 'acertr', 'Atru.chr4.2347' => 'acertr', 'Atru.chr4.2348' => 'acertr', 'Atru.chr4.2355' => 'acertr', 'Atru.chr4.2356' => 'acertr', 'Atru.chr4.2358' => 'acertr', 'Atru.chr4.2359' => 'acertr', 'Atru.chr4.2360' => 'acertr', 'Atru.chr4.2361' => 'acertr', 'AUR62030476' => 'cqu', 'AUR62030478' => 'cqu', 'AUR62030819' => 'cqu', 'AUR62030820' => 'cqu', 'BcaB03g14648' => 'bca', 'BcaB04g20492' => 'bca', 'BcaB06g26399' => 'bca', 'BcaC01g03416' => 'bca', 'BcaC01g03419' => 'bca', 'BcaC01g03421' => 'bca', 'BcaC01g03424' => 'bca', 'BcaC05g28012' => 'bca', 'BcaC09g49212' => 'bca', 'BcaC09g50140' => 'bca', 'BcaNung00346' => 'bca', 'BolC1t02785H' => 'bol', 'BolC1t04095H' => 'bol', 'BolC3t17545H' => 'bol', 'BolC5t32769H' => 'bol', 'BraA01t02211Z' => 'bra', 'BraA01t03359Z' => 'bra', 'BraA03t13441Z' => 'bra', 'BraA05t21476Z' => 'bra', 'C01p28420' => 'bna', 'C01p41350' => 'bna', 'C03p52750' => 'bna', 'C03p52780' => 'bna', 'C05p40270' => 'bna', 'CAN.G1437.9' => 'can', 'CANSAT78G0035' => 'cansat', 'CANSAT78G1036' => 'cansat', 'CANSAT78G2272' => 'cansat', 'CANSAT78G2478' => 'cansat', 'CARHR098700' => 'chi', 'CARHR221120' => 'chi', 'CARHR221150' => 'chi', 'Carub.0003s2297' => 'cru', 'Carub.0007s2749' => 'cru', 'Carub.0007s2750' => 'cru', 'Carub.0007s2751' => 'cru', 'Ca_10849_v3' => 'car', 'Cc03_g04300' => 'ccan', 'CDE02G3648' => 'cde', 'CDE05G0060' => 'cde', 'CDE05G0692' => 'cde', 'CDE05G2285' => 'cde', 'CDE05G2884' => 'cde', 'CDE05G3072' => 'cde', 'Cfa008439' => 'cfa', 'Cfa008441' => 'cfa', 'Cfa008443' => 'cfa', 'Cfa008448' => 'cfa', 'Ciclev10005974m.g' => 'ccl', 'Ciclev10006006m.g' => 'ccl', 'Ciclev10006775m.g' => 'ccl', 'CiPaw.02G120400' => 'cil', 'CiPaw.02G120500' => 'cil', 'CiPaw.02G120600' => 'cil', 'ClCG05G004850' => 'cla', 'COL.COLO4_21566' => 'col', 'Cpa.g.sc44.124' => 'cpa', 'Cre07.g320400' => 'cre', 'Cre07.g320450' => 'cre', 'Cre08.g384650' => 'cre', 'Cre09.g393173' => 'cre', 'Cre09.g394325' => 'cre', 'Cre14.g626750' => 'cre', 'Cre16.g679250' => 'cre', 'CsaV3_3G012890' => 'csa', 'CSS0010865' => 'camsi', 'CSS0044338' => 'camsi', 'DCAR_002366' => 'dca', 'DCAR_030687' => 'dca', 'DCAR_030688' => 'dca', 'Dinv14047' => 'din', 'Dinv14048' => 'din', 'Duzib151G0105' => 'dzi', 'Duzib151G0114' => 'dzi', 'Duzib212G1029' => 'dzi', 'ECA232G3536' => 'eca', 'ECA240G0786' => 'eca', 'ECA240G1802' => 'eca', 'ECA240G3760' => 'eca', 'ECA240G3920' => 'eca', 'EL10Ac5g12536' => 'bvu', 'EL10Ac5g12537' => 'bvu', 'EL10Ac5g12538' => 'bvu', 'Eucgr.B01004' => 'egr', 'Eucgr.B01006' => 'egr', 'Eucgr.B01007' => 'egr', 'Eucgr.B01008' => 'egr', 'Eucgr.B01895' => 'egr', 'Eucgr.B01896' => 'egr', 'FAN04G1456' => 'fan', 'FAN08G1769' => 'fan', 'FAN08G2160' => 'fan', 'FAN13G2403' => 'fan', 'FAN13G3303' => 'fan', 'FAN15G2435' => 'fan', 'FAN17G0672' => 'fan', 'FAN17G2441' => 'fan', 'FAN18G1024' => 'fan', 'FAN22G1458' => 'fan', 'FAN24G0037' => 'fan', 'FAN24G0429' => 'fan', 'FAN24G2387' => 'fan', 'FAN27G2746' => 'fan', 'FvH4_2g20400' => 'fve', 'FvH4_2g20420' => 'fve', 'FvH4_2g20430' => 'fve', 'FvH4_4g01270' => 'fve', 'FvH4_4g01290' => 'fve', 'FvH4_4g01300' => 'fve', 'FvH4_4g01310' => 'fve', 'FvH4_4g01330' => 'fve', 'FvH4_5g09070' => 'fve', 'Glyma.10G243800' => 'gma', 'Glyma.20G150600' => 'gma', 'Gohir.A09G219200' => 'ghi', 'Gohir.A09G219300' => 'ghi', 'Gohir.D09G221400' => 'ghi', 'Gohir.D09G221500' => 'ghi', 'Gorai.006G242600' => 'gra', 'Gorai.006G242700' => 'gra', 'GSVIVG01018044001' => 'vvi', 'HanXRQChr03g0083821' => 'han', 'HanXRQChr03g0083841' => 'han', 'HanXRQChr03g0083881' => 'han', 'HanXRQChr03g0083901' => 'han', 'HanXRQChr03g0083921' => 'han', 'HanXRQChr03g0085331' => 'han', 'HanXRQChr03g0085361' => 'han', 'HanXRQChr03g0085411' => 'han', 'HanXRQChr03g0085421' => 'han', 'HanXRQChr03g0085431' => 'han', 'HanXRQChr08g0221991' => 'han', 'HanXRQChr11g0336061' => 'han', 'HanXRQChr11g0336411' => 'han', 'Haze_11234' => 'cav', 'Hma1.2p1_0549F.1_g177010' => 'hma', 'Hma1.2p1_0602F.1_g187630' => 'hma', 'Hund14876' => 'sun', 'Hund14879' => 'sun', 'Lalb_Chr06g0160741' => 'lal', 'Lalb_Chr21g0304781' => 'lal', 'Lj3A726G19' => 'lonja', 'Lj3A726T23' => 'lonja', 'Lj3A726T24' => 'lonja', 'Lj3A726T25' => 'lonja', 'Lj3A727T17' => 'lonja', 'Lj3C726T0' => 'lonja', 'Lj3C726T2' => 'lonja', 'Lj3P725T35' => 'lonja', 'Lj3P727T10' => 'lonja', 'Lj3P727T12' => 'lonja', 'Lj3P727T14' => 'lonja', 'Lj5g0023109' => 'lja', 'Lj6P646T44' => 'lonja', 'Lsat_1_v5_gn_6_75760' => 'lsa', 'Lsat_1_v5_gn_6_75800' => 'lsa', 'Lsat_1_v5_gn_6_75900' => 'lsa', 'Lsat_1_v5_gn_6_76240' => 'lsa', 'Lsat_1_v5_gn_6_76441' => 'lsa', 'Lsat_1_v5_gn_6_76700' => 'lsa', 'Lsat_1_v5_gn_6_76760' => 'lsa', 'Manes.15G033100' => 'mes', 'Mapoly0004s0074' => 'mpo', 'Mapoly0004s0075' => 'mpo', 'Mapoly0004s0163' => 'mpo', 'Mapoly0004s0164' => 'mpo', 'Mapoly0021s0018' => 'mpo', 'Mapoly0041s0136' => 'mpo', 'Mapoly0041s0137' => 'mpo', 'Mapoly0041s0138' => 'mpo', 'Mapoly0041s0139' => 'mpo', 'Mapoly0041s0141' => 'mpo', 'Mapoly0041s0142' => 'mpo', 'Mapoly0041s0143' => 'mpo', 'Mapoly0041s0144' => 'mpo', 'Mapoly0041s0145' => 'mpo', 'Mapoly0047s0106' => 'mpo', 'Mapoly0047s0108' => 'mpo', 'Mapoly0050s0051' => 'mpo', 'Mapoly0050s0052' => 'mpo', 'Mapoly0050s0053' => 'mpo', 'Mapoly0058s0013' => 'mpo', 'Mapoly0091s0078' => 'mpo', 'Mapoly0091s0079' => 'mpo', 'Mapoly0091s0080' => 'mpo', 'Mapoly0091s0081' => 'mpo', 'Mapoly0278s0004' => 'mpo', 'Mapoly0278s0005' => 'mpo', 'Mapoly0278s0006' => 'mpo', 'MBI11_g30648_MAGBIO' => 'mbi', 'MCO03G194' => 'mco', 'MCO03G590' => 'mco', 'MCO07G312' => 'mco', 'MCO10G318' => 'mco', 'MCO12G244' => 'mco', 'MCO13G148' => 'mco', 'MCO13G194' => 'mco', 'MCO16G238' => 'mco', 'MD06G1134100' => 'mdo', 'MD13G1200100' => 'mdo', 'MD13G1200300' => 'mdo', 'MD13G1200600' => 'mdo', 'MD14G1150400' => 'mdo', 'MD16G1200000' => 'mdo', 'Medtr1g102570' => 'mtr', 'Medtr1g102780' => 'mtr', 'Medtr1g102800' => 'mtr', 'Medtr1g102810' => 'mtr', 'Medtr1g102830' => 'mtr', 'MELO3C006499.2' => 'cme', 'Migut.G00385' => 'egut', 'MSTRG.4063' => 'ama', 'Nitab4.5_0000090g0260' => 'nta', 'Nitab4.5_0000977g0030' => 'nta', 'Nitab4.5_0002541g0040' => 'nta', 'Nitab4.5_0007068g0040' => 'nta', 'Nn005s41408' => 'nnu', 'Nn005s41410' => 'nnu', 'Oeu010310.1' => 'oeu', 'Oeu010311.1' => 'oeu', 'Oeu043472.1' => 'oeu', 'Os01g0246400' => 'osa', 'Os04g0267950' => 'osa', 'Os07g0178700' => 'osa', 'Os07g0178800' => 'osa', 'Peaxi162Scf00316g00046' => 'pax', 'Peaxi162Scf00316g00049' => 'pax', 'Peaxi162Scf00316g00059' => 'pax', 'Peaxi162Scf00316g00328' => 'pax', 'Peaxi162Scf00316g00329' => 'pax', 'Peaxi162Scf00316g00411' => 'pax', 'Peaxi162Scf00316g00521' => 'pax', 'Peaxi162Scf00492g00068' => 'pax', 'Peaxi162Scf35631g00002' => 'pax', 'PGR142G3720' => 'pgr', 'PGSC0003DMG400006442' => 'stu', 'Phvul.007G062000' => 'pvu', 'Potri.008G157750' => 'ptr', 'Potri.008G157900' => 'ptr', 'Potri.008G158000' => 'ptr', 'Potri.008G158200' => 'ptr', 'Pp3c11_7280' => 'ppa', 'Pp3c11_7980' => 'ppa', 'Pp3c12_19450' => 'ppa', 'Pp3c14_1480' => 'ppa', 'Pp3c14_1501' => 'ppa', 'Pp3c16_4900' => 'ppa', 'Pp3c16_5010' => 'ppa', 'Pp3c16_5060' => 'ppa', 'Pp3c19_18250' => 'ppa', 'Pp3c23_8530' => 'ppa', 'Pp3c23_8550' => 'ppa', 'Pp3c24_9670' => 'ppa', 'Pp3c2_21390' => 'ppa', 'Pp3c2_31380' => 'ppa', 'Pp3c3_16620' => 'ppa', 'Pp3c3_8090' => 'ppa', 'Pp3c3_8110' => 'ppa', 'Pp3c3_8130' => 'ppa', 'Pp3c3_8150' => 'ppa', 'Pp3c4_14320' => 'ppa', 'Pp3c6_2560' => 'ppa', 'Pp3c9_16700' => 'ppa', 'PRCOL_00000234' => 'pco', 'PRCOL_00000235' => 'pco', 'PRCOL_00000777' => 'pco', 'PRCOL_00002344' => 'pco', 'PRCOL_00002372' => 'pco', 'PRCOL_00006120' => 'pco', 'Prupe.1G021400' => 'ppe', 'Prupe.1G021500' => 'ppe', 'Prupe.1G021600' => 'ppe', 'Prupe.1G021700' => 'ppe', 'Prupe.1G021800' => 'ppe', 'Prupe.5G145100' => 'ppe', 'Psat6g204040' => 'psa', 'Psat6g204800' => 'psa', 'Psat6g204920' => 'psa', 'Psat6g204960' => 'psa', 'Psat6g205080' => 'psa', 'PSO017G0271' => 'pso', 'PSO017G1276' => 'pso', 'PSO017G1429' => 'pso', 'PSO017G1861' => 'pso', 'PSO017G2787' => 'pso', 'PSO017G4466' => 'pso', 'PSO017G5118' => 'pso', 'PSO017G5420' => 'pso', 'PSO063G3678' => 'pso', 'PSO210G0546' => 'pso', 'PSO317G0001' => 'pso', 'PSO357G0512' => 'pso', 'PSO478G2682' => 'pso', 'PSO647G0001' => 'pso', 'PSO675G0001' => 'pso', 'PSO675G2699' => 'pso', 'PSO675G2849' => 'pso', 'PSO675G4991' => 'pso', 'PSO689G0001' => 'pso', 'QL06p000916' => 'qlo', 'QL06p000921' => 'qlo', 'QL06p001398' => 'qlo', 'QL06p001407' => 'qlo', 'QL06p002031' => 'qlo', 'RcHm_v2.0_Chr4g0387791' => 'rch', 'RcHm_v2.0_Chr4g0387801' => 'rch', 'RcHm_v2.0_Chr6g0286501' => 'rch', 'RcHm_v2.0_Chr6g0286511' => 'rch', 'RcHm_v2.0_Chr6g0286521' => 'rch', 'RcHm_v2.0_Chr6g0286531' => 'rch', 'RcHm_v2.0_Chr7g0189141' => 'rch', 'Rhsim02G0028700' => 'rsi', 'Rhsim02G0028800' => 'rsi', 'Rhsim02G0028900' => 'rsi', 'Rhsim02G0029000' => 'rsi', 'Rhsim02G0029100' => 'rsi', 'Rhsim02G0029200' => 'rsi', 'Rhsim02G0029300' => 'rsi', 'Rhsim02G0029400' => 'rsi', 'Rhsim02G0029500' => 'rsi', 'Rhsim02G0029600' => 'rsi', 'RhsimUnG0024000' => 'rsi', 'RhsimUnG0024100' => 'rsi', 'RhsimUnG0024200' => 'rsi', 'RhsimUnG0024300' => 'rsi', 'RhsimUnG0024400' => 'rsi', 'RhsimUnG0024500' => 'rsi', 'RhsimUnG0024700' => 'rsi', 'RhsimUnG0024800' => 'rsi', 'RhsimUnG0024900' => 'rsi', 'RhsimUnG0025100' => 'rsi', 'Sabra08G0120200' => 'sbr', 'Sabra08G0120300' => 'sbr', 'Sabra08G0120500' => 'sbr', 'Sabra08G0120600' => 'sbr', 'Sabra10G0158900' => 'sbr', 'SalBow2G3492' => 'sbo', 'Sc13g0004760' => 'sci', 'Sc13g0004770' => 'sci', 'Sed0003417' => 'sed', 'Sed0019750' => 'sed', 'SEGI_03419' => 'sgi', 'SEGI_05907' => 'sgi', 'SEGI_10682' => 'sgi', 'SEGI_13528' => 'sgi', 'SEGI_16081' => 'sgi', 'SEGI_19370' => 'sgi', 'SEGI_21015' => 'sgi', 'SEGI_21944' => 'sgi', 'SEGI_32906' => 'sgi', 'SEGI_33093' => 'sgi', 'SEGI_36110' => 'sgi', 'SEGI_40397' => 'sgi', 'SGA_v2.0_scaffold191G40426' => 'sas', 'SGA_v2.0_scaffold353G49717' => 'sas', 'SGA_v2.0_scaffold50G18550' => 'sas', 'SMO119G0173' => 'smo', 'SMO172G0002' => 'smo', 'Solyc09g082690.3' => 'sly', 'Solyc09g082700.2' => 'sly', 'Sopen09g031550' => 'spe', 'Sopen09g031560' => 'spe', 'Sp3g20540' => 'spa', 'Sp7g07580' => 'spa', 'TAR134G0002' => 'tar', 'TAR236G0001' => 'tar', 'TAR365G0892' => 'tar', 'TAR636G0166' => 'tar', 'TAR636G0646' => 'tar', 'TAR636G0869' => 'tar', 'TAR636G1317' => 'tar', 'TAR636G1744' => 'tar', 'TAR636G3358' => 'tar', 'TAR636G3436' => 'tar', 'THA.LOC104803047' => 'tha', 'Thecc.04G238900' => 'tca', 'Thhalv10021557m.g' => 'esa', 'Thhalv10026318m.g' => 'esa', 'Thhalv10026335m.g' => 'esa', 'TPR.G17433' => 'tpr', 'TPR.G18915' => 'tpr', 'TPR.G26125' => 'tpr', 'TWI09G0677' => 'twi', 'TWI73G0287' => 'twi', 'unitig_748.g8326' => 'ugi', 'vmacro15370' => 'vma', 'vmacro15371' => 'vma', 'vmacro15372' => 'vma', 'vmacro15373' => 'vma', 'vmacro15374' => 'vma', 'VMungo0720G2826' => 'vmu', 'Zm00001eb116960' => 'zma', 'Zm00001eb301260' => 'zma', 'Zm00001eb301270' => 'zma' ) $gf_id = 'HOM05D001460' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001460' ) $data_identifier = 'HOM05D001460' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 4, 'aag' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 2, 'aox' => (int) 2, 'arhy' => (int) 4, 'ath' => (int) 2, 'atr' => (int) 1, 'acertr' => (int) 10, 'cqu' => (int) 4, 'bca' => (int) 11, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 1, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 1, 'ccan' => (int) 1, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 1, 'col' => (int) 1, 'cpa' => (int) 1, 'cre' => (int) 7, 'csa' => (int) 1, 'camsi' => (int) 2, 'dca' => (int) 3, 'din' => (int) 2, 'dzi' => (int) 3, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 14, 'fve' => (int) 9, 'gma' => (int) 2, 'ghi' => (int) 4, 'gra' => (int) 2, 'vvi' => (int) 1, 'han' => (int) 13, 'cav' => (int) 1, 'hma' => (int) 2, 'sun' => (int) 2, 'lal' => (int) 2, 'lonja' => (int) 12, 'lja' => (int) 1, 'lsa' => (int) 7, 'mes' => (int) 1, 'mpo' => (int) 27, 'mbi' => (int) 1, 'mco' => (int) 8, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 1, 'egut' => (int) 1, 'ama' => (int) 1, 'nta' => (int) 4, 'nnu' => (int) 2, 'oeu' => (int) 3, 'osa' => (int) 4, 'pax' => (int) 9, 'pgr' => (int) 1, 'stu' => (int) 1, 'pvu' => (int) 1, 'ptr' => (int) 4, 'ppa' => (int) 22, 'pco' => (int) 6, 'ppe' => (int) 6, 'psa' => (int) 5, 'pso' => (int) 19, 'qlo' => (int) 5, 'rch' => (int) 7, 'rsi' => (int) 20, 'sbr' => (int) 5, 'sbo' => (int) 1, 'sci' => (int) 2, 'sed' => (int) 2, 'sgi' => (int) 12, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 2, 'tar' => (int) 10, 'tha' => (int) 1, 'tca' => (int) 1, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 2, 'ugi' => (int) 1, 'vma' => (int) 5, 'vmu' => (int) 1, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb301270' $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' => 'HOM05D001460', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '433', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p22980' => 'bna', 'A01p32340' => 'bna', 'A03p42970' => 'bna', 'A05p25880' => 'bna', 'Aa31LG8G9320' => 'aar', 'Aa31LG8G9330' => 'aar', 'Aa31LG8G9340' => 'aar', 'Aa31sc221G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1034' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1528' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.829' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2222' => 'aag', 'Ah.12g058830' => 'amhyb', 'Ah.12g058840' => 'amhyb', 'AL3G37160' => 'aly', 'AL7G41310' => 'aly', 'Aqoxy5G00395' => 'aox', 'Aqoxy5G00396' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0C8NZA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5185HY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JZ1PRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MD3LS0' => 'arhy', 'AT3G22840' => 'ath', 'AT4G14690' => 'ath', 'ATR0665G054' => 'atr', 'Atru.chr4.2344' => 'acertr', 'Atru.chr4.2346' => 'acertr', 'Atru.chr4.2347' => 'acertr', 'Atru.chr4.2348' => 'acertr', 'Atru.chr4.2355' => 'acertr', 'Atru.chr4.2356' => 'acertr', 'Atru.chr4.2358' => 'acertr', 'Atru.chr4.2359' => 'acertr', 'Atru.chr4.2360' => 'acertr', 'Atru.chr4.2361' => 'acertr', 'AUR62030476' => 'cqu', 'AUR62030478' => 'cqu', 'AUR62030819' => 'cqu', 'AUR62030820' => 'cqu', 'BcaB03g14648' => 'bca', 'BcaB04g20492' => 'bca', 'BcaB06g26399' => 'bca', 'BcaC01g03416' => 'bca', 'BcaC01g03419' => 'bca', 'BcaC01g03421' => 'bca', 'BcaC01g03424' => 'bca', 'BcaC05g28012' => 'bca', 'BcaC09g49212' => 'bca', 'BcaC09g50140' => 'bca', 'BcaNung00346' => 'bca', 'BolC1t02785H' => 'bol', 'BolC1t04095H' => 'bol', 'BolC3t17545H' => 'bol', 'BolC5t32769H' => 'bol', 'BraA01t02211Z' => 'bra', 'BraA01t03359Z' => 'bra', 'BraA03t13441Z' => 'bra', 'BraA05t21476Z' => 'bra', 'C01p28420' => 'bna', 'C01p41350' => 'bna', 'C03p52750' => 'bna', 'C03p52780' => 'bna', 'C05p40270' => 'bna', 'CAN.G1437.9' => 'can', 'CANSAT78G0035' => 'cansat', 'CANSAT78G1036' => 'cansat', 'CANSAT78G2272' => 'cansat', 'CANSAT78G2478' => 'cansat', 'CARHR098700' => 'chi', 'CARHR221120' => 'chi', 'CARHR221150' => 'chi', 'Carub.0003s2297' => 'cru', 'Carub.0007s2749' => 'cru', 'Carub.0007s2750' => 'cru', 'Carub.0007s2751' => 'cru', 'Ca_10849_v3' => 'car', 'Cc03_g04300' => 'ccan', 'CDE02G3648' => 'cde', 'CDE05G0060' => 'cde', 'CDE05G0692' => 'cde', 'CDE05G2285' => 'cde', 'CDE05G2884' => 'cde', 'CDE05G3072' => 'cde', 'Cfa008439' => 'cfa', 'Cfa008441' => 'cfa', 'Cfa008443' => 'cfa', 'Cfa008448' => 'cfa', 'Ciclev10005974m.g' => 'ccl', 'Ciclev10006006m.g' => 'ccl', 'Ciclev10006775m.g' => 'ccl', 'CiPaw.02G120400' => 'cil', 'CiPaw.02G120500' => 'cil', 'CiPaw.02G120600' => 'cil', 'ClCG05G004850' => 'cla', 'COL.COLO4_21566' => 'col', 'Cpa.g.sc44.124' => 'cpa', 'Cre07.g320400' => 'cre', 'Cre07.g320450' => 'cre', 'Cre08.g384650' => 'cre', 'Cre09.g393173' => 'cre', 'Cre09.g394325' => 'cre', 'Cre14.g626750' => 'cre', 'Cre16.g679250' => 'cre', 'CsaV3_3G012890' => 'csa', 'CSS0010865' => 'camsi', 'CSS0044338' => 'camsi', 'DCAR_002366' => 'dca', 'DCAR_030687' => 'dca', 'DCAR_030688' => 'dca', 'Dinv14047' => 'din', 'Dinv14048' => 'din', 'Duzib151G0105' => 'dzi', 'Duzib151G0114' => 'dzi', 'Duzib212G1029' => 'dzi', 'ECA232G3536' => 'eca', 'ECA240G0786' => 'eca', 'ECA240G1802' => 'eca', 'ECA240G3760' => 'eca', 'ECA240G3920' => 'eca', 'EL10Ac5g12536' => 'bvu', 'EL10Ac5g12537' => 'bvu', 'EL10Ac5g12538' => 'bvu', 'Eucgr.B01004' => 'egr', 'Eucgr.B01006' => 'egr', 'Eucgr.B01007' => 'egr', 'Eucgr.B01008' => 'egr', 'Eucgr.B01895' => 'egr', 'Eucgr.B01896' => 'egr', 'FAN04G1456' => 'fan', 'FAN08G1769' => 'fan', 'FAN08G2160' => 'fan', 'FAN13G2403' => 'fan', 'FAN13G3303' => 'fan', 'FAN15G2435' => 'fan', 'FAN17G0672' => 'fan', 'FAN17G2441' => 'fan', 'FAN18G1024' => 'fan', 'FAN22G1458' => 'fan', 'FAN24G0037' => 'fan', 'FAN24G0429' => 'fan', 'FAN24G2387' => 'fan', 'FAN27G2746' => 'fan', 'FvH4_2g20400' => 'fve', 'FvH4_2g20420' => 'fve', 'FvH4_2g20430' => 'fve', 'FvH4_4g01270' => 'fve', 'FvH4_4g01290' => 'fve', 'FvH4_4g01300' => 'fve', 'FvH4_4g01310' => 'fve', 'FvH4_4g01330' => 'fve', 'FvH4_5g09070' => 'fve', 'Glyma.10G243800' => 'gma', 'Glyma.20G150600' => 'gma', 'Gohir.A09G219200' => 'ghi', 'Gohir.A09G219300' => 'ghi', 'Gohir.D09G221400' => 'ghi', 'Gohir.D09G221500' => 'ghi', 'Gorai.006G242600' => 'gra', 'Gorai.006G242700' => 'gra', 'GSVIVG01018044001' => 'vvi', 'HanXRQChr03g0083821' => 'han', 'HanXRQChr03g0083841' => 'han', 'HanXRQChr03g0083881' => 'han', 'HanXRQChr03g0083901' => 'han', 'HanXRQChr03g0083921' => 'han', 'HanXRQChr03g0085331' => 'han', 'HanXRQChr03g0085361' => 'han', 'HanXRQChr03g0085411' => 'han', 'HanXRQChr03g0085421' => 'han', 'HanXRQChr03g0085431' => 'han', 'HanXRQChr08g0221991' => 'han', 'HanXRQChr11g0336061' => 'han', 'HanXRQChr11g0336411' => 'han', 'Haze_11234' => 'cav', 'Hma1.2p1_0549F.1_g177010' => 'hma', 'Hma1.2p1_0602F.1_g187630' => 'hma', 'Hund14876' => 'sun', 'Hund14879' => 'sun', 'Lalb_Chr06g0160741' => 'lal', 'Lalb_Chr21g0304781' => 'lal', 'Lj3A726G19' => 'lonja', 'Lj3A726T23' => 'lonja', 'Lj3A726T24' => 'lonja', 'Lj3A726T25' => 'lonja', 'Lj3A727T17' => 'lonja', 'Lj3C726T0' => 'lonja', 'Lj3C726T2' => 'lonja', 'Lj3P725T35' => 'lonja', 'Lj3P727T10' => 'lonja', 'Lj3P727T12' => 'lonja', 'Lj3P727T14' => 'lonja', 'Lj5g0023109' => 'lja', 'Lj6P646T44' => 'lonja', 'Lsat_1_v5_gn_6_75760' => 'lsa', 'Lsat_1_v5_gn_6_75800' => 'lsa', 'Lsat_1_v5_gn_6_75900' => 'lsa', 'Lsat_1_v5_gn_6_76240' => 'lsa', 'Lsat_1_v5_gn_6_76441' => 'lsa', 'Lsat_1_v5_gn_6_76700' => 'lsa', 'Lsat_1_v5_gn_6_76760' => 'lsa', 'Manes.15G033100' => 'mes', 'Mapoly0004s0074' => 'mpo', 'Mapoly0004s0075' => 'mpo', 'Mapoly0004s0163' => 'mpo', 'Mapoly0004s0164' => 'mpo', 'Mapoly0021s0018' => 'mpo', 'Mapoly0041s0136' => 'mpo', 'Mapoly0041s0137' => 'mpo', 'Mapoly0041s0138' => 'mpo', 'Mapoly0041s0139' => 'mpo', 'Mapoly0041s0141' => 'mpo', 'Mapoly0041s0142' => 'mpo', 'Mapoly0041s0143' => 'mpo', 'Mapoly0041s0144' => 'mpo', 'Mapoly0041s0145' => 'mpo', 'Mapoly0047s0106' => 'mpo', 'Mapoly0047s0108' => 'mpo', 'Mapoly0050s0051' => 'mpo', 'Mapoly0050s0052' => 'mpo', 'Mapoly0050s0053' => 'mpo', 'Mapoly0058s0013' => 'mpo', 'Mapoly0091s0078' => 'mpo', 'Mapoly0091s0079' => 'mpo', 'Mapoly0091s0080' => 'mpo', 'Mapoly0091s0081' => 'mpo', 'Mapoly0278s0004' => 'mpo', 'Mapoly0278s0005' => 'mpo', 'Mapoly0278s0006' => 'mpo', 'MBI11_g30648_MAGBIO' => 'mbi', 'MCO03G194' => 'mco', 'MCO03G590' => 'mco', 'MCO07G312' => 'mco', 'MCO10G318' => 'mco', 'MCO12G244' => 'mco', 'MCO13G148' => 'mco', 'MCO13G194' => 'mco', 'MCO16G238' => 'mco', 'MD06G1134100' => 'mdo', 'MD13G1200100' => 'mdo', 'MD13G1200300' => 'mdo', 'MD13G1200600' => 'mdo', 'MD14G1150400' => 'mdo', 'MD16G1200000' => 'mdo', 'Medtr1g102570' => 'mtr', 'Medtr1g102780' => 'mtr', 'Medtr1g102800' => 'mtr', 'Medtr1g102810' => 'mtr', 'Medtr1g102830' => 'mtr', 'MELO3C006499.2' => 'cme', 'Migut.G00385' => 'egut', 'MSTRG.4063' => 'ama', 'Nitab4.5_0000090g0260' => 'nta', 'Nitab4.5_0000977g0030' => 'nta', 'Nitab4.5_0002541g0040' => 'nta', 'Nitab4.5_0007068g0040' => 'nta', 'Nn005s41408' => 'nnu', 'Nn005s41410' => 'nnu', 'Oeu010310.1' => 'oeu', 'Oeu010311.1' => 'oeu', 'Oeu043472.1' => 'oeu', 'Os01g0246400' => 'osa', 'Os04g0267950' => 'osa', 'Os07g0178700' => 'osa', 'Os07g0178800' => 'osa', 'Peaxi162Scf00316g00046' => 'pax', 'Peaxi162Scf00316g00049' => 'pax', 'Peaxi162Scf00316g00059' => 'pax', 'Peaxi162Scf00316g00328' => 'pax', 'Peaxi162Scf00316g00329' => 'pax', 'Peaxi162Scf00316g00411' => 'pax', 'Peaxi162Scf00316g00521' => 'pax', 'Peaxi162Scf00492g00068' => 'pax', 'Peaxi162Scf35631g00002' => 'pax', 'PGR142G3720' => 'pgr', 'PGSC0003DMG400006442' => 'stu', 'Phvul.007G062000' => 'pvu', 'Potri.008G157750' => 'ptr', 'Potri.008G157900' => 'ptr', 'Potri.008G158000' => 'ptr', 'Potri.008G158200' => 'ptr', 'Pp3c11_7280' => 'ppa', 'Pp3c11_7980' => 'ppa', 'Pp3c12_19450' => 'ppa', 'Pp3c14_1480' => 'ppa', 'Pp3c14_1501' => 'ppa', 'Pp3c16_4900' => 'ppa', 'Pp3c16_5010' => 'ppa', 'Pp3c16_5060' => 'ppa', 'Pp3c19_18250' => 'ppa', 'Pp3c23_8530' => 'ppa', 'Pp3c23_8550' => 'ppa', 'Pp3c24_9670' => 'ppa', 'Pp3c2_21390' => 'ppa', 'Pp3c2_31380' => 'ppa', 'Pp3c3_16620' => 'ppa', 'Pp3c3_8090' => 'ppa', 'Pp3c3_8110' => 'ppa', 'Pp3c3_8130' => 'ppa', 'Pp3c3_8150' => 'ppa', 'Pp3c4_14320' => 'ppa', 'Pp3c6_2560' => 'ppa', 'Pp3c9_16700' => 'ppa', 'PRCOL_00000234' => 'pco', 'PRCOL_00000235' => 'pco', 'PRCOL_00000777' => 'pco', 'PRCOL_00002344' => 'pco', 'PRCOL_00002372' => 'pco', 'PRCOL_00006120' => 'pco', 'Prupe.1G021400' => 'ppe', 'Prupe.1G021500' => 'ppe', 'Prupe.1G021600' => 'ppe', 'Prupe.1G021700' => 'ppe', 'Prupe.1G021800' => 'ppe', 'Prupe.5G145100' => 'ppe', 'Psat6g204040' => 'psa', 'Psat6g204800' => 'psa', 'Psat6g204920' => 'psa', 'Psat6g204960' => 'psa', 'Psat6g205080' => 'psa', 'PSO017G0271' => 'pso', 'PSO017G1276' => 'pso', 'PSO017G1429' => 'pso', 'PSO017G1861' => 'pso', 'PSO017G2787' => 'pso', 'PSO017G4466' => 'pso', 'PSO017G5118' => 'pso', 'PSO017G5420' => 'pso', 'PSO063G3678' => 'pso', 'PSO210G0546' => 'pso', 'PSO317G0001' => 'pso', 'PSO357G0512' => 'pso', 'PSO478G2682' => 'pso', 'PSO647G0001' => 'pso', 'PSO675G0001' => 'pso', 'PSO675G2699' => 'pso', 'PSO675G2849' => 'pso', 'PSO675G4991' => 'pso', 'PSO689G0001' => 'pso', 'QL06p000916' => 'qlo', 'QL06p000921' => 'qlo', 'QL06p001398' => 'qlo', 'QL06p001407' => 'qlo', 'QL06p002031' => 'qlo', 'RcHm_v2.0_Chr4g0387791' => 'rch', 'RcHm_v2.0_Chr4g0387801' => 'rch', 'RcHm_v2.0_Chr6g0286501' => 'rch', 'RcHm_v2.0_Chr6g0286511' => 'rch', 'RcHm_v2.0_Chr6g0286521' => 'rch', 'RcHm_v2.0_Chr6g0286531' => 'rch', 'RcHm_v2.0_Chr7g0189141' => 'rch', 'Rhsim02G0028700' => 'rsi', 'Rhsim02G0028800' => 'rsi', 'Rhsim02G0028900' => 'rsi', 'Rhsim02G0029000' => 'rsi', 'Rhsim02G0029100' => 'rsi', 'Rhsim02G0029200' => 'rsi', 'Rhsim02G0029300' => 'rsi', 'Rhsim02G0029400' => 'rsi', 'Rhsim02G0029500' => 'rsi', 'Rhsim02G0029600' => 'rsi', 'RhsimUnG0024000' => 'rsi', 'RhsimUnG0024100' => 'rsi', 'RhsimUnG0024200' => 'rsi', 'RhsimUnG0024300' => 'rsi', 'RhsimUnG0024400' => 'rsi', 'RhsimUnG0024500' => 'rsi', 'RhsimUnG0024700' => 'rsi', 'RhsimUnG0024800' => 'rsi', 'RhsimUnG0024900' => 'rsi', 'RhsimUnG0025100' => 'rsi', 'Sabra08G0120200' => 'sbr', 'Sabra08G0120300' => 'sbr', 'Sabra08G0120500' => 'sbr', 'Sabra08G0120600' => 'sbr', 'Sabra10G0158900' => 'sbr', 'SalBow2G3492' => 'sbo', 'Sc13g0004760' => 'sci', 'Sc13g0004770' => 'sci', 'Sed0003417' => 'sed', 'Sed0019750' => 'sed', 'SEGI_03419' => 'sgi', 'SEGI_05907' => 'sgi', 'SEGI_10682' => 'sgi', 'SEGI_13528' => 'sgi', 'SEGI_16081' => 'sgi', 'SEGI_19370' => 'sgi', 'SEGI_21015' => 'sgi', 'SEGI_21944' => 'sgi', 'SEGI_32906' => 'sgi', 'SEGI_33093' => 'sgi', 'SEGI_36110' => 'sgi', 'SEGI_40397' => 'sgi', 'SGA_v2.0_scaffold191G40426' => 'sas', 'SGA_v2.0_scaffold353G49717' => 'sas', 'SGA_v2.0_scaffold50G18550' => 'sas', 'SMO119G0173' => 'smo', 'SMO172G0002' => 'smo', 'Solyc09g082690.3' => 'sly', 'Solyc09g082700.2' => 'sly', 'Sopen09g031550' => 'spe', 'Sopen09g031560' => 'spe', 'Sp3g20540' => 'spa', 'Sp7g07580' => 'spa', 'TAR134G0002' => 'tar', 'TAR236G0001' => 'tar', 'TAR365G0892' => 'tar', 'TAR636G0166' => 'tar', 'TAR636G0646' => 'tar', 'TAR636G0869' => 'tar', 'TAR636G1317' => 'tar', 'TAR636G1744' => 'tar', 'TAR636G3358' => 'tar', 'TAR636G3436' => 'tar', 'THA.LOC104803047' => 'tha', 'Thecc.04G238900' => 'tca', 'Thhalv10021557m.g' => 'esa', 'Thhalv10026318m.g' => 'esa', 'Thhalv10026335m.g' => 'esa', 'TPR.G17433' => 'tpr', 'TPR.G18915' => 'tpr', 'TPR.G26125' => 'tpr', 'TWI09G0677' => 'twi', 'TWI73G0287' => 'twi', 'unitig_748.g8326' => 'ugi', 'vmacro15370' => 'vma', 'vmacro15371' => 'vma', 'vmacro15372' => 'vma', 'vmacro15373' => 'vma', 'vmacro15374' => 'vma', 'VMungo0720G2826' => 'vmu', 'Zm00001eb116960' => 'zma', 'Zm00001eb301260' => 'zma', 'Zm00001eb301270' => 'zma' ), 'gf_id' => 'HOM05D001460', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001460' ), 'data_identifier' => 'HOM05D001460', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001460', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '433', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p22980' => 'bna', 'A01p32340' => 'bna', 'A03p42970' => 'bna', 'A05p25880' => 'bna', 'Aa31LG8G9320' => 'aar', 'Aa31LG8G9330' => 'aar', 'Aa31LG8G9340' => 'aar', 'Aa31sc221G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1034' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1528' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.829' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2222' => 'aag', 'Ah.12g058830' => 'amhyb', 'Ah.12g058840' => 'amhyb', 'AL3G37160' => 'aly', 'AL7G41310' => 'aly', 'Aqoxy5G00395' => 'aox', 'Aqoxy5G00396' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0C8NZA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5185HY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JZ1PRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MD3LS0' => 'arhy', 'AT3G22840' => 'ath', 'AT4G14690' => 'ath', 'ATR0665G054' => 'atr', 'Atru.chr4.2344' => 'acertr', 'Atru.chr4.2346' => 'acertr', 'Atru.chr4.2347' => 'acertr', 'Atru.chr4.2348' => 'acertr', 'Atru.chr4.2355' => 'acertr', 'Atru.chr4.2356' => 'acertr', 'Atru.chr4.2358' => 'acertr', 'Atru.chr4.2359' => 'acertr', 'Atru.chr4.2360' => 'acertr', 'Atru.chr4.2361' => 'acertr', 'AUR62030476' => 'cqu', 'AUR62030478' => 'cqu', 'AUR62030819' => 'cqu', 'AUR62030820' => 'cqu', 'BcaB03g14648' => 'bca', 'BcaB04g20492' => 'bca', 'BcaB06g26399' => 'bca', 'BcaC01g03416' => 'bca', 'BcaC01g03419' => 'bca', 'BcaC01g03421' => 'bca', 'BcaC01g03424' => 'bca', 'BcaC05g28012' => 'bca', 'BcaC09g49212' => 'bca', 'BcaC09g50140' => 'bca', 'BcaNung00346' => 'bca', 'BolC1t02785H' => 'bol', 'BolC1t04095H' => 'bol', 'BolC3t17545H' => 'bol', 'BolC5t32769H' => 'bol', 'BraA01t02211Z' => 'bra', 'BraA01t03359Z' => 'bra', 'BraA03t13441Z' => 'bra', 'BraA05t21476Z' => 'bra', 'C01p28420' => 'bna', 'C01p41350' => 'bna', 'C03p52750' => 'bna', 'C03p52780' => 'bna', 'C05p40270' => 'bna', 'CAN.G1437.9' => 'can', 'CANSAT78G0035' => 'cansat', 'CANSAT78G1036' => 'cansat', 'CANSAT78G2272' => 'cansat', 'CANSAT78G2478' => 'cansat', 'CARHR098700' => 'chi', 'CARHR221120' => 'chi', 'CARHR221150' => 'chi', 'Carub.0003s2297' => 'cru', 'Carub.0007s2749' => 'cru', 'Carub.0007s2750' => 'cru', 'Carub.0007s2751' => 'cru', 'Ca_10849_v3' => 'car', 'Cc03_g04300' => 'ccan', 'CDE02G3648' => 'cde', 'CDE05G0060' => 'cde', 'CDE05G0692' => 'cde', 'CDE05G2285' => 'cde', 'CDE05G2884' => 'cde', 'CDE05G3072' => 'cde', 'Cfa008439' => 'cfa', 'Cfa008441' => 'cfa', 'Cfa008443' => 'cfa', 'Cfa008448' => 'cfa', 'Ciclev10005974m.g' => 'ccl', 'Ciclev10006006m.g' => 'ccl', 'Ciclev10006775m.g' => 'ccl', 'CiPaw.02G120400' => 'cil', 'CiPaw.02G120500' => 'cil', 'CiPaw.02G120600' => 'cil', 'ClCG05G004850' => 'cla', 'COL.COLO4_21566' => 'col', 'Cpa.g.sc44.124' => 'cpa', 'Cre07.g320400' => 'cre', 'Cre07.g320450' => 'cre', 'Cre08.g384650' => 'cre', 'Cre09.g393173' => 'cre', 'Cre09.g394325' => 'cre', 'Cre14.g626750' => 'cre', 'Cre16.g679250' => 'cre', 'CsaV3_3G012890' => 'csa', 'CSS0010865' => 'camsi', 'CSS0044338' => 'camsi', 'DCAR_002366' => 'dca', 'DCAR_030687' => 'dca', 'DCAR_030688' => 'dca', 'Dinv14047' => 'din', 'Dinv14048' => 'din', 'Duzib151G0105' => 'dzi', 'Duzib151G0114' => 'dzi', 'Duzib212G1029' => 'dzi', 'ECA232G3536' => 'eca', 'ECA240G0786' => 'eca', 'ECA240G1802' => 'eca', 'ECA240G3760' => 'eca', 'ECA240G3920' => 'eca', 'EL10Ac5g12536' => 'bvu', 'EL10Ac5g12537' => 'bvu', 'EL10Ac5g12538' => 'bvu', 'Eucgr.B01004' => 'egr', 'Eucgr.B01006' => 'egr', 'Eucgr.B01007' => 'egr', 'Eucgr.B01008' => 'egr', 'Eucgr.B01895' => 'egr', 'Eucgr.B01896' => 'egr', 'FAN04G1456' => 'fan', 'FAN08G1769' => 'fan', 'FAN08G2160' => 'fan', 'FAN13G2403' => 'fan', 'FAN13G3303' => 'fan', 'FAN15G2435' => 'fan', 'FAN17G0672' => 'fan', 'FAN17G2441' => 'fan', 'FAN18G1024' => 'fan', 'FAN22G1458' => 'fan', 'FAN24G0037' => 'fan', 'FAN24G0429' => 'fan', 'FAN24G2387' => 'fan', 'FAN27G2746' => 'fan', 'FvH4_2g20400' => 'fve', 'FvH4_2g20420' => 'fve', 'FvH4_2g20430' => 'fve', 'FvH4_4g01270' => 'fve', 'FvH4_4g01290' => 'fve', 'FvH4_4g01300' => 'fve', 'FvH4_4g01310' => 'fve', 'FvH4_4g01330' => 'fve', 'FvH4_5g09070' => 'fve', 'Glyma.10G243800' => 'gma', 'Glyma.20G150600' => 'gma', 'Gohir.A09G219200' => 'ghi', 'Gohir.A09G219300' => 'ghi', 'Gohir.D09G221400' => 'ghi', 'Gohir.D09G221500' => 'ghi', 'Gorai.006G242600' => 'gra', 'Gorai.006G242700' => 'gra', 'GSVIVG01018044001' => 'vvi', 'HanXRQChr03g0083821' => 'han', 'HanXRQChr03g0083841' => 'han', 'HanXRQChr03g0083881' => 'han', 'HanXRQChr03g0083901' => 'han', 'HanXRQChr03g0083921' => 'han', 'HanXRQChr03g0085331' => 'han', 'HanXRQChr03g0085361' => 'han', 'HanXRQChr03g0085411' => 'han', 'HanXRQChr03g0085421' => 'han', 'HanXRQChr03g0085431' => 'han', 'HanXRQChr08g0221991' => 'han', 'HanXRQChr11g0336061' => 'han', 'HanXRQChr11g0336411' => 'han', 'Haze_11234' => 'cav', 'Hma1.2p1_0549F.1_g177010' => 'hma', 'Hma1.2p1_0602F.1_g187630' => 'hma', 'Hund14876' => 'sun', 'Hund14879' => 'sun', 'Lalb_Chr06g0160741' => 'lal', 'Lalb_Chr21g0304781' => 'lal', 'Lj3A726G19' => 'lonja', 'Lj3A726T23' => 'lonja', 'Lj3A726T24' => 'lonja', 'Lj3A726T25' => 'lonja', 'Lj3A727T17' => 'lonja', 'Lj3C726T0' => 'lonja', 'Lj3C726T2' => 'lonja', 'Lj3P725T35' => 'lonja', 'Lj3P727T10' => 'lonja', 'Lj3P727T12' => 'lonja', 'Lj3P727T14' => 'lonja', 'Lj5g0023109' => 'lja', 'Lj6P646T44' => 'lonja', 'Lsat_1_v5_gn_6_75760' => 'lsa', 'Lsat_1_v5_gn_6_75800' => 'lsa', 'Lsat_1_v5_gn_6_75900' => 'lsa', 'Lsat_1_v5_gn_6_76240' => 'lsa', 'Lsat_1_v5_gn_6_76441' => 'lsa', 'Lsat_1_v5_gn_6_76700' => 'lsa', 'Lsat_1_v5_gn_6_76760' => 'lsa', 'Manes.15G033100' => 'mes', 'Mapoly0004s0074' => 'mpo', 'Mapoly0004s0075' => 'mpo', 'Mapoly0004s0163' => 'mpo', 'Mapoly0004s0164' => 'mpo', 'Mapoly0021s0018' => 'mpo', 'Mapoly0041s0136' => 'mpo', 'Mapoly0041s0137' => 'mpo', 'Mapoly0041s0138' => 'mpo', 'Mapoly0041s0139' => 'mpo', 'Mapoly0041s0141' => 'mpo', 'Mapoly0041s0142' => 'mpo', 'Mapoly0041s0143' => 'mpo', 'Mapoly0041s0144' => 'mpo', 'Mapoly0041s0145' => 'mpo', 'Mapoly0047s0106' => 'mpo', 'Mapoly0047s0108' => 'mpo', 'Mapoly0050s0051' => 'mpo', 'Mapoly0050s0052' => 'mpo', 'Mapoly0050s0053' => 'mpo', 'Mapoly0058s0013' => 'mpo', 'Mapoly0091s0078' => 'mpo', 'Mapoly0091s0079' => 'mpo', 'Mapoly0091s0080' => 'mpo', 'Mapoly0091s0081' => 'mpo', 'Mapoly0278s0004' => 'mpo', 'Mapoly0278s0005' => 'mpo', 'Mapoly0278s0006' => 'mpo', 'MBI11_g30648_MAGBIO' => 'mbi', 'MCO03G194' => 'mco', 'MCO03G590' => 'mco', 'MCO07G312' => 'mco', 'MCO10G318' => 'mco', 'MCO12G244' => 'mco', 'MCO13G148' => 'mco', 'MCO13G194' => 'mco', 'MCO16G238' => 'mco', 'MD06G1134100' => 'mdo', 'MD13G1200100' => 'mdo', 'MD13G1200300' => 'mdo', 'MD13G1200600' => 'mdo', 'MD14G1150400' => 'mdo', 'MD16G1200000' => 'mdo', 'Medtr1g102570' => 'mtr', 'Medtr1g102780' => 'mtr', 'Medtr1g102800' => 'mtr', 'Medtr1g102810' => 'mtr', 'Medtr1g102830' => 'mtr', 'MELO3C006499.2' => 'cme', 'Migut.G00385' => 'egut', 'MSTRG.4063' => 'ama', 'Nitab4.5_0000090g0260' => 'nta', 'Nitab4.5_0000977g0030' => 'nta', 'Nitab4.5_0002541g0040' => 'nta', 'Nitab4.5_0007068g0040' => 'nta', 'Nn005s41408' => 'nnu', 'Nn005s41410' => 'nnu', 'Oeu010310.1' => 'oeu', 'Oeu010311.1' => 'oeu', 'Oeu043472.1' => 'oeu', 'Os01g0246400' => 'osa', 'Os04g0267950' => 'osa', 'Os07g0178700' => 'osa', 'Os07g0178800' => 'osa', 'Peaxi162Scf00316g00046' => 'pax', 'Peaxi162Scf00316g00049' => 'pax', 'Peaxi162Scf00316g00059' => 'pax', 'Peaxi162Scf00316g00328' => 'pax', 'Peaxi162Scf00316g00329' => 'pax', 'Peaxi162Scf00316g00411' => 'pax', 'Peaxi162Scf00316g00521' => 'pax', 'Peaxi162Scf00492g00068' => 'pax', 'Peaxi162Scf35631g00002' => 'pax', 'PGR142G3720' => 'pgr', 'PGSC0003DMG400006442' => 'stu', 'Phvul.007G062000' => 'pvu', 'Potri.008G157750' => 'ptr', 'Potri.008G157900' => 'ptr', 'Potri.008G158000' => 'ptr', 'Potri.008G158200' => 'ptr', 'Pp3c11_7280' => 'ppa', 'Pp3c11_7980' => 'ppa', 'Pp3c12_19450' => 'ppa', 'Pp3c14_1480' => 'ppa', 'Pp3c14_1501' => 'ppa', 'Pp3c16_4900' => 'ppa', 'Pp3c16_5010' => 'ppa', 'Pp3c16_5060' => 'ppa', 'Pp3c19_18250' => 'ppa', 'Pp3c23_8530' => 'ppa', 'Pp3c23_8550' => 'ppa', 'Pp3c24_9670' => 'ppa', 'Pp3c2_21390' => 'ppa', 'Pp3c2_31380' => 'ppa', 'Pp3c3_16620' => 'ppa', 'Pp3c3_8090' => 'ppa', 'Pp3c3_8110' => 'ppa', 'Pp3c3_8130' => 'ppa', 'Pp3c3_8150' => 'ppa', 'Pp3c4_14320' => 'ppa', 'Pp3c6_2560' => 'ppa', 'Pp3c9_16700' => 'ppa', 'PRCOL_00000234' => 'pco', 'PRCOL_00000235' => 'pco', 'PRCOL_00000777' => 'pco', 'PRCOL_00002344' => 'pco', 'PRCOL_00002372' => 'pco', 'PRCOL_00006120' => 'pco', 'Prupe.1G021400' => 'ppe', 'Prupe.1G021500' => 'ppe', 'Prupe.1G021600' => 'ppe', 'Prupe.1G021700' => 'ppe', 'Prupe.1G021800' => 'ppe', 'Prupe.5G145100' => 'ppe', 'Psat6g204040' => 'psa', 'Psat6g204800' => 'psa', 'Psat6g204920' => 'psa', 'Psat6g204960' => 'psa', 'Psat6g205080' => 'psa', 'PSO017G0271' => 'pso', 'PSO017G1276' => 'pso', 'PSO017G1429' => 'pso', 'PSO017G1861' => 'pso', 'PSO017G2787' => 'pso', 'PSO017G4466' => 'pso', 'PSO017G5118' => 'pso', 'PSO017G5420' => 'pso', 'PSO063G3678' => 'pso', 'PSO210G0546' => 'pso', 'PSO317G0001' => 'pso', 'PSO357G0512' => 'pso', 'PSO478G2682' => 'pso', 'PSO647G0001' => 'pso', 'PSO675G0001' => 'pso', 'PSO675G2699' => 'pso', 'PSO675G2849' => 'pso', 'PSO675G4991' => 'pso', 'PSO689G0001' => 'pso', 'QL06p000916' => 'qlo', 'QL06p000921' => 'qlo', 'QL06p001398' => 'qlo', 'QL06p001407' => 'qlo', 'QL06p002031' => 'qlo', 'RcHm_v2.0_Chr4g0387791' => 'rch', 'RcHm_v2.0_Chr4g0387801' => 'rch', 'RcHm_v2.0_Chr6g0286501' => 'rch', 'RcHm_v2.0_Chr6g0286511' => 'rch', 'RcHm_v2.0_Chr6g0286521' => 'rch', 'RcHm_v2.0_Chr6g0286531' => 'rch', 'RcHm_v2.0_Chr7g0189141' => 'rch', 'Rhsim02G0028700' => 'rsi', 'Rhsim02G0028800' => 'rsi', 'Rhsim02G0028900' => 'rsi', 'Rhsim02G0029000' => 'rsi', 'Rhsim02G0029100' => 'rsi', 'Rhsim02G0029200' => 'rsi', 'Rhsim02G0029300' => 'rsi', 'Rhsim02G0029400' => 'rsi', 'Rhsim02G0029500' => 'rsi', 'Rhsim02G0029600' => 'rsi', 'RhsimUnG0024000' => 'rsi', 'RhsimUnG0024100' => 'rsi', 'RhsimUnG0024200' => 'rsi', 'RhsimUnG0024300' => 'rsi', 'RhsimUnG0024400' => 'rsi', 'RhsimUnG0024500' => 'rsi', 'RhsimUnG0024700' => 'rsi', 'RhsimUnG0024800' => 'rsi', 'RhsimUnG0024900' => 'rsi', 'RhsimUnG0025100' => 'rsi', 'Sabra08G0120200' => 'sbr', 'Sabra08G0120300' => 'sbr', 'Sabra08G0120500' => 'sbr', 'Sabra08G0120600' => 'sbr', 'Sabra10G0158900' => 'sbr', 'SalBow2G3492' => 'sbo', 'Sc13g0004760' => 'sci', 'Sc13g0004770' => 'sci', 'Sed0003417' => 'sed', 'Sed0019750' => 'sed', 'SEGI_03419' => 'sgi', 'SEGI_05907' => 'sgi', 'SEGI_10682' => 'sgi', 'SEGI_13528' => 'sgi', 'SEGI_16081' => 'sgi', 'SEGI_19370' => 'sgi', 'SEGI_21015' => 'sgi', 'SEGI_21944' => 'sgi', 'SEGI_32906' => 'sgi', 'SEGI_33093' => 'sgi', 'SEGI_36110' => 'sgi', 'SEGI_40397' => 'sgi', 'SGA_v2.0_scaffold191G40426' => 'sas', 'SGA_v2.0_scaffold353G49717' => 'sas', 'SGA_v2.0_scaffold50G18550' => 'sas', 'SMO119G0173' => 'smo', 'SMO172G0002' => 'smo', 'Solyc09g082690.3' => 'sly', 'Solyc09g082700.2' => 'sly', 'Sopen09g031550' => 'spe', 'Sopen09g031560' => 'spe', 'Sp3g20540' => 'spa', 'Sp7g07580' => 'spa', 'TAR134G0002' => 'tar', 'TAR236G0001' => 'tar', 'TAR365G0892' => 'tar', 'TAR636G0166' => 'tar', 'TAR636G0646' => 'tar', 'TAR636G0869' => 'tar', 'TAR636G1317' => 'tar', 'TAR636G1744' => 'tar', 'TAR636G3358' => 'tar', 'TAR636G3436' => 'tar', 'THA.LOC104803047' => 'tha', 'Thecc.04G238900' => 'tca', 'Thhalv10021557m.g' => 'esa', 'Thhalv10026318m.g' => 'esa', 'Thhalv10026335m.g' => 'esa', 'TPR.G17433' => 'tpr', 'TPR.G18915' => 'tpr', 'TPR.G26125' => 'tpr', 'TWI09G0677' => 'twi', 'TWI73G0287' => 'twi', 'unitig_748.g8326' => 'ugi', 'vmacro15370' => 'vma', 'vmacro15371' => 'vma', 'vmacro15372' => 'vma', 'vmacro15373' => 'vma', 'vmacro15374' => 'vma', 'VMungo0720G2826' => 'vmu', 'Zm00001eb116960' => 'zma', 'Zm00001eb301260' => 'zma', 'Zm00001eb301270' => 'zma' ) $gf_id = 'HOM05D001460' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001460' ) $data_identifier = 'HOM05D001460' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 4, 'aag' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 2, 'aox' => (int) 2, 'arhy' => (int) 4, 'ath' => (int) 2, 'atr' => (int) 1, 'acertr' => (int) 10, 'cqu' => (int) 4, 'bca' => (int) 11, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 1, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 1, 'ccan' => (int) 1, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 1, 'col' => (int) 1, 'cpa' => (int) 1, 'cre' => (int) 7, 'csa' => (int) 1, 'camsi' => (int) 2, 'dca' => (int) 3, 'din' => (int) 2, 'dzi' => (int) 3, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 14, 'fve' => (int) 9, 'gma' => (int) 2, 'ghi' => (int) 4, 'gra' => (int) 2, 'vvi' => (int) 1, 'han' => (int) 13, 'cav' => (int) 1, 'hma' => (int) 2, 'sun' => (int) 2, 'lal' => (int) 2, 'lonja' => (int) 12, 'lja' => (int) 1, 'lsa' => (int) 7, 'mes' => (int) 1, 'mpo' => (int) 27, 'mbi' => (int) 1, 'mco' => (int) 8, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 1, 'egut' => (int) 1, 'ama' => (int) 1, 'nta' => (int) 4, 'nnu' => (int) 2, 'oeu' => (int) 3, 'osa' => (int) 4, 'pax' => (int) 9, 'pgr' => (int) 1, 'stu' => (int) 1, 'pvu' => (int) 1, 'ptr' => (int) 4, 'ppa' => (int) 22, 'pco' => (int) 6, 'ppe' => (int) 6, 'psa' => (int) 5, 'pso' => (int) 19, 'qlo' => (int) 5, 'rch' => (int) 7, 'rsi' => (int) 20, 'sbr' => (int) 5, 'sbo' => (int) 1, 'sci' => (int) 2, 'sed' => (int) 2, 'sgi' => (int) 12, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 2, 'tar' => (int) 10, 'tha' => (int) 1, 'tca' => (int) 1, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 2, 'ugi' => (int) 1, 'vma' => (int) 5, 'vmu' => (int) 1, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb301270' $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' => 'HOM05D001460', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '433', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p22980' => 'bna', 'A01p32340' => 'bna', 'A03p42970' => 'bna', 'A05p25880' => 'bna', 'Aa31LG8G9320' => 'aar', 'Aa31LG8G9330' => 'aar', 'Aa31LG8G9340' => 'aar', 'Aa31sc221G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1034' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1528' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.829' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2222' => 'aag', 'Ah.12g058830' => 'amhyb', 'Ah.12g058840' => 'amhyb', 'AL3G37160' => 'aly', 'AL7G41310' => 'aly', 'Aqoxy5G00395' => 'aox', 'Aqoxy5G00396' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0C8NZA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5185HY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JZ1PRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MD3LS0' => 'arhy', 'AT3G22840' => 'ath', 'AT4G14690' => 'ath', 'ATR0665G054' => 'atr', 'Atru.chr4.2344' => 'acertr', 'Atru.chr4.2346' => 'acertr', 'Atru.chr4.2347' => 'acertr', 'Atru.chr4.2348' => 'acertr', 'Atru.chr4.2355' => 'acertr', 'Atru.chr4.2356' => 'acertr', 'Atru.chr4.2358' => 'acertr', 'Atru.chr4.2359' => 'acertr', 'Atru.chr4.2360' => 'acertr', 'Atru.chr4.2361' => 'acertr', 'AUR62030476' => 'cqu', 'AUR62030478' => 'cqu', 'AUR62030819' => 'cqu', 'AUR62030820' => 'cqu', 'BcaB03g14648' => 'bca', 'BcaB04g20492' => 'bca', 'BcaB06g26399' => 'bca', 'BcaC01g03416' => 'bca', 'BcaC01g03419' => 'bca', 'BcaC01g03421' => 'bca', 'BcaC01g03424' => 'bca', 'BcaC05g28012' => 'bca', 'BcaC09g49212' => 'bca', 'BcaC09g50140' => 'bca', 'BcaNung00346' => 'bca', 'BolC1t02785H' => 'bol', 'BolC1t04095H' => 'bol', 'BolC3t17545H' => 'bol', 'BolC5t32769H' => 'bol', 'BraA01t02211Z' => 'bra', 'BraA01t03359Z' => 'bra', 'BraA03t13441Z' => 'bra', 'BraA05t21476Z' => 'bra', 'C01p28420' => 'bna', 'C01p41350' => 'bna', 'C03p52750' => 'bna', 'C03p52780' => 'bna', 'C05p40270' => 'bna', 'CAN.G1437.9' => 'can', 'CANSAT78G0035' => 'cansat', 'CANSAT78G1036' => 'cansat', 'CANSAT78G2272' => 'cansat', 'CANSAT78G2478' => 'cansat', 'CARHR098700' => 'chi', 'CARHR221120' => 'chi', 'CARHR221150' => 'chi', 'Carub.0003s2297' => 'cru', 'Carub.0007s2749' => 'cru', 'Carub.0007s2750' => 'cru', 'Carub.0007s2751' => 'cru', 'Ca_10849_v3' => 'car', 'Cc03_g04300' => 'ccan', 'CDE02G3648' => 'cde', 'CDE05G0060' => 'cde', 'CDE05G0692' => 'cde', 'CDE05G2285' => 'cde', 'CDE05G2884' => 'cde', 'CDE05G3072' => 'cde', 'Cfa008439' => 'cfa', 'Cfa008441' => 'cfa', 'Cfa008443' => 'cfa', 'Cfa008448' => 'cfa', 'Ciclev10005974m.g' => 'ccl', 'Ciclev10006006m.g' => 'ccl', 'Ciclev10006775m.g' => 'ccl', 'CiPaw.02G120400' => 'cil', 'CiPaw.02G120500' => 'cil', 'CiPaw.02G120600' => 'cil', 'ClCG05G004850' => 'cla', 'COL.COLO4_21566' => 'col', 'Cpa.g.sc44.124' => 'cpa', 'Cre07.g320400' => 'cre', 'Cre07.g320450' => 'cre', 'Cre08.g384650' => 'cre', 'Cre09.g393173' => 'cre', 'Cre09.g394325' => 'cre', 'Cre14.g626750' => 'cre', 'Cre16.g679250' => 'cre', 'CsaV3_3G012890' => 'csa', 'CSS0010865' => 'camsi', 'CSS0044338' => 'camsi', 'DCAR_002366' => 'dca', 'DCAR_030687' => 'dca', 'DCAR_030688' => 'dca', 'Dinv14047' => 'din', 'Dinv14048' => 'din', 'Duzib151G0105' => 'dzi', 'Duzib151G0114' => 'dzi', 'Duzib212G1029' => 'dzi', 'ECA232G3536' => 'eca', 'ECA240G0786' => 'eca', 'ECA240G1802' => 'eca', 'ECA240G3760' => 'eca', 'ECA240G3920' => 'eca', 'EL10Ac5g12536' => 'bvu', 'EL10Ac5g12537' => 'bvu', 'EL10Ac5g12538' => 'bvu', 'Eucgr.B01004' => 'egr', 'Eucgr.B01006' => 'egr', 'Eucgr.B01007' => 'egr', 'Eucgr.B01008' => 'egr', 'Eucgr.B01895' => 'egr', 'Eucgr.B01896' => 'egr', 'FAN04G1456' => 'fan', 'FAN08G1769' => 'fan', 'FAN08G2160' => 'fan', 'FAN13G2403' => 'fan', 'FAN13G3303' => 'fan', 'FAN15G2435' => 'fan', 'FAN17G0672' => 'fan', 'FAN17G2441' => 'fan', 'FAN18G1024' => 'fan', 'FAN22G1458' => 'fan', 'FAN24G0037' => 'fan', 'FAN24G0429' => 'fan', 'FAN24G2387' => 'fan', 'FAN27G2746' => 'fan', 'FvH4_2g20400' => 'fve', 'FvH4_2g20420' => 'fve', 'FvH4_2g20430' => 'fve', 'FvH4_4g01270' => 'fve', 'FvH4_4g01290' => 'fve', 'FvH4_4g01300' => 'fve', 'FvH4_4g01310' => 'fve', 'FvH4_4g01330' => 'fve', 'FvH4_5g09070' => 'fve', 'Glyma.10G243800' => 'gma', 'Glyma.20G150600' => 'gma', 'Gohir.A09G219200' => 'ghi', 'Gohir.A09G219300' => 'ghi', 'Gohir.D09G221400' => 'ghi', 'Gohir.D09G221500' => 'ghi', 'Gorai.006G242600' => 'gra', 'Gorai.006G242700' => 'gra', 'GSVIVG01018044001' => 'vvi', 'HanXRQChr03g0083821' => 'han', 'HanXRQChr03g0083841' => 'han', 'HanXRQChr03g0083881' => 'han', 'HanXRQChr03g0083901' => 'han', 'HanXRQChr03g0083921' => 'han', 'HanXRQChr03g0085331' => 'han', 'HanXRQChr03g0085361' => 'han', 'HanXRQChr03g0085411' => 'han', 'HanXRQChr03g0085421' => 'han', 'HanXRQChr03g0085431' => 'han', 'HanXRQChr08g0221991' => 'han', 'HanXRQChr11g0336061' => 'han', 'HanXRQChr11g0336411' => 'han', 'Haze_11234' => 'cav', 'Hma1.2p1_0549F.1_g177010' => 'hma', 'Hma1.2p1_0602F.1_g187630' => 'hma', 'Hund14876' => 'sun', 'Hund14879' => 'sun', 'Lalb_Chr06g0160741' => 'lal', 'Lalb_Chr21g0304781' => 'lal', 'Lj3A726G19' => 'lonja', 'Lj3A726T23' => 'lonja', 'Lj3A726T24' => 'lonja', 'Lj3A726T25' => 'lonja', 'Lj3A727T17' => 'lonja', 'Lj3C726T0' => 'lonja', 'Lj3C726T2' => 'lonja', 'Lj3P725T35' => 'lonja', 'Lj3P727T10' => 'lonja', 'Lj3P727T12' => 'lonja', 'Lj3P727T14' => 'lonja', 'Lj5g0023109' => 'lja', 'Lj6P646T44' => 'lonja', 'Lsat_1_v5_gn_6_75760' => 'lsa', 'Lsat_1_v5_gn_6_75800' => 'lsa', 'Lsat_1_v5_gn_6_75900' => 'lsa', 'Lsat_1_v5_gn_6_76240' => 'lsa', 'Lsat_1_v5_gn_6_76441' => 'lsa', 'Lsat_1_v5_gn_6_76700' => 'lsa', 'Lsat_1_v5_gn_6_76760' => 'lsa', 'Manes.15G033100' => 'mes', 'Mapoly0004s0074' => 'mpo', 'Mapoly0004s0075' => 'mpo', 'Mapoly0004s0163' => 'mpo', 'Mapoly0004s0164' => 'mpo', 'Mapoly0021s0018' => 'mpo', 'Mapoly0041s0136' => 'mpo', 'Mapoly0041s0137' => 'mpo', 'Mapoly0041s0138' => 'mpo', 'Mapoly0041s0139' => 'mpo', 'Mapoly0041s0141' => 'mpo', 'Mapoly0041s0142' => 'mpo', 'Mapoly0041s0143' => 'mpo', 'Mapoly0041s0144' => 'mpo', 'Mapoly0041s0145' => 'mpo', 'Mapoly0047s0106' => 'mpo', 'Mapoly0047s0108' => 'mpo', 'Mapoly0050s0051' => 'mpo', 'Mapoly0050s0052' => 'mpo', 'Mapoly0050s0053' => 'mpo', 'Mapoly0058s0013' => 'mpo', 'Mapoly0091s0078' => 'mpo', 'Mapoly0091s0079' => 'mpo', 'Mapoly0091s0080' => 'mpo', 'Mapoly0091s0081' => 'mpo', 'Mapoly0278s0004' => 'mpo', 'Mapoly0278s0005' => 'mpo', 'Mapoly0278s0006' => 'mpo', 'MBI11_g30648_MAGBIO' => 'mbi', 'MCO03G194' => 'mco', 'MCO03G590' => 'mco', 'MCO07G312' => 'mco', 'MCO10G318' => 'mco', 'MCO12G244' => 'mco', 'MCO13G148' => 'mco', 'MCO13G194' => 'mco', 'MCO16G238' => 'mco', 'MD06G1134100' => 'mdo', 'MD13G1200100' => 'mdo', 'MD13G1200300' => 'mdo', 'MD13G1200600' => 'mdo', 'MD14G1150400' => 'mdo', 'MD16G1200000' => 'mdo', 'Medtr1g102570' => 'mtr', 'Medtr1g102780' => 'mtr', 'Medtr1g102800' => 'mtr', 'Medtr1g102810' => 'mtr', 'Medtr1g102830' => 'mtr', 'MELO3C006499.2' => 'cme', 'Migut.G00385' => 'egut', 'MSTRG.4063' => 'ama', 'Nitab4.5_0000090g0260' => 'nta', 'Nitab4.5_0000977g0030' => 'nta', 'Nitab4.5_0002541g0040' => 'nta', 'Nitab4.5_0007068g0040' => 'nta', 'Nn005s41408' => 'nnu', 'Nn005s41410' => 'nnu', 'Oeu010310.1' => 'oeu', 'Oeu010311.1' => 'oeu', 'Oeu043472.1' => 'oeu', 'Os01g0246400' => 'osa', 'Os04g0267950' => 'osa', 'Os07g0178700' => 'osa', 'Os07g0178800' => 'osa', 'Peaxi162Scf00316g00046' => 'pax', 'Peaxi162Scf00316g00049' => 'pax', 'Peaxi162Scf00316g00059' => 'pax', 'Peaxi162Scf00316g00328' => 'pax', 'Peaxi162Scf00316g00329' => 'pax', 'Peaxi162Scf00316g00411' => 'pax', 'Peaxi162Scf00316g00521' => 'pax', 'Peaxi162Scf00492g00068' => 'pax', 'Peaxi162Scf35631g00002' => 'pax', 'PGR142G3720' => 'pgr', 'PGSC0003DMG400006442' => 'stu', 'Phvul.007G062000' => 'pvu', 'Potri.008G157750' => 'ptr', 'Potri.008G157900' => 'ptr', 'Potri.008G158000' => 'ptr', 'Potri.008G158200' => 'ptr', 'Pp3c11_7280' => 'ppa', 'Pp3c11_7980' => 'ppa', 'Pp3c12_19450' => 'ppa', 'Pp3c14_1480' => 'ppa', 'Pp3c14_1501' => 'ppa', 'Pp3c16_4900' => 'ppa', 'Pp3c16_5010' => 'ppa', 'Pp3c16_5060' => 'ppa', 'Pp3c19_18250' => 'ppa', 'Pp3c23_8530' => 'ppa', 'Pp3c23_8550' => 'ppa', 'Pp3c24_9670' => 'ppa', 'Pp3c2_21390' => 'ppa', 'Pp3c2_31380' => 'ppa', 'Pp3c3_16620' => 'ppa', 'Pp3c3_8090' => 'ppa', 'Pp3c3_8110' => 'ppa', 'Pp3c3_8130' => 'ppa', 'Pp3c3_8150' => 'ppa', 'Pp3c4_14320' => 'ppa', 'Pp3c6_2560' => 'ppa', 'Pp3c9_16700' => 'ppa', 'PRCOL_00000234' => 'pco', 'PRCOL_00000235' => 'pco', 'PRCOL_00000777' => 'pco', 'PRCOL_00002344' => 'pco', 'PRCOL_00002372' => 'pco', 'PRCOL_00006120' => 'pco', 'Prupe.1G021400' => 'ppe', 'Prupe.1G021500' => 'ppe', 'Prupe.1G021600' => 'ppe', 'Prupe.1G021700' => 'ppe', 'Prupe.1G021800' => 'ppe', 'Prupe.5G145100' => 'ppe', 'Psat6g204040' => 'psa', 'Psat6g204800' => 'psa', 'Psat6g204920' => 'psa', 'Psat6g204960' => 'psa', 'Psat6g205080' => 'psa', 'PSO017G0271' => 'pso', 'PSO017G1276' => 'pso', 'PSO017G1429' => 'pso', 'PSO017G1861' => 'pso', 'PSO017G2787' => 'pso', 'PSO017G4466' => 'pso', 'PSO017G5118' => 'pso', 'PSO017G5420' => 'pso', 'PSO063G3678' => 'pso', 'PSO210G0546' => 'pso', 'PSO317G0001' => 'pso', 'PSO357G0512' => 'pso', 'PSO478G2682' => 'pso', 'PSO647G0001' => 'pso', 'PSO675G0001' => 'pso', 'PSO675G2699' => 'pso', 'PSO675G2849' => 'pso', 'PSO675G4991' => 'pso', 'PSO689G0001' => 'pso', 'QL06p000916' => 'qlo', 'QL06p000921' => 'qlo', 'QL06p001398' => 'qlo', 'QL06p001407' => 'qlo', 'QL06p002031' => 'qlo', 'RcHm_v2.0_Chr4g0387791' => 'rch', 'RcHm_v2.0_Chr4g0387801' => 'rch', 'RcHm_v2.0_Chr6g0286501' => 'rch', 'RcHm_v2.0_Chr6g0286511' => 'rch', 'RcHm_v2.0_Chr6g0286521' => 'rch', 'RcHm_v2.0_Chr6g0286531' => 'rch', 'RcHm_v2.0_Chr7g0189141' => 'rch', 'Rhsim02G0028700' => 'rsi', 'Rhsim02G0028800' => 'rsi', 'Rhsim02G0028900' => 'rsi', 'Rhsim02G0029000' => 'rsi', 'Rhsim02G0029100' => 'rsi', 'Rhsim02G0029200' => 'rsi', 'Rhsim02G0029300' => 'rsi', 'Rhsim02G0029400' => 'rsi', 'Rhsim02G0029500' => 'rsi', 'Rhsim02G0029600' => 'rsi', 'RhsimUnG0024000' => 'rsi', 'RhsimUnG0024100' => 'rsi', 'RhsimUnG0024200' => 'rsi', 'RhsimUnG0024300' => 'rsi', 'RhsimUnG0024400' => 'rsi', 'RhsimUnG0024500' => 'rsi', 'RhsimUnG0024700' => 'rsi', 'RhsimUnG0024800' => 'rsi', 'RhsimUnG0024900' => 'rsi', 'RhsimUnG0025100' => 'rsi', 'Sabra08G0120200' => 'sbr', 'Sabra08G0120300' => 'sbr', 'Sabra08G0120500' => 'sbr', 'Sabra08G0120600' => 'sbr', 'Sabra10G0158900' => 'sbr', 'SalBow2G3492' => 'sbo', 'Sc13g0004760' => 'sci', 'Sc13g0004770' => 'sci', 'Sed0003417' => 'sed', 'Sed0019750' => 'sed', 'SEGI_03419' => 'sgi', 'SEGI_05907' => 'sgi', 'SEGI_10682' => 'sgi', 'SEGI_13528' => 'sgi', 'SEGI_16081' => 'sgi', 'SEGI_19370' => 'sgi', 'SEGI_21015' => 'sgi', 'SEGI_21944' => 'sgi', 'SEGI_32906' => 'sgi', 'SEGI_33093' => 'sgi', 'SEGI_36110' => 'sgi', 'SEGI_40397' => 'sgi', 'SGA_v2.0_scaffold191G40426' => 'sas', 'SGA_v2.0_scaffold353G49717' => 'sas', 'SGA_v2.0_scaffold50G18550' => 'sas', 'SMO119G0173' => 'smo', 'SMO172G0002' => 'smo', 'Solyc09g082690.3' => 'sly', 'Solyc09g082700.2' => 'sly', 'Sopen09g031550' => 'spe', 'Sopen09g031560' => 'spe', 'Sp3g20540' => 'spa', 'Sp7g07580' => 'spa', 'TAR134G0002' => 'tar', 'TAR236G0001' => 'tar', 'TAR365G0892' => 'tar', 'TAR636G0166' => 'tar', 'TAR636G0646' => 'tar', 'TAR636G0869' => 'tar', 'TAR636G1317' => 'tar', 'TAR636G1744' => 'tar', 'TAR636G3358' => 'tar', 'TAR636G3436' => 'tar', 'THA.LOC104803047' => 'tha', 'Thecc.04G238900' => 'tca', 'Thhalv10021557m.g' => 'esa', 'Thhalv10026318m.g' => 'esa', 'Thhalv10026335m.g' => 'esa', 'TPR.G17433' => 'tpr', 'TPR.G18915' => 'tpr', 'TPR.G26125' => 'tpr', 'TWI09G0677' => 'twi', 'TWI73G0287' => 'twi', 'unitig_748.g8326' => 'ugi', 'vmacro15370' => 'vma', 'vmacro15371' => 'vma', 'vmacro15372' => 'vma', 'vmacro15373' => 'vma', 'vmacro15374' => 'vma', 'VMungo0720G2826' => 'vmu', 'Zm00001eb116960' => 'zma', 'Zm00001eb301260' => 'zma', 'Zm00001eb301270' => 'zma' ), 'gf_id' => 'HOM05D001460', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001460' ), 'data_identifier' => 'HOM05D001460', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001460', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '433', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p22980' => 'bna', 'A01p32340' => 'bna', 'A03p42970' => 'bna', 'A05p25880' => 'bna', 'Aa31LG8G9320' => 'aar', 'Aa31LG8G9330' => 'aar', 'Aa31LG8G9340' => 'aar', 'Aa31sc221G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1034' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1528' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.829' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2222' => 'aag', 'Ah.12g058830' => 'amhyb', 'Ah.12g058840' => 'amhyb', 'AL3G37160' => 'aly', 'AL7G41310' => 'aly', 'Aqoxy5G00395' => 'aox', 'Aqoxy5G00396' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0C8NZA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5185HY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JZ1PRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MD3LS0' => 'arhy', 'AT3G22840' => 'ath', 'AT4G14690' => 'ath', 'ATR0665G054' => 'atr', 'Atru.chr4.2344' => 'acertr', 'Atru.chr4.2346' => 'acertr', 'Atru.chr4.2347' => 'acertr', 'Atru.chr4.2348' => 'acertr', 'Atru.chr4.2355' => 'acertr', 'Atru.chr4.2356' => 'acertr', 'Atru.chr4.2358' => 'acertr', 'Atru.chr4.2359' => 'acertr', 'Atru.chr4.2360' => 'acertr', 'Atru.chr4.2361' => 'acertr', 'AUR62030476' => 'cqu', 'AUR62030478' => 'cqu', 'AUR62030819' => 'cqu', 'AUR62030820' => 'cqu', 'BcaB03g14648' => 'bca', 'BcaB04g20492' => 'bca', 'BcaB06g26399' => 'bca', 'BcaC01g03416' => 'bca', 'BcaC01g03419' => 'bca', 'BcaC01g03421' => 'bca', 'BcaC01g03424' => 'bca', 'BcaC05g28012' => 'bca', 'BcaC09g49212' => 'bca', 'BcaC09g50140' => 'bca', 'BcaNung00346' => 'bca', 'BolC1t02785H' => 'bol', 'BolC1t04095H' => 'bol', 'BolC3t17545H' => 'bol', 'BolC5t32769H' => 'bol', 'BraA01t02211Z' => 'bra', 'BraA01t03359Z' => 'bra', 'BraA03t13441Z' => 'bra', 'BraA05t21476Z' => 'bra', 'C01p28420' => 'bna', 'C01p41350' => 'bna', 'C03p52750' => 'bna', 'C03p52780' => 'bna', 'C05p40270' => 'bna', 'CAN.G1437.9' => 'can', 'CANSAT78G0035' => 'cansat', 'CANSAT78G1036' => 'cansat', 'CANSAT78G2272' => 'cansat', 'CANSAT78G2478' => 'cansat', 'CARHR098700' => 'chi', 'CARHR221120' => 'chi', 'CARHR221150' => 'chi', 'Carub.0003s2297' => 'cru', 'Carub.0007s2749' => 'cru', 'Carub.0007s2750' => 'cru', 'Carub.0007s2751' => 'cru', 'Ca_10849_v3' => 'car', 'Cc03_g04300' => 'ccan', 'CDE02G3648' => 'cde', 'CDE05G0060' => 'cde', 'CDE05G0692' => 'cde', 'CDE05G2285' => 'cde', 'CDE05G2884' => 'cde', 'CDE05G3072' => 'cde', 'Cfa008439' => 'cfa', 'Cfa008441' => 'cfa', 'Cfa008443' => 'cfa', 'Cfa008448' => 'cfa', 'Ciclev10005974m.g' => 'ccl', 'Ciclev10006006m.g' => 'ccl', 'Ciclev10006775m.g' => 'ccl', 'CiPaw.02G120400' => 'cil', 'CiPaw.02G120500' => 'cil', 'CiPaw.02G120600' => 'cil', 'ClCG05G004850' => 'cla', 'COL.COLO4_21566' => 'col', 'Cpa.g.sc44.124' => 'cpa', 'Cre07.g320400' => 'cre', 'Cre07.g320450' => 'cre', 'Cre08.g384650' => 'cre', 'Cre09.g393173' => 'cre', 'Cre09.g394325' => 'cre', 'Cre14.g626750' => 'cre', 'Cre16.g679250' => 'cre', 'CsaV3_3G012890' => 'csa', 'CSS0010865' => 'camsi', 'CSS0044338' => 'camsi', 'DCAR_002366' => 'dca', 'DCAR_030687' => 'dca', 'DCAR_030688' => 'dca', 'Dinv14047' => 'din', 'Dinv14048' => 'din', 'Duzib151G0105' => 'dzi', 'Duzib151G0114' => 'dzi', 'Duzib212G1029' => 'dzi', 'ECA232G3536' => 'eca', 'ECA240G0786' => 'eca', 'ECA240G1802' => 'eca', 'ECA240G3760' => 'eca', 'ECA240G3920' => 'eca', 'EL10Ac5g12536' => 'bvu', 'EL10Ac5g12537' => 'bvu', 'EL10Ac5g12538' => 'bvu', 'Eucgr.B01004' => 'egr', 'Eucgr.B01006' => 'egr', 'Eucgr.B01007' => 'egr', 'Eucgr.B01008' => 'egr', 'Eucgr.B01895' => 'egr', 'Eucgr.B01896' => 'egr', 'FAN04G1456' => 'fan', 'FAN08G1769' => 'fan', 'FAN08G2160' => 'fan', 'FAN13G2403' => 'fan', 'FAN13G3303' => 'fan', 'FAN15G2435' => 'fan', 'FAN17G0672' => 'fan', 'FAN17G2441' => 'fan', 'FAN18G1024' => 'fan', 'FAN22G1458' => 'fan', 'FAN24G0037' => 'fan', 'FAN24G0429' => 'fan', 'FAN24G2387' => 'fan', 'FAN27G2746' => 'fan', 'FvH4_2g20400' => 'fve', 'FvH4_2g20420' => 'fve', 'FvH4_2g20430' => 'fve', 'FvH4_4g01270' => 'fve', 'FvH4_4g01290' => 'fve', 'FvH4_4g01300' => 'fve', 'FvH4_4g01310' => 'fve', 'FvH4_4g01330' => 'fve', 'FvH4_5g09070' => 'fve', 'Glyma.10G243800' => 'gma', 'Glyma.20G150600' => 'gma', 'Gohir.A09G219200' => 'ghi', 'Gohir.A09G219300' => 'ghi', 'Gohir.D09G221400' => 'ghi', 'Gohir.D09G221500' => 'ghi', 'Gorai.006G242600' => 'gra', 'Gorai.006G242700' => 'gra', 'GSVIVG01018044001' => 'vvi', 'HanXRQChr03g0083821' => 'han', 'HanXRQChr03g0083841' => 'han', 'HanXRQChr03g0083881' => 'han', 'HanXRQChr03g0083901' => 'han', 'HanXRQChr03g0083921' => 'han', 'HanXRQChr03g0085331' => 'han', 'HanXRQChr03g0085361' => 'han', 'HanXRQChr03g0085411' => 'han', 'HanXRQChr03g0085421' => 'han', 'HanXRQChr03g0085431' => 'han', 'HanXRQChr08g0221991' => 'han', 'HanXRQChr11g0336061' => 'han', 'HanXRQChr11g0336411' => 'han', 'Haze_11234' => 'cav', 'Hma1.2p1_0549F.1_g177010' => 'hma', 'Hma1.2p1_0602F.1_g187630' => 'hma', 'Hund14876' => 'sun', 'Hund14879' => 'sun', 'Lalb_Chr06g0160741' => 'lal', 'Lalb_Chr21g0304781' => 'lal', 'Lj3A726G19' => 'lonja', 'Lj3A726T23' => 'lonja', 'Lj3A726T24' => 'lonja', 'Lj3A726T25' => 'lonja', 'Lj3A727T17' => 'lonja', 'Lj3C726T0' => 'lonja', 'Lj3C726T2' => 'lonja', 'Lj3P725T35' => 'lonja', 'Lj3P727T10' => 'lonja', 'Lj3P727T12' => 'lonja', 'Lj3P727T14' => 'lonja', 'Lj5g0023109' => 'lja', 'Lj6P646T44' => 'lonja', 'Lsat_1_v5_gn_6_75760' => 'lsa', 'Lsat_1_v5_gn_6_75800' => 'lsa', 'Lsat_1_v5_gn_6_75900' => 'lsa', 'Lsat_1_v5_gn_6_76240' => 'lsa', 'Lsat_1_v5_gn_6_76441' => 'lsa', 'Lsat_1_v5_gn_6_76700' => 'lsa', 'Lsat_1_v5_gn_6_76760' => 'lsa', 'Manes.15G033100' => 'mes', 'Mapoly0004s0074' => 'mpo', 'Mapoly0004s0075' => 'mpo', 'Mapoly0004s0163' => 'mpo', 'Mapoly0004s0164' => 'mpo', 'Mapoly0021s0018' => 'mpo', 'Mapoly0041s0136' => 'mpo', 'Mapoly0041s0137' => 'mpo', 'Mapoly0041s0138' => 'mpo', 'Mapoly0041s0139' => 'mpo', 'Mapoly0041s0141' => 'mpo', 'Mapoly0041s0142' => 'mpo', 'Mapoly0041s0143' => 'mpo', 'Mapoly0041s0144' => 'mpo', 'Mapoly0041s0145' => 'mpo', 'Mapoly0047s0106' => 'mpo', 'Mapoly0047s0108' => 'mpo', 'Mapoly0050s0051' => 'mpo', 'Mapoly0050s0052' => 'mpo', 'Mapoly0050s0053' => 'mpo', 'Mapoly0058s0013' => 'mpo', 'Mapoly0091s0078' => 'mpo', 'Mapoly0091s0079' => 'mpo', 'Mapoly0091s0080' => 'mpo', 'Mapoly0091s0081' => 'mpo', 'Mapoly0278s0004' => 'mpo', 'Mapoly0278s0005' => 'mpo', 'Mapoly0278s0006' => 'mpo', 'MBI11_g30648_MAGBIO' => 'mbi', 'MCO03G194' => 'mco', 'MCO03G590' => 'mco', 'MCO07G312' => 'mco', 'MCO10G318' => 'mco', 'MCO12G244' => 'mco', 'MCO13G148' => 'mco', 'MCO13G194' => 'mco', 'MCO16G238' => 'mco', 'MD06G1134100' => 'mdo', 'MD13G1200100' => 'mdo', 'MD13G1200300' => 'mdo', 'MD13G1200600' => 'mdo', 'MD14G1150400' => 'mdo', 'MD16G1200000' => 'mdo', 'Medtr1g102570' => 'mtr', 'Medtr1g102780' => 'mtr', 'Medtr1g102800' => 'mtr', 'Medtr1g102810' => 'mtr', 'Medtr1g102830' => 'mtr', 'MELO3C006499.2' => 'cme', 'Migut.G00385' => 'egut', 'MSTRG.4063' => 'ama', 'Nitab4.5_0000090g0260' => 'nta', 'Nitab4.5_0000977g0030' => 'nta', 'Nitab4.5_0002541g0040' => 'nta', 'Nitab4.5_0007068g0040' => 'nta', 'Nn005s41408' => 'nnu', 'Nn005s41410' => 'nnu', 'Oeu010310.1' => 'oeu', 'Oeu010311.1' => 'oeu', 'Oeu043472.1' => 'oeu', 'Os01g0246400' => 'osa', 'Os04g0267950' => 'osa', 'Os07g0178700' => 'osa', 'Os07g0178800' => 'osa', 'Peaxi162Scf00316g00046' => 'pax', 'Peaxi162Scf00316g00049' => 'pax', 'Peaxi162Scf00316g00059' => 'pax', 'Peaxi162Scf00316g00328' => 'pax', 'Peaxi162Scf00316g00329' => 'pax', 'Peaxi162Scf00316g00411' => 'pax', 'Peaxi162Scf00316g00521' => 'pax', 'Peaxi162Scf00492g00068' => 'pax', 'Peaxi162Scf35631g00002' => 'pax', 'PGR142G3720' => 'pgr', 'PGSC0003DMG400006442' => 'stu', 'Phvul.007G062000' => 'pvu', 'Potri.008G157750' => 'ptr', 'Potri.008G157900' => 'ptr', 'Potri.008G158000' => 'ptr', 'Potri.008G158200' => 'ptr', 'Pp3c11_7280' => 'ppa', 'Pp3c11_7980' => 'ppa', 'Pp3c12_19450' => 'ppa', 'Pp3c14_1480' => 'ppa', 'Pp3c14_1501' => 'ppa', 'Pp3c16_4900' => 'ppa', 'Pp3c16_5010' => 'ppa', 'Pp3c16_5060' => 'ppa', 'Pp3c19_18250' => 'ppa', 'Pp3c23_8530' => 'ppa', 'Pp3c23_8550' => 'ppa', 'Pp3c24_9670' => 'ppa', 'Pp3c2_21390' => 'ppa', 'Pp3c2_31380' => 'ppa', 'Pp3c3_16620' => 'ppa', 'Pp3c3_8090' => 'ppa', 'Pp3c3_8110' => 'ppa', 'Pp3c3_8130' => 'ppa', 'Pp3c3_8150' => 'ppa', 'Pp3c4_14320' => 'ppa', 'Pp3c6_2560' => 'ppa', 'Pp3c9_16700' => 'ppa', 'PRCOL_00000234' => 'pco', 'PRCOL_00000235' => 'pco', 'PRCOL_00000777' => 'pco', 'PRCOL_00002344' => 'pco', 'PRCOL_00002372' => 'pco', 'PRCOL_00006120' => 'pco', 'Prupe.1G021400' => 'ppe', 'Prupe.1G021500' => 'ppe', 'Prupe.1G021600' => 'ppe', 'Prupe.1G021700' => 'ppe', 'Prupe.1G021800' => 'ppe', 'Prupe.5G145100' => 'ppe', 'Psat6g204040' => 'psa', 'Psat6g204800' => 'psa', 'Psat6g204920' => 'psa', 'Psat6g204960' => 'psa', 'Psat6g205080' => 'psa', 'PSO017G0271' => 'pso', 'PSO017G1276' => 'pso', 'PSO017G1429' => 'pso', 'PSO017G1861' => 'pso', 'PSO017G2787' => 'pso', 'PSO017G4466' => 'pso', 'PSO017G5118' => 'pso', 'PSO017G5420' => 'pso', 'PSO063G3678' => 'pso', 'PSO210G0546' => 'pso', 'PSO317G0001' => 'pso', 'PSO357G0512' => 'pso', 'PSO478G2682' => 'pso', 'PSO647G0001' => 'pso', 'PSO675G0001' => 'pso', 'PSO675G2699' => 'pso', 'PSO675G2849' => 'pso', 'PSO675G4991' => 'pso', 'PSO689G0001' => 'pso', 'QL06p000916' => 'qlo', 'QL06p000921' => 'qlo', 'QL06p001398' => 'qlo', 'QL06p001407' => 'qlo', 'QL06p002031' => 'qlo', 'RcHm_v2.0_Chr4g0387791' => 'rch', 'RcHm_v2.0_Chr4g0387801' => 'rch', 'RcHm_v2.0_Chr6g0286501' => 'rch', 'RcHm_v2.0_Chr6g0286511' => 'rch', 'RcHm_v2.0_Chr6g0286521' => 'rch', 'RcHm_v2.0_Chr6g0286531' => 'rch', 'RcHm_v2.0_Chr7g0189141' => 'rch', 'Rhsim02G0028700' => 'rsi', 'Rhsim02G0028800' => 'rsi', 'Rhsim02G0028900' => 'rsi', 'Rhsim02G0029000' => 'rsi', 'Rhsim02G0029100' => 'rsi', 'Rhsim02G0029200' => 'rsi', 'Rhsim02G0029300' => 'rsi', 'Rhsim02G0029400' => 'rsi', 'Rhsim02G0029500' => 'rsi', 'Rhsim02G0029600' => 'rsi', 'RhsimUnG0024000' => 'rsi', 'RhsimUnG0024100' => 'rsi', 'RhsimUnG0024200' => 'rsi', 'RhsimUnG0024300' => 'rsi', 'RhsimUnG0024400' => 'rsi', 'RhsimUnG0024500' => 'rsi', 'RhsimUnG0024700' => 'rsi', 'RhsimUnG0024800' => 'rsi', 'RhsimUnG0024900' => 'rsi', 'RhsimUnG0025100' => 'rsi', 'Sabra08G0120200' => 'sbr', 'Sabra08G0120300' => 'sbr', 'Sabra08G0120500' => 'sbr', 'Sabra08G0120600' => 'sbr', 'Sabra10G0158900' => 'sbr', 'SalBow2G3492' => 'sbo', 'Sc13g0004760' => 'sci', 'Sc13g0004770' => 'sci', 'Sed0003417' => 'sed', 'Sed0019750' => 'sed', 'SEGI_03419' => 'sgi', 'SEGI_05907' => 'sgi', 'SEGI_10682' => 'sgi', 'SEGI_13528' => 'sgi', 'SEGI_16081' => 'sgi', 'SEGI_19370' => 'sgi', 'SEGI_21015' => 'sgi', 'SEGI_21944' => 'sgi', 'SEGI_32906' => 'sgi', 'SEGI_33093' => 'sgi', 'SEGI_36110' => 'sgi', 'SEGI_40397' => 'sgi', 'SGA_v2.0_scaffold191G40426' => 'sas', 'SGA_v2.0_scaffold353G49717' => 'sas', 'SGA_v2.0_scaffold50G18550' => 'sas', 'SMO119G0173' => 'smo', 'SMO172G0002' => 'smo', 'Solyc09g082690.3' => 'sly', 'Solyc09g082700.2' => 'sly', 'Sopen09g031550' => 'spe', 'Sopen09g031560' => 'spe', 'Sp3g20540' => 'spa', 'Sp7g07580' => 'spa', 'TAR134G0002' => 'tar', 'TAR236G0001' => 'tar', 'TAR365G0892' => 'tar', 'TAR636G0166' => 'tar', 'TAR636G0646' => 'tar', 'TAR636G0869' => 'tar', 'TAR636G1317' => 'tar', 'TAR636G1744' => 'tar', 'TAR636G3358' => 'tar', 'TAR636G3436' => 'tar', 'THA.LOC104803047' => 'tha', 'Thecc.04G238900' => 'tca', 'Thhalv10021557m.g' => 'esa', 'Thhalv10026318m.g' => 'esa', 'Thhalv10026335m.g' => 'esa', 'TPR.G17433' => 'tpr', 'TPR.G18915' => 'tpr', 'TPR.G26125' => 'tpr', 'TWI09G0677' => 'twi', 'TWI73G0287' => 'twi', 'unitig_748.g8326' => 'ugi', 'vmacro15370' => 'vma', 'vmacro15371' => 'vma', 'vmacro15372' => 'vma', 'vmacro15373' => 'vma', 'vmacro15374' => 'vma', 'VMungo0720G2826' => 'vmu', 'Zm00001eb116960' => 'zma', 'Zm00001eb301260' => 'zma', 'Zm00001eb301270' => 'zma' ) $gf_id = 'HOM05D001460' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001460' ) $data_identifier = 'HOM05D001460' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 4, 'aag' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 2, 'aox' => (int) 2, 'arhy' => (int) 4, 'ath' => (int) 2, 'atr' => (int) 1, 'acertr' => (int) 10, 'cqu' => (int) 4, 'bca' => (int) 11, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 1, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 1, 'ccan' => (int) 1, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 1, 'col' => (int) 1, 'cpa' => (int) 1, 'cre' => (int) 7, 'csa' => (int) 1, 'camsi' => (int) 2, 'dca' => (int) 3, 'din' => (int) 2, 'dzi' => (int) 3, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 14, 'fve' => (int) 9, 'gma' => (int) 2, 'ghi' => (int) 4, 'gra' => (int) 2, 'vvi' => (int) 1, 'han' => (int) 13, 'cav' => (int) 1, 'hma' => (int) 2, 'sun' => (int) 2, 'lal' => (int) 2, 'lonja' => (int) 12, 'lja' => (int) 1, 'lsa' => (int) 7, 'mes' => (int) 1, 'mpo' => (int) 27, 'mbi' => (int) 1, 'mco' => (int) 8, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 1, 'egut' => (int) 1, 'ama' => (int) 1, 'nta' => (int) 4, 'nnu' => (int) 2, 'oeu' => (int) 3, 'osa' => (int) 4, 'pax' => (int) 9, 'pgr' => (int) 1, 'stu' => (int) 1, 'pvu' => (int) 1, 'ptr' => (int) 4, 'ppa' => (int) 22, 'pco' => (int) 6, 'ppe' => (int) 6, 'psa' => (int) 5, 'pso' => (int) 19, 'qlo' => (int) 5, 'rch' => (int) 7, 'rsi' => (int) 20, 'sbr' => (int) 5, 'sbo' => (int) 1, 'sci' => (int) 2, 'sed' => (int) 2, 'sgi' => (int) 12, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 2, 'tar' => (int) 10, 'tha' => (int) 1, 'tca' => (int) 1, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 2, 'ugi' => (int) 1, 'vma' => (int) 5, 'vmu' => (int) 1, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb301270' $species_info = array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ) $local_species = 'vmu' $disabled = '' $selected = '' $num_hits = (int) 0include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001460', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '433', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p22980' => 'bna', 'A01p32340' => 'bna', 'A03p42970' => 'bna', 'A05p25880' => 'bna', 'Aa31LG8G9320' => 'aar', 'Aa31LG8G9330' => 'aar', 'Aa31LG8G9340' => 'aar', 'Aa31sc221G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1034' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1528' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.829' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2222' => 'aag', 'Ah.12g058830' => 'amhyb', 'Ah.12g058840' => 'amhyb', 'AL3G37160' => 'aly', 'AL7G41310' => 'aly', 'Aqoxy5G00395' => 'aox', 'Aqoxy5G00396' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0C8NZA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5185HY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JZ1PRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MD3LS0' => 'arhy', 'AT3G22840' => 'ath', 'AT4G14690' => 'ath', 'ATR0665G054' => 'atr', 'Atru.chr4.2344' => 'acertr', 'Atru.chr4.2346' => 'acertr', 'Atru.chr4.2347' => 'acertr', 'Atru.chr4.2348' => 'acertr', 'Atru.chr4.2355' => 'acertr', 'Atru.chr4.2356' => 'acertr', 'Atru.chr4.2358' => 'acertr', 'Atru.chr4.2359' => 'acertr', 'Atru.chr4.2360' => 'acertr', 'Atru.chr4.2361' => 'acertr', 'AUR62030476' => 'cqu', 'AUR62030478' => 'cqu', 'AUR62030819' => 'cqu', 'AUR62030820' => 'cqu', 'BcaB03g14648' => 'bca', 'BcaB04g20492' => 'bca', 'BcaB06g26399' => 'bca', 'BcaC01g03416' => 'bca', 'BcaC01g03419' => 'bca', 'BcaC01g03421' => 'bca', 'BcaC01g03424' => 'bca', 'BcaC05g28012' => 'bca', 'BcaC09g49212' => 'bca', 'BcaC09g50140' => 'bca', 'BcaNung00346' => 'bca', 'BolC1t02785H' => 'bol', 'BolC1t04095H' => 'bol', 'BolC3t17545H' => 'bol', 'BolC5t32769H' => 'bol', 'BraA01t02211Z' => 'bra', 'BraA01t03359Z' => 'bra', 'BraA03t13441Z' => 'bra', 'BraA05t21476Z' => 'bra', 'C01p28420' => 'bna', 'C01p41350' => 'bna', 'C03p52750' => 'bna', 'C03p52780' => 'bna', 'C05p40270' => 'bna', 'CAN.G1437.9' => 'can', 'CANSAT78G0035' => 'cansat', 'CANSAT78G1036' => 'cansat', 'CANSAT78G2272' => 'cansat', 'CANSAT78G2478' => 'cansat', 'CARHR098700' => 'chi', 'CARHR221120' => 'chi', 'CARHR221150' => 'chi', 'Carub.0003s2297' => 'cru', 'Carub.0007s2749' => 'cru', 'Carub.0007s2750' => 'cru', 'Carub.0007s2751' => 'cru', 'Ca_10849_v3' => 'car', 'Cc03_g04300' => 'ccan', 'CDE02G3648' => 'cde', 'CDE05G0060' => 'cde', 'CDE05G0692' => 'cde', 'CDE05G2285' => 'cde', 'CDE05G2884' => 'cde', 'CDE05G3072' => 'cde', 'Cfa008439' => 'cfa', 'Cfa008441' => 'cfa', 'Cfa008443' => 'cfa', 'Cfa008448' => 'cfa', 'Ciclev10005974m.g' => 'ccl', 'Ciclev10006006m.g' => 'ccl', 'Ciclev10006775m.g' => 'ccl', 'CiPaw.02G120400' => 'cil', 'CiPaw.02G120500' => 'cil', 'CiPaw.02G120600' => 'cil', 'ClCG05G004850' => 'cla', 'COL.COLO4_21566' => 'col', 'Cpa.g.sc44.124' => 'cpa', 'Cre07.g320400' => 'cre', 'Cre07.g320450' => 'cre', 'Cre08.g384650' => 'cre', 'Cre09.g393173' => 'cre', 'Cre09.g394325' => 'cre', 'Cre14.g626750' => 'cre', 'Cre16.g679250' => 'cre', 'CsaV3_3G012890' => 'csa', 'CSS0010865' => 'camsi', 'CSS0044338' => 'camsi', 'DCAR_002366' => 'dca', 'DCAR_030687' => 'dca', 'DCAR_030688' => 'dca', 'Dinv14047' => 'din', 'Dinv14048' => 'din', 'Duzib151G0105' => 'dzi', 'Duzib151G0114' => 'dzi', 'Duzib212G1029' => 'dzi', 'ECA232G3536' => 'eca', 'ECA240G0786' => 'eca', 'ECA240G1802' => 'eca', 'ECA240G3760' => 'eca', 'ECA240G3920' => 'eca', 'EL10Ac5g12536' => 'bvu', 'EL10Ac5g12537' => 'bvu', 'EL10Ac5g12538' => 'bvu', 'Eucgr.B01004' => 'egr', 'Eucgr.B01006' => 'egr', 'Eucgr.B01007' => 'egr', 'Eucgr.B01008' => 'egr', 'Eucgr.B01895' => 'egr', 'Eucgr.B01896' => 'egr', 'FAN04G1456' => 'fan', 'FAN08G1769' => 'fan', 'FAN08G2160' => 'fan', 'FAN13G2403' => 'fan', 'FAN13G3303' => 'fan', 'FAN15G2435' => 'fan', 'FAN17G0672' => 'fan', 'FAN17G2441' => 'fan', 'FAN18G1024' => 'fan', 'FAN22G1458' => 'fan', 'FAN24G0037' => 'fan', 'FAN24G0429' => 'fan', 'FAN24G2387' => 'fan', 'FAN27G2746' => 'fan', 'FvH4_2g20400' => 'fve', 'FvH4_2g20420' => 'fve', 'FvH4_2g20430' => 'fve', 'FvH4_4g01270' => 'fve', 'FvH4_4g01290' => 'fve', 'FvH4_4g01300' => 'fve', 'FvH4_4g01310' => 'fve', 'FvH4_4g01330' => 'fve', 'FvH4_5g09070' => 'fve', 'Glyma.10G243800' => 'gma', 'Glyma.20G150600' => 'gma', 'Gohir.A09G219200' => 'ghi', 'Gohir.A09G219300' => 'ghi', 'Gohir.D09G221400' => 'ghi', 'Gohir.D09G221500' => 'ghi', 'Gorai.006G242600' => 'gra', 'Gorai.006G242700' => 'gra', 'GSVIVG01018044001' => 'vvi', 'HanXRQChr03g0083821' => 'han', 'HanXRQChr03g0083841' => 'han', 'HanXRQChr03g0083881' => 'han', 'HanXRQChr03g0083901' => 'han', 'HanXRQChr03g0083921' => 'han', 'HanXRQChr03g0085331' => 'han', 'HanXRQChr03g0085361' => 'han', 'HanXRQChr03g0085411' => 'han', 'HanXRQChr03g0085421' => 'han', 'HanXRQChr03g0085431' => 'han', 'HanXRQChr08g0221991' => 'han', 'HanXRQChr11g0336061' => 'han', 'HanXRQChr11g0336411' => 'han', 'Haze_11234' => 'cav', 'Hma1.2p1_0549F.1_g177010' => 'hma', 'Hma1.2p1_0602F.1_g187630' => 'hma', 'Hund14876' => 'sun', 'Hund14879' => 'sun', 'Lalb_Chr06g0160741' => 'lal', 'Lalb_Chr21g0304781' => 'lal', 'Lj3A726G19' => 'lonja', 'Lj3A726T23' => 'lonja', 'Lj3A726T24' => 'lonja', 'Lj3A726T25' => 'lonja', 'Lj3A727T17' => 'lonja', 'Lj3C726T0' => 'lonja', 'Lj3C726T2' => 'lonja', 'Lj3P725T35' => 'lonja', 'Lj3P727T10' => 'lonja', 'Lj3P727T12' => 'lonja', 'Lj3P727T14' => 'lonja', 'Lj5g0023109' => 'lja', 'Lj6P646T44' => 'lonja', 'Lsat_1_v5_gn_6_75760' => 'lsa', 'Lsat_1_v5_gn_6_75800' => 'lsa', 'Lsat_1_v5_gn_6_75900' => 'lsa', 'Lsat_1_v5_gn_6_76240' => 'lsa', 'Lsat_1_v5_gn_6_76441' => 'lsa', 'Lsat_1_v5_gn_6_76700' => 'lsa', 'Lsat_1_v5_gn_6_76760' => 'lsa', 'Manes.15G033100' => 'mes', 'Mapoly0004s0074' => 'mpo', 'Mapoly0004s0075' => 'mpo', 'Mapoly0004s0163' => 'mpo', 'Mapoly0004s0164' => 'mpo', 'Mapoly0021s0018' => 'mpo', 'Mapoly0041s0136' => 'mpo', 'Mapoly0041s0137' => 'mpo', 'Mapoly0041s0138' => 'mpo', 'Mapoly0041s0139' => 'mpo', 'Mapoly0041s0141' => 'mpo', 'Mapoly0041s0142' => 'mpo', 'Mapoly0041s0143' => 'mpo', 'Mapoly0041s0144' => 'mpo', 'Mapoly0041s0145' => 'mpo', 'Mapoly0047s0106' => 'mpo', 'Mapoly0047s0108' => 'mpo', 'Mapoly0050s0051' => 'mpo', 'Mapoly0050s0052' => 'mpo', 'Mapoly0050s0053' => 'mpo', 'Mapoly0058s0013' => 'mpo', 'Mapoly0091s0078' => 'mpo', 'Mapoly0091s0079' => 'mpo', 'Mapoly0091s0080' => 'mpo', 'Mapoly0091s0081' => 'mpo', 'Mapoly0278s0004' => 'mpo', 'Mapoly0278s0005' => 'mpo', 'Mapoly0278s0006' => 'mpo', 'MBI11_g30648_MAGBIO' => 'mbi', 'MCO03G194' => 'mco', 'MCO03G590' => 'mco', 'MCO07G312' => 'mco', 'MCO10G318' => 'mco', 'MCO12G244' => 'mco', 'MCO13G148' => 'mco', 'MCO13G194' => 'mco', 'MCO16G238' => 'mco', 'MD06G1134100' => 'mdo', 'MD13G1200100' => 'mdo', 'MD13G1200300' => 'mdo', 'MD13G1200600' => 'mdo', 'MD14G1150400' => 'mdo', 'MD16G1200000' => 'mdo', 'Medtr1g102570' => 'mtr', 'Medtr1g102780' => 'mtr', 'Medtr1g102800' => 'mtr', 'Medtr1g102810' => 'mtr', 'Medtr1g102830' => 'mtr', 'MELO3C006499.2' => 'cme', 'Migut.G00385' => 'egut', 'MSTRG.4063' => 'ama', 'Nitab4.5_0000090g0260' => 'nta', 'Nitab4.5_0000977g0030' => 'nta', 'Nitab4.5_0002541g0040' => 'nta', 'Nitab4.5_0007068g0040' => 'nta', 'Nn005s41408' => 'nnu', 'Nn005s41410' => 'nnu', 'Oeu010310.1' => 'oeu', 'Oeu010311.1' => 'oeu', 'Oeu043472.1' => 'oeu', 'Os01g0246400' => 'osa', 'Os04g0267950' => 'osa', 'Os07g0178700' => 'osa', 'Os07g0178800' => 'osa', 'Peaxi162Scf00316g00046' => 'pax', 'Peaxi162Scf00316g00049' => 'pax', 'Peaxi162Scf00316g00059' => 'pax', 'Peaxi162Scf00316g00328' => 'pax', 'Peaxi162Scf00316g00329' => 'pax', 'Peaxi162Scf00316g00411' => 'pax', 'Peaxi162Scf00316g00521' => 'pax', 'Peaxi162Scf00492g00068' => 'pax', 'Peaxi162Scf35631g00002' => 'pax', 'PGR142G3720' => 'pgr', 'PGSC0003DMG400006442' => 'stu', 'Phvul.007G062000' => 'pvu', 'Potri.008G157750' => 'ptr', 'Potri.008G157900' => 'ptr', 'Potri.008G158000' => 'ptr', 'Potri.008G158200' => 'ptr', 'Pp3c11_7280' => 'ppa', 'Pp3c11_7980' => 'ppa', 'Pp3c12_19450' => 'ppa', 'Pp3c14_1480' => 'ppa', 'Pp3c14_1501' => 'ppa', 'Pp3c16_4900' => 'ppa', 'Pp3c16_5010' => 'ppa', 'Pp3c16_5060' => 'ppa', 'Pp3c19_18250' => 'ppa', 'Pp3c23_8530' => 'ppa', 'Pp3c23_8550' => 'ppa', 'Pp3c24_9670' => 'ppa', 'Pp3c2_21390' => 'ppa', 'Pp3c2_31380' => 'ppa', 'Pp3c3_16620' => 'ppa', 'Pp3c3_8090' => 'ppa', 'Pp3c3_8110' => 'ppa', 'Pp3c3_8130' => 'ppa', 'Pp3c3_8150' => 'ppa', 'Pp3c4_14320' => 'ppa', 'Pp3c6_2560' => 'ppa', 'Pp3c9_16700' => 'ppa', 'PRCOL_00000234' => 'pco', 'PRCOL_00000235' => 'pco', 'PRCOL_00000777' => 'pco', 'PRCOL_00002344' => 'pco', 'PRCOL_00002372' => 'pco', 'PRCOL_00006120' => 'pco', 'Prupe.1G021400' => 'ppe', 'Prupe.1G021500' => 'ppe', 'Prupe.1G021600' => 'ppe', 'Prupe.1G021700' => 'ppe', 'Prupe.1G021800' => 'ppe', 'Prupe.5G145100' => 'ppe', 'Psat6g204040' => 'psa', 'Psat6g204800' => 'psa', 'Psat6g204920' => 'psa', 'Psat6g204960' => 'psa', 'Psat6g205080' => 'psa', 'PSO017G0271' => 'pso', 'PSO017G1276' => 'pso', 'PSO017G1429' => 'pso', 'PSO017G1861' => 'pso', 'PSO017G2787' => 'pso', 'PSO017G4466' => 'pso', 'PSO017G5118' => 'pso', 'PSO017G5420' => 'pso', 'PSO063G3678' => 'pso', 'PSO210G0546' => 'pso', 'PSO317G0001' => 'pso', 'PSO357G0512' => 'pso', 'PSO478G2682' => 'pso', 'PSO647G0001' => 'pso', 'PSO675G0001' => 'pso', 'PSO675G2699' => 'pso', 'PSO675G2849' => 'pso', 'PSO675G4991' => 'pso', 'PSO689G0001' => 'pso', 'QL06p000916' => 'qlo', 'QL06p000921' => 'qlo', 'QL06p001398' => 'qlo', 'QL06p001407' => 'qlo', 'QL06p002031' => 'qlo', 'RcHm_v2.0_Chr4g0387791' => 'rch', 'RcHm_v2.0_Chr4g0387801' => 'rch', 'RcHm_v2.0_Chr6g0286501' => 'rch', 'RcHm_v2.0_Chr6g0286511' => 'rch', 'RcHm_v2.0_Chr6g0286521' => 'rch', 'RcHm_v2.0_Chr6g0286531' => 'rch', 'RcHm_v2.0_Chr7g0189141' => 'rch', 'Rhsim02G0028700' => 'rsi', 'Rhsim02G0028800' => 'rsi', 'Rhsim02G0028900' => 'rsi', 'Rhsim02G0029000' => 'rsi', 'Rhsim02G0029100' => 'rsi', 'Rhsim02G0029200' => 'rsi', 'Rhsim02G0029300' => 'rsi', 'Rhsim02G0029400' => 'rsi', 'Rhsim02G0029500' => 'rsi', 'Rhsim02G0029600' => 'rsi', 'RhsimUnG0024000' => 'rsi', 'RhsimUnG0024100' => 'rsi', 'RhsimUnG0024200' => 'rsi', 'RhsimUnG0024300' => 'rsi', 'RhsimUnG0024400' => 'rsi', 'RhsimUnG0024500' => 'rsi', 'RhsimUnG0024700' => 'rsi', 'RhsimUnG0024800' => 'rsi', 'RhsimUnG0024900' => 'rsi', 'RhsimUnG0025100' => 'rsi', 'Sabra08G0120200' => 'sbr', 'Sabra08G0120300' => 'sbr', 'Sabra08G0120500' => 'sbr', 'Sabra08G0120600' => 'sbr', 'Sabra10G0158900' => 'sbr', 'SalBow2G3492' => 'sbo', 'Sc13g0004760' => 'sci', 'Sc13g0004770' => 'sci', 'Sed0003417' => 'sed', 'Sed0019750' => 'sed', 'SEGI_03419' => 'sgi', 'SEGI_05907' => 'sgi', 'SEGI_10682' => 'sgi', 'SEGI_13528' => 'sgi', 'SEGI_16081' => 'sgi', 'SEGI_19370' => 'sgi', 'SEGI_21015' => 'sgi', 'SEGI_21944' => 'sgi', 'SEGI_32906' => 'sgi', 'SEGI_33093' => 'sgi', 'SEGI_36110' => 'sgi', 'SEGI_40397' => 'sgi', 'SGA_v2.0_scaffold191G40426' => 'sas', 'SGA_v2.0_scaffold353G49717' => 'sas', 'SGA_v2.0_scaffold50G18550' => 'sas', 'SMO119G0173' => 'smo', 'SMO172G0002' => 'smo', 'Solyc09g082690.3' => 'sly', 'Solyc09g082700.2' => 'sly', 'Sopen09g031550' => 'spe', 'Sopen09g031560' => 'spe', 'Sp3g20540' => 'spa', 'Sp7g07580' => 'spa', 'TAR134G0002' => 'tar', 'TAR236G0001' => 'tar', 'TAR365G0892' => 'tar', 'TAR636G0166' => 'tar', 'TAR636G0646' => 'tar', 'TAR636G0869' => 'tar', 'TAR636G1317' => 'tar', 'TAR636G1744' => 'tar', 'TAR636G3358' => 'tar', 'TAR636G3436' => 'tar', 'THA.LOC104803047' => 'tha', 'Thecc.04G238900' => 'tca', 'Thhalv10021557m.g' => 'esa', 'Thhalv10026318m.g' => 'esa', 'Thhalv10026335m.g' => 'esa', 'TPR.G17433' => 'tpr', 'TPR.G18915' => 'tpr', 'TPR.G26125' => 'tpr', 'TWI09G0677' => 'twi', 'TWI73G0287' => 'twi', 'unitig_748.g8326' => 'ugi', 'vmacro15370' => 'vma', 'vmacro15371' => 'vma', 'vmacro15372' => 'vma', 'vmacro15373' => 'vma', 'vmacro15374' => 'vma', 'VMungo0720G2826' => 'vmu', 'Zm00001eb116960' => 'zma', 'Zm00001eb301260' => 'zma', 'Zm00001eb301270' => 'zma' ), 'gf_id' => 'HOM05D001460', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001460' ), 'data_identifier' => 'HOM05D001460', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001460', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '433', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p22980' => 'bna', 'A01p32340' => 'bna', 'A03p42970' => 'bna', 'A05p25880' => 'bna', 'Aa31LG8G9320' => 'aar', 'Aa31LG8G9330' => 'aar', 'Aa31LG8G9340' => 'aar', 'Aa31sc221G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1034' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1528' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.829' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2222' => 'aag', 'Ah.12g058830' => 'amhyb', 'Ah.12g058840' => 'amhyb', 'AL3G37160' => 'aly', 'AL7G41310' => 'aly', 'Aqoxy5G00395' => 'aox', 'Aqoxy5G00396' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0C8NZA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5185HY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JZ1PRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MD3LS0' => 'arhy', 'AT3G22840' => 'ath', 'AT4G14690' => 'ath', 'ATR0665G054' => 'atr', 'Atru.chr4.2344' => 'acertr', 'Atru.chr4.2346' => 'acertr', 'Atru.chr4.2347' => 'acertr', 'Atru.chr4.2348' => 'acertr', 'Atru.chr4.2355' => 'acertr', 'Atru.chr4.2356' => 'acertr', 'Atru.chr4.2358' => 'acertr', 'Atru.chr4.2359' => 'acertr', 'Atru.chr4.2360' => 'acertr', 'Atru.chr4.2361' => 'acertr', 'AUR62030476' => 'cqu', 'AUR62030478' => 'cqu', 'AUR62030819' => 'cqu', 'AUR62030820' => 'cqu', 'BcaB03g14648' => 'bca', 'BcaB04g20492' => 'bca', 'BcaB06g26399' => 'bca', 'BcaC01g03416' => 'bca', 'BcaC01g03419' => 'bca', 'BcaC01g03421' => 'bca', 'BcaC01g03424' => 'bca', 'BcaC05g28012' => 'bca', 'BcaC09g49212' => 'bca', 'BcaC09g50140' => 'bca', 'BcaNung00346' => 'bca', 'BolC1t02785H' => 'bol', 'BolC1t04095H' => 'bol', 'BolC3t17545H' => 'bol', 'BolC5t32769H' => 'bol', 'BraA01t02211Z' => 'bra', 'BraA01t03359Z' => 'bra', 'BraA03t13441Z' => 'bra', 'BraA05t21476Z' => 'bra', 'C01p28420' => 'bna', 'C01p41350' => 'bna', 'C03p52750' => 'bna', 'C03p52780' => 'bna', 'C05p40270' => 'bna', 'CAN.G1437.9' => 'can', 'CANSAT78G0035' => 'cansat', 'CANSAT78G1036' => 'cansat', 'CANSAT78G2272' => 'cansat', 'CANSAT78G2478' => 'cansat', 'CARHR098700' => 'chi', 'CARHR221120' => 'chi', 'CARHR221150' => 'chi', 'Carub.0003s2297' => 'cru', 'Carub.0007s2749' => 'cru', 'Carub.0007s2750' => 'cru', 'Carub.0007s2751' => 'cru', 'Ca_10849_v3' => 'car', 'Cc03_g04300' => 'ccan', 'CDE02G3648' => 'cde', 'CDE05G0060' => 'cde', 'CDE05G0692' => 'cde', 'CDE05G2285' => 'cde', 'CDE05G2884' => 'cde', 'CDE05G3072' => 'cde', 'Cfa008439' => 'cfa', 'Cfa008441' => 'cfa', 'Cfa008443' => 'cfa', 'Cfa008448' => 'cfa', 'Ciclev10005974m.g' => 'ccl', 'Ciclev10006006m.g' => 'ccl', 'Ciclev10006775m.g' => 'ccl', 'CiPaw.02G120400' => 'cil', 'CiPaw.02G120500' => 'cil', 'CiPaw.02G120600' => 'cil', 'ClCG05G004850' => 'cla', 'COL.COLO4_21566' => 'col', 'Cpa.g.sc44.124' => 'cpa', 'Cre07.g320400' => 'cre', 'Cre07.g320450' => 'cre', 'Cre08.g384650' => 'cre', 'Cre09.g393173' => 'cre', 'Cre09.g394325' => 'cre', 'Cre14.g626750' => 'cre', 'Cre16.g679250' => 'cre', 'CsaV3_3G012890' => 'csa', 'CSS0010865' => 'camsi', 'CSS0044338' => 'camsi', 'DCAR_002366' => 'dca', 'DCAR_030687' => 'dca', 'DCAR_030688' => 'dca', 'Dinv14047' => 'din', 'Dinv14048' => 'din', 'Duzib151G0105' => 'dzi', 'Duzib151G0114' => 'dzi', 'Duzib212G1029' => 'dzi', 'ECA232G3536' => 'eca', 'ECA240G0786' => 'eca', 'ECA240G1802' => 'eca', 'ECA240G3760' => 'eca', 'ECA240G3920' => 'eca', 'EL10Ac5g12536' => 'bvu', 'EL10Ac5g12537' => 'bvu', 'EL10Ac5g12538' => 'bvu', 'Eucgr.B01004' => 'egr', 'Eucgr.B01006' => 'egr', 'Eucgr.B01007' => 'egr', 'Eucgr.B01008' => 'egr', 'Eucgr.B01895' => 'egr', 'Eucgr.B01896' => 'egr', 'FAN04G1456' => 'fan', 'FAN08G1769' => 'fan', 'FAN08G2160' => 'fan', 'FAN13G2403' => 'fan', 'FAN13G3303' => 'fan', 'FAN15G2435' => 'fan', 'FAN17G0672' => 'fan', 'FAN17G2441' => 'fan', 'FAN18G1024' => 'fan', 'FAN22G1458' => 'fan', 'FAN24G0037' => 'fan', 'FAN24G0429' => 'fan', 'FAN24G2387' => 'fan', 'FAN27G2746' => 'fan', 'FvH4_2g20400' => 'fve', 'FvH4_2g20420' => 'fve', 'FvH4_2g20430' => 'fve', 'FvH4_4g01270' => 'fve', 'FvH4_4g01290' => 'fve', 'FvH4_4g01300' => 'fve', 'FvH4_4g01310' => 'fve', 'FvH4_4g01330' => 'fve', 'FvH4_5g09070' => 'fve', 'Glyma.10G243800' => 'gma', 'Glyma.20G150600' => 'gma', 'Gohir.A09G219200' => 'ghi', 'Gohir.A09G219300' => 'ghi', 'Gohir.D09G221400' => 'ghi', 'Gohir.D09G221500' => 'ghi', 'Gorai.006G242600' => 'gra', 'Gorai.006G242700' => 'gra', 'GSVIVG01018044001' => 'vvi', 'HanXRQChr03g0083821' => 'han', 'HanXRQChr03g0083841' => 'han', 'HanXRQChr03g0083881' => 'han', 'HanXRQChr03g0083901' => 'han', 'HanXRQChr03g0083921' => 'han', 'HanXRQChr03g0085331' => 'han', 'HanXRQChr03g0085361' => 'han', 'HanXRQChr03g0085411' => 'han', 'HanXRQChr03g0085421' => 'han', 'HanXRQChr03g0085431' => 'han', 'HanXRQChr08g0221991' => 'han', 'HanXRQChr11g0336061' => 'han', 'HanXRQChr11g0336411' => 'han', 'Haze_11234' => 'cav', 'Hma1.2p1_0549F.1_g177010' => 'hma', 'Hma1.2p1_0602F.1_g187630' => 'hma', 'Hund14876' => 'sun', 'Hund14879' => 'sun', 'Lalb_Chr06g0160741' => 'lal', 'Lalb_Chr21g0304781' => 'lal', 'Lj3A726G19' => 'lonja', 'Lj3A726T23' => 'lonja', 'Lj3A726T24' => 'lonja', 'Lj3A726T25' => 'lonja', 'Lj3A727T17' => 'lonja', 'Lj3C726T0' => 'lonja', 'Lj3C726T2' => 'lonja', 'Lj3P725T35' => 'lonja', 'Lj3P727T10' => 'lonja', 'Lj3P727T12' => 'lonja', 'Lj3P727T14' => 'lonja', 'Lj5g0023109' => 'lja', 'Lj6P646T44' => 'lonja', 'Lsat_1_v5_gn_6_75760' => 'lsa', 'Lsat_1_v5_gn_6_75800' => 'lsa', 'Lsat_1_v5_gn_6_75900' => 'lsa', 'Lsat_1_v5_gn_6_76240' => 'lsa', 'Lsat_1_v5_gn_6_76441' => 'lsa', 'Lsat_1_v5_gn_6_76700' => 'lsa', 'Lsat_1_v5_gn_6_76760' => 'lsa', 'Manes.15G033100' => 'mes', 'Mapoly0004s0074' => 'mpo', 'Mapoly0004s0075' => 'mpo', 'Mapoly0004s0163' => 'mpo', 'Mapoly0004s0164' => 'mpo', 'Mapoly0021s0018' => 'mpo', 'Mapoly0041s0136' => 'mpo', 'Mapoly0041s0137' => 'mpo', 'Mapoly0041s0138' => 'mpo', 'Mapoly0041s0139' => 'mpo', 'Mapoly0041s0141' => 'mpo', 'Mapoly0041s0142' => 'mpo', 'Mapoly0041s0143' => 'mpo', 'Mapoly0041s0144' => 'mpo', 'Mapoly0041s0145' => 'mpo', 'Mapoly0047s0106' => 'mpo', 'Mapoly0047s0108' => 'mpo', 'Mapoly0050s0051' => 'mpo', 'Mapoly0050s0052' => 'mpo', 'Mapoly0050s0053' => 'mpo', 'Mapoly0058s0013' => 'mpo', 'Mapoly0091s0078' => 'mpo', 'Mapoly0091s0079' => 'mpo', 'Mapoly0091s0080' => 'mpo', 'Mapoly0091s0081' => 'mpo', 'Mapoly0278s0004' => 'mpo', 'Mapoly0278s0005' => 'mpo', 'Mapoly0278s0006' => 'mpo', 'MBI11_g30648_MAGBIO' => 'mbi', 'MCO03G194' => 'mco', 'MCO03G590' => 'mco', 'MCO07G312' => 'mco', 'MCO10G318' => 'mco', 'MCO12G244' => 'mco', 'MCO13G148' => 'mco', 'MCO13G194' => 'mco', 'MCO16G238' => 'mco', 'MD06G1134100' => 'mdo', 'MD13G1200100' => 'mdo', 'MD13G1200300' => 'mdo', 'MD13G1200600' => 'mdo', 'MD14G1150400' => 'mdo', 'MD16G1200000' => 'mdo', 'Medtr1g102570' => 'mtr', 'Medtr1g102780' => 'mtr', 'Medtr1g102800' => 'mtr', 'Medtr1g102810' => 'mtr', 'Medtr1g102830' => 'mtr', 'MELO3C006499.2' => 'cme', 'Migut.G00385' => 'egut', 'MSTRG.4063' => 'ama', 'Nitab4.5_0000090g0260' => 'nta', 'Nitab4.5_0000977g0030' => 'nta', 'Nitab4.5_0002541g0040' => 'nta', 'Nitab4.5_0007068g0040' => 'nta', 'Nn005s41408' => 'nnu', 'Nn005s41410' => 'nnu', 'Oeu010310.1' => 'oeu', 'Oeu010311.1' => 'oeu', 'Oeu043472.1' => 'oeu', 'Os01g0246400' => 'osa', 'Os04g0267950' => 'osa', 'Os07g0178700' => 'osa', 'Os07g0178800' => 'osa', 'Peaxi162Scf00316g00046' => 'pax', 'Peaxi162Scf00316g00049' => 'pax', 'Peaxi162Scf00316g00059' => 'pax', 'Peaxi162Scf00316g00328' => 'pax', 'Peaxi162Scf00316g00329' => 'pax', 'Peaxi162Scf00316g00411' => 'pax', 'Peaxi162Scf00316g00521' => 'pax', 'Peaxi162Scf00492g00068' => 'pax', 'Peaxi162Scf35631g00002' => 'pax', 'PGR142G3720' => 'pgr', 'PGSC0003DMG400006442' => 'stu', 'Phvul.007G062000' => 'pvu', 'Potri.008G157750' => 'ptr', 'Potri.008G157900' => 'ptr', 'Potri.008G158000' => 'ptr', 'Potri.008G158200' => 'ptr', 'Pp3c11_7280' => 'ppa', 'Pp3c11_7980' => 'ppa', 'Pp3c12_19450' => 'ppa', 'Pp3c14_1480' => 'ppa', 'Pp3c14_1501' => 'ppa', 'Pp3c16_4900' => 'ppa', 'Pp3c16_5010' => 'ppa', 'Pp3c16_5060' => 'ppa', 'Pp3c19_18250' => 'ppa', 'Pp3c23_8530' => 'ppa', 'Pp3c23_8550' => 'ppa', 'Pp3c24_9670' => 'ppa', 'Pp3c2_21390' => 'ppa', 'Pp3c2_31380' => 'ppa', 'Pp3c3_16620' => 'ppa', 'Pp3c3_8090' => 'ppa', 'Pp3c3_8110' => 'ppa', 'Pp3c3_8130' => 'ppa', 'Pp3c3_8150' => 'ppa', 'Pp3c4_14320' => 'ppa', 'Pp3c6_2560' => 'ppa', 'Pp3c9_16700' => 'ppa', 'PRCOL_00000234' => 'pco', 'PRCOL_00000235' => 'pco', 'PRCOL_00000777' => 'pco', 'PRCOL_00002344' => 'pco', 'PRCOL_00002372' => 'pco', 'PRCOL_00006120' => 'pco', 'Prupe.1G021400' => 'ppe', 'Prupe.1G021500' => 'ppe', 'Prupe.1G021600' => 'ppe', 'Prupe.1G021700' => 'ppe', 'Prupe.1G021800' => 'ppe', 'Prupe.5G145100' => 'ppe', 'Psat6g204040' => 'psa', 'Psat6g204800' => 'psa', 'Psat6g204920' => 'psa', 'Psat6g204960' => 'psa', 'Psat6g205080' => 'psa', 'PSO017G0271' => 'pso', 'PSO017G1276' => 'pso', 'PSO017G1429' => 'pso', 'PSO017G1861' => 'pso', 'PSO017G2787' => 'pso', 'PSO017G4466' => 'pso', 'PSO017G5118' => 'pso', 'PSO017G5420' => 'pso', 'PSO063G3678' => 'pso', 'PSO210G0546' => 'pso', 'PSO317G0001' => 'pso', 'PSO357G0512' => 'pso', 'PSO478G2682' => 'pso', 'PSO647G0001' => 'pso', 'PSO675G0001' => 'pso', 'PSO675G2699' => 'pso', 'PSO675G2849' => 'pso', 'PSO675G4991' => 'pso', 'PSO689G0001' => 'pso', 'QL06p000916' => 'qlo', 'QL06p000921' => 'qlo', 'QL06p001398' => 'qlo', 'QL06p001407' => 'qlo', 'QL06p002031' => 'qlo', 'RcHm_v2.0_Chr4g0387791' => 'rch', 'RcHm_v2.0_Chr4g0387801' => 'rch', 'RcHm_v2.0_Chr6g0286501' => 'rch', 'RcHm_v2.0_Chr6g0286511' => 'rch', 'RcHm_v2.0_Chr6g0286521' => 'rch', 'RcHm_v2.0_Chr6g0286531' => 'rch', 'RcHm_v2.0_Chr7g0189141' => 'rch', 'Rhsim02G0028700' => 'rsi', 'Rhsim02G0028800' => 'rsi', 'Rhsim02G0028900' => 'rsi', 'Rhsim02G0029000' => 'rsi', 'Rhsim02G0029100' => 'rsi', 'Rhsim02G0029200' => 'rsi', 'Rhsim02G0029300' => 'rsi', 'Rhsim02G0029400' => 'rsi', 'Rhsim02G0029500' => 'rsi', 'Rhsim02G0029600' => 'rsi', 'RhsimUnG0024000' => 'rsi', 'RhsimUnG0024100' => 'rsi', 'RhsimUnG0024200' => 'rsi', 'RhsimUnG0024300' => 'rsi', 'RhsimUnG0024400' => 'rsi', 'RhsimUnG0024500' => 'rsi', 'RhsimUnG0024700' => 'rsi', 'RhsimUnG0024800' => 'rsi', 'RhsimUnG0024900' => 'rsi', 'RhsimUnG0025100' => 'rsi', 'Sabra08G0120200' => 'sbr', 'Sabra08G0120300' => 'sbr', 'Sabra08G0120500' => 'sbr', 'Sabra08G0120600' => 'sbr', 'Sabra10G0158900' => 'sbr', 'SalBow2G3492' => 'sbo', 'Sc13g0004760' => 'sci', 'Sc13g0004770' => 'sci', 'Sed0003417' => 'sed', 'Sed0019750' => 'sed', 'SEGI_03419' => 'sgi', 'SEGI_05907' => 'sgi', 'SEGI_10682' => 'sgi', 'SEGI_13528' => 'sgi', 'SEGI_16081' => 'sgi', 'SEGI_19370' => 'sgi', 'SEGI_21015' => 'sgi', 'SEGI_21944' => 'sgi', 'SEGI_32906' => 'sgi', 'SEGI_33093' => 'sgi', 'SEGI_36110' => 'sgi', 'SEGI_40397' => 'sgi', 'SGA_v2.0_scaffold191G40426' => 'sas', 'SGA_v2.0_scaffold353G49717' => 'sas', 'SGA_v2.0_scaffold50G18550' => 'sas', 'SMO119G0173' => 'smo', 'SMO172G0002' => 'smo', 'Solyc09g082690.3' => 'sly', 'Solyc09g082700.2' => 'sly', 'Sopen09g031550' => 'spe', 'Sopen09g031560' => 'spe', 'Sp3g20540' => 'spa', 'Sp7g07580' => 'spa', 'TAR134G0002' => 'tar', 'TAR236G0001' => 'tar', 'TAR365G0892' => 'tar', 'TAR636G0166' => 'tar', 'TAR636G0646' => 'tar', 'TAR636G0869' => 'tar', 'TAR636G1317' => 'tar', 'TAR636G1744' => 'tar', 'TAR636G3358' => 'tar', 'TAR636G3436' => 'tar', 'THA.LOC104803047' => 'tha', 'Thecc.04G238900' => 'tca', 'Thhalv10021557m.g' => 'esa', 'Thhalv10026318m.g' => 'esa', 'Thhalv10026335m.g' => 'esa', 'TPR.G17433' => 'tpr', 'TPR.G18915' => 'tpr', 'TPR.G26125' => 'tpr', 'TWI09G0677' => 'twi', 'TWI73G0287' => 'twi', 'unitig_748.g8326' => 'ugi', 'vmacro15370' => 'vma', 'vmacro15371' => 'vma', 'vmacro15372' => 'vma', 'vmacro15373' => 'vma', 'vmacro15374' => 'vma', 'VMungo0720G2826' => 'vmu', 'Zm00001eb116960' => 'zma', 'Zm00001eb301260' => 'zma', 'Zm00001eb301270' => 'zma' ) $gf_id = 'HOM05D001460' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001460' ) $data_identifier = 'HOM05D001460' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 4, 'aag' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 2, 'aox' => (int) 2, 'arhy' => (int) 4, 'ath' => (int) 2, 'atr' => (int) 1, 'acertr' => (int) 10, 'cqu' => (int) 4, 'bca' => (int) 11, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 1, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 1, 'ccan' => (int) 1, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 1, 'col' => (int) 1, 'cpa' => (int) 1, 'cre' => (int) 7, 'csa' => (int) 1, 'camsi' => (int) 2, 'dca' => (int) 3, 'din' => (int) 2, 'dzi' => (int) 3, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 14, 'fve' => (int) 9, 'gma' => (int) 2, 'ghi' => (int) 4, 'gra' => (int) 2, 'vvi' => (int) 1, 'han' => (int) 13, 'cav' => (int) 1, 'hma' => (int) 2, 'sun' => (int) 2, 'lal' => (int) 2, 'lonja' => (int) 12, 'lja' => (int) 1, 'lsa' => (int) 7, 'mes' => (int) 1, 'mpo' => (int) 27, 'mbi' => (int) 1, 'mco' => (int) 8, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 1, 'egut' => (int) 1, 'ama' => (int) 1, 'nta' => (int) 4, 'nnu' => (int) 2, 'oeu' => (int) 3, 'osa' => (int) 4, 'pax' => (int) 9, 'pgr' => (int) 1, 'stu' => (int) 1, 'pvu' => (int) 1, 'ptr' => (int) 4, 'ppa' => (int) 22, 'pco' => (int) 6, 'ppe' => (int) 6, 'psa' => (int) 5, 'pso' => (int) 19, 'qlo' => (int) 5, 'rch' => (int) 7, 'rsi' => (int) 20, 'sbr' => (int) 5, 'sbo' => (int) 1, 'sci' => (int) 2, 'sed' => (int) 2, 'sgi' => (int) 12, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 2, 'tar' => (int) 10, 'tha' => (int) 1, 'tca' => (int) 1, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 2, 'ugi' => (int) 1, 'vma' => (int) 5, 'vmu' => (int) 1, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb301270' $species_info = array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ) $local_species = 'vmu' $disabled = '' $selected = '' $num_hits = (int) 0
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001460', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '433', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p22980' => 'bna', 'A01p32340' => 'bna', 'A03p42970' => 'bna', 'A05p25880' => 'bna', 'Aa31LG8G9320' => 'aar', 'Aa31LG8G9330' => 'aar', 'Aa31LG8G9340' => 'aar', 'Aa31sc221G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1034' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1528' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.829' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2222' => 'aag', 'Ah.12g058830' => 'amhyb', 'Ah.12g058840' => 'amhyb', 'AL3G37160' => 'aly', 'AL7G41310' => 'aly', 'Aqoxy5G00395' => 'aox', 'Aqoxy5G00396' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0C8NZA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5185HY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JZ1PRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MD3LS0' => 'arhy', 'AT3G22840' => 'ath', 'AT4G14690' => 'ath', 'ATR0665G054' => 'atr', 'Atru.chr4.2344' => 'acertr', 'Atru.chr4.2346' => 'acertr', 'Atru.chr4.2347' => 'acertr', 'Atru.chr4.2348' => 'acertr', 'Atru.chr4.2355' => 'acertr', 'Atru.chr4.2356' => 'acertr', 'Atru.chr4.2358' => 'acertr', 'Atru.chr4.2359' => 'acertr', 'Atru.chr4.2360' => 'acertr', 'Atru.chr4.2361' => 'acertr', 'AUR62030476' => 'cqu', 'AUR62030478' => 'cqu', 'AUR62030819' => 'cqu', 'AUR62030820' => 'cqu', 'BcaB03g14648' => 'bca', 'BcaB04g20492' => 'bca', 'BcaB06g26399' => 'bca', 'BcaC01g03416' => 'bca', 'BcaC01g03419' => 'bca', 'BcaC01g03421' => 'bca', 'BcaC01g03424' => 'bca', 'BcaC05g28012' => 'bca', 'BcaC09g49212' => 'bca', 'BcaC09g50140' => 'bca', 'BcaNung00346' => 'bca', 'BolC1t02785H' => 'bol', 'BolC1t04095H' => 'bol', 'BolC3t17545H' => 'bol', 'BolC5t32769H' => 'bol', 'BraA01t02211Z' => 'bra', 'BraA01t03359Z' => 'bra', 'BraA03t13441Z' => 'bra', 'BraA05t21476Z' => 'bra', 'C01p28420' => 'bna', 'C01p41350' => 'bna', 'C03p52750' => 'bna', 'C03p52780' => 'bna', 'C05p40270' => 'bna', 'CAN.G1437.9' => 'can', 'CANSAT78G0035' => 'cansat', 'CANSAT78G1036' => 'cansat', 'CANSAT78G2272' => 'cansat', 'CANSAT78G2478' => 'cansat', 'CARHR098700' => 'chi', 'CARHR221120' => 'chi', 'CARHR221150' => 'chi', 'Carub.0003s2297' => 'cru', 'Carub.0007s2749' => 'cru', 'Carub.0007s2750' => 'cru', 'Carub.0007s2751' => 'cru', 'Ca_10849_v3' => 'car', 'Cc03_g04300' => 'ccan', 'CDE02G3648' => 'cde', 'CDE05G0060' => 'cde', 'CDE05G0692' => 'cde', 'CDE05G2285' => 'cde', 'CDE05G2884' => 'cde', 'CDE05G3072' => 'cde', 'Cfa008439' => 'cfa', 'Cfa008441' => 'cfa', 'Cfa008443' => 'cfa', 'Cfa008448' => 'cfa', 'Ciclev10005974m.g' => 'ccl', 'Ciclev10006006m.g' => 'ccl', 'Ciclev10006775m.g' => 'ccl', 'CiPaw.02G120400' => 'cil', 'CiPaw.02G120500' => 'cil', 'CiPaw.02G120600' => 'cil', 'ClCG05G004850' => 'cla', 'COL.COLO4_21566' => 'col', 'Cpa.g.sc44.124' => 'cpa', 'Cre07.g320400' => 'cre', 'Cre07.g320450' => 'cre', 'Cre08.g384650' => 'cre', 'Cre09.g393173' => 'cre', 'Cre09.g394325' => 'cre', 'Cre14.g626750' => 'cre', 'Cre16.g679250' => 'cre', 'CsaV3_3G012890' => 'csa', 'CSS0010865' => 'camsi', 'CSS0044338' => 'camsi', 'DCAR_002366' => 'dca', 'DCAR_030687' => 'dca', 'DCAR_030688' => 'dca', 'Dinv14047' => 'din', 'Dinv14048' => 'din', 'Duzib151G0105' => 'dzi', 'Duzib151G0114' => 'dzi', 'Duzib212G1029' => 'dzi', 'ECA232G3536' => 'eca', 'ECA240G0786' => 'eca', 'ECA240G1802' => 'eca', 'ECA240G3760' => 'eca', 'ECA240G3920' => 'eca', 'EL10Ac5g12536' => 'bvu', 'EL10Ac5g12537' => 'bvu', 'EL10Ac5g12538' => 'bvu', 'Eucgr.B01004' => 'egr', 'Eucgr.B01006' => 'egr', 'Eucgr.B01007' => 'egr', 'Eucgr.B01008' => 'egr', 'Eucgr.B01895' => 'egr', 'Eucgr.B01896' => 'egr', 'FAN04G1456' => 'fan', 'FAN08G1769' => 'fan', 'FAN08G2160' => 'fan', 'FAN13G2403' => 'fan', 'FAN13G3303' => 'fan', 'FAN15G2435' => 'fan', 'FAN17G0672' => 'fan', 'FAN17G2441' => 'fan', 'FAN18G1024' => 'fan', 'FAN22G1458' => 'fan', 'FAN24G0037' => 'fan', 'FAN24G0429' => 'fan', 'FAN24G2387' => 'fan', 'FAN27G2746' => 'fan', 'FvH4_2g20400' => 'fve', 'FvH4_2g20420' => 'fve', 'FvH4_2g20430' => 'fve', 'FvH4_4g01270' => 'fve', 'FvH4_4g01290' => 'fve', 'FvH4_4g01300' => 'fve', 'FvH4_4g01310' => 'fve', 'FvH4_4g01330' => 'fve', 'FvH4_5g09070' => 'fve', 'Glyma.10G243800' => 'gma', 'Glyma.20G150600' => 'gma', 'Gohir.A09G219200' => 'ghi', 'Gohir.A09G219300' => 'ghi', 'Gohir.D09G221400' => 'ghi', 'Gohir.D09G221500' => 'ghi', 'Gorai.006G242600' => 'gra', 'Gorai.006G242700' => 'gra', 'GSVIVG01018044001' => 'vvi', 'HanXRQChr03g0083821' => 'han', 'HanXRQChr03g0083841' => 'han', 'HanXRQChr03g0083881' => 'han', 'HanXRQChr03g0083901' => 'han', 'HanXRQChr03g0083921' => 'han', 'HanXRQChr03g0085331' => 'han', 'HanXRQChr03g0085361' => 'han', 'HanXRQChr03g0085411' => 'han', 'HanXRQChr03g0085421' => 'han', 'HanXRQChr03g0085431' => 'han', 'HanXRQChr08g0221991' => 'han', 'HanXRQChr11g0336061' => 'han', 'HanXRQChr11g0336411' => 'han', 'Haze_11234' => 'cav', 'Hma1.2p1_0549F.1_g177010' => 'hma', 'Hma1.2p1_0602F.1_g187630' => 'hma', 'Hund14876' => 'sun', 'Hund14879' => 'sun', 'Lalb_Chr06g0160741' => 'lal', 'Lalb_Chr21g0304781' => 'lal', 'Lj3A726G19' => 'lonja', 'Lj3A726T23' => 'lonja', 'Lj3A726T24' => 'lonja', 'Lj3A726T25' => 'lonja', 'Lj3A727T17' => 'lonja', 'Lj3C726T0' => 'lonja', 'Lj3C726T2' => 'lonja', 'Lj3P725T35' => 'lonja', 'Lj3P727T10' => 'lonja', 'Lj3P727T12' => 'lonja', 'Lj3P727T14' => 'lonja', 'Lj5g0023109' => 'lja', 'Lj6P646T44' => 'lonja', 'Lsat_1_v5_gn_6_75760' => 'lsa', 'Lsat_1_v5_gn_6_75800' => 'lsa', 'Lsat_1_v5_gn_6_75900' => 'lsa', 'Lsat_1_v5_gn_6_76240' => 'lsa', 'Lsat_1_v5_gn_6_76441' => 'lsa', 'Lsat_1_v5_gn_6_76700' => 'lsa', 'Lsat_1_v5_gn_6_76760' => 'lsa', 'Manes.15G033100' => 'mes', 'Mapoly0004s0074' => 'mpo', 'Mapoly0004s0075' => 'mpo', 'Mapoly0004s0163' => 'mpo', 'Mapoly0004s0164' => 'mpo', 'Mapoly0021s0018' => 'mpo', 'Mapoly0041s0136' => 'mpo', 'Mapoly0041s0137' => 'mpo', 'Mapoly0041s0138' => 'mpo', 'Mapoly0041s0139' => 'mpo', 'Mapoly0041s0141' => 'mpo', 'Mapoly0041s0142' => 'mpo', 'Mapoly0041s0143' => 'mpo', 'Mapoly0041s0144' => 'mpo', 'Mapoly0041s0145' => 'mpo', 'Mapoly0047s0106' => 'mpo', 'Mapoly0047s0108' => 'mpo', 'Mapoly0050s0051' => 'mpo', 'Mapoly0050s0052' => 'mpo', 'Mapoly0050s0053' => 'mpo', 'Mapoly0058s0013' => 'mpo', 'Mapoly0091s0078' => 'mpo', 'Mapoly0091s0079' => 'mpo', 'Mapoly0091s0080' => 'mpo', 'Mapoly0091s0081' => 'mpo', 'Mapoly0278s0004' => 'mpo', 'Mapoly0278s0005' => 'mpo', 'Mapoly0278s0006' => 'mpo', 'MBI11_g30648_MAGBIO' => 'mbi', 'MCO03G194' => 'mco', 'MCO03G590' => 'mco', 'MCO07G312' => 'mco', 'MCO10G318' => 'mco', 'MCO12G244' => 'mco', 'MCO13G148' => 'mco', 'MCO13G194' => 'mco', 'MCO16G238' => 'mco', 'MD06G1134100' => 'mdo', 'MD13G1200100' => 'mdo', 'MD13G1200300' => 'mdo', 'MD13G1200600' => 'mdo', 'MD14G1150400' => 'mdo', 'MD16G1200000' => 'mdo', 'Medtr1g102570' => 'mtr', 'Medtr1g102780' => 'mtr', 'Medtr1g102800' => 'mtr', 'Medtr1g102810' => 'mtr', 'Medtr1g102830' => 'mtr', 'MELO3C006499.2' => 'cme', 'Migut.G00385' => 'egut', 'MSTRG.4063' => 'ama', 'Nitab4.5_0000090g0260' => 'nta', 'Nitab4.5_0000977g0030' => 'nta', 'Nitab4.5_0002541g0040' => 'nta', 'Nitab4.5_0007068g0040' => 'nta', 'Nn005s41408' => 'nnu', 'Nn005s41410' => 'nnu', 'Oeu010310.1' => 'oeu', 'Oeu010311.1' => 'oeu', 'Oeu043472.1' => 'oeu', 'Os01g0246400' => 'osa', 'Os04g0267950' => 'osa', 'Os07g0178700' => 'osa', 'Os07g0178800' => 'osa', 'Peaxi162Scf00316g00046' => 'pax', 'Peaxi162Scf00316g00049' => 'pax', 'Peaxi162Scf00316g00059' => 'pax', 'Peaxi162Scf00316g00328' => 'pax', 'Peaxi162Scf00316g00329' => 'pax', 'Peaxi162Scf00316g00411' => 'pax', 'Peaxi162Scf00316g00521' => 'pax', 'Peaxi162Scf00492g00068' => 'pax', 'Peaxi162Scf35631g00002' => 'pax', 'PGR142G3720' => 'pgr', 'PGSC0003DMG400006442' => 'stu', 'Phvul.007G062000' => 'pvu', 'Potri.008G157750' => 'ptr', 'Potri.008G157900' => 'ptr', 'Potri.008G158000' => 'ptr', 'Potri.008G158200' => 'ptr', 'Pp3c11_7280' => 'ppa', 'Pp3c11_7980' => 'ppa', 'Pp3c12_19450' => 'ppa', 'Pp3c14_1480' => 'ppa', 'Pp3c14_1501' => 'ppa', 'Pp3c16_4900' => 'ppa', 'Pp3c16_5010' => 'ppa', 'Pp3c16_5060' => 'ppa', 'Pp3c19_18250' => 'ppa', 'Pp3c23_8530' => 'ppa', 'Pp3c23_8550' => 'ppa', 'Pp3c24_9670' => 'ppa', 'Pp3c2_21390' => 'ppa', 'Pp3c2_31380' => 'ppa', 'Pp3c3_16620' => 'ppa', 'Pp3c3_8090' => 'ppa', 'Pp3c3_8110' => 'ppa', 'Pp3c3_8130' => 'ppa', 'Pp3c3_8150' => 'ppa', 'Pp3c4_14320' => 'ppa', 'Pp3c6_2560' => 'ppa', 'Pp3c9_16700' => 'ppa', 'PRCOL_00000234' => 'pco', 'PRCOL_00000235' => 'pco', 'PRCOL_00000777' => 'pco', 'PRCOL_00002344' => 'pco', 'PRCOL_00002372' => 'pco', 'PRCOL_00006120' => 'pco', 'Prupe.1G021400' => 'ppe', 'Prupe.1G021500' => 'ppe', 'Prupe.1G021600' => 'ppe', 'Prupe.1G021700' => 'ppe', 'Prupe.1G021800' => 'ppe', 'Prupe.5G145100' => 'ppe', 'Psat6g204040' => 'psa', 'Psat6g204800' => 'psa', 'Psat6g204920' => 'psa', 'Psat6g204960' => 'psa', 'Psat6g205080' => 'psa', 'PSO017G0271' => 'pso', 'PSO017G1276' => 'pso', 'PSO017G1429' => 'pso', 'PSO017G1861' => 'pso', 'PSO017G2787' => 'pso', 'PSO017G4466' => 'pso', 'PSO017G5118' => 'pso', 'PSO017G5420' => 'pso', 'PSO063G3678' => 'pso', 'PSO210G0546' => 'pso', 'PSO317G0001' => 'pso', 'PSO357G0512' => 'pso', 'PSO478G2682' => 'pso', 'PSO647G0001' => 'pso', 'PSO675G0001' => 'pso', 'PSO675G2699' => 'pso', 'PSO675G2849' => 'pso', 'PSO675G4991' => 'pso', 'PSO689G0001' => 'pso', 'QL06p000916' => 'qlo', 'QL06p000921' => 'qlo', 'QL06p001398' => 'qlo', 'QL06p001407' => 'qlo', 'QL06p002031' => 'qlo', 'RcHm_v2.0_Chr4g0387791' => 'rch', 'RcHm_v2.0_Chr4g0387801' => 'rch', 'RcHm_v2.0_Chr6g0286501' => 'rch', 'RcHm_v2.0_Chr6g0286511' => 'rch', 'RcHm_v2.0_Chr6g0286521' => 'rch', 'RcHm_v2.0_Chr6g0286531' => 'rch', 'RcHm_v2.0_Chr7g0189141' => 'rch', 'Rhsim02G0028700' => 'rsi', 'Rhsim02G0028800' => 'rsi', 'Rhsim02G0028900' => 'rsi', 'Rhsim02G0029000' => 'rsi', 'Rhsim02G0029100' => 'rsi', 'Rhsim02G0029200' => 'rsi', 'Rhsim02G0029300' => 'rsi', 'Rhsim02G0029400' => 'rsi', 'Rhsim02G0029500' => 'rsi', 'Rhsim02G0029600' => 'rsi', 'RhsimUnG0024000' => 'rsi', 'RhsimUnG0024100' => 'rsi', 'RhsimUnG0024200' => 'rsi', 'RhsimUnG0024300' => 'rsi', 'RhsimUnG0024400' => 'rsi', 'RhsimUnG0024500' => 'rsi', 'RhsimUnG0024700' => 'rsi', 'RhsimUnG0024800' => 'rsi', 'RhsimUnG0024900' => 'rsi', 'RhsimUnG0025100' => 'rsi', 'Sabra08G0120200' => 'sbr', 'Sabra08G0120300' => 'sbr', 'Sabra08G0120500' => 'sbr', 'Sabra08G0120600' => 'sbr', 'Sabra10G0158900' => 'sbr', 'SalBow2G3492' => 'sbo', 'Sc13g0004760' => 'sci', 'Sc13g0004770' => 'sci', 'Sed0003417' => 'sed', 'Sed0019750' => 'sed', 'SEGI_03419' => 'sgi', 'SEGI_05907' => 'sgi', 'SEGI_10682' => 'sgi', 'SEGI_13528' => 'sgi', 'SEGI_16081' => 'sgi', 'SEGI_19370' => 'sgi', 'SEGI_21015' => 'sgi', 'SEGI_21944' => 'sgi', 'SEGI_32906' => 'sgi', 'SEGI_33093' => 'sgi', 'SEGI_36110' => 'sgi', 'SEGI_40397' => 'sgi', 'SGA_v2.0_scaffold191G40426' => 'sas', 'SGA_v2.0_scaffold353G49717' => 'sas', 'SGA_v2.0_scaffold50G18550' => 'sas', 'SMO119G0173' => 'smo', 'SMO172G0002' => 'smo', 'Solyc09g082690.3' => 'sly', 'Solyc09g082700.2' => 'sly', 'Sopen09g031550' => 'spe', 'Sopen09g031560' => 'spe', 'Sp3g20540' => 'spa', 'Sp7g07580' => 'spa', 'TAR134G0002' => 'tar', 'TAR236G0001' => 'tar', 'TAR365G0892' => 'tar', 'TAR636G0166' => 'tar', 'TAR636G0646' => 'tar', 'TAR636G0869' => 'tar', 'TAR636G1317' => 'tar', 'TAR636G1744' => 'tar', 'TAR636G3358' => 'tar', 'TAR636G3436' => 'tar', 'THA.LOC104803047' => 'tha', 'Thecc.04G238900' => 'tca', 'Thhalv10021557m.g' => 'esa', 'Thhalv10026318m.g' => 'esa', 'Thhalv10026335m.g' => 'esa', 'TPR.G17433' => 'tpr', 'TPR.G18915' => 'tpr', 'TPR.G26125' => 'tpr', 'TWI09G0677' => 'twi', 'TWI73G0287' => 'twi', 'unitig_748.g8326' => 'ugi', 'vmacro15370' => 'vma', 'vmacro15371' => 'vma', 'vmacro15372' => 'vma', 'vmacro15373' => 'vma', 'vmacro15374' => 'vma', 'VMungo0720G2826' => 'vmu', 'Zm00001eb116960' => 'zma', 'Zm00001eb301260' => 'zma', 'Zm00001eb301270' => 'zma' ), 'gf_id' => 'HOM05D001460', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001460' ), 'data_identifier' => 'HOM05D001460', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001460', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '433', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p22980' => 'bna', 'A01p32340' => 'bna', 'A03p42970' => 'bna', 'A05p25880' => 'bna', 'Aa31LG8G9320' => 'aar', 'Aa31LG8G9330' => 'aar', 'Aa31LG8G9340' => 'aar', 'Aa31sc221G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1034' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1528' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.829' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2222' => 'aag', 'Ah.12g058830' => 'amhyb', 'Ah.12g058840' => 'amhyb', 'AL3G37160' => 'aly', 'AL7G41310' => 'aly', 'Aqoxy5G00395' => 'aox', 'Aqoxy5G00396' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0C8NZA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5185HY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JZ1PRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MD3LS0' => 'arhy', 'AT3G22840' => 'ath', 'AT4G14690' => 'ath', 'ATR0665G054' => 'atr', 'Atru.chr4.2344' => 'acertr', 'Atru.chr4.2346' => 'acertr', 'Atru.chr4.2347' => 'acertr', 'Atru.chr4.2348' => 'acertr', 'Atru.chr4.2355' => 'acertr', 'Atru.chr4.2356' => 'acertr', 'Atru.chr4.2358' => 'acertr', 'Atru.chr4.2359' => 'acertr', 'Atru.chr4.2360' => 'acertr', 'Atru.chr4.2361' => 'acertr', 'AUR62030476' => 'cqu', 'AUR62030478' => 'cqu', 'AUR62030819' => 'cqu', 'AUR62030820' => 'cqu', 'BcaB03g14648' => 'bca', 'BcaB04g20492' => 'bca', 'BcaB06g26399' => 'bca', 'BcaC01g03416' => 'bca', 'BcaC01g03419' => 'bca', 'BcaC01g03421' => 'bca', 'BcaC01g03424' => 'bca', 'BcaC05g28012' => 'bca', 'BcaC09g49212' => 'bca', 'BcaC09g50140' => 'bca', 'BcaNung00346' => 'bca', 'BolC1t02785H' => 'bol', 'BolC1t04095H' => 'bol', 'BolC3t17545H' => 'bol', 'BolC5t32769H' => 'bol', 'BraA01t02211Z' => 'bra', 'BraA01t03359Z' => 'bra', 'BraA03t13441Z' => 'bra', 'BraA05t21476Z' => 'bra', 'C01p28420' => 'bna', 'C01p41350' => 'bna', 'C03p52750' => 'bna', 'C03p52780' => 'bna', 'C05p40270' => 'bna', 'CAN.G1437.9' => 'can', 'CANSAT78G0035' => 'cansat', 'CANSAT78G1036' => 'cansat', 'CANSAT78G2272' => 'cansat', 'CANSAT78G2478' => 'cansat', 'CARHR098700' => 'chi', 'CARHR221120' => 'chi', 'CARHR221150' => 'chi', 'Carub.0003s2297' => 'cru', 'Carub.0007s2749' => 'cru', 'Carub.0007s2750' => 'cru', 'Carub.0007s2751' => 'cru', 'Ca_10849_v3' => 'car', 'Cc03_g04300' => 'ccan', 'CDE02G3648' => 'cde', 'CDE05G0060' => 'cde', 'CDE05G0692' => 'cde', 'CDE05G2285' => 'cde', 'CDE05G2884' => 'cde', 'CDE05G3072' => 'cde', 'Cfa008439' => 'cfa', 'Cfa008441' => 'cfa', 'Cfa008443' => 'cfa', 'Cfa008448' => 'cfa', 'Ciclev10005974m.g' => 'ccl', 'Ciclev10006006m.g' => 'ccl', 'Ciclev10006775m.g' => 'ccl', 'CiPaw.02G120400' => 'cil', 'CiPaw.02G120500' => 'cil', 'CiPaw.02G120600' => 'cil', 'ClCG05G004850' => 'cla', 'COL.COLO4_21566' => 'col', 'Cpa.g.sc44.124' => 'cpa', 'Cre07.g320400' => 'cre', 'Cre07.g320450' => 'cre', 'Cre08.g384650' => 'cre', 'Cre09.g393173' => 'cre', 'Cre09.g394325' => 'cre', 'Cre14.g626750' => 'cre', 'Cre16.g679250' => 'cre', 'CsaV3_3G012890' => 'csa', 'CSS0010865' => 'camsi', 'CSS0044338' => 'camsi', 'DCAR_002366' => 'dca', 'DCAR_030687' => 'dca', 'DCAR_030688' => 'dca', 'Dinv14047' => 'din', 'Dinv14048' => 'din', 'Duzib151G0105' => 'dzi', 'Duzib151G0114' => 'dzi', 'Duzib212G1029' => 'dzi', 'ECA232G3536' => 'eca', 'ECA240G0786' => 'eca', 'ECA240G1802' => 'eca', 'ECA240G3760' => 'eca', 'ECA240G3920' => 'eca', 'EL10Ac5g12536' => 'bvu', 'EL10Ac5g12537' => 'bvu', 'EL10Ac5g12538' => 'bvu', 'Eucgr.B01004' => 'egr', 'Eucgr.B01006' => 'egr', 'Eucgr.B01007' => 'egr', 'Eucgr.B01008' => 'egr', 'Eucgr.B01895' => 'egr', 'Eucgr.B01896' => 'egr', 'FAN04G1456' => 'fan', 'FAN08G1769' => 'fan', 'FAN08G2160' => 'fan', 'FAN13G2403' => 'fan', 'FAN13G3303' => 'fan', 'FAN15G2435' => 'fan', 'FAN17G0672' => 'fan', 'FAN17G2441' => 'fan', 'FAN18G1024' => 'fan', 'FAN22G1458' => 'fan', 'FAN24G0037' => 'fan', 'FAN24G0429' => 'fan', 'FAN24G2387' => 'fan', 'FAN27G2746' => 'fan', 'FvH4_2g20400' => 'fve', 'FvH4_2g20420' => 'fve', 'FvH4_2g20430' => 'fve', 'FvH4_4g01270' => 'fve', 'FvH4_4g01290' => 'fve', 'FvH4_4g01300' => 'fve', 'FvH4_4g01310' => 'fve', 'FvH4_4g01330' => 'fve', 'FvH4_5g09070' => 'fve', 'Glyma.10G243800' => 'gma', 'Glyma.20G150600' => 'gma', 'Gohir.A09G219200' => 'ghi', 'Gohir.A09G219300' => 'ghi', 'Gohir.D09G221400' => 'ghi', 'Gohir.D09G221500' => 'ghi', 'Gorai.006G242600' => 'gra', 'Gorai.006G242700' => 'gra', 'GSVIVG01018044001' => 'vvi', 'HanXRQChr03g0083821' => 'han', 'HanXRQChr03g0083841' => 'han', 'HanXRQChr03g0083881' => 'han', 'HanXRQChr03g0083901' => 'han', 'HanXRQChr03g0083921' => 'han', 'HanXRQChr03g0085331' => 'han', 'HanXRQChr03g0085361' => 'han', 'HanXRQChr03g0085411' => 'han', 'HanXRQChr03g0085421' => 'han', 'HanXRQChr03g0085431' => 'han', 'HanXRQChr08g0221991' => 'han', 'HanXRQChr11g0336061' => 'han', 'HanXRQChr11g0336411' => 'han', 'Haze_11234' => 'cav', 'Hma1.2p1_0549F.1_g177010' => 'hma', 'Hma1.2p1_0602F.1_g187630' => 'hma', 'Hund14876' => 'sun', 'Hund14879' => 'sun', 'Lalb_Chr06g0160741' => 'lal', 'Lalb_Chr21g0304781' => 'lal', 'Lj3A726G19' => 'lonja', 'Lj3A726T23' => 'lonja', 'Lj3A726T24' => 'lonja', 'Lj3A726T25' => 'lonja', 'Lj3A727T17' => 'lonja', 'Lj3C726T0' => 'lonja', 'Lj3C726T2' => 'lonja', 'Lj3P725T35' => 'lonja', 'Lj3P727T10' => 'lonja', 'Lj3P727T12' => 'lonja', 'Lj3P727T14' => 'lonja', 'Lj5g0023109' => 'lja', 'Lj6P646T44' => 'lonja', 'Lsat_1_v5_gn_6_75760' => 'lsa', 'Lsat_1_v5_gn_6_75800' => 'lsa', 'Lsat_1_v5_gn_6_75900' => 'lsa', 'Lsat_1_v5_gn_6_76240' => 'lsa', 'Lsat_1_v5_gn_6_76441' => 'lsa', 'Lsat_1_v5_gn_6_76700' => 'lsa', 'Lsat_1_v5_gn_6_76760' => 'lsa', 'Manes.15G033100' => 'mes', 'Mapoly0004s0074' => 'mpo', 'Mapoly0004s0075' => 'mpo', 'Mapoly0004s0163' => 'mpo', 'Mapoly0004s0164' => 'mpo', 'Mapoly0021s0018' => 'mpo', 'Mapoly0041s0136' => 'mpo', 'Mapoly0041s0137' => 'mpo', 'Mapoly0041s0138' => 'mpo', 'Mapoly0041s0139' => 'mpo', 'Mapoly0041s0141' => 'mpo', 'Mapoly0041s0142' => 'mpo', 'Mapoly0041s0143' => 'mpo', 'Mapoly0041s0144' => 'mpo', 'Mapoly0041s0145' => 'mpo', 'Mapoly0047s0106' => 'mpo', 'Mapoly0047s0108' => 'mpo', 'Mapoly0050s0051' => 'mpo', 'Mapoly0050s0052' => 'mpo', 'Mapoly0050s0053' => 'mpo', 'Mapoly0058s0013' => 'mpo', 'Mapoly0091s0078' => 'mpo', 'Mapoly0091s0079' => 'mpo', 'Mapoly0091s0080' => 'mpo', 'Mapoly0091s0081' => 'mpo', 'Mapoly0278s0004' => 'mpo', 'Mapoly0278s0005' => 'mpo', 'Mapoly0278s0006' => 'mpo', 'MBI11_g30648_MAGBIO' => 'mbi', 'MCO03G194' => 'mco', 'MCO03G590' => 'mco', 'MCO07G312' => 'mco', 'MCO10G318' => 'mco', 'MCO12G244' => 'mco', 'MCO13G148' => 'mco', 'MCO13G194' => 'mco', 'MCO16G238' => 'mco', 'MD06G1134100' => 'mdo', 'MD13G1200100' => 'mdo', 'MD13G1200300' => 'mdo', 'MD13G1200600' => 'mdo', 'MD14G1150400' => 'mdo', 'MD16G1200000' => 'mdo', 'Medtr1g102570' => 'mtr', 'Medtr1g102780' => 'mtr', 'Medtr1g102800' => 'mtr', 'Medtr1g102810' => 'mtr', 'Medtr1g102830' => 'mtr', 'MELO3C006499.2' => 'cme', 'Migut.G00385' => 'egut', 'MSTRG.4063' => 'ama', 'Nitab4.5_0000090g0260' => 'nta', 'Nitab4.5_0000977g0030' => 'nta', 'Nitab4.5_0002541g0040' => 'nta', 'Nitab4.5_0007068g0040' => 'nta', 'Nn005s41408' => 'nnu', 'Nn005s41410' => 'nnu', 'Oeu010310.1' => 'oeu', 'Oeu010311.1' => 'oeu', 'Oeu043472.1' => 'oeu', 'Os01g0246400' => 'osa', 'Os04g0267950' => 'osa', 'Os07g0178700' => 'osa', 'Os07g0178800' => 'osa', 'Peaxi162Scf00316g00046' => 'pax', 'Peaxi162Scf00316g00049' => 'pax', 'Peaxi162Scf00316g00059' => 'pax', 'Peaxi162Scf00316g00328' => 'pax', 'Peaxi162Scf00316g00329' => 'pax', 'Peaxi162Scf00316g00411' => 'pax', 'Peaxi162Scf00316g00521' => 'pax', 'Peaxi162Scf00492g00068' => 'pax', 'Peaxi162Scf35631g00002' => 'pax', 'PGR142G3720' => 'pgr', 'PGSC0003DMG400006442' => 'stu', 'Phvul.007G062000' => 'pvu', 'Potri.008G157750' => 'ptr', 'Potri.008G157900' => 'ptr', 'Potri.008G158000' => 'ptr', 'Potri.008G158200' => 'ptr', 'Pp3c11_7280' => 'ppa', 'Pp3c11_7980' => 'ppa', 'Pp3c12_19450' => 'ppa', 'Pp3c14_1480' => 'ppa', 'Pp3c14_1501' => 'ppa', 'Pp3c16_4900' => 'ppa', 'Pp3c16_5010' => 'ppa', 'Pp3c16_5060' => 'ppa', 'Pp3c19_18250' => 'ppa', 'Pp3c23_8530' => 'ppa', 'Pp3c23_8550' => 'ppa', 'Pp3c24_9670' => 'ppa', 'Pp3c2_21390' => 'ppa', 'Pp3c2_31380' => 'ppa', 'Pp3c3_16620' => 'ppa', 'Pp3c3_8090' => 'ppa', 'Pp3c3_8110' => 'ppa', 'Pp3c3_8130' => 'ppa', 'Pp3c3_8150' => 'ppa', 'Pp3c4_14320' => 'ppa', 'Pp3c6_2560' => 'ppa', 'Pp3c9_16700' => 'ppa', 'PRCOL_00000234' => 'pco', 'PRCOL_00000235' => 'pco', 'PRCOL_00000777' => 'pco', 'PRCOL_00002344' => 'pco', 'PRCOL_00002372' => 'pco', 'PRCOL_00006120' => 'pco', 'Prupe.1G021400' => 'ppe', 'Prupe.1G021500' => 'ppe', 'Prupe.1G021600' => 'ppe', 'Prupe.1G021700' => 'ppe', 'Prupe.1G021800' => 'ppe', 'Prupe.5G145100' => 'ppe', 'Psat6g204040' => 'psa', 'Psat6g204800' => 'psa', 'Psat6g204920' => 'psa', 'Psat6g204960' => 'psa', 'Psat6g205080' => 'psa', 'PSO017G0271' => 'pso', 'PSO017G1276' => 'pso', 'PSO017G1429' => 'pso', 'PSO017G1861' => 'pso', 'PSO017G2787' => 'pso', 'PSO017G4466' => 'pso', 'PSO017G5118' => 'pso', 'PSO017G5420' => 'pso', 'PSO063G3678' => 'pso', 'PSO210G0546' => 'pso', 'PSO317G0001' => 'pso', 'PSO357G0512' => 'pso', 'PSO478G2682' => 'pso', 'PSO647G0001' => 'pso', 'PSO675G0001' => 'pso', 'PSO675G2699' => 'pso', 'PSO675G2849' => 'pso', 'PSO675G4991' => 'pso', 'PSO689G0001' => 'pso', 'QL06p000916' => 'qlo', 'QL06p000921' => 'qlo', 'QL06p001398' => 'qlo', 'QL06p001407' => 'qlo', 'QL06p002031' => 'qlo', 'RcHm_v2.0_Chr4g0387791' => 'rch', 'RcHm_v2.0_Chr4g0387801' => 'rch', 'RcHm_v2.0_Chr6g0286501' => 'rch', 'RcHm_v2.0_Chr6g0286511' => 'rch', 'RcHm_v2.0_Chr6g0286521' => 'rch', 'RcHm_v2.0_Chr6g0286531' => 'rch', 'RcHm_v2.0_Chr7g0189141' => 'rch', 'Rhsim02G0028700' => 'rsi', 'Rhsim02G0028800' => 'rsi', 'Rhsim02G0028900' => 'rsi', 'Rhsim02G0029000' => 'rsi', 'Rhsim02G0029100' => 'rsi', 'Rhsim02G0029200' => 'rsi', 'Rhsim02G0029300' => 'rsi', 'Rhsim02G0029400' => 'rsi', 'Rhsim02G0029500' => 'rsi', 'Rhsim02G0029600' => 'rsi', 'RhsimUnG0024000' => 'rsi', 'RhsimUnG0024100' => 'rsi', 'RhsimUnG0024200' => 'rsi', 'RhsimUnG0024300' => 'rsi', 'RhsimUnG0024400' => 'rsi', 'RhsimUnG0024500' => 'rsi', 'RhsimUnG0024700' => 'rsi', 'RhsimUnG0024800' => 'rsi', 'RhsimUnG0024900' => 'rsi', 'RhsimUnG0025100' => 'rsi', 'Sabra08G0120200' => 'sbr', 'Sabra08G0120300' => 'sbr', 'Sabra08G0120500' => 'sbr', 'Sabra08G0120600' => 'sbr', 'Sabra10G0158900' => 'sbr', 'SalBow2G3492' => 'sbo', 'Sc13g0004760' => 'sci', 'Sc13g0004770' => 'sci', 'Sed0003417' => 'sed', 'Sed0019750' => 'sed', 'SEGI_03419' => 'sgi', 'SEGI_05907' => 'sgi', 'SEGI_10682' => 'sgi', 'SEGI_13528' => 'sgi', 'SEGI_16081' => 'sgi', 'SEGI_19370' => 'sgi', 'SEGI_21015' => 'sgi', 'SEGI_21944' => 'sgi', 'SEGI_32906' => 'sgi', 'SEGI_33093' => 'sgi', 'SEGI_36110' => 'sgi', 'SEGI_40397' => 'sgi', 'SGA_v2.0_scaffold191G40426' => 'sas', 'SGA_v2.0_scaffold353G49717' => 'sas', 'SGA_v2.0_scaffold50G18550' => 'sas', 'SMO119G0173' => 'smo', 'SMO172G0002' => 'smo', 'Solyc09g082690.3' => 'sly', 'Solyc09g082700.2' => 'sly', 'Sopen09g031550' => 'spe', 'Sopen09g031560' => 'spe', 'Sp3g20540' => 'spa', 'Sp7g07580' => 'spa', 'TAR134G0002' => 'tar', 'TAR236G0001' => 'tar', 'TAR365G0892' => 'tar', 'TAR636G0166' => 'tar', 'TAR636G0646' => 'tar', 'TAR636G0869' => 'tar', 'TAR636G1317' => 'tar', 'TAR636G1744' => 'tar', 'TAR636G3358' => 'tar', 'TAR636G3436' => 'tar', 'THA.LOC104803047' => 'tha', 'Thecc.04G238900' => 'tca', 'Thhalv10021557m.g' => 'esa', 'Thhalv10026318m.g' => 'esa', 'Thhalv10026335m.g' => 'esa', 'TPR.G17433' => 'tpr', 'TPR.G18915' => 'tpr', 'TPR.G26125' => 'tpr', 'TWI09G0677' => 'twi', 'TWI73G0287' => 'twi', 'unitig_748.g8326' => 'ugi', 'vmacro15370' => 'vma', 'vmacro15371' => 'vma', 'vmacro15372' => 'vma', 'vmacro15373' => 'vma', 'vmacro15374' => 'vma', 'VMungo0720G2826' => 'vmu', 'Zm00001eb116960' => 'zma', 'Zm00001eb301260' => 'zma', 'Zm00001eb301270' => 'zma' ) $gf_id = 'HOM05D001460' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001460' ) $data_identifier = 'HOM05D001460' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 4, 'aag' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 2, 'aox' => (int) 2, 'arhy' => (int) 4, 'ath' => (int) 2, 'atr' => (int) 1, 'acertr' => (int) 10, 'cqu' => (int) 4, 'bca' => (int) 11, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 1, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 1, 'ccan' => (int) 1, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 1, 'col' => (int) 1, 'cpa' => (int) 1, 'cre' => (int) 7, 'csa' => (int) 1, 'camsi' => (int) 2, 'dca' => (int) 3, 'din' => (int) 2, 'dzi' => (int) 3, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 14, 'fve' => (int) 9, 'gma' => (int) 2, 'ghi' => (int) 4, 'gra' => (int) 2, 'vvi' => (int) 1, 'han' => (int) 13, 'cav' => (int) 1, 'hma' => (int) 2, 'sun' => (int) 2, 'lal' => (int) 2, 'lonja' => (int) 12, 'lja' => (int) 1, 'lsa' => (int) 7, 'mes' => (int) 1, 'mpo' => (int) 27, 'mbi' => (int) 1, 'mco' => (int) 8, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 1, 'egut' => (int) 1, 'ama' => (int) 1, 'nta' => (int) 4, 'nnu' => (int) 2, 'oeu' => (int) 3, 'osa' => (int) 4, 'pax' => (int) 9, 'pgr' => (int) 1, 'stu' => (int) 1, 'pvu' => (int) 1, 'ptr' => (int) 4, 'ppa' => (int) 22, 'pco' => (int) 6, 'ppe' => (int) 6, 'psa' => (int) 5, 'pso' => (int) 19, 'qlo' => (int) 5, 'rch' => (int) 7, 'rsi' => (int) 20, 'sbr' => (int) 5, 'sbo' => (int) 1, 'sci' => (int) 2, 'sed' => (int) 2, 'sgi' => (int) 12, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 2, 'tar' => (int) 10, 'tha' => (int) 1, 'tca' => (int) 1, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 2, 'ugi' => (int) 1, 'vma' => (int) 5, 'vmu' => (int) 1, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb301270' $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' => 'HOM05D001460', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '433', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p22980' => 'bna', 'A01p32340' => 'bna', 'A03p42970' => 'bna', 'A05p25880' => 'bna', 'Aa31LG8G9320' => 'aar', 'Aa31LG8G9330' => 'aar', 'Aa31LG8G9340' => 'aar', 'Aa31sc221G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1034' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1528' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.829' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2222' => 'aag', 'Ah.12g058830' => 'amhyb', 'Ah.12g058840' => 'amhyb', 'AL3G37160' => 'aly', 'AL7G41310' => 'aly', 'Aqoxy5G00395' => 'aox', 'Aqoxy5G00396' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0C8NZA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5185HY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JZ1PRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MD3LS0' => 'arhy', 'AT3G22840' => 'ath', 'AT4G14690' => 'ath', 'ATR0665G054' => 'atr', 'Atru.chr4.2344' => 'acertr', 'Atru.chr4.2346' => 'acertr', 'Atru.chr4.2347' => 'acertr', 'Atru.chr4.2348' => 'acertr', 'Atru.chr4.2355' => 'acertr', 'Atru.chr4.2356' => 'acertr', 'Atru.chr4.2358' => 'acertr', 'Atru.chr4.2359' => 'acertr', 'Atru.chr4.2360' => 'acertr', 'Atru.chr4.2361' => 'acertr', 'AUR62030476' => 'cqu', 'AUR62030478' => 'cqu', 'AUR62030819' => 'cqu', 'AUR62030820' => 'cqu', 'BcaB03g14648' => 'bca', 'BcaB04g20492' => 'bca', 'BcaB06g26399' => 'bca', 'BcaC01g03416' => 'bca', 'BcaC01g03419' => 'bca', 'BcaC01g03421' => 'bca', 'BcaC01g03424' => 'bca', 'BcaC05g28012' => 'bca', 'BcaC09g49212' => 'bca', 'BcaC09g50140' => 'bca', 'BcaNung00346' => 'bca', 'BolC1t02785H' => 'bol', 'BolC1t04095H' => 'bol', 'BolC3t17545H' => 'bol', 'BolC5t32769H' => 'bol', 'BraA01t02211Z' => 'bra', 'BraA01t03359Z' => 'bra', 'BraA03t13441Z' => 'bra', 'BraA05t21476Z' => 'bra', 'C01p28420' => 'bna', 'C01p41350' => 'bna', 'C03p52750' => 'bna', 'C03p52780' => 'bna', 'C05p40270' => 'bna', 'CAN.G1437.9' => 'can', 'CANSAT78G0035' => 'cansat', 'CANSAT78G1036' => 'cansat', 'CANSAT78G2272' => 'cansat', 'CANSAT78G2478' => 'cansat', 'CARHR098700' => 'chi', 'CARHR221120' => 'chi', 'CARHR221150' => 'chi', 'Carub.0003s2297' => 'cru', 'Carub.0007s2749' => 'cru', 'Carub.0007s2750' => 'cru', 'Carub.0007s2751' => 'cru', 'Ca_10849_v3' => 'car', 'Cc03_g04300' => 'ccan', 'CDE02G3648' => 'cde', 'CDE05G0060' => 'cde', 'CDE05G0692' => 'cde', 'CDE05G2285' => 'cde', 'CDE05G2884' => 'cde', 'CDE05G3072' => 'cde', 'Cfa008439' => 'cfa', 'Cfa008441' => 'cfa', 'Cfa008443' => 'cfa', 'Cfa008448' => 'cfa', 'Ciclev10005974m.g' => 'ccl', 'Ciclev10006006m.g' => 'ccl', 'Ciclev10006775m.g' => 'ccl', 'CiPaw.02G120400' => 'cil', 'CiPaw.02G120500' => 'cil', 'CiPaw.02G120600' => 'cil', 'ClCG05G004850' => 'cla', 'COL.COLO4_21566' => 'col', 'Cpa.g.sc44.124' => 'cpa', 'Cre07.g320400' => 'cre', 'Cre07.g320450' => 'cre', 'Cre08.g384650' => 'cre', 'Cre09.g393173' => 'cre', 'Cre09.g394325' => 'cre', 'Cre14.g626750' => 'cre', 'Cre16.g679250' => 'cre', 'CsaV3_3G012890' => 'csa', 'CSS0010865' => 'camsi', 'CSS0044338' => 'camsi', 'DCAR_002366' => 'dca', 'DCAR_030687' => 'dca', 'DCAR_030688' => 'dca', 'Dinv14047' => 'din', 'Dinv14048' => 'din', 'Duzib151G0105' => 'dzi', 'Duzib151G0114' => 'dzi', 'Duzib212G1029' => 'dzi', 'ECA232G3536' => 'eca', 'ECA240G0786' => 'eca', 'ECA240G1802' => 'eca', 'ECA240G3760' => 'eca', 'ECA240G3920' => 'eca', 'EL10Ac5g12536' => 'bvu', 'EL10Ac5g12537' => 'bvu', 'EL10Ac5g12538' => 'bvu', 'Eucgr.B01004' => 'egr', 'Eucgr.B01006' => 'egr', 'Eucgr.B01007' => 'egr', 'Eucgr.B01008' => 'egr', 'Eucgr.B01895' => 'egr', 'Eucgr.B01896' => 'egr', 'FAN04G1456' => 'fan', 'FAN08G1769' => 'fan', 'FAN08G2160' => 'fan', 'FAN13G2403' => 'fan', 'FAN13G3303' => 'fan', 'FAN15G2435' => 'fan', 'FAN17G0672' => 'fan', 'FAN17G2441' => 'fan', 'FAN18G1024' => 'fan', 'FAN22G1458' => 'fan', 'FAN24G0037' => 'fan', 'FAN24G0429' => 'fan', 'FAN24G2387' => 'fan', 'FAN27G2746' => 'fan', 'FvH4_2g20400' => 'fve', 'FvH4_2g20420' => 'fve', 'FvH4_2g20430' => 'fve', 'FvH4_4g01270' => 'fve', 'FvH4_4g01290' => 'fve', 'FvH4_4g01300' => 'fve', 'FvH4_4g01310' => 'fve', 'FvH4_4g01330' => 'fve', 'FvH4_5g09070' => 'fve', 'Glyma.10G243800' => 'gma', 'Glyma.20G150600' => 'gma', 'Gohir.A09G219200' => 'ghi', 'Gohir.A09G219300' => 'ghi', 'Gohir.D09G221400' => 'ghi', 'Gohir.D09G221500' => 'ghi', 'Gorai.006G242600' => 'gra', 'Gorai.006G242700' => 'gra', 'GSVIVG01018044001' => 'vvi', 'HanXRQChr03g0083821' => 'han', 'HanXRQChr03g0083841' => 'han', 'HanXRQChr03g0083881' => 'han', 'HanXRQChr03g0083901' => 'han', 'HanXRQChr03g0083921' => 'han', 'HanXRQChr03g0085331' => 'han', 'HanXRQChr03g0085361' => 'han', 'HanXRQChr03g0085411' => 'han', 'HanXRQChr03g0085421' => 'han', 'HanXRQChr03g0085431' => 'han', 'HanXRQChr08g0221991' => 'han', 'HanXRQChr11g0336061' => 'han', 'HanXRQChr11g0336411' => 'han', 'Haze_11234' => 'cav', 'Hma1.2p1_0549F.1_g177010' => 'hma', 'Hma1.2p1_0602F.1_g187630' => 'hma', 'Hund14876' => 'sun', 'Hund14879' => 'sun', 'Lalb_Chr06g0160741' => 'lal', 'Lalb_Chr21g0304781' => 'lal', 'Lj3A726G19' => 'lonja', 'Lj3A726T23' => 'lonja', 'Lj3A726T24' => 'lonja', 'Lj3A726T25' => 'lonja', 'Lj3A727T17' => 'lonja', 'Lj3C726T0' => 'lonja', 'Lj3C726T2' => 'lonja', 'Lj3P725T35' => 'lonja', 'Lj3P727T10' => 'lonja', 'Lj3P727T12' => 'lonja', 'Lj3P727T14' => 'lonja', 'Lj5g0023109' => 'lja', 'Lj6P646T44' => 'lonja', 'Lsat_1_v5_gn_6_75760' => 'lsa', 'Lsat_1_v5_gn_6_75800' => 'lsa', 'Lsat_1_v5_gn_6_75900' => 'lsa', 'Lsat_1_v5_gn_6_76240' => 'lsa', 'Lsat_1_v5_gn_6_76441' => 'lsa', 'Lsat_1_v5_gn_6_76700' => 'lsa', 'Lsat_1_v5_gn_6_76760' => 'lsa', 'Manes.15G033100' => 'mes', 'Mapoly0004s0074' => 'mpo', 'Mapoly0004s0075' => 'mpo', 'Mapoly0004s0163' => 'mpo', 'Mapoly0004s0164' => 'mpo', 'Mapoly0021s0018' => 'mpo', 'Mapoly0041s0136' => 'mpo', 'Mapoly0041s0137' => 'mpo', 'Mapoly0041s0138' => 'mpo', 'Mapoly0041s0139' => 'mpo', 'Mapoly0041s0141' => 'mpo', 'Mapoly0041s0142' => 'mpo', 'Mapoly0041s0143' => 'mpo', 'Mapoly0041s0144' => 'mpo', 'Mapoly0041s0145' => 'mpo', 'Mapoly0047s0106' => 'mpo', 'Mapoly0047s0108' => 'mpo', 'Mapoly0050s0051' => 'mpo', 'Mapoly0050s0052' => 'mpo', 'Mapoly0050s0053' => 'mpo', 'Mapoly0058s0013' => 'mpo', 'Mapoly0091s0078' => 'mpo', 'Mapoly0091s0079' => 'mpo', 'Mapoly0091s0080' => 'mpo', 'Mapoly0091s0081' => 'mpo', 'Mapoly0278s0004' => 'mpo', 'Mapoly0278s0005' => 'mpo', 'Mapoly0278s0006' => 'mpo', 'MBI11_g30648_MAGBIO' => 'mbi', 'MCO03G194' => 'mco', 'MCO03G590' => 'mco', 'MCO07G312' => 'mco', 'MCO10G318' => 'mco', 'MCO12G244' => 'mco', 'MCO13G148' => 'mco', 'MCO13G194' => 'mco', 'MCO16G238' => 'mco', 'MD06G1134100' => 'mdo', 'MD13G1200100' => 'mdo', 'MD13G1200300' => 'mdo', 'MD13G1200600' => 'mdo', 'MD14G1150400' => 'mdo', 'MD16G1200000' => 'mdo', 'Medtr1g102570' => 'mtr', 'Medtr1g102780' => 'mtr', 'Medtr1g102800' => 'mtr', 'Medtr1g102810' => 'mtr', 'Medtr1g102830' => 'mtr', 'MELO3C006499.2' => 'cme', 'Migut.G00385' => 'egut', 'MSTRG.4063' => 'ama', 'Nitab4.5_0000090g0260' => 'nta', 'Nitab4.5_0000977g0030' => 'nta', 'Nitab4.5_0002541g0040' => 'nta', 'Nitab4.5_0007068g0040' => 'nta', 'Nn005s41408' => 'nnu', 'Nn005s41410' => 'nnu', 'Oeu010310.1' => 'oeu', 'Oeu010311.1' => 'oeu', 'Oeu043472.1' => 'oeu', 'Os01g0246400' => 'osa', 'Os04g0267950' => 'osa', 'Os07g0178700' => 'osa', 'Os07g0178800' => 'osa', 'Peaxi162Scf00316g00046' => 'pax', 'Peaxi162Scf00316g00049' => 'pax', 'Peaxi162Scf00316g00059' => 'pax', 'Peaxi162Scf00316g00328' => 'pax', 'Peaxi162Scf00316g00329' => 'pax', 'Peaxi162Scf00316g00411' => 'pax', 'Peaxi162Scf00316g00521' => 'pax', 'Peaxi162Scf00492g00068' => 'pax', 'Peaxi162Scf35631g00002' => 'pax', 'PGR142G3720' => 'pgr', 'PGSC0003DMG400006442' => 'stu', 'Phvul.007G062000' => 'pvu', 'Potri.008G157750' => 'ptr', 'Potri.008G157900' => 'ptr', 'Potri.008G158000' => 'ptr', 'Potri.008G158200' => 'ptr', 'Pp3c11_7280' => 'ppa', 'Pp3c11_7980' => 'ppa', 'Pp3c12_19450' => 'ppa', 'Pp3c14_1480' => 'ppa', 'Pp3c14_1501' => 'ppa', 'Pp3c16_4900' => 'ppa', 'Pp3c16_5010' => 'ppa', 'Pp3c16_5060' => 'ppa', 'Pp3c19_18250' => 'ppa', 'Pp3c23_8530' => 'ppa', 'Pp3c23_8550' => 'ppa', 'Pp3c24_9670' => 'ppa', 'Pp3c2_21390' => 'ppa', 'Pp3c2_31380' => 'ppa', 'Pp3c3_16620' => 'ppa', 'Pp3c3_8090' => 'ppa', 'Pp3c3_8110' => 'ppa', 'Pp3c3_8130' => 'ppa', 'Pp3c3_8150' => 'ppa', 'Pp3c4_14320' => 'ppa', 'Pp3c6_2560' => 'ppa', 'Pp3c9_16700' => 'ppa', 'PRCOL_00000234' => 'pco', 'PRCOL_00000235' => 'pco', 'PRCOL_00000777' => 'pco', 'PRCOL_00002344' => 'pco', 'PRCOL_00002372' => 'pco', 'PRCOL_00006120' => 'pco', 'Prupe.1G021400' => 'ppe', 'Prupe.1G021500' => 'ppe', 'Prupe.1G021600' => 'ppe', 'Prupe.1G021700' => 'ppe', 'Prupe.1G021800' => 'ppe', 'Prupe.5G145100' => 'ppe', 'Psat6g204040' => 'psa', 'Psat6g204800' => 'psa', 'Psat6g204920' => 'psa', 'Psat6g204960' => 'psa', 'Psat6g205080' => 'psa', 'PSO017G0271' => 'pso', 'PSO017G1276' => 'pso', 'PSO017G1429' => 'pso', 'PSO017G1861' => 'pso', 'PSO017G2787' => 'pso', 'PSO017G4466' => 'pso', 'PSO017G5118' => 'pso', 'PSO017G5420' => 'pso', 'PSO063G3678' => 'pso', 'PSO210G0546' => 'pso', 'PSO317G0001' => 'pso', 'PSO357G0512' => 'pso', 'PSO478G2682' => 'pso', 'PSO647G0001' => 'pso', 'PSO675G0001' => 'pso', 'PSO675G2699' => 'pso', 'PSO675G2849' => 'pso', 'PSO675G4991' => 'pso', 'PSO689G0001' => 'pso', 'QL06p000916' => 'qlo', 'QL06p000921' => 'qlo', 'QL06p001398' => 'qlo', 'QL06p001407' => 'qlo', 'QL06p002031' => 'qlo', 'RcHm_v2.0_Chr4g0387791' => 'rch', 'RcHm_v2.0_Chr4g0387801' => 'rch', 'RcHm_v2.0_Chr6g0286501' => 'rch', 'RcHm_v2.0_Chr6g0286511' => 'rch', 'RcHm_v2.0_Chr6g0286521' => 'rch', 'RcHm_v2.0_Chr6g0286531' => 'rch', 'RcHm_v2.0_Chr7g0189141' => 'rch', 'Rhsim02G0028700' => 'rsi', 'Rhsim02G0028800' => 'rsi', 'Rhsim02G0028900' => 'rsi', 'Rhsim02G0029000' => 'rsi', 'Rhsim02G0029100' => 'rsi', 'Rhsim02G0029200' => 'rsi', 'Rhsim02G0029300' => 'rsi', 'Rhsim02G0029400' => 'rsi', 'Rhsim02G0029500' => 'rsi', 'Rhsim02G0029600' => 'rsi', 'RhsimUnG0024000' => 'rsi', 'RhsimUnG0024100' => 'rsi', 'RhsimUnG0024200' => 'rsi', 'RhsimUnG0024300' => 'rsi', 'RhsimUnG0024400' => 'rsi', 'RhsimUnG0024500' => 'rsi', 'RhsimUnG0024700' => 'rsi', 'RhsimUnG0024800' => 'rsi', 'RhsimUnG0024900' => 'rsi', 'RhsimUnG0025100' => 'rsi', 'Sabra08G0120200' => 'sbr', 'Sabra08G0120300' => 'sbr', 'Sabra08G0120500' => 'sbr', 'Sabra08G0120600' => 'sbr', 'Sabra10G0158900' => 'sbr', 'SalBow2G3492' => 'sbo', 'Sc13g0004760' => 'sci', 'Sc13g0004770' => 'sci', 'Sed0003417' => 'sed', 'Sed0019750' => 'sed', 'SEGI_03419' => 'sgi', 'SEGI_05907' => 'sgi', 'SEGI_10682' => 'sgi', 'SEGI_13528' => 'sgi', 'SEGI_16081' => 'sgi', 'SEGI_19370' => 'sgi', 'SEGI_21015' => 'sgi', 'SEGI_21944' => 'sgi', 'SEGI_32906' => 'sgi', 'SEGI_33093' => 'sgi', 'SEGI_36110' => 'sgi', 'SEGI_40397' => 'sgi', 'SGA_v2.0_scaffold191G40426' => 'sas', 'SGA_v2.0_scaffold353G49717' => 'sas', 'SGA_v2.0_scaffold50G18550' => 'sas', 'SMO119G0173' => 'smo', 'SMO172G0002' => 'smo', 'Solyc09g082690.3' => 'sly', 'Solyc09g082700.2' => 'sly', 'Sopen09g031550' => 'spe', 'Sopen09g031560' => 'spe', 'Sp3g20540' => 'spa', 'Sp7g07580' => 'spa', 'TAR134G0002' => 'tar', 'TAR236G0001' => 'tar', 'TAR365G0892' => 'tar', 'TAR636G0166' => 'tar', 'TAR636G0646' => 'tar', 'TAR636G0869' => 'tar', 'TAR636G1317' => 'tar', 'TAR636G1744' => 'tar', 'TAR636G3358' => 'tar', 'TAR636G3436' => 'tar', 'THA.LOC104803047' => 'tha', 'Thecc.04G238900' => 'tca', 'Thhalv10021557m.g' => 'esa', 'Thhalv10026318m.g' => 'esa', 'Thhalv10026335m.g' => 'esa', 'TPR.G17433' => 'tpr', 'TPR.G18915' => 'tpr', 'TPR.G26125' => 'tpr', 'TWI09G0677' => 'twi', 'TWI73G0287' => 'twi', 'unitig_748.g8326' => 'ugi', 'vmacro15370' => 'vma', 'vmacro15371' => 'vma', 'vmacro15372' => 'vma', 'vmacro15373' => 'vma', 'vmacro15374' => 'vma', 'VMungo0720G2826' => 'vmu', 'Zm00001eb116960' => 'zma', 'Zm00001eb301260' => 'zma', 'Zm00001eb301270' => 'zma' ), 'gf_id' => 'HOM05D001460', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001460' ), 'data_identifier' => 'HOM05D001460', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001460', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '433', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p22980' => 'bna', 'A01p32340' => 'bna', 'A03p42970' => 'bna', 'A05p25880' => 'bna', 'Aa31LG8G9320' => 'aar', 'Aa31LG8G9330' => 'aar', 'Aa31LG8G9340' => 'aar', 'Aa31sc221G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1034' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1528' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.829' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2222' => 'aag', 'Ah.12g058830' => 'amhyb', 'Ah.12g058840' => 'amhyb', 'AL3G37160' => 'aly', 'AL7G41310' => 'aly', 'Aqoxy5G00395' => 'aox', 'Aqoxy5G00396' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0C8NZA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5185HY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JZ1PRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MD3LS0' => 'arhy', 'AT3G22840' => 'ath', 'AT4G14690' => 'ath', 'ATR0665G054' => 'atr', 'Atru.chr4.2344' => 'acertr', 'Atru.chr4.2346' => 'acertr', 'Atru.chr4.2347' => 'acertr', 'Atru.chr4.2348' => 'acertr', 'Atru.chr4.2355' => 'acertr', 'Atru.chr4.2356' => 'acertr', 'Atru.chr4.2358' => 'acertr', 'Atru.chr4.2359' => 'acertr', 'Atru.chr4.2360' => 'acertr', 'Atru.chr4.2361' => 'acertr', 'AUR62030476' => 'cqu', 'AUR62030478' => 'cqu', 'AUR62030819' => 'cqu', 'AUR62030820' => 'cqu', 'BcaB03g14648' => 'bca', 'BcaB04g20492' => 'bca', 'BcaB06g26399' => 'bca', 'BcaC01g03416' => 'bca', 'BcaC01g03419' => 'bca', 'BcaC01g03421' => 'bca', 'BcaC01g03424' => 'bca', 'BcaC05g28012' => 'bca', 'BcaC09g49212' => 'bca', 'BcaC09g50140' => 'bca', 'BcaNung00346' => 'bca', 'BolC1t02785H' => 'bol', 'BolC1t04095H' => 'bol', 'BolC3t17545H' => 'bol', 'BolC5t32769H' => 'bol', 'BraA01t02211Z' => 'bra', 'BraA01t03359Z' => 'bra', 'BraA03t13441Z' => 'bra', 'BraA05t21476Z' => 'bra', 'C01p28420' => 'bna', 'C01p41350' => 'bna', 'C03p52750' => 'bna', 'C03p52780' => 'bna', 'C05p40270' => 'bna', 'CAN.G1437.9' => 'can', 'CANSAT78G0035' => 'cansat', 'CANSAT78G1036' => 'cansat', 'CANSAT78G2272' => 'cansat', 'CANSAT78G2478' => 'cansat', 'CARHR098700' => 'chi', 'CARHR221120' => 'chi', 'CARHR221150' => 'chi', 'Carub.0003s2297' => 'cru', 'Carub.0007s2749' => 'cru', 'Carub.0007s2750' => 'cru', 'Carub.0007s2751' => 'cru', 'Ca_10849_v3' => 'car', 'Cc03_g04300' => 'ccan', 'CDE02G3648' => 'cde', 'CDE05G0060' => 'cde', 'CDE05G0692' => 'cde', 'CDE05G2285' => 'cde', 'CDE05G2884' => 'cde', 'CDE05G3072' => 'cde', 'Cfa008439' => 'cfa', 'Cfa008441' => 'cfa', 'Cfa008443' => 'cfa', 'Cfa008448' => 'cfa', 'Ciclev10005974m.g' => 'ccl', 'Ciclev10006006m.g' => 'ccl', 'Ciclev10006775m.g' => 'ccl', 'CiPaw.02G120400' => 'cil', 'CiPaw.02G120500' => 'cil', 'CiPaw.02G120600' => 'cil', 'ClCG05G004850' => 'cla', 'COL.COLO4_21566' => 'col', 'Cpa.g.sc44.124' => 'cpa', 'Cre07.g320400' => 'cre', 'Cre07.g320450' => 'cre', 'Cre08.g384650' => 'cre', 'Cre09.g393173' => 'cre', 'Cre09.g394325' => 'cre', 'Cre14.g626750' => 'cre', 'Cre16.g679250' => 'cre', 'CsaV3_3G012890' => 'csa', 'CSS0010865' => 'camsi', 'CSS0044338' => 'camsi', 'DCAR_002366' => 'dca', 'DCAR_030687' => 'dca', 'DCAR_030688' => 'dca', 'Dinv14047' => 'din', 'Dinv14048' => 'din', 'Duzib151G0105' => 'dzi', 'Duzib151G0114' => 'dzi', 'Duzib212G1029' => 'dzi', 'ECA232G3536' => 'eca', 'ECA240G0786' => 'eca', 'ECA240G1802' => 'eca', 'ECA240G3760' => 'eca', 'ECA240G3920' => 'eca', 'EL10Ac5g12536' => 'bvu', 'EL10Ac5g12537' => 'bvu', 'EL10Ac5g12538' => 'bvu', 'Eucgr.B01004' => 'egr', 'Eucgr.B01006' => 'egr', 'Eucgr.B01007' => 'egr', 'Eucgr.B01008' => 'egr', 'Eucgr.B01895' => 'egr', 'Eucgr.B01896' => 'egr', 'FAN04G1456' => 'fan', 'FAN08G1769' => 'fan', 'FAN08G2160' => 'fan', 'FAN13G2403' => 'fan', 'FAN13G3303' => 'fan', 'FAN15G2435' => 'fan', 'FAN17G0672' => 'fan', 'FAN17G2441' => 'fan', 'FAN18G1024' => 'fan', 'FAN22G1458' => 'fan', 'FAN24G0037' => 'fan', 'FAN24G0429' => 'fan', 'FAN24G2387' => 'fan', 'FAN27G2746' => 'fan', 'FvH4_2g20400' => 'fve', 'FvH4_2g20420' => 'fve', 'FvH4_2g20430' => 'fve', 'FvH4_4g01270' => 'fve', 'FvH4_4g01290' => 'fve', 'FvH4_4g01300' => 'fve', 'FvH4_4g01310' => 'fve', 'FvH4_4g01330' => 'fve', 'FvH4_5g09070' => 'fve', 'Glyma.10G243800' => 'gma', 'Glyma.20G150600' => 'gma', 'Gohir.A09G219200' => 'ghi', 'Gohir.A09G219300' => 'ghi', 'Gohir.D09G221400' => 'ghi', 'Gohir.D09G221500' => 'ghi', 'Gorai.006G242600' => 'gra', 'Gorai.006G242700' => 'gra', 'GSVIVG01018044001' => 'vvi', 'HanXRQChr03g0083821' => 'han', 'HanXRQChr03g0083841' => 'han', 'HanXRQChr03g0083881' => 'han', 'HanXRQChr03g0083901' => 'han', 'HanXRQChr03g0083921' => 'han', 'HanXRQChr03g0085331' => 'han', 'HanXRQChr03g0085361' => 'han', 'HanXRQChr03g0085411' => 'han', 'HanXRQChr03g0085421' => 'han', 'HanXRQChr03g0085431' => 'han', 'HanXRQChr08g0221991' => 'han', 'HanXRQChr11g0336061' => 'han', 'HanXRQChr11g0336411' => 'han', 'Haze_11234' => 'cav', 'Hma1.2p1_0549F.1_g177010' => 'hma', 'Hma1.2p1_0602F.1_g187630' => 'hma', 'Hund14876' => 'sun', 'Hund14879' => 'sun', 'Lalb_Chr06g0160741' => 'lal', 'Lalb_Chr21g0304781' => 'lal', 'Lj3A726G19' => 'lonja', 'Lj3A726T23' => 'lonja', 'Lj3A726T24' => 'lonja', 'Lj3A726T25' => 'lonja', 'Lj3A727T17' => 'lonja', 'Lj3C726T0' => 'lonja', 'Lj3C726T2' => 'lonja', 'Lj3P725T35' => 'lonja', 'Lj3P727T10' => 'lonja', 'Lj3P727T12' => 'lonja', 'Lj3P727T14' => 'lonja', 'Lj5g0023109' => 'lja', 'Lj6P646T44' => 'lonja', 'Lsat_1_v5_gn_6_75760' => 'lsa', 'Lsat_1_v5_gn_6_75800' => 'lsa', 'Lsat_1_v5_gn_6_75900' => 'lsa', 'Lsat_1_v5_gn_6_76240' => 'lsa', 'Lsat_1_v5_gn_6_76441' => 'lsa', 'Lsat_1_v5_gn_6_76700' => 'lsa', 'Lsat_1_v5_gn_6_76760' => 'lsa', 'Manes.15G033100' => 'mes', 'Mapoly0004s0074' => 'mpo', 'Mapoly0004s0075' => 'mpo', 'Mapoly0004s0163' => 'mpo', 'Mapoly0004s0164' => 'mpo', 'Mapoly0021s0018' => 'mpo', 'Mapoly0041s0136' => 'mpo', 'Mapoly0041s0137' => 'mpo', 'Mapoly0041s0138' => 'mpo', 'Mapoly0041s0139' => 'mpo', 'Mapoly0041s0141' => 'mpo', 'Mapoly0041s0142' => 'mpo', 'Mapoly0041s0143' => 'mpo', 'Mapoly0041s0144' => 'mpo', 'Mapoly0041s0145' => 'mpo', 'Mapoly0047s0106' => 'mpo', 'Mapoly0047s0108' => 'mpo', 'Mapoly0050s0051' => 'mpo', 'Mapoly0050s0052' => 'mpo', 'Mapoly0050s0053' => 'mpo', 'Mapoly0058s0013' => 'mpo', 'Mapoly0091s0078' => 'mpo', 'Mapoly0091s0079' => 'mpo', 'Mapoly0091s0080' => 'mpo', 'Mapoly0091s0081' => 'mpo', 'Mapoly0278s0004' => 'mpo', 'Mapoly0278s0005' => 'mpo', 'Mapoly0278s0006' => 'mpo', 'MBI11_g30648_MAGBIO' => 'mbi', 'MCO03G194' => 'mco', 'MCO03G590' => 'mco', 'MCO07G312' => 'mco', 'MCO10G318' => 'mco', 'MCO12G244' => 'mco', 'MCO13G148' => 'mco', 'MCO13G194' => 'mco', 'MCO16G238' => 'mco', 'MD06G1134100' => 'mdo', 'MD13G1200100' => 'mdo', 'MD13G1200300' => 'mdo', 'MD13G1200600' => 'mdo', 'MD14G1150400' => 'mdo', 'MD16G1200000' => 'mdo', 'Medtr1g102570' => 'mtr', 'Medtr1g102780' => 'mtr', 'Medtr1g102800' => 'mtr', 'Medtr1g102810' => 'mtr', 'Medtr1g102830' => 'mtr', 'MELO3C006499.2' => 'cme', 'Migut.G00385' => 'egut', 'MSTRG.4063' => 'ama', 'Nitab4.5_0000090g0260' => 'nta', 'Nitab4.5_0000977g0030' => 'nta', 'Nitab4.5_0002541g0040' => 'nta', 'Nitab4.5_0007068g0040' => 'nta', 'Nn005s41408' => 'nnu', 'Nn005s41410' => 'nnu', 'Oeu010310.1' => 'oeu', 'Oeu010311.1' => 'oeu', 'Oeu043472.1' => 'oeu', 'Os01g0246400' => 'osa', 'Os04g0267950' => 'osa', 'Os07g0178700' => 'osa', 'Os07g0178800' => 'osa', 'Peaxi162Scf00316g00046' => 'pax', 'Peaxi162Scf00316g00049' => 'pax', 'Peaxi162Scf00316g00059' => 'pax', 'Peaxi162Scf00316g00328' => 'pax', 'Peaxi162Scf00316g00329' => 'pax', 'Peaxi162Scf00316g00411' => 'pax', 'Peaxi162Scf00316g00521' => 'pax', 'Peaxi162Scf00492g00068' => 'pax', 'Peaxi162Scf35631g00002' => 'pax', 'PGR142G3720' => 'pgr', 'PGSC0003DMG400006442' => 'stu', 'Phvul.007G062000' => 'pvu', 'Potri.008G157750' => 'ptr', 'Potri.008G157900' => 'ptr', 'Potri.008G158000' => 'ptr', 'Potri.008G158200' => 'ptr', 'Pp3c11_7280' => 'ppa', 'Pp3c11_7980' => 'ppa', 'Pp3c12_19450' => 'ppa', 'Pp3c14_1480' => 'ppa', 'Pp3c14_1501' => 'ppa', 'Pp3c16_4900' => 'ppa', 'Pp3c16_5010' => 'ppa', 'Pp3c16_5060' => 'ppa', 'Pp3c19_18250' => 'ppa', 'Pp3c23_8530' => 'ppa', 'Pp3c23_8550' => 'ppa', 'Pp3c24_9670' => 'ppa', 'Pp3c2_21390' => 'ppa', 'Pp3c2_31380' => 'ppa', 'Pp3c3_16620' => 'ppa', 'Pp3c3_8090' => 'ppa', 'Pp3c3_8110' => 'ppa', 'Pp3c3_8130' => 'ppa', 'Pp3c3_8150' => 'ppa', 'Pp3c4_14320' => 'ppa', 'Pp3c6_2560' => 'ppa', 'Pp3c9_16700' => 'ppa', 'PRCOL_00000234' => 'pco', 'PRCOL_00000235' => 'pco', 'PRCOL_00000777' => 'pco', 'PRCOL_00002344' => 'pco', 'PRCOL_00002372' => 'pco', 'PRCOL_00006120' => 'pco', 'Prupe.1G021400' => 'ppe', 'Prupe.1G021500' => 'ppe', 'Prupe.1G021600' => 'ppe', 'Prupe.1G021700' => 'ppe', 'Prupe.1G021800' => 'ppe', 'Prupe.5G145100' => 'ppe', 'Psat6g204040' => 'psa', 'Psat6g204800' => 'psa', 'Psat6g204920' => 'psa', 'Psat6g204960' => 'psa', 'Psat6g205080' => 'psa', 'PSO017G0271' => 'pso', 'PSO017G1276' => 'pso', 'PSO017G1429' => 'pso', 'PSO017G1861' => 'pso', 'PSO017G2787' => 'pso', 'PSO017G4466' => 'pso', 'PSO017G5118' => 'pso', 'PSO017G5420' => 'pso', 'PSO063G3678' => 'pso', 'PSO210G0546' => 'pso', 'PSO317G0001' => 'pso', 'PSO357G0512' => 'pso', 'PSO478G2682' => 'pso', 'PSO647G0001' => 'pso', 'PSO675G0001' => 'pso', 'PSO675G2699' => 'pso', 'PSO675G2849' => 'pso', 'PSO675G4991' => 'pso', 'PSO689G0001' => 'pso', 'QL06p000916' => 'qlo', 'QL06p000921' => 'qlo', 'QL06p001398' => 'qlo', 'QL06p001407' => 'qlo', 'QL06p002031' => 'qlo', 'RcHm_v2.0_Chr4g0387791' => 'rch', 'RcHm_v2.0_Chr4g0387801' => 'rch', 'RcHm_v2.0_Chr6g0286501' => 'rch', 'RcHm_v2.0_Chr6g0286511' => 'rch', 'RcHm_v2.0_Chr6g0286521' => 'rch', 'RcHm_v2.0_Chr6g0286531' => 'rch', 'RcHm_v2.0_Chr7g0189141' => 'rch', 'Rhsim02G0028700' => 'rsi', 'Rhsim02G0028800' => 'rsi', 'Rhsim02G0028900' => 'rsi', 'Rhsim02G0029000' => 'rsi', 'Rhsim02G0029100' => 'rsi', 'Rhsim02G0029200' => 'rsi', 'Rhsim02G0029300' => 'rsi', 'Rhsim02G0029400' => 'rsi', 'Rhsim02G0029500' => 'rsi', 'Rhsim02G0029600' => 'rsi', 'RhsimUnG0024000' => 'rsi', 'RhsimUnG0024100' => 'rsi', 'RhsimUnG0024200' => 'rsi', 'RhsimUnG0024300' => 'rsi', 'RhsimUnG0024400' => 'rsi', 'RhsimUnG0024500' => 'rsi', 'RhsimUnG0024700' => 'rsi', 'RhsimUnG0024800' => 'rsi', 'RhsimUnG0024900' => 'rsi', 'RhsimUnG0025100' => 'rsi', 'Sabra08G0120200' => 'sbr', 'Sabra08G0120300' => 'sbr', 'Sabra08G0120500' => 'sbr', 'Sabra08G0120600' => 'sbr', 'Sabra10G0158900' => 'sbr', 'SalBow2G3492' => 'sbo', 'Sc13g0004760' => 'sci', 'Sc13g0004770' => 'sci', 'Sed0003417' => 'sed', 'Sed0019750' => 'sed', 'SEGI_03419' => 'sgi', 'SEGI_05907' => 'sgi', 'SEGI_10682' => 'sgi', 'SEGI_13528' => 'sgi', 'SEGI_16081' => 'sgi', 'SEGI_19370' => 'sgi', 'SEGI_21015' => 'sgi', 'SEGI_21944' => 'sgi', 'SEGI_32906' => 'sgi', 'SEGI_33093' => 'sgi', 'SEGI_36110' => 'sgi', 'SEGI_40397' => 'sgi', 'SGA_v2.0_scaffold191G40426' => 'sas', 'SGA_v2.0_scaffold353G49717' => 'sas', 'SGA_v2.0_scaffold50G18550' => 'sas', 'SMO119G0173' => 'smo', 'SMO172G0002' => 'smo', 'Solyc09g082690.3' => 'sly', 'Solyc09g082700.2' => 'sly', 'Sopen09g031550' => 'spe', 'Sopen09g031560' => 'spe', 'Sp3g20540' => 'spa', 'Sp7g07580' => 'spa', 'TAR134G0002' => 'tar', 'TAR236G0001' => 'tar', 'TAR365G0892' => 'tar', 'TAR636G0166' => 'tar', 'TAR636G0646' => 'tar', 'TAR636G0869' => 'tar', 'TAR636G1317' => 'tar', 'TAR636G1744' => 'tar', 'TAR636G3358' => 'tar', 'TAR636G3436' => 'tar', 'THA.LOC104803047' => 'tha', 'Thecc.04G238900' => 'tca', 'Thhalv10021557m.g' => 'esa', 'Thhalv10026318m.g' => 'esa', 'Thhalv10026335m.g' => 'esa', 'TPR.G17433' => 'tpr', 'TPR.G18915' => 'tpr', 'TPR.G26125' => 'tpr', 'TWI09G0677' => 'twi', 'TWI73G0287' => 'twi', 'unitig_748.g8326' => 'ugi', 'vmacro15370' => 'vma', 'vmacro15371' => 'vma', 'vmacro15372' => 'vma', 'vmacro15373' => 'vma', 'vmacro15374' => 'vma', 'VMungo0720G2826' => 'vmu', 'Zm00001eb116960' => 'zma', 'Zm00001eb301260' => 'zma', 'Zm00001eb301270' => 'zma' ) $gf_id = 'HOM05D001460' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001460' ) $data_identifier = 'HOM05D001460' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 4, 'aag' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 2, 'aox' => (int) 2, 'arhy' => (int) 4, 'ath' => (int) 2, 'atr' => (int) 1, 'acertr' => (int) 10, 'cqu' => (int) 4, 'bca' => (int) 11, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 1, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 1, 'ccan' => (int) 1, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 1, 'col' => (int) 1, 'cpa' => (int) 1, 'cre' => (int) 7, 'csa' => (int) 1, 'camsi' => (int) 2, 'dca' => (int) 3, 'din' => (int) 2, 'dzi' => (int) 3, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 14, 'fve' => (int) 9, 'gma' => (int) 2, 'ghi' => (int) 4, 'gra' => (int) 2, 'vvi' => (int) 1, 'han' => (int) 13, 'cav' => (int) 1, 'hma' => (int) 2, 'sun' => (int) 2, 'lal' => (int) 2, 'lonja' => (int) 12, 'lja' => (int) 1, 'lsa' => (int) 7, 'mes' => (int) 1, 'mpo' => (int) 27, 'mbi' => (int) 1, 'mco' => (int) 8, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 1, 'egut' => (int) 1, 'ama' => (int) 1, 'nta' => (int) 4, 'nnu' => (int) 2, 'oeu' => (int) 3, 'osa' => (int) 4, 'pax' => (int) 9, 'pgr' => (int) 1, 'stu' => (int) 1, 'pvu' => (int) 1, 'ptr' => (int) 4, 'ppa' => (int) 22, 'pco' => (int) 6, 'ppe' => (int) 6, 'psa' => (int) 5, 'pso' => (int) 19, 'qlo' => (int) 5, 'rch' => (int) 7, 'rsi' => (int) 20, 'sbr' => (int) 5, 'sbo' => (int) 1, 'sci' => (int) 2, 'sed' => (int) 2, 'sgi' => (int) 12, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 2, 'tar' => (int) 10, 'tha' => (int) 1, 'tca' => (int) 1, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 2, 'ugi' => (int) 1, 'vma' => (int) 5, 'vmu' => (int) 1, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb301270' $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' => 'HOM05D001460', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '433', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p22980' => 'bna', 'A01p32340' => 'bna', 'A03p42970' => 'bna', 'A05p25880' => 'bna', 'Aa31LG8G9320' => 'aar', 'Aa31LG8G9330' => 'aar', 'Aa31LG8G9340' => 'aar', 'Aa31sc221G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1034' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1528' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.829' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2222' => 'aag', 'Ah.12g058830' => 'amhyb', 'Ah.12g058840' => 'amhyb', 'AL3G37160' => 'aly', 'AL7G41310' => 'aly', 'Aqoxy5G00395' => 'aox', 'Aqoxy5G00396' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0C8NZA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5185HY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JZ1PRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MD3LS0' => 'arhy', 'AT3G22840' => 'ath', 'AT4G14690' => 'ath', 'ATR0665G054' => 'atr', 'Atru.chr4.2344' => 'acertr', 'Atru.chr4.2346' => 'acertr', 'Atru.chr4.2347' => 'acertr', 'Atru.chr4.2348' => 'acertr', 'Atru.chr4.2355' => 'acertr', 'Atru.chr4.2356' => 'acertr', 'Atru.chr4.2358' => 'acertr', 'Atru.chr4.2359' => 'acertr', 'Atru.chr4.2360' => 'acertr', 'Atru.chr4.2361' => 'acertr', 'AUR62030476' => 'cqu', 'AUR62030478' => 'cqu', 'AUR62030819' => 'cqu', 'AUR62030820' => 'cqu', 'BcaB03g14648' => 'bca', 'BcaB04g20492' => 'bca', 'BcaB06g26399' => 'bca', 'BcaC01g03416' => 'bca', 'BcaC01g03419' => 'bca', 'BcaC01g03421' => 'bca', 'BcaC01g03424' => 'bca', 'BcaC05g28012' => 'bca', 'BcaC09g49212' => 'bca', 'BcaC09g50140' => 'bca', 'BcaNung00346' => 'bca', 'BolC1t02785H' => 'bol', 'BolC1t04095H' => 'bol', 'BolC3t17545H' => 'bol', 'BolC5t32769H' => 'bol', 'BraA01t02211Z' => 'bra', 'BraA01t03359Z' => 'bra', 'BraA03t13441Z' => 'bra', 'BraA05t21476Z' => 'bra', 'C01p28420' => 'bna', 'C01p41350' => 'bna', 'C03p52750' => 'bna', 'C03p52780' => 'bna', 'C05p40270' => 'bna', 'CAN.G1437.9' => 'can', 'CANSAT78G0035' => 'cansat', 'CANSAT78G1036' => 'cansat', 'CANSAT78G2272' => 'cansat', 'CANSAT78G2478' => 'cansat', 'CARHR098700' => 'chi', 'CARHR221120' => 'chi', 'CARHR221150' => 'chi', 'Carub.0003s2297' => 'cru', 'Carub.0007s2749' => 'cru', 'Carub.0007s2750' => 'cru', 'Carub.0007s2751' => 'cru', 'Ca_10849_v3' => 'car', 'Cc03_g04300' => 'ccan', 'CDE02G3648' => 'cde', 'CDE05G0060' => 'cde', 'CDE05G0692' => 'cde', 'CDE05G2285' => 'cde', 'CDE05G2884' => 'cde', 'CDE05G3072' => 'cde', 'Cfa008439' => 'cfa', 'Cfa008441' => 'cfa', 'Cfa008443' => 'cfa', 'Cfa008448' => 'cfa', 'Ciclev10005974m.g' => 'ccl', 'Ciclev10006006m.g' => 'ccl', 'Ciclev10006775m.g' => 'ccl', 'CiPaw.02G120400' => 'cil', 'CiPaw.02G120500' => 'cil', 'CiPaw.02G120600' => 'cil', 'ClCG05G004850' => 'cla', 'COL.COLO4_21566' => 'col', 'Cpa.g.sc44.124' => 'cpa', 'Cre07.g320400' => 'cre', 'Cre07.g320450' => 'cre', 'Cre08.g384650' => 'cre', 'Cre09.g393173' => 'cre', 'Cre09.g394325' => 'cre', 'Cre14.g626750' => 'cre', 'Cre16.g679250' => 'cre', 'CsaV3_3G012890' => 'csa', 'CSS0010865' => 'camsi', 'CSS0044338' => 'camsi', 'DCAR_002366' => 'dca', 'DCAR_030687' => 'dca', 'DCAR_030688' => 'dca', 'Dinv14047' => 'din', 'Dinv14048' => 'din', 'Duzib151G0105' => 'dzi', 'Duzib151G0114' => 'dzi', 'Duzib212G1029' => 'dzi', 'ECA232G3536' => 'eca', 'ECA240G0786' => 'eca', 'ECA240G1802' => 'eca', 'ECA240G3760' => 'eca', 'ECA240G3920' => 'eca', 'EL10Ac5g12536' => 'bvu', 'EL10Ac5g12537' => 'bvu', 'EL10Ac5g12538' => 'bvu', 'Eucgr.B01004' => 'egr', 'Eucgr.B01006' => 'egr', 'Eucgr.B01007' => 'egr', 'Eucgr.B01008' => 'egr', 'Eucgr.B01895' => 'egr', 'Eucgr.B01896' => 'egr', 'FAN04G1456' => 'fan', 'FAN08G1769' => 'fan', 'FAN08G2160' => 'fan', 'FAN13G2403' => 'fan', 'FAN13G3303' => 'fan', 'FAN15G2435' => 'fan', 'FAN17G0672' => 'fan', 'FAN17G2441' => 'fan', 'FAN18G1024' => 'fan', 'FAN22G1458' => 'fan', 'FAN24G0037' => 'fan', 'FAN24G0429' => 'fan', 'FAN24G2387' => 'fan', 'FAN27G2746' => 'fan', 'FvH4_2g20400' => 'fve', 'FvH4_2g20420' => 'fve', 'FvH4_2g20430' => 'fve', 'FvH4_4g01270' => 'fve', 'FvH4_4g01290' => 'fve', 'FvH4_4g01300' => 'fve', 'FvH4_4g01310' => 'fve', 'FvH4_4g01330' => 'fve', 'FvH4_5g09070' => 'fve', 'Glyma.10G243800' => 'gma', 'Glyma.20G150600' => 'gma', 'Gohir.A09G219200' => 'ghi', 'Gohir.A09G219300' => 'ghi', 'Gohir.D09G221400' => 'ghi', 'Gohir.D09G221500' => 'ghi', 'Gorai.006G242600' => 'gra', 'Gorai.006G242700' => 'gra', 'GSVIVG01018044001' => 'vvi', 'HanXRQChr03g0083821' => 'han', 'HanXRQChr03g0083841' => 'han', 'HanXRQChr03g0083881' => 'han', 'HanXRQChr03g0083901' => 'han', 'HanXRQChr03g0083921' => 'han', 'HanXRQChr03g0085331' => 'han', 'HanXRQChr03g0085361' => 'han', 'HanXRQChr03g0085411' => 'han', 'HanXRQChr03g0085421' => 'han', 'HanXRQChr03g0085431' => 'han', 'HanXRQChr08g0221991' => 'han', 'HanXRQChr11g0336061' => 'han', 'HanXRQChr11g0336411' => 'han', 'Haze_11234' => 'cav', 'Hma1.2p1_0549F.1_g177010' => 'hma', 'Hma1.2p1_0602F.1_g187630' => 'hma', 'Hund14876' => 'sun', 'Hund14879' => 'sun', 'Lalb_Chr06g0160741' => 'lal', 'Lalb_Chr21g0304781' => 'lal', 'Lj3A726G19' => 'lonja', 'Lj3A726T23' => 'lonja', 'Lj3A726T24' => 'lonja', 'Lj3A726T25' => 'lonja', 'Lj3A727T17' => 'lonja', 'Lj3C726T0' => 'lonja', 'Lj3C726T2' => 'lonja', 'Lj3P725T35' => 'lonja', 'Lj3P727T10' => 'lonja', 'Lj3P727T12' => 'lonja', 'Lj3P727T14' => 'lonja', 'Lj5g0023109' => 'lja', 'Lj6P646T44' => 'lonja', 'Lsat_1_v5_gn_6_75760' => 'lsa', 'Lsat_1_v5_gn_6_75800' => 'lsa', 'Lsat_1_v5_gn_6_75900' => 'lsa', 'Lsat_1_v5_gn_6_76240' => 'lsa', 'Lsat_1_v5_gn_6_76441' => 'lsa', 'Lsat_1_v5_gn_6_76700' => 'lsa', 'Lsat_1_v5_gn_6_76760' => 'lsa', 'Manes.15G033100' => 'mes', 'Mapoly0004s0074' => 'mpo', 'Mapoly0004s0075' => 'mpo', 'Mapoly0004s0163' => 'mpo', 'Mapoly0004s0164' => 'mpo', 'Mapoly0021s0018' => 'mpo', 'Mapoly0041s0136' => 'mpo', 'Mapoly0041s0137' => 'mpo', 'Mapoly0041s0138' => 'mpo', 'Mapoly0041s0139' => 'mpo', 'Mapoly0041s0141' => 'mpo', 'Mapoly0041s0142' => 'mpo', 'Mapoly0041s0143' => 'mpo', 'Mapoly0041s0144' => 'mpo', 'Mapoly0041s0145' => 'mpo', 'Mapoly0047s0106' => 'mpo', 'Mapoly0047s0108' => 'mpo', 'Mapoly0050s0051' => 'mpo', 'Mapoly0050s0052' => 'mpo', 'Mapoly0050s0053' => 'mpo', 'Mapoly0058s0013' => 'mpo', 'Mapoly0091s0078' => 'mpo', 'Mapoly0091s0079' => 'mpo', 'Mapoly0091s0080' => 'mpo', 'Mapoly0091s0081' => 'mpo', 'Mapoly0278s0004' => 'mpo', 'Mapoly0278s0005' => 'mpo', 'Mapoly0278s0006' => 'mpo', 'MBI11_g30648_MAGBIO' => 'mbi', 'MCO03G194' => 'mco', 'MCO03G590' => 'mco', 'MCO07G312' => 'mco', 'MCO10G318' => 'mco', 'MCO12G244' => 'mco', 'MCO13G148' => 'mco', 'MCO13G194' => 'mco', 'MCO16G238' => 'mco', 'MD06G1134100' => 'mdo', 'MD13G1200100' => 'mdo', 'MD13G1200300' => 'mdo', 'MD13G1200600' => 'mdo', 'MD14G1150400' => 'mdo', 'MD16G1200000' => 'mdo', 'Medtr1g102570' => 'mtr', 'Medtr1g102780' => 'mtr', 'Medtr1g102800' => 'mtr', 'Medtr1g102810' => 'mtr', 'Medtr1g102830' => 'mtr', 'MELO3C006499.2' => 'cme', 'Migut.G00385' => 'egut', 'MSTRG.4063' => 'ama', 'Nitab4.5_0000090g0260' => 'nta', 'Nitab4.5_0000977g0030' => 'nta', 'Nitab4.5_0002541g0040' => 'nta', 'Nitab4.5_0007068g0040' => 'nta', 'Nn005s41408' => 'nnu', 'Nn005s41410' => 'nnu', 'Oeu010310.1' => 'oeu', 'Oeu010311.1' => 'oeu', 'Oeu043472.1' => 'oeu', 'Os01g0246400' => 'osa', 'Os04g0267950' => 'osa', 'Os07g0178700' => 'osa', 'Os07g0178800' => 'osa', 'Peaxi162Scf00316g00046' => 'pax', 'Peaxi162Scf00316g00049' => 'pax', 'Peaxi162Scf00316g00059' => 'pax', 'Peaxi162Scf00316g00328' => 'pax', 'Peaxi162Scf00316g00329' => 'pax', 'Peaxi162Scf00316g00411' => 'pax', 'Peaxi162Scf00316g00521' => 'pax', 'Peaxi162Scf00492g00068' => 'pax', 'Peaxi162Scf35631g00002' => 'pax', 'PGR142G3720' => 'pgr', 'PGSC0003DMG400006442' => 'stu', 'Phvul.007G062000' => 'pvu', 'Potri.008G157750' => 'ptr', 'Potri.008G157900' => 'ptr', 'Potri.008G158000' => 'ptr', 'Potri.008G158200' => 'ptr', 'Pp3c11_7280' => 'ppa', 'Pp3c11_7980' => 'ppa', 'Pp3c12_19450' => 'ppa', 'Pp3c14_1480' => 'ppa', 'Pp3c14_1501' => 'ppa', 'Pp3c16_4900' => 'ppa', 'Pp3c16_5010' => 'ppa', 'Pp3c16_5060' => 'ppa', 'Pp3c19_18250' => 'ppa', 'Pp3c23_8530' => 'ppa', 'Pp3c23_8550' => 'ppa', 'Pp3c24_9670' => 'ppa', 'Pp3c2_21390' => 'ppa', 'Pp3c2_31380' => 'ppa', 'Pp3c3_16620' => 'ppa', 'Pp3c3_8090' => 'ppa', 'Pp3c3_8110' => 'ppa', 'Pp3c3_8130' => 'ppa', 'Pp3c3_8150' => 'ppa', 'Pp3c4_14320' => 'ppa', 'Pp3c6_2560' => 'ppa', 'Pp3c9_16700' => 'ppa', 'PRCOL_00000234' => 'pco', 'PRCOL_00000235' => 'pco', 'PRCOL_00000777' => 'pco', 'PRCOL_00002344' => 'pco', 'PRCOL_00002372' => 'pco', 'PRCOL_00006120' => 'pco', 'Prupe.1G021400' => 'ppe', 'Prupe.1G021500' => 'ppe', 'Prupe.1G021600' => 'ppe', 'Prupe.1G021700' => 'ppe', 'Prupe.1G021800' => 'ppe', 'Prupe.5G145100' => 'ppe', 'Psat6g204040' => 'psa', 'Psat6g204800' => 'psa', 'Psat6g204920' => 'psa', 'Psat6g204960' => 'psa', 'Psat6g205080' => 'psa', 'PSO017G0271' => 'pso', 'PSO017G1276' => 'pso', 'PSO017G1429' => 'pso', 'PSO017G1861' => 'pso', 'PSO017G2787' => 'pso', 'PSO017G4466' => 'pso', 'PSO017G5118' => 'pso', 'PSO017G5420' => 'pso', 'PSO063G3678' => 'pso', 'PSO210G0546' => 'pso', 'PSO317G0001' => 'pso', 'PSO357G0512' => 'pso', 'PSO478G2682' => 'pso', 'PSO647G0001' => 'pso', 'PSO675G0001' => 'pso', 'PSO675G2699' => 'pso', 'PSO675G2849' => 'pso', 'PSO675G4991' => 'pso', 'PSO689G0001' => 'pso', 'QL06p000916' => 'qlo', 'QL06p000921' => 'qlo', 'QL06p001398' => 'qlo', 'QL06p001407' => 'qlo', 'QL06p002031' => 'qlo', 'RcHm_v2.0_Chr4g0387791' => 'rch', 'RcHm_v2.0_Chr4g0387801' => 'rch', 'RcHm_v2.0_Chr6g0286501' => 'rch', 'RcHm_v2.0_Chr6g0286511' => 'rch', 'RcHm_v2.0_Chr6g0286521' => 'rch', 'RcHm_v2.0_Chr6g0286531' => 'rch', 'RcHm_v2.0_Chr7g0189141' => 'rch', 'Rhsim02G0028700' => 'rsi', 'Rhsim02G0028800' => 'rsi', 'Rhsim02G0028900' => 'rsi', 'Rhsim02G0029000' => 'rsi', 'Rhsim02G0029100' => 'rsi', 'Rhsim02G0029200' => 'rsi', 'Rhsim02G0029300' => 'rsi', 'Rhsim02G0029400' => 'rsi', 'Rhsim02G0029500' => 'rsi', 'Rhsim02G0029600' => 'rsi', 'RhsimUnG0024000' => 'rsi', 'RhsimUnG0024100' => 'rsi', 'RhsimUnG0024200' => 'rsi', 'RhsimUnG0024300' => 'rsi', 'RhsimUnG0024400' => 'rsi', 'RhsimUnG0024500' => 'rsi', 'RhsimUnG0024700' => 'rsi', 'RhsimUnG0024800' => 'rsi', 'RhsimUnG0024900' => 'rsi', 'RhsimUnG0025100' => 'rsi', 'Sabra08G0120200' => 'sbr', 'Sabra08G0120300' => 'sbr', 'Sabra08G0120500' => 'sbr', 'Sabra08G0120600' => 'sbr', 'Sabra10G0158900' => 'sbr', 'SalBow2G3492' => 'sbo', 'Sc13g0004760' => 'sci', 'Sc13g0004770' => 'sci', 'Sed0003417' => 'sed', 'Sed0019750' => 'sed', 'SEGI_03419' => 'sgi', 'SEGI_05907' => 'sgi', 'SEGI_10682' => 'sgi', 'SEGI_13528' => 'sgi', 'SEGI_16081' => 'sgi', 'SEGI_19370' => 'sgi', 'SEGI_21015' => 'sgi', 'SEGI_21944' => 'sgi', 'SEGI_32906' => 'sgi', 'SEGI_33093' => 'sgi', 'SEGI_36110' => 'sgi', 'SEGI_40397' => 'sgi', 'SGA_v2.0_scaffold191G40426' => 'sas', 'SGA_v2.0_scaffold353G49717' => 'sas', 'SGA_v2.0_scaffold50G18550' => 'sas', 'SMO119G0173' => 'smo', 'SMO172G0002' => 'smo', 'Solyc09g082690.3' => 'sly', 'Solyc09g082700.2' => 'sly', 'Sopen09g031550' => 'spe', 'Sopen09g031560' => 'spe', 'Sp3g20540' => 'spa', 'Sp7g07580' => 'spa', 'TAR134G0002' => 'tar', 'TAR236G0001' => 'tar', 'TAR365G0892' => 'tar', 'TAR636G0166' => 'tar', 'TAR636G0646' => 'tar', 'TAR636G0869' => 'tar', 'TAR636G1317' => 'tar', 'TAR636G1744' => 'tar', 'TAR636G3358' => 'tar', 'TAR636G3436' => 'tar', 'THA.LOC104803047' => 'tha', 'Thecc.04G238900' => 'tca', 'Thhalv10021557m.g' => 'esa', 'Thhalv10026318m.g' => 'esa', 'Thhalv10026335m.g' => 'esa', 'TPR.G17433' => 'tpr', 'TPR.G18915' => 'tpr', 'TPR.G26125' => 'tpr', 'TWI09G0677' => 'twi', 'TWI73G0287' => 'twi', 'unitig_748.g8326' => 'ugi', 'vmacro15370' => 'vma', 'vmacro15371' => 'vma', 'vmacro15372' => 'vma', 'vmacro15373' => 'vma', 'vmacro15374' => 'vma', 'VMungo0720G2826' => 'vmu', 'Zm00001eb116960' => 'zma', 'Zm00001eb301260' => 'zma', 'Zm00001eb301270' => 'zma' ), 'gf_id' => 'HOM05D001460', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001460' ), 'data_identifier' => 'HOM05D001460', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001460', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '433', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p22980' => 'bna', 'A01p32340' => 'bna', 'A03p42970' => 'bna', 'A05p25880' => 'bna', 'Aa31LG8G9320' => 'aar', 'Aa31LG8G9330' => 'aar', 'Aa31LG8G9340' => 'aar', 'Aa31sc221G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1034' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1528' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.829' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2222' => 'aag', 'Ah.12g058830' => 'amhyb', 'Ah.12g058840' => 'amhyb', 'AL3G37160' => 'aly', 'AL7G41310' => 'aly', 'Aqoxy5G00395' => 'aox', 'Aqoxy5G00396' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0C8NZA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5185HY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JZ1PRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MD3LS0' => 'arhy', 'AT3G22840' => 'ath', 'AT4G14690' => 'ath', 'ATR0665G054' => 'atr', 'Atru.chr4.2344' => 'acertr', 'Atru.chr4.2346' => 'acertr', 'Atru.chr4.2347' => 'acertr', 'Atru.chr4.2348' => 'acertr', 'Atru.chr4.2355' => 'acertr', 'Atru.chr4.2356' => 'acertr', 'Atru.chr4.2358' => 'acertr', 'Atru.chr4.2359' => 'acertr', 'Atru.chr4.2360' => 'acertr', 'Atru.chr4.2361' => 'acertr', 'AUR62030476' => 'cqu', 'AUR62030478' => 'cqu', 'AUR62030819' => 'cqu', 'AUR62030820' => 'cqu', 'BcaB03g14648' => 'bca', 'BcaB04g20492' => 'bca', 'BcaB06g26399' => 'bca', 'BcaC01g03416' => 'bca', 'BcaC01g03419' => 'bca', 'BcaC01g03421' => 'bca', 'BcaC01g03424' => 'bca', 'BcaC05g28012' => 'bca', 'BcaC09g49212' => 'bca', 'BcaC09g50140' => 'bca', 'BcaNung00346' => 'bca', 'BolC1t02785H' => 'bol', 'BolC1t04095H' => 'bol', 'BolC3t17545H' => 'bol', 'BolC5t32769H' => 'bol', 'BraA01t02211Z' => 'bra', 'BraA01t03359Z' => 'bra', 'BraA03t13441Z' => 'bra', 'BraA05t21476Z' => 'bra', 'C01p28420' => 'bna', 'C01p41350' => 'bna', 'C03p52750' => 'bna', 'C03p52780' => 'bna', 'C05p40270' => 'bna', 'CAN.G1437.9' => 'can', 'CANSAT78G0035' => 'cansat', 'CANSAT78G1036' => 'cansat', 'CANSAT78G2272' => 'cansat', 'CANSAT78G2478' => 'cansat', 'CARHR098700' => 'chi', 'CARHR221120' => 'chi', 'CARHR221150' => 'chi', 'Carub.0003s2297' => 'cru', 'Carub.0007s2749' => 'cru', 'Carub.0007s2750' => 'cru', 'Carub.0007s2751' => 'cru', 'Ca_10849_v3' => 'car', 'Cc03_g04300' => 'ccan', 'CDE02G3648' => 'cde', 'CDE05G0060' => 'cde', 'CDE05G0692' => 'cde', 'CDE05G2285' => 'cde', 'CDE05G2884' => 'cde', 'CDE05G3072' => 'cde', 'Cfa008439' => 'cfa', 'Cfa008441' => 'cfa', 'Cfa008443' => 'cfa', 'Cfa008448' => 'cfa', 'Ciclev10005974m.g' => 'ccl', 'Ciclev10006006m.g' => 'ccl', 'Ciclev10006775m.g' => 'ccl', 'CiPaw.02G120400' => 'cil', 'CiPaw.02G120500' => 'cil', 'CiPaw.02G120600' => 'cil', 'ClCG05G004850' => 'cla', 'COL.COLO4_21566' => 'col', 'Cpa.g.sc44.124' => 'cpa', 'Cre07.g320400' => 'cre', 'Cre07.g320450' => 'cre', 'Cre08.g384650' => 'cre', 'Cre09.g393173' => 'cre', 'Cre09.g394325' => 'cre', 'Cre14.g626750' => 'cre', 'Cre16.g679250' => 'cre', 'CsaV3_3G012890' => 'csa', 'CSS0010865' => 'camsi', 'CSS0044338' => 'camsi', 'DCAR_002366' => 'dca', 'DCAR_030687' => 'dca', 'DCAR_030688' => 'dca', 'Dinv14047' => 'din', 'Dinv14048' => 'din', 'Duzib151G0105' => 'dzi', 'Duzib151G0114' => 'dzi', 'Duzib212G1029' => 'dzi', 'ECA232G3536' => 'eca', 'ECA240G0786' => 'eca', 'ECA240G1802' => 'eca', 'ECA240G3760' => 'eca', 'ECA240G3920' => 'eca', 'EL10Ac5g12536' => 'bvu', 'EL10Ac5g12537' => 'bvu', 'EL10Ac5g12538' => 'bvu', 'Eucgr.B01004' => 'egr', 'Eucgr.B01006' => 'egr', 'Eucgr.B01007' => 'egr', 'Eucgr.B01008' => 'egr', 'Eucgr.B01895' => 'egr', 'Eucgr.B01896' => 'egr', 'FAN04G1456' => 'fan', 'FAN08G1769' => 'fan', 'FAN08G2160' => 'fan', 'FAN13G2403' => 'fan', 'FAN13G3303' => 'fan', 'FAN15G2435' => 'fan', 'FAN17G0672' => 'fan', 'FAN17G2441' => 'fan', 'FAN18G1024' => 'fan', 'FAN22G1458' => 'fan', 'FAN24G0037' => 'fan', 'FAN24G0429' => 'fan', 'FAN24G2387' => 'fan', 'FAN27G2746' => 'fan', 'FvH4_2g20400' => 'fve', 'FvH4_2g20420' => 'fve', 'FvH4_2g20430' => 'fve', 'FvH4_4g01270' => 'fve', 'FvH4_4g01290' => 'fve', 'FvH4_4g01300' => 'fve', 'FvH4_4g01310' => 'fve', 'FvH4_4g01330' => 'fve', 'FvH4_5g09070' => 'fve', 'Glyma.10G243800' => 'gma', 'Glyma.20G150600' => 'gma', 'Gohir.A09G219200' => 'ghi', 'Gohir.A09G219300' => 'ghi', 'Gohir.D09G221400' => 'ghi', 'Gohir.D09G221500' => 'ghi', 'Gorai.006G242600' => 'gra', 'Gorai.006G242700' => 'gra', 'GSVIVG01018044001' => 'vvi', 'HanXRQChr03g0083821' => 'han', 'HanXRQChr03g0083841' => 'han', 'HanXRQChr03g0083881' => 'han', 'HanXRQChr03g0083901' => 'han', 'HanXRQChr03g0083921' => 'han', 'HanXRQChr03g0085331' => 'han', 'HanXRQChr03g0085361' => 'han', 'HanXRQChr03g0085411' => 'han', 'HanXRQChr03g0085421' => 'han', 'HanXRQChr03g0085431' => 'han', 'HanXRQChr08g0221991' => 'han', 'HanXRQChr11g0336061' => 'han', 'HanXRQChr11g0336411' => 'han', 'Haze_11234' => 'cav', 'Hma1.2p1_0549F.1_g177010' => 'hma', 'Hma1.2p1_0602F.1_g187630' => 'hma', 'Hund14876' => 'sun', 'Hund14879' => 'sun', 'Lalb_Chr06g0160741' => 'lal', 'Lalb_Chr21g0304781' => 'lal', 'Lj3A726G19' => 'lonja', 'Lj3A726T23' => 'lonja', 'Lj3A726T24' => 'lonja', 'Lj3A726T25' => 'lonja', 'Lj3A727T17' => 'lonja', 'Lj3C726T0' => 'lonja', 'Lj3C726T2' => 'lonja', 'Lj3P725T35' => 'lonja', 'Lj3P727T10' => 'lonja', 'Lj3P727T12' => 'lonja', 'Lj3P727T14' => 'lonja', 'Lj5g0023109' => 'lja', 'Lj6P646T44' => 'lonja', 'Lsat_1_v5_gn_6_75760' => 'lsa', 'Lsat_1_v5_gn_6_75800' => 'lsa', 'Lsat_1_v5_gn_6_75900' => 'lsa', 'Lsat_1_v5_gn_6_76240' => 'lsa', 'Lsat_1_v5_gn_6_76441' => 'lsa', 'Lsat_1_v5_gn_6_76700' => 'lsa', 'Lsat_1_v5_gn_6_76760' => 'lsa', 'Manes.15G033100' => 'mes', 'Mapoly0004s0074' => 'mpo', 'Mapoly0004s0075' => 'mpo', 'Mapoly0004s0163' => 'mpo', 'Mapoly0004s0164' => 'mpo', 'Mapoly0021s0018' => 'mpo', 'Mapoly0041s0136' => 'mpo', 'Mapoly0041s0137' => 'mpo', 'Mapoly0041s0138' => 'mpo', 'Mapoly0041s0139' => 'mpo', 'Mapoly0041s0141' => 'mpo', 'Mapoly0041s0142' => 'mpo', 'Mapoly0041s0143' => 'mpo', 'Mapoly0041s0144' => 'mpo', 'Mapoly0041s0145' => 'mpo', 'Mapoly0047s0106' => 'mpo', 'Mapoly0047s0108' => 'mpo', 'Mapoly0050s0051' => 'mpo', 'Mapoly0050s0052' => 'mpo', 'Mapoly0050s0053' => 'mpo', 'Mapoly0058s0013' => 'mpo', 'Mapoly0091s0078' => 'mpo', 'Mapoly0091s0079' => 'mpo', 'Mapoly0091s0080' => 'mpo', 'Mapoly0091s0081' => 'mpo', 'Mapoly0278s0004' => 'mpo', 'Mapoly0278s0005' => 'mpo', 'Mapoly0278s0006' => 'mpo', 'MBI11_g30648_MAGBIO' => 'mbi', 'MCO03G194' => 'mco', 'MCO03G590' => 'mco', 'MCO07G312' => 'mco', 'MCO10G318' => 'mco', 'MCO12G244' => 'mco', 'MCO13G148' => 'mco', 'MCO13G194' => 'mco', 'MCO16G238' => 'mco', 'MD06G1134100' => 'mdo', 'MD13G1200100' => 'mdo', 'MD13G1200300' => 'mdo', 'MD13G1200600' => 'mdo', 'MD14G1150400' => 'mdo', 'MD16G1200000' => 'mdo', 'Medtr1g102570' => 'mtr', 'Medtr1g102780' => 'mtr', 'Medtr1g102800' => 'mtr', 'Medtr1g102810' => 'mtr', 'Medtr1g102830' => 'mtr', 'MELO3C006499.2' => 'cme', 'Migut.G00385' => 'egut', 'MSTRG.4063' => 'ama', 'Nitab4.5_0000090g0260' => 'nta', 'Nitab4.5_0000977g0030' => 'nta', 'Nitab4.5_0002541g0040' => 'nta', 'Nitab4.5_0007068g0040' => 'nta', 'Nn005s41408' => 'nnu', 'Nn005s41410' => 'nnu', 'Oeu010310.1' => 'oeu', 'Oeu010311.1' => 'oeu', 'Oeu043472.1' => 'oeu', 'Os01g0246400' => 'osa', 'Os04g0267950' => 'osa', 'Os07g0178700' => 'osa', 'Os07g0178800' => 'osa', 'Peaxi162Scf00316g00046' => 'pax', 'Peaxi162Scf00316g00049' => 'pax', 'Peaxi162Scf00316g00059' => 'pax', 'Peaxi162Scf00316g00328' => 'pax', 'Peaxi162Scf00316g00329' => 'pax', 'Peaxi162Scf00316g00411' => 'pax', 'Peaxi162Scf00316g00521' => 'pax', 'Peaxi162Scf00492g00068' => 'pax', 'Peaxi162Scf35631g00002' => 'pax', 'PGR142G3720' => 'pgr', 'PGSC0003DMG400006442' => 'stu', 'Phvul.007G062000' => 'pvu', 'Potri.008G157750' => 'ptr', 'Potri.008G157900' => 'ptr', 'Potri.008G158000' => 'ptr', 'Potri.008G158200' => 'ptr', 'Pp3c11_7280' => 'ppa', 'Pp3c11_7980' => 'ppa', 'Pp3c12_19450' => 'ppa', 'Pp3c14_1480' => 'ppa', 'Pp3c14_1501' => 'ppa', 'Pp3c16_4900' => 'ppa', 'Pp3c16_5010' => 'ppa', 'Pp3c16_5060' => 'ppa', 'Pp3c19_18250' => 'ppa', 'Pp3c23_8530' => 'ppa', 'Pp3c23_8550' => 'ppa', 'Pp3c24_9670' => 'ppa', 'Pp3c2_21390' => 'ppa', 'Pp3c2_31380' => 'ppa', 'Pp3c3_16620' => 'ppa', 'Pp3c3_8090' => 'ppa', 'Pp3c3_8110' => 'ppa', 'Pp3c3_8130' => 'ppa', 'Pp3c3_8150' => 'ppa', 'Pp3c4_14320' => 'ppa', 'Pp3c6_2560' => 'ppa', 'Pp3c9_16700' => 'ppa', 'PRCOL_00000234' => 'pco', 'PRCOL_00000235' => 'pco', 'PRCOL_00000777' => 'pco', 'PRCOL_00002344' => 'pco', 'PRCOL_00002372' => 'pco', 'PRCOL_00006120' => 'pco', 'Prupe.1G021400' => 'ppe', 'Prupe.1G021500' => 'ppe', 'Prupe.1G021600' => 'ppe', 'Prupe.1G021700' => 'ppe', 'Prupe.1G021800' => 'ppe', 'Prupe.5G145100' => 'ppe', 'Psat6g204040' => 'psa', 'Psat6g204800' => 'psa', 'Psat6g204920' => 'psa', 'Psat6g204960' => 'psa', 'Psat6g205080' => 'psa', 'PSO017G0271' => 'pso', 'PSO017G1276' => 'pso', 'PSO017G1429' => 'pso', 'PSO017G1861' => 'pso', 'PSO017G2787' => 'pso', 'PSO017G4466' => 'pso', 'PSO017G5118' => 'pso', 'PSO017G5420' => 'pso', 'PSO063G3678' => 'pso', 'PSO210G0546' => 'pso', 'PSO317G0001' => 'pso', 'PSO357G0512' => 'pso', 'PSO478G2682' => 'pso', 'PSO647G0001' => 'pso', 'PSO675G0001' => 'pso', 'PSO675G2699' => 'pso', 'PSO675G2849' => 'pso', 'PSO675G4991' => 'pso', 'PSO689G0001' => 'pso', 'QL06p000916' => 'qlo', 'QL06p000921' => 'qlo', 'QL06p001398' => 'qlo', 'QL06p001407' => 'qlo', 'QL06p002031' => 'qlo', 'RcHm_v2.0_Chr4g0387791' => 'rch', 'RcHm_v2.0_Chr4g0387801' => 'rch', 'RcHm_v2.0_Chr6g0286501' => 'rch', 'RcHm_v2.0_Chr6g0286511' => 'rch', 'RcHm_v2.0_Chr6g0286521' => 'rch', 'RcHm_v2.0_Chr6g0286531' => 'rch', 'RcHm_v2.0_Chr7g0189141' => 'rch', 'Rhsim02G0028700' => 'rsi', 'Rhsim02G0028800' => 'rsi', 'Rhsim02G0028900' => 'rsi', 'Rhsim02G0029000' => 'rsi', 'Rhsim02G0029100' => 'rsi', 'Rhsim02G0029200' => 'rsi', 'Rhsim02G0029300' => 'rsi', 'Rhsim02G0029400' => 'rsi', 'Rhsim02G0029500' => 'rsi', 'Rhsim02G0029600' => 'rsi', 'RhsimUnG0024000' => 'rsi', 'RhsimUnG0024100' => 'rsi', 'RhsimUnG0024200' => 'rsi', 'RhsimUnG0024300' => 'rsi', 'RhsimUnG0024400' => 'rsi', 'RhsimUnG0024500' => 'rsi', 'RhsimUnG0024700' => 'rsi', 'RhsimUnG0024800' => 'rsi', 'RhsimUnG0024900' => 'rsi', 'RhsimUnG0025100' => 'rsi', 'Sabra08G0120200' => 'sbr', 'Sabra08G0120300' => 'sbr', 'Sabra08G0120500' => 'sbr', 'Sabra08G0120600' => 'sbr', 'Sabra10G0158900' => 'sbr', 'SalBow2G3492' => 'sbo', 'Sc13g0004760' => 'sci', 'Sc13g0004770' => 'sci', 'Sed0003417' => 'sed', 'Sed0019750' => 'sed', 'SEGI_03419' => 'sgi', 'SEGI_05907' => 'sgi', 'SEGI_10682' => 'sgi', 'SEGI_13528' => 'sgi', 'SEGI_16081' => 'sgi', 'SEGI_19370' => 'sgi', 'SEGI_21015' => 'sgi', 'SEGI_21944' => 'sgi', 'SEGI_32906' => 'sgi', 'SEGI_33093' => 'sgi', 'SEGI_36110' => 'sgi', 'SEGI_40397' => 'sgi', 'SGA_v2.0_scaffold191G40426' => 'sas', 'SGA_v2.0_scaffold353G49717' => 'sas', 'SGA_v2.0_scaffold50G18550' => 'sas', 'SMO119G0173' => 'smo', 'SMO172G0002' => 'smo', 'Solyc09g082690.3' => 'sly', 'Solyc09g082700.2' => 'sly', 'Sopen09g031550' => 'spe', 'Sopen09g031560' => 'spe', 'Sp3g20540' => 'spa', 'Sp7g07580' => 'spa', 'TAR134G0002' => 'tar', 'TAR236G0001' => 'tar', 'TAR365G0892' => 'tar', 'TAR636G0166' => 'tar', 'TAR636G0646' => 'tar', 'TAR636G0869' => 'tar', 'TAR636G1317' => 'tar', 'TAR636G1744' => 'tar', 'TAR636G3358' => 'tar', 'TAR636G3436' => 'tar', 'THA.LOC104803047' => 'tha', 'Thecc.04G238900' => 'tca', 'Thhalv10021557m.g' => 'esa', 'Thhalv10026318m.g' => 'esa', 'Thhalv10026335m.g' => 'esa', 'TPR.G17433' => 'tpr', 'TPR.G18915' => 'tpr', 'TPR.G26125' => 'tpr', 'TWI09G0677' => 'twi', 'TWI73G0287' => 'twi', 'unitig_748.g8326' => 'ugi', 'vmacro15370' => 'vma', 'vmacro15371' => 'vma', 'vmacro15372' => 'vma', 'vmacro15373' => 'vma', 'vmacro15374' => 'vma', 'VMungo0720G2826' => 'vmu', 'Zm00001eb116960' => 'zma', 'Zm00001eb301260' => 'zma', 'Zm00001eb301270' => 'zma' ) $gf_id = 'HOM05D001460' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001460' ) $data_identifier = 'HOM05D001460' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 4, 'aag' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 2, 'aox' => (int) 2, 'arhy' => (int) 4, 'ath' => (int) 2, 'atr' => (int) 1, 'acertr' => (int) 10, 'cqu' => (int) 4, 'bca' => (int) 11, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 1, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 1, 'ccan' => (int) 1, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 1, 'col' => (int) 1, 'cpa' => (int) 1, 'cre' => (int) 7, 'csa' => (int) 1, 'camsi' => (int) 2, 'dca' => (int) 3, 'din' => (int) 2, 'dzi' => (int) 3, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 14, 'fve' => (int) 9, 'gma' => (int) 2, 'ghi' => (int) 4, 'gra' => (int) 2, 'vvi' => (int) 1, 'han' => (int) 13, 'cav' => (int) 1, 'hma' => (int) 2, 'sun' => (int) 2, 'lal' => (int) 2, 'lonja' => (int) 12, 'lja' => (int) 1, 'lsa' => (int) 7, 'mes' => (int) 1, 'mpo' => (int) 27, 'mbi' => (int) 1, 'mco' => (int) 8, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 1, 'egut' => (int) 1, 'ama' => (int) 1, 'nta' => (int) 4, 'nnu' => (int) 2, 'oeu' => (int) 3, 'osa' => (int) 4, 'pax' => (int) 9, 'pgr' => (int) 1, 'stu' => (int) 1, 'pvu' => (int) 1, 'ptr' => (int) 4, 'ppa' => (int) 22, 'pco' => (int) 6, 'ppe' => (int) 6, 'psa' => (int) 5, 'pso' => (int) 19, 'qlo' => (int) 5, 'rch' => (int) 7, 'rsi' => (int) 20, 'sbr' => (int) 5, 'sbo' => (int) 1, 'sci' => (int) 2, 'sed' => (int) 2, 'sgi' => (int) 12, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 2, 'tar' => (int) 10, 'tha' => (int) 1, 'tca' => (int) 1, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 2, 'ugi' => (int) 1, 'vma' => (int) 5, 'vmu' => (int) 1, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb301270' $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' => 'HOM05D001460', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '433', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p22980' => 'bna', 'A01p32340' => 'bna', 'A03p42970' => 'bna', 'A05p25880' => 'bna', 'Aa31LG8G9320' => 'aar', 'Aa31LG8G9330' => 'aar', 'Aa31LG8G9340' => 'aar', 'Aa31sc221G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1034' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1528' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.829' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2222' => 'aag', 'Ah.12g058830' => 'amhyb', 'Ah.12g058840' => 'amhyb', 'AL3G37160' => 'aly', 'AL7G41310' => 'aly', 'Aqoxy5G00395' => 'aox', 'Aqoxy5G00396' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0C8NZA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5185HY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JZ1PRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MD3LS0' => 'arhy', 'AT3G22840' => 'ath', 'AT4G14690' => 'ath', 'ATR0665G054' => 'atr', 'Atru.chr4.2344' => 'acertr', 'Atru.chr4.2346' => 'acertr', 'Atru.chr4.2347' => 'acertr', 'Atru.chr4.2348' => 'acertr', 'Atru.chr4.2355' => 'acertr', 'Atru.chr4.2356' => 'acertr', 'Atru.chr4.2358' => 'acertr', 'Atru.chr4.2359' => 'acertr', 'Atru.chr4.2360' => 'acertr', 'Atru.chr4.2361' => 'acertr', 'AUR62030476' => 'cqu', 'AUR62030478' => 'cqu', 'AUR62030819' => 'cqu', 'AUR62030820' => 'cqu', 'BcaB03g14648' => 'bca', 'BcaB04g20492' => 'bca', 'BcaB06g26399' => 'bca', 'BcaC01g03416' => 'bca', 'BcaC01g03419' => 'bca', 'BcaC01g03421' => 'bca', 'BcaC01g03424' => 'bca', 'BcaC05g28012' => 'bca', 'BcaC09g49212' => 'bca', 'BcaC09g50140' => 'bca', 'BcaNung00346' => 'bca', 'BolC1t02785H' => 'bol', 'BolC1t04095H' => 'bol', 'BolC3t17545H' => 'bol', 'BolC5t32769H' => 'bol', 'BraA01t02211Z' => 'bra', 'BraA01t03359Z' => 'bra', 'BraA03t13441Z' => 'bra', 'BraA05t21476Z' => 'bra', 'C01p28420' => 'bna', 'C01p41350' => 'bna', 'C03p52750' => 'bna', 'C03p52780' => 'bna', 'C05p40270' => 'bna', 'CAN.G1437.9' => 'can', 'CANSAT78G0035' => 'cansat', 'CANSAT78G1036' => 'cansat', 'CANSAT78G2272' => 'cansat', 'CANSAT78G2478' => 'cansat', 'CARHR098700' => 'chi', 'CARHR221120' => 'chi', 'CARHR221150' => 'chi', 'Carub.0003s2297' => 'cru', 'Carub.0007s2749' => 'cru', 'Carub.0007s2750' => 'cru', 'Carub.0007s2751' => 'cru', 'Ca_10849_v3' => 'car', 'Cc03_g04300' => 'ccan', 'CDE02G3648' => 'cde', 'CDE05G0060' => 'cde', 'CDE05G0692' => 'cde', 'CDE05G2285' => 'cde', 'CDE05G2884' => 'cde', 'CDE05G3072' => 'cde', 'Cfa008439' => 'cfa', 'Cfa008441' => 'cfa', 'Cfa008443' => 'cfa', 'Cfa008448' => 'cfa', 'Ciclev10005974m.g' => 'ccl', 'Ciclev10006006m.g' => 'ccl', 'Ciclev10006775m.g' => 'ccl', 'CiPaw.02G120400' => 'cil', 'CiPaw.02G120500' => 'cil', 'CiPaw.02G120600' => 'cil', 'ClCG05G004850' => 'cla', 'COL.COLO4_21566' => 'col', 'Cpa.g.sc44.124' => 'cpa', 'Cre07.g320400' => 'cre', 'Cre07.g320450' => 'cre', 'Cre08.g384650' => 'cre', 'Cre09.g393173' => 'cre', 'Cre09.g394325' => 'cre', 'Cre14.g626750' => 'cre', 'Cre16.g679250' => 'cre', 'CsaV3_3G012890' => 'csa', 'CSS0010865' => 'camsi', 'CSS0044338' => 'camsi', 'DCAR_002366' => 'dca', 'DCAR_030687' => 'dca', 'DCAR_030688' => 'dca', 'Dinv14047' => 'din', 'Dinv14048' => 'din', 'Duzib151G0105' => 'dzi', 'Duzib151G0114' => 'dzi', 'Duzib212G1029' => 'dzi', 'ECA232G3536' => 'eca', 'ECA240G0786' => 'eca', 'ECA240G1802' => 'eca', 'ECA240G3760' => 'eca', 'ECA240G3920' => 'eca', 'EL10Ac5g12536' => 'bvu', 'EL10Ac5g12537' => 'bvu', 'EL10Ac5g12538' => 'bvu', 'Eucgr.B01004' => 'egr', 'Eucgr.B01006' => 'egr', 'Eucgr.B01007' => 'egr', 'Eucgr.B01008' => 'egr', 'Eucgr.B01895' => 'egr', 'Eucgr.B01896' => 'egr', 'FAN04G1456' => 'fan', 'FAN08G1769' => 'fan', 'FAN08G2160' => 'fan', 'FAN13G2403' => 'fan', 'FAN13G3303' => 'fan', 'FAN15G2435' => 'fan', 'FAN17G0672' => 'fan', 'FAN17G2441' => 'fan', 'FAN18G1024' => 'fan', 'FAN22G1458' => 'fan', 'FAN24G0037' => 'fan', 'FAN24G0429' => 'fan', 'FAN24G2387' => 'fan', 'FAN27G2746' => 'fan', 'FvH4_2g20400' => 'fve', 'FvH4_2g20420' => 'fve', 'FvH4_2g20430' => 'fve', 'FvH4_4g01270' => 'fve', 'FvH4_4g01290' => 'fve', 'FvH4_4g01300' => 'fve', 'FvH4_4g01310' => 'fve', 'FvH4_4g01330' => 'fve', 'FvH4_5g09070' => 'fve', 'Glyma.10G243800' => 'gma', 'Glyma.20G150600' => 'gma', 'Gohir.A09G219200' => 'ghi', 'Gohir.A09G219300' => 'ghi', 'Gohir.D09G221400' => 'ghi', 'Gohir.D09G221500' => 'ghi', 'Gorai.006G242600' => 'gra', 'Gorai.006G242700' => 'gra', 'GSVIVG01018044001' => 'vvi', 'HanXRQChr03g0083821' => 'han', 'HanXRQChr03g0083841' => 'han', 'HanXRQChr03g0083881' => 'han', 'HanXRQChr03g0083901' => 'han', 'HanXRQChr03g0083921' => 'han', 'HanXRQChr03g0085331' => 'han', 'HanXRQChr03g0085361' => 'han', 'HanXRQChr03g0085411' => 'han', 'HanXRQChr03g0085421' => 'han', 'HanXRQChr03g0085431' => 'han', 'HanXRQChr08g0221991' => 'han', 'HanXRQChr11g0336061' => 'han', 'HanXRQChr11g0336411' => 'han', 'Haze_11234' => 'cav', 'Hma1.2p1_0549F.1_g177010' => 'hma', 'Hma1.2p1_0602F.1_g187630' => 'hma', 'Hund14876' => 'sun', 'Hund14879' => 'sun', 'Lalb_Chr06g0160741' => 'lal', 'Lalb_Chr21g0304781' => 'lal', 'Lj3A726G19' => 'lonja', 'Lj3A726T23' => 'lonja', 'Lj3A726T24' => 'lonja', 'Lj3A726T25' => 'lonja', 'Lj3A727T17' => 'lonja', 'Lj3C726T0' => 'lonja', 'Lj3C726T2' => 'lonja', 'Lj3P725T35' => 'lonja', 'Lj3P727T10' => 'lonja', 'Lj3P727T12' => 'lonja', 'Lj3P727T14' => 'lonja', 'Lj5g0023109' => 'lja', 'Lj6P646T44' => 'lonja', 'Lsat_1_v5_gn_6_75760' => 'lsa', 'Lsat_1_v5_gn_6_75800' => 'lsa', 'Lsat_1_v5_gn_6_75900' => 'lsa', 'Lsat_1_v5_gn_6_76240' => 'lsa', 'Lsat_1_v5_gn_6_76441' => 'lsa', 'Lsat_1_v5_gn_6_76700' => 'lsa', 'Lsat_1_v5_gn_6_76760' => 'lsa', 'Manes.15G033100' => 'mes', 'Mapoly0004s0074' => 'mpo', 'Mapoly0004s0075' => 'mpo', 'Mapoly0004s0163' => 'mpo', 'Mapoly0004s0164' => 'mpo', 'Mapoly0021s0018' => 'mpo', 'Mapoly0041s0136' => 'mpo', 'Mapoly0041s0137' => 'mpo', 'Mapoly0041s0138' => 'mpo', 'Mapoly0041s0139' => 'mpo', 'Mapoly0041s0141' => 'mpo', 'Mapoly0041s0142' => 'mpo', 'Mapoly0041s0143' => 'mpo', 'Mapoly0041s0144' => 'mpo', 'Mapoly0041s0145' => 'mpo', 'Mapoly0047s0106' => 'mpo', 'Mapoly0047s0108' => 'mpo', 'Mapoly0050s0051' => 'mpo', 'Mapoly0050s0052' => 'mpo', 'Mapoly0050s0053' => 'mpo', 'Mapoly0058s0013' => 'mpo', 'Mapoly0091s0078' => 'mpo', 'Mapoly0091s0079' => 'mpo', 'Mapoly0091s0080' => 'mpo', 'Mapoly0091s0081' => 'mpo', 'Mapoly0278s0004' => 'mpo', 'Mapoly0278s0005' => 'mpo', 'Mapoly0278s0006' => 'mpo', 'MBI11_g30648_MAGBIO' => 'mbi', 'MCO03G194' => 'mco', 'MCO03G590' => 'mco', 'MCO07G312' => 'mco', 'MCO10G318' => 'mco', 'MCO12G244' => 'mco', 'MCO13G148' => 'mco', 'MCO13G194' => 'mco', 'MCO16G238' => 'mco', 'MD06G1134100' => 'mdo', 'MD13G1200100' => 'mdo', 'MD13G1200300' => 'mdo', 'MD13G1200600' => 'mdo', 'MD14G1150400' => 'mdo', 'MD16G1200000' => 'mdo', 'Medtr1g102570' => 'mtr', 'Medtr1g102780' => 'mtr', 'Medtr1g102800' => 'mtr', 'Medtr1g102810' => 'mtr', 'Medtr1g102830' => 'mtr', 'MELO3C006499.2' => 'cme', 'Migut.G00385' => 'egut', 'MSTRG.4063' => 'ama', 'Nitab4.5_0000090g0260' => 'nta', 'Nitab4.5_0000977g0030' => 'nta', 'Nitab4.5_0002541g0040' => 'nta', 'Nitab4.5_0007068g0040' => 'nta', 'Nn005s41408' => 'nnu', 'Nn005s41410' => 'nnu', 'Oeu010310.1' => 'oeu', 'Oeu010311.1' => 'oeu', 'Oeu043472.1' => 'oeu', 'Os01g0246400' => 'osa', 'Os04g0267950' => 'osa', 'Os07g0178700' => 'osa', 'Os07g0178800' => 'osa', 'Peaxi162Scf00316g00046' => 'pax', 'Peaxi162Scf00316g00049' => 'pax', 'Peaxi162Scf00316g00059' => 'pax', 'Peaxi162Scf00316g00328' => 'pax', 'Peaxi162Scf00316g00329' => 'pax', 'Peaxi162Scf00316g00411' => 'pax', 'Peaxi162Scf00316g00521' => 'pax', 'Peaxi162Scf00492g00068' => 'pax', 'Peaxi162Scf35631g00002' => 'pax', 'PGR142G3720' => 'pgr', 'PGSC0003DMG400006442' => 'stu', 'Phvul.007G062000' => 'pvu', 'Potri.008G157750' => 'ptr', 'Potri.008G157900' => 'ptr', 'Potri.008G158000' => 'ptr', 'Potri.008G158200' => 'ptr', 'Pp3c11_7280' => 'ppa', 'Pp3c11_7980' => 'ppa', 'Pp3c12_19450' => 'ppa', 'Pp3c14_1480' => 'ppa', 'Pp3c14_1501' => 'ppa', 'Pp3c16_4900' => 'ppa', 'Pp3c16_5010' => 'ppa', 'Pp3c16_5060' => 'ppa', 'Pp3c19_18250' => 'ppa', 'Pp3c23_8530' => 'ppa', 'Pp3c23_8550' => 'ppa', 'Pp3c24_9670' => 'ppa', 'Pp3c2_21390' => 'ppa', 'Pp3c2_31380' => 'ppa', 'Pp3c3_16620' => 'ppa', 'Pp3c3_8090' => 'ppa', 'Pp3c3_8110' => 'ppa', 'Pp3c3_8130' => 'ppa', 'Pp3c3_8150' => 'ppa', 'Pp3c4_14320' => 'ppa', 'Pp3c6_2560' => 'ppa', 'Pp3c9_16700' => 'ppa', 'PRCOL_00000234' => 'pco', 'PRCOL_00000235' => 'pco', 'PRCOL_00000777' => 'pco', 'PRCOL_00002344' => 'pco', 'PRCOL_00002372' => 'pco', 'PRCOL_00006120' => 'pco', 'Prupe.1G021400' => 'ppe', 'Prupe.1G021500' => 'ppe', 'Prupe.1G021600' => 'ppe', 'Prupe.1G021700' => 'ppe', 'Prupe.1G021800' => 'ppe', 'Prupe.5G145100' => 'ppe', 'Psat6g204040' => 'psa', 'Psat6g204800' => 'psa', 'Psat6g204920' => 'psa', 'Psat6g204960' => 'psa', 'Psat6g205080' => 'psa', 'PSO017G0271' => 'pso', 'PSO017G1276' => 'pso', 'PSO017G1429' => 'pso', 'PSO017G1861' => 'pso', 'PSO017G2787' => 'pso', 'PSO017G4466' => 'pso', 'PSO017G5118' => 'pso', 'PSO017G5420' => 'pso', 'PSO063G3678' => 'pso', 'PSO210G0546' => 'pso', 'PSO317G0001' => 'pso', 'PSO357G0512' => 'pso', 'PSO478G2682' => 'pso', 'PSO647G0001' => 'pso', 'PSO675G0001' => 'pso', 'PSO675G2699' => 'pso', 'PSO675G2849' => 'pso', 'PSO675G4991' => 'pso', 'PSO689G0001' => 'pso', 'QL06p000916' => 'qlo', 'QL06p000921' => 'qlo', 'QL06p001398' => 'qlo', 'QL06p001407' => 'qlo', 'QL06p002031' => 'qlo', 'RcHm_v2.0_Chr4g0387791' => 'rch', 'RcHm_v2.0_Chr4g0387801' => 'rch', 'RcHm_v2.0_Chr6g0286501' => 'rch', 'RcHm_v2.0_Chr6g0286511' => 'rch', 'RcHm_v2.0_Chr6g0286521' => 'rch', 'RcHm_v2.0_Chr6g0286531' => 'rch', 'RcHm_v2.0_Chr7g0189141' => 'rch', 'Rhsim02G0028700' => 'rsi', 'Rhsim02G0028800' => 'rsi', 'Rhsim02G0028900' => 'rsi', 'Rhsim02G0029000' => 'rsi', 'Rhsim02G0029100' => 'rsi', 'Rhsim02G0029200' => 'rsi', 'Rhsim02G0029300' => 'rsi', 'Rhsim02G0029400' => 'rsi', 'Rhsim02G0029500' => 'rsi', 'Rhsim02G0029600' => 'rsi', 'RhsimUnG0024000' => 'rsi', 'RhsimUnG0024100' => 'rsi', 'RhsimUnG0024200' => 'rsi', 'RhsimUnG0024300' => 'rsi', 'RhsimUnG0024400' => 'rsi', 'RhsimUnG0024500' => 'rsi', 'RhsimUnG0024700' => 'rsi', 'RhsimUnG0024800' => 'rsi', 'RhsimUnG0024900' => 'rsi', 'RhsimUnG0025100' => 'rsi', 'Sabra08G0120200' => 'sbr', 'Sabra08G0120300' => 'sbr', 'Sabra08G0120500' => 'sbr', 'Sabra08G0120600' => 'sbr', 'Sabra10G0158900' => 'sbr', 'SalBow2G3492' => 'sbo', 'Sc13g0004760' => 'sci', 'Sc13g0004770' => 'sci', 'Sed0003417' => 'sed', 'Sed0019750' => 'sed', 'SEGI_03419' => 'sgi', 'SEGI_05907' => 'sgi', 'SEGI_10682' => 'sgi', 'SEGI_13528' => 'sgi', 'SEGI_16081' => 'sgi', 'SEGI_19370' => 'sgi', 'SEGI_21015' => 'sgi', 'SEGI_21944' => 'sgi', 'SEGI_32906' => 'sgi', 'SEGI_33093' => 'sgi', 'SEGI_36110' => 'sgi', 'SEGI_40397' => 'sgi', 'SGA_v2.0_scaffold191G40426' => 'sas', 'SGA_v2.0_scaffold353G49717' => 'sas', 'SGA_v2.0_scaffold50G18550' => 'sas', 'SMO119G0173' => 'smo', 'SMO172G0002' => 'smo', 'Solyc09g082690.3' => 'sly', 'Solyc09g082700.2' => 'sly', 'Sopen09g031550' => 'spe', 'Sopen09g031560' => 'spe', 'Sp3g20540' => 'spa', 'Sp7g07580' => 'spa', 'TAR134G0002' => 'tar', 'TAR236G0001' => 'tar', 'TAR365G0892' => 'tar', 'TAR636G0166' => 'tar', 'TAR636G0646' => 'tar', 'TAR636G0869' => 'tar', 'TAR636G1317' => 'tar', 'TAR636G1744' => 'tar', 'TAR636G3358' => 'tar', 'TAR636G3436' => 'tar', 'THA.LOC104803047' => 'tha', 'Thecc.04G238900' => 'tca', 'Thhalv10021557m.g' => 'esa', 'Thhalv10026318m.g' => 'esa', 'Thhalv10026335m.g' => 'esa', 'TPR.G17433' => 'tpr', 'TPR.G18915' => 'tpr', 'TPR.G26125' => 'tpr', 'TWI09G0677' => 'twi', 'TWI73G0287' => 'twi', 'unitig_748.g8326' => 'ugi', 'vmacro15370' => 'vma', 'vmacro15371' => 'vma', 'vmacro15372' => 'vma', 'vmacro15373' => 'vma', 'vmacro15374' => 'vma', 'VMungo0720G2826' => 'vmu', 'Zm00001eb116960' => 'zma', 'Zm00001eb301260' => 'zma', 'Zm00001eb301270' => 'zma' ), 'gf_id' => 'HOM05D001460', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001460' ), 'data_identifier' => 'HOM05D001460', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001460', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '433', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p22980' => 'bna', 'A01p32340' => 'bna', 'A03p42970' => 'bna', 'A05p25880' => 'bna', 'Aa31LG8G9320' => 'aar', 'Aa31LG8G9330' => 'aar', 'Aa31LG8G9340' => 'aar', 'Aa31sc221G30' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.1034' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.1528' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_117.829' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.2222' => 'aag', 'Ah.12g058830' => 'amhyb', 'Ah.12g058840' => 'amhyb', 'AL3G37160' => 'aly', 'AL7G41310' => 'aly', 'Aqoxy5G00395' => 'aox', 'Aqoxy5G00396' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0C8NZA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.5185HY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JZ1PRS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MD3LS0' => 'arhy', 'AT3G22840' => 'ath', 'AT4G14690' => 'ath', 'ATR0665G054' => 'atr', 'Atru.chr4.2344' => 'acertr', 'Atru.chr4.2346' => 'acertr', 'Atru.chr4.2347' => 'acertr', 'Atru.chr4.2348' => 'acertr', 'Atru.chr4.2355' => 'acertr', 'Atru.chr4.2356' => 'acertr', 'Atru.chr4.2358' => 'acertr', 'Atru.chr4.2359' => 'acertr', 'Atru.chr4.2360' => 'acertr', 'Atru.chr4.2361' => 'acertr', 'AUR62030476' => 'cqu', 'AUR62030478' => 'cqu', 'AUR62030819' => 'cqu', 'AUR62030820' => 'cqu', 'BcaB03g14648' => 'bca', 'BcaB04g20492' => 'bca', 'BcaB06g26399' => 'bca', 'BcaC01g03416' => 'bca', 'BcaC01g03419' => 'bca', 'BcaC01g03421' => 'bca', 'BcaC01g03424' => 'bca', 'BcaC05g28012' => 'bca', 'BcaC09g49212' => 'bca', 'BcaC09g50140' => 'bca', 'BcaNung00346' => 'bca', 'BolC1t02785H' => 'bol', 'BolC1t04095H' => 'bol', 'BolC3t17545H' => 'bol', 'BolC5t32769H' => 'bol', 'BraA01t02211Z' => 'bra', 'BraA01t03359Z' => 'bra', 'BraA03t13441Z' => 'bra', 'BraA05t21476Z' => 'bra', 'C01p28420' => 'bna', 'C01p41350' => 'bna', 'C03p52750' => 'bna', 'C03p52780' => 'bna', 'C05p40270' => 'bna', 'CAN.G1437.9' => 'can', 'CANSAT78G0035' => 'cansat', 'CANSAT78G1036' => 'cansat', 'CANSAT78G2272' => 'cansat', 'CANSAT78G2478' => 'cansat', 'CARHR098700' => 'chi', 'CARHR221120' => 'chi', 'CARHR221150' => 'chi', 'Carub.0003s2297' => 'cru', 'Carub.0007s2749' => 'cru', 'Carub.0007s2750' => 'cru', 'Carub.0007s2751' => 'cru', 'Ca_10849_v3' => 'car', 'Cc03_g04300' => 'ccan', 'CDE02G3648' => 'cde', 'CDE05G0060' => 'cde', 'CDE05G0692' => 'cde', 'CDE05G2285' => 'cde', 'CDE05G2884' => 'cde', 'CDE05G3072' => 'cde', 'Cfa008439' => 'cfa', 'Cfa008441' => 'cfa', 'Cfa008443' => 'cfa', 'Cfa008448' => 'cfa', 'Ciclev10005974m.g' => 'ccl', 'Ciclev10006006m.g' => 'ccl', 'Ciclev10006775m.g' => 'ccl', 'CiPaw.02G120400' => 'cil', 'CiPaw.02G120500' => 'cil', 'CiPaw.02G120600' => 'cil', 'ClCG05G004850' => 'cla', 'COL.COLO4_21566' => 'col', 'Cpa.g.sc44.124' => 'cpa', 'Cre07.g320400' => 'cre', 'Cre07.g320450' => 'cre', 'Cre08.g384650' => 'cre', 'Cre09.g393173' => 'cre', 'Cre09.g394325' => 'cre', 'Cre14.g626750' => 'cre', 'Cre16.g679250' => 'cre', 'CsaV3_3G012890' => 'csa', 'CSS0010865' => 'camsi', 'CSS0044338' => 'camsi', 'DCAR_002366' => 'dca', 'DCAR_030687' => 'dca', 'DCAR_030688' => 'dca', 'Dinv14047' => 'din', 'Dinv14048' => 'din', 'Duzib151G0105' => 'dzi', 'Duzib151G0114' => 'dzi', 'Duzib212G1029' => 'dzi', 'ECA232G3536' => 'eca', 'ECA240G0786' => 'eca', 'ECA240G1802' => 'eca', 'ECA240G3760' => 'eca', 'ECA240G3920' => 'eca', 'EL10Ac5g12536' => 'bvu', 'EL10Ac5g12537' => 'bvu', 'EL10Ac5g12538' => 'bvu', 'Eucgr.B01004' => 'egr', 'Eucgr.B01006' => 'egr', 'Eucgr.B01007' => 'egr', 'Eucgr.B01008' => 'egr', 'Eucgr.B01895' => 'egr', 'Eucgr.B01896' => 'egr', 'FAN04G1456' => 'fan', 'FAN08G1769' => 'fan', 'FAN08G2160' => 'fan', 'FAN13G2403' => 'fan', 'FAN13G3303' => 'fan', 'FAN15G2435' => 'fan', 'FAN17G0672' => 'fan', 'FAN17G2441' => 'fan', 'FAN18G1024' => 'fan', 'FAN22G1458' => 'fan', 'FAN24G0037' => 'fan', 'FAN24G0429' => 'fan', 'FAN24G2387' => 'fan', 'FAN27G2746' => 'fan', 'FvH4_2g20400' => 'fve', 'FvH4_2g20420' => 'fve', 'FvH4_2g20430' => 'fve', 'FvH4_4g01270' => 'fve', 'FvH4_4g01290' => 'fve', 'FvH4_4g01300' => 'fve', 'FvH4_4g01310' => 'fve', 'FvH4_4g01330' => 'fve', 'FvH4_5g09070' => 'fve', 'Glyma.10G243800' => 'gma', 'Glyma.20G150600' => 'gma', 'Gohir.A09G219200' => 'ghi', 'Gohir.A09G219300' => 'ghi', 'Gohir.D09G221400' => 'ghi', 'Gohir.D09G221500' => 'ghi', 'Gorai.006G242600' => 'gra', 'Gorai.006G242700' => 'gra', 'GSVIVG01018044001' => 'vvi', 'HanXRQChr03g0083821' => 'han', 'HanXRQChr03g0083841' => 'han', 'HanXRQChr03g0083881' => 'han', 'HanXRQChr03g0083901' => 'han', 'HanXRQChr03g0083921' => 'han', 'HanXRQChr03g0085331' => 'han', 'HanXRQChr03g0085361' => 'han', 'HanXRQChr03g0085411' => 'han', 'HanXRQChr03g0085421' => 'han', 'HanXRQChr03g0085431' => 'han', 'HanXRQChr08g0221991' => 'han', 'HanXRQChr11g0336061' => 'han', 'HanXRQChr11g0336411' => 'han', 'Haze_11234' => 'cav', 'Hma1.2p1_0549F.1_g177010' => 'hma', 'Hma1.2p1_0602F.1_g187630' => 'hma', 'Hund14876' => 'sun', 'Hund14879' => 'sun', 'Lalb_Chr06g0160741' => 'lal', 'Lalb_Chr21g0304781' => 'lal', 'Lj3A726G19' => 'lonja', 'Lj3A726T23' => 'lonja', 'Lj3A726T24' => 'lonja', 'Lj3A726T25' => 'lonja', 'Lj3A727T17' => 'lonja', 'Lj3C726T0' => 'lonja', 'Lj3C726T2' => 'lonja', 'Lj3P725T35' => 'lonja', 'Lj3P727T10' => 'lonja', 'Lj3P727T12' => 'lonja', 'Lj3P727T14' => 'lonja', 'Lj5g0023109' => 'lja', 'Lj6P646T44' => 'lonja', 'Lsat_1_v5_gn_6_75760' => 'lsa', 'Lsat_1_v5_gn_6_75800' => 'lsa', 'Lsat_1_v5_gn_6_75900' => 'lsa', 'Lsat_1_v5_gn_6_76240' => 'lsa', 'Lsat_1_v5_gn_6_76441' => 'lsa', 'Lsat_1_v5_gn_6_76700' => 'lsa', 'Lsat_1_v5_gn_6_76760' => 'lsa', 'Manes.15G033100' => 'mes', 'Mapoly0004s0074' => 'mpo', 'Mapoly0004s0075' => 'mpo', 'Mapoly0004s0163' => 'mpo', 'Mapoly0004s0164' => 'mpo', 'Mapoly0021s0018' => 'mpo', 'Mapoly0041s0136' => 'mpo', 'Mapoly0041s0137' => 'mpo', 'Mapoly0041s0138' => 'mpo', 'Mapoly0041s0139' => 'mpo', 'Mapoly0041s0141' => 'mpo', 'Mapoly0041s0142' => 'mpo', 'Mapoly0041s0143' => 'mpo', 'Mapoly0041s0144' => 'mpo', 'Mapoly0041s0145' => 'mpo', 'Mapoly0047s0106' => 'mpo', 'Mapoly0047s0108' => 'mpo', 'Mapoly0050s0051' => 'mpo', 'Mapoly0050s0052' => 'mpo', 'Mapoly0050s0053' => 'mpo', 'Mapoly0058s0013' => 'mpo', 'Mapoly0091s0078' => 'mpo', 'Mapoly0091s0079' => 'mpo', 'Mapoly0091s0080' => 'mpo', 'Mapoly0091s0081' => 'mpo', 'Mapoly0278s0004' => 'mpo', 'Mapoly0278s0005' => 'mpo', 'Mapoly0278s0006' => 'mpo', 'MBI11_g30648_MAGBIO' => 'mbi', 'MCO03G194' => 'mco', 'MCO03G590' => 'mco', 'MCO07G312' => 'mco', 'MCO10G318' => 'mco', 'MCO12G244' => 'mco', 'MCO13G148' => 'mco', 'MCO13G194' => 'mco', 'MCO16G238' => 'mco', 'MD06G1134100' => 'mdo', 'MD13G1200100' => 'mdo', 'MD13G1200300' => 'mdo', 'MD13G1200600' => 'mdo', 'MD14G1150400' => 'mdo', 'MD16G1200000' => 'mdo', 'Medtr1g102570' => 'mtr', 'Medtr1g102780' => 'mtr', 'Medtr1g102800' => 'mtr', 'Medtr1g102810' => 'mtr', 'Medtr1g102830' => 'mtr', 'MELO3C006499.2' => 'cme', 'Migut.G00385' => 'egut', 'MSTRG.4063' => 'ama', 'Nitab4.5_0000090g0260' => 'nta', 'Nitab4.5_0000977g0030' => 'nta', 'Nitab4.5_0002541g0040' => 'nta', 'Nitab4.5_0007068g0040' => 'nta', 'Nn005s41408' => 'nnu', 'Nn005s41410' => 'nnu', 'Oeu010310.1' => 'oeu', 'Oeu010311.1' => 'oeu', 'Oeu043472.1' => 'oeu', 'Os01g0246400' => 'osa', 'Os04g0267950' => 'osa', 'Os07g0178700' => 'osa', 'Os07g0178800' => 'osa', 'Peaxi162Scf00316g00046' => 'pax', 'Peaxi162Scf00316g00049' => 'pax', 'Peaxi162Scf00316g00059' => 'pax', 'Peaxi162Scf00316g00328' => 'pax', 'Peaxi162Scf00316g00329' => 'pax', 'Peaxi162Scf00316g00411' => 'pax', 'Peaxi162Scf00316g00521' => 'pax', 'Peaxi162Scf00492g00068' => 'pax', 'Peaxi162Scf35631g00002' => 'pax', 'PGR142G3720' => 'pgr', 'PGSC0003DMG400006442' => 'stu', 'Phvul.007G062000' => 'pvu', 'Potri.008G157750' => 'ptr', 'Potri.008G157900' => 'ptr', 'Potri.008G158000' => 'ptr', 'Potri.008G158200' => 'ptr', 'Pp3c11_7280' => 'ppa', 'Pp3c11_7980' => 'ppa', 'Pp3c12_19450' => 'ppa', 'Pp3c14_1480' => 'ppa', 'Pp3c14_1501' => 'ppa', 'Pp3c16_4900' => 'ppa', 'Pp3c16_5010' => 'ppa', 'Pp3c16_5060' => 'ppa', 'Pp3c19_18250' => 'ppa', 'Pp3c23_8530' => 'ppa', 'Pp3c23_8550' => 'ppa', 'Pp3c24_9670' => 'ppa', 'Pp3c2_21390' => 'ppa', 'Pp3c2_31380' => 'ppa', 'Pp3c3_16620' => 'ppa', 'Pp3c3_8090' => 'ppa', 'Pp3c3_8110' => 'ppa', 'Pp3c3_8130' => 'ppa', 'Pp3c3_8150' => 'ppa', 'Pp3c4_14320' => 'ppa', 'Pp3c6_2560' => 'ppa', 'Pp3c9_16700' => 'ppa', 'PRCOL_00000234' => 'pco', 'PRCOL_00000235' => 'pco', 'PRCOL_00000777' => 'pco', 'PRCOL_00002344' => 'pco', 'PRCOL_00002372' => 'pco', 'PRCOL_00006120' => 'pco', 'Prupe.1G021400' => 'ppe', 'Prupe.1G021500' => 'ppe', 'Prupe.1G021600' => 'ppe', 'Prupe.1G021700' => 'ppe', 'Prupe.1G021800' => 'ppe', 'Prupe.5G145100' => 'ppe', 'Psat6g204040' => 'psa', 'Psat6g204800' => 'psa', 'Psat6g204920' => 'psa', 'Psat6g204960' => 'psa', 'Psat6g205080' => 'psa', 'PSO017G0271' => 'pso', 'PSO017G1276' => 'pso', 'PSO017G1429' => 'pso', 'PSO017G1861' => 'pso', 'PSO017G2787' => 'pso', 'PSO017G4466' => 'pso', 'PSO017G5118' => 'pso', 'PSO017G5420' => 'pso', 'PSO063G3678' => 'pso', 'PSO210G0546' => 'pso', 'PSO317G0001' => 'pso', 'PSO357G0512' => 'pso', 'PSO478G2682' => 'pso', 'PSO647G0001' => 'pso', 'PSO675G0001' => 'pso', 'PSO675G2699' => 'pso', 'PSO675G2849' => 'pso', 'PSO675G4991' => 'pso', 'PSO689G0001' => 'pso', 'QL06p000916' => 'qlo', 'QL06p000921' => 'qlo', 'QL06p001398' => 'qlo', 'QL06p001407' => 'qlo', 'QL06p002031' => 'qlo', 'RcHm_v2.0_Chr4g0387791' => 'rch', 'RcHm_v2.0_Chr4g0387801' => 'rch', 'RcHm_v2.0_Chr6g0286501' => 'rch', 'RcHm_v2.0_Chr6g0286511' => 'rch', 'RcHm_v2.0_Chr6g0286521' => 'rch', 'RcHm_v2.0_Chr6g0286531' => 'rch', 'RcHm_v2.0_Chr7g0189141' => 'rch', 'Rhsim02G0028700' => 'rsi', 'Rhsim02G0028800' => 'rsi', 'Rhsim02G0028900' => 'rsi', 'Rhsim02G0029000' => 'rsi', 'Rhsim02G0029100' => 'rsi', 'Rhsim02G0029200' => 'rsi', 'Rhsim02G0029300' => 'rsi', 'Rhsim02G0029400' => 'rsi', 'Rhsim02G0029500' => 'rsi', 'Rhsim02G0029600' => 'rsi', 'RhsimUnG0024000' => 'rsi', 'RhsimUnG0024100' => 'rsi', 'RhsimUnG0024200' => 'rsi', 'RhsimUnG0024300' => 'rsi', 'RhsimUnG0024400' => 'rsi', 'RhsimUnG0024500' => 'rsi', 'RhsimUnG0024700' => 'rsi', 'RhsimUnG0024800' => 'rsi', 'RhsimUnG0024900' => 'rsi', 'RhsimUnG0025100' => 'rsi', 'Sabra08G0120200' => 'sbr', 'Sabra08G0120300' => 'sbr', 'Sabra08G0120500' => 'sbr', 'Sabra08G0120600' => 'sbr', 'Sabra10G0158900' => 'sbr', 'SalBow2G3492' => 'sbo', 'Sc13g0004760' => 'sci', 'Sc13g0004770' => 'sci', 'Sed0003417' => 'sed', 'Sed0019750' => 'sed', 'SEGI_03419' => 'sgi', 'SEGI_05907' => 'sgi', 'SEGI_10682' => 'sgi', 'SEGI_13528' => 'sgi', 'SEGI_16081' => 'sgi', 'SEGI_19370' => 'sgi', 'SEGI_21015' => 'sgi', 'SEGI_21944' => 'sgi', 'SEGI_32906' => 'sgi', 'SEGI_33093' => 'sgi', 'SEGI_36110' => 'sgi', 'SEGI_40397' => 'sgi', 'SGA_v2.0_scaffold191G40426' => 'sas', 'SGA_v2.0_scaffold353G49717' => 'sas', 'SGA_v2.0_scaffold50G18550' => 'sas', 'SMO119G0173' => 'smo', 'SMO172G0002' => 'smo', 'Solyc09g082690.3' => 'sly', 'Solyc09g082700.2' => 'sly', 'Sopen09g031550' => 'spe', 'Sopen09g031560' => 'spe', 'Sp3g20540' => 'spa', 'Sp7g07580' => 'spa', 'TAR134G0002' => 'tar', 'TAR236G0001' => 'tar', 'TAR365G0892' => 'tar', 'TAR636G0166' => 'tar', 'TAR636G0646' => 'tar', 'TAR636G0869' => 'tar', 'TAR636G1317' => 'tar', 'TAR636G1744' => 'tar', 'TAR636G3358' => 'tar', 'TAR636G3436' => 'tar', 'THA.LOC104803047' => 'tha', 'Thecc.04G238900' => 'tca', 'Thhalv10021557m.g' => 'esa', 'Thhalv10026318m.g' => 'esa', 'Thhalv10026335m.g' => 'esa', 'TPR.G17433' => 'tpr', 'TPR.G18915' => 'tpr', 'TPR.G26125' => 'tpr', 'TWI09G0677' => 'twi', 'TWI73G0287' => 'twi', 'unitig_748.g8326' => 'ugi', 'vmacro15370' => 'vma', 'vmacro15371' => 'vma', 'vmacro15372' => 'vma', 'vmacro15373' => 'vma', 'vmacro15374' => 'vma', 'VMungo0720G2826' => 'vmu', 'Zm00001eb116960' => 'zma', 'Zm00001eb301260' => 'zma', 'Zm00001eb301270' => 'zma' ) $gf_id = 'HOM05D001460' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001460' ) $data_identifier = 'HOM05D001460' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 9, 'aar' => (int) 4, 'aag' => (int) 4, 'amhyb' => (int) 2, 'aly' => (int) 2, 'aox' => (int) 2, 'arhy' => (int) 4, 'ath' => (int) 2, 'atr' => (int) 1, 'acertr' => (int) 10, 'cqu' => (int) 4, 'bca' => (int) 11, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 1, 'cansat' => (int) 4, 'chi' => (int) 3, 'cru' => (int) 4, 'car' => (int) 1, 'ccan' => (int) 1, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 1, 'col' => (int) 1, 'cpa' => (int) 1, 'cre' => (int) 7, 'csa' => (int) 1, 'camsi' => (int) 2, 'dca' => (int) 3, 'din' => (int) 2, 'dzi' => (int) 3, 'eca' => (int) 5, 'bvu' => (int) 3, 'egr' => (int) 6, 'fan' => (int) 14, 'fve' => (int) 9, 'gma' => (int) 2, 'ghi' => (int) 4, 'gra' => (int) 2, 'vvi' => (int) 1, 'han' => (int) 13, 'cav' => (int) 1, 'hma' => (int) 2, 'sun' => (int) 2, 'lal' => (int) 2, 'lonja' => (int) 12, 'lja' => (int) 1, 'lsa' => (int) 7, 'mes' => (int) 1, 'mpo' => (int) 27, 'mbi' => (int) 1, 'mco' => (int) 8, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 1, 'egut' => (int) 1, 'ama' => (int) 1, 'nta' => (int) 4, 'nnu' => (int) 2, 'oeu' => (int) 3, 'osa' => (int) 4, 'pax' => (int) 9, 'pgr' => (int) 1, 'stu' => (int) 1, 'pvu' => (int) 1, 'ptr' => (int) 4, 'ppa' => (int) 22, 'pco' => (int) 6, 'ppe' => (int) 6, 'psa' => (int) 5, 'pso' => (int) 19, 'qlo' => (int) 5, 'rch' => (int) 7, 'rsi' => (int) 20, 'sbr' => (int) 5, 'sbo' => (int) 1, 'sci' => (int) 2, 'sed' => (int) 2, 'sgi' => (int) 12, 'sas' => (int) 3, 'smo' => (int) 2, 'sly' => (int) 2, 'spe' => (int) 2, 'spa' => (int) 2, 'tar' => (int) 10, 'tha' => (int) 1, 'tca' => (int) 1, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 2, 'ugi' => (int) 1, 'vma' => (int) 5, 'vmu' => (int) 1, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb301270' $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